title: Single cell RNA-seq analysis of mature thymic epithelial cells

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

summary: This study set out to assay the (polyA+) transcriptomes of single mature (MHCII high) mouse medullary thymic epithelial cells (mTEC).

overall_design: Following isolation by FACs, the transcriptomes of single mature mTEC was assayed using the Fluidigm C1 microfluidics platform and Illumina RNA-seq.

first: Noriko

last: Shikama-Dorn

first: Saule

last: Zhanybekova

first: Gretel

last: Nusspaumer

first: Iain

last: Macaulay

first: Mary

last: Deadman

first: Andreas

last: Heger

first: Chris

last: Ponting

first: Georg

last: Hollander


title: Conserved non-coding sequence 2 (CNS2) of the Foxp3 genomic locus is essential for the function and stability of regulatory T cells during their activation

status: Public on Sep 04 2014

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

country: USA

institute: University of California, San Diego (UCSD)

type: Expression profiling by high throughput sequencing

summary: Regulatory T (Treg) cells play an indispensable role in immune homeostasis. The development and function of Tregs are dependent on transcriptional factor Foxp3, but how constant expression of Foxp3 is maintained in Tregs is not clear.  Here we show that ablation of the conserved non-coding DNA sequence 2 (CNS2) at the Foxp3 locus in mice led to spontaneous lymphoproliferative disease and exacerbation of experimental autoimmune encephalomyelitis (EAE). CNS2 is required for activated Treg cells to maintain elevated Foxp3 expression, which is critical for their suppressor function and lineage stability. Mechanistically, upon TCR stimulation, NFAT binds to both CNS2 and Foxp3 promoter and mediates the interaction between CNS2 and Foxp3 promoter. Our findings demonstrated an essential role for CNS2 in maintaining the stability and function of activated Treg cells and identified NFAT as a key mediator of its function.

overall_design: Gene expression was profiled in T regulatory cells (Treg) in WT and CNS2 knockout mice.   CNS2 knockout mice lack a conserved non-coding DNA sequence 2 (CNS2) at the Foxp3 locus.  Treg cells were further sorted into Foxp3-high and Foxp3-low populations based on the  expression level of Foxp3.   mRNA was profiled using RNA-Seq  (unstranded, polyA+, SE100) in replicate for each condition

first: Xudong

last: Li

first: Yuqiong

last: Liang

first: Mathias

last: LeBlanc

first: Christophter

first: Ye

last: Zheng


title: Genome wide occupancy of Msgn1 in differentiating embryonic stem cells

city: Frederick

first: Ravindra B

last: Chalamalasetty

state: MD

address: 1050 Boyles St, Bldg 539,Rm205

department: Cancer and Developmental Biology

institute: National Cancer Institute-Frederick

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Msgn1 is a bHLH transcription factor and is a direct target gene of the Wnt/b-catenin signaling pathway. During mouse embryogenesis, Msgn1 is expressed in the mesodermal compartment of the primitive streak and is required for the differentiation of presomitic mesoderm. Msgn1-/- mutants show defects in somitogenesis leading to a lack of trunk skeletal muscles, vertebra and ribs. The goal of this study is to dissect the molecular and cellular function of Msgn1 in Embryonic Stem Cells (ESC) and mouse development. In order to identify direct Msgn1 targets, we performed transcriptional profiling and CHIP-seq of Msgn1 expressing differentiating ES cells. Integration of these data sets, we found that Msgn1 is a master regulator of PSM differentiation regulating gene expression programs of PSM identity, EMT, motility and Notch segmentation clock.

overall_design: Inducible Flag Msgn1 ES cells were differentiated to form Embryoid bodies (EBs) for 2 days. Flag-Msgn1 was induced on day 2 with doxycycline and samples were collected 36h later. Here Input DNA is used as control.

first: Ravindra

middle: B

first: Terry

middle: P

last: Yamaguchi


title: Chromatin state in thymic epithelial cells [ChIP-seq]

first: Stephen

country: United Kingdom

summary: The study set out to assess the genome-wide distribution of the chromatin modifications H3K4me3 and H3K27me3 in mature thymic epithelial cells.

overall_design: ChIP and input DNA was prepared from biological replicated FACS sorted mature mTEC samples and sequenced.

middle: N

first: Noriko

middle: A


title: Gene expression in thymic epithelial cells [RNA-seq]

summary: This study set out to assay the (polyA+) transcriptomes of specific FACS sorted populations of mouse thymic epithelial cells (TEC).

overall_design: Two biological replicates of each of seven murine TEC populations were FACS sorted and sequenced.

first: Saule

first: Gretel


title: Aire secures the transcription of polycomb marked genes to complete a comprehensive program of promiscuous gene expression in the thymic epithelial cell lineage

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

overall_design: Refer to individual Series


title: Gcn5 and PCAF negatively regulate interferon β production through HAT-independent inhibition of TBK1 [RNA-Seq]

status: Public on Sep 03 2014

city: Bethesda

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

summary: Gcn5/PCAF double knockout (dKO) leads to loss of the global H3K9ac. RNA-Seq was performed to define the changes of gene expression in response to Gcn5/PCAF deletion and H3K9ac loss

overall_design: PCAF-/-;Gcn5f/D MEFs were infected with retroviral Cre to delete Gcn5 to generate Gcn5/PCAF dKO cells, followed by RNA-Seq analysis using spike-in RNA as controls

first: Qihuang

last: Jin

first: Binbin

last: Lai

first: Yue

last: Lu

first: Weiqun

last: Peng

first: Sharon

middle: Y

last: Dent


title: Gcn5 and PCAF negatively regulate interferon β production through HAT-independent inhibition of TBK1 [ChIP-Seq]

summary: Gcn5/PCAF dobule knockout (dKO) in MEFs leads to loss of the global H3K9ac, but only affect expression of a small nubmer of genes according to RNA-Seq data. To examine the function of H3K9ac on gene activation, H3K9ac ChIP-Seq was performed. We found that H3K9ac at Transcriptional Start sites (TSSs) of no-changed, up-regulated and down-regulated genes are all dramatially decreased in Gcn5/PCAF dKO cells, suggesting that H3K9ac is largely not required for gene activation.

overall_design: PCAF-/-;Gcn5f/D MEFs were infected with retroviral Cre to delete Gcn5 to generate Gcn5/PCAF dKO cells, followed by H3K9ac ChIP-Seq analysis


title: Gcn5 and PCAF negatively regulate interferon β production through HAT-independent inhibition of TBK1


title: Genome-wide profiling of the DNA methylation landscape in primary and matastatic breast cancer types [468LN and 468PT]

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by high throughput sequencing

summary: Whole genome bisulphite sequencing of 2 human breast cancer cell lines representing a breast primary tumor and a matched lymph node metastasis.

overall_design: Sequencing of bisulfite converted DNA of cancer cell line samples.

first: Holger

last: Heyn


title: RNA-Seq analysis of prostate tumors with or without androgen receptor splice variant

city: Baltimore

first: Jun

last: Luo

address: 411 Marburg Building, 600 N Wolf St.

department: Urology

institute: Johns Hopkins Medical Institutions

summary:
Background.  Androgen receptor splice variant-7 (AR-V7) is a truncated form of the androgen receptor protein which lacks the ligand-binding domain, the target of enzalutamide and abiraterone, but remains constitutively active as a transcription factor. We hypothesized that detection of AR-V7 in circulating tumor cells (CTCs) from men with advanced prostate cancer would be associated with resistance to enzalutamide and abiraterone.
Methods.  We used quantitative reverse-transcription polymerase-chain-reaction (qRT-PCR) to interrogate CTCs for the presence or absence of AR-V7 from prospectively enrolled patients with metastatic castration-resistant prostate cancer initiating treatment with either enzalutamide or abiraterone. We examined associations between AR-V7 status and PSA response rates, PSA-progression-free-survival (PSA-PFS), clinical/radiographic-progression-free-survival (PFS), and overall survival (OS). Multivariable Cox regression analyses were performed to determine the independent effect of AR-V7 status on clinical outcomes.
Results.  Thirty-one enzalutamide-treated patients and thirty-one abiraterone-treated patients were enrolled, of which 38.7% and 19.4% had detectable AR-V7 from CTCs, respectively. Among men receiving enzalutamide, AR-V7–positive patients had inferior PSA response rates (0% vs 52.6%, P=0.004), PSA-PFS (median: 1.4 vs 6.0 months, P<0.001), PFS (median: 2.1 vs 6.1 months, P<0.001), and OS (median: 5.5 months vs not reached, P=0.002) compared to AR-V7–negative patients. Similarly, among men receiving abiraterone, AR-V7–positive patients had inferior PSA response rates (0% vs 68.0%, P=0.004), PSA-PFS (median: 1.3 months vs not reached, P<0.001), PFS (median: 2.3 months vs not reached, P<0.001), and OS (median: 10.6 months vs not reached, P=0.006). The negative prognostic impact of AR-V7 was maintained after adjusting for full-length-AR expression.
Conclusions.  Detection of AR-V7 in CTCs from patients with castration-resistant prostate cancer is associated with resistance to enzalutamide and abiraterone.

overall_design: A total of four metastatic castration-resistant prostate tumor samples from four patients were subjected to RNA-seq. Two samples were positive for androgen receptor splice variant 7 and the other two were negative for this variant.

first: Yidong

last: Chen

first: Tabrez

last: Mohammad


title: Investigating gene expression changes in wildtype and TMPRSS2-ERG homozygous mouse prostate tissue

city: Cambridge

first: Joshua

middle: M

last: Korn

state: MA

address: 250 Mass Ave

institute: Novartis

summary:
A transgenic TMPRSS2:ERG  mouse model was engineered in FVB background and compared to its wildtype counterpart in the absence of any treatment
This experiment is designed to look at ERG-dependent changes in phenotype and gene expression

overall_design: A loxP-GFP-loxP-hERG exon 4-11 cassette was inserted into a BAC clone containing the TMPRSS2 locus using a recombineering kit.  This modified BAC was used for pronuclear injection and generation of germline-transmitting mice. One line expressing high GFP was used for pronuclear injection of Cre protein and one sub-line that transmitted the TMPRSS2:ERG transgene into the germline  was subsequently bred to homozygosity.

