title: RNA-seq profiling of the bovine cervix at 6 timepoints during the peri-oestrus period.

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

summary: The estrous cycles of Limousin heifers (n = 30) were synchronized by insertion of a controlled internal drug release (CIDR) device (1.94 g progesterone; Pfizer Animal Health) placed into the vagina for 8 days. A 0.5 mg intramuscular injection of a prostaglandin F2α (PG) analogue (PG, Estrumate, Shering-Plough Animal Health, Hertfordshire, UK) was administered 1 day before CIDR removal.  Heifers were checked for standing  estrus  and only those exhibiting  estrus  (Day 0) were used. All animals were expected to come in heat between 48 and 72 hours after CIDR removal. Cervical tissues were collected at slaughter from heifers 12h after CIDR removal (Group 1: CIDR + 12 h, n = 6), 24h after CIDR removal (Group 2: CIDR + 24 h, n = 6), at the onset of  estrus  (Group 3: Estrus, n = 4), 12 h after the onset of  estrus  (Group 4:  estrus  + 12 h, n = 5), 48 h after the onset of  estrus  (Group 5: Estrus+48h, n = 4) and on day 7 after the onset of  estrus  (Group 6: Luteal phase, n = 5).

overall_design: Cervical tissue from 30 animals taken at 6 timepoints in the peri-oestrus period. +12hrs post CIDR, Onset of Oestrus,+12hrs post Oestrus, +48hrs post Oestrus, Luteal phase

first: Katarzyna

last: Pluta

first: John

last: Browne

first: Amanda

last: Lohan

first: Jane

last: Irwin

first: Colm

last: Reid

first: Brendan

last: Loftus

first: Alexander

middle: C

last: Evans

first: Stephen

middle: D

last: Carrington


title: Ogt chromatin recruitment is mediated by TET proteins in mouse ES cells [ChIP-Seq]

status: Public on Jan 06 2013

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

type: Genome binding/occupancy profiling by high throughput sequencing

summary: These data include the genome wide location analysis of Ogt by ChIP of Ogt in mouse ES cells.

overall_design: Precipitation of formaldehyde cross-linked chromatin prepared from mouse ES cell using specific antibody against OGT and IgG as control.

first: Pietro

last: Vella

first: Kristine

last: Williams

first: Jesper

last: Christensen

first: Kristian

last: Helin

first: Andrea

last: Scelfo

first: Sri

middle: G

first: Diego

last: Pasini


title: Estrogen Receptor alpha ChIP-Seq in mouse mammary gland

status: Public on Jan 11 2013

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

country: Netherlands

institute: NKI

summary: Estrogen Receptor is a key transcriptional regulator in mammary gland development and breast cancer. In this study, we have mapped the Estrogen Receptor chromatin binding patterns in healthy mouse mammary gland

overall_design: A minimum of 6 pairs of mouse mammary gland pads from mice at 5-6 weeks of age were excised and Estrogen Receptor ChIp-seq was performed.

first: Arno

last: Velds

first: Jaya

last: Nautiyal

first: Malcolm

last: Parker


title: Adaptive evolution of Corynebacterium glutamicum resistant to oxidative stress and its global gene expression profiling

city: Bucheon

first: Joo-Young

last: Lee

state: Gyonggi

address: 43-1 Yokgok2-dong

department: Department of Biotechnology

country: South Korea

institute: The Catholic University of Korea

type: Expression profiling by high throughput sequencing

summary: Corynebacterium glutamicum was adapted in a chemostat for 1,900 h with gradually increasing H2O2 stress to understand the oxidative stress response of an industrial host. After 411 generations of adaptation, C. glutamicum developed the ability to grow under stress of 10 mM H2O2, whereas the wild-type did not. The adapted strain also showed increased stress resistance to diamide and menadione, SDS, Tween 20, HCl, NaOH, and ampicillin. A total of 1,180 genes in the RNA-seq transcriptome analysis of the adapted strain were up-regulated twice or higher (corresponding to 38.6 % of the genome), and 126 genes were down-regulated half or less (4.1 % of genome) under 10 mM H2O2-stress conditions compared with those of the wild-type under a no stress condition. Especially the aromatic compound-degrading gene clusters (vanRABK, pcaJIRFLO, and benABCDRKE) were more than threefold up-regulated. Plausible reasons for the H2O2-stress tolerance of the adapted strain are discussed as well as the potential strategy for development of oxidative stress-tolerant strain.

overall_design:
Comparison of global gene expression profiling using RNA-seq data of wild-type strain under normal condition (WT_MCGC) vs. 10 mM H2O2-adapted strain under oxidative stress condition
Global gene expression profiling_WT vs. H2O2 adapted C. glutamicum strains

first: Pil

last: Kim

middle: Y


title: Paternally induced transgenerational inheritance of susceptibility to diabetes in mammals

status: Public on Jan 02 2013

city: Beijing

first: yanchang

last: wei

address: #1 Beichen West Rd

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Paternally induced transgenerational inheritance of susceptibility to diabetes in mammals (MeDIP-Seq)

summary: The global prevalence of type 2 diabetes (T2D) is increasing, and it is contributing to the susceptibility to diabetes and its related epidemic in offspring. Although the impacts of paternal T2D on metabolism of offspring have been well established, the exact molecular and mechanistic basis that mediates these impacts remains largely unclear. Here we show that paternal T2D increases the susceptibility to diabetes in offspring through the gametic epigenetic alterations. Paternal T2D led to glucose intolerance and insulin resistance in offspring. Relative to controls, offspring of T2D fathers exhibited altered gene expression patterns in the pancreatic islets, with downregulation of several genes involved in glucose metabolism and insulin signaling pathway. Epigenomic profiling of offspring pancreatic islets revealed numerous changes in cytosine methylation depending on paternal T2D, including reproducible changes in methylation over several insulin signaling genes. Paternal T2D altered overall methylome patterns in sperm, with a large portion of differentially methylated genes overlapped with that of pancreatic islets in offspring. Our study revealed, for the first time, that T2D can be inherited transgenerationally through the mammalian germline by an epigenetic manner.

overall_design: Examination of the effect of paternal T2D on the DNA methylation in the pancreatic islets of offspring and in the sperm of father.

first: Yanchang

last: Wei

first: Qing-Yuan

last: Sun


title: Widespread regulation of translation by elongation pausing in heat shock

status: Public on Jan 03 2013

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

summary: RNA-seq and ribosome footprinting libraries of mouse 3T3 and human 293T cellsrelated to Shalgi et al.  2013

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 36bases paired-end RNA-seq, and ribosome footprinting libraries for: 3T3 cells - Control, 8 hours of mild heat shock (42) and 2 hours of severe heat shock (44) - in replicates, as well as 3T3 cells treated by mild followed by severe heat shock. In addition, 3T3 cells treated with Hsp70 inhibitor VER-155008 (Massey et al. 2010), and 293T cells transfected with Hspa1a or GFP, before and after 2 hours of severe heat shock.

first: Jessica

middle: A

last: Hurt

first: Irina

last: Krykbaeva

first: Mikko

last: Taipale

first: Susan

last: Lindquist

first: Christopher

middle: B

last: Burge


title: Transcriptional Profiling of Mouse Uterus at Pre-implantation Stage under VEGF Repression

status: Public on Jan 09 2013

city: changchun

first: zhong

middle: q

last: p

address: nenu

institute: Mouse Uterus

summary: In this study, a genetically repressed VEGF mouse model was used to analyze uterus transcriptome at G2.5 (gestation day 2.5) by Solexa/ Illumina’s digital gene expression (DGE) system. 831 uterus-specific and 2398 VEGF regulated genes were identified. Gene ontology analysis indicated that genes actively involved in uterus development were members of collagen biosynthesis, cell proliferation and cell apoptosis. Uterus-specific genes were enriched in activities of phosphatidyl inositol phosphate kinase, histone H3-K36 demethylation and protein acetylation. Among VEGF regulated genes, up-regulated genes were associated with RNA polymerase III activity while down-regulated genes were strongly associated with muscle development.Comparable numbers of antisense RNA transcripts were also identified. Expression levels of the antisense RNAs were found tightly correlated with their sense expression levels, an indication of possibly non-specific transcripts generated around the active promoters and enhancers. The antisense RNAs with exceptionally high or low expression levels and the antisense RNAs under VEGF regulation were also identified. These transcripts may be important candidates in regulation of uterus development. This study provides a global survey on genes and antisense transcripts regulated by VEGF in the pre-implantation stage. Results will contribute to the further studies of candidate genes and pathways in regulating implantation process and related diseases.

overall_design: Uteri mRNA profiles of G2.5 VEGF-normal (Dox+) and VEGF-repression (Dox-) were generated by Solexa/ Illumina’s digital gene expression (DGE) system.

first: Yan

last: Ji

first: Qingping

last: Zhong

first: Yaowu

last: Zheng


title: Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival

status: Public on Jan 10 2013

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

country: USA

institute: University of California Los Angeles

summary: Here we show that the phytochrome-less chlorophyte Chlamydomonas reinhardtii retains a functional pathway to synthesize the linear tetrapyrrole (bilin) precursor of the phytochrome chromophore. Reverse genetic, metabolic inactivation and bilin rescue experiments establish that this pathway is needed for heme iron acquisition and for the diurnal transition to phototrophic growth. RNA-Seq measurements reveal a bilin-dependent signaling network that is necessary for the heterotrophic to phototrophic transition. These results imply the presence of a novel bilin sensor pathway that may be widely distributed amongst oxygenic photosynthetic organisms.

overall_design: We isolated RNA from heterotrophic suspension cultures of 4A+ WT and the hmox1 mutant grown in the presence or absence of 0.1 mM BV IXα before and after transfer to low light.

first: Deqiang

last: Duanmu

first: David

last: Casero

first: Rachel

middle: M

last: Dent

first: Sean

last: Gallaher

first: Wenqiang

last: Yang

first: Nathan

last: Rockwell

first: Shelley

middle: S

last: Martin

first: Matteo

last: Pellegrini

first: Krishna

middle: K

last: Niyogi

first: Arthur

middle: R

last: Grossman

first: J

last: Lagarias


title: Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers [ChIP-seq]

