title: b-Catenin Mediates the Development of Behavioral Resilience [ChIP-Seq]

city: New York

first: Li

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Here we show that β-catenin mediates pro-resilient and anxiolytic effects in mice in the nucleus accumbens (NAc), a key brain reward region, an effect that is mediated by β-catenin signaling in D2-type medium spiny neurons (MSNs) specifically.  Conversely, blocking β-catenin function in NAc promotes susceptibility to chronic stress, and we show evidence of robust suppression of β-catenin transcriptional activity in the NAc both of depressed humans examined postmortem as well as of mice that display a susceptible phenotype after chronic stress, with a converse upregulation in mice that are stress resilient.  Using ChIP-seq, we demonstrate a global, genome-wide enrichment of β-catenin in the NAc of resilient mice, and specifically identify Dicer1—important in small RNA (e.g., microRNA [miRNA]) biogenesis—as a critical β-catenin target gene involved in mediating a resilient phenotype.  Small RNA-seq after excising β-catenin from the NAc in the context of chronic stress reveals dynamic β-catenin-dependent miRNA regulation associated with resilience.

overall_design: Control: 2 samples, Resilient: 2 samples, Susceptible: 2 samples; DNA input: 1 sample.

first: Ning-Yi

last: SHAO

first: Caroline

last: DIAS

last: SHEN

first: Eric

last: NESTLER


title: b-Catenin Mediates the Development of Behavioral Resilience [smallRNA-Seq]

status: Public on Nov 13 2014

country: USA

type: Non-coding RNA profiling by high throughput sequencing

overall_design: GFP_Control: 12 samples, GFP_Resilient: 12 samples, GFP_Susceptible: 4 samples; CRE_Control: 12 samples, CRE_Susceptible: 8 samples.

first: Jian

last: FENG

last: NESTELER


title: b-Catenin Mediates the Development of Behavioral Resilience

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The putative cellodextrin transporter-like protein CLP1 is involved in cellulase induction in Neurospora crassa

city: Tianjin

first: Pengli

last: Cai

address: Xiqi Dao 32, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, CAS

type: Expression profiling by high throughput sequencing

summary: Neurospora crassa recently has become a novel system to investigate cellulase induction. Here, we discovered a novel membrane protein, CLP1 (NCU05853), a putative cellodextrin transporter-like protein, that is a critical component of the cellulase induction pathway in N. crassa. Although CLP1 protein cannot transport cellodextrin, the suppression of cellulase induction by this protein was discovered on both cellobiose and Avicel. The co-disruption of the cellodextrin transporters cdt2 and clp1 in strain Δ3βG formed strain CPL7. With induction by cellobiose, cellulase production was enhanced 6.9-fold in CPL7 compared with Δ3βG. We also showed that the suppression of cellulase expression by CLP1 occurred by repressing the expression of cellodextrin transporters, particularly cdt1 expression. Transcriptome analysis of the hypercellulase-producing strain CPL7 showed that the cellulase expression machinery was dramatically stimulated, as were the cellulase enzyme genes including the inducer transporters and the major transcriptional regulators.

overall_design: N. crassa was pregrown in sucrose and transferred to cellobiose media. Up regulated and down regulated genes expressions were compared with Δ3βG and Δ3βGΔclp1 strain.

first: Chaoguang

last: Tian

first: Bang

last: Wang

first: Jingxiao

last: Ji

first: Yongsheng

last: Jiang

last: Wan

first: Yanhe

last: Ma


title: mRNA sequencing of small intestinal tissue of germfree mice

first: Elisabeth

last: Kernbauer

address: 540 First Avenue

institute: New York University School of Medicine, Skirball Institute

summary: With this study we wanted to evaluate the impact of murine norovirus infection of germfree mice and to compare it to germfree mice which have received fecal transplants of conventional mice.

overall_design: whole small intestinal tissue analysis of 3 germfree, 3 germfree mice infected with murine norovirus and 3 conventionalized germfree mice

first: Ken

last: Cadwell


title: Transcriptome comparisons of "expandable hemangioblasts" (eHBs) and their progeny to control cells

city: Madison

first: David

last: Vereide

state: WI

address: 330 North Orchard Street

department: Regenerative Biology

institute: Morgridge Institute for Research

summary: We examined the transcriptomes of murine "expandable hemangioblasts" (eHBs) and their blood and endothelial progeny, comparing them to the transcriptomes of murine embryonic stem (ES) cells, primary murine endothelial cells isolated from E11.5 yolk sacs or embryos, and E14.5 fetal liver hematopoietic stem cells.

overall_design: Total RNAs were purified from lysates of cultured or primary cells, reverse transcribed, and sequenced on an Illumina HiSeq 2500.

middle: T

first: Vernella

last: Vickerman

first: Scott

middle: A

last: Swanson

first: Li-Fang

last: Chu

first: Brian

middle: E

last: McIntosh

first: James

last: Thomson


title: Transcriptional Program of Kpna2 (Importin-alpha2) Regulates Cellular Differentiation-Coupled Circadian Clock Development in Mammalian Cells

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: The circadian clock in mammalian cells is cell-autonomously generated during the cellular differentiation process, but the underlying mechanisms are not understood. Here we show that perturbation of transcriptional program by constitutive expression of c-Myc and Dnmt1 ablation disrupts the differentiation-coupled emergence of the clock from mouse embryonic stem cells (ESCs). Using these model ESCs, 484 genes are identified by global gene expression analysis as correlating factors with differentiation-coupled circadian clock development. Among them, we find the misregulation of Kpna2 (Importin-alpha2) during the differentiation of the c-Myc over-expressed and Dnmt1-/- ESCs, in which sustaining cytoplasmic accumulation of PER proteins is observed. Moreover, constitutive expression of Kpna2 during the differentiation culture of ESCs significantly impairs clock development and KPNA2 facilitates cytoplasmic localization of PER1/2. These results suggest that the programmed gene expression network regulates the differentiation-coupled circadian clock development in mammalian cells, at least in part via post-transcriptional regulation of clock proteins.

overall_design: Examination of whole transcriptome in ES cells and in vitro differentiated cells.

first: Yasuhiro

last: Umemura

first: Nobuya

last: Koike

first: Tsuguhiro

last: Matsumoto

first: Seung-Hee

last: Yoo

first: Zheng

last: Chen

first: Noriko

last: Yasuhara

first: Joseph

middle: S

last: Takahashi


title: The Parathyroid Hormone-Regulated Transcriptome in Osteocytes: Parallel Actions with 1,25-Dihydroxyvitamin D3 to Oppose Gene Expression Changes During Differentiation and to Promote Mature Cell Function

status: Public on Nov 14 2014

first: Mark

middle: B

last: Meyer

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison


title: TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

summary: Ten eleven translocation (TET) enzymes catalyse the oxidative reactions of 5-methylcytosine (5mC) to promote the demethylation process. The reaction intermediate 5-hydroxymethylcytosine (5hmC) has been shown to be abundant in embryonic stem cells and tissues, but strongly depleted in human cancers. Genetic mutations of TET2 gene were associated with lleukemia, whereas TET1 downregulation has been shown to promote malignancy in breast cancer.  Here, we report that TET1 is downregulated in colon tumours from the initial stage. TET1 silencing in primary epithelial colon cells increase their cellular proliferation while its   re-expression in colon cancer cells inhibits their proliferation and the growth of tumour xenografts even at later stages. We found that TET1 binds and maintains hypomethylated the promoter of the DKK genes inhibitors of the WNT signalling to promote their expression. Downregulation of TET1 during colon cancer initiation leads to repression, by DNA methylation the promoters of the inhibitors of the WNT pathway resulting in a constitutive activation of the WNT pathway. Thus the DNA hydroxymethylation mediated by TET1 controlling the WNT signalling is a key player of tumour growth. These results provide new insights for understanding how tumours escape cellular controls

overall_design: Transcriptome analysis of Caco-2 cell line expressing TET1 protein.

first: Salvatore

last: Oliviero


title: An Oncogenic Super-Enhancer Formed through Somatic Mutation of a Noncoding Intergenic Element

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: In many cancers, critical oncogenes are driven from large regulatory elements, called super-enhancers, which recruit much of the cell’s transcriptional apparatus and are defined by extensive H3K27 acetylation.  We found that in T-cell acute lymphoblastic leukemia (T-ALL), somatic heterozygous mutations introduce MYB binding motifs in a precise noncoding site, which nucleate a super-enhancer upstream of the TAL1 oncogene.   Further analysis of genome-wide binding identified MYB and its histone acetylase binding partner CBP as core components of the TAL1 complex and of the TAL1-mediated feed-forward auto-regulatory loop that drives T-ALL.  Furthermore, MYB and CBP occupy endogenous MYB binding sites in the majority of super-enhancer sites found in T-ALL cells.  Thus, our study reveals a new mechanism for the generation of super-enhancers in malignant cells involving the introduction of somatic indel mutations within non-coding sequences, which introduce aberrant binding sites for the MYB master transcription factor.

overall_design: ChIP-Seq for transcription factors and co-factors in T cell acute lymphoblastic leukemia cell lines

first: Marc

middle: R

last: Mansour

middle: J

last: Abraham

first: Lars

last: Anders

first: Alla

last: Berezovskaya

first: Alejandro

last: Gutierrez

first: Adam

middle: D

last: Durbin

first: Lee

middle: N

last: Lawton

first: Stephen

last: Sallan

first: Lewis

last: Silverman

first: Mignon

middle: L

last: Loh

middle: P

last: Hunger

first: Takaomi

last: Sanda

first: Jessica

last: Reddy

first: A

last: Look


title: MicroRNA analysis of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by miRNA regulation of endocytosis and lysosome trafficking

city: Dunsany

first: Peter

last: Vegh

state: Meath

address: Grange, Batterjohn Crossroads

department: Animal & Bioscience Research Department

country: Ireland

institute: Teagasc

summary: Purpose: The goal of this RNA-seq study was to profile changes in miRNA expression in bovine alveolar macrophages isolated from Holstein-Friesian and challenged with M. bovis over a 48 hour time course. Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major infectious disease problem for global agriculture, resulting in losses of billions of Euros annually. The bacterium spreads via an airborne route and is taken up by alveolar macrophages in the lung. MicroRNAs (miRNAs) — short non-coding RNAs that post-transcriptionally regulate gene expression — are increasingly being recognised as key regulators of the immune system. There is mounting evidence for the role of miRNAs in regulating the early innate immune response to mycobacterial infections; however, the underlying processes are not fully understood yet. Results: In total, 2.5 billion raw sequencing reads were generated. 93% of post-filtered reads aligned to known miRNAs. The expression of miRNAs varied over a wide range: miR-21 was expressed at approximately 430,000 reads per million (RPM), but the majority were more lowly expressed (1000-10,000 RPM). One, six, and 40 miRNAs were identified as significantly differentially expressed at 2, 24 and 48 h post-infection (hpi), respectively (FDR < 0.05); the differential expression at 48 hpi of three (out of four) of these miRNAs was confirmed by RT-qPCR. No miRNAs were detected to be differentially expressed 6 hpi. Many of the differentially expressed miRNAs have been shown to have a role in the host response to mycobacterial pathogens and other infections in other species. MicroRNA-155, for example, which we observed to be upregulated in response to M. bovis has recently been shown to control autophagy in murine macrophages infected with the human pathogen Mycobacterium tuberculosis. Pathway analysis suggests that upregulated miRNAs target endocytosis and lysosome trafficking, thus potentially enhancing bacterial survival. An independent gene silencing experiment with a bovine macrophage cell line (Bomac) has confirmed downregulation of IRAK1 by miR-146a and miR-146b. Moreover, downregulation of another predicted target, TGFRB2, by miR-146a was also confirmed. These findings support the target prediction and pathway analysis results. Our results suggest that several miRNAs have an important role in the alveolar macrophage response to pathogenic mycobacteria.

