title: ChIP-seq analysis of CTCF binding sites in lymphocyte subsets

first: Ali

last: Torkamani

address: 3344 North Torrey Pines Court Suite 300

institute: TSRI

first: Ann

last: Feeney

first: Jiyoti

last: Verma-Gaur


title: ChIP-seq analysis of CTCF binding sites in lymphocyte subsets [DP thymocytes]

status: Public on Dec 03 2012

city: La Jolla

state: CA

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we compare the binding pattern of CTCF at the T  cell receptor alpha locus in different subsets of developing lymphocytes

overall_design: For the ChIP-seq, input and immunoprecipitated DNA was given to The Scripps DNA Array Facility, where it was prepared for massively parallel sequencing on Illumina Genome Analyzer IIx.

middle: J


title: ChIP-seq analysis of CTCF binding sites in lymphocyte subsets [pro-B cells]

overall_design: For the ChIP-seq, input and immunoprecipitated DNA was given to The Scripps DNA Array Facility, where it was prepared for massively parallel sequencing on Illumina Hi-Seq.


title: ChIP-seq analysis of CTCF binding sites in lymphocyte subsets [DN thymocytes]

summary: In this study, we compare the binding pattern of CTCF at the T  cell receptor alpha locus in different subsets of developing lymphocytes.


title: Digital gene expression analysis of early root infection of Sporisorium reilianum f.sp.zeae in maize based on susceptible and resistant lines

city: wuhan

first: shaopeng

last: zhang

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huangzhong agricultural university

type: Expression profiling by high throughput sequencing

summary: The maize smut fungus, Sporisorium reilianum f. sp. zeae, which is an important biotrophic pathogen responsible for extensive crop losses, infects maize by invading the root during the early seedling stage. In order to investigate disease-resistance mechanisms at this early seedling stage, digital gene expression (DGE) analysis, which applies a dual-enzyme approach (DpnII and NlaIII), was used to identify the transcriptional changes in roots of Huangzao4 (susceptible) and Mo17 (resistant) after inoculation with teliospores of S. reilianum. Before and after inoculation, pathogenesis-related genes were differentially regulated and enzymes involved in controlling reactive oxygen species (ROS) levels showed different activity between Huangzao4 and Mo17, which can potentially lead to changes in the growth of S. reilianum and ROS production in maize. Moreover, lignin depositions of roots were also changed differentially during root colonization of hyphae between Huangzao4 and Mo17. These results suggest that the interplays between S. reilianum and maize during the early infection stage involve many interesting transcriptional and physiological changes, which offer several novel insights for understanding the mechanisms of resistance to the fungal infection.

overall_design: Examination of control stage (ck), post-inoculation stage1 (P1) and post-inoculation stage2 (P2) in Huangzao4 (susceptible) and Mo17 (resistant)

first: Shaopeng

last: Zhang

first: Andrea

middle: L

last: Eveland

first: Lifang


title: Insect larvae fed on resistant Zea mays (corn) expressing maize insect resistant 1 cysteine protease (Mir1-CP) compensate for Mir1-CP degradation of their peritrophic membrane by altering expression of midgut transcripts as revealed through mRNA-seq

status: Public on Dec 01 2012

city: University Park

first: Howard

middle: W

last: Fescemyer

state: PA

address: 208 Mueller Lab

department: Biology

institute: The Pennsylvania State University

summary: Native host plant insect resistance in the maize inbred line Mp708 was developed by traditional plant breeding.  Resistant Mp708 thwarts feeding by fall armyworm (Spodoptera frugiperda [J.E. Smith]; Lepidoptera: Noctuidae), numerous other lepidopteran pests, and the coleopteran western corn rootworm.  This broad resistance makes it an excellent model for studying native host plant resistance mechanisms.  In response to caterpillar feeding, Mp708 rapidly mobilizes Mir1-CP, a unique cysteine protease that appears to translocate from roots to the maize midwhorl where it accumulates.  This accumulation correlates with a significant reduction in caterpillar growth resulting from diminished food utilization.  In addition, the peritrophic membrane (PM) that surrounds the food bolus in the mudgut (MG) is severely damaged in caterpillars fed on sweet corn callus transformed to express the gene encoding Mir1-CP or on midwhorl tissue from resistant Mp708 maize.  Functions of the PM include assisting digestion and protecting the epithelium of the caterpillar MG from physical and chemical damage.  Consequently, the reduced growth of caterpillars that feed on Mp708 is probably due to the action of Mir1-CP on PM physiology. In fact, previous in vitro studies indicated that Mir1-CP was capable of permeabilizing the PM. The present study used both targeted (qRT-PCR) and global (mRNA-seq) transcriptome analyses to explore the effect of eating Mir1-CP expressing Mp708 maize on abundance of transcripts in the MG of fall armyworm larvae in comparison to MGs from larvae fed on susceptible Tx601 maize that does not express Mir1-CP.  Expression of genes encoding proteins involved in PM production is upregulated in MGs from fall armyworm fed on Mp708.  Also, several digestive enzymes (endopeptidases, aminopeptidases, lipases, amylase) were more highly expressed in MGs from larvae fed on Mp708 than MGs from larvae fed on Tx601.  Impaired growth of larvae fed on Mp708 probably results from metabolic costs associated with higher production of PM constituents and digestive enzymes in a compensatory attempt to maintain MG function.

overall_design: Beginning as neonates, fall armyworm larvae used in the mRNA-seq experiment were reared on yellow-green midwhorl foliage from resistant Mp708 maize or susceptible Tx601 maize.  Old foliage and frass were removed every other day and replaced with fresh foliage.  Larvae were reared in an environmental chamber at 27°C, 14:10 (light:dark) photoperiod, and 70% relative humidity.  Midguts were dissected from larvae 2 d after molting to the last instar with masses between 300 and 400 mg.  Dissections were done with cold anesthetized larvae submerged in Bombyx saline.  After removing Malpighian tubules, foregut anterior to the stomodial valve, hindgut and food bolus, the MG was transferred from the body cavity, rinsed well with cold saline, and preserved in RNAlater®.  Equal amounts (3 µg) of total RNA from an individual MG were randomly pooled into three replicates per treatment (i.e., Mp708 or Tx601) such that each treatment replicate derived from 12-13 MGs.  Each pool of total RNA was separately enriched for poly(A+) RNA and submitted to the Penn State Genomics Core Facility (University Park, PA) where barcoded cDNA libraries were prepared and equimolar quantities of each library sequenced on the SOLiD 3 Plus System.  Sequence reads were filtered to accept reads whose median score threshold was ≥12, contained ≥25 bases and contained one or more bases with a quality score ≥14.  The 138911 Sanger ESTs in SPODOBASE (http://bioweb.ensam.inra.fr/spodobase) were assembled into a reference transcriptome using SeqMan Pro version 8.0.2.  Filtered reads from each library representing a replicate within a maize inbred treatment were mapped separately to the reference transcriptome using the Bowtie-like algorithm in NextGENe® with the requirement that 85% of 12 or more nucleotides comprising a read must match the reference.  A read was allowed to map only once (i.e., no ambiguous mapping).  The number of mapped reads per contig (i.e., gene model) in each treatment replicate-library were summed by NextGENe® as read counts per gene and subsequently used in differential expression analyses.

first: Dawn

middle: S

last: Luthe

first: James

middle: H

last: Marden


title: Enhancer-associated H3K4 mono-methylation by Drosophila Trithorax-related, the Drosophila homolog of Mll3/Mll4

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Mono-methylation of histone H3 on lysine 4 (H3K4me1) and acetylation of histone H3 on lysine 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and enhancers. Although in yeast all H3K4 methylation patterns including H3K4me1 are implemented by Set1/COMPASS, there are three classes of COMPASS-like complexes in Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax and Trithorax-related (Trr). Here, we report that Trr, the Drosophila homolog of mammalian Mll3/4, can function as a major H3K4 mono-methyltransferase on enhancers in vivo. Loss of Trr results in a global decrease of H3K4me1 and H3K27ac in various tissues. Assays with the cut wing margin enhancer imply a functional role for Trr in enhancer-mediated processes. A genome-wide analysis demonstrates that Trr is required for H3K4me1 and H3K27ac on chromatin signatures that resemble the histone modification patterns described for enhancers. Since Trr and mammalian Mll3/4 complexes are distinguished by bearing a unique subunit, the H3K27 demethylase UTX, we propose a model in which the H3K4 mono-methyltransferase Trr, and the H3K27 demethylase, UTX, cooperate to regulate the transition from inactive/poised to active enhancers.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: ChIP-seq of Trr, LPT, UTX in Drosophila S2 Cells.  ChIP-seq of H3K4me1, H3K4me3, H3K27ac, H3K27me3 in WT and Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1, H3K27me3 in LPT knock-down Drosophila S2 cells.  ChIP-seq of LPT and UTX in Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1 and H3K27me3 in MLL1(+/+), MLL1(-/-), MLL3(+/+), and MLL3(-/-) Mouse Embryonic Fibroblasts (MEFs).

first: Hans-Martin

last: Herz

last: Shilatifard


title: RNA-seq HL60 cells

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

summary: Identification of the all RNA species coding and non-coding in total RNA

overall_design: Relationship between DNMT1-RNA interactions, DNA methylation and gene expression

first: Annalisa

last: Di Ruscio

middle: K

last: Ebralidze

first: Loyal

middle: A

last: Goff

first: John

last: Rinn

first: Daniel

middle: G

last: Tenen


title: Nucleosome driven transcription factor binding and gene regulati

city: Barcelona

first: Miguel

last: Beato

address: Aiguader 88

country: Spain

institute: CRG

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: YM500: An integrative small RNA sequencing (smRNA-seq) database for microRNA research

city: hsinchu

first: wei-chung

last: cheng

address: adqwerqr ew

country: Taiwan

institute: NTHU

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are small RNAs of ~22 nucleotides in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next generation sequencing applications, have reshaped the miRNA research landscape. In this study, we established an integrative database containing analysis pipelines and analysis results of 609 human and mice smRNA-seq results, including public data from GEO and private ones. YM500 collects analysis results for miRNA quantification, for isomiR identification (incl. RNA editing), for arm switching discovery, and, more importantly, for novel miRNA predictions. Wetlab validation on >100 miRNAs confirmed high correlation between miRNA profiling and RT-qPCR results (R=0.84). This database allows researchers to search these 4 different types of analysis results via our interactive web interface. YM500 allows researchers to define the criteria of isomiRs, as well as integrates the information of dbSNP to help researchers to distinguish isomiRs from SNPs. A user-friendly interface is provided to integrate miRNA-related information and existing evidences from hundreds of sequencing datasets. The identified novel miRNAs and isomiRs hold the potentials for both basic research and biotech applications. YM500 is now available on http://ngs.ym.edu.tw/ym500/.