first: Zineb

last: Mounir

first: Victor

middle: G

last: Lin

first: Yi

last: Yang

first: Raymond

last: Pagliarini


title: Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling

status: Public on Sep 02 2014

city: Kansas City

first: Joan

last: Conaway

state: MO

institute: Stowers Institute

summary: Histone H3 lysine27-to-methionine (H3K27M) gain-of-function mutations occur in highly aggressive pediatric gliomas. Here, we establish a Drosophila animal model for the pathogenic histone H3K27M mutation and show that its overexpression resembles Polycomb repressive complex 2 (PRC2) loss-of-function phenotypes, causing de-repression of PRC2 target genes and developmental perturbations. Similarly, a H3K9M mutant depletes H3K9 methylation levels and suppresses position-effect variegation in various Drosophila tissues. The histone H3K9 demethylase KDM3B/JHDM2 associates with H3K9M nucleosomes and its overexpression in Drosophila results in loss of H3K9 methylation levels and heterochromatic silencing defects. Here we establish histone lysine-to-methionine mutants as robust in vivo tools for inhibiting methylation pathways that also function as biochemical reagents for capturing site-specific histone-modifying enzymes, thus providing molecular insight into chromatin-signaling pathways.

overall_design: RNA-seq of wing imaginal discs expressing either H3.3WT-FLAG-HA or H3.3K27M-FLAG-HA.

first: Hans

last: Herz

first: Marc

last: Morgan

first: Xin

last: Gao

first: Ali

last: Shilatifard


title: A histone H3.3 Lysine 36 Trimethylation Reader Connects Chromatin to Regulated Pre-mRNA Processing

city: Shanghai

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

country: China

institute: Fudan university

summary: BS69 (aka ZMYND11) was initially discovered as a direct target of adenoviral E1A oncoprotein1. Subsequent studies implicated BS69 as a tumor suppressor and a transcriptional regulator2. But exactly how BS69 regulates gene expression has remained elusive. BS69 contains tandemly arranged PHD, BROMO and PWWP domains, which are known to function as chromatin recognition modalities. Here we show that BS69 selectively recognizes histone variant H3.3 lysine 36 trimethylation (H3.3K36me3) via these chromatin recognition modules. Using a proteomics approach, we further identified association of BS69 with a host of RNA splicing regulators including EFTUD2 and other U5 snRNP components of the spliceosome. Remarkably, RNA-seq analysis shows that BS69 mainly regulates intron retention (IR), which is one of the least well-understood RNA alternative splicing events in mammalian cells. Specifically, loss of BS69 results in a decrease in IR, while in contrast, knockdown of EFTUD2 leads to an increase in IR, consistent with its role as a core member of the splicesome machinery. Importantly, wildtype BS69, but not a BS69 mutant defective in its interaction with EFTUD2, rescues the IR events. We also show that knockdown of SETD2, the main enzyme that mediates H3K36 trimethylation3, similarly results in a decreased retention of the same introns regulated by BS69. Significantly, a BS69 mutant unable to bind H3.3K36me3 in vitro fails to rescue the reduced IR phenotype associated with the loss of BS69. Taken together, our findings identify an antagonistic relationship between BS69 and the core splicing machinery and demonstrate that BS69-mediated RNA splicing regulation is dependent both on its ability to bind chromatin decorated by H3K36me3 and its ability to physically interact with the core spliceosome machinery. Our study reveals a novel and unexpected role of BS69 in connecting histone H3.3K36 trimethylation to regulated RNA splicing, providing significant new insights into chromatin regulation of RNA splicing.

overall_design: HeLaS cells stably expressing BS69 were used for HA-tagged BS69 ChIP-seq. HeLa cells were used for BS69 ChIP-seq. HeLa cells were used for H3K36me3 ChIP-seq.

first: Y

first: R

last: Guo

first: J

last: Zheng


title: Genome-wide transcriptome analysis revealed extensive alternative RNA splicing in gene expression in the zoonotic parasite Schistosoma japonicum

city: Beijing

first: Xianyu

last: Piao

address: Dong Dan San Tiao 9

department: Institute of Pathogen Biology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Background: Schistosoma japonicum is a pathogen of the phylum Platyhelminths  that causes zoonotic schistosomiasis endemic in China and Southeast Asian countries. Control of the disease has been hampered by the lack of efficient measures. The development of tools for diagnosis of acute and chronic infection, and novel antiparasite reagents all relies on the understanding of the biological mechanism of the parasite.   Results: In this study, the polyadenylated transcripts from the male and female S. japonicum were sequenced by a high-through-put RNA-seq technique. Bioinformatic and experimental analyses were focused on the posttranscriptional RNA processing, which at the first time revealed the extensive alternative splicing events occurred in the adult stage of the parasite. The number of protein-coding sequences identified in the transcriptomes of the female and male S. japonicum was 15,939 and 19,501 respectively, which is more than that predicted from the annotated genome sequence. Further, we identified four types of posttranscriptional processing, also called alternative splicing, in both female and male worms of S. japonicum, including exon skipping, intron retention, alternative donor site, and alternative acceptor site. Unlike mammalian organisms, alternative donor site and alternative acceptor site were found to be more common than the other two types of posttranscriptional processing in S. japonicum. In total, 13,438 and 16,507 alternative splicing events were respectively predicted in the transcriptomes of female and male S. japonicum.   Conclusions: By using RNA-seq technology, we obtained the global transcriptomes of male and female S. japonicum. These results further provide a comprehensive view of the global transcriptome of S. japonicum. The findings of a substantial level of alternative splicing events dynamically occurring in the parasitation of the S. japonicum in the mammalian hosts suggested a complicate transcriptional and post-transcriptional regulation mechanisms employed by the parasite. The data will not only significantly improve the re-annotation of the genome sequences, but will also provide new information in the biology of the parasite.

overall_design: Two samples are analyzed.

first: Qijun


title: Transcriptome impact of acute deletion of Gata3 in murine pro-T cells

city: Pasadena

first: Ellen

last: Rothenberg

state: CA

address: 1200 E. California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology

summary: The purpose of the study was to determine what genes in DN2 pro-T cells are immediately regulated by the transcription factor GATA-3, either as activation targets or as repression targets.  To do this, two pairs of Gata3-floxed and control pro-T cells were generated and analyzed by RNA-seq within the first day of deletion of the Gata3 gene. Pro-T cells were generated by differentiation in vitro on OP9-DL1 monolayers of fetal liver-derive precursors from wildtype or Gata3-floxed mice, and the Gata3 gene was acutely deleted by transduction with Cre retroviral vector.  Within 20 hr after transduction, samples of acutely Gata3-deleted and control DN2 cells were sorted and RNA prepared for RNA-seq analysis.   High-throughput sequencing of the samples was carried out.   Experimental Gata3 deleted samples in both cases were Gata3-floxed, ROSA26R-EYFP samples infected with Cre retrovirus and sorted for EYFP+ (Cre-activated) DN2 phenotype. Control for experiment 1: wildtype (C57BL/6) DN2 pro-T cells generated in parallel, also treated with Cre retrovirus but sorted only for DN2 phenotype.  Control for experiment 2: same genotype as experimental, but infected with a GFP+ empty retroviral vector and sorted for GFP+ DN2 phenotype.

overall_design: Two pairs of RNA-seq samples of DN2 pro-T cells were generated for comparison, each pair consisting of a Gata3-deleted sample plus a stage-matched control.

first: Sagar

middle: S

last: Damle

middle: V


title: Subcellular localization of coagulation factor II receptor-like 1 in neurons governs angiogenesis

city: Montreal

first: Jean-Sebastien

last: Joyal

state: Québec

address: 3175 Cote-Ste-Catherine

department: Paediatrics

country: Canada

institute: CHU Sainte-Justine

summary: Chip-Seq on HEK293 cells using an antibody against PAR2 in order to determe binding to promoter and  enhancer sequences

overall_design: PAR2-GFP expressing HEK293 cells were lysed and immunoprecipitated with antibodies against PAR2. Short-read sequencing of ChIP DNA fragments was processed using the Solexa/Illumina Genome Analyzer II platform. Results were converted to BED files for processing and visualization for peak detection.

first: Jean-Sebastian

first: Sylvain

last: Chemtob


title: Transcriptome wide identification of retained introns upon depletion of the splicing factors SNW1 or PRPF8

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

summary: We identified which mRNAs are dependent on the splicing factors SNW1 or PRPF8. These factors were depleted in HeLa cells by RNAi, and the levels of intronic reads in mRNAs was compared to control RNAi.

overall_design: Intronic reads from polyA containing RNAs from HeLa cells and mSnw1-LAP 'rescued' cells, both depleted for endogenous SNW1, were compared. Furthermore, intronic reads from polyA containing RNAs from HeLa cells depleted for SNW1 or PRPF8 were compared to control depleted HeLa cells.

first: Petra

last: van der Lelij


title: Identification of a Facial Enhancer

city: New York

first: Juhee

last: Jeong

state: New York

address: 345 E 24th St

department: Basic sciences and Craniofacial development

institute: New York University College of Dentistry

summary: We generated a genome-wide map of candidate enhancers from the maxillary arch (primordium for the upper jaw) of mouse embryos

overall_design: Examination of histone modification H3K27ac (distinguishes active enhancers from inactive enhancer elements)  in the maxillary arch tissue

first: Andre

last: Landin Malt


title: Genome sequencing coupled with iPSC technology identifies GTDC1 as a novel candidate gene involved in Neurodevelopmental Disorders

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

country: Germany

institute: University of Cologne

type: Genome variation profiling by high throughput sequencing

summary: We identified genomic structural alterations of six patients with signs of neurodevelopmental disorder (NDDs) that harbour chromosomal rearrangements using large-insert paired-end tag sequencing (DNA-PET). This technique allowed the refinement of chromosomal breakpoints and lead to the identification of seven disrupted genes (GNAQ, RBFOX3, UNC5D, TMEM47, NCAPG2, GTDC1 and XIAP). For one patient we filtered the entire panel of structural variations (SVs) with his parents and identified a unique SV that disrupted a single gene: GTDC1. We then validated the functional consequences of the chromosomal breakpoint disruption of GTDC1 by using patient-derived iPSCs. By differentiating these cells into neural progenitor cells (NPCs) and neurons, we interrogated the disease process at the cellular level and observed defects in the proliferation and glycosylation status of NPCs and also defects in neuronal maturation and function. We compared these results with GTDC1-deficient wild-type human NPCs and neurons, and observed similar phenotypic features as in the patient-derived cells which confirm that GTDC1 is involved in the patient’s phenotype. We show here that the combination of genomic screening with iPSCs technology provides a mechanistic insight into possible contributory effects of candidate genes implicated in NDDs and for personalized medicine.

overall_design: Structural variations were identified by long insert DNA paired-end tag (DNA-PET) sequencing, a mate-pair sequencing approach.