overall_design: 10 animals (biological replicates) were used. Alveolar macrophages from each animal were treated with M. bovis and miRNA expression was analyzed at 4 timepoints (2hpi, 6hpi, 24hpi, 48hpi), in addition to the 0h control. Uninfected samples was used for each timepoint for each animals.

first: David

last: Magee

first: Nicolas

middle: C

last: Nalpas

first: Kenneth

last: Bryan

first: Matthew

last: McCabe

first: John

last: Browne

first: Kevin

middle: M

last: Conlon

middle: V

last: Gordon

first: Daniel

middle: G

last: Bradley

last: MacHugh

last: Lynn


title: p53 activation effect on GM12878 lymphoblastoid cells

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH


title: Genome-wide binding sites of AtDEK3 in Arabidopsis thaliana.

city: Vienna

first: Sascha

last: Waidmann

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

summary: The scope of the project is to find DNA binding sites of the DNA binding protein AtDEK3. For the experiments AtDEK3 overexpressor (OE) plants have been obtained. The AtDEK3 was tagged with a CFP-tag. With ChIP the protein was pulled down and eluted DNA was send for sequencing. Gene ontology (GO) term classification of genes enriched for AtDEK3 binding indicated that AtDEK3 target genes are involved in diverse biological processes.

overall_design: ChIP Seq of three indenpendendt AtDEK3 OE and their respective inputs were used.

first: Branislav

last: Kusenda

first: Claudia

last: Jonak


title: Restoration of Progranulin Expression Rescues Cortical Neuron Generation in Induced Pluripotent Stem Cell Model of Frontotemporal Dementia

status: Public on Nov 12 2014

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: To understand how haploinsufficiency of progranulin (PGRN) protein causes frontotemporal dementia (FTD), we created induced pluripotent stem cells (iPSC) from patients carrying the GRNIVS1+5G>C mutation (FTD-iPSCs). FTD-iPSCs were fated to cortical neurons, the cells most affected in FTD and known to express PGRN. Although generation of neuroprogenitors was unaffected, their further differentiation into neurons, especially CTIP2-, FOXP2- or TBR1-TUJ1 double positive cortical neurons, was significantly decreased in FTD-neural progeny. Zinc finger nuclease-mediated introduction of PGRN cDNA into the AAVS1 locus corrected defects in cortical neurogenesis, demonstrating that PGRN haploinsufficiency causes inefficient cortical neuron generation. RNAseq analysis confirmed reversal of altered gene expression profile following genetic correction. Wnt signaling pathway, one of the top defective pathways in FTD-iPSC-derived neurons coupled with its reversal following genetic correction, makes it an important candidate. Therefore, we demonstrate for the first time that PGRN haploinsufficiency hampers corticogenesis in vitro.

overall_design: We profiled 6 samples: two biological replicates for 3 conditions. Condition 1 consists of neuronal progeny derived from human Embryonic Stem Cells. Condition 2 consists of neuronal progeny derived from induced pluripotent stem cells generated from patients carrying PGRN mutation. Condition 3 consists of neuronal progeny derived from induced pluripotent stem cells generated from patients carrying PGRN mutation, genetically modified to correct the PGRN defect.

first: Susanna

last: Raitano

first: Laura

last: Ordovàs

first: Louis

last: De Muynck

first: Ira

last: Espuny-Camacho

first: Martine

last: Geraerts

first: Satish

last: Khurana

first: Kim

last: Vanuytsel

first: Balazs

middle: I

last: Tóth

first: Thomas

last: Voets

first: Rik

last: Vandenberghe

first: Toni

last: Cathomen

first: Pierre

last: Vanderhaeghen

first: Philip

last: Van Damme

first: Catherine

last: Verfaillie


title: 293T cells transfected with HIV-1 proviral plasmids

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: Missouri

address: Washington University School of Medicine

summary: The HIV-1 Gag protein orchestrates all steps of virion genesis, including RNA recruitment into virions. However, the identities of specific RNA sequences recognized by Gag in cells and virions are largely unknown. Using crosslinking-immunoprecipitation (CLIP) sequencing, we uncover dramatic changes in the RNA binding specificity of Gag during virion genesis that are induced by its membrane binding, multimerization and proteolytic maturation. Prior to assembly, and also in mature virions, the nucleocapsid domain of Gag preferentially binds to psi and Rev Response elements in the viral genome, and GU-rich mRNA sequences. However, during assembly of immature virions, this specificity changes in a manner that facilitates genome packaging, as nucleocapsid binds to many sites on the viral genome and mRNA sequences with a similar A-rich nucleotide composition. Additionally, we find that the matrix domain of Gag binds almost exclusively to specific tRNAs in the cytosol, and this association regulates Gag binding to cellular membranes.

overall_design: CLIP-seq data sets from 293T cells

first: Paul

last: Bieniasz


title: Paternal poly(ADP-ribose) metabolism modulates retention of inheritable sperm histones and early embryonic gene expression

city: Logan

first: Ralph

last: Meyer

state: UT

address: 4700 Old Main Hill

department: School of Veterinary Medicine

institute: Utah State University

summary: To achieve the extreme nuclear condensation necessary for sperm function, most histones are replaced with protamines during spermiogenesis in mammals.  Mature sperm retain only a small fraction of nucleosomes, which are, in part, enriched on gene regulatory sequences, and recent findings suggest that these retained histones provide epigenetic information that regulates expression of a subset of genes involved in embryo development after fertilization.  We addressed this tantalizing hypothesis by analyzing two mouse models exhibiting abnormal histone positioning in mature sperm due to impaired poly(ADP-ribose) (PAR) metabolism during spermiogenesis and identified altered sperm histone retention in specific gene loci genome-wide using MNase digestion-based enrichment of mononucleosomal DNA.  We then set out to determine the extent to which expression of these genes was altered in embryos generated with these sperm.  For control sperm, most genes showed some degree of histone association, unexpectedly suggesting that histone retention in sperm genes is not an all-or-none phenomenon and that a small number of histones may remain associated with genes throughout the genome.  The amount of retained histones, however, was altered in many loci when PAR metabolism was impaired.  To ascertain whether sperm histone association and embryonic gene expression are linked, the transcriptome of individual 2-cell embryos derived from such sperm was determined using microarrays and RNA sequencing.  Strikingly, a moderate but statistically significant portion of the genes that were differentially expressed in these embryos also showed different histone retention in the corresponding gene loci in sperm of their fathers.  These findings provide new evidence for the existence of a linkage between sperm histone retention and gene expression in the embryo.

overall_design: 9 WT samples in 3 groups of 3. Each group consists of 3 eggs fertilized by the same father. 9 KO samples in the same setup.

first: Motomasa

last: Ihara

first: Mirella

last: Meyer-Ficca

first: N

last: Leu

first: Shilpa

last: Rao

first: Fan

last: Li

first: Brian

last: Gregory

first: Irina

last: Zalenskaya

first: Richard

last: Schultz


title: Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: Combinatorial actions of relatively few transcription factors control hematopoietic differentiation. To investigate this process in erythro-megakaryopoiesis, we correlated the genome-wide chromatin occupancy signatures of four master hematopoietic transcription factors (GATA1, GATA2, TAL1, and FLI1) and three diagnostic histone modification marks with the gene expression changes that occur during development of primary cultured megakaryocytes (MEG) and primary erythroblasts (ERY) from murine fetal liver hematopoietic stem/progenitor cells. We identified a robust, genome-wide mechanism of MEG-specific lineage priming by a previously described stem/progenitor cell-expressed transcription factor heptad (GATA2, LYL1, TAL1, FLI1, ERG, RUNX1, LMO2) binding to MEG-associated cis-regulatory modules (CRMs) in multipotential progenitors. This is followed by genome-wide GATA factor switching that mediates further induction of MEG-specific genes following lineage commitment. Interaction between GATA and ETS factors appears to be a key determinant of these processes. In contrast, ERY-specific lineage priming is biased toward GATA2-independent mechanisms. In addition to its role in MEG lineage priming, GATA2 plays an extensive role in late megakaryopoiesis as a transcriptional repressor at loci defined by a specific DNA signature. Our findings reveal important new insights into how ERY and MEG lineages arise from a common bipotential progenitor via overlapping and divergent functions of shared hematopoietic transcription factors.

overall_design: Genome-wide chromatin occupancy using ChIP-seq on 4 transcription factors (GATA1, GATA2, TAL1, and FLII) and three histone marks (H3K4me1, H3K4me3, and H3K27me3) in lineage-commited primary erythoblasts (ERY) and primary cultured megakaryocytes (MEG).