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Chromatin regulators have become highly attractive targets for cancer therapy, yet many of these regulators are expressed in a broad range of healthy cells and contribute generally to gene expression.  An important conundrum has thus emerged: how can inhibition of a general regulator of gene expression produce selective effects at specific oncogenes? Here we investigate how inhibition of the transcriptional coactivator BRD4 (Bromodomain containing 4) leads to selective inhibition of disease-critical oncogenes in a highly malignant blood cancer, multiple myeloma (MM).  We found that BRD4 generally occupies the promoter elements of active genes together with the Mediator coactivator, but remarkably high levels of these two coactivator proteins were associated with a small set of exceptionally large enhancers.  These super-enhancers are associated with genes that feature prominently in MM biology, including the MYC oncogene. Treatment of MM tumor cells with the BET-bromodomain inhibitor JQ1 led to preferential loss of BRD4 at super-enhancers and consequent transcription elongation defects that preferentially impact genes with super-enhancers, including the c-MYC oncogene.  Super-enhancers were found at key oncogenic drivers in many other tumor cells.  Thus, super-enhancers can regulate oncogenic drivers in tumor cells, which in some cells can be preferentially disrupted by BRD4 inhibition, which in turn contributes to the selective transcriptional effects observed at these oncogenes. These observations have implications for the discovery of novel cancer therapeutics directed at components of super-enhancers in diverse tumor types.

overall_design: ChIP-Seq for chromatin regulators and RNA Polymerase II in multiple myeloma, glioblastoma multiforme, and small cell lung cancer

first: Jakob

last: Lovén

first: Heather

last: Hoke

first: Charles

last: Lin


title: Divergent transcription of lncRNA/mRNA gene pairs in embryonic stem cells

type: Non-coding RNA profiling by high throughput sequencing

summary: Many long non-coding RNA (lncRNA) species have been identified in mammalian cells, but the genomic origin, regulation and function of these molecules in individual cell types is poorly understood.  We have generated comprehensive catalogs of lncRNA species expressed in human and murine embryonic stem cells (ESCs) and mapped their genomic origin.  A surprisingly large fraction of these transcripts (>60%) originate from divergent transcription at promoters of active protein-coding genes.  The divergently transcribed lncRNA/mRNA gene pairs exhibit coordinated changes in transcription when ESCs are differentiated into endoderm.  A significant number of the divergently transcribed lncRNAs/mRNA pairs are conserved between human and mouse ESCs.  Disruption of promoter-associated lncRNA orthologs in a zebrafish model of early development causes gross developmental defects.  Our results reveal that transcription of most lncRNA genes is coordinated with transcription of protein-coding genes and that these lncRNAs have roles in early development.

overall_design: Analysis of genome-wide lncRNA transcription in human embryonic stem cells and early differentiation using RNA-seq, GRO-seq and ChIP-seq

first: Alla

last: Sigova

first: Alan

last: Mullen

first: Benoit

last: Moline

first: Sumeet

last: Gupta

last: Orlando

first: Cosmas

last: Giallourakis


title: Identification of Novel Molecular Markers through Transcriptomic Analysis in Human Fetal and Adult Corneal Endothelial Cells

status: Public on Jan 08 2013

first: Kevin

last: Huang

state: CA

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

summary: Corneal endothelium is composed of a monolayer of corneal endothelial cells (CECs) in the inner layer of cornea, which is essential for maintaining corneal transparency. In order to better characterize CECs in different developmental stages, we profiled mRNA transcriptomes in human fetal and adult corneal endothelium with the goal to identify novel molecular markers in these cells. By comparing CECs with 12 other types of tissues, we identified 245 and 284 signature genes that are highly expressed in fetal and adult CECs, respectively. Functionally, these genes are characteristic of CECs, involving in cell adhesion, proteoglycan and sulfur metabolic process. Importantly, several of these genes are disease target genes in hereditary corneal dystrophies, consistent with their functional significance in CEC physiology. By comparing fetal and adult CECs, we also identified stage-specific markers associated with CEC maturation, such as the activation of the Wnt pathway genes in fetal, but not in adult CECs. Lastly, by immunohistochemistry of ocular tissues, we further confirmed the unique protein expression patterns for Wnt5a, S100A4, S100A6, and IER3, the four novel markers for either fetal or adult CECs.  The identification of a new panel of molecular markers for fetal and mature CECs would be very useful for characterizing and quality controlling CECs through ex vivo expansion or stem cell differentiation for cell replacement therapy.

overall_design: mRNA profile between adult and fetal CECs by high-throughput sequencing

first: Guoping

last: Fan


title: RPA accumulation during class switch recombination represents 5'-3' DNA end resection during the S-G2/M phase of the cell cycle

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: AID promotes chromosomal translocations by inducing DNA double-strand breaks (DSBs) at immunoglobulin (Ig) genes and oncogenes in G1.  RPA is a ssDNA-binding protein that associates with resected DSBs in the S phase and facilitates the assembly of factors involved in homologous repair (HR) such as Rad51. Notably, RPA deposition also marks sites of AID-mediated damage, but its role in Ig gene recombination remains unclear. Here we demonstrate that RPA associates asymmetrically with resected ssDNA in response to lesions created by AID, RAG, or other nucleases. Small amounts of RPA are deposited at AID targets in G1 in an ATM-dependent manner. In contrast, recruitment in S-G2/M is extensive, ATM-independent, and associated with Rad51 accumulation. RPA in S-G2/M increases in NHEJ-deficient lymphocytes, where there is more extensive DNA-end resection. Thus, most RPA recruitment during CSR represents salvage of un-repaired breaks by homology-based pathways during the S-G2/M phases of the cell cycle.

overall_design: Chip-Seq of RPA from mouse activated B cells (n = 40), mouse thymocytes (n = 6), and MEFs (n = 1). Different genotypes and/or inhibitors were used.

first: Arito

last: Yamane

first: Davide

middle: F

last: Robbiani

first: Wolfgang

last: Resch

first: Anne

last: Bothmer

first: Hirotaka

last: Nakahashi

first: Thiago

last: Oliveira

first: Philipp

last: Rommel

first: Eric

middle: J

last: Brown

first: Andre

last: Nussenzweig

first: Michel

first: Rafael

last: Casellas


title: Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe

first: Ian

middle: O'Brien

last: Carter-O'Connell

address: 52 Oxford St. NW 440

department: MCB

institute: Harvard University

platform_organism:
Schizosaccharomyces pombe
Schizosaccharomyces pombe 972h-

middle: O

first: Michael

middle: T

last: Peel

first: Dennis

last: Wykoff

first: Erin

last: O'Shea


title: Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe [ChIP-Seq data]

summary: Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway leading to the expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway. The genes induced by phosphate limitation and the molecular mechanism by which the genetically identified positive (pho7+) and negative (csk1+) regulators function are not known. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response for the ScPHO5 (pho1+), ScPHO84 (spbc8e4.01c+), and ScGIT1 (spbc1271.09+) orthologs. We use ChIP-Seq to identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. We provide a global analysis of the PHO pathway in S. pombe. Our results elucidate the conserved core regulon required for responding to phosphate starvation between distantly related ascomycetes and a better understanding of flexibility in environmental stress response networks.

overall_design: ChIP Sequencing of the Schizosaccharomyces pombe 972h- transcription factor Pho7-TAP in high-Pi, no-Pi, and csk1Δ conditions


title: Ogt chromatin recruitment is mediated by TET proteins in mouse ES cells

first: Sri Ganesh

last: Jammula


title: High throughput sequencing of small RNAs from Drosophila cells infected with a panel of viruses

status: Public on Jan 01 2013

city: Philadelphia

first: Sara

last: Cherry

address: 304K Lynch Labs

institute: University of Pennsylvania

summary: We report the cloning and sequencing of both endogenous small RNAs and virus-derived siRNAs produced by the antiviral RNAi pathway in Drosophila. We find that a diverse panel of viruses are targeted by the RNAi pathway in Drosophila to produce abundant virus-derived siRNAs, and these siRNAs map to various locations within the viral genomes. Knockdown of various RNAi and miRNA pathway components alters the levels of these viral small RNAs.

overall_design: Drosophila DL1 cells were treated with dsRNA for 3 days to deplete factors involved in the antiviral RNAi pathway and miRNA pathway, then were challenged with one of four viruses for 4 days. Total RNA was collected, and the small RNA populations from 15-29 nt were cloned and sequenced.

first: Leah

last: Sabin


title: Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes [ChIP-Seq and RNA-seq]

first: Richard

last: Young

summary: The master transcription factors Oct4, Sox2 and Nanog bind enhancer elements and recruit the Mediator co-activator to activate much of the gene expression program of embryonic stem cells (ESCs).  We report here that these ESC master transcription factors and Mediator form “super-enhancers” at most genes that are known to control the pluripotent state, including those encoding the master transcription factors themselves. These super-enhancers consist of extraordinarily large genomic domains occupied by exceptional amounts of Oct4 and Mediator.  Super-enhancers stimulate considerably higher transcription than typical enhancers in reporter vectors.  ESC differentiation causes preferential loss of expression of super-enhancer -associated genes.  Super-enhancers are also found at key cell identity genes in differentiated cells. These results implicate super-enhancers in the control of mammalian cell identity and differentiation and suggest that these elements might generally be used to identify genes that control cell-type specific gene expression programs in many mammalian cells.

overall_design: ChIP-Seq and RNA-seq of Med1 in ZHBTc4 ES during treatment with doxycycline. ChIP-Seq data of Med1 in 38B9 pro-B cells.

first: Warren

last: Whyte

first: Denes

last: Hnisz

first: Alan

last: Mullen

first: David

last: Orlando


title: High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells

city: Ipswich

first: Yu

last: Zheng

address: 240 County Road

institute: New England Biolabs

summary: We describe the use of a novel DNA modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq) to map high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The specificity of AbaSI enables sensitive detection of 5hmC at low occupancy regions. Bioinformatic analysis suggests 5hmCs in genic regions closely follows the 5mC distribution. 5hmC is generally depleted in CpG islands and only enriched in a small set of repetitive elements. A regularly spaced and oscillating 5hmC pattern was observed at the binding sites of CTCF. 5hmC is enriched at the poised enhancers with the mono-methylated histone H3 lysine 4 (H3K4me1) marks, but not at the active enhancers with the acetylated histone H3 lysine 27 (H3K27Ac) marks. Non-CG hydroxymethylation appears to be prevalent in the mitochondrial genome. We propose that some amounts of transiently stable 5hmCs may indicate a poised epigenetic state or de-methylation intermediate, while others may suggest a locally accessible chromosomal environment to the TET enzymatic apparatus.

overall_design: Mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cell by enzymatic digistion of  AbaSI coupled with high-throughput sequencing, in replicates.