overall_design: There are 34 in-house datasets in YM500 . They are 9 human embryonal tumors, 9 human germ cell tumors, and 16 human gliomas.

first: Wei-Chung

last: Cheng

first: Hsei-Wei

last: Wang


title: Nucleosome driven transcription factor binding and gene regulation [ChIP-Seq]

summary: Elucidating the global function of a transcription factor implies the identification of its target genes and genomic binding sites. The role of chromatin in this context is unclear, but the dominant view is that factors bind preferentially to nucleosome-depleted regions, identified as DNaseI-hypersensitive sites (DHS). Here we show by chromatin-IP, MNase and DNaseI assays followed by deep sequencing that the progesterone receptor (PR) requires nucleosomes for optimal binding and function. In breast cancer cells treated with progestins we identified 25,000 PR binding sites (PRbs), the majority encompassing several copies of the hexanucleotide TGTYCY, highly abundant in the genome. We found that functional PRbs accumulate around progesterone-induced genes mainly in enhancers, are enriched in DHS but exhibit high nucleosome occupancy. Progestin stimulation results in remodeling of these nucleosomes with displacement of histones H1 and H2A/H2B dimers. Our results strongly suggest that nucleosomes are crucial for PR binding and hormonal gene regulation.

overall_design: T47D-MTVL human breast cancer cells were incubated with the progestin R5020 for different times between 0 to 360 minutes at 37C. ChIP-seq experiments were performed using antibodies against progesterone receptor. Mononucleosomal DNA was prepared from cells untreated or stimulated 60 min with R5020 and subjected to deep sequencing using the Solexa Genome Analyzer.

first: Cecilia

last: Ballare

first: Giancarlo

last: Castellanos

first: Laura

last: Gaveglia

first: Sonja

last: Althammer

first: Juan

last: Gonzalez-Vallinas

first: Eduardo

last: Eyras

first: Roser

last: Zaurin

last: Soronellas

first: Guillermo

last: Vicent


title: Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements

city: Athens

first: Carlos

middle: Rafael

last: Infante

state: GA

address: 500 D.W. Brooks Dr

department: Genetics

institute: University of Georgia

summary: Extensive functional analyses have demonstrated that the pituitary homeodomain transcription factor Pitx1 plays a critical role in specifying hindlimb morphology in vertebrates. However, much less is known regarding the target genes and cis-regulatory elements through which Pitx1 acts. Earlier studies suggested that the hindlimb transcription factors Tbx4, HoxC10, and HoxC11 might be transcriptional targets of Pitx1, but definitive evidence for direct regulatory interactions has been lacking. Using ChIP-Seq on embryonic mouse hindlimbs, we have pinpointed the genome-wide location of Pitx1 binding sites during mouse hindlimb development and identified potential gene targets for Pitx1. We determined that Pitx1 binding is significantly enriched near genes involved in limb morphogenesis, including Tbx4, HoxC10, and HoxC11. Notably, Pitx1 is bound to the previously identified HLEA and HLEB hindlimb enhancers of the Tbx4 gene and to a newly identified Tbx2 hindlimb enhancer. Moreover, Pitx1 binding is significantly enriched on hindlimb relative to forelimb-specific cis-regulatory features that are differentially marked by H3K27ac. However, our analysis revealed that Pitx1 also strongly associates with many functionally verified limb enhancers that exhibit similar levels of activity in the embryonic mesenchyme of forelimbs and hindlimbs. We speculate that Pitx1 influences hindlimb morphology both through the activation of hindlimb specific enhancers as well as through the hindlimb-specific modulation of enhancers that are active in both sets of limbs.

overall_design: Embryonic hindlimb buds from 4 ICR mouse samples were used.

middle: R

first: Sungdae

last: Park

first: Douglas

middle: B

last: Menke


title: The Growth factor independence 1 (GFI1) 36N variant predisposes to Acute Myeloid Leukemia (AML) by inducing epigenetic changes at the Hoxa9 locus

status: Public on Dec 04 2012

city: Cambridge

first: Judith

last: Schütte

address: Hills Road

country: United Kingdom

institute: Cambridge Institue for Medical Research

summary: GFI136N is a coding Single Nucleotide Polymorphism (SNP) in the gene GFI1 that increases the risk for Acute myeloid leukemia (AML) by 60%. It is present in 3-5% of Caucasians and has a prevalence of 12% among AML patients. We generated knockin mice expressing either the human GFI136N variant or the more common GFI136S form and observed that GFI136N, in contrast to GFI136S, lacked the ability to bind to the Gfi1 target gene and leukemia associated transcription factor Hoxa9 in myeloid precursors and failed to initiate the histone modifications that regulate HoxA9 expression. Consistent with this, GFI136N heterozygous AML patients showed increased HOXA9 expression compared to control patients. In the knockin mice, granulo-monocytic pogenitors (GMPs), a bone marrow subset from which AML can arise, show a proliferative expansion in the presence of the GFI136N variant. Finally, the GFI136N variant increased colony formation and proliferation of myeloid precursors induced by the onco-fusion proteins MLL/AF9 or AML1/Eto9a and accelerated the onset of a KRAS-driven myelo-proliferative disease. Our data suggest that GFI136N predisposes to AML by deregulating the expression of Hoxa9, a locus highly relevant for AML, thereby inducing a pre-leukemic state in myeloid precursors that can give rise to AML.

overall_design: 3 samples (2 histone modifications, 1 transcription factor)

first: Cyrus

last: Khandanpour

first: Joseph

last: Krongold

first: Frederique

last: Bouwman

first: Lothar

last: Vassen

first: Marie-Claude

last: Gaudreau

first: Riyan

last: Chen

first: Fernando

last: Calero-Nieto

first: Evangelia

last: Diamanti

first: Rebecca

last: Hannah

first: Sara

middle: E

last: Meyer

first: Leighton

last: Grimes

first: Bert

last: van der Reijden

first: Joop

last: Jansen

first: Chandrashekhar

middle: V

last: Patel

first: Justine

last: Peeters

first: Bob

last: Löwenberg

first: Ulrich

last: Dührsen

first: Bertie

last: Göttgens

first: Tarik

last: Möröy


title: A SWI/SNF nucleosome remodeling complex acts in non-coding RNA-mediated transcriptional silencing

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

summary: RNA-mediated transcriptional silencing prevents deleterious effects of transposon activity and controls the expression of protein-coding genes. It involves long non-coding RNAs (lncRNAs)1, which in Arabidopsis thaliana are produced by a specialized RNA Polymerase V (Pol V)2. lncRNAs guide Argonaute-siRNA complexes to specific genomic loci and mediate the establishment of DNA methylation3,4. The mechanism by which lncRNAs affect chromatin structure and mRNA production remains mostly unknown. Here we identify the SWI/SNF nucleosome remodeling complex as a component of the RNA-mediated transcriptional silencing pathway. We found that SWI3, an essential subunit of the SWI/SNF complex, physically interacts with a lncRNA-binding IDN2 protein5,6. RNA-mediated DNA methylation and transcriptional silencing was compromised in the swi3 mutant. Moreover, targets of SWI/SNF significantly overlapped with genes controlled by Pol V, which shows that the physical interaction reflects a functional relationship. We further found that non-coding transcription by Pol V affects nucleosome positioning on silenced regions. We propose that lncRNAs mediate transcriptional silencing by guiding the SWI/SNF complex and establishing positioned nucleosomes on specific genomic loci. We further propose that guiding ATP-dependent chromatin remodeling complexes may be a more general function of lncRNAs.

overall_design: RNA-seq of 3 samples (Col-0, nrpe1, swi3b, idn2) with 3 biological replicates.

first: Yongyou

last: Zhu

first: Gudrun

last: Böhmdorfer

first: Andrzej

middle: T

last: Wierzbicki


title: Nucleosome remodeling by the SWI/SNF complex in non-coding RNA-mediated transcriptional gene silencing


title: Nucleosome remodeling by the SWI/SNF complex in non-coding RNA-mediated transcriptional gene silencing (ChIP-seq)

overall_design: H3 ChIP-seq of 2 samples (Col-0 and nrpe1) with 2 biological repeats.


title: High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (RNA-seq)

city: Lausanne

first: Swapna

last: Uplekar

address: Station 19, EPFL-GHI-UPCOL

country: Switzerland

institute: EPFL

summary: To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches, strand-specific RNA-seq and ChIP-seq, to survey the global transcriptome and monitor genome-wide dynamics of RNA polymerase (RNAP) and NusA.  ChIP-seq revealed that RNAP and the antiterminator, NusA, occurred ubiquitously with the NusA profile mirroring RNAP distribution in both the exponential and stationary phases of growth.  Generally, promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease in signal strength reflecting transcriptional polarity.  Differential binding of RNAP and NusA in the two growth conditions correlated with transcriptional activity as reflected by RNA abundance.  Indeed, a significant association between expression levels and the presence of NusA throughout the gene body was detected, confirming the peculiar transcription-promoting role of NusA.  Integration of the datasets pinpointed transcriptional units, mapped promoters and uncovered new anti-sense and non-coding transcripts.  Highly expressed transcriptional units were situated mainly on the leading strand, despite the relatively unbiased distribution of genes throughout the genome, thus helping the replicative and transcriptional complexes to align.

overall_design: RNA-Seq in exponential and stationary phase cultures

first: Jacques

last: Rougemont

first: Stewart

last: Cole

first: Claudia

last: Sala


title: RIPSEQ DNMT1 HL60

first: Touati

last: Benoukraf

summary: Identification of the all RNA species associated with DNMT1. Using a comparative genome-scale approach we identified and correlated the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci and expression levels of the respective genes. This comparative approach delineated the first -DNMT1 centered- 'epitranscriptome' map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile.

first: Annalisa

last: Di Ruscio

first: Alexander

last: Ebralidze

first: Mengchu

last: Wu

first: Daniel

last: Tenen


title: High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (ChIP-seq)

overall_design: ChIP-Seq of RNAP and NusA in Mtb H37Rv at exponential and stationary phase cultures. Each experiment was performed in duplicate. Input DNA (No IP) was used as a control.


title: Relationship between DNMT1-RNA interactions, DNA methylation and gene expression

type: Methylation profiling by high throughput sequencing


title: High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis


title: Species-specific splicing differences are primarily governed by changes in  cis-acting sequences