first: Maxim

last: Pimkin

first: Andrew

last: Kossenkov

first: Tejaswini

last: Mishra

first: Christapher

last: Morrissey

first: Weisheng

last: Wu

first: Cheryl

last: Keller

first: Gerd

last: Blobel

first: Dongwon

last: Lee

first: Michael

last: Beer

first: Ross

last: Hardison

first: Mitchell

last: Weiss


title: RNA-Seq Analysis of CNF2 and GPF1-dependent Genes in Magnaporthe oryzae 70-15

city: Hangzhou

first: Jianping

last: Lu

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

institute: Zhejiang University

summary:
Purpose: The goals of this study are to find out the genes regulated directly or indirectly by Zn2Cys6 transcription factors Cnf2 and Gpf1 by RNA-seq and to evaluate the similarities and differences in gene regulation mechanisms of Cnf2 and Gpf1 in the rice blast fungus
Methods: Mycelial mRNAs of the wild type strain 70-15, mutants Δgpf1 (01F1-1) and Δcnf2 (03C7-2) incubated in H2O at 25˚C for 4 h, in triplicate independently for each strain, were extracted and isolated by RNeasy Plant mini kit (QIAGEN) and AMPure XP beads (Beckman). RNA-sequencing libraries were constructed using NEBNext RNA sample preparation kit (NEB). Samples were sequenced in a 1 x 100 nt way on Illumina Hiseq2500 instrument using TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).The M. oryzae genome database (Version 7) (www.broadinstitute.org) was used as a reference gene database. Genome-wide transcript levels of genes were quantified in fragments per kilobase of exon model per million mapped reads (FPKM) (Trapnell 2010). Gene Ontology (GO) enrichment analyses for differentially expressed genes were performed using hypergeometric test with topGO, and p-values were adjusted with Bonferroni for multiple testing (Alexa 2006). And we selected FDR < 0.05 as enrichment terms.
Results and Conclusions: We identified 2641 genes regulated by GPF1 and 3144 genes by CNF2 through RNA-Seq. Interestingly, 2021 genes were regulated in same direction in Δgpf1 and Δcnf2. This fact suggested GPF1 and CNF2 have similar mechanisms in the regulation of fungal pathogenicity. More than sixty differentially expressed genes in Δgpf1 and Δcnf2 were confirmed to be required for fungal pathogenicity. Nearly half of Zn2Cys6 transcription factor genes and many other DNA binding domain transcription factor genes were regulated by GPF1 and CNF2. These data primarily revealed the gene expression network in the regulation of fungal pathogenicity controlled by GPF1 and CNF2.

overall_design: Mycelial mRNA profiles of wild type strain 70-15 (WT), Δgpf1 and Δcnf2 incubated in H2O for 4 h were generated, in biologic triplicate, by Illumina Hiseq2500 in a 1 x 100 nt way

first: Jian

first: Hui

last: Cao

first: Li

last: Zhang

first: Peng

middle: Y

last: Huang

first: Fu

last: Lin


title: Endometrial gene expression and cow fertility

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

institute: St. Vincent's University Hospital

summary: Profitable milk production in dairy cows requires good reproductive performance. Calving interval is a trait used to measure reproductive efficiency. Here we used a novel lactating Holstein cow model with genetic and phenotypic divergence in calving interval. Cows had similar genetic merit for milk production traits, but either very good genetic merit for fertility (Fert+; n = 7) or very poor genetic merit for fertility (Fert-; n = 6). We sequenced the transcriptome of endometrial biopsies collected on day 7 of the estrous cycle, a crucial stage for establishment of pregnancy. Significant differential expression (FDR adjusted p < 0.1) of 403 genes was found between the  Fert+ and Fert- animals. A standard over-representation analysis resulted in 12 lowly populated canonical pathways; however a novel in-depth analysis revealed a core of eighteen genes both differentially expressed and highly abundant. Almost all of these genes were related to actin-related and cytoskeletal components of the endometrium; fundamental cell-structure differences existed between  Fert+ and Fert- phenotypes. We also present results indicating inflammation-related genes are down-regulated, and that multiple ion transporters and gated-voltage channels were up-regulated, in Fert+ cows. These three topics are discussed in terms of the uterus and in the context of fertility during early embryo development. Transcriptomic data analysis is complex; we use a method that filters those genes that may be of greatest importance to the tissue at the timepoint of sampling. Our findings support the utility of this approach, as well as highlighting clear physiological differences in our animal model.

overall_design: 14 samples total; 7 Fert+ ('high fertility'), 7 Fert- ('low fertility'); no controls; Fert+, Fert- differential gene expression analysis

first: Stephen

middle: T

last: Butler

first: Christopher

last: Creevey


title: Localization of the Rb tumor suppressor in MEFs during reprogramming to iPS and the consequence of Rb loss on the transcriptional profile and histone landscape in these cells

first: Julien

last: Sage

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

summary: The reprogramming of differentiated cells to an embryonic stem cell-like state provides a powerful system to explore fundamental mechanisms of development, including how mammalian cells establish and maintain pluripotency and long-term self-renewal capability. Based on the similarities between embryonic stem cells and cancer cells, we investigated the potential role of the retinoblastoma tumor suppressor and cell cycle regulator RB in the reprogramming of fibroblasts into induced pluripotent stem cells (iPS cells). Herein we demonstrate that loss of RB function leads to both an acceleration of the reprogramming process and the generation of more iPS clones from fibroblasts. This effect is largely due to a restrictive role for RB at the early stages of reprogramming. Surprisingly, however, RB inactivation does not enhance the formation of iPS clones by accelerating the proliferation of cells undergoing reprogramming. Rather, a genome-wide investigation of RB targets indicates that RB binds to regulatory regions of pluripotency genes such as Sox2 and Oct4 and contributes to their full repression in differentiated cells. This effect correlates with the maintenance of a repressive chromatin structure at these loci. Accordingly, Rb-deficient fibroblasts can be reprogrammed into iPS cells even in the absence of exogenous Sox2, which is normally required to initiate reprogramming from fibroblasts. These experiments identify a novel barrier in the reprogramming process, mainly the repression of certain pluripotency genes such as Sox2 by RB, which provides a new link between tumor suppressor mechanisms and cellular reprogramming.

overall_design: RNAseq from MEFs with 2 biological replicates (save CP), Rb ChIPseq from MEFs with 2 biological replicates, Histone H3 modification ChIPseq from MEFs with 1 biological replicate

last: Kareta

first: Laura

last: Gorges

first: Sana

last: Hafeez

first: Damek

last: Spacek

first: Luis

middle: F

last: Batista

first: Dedeepya

last: Vaka

first: Steven

middle: E

last: Artandi

first: Marius

last: Wernig


title: Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia

status: Public on Nov 11 2014

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

summary: Notch is needed for T cell development and is a common oncogenic driver in T cell acute lymphoblastic leukemia. Myc is a critical target of Notch in normal and malignant pre-T cells, but how Notch regulates Myc is unknown. Here, we identify a distal enhancer located >1 Mb 3' of human and murine Myc that binds Notch transcription complexes and physically interacts with the Myc proximal promoter. The Notch1 binding element in this region activates reporter genes in a Notch-dependent, cell context-specific fashion that requires a conserved Notch complex binding site. Acute changes in Notch activation produce rapid changes in H3K27 acetylation across the entire enhancer (a region spanning >600 kb) that correlate with Myc expression. This broad Notch-influenced region is comprised of an enhancer region containing multiple domains, recognizable as discrete H3K27 acetylation peaks. Leukemia cells selected for resistance to Notch inhibitors express Myc despite epigenetic silencing of enhancer domains near the Notch transcription complex binding sites. Notch-independent expression of Myc in resistant cells is highly sensitive to inhibitors of Brd4, a change in drug sensitivity that is accompanied by preferential association of the Myc promoter with more 3’ enhancer domains that are strongly dependent on Brd4 for function. These findings indicate that altered long-range enhancer activity can mediate resistance to targeted therapies and provide a mechanistic rationale for combined targeting of Notch and Brd4 in leukemia.

overall_design: Identifying of Notch1 and CSL binding region and 3 different histone modifications in T cell acute lymphocytic leukemia.

first: Yumi

last: Yashiro-Ohtani

first: Hongfang

last: Wang

first: X

middle: S

last: Liu

first: Jon

last: Aster

first: Warren

last: Pear


title: Chromatin dynamics of p53 binding sites in IMR90

city: Philadelphia

first: Morgan

last: Sammons

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary:
We report the chromatin modification dynamics at p53 binding sites upon treatment with DMSO or nutlin3-a (5uM) in IMR90 human lung fibroblasts using ChIP-seq and RNA-seq analyses.
We assessed the genomewide changes in H3, H3K4me3, H3K4me2, H3K4me1, H3K27ac, H4K16ac, RNA polymerase II, and p53 in response to p53 activation.

overall_design: ChIP-seq of 8 histone modifications or proteins for 2 conditions in 1 cell line.

first: Shelley

last: Berger


title: TGIF1 is a negative regulator of MLL-rearranged acute myeloid leukemias

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaloesvej 5

department: Finsen Centre

country: Denmark

institute: Rigshospitalet

summary: Members of the TALE (Three-amino acid loop extension) family of atypical homeodomain-containing transcription factors are prominent downstream effectors of oncogenic fusion proteins generated from translocations involving the mixed lineage leukemia (MLL) gene. A particular well-characterized member of this protein family is MEIS1, which together with HOXA proteins, orchestrates a transcriptional program required for the maintenance of MLL-rearranged acute myeloid leukemia (AML). Although TALE family proteins are mainly described as transcriptional activators TGIF1 (TGF-β induced factor) / TGIF2 are considered as transcriptional repressors. However, as their function in MLL-rearranged AML is largely unknown, we tested the potential importance of TGIF1 in the maintenance of MLL-rearranged AML. We find that expression of TGIF1 in MLL-AF9 transformed cells (MAF9) leads to cell cycle exit and differentiation in vitro and delayed leukemic onset in vivo. In accordance, MLL-rearranged patient blasts display lower levels of TGIF1 and TGIF1 expression in general correlates positively with survival. Mechanistically, we show that TGIF1 interferes with a MEIS1-dependent transcriptional program by associating to MEIS1-bound region in a competitive manner. Collectively, these findings demonstrate that TALE family members can act both positively and negatively on transcriptional programs responsible for the maintenance of MLL-rearranged AML.

overall_design: Examination of TGIF1 and Meis1 binding in MLL-AF9 transformed cells. ChIP-seq was carried out in dublicates

first: Anton

last: Willer


title: Enhancer landscape of mouse developing forebrain at 11.5 dpc embryos [ChIP-seq]

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: We report the distribution of histone H3K4me1 and H3K27ac within the genome of mouse embryonic forebrain. We prepared the chromatin from 11 dpc embryonic forebrain and made chromatin precipitation with antibody against H3K4me1 and H3K27ac (rabbit polyclonal antibody). High-throughput sequencing applied for the ChIP analysis revealed the differential distribution of modified histone within developing forebrain.

overall_design:
ChIP analysis of mouse 11 dpc embryonic forebrain against anti-H3K4me1 and H3K27ac antibody.
Forebrain isolated and disected from 11 dpc embryos are fixed by 1% formaldehyde. After conventional ChIP reaction, ChIP library for highthroughput sequence is prepared by NEBNext ChIP-seq library Prep Master Mix Set for Illumina.