first: Zhiyi

last: Sun

first: Terragni

last: Jolyon

first: Zhenyu

last: Zhu

first: Sriharsa

last: Pradhan


title: RYBP and Cbx7 define specific biological functions of PRC1 complexes in mouse embryonic stem cells

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

summary: We report the ChIP-seq data of several PRC1 and PRC2 members from mouse embryonic stem cells

overall_design: Examination of DNA binding profile of Polycomb subunits

first: Lluis

last: Morey

first: Luca

last: Cozzuto


title: Nuclear Receptor Corepressors are Required for the Histone Deacetylase Activity of HDAC3 In Vivo (ChIP-Seq)

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: We report the genomic regions enriched in Histone Deacetylase 3 (HDAC3) in mouse livers. We also report the change of HDAC3 occupancy upon DAD mutations in NCOR and SMRT.

overall_design: HDAC3 enriched genomic regions in WT and NS-DADm mice livers using Illumina GAIIx.

first: Seo-Hee

last: You

first: Zheng

first: Molly

last: Broache

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: Nuclear Receptor Corepressors are Required for the Histone Deacetylase Activity of HDAC3 In Vivo

summary:
Histone deacetylase 3 (HDAC3) is an epigenome-modifying enzyme that is required for normal mouse development and tissue-specific functions. In vitro, HDAC3 protein itself has minimal enzyme activity, but gains its histone deacetylation function from stable association with the conserved deacetylase activation domain (DAD) contained in nuclear receptor corepressors NCOR1 and SMRT.  Here we show that HDAC3 enzyme activity is undetectable in mice bearing point mutations in the DAD of both NCOR1 and SMRT (NS-DADm), despite normal levels of HDAC3 protein.  Local histone acetylation is increased, and genomic HDAC3 recruitment is reduced though not abrogated. Remarkably, the NS-DADm mice are born and live to adulthood, whereas genetic deletion of HDAC3 is embryonic lethal. These findings demonstrate that nuclear receptor corepressors are required for HDAC3 enzyme activity in vivo, and suggest that a deacetylase-independent function of HDAC3 may be required for life.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: PKCz restrains cancer cell transformation by inhibiting nutrient stress-induced metabolic reprogramming

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Tumor cells utilize the so-called Warburg effect to allow for rapid proliferation with glucose as the main nutrient. We show here that, although PKCz is critical for that effect, its deficiency promotes the plasticity necessary for nutrient-stressed cancer cells to reprogram their metabolism to utilize glutamine through the serine biosynthetic pathway, empowering them to survive and proliferate in the absence of glucose. We show that PKCz deficiency enhances glutamine utilization and expression of two key enzymes of the pathway, PGHDGH and PSAT1, in cells cultured in the absence of glucose. The loss of PKCz in mice results in enhanced intestinal tumorigenesis and increased levels of these two metabolic enzymes, while patients with low levels of PKCz have a poor prognosis. Taken together, this suggests that PKCz is a critical metabolic tumor suppressor.

overall_design: SW480 cells were infected with lentivirus expressing PKCz RNA interference (shPKCz) and a control lentivirus (shNT). The elimination of endogenous PKCz with shPKCz transfection was >90% efficient. Cells transfected with shNT had unaltered levels of PKCz. To mimic the conditions of nutrient stress to which tumor cells are normally exposed, both cell types were initially seeded in DMEM with 10% FBS, and cultured without subsequent further media changes, which led to nutrient exhaustion over time. Total RNA was harvested from three independent biological replicates for shPKCz and shNT transfected cells.

first: Li

last: Ma

first: Yongzhen

last: Tao

first: Anita

last: Galvez

first: Jennifer

last: Barger

first: Elias

last: Castilla

first: Jing

last: Chen

first: Alekxey

last: Porollo

last: Plas

first: Maria

last: Diaz-Meco

first: Adam

last: Richardson

first: Jorge

last: Moscat


title: Transcription factors interfering with dedifferentiation induce direct conversion

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

summary: Although transcription factor(TF)s regulate differentiation-related processes, including dedifferentiation and direct conversion, functional interactions between TFs regulating these processes are not well understood. Here we show that TFs preventing dedifferentiation are able to induce direct conversion. Using a neural lineage cell line and a large number of TFs expressed in it, we found a subset of TFs whose overexpression strongly interfered with dedifferentiation triggered by a procedure to induce induced pluripotent stem cells (iPSC), through a maintenance mechanism of the cell-type-specific transcriptional profile. Strikingly, the maintenance activity of the interfering TF set was strong enough to induce the cell line-specific transcriptional profile when overexpressed in a heterologous cell type. In addition, TFs that interfered with dedifferentiation in hepatic lineage cells involved known TFs with induction activity for hepatic lineage cells. Our results suggest that dedifferentiation suppresses a cell-type-specific transcriptional profile, which is primarily maintained by a small subset of TFs capable of inducing direct conversion. We anticipate that this functional correlation might be applicable in various cell types, which may include cancer cells, and might facilitate identification of TFs with induction activity to understand differentiation and tumorigenesis

overall_design: Examination of binding of 3 transcription factors and histone modifications in Neural progenitor like cells.

first: Shinji

last: Masui


title: VL30 retro-transposons are TRIM24-repressed enhancers that generate non-coding RNA to regulate gene expression in mouse hepatocytes. [ChIP-Seq]

city: ILLKIRCH Cedex

first: Stephanie

last: Le Gras

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary: TRIM24 and TRIM33 interact to form a corepressor complex that suppresses murine hepatocellular carcinoma (HCC). TRIM24 and TRIM33 cooperatively repress retinoic acid receptor dependent activity of VL30 retro-transposons in hepatocytes in vivo. In TRIM24 knockout hepatocytes, VL30 long terminal repeats (LTRs) generate enhancer (e)RNAs and act as surrogate promoter and enhancer elements deregulating expression of neighbouring genes. We show that a VL30 LTR-derived eRNA is essential to activate the lipocalin 13 gene in hepatocytes in vivo. A further consequence of VL30 de-repression is the accumulation of retro-transcribed VL30 DNA in the cytoplasm of TRIM24-mutant hepatocytes and activation of the viral defence/interferon response. VL30 activation therefore modulates gene expression via the enhancer activity of the LTRs and by activation of the interferon response. Both of these processes are genetically linked to HCC development suggesting that VL30 repression by TRIM24 plays an important role in tumour suppression.

overall_design: Examination of H3k4me3 and RNA pol II in liver by deep sequencing.

first: Benjamin

last: Herquel

first: Irwin

last: Davidson


title: miRNA expression profile and small RNA transcriptome in the Squalius alburnoides complex

city: Lisbon

first: Angela

last: Inácio

address: Campo Grande

country: Portugal

institute: centro de Biologia Ambiental

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

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus
Takifugu rubripes
Squalius alburnoides
Squalius pyrenaicus

overall_design: Refer to individual Series


title: VL30 retro-transposons are TRIM24-repressed enhancers that generate non-coding RNA to regulate gene expression in mouse hepatocytes. [RNA-Seq]

overall_design: RNA profiles in liver of wild type (WT) and Trim24-/- mice by deep sequencing using Illumina GAIIx.


title: Small RNA transcriptome in the Squalius alburnoides complex

summary: The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was shown that in response to the increase in the genome dosage, triploid hybrids could regulate gene expression to a diploid state. In this work, we compared the small RNA profiles in the different genomic compositions interacting in the complex. Using high-throughput arrays and sequencing technologies, we were able to verify that diploid and triploid hybrids were closely related: they shared most of their sequences and their miRNA expression profiles were highly correlated. However, an overall view indicates an up-regulation of a substantial number of miRNAs in triploids. Also, the global miRNA expression in triploids was higher than predicted from an additive model. These results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.

sample_organism:
Squalius alburnoides
Squalius pyrenaicus

overall_design: 4 samples were analyzed corresponding to 4 genomic constitutions: PAA, PA, AA and PP. For each sample, a library based on 3 individuals of the same genomic constitution was prepared. From each individual, 3 types of tissues were collected for RNA extraction (brain, liver and muscle).

first: Joana

last: Pinho

first: Patricia

last: Pereira

first: Luca

last: Comai

last: Coelho


title: Genome-wide maps of H3K27ac localization in HUVECs

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

institute: LSBM, RCAST

summary: H3K27Ac is one of the expressed enhancer markers in endothelial cells, but its genomic localization is unknown.  This time, we established a new antibody for H3K27ac, and performed ChIP-seq to identify H3K27ac binding site in whole genome manner under hypoxia.

overall_design: We used chromatin immunoprecipitation with deep sequencing (ChIP-seq) of HUVECs treated with or without hypoxia (1%O2) for 24hours, then H3K27ac binding regions were identified.  Normoxia was used as a control condition.  HUVECs were used within the first 6 passages.

first: Tsuyoshi

last: Inoue

first: Youichiro

last: Wada

first: Akashi

last: Taguchi

first: Shogo

last: Yamamoto

first: Tatsuhiko

last: Kodama


title: Myc correlates globally with transcription complexes rather than specific DNA elements

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary: The Myc-Max heterodimer has been thought of as a sequence specific DNA binding protein that regulates transcription of a large number of genes. We demonstrate here that the positions of the human genome occupied by Myc-Max correlate with the RNA polymerase II (Pol II) transcription complex rather than to the canonical DNA binding sequence element CACGTG. The heterodimer is positioned slightly upstream of essentially all promoter proximal paused polymerases and is found throughout the transcribed regions of genes. Using a multi-genome analysis of promoter regions we show that the heterodimers are oriented with respect to the direction of transcription with Myc downstream of Max. In strong support of a model in which the Myc is recruited by transcription complexes rather than specific DNA sequences, we found that the difference in affinities of Myc-Max heterodimers for CACGTG versus non-specific DNA is not great enough to drive the pattern of genome occupancy exhibited.

overall_design: A total of 2 ChIP-Seq data for Myc and Max in human HeLa cell.

first: David

middle: H

last: Price


title: Identifying reference genes with stable expression from high throughput sequence data

city: Woods Hole

first: Sonya

last: Dyhrman

address: 266 Woods Hole Road

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and Analysis of Sequence Counts (ASC) to identify putative reference genes. A total of 9759 genes were identified and screened for stable expression. Literature-based searches surveyed 18 generally accepted reference genes, revealing 101 homologs in T. pseudonana with variable expression and a wide range of mean tags per million. K-means analysis parsed the whole transcriptome into 15 clusters. The two most stable clusters contained 709 genes but still had distinct patterns in expression. ASC analyses identified 179 genes that were stably expressed (posterior probability < 0.1 for 1.25 fold change). Genes known to have a stable expression pattern across the test treatments, like actin, were identified in this pool of 179 candidate genes. ASC can be employed on data without biological replicates and was more robust than the k-means approach in isolating genes with stable expression. The intersection of the genes identified through ASC with commonly used reference genes from the literature suggests that actin and ubiquitin ligase may be useful reference genes for T. pseudonana and potentially other diatoms. With the wealth of transcriptome sequence data becoming available, ASC can be easily applied to transcriptome datasets from other phytoplankton to identify reference genes.