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

summary: We assessed whether human transcripts expressed in an aneuploid mouse that carries human chromosome 21 (HsChr21) are spliced in a human-specific or mouse-specific fashion. In almost all cases, human-specific alternative splicing is maintained in the mouse nucleus. Species-specific splicing therefore appears to be primarily directed by cis-acting elements, rather than changes in the levels or activities of trans-acting factors.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Approximately 485 million Illumina 50-nt sequence reads were generated for brain and liver tissues from normal human, Tc0 (wildtype) mouse and Tc1 mouse strains.  Sequence reads were mapped to splice junctions and %in levels were estimated.

first: Valentina

last: Slobodeniuc

first: Nuno

last: Barbosa-Morais

first: Michael

middle: D

last: Wilson

last: Kutter

first: Hong

last: Han

first: Duncan

last: Odom

first: Benjamin

last: Blencowe


title: Porphyromonas gingivalis investigated by RNA-Seq

city: Seattle

first: David

middle: A. C.

last: Beck

state: WA

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

summary: Comparison of transcriptomes for wild-type and the following mutants: LuxS, GppX, cdhR

overall_design: Four conditions are compared with at least two replicates for each

first: Takanori

last: Hirano

first: Erik

last: Hendrickson

first: Murray

last: Hackett

first: Donald

last: Demuth

first: Richard

middle: J

last: Lamont


title: RRBS (Reduced Representation Bisulfite Sequencing) of HL60

first: Touati

last: Benoukraf

summary: We exploited the methylation genome-scale screening RRBS to correlate the RNA species physically associated with DNMT1 and proximal to the annotated genes to the methylation status of the corresponding loci. Out of 15275 non ambiguous gene loci identified by DNMT1 RIP-Seq, 9436 loci were covered by RRBS. These 9436 loci were clustered according to the fold of specific DNMT1 library peaks enrichment (defined as the ratio of the sum of the area under the curve of specific DNMT1 library peaks covering the gene loci). Genes were then stratified by the expression profile ultimately leading to the epitranscriptome map, a comprehensive map cross-referencing DNMT1-interacting transcripts to (i) DNA methylation and (ii) gene expression profile.

first: Annalisa

last: Di Ruscio

last: Ebralidze


title: Deep sequencing analysis of the murine transcriptome response to different virulent parenthood B. melitensis infection

city: Harbin

first: Fangkun

last: Wang

address: 427 Maduan Street

department: Harbin Veterinary Research Institute

institute: Chinese Academy of Agricultural Sciences

summary: In this study, we employed the Illumina Genome Analyzer platform to perform a Digital Gene Expression (DGE) analysis of the peritoneal macrophages genome-wide transcriptome response to B.melitensis infection. Common changes in gene expression were observed among Brucella app. infected macrophages suggesting similar strategies were employed for their survival and replication, inducing anti-inflammatory and anti-apoptotic. A total of 1019 differentially expressed (DE) transcripts were identified in the macrophages 4 hours after differ virluent B.melitensis infection, especially genes participated lysosome pathway and MAPK pathway. Our findings demonstrate previously unrecognized changes in gene transcription that are associated with B.melitensis infection in the macrophages, and many significant pathways (cascades) identified in the study clearly merit further investigation. Our data provide new clues to understand the molecular attenuation mechanism of M5-90 and a firm foundation for reducing vaccine residual virulence, enhancing vaccine efficacy.

overall_design: Examination oftwo peritoneal macrophages infected brucella and one blank control.

first: F

first: Z.

last: Bu


title: Genomic analysis of the combined effects of H-NS and co-regulators on E. coli gene expression

city: Hinxton

first: Aswin Sai Narain

last: Seshasayee

address: Wellcome Trust Genome Campus

institute: EMBL-EBI

summary: This entry refers to transcriptome analysis of E. coli with single deletions of hns, stpA, hha and ydgT and double deletions of hns with each of the other three regulators mentioned.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: 8 samples with 2 replicates each

first: Aswin

first: Rajalakshmi

last: Srinivasan


title: Gene expression analysis of murine SAMHD1 deficient peritoneal macrophages

city: Dresden

first: Tina

last: Schumann

address: Fetscherstraße 74

department: Medical Faculty "Carl Gustav Carus"

country: Germany

institute: Institute of Immunology

summary: To elucidate responses of myeloid cells to SAMHD1 deficiency in the absence of exogenous viral infection, we performed global gene expression analysis of SAMHD1 deficient macrophages.

overall_design: Peritoneal macrophages from nine mutants and nine controls were FACS sorted. Cells from three animals were pooled to yield three poolls per group. RNA from these pools was subjected to next generation mRNA sequencing

first: Rayk

last: Behrendt

first: Andreas

last: Dahl

first: Dimitra

last: Alexopoulou


title: Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 in pancreas cancer

status: Public on Nov 30 2012

first: Andrew

last: Deonarine

institute: Laboratory of Molecular Biology

summary: An autochthonous model of pancreatic ductal adenocarcinoma (PDA) permitted the analysis of why immunotherapy is ineffective in this human disease. Despite finding that PDA-bearing mice had cancer cell-specific CD8+ T cells, the mice, like human PDA patients, did not respond to two immunological checkpoint antagonists that promote the function of T cells, α-CTLA-4 and α-PD-L1. Immune control of PDA growth was achieved, however, by depleting carcinoma-associated fibroblasts (CAFs) that express Fibroblast Activation Protein (FAP).  The depletion of the FAP+ stromal cell also uncovered the anti-tumor effects of α-CTLA-4 and α-PD-L1, indicating that its immune suppressive activity accounts for the failure of these T cell checkpoint antagonists. Three findings suggested that CXCL12 explained the overriding immunosuppression by the FAP+ cell: T cells were absent from regions of the tumor containing cancer cells; cancer cells were coated with the chemokine, CXCL12; and the FAP+ CAF was the principle source of CXCL12 in the tumor. Administering AMD3100, a CXCL12 receptor (CXCR4) inhibitor, induced rapid T cell accumulation among cancer cells, and acted synergistically with α-PD-L1 to selectively and greatly diminish cancer cells, identified by their loss-of-heterozygosity (LOH) of Trp53. The residual tumor was comprised only of pre-malignant epithelial cells and inflammatory cells.  Thus, a single protein, CXCL12, from a single stromal cell type, the FAP+ CAF, may direct tumor immune evasion in a model of human PDA.

overall_design: FAP+ cells were sorted from pancreatic ductal adenocarcinoma. Cells were isolated in duplicate experiments and these were analysed separately. These were compared separately to previously published publicly available CD4+ T-cell subset data (C57BL/6 mice and Foxp3-RFP mice (Line 8374) GEO accession GSE20898), and previously published FAP+ cell datasets (transgenic albino (Tyr-/-) C57BL/6 mouse, GEO accession GSE39438).

first: C

last: Feig

first: J

middle: O

last: Jones

first: M

last: Kraman

first: R

last: Wells

first: A

first: D

last: Chan

middle: M

last: Connell

first: E

middle: W

last: Roberts

first: Q

last: Zhao

first: O

middle: L

last: Caballero

first: S

last: Teichmann

first: T

last: Janowitz

middle: I

last: Jodrell

last: Tuveson

last: Fearon


title: Chromatin occupancy of key transcriptional regulators in the presence of the BET bromodomain inhibitor JQ1

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: MM1.S cells are an aggressive dexamethasone sensitive multiple myeloma cell line whose transcritional program is driven by deregulated c-Myc activity.  We present ChIP-seq analysis of key transcritional regulators that are implicated the c-Myc transcriptional network in MM1.S cells treated with vehicle or 500nM JQ1.

overall_design: Brd4, Cdk9, cMyc, Max, Med1, RNA Pol II, and the chromatin modifications H3K4me3 and H3K27Ac were profiled in MM1.S cells treated with 500nM JQ1 for 24hr

first: Rahl

last: Peter

first: Jakob

last: Loven


title: Tissue-specific regulation of chromatin insulator function

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Chromatin insulators organize the genome into distinct transcriptional domains and contribute to cell type-specific chromatin organization. However, factors regulating tissue-specific insulator function have not yet been discovered. Here we identify the RNA recognition motif-containing protein, Shep, as a direct interactor of two individual components of the gypsy insulator complex in Drosophila. Mutation of shep improves gypsy-dependent enhancer blocking, indicating a role as a negative regulator of insulator activity. Unlike ubiquitously expressed core gypsy insulator proteins, Shep is highly expressed in the central nervous system (CNS) with lower expression in other tissues. We developed a novel, quantitative tissue-specific barrier assay to demonstrate that Shep functions as a negative regulator of insulator activity in the CNS but not in muscle tissue. Additionally, mutation of shep alters insulator complex nuclear localization in the CNS but not other tissues. Consistent with negative regulatory activity, ChIP-seq analysis of Shep in a CNS-derived cell line indicates substantial genome-wide colocalization with a single gypsy insulator component but limited overlap with intact insulator complexes. Taken together, these data reveal a novel, tissue-specific mode of regulation of a chromatin insulator.

overall_design: ChIP-seq of Shep, Su(Hw), and Mod(mdg4)2.2 in Drosophila BG3 cells along with alternate antibodies

first: Leah

middle: H

last: Matzat

middle: K

first: Elissa

middle: P

last: Lei


title: Role of PRC2 complex components in prostate cancer cell lines

city: San Antonio

first: Kexin

last: Xu

state: TX

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Nucleosome remodeling by the SWI/SNF complex in non-coding RNA-mediated transcriptional gene silencing (MNase-Seq)

last: Rowley

overall_design: Mnase-seq of 2 samples (Col-0 and nrpe1).

first: Yongyou

last: Zhu

first: Gudrun

last: Böhmdorfer

first: Andrzej

last: Wierzbicki


title: Chromatin Looping of Normal and Cancerous Prostate Cells

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

summary: Mapping the locations of the DNA binding protein CTCF genome-wide to assess its colocalisation with expression domain boundaries.

overall_design: One PrEC sample, a normal cell line. One LNCaP sample, a cancer cell line.