first: Takashi

last: Kondo

middle: A

first: Haruhiko

last: Koseki


title: Detection of Pol IV-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis

city: Beijing

first: shaofang

last: Li

state: Beijing

address: No 50, ZhanghuaLu, HAIDIAN

department: Beijing Vegetable Research Center

institute: Beijing Academy of Agriculture and Forestry Science

summary: 24 nucleotide siRNAs are central players in RNA-directed DNA methylation (RdDM), a process that establishes DNA methylation at transposable elements to ensure genome stability. The plant-specific RNA polymerase IV (Pol IV) is required for siRNA biogenesis and is thought to transcribe RdDM loci to produce primary transcripts that serve as precursors to siRNAs. Yet, no such transcripts have ever been reported. Here, through RNA sequencing and double-stranded RNA sequencing in genotypes that compromise the dicing of siRNA precursors, we were able to identify Pol IV-dependent transcripts from tens of thousands of loci. We show that Pol IV-dependent transcripts correspond to both DNA strands, while the Pol II-dependent transcripts produced upon de-repression of the loci are derived from primarily one strand. We show that Pol IV-dependent transcripts have a 5’ monophosphate, lack a polyA tail at the 3’ end, and contain no introns; these features distinguish them from Pol II-dependent transcripts. Moreover, RDR2 is shown to play similar roles with Pol IV in both the abundance of siRNA precursors and siRNAs as well as the CHH DNA methylation. The decreased CHH methylation at dcl234 can inhibit the transcription of Pol IV at DRM2-target sites. Finally, the regulations of siRNA biogenesis were explored.

overall_design: To detect siRNA precursors transcribed by RNA polymerase IV, the genome wide profiling of RNA were carried out at  dcl234 and dcl234 nrpd1.  Different types of RNA (including Total RNA, polyA+ RNA, polyA- RNA, double stranded RNA) libraries were built to detect different transcripts. RDR2 is a RNA-dependent RNA polymerase in Pol IV complex, so the RNA-seq libraries with the mutation of RDR2 were also built. In addition, smRNA libraries with mutations blocking siRNA biogenesis were also built

first: Shaofang

first: Xuemei

last: Chen


title: Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition, based on hierarchical binding affinities (mRNA)

status: Public on Nov 10 2014

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

summary: Target competition (ceRNA crosstalk) within miRNA-regulated gene networks has been proposed to influence biological systems. To assess target competition, we characterize and quantitate miRNA networks in two cell types. Argonaute iCLIP reveals that hierarchical binding of high to low affinity miRNA targets is a key characteristic of in vivo activity. Quantification of cellular miRNA and mRNA/ncRNA target pool levels indicates that miRNA-Target pool ratios and an affinity partitioned target pool accurately predict in vivo Ago binding profiles and miRNA susceptibility to target competition. Using single-cell reporters, we directly test predictions and estimate ~3,000 additional high affinity target sites can affect active miRNA families with low endogenous miRNA-Target ratios, such as miR-92/25. In contrast, the highly expressed miR-294 and let-7 families are not susceptible to increases of nearly 10,000 sites. These results show differential susceptibility based on endogenous miRNA-Target pool ratios and provide a physiological context for ceRNA competition in vivo.

overall_design: mRNA seq from TT-FHAgo2 mouse embryonic stem cells or Meschencymal stem cells grown with 2.5 μg/mL Dox to express Ago2 or removed from doxycycline for 96h.


title: Targeting and Plasticity of Mitochondrial Proteins Revealed by Proximity-Specific Ribosome Profiling

city: San Francisco

first: Jonathan

last: Weissman

address: 1700 4th Street

institute: UCSF

summary: Nearly all mitochondrial proteins are nuclear-encoded and are targeted to their mitochondrial destination from the cytosol. Here, we used proximity-specific ribosome profiling to comprehensively measure translation at the mitochondrial surface in yeast. The majority of inner membrane proteins were co-translationally targeted to mitochondria, reminiscent of proteins entering the endoplasmic reticulum (ER). Comparison between mitochondrial and ER localization demonstrated that the vast majority of proteins were targeted to a specific organelle. A prominent exception was the fumarate reductase Osm1, known to reside in mitochondria. We identified a conserved ER isoform of Osm1, which contributes to the oxidative protein folding capacity of the organelle. This dual localization was enabled by alternative translation initiation sites encoding distinct targeting signals. These findings highlight the exquisite in vivo specificity of organellar targeting mechanisms.

overall_design: Ribosome profiling of whole cell or streptavidin-purified ribosomes biotinylated by cytosolic, ER or mitochondrially localized biotin ligase in yeast and mammalian cells

first: Christopher

last: Williams

first: Calvin

middle: H

last: Jan


title: Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition, based on hierarchical binding affinities (small RNA)

overall_design: Total small RNA sequencing from TT-FHAgo2 mouse embryonic stem cells grown with 2.5 μg/mL Dox to express Ago2 near wildtype levels. This is a biological replicate of GSM1224440.


title: Delineating Tumor-infiltrating Antigen Presenting Cell populations

first: Joshua

last: Pollack

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

summary:
The goal of this study is to compare tumor-infiltrating antigen presenting cell populations by global transcriptome profiling (RNA-seq) to help further delineate sub-populations of infiltrating myeloid cells in tumor.
Methods: Four tumor antigen presenting cell populations were sorted from digested B78chOVA (melanoma variant) tumors in biological triplicate
Results: RNA was extracted from the 4 groups (n=3 per group) and prepared for RNAseq.  Sequencing yielded ~405 million reads with an average read depth of 33.7 million  reads/sample.  Reads were then aligned to the mouse genome (UCSC mm10) and those  that mapped uniquely to known mRNAs were used to assess differential expression.

overall_design: Examination of four tumor infiltrating myeliod populations

first: Matthew

last: Krummel

first: Miranda

last: Broz

first: Mikhail

last: Binnewies


title: Principles of ER Co-Translational Translocation Revealed by Proximity-Specific Ribosome Profiling

summary: Localized protein synthesis is a fundamental mechanism for creating distinct subcellular environments. Here we developed a generalizable proximity-specific ribosome profiling strategy that enables global interrogation of translation in defined subcellular locations. We applied this approach to the endoplasmic reticulum (ER) in yeast and mammals. We observed the vast majority of secretory proteins to be co-translationally translocated, including substrates capable of post-translational insertion in vitro. Distinct translocon complexes engaged nascent chains at different points during synthesis. Whereas most proteins engaged the ER immediately following or even before signal sequence (SS) emergence, a class of Sec66-dependent proteins entered with a looped SS conformation. Finally, we observed rapid ribosome exchange into the cytosol following translation termination. These data provide insights into how distinct translocation mechanisms act in concert to promote efficient co-translational recruitment.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens


title: Product binding enforces the genomic specificity of a yeast Polycomb repressive complex

first: Phillip

middle: Anthony

last: Dumesic

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: University of California, San Francisco

summary: We characterize the Polycomb system that assembles repressive subtelomeric domains of H3K27 methylation (H3K27me) in the yeast Cryptococcus neoformans.  Purification of this PRC2-like protein complex reveals orthologs of animal PRC2 components as well as a chromodomain-containing subunit, Ccc1, which recognizes H3K27me.  Whereas removal of either the EZH or EED ortholog eliminates H3K27me, disruption of mark recognition by Ccc1 causes H3K27me to redistribute.  Strikingly, the resulting pattern of H3K27me coincides with domains of heterochromatin marked by H3K9me.  Indeed, additional removal of the C. neoformans H3K9 methyltransferase Clr4 results in loss of both H3K9me and the redistributed H3K27me marks.  These findings indicate that the anchoring of a chromatin-modifying complex to its product suppresses its attraction to a different chromatin type, explaining how enzymes that act on histones, which often harbor product recognition modules, may deposit distinct chromatin domains despite sharing a highly abundant and largely identical substrate—the nucleosome.

overall_design: RNA-seq or ChIP-seq to compare multiple Cryptococcus neoformans genotypes using the HiSeq 2500 platform

first: Christina

last: Homer

first: James

middle: J

last: Moresco

first: Lindsey

last: Pack

first: Scott

last: Coyle

first: Brian

middle: D

last: Strahl

first: Danica

last: Fujimori

first: John

last: Yates III

first: Hiten

last: Madhani


title: Analysis of transcription start sites from nascent RNA identifies a unified architecture of initiation at mammalian promoters and enhancers (GRO-cap)

city: Ithaca

first: Leighton

middle: James

last: Core

address: 417 Biotechnology Building

department: Moleular Biology and Genetics

institute: Cornell University

summary: Despite the conventional distinction between promoters and enhancers, they share many features in mammals, including divergent transcription and similar modes of transcription factor (TF) binding. Here, we examine the architecture of transcription initiation genome-wide through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid B-cell (GM12878) and chronic myelogenous leukemic (K562) tier 1, ENCODE cell lines using a nuclear run-on protocol called GRO-cap. This method captures TSSs for both stable and unstable transcripts, thus allowing us to conduct detailed comparisons between thousands of promoters and enhancers in human cells. These analyses reveal a common architecture of initiation at both promoters and enhancers, including tightly spaced (110 bp) divergent initiation that features similar frequencies of core-promoter sequence elements, highly-positioned flanking nucleosomes, and two modes of TF binding. Transcript elongation stability, a feature determined after transcription initiation, provides a more fundamental distinction between promoters and enhancers than the relative abundance of histone modifications and the presence of TFs or coactivators. These results support a unified model of transcription initiation at both promoters and enhancers.

overall_design: We sequenced nascent RNAs purified from run-on sequencing reactions (GRO-seq) performed in two ENCODE cells lines: K562 and GM12878. Precision Run-on sequencing (PRO-seq was also performed in K562 cells). We also enriched separate libraries from the same cells for the 5-meG cap associated with transcription start sites (TSSs) in order to produce a comprehensive mapping of nascent TSSs in these cells. This assay is called GRO-cap. We compared these TSSs to those identified in stable RNAs from CAGE assays to generate annotations for all TSSs based on the stability of the resulting transcript.

last: Lis

first: Andre

middle: L

last: Martins


title: Analysis of transcription start sites from nascent RNA identifies a unified architecture of initiation at mammalian promoters and enhancers (PRO-seq)

overall_design: We sequenced nascent RNAs purified from run-on sequencing reactions (GRO-seq and PRO-seq) performed in two ENCODE cells lines: K562 and GM12878. We also enriched separate libraries from the same cells for the 5-meG cap associated with transcription start sites (TSSs) in order to produce a comprehensive mapping of nascent TSSs in these cells. This assay is called GRO-cap. We compared these TSSs to those identified in stable RNAs from CAGE assays to generate annotations for all TSSs based on the stability of the resulting transcript.