overall_design: Axenic T. pseudonana CCMP 1335 was grown at 14°C under 24 hour light (120 µmol photons m-2 s-1) after Dyhrman et al. (2012) in f/2 plus silica chelated media made from surface Sargasso Sea water. Nitrate, silica, vitamins, and trace metals were at f/2 concentrations (Guillard and Ryther 1962), while iron and phosphate were modified across treatments. In brief, triplicate cultures of replete (36 µM PO4, 400 nM Fe), P-limited (0.4 µM PO4, 400 nM Fe), Fe-limited (36 µM PO4, 40 nM Fe), and Co-limited (0.4 µM PO4, 40 nM Fe) treatments were harvested when growth deviated from the replete control. Growth was monitored by cell counts. Biomass was harvested onto 0.2 µm filters and flash frozen in liquid nitrogen and total RNA was extracted as described in Dyhrman et al. (2012). Tag-seq sequencing of the transcriptome was performed by Illumina with a polyA selection and NlaIII digestion, resulting in 21 bp sequence reads or tags (Dyhrman et al., 2012). Libraries were of varied sizes as follows: replete (~12 million), P-limited (~13 million), Fe-limited (~23 million), and Co-limited (~26 million). Tags were mapped to gene models (predicted protein coding regions) with a pipeline designed by Genesifter Inc., requiring 100% identity and covering 9759 genes. Tag counts within a gene were pooled and normalized to the size of the library, with resulting data expressed in tags per million (tpm). Genes with normalized tag counts less than 2.5 tpm for each of the four treatments were excluded (Figure S1) , leaving 7380 genes in the analysis.

first: Harriet

last: Alexander

first: Bethany

last: Jenkins

first: Tatiana

last: Rynearson

first: Mak

last: Saito

first: Melissa

middle: L

last: Mercier

last: Dyhran


title: OsJMJ703, a Histone H3K4 Demethylase, Controls Transposon Activity in Rice

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

summary: Retrotransposons are classified into long terminal repeat (LTR) or non-LTR retrotransoposons, and both types can mobilize in a “copy and paste” manner. Rice genome contains >40% of repetitive sequences or transposable elements (TEs) that scattered throughout the genome. TE activities are tightly regulated by distinct epigenetic mechanisms. Histone lysine methylation is catalyzed by SET domain group (SDG) protein and reversed by a family of Jumonji C (JmjC) domain-containing proteins. In rice, DNA methylation and histone methylation have been implicated in controlling copia-like LTR retrotransposon Tos17 activities. Whether any TEs are controlled by histone demethylase remains to be elusive. Here, we show that JMJ703 is a histone H3K4 specific demethylase in rice. Impaired JMJ703 disrupted genome-wide transcriptome and enhanced H3K4me3 resulting in pleiotropic defects. Two LINE elements, Karma and its N-terminal truncation were identified as direct targets of JMJ703 with increased frequency of transposition in jmj703, while Tos17 is unaffected. Our findings show that plants use H3K4me3 demethylase to constitutively remove active chromatin mark and maintain silencing status at a subset retrotransposons which localize in heterochromatin regions. Therefore, our work uncovers a novel mechanism to control retrotransposon activity by histone demethylation, which further strengthens the link between epigenetic silencing and genome stability.

overall_design: Examination of differences in H3K4 between jmj703 and wild type.

first: Xiaofeng

last: Cao


title: Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [ChIP-seq]

city: Vienna

first: Denes

last: Hnisz

address: Dr Bohr-gasse

department: Medical Biochemistry

country: Austria

institute: Max F Perutz Laboratories

summary: The dataset contains ChIP-Seq data of the Set3 and Hos2 proteins in Candida albicans, assayed in two morphological phases (yeast and hypha). The Set3 and Hos2 proteins in the respective strains carry 9myc epitopes and ChIP was performed with an anti-myc antibody. Included samples are the following: 1 input and 1 ChIP sample of an untagged wild type strain as negative control assayed in the yeast phase, 1 input and 3 ChIP biological replicates of the Set3-9myc strain in the yeast phase, 1 input and 2 ChIP biological replicates of the Set3-9myc strain in the hypha phase, 1 input and 2 ChIP biological replicates of the Hos2-9myc strain in the yeast phase, 1 input and 2 ChIP biological replicates of the Hos2-9myc strain in the hypha phase, 1 input and 3 ChIP biological replicates of Set3-9myc in a set1delta/delta background in the yeast phase.

overall_design: ChIP-Seq was performed of Candida albicans strains in two morphological phases (yeast and hypha). Yeast-phase cells were grown to the exponential phase in YPD at 30C. Hyphal differentiation was induced by resuspending the cells in YPD+20% Fetal Calf Serum and a shift of the growth temperature to 37C. Induction was performed for 30 minutes. Cells were crosslinked with 1% formaldehyde for 15 minutes at room temperature.


title: Differential expression analysis of miRNAs in goat (Capra hircus) mammary gland  between peak and late lactation by Solexa sequencing

city: Tai'an

first: Dong

last: fei

state: Shandong

address: No.61 Daizong street

institute: Shandong Agricultural University

summary: We report the application of Solexa high-throuthput sequencing technology for miRNA differential expression profiles.  Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to Ovis aries genome.  The results were validated by qRT-PCR.  Our study represents the first detailed analysis of miRNA expression profiles in goat mammary gland tissues, with biologic replicates generated by RNA-seq technology.

overall_design: miRNA  expression profiles of goat mammary gland tissues between peak lactation and late lactation were generated by Illumina/Solexa sequencing

first: Jianmin

last: Wang

first: Zhibin

last: Ji


title: Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [RNA-seq]

summary: Transcriptome analysis of wild type and set3-deficient Candida albicans cells in yeast and hyphal morphological phases

overall_design: RNA Sequencing was performed of wild type and set3-deficient Candida albicans strains in two morphological phases (yeast and hypha). Yeast-phase cells were grown to the exponential phase in YPD at 30oC. Hyphal differentiation was induced by resuspending the cells in YPD+20% Fetal Calf Serum and a shift of the growth temperature to 37oC. Induction was performed for 30 minutes. Three biological replicates of both genotypes in each morphological phases were analyzed.


title: Daily cycling of genome-wide histone methylation

first: Utham Kashyap

last: Valekunja

state: PA

address: 3400 Civic Center Boulevard,

department: Department of Systems Pharmacology & Therapeutics, Perelman School of Medicine,

summary: Daily (circadian) clocks are essential for regulating and coordinating physiology in mammals. Modulation of local chromatin structure has been shown for only a small number of genes, principally thought to be directly modulated by Clock-mediated histone acetylation. Here we show that genome-wide changes of active and suppressive histone marks control global chromatin architecture over the day and night.

overall_design: Examination of mouse liver tissue at 4 time-points around the clock in "free-running", continuous conditions (constant darkness, temperature and food available ad libitum).

first: Utham

first: Akhilesh

last: Reddy


title: SNF5 is an essential executor of epigenetic regulation in pluripotency and differentiation

city: LA

first: jueng soo

last: You

address: 1441 Eastlake Ave

department: Norris Comprehensive Cancer Center

institute: USC


title: Genome-wide maps of chromatin remodeler SNF5 in human pluripotent cells.

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of SNF5 binding in human pluripotent embryonic carcinoma NCCIT and SNF5 overexpressed NCCIT cells. We generated genome-wide cSNF5 maps of NCCIT and SNF5 overexpressed NCCIT cells from chromatin immunoprecipitated DNA. SNF5 and OCT4 seem not to share their binding in OCT4 centered binding plot in control, while SNF5 overexpression directs SNF5 to OCT4 target genes.

overall_design: Examination of the relationship between SNF5 and OCT4 binding in control and SNF5 overexpressed cells.

first: Peter

last: Jones


title: Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis.


title: Genome-wide maps of RNA Polymerase II and p65 localization in HUVECs stimulated with TNF alpha

first: Takahide

last: Kohro

summary: TNF alpha is one of the inflammatory mediator and induce genes mainly by  transcriptional factor, p65,  in endothelial cells. This time, we performed a time course study to detect the change of localization of p65 and Pol II.

overall_design: To identify p65 and Pol II binding sites, we used chromatin immunoprecipitation with deep sequencing (ChIP-seq) of HUVECs treated with or without TNF alpha for 30 mins.  Cells were starved before stimulation longer than 16 hours.  HUVECs were used within the first 6 passages.  For crosslinking, 10 mM of EGS in 50% glacial acetic acid was used for 45 min, followed by 20 min of 1% paraformaldehyde treatmet was used.

first: Wada

last: Youichiro

first: Kohro

last: Takahide

first: Kobayashi

last: Mika

first: Shogo

last: Yamamoto

first: Tatsuhiko

last: Kodama


title: The histone methyltransferase MLL3 regulates genome-scale circadian transcription


title: Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling

city: New York

first: Shao-shan

middle: Carol

last: Huang

state: NY

address: 12 Waverly Pl

institute: New York University


title: Transcriptome of normal, paracancerouse and cancerous bladder tissues based on RNA-Seq method

city: haikou

first: shufang

last: zhang

address: people avenue NO.43

institute: haikou people hospital

summary: In order to support our research of bladder cancer in human genome, we conducted massively parallel pyrosequencing of mRNAs (RNA-Seq) using normal, paracancerouse and cancerous human bladder tissues. We obtained a total of 30.0 million read pairs from normal, 33.1 million read pairs from paracancerous and 36.5 million read pairs from cancerous. The RNA-Seq data derived from the sample illustrated the differencially expression genes among normal, paracancerous and cancerous bladder tissues of human.

overall_design: 3 samples examined: normal tissue, paracancerous tissue, cancerous tissue.