last: Hillmer

first: Valere

last: Cacheux


title: Hybrid mice reveal parent-of-origin and cis- and trans-regulatory effects in the retina

status: Public on Sep 01 2014

city: St. Louis

first: Joseph

middle: C

last: Corbo

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

summary: A fundamental challenge in genomics is to map DNA sequence variants onto changes in gene expression. Gene expression is regulated by cis-regulatory elements (CREs, i.e., enhancers, promoters, and silencers) and the trans factors (e.g., transcription factors) that act upon them. A powerful approach to dissecting cis and trans effects is to compare F1 hybrids with F0 homozygotes. Using this approach and taking advantage of the high frequency of polymorphisms in wild-derived inbred Cast/EiJ mice relative to the reference strain C57BL/6J, we conducted allele-specific mRNA-seq analysis in the adult mouse retina, a disease-relevant neural tissue. We found that cis effects account for the bulk of gene regulatory divergence in the retina. Many CREs contained functional (i.e., activating or silencing) cis-regulatory variants mapping onto altered expression of genes, including genes associated with retinal disease. By comparing our retinal data with previously published liver data, we found that most of the cis effects identified were tissue-specific. Lastly, by comparing reciprocal F1 hybrids, we identified evidence of imprinting in the retina for the first time. Our study provides a framework and resource for mapping cis-regulatory variants onto changes in gene expression, and underscores the importance of studying cis-regulatory variants in the context of retinal disease.

overall_design: Retinas from four classes of 8 week old male mice were collected: F0 C57BL/6J (B6), F0 Cast/EiJ (Cast), F1 B6xCast, and F1 CastxB6. Three replicates per class were generated. Each replicate consisted of a pool of 6-8 retinas. The mRNA-seq was conducted with paired-end 2x101 sequencing on the Illumina HiSeq 2000 platform. One lane of sequencing was run for all twelve samples. An additional lane of sequencing was run for the six F1 samples.

first: Susan

middle: Q

last: Shen

first: Ernest

last: Turro


title: A trans-generational epigenetic process defines piRNA biogenesis in Drosophila virilis

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary:
Piwi interacting (pi)RNAs repress diverse transposable elements in the germ cells of metazoans and are essential for fertility in both invertebrates and vertebrates. The precursors of piRNAs are transcribed from distinct genomic regions, the so-called piRNA clusters; however, how piRNA clusters are differentiated from the rest of the genome is not known. To address this question, we studied piRNA biogenesis in two Drosophila  virilis strains that show differential ability to generate piRNAs from several genomic regions. We found that active piRNA biogenesis correlates with high levels of histone 3 lysine 9 trimethylation (H3K9me3) over genomic regions that give rise to piRNAs. Furthermore, piRNA biogenesis in the progeny requires the trans-generational inheritance of an epigenetic signal, presumably in form of homologous piRNAs that are generated in the maternal germline and deposited into the oocyte. The inherited piRNAs enhance piRNA biogenesis by installment of H3K9me3 mark on piRNA clusters and by promoting ping-pong processing of homologous transcripts into mature piRNAs.

We submitted the resequencing data together with the functional genomic datasets because it was generated with the sole purpose of supporting those. The SRA accession numbers are SRR1536176 and SRR1536175.

overall_design: ChIP-seq against H3K9me3 and Pol2, Total RNA-seq, in Drosophila virilis Strain9 and Strain160 as well as crosses between them

middle: K

first: Adrien

middle: L

last: Thomas

first: Alexei

last: Aravin


title: RNA-seq transcriptional profile of Toxoplasma gondii strains RH, PLK, CTG as tachyzoites and bradyzoites

city: Tampa

first: Kami

last: Kim

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Internal Medicine Medicine

institute: University of South Florida

summary: Using high through-put RNA sequencing, we assayed the transcriptomes of three different strains of Toxoplasma gondii representing three common genotypes under both in vitro tachyzoite and in vitro bradyzoite-inducing alkaline stress culture conditions. Strikingly, the differences in transcriptional profiles between the strains, RH, PLK, and CTG, is much greater than differences between tachyzoites and alkaline stressed in vitro bradyzoites. With an FDR of 10%, we identify 241 genes differentially expressed between CTG tachyzoites and in vitro bradyzoites, including 5 putative AP2 transcription factors. We also observe close association between cell cycle regulated genes and differentiation. By Gene Set Enrichment Analysis (GSEA), there are a number of KEGG pathways associated with the in vitro bradyzoite transcriptomes of PLK and CTG, including pyrimidine metabolism and DNA replication. These functions are likely associated with cell-cycle arrest. When comparing mRNA levels between strains, we identify 1,526 genes that are differentially expressed regardless of culture-condition as well as 846 differentially expressed only in bradyzoites and 542 differentially expressed only in tachyzoites between at least two strains. Using GSEA, we identify ribosomal proteins as being expressed at significantly higher levels in the CTG strain than in either the RH or PLK strains. This association holds true regardless of life cycle stage.

overall_design: Type I – RH, Type II – PLK, and Type III CTG parasites were each grown in either alkaline, bradyzoite conditions or pH neutral, tachyzoites conditions. 6 conditions, 3 replicates each, 18 total samples

first: Matthew

last: Croken

first: Yan

middle: F

last: Ma

first: Lye

last: Markillie

first: Ronald

last: Taylor

first: Galya

last: Orr

first: Louis

last: Weiss


title: Identification and comparative analysis of miRNAs and their targets associated with curd-forming capacity at high temperature in two broccoli genotypes

city: Changhua

first: Shih-Feng

last: Fu

address: No.1, Jin-De Road, Changhua City, 500

country: Taiwan

institute: Department of Biology, National Changhua University

type: Non-coding RNA profiling by high throughput sequencing

summary: We report miRNA expression profiles underlying curd-forming capacity at high temperature in two broccoli lines by high-throughput sequencing.

overall_design: Examination of miRNA expression profiles in 2  broccoli isogenic lines with different curd-forming capacity at high temperature  (High curd-forming capacity: E22 sample; Low-curd forming capacity: L22 sample)

first: Chi-Chien

last: Chen

first: Hao-Jen

last: Huang


title: Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences [RNA-Seq]

city: Buffalo

first: Jiho

last: Sohn

address: 3435 Main Street, 644 Biomedical Research Building

department: Oral Biology

institute: SUNY Buffalo

summary: Acquisition of the intestinal microbiota begins at birth, and a stable microbial community develops from a succession of key organisms. Disruption of the microbiota during maturation by low-dose antibiotic exposure can alter host metabolism and adiposity. We now show that low-dose penicillin (LDP), delivered from birth, induces metabolic alterations and affects ileal expression of genes involved in immunity. LDP that is limited to early life transiently perturbs the microbiota, which is sufficient to induce sustained effects on body composition, indicating that microbiota interactions in infancy may be critical determinants of long-term host metabolic effects. In addition, LDP enhances the effect of high-fat diet induced obesity. The growth promotion phenotype is transferrable to germ-free hosts by LDP-selected microbiota, showing that the altered microbiota, not antibiotics per se, play a causal role. These studies characterize important variables in early-life microbe-host metabolic interaction and identify several taxa consistently linked with metabolic alterations.

overall_design: Male and female mice were exposed to low-dose penicillin from birth. In a second experiment, microbiota from female control and LDP mice was transferred to 3-week old female germ-free mice.  Livers were collected at 8 weeks of age, RNA was extracted, and transcriptional differences were measured by RNAseq.

first: Laura

last: Cox

first: Shingo

last: Yamanishi

first: Alexander

last: Alekseyenko

first: Jacqueline

last: Leung

first: Ilseung

last: Cho

first: Sungheon

first: Huilin

last: Li

first: Zhan

last: Gao

first: Douglas

last: Mahana

first: Jorge

last: Zarate Rodriguez

first: Arlin

last: Rogers

first: Nicolas

last: Robine

first: P’ng

last: Loke

first: Martin

middle: J

last: Blaser


title: mRNA Expression Comparison Between Igfbp7-null and wild type mice at Lactation Day 3

city: Toronto

first: Yutaka

last: Amemiya

state: ON

address: 2075 Bayview Ave.

institute: Sunnybrook Research Institute

summary:
Insulin like growth factor binding protein 7, Igfbp7, is a secreted protein that in addition to modulating insulin and insulin-like growth factor signaling, it acts as a tumor suppressor gene in breast and other cancers.
To elucidate the role of Igfbp7 in regulating the proliferation and differentiation of mammary epithelial cells, we examined the growth and differentiation of mammary gland through different stages of its development in Igfbp7-null mice.
Using transcriptome profiling in addition to functional assays we demonstrate that loss of Igfbp7 leads to diminished luminal cell differentiation and  expansion of the luminal progenitors.
These studies identify the endocrine factor Igfbp7, as a key regulator of luminal progenitor functions in the mammary gland.

overall_design: Mammary gland mRNA profiles of lactation day 3  wild type (WT) and Igfbp7-/- (KO) mice were generated by deep sequencing using SOLiD5500xl

first: Stephanie

last: Bacopulos

first: Sumanta

last: Chatterjee

first: Afshin

last: Raouf

first: Arun

last: Seth


title: Human hepatocyte metaplasia in injured humanized mouse livers

city: Portland

first: Branden

last: Tarlow

state: OR

address: 3181 SW Sam Jackson Park Road

department: Pediatrics

institute: Oregon Health & Science University

summary: The goal of this experiment was to test whether human hepatocytes could give rise to biliary-like progenitor cells in an in vivo context.  Here Fah-/- Il2ry-/- Rag2-/-NOD mouse livers were humanized with human hepatocytes. Only hepatocytes engraft in the Fah-/- mouse at detectable levels in this model.  Then animals were given chronic liver injury with 0.1% ddc.  After injury we measured human-specific transcripts to determine whether the phenotype of the human cells had changed.  Specifically, we evaluated the relative levels of human biliary duct markers such as Spp1, Sox9, Krt7, etc.  and hepatocyte markers such as Alb, Ttr, Fah, etc.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 3 DDC treated chimeras and 6 untreated chimeras are included.  Additional controls include a normal human liver biopsy, FACS sorted primary intrahepatic human bile duct cells, mouse hepatocytes, and mouse intrahepatic biliary cells in ddc treated animal.