first: Adam

last: Siepel


title: BRD4 assists elongation of both coding and enhancer RNAs guided by histone acetylation

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

summary: In serum-starved and re-fed mouse fibroblast, nascent RNA-seq analysis showed that the BET inhibitor JQ1 antagonized a process regulating PIC formation and a downstream process involved in progressive elongation. To specifically address the role of BRD4 and its interactions with acetylated histones and P-TEFb, YFP-tagged BRD4 proteins (wild type and mutant BRD4) were stably expressed in cells, endogenous BRD4 of which was knocked down by shRNA (shBRD4). Nascent RNA-seq analysis showed that BRD4 facilitated transcript elongation in a manner dependent on acetylated histone interaction but not P-TEFb. Furthermore, the role of BRD4 in enhancer activity was evaluated by mapping the intergenic distributions of Pol II, CDK9, H3K27 acetylation (Ac) and H4 Ac as well as BRD4 by ChIP-seq analysis. The results suggest that the role of intergenic BRD4 on nearby gene expression is mediated through enhanced synthesis of eRNA.

overall_design: Mouse fibroblasts were synchronized by serum-starvation (48 hours) and then re-fed (30 min) so that the transcriptional initiation of serum-response genes could be easily and uniformly captured by nascent RNA sequencing. To understand the basis of the reduced transcription initiation of protein-coding genes by JQ1, the role of BRD4 in enhancer activity was evaluated by mapping the genomic distributions of Pol II, CDK9, H3K27 acetylation (Ac) and H4 Ac as well as BRD4 by ChIP-seq analysis. To specifically address the role of BRD4 and its interaction with acetylated histone via bromodomain (BD) or with P-TEFb, YFP-tagged BRD4 proteins (wild type and mutant BRD4) were stably expressed in cells, endogenous BRD4 of which was knocked down by shRNA (shBRD4). The “mBD” mutants carry a point mutation in each BD so that they do not bind acetylated histones. A short form of BRD4 termed BRD4short lacks the P-TEFb interacting C-terminal region. Nascent RNA-seq analysis was performed to monitor the progression of transcripts.

first: Tomohiko

first: Gary

last: LeRoy

first: Eric

last: Campos

first: Stephen

last: Brooks

first: Hong-Wei

last: Sun

first: Golnaz

last: Vahedi

first: Tom

last: Heightman

first: Benjamin

last: Garcia

first: Keiko

last: Ozato

first: Danny

last: Reinberg

last: O'Shea

first: Ulrich

last: Siebenlist


title: ETS trancription factors PU.1 and Spi-B binding in mouse lymphoma cells

city: LONDON

first: Rodney

last: DeKoter

state: Ontario

address: 1151 Richmond street

department: Microbiology and Immunology

country: Canada

institute: University of Western Ontario

summary: Spi-B and PU.1 are highly related members of the E26-transformation-specific (ETS) family of transcription factors that have similar, but not identical, functions in B cell development. PU.1 and Spi-B are both expressed at high levels in lymphoma cell lines. We hypothesized that Spi-B and PU.1 occupy similar sites in the genome. To determine binding sites of Spi-B and PU.1, WEHI-279 mouse lymphoma cells were infected with retroviral vectors encoding 3XFLAG-tagged PU.1 or Spi-B. Anti-FLAG chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) was performed. Both transcription factors occupied approximately 2000 sites in the genome, and approximately half of these sites were bound by both factors while the other sites were unique to each factor.

overall_design: ChIP-seq analysis for PU.1 and Spi-B was conducted in duplicate, in WEHI-279 mouse lymphoma cells were infected with retroviral vectors encoding 3XFLAG-tagged PU.1 or Spi-B. Immuno-precipitated chromatin was sequenced using Next-generation Illimuna Sequencing conducted independantly at two different sequencing cores. Between-laboratory ChIP-seq datasets were combined using mmCHIP, and  ChIP-enriched regions compared and contrasted between the two transcription factors.

middle: P

first: Lauren

last: Solomon


title: SuUR role in regulation of DNA replication

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Iron-responsive chromatin remodelling and MAPK signalling enhance adhesion in Candida albicans

city: Buffalo

first: Michael

last: Buck

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

summary: Recent cumulative data shows that various transcription factors are recruited to the chromatin in an iron-responsive manner to affect diverse cellular functions in the pathogenic fungus Candida albicans. Here, we identified groups of iron-responsive genes in C. albicans by chromatin remodeling analysis at gene promoters, using micrococcal nuclease (MNase) digestion followed by deep sequencing. Chromatin in the promoter regions of iron uptake and utilization genes showed repressed and active configuration, respectively, under iron-replete conditions. GO Term enrichment analysis of genes with differentially remodeled chromatin, in respective promoter locales, suggested that many genes involved in adhesion are also iron-responsive. C. albicans was observed to be more self-adherent (2-fold increase) and formed higher biofilm mass (77% increase) in the presence of iron. Furthermore, we identified various known and novel adhesion-related genes with iron-dependent active chromatin profiles that are indicative of potential up-regulation under iron-replete conditions. Transcription factor Cph1 that is activated upon Cek1 phosphorylation also showed an active chromatin profile under iron-replete conditions and cells showed iron-responsive Cek1 MAPK phosphorylation in the presence of iron. Thus, iron affects diverse biological functions by modulating chromatin profiles of large gene sets and by signaling through Cek1 MAPK in C. albicans.

overall_design: Two matched MNase-seq replicates in the presence and absence of iron in the media.

first: Jason

last: Rizzo

first: William

last: Lai

first: Sumant

last: Puri

first: Mira

last: Edgerton


title: Spring Varaemia of Carp Virus (SVCV) infection of adult zebrafish

city: Wuhan

first: Jianfang

last: Gui

address: No.7 Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

summary: During viral infection, a large number of immune response signaling molecules including the interferon regulatory (IRF) family and type I interferon (IFN) transcribe. The exact identity and expression levels of fish IRFs and type-I IFNs during viral infection remains largely unknown. Here, we utilized Illumina sequencing technology to determine differential expression patterns for both zebrafish IRFs and type-I IFNs during two stages of SVCV infection, i.e. 6h and 24h post-infection. For 12 zebrafish IRFs, we identified DrIRF1 mRNA as one of the most abundant in normal tissues and also in SVCV-infected tissues, but DrIRF11 had a very weak basal expression and was almost not induced by SVCV infection. We also identified the highly basal expression of DrIRF7, which together with DrIRF3, was highly induced by SVCV infection. For type-I IFNs, zebrafish has four IFN genes, three of which, IFN1/2/3, particularly IFN 1 and IFN 3, were significantly transcribed under the same conditions.

overall_design: 12 adult healthy male and female (1:1) zebrafish were infected by intraperitoneal inoculation with approximately  50 μL SVCV (10-8TCID50/mL). 6 infected fish (male:female=1:1) were sacrificed at 6h post-injection, and 6 (male:female=1:1) were sacrificed at 24h post-injection for head kidney (6K and 24K) and spleen (6S and 24S). Head kidney and spleen (0K and 0S) from the 6 control adult zebrafish (male:female=1:1) were collected as negative control.

first: Hui

last: Feng

first: Yibing

last: Zhang

first: Zhi

last: Li


title: ChIP-Seq of gamma-H2Av bound to third instar salivary gland DNA in WT and SuUR mutant Drosophila; ChIP-Seq of SUUR and Cdc45 bound to egg chamber DNA from early and late stage egg chambers

summary:
We analyzed gamma-H2Av ChIP-Seq from hand dissected salivary glands of wandering third instar larvae from wild-type (OrR) or suppressor of under-replication (SuUR) mutant Drosophila. Goals were to determine the DNA damage profile relative to underreplicated domains.
We analyzed SUUR and Cdc45 ChIP-Seq from hand dissected early (stage 10) and late (stage 12/13) egg chambers from adult Drosophila ovaries. The goals was to determine the localization of SUUR relative to replication forks.

overall_design:
ChIP-Seq of gamma-H2Av bound to third instar salivary gland DNA in WT and SuUR mutant Drosophila, analyzed by Illumina sequencing. One replicate is included for each of OrR (WT) or SuUR salivary glands.Rabbit IgG controls are included for OrR (WT).
ChIP-Seq of SUUR and Cdc45 bound to egg chamber DNA from early and late stage egg chambers, analyzed by Illumina sequencing. One replicate is included for each ChIP reaction.

first: Jared

last: Nordman


title: Transcriptionally repressive histone modifying enzymes – a role in olfactory receptor expression

first: Stavros

last: Lomvardas

institute: Univ of California - SF

summary: identification of a role for g9a and glp histone methyltransferases in the stochastic fate decision of the olfactory sensory neuron

overall_design: generate knockout mice and perform rna-seq and other expression analyses

first: David

last: Lyons


title: RNA bisulfite sequencing of 25S rRNA (C2278) in S. cerevisiae and of 28S rRNA (C3381) in C. elegans

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

institute: Medical University of Vienna

summary: The RNA methyltransferase NSUN5 modulates the lifespans of yeast, worms and flies by re-programming the translation of specific subsets of mRNAs, which are associated with the cellular stress response. Here we show by RNA bisulfite sequencing that Rcm1 specifically methylates C2278 of yeast 25S rRNA and nsun-5 C3381 of C. elegans 28S rRNA.

sample_organism:
Saccharomyces cerevisiae
Caenorhabditis elegans

overall_design: In S. cerevisiae RNA was isolated from polysome and monosome fractions of two genotypes (wild-type and rcm1 deletion) and three stress treatments (unstressed, 30 min and 90 min H2O2) in single replicates. In C. elegans total RNA of wild-type (N2) and JGG1 (nsun-5 mutant) were compared in single replicates.

first: Johannes

last: Grillari

first: Lore

last: Breitenbach-Koller

first: Matthias

last: Gerstl

first: Andreas

last: Weinhaeusel

last: Sonntagbauer


title: C elegans N2 Late embryo input control

status: Public on Nov 09 2014

city: Chapel Hill

first: Tristan

last: De Buysscher

address: CB# 3280, Coker Hall

department: Biology

institute: University of North Carolina at Chapel Hill

summary: Input lanes for ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus.

overall_design: Control sample from late embryo N2 worms.