first: A


title: Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans

city: Nijmegen

first: Eugene

middle: Thomas Pieter

last: Verwiel

state: Gelderland

address: Geert Grooteplein zuid 10

department: Human Genetics

country: Netherlands

institute: Radboud University Medical Centre

summary: Candida albicans is the most common human fungal pathogen causing mucosal and systemic infections. However, human antifungal immunity remains poorly defined. By integrating transcriptional analysis and functional genomics we identified Candida-specific host defense mechanisms in humans. Candida induced significant (p<10-35) expression of genes from the type I interferon (IFN) pathway in human peripheral blood mononuclear cells. This unexpectedly prominent role of type I IFN pathway in anti-Candida host defense was supported by additional evidence. Polymorphisms in type I IFN genes modulated Candida-induced cytokine production and were correlated with susceptibility to systemic candidiasis. In in-vitro experiments, type I IFNs skewed Candida-induced inflammation from a Th17-response toward a Th1-response. Patients with chronic mucocutaneaous candidiasis displayed defective expression of genes in the type I IFN pathway. These findings indicate that the type I IFN pathway is a main signature of Candida-induced inflammation and plays a crucial role in anti-Candida host defense in humans.

overall_design: 3 healthy controls and 2 CMC patients

first: Sanne

last: Smeekens

first: Aylwin

last: Ng

first: Vinod

last: Kumar

first: Melissa

last: Johnson

first: Theo

middle: S

last: Plantinga

first: Cleo

last: van Diemen

first: Peer

last: Arts

first: Eugène

first: Mark

last: Gresnigt

first: Karin

last: Fransen

first: Suzanne

last: van Sommeren

first: Marije

last: Oosting

first: Shih-Chin

last: Cheng

first: Leo

last: Joosten

first: Alexander

last: Hoischen

first: Bart-Jan

last: Kullberg

first: William

last: Scott

first: John

middle: R

last: Perfect

first: Jos

last: van der Meer

first: Cisca

last: Wijmenga

first: Mihai

middle: G

last: Netea

first: Ramnik

last: Xavier


title: H3K27me3 Marks in Normal and Cancerous Prostate Cells

first: Aaron

last: Statham

summary: The histone modification H3K27me3 is representative of silenced regions of the genome. Changes between the normal and cancer state were investigated.

overall_design: Three PrEC samples, a normal cell line. Four LNCaP sample, a cancer cell line. Technical replicates.

first: A


title: Genome-wide maps of PRC2 complex components and chromatin states in prostate cancer cell lines

first: Kexin

last: Xu

summary: We report the high-throughput profiling of PRC2 core subunits chromatin states and histone modifications in two prostate cancer cell lines, androgen-dependent cells LNCaP and androgen-independent cells LNCaP-abl (abl). By obtaining over 1 billion bases of sequence from chromatin immunoprecipitated DNA, we generated the genome-wide localizations of EZH2, SUZ12 and H3K27 trimethylation in both cell lines, and found that EZH2 can be localized to a subsets of chromating sites that don't have H3K27me3 or SUZ12 signals nearby. Interestingly, these sites are enriched for the active histone marks H3K4 di/trimethylation as well as the RNA polymerase II, which suggest the potential function of these peaks in gene activation. Indeed, these sites are enriched near the transcription start sites of EZH2-activated genes. Further analysis of the transcription factor motifs enriched at these peaks revealed the enrichement of androgen receptor motif, suggesting a co-activator role for EZH2 in concert with AR. Our work demonstrated a novel funtion of EZH2 in transcriptional activation by directly binding to the chromatin sites that cooperate with AR.

overall_design: Study of the chromatin localizations of PRC2 complex core subunits and different histone marks in 2 cell types

first: Zhenhua

last: Wu


title: H3K4me3 Marks in Normal and Cancerous Prostate Cells

summary: H3K4me3 ChIP-seq was done to examine transcription start sites in a genome wide manner, and compare results to CAGE-seq


title: DNA Methylation in IMR90 cells

summary: DNA methylation was measured by MBD2 enrichment of DNA fragments in IMR90. A statistical model was developed to estimate absolute methylation levels, and compared to whole genome bisulfite sequencing results (Lister, R. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature)

overall_design: Two techincal replicates of MBD2 methylated DNA enrichment in IMR90 cells.


title: Mapping of Transcription Start Sites of Normal and Cancerous Prostate Cells

summary: Capped analysis of gene expression (CAGE) sequencing was done on a normal and a cancer cell line to examine how promoter usage changes between these two states.


title: Expression Analysis of Normal and Cancerous Prostate Cells

summary: Strand-specific RNA sequencing was done on a normal and a cancer cell line to examine how isoforms are used differently between these two states.


title: RNA polymerase II collision interrupts convergent transcription (RNA-seq)

city: Heidelberg

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

institute: EMBL Heidelberg

summary: Anti-sense non-coding transcripts, genes-within-genes, and convergent gene pairs are prevalent among eukaryotes. The existence of such transcription units raises the question of what happens when RNA polymerase II (RNAPII) molecules collide head-to-head. Here we use a combination of biochemical and genetic approaches in yeast to show that polymerases transcribing opposite DNA strands cannot bypass each other. RNAPII stops, but does not dissociate upon head-to-head collision in vitro, suggesting that opposing polymerases represent insurmountable obstacles for each other. Head-to-head collision in vivo results in RNAPII stopping as well, and removal of collided RNAPII from the DNA template can be achieved via ubiquitylation-directed proteolysis. Indeed, in cells lacking efficient RNAPII poly-ubiquitylation, the half-life of collided polymerases increases, so that these can be detected between convergent genes by ChIP-Seq. These results provide new insight into fundamental mechanisms of gene traffic control, and point to an unexplored effect of anti-sense transcription on gene regulation via polymerase collision.

overall_design: Total RNA was extracted from WT or Elongin C deletion mutant (elc1∆) cells and strand-specific RNA-Seq was performed. Three biological replicates were performed for WT and elc1∆.

first: David

last: Hobson

first: Lars

last: Steinmetz

first: Jesper

middle: Q

last: Svejstrup


title: RNA polymerase II collision interrupts convergent transcription


title: RNA polymerase II collision interrupts convergent transcription (ChIP-seq)

overall_design: ChIP-Seq of RNA polymerase II was performed with WT and Elongain C deletion mutant (elc1∆) cells. 4H8 antibody against the Rpb1 C-terminal domain was used for RNA polymerase II immunoprecipitation, whilst mouse IgG antibody was used for control immunoprecipitations. Two biological replicates were performed for both WT and elc1∆.


title: Genomic DNA in Normal and Cancerous Prostate Cells

type: Genome variation profiling by high throughput sequencing

summary: To investiagate copy number differences between PrEC and LNCaP cells, each was DNA sequenced.


title: Decoupling epigenetic and genetic effects through systematic analysis of gene position

status: Public on Nov 28 2012

city: La Jolla

first: Menzies

last: Chen

address: 9500 Gilman Drive MC 0688

department: Bioengineering

institute: UCSD

summary: Classic ‘position effect’ experiments repositioned genes to the telomere to demonstrate that the epigenetic landscape can dramatically alter gene expression. Here we show that systematic gene knockout collections provide an exceptional resource for interrogating position effects, not only at the telomere but at every single genetic locus. Because deleted genes are replaced by the same reporter gene, interrogation of this reporter provides a sensitive probe into many different chromatin environments while controlling for genetic context. Using this approach we find that, whereas replacement of yeast genes with the kanMX marker does not perturb the chromatin landscape, differences due to gene position account for more than 35% of marker gene activity. We observe chromatin influences different from those reported previously, including an antagonistic interaction between histone H3 lysine 36 trimethylation (H3K36me3) and the Rap1 transcriptional activation site in kanMX that is mediated through a Set2-Rpd3-dependent pathway. This interaction explains why some yeast genes have been resistant to deletion and allows successful generation of these deletion strains using a modified transformation procedure. These findings demonstrate that chromatin regulation is not governed by a uniform ‘histone code’, but by specific interactions between chromatin and genetic factors.

overall_design: Data included are RNA-Seq data for 4 heterzygous diploid yeast strains and diploid wild-type. Therea re three replicates for each heterzygous strain, and six replicates for wild-type.

first: Chen

last: Menzies

first: Zhang

last: Fan


title: CpG underrepresentation and the new bacterial CpG specific DNA methyltransferase M.MpeI

status: Public on Nov 29 2012

city: Warsaw

first: Matthias

last: Bochtler

address: Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology

summary: The CpG depleted Mycoplasma penetrans harbors a CpG specific C5 methyltransferase. The aim of this experiment was to confirm the specificity of the methyltransferase in vivo and in vitro.

sample_organism:
Escherichia coli
Malacoplasma penetrans

platform_organism:
Escherichia coli
Malacoplasma penetrans

overall_design: Genomic DNA from Mycoplasma penetrans and Escherichia coli genomic DNA that either was or was not methylated in vitro by M.MpeI were subjected to Illumina MiSeq bisulfite sequencing.

first: Marek

last: Wojciechowski

first: Honorata

last: Czapinska


title: Genetics of gene expression responses to temperature stress in a sea urchin gene network (HTS)

city: Durham

first: Daniel

last: Runcie

state: NC

department: Biology Department

institute: Duke University

summary: Stress responses play an important role in shaping species distributions and robustness to climate change. We investigated how stress responses alter the contribution of additive genetic variation to gene expression during development of the purple sea urchin, Strongylocentrotus purpuratus, under increased temperatures that model realistic climate change scenarios. We first measured gene expression responses in the embryos by RNA-seq to characterize molecular signatures of mild, chronic temperature stress in an unbiased manner. We found that an increase from 12 °C to 18 °C caused widespread alterations in gene expression including in genes involved in protein folding, RNA processing, and development. To understand the quantitative genetic architecture of this response, we then focused on a well-characterized gene network involved in endomesoderm and ectoderm specification. Using a breeding design with wild-caught individuals, we measured genetic and gene-environment interaction effects on 72 genes within this network. We found genetic or maternal effects in 33 of these genes, and that the genetic effects were correlated in the network. 14 network genes also responded to higher temperatures, but we found no significant genotype-environment interactions in any of the genes. This absence may be due to an effective buffering of the temperature perturbations within the network. In support of this hypothesis, perturbations to regulatory genes did not affect the expression of the genes that they regulate. Together, these results provide novel insights into the relationship between environmental change and developmental evolution and suggest that climate change may not expose large amounts of cryptic genetic variation to selection in this species.

overall_design: 7 RNAseq samples representing embryos grown at 2 temperatures, from 3 female parents and 2 male parents

middle: E

last: Garfield

first: Courtney

middle: C

last: Babbitt

first: Jennifer

last: Wygoda

first: Sayan

last: Mukherjee

first: Gregory

last: Wray


title: UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery [RNA-Seq and RIP-Seq]

city: Worcester

first: Jie

last: Wang

address: 364 Plantation St.