middle: D

first: Markus

last: Grompe


title: Treatment of multiple myeloma cells with EZH2 small molecule inhibitor

city: Chicago

first: Relja

last: Popovic

address: 303 East Superior Street

institute: Northwestern University

summary: We investigated differential gene expression in response to treatment of multiple myeloma cells with EZH2 inhibitor

overall_design: RNA-seq in two cell lines


title: MMSET Induces Global and Focal Changes in Histone Methylation in Myeloma Cells

summary: We investigated genome wide distribution of H3K36me2, H3K36me3 and H3K27me3 in the presence and absence of MMSET protein. MMSET overexpression in t(4;14)+ myeloma leads to global loss redistribution of H3K36me2 and genome-wide loss of  H3K27 methylation. Despite the gloal decrease in H3K27me3, specific regions of the genome show enhanced H3K27me3 enrichment through increased recruitment of EZH2 methyltransferase

overall_design: ChIP-seq for H3K36me2, H3K36me3 and H3K27me3 in two cell types


title: Transcriptome profiling of developing photoreceptor subtypes reveals candidate genes for avian photoreceptor diversification

city: Saint Louis

first: Jennifer

last: Enright

address: 660 S. Euclid, Box 8118

summary:
Purpose: Avian photoreceptors are a diverse class of neurons, comprised of four single cones, the two members of the double cone, and rods. Many distinctive features of photoreceptor subtypes, including spectral tuning, oil droplet size and pigmentation, synaptic targets and spatial patterning, have been well characterized, but the molecular mechanisms underlying these attributes have not been explored. Furthermore, the signaling events and transcriptional regulators driving the differentiation of these diverse photoreceptors are currently unknown.
Methods: To identify genes specifically expressed in distinct chicken (Gallus gallus) photoreceptor subtypes, we developed fluorescent reporters that label photoreceptor subpopulations, isolated these subpopulations using fluorescence-activated cell sorting, subjected them to next-generation sequencing, and conducted differential expression analysis.
Results: We identified hundreds of differentially expressed genes from photoreceptor subpopulations labeled with rhodopsin, red opsin, green opsin, and violet opsin reporters. These genes are involved in a variety of processes, including phototransduction, transcriptional regulation, cell adhesion, maintenance of intra- and extra-cellular structure, and metabolism. Of particular note are a variety of differentially expressed transcription factors, which may drive and maintain photoreceptor diversity, and cell adhesion molecules that may mediate spatial patterning of photoreceptors and act to establish retinal circuitry.
Conclusions: These analyses provide a framework for future studies that will dissect the role of these various factors in the differentiation of avian photoreceptor subtypes.

overall_design: mRNA expression profiling of 5 pairs of photoreceptor subtypes isolated from chicken retinal explants, 3 replicates per sample

first: Karen

last: Lawrence

first: Tarik

last: Hadzic

first: Joseph

last: Corbo


title: Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta

city: Tartu

first: Tauno

last: Metsalu

address: Liivi 2

country: Estonia

institute: University of Tartu

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

overall_design: Refer to individual Series


title: MMSET alters EZH2 Binding in Myeloma Cells

summary: We investigated EZH2 binding in the presence and absence of MMSET protein. MMSET overexpression in t(4;14)+ myeloma leads to global loss of H3K27 methylation and redistribution of EZH2 binding throughout the genome

overall_design: ChIP-seq for EZH2 in two cell types


title: Hepatocyte ductal metaplasia in chronic mouse liver injury

summary: Expression profiling of hepatocytes-derived ductal cells with properties intermediate between mature hepatocytes and cholangiocytes

overall_design: Chimeric adult mice were generated where mature hepatocytes were marked with a fluorescent red marker.  Chronic injury was induced for ~6weeks and three cell types were isolated by FACS (Influx, BD) for expression analysis by RNAseq based on cell surface phenotype and origin: hepatocytes (n=3), hepatocyte-derived oval cells (1c3+, n=5), and cholangiocyte-derived oval cells (1c3+, n=5).


title: Transcriptome of EBV-infected gastric cancer cell lines

city: Goyaongsi

first: Charny

last: Park

state: Gyeonggi-do

address: 323 Ilsan-ro,

country: South Korea

institute: National Cancer Center

summary: To understand epigenic dysregulation of host and viral genes upon EBV infection in human gastric cancer, genome wide transcripts by RNAseq were undertaken for total RNAs of 3 EBVnGC, their isogenic cell lines converted by in vitro EBV-infection and 3 EBV-naturally infected GC cell lines.

overall_design: Three independent gastric cancer (GC) cell lines (NUGC3, SNU-484, SNU-638) were experimentally infected with AKATA strain of EBV to derive EBV-infected isogenic GC cell lines (NUGC3EBV, SNU-484EBV, SNU-638EBV). Three indepedent GC cell lines with natural EBV-infection (SNU-719, NCC24, YCCEL1)) were also included in this study.

first: Myung-Soo

last: KANG


title: Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T-Cell Function

city: Cambridge

first: Yang

middle: Eric

last: Guo

address: 455 Main St

institute: Whitehead Institute MIT

summary: In marmoset T cells transformed by Herpesvirus saimiri (HVS), a viral U-rich noncoding RNA, HSUR 1, specifically mediates degradation of host microRNA-27 (miR-27). High-throughput sequencing of RNA after crosslinking immunoprecipitation (HITS-CLIP) identified mRNAs targeted by miR-27 as enriched in the T-cell receptor (TCR) signaling pathway, including GRB2. Accordingly, transfection of miR-27 into human T cells attenuates TCR-induced activation of mitogen-activated protein kinases (MAPKs) and induction of CD69. MiR-27 also robustly regulates SEMA7A and IFN-γ, key modulators and effectors of T-cell function. Knockdown or ectopic expression of HSUR 1 alters levels of these proteins in virally-transformed cells. Two other T-lymphotropic γ-herpesviruses, AlHV-1 and OvHV-2, do not produce a noncoding RNA to downregulate miR-27, but instead encode homologs of miR-27 target genes. Thus, oncogenic γ-herpesviruses have evolved diverse strategies to converge on common targets in host T cells.

overall_design: HVS-transformed marmoset T cells were transfected with ASOs against HSUR 1 or control, or with LNAs against miR-27 or control, in replicates; poly A+ RNAs were selected and sequenced on HiSeq 2000.

first: Y

middle: E

first: Kasandra

last: Riley

first: Akiko

last: Iwasaki

first: Joan

last: Steitz


title: Transcriptome sequencing of a large human family identifies the impact of rare non-coding variants

first: Xin

last: Li

address: 300 Pasteur Dr

department: Pathology

institute: Stanford University

summary: We have combined high-quality genome sequencing and RNA-sequencing data within a 17-individual, three generation family. Using these data, we have contrasted cis-acting expression, allele-specific expression and splicing quantitative trait loci (collectively termed eQTLs) within the family to eQTLs discovered within a cell-type and ethnicity-matched population sample. We identified that eQTL that exhibit larger effects in the family compared to the population are enriched for rare regulatory and splicing variants and were more likely to influence essential genes. In addition, we identify several large effect-size eQTLs within the family for genes involved in complex disease. Through analysis of eQTLs in a large family we also report the utility of non-coding genome annotation to predicting the effect of rare non-coding variants. We find that a combination of distance to the transcription start site, evolutionary constraint and epigenetic annotation is considerably more informative for predicting the consequence of rare non-coding variants than for common variants. In summary, through transcriptome analyses within a large family we are able to identify the contribution of rare non-coding variants to expression phenotypes and further demonstrate the predictive potential of diverse non-coding genome annotation for interpretation of the impact of rare non-coding variants.

overall_design: RNA-Sequencing of CEPH/UTAH family 1463

first: Stephen

middle: B

last: Montgomery


title: ChIP-seq mapping of histone modifications in CD14++ CD16- monocytes from human blood samples

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

summary: Chromatin immunoprecipitation in combination with a genome-wide analysis via high-throughput sequencing is the state of the art method to gain genome-wide representation of histone modification or transcription factor binding profiles. However, chromatin immunoprecipitation analysis in the context of human experimental samples is limited, especially in the case of blood cells. The typically extremely low yields of precipitated DNA are usually not compatible with library amplification for next generation sequencing. We developed a highly reproducible protocol to present a guideline from the first step of isolating monocytes from a blood sample to analyse the distribution of histone modifications in a genome-wide manner.

overall_design:
ChIP-seq
histone modifications in CD14++ CD16- monocytes from human blood samples

first: Sebastian

last: Weiterer


title: Analysis of transcriptome of Chlamydomonas upon ClpP1 depletion and rapamycin treatment

city: Geneva 4

first: Jean-David

last: Rochaix

address: 30, quai Ernest-Ansermet

department: Department of Molecular biology and Plant Biology

country: Switzerland

institute: University of geneva

summary: All the proteases and chaperones involved in plastid protein quality control are encoded by the nucleus with exception of the catalytic subunit of the evolutionarily conserved serine-protease ClpP which is essential for the viability of Chlamydomonas cells. To study its function, we have induced a selective gradual depletion of ClpP in this alga which leads to a progressive alteration of chloroplast morphology, causes formation of vesicles and induces extensive cytoplasmic vacuolization, reminiscent of an autophagy phenotype. A high-throughput time-course analysis of the transcriptome and proteome during ClpP depletion revealed a set of proteins that are more abundant at the protein but not at the RNA level upon ClpP depletion which may comprise some of its substrates. Moreover, the specific increase in accumulation, both at the RNA and protein level, of small heat shock proteins, chaperones, proteases and proteins involved in thylakoid maintenance upon perturbation of plastid protein homeostasis suggests the existence of a chloroplast-to-nucleus signaling pathway involved in organelle quality control.

overall_design: Kinetic analysis using deep sequencing of mRNA levels in triplicates upon progressive deletion of ClpP1 protease (0, 12, 31, 43, 48 h) and inhibition of the TOR kinase by rapamycin (0, 2, 8 h).

first: Silvia

last: Ramundo

first: David

last: Casero

first: Olivier

last: Schaad

first: Natacha

last: Civic


title: Macrophage-Expressed Perforins Mpeg1 and Mpeg1.2 Have an Anti-Bacterial Function in Zebrafish