first: Susan

last: Strome

first: Jacob

last: Garrigues


title: Epigenetic modifications are associated with inter-species gene expression variation in primates

city: Ann Arbor

first: Xiang

last: Zhou

state: MI

address: 1415 Washington Heights

department: Biostatistics

institute: UNIVERSITY OF MICHIGAN

summary: Changes in gene regulation level have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels yet we know much less about the extent to which regulatory mechanisms differ between species. To begin addressing this gap, we performed a comparative epigenetic study in primate lymphoblastoid cell lines (LCLs), to query the contribution of RNA polymerase II (Pol II) and four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) to inter-species variation in gene expression levels. We found that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also found that first-order interactions among the histone marks and Pol II do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: ChIP-seq of RNA polymerase II and 4 histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K27me3), and RNA-seq, in 8 chimpanzee and 8 rhesus macaque lymphoblastoid cell lines

first: Carolyn

last: Cain

first: Marsha

last: Myrthil

first: Noah

last: Lewellen

first: Katelyn

last: Michelini

first: Emily

last: Davenport

first: Matthew

last: Stephens

first: Johathan

middle: K

last: Pritchard

first: Yoav

last: Gilad


title: Ethylmalonyl-CoA mutase Operates as a Metabolic Control Point in Methylobacterium extorquens AM1

status: Public on Nov 08 2014

city: East Lansing

first: Nathan

middle: M

last: Good

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: We report RNA-seq datasets profiling the transcriptional response to a sudden change in growth substrate, from succinate to ethylamine. This detailed combined dataset provides a dynamic assessment of the transcriptional response to a metabolic perturbation. These datasets are the first reported RNA-seq datasets for gene expression in Methylobacterium extorquens AM1

overall_design: Time course of transcriptome datasets from time zero (succinate growth) and several points after the substrate switch.

first: Norma

middle: C

last: Martinez-Gomez

first: Mary

last: Lidstrom


title: Genome-wide Profiling of Steroid Receptor Coactivator 2 in mouse liver

city: Houston

first: Erin

last: Stashi

state: TX

address: One Baylor Plaza

institute: Bayolor College of Medicine

summary: Steroid Receptor 2 (SRC-2) is a coactivator involved in hepatic metabolism.  To better understand its temporal involvement in metabolism genome wide profiling was performed at 2 time ZT4 and ZT18 as well as in the SRC-2 knockout mouse.

overall_design: SRC-2 ChIP-Seq at two time ZT4 and ZT18 and in the SRC-2 knockout mouse liver

first: Bert

last: O'Malley


title: Genome-wide maps of Scl/TAL1 in human erythroid cells.

city: Oxford

first: Richard

last: Gibbons

state: Oxon

address: John Radcliffe Hospital,

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

summary: ChIP-Seq experiments using an Scl/TAL1 antibody were carried out in primary erythroid cells cultured from two individuals of Caucasian origin. ChIP-Seq libraries were prepared from two biological replicates for each individual. ChIP DNA was processed for Illumina High-throughput sequencing according to Illumina protocol. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA from each experiments, we generated a high-resolution map of Scl/TAL1 genomic targets in human  erythroid cells. We find that WGATAR and the combinatorial CTG(n9)GATA are the most significant motifs responsible for the chromatin occupancy by Scl/TAL1. In addition, other motifs are also significantly enriched at the Scl/TAL1 targets. Amongst these were binding sites for known TFs (Sp/XKLF, RUNX1, NFE2). We next investigated how many of these targets varied between these two individuals. We find that 0.8% of Scl/TAL1 binding regions differ significantly between the two individuals.

overall_design: We have compared the genome-wide occupancy of Scl/TAL1 in erythroid cells between two different individuals

first: Marco

last: De Gobbi

first: Karen

last: Lower

first: Jim

last: Hughes

first: Douglas

last: Higgs


title: Methylation Affects Transposition and Splicing of a Large CACTA Transposable Element From a MYB Transcription Factor Regulating Anthocyanin Synthase (ANS) Genes in Soybean Seed Coats

status: Public on Nov 07 2014

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

type: Methylation profiling by high throughput sequencing


title: Epigenetic stability in the adult cortex is counterbalanced by the expression of long non-coding RNA

city: New Haven

first: Pasko

last: Rakic

state: CT

address: 333 Cedar Street

department: Neurobiology

institute: Yale University

summary: Adult neural tissue was treated with an HDAC inhibitor, TSA to assess changes in gene expression, which was then correlated with control adult tissue as well as early postnatal controls

overall_design: Total RNA obtained from P26 occipital cortex as well as P180 TSA-treated and control occipital and frontal cortex, hippocampus and olfactory bulb. Cortical areas are subdivided by lamina, which were microdissected.

first: Jamie

last: Benoit


title: Next generation sequencing reveals microRNA isoforms in liver cirrhosis and hepatocellular carcinoma

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

summary:
Hepatocellular carcinoma (HCC) represents the major histological subtype of liver cancer. Tumorigenic changes in hepatic cells potentially result from aberrant expression of microRNAs (miRNAs). Individual microRNA gene may give rise to miRNAs of different length, named isomiRNAs that proved to be functionally relevant.
Results: We detected 374 microRNAs expressed in liver, including miR-122-5p that constituted over 39% ofthe hepatic miRnome. Among the liver expressed miRs, the levels of 64 significantly differed between tumor and control samples (FDR < 0.05, fold change > 2). Almost all miRNA genes produced several mature molecules differing in length (isomiRNAs). The reference sequence was not the most prevalent in 38.6% and completely absent in 10.5% of isomiRNAs. Over 26.1% of miRNAs produced isoforms carrying ≥ 2 alternative seed regions, of which 35.5% constituted novel, previously unknown seeds. This fact sheds new light on the percentage of the human genome regulated by microRNAs and their variants.
Conclusions: The study reveals the comprehensive miRNome of hepatic tissue and provides new tools for investigation of microRNA-dependent pathways in cirrhotic liver and hepatocellular carcinoma.

overall_design: We employed next-generation sequencing to comprehensively analyze microRNA transcriptome in HCCtumors (n = 24) and unaffected tissue adjacent to tumors (n = 24), including samples with (n = 15) and without cirrhosis (n = 9).

first: Krystian

last: Jazdzewski


title: Checkpoint Blockade Cancer Immunotherapy Targets Tumor-Specific Mutant Antigens

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Cytotoxic T-lymphocyte associated antigen-4 (CTLA-4) and Programmed death-1 (PD-1) are immunoregulatory receptors expressed on T cells that play important roles in suppressing immune responses to cancer. Although monoclonal antibodies that target CTLA-4 or PD-1 stimulate therapeutic anti-tumour T cell responses, the tumour antigens recognized by checkpoint blockade immunotherapy remain undefined. Herein, we use genomics and bioinformatics approaches to identify tumour-specific mutant proteins as a major class of T cell rejection antigens following αPD-1 and/or αCTLA-4 treatment of mice bearing progressively growing sarcomas. We validate this conclusion by showing that (a) the predicted mutant epitopes associate with MHC class I molecules of the tumour; (b) T cells specific for these mutant epitopes infiltrate tumours; and (c) therapeutic vaccines incorporating these mutant epitopes induce tumour rejection comparably to checkpoint blockade immunotherapy. Whereas, T cells with the same antigen specificity are present in progressively growing tumours in control mice, tumour-specific T cells in αPD-1- and/or αCTLA-4-treated mice express some overlapping but mostly treatment-specific transcriptional profiles that render them capable of tumour rejection. Thus, tumour-specific mutant antigens are not only important targets of checkpoint blockade therapy but also can be used to identify tumour antigen-specific T cells that function as biomarkers of successful anti-tumour responses.

overall_design: For sorting of mLama4-specific cells, tumour-infiltrating cells were enriched for CD45+ cells using CD45 cell purification magnetic beads (Miltenyi Biotec). CD45 enriched cells were then sorted gating for PI- CD3ε+ CD8α+ mLama4-tetramer-PE+ or PI- CD3ε+ CD8α+ mLama4-tetramer-PE- cells. Sorting was performed on a BD FACSAria II (BD Biosciences). Sorted cells were pelleted and processed for RNA analysis. All flow cytometry was performed on the FACSCalibur (BD Biosciences) or LSR Fortessa (BD Biosciences) and analysed using FlowJo software (TreeStar).

middle: N


title: Multiplex-NGS for identification of differentially expressed miRNAs between colon cancer patients with and without metachronous metastases

city: Leiden

first: Peter

middle: J. K.

last: Kuppen

address: PO Box 9600

department: Surgery

country: Netherlands

institute: Leiden University Medical Center

summary:
Purpose: The goal of this experiment was to identify differentially expressed miRNAs between colon cancer patients with and without metachronous metastases.

Background: Colon cancer prognosis and treatment are currently based on a classification system still showing large heterogeneity in clinical outcome, especially in TNM-stages II-III. Prognostic biomarkers for metastasis risk are warranted, as development of distant recurrent disease mainly accounts for the high lethality rates of colon cancer. MicroRNAs have been proposed as potential biomarkers for cancer. Furthermore, a verified standard for normalization of the amount of input material in PCR-based relative quantification of miRNA expression is lacking.

Methods: A selection of frozen tumor specimens from two independent patient cohorts with TNM-stage II-III microsatellite stable primary adenocarcinomas were used for laser capture microdissection. Next-generation sequencing was performed on small RNAs isolated from colorectal tumors from the Dutch cohort (N=50). Differential expression analysis, comparing in metastasized- and non-metastasized tumors, identified prognostic microRNAs. Validation was performed on colon tumors from the German cohort (N=43) using qPCR.

Results: MiR-25-3p and miR-339-5p were identified and validated as independent prognostic markers and used to construct a multivariate nomogram for metastasis risk prediction. The nomogram showed good probability prediction in validation. Additionally, we recommend combination of miR-16-5p and miR-26a-5p as standard for normalization in qPCR of colon cancer tissue-derived microRNA expression.