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: The transposon silencing piRNAs are produced from precursors that are encoded by heterochromatic clusters and processed in the perinuclear nuage. We show that the Drosophila nuclear DEAD box protein UAP56, previously implicated in mRNA splicing and nuclear export, co-localizes with the cluster-associated HP1 homologue Rhino. Prominent nuclear foci containing Rhi and UAP56 localize directly across the nuclear envelope from Vasa, a conserved DEAD box protein and core nuage component that is required for piRNA production, and piRNA precursors immunoprecipitate with both UAP56 and Vasa.   A uap56 point mutation that prevents UAP56 protein co-localization with Rhino also disrupts nuage organization, transposon silencing, and expression of dual strand piRNA clusters.  By contrast, this allele significantly increases ectopic piRNAs from protein coding genes.  We therefore propose that UAP56 and Vasa organize a piRNA-processing compartment that spans the nuclear envelope, increasing the efficiency and specificity of piRNA biogenesis.

overall_design:
RNA-Seq: 3 samples examined: w1118, uap56 mutant un-oxidized, uap56 mutant oxidized
RIP-Seq: 6 samples: UAP56-Venus, sz-Venus, and wild type w1 with anti-flag and input control each.

first: Fan

last: Zhang

first: Zhao


title: Mouse Model of Clear Cell Sarcoma

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

summary: Profile gene expression from tumors that develop in mice bearing conditional activation of EWS-ATF1, compared to control mouse tissues from the chest wall as well as tumor samples from mouse models of synovial sarcoma and osteosarcoma achieved by conditional disruption of Rb1 and p53

overall_design: 13 clear cell sarcomas (5 started with Rosa26CreER, 4 with TATCre, 2 with Prx1CreERT2, and 2 with Bmi1IRESCreERT2), 7 osteosarcomas, 6 synovial sarcomas, 6 control samples

first: Mario

last: Capecchi


title: Genome-wide DNA methylation profiling of human dorsolateral prefrontal cortex

city: Huntsville

first: Kevin

last: Bowling

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

summary: Reduced representation bisulfite sequencing (RRBS) was conducted on dorsolateral prefrontal cortex tissue samples taken from the brains of control individuals not affected by neurological disorder

overall_design: DNA methylation profiling was conducted using RRBS and the Illumina Genome Analyzer IIx

first: Katherine

last: Varley

first: Richard

last: Myers


title: UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery

summary: This SuperSeries is composed of the SubSeries listed below.


title: Genome-wide TNFα-induced p65 binding before and after telomerase inhibition in HeLa cells

status: Public on Nov 26 2012

city: Singapore

first: Gaye

last: Saginc

address: 60 Biopolis Street

department: Genome Institute of Singapore

country: Singapore

institute: A*STAR

summary: Chromatin immunoprecipitation sequencing (ChIP-seq) was performed to analyze the effect of telomerase inhibition on TNFα-induced genome-wide p65 binding in HeLa cells. By obtaining over 40 million uniquely mappable reads per sample from ChIP-seq, maps for TNFα-induced p65 binding in absence and presence of an hTERT inhibitor, MST-312, were generated. As expected, TNFα treatment significantly increased genome-wide p65 occupancy. Interestingly, when cells were treated with MST-312 prior to TNFα stimulation, the number of p65 binding sites was reduced. In addition, some binding sites, including important p65 targets like IL6 and TNF, showed a reduced p65 occupancy with a minimum fold change of 1.5, after MST-312 exposure. Taken together, our ChIP-seq data indicate that telomerase is required for optimal p65 binding at a small proportion of p65 target sites upon inflammatory stimuli.

overall_design: Examination of p65 binding in HeLa cells in absence and presence of TNFα and MST-312.

first: Zhizhuo

first: Guoliang

last: Li

first: Arka

last: Ghosh

first: Shi

last: Leow

first: Edison

middle: T

last: Liu

first: Vinay

last: Tergaonkar


title: An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants

city: St Paul

first: Sam

last: Yang

state: MN

address: 411 Upper Buford Circle

department: ARS

institute: USDA

summary: Phosphorus, in its orthophosphate form (P(i)), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole-genome molecular mechanisms contributing to plant acclimation to P(i) deficiency remain largely unknown. White lupin (Lupinus albus) has evolved unique adaptations for growth in P(i)-deficient soils, including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to P(i) supply. We de novo assembled 277,224,180 Illumina reads from 12 complementary DNA libraries to build what is to our knowledge the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 50,734 were transcriptionally active (reads per kilobase per million reads ≥ 3), representing approximately 7.8% of the white lupin genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to P(i) deficiency with a 2-fold or greater change and P ≤ 0.05. Twelve sequences were consistently differentially expressed due to P(i) deficiency stress in three species, Arabidopsis (Arabidopsis thaliana), potato (Solanum tuberosum), and white lupin, making them ideal candidates to monitor the P(i) status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in P(i) deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to P(i) deficiency.

overall_design: Examination of 2 different tissue types (roots and leaves) under phosphorus (P) -sufficient or P-deficient condition with 3 biological replications per condition in white lupin (Lupinus albus).

first: Carroll

last: Vance

first: Jamie

last: O'Rourke


title: Transcriptional silencing of transposable elements by Piwi and its impact on chromatin and gene expression

city: Vienna

first: Grzegorz

last: Sienski

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

summary: Eukaryotic genomes are colonized by transposable elements whose uncontrolled activity results in genomic instability. The piRNA pathway silences transposons in animal gonads, yet how this is achieved molecularly remains controversial. We assign an essential role to the HMG protein Maelstrom in the process of Piwi mediated silencing in Drosophila. Genome wide assays revealed highly correlated changes in RNA Polymerase II recruitment, nascent RNA output and steady state RNA levels of transposons upon loss of Piwi or Maelstrom. Our data demonstrate piRNA-mediated trans- silencing of hundreds of transposon copies at the transcriptional level. We show that Piwi is required for establishing heterochromatic H3K9me3 marks on transposons and their genomic surrounding. In contrast, loss of Maelstrom impacts transposon H3K9me3 patterns only marginally yet leads to increased heterochromatin spreading, suggesting that Maelstrom acts downstream of or in parallel to H3K9me3. Our work uncovers the widespread influence of transposons and the piRNA pathway on chromatin patterns and gene expression programs.

overall_design:
RNA Polymerase II and H3K9me3 occupancy, and steady-state and nascent RNA levels in wild-type ovarian somatic cells (OSC) and RNAi knock-downs of the piRNA pathway components.
RNA Polymerase II occupancy in tissue-specific knockdowns of tejas (control) and armi in somatic cells of Drosophila ovary.

first: Julius

last: Brennecke


title: RNAi triggered by specialized machinery silences developmental genes and retrotransposons (RNA-Seq)

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: RNAi is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, genes encoding transmembrane proteins, and retrotransposons that are also targeted by the exosome RNA degradation machinery. In the absence of the exosome, transcripts are processed preferentially by the RNAi machinery, revealing widespread occurrence of siRNA clusters and corresponding increase in heterochromatin modifications across large domains. We show that the generation of siRNAs and heterochromatin assembly by RNAi is triggered by a mechanism involving the canonical poly(A) polymerase Pla1 and an associated RNA surveillance factor Red1, which also activate the exosome. Remarkably, siRNA production and heterochromatin modifications at genes are regulated by environmental growth conditions, and by developmental signals that induce gene expression during sexual differentiation. Our analyses uncover interplay between RNAi and the exosome that is conserved in higher eukaryotes, and show that differentiation signals modulate RNAi silencing to regulate developmental genes.

sample_organism:
Schizosaccharomyces pombe
Drosophila melanogaster

overall_design: We sequenced 7 samples from Schizosaccharomyces pombe and 2 samples from Drosophila melanogaster.

first: Soichiro

last: Yamanaka

first: Sameet

last: Mehta

first: Fanglei

last: Shuang

first: Ryan

last: Fuchs

first: Yikang

last: Rong

first: Gregory

middle: B

last: Robb


title: Integrative Epigenomic Analysis Identifies Biomarkers and Therapeutic Targets in Adult B-Acute Lymphoblastic Leukemia

status: Public on Nov 27 2012

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

type: Methylation profiling by genome tiling array

overall_design: Refer to individual Series


title: Genetics of gene expression responses to temperature stress in a sea urchin gene network

first: Daniel

last: Runcie

first: David

last: Garfield

first: Courtney

last: Babbitt

first: Jennifer

last: Wygoda

first: Sayan

last: Mukherjee

last: Wray


title: Expression profiles of microRNAs from lactating and non-lactating bovine mammary glands and identification of miRNA related to lactation.

city: Hangzhou

first: Zhen

last: Li

address: 866 Yuhang Tang Road

institute: College of Animal Science, Zhejiang University

summary: miRNAs have been implicated in the regulation of milk protein synthesis and development of mammary gland. However, the function of miRNAs in regulating lactation is unclear. Therefore, the elucidation of miRNA expression profiles in MG provides a crucial entry into the understanding of the mechanisms of lactation initiation. Our present work is to examine miRNA expression profiles in bovine mammary gland, and to evaluate miRNAs function through the identification of differentially expressed miRNA between lactation and non-lactation mammary gland. Identification of novel miRNAs highlights the important function of low abundance and less conserved miRNAs. An interaction network of known miRNAs and their target genes around the lactation function was constructed to postulate the functional roles of miRNAs in mammary gland. This integrated analysis provides important information that will inspire further experimental investigations into the field of miRNAs and their targets during lactation.

overall_design: Examination of 2 different miRNA expression profilings in bovine mammary gland

first: Hongyun

last: Liu

first: Xiaolu

last: Jin

first: Lijan

last: Lo

first: Jianxin


title: Genomic Study of RNA Polymerase II and III SNAPc-Bound Promoters Reveals a Gene Transcribed by both Enzymes and a Broad Use of Common Activators

status: Public on Nov 22 2012

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV

summary: SNAPc-dependent promoters are unique among cellular promoters in being very similar to each other, even though some of them recruit RNA polymerase II and other RNA polymerase III. We have examined all SNAPc-bound promoters present in the human genome. We find that there is a surprisingly small number of them, some 70 promoters. Among these, the large majority is bound by either RNA polymerase II or RNA polymerase III, as expected, but one gene hitherto considered an RNA polymerase III gene is also occupied by significant levels of RNA polymerase II, which synthesizes an RNA distinct from that synthesized by RNA polymerase III. Both RNA polymerase II and RNA polymerase III SNAPc- dependent promoters use a largely overlapping set of a few transcription activators, including GABP, a novel factor implicated in snRNA gene transcription.