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

country: Netherlands

institute: Institute of Biology, Leiden University

summary: Macrophage expressed gene 1 (MPEG1) encodes an evolutionary conserved protein with a predicted Membrane Attack Complex/Perforin domain associated with host defence against invading pathogens. In vertebrates, MPEG1 is an integral membrane protein of macrophages, but how it contributes to the macrophage defence mechanisms remains unknown. Zebrafish have three copies of MPEG1, two of which (mpeg1 and mpeg1.2) are expressed in macrophages whereas the third could be a pseudogene. The mpeg1 and mpeg1.2 genes show differential regulation during infection of zebrafish embryos with the bacterial pathogens, Mycobacterium marinum and Salmonella typhimurium. While mpeg1 is down-regulated during infection with both pathogens, mpeg1.2 is infection inducible. Up-regulation of mpeg1.2 is partially dependent on the presence of functional Mpeg1, and requires the Toll-like receptor adaptor molecule MyD88 and transcription factor NFκB. Knockdown of mpeg1 alters the immune response to M. marinum infection and results in increased bacterial burden. In S. typhimurium infection, both mpeg1 and mpeg1.2 knockdown increase bacterial burdens, but mpeg1 morphants show an increased survival rate. The combined results of these two in vivo infection models support the anti-bacterial function of the Mpeg1 family and indicate that the intricate cross-regulation of the two  mpeg1 copies aids the zebrafish host in combatting infection

overall_design: Embryos were injected at the one cell stage with a morpholino targeting mpeg1, or with the standard control morpholino from GeneTools, or with a morpholino targeting ptpn6 (Kanwal et al., 2013, J. Immunol 190:1631-45) for comparison. Subsequently, at 24 hours post fertilisation (hpf) the morphants and their controls were manually dechorionated at 24 hpf and at 28 hpf they were infected by injecting 200 colony forming units of M. marinum Mma20 into the caudal vein, or mock-injected with PBS/2%PVP. After injections embryos were transferred into fresh egg water containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) to prevent melanisation and incubated for 4 days at 28°C. After the incubation period, infected and uninfected morphants, mutants and their controls were imaged and groups of 30 embryos were snap-frozen in liquid nitrogen and RNA was isolated for Illumina RNAseq analysis.

first: Erica

last: Benard

first: Peter

middle: I

last: Racz

first: Julien

last: Rougeot

first: Alexander

last: Nezhinsky

first: Fons

last: Verbeek

first: Herman

middle: P

last: Spaink

middle: H


title: Grhl3 is essential for epidermal barrier repair from both physical and immune injury, relevance to lesional skin disease

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

summary: Epidermal barrier repair mechanisms activated in psoriasis lesions are likely involved in limiting the severity of this disease. We show that loss of grainyhead-like 3 (Grhl3), a pro-terminal differentiation factor in the epidermis, is sufficient to trigger greater sensitivity to and delayed resolution of epidermal lesions resulting from either physical or immune mediated barrier injury. After stimulation of Toll like receptors, the loss of Grhl3 resulted in increased epidermal damage with a striking increase in basal cell proliferation, hyperplasia of partially differentiated suprabasal layers, and a transcriptional profile highlighted by the overexpression of epidermal wound response and alarmin genes. This study reveals an important role for the epidermis in the initiation and recovery from immune-mediated lesions, and indicated that the epidermal regulator Grhl3 acts to both suppress disease initiation and resolve existing lesions. This work suggests that treatments focused on improving barrier function could be used preventatively and therapeutically in psoriasis.

overall_design: Whole skin was collected from E16.5 mouse backskins for Grhl3 ChIP. Adult epidermis for depilation and imiquimod experiments was seperated from dermis using dispase prior to Grhl3 ChIP.

first: William

last: Gordon


title: Small molecule inhibitor of BCL2 in combination with RCHOP is effective in CD20 negative lymphoma

city: Waltham

first: Zhongwu

last: Lai

state: Massachusetts

address: 35 Gatehouse Dr.

department: Cancer Informatics

institute: AstraZeneca

summary: Rituximab alone or in combination with chemotherapeutics is the first-line therapy for variety of lymphoproliferative disorders including low- and high grade non-Hodgkin’s lymphomas (NHL). Although the complete response rate is quite impressive, vast majority of patient presents recurrent disease. The association between CD20 expression and clinical outcome in patients strongly suggests that reduced CD20 expression leads to inferior response to RCHOP (rituximab, cyclophosphamide, vincristine, doxorubicin and prednisone). In order to understand how loss of CD20 leads to development of RCHOP resistance, we developed rituximab resistant DOHH2 model in vivo by chronic exposure to rituximab. Characterization of several resistant in vivo xenografts revealed one model that maintained resistance to an acute dose of rituximab and demonstrated loss of CD20. Further characterization of the model demonstrated a loss of CD20 is associated with over expression of BCL2 and BIM. In vivo efficacy studies showed resistant line is insensitive to acute dose of RCHOP and treatment with an inhibitor of BCL2 (ABT199) in combination with chemotherapy resulted in better efficacy than RCHOP alone. We have identified an in vivo model of DLBCL where loss of CD20 and over expression of anti-apoptotic protein BCL2 leads to RCHOP resistance. These data suggest the addition of BCL2 inhibitor to chemotherapy might be effective in treating CD20 negative lymphomas.

overall_design: mRNA profiles of parental and rituximab resistant DOHH2 xenograft were generated by deep sequencing using Illumina HiSeq

first: Bradford

last: James

first: Qi

last: Zhang

first: Sara

last: Dempster

first: Celina

last: D'Cruz

first: Chaitali

last: Dutta

first: Corinne

last: Reimer


title: RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

summary: We developed a general method based on RNA Antisense Purification (RAP) to identify the intermolecular RNA-RNA interactions of a target RNA (RAP-RNA). RAP-RNA identifies endogenous RNA-RNA complexes through in vivo crosslinking, RNA capture with antisense oligonucleotides, and high-throughput RNA sequencing. This approach provides a systematic view of other RNAs that interact with a target RNA, and furthermore can distinguish between direct and indirect RNA-RNA interactions through the use of crosslinking reagents with different reactivities with proteins and nucleic acids.  We applied this method to numerous small and large noncoding RNAs, including U1 snRNA, Malat1 lncRNA, Xist lncRNA, U3 snoRNA, U17/Snora73a snoRNA and U12 snRNA.

overall_design: We examined the RNA and chromatin interactions of ncRNAs in mouse embryonic stem cells.  We developed and applied three related protocols: RAP-RNA[AMT], RAP-RNA[FA], and RAP-RNA[FA-DSG]. In the RAP-RNA[AMT] protocol, we fixed direct RNA-RNA hybrids in mouse embryonic stem (ES) cells with 4'-aminomethyltrioxalen (AMT), a psoralen-derivative crosslinker; AMT generates inter-strand crosslinks between uridine bases in RNA but does not react with proteins. In the RAP-RNA[FA] protocol, we used a different crosslinking strategy to capture both direct and indirect RNA-RNA interactions: we fixed ES cells using formaldehyde (FA), which crosslinks protein-RNA and protein-protein interactions and thus can capture both indirect interactions as well as direct interactions that are caged or flanked by proteins. In the RAP-RNA[FA-DSG] protocol, we fixed with both FA and disuccinimidyl glutarate (DSG), a strong protein-protein crosslinker, to more efficiently capture RNAs linked indirectly through multiple protein intermediates.

middle: M

first: Klara

last: Sirokman

first: Patrick

last: McDonel

last: Shishkin

first: Christine

last: Surka

first: Amy

last: Chow

first: Pamela

last: Russell

first: Sharon

last: Grossman

first: Mitchell

last: Guttman

first: Eric

middle: S

last: Lander


title: Whole transcriptome analyses of three Berkshire and three Korean native pig fat, liver and muscle tissue using RNA-Seq

city: Seoul

first: WonCheoul

last: Park

state: Gwanak-gu

address: 599 Gwanangno

institute: Seoul national university

summary: We sequenced the whole mRNA of six pig (Sus scrofa) fat, liver and muscle tissues, generating a total of 1.3 billion short reads with 90-bp pair-end sequences from 24 samples. Comparing with current genome annotation, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) unigene clusters did not match any current equine gene model. We identified 189,973 single nucleotide variations (SNVs) from the aligned sequences against the horse reference. Most SNVs (171,558 SNVs; 90.31%) were novel compared with over 1.1 million equine SNPs from two databases. Some genes have significantly different expression levels under different environment. We define those identical genes which have different expression levels are ‘differentially expressed’ and carried out differentially expressed gene analysis before and after exercise conditions. We discovered, 62 up- and 80 down-regulated genes in the blood and 878 up- and 285 down-regulated genes in the muscle from the 24 samples. Six out of 28 previously exercise-related known genes, HIF1A, ADRB2, PPARD, VEGF, TNC, and BDNF, were highly expressed in the muscle after exercise. We discovered 56 functionally unknown transcription factors that are probably associated with an early regulatory exercise mechanism from 91 differentially expressed transcription factors. We found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.

overall_design: whole mRNA sequencing profiles of six pig (Sus scrofa) fat, liver and muscle tissues

first: Dong-Ki

last: Jeong

first: Hee-Bal

last: Kim

first: Jin-Nam


title: Genome-scale methylation changes induced by photoperiods in Nasonia vitripennis

city: Leicester

first: Eran

last: Tauber

address: University Road

institute: University of Leicester

summary: Seasonal photoperiodic changes have strong impact on development in Nasonia vitripennis. Here, Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps of female wasps maintained in long vs short day. We have identified differential methylated loci that encode the photoperiodic change.

overall_design: analysis of  DNA methylation in female wasps maintained in long vs short day, using RRBS followed by Illumina sequencing

first: Nathaniel

last: Davies


title: A histone H3.3 Lysine 36 Trimethylation Reader Connects Chromatin to Regulated Pre-mRNA Processing

city: Los Angeles

first: Yi

last: Xing

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA

summary: BS69 (aka ZMYND11) was initially discovered as a direct target of adenoviral E1A oncoprotein1. Subsequent studies implicated BS69 as a tumor suppressor and a transcriptional regulator2. But exactly how BS69 regulates gene expression has remained elusive. BS69 contains tandemly arranged PHD, BROMO and PWWP domains, which are known to function as chromatin recognition modalities. Here we show that BS69 selectively recognizes histone variant H3.3 lysine 36 trimethylation (H3.3K36me3) via these chromatin recognition modules. Using a proteomics approach, we further identified association of BS69 with a host of RNA splicing regulators including EFTUD2 and other U5 snRNP components of the spliceosome. Remarkably, RNA-seq analysis shows that BS69 mainly regulates intron retention (IR), which is one of the least well-understood RNA alternative splicing events in mammalian cells. Specifically, loss of BS69 results in a decrease in IR, while in contrast, knockdown of EFTUD2 leads to an increase in IR, consistent with its role as a core member of the splicesome machinery. Importantly, wildtype BS69, but not a BS69 mutant defective in its interaction with EFTUD2, rescues the IR events. We also show that knockdown of SETD2, the main enzyme that mediates H3K36 trimethylation3, similarly results in a decreased retention of the same introns regulated by BS69. Significantly, a BS69 mutant unable to bind H3.3K36me3 in vitro fails to rescue the reduced IR phenotype associated with the loss of BS69. Taken together, our findings identify an antagonistic relationship between BS69 and the core splicing machinery and demonstrate that BS69-mediated RNA splicing regulation is dependent both on its ability to bind chromatin decorated by H3K36me3 and its ability to physically interact with the core spliceosome machinery. Our study reveals a novel and unexpected role of BS69 in connecting histone H3.3K36 trimethylation to regulated RNA splicing, providing significant new insights into chromatin regulation of RNA splicing.