Conclusions: In this international study, we identified and validated an miRNA classifier in primary cancers, and propose a nomogram capable of predicting metastasis risk in microsatellite stable TNM-stage II-III colon cancer.

overall_design: Small RNAs of 50 primary colon adenocarcinomas, with and without metachronous metastases, were sequenced using the Illunina HiSeq 2000.

first: Inès

last: Goossens-Beumer


title: Methylation Affects Transposition and Splicing of a Large CACTA Transposable Element From a MYB Transcription Factor Regulating Anthocyanin Synthase (ANS) Genes in Soybean Seed Coats (RNA-Seq)

summary: We determined the molecular basis of three soybean lines that vary in seed coat color at the R locus which is thought to encode a MYB transcription factor.  RM55-rm is homozygous for a mutable allele (rm) that specifies black and brown striped seeds; RM30-R* is a stable black revertant isoline derived from the mutable line; and RM38-r has brown seed coats due to a recessive r allele shown to translate a truncated MYB protein. Using long range PCR, 454 sequencing of amplicons, and whole genome re-sequencing, we determined that the variegated  RM55-rm line had a 13 kb CACTA subfamily transposon insertion (designated TgmR*) at a position 110 bp from the beginning of Intron2 of the R locus, Glyma09g36983. Although the MYB encoded by R was expressed at only very low levels in older seed coats of the black revertant RM30-R* line, it upregulated expression of anthocyanidin synthase genes (ANS2, ANS3) to promote the synthesis of anthocyanins. Surprisingly, the RM30-R* revertant also carried the 13 kb TgmR* insertion in Intron2. Using RNA-Seq, we showed that intron splicing was accurate, albeit at lower levels, despite the presence of the 13kb TgmR* element. As determined by whole genome methylation sequencing, we demonstrate that the TgmR* sequence was relatively more methylated in RM30-R* than in the mutable RM55-rm progenitor line. The stabilized and more methylated RM30-R* revertant line apparently lacks effective binding of a transposae to its subterminal repeats, thus allowing intron splicing to proceed resulting in sufficient MYB protein to stimulate anthocyanin production and thus black seed coats. In this regard, the TgmR* element in soybean resembles McClintock’s Spm-suppressible and change-of-state alleles of maize. This comparison explains the opposite effects of the TgmR* element on intron splicing of the MYB gene in which it resides depending on the methylation state of the element.

overall_design: Differential RNA expression of anthocyanin pathway genes in the seed coats of two seed color lines: RM30-R* (black) and RM38-r (brown). The multiple gene expression analysis  was performed at five different stages of seed development which were chosen based on the fresh weight (fwt) of entire seeds: 100-200, 200-300, 300-400 and 400-500 mg with green cotyledons, and a later stage in which seed desiccation had initiated judging by the yellowing of cotyledons and a lower fresh weight of 300-400 mg

first: Gracia

last: Zabala

middle: O


title: Methylation Affects Transposition and Splicing of a Large CACTA Transposable Element From a MYB Transcription Factor Regulating Anthocyanin Synthase (ANS) Genes in Soybean Seed Coats (Bisulfite-Seq)

overall_design: The genomic DNAs extracted from shoot tips of two seed color soybean lines, RM55-rm (black/brown striped) and RM30-R* (black) were sequenced in an Illumina HiSeq 2000 following the the Bisulfite (BS) sequencing method.


title: Identification of epigenetic barrier that prevents reprogramming in somatic cell nuclear transfer

city: Brookline

first: Yuting

last: Liu

state: MA

address: 82 Walnut St. Unit 3

department: Department of Genetics

institute: Harvard Medical School

summary: Mammalian oocytes can reprogram somatic cells into totipotent state, which allows animal cloning through somatic cell nuclear transfer (SCNT). However, the great majority of SCNT embryos fail to develop to term due to poorly defined reprogramming defects. Here we demonstrate that histone H3 lysine 9 trimethylation (H3K9me3) in donor nuclei is a major epigenetic barrier that prevents efficient nuclear reprogramming in mouse oocytes. Comparative transcriptome analysis of early embryos revealed reprogramming resistant regions (RRRs) where transcriptional activation at 2-cell embryos is inhibited by SCNT compared to in vitro fertilization (IVF). RRRs significantly overlap with H3K9me3 enrichment in donor somatic cells. Importantly, removal of the H3K9me3 by ectopic expression of an H3K9me3 demethylase Kdm4d in recipient oocytes not only reactivates most RRRs, but also greatly improves development of SCNT embryos. Furthermore, the use of Suv39h1/2-depleted somatic nuclei as donors also greatly improves the development of SCNT embryos. Our study thus reveals H3K9me3 as an epigenetic barrier in SCNT-mediated reprogramming and provides a feasible method for improving mammalian cloning efficiency.

overall_design: Here we perform RNA-seq based transcriptome profiling in Donor (cumulus cells), in vitro fertilized (IVF) embryos at 1- and 2-cell stages, somatic cell nuclear transfer (SCNT) embryos at 1- and 2-cell stages, Kdm4d over-expressed 2-cell SCNT embryos, and catalytic domain mutated Kdm4d over-expressed 2-cell SCNT embryos with duplicates.

first: Shogo

last: Matoba

first: Yi

last: Zhang


title: A Selective Phenelzine Analog Inhibitor of Histone Demethylase LSD1

city: Guangzhou

first: Xin

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

summary: Lysine-specific demethylase 1 (LSD1) is an epigenetic enzyme that oxidatively cleaves methyl groups from monomethyl and dimethyl Lys4 of histone H3 (H3K4Me1, H3K4Me2) and can contribute to gene silencing. This study describes the design and synthesis of analogs of a monoamine oxidase antidepressant, phenelzine, and their LSD1 inhibitory properties. A novel phenelzine analog (bizine) containing a phenyl-butyrylamide appendage was shown to be a potent LSD1 inhibitor in vitro and was selective versus monoamine oxidases A/B and the LSD1 homolog, LSD2. LSD1 inhibitor bizine was found to be effective at modulating bulk histone methylation in cancer cells, and ChIP-seq experiments revealed a statistically significant overlap in the H3K4 methylation pattern of genes affected by bizine and those altered in LSD1-/- cells. Treatment of two cancer cell lines, LNCaP and H460 with bizine conferred a reduction in proliferation rate, and bizine showed additive to synergistic effects on cell growth when used in combination with two out of five HDAC inhibitors tested. Moreover, neurons exposed to oxidative stress were protected by the presence of bizine, suggesting potential applications in neurodegenerative disease.

overall_design: To identify the effect of LSD1 inhibition by bizine on chromatin H3 Lys-methylation with individual gene resolution in LNCaP cells treated for 48 hours.

first: Polina

last: Prusevich

first: Oliver

middle: G

last: McDonald

first: Andrew

last: Feinberg

first: Philip

middle: A

last: Cole


title: Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [ChIP-seq]

city: Irvine

first: William

last: Chiu

address: Room 4410 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: We defined the genome-wide binding regions of Smad2/3 and Foxh1 at mid-gastrula stage Xenopus tropicalis embryos, at which Nodal signaling and Foxh1 are critical in mesendoderm specification program.

overall_design: Binding profile of the TFs Smad2/3 and Foxh1 in gastrula stage (st10.5) Xenopus tropicalis embryos using ChIP-seq approach.

middle: T

first: Ken

middle: W

last: Cho


title: Global analyses of cell cycle dependent changes in fission yeast genome organization reveal correlations with alterations in transcript levels [RNA-Seq]

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary: The successful progression of a cell through the cell cycle requires the temporal regulation of many biological processes, including gene transcript levels and the number and condensation of chromosomes. Fission yeast (Schizosaccharomyces pombe) is a paradigm for cell cycle research and model for higher eukaryotic cells. Due to the small size of its genome, it is highly amenable to high resolution studies of the spatial organization of its genome. Here we present the results of a high resolution study in which we used synchronised S. pombe cells to investigate cell cycle phase dependent changes in genome organization and transcription patterns. We reveal cell cycle dependant changes in connections within and between chromosomes while confirming previously observed features of genome organization, such as telomere clustering. Our results show that chromosomes are effectively circular throughout the cell cycle and that they remain connected even during the M phase. Determining the structure and transcript levels for matched synchronized cells revealed: 1) that genes with high transcript levels are highly connected with the genome at specific stages of the cell cycle; and 2) that interactions have positive and negative effects on transcript levels. We hypothesize that the observed correlations between transcript levels and the formation and disruption of cell cycle specific chromosomal interactions implicate genome organization in epigenetic inheritance and bookmarking.

overall_design: RNA sequencing was used to determine gene transcript levels in Schizosaccharomyces pombe cells synchronized at three pahses of the cell cycle; G1, G2 and M phase.

first: Ralph

middle: S

last: Grand


title: Global analyses of cell cycle dependent changes in fission yeast genome organization reveal correlations with alterations in transcript levels [GCC]

overall_design: Genome Conformation Capture was used to determine the three dimensional organization of Schizosaccharomyces pombe cells synchronized at three pahses of the cell cycle; G1, G2 and M phase.


title: Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program

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

overall_design: Refer to individual Series


title: Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors

status: Public on Nov 06 2014

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem


title: Global analyses of cell cycle dependent changes in fission yeast genome organization reveal correlations with alterations in transcript levels


title: The Role of cis Regulatory Evolution in Maize Domestication

city: Madison;

first: John

last: Doebley

state: WI

address: 425-G Henry Mall

department: Genetics Department

institute: University of Wisconsin - Madison

summary: Modification of cis regulatory elements to produce differences in gene expression level, localization, and timing is an important mechanism by which organisms evolve divergent adaptations. To examine gene regulatory change during the domestication of maize from its wild progenitor, teosinte, we assessed allele-specific expression in a collection of maize and teosinte inbreds and their F1 hybrids using three tissues from different developmental stages. Our use of F1 hybrids represents the first study in a domesticated crop and wild progenitor that dissects cis and trans regulatory effects to examine characteristics of genes under various cis and trans regulatory regimes. We find evidence for consistent cis regulatory divergence that differentiates maize from teosinte in approximately 4% of genes. These genes are significantly correlated with genes under selection during domestication and crop improvement, suggesting an important role for cis regulatory elements in maize evolution.

overall_design: We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem) followed by assessment of allele-specific gene expression.

first: Zachary

middle: H

last: Lemmon

first: Robert

last: Bukowski

first: Qi

last: Sun

middle: F


title: Genome-wide view of TGFb/Foxh1 regulation of the early mesendoderm program [RNA-seq]

state: CA

summary: We identified Nodal and Foxh1 downstream targets by performing RNA-seq of embryos either treated with small molecule SB431542 or microinjected morpholino anti-sense oligo against Foxh1.

overall_design: Differential gene expression analyses of perturbed embryos (SB431542 treated, or Foxh1 MO injected) using RNA-seq


title: Coilin ChIP-seq in cycling HeLa cells

first: Karla

last: Neugebauer

department: Molecular Biophysics & Biochemistry

summary: To investigate location of Cajal bodies (CB) inside the cell nucleus, we created a stable cell line expressing the GFP version of CB-marker protein coilin at endogenous levels and performed ChIP-seq with anti-EGFP antibody. ChIP-seq revealed close association of CBs wih U3 genes, snRNA genes and histone genes in histone cluster 1 and 2.

overall_design: 1 biological replicate of coilin ChIP-seq and input sample

first: Martin

last: Machyna


title: RNA-seq of young and quiescent MRC-5 human fibroblasts

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Quiescent MRC-5 fibroblasts were compared to young fibroblasts