overall_design: SNAPc-dependent promoters in the human genome

first: Nicole

middle: J

last: Faresse

first: Donatella

last: Canella

first: Viviane

last: Praz

first: Joëlle

last: Michaud

last: Romascano

first: Nouria

last: Hernandez


title: H2A.Z inheritance during the cell cycle and its impact on promoter organization and dynamics [ChIP-seq]

status: Public on Nov 23 2012

first: Rohan

last: Williams

address: Medical Drive

institute: SCELSE-NUS

summary: While it has been clearly established that well positioned H2A.Z-containing nucleosomes flank the nucleosome depleted region (NDR) at the transcriptional start site (TSS) of active mammalian genes, how this chromatin-based information is transmitted through the cell cycle is unknown. We show here that in trophoblast stem (TS) cells, the level of H2A.Z at promoters decreases during S phase coinciding with homotypic (H2A.Z/H2A.Z) nucleosomes flanking the TSS becoming heterotypic (H2A.Z/H2A). Surprisingly, these nucleosomes remain heterotypic at M phase. At the TSS, we identify an unstable heterotypic H2A.Z-containing nucleosome in G1 which, strikingly, is lost following DNA replication. These dynamic changes in H2A.Z at the TSS mirror a global expansion of the NDR at S and M which, unexpectedly, is unrelated to transcriptional activity. Coincident with the loss of H2A.Z at promoters, it is targeted to the centromere when mitosis begins

overall_design: We performed ChIP-Seq experiments (on mouse Trophoblast Stem cells arrested at G1; S and M stages of thecell cycle) using antibodies against histone variant H2A.Z and sequentional ChIP-re-ChIP-Seq experiments using H2A.Z antibody and H2A antibody in sequence. Combining those data sets with microarray gene expression expression data allowed us to see H2A.Z distribution over promoters of mouse coding genes in cell cycle dependant manner. Interestingly, Input also showed cell-cycle dependent effects, but histone H3 could be used as a cell-cycle independent normalisation factor. We also performed ChIP-seq with a CTCF pull-down to investigate its cell-cycle dependent relationship with heterochromatin.

first: Max

last: Nekrasov

first: Cameron

last: Jack

first: Brian

last: Parker


title: High-throughput sequencing of small RNA transcriptome reveals salt stressed regulated microRNAs in sugarcane

status: Public on Nov 24 2012

city: Rio de Janeiro

first: Paulo

last: Ferreira

address: Rua Rodolpho Paulo Rocco s/nº, CCS, Bl.L, Cidade Universitária

country: Brazil

institute: Universidade Federal do Rio de Janeiro

summary: Salt stress is a primary cause of crop losses worldwide, and it has been the subject of intense investigation to unravel the complex mechanisms responsible for salinity tolerance. MicroRNA is implicated in many developmental processes and in responses to various abiotic stresses, playing pivotal roles in plant adaptation. Deep sequencing technology was chosen to determine the small RNA transcriptome of Saccharum sp cultivars grown on saline conditions. We constructed four small RNAs libraries prepared from plants grown on hydroponic culture submitted to 170 mM NaCl and harvested after 1 h, 6 hs and 24 hs. Each library was sequenced individually and together generated more than 50 million short reads. Ninety-eight conserved miRNAs and 33 miRNAs* were identified by bioinformatics. Several of the microRNA showed considerable differences of expression in the four libraries. To confirm the results of the bioinformatics-based analysis, we studied the expression of the 10 most abundant miRNAs and 1 miRNA* in plants treated with 170 mM NaCl and in plants with a severe treatment of 340 mM NaCl. The results showed that 11 selected miRNAs had higher expression in samples treated with severe salt treatment compared to the mild one. We also investigated the regulation of the same miRNAs in shoots of four cultivars grown on soil treated with 170 mM NaCl. Cultivars could be grouped according to miRNAs expression in response to salt stress. Furthermore, the majority of the predicted target genes had an inverse regulation with their correspondent microRNAs. The targets encode a wide range of proteins, including transcription factors, metabolic enzymes and genes involved in hormone signaling, probably assisting the plants to develop tolerance to salinity. Our work provides insights into the regulatory functions of miRNAs, thereby expanding our knowledge on potential salt-stressed regulated genes.

overall_design: Screenning of sRNA transcriptome of sugarcane plants infected with Acidovorax avenae subsp avenae after seven days

first: Mariana

last: Carnavale-Bottino

first: Sabrina

last: do Rosario

first: Clícia

last: Grativol

first: Flávia

last: Thiebaut

first: Cristian

last: Rojas

first: Laurent

last: Farinelli

first: Adriana

last: Hemerly


title: H2A.Z inheritance during the cell cycle


title: Differential sRNA regulation in leaves and roots of sugarcane under water depletion

summary: In order to increase our understanding on the epigenetic regulation in response to abiotic stresses in plants, sRNA regulation in sugarcane plants submitted to drought stress was analyzed. Deep sequencing analysis was carried out to identify the sRNA regulated in leaves and roots of sugarcane cultivars with different drought sensitivities.  An enrichment of 22-nt sRNA species was observed in leaf libraries. The pool of sRNA selected allowed the analysis of different sRNA classes (miRNA and siRNA). Twenty eight and 36 families of conserved miRNA were identified in leaf and root libraries, respectively. Dynamic regulation of miRNA was observed and the expression profile of eight miRNA was verified in leaf samples by stem-loop qRT-PCR assay. Altered miRNA regulation was correlated with changes in mRNA levels of specific targets. 22-nt miRNA triggered siRNA-candidates production by cleavage of their targets in response to drought stress. Some genes of sRNA biogenesis were down-regulated in tolerant genotypes and up-regulated in sensitive in response to drought stress. Our analysis contributes to increase the knowledge on the roles of sRNA in epigenetic-regulatory pathways in sugarcane submitted to drought stress.

sample_organism:
Saccharum hybrid cultivar (mixed)
Saccharum hybrid cultivar CTC6
Saccharum hybrid cultivar SP90-3414

overall_design: Screenning of sRNA transcriptome of sugarcane plants under drougth stress

first: Milos

last: Tanurdzic

first: Tauan

last: Vieira

last: Motta

first: Renato

last: Vincentini

first: Robert

last: Martienssen


title: Transcriptomic analysis of copper tolerance and wood decay in the brown rot fungus Fibroporia radiculosa

city: Mississippi State

first: Juliet

middle: D

last: Tang

state: MS

department: Forest Products

institute: Mississippi State University

summary: Many brown rot fungi are capable of rapidly degrading wood and are copper-tolerant.  To better understand the genes that control these processes, we examined gene expression of Fibroporia radiculosa growing on wood treated with a copper-based preservative that combined copper carbonate with dimethyldidecylammonium carbonate.  A global profiling strategy called RNA-Seq was used to quantify gene expression of the fungus at days 31 and 154.  At day 31, the preservative was still protecting the wood, which showed no strength loss.  At day 154, the effects of the preservative were gone, and the wood exhibited 52% strength loss.  Statistical analysis identified 917 genes that were differentially expressed (FDR < 1E-4).  Transcripts that showed higher expression levels at the early time point were controlling increased oxalate metabolism, laccase for hydroquinone-driven hydroxyl free radical production, pectin degradation, ATP production, xenobiotic detoxification, copper resistance, and stress response.  Transcripts that showed higher expression levels at the late time point were involved in degradation of cellulose, hemicellulose, and pectin, hexose transport, oxalate catabolism, catabolism of laccase substrates, extracellular proton reduction, and remodeling of the fungal cell membrane and cell wall to enhance survival at low pH.

overall_design: 7 samples were analyzed.  The comparison was day 31 (n=3) vs day 154 (n=4).

first: Andy

last: Perkins

first: Tad

last: Sonstegard

first: Steven

last: Schroeder

first: Darrel

last: Nicholas

first: Susan

middle: V

last: Diehl


title: A chromatin link to caste identity in the carpenter ant Camponotus floridanus

city: Philadelphia

first: Daniel

middle: Francis

last: Simola

state: PA

address: 1041 BRB II/III

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: The goal of this study was to assay the extent of variation in chromatin organization between 3 ant castes (major and minor female workers and males) in one colony of Camponotus floridanus carpenter ant using ChIPseq.

overall_design: 45 samples total: 30 ChIP samples and 3 inputs for total histone H3, 7 histone H3 PTMs and RNA Pol II in major, minor, and male ants; CBP in major and minor ants; the major H3K27ac sample was replicated. 4 ChIP samples for H3 and H3K27ac in brains of majors and minors, and 2 inputs. 2 RNAseq samples for major and minor ants head+thorax; 4 RNAseq samples for brain (majors and minors with 2 replicates each).

middle: F

first: Chaoyang

last: Ye

first: Roberto

last: Bonasio

first: Navdeep

last: Mutti

first: Kelly

last: Dolezal

first: Shelley

middle: L

last: Berger

first: Danny

last: Reinberg

first: Juergen

last: Liebig


title: RNAi triggered by specialized machinery silences developmental genes and retrotransposons

city: Bethesda

first: Shiv

last: Grewal

type: Genome binding/occupancy profiling by array

platform_organism:
Schizosaccharomyces pombe
Drosophila melanogaster


title: Population and sex differences in Drosophila melanogaster brain gene expression

status: Public on Nov 21 2012

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

institute: University of Munich

summary:
Background: Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-throughput RNA sequencing of a single Drosophila melanogaster tissue to detect brain-specific differences in gene expression between the sexes and between two populations, one from the ancestral species range in sub-Saharan Africa and one from the recently colonized species range in Europe.
Results: Relatively few genes (<100) displayed sexually dimorphic expression in the brain, but there was an enrichment of sex-biased genes, especially male-biased genes, on the X chromosome. Over 340 genes differed in brain expression between flies from the African and European populations, with the between-population divergence being highly correlated between males and females. The differentially expressed genes include those involved in stress response, olfaction, and detoxification. Expression differences were associated with transposable element insertions at two genes implicated in insecticide resistance (Cyp6g1 and CHKov1).
Conclusions: Analysis of the brain transcriptome revealed many genes differing in expression between populations that were not detected in previous studies using whole flies. There was little evidence for sex-specific regulatory adaptation in the brain, as most expression differences between populations were observed in both males and females. The enrichment of genes with sexually dimorphic expression on the X chromosome is consistent with dosage compensation mechanisms affecting sex-biased expression in somatic tissues.

overall_design: mRNA profiles of Drosophila melanogaster brains from adult males and females from a European and an African population (2 biological replicates each)

first: Ana

last: Catalán

first: John

last: Parsch


title: GATA3 acts upstream of FOXA1 in mediating ER binding by shaping enhancer accessibility