overall_design: HeLa cells were infected with lentiviruses carrying control and BS69 shRNA and deep sequencing data were generated, in triplicate, using Illumina HiSeq 2000

first: Yang

last: Shi


title: Integrated analyses of DNA methylation and hydroxymethylation reveal tumor suppressive roles of ECM1, ATF5 and EOMES in human hepatocellular carcinoma

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

summary: The newly discovered 5-hydroxymethylcytosine (5hmC) may complicate previous observations of abnormal cytosine methylation statuses used for the identification of new tumor suppressor gene candidates relevant to human hepatocarcinogenesis. The simultaneous detection of 5mC and 5hmC will stimulate the discovery of aberrantly methylated genes with increased accuracy in human hepatocellular carcinoma (HCC). Here, we performed a newly developed single-base high-throughput sequencing approach (hydroxymethylation and methylation Sensitive Tag sequencing, HMST-seq) to synchronously measure these two modifications in HCC samples. After identifying the differentially methylated and hydroxymethylated genes in HCC, we integrated the DNA copy-number alterations as determined using array-based comparative genomic hybridization (aCGH) data with gene expression to identify genes potentially silenced by promoter hypermethylation. As a result, we report a high enrichment of genes with epigenetic aberrations in cancer signaling pathways. Six genes were selected as tumor suppressor gene (TSG) candidates, among which, ECM1, ATF5 and EOMES were confirmed to have potential anti-cancer function via siRNA experiments.

overall_design: To fully examine 5mC and 5hmC status in HCC, we used  a newly developed single-base high-throughput sequencing approach (hydroxymethylation and methylation sensitive tag sequencing, HMST-seq) to synchronously measure these two modifications in HCC samples and their adjacent non-cancerous liver tissues (non-HCCs).

first: Fei

last: Gao

first: Yudong

last: Xia

first: Junwen

last: Wang

first: Jian

last: Huang


title: Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (RNA-seq)

first: Tauno

last: Metsalu

summary: Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle.

overall_design: Placentas from ten family trios were analysed using RNA-Seq.

first: Triin

last: Viltrop

first: Airi

last: Tiirats

first: Balaji

last: Rajashekar

first: Ene

last: Reimann

first: Sulev

last: Kõks

first: Kristiina

last: Rull

first: Lili

last: Milani

first: Ganesh

last: Acharya

first: Purusotam

last: Basnet

first: Jaak

last: Vilo

first: Reedik

last: Mägi

first: Andres

last: Metspalu

first: Maire

last: Peters

first: Kadri

last: Haller-Kikkatalo

last: Salumets


title: Apparently Balanced Chromosomal Rearrangements (BCRs) as a model for random mutagenesis in humans

city: Copenhagen

first: Mads

last: Bak

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

summary: Transcribed regions in adult temporal lobe, hippocampus and frontal lobe were assesed by strand specific next generation sequencing of polyA RNA.

overall_design: Strand specific mRNA expression profiles of three human adult brain regions were generated by next generation sequencing using Illumina GAIIx

first: Christina

last: Halgren

first: Niels

last: Tommerup


title: Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences

city: Buffalo

first: Jiho

last: Sohn

address: 3435 Main Street, 644 Biomedical Research Building

institute: SUNY Buffalo

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

Acquisition of the intestinal microbiota begins at birth, and a stable microbial community develops from a succession of key organisms. Disruption of the microbiota during maturation by low-dose antibiotic exposure can alter host metabolism and adiposity. We now show that low-dose penicillin (LDP), delivered from birth, induces metabolic alterations and affects ileal expression of genes involved in immunity. LDP that is limited to early life transiently perturbs the microbiota, which is sufficient to induce sustained effects on body composition, indicating that microbiota interactions in infancy may be critical determinants of long-term host metabolic effects. In addition, LDP enhances the effect of high-fat diet induced obesity. The growth promotion phenotype is transferrable to germ-free hosts by LDP-selected microbiota, showing that the altered microbiota, not antibiotics per se, play a causal role. These studies characterize important variables in early-life microbe-host metabolic interaction and identify several taxa consistently linked with metabolic alterations.

overall_design: Refer to individual Series


title: ChIP-Seq analysis of HNF4A and FOXA2 in embryonic mouse liver

status: Public on Aug 31 2014

city: Vancouver

first: Pamela

last: Hoodless

state: BC

address: 675 W 10th Ave

department: Terry Fox Laboratory

institute: BC Cancer Agency - Research Centre

summary: HNF4a and FOXA2 are two liver enriched transcription factors that have been shown capable of reprogramming fibroblasts into hepatocyte-like cells. However to date it is not yet understood how these master regulators, expressed in both embryonic and adult liver contribute to the transcriptional changes necessary for hepatocyte maturation during development. Consequently we undertook to identify binding sites and target genes for HNF4a and FOXA2 in the embryonic liver. A comparison of embryonic and adult liver TF binding patterns revealed widespread differentiation-dependent genome occupancy associated with changes in target gene expression during liver development.

overall_design: Examination of HNF4a and FOXA2 binding sites in hepatoblasts purfied from embryonic liver (E14.5).

middle: A

first: Marco

last: Marra

first: Steven

last: Jones

first: Yongjun

last: Zhao

first: Nina

last: Thiessen

first: Gordon

last: Robertson

first: Misha

last: Bilenky

first: Sorana

last: Morrissy

first: Malachi

last: Griffiths

first: Rebecca

last: Cullum

first: Sam

last: Lee

first: Olivia

last: Alder


title: Integrating Genomics, Transcriptomics, and T-Cell Biology: An RNA-seq Atlas of the Murine CD4+ Transcriptome

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Rd

institute: University of Warwick

summary: CD4+ cells are key regulators of the adaptive immune system and can be classified into two main groups: T helper cells (naive, Th1, Th2 and Th17 cells), and regulatory T cells, iTreg and nTreg cells). We performed mRNA-sequencing on these major CD4+ cell subtypes, and integrated multiple computational methods for analyzing gene/isoform expression, differential expression, and functional annotation. Our primary analysis not only provides evidence for the very high quality of the sequence data, but also reveals novel patterns of read distributions inside and adjacent to genes. We identify 168 novel transcripts, which are differentially expressed in the various CD4+ cell subtypes. Further, we identify a wealth of novel, uniquely differentially expressed 'signature' transcripts for each cell type.  nTreg  cells have the largest number of these, with 477 signature genes in total, of which 58 are transcription factors. The data is compiled into an easily accessible online database publically available at http://www.thelpercell.com.

overall_design: RNA-seq data of Murine CD4+ cells

first: Andrew

last: Deonarine

first: Muxin

last: Gu

first: Jesper

last: Nissen

first: Alexander

middle: G

last: Betz

first: Sarah

last: Teichmann


title: Melatonin enhances plant growth and abiotic stress tolerance in soybean plants

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No.2

department: State Key Lab of Plant Genomics

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Melatonin is a well-known agent that plays multiple roles in animals. Its possible function in plants is less clear. In the present study, we tested the effect of melatonin (N-acetyl-5-methoxytryptamine) on soybean growth and development. Both spraying of leaves and seed-coating with melatonin significantly promoted soybean growth as judged from leaf size and plant height. This enhancement was also observed in soybean production and their fatty acid content. Melatonin increased pod number, seed number and seed weight. However, the 100-seed weight was not influenced by melatonin application. Melatonin also improved soybean tolerance to salt and drought stresses. Transcriptome analysis revealed that melatonin up-regulated the expression of many genes and alleviated the inhibitory effects of salt stress on gene expressions. Further detailed analysis of the affected pathways documents that melatonin likely achieved its promotional roles in soybean through enhancement of genes involved in cell division, photosynthesis, carbohydrate metabolism, fatty acid biosynthesis and ascorbate metabolism. Our results demonstrate that melatonin has significant potential for improving of soybean growth and seed production. Further study should uncover more about the molecular mechanisms of melatonin’s function in soybeans and other crops.

overall_design: Four different treatments were chosen, water, salt, 100µM melatonin and salt plus 100µM melatonin. The comparison of salt/melatonin-treated sample versus water-treated sample reveals salt or melatonin induced transcriptome changes. The comparison of melatonin plus salt treated sample versus salt-treated sample reveals melatonin induced changes when salt exists.

first: Qing-Tian

last: Li

first: Ya-Nan

last: Chu

first: Russel

last: Reiter

first: Wan-Ke

last: Zhang

first: Biao

last: Ma

first: Qing

last: Lin

first: Jin-Song

first: Shou-Yi

last: Chen


title: Identification of Highly Conserved Putative Developmental Enhancers Bound by SOX3 in Neural Progenitors Using ChIP-Seq

city: Adelaide

first: Dale

last: McAninch

state: SA

address: North Terrace

country: Australia

institute: The University of Adelaide

summary: SOX3 is highly expressed in neural progenitor cells (NPC) within the developing mouse cetral nervous system. A ChIP-Seq experiement was performed for SOX3 in NPCs derived from embryonic stem cells.

overall_design: Identification of SOX3 binidng sites from 3 independent ChIP-seq samples in NPCs

first: Paul

middle: Q

last: Thomas


title: RNA-guided Location and Function of the Cas9 CRISPR Endonuclease in Mammalian Cells

status: Public on Aug 29 2014

city: Montreal

first: Jerry

last: Pelletier

state: Quebec

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

department: Department of Biochemistry

institute: McGill university

summary: The clustered regularly interspaced short palindromic repeat (CRISPR)-associated enzyme Cas9 is an RNA-guided nuclease that has been widely adapted for genome editing in eukaryotic cells. However, the in vivo target specificity of Cas9 is poorly understood and most studies rely on in silico predictions to define the potential off-target editing spectrum. Using chromatin immunoprecipitation followed by sequencing (ChIP-seq), we delineate the genome-wide binding panorama of catalytically inactive Cas9 directed by two different single guide (sg) RNAs targeting the Trp53 locus. Cas9:sgRNA complexes are able to load onto multiple sites with short seed regions adjacent to 5’NGG3’ protospacer adjacent motifs (PAM).

overall_design: Examination of dmCas9 binding sites using two Trp53 targeting  sgRNAs in Arf -/- MEF cell line (mouse).

first: Hisashi

last: Miura

first: Abba

last: Malina

first: Regina

last: Cencic

first: Robert

last: Francis


title: Effects of acute prenatal exposure to ethanol on microRNA expression are ameliorated by environmental manipulation