first: Zhang

last: ShuFang


title: Progressive degeneration of human neural stem cells caused by pathogenic LRRK2

city: Zurich

first: Ulrich

last: Wagner

address: Schmelzbergstrasse 12

country: Switzerland

institute: Uiversity Hospital Zurich

summary: Aging and its physiological manifestations have been correlated with adult stem cell exhaustion and a failure to maintain tissue homeostasis1-10. Since multiple morphological cellular defects are associated with aging-related disorders, we hypothesized that late onset disorders might be linked to adult stem cell abnormalities compromising cellular function over time. Our work shows that a dominant G2019S mutation in the human LRRK2 gene, which is associated with central nervous system disorders, including Parkinson’s disease, the second most prevalent neurodegenerative disease in the aging population, causes alterations in neural stem cell homeostasis in aging-related cellular contexts. They include disruption of the nuclear architecture, deficiencies in clonal expansion and alterations in neural differentiation assays as well as an increased susceptibility to proteasomal stress. These phenotypic changes are dependent on differential kinase activity manifested during cellular passaging. Our studies might open new venues for studying the influence of aging in neural stem cell dependent processes, such as cognitive impairments, in the degenerating diseased brain.

overall_design: Genome-wide localization of Histon K4 trimethylation in human iPSC and iPSC-derived neural stem cell using ChIP-seq

first: Guang-Hui

last: Liu

first: Jing

last: Qu

first: Keiichiro

last: Suzuki

first: Mo

last: Li

first: Ignacio

last: Sancho-Martinez

first: Fei

last: Yi

first: Emmanuel

last: Nivet

first: Sergio

last: Ruiz

first: Nuria

last: Montserrat

first: Weiqi

last: Zhang

first: Audrey

last: Kim

first: Bing

last: Ren

first: April

last: Goebl

first: Jessica

first: R

middle: D

last: Soligalla

first: Ilir

last: Dubova

first: Concepcion

last: Rodriguez Esteban

first: Juan

middle: C

last: Izpisua Belmonte


title: Linking oncogenic signaling to transcriptional changes by epigenomic data in a cell line model of human glioblastoma

first: Shao-shan

last: Huang

summary: We present a computational method for building a regulatory network from global phosphoproteomic and transcription profiling data. To recover the critical missing links between signaling events and transcriptional responses, we relate changes in chromatin accessibility to changes in expression and then uses these links to connect proteomic and transcriptome data.  We applied our approach to integrate epigenomic, phosphoproteomic and transcriptome changes induced by the variant III mutation of the epidermal growth factor receptor (EGFRvIII) in a cell line model of glioblastoma multiforme (GBM).

overall_design: Genome-wide DNase I hypersensitivity followed by sequencing (DNase-Seq) to measure chromatin accessibility in a cell line derived from the U87MG glioblastoma cell line to express high level of EGFRvIII (U87H; 2 million copies of EGFRvIII per cell) and a control cell line expressing kinase dead EGFRvIII (U87DK; 2 million kinase dead EGFRvIII per cell).  A prediction from the computational method, the transcriptional co-regulator p300, was experimentally validated by chromatin immunoprecipitation followed by sequencing (ChIP-Seq).

first: Ernest

last: Fraenkel


title: VL30 retro-transposons are TRIM24-repressed enhancers that generate non-coding RNA to regulate gene expression in mouse hepatocytes.

first: Stephanie

last: Le Gras


title: Genome-wide maps of MEF2C and H3K27ac localization in HUVECs

first: Takahide

last: Kohro

summary: MEF2C is one of the substantially expressed transcriptional factors in endothelial cells, but its genomic localization is unknown. This time, we established a new antibody for MEF2C, and performed ChIP-seq to identify MEF2C binding site in whole genome manner.   H3K27Ac binding sites were also detected in the same way.

overall_design: We used chromatin immunoprecipitation with deep sequencing (ChIP-seq) of HUVECs treated with or without pitavastatin for 4hours, we identified MEF2C and H3K27Ac binding regions.HUVECs were used within the first 6 passages.  For MEF2C studies, HUVECs were cultivated in medium EGM2MV containing pitavastatin at a concentration of 1 μM, and same concentration of DMSO was used as a control sample. For H3K27ac, HUVECs were starved for 16 hours and harvested without statin treatment.

first: Takashi

last: Maejima

first: Shuichi

last: Tsutsumi

first: Shogo

last: Yamamoto

first: Hiroshi

last: Kimura

first: Tatsuhiko

last: Kodama

first: Youichiro

last: Wada


title: A global analysis of tandem 3'UTRs in eosinophilic chronic rhinosinusitis with nasal polyps

status: Public on Dec 31 2012

city: Guang Zhou

first: Peng

last: Tian

state: Guang dong

address: Yan Jiang Xi Road 107#

department: Department of Biochemistry, Department of Otorhinolaryngology-Head and Neck Surgery

institute: Sun Yat-sen University

summary:
Background: Alternative polyadenylation (APA) is emerging as a widespread mechanism of gene regulation. The usage of APA sites allows a single gene to encode multiple mRNA transcripts with different 3'-untranslated region (3'UTR) lengths. Many disease processes reflect the importance of the regulation of APA site switching. The objective of this study was to explore the profiling of tandem APA sites in nasal polyps compared with nasal uncinate process mucosa.
Methods: Sequencing of APA sites (SAPAS) based on second-generation sequencing technology was undertaken to investigate the use of tandem APA sites and identify gene expression patterns in samples from the nasal polyps and nasal uncinate process mucosa of two patients with chronic rhinosinusitis with nasal polyps. The findings of the SAPAS analysis were validated via quantitative reverse-transcription polymerase chain reaction (qRT-PCR).
Results: First, the results showed a switching of 3'UTR lengths in nasal polyps compared with nasal uncinate process mucosa. From the two patients, 105 overlapping genes in the nasal polyps were switched to distal poly(A) sites, and 90 such genes were switched to proximal poly(A) sites. Several Gene Ontology terms were enriched in the list of genes with switched APA sites, including transcription regulation, cell cycle, apoptosis, and metabolism. Second, we detected genes that showed differential expression with at least a 3-fold difference between nasal polyp tissue and nasal uncinate process mucosa. Between the two sample types, 627 genes exhibited differential expression. The qRT-PCR results confirmed our SAPAS results.
Conclusion: APA site-switching events of 3'UTRs are prevalent in nasal polyp tissue, and the regulation of gene expression mediated by APA may play an important role in the formation and persistence of nasal polyps. Our results may provide new insights into the possible pathophysiologic processes involved in nasal polyps.

overall_design: Investigate the use of tandem APA sites of 3'ends of mRNAs using second-generation sequencing technology.

first: Yonggui

last: Fu

first: Hua

last: Zou


title: Regulation of Oxidative Stress Responses by the Arabidopsis Heat Shock Factor A4A

city: Morahalom

first: Balazs

last: Horvath

address: Vallalkozok u. 7.

department: NGSP

country: Hungary

institute: SeqOmics Biotechnology Ltd.

summary: Identification of target genes for the transcription factor HSFA4A  in Arabidopsis thaliana.

overall_design: Two weeks-old Col-0 wild-type and transgenic plants overexpressing the HSFA4A transcription factor under the estradiol-inducible promoter lexA (HSFA4Aox2) were treated by 5µM estradiol with or without 1mM H2O2 for 6h in liquid 0.5 MS medium and the isolated RNA samples were used for RNAseq analysis.

first: László

last: Szabados

first: Imma

middle: P

last: Salamó

first: István

last: Nagy

first: Balázs

last: Horváth


title: Transcriptomic response of goat mammary epithelial cells to Mycoplasma agalactiae challenge – a preliminary study

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

summary: Mycoplasma agalactiae (Ma) is one of the main aetiological agents of intramammary infections in small ruminants, causing contagious agalactia. To better understand the underlying disease patterns a primary goat mammary epithelial cell (pgMEC) culture was established from the mammary tissue and it was challenged with Ma. High-throughput mRNA sequencing was performed to reveal differentially expressed genes (DEG) at different time-points (3 h, 12 h, and 24 h) post infection (PI). The pathway enrichment analysis of the DEG showed that infection significantly affected pathways associated with immune response, steroid metabolism, fatty acid metabolism, apoptosis signalling, transcription regulation, and cell cycle regulation. Based on the results we suggest that mammary epithelial cells in vivo contribute to the immune system by the induced expression of cytokines and other chemotactic agents, activation of the complement system and apoptosis pathways, and expression of genes coding for antimicrobial molecules and peptides. In our study we attempted to interpret the detected transcriptomic changes in a biological context and infer mammary infection resistance candidate genes, interesting for further validation. Additionally, the results represent comprehensive goat mammary transcriptome information and demonstrate the applicability of the comparative genomics approach for annotation of goat data, using transcriptome information of a closely related species (Bos taurus) as a reference.

overall_design: Transcriptome analysis of 12 samples; 3 replicated samples from control cells, and from cells 3 h, 12 h, and 24 h post infection.

first: Jernej

last: Ogorevc

first: Sonja

last: Prpar

first: Dusan

last: Bencina

first: Tanja

last: Kunej

first: Peter

last: Dovc


title: RNAPII progression through H3K27me3 enriched gene bodies require JMJD3 HDM activity

city: Barcelona

first: Conchi

last: EI

address: Baldiri Reixac 15

institute: IBMB

summary: Several signaling pathways require JMJD3 binding to promoters to activate the expression of target genes. Despite the known H3K27me3 demethylase activity of JMJD3 the transcriptional coactivator mechanism remains unclear. Here we reveal that JMJD3 promotes transcription of TGFb responsive genes through regulation of RNAPII progression on gene bodies. ChIPseq experiments demonstrate that upon TGFb treatment, JMJD3 and RNAPII.ser2P colocalyze extensively along intragenic regions of TGF target genes.  According to these data, genome wide analysis shows that JMJD3 dependent TGF target genes are enriched in H3K27me3 prior to TGF signaling pathway activation.  Further molecular analysis indicate that JMJD3  removes H3K27me3 and pave the way for the RNAPII.Overall, these findings uncover the mechanism of JMJD3 function in transcriptional activation

overall_design: We performed chromatin immunoprecipitation followed by sequencing (ChIPseq) of H3K27me3 mark in mouse neural stem cells growing under standard conditions. We also performed ChIPseq of elongating RNAPII (Ser2P) and JMJD3 in neural stem cells stimulated with TGFb cytokine.

last: Estarás


title: Genome-wide cistromes of thyroid hormone receptors alpha and beta in C17.2 cells