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design:
6 samples: 3 biological replicates for each age group: young and quiescent MRC-5 cells.
50bp, single-end reads, no strand-specific reads

first: Shiva

last: Marthandan

first: Karolin

last: Klement

first: Steffen

last: Priebe

first: Marco

last: Groth

first: Matthias

last: Platzer

first: Peter

last: Hemmerich

first: Stephan

last: Diekmann


title: Profiling of mRNA N6-Adenosine Methylation (m6A) in Arabidopsis

city: Chicago

first: Guan-Zheng

last: Luo

address: 929 E 57th St

department: Chemistry

institute: UChicago

summary: m6A profiling in two accessions of Arabidopsis thaliana (Can-0 and Hen-16) using the m6A-targeted antibody coupled with high-throughput sequencing

overall_design: m6A-seq in two accessions of Arabidopsis, two replicates for each sample

first: Guifang

last: Jia

first: Chuan

last: He


title: HeLa cell polyA- RNA-seq

summary: Coilin iCLIP data revealed 42 novel human snoRNAs of intronic origin. To validate their expression and estimate abundance  of novel and annotated snoRNAs, we performed RNA-seq on polyA- and rRNA-depleted RNA isolated from HeLa cells. Results show that expression of novel snoRNAs is comparable to the previously annotated snoRNAs.

overall_design: 1 replicate of RNA depleted of polyA and ribosomal RNA.


title: Non-coding roX RNAs Prevent the Binding of the MSL-complex to Heterochromatic Regions

city: Umeå

first: Jan

last: Larsson

state: Västerbotten

address: University Hospital, buildings 6 K and 6 L

department: Molecular Biology

country: Sweden

institute: Umeå University

summary: Long non-coding RNAs are involved in dosage compensation both in mammals and in Drosophila by inducing changes in the X-chromosome chromatin structure. In Drosophila melanogaster, roX1 and roX2 are long non-coding RNAs that together with proteins form the male-specific lethal (MSL) complex, which coats the entire male X-chromosome and mediates dosage compensation by increased transcriptional output. It has been shown that in polytene chromosomes, in absence of both roX1 and roX2, the MSL-complex is decreased on the male X-chromosome and found relocated to the chromocenter, and the 4th chromosome. Here we address the role of roX RNAs in MSL-complex targeting and in the evolution of dosage compensation in Drosophila. We performed ChIP-seq experiments and show that MSL-complex recruitment to high affinity sites (HAS) on the X-chromosome is independent on roX and that the HAS sequence motif is conserved in D. simulans. Additionally, a complete and enzymatically active MSL-complex is recruited to six specific genes on the 4th chromosome. Interestingly, our sequence analysis shows that in the absence of roX RNAs, the MSL-complex has affinity to regions enriched in Hoppel transposable elements and to repeats in general. We hypothesize that roX mutants reveal an ancient targeting of the MSL-complex and propose that the role of roX RNAs is to restrict MSL-complex from binding to heterochromatin.

sample_organism:
Drosophila melanogaster
Drosophila simulans

overall_design: ChIP-seq

first: Margarida

middle: L

last: Figueiredo

first: Maria

last: Kim

first: Philge

last: Philip

first: Anders

last: Allgardsson

first: Per

last: Stenberg


title: iCLIP mapping of coilin-RNA interactions in HeLa and P19 cells

first: Karla

last: Neugebauer

summary: Our ChIP resuls suggested that coilin association with U3, snRNA and histone genes might be dependent on coilin-RNA interaction. We used iCLIP of coilin-GFP expressed in HeLa and P19 cell lines at endogenous levels to identify coilin RNA targets and investigate RNA-binding specificity. P19 cells expressing GFP fused to a nuclear localization signal (GFP-NLS) was used as a negative control. iCLIP results revealed that coilin binds several classes of ncRNA including snRNAs, U3 snoRNA and scaRNAs. Interestlignly the majority of coilin targets were intronic snoRNAs, suggesting a novel role of CBs in snoRNA biogenesis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 5 biological replicates from P19 and 2 biological replicates from HeLa cells after UV-crosslinking. Negative control samples prepared from GFP-NLS fusion protein are stored uder accession E-MTAB-747.

first: Martin

last: Machyna


title: Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification

status: Public on Nov 05 2014

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

summary: The aim of this study was to determine the genomic binding sites of an HA-tagged Transcription Activator-Like Effector (TALE) fused to a VP64 domain with a DNA binding domain designed to bind the sequence GGGCGCTTCCTGTTTTCTCA (found in the PU.1-14kb enhancer element in mouse and human genome), termed HA-T-VP64-PU.1-14, in the 416B mouse myeloid progenitor cell line.

overall_design: Inducible T-VP64-PU.1-14 transgene contained within the piggyBac vector was stably integrated into 416B cells by transfection along with a constituteively expressed rtTA plasmid (pCAG-rtTA-piggyBac) and a piggyBac transposase. 416Bs carrying stably integrated transgenes were FACS sorted based on their ability to expressed the transgene and expanded before HA-T-VP64-PU.1-14 expression was induced for 48 hours by addition of dox before cells were fixed with 1% formaldehyde for 10 mins. Chromatin was isolated, sonicated for 7 mins (30 sec on, 30 sec off), and an anti-HA antibody used to pull down the HA-T-VP64-PU.1-14 after a pre-clearing step. Chromatin was washed, de-crosslinked, amplified, size selected by gel purification and sequenced. As a control, untransfected 416B cells were similarly ChIP'd.

first: Adam

last: Wilkinson


title: Deep Sequencing Analysis of miRNAs Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers

first: OuYang

last: Hongjia

address: Wushan street 483

department: College of Animal Science

institute: South China Agricultural University

summary: To investigate the function of miRNAs in chicken growth, breast muscle tissues of the two-tail samples (highest and lowest body weight) from Recessive White Rock (WRR) and Xinghua Chickens (XH) were performed on high throughput small RNA deep sequencing. In this study, a total of 921 miRNAs were identified, including 733 known mature miRNAs and 188 novel miRNAs. There were 200, 279, 257 and 297 differentially expressed miRNAs in the contrasts of WRRh Vs. WRRl, WRRh Vs. XHh, WRRl Vs. XHl, and XHh Vs. XHl group, respectively. A total of 22 serious differentially expressed miRNAs (fold change > 2 or < 0.5; P-value < 0.05; q-value < 0.01) which also have abundant expression (read counts > 1,000) were found in our contrasts. As far as two contrasts (WRRh Vs. WRRl, and XHh Vs. XHl) are concerned, we found 80 common differentially expressed miRNAs, meanwhile 110 miRNAs were found in WRRh Vs. XHh and WRRl Vs. XHl. Furthermore, only 26 common miRNAs were identified among all of four contrasts.

overall_design: Examination of miRNA profiles in two-tail samples of WRR and XH strains.

first: Hongjia

last: Ouyang

first: Xiaomei

first: Qinghua

last: Nie


title: Transcriptome profiling from roots of jatropha in response to waterlogging

city: Chatujak

first: Piyada

last: Juntawong

state: Bangkok

address: 50 Ngamwongwan rd.

country: Thailand

institute: Kasetsart University

summary: Gene expression analysis by high-throughtput RNA-sequencing from roots of waterlogged jatropha (Jatropha curcas). Six leaf stage seedlings (~30 d.o.) were subjected to 24 h of soil waterlogging.

overall_design: 4 samples, 2 conditions  (24 h nonstress and 24 h waterlogging stress) and 2 independent biological replicates of 2 mRNA pools


title: Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors [RNA-Seq]

first: Ido

last: Sagi

summary: Human pluripotent stem cells can be derived from somatic cells by forced expression of defined factors, and more recently by nuclear-transfer into human oocytes, revitalizing a debate on whether one reprogramming approach might be advantageous over the other. Here we compared the genetic and epigenetic stability of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal and adult origin. Both cell types shared similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs have comparable numbers of de novo coding mutations but significantly higher than parthenogenetic ESCs. Similar to iPSCs NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes, similarly to iPSCs. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of the underlying technique.

overall_design: RNA sequencing analysis was performed on a total of 12 human cell lines, including: an isogenic set of 3 nuclear-transfer embryonic stem cell (NT-ESC) lines, 2 RNA-reprogrammed induced pluripotent stem cell (iPSC) lines and their parental neonatal fibroblast cell line; an isogenic set of 1 NT-ESC line, 3 iPSC lines and their parental adult fibroblast cell line (derived from a type 1 diabetic subject); as well as 1 control embryonic stem cell (ESC) line.

first: Bjarki

last: Johannesson

first: Mitsutoshi

last: Yamada

first: Nissim

last: Benvenisty

first: Dieter

last: Egli


title: ATRX regulates binding of Polycomb repressive complex 2 to Xist RNA and Polycomb targets

city: Boston

first: Jeannie

last: Lee

address: 185 Cambridge St, CPZN6

department: Department of Molecular Biology

country: USA

institute: Massachusetts General Hospital

summary: In mammals, dosage compensation entails inactivation of an entire X chromosome in female cells. X-chromosome inactivation (XCI) depends on the long noncoding RNA Xist and its recruitment of Polycomb Repressive Complex 2 (PRC2). How PRC2 specifically interacts with Xist and other Polycomb targets remains unclear. Using XCI as a model, we take an unbiased proteomics approach to search for new Xist and PRC2 regulators. We identify ATRX, a chromatin remodeler associated with mental retardation, alpha thalassemia, and cancer in humans. We show that ATRX is a high-affinity RNA-binding protein. ATRX directly interacts with RepA/Xist RNA and is required for loading of PRC2 onto the RNA in vivo.  The Xist gene is a hotspot of ATRX occupancy. Without ATRX, PRC2 cannot load onto Xist RNA nor spread in cis along the X-chromosome. Epigenomic profiling reveals a dependency of PRC2 on ATRX that extends beyond XCI. Depleting ATRX results in genome-wide disruptions to PRC2 localization and trimethylation of histone H3-lysine 27 (H3K27me3). PRC2 is displaced from genes and relocalized to intergenic space, causing reduced H3K27me3 and concomitant changes in expression of Polycomb targets. We conclude that ATRX is a required specificity determinant for PRC2 targeting and function.

overall_design: Distribution of ATRX in a transformed female mouse embryonic fibroblast cell line (EY.T4) and female mouse embryonic stem cells and examination of changes in EZH2 and H3K27me3 marks in transformed male embryonic fibroblast cell lines that contain autosomal integrated copies of full length Xist RNA gene upon ATRX knock down.

first: Kavitha

last: Sarma

first: Catherine

last: Cifuentes-Rojas

first: Ayla

last: Ergun

first: Amanda

last: del Rosario

first: Yesu

last: Jeon

first: Forest

last: White

first: Ruslan

last: Sadreyev