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Estrogen Receptor (ESR1) drives growth in the majority of human breast cancers by binding to regulatory elements and inducing transcription events that promote tumor growth. Differences in enhancer occupancy by ESR1, contribute to the diverse expression profiles and clinical outcome observed in breast cancer patients. GATA3 is an ESR1 co-operating transcription factor mutated in breast tumors, however its genomic properties are not fully defined. In order to investigate the composition of enhancers involved in estrogen-induced transcription and the potential role of GATA3, we performed extensive ChIP-sequencing in unstimulated breast cancer cells and following estrogen treatment. We find that GATA3 is pivotal in mediating enhancer accessibility at regulatory regions involved in ESR1-mediated transcription. GATA3 silencing resulted in a global redistribution of co-factors and active histone marks prior to estrogen stimulation. These global genomic changes altered the ESR1 binding profile that subsequently occurred following estrogen, with events exhibiting both loss and gain in binding affinity, implying a GATA3 mediated re-distribution of ESR1 binding. The GATA3-mediated re-distributed ESR1 profile correlated with changes in gene expression, suggestive of its functionality. Chromatin loops at the TFF locus involving ESR1 bound enhancers occurred independently of ESR1 when GATA3 was silenced, indicating that GATA3, when present on the chromatin, may serve as a licensing factor for estrogen- ESR1 mediated interactions between cis-regulatory elements. Together these experiments suggest that GATA3 directly impacts ESR1 enhancer accessibility and may potentially explain the contribution of mutant-GATA3 in the heterogeneity of ESR1+ breast cancer.

overall_design: GATA and ER binding studied by chromatin immunoprecipitation in breast cancer cell lines, with and without estrogen stimulation and by knocking down GATA

first: Vasiliki

last: Theodorou

first: Jason

last: Carroll

first: Rory

last: Stark


title: Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, Pol IV and Pol V, in a process called RNA-directed DNA methylation.  By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues.

overall_design: We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). We also examined small RNA abundance at individual CRP genes in the wild type plant, nrpd1, and rdr2 mutant plants.

first: Wanhui

last: You

first: Agata

last: Tyczewska

first: Matthew

last: Spencer

first: Lucia

last: Daxinger

first: Marc

last: Schmid

first: Ueli

last: Grossniklaus

first: Stacey

middle: A

last: Simon

first: Antonius

last: Matzke

first: Marjori


title: The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis

first: Philipp

last: Kimmig

state: CA

address: Genentech Hall N316, 600 16th Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary: Homeostatic control mechanisms are essentil to life. One such mechanism, the unfolded protein response (UPR) operates in all eukarytic cells to adjust protein folding capacity of the endoplasmic reticulum (ER) according to need. UPR induction in all eurkarytic cells to date involves Ire1 (kinase/endonuclease transmembrane protein) mediated a non-convential splicing of Hac1/XBP1 mRNA, encoding for a potent transcription factor. UPR induction causes a comprehensive transcriptional upregulation of the folding capacity in the ER. Here we studied the global transcriptional profile of the UPR in fission yeast. Fission yeast lacks a clear homolog of Hac1/XBP1. Instead Ire1 maintains ER homeostasis through two post-transciptional programs: selective mRNA decay and processing of Bip1 mRNA (encoding for a major HS70-familiy member in the ER) thereby stabilizing it.

overall_design: S. pombe cells were grown in liquid medium (YE5S) to OD600=0.25. Cells were treated with or without 2 mM DTT (Dithiothreitol, impairs disulfid bond formation) for 60 min at 30℃. Total RNA was extracted from cells using hot phenol method. PolyA+ mRNA were enriched by two sequential rounds of oligo-dT (Invitrogen) selection. rRNA depletion was performed by depletion of ll RNA smaller than 200nt (mirVana miRNA Purification Kit (Ambion) followed by two rounds of subtractive hybridization using Ribominus EukaryoteKit for RNA-seq (Invitrogen). To sequence 2',3'-cyclic phosphate cleavage products tRNA ligase was used to selectively ligate an RNA linker to all 2',3'-cyclic phosphatesin total RNA. (described in Schutz et al., 2010). Two biological repeats were performed for the following samples with different conditions and yeast strains: poly A+ mRNA sample and mRNA enriched (ribosome depletion). On replicate was performed for RNA 3' end mapping carrying a 2',3'-cyclic phosphate: 1 replicate

first: Marcy

last: Diaz

first: Alexander

last: Lang

first: Jiashun

last: Zheng

first: Christopher

last: Williams

first: Tomas

last: Aragón

first: Hao

last: Li

first: Peter

last: Walter


title: Transcriptome profiling of wild type and Tet1-null primordial germ cells (PGC) by Bisulfite-seq

status: Public on Nov 20 2012

city: La Jolla

first: Kun

last: Zhang

address: 9500 Gilman Dr Mailcode: 0412

institute: University of California, San Diego

summary:
Purpose: To investigate the effect of Tet1 depletion on global DNA methylation, we performed whole-genome bisulfite sequencing (WGBS).
Methods: Starting with as little as 1400-5251 manually micro-dissected PGCs, we used an ultra-low input method, Tn5mC-seq.
Results: We generated 945 million reads for Tet1Gt/Gt PGCs and 302 million reads for wild-type PGCs. We obtained 14-16 million CpG sites per genotype at 1.76-2.66x genome coverage, which enables a comprehensive view of genome-wide DNA methylation patterns in E13.5 PGCs. PGCs are almost completely unmethylated genome-wide. Loss of Tet1 led to a subtle increase of methylation level in various genomic elements including promoters, exons, introns and repetitive elements in Tet1Gt/Gt PGCs (p<0.01). Local analysis identified 4,337 differentially methylated regions (DMRs) between Tet1-/- PGCs and wild-type cells. These DMRs are associated with 5,261 genes, among which 271 genes also exhibited differential gene expression and enriched for the cell cycle pathway (FDR=0.02).
Conclusions: This result revealed that demethylation of certain set of cell cycle genes is largely abolished in the Tet1-/- PGCs.

overall_design: Genome-wide methylation profiles of primordial germ cells derived from the wild type (WT) and Tet1-null female embryos at E13.5 were generated by whole genome bisulfite sequencing using Illumina Hiseq.


title: Rescue Of Dysfunctional Autophagy By Peptide IDR-1018 Attenuates Hyperinflammatory Phenotype Of Cystic Fibrosis Cells (RNA-seq)

city: Vancouver

last: Fjell

state: BC

address: Room 166 - 1081 Burrard Street

department: Medicine

institute: University of British Columbia

summary:
Genome-wide gene expression was measured in peripheral blood mononuclear cells (PBMCs) from patients with cystic fibrosis (CF) after treatment in vitro with the flagellin protein fliC, and/or synthetic peptide IDR-1018 to assess patterns of gene expression.
The patterns of gene expression suggest that CF cells have a hyperinflammatory phenotype including dysfunctional autophagy processes. The synthetic peptide IDR-1018 attentuates this hyperinflammatory phenotype.

overall_design: Total RNA was obtained from PBMCs obtained from CF patients after treatment with the fliC flagellin protein (that is known to play a role in CF lung inflammation), and/or the peptide IDR-1018 that has anti-inflammatory properties. Comparison of genes and pathways affected by these treatments indicated the role of autophagy process in CF disease.

first: Matt

last: Mayer

first: Christoph

last: Blohmke

first: Reza

last: Falsafi

first: Laurence

last: Madera

first: Stuart

last: Turvey

first: Robert

last: Hancock


title: ChIP-chip from H9 hESCs for RNA Polymerase II, TBP, TAF3, TAF5, TAF7, and TAF11

status: Public on Nov 19 2012

city: Worcester

first: Michael

middle: R.

last: Green

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary:
The general transcription factor TFIID is composed of the TATA-box-binding protein (TBP) and approximately 14 TBP-associated factors (TAFs). Here we find, unexpectedly, that undifferentiated human embryonic stem cells (hESCs) contain only six TAFs (TAFs 2, 3, 5, 6, 7 and 11), whereas following differentiation all TAFs are expressed. Directed and global chromatin immunoprecipitation analyses reveal an unprecedented promoter occupancy pattern: most active genes are bound by only TAFs 3 and 5 along with TBP, whereas the remaining active genes are bound by TBP and all six hESC TAFs. Consistent with these results, hESCs contain a previously undescribed complex containing TAFs 2, 6, 7, 11 and TBP. Altering the composition of hESC TAFs, either by depletion of TAFs that are present or ectopic expression of TAFs that are absent, results in misregulation of pluripotency gene expression and induction of differentiation. Thus, the selective expression and use of TAFs underlies the ability of hESCs to self-renew.
ChIP-chip was used in this study to assess the global pattern of TAF recruitment at a gene promoters, to verify the existence of two classes of genes which differentially recruit and use TAF proteins for transcription initiation.

overall_design: Comparison of recruitment of 4 TAFs (TAF3, TAF5, TAF7 and TAf11) with the recruitment of TBP and RNA Polymerase II in wild-type H9 embryonic stem cells from replicate experiments

first: Glenn

last: Maston

first: Lihua

last: Zhu

first: Lynn

last: Chamberlain

first: Ling

last: Lin


title: Analysis of H3K9 trimethylation in unstimulated and stimulated dendritic cells and fibroblasts

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

country: France

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

summary: The distribution of H3K9me3 was analyzed in order to investigate the influence of H3K9me3 levels surrounding candidate enhancers and other cis-regulatory elements.

overall_design: ChIP-seq for H3K9me3 and input DNA controls, from 2 cell types (DCs & fibroblasts) under 2 conditions (unstimulated & stimulated)

first: Yina

first: Simona

last: Saccani


title: Analysis of JmjD2d-bound regions in unstimulated and stimulated dendritic cells

summary: To examine JmjD2d-binding, ChIP was performed using monoclonal antibodies specific for JmjD2d, or for the JmjN domain of all JmjD2-family members.

overall_design: ChIP-seq for JmjD2d, Jmjd2-family, and input DNA controls, from dendritic cells under 2 conditions (unstimulated & stimulated)


title: OSKM factors cooperatively engage chromatin to initiate reprogramming

status: Public on Nov 16 2012

first: Kenneth

middle: S.