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: In this study, we tested if miRNAs are altered in amygdala and ventral striatum as a consequence of prenatal ethanol exposure and/or social enrichment. miRNA samples from 72 male and female adolescent rats were analyzed by RNA-Seq analysis and Affymetrix miRNA arrays. Several miRNAs showed significant changes due to prenatal ethanol exposure or social enrichment in one or both brain regions. Some of the miRNA changes caused by ethanol were reversed by social enrichment. The top predicted gene targets of these miRNAs were mapped and subjected to pathway enrichment analysis. We also directly examined the evidence for modulation of target mRNAs in whole transcriptome microarray data from the same rats. Among the pathways most strongly affected were p53, CREB, Glutamate and GABA signaling. Together, our data suggest a number of novel epigenetic mechanisms for social enrichment to reverse the effects of ethanol exposure.

overall_design: A total of 48 samples were analyzed by small RNA-Sequencing using RNA purified from 2 brain regions (amygdala and ventral striatum) of postnatal day 42 Long Evans rats. 3 replicate sequencing runs were performed for each gender within 4 different treatment groups (prenatal ethanol or prenatal saline exposed; postnatal socially-enriched or non-enriched environment)

first: Sandra

last: Mooney

first: Cherry

last: Ignacio


title: The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription [Yeast cells]

city: Illkirch

first: Didier

last: Devys

address: 1 rue Laurent Fries / BP 10142

country: France

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)

summary: The SAGA co-activator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Surprisingly, recent studies revealed little overlap between genome-wide SAGA-binding profiles and changes in gene expression upon depletion of subunits of the complex. As indicators of SAGA recruitment on chromatin, we monitored in yeast and human cells the genome-wide distribution of histone H3K9 acetylation and H2B ubiquitination, which are respectively deposited or removed by SAGA. Changes in these modifications after inactivation of the corresponding enzyme revealed that SAGA acetylates the promoters and deubiquitinates the transcribed region of all expressed genes. In agreement with this broad distribution, we show that SAGA plays a critical role for RNA polymerase II recruitment at all expressed genes. In addition, through quantification of newly synthesized RNA, we demonstrated that SAGA inactivation induced a strong decrease of mRNA synthesis at all tested genes. Analysis of the SAGA deubiquitination activity further revealed that SAGA acts on the whole transcribed genome in a very fast manner indicating a highly dynamic association of the complex with chromatin. Thus, our study uncovers a new function for SAGA as a bone fide co-factor for all RNA Polymerase II transcription.

overall_design: Comparison of H3K9ac, H2Bub and RNA Pol II distributions in WT yeast cells and upon the loss of SAGA activities.

first: Chen-Yi

middle: Y

last: Wang

first: Jacques

last: Bonnet

first: Tiago

last: Baptista

first: Stéphane

last: Vincent

first: Wei-Chun

middle: C

last: Hsiao

first: Matthieu

last: Stierle

first: Cheng-Fu

last: Kao

first: László

last: Tora


title: Comparison of small RNA-seq and microarray analysis for determining the effects of acute prenatal ethanol exposure on microRNA expression and its amelioration by environmental manipulation

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

platform_organism:
Rattus norvegicus
synthetic construct


title: Selection of epigenetic variation in Arabidopsis [SNP data]

city: Zürich

first: Christian

last: Heichinger

state: Zürich

address: Zollikerstrasse 107

department: Institute of Plant Biology

institute: Zürich University

summary: In Arabidopsis thaliana a high rate of spontaneous epigenetic variation can occur in the DNA methylome in the absence of genetic variation and selection. It has been of great interest, whether natural epigenetic variation is subject to selection and contributes to fitness and adaptation in selective environments. We compared the variation in selected phenotypic traits, genome-wide cytosine DNA methylation and gene expression in two Arabidopsis recombinant inbred lines, which had undergone five generations of selection in experimental landscapes relative to their genetically identical ancestors. Selected populations exerted significant differences in flowering time and the number of branches and fruits, differences that were maintained over two to three generations in the absence of selection. We identified 4,629 and 5,158 differentially methylated cytosines which were overrepresented in genes that regulate flowering time, epigenetic processes, development and morphogenesis. Differentially methylated genes were enriched in differentially expressed genes. Thus, epigenetic variation is subject to selection and may play an important role in the adaptive response of populations in rapidly changing natural environments.

overall_design: Genomic DNA was extracted from whole-plant above-ground tissue of individual 25-day-old plants with the Qiagen DNeasy kit (Qiagen). DNA from two randomly chosen CVL39 individuals from ancestral (A3) lines and from 7 selected (S3) lines that had experienced 5 generations of selection in the three replicated dynamic landscapes (2xD1, 3xD5,2xD6)  was  sequenced (paired-end, 100 bp) using the Illumina Highseq 2000 Instrument. Single nucleotide polymorphisms and TE insertions were mapped with respect to the recombinant reference genome and compared between selected and ancestral lines.

first: Marc

middle: W

last: Schmid

first: Daniela

last: Guthörl

first: Rémy

last: Bruggmann

first: Sirisha

last: Aluri

first: Marzanna

last: Künzli

first: Lindsay

last: Turnbull

first: Bernhard

first: Ueli

last: Grossniklaus


title: The NF-kB genomic landscape in lymphoblastoid B-cells

city: Boston

first: Benjamin

last: Gewurz

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

summary: The nuclear factor kB (NF-kB) subunits RelA, RelB, c-Rel, p50 and p52 are each critical for B-cell development and function.  To systematically characterize their responses to canonical and non-canonical NF-kB pathways activity, we performed ChIP-seq analysis in lymphoblastoid B-cells. We found a surprisingly complex NF-kB binding landscape, which did not readily reflect the two NF-kB pathway paradigm.  Instead, ten subunit binding patterns were observed at promoters and eleven at enhancers.  Surprisingly, nearly one-third of NF-kB binding sites lacked kB motifs. De novo motif finding uncovered distinct modes of NF-kB recruitment at these sites. The oncogenic forkhead box protein FOXM1 and NF-kB co-occupied many kB sites despite the absence of a FOXM1 DNA motif.  FoxM1 knockdown decreased expression of key NF-kB targets and caused apoptosis.  Our study highlights opportunities for selective therapeutic NF-kB blockade.

overall_design:
ChIP-seq was used to define the genomic landscape of NF-kB DNA binding in lymphoblastoid cells.

The raw data for GSM2628089 are not available.

first: Bo

last: Zhao

first: Luis

last: Barrera

first: Ina

last: Ersing

first: Brad

last: Willox

first: Stephanie

last: Schmidt

first: Hufeng

last: Zhou

first: Tommy

last: Shi

first: Sarah

last: Mollo

first: Hannah

last: Greenfeld

first: Kaoru

last: Takasaki

first: Sizun

last: Jiang

first: Ellen

last: Cahir-McFarland

first: Manolis

last: Kellis

first: Martha

middle: L

last: Bulyk

first: Elliott

last: Kieff


title: RNA-Seq and BS-Seq of Sorghum bicolor tissues

city: Cold Spring Harbor

first: Andrew

middle: J

last: Olson

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: This study utilized next generation sequencing technology (RNA-Seq and BS-Seq) to examine the transcriptome and methylome of various tissues within sorghum plants with the ultimate goal of improving the Sorghum bicolor annotation

overall_design: We examined the mRNA of various Sorghum bicolor (BTx623) tissues (flowers, vegitative and floral meristems, embryos, roots and shoots) and bisulfite treated DNA from two root samples

first: Diana

middle: V

last: Dugas

first: Robert

middle: R

last: Klein

first: Doreen

last: Ware

first: Zhenyuan

last: Lu

first: Michael

last: Regulski

first: Patricia


title: Potent antitumor activity of Cabozantinib, a c-MET and VEGFR2 Inhibitor, in a Colorectal Cancer Patient-derived Tumor Explant Model

status: Public on Aug 30 2014

city: Aurora

first: John

last: Arcaroli

state: CO

address: 12801 E. 17th Avenue

department: Department of Medicine

institute: University of Colorado Denver

summary: Anti-angiogenic therapy is commonly used for the treatment of CRC. Although patients derive some clinical benefit, treatment resistance inevitably occurs. The MET signaling pathway has been proposed to be a major contributor of resistance to anti-angiogenic therapy. MET is upregulated in response to VEGF pathway inhibition and plays an essential role in tumorigenesis and progression of tumors. In this study we set out to determine the efficacy of cabozantinib in a preclinical CRC PDTX model. We demonstrate potent inhibitory effects on tumor growth in 80% of tumors treated. The greatest antitumor effects were observed in tumors that possess a mutation in the PIK3CA gene. The underlying antitumor mechanisms of cabozantinib consisted of inhibition of angiogenesis and Akt activation and significantly decreased expression of genes involved in the PI3K pathway. These findings support further evaluation of cabozantinib in patients with CRC. PIK3CA mutation as a predictive biomarker of sensitivity is intriguing and warrants further elucidation. A clinical trial of cabozantinib in refractory metastatic CRC is being activated.

overall_design: CRC PDTX Model treated with cabozantinib

first: Guoliang

last: Wang


title: Selection of epigenetic variation in Arabidopsis [Bisulfite-Seq]

first: Christian

last: Heichinger

overall_design: Genomic DNA was extracted from whole-plant above-ground tissue of individual 25-day-old plants with the Qiagen DNeasy kit (Qiagen). DNA from four randomly chosen individuals was pooled from selected (S2) lines that had experienced 5 generations of selection in the three replicated dynamic landscapes (D1, D5, D6) and from the ancestrals (A2) for both CVL39 and CVL125 respectively, yielding eight samples for bisulfite sequencing. DNA was treated with bisulfite which converts unmethylated cytosines to thymines but leaves methylated cytosines unconverted. DNA was then sequenced using the SOLIDTM Life technologiesTM System. DNA cytosine methylation profiles of selected lines (S2) were compared to methylation profiles from ancestral (A2) lines.

first: Marc

last: Schmid

first: Daniela

last: Kleen

first: Remy

last: Bruggmann

first: Sirisha

last: Aluri

first: Marzanna

last: Künzli

first: Lindsay

last: Turnbull

first: Bernhard

first: Ueli

last: Grossniklaus


title: The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription

first: Didier

last: Devys

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

The SAGA co-activator complex contains distinct chromatin-modifying activities and is recruited by DNA-bound activators to regulate the expression of a subset of genes. Surprisingly, recent studies revealed little overlap between genome-wide SAGA-binding profiles and changes in gene expression upon depletion of subunits of the complex. As indicators of SAGA recruitment on chromatin, we monitored in yeast and human cells the genome-wide distribution of histone H3K9 acetylation and H2B ubiquitination, which are respectively deposited or removed by SAGA. Changes in these modifications after inactivation of the corresponding enzyme revealed that SAGA acetylates the promoters and deubiquitinates the transcribed region of all expressed genes. In agreement with this broad distribution, we show that SAGA plays a critical role for RNA polymerase II recruitment at all expressed genes. In addition, through quantification of newly synthesized RNA, we demonstrated that SAGA inactivation induced a strong decrease of mRNA synthesis at all tested genes. Analysis of the SAGA deubiquitination activity further revealed that SAGA acts on the whole transcribed genome in a very fast manner indicating a highly dynamic association of the complex with chromatin. Thus, our study uncovers a new function for SAGA as a bone fide co-factor for all RNA Polymerase II transcription.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens


title: Genome-wide expression profiling of B Lymphocytes reveals IL4R increase in allergic asthma

status: Public on Aug 28 2014

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

institute: University of Navarra

summary: In this study we present the first genome-wide expression profiling of peripheral B cells by massive parallel RNA sequencing in patients with allergic asthma validating the discovery potential of this approach in allergy.