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

institute: INSERM

summary: Tagged versions of thyroid hormone receptors alpha (TRa) and beta (TRb) were stably transfected in two C17.2 cell lines, C17.2a and C17.2b, respectively. We performed an affinity-based purification of chromatin (ChAP), and high-throughput sequencing was used to assess binding sites of both receptors (ChAP-Seq). Standard ChIP-Seq for RXR was also performed in C17.2a cells. These data allow us to compare binding sites for both receptors and to conclude that they were only partially redundant, with co-existence of receptor-specific sites.

overall_design: Examination of binding sites of the two thyroid hormone receptors (alpha, beta) in two cell lines (C17.2a, C17.2b), each expressing one of the receptors. Examination of RXR binding sites in C17.2a cells.

first: Romain

last: Guyot

first: Gérard

last: Benoît

first: Frédéric

last: Flamant


title: Fbxl10 regulates PRC1 recruitment to CpG islands and H2A ubiquitination

city: Copenhagen

first: Xudong

last: Wu

address: Ole Maaløes Vej 5

institute: Biotech Research and Innovation Centre

summary: Polycomb repressive complex 1 (PRC1) catalyzes H2A monoubiquitination (uH2A) and regulates pluripotency in embryonic stem cells (ESCs). However the mechanisms controlling PRC1 recruitment and activity are largely unknown. Here we show that Fbxl10 interacts with Ring1B and Nspc1, forming a non-canonical PRC1. We demonstrate that Fbxl10-PRC1 is essential for H2A ubiquitination in mouse ESCs. Genome-wide analyses reveal that Fbxl10 preferentially binds to CpG islands and co-localizes with Ring1B on Polycomb target genes. Notably, Fbxl10 depletion causes modest dissociation of Ring1B but a major loss of uH2A on target genes. Furthermore rescue experiments for Fbxl10 reveal that its DNA binding capability and integration into PRC1 are required for proper H2A ubiquitination. ES cells lacking Fbxl10, like previously characterized Polycomb mutants, show a severely compromised capacity for successful differentiation. Our results shed light on a novel mechanism how CpG islands regulate chromatin function by affecting polycomb recruitment and activity.

overall_design: All  ChIP-seq reactions were performed in either untransfected cells, cells expressing scrambled shRNA or Fbxl10 shRNA, Ring1b-/- or Suz12-/- mouse ES cells

first: Jens

middle: V

last: Johansen


title: Pronounced and Extensive Microtubule Defects in a Saccharomyces cerevisiae DIS3 Mutant

city: Cleveland

first: Daniel

middle: Louis

last: Kiss

address: 2109 Adelbert Road

department: Molceular Biology and Microbiology

institute: Case Western Reserve University

summary: The recently proposed exozyme hypothesis posits that subunits of the RNA processing exosome assemble into structurally distinct protein complexes that function in disparate cellular compartments and RNA metabolic pathways.  Here, in a genetic test of this hypothesis, we examine the role of Dis3 -- an essential polypeptide with endo- and 3' to 5' exo-ribonuclease activity -- in cell cycle progression.  We present several lines of evidence that perturbation of DIS3 affects microtubule (MT) localization and structure in Saccharomyces cerevisiae.  Cells with a DIS3 mutation: (i) accumulate anaphase and pre-anaphase mitotic spindles; (ii) exhibit spindles that are mis-oriented and displaced from the bud neck; (iii) harbor elongated spindle-associated astral MTs; (iv) have an increased G1 astral MT length and number; and (v) are hypersensitive to MT poisons.  Mutations in the core exosome genes RRP4 and MTR3 and the exosome cofactor gene MTR4 -- but not other exosome subunit gene mutants -- also elicit MT phenotypes.  RNA deep sequencing analysis (RNA-seq) shows broad changes in the levels of cell cycle- and microtubule-related transcripts in mutant strains.  Collectively, the different mitotic phenotypes and distinct sets of mRNAs affected by the exosome subunit and cofactor mutants studied here suggest that Dis3 has a core exosome-independent role(s) in cell cycle progression.  These observations are consistent with the predictions of the exozyme hypothesis and also suggest an evolutionarily conserved role for Dis3 in linking RNA metabolism, MTs, and mitotic progression.

overall_design: RNA-seq analysis of total RNA harvested from WT, mtr3-1, mtr4-1, and Dis3^mtr (rrp44-1/mtr17-1) Saccharomyces cerevisiae strains after a temperature shift.

first: Erik

last: Andrulis


title: Small RNA sequencing of NIH 3T12 cells infected by murine gammaherpesvirus

city: St. Louis

first: Jing

last: Xia

address: Campus Box 1045 One Brookings Drive

department: Department of Computer Science and Engineering

institute: Washington University in St. Louis

summary: MicroRNA (miRNA) and endogenous siRNA (endo-siRNA) are two essential classes of small noncoding RNAs (sncRNAs) in eukaryotic organisms. The class of miRNA is diverse and there exist noncanonical miRNAs that bypass the canonical miRNA biogenesis pathway. In order to identify noncanonical miRNAs and endo-siRNAs responding to virus infection and study their potential function, we sequenced small-RNA species from cells lytically infected with murine gammaherpesvirus 68. In addition to 3 novel canonical miRNAs in mouse, two antisense miRNAs in virus and 25 novel noncanonical miRNAs, including miRNAs derived from tRNAs, snoRNAs and introns, in the host were identified. These noncanonical miRNAs exhibited features distinct from canonical miRNAs in the lengths and structures of miRNA hairpins as well as base pairings and first nucleotide preference. Many of the novel miRNAs are conserved in mammals. In addition to several known murine endo-siRNAs detected by the sequencing profiling, a novel locus in the mouse genome was identified to give rise to endo-siRNAs. This novel endo-siRNA locus is comprised of two tandem inverted B4 short interspersed nuclear elements (SINEs). Unexpectedly, the SINE-derived endo-siRNAs were found in a variety of sequencing data as well as virus-infected cells. Moreover, a murine miRNA was up-regulated more than 35 fold in infected than in mock-treated cells. The putative target genes of the viral and the up-regulated murine miRNAs were potentially involved in processes of gene transcription and protein phosphorylation and localized to membranes, suggesting their role in manipulating the host basal immune system during lytic infection. Our results extended the number of noncanonical miRNAs in mammals and shed new lights on their potential functions of lytic infection of MHV68.

overall_design: Mouse NIH 3T12 cells infectd with MHV68 (3 samples) and mock-treated (2 samples) were examined. Noncanonical microRNAs and endogenous siRNAs discovery in lytic infection of murine gammaherpesvirus MHV68 (NC_001826.2).

first: Tiffany

middle: A

last: Reese

first: Steven

last: Johnson

first: Xiang

last: Zhou

first: Weixiong

last: Zhang

first: Herbert

middle: W

last: Virgin


title: Quantitative polyadenylation map of mouse embryonic epidermal lineages

city: Boulder

first: Li

last: Wang

state: CO

address: 347 UCB

institute: University of Colorado, Boulder

summary: We establish an experimental and bioinformatic pipeline using 3SEQ to quantitatively measure mRNA expression and reliably determine 3' end formation by sequencing polyadenylated transcripts. When applied to purified mouse embryonic skin stem cells direct differentiation lineages, we identify 15,651 UTRs representing 10,442 distinct mRNAs that are abundantly expressed in the skin. We determine that ~80% of UTRs are formed by using canonical A[A/U]UAAA polyadenylation signals, whereas ~20% of UTRs utilize alternative signals. We demonstrate that comparing with qPCR, our RNA-Seq approach can precisely measure mRNA fold-change and accurately determine the expression of mRNAs over four orders of magnitude. We also reported 453 out of 10,442 genes (4.3%) show differential 3' end usage between skin stem cells and their direct differentiation lineages. Among them, core components of the miRNA pathway, including Dicer, Dgcr8, Xpo5 and Ago2, show dynamic 3' UTR formation patterns, indicating a self-regulatory mechanism. Together, our quantitative analysis reveals a dynamic picture of mRNA 3' end formation in closely related somatic stem cell lineages.

overall_design: Perform 3SEQ in E14 epidermal basal cells and E14 epidermal suprabasal cells.

first: D

last: Dowell

first: Rui

last: Yi


title: Genome-wide analysis of thyroid hormone receptors' shared and specific functions in neural cells

first: Fabrice

last: Chatonnet

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

overall_design: Refer to individual Series

first: Gerard

last: Benoit

first: Frederic


title: Dosage imbalance of NMD genes is associated with intellectual disability

city: North Adelaide

first: Jozef

last: Gecz

state: South Australia

address: 72 King William Rd

department: Genetics Medicine

country: Australia

institute: SA Pathology

summary: Nonsense-mediated mRNA decay (NMD) functions to degrade transcripts bearing premature stop codon (PTC) and is a crucial regulator of gene expression. NMD and the UPF3B gene have been implicated as the cause of various forms of intellectual disability (ID) and other neurological symptoms. Here, we reports three patients with global developmental delay carrying hemizygous deletions of the UPF2 gene, another important member of the NMD pathway and direct interacting partner of UPF3B.

overall_design: Using RNA-SEQ on lymphoblastoid cells from UPF2 deletion patients, we identified 1009 differently expressed genes (DEGs). 38% of these DEGs overlapped with DEGs identified in UPF3B patients. More importantly, 95% of all DEGs in either UPF2 or UPF3B patients share the same trend of de-regulation. This demonstrates that the transcriptome deregulation in these two patient groups is similar and that UPF2 should be considered as a new candidate gene for ID in man. We expanded our inq`uiries and performed a comprehensive search for copy number variations (CNVs) encompassing all NMD genes in cohorts of ID patients and controls. We found that UPF2, UPF3A, Y14, SMG6 and EIF4A3 are frequently deleted and/or duplicated in ID patients. These CNVs are likely to be the root of the problems or to act as predisposing factors. Our results suggest that dosage imbalance of NMD factors is associated with ID and further emphasize the importance of NMD in normal learning and memory processes.

first: Lam

middle: S

last: Nguyen

first: Hyung

middle: G

last: Kim

first: Jill

last: Mokry

first: Lulu

last: Huang

first: Miles

last: Wilkinson

first: Lisa

last: Schaffer


title: Expression data from the human parietal cortex brain

city: Changsha

first: Chao

last: Chen

address: 110 Xiangya Road

institute: Central South University

summary:
Schizophrenia (SCZ) and bipolar disorder (BD) are highly heritable psychiatric disorders. Associated genetic and gene expression
changes have been identified, but many have not been replicated and have unknown functions. We identified groups of genes
whose expressions varied together, that is co-expression modules, then tested them for association with SCZ. Using weighted gene
co-expression network analysis, we show that two modules were differentially expressed in patients versus controls. One,
upregulated in cerebral cortex, was enriched with neuron differentiation and neuron development genes, as well as disease
genome-wide association study genetic signals; the second, altered in cerebral cortex and cerebellum, was enriched with genes
involved in neuron protection functions. The findings were preserved in five expression data sets, including sets from three brain
regions, from a different microarray platform, and from BD patients. From those observations, we propose neuron differentiation
and development pathways may be involved in etiologies of both SCZ and BD, and neuron protection function participates in
pathological process of the diseases.