last: Zaret

address: 9-132, SCTR, 3400 Civic Center Boulevard

institute: University of Pennsylvania School of Medicine

summary: Reprogramming cells from one fate to another, using transcription factors, generates cells for research and potential therapy, yet little is known about the initial engagement of reprogramming factors with the genome.  We mapped the interactions between Oct4, Sox2, Klf4, and c-Myc (OSKM) and the human genome during the first 48 hours of cellular reprogramming to pluripotency.  Unlike that reported in ES/iPS cells, we find extensive overlap in the initial binding of OSKM, demonstrating that the initial regulatory network differs markedly from that in pluripotency.  OSK act as pioneer factors for c-Myc, and c-Myc enhances the engagement of OSK, including at many genes that are required for conversion to pluripotency.  Distal enhancer sites in closed chromatin dominate the initial OSKM distribution.  Hierarchical chromatin binding during reprogramming resembles that employed during development.

overall_design: Four chIP-seq data sets (Oct4, Sox2, Klf4, and c-Myc) are included, one lane per factor, no replicates. Also included is an input lane from the same conditions and two mock lentiviral controls (no exogenous OSKM factors) treated with Oct4 IP and c-Myc IP.

first: Abdenour

last: Soufi

first: Greg

last: Donahue

middle: S


title: Study of gene expression in Chromolaena odorata cuttings using a combination of RNA-seq and digital gene expression analysis

city: Nanning

first: Haiwang

last: He

state: Guangxi

address: 100, Daxue Road

department: College of Agronomy

institute: Guangxi University

summary: 4,392 differentially expressed genes were generated by DGE analysis, and 3,074 had good comparability with known gene sequences in existing species. 1,152 differentially expressed sequences were mapped to the reference canonical pathways in the KEGG database, and were assigned to 110 KEGG pathways, 11 pathways less then with the transcriptome database. Differentially expressed genes were classed according to their function, which includes phytohormones, growth and developmental processes, defense, peroxidase and P450-related genes. Pathway analysis also revealed that the principal secondary metabolites in the C. odorata cuttings were phytohormones and flavonoids.

overall_design: Examination of 2 different stage of adventitious root formation

first: Hai-wang

first: Long-fei

first: Ai-qin

last: Wang

first: Chun-yan

last: Xu

first: Chuang-zhen

last: Li

first: Shan-qing

last: Wei


title: Genome-wide identification of functional elements regulated by T-bet and GATA3 in human T-cells

city: Liverpool

first: Aditi

last: Kanhere

address: Institute of Systems, Molecular and Integrative Biology

institute: University of Liverpool

summary: T-bet and GATA3 induce differentiation of CD4+ T-cells into Th1 or Th2 effectors. These exhibit a range of different properties but understanding of T-bet and GATA3 function is mostly limited to the murine Ifng and Il4/Il5/Il13 loci. We hypothesised that extending such analyses across the human genome would allow further insight into T-bet and GATA3 function. We have discovered that T-bet and GATA3 bind to multiple distal sites at a set of key immune regulatory genes. These sites display markers of functional elements, act as enhancers in reporter assays and are associated with lineage-specific expression regulated by T-bet and GATA3. Our approach also reveals that GATA3 is distributed at T-bet binding sites in Th1 cells and that T-bet directly activates its own expression. We propose that these aspects of T-bet and GATA3 function are critical for Th1/ Th2 differentiation and provide a model for the relationship between other lineage-specific regulators.

overall_design: ChIP was performed using antibody against T-bet in Th1 cells and against GATA3 in Th1 cells as well as Th2 cells. A sample of whole cell extract (WCE) from Th1 cells and Th2 cells was sequenced. Th1 WCE was used as the background to determine enrichment.

first: Arnulf

last: Hertweck

first: Graham

middle: M

last: Lord

first: Richard

last: Jenner


title: Time-course RNA-seq analysis of the barley MLA1 immune receptor-mediated response to barley powdery mildew fungus Bgh in Arabidopsis thaliana

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

institute: Max Planck Institute

summary:
We report that an intracellular NLR immune receptor from monocotyledonous barley is fully functional in dicotyledonous Arabidopsis thaliana. In contrast to common belief in plant NLR biology, this implies ~150 million years of evolutionary conservation of the underlying immune mechanism. This also suggests a conserved translocation mechanism for pathogen effectors in flowering plants. The deduced connectivity of the NLR to bifurcated signaling pathways likely confers increased robustness against pathogen interception, which could have contributed to the evolutionary preservation of the immune mechanism.

RNA-seq experiments in Arabidopsis detected sustained expression of a single major MLA1-dependent gene cluster.

overall_design: 3 biological replicates per condition. The Arabidopsis plants without (pps) or with (B12) the MLA1-HA construct in a pen2 pad4 sag101 background were challenged with either the Bgh isolate K1 expressing the cognate AVRA1 effector for MLA1 or the Bgh isolate A6 expressing other AVRA effectors. Samples were collected at 6, 12, 18, 24 hours post inoculation (hpi) of Bgh.

first: Takaki

last: Maekawa

first: Barbara

last: Kracher

first: Saskia

last: Vernaldi

first: Paul

last: Schulze-Lefert


title: Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (RNA-Seq)

city: Maastricht

first: Stan

last: Gaj

state: Limburg

address: Universiteitssingel 50

department: Department of Toxicogenomics

institute: Maastricht University

summary: Whole-genome transcriptome measurements are pivotal for characterizing carcinogenic mechanisms of chemicals and predicting toxic classes, such as genotoxicity, from in vitro and in vivo assays. DNA microarrays have evolved as the gold standard for this purpose. In recent years deep sequencing technologies have been developed that hold the promise of measuring the transcriptome with RNA-seq in a more accurate and unbiased manner than microarrays. So far, however, few applications have been published that assess the performance of RNA-seq within a toxicogenomics context. Here, we applied RNA-seq for the characterization of the in vitro transcriptomic responses in HepG2 cells upon exposure to benzo[a]pyrene (BaP), a well-known DNA damaging carcinogen. We demonstrate the performance of RNA-seq with respect to the identification of differentially expressed genes and associated pathways, in comparison with microarray technology. RNA-seq data generates more complete and thus accurate data on differentially expressed genes and affected pathways than microarrays. Additionally, we highlight the potential of RNA-seq for characterizing mechanisms related to alternative splicing and thereby gathering new information. Exposure to BaP alters the isoform distribution for many genes, including regulators of cell death and DNA repair such as TP53, BCL2 and XPA, which are relevant for genotoxic responses. Finally, we demonstrate that RNA-seq enables to investigate allele-specific gene expression, although no changes for that could be observed. Our results provide evidence that RNA-seq is a powerful tool for toxicology which, compared to microarrays, is capable of adding valuable information at the transcriptome level for characterizing toxic effects caused by chemicals.

overall_design: Examination of 2 biological replicates at 2 different timepoints

first: Joost

last: vanDelft

first: Jos

last: Kleinjans


title: Two isoforms of Fs(1)h ChIP-seq

status: Public on Nov 15 2012

city: Atlanta

first: Wendy

last: Kellner

state: GA

address: 1510 Clifton Road

department: Biology

institute: Emory University

summary: ChIP-seq was performed using Drosophila Kc167 cells using antibodies against the two isoforms of Fs(1)h, the Brd4 homologue. Differences in binding patterns between the two isoforms are described.

overall_design: We examined the differences in Fs(1)h isoform binding across the genome and describe the short isoform to be correlated with transcription at enhancers and promoters. The long isoform is found predominately at insulator binding sites where multiple insulators are bound.

first: Victor

middle: G

last: Corces

first: Edward

last: Ramos

first: Kevin

last: Van Bortle

first: Naomi

last: Takenaka

first: Li


title: Site-specific silencing of regulatory elements as a mechanism of X-inactivation

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC-Chapel Hill

summary: The inactive X chromosome’s (Xi) physical territory is microscopically devoid of transcriptional hallmarks and enriched in silencing-associated modifications. How these microscopic signatures relate to specific Xi sequence is unknown. This study reports the profiling of Xi gene expression and chromatin states at high-resolution via allele-specific sequencing in F1 hybrid mouse trophoblast stem cells (TSCs). Datasets provided include those generated from strand-specific RNA-Seq, ChIP-Seq, FAIRE-Seq, and DNase-Seq protocols. Included for each dataset are FASTQ files, BED alignments and WIG files with coordinates relative to UCSC genome build mm9, and _snp files that report the location of all SNP-overlapping reads.

overall_design: The F1 TSC lines profiled were generated from crosses between CAST/EiJ (Cast) and C57BL/6J (B6) mice. C/B denotes a Cast mother and B6 father, and B/C denotes a B6 mother and Cast father.


title: Characterization of the EZH2-MMSET histone methyltransferase regulatory axis in cancer [ChIP-seq]

first: Meng

last: Zhao

address: 1518 Clifton Rd, #369

department: BIOS

summary: Histone methyltransferases (HMTases), as chromatin modifiers, regulate the transcriptomic landscape in normal development as well in diseases such as cancer.  Here, we molecularly order two HMTases, EZH2 and MMSET that have established genetic links to oncogenesis. EZH2, which mediates histone H3K27 trimethylation and is associated with gene silencing, was shown to be coordinately expressed and function upstream of MMSET, which mediates H3K36 dimethylation and is associated with active transcription. We found that the EZH2-MMSET HMTase axis is coordinated by a microRNA network and that the oncogenic functions of EZH2 require MMSET activity. Together, these results suggest that the EZH2-MMSET HMTase axis coordinately functions as a master regulator of transcriptional repression, activation, and oncogenesis and may represent an attractive therapeutic target in cancer.

overall_design: Examination of H3K36me2 mark in control and stable EZH2 knockdown cells

first: Irfan

last: Asangani


title: Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Genome-wide maps of 5hmC state in pluripotent and (T-)iPS induction cells.

status: Public on Nov 17 2012

city: Beijing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute Of Biological Sciences, Beijing (NIBS)

summary: We performed 5hmC DNA Immunoprecipitation followed high-throughput sequencing using R1 ESCs, OT ESCs, TSKM ESCs, Day3 TSKM and OSKM induction cells. We compared the profiling of 5-hydroxymethylcytosine modifications in these different cell lines. We found that: the TSKM and OT iPSCs shared similar 5hmC modification pattern while apart from that of R1 ESCs. However the comparison based on the gene promoter (-1000/+500 of gene’s TSS) showed less differences. The TSKM 2nd induction samples were quite like each other and have shared the basic pattern with traditional OSKM 2nd sample. However comparison based on the gene promoter showed sharp increase. Moreover higher enrichment of 5hmC on the distal enhancer of Oct4 was specifically detected in Day 3 TSKM 2nd cells as well as TSKM and OT iPSCs, which might be helpful for us to study the Tet1-mediated somatic reprogramming.

overall_design: Examination of 5-hydroxymethylcytosine modifications in 5 different cell lines.

first: Yawei

last: Gao

first: Jiayu

last: Chen

first: Shaorong