overall_design: RNA-seq was used to asses expression differences in B CD19 Lymphocytes from house dust mite allergic patients and healthy controls.

first: Marien

last: Pascual

first: Sergio

last: Roa

first: Asunción

last: García-Sánchez

first: Catalina

last: Sanz

first: Laura

last: Hernandez-Hernandez

last: Greally

first: Félix

last: Lorente

first: Ignacio

last: Dávila

first: María

last: Isidoro-García


title: Role of small RNA in post-natal olfactory bulb neurogenesis in mouse

city: Marseille

first: christophe

last: beclin

state: Bouches du Rhone

address: campus de Luminy, case 907

department: Aix-Marseille université

institute: CNRS

summary: We performed deep-sequencing analysis of small RNA extracted from neuronal progenitors at different developmental stages. The RNA samples were extracted from microdissected tissues of dorsal or lateral sub-ventricular zone (SVZ) (to analyze the immature progenitor pools), of rostral migration stream (RMS) (to analyze the migrating neuroblasts) or of olfactory bulbs (OB) (to analyze both immature and mature neurons). These tissues were dissected from animals at variable ages: P1 and P6 for SVZ samples, P15 and P28 for RMS and OB samples.

overall_design: Expression profile of microRNA  in time and space along post-natal neurogenesis

first: Christophe

last: Beclin

first: Phillip

last: Follert

first: Harold

last: Cremer

first: Pascal

last: Barbry


title: Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine

city: College Park

first: Jose

middle: Adrian

last: Carrillo

state: MD

address: 1413 Animal Sciences Center

department: Department of Animal and Avian Sciences

institute: University of Maryland

summary: In this study we investigated the methylome of chickens immunized with Infectious laryngotracheitis (ILT) vaccine derived from chicken embryos. Methyl-CpG binding domain protein-enriched genome sequencing (MBD-Seq) method was employed in the detection of the 1,155 differentially methylated regions (DMRs) across the entire genome. After validation, we ascertained the genomic DMRs distribution and annotated them regarding genes, transcription start sites (TSS) and CpG islands. We found that global DNA methylation decreased in vaccinated birds, presenting 704 hypomethylated and 451 hypermethylated DMRs, respectively. Additionally, we performed an enrichment analysis detecting gene networks, in which cancer and RNA post-transcriptional modification appeared in the first place, followed by humoral immune response, immunological disease and inflammatory disease. The top four identified canonical pathways were EIF2 signaling, regulation of EIF4 and p70S6K signaling, axonal guidance signaling and mTOR signaling, providing new insight regarding the mechanisms of ILT etiology. Lastly, the association between DNA methylation and differentially expressed genes was examined, and detected negative correlation in seventeen of the eighteen genes.

overall_design: DNA methylation analysis employing MBD-Seq with 3 salt concentrations, in vaccinated and control group of chickens with 2 biological replications

first: José

first: YangHua

last: He

first: Juan

last: Luo

first: Kimberly

last: Menendez

first: Nathaniel

last: Tablante

first: Keji

last: Zhao

first: Joseph

middle: N

last: Paulson

first: Bichun

last: Li

first: Jiuzhou

last: Song


title: The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription [HeLa cells]

first: Didier

last: Devys

overall_design: Comparison of H3K9ac and H2Bub distributions in control HeLa cells and upon the inactivation of SAGA enzymatic activities

first: Jacques

last: Bonnet

first: Chen-Yi

last: Wang

first: Tiago

last: Baptista

first: Stéphane

middle: D

last: Vincent

first: Wei-Chun

last: Hsiao

first: Matthieu

last: Stierle

first: Cheng-Fu

middle: F

last: Kao

first: László

last: Tora


title: Comparison of the transcriptional profiles of male E13.5 wild type and L/H-Pgds-/- gonads

status: Public on Aug 26 2014

city: Montpellier

first: Brigitte

last: Boizet-Bonhoure

address: 141 rue de la Cardonille

department: Genetic and Development

summary: The goals of this study are to compare transcriptome profiling of  L/H-Pgds-/- gonads to that of WT (RNA-seq)

overall_design: Methods:  mRNA profiles of E13.5 wild-type (WT) and L- and H- prostaglandin D synthases (L/H-Pgds−/−) embryonic gonad were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.  qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Francis

last: Poulat


title: Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis

first: Peng

last: Du

state: MA

address: 1 Blackfan Circle

institute: Boston Children’s Hospital, Harvard Medical School

overall_design: This study constructed and sequenced two independent small RNA libraries from the upper uninoculated leaves of (i) WT Arabidopsis plants 14 d after mock inoculation and of (ii) rdr1 rdr6 plants 14 d after infection with Fny CMV-Δ2b, and one library each from the upper uninoculated leaves of (iii) WT, (iv) rdr1, and (v) rdr6 plants 14 d after infection with TuMV-GFP. Coimmunoprecipitation with FLAG- and HA-specific antibodies was used to obtain (vi,vii) AGO1 and (viii,ix) AGO2 complexes, respectively, from the FLAG-AGO1/ago1-36 and HA-AGO2 plants 14 d after infection with Fny CMV-Δ2b for extracting total loaded small RNAs for the construction and sequencing of small RNA libraries.

first: Shou-wei

last: Ding

first: Yi

first: Mengji

last: Cao

first: Xian-bing


title: RRHP : a tag-based approach for 5-hydroxymethylcytosine mapping at single-site resolution

city: Irvine

first: Xueguang

last: Sun

state: CA

address: 17062 Murphy Ave

institute: zymo research corp

summary: We present here a novel approach called Reduced Representation 5-Hydroxymethylcytosine Profiling (RRHP), which exploits β-glucosyltransferase (β-GT) to inhibit restriction digestion at adapters ligated to a genomic library, such that only fragments presenting glucosylated 5hmC residues at adapter junctions will be amplified and sequenced. This assay profiles 5hmC sites with single-base resolution in a strand-specific manner. The absence of harsh chemical conversion steps allows for sequencing of native DNA with less inputs, enhancing both sequencing quality and mapping efficiency. Most importantly, the method proves highly reproducible and is a positive display method, sensitive enough to interrogate 5hmC sites with low abundance. When combined with existing RRBS data, it allows simultaneous comparison of 5mC and 5hmC at specific site.

overall_design: developing a new assay for genomic profiling of 5hmC

first: Adam

last: Petterson

first: Tzu Hung

last: Chung

first: Darany

last: Tan

first: Xi-Yu

last: Jua


title: Transcriptome analysis of NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, NTHi 86-028NPrpsL∆fur∆hrrF, NTHi 86-028NPrpsL∆fur∆hrrF3' strains

city: Columbus

first: Alistair

last: Harrison

state: OH

address: 700 Children's Drive

department: Center for Microbial Pathogenesis

institute: The Research Institute at Nationwide Children's Hospital

summary: Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the normal human nasopharyngeal flora, yet also an opportunistic pathogen of the upper and lower respiratory tracts. Changes in gene expression patterns in response to host microenvironments are likely critical for survival. One such system of gene regulation is the ability to carefully regulate iron uptake. A central regulatory system that controls iron uptake, mediated by the ferric uptake regulator Fur, is present in multiple bacteria, including NTHi. Previous work has identified a small RNA, HrrF, that is Fur-regulated in NTHi 86-028NPrpsL.To understand the contribution made by HrrF to gene regulation in NTHi, hrrF was deleted in the NTHi strain 86-028NPrpsL∆fur. Using RNA-Seq, we identified protein-encoding genes whose expression was repressed or activated by HrrF.

overall_design:
These data comprise transcriptional anaylses of an rpsL mutant of 86-028NP, an isogenic fur mutant of 86-028NPrpsL, an isogenic fur mutant of 86-028NPrpsL also containing a full deletion of hrrF, and an isogenic fur mutant of 86-028NPrpsL also containing a deletion of only the 3' portion of hrrF. All strains were grown in defined medium containing 10 µg/ml human hemoglobin to mid-log phase. Cells were then harvested and RNA extracted. A total of three biological replicates were generated for these analyses.
Analysis of transcriptomes using the Illumina HiSeq 2000 of four strains of nontypeable Haemophilus influenzae which include NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur,  NTHi 86-028NPrpsL∆fur∆hrrF, and NTHi 86-028NPrpsL∆fur∆hrrF3' strains. For each strain three biological replicates were analyzed.

first: Robert

last: Munson Jr

first: Estevan

last: Santana


title: Staphylococcus epidermidis biofilms transcriptome alterations upon incubation with whole human blood

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

summary: The ability of S. epidermidis to withstand the high bactericidal activity of the host’s blood is crucial for its systemic dissemination. Hence, in order to identify genes and pathways involved in the bacterium’s survival in human blood, we have characterized the transcriptome of S. epidermidis biofilms upon contact with human blood. Our results showed that genes whose transcription was increased in blood included those involved in biosynthesis and metabolism of amino acids, small molecules, carboxylic and organic acids, and cellular ketones. One of the striking changes, observed after 4 hours of exposure to human blood, was the increase in the expression of genes involved in iron utilization, suggesting iron acquisition is an important component of S. epidermidis survival in human blood.

overall_design: Twenty-four hour S. epidermidis biofilms were incubated with either whole human blood or tryptic soy broth (TSB) during 2 or 4 hours at 37oC, 5% CO2 and slight agitation. RNA was then extracted and the transcriptomic libraries constructed. Differential gene expression calculations were performed using the transcriptome of biofilms at the start of the culture (T0h) as a control. This experiment was performed twice with blood collected from 6 healthy human donors under a protocol approved by the Partner’s Health Care System Institutional Review Board (Boston, MA, USA).

first: Angela

first: Virginia

last: Carvalhais

first: Tomás

last: Maira-Litrán

first: Manuel

last: Vilanova

first: Nuno

last: Cerca

first: Gerald

last: Pier