overall_design: We use microarray technology to understand the etiology and pathology of psychiatric diseases at the transcriptomic level. Postmortem human brain samples came from the Stanley Medical Research Institute’s Neuropathology Consortium and Array collections, including schizophrenia, bipolar disorder and control samples.

first: Chunyu

last: Liu


title: Expression data from the human cerebellum and parietal cortex brain


title: The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation

status: Public on Dec 30 2012

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Enhancers play a central role in precisely regulating the spatiotemporal expression of developmentally regulated genes. The molecular mechanisms and factors required for controlling the inactive or poised enhancers and their function in future gene activation remain elusive. Here, we have identified that Ell3, a member of the Ell (Eleven-nineteen Lysine-rich Leukemia gene) family of RNA Pol II elongation factors, predominately occupies active and inactive enhancers of many developmentally regulated genes in mouse embryonic stem cells. Ell3 localizes to active enhancers of key stem cell renewal genes, but is not required for maintaining the undifferentiated state. Instead, Ell3 binding to inactive or poised enhancers is essential for marking them for stem cell specification through regulating the activation of key lineage-specific genes throughout differentiation. Ell3’s association with enhancers is required for setting up proper Pol II occupancy at the proximal promoter regions of neighboring genes. This functional interaction between Ell3 and proximal promoter Pol II is dependent on cohesin. The depletion of cohesin subunits removes Ell3 from the enhancers and results in reduction in the levels of promoter proximally paused Pol II. Our study demonstrates that Ell3 is required for stem cell fate specification through regulating Pol II pausing on key developmental genes in the undifferentiated state and for their proper expression during differentiation.

overall_design: ChIP-seq of Ell3 in mES cells.  ChIP-seq of Pol II in mES cells after Ell3 shRNA and non-targeting shRNA.  RNA-seq of mES cells after Ell3 shRNA and non-targeting shRNA.  RNA-seq of mouse embryoid bodies at day five after non-targeting shRNA.

first: Chengqi

last: Lin

first: Ali

last: Shilatifard


title: Marek's Disease Virus Infection Induces Differential Chromatin Marks and Tissue-specific effects in inbred chicken lines

city: Bethesda

first: Apratim

last: Mitra

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

summary: Marek’s disease (MD) is a viral neoplastic disease in chickens caused by the MD virus (MDV). Successful vaccination strategies against MD have resulted in a progressive increase in the virulence of MDV and therefore, the understanding of genetic resistance to MD is considered crucial to the long-term control of the disease. Here we examine whether MDV infection induces changes in the epigenetic status of genes and whether this response is dependent on the host genotype. We generated genome-wide histone 3 lysine 4 (H3K4) and histone 3 lysine 27 (H3K27) trimethylation maps in thymus tissues from chicken lines with varying resistance to MD. Differential chromatin marks were observed on several genes previously implicated in MD such as MX1, MMP2 and CTLA-4 and also on novel genes such as EAF2, IGF2BP1 and GAL. We also detected bivalent domains on transcriptional regulators such as BCL6, CITED2 and EGR1 that have particular functions in immune response. Moreover, novel putative roles for GAL and CITED2 in the mechanism of MD progression were uncovered. We also found tissue-specific effects of MDV infection with certain genes exhibiting differential marks only in spleen. Our results suggest widespread epigenetic changes are induced by MDV infection extent of which is determined by the level of MD resistance of the host.

overall_design: 8 samples examined: 2 histone modifications X 2 chicken lines with varying resistance to MD X 2 groups - infected and control.

first: Juan

last: Luo

first: Jiuzhou

last: Song


title: ZNF335 regulates stem cell proliferation and neuronal differentiation via Trithorax complex and REST/NRSF [ChIP-Seq]

city: Boston

first: Christopher

last: Walsh

address: 3 Blackfan Circle

department: Genetics

institute: Children's Hospital Boston

summary: The progression from stem cell to differentiated neuron is associated with extensive chromatin remodeling that controls gene expression, but the mechanisms that connect chromatin to gene expression are not well defined. Here we show that mutation of ZNF335 causes severe human microcephaly ("small brain"), small somatic size, and neonatal death. Germline Znf335 null mutations are embryonically lethal in mice, whereas RNA-interference studies and postmortem human studies show that Znf335 is essential for neural progenitor self-renewal, neurogenesis, and neuronal differentiation. Znf335 is a component of a vertebrate-specific, trithorax H3K4 methylation complex, while global ChIP-seq and mRNA expression studies show that Znf335 is a previously unsuspected, direct regulator of REST/NRSF, a master regulator of neural gene expression and neural cell fate, as well as other essential neural-specific genes. Our results reveal ZNF335 as an essential link between H3K4 complexes and REST/NRSF, and provide the first direct evidence that this pathway regulates human neurogenesis and neuronal differentiation.

overall_design: Examination of Znf335-bound genes with two separate antisera

first: Yawei

middle: J

last: Yang


title: Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth

city: Campinas

first: Renato

last: Vicentini

state: SP

address: Cidade Universitaria "Zeferino Vaz"

department: Centro de Biologia Molecular e Engenharia Genetica - CBMEG

country: Brazil

institute: Universidade Estadual de Campinas - UNICAMP

summary: Axillary bud outgrowth determines plant shoot architecture and is under control of endogenous hormones and a fine-tuned gene expression network. Some genes associated with shoot development are known targets of small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets in axillary buds are unknown. In this study, we employed next-generation sequencing, gene expression analysis and metabolite profiling to identify sRNAs and quantify distinct hormones, respectively, in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.). Differential accumulation of abscisic acid (ABA), gibberellins (GA), and cytokinins indicates a dynamic balance of these hormones during sugarcane bud outgrowth. A number of repeat-associated siRNAs generated from distinct transposable elements and genes were highly expressed in both inactive and developing buds. RT-qPCR results revealed that specific miRNAs were differentially expressed in developing buds and some correlate negatively with the expression of their targets. Expression patterns of miR159 and its experimentally confirmed target GAMYB suggest they play roles in regulating ABA and GA-signaling pathways during bud outgrowth. Our work reveals, for the first time, differences in composition and expression profiles of small RNAs and targets between inactive and developing buds that, together with the endogenous balance of specific hormones, may be important to regulate axillary bud outgrowth in plants.

overall_design: Examination of small RNA populations in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.)

first: Fausto

last: Ortiz-Morea

first: Geraldo

middle: F

last: Silva

first: Eder

middle: M

first: Helaine

last: Carrer

first: Ana

last: Rodrigues

first: Fabio

last: Nogueira


title: RIP-seq data for CCNT1

status: Public on Dec 28 2012

city: Cambridge

first: Yue

last: Li

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

summary: To demonstrate RIPSeeker program that is developed for RIP-seq analyses, we generated RIP-seq data corresponding to the protein CCNT1 in HEK293 cell line using standard RIP-seq protocols described in Zhao et al., (2010).

overall_design: We performed two in-house RIP-seq experiments both for CCNT1 in human HEK293 cells.  Briefly, we generated tagged CCNT1 using a triple tag system that supports lentiviral stable expression and mammalian affinity purification (MAPLE) Mak et al (2010).  The HEK293 cells stably expressing tagged CCNT1 was purified by M2 agarose beads, followed by RNA extraction by Trizol.  The library synthesis was carried out according to the RIP-seq protocol described in Zhao et al., (2010) except that one of the two experiments was done with non-strand-specific sequencing.

first: Dorothy

middle: Y

last: Zhao

first: Jack

last: Greenblatt

first: Zhaolei

last: Zhang


title: KDM2B binds CpG islands and modulates recruitment of Ring1b

status: Public on Dec 26 2012

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

summary: CpG island elements are associated with most mammalian gene promoters, yet how they contribute to gene regulation remains poorly understood. Recently it has become clear that a subset of CpG islands in embryonic stem cells can act as polycomb response elements and are recognized by the polycomb silencing systems to regulate the expression of genes involved in pluripotency and early developmental transcription programs. How CpG islands function mechanistically as nucleation sites for polycomb repressive complexes remains unknown. Here we discover that the KDM2B protein, by virtue of its ZF-CxxC DNA binding domain, specifically recognizes non-methylated DNA in CpG islands elements genome-wide. Through a physical interaction with the polycomb repressive complex 1 (PRC1), KDM2B targets PRC1 to CpG islands where it contributes to H2AK119ub1 and gene repression at a subset of polycomb targets. Unexpectedly, we also find that CpG islands are occupied by low levels of PRC1 throughout the genome, suggesting that the KDM2B-PRC1 complex may sample CpG island associated genes for susceptibility to polycomb mediated silencing. These observations demonstrate an unexpected and direct link between recognition of CpG islands by KDM2B and targeting of the polycomb repressive system. This provides the basis for a new model describing the functionality of CpG islands as mammalian PREs.

overall_design: ChIP-Seq to compare KDM2A vs. KDM2B genome-wide binding profiles and to understand the contribution of KDM2B to RING1B nucleation. Binding of Kdm2a and Kdm2b to the genome was examined in wildtype mESC, and Kdm2b and Ring1b in mESC where Kdm2b has been stably knocked down by shRNA.

first: Robert

last: Klose

first: Anca

last: Farcas


title: KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands


title: High-throughput sequencing of  small RNAs from seedling of Larix leptolepis

city: Beijing

first: Liwang

last: Qi

address: Xiang shan Road

department: The Research Institute of Forestry

institute: The Chinese Academy of Forestry

summary: MicroRNAs (miRNAs) are emerging as essential, albeit poorly characterized, regulators of biological processes. The miRNA in gymnosperms is under-identified, which limits the progress of miRNA in gymnoperms. Using the high-throughput sequencing, a total of 87 conserved miRNAs were identified from Larix leptolepis. Eighteen novel miRNAs were discovered in our library, most of which were Larix-specific miRNAs.

overall_design: Identification of  small RNA in Larix seedling

first: Tao

last: Wu

first: Junhong


title: The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer.

status: Public on Dec 27 2012

city: Darlinghurst

first: Mark

last: Cowley

state: NSW

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

institute: Garvan Institute of Medical Research


title: FOXO3 regulates gene expression from distal enhancers

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

institute: Hubrecht Institute

type: Genome variation profiling by high throughput sequencing

summary: FOXO transcription factors are key players in diverse cellular responses affecting tumorigenesis, stem cell maintenance and lifespan. To gain insight into mechanisms of FOXO regulated gene expression, we studied genome-wide effects of FOXO3 activation. Profiling RNA polymerase II (RNAPII) changes shows FOXO3 regulates gene expression through transcription initiation. Correlative analysis of FOXO3 and RNAPII ChIP-seq profiles demonstrates FOXO3 to act as a transcriptional activator. Furthermore, this analysis reveals a significant part of FOXO3 gene regulation proceeds through enhancer regions. FOXO3 binds to and activates enhancers as shown by the presence of and changes in enhancer-specific histone modifications and RNAPII occupancy. In addition, FOXO3-mediated enhancer regulation correlates with regulation of adjacent genes and existence of chromatin loops between FOXO3 bound enhancers and regulated genes. Combined, our data elucidate how FOXOs regulate gene transcription and provide insight into mechanisms by which FOXOs can induce different gene expression programs depending on chromatin architecture.

overall_design: seven 4C view point were analyzed on DLD1 colon carcinoma cells containing 4OH-Tamoxifen inducible FOXO3A3-ER (DL23 cells, Kops et al., 2002, Mol Cell Biol), to investigate 3D topology around FOXO3 bound regions and FOXO3 regulated genes before and 4 hours after addition of tamoxifen. 4C procedure, as published before (Splinter et al., 2001, Genes Dev). Cells are cross linked using 1% formaldehyde for 10min at room temperature, nuclei are isolated, after which chromatin is digested with DpnII and subsequently ligated under diluted conditions. After reversal of the cross links the DNA is purified and treated with the second restriction enzyme treatment (Csp). After a second re-ligation step the sample is purified and ligated fragments are analyzed by inverse PCR.

first: Astrid

last: Eijkelenboom

first: Michal

last: Mokry

first: Paulien

middle: E

last: Polderman

first: Almut

last: Schulze

first: Wouter

last: de Laat

first: Edwin

last: Cuppen

first: Boudewijn

last: Burgering


title: The loop position of shRNAs and pre-miRNAs is critical for the accuracy of Dicer processing in vivo

status: Public on Dec 25 2012

city: Palo Alto

first: shuo

last: gu

state: CA

address: 269 Campus Drive

department: Pediatrics

institute: Stanford University

summary: Short-hairpin RNA (shRNA)-induced RNAi is used for biological discovery and therapeutics. Dicer, whose normal role is to liberate endogenous miRNAs from their precursors, processes shRNAs into different biologically active siRNAs, affecting their efficacy and potential for off-targeting. We found that in cells, Dicer induced imprecise cleavage events around the expected sites based on the previously described 5'/3'-counting rules. These promiscuous non-canonical cleavages were abrogated when the cleavage site was positioned 2 nt from a bulge or loop. Interestingly, we observed that the ~1/3 of mammalian endogenous pre-miRNAs that contained such structures were more precisely processed by Dicer. Implementing a new "loop-counting rule", we designed potent anti-HCV shRNAs with substantially reduced off-target effects. Our results suggest that Dicer recognizes the loop/bulge structure in addition to the ends of shRNAs/pre-miRNAs for accurate processing. This has important implications for both miRNA processing and future design of shRNAs for RNAi-based genetic screens and therapies.

overall_design: Various shRNAs were expressed in Cell and processed by the RNase III enzyme Dicer.  The profiles of the siRNA products were generated by deep sequencing with or without the Ago2-IP.

first: Shuo

last: Gu

last: Kay


title: Transcriptome sequencing of Capra hircus for different tissues.

status: Public on Dec 23 2012

city: Shenzhen

first: Zhijun

last: Zheng

address: #11 Building 2/F│Beishan Industrial Zone│Yantian District

institute: BGI

summary:
The domestic goat, Capra hircus (2n=60), is one of the most important domestic livestock species in the world. Here we report its high quality reference genome generated by combining Illumina short reads sequencing and a new automated and high throughput whole genome mapping system based on the optical mapping technology which was used to generate extremely long super-scaffolds. The N50 size of contigs, scaffolds, and super-scaffolds for the sequence assembly reported herein are 18.7 kb, 3.06 Mb, and 18.2 Mb, respectively. Almost 95% of the supper-scaffolds are anchored on chromosomes based on conserved syntenic information with cattle. The assembly is strongly supported by the RH map of goat chromosome 1. We annotated 22,175 protein-coding genes, most of which are recovered by RNA-seq data of ten tissues. Rapidly evolving genes and gene families are enriched in metabolism and immune systems, consistent with the fact that the goat is one of the most adaptable and geographically widespread livestock species. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat revealed 51 genes that were significantly differentially expressed between the two types of hair follicles. This study not only provides a high quality reference genome for an important livestock species, but also shows that the new automated optical mapping technology can be used in a de novo assembly of large genomes.

We have sequenced a 3-year-old female Yunnan black goat and constructed a reference sequence for this breed. In order to improve quality of gene models, RNA samples of ten tissues(Bladder, Brain, Heart, Kidney, Liver, Lung, Lymph, Muscle, Ovarian, Spleen) were extracted from the same goat which was sequenced. To investigate the genic basis underlying the development of cashmere fibers using the goat reference genome assembly and annotated genes, we extracted RNA samples of primary hair follicle and secondary hair follicle from three Inner Mongolia cashmere goats and conducted transcriptome sequencing and DEG analysis.

Corresponding whole genome sequencing is available in NCBI BioProject PRJNA158393.

overall_design:
We have sequenced a 3-year-old female Yunnan black goat and constructed a reference sequence for this breed. In order to improve quality of gene models, RNA samples of ten tissues (Bladder, Brain, Heart, Kidney, Liver, Lung, Lymph, Muscle, Ovarian, Spleen) were extracted from the same goat which was sequenced. To investigate the genic basis underlying the development of cashmere fibers using the goat reference genome assembly and annotated genes, we extracted RNA samples of primary hair follicle and secondary hair follicle from three Inner Mongolia cashmere goats and conducted transcriptome sequencing and DGE analysis.

Ten RNA pools were created corresponding to different tissues of a 3-year-old female Yunnan Black goat. Secondary hair folicle and primary hair folicle were compared with 3 dulicated sample paires from three different Inner Mongolia cashmere goat individules.

This submission represents RNA-Seq component of study.

first: Wen

last: Wang

first: Yang

last: Dong

first: Xun

last: Xu

first: Min

last: Xie


title: ZNF335 regulates stem cell proliferation and neuronal differentiation via Trithorax complex and REST/NRSF

first: Christopher

last: Walsh

state: MA


title: DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation (RNA-seq)

status: Public on Dec 29 2012

city: La Jolla

first: MICHAEL

last: ROSENFELD

address: 9500 Gilman Drive

institute: HHMI/UCSD

summary: Although liganded nuclear receptors have been established to regulate RNA polymerase II (Pol II)-dependent transcription units, their role in regulating Pol III-transcribed DNA repeats remains largely unknown. Here we report that ~2-3% of the ~100,000-200,000 total human DR2 Alu repeats located in proximity to activated Pol II transcription units are activated by the retinoic acid receptor (RAR) in human embryonic stem cells to generate Pol III-dependent RNAs. These transcripts are processed, initially in a DICER-dependent fashion, into small RNAs (~28-65 nt) referred to as repeat-induced RNAs that cause the degradation of a subset of crucial stem-cell mRNAs, including Nanog mRNA, which modulate exit from the proliferative stem-cell state. This regulation requires AGO3-dependent accumulation of processed DR2 Alu transcripts and the subsequent recruitment of AGO3-associated decapping complexes to the target mRNA. In this way, the RAR-dependent and Pol III-dependent DR2 Alu transcriptional events in stem cells functionally complement the Pol II-dependent neuronal transcriptional program.

overall_design: RNA-sequencing of polyA selected RNA molecules in NTera2/D1 cells and Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq).

first: Qidong

last: Hu

first: Bogdan

last: Tanasa

first: Michele

last: Trabucchi

first: Wenbo

last: Li

first: Jie

last: Zhang

first: Kenneth

middle: H

last: Ohgi

middle: K

last: Glass

first: David

last: Rose

first: Michael

last: Rosenfeld


title: C. elegans piRNAs are processed from capped-small RNAs transcribed at promoters throughout the genome

status: Public on Dec 22 2012

city: Worcester

first: Craig

last: Mello

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Piwi-interacting (pi) RNAs are a class of germline-expressed small RNAs that have been linked to epigenetic programming in metazoa. C. elegans piRNAs known as 21U-RNAs are defined by more than 15,000 genome-encoded species. To explore the origin of 21U-RNAs we employed methods to enrich the 5' ends of Pol II transcripts. We show that a species of capped-short (cs) RNA is frequently expressed bidirectionally at Pol II loci in C. elegans. Interestingly, at annotated 21U-RNA loci, csRNAs originate precisely 2 nt upstream of the mature piRNA species suggesting that csRNAs are piRNA precursors. In addition, we show that csRNAs associated with TS sites genome-wide define a previously overlooked class of 21U-RNA loci, and nearly double the number of piRNA species available for genome surveillance. Our methods should be of general utility in TS site identification and 5' anchored RNA-expression profiling.

sample_organism:
Caenorhabditis elegans
Mus musculus

platform_organism:
Caenorhabditis elegans
Mus musculus

overall_design: Identification of capped RNA including capped small RNA and long capped RNA in C. elegans. The mouse data are independent data to test the CapSeq sequencing protocol.

first: Heng-Chi

last: Lee

first: Daniel

last: Chaves

first: Darryl

last: Conte


title: To detect CENP-A enrichment on Chromosome 1,5 &7 in C. albicans centromere deleted clones

status: Public on Dec 21 2012

city: Bangalore

first: Kaustuv

last: Sanyal

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

summary: ChIP Seq revealed presence of unique CEN-proximal neocentromere peaks in CEN deleted clones. Using 10 million reads generated from ChIP-seq for each sample,  chromosome wide maps for CENP-A  enrichment were generated .

overall_design: Examination of CENP-A enrichment in Input/IP  samples of various CEN deleted C. albicans clones

first: Jitendra

last: Thakur