title: Selective suppression of endothelial cytokine production by progesterone receptor [RNA-seq]

city: Los Angeles

first: Lauren

last: Goddard

address: 621 Charles E. Young Dr. S.

department: Molecular, Cell, and Developmental Biology

institute: University of California-Los Angeles

summary: Steroid hormones are well-recognized suppressors of the inflammatory response, however, their cell- and tissue-specific effects in the regulation of inflammation are far less understood, particularly for the sex-related steroids. To determine the contribution of progesterone in the endothelium, we have characterized and validated an in vitro culture system in which human umbilical vein endothelial cells constitutively express human progesterone receptor (PR). Using next generation RNA-sequencing, we identified a selective group of cytokines that are suppressed by progesterone both under physiological conditions and during pathological activation by lipopolysaccharide. In particular, IL-6, IL-8, CXCL2/3, and CXCL1 were found to be direct targets of PR, as determined by ChIP-sequencing. Regulation of these cytokines by progesterone was also confirmed by bead-based multiplex cytokine assays and quantitative PCR. These findings provide a novel role for PR in the direct regulation of cytokine levels secreted by the endothelium. They also suggest that progesterone-PR signaling in the endothelium directly impacts leukocyte trafficking in PR-expressing tissues

overall_design:
Examination of PR target genes in human umbilical vein endothelial cells (HUVECs) using RNA-seq
PR infected only (PR);
PR infected followed by ligand treatment (PR+P);
PR infected followed by 4h LPS treatment (PR+LPs_4h);
PR infected followed by 8h LPS treatment (PR+LPs_8h);
PR infected followed by 4h LPS and progesterone treatment (PR+LPS+P_4h);
PR infected followed by 8h LPS and progesterone treatment (PR+LPS+P_8h)

first: Amy

last: Ton

first: Tonis

last: Org

first: Hanna

last: Mikkola

first: M

middle: L

last: Iruela-Arispe


title: Tissue-specific RNA-seq in human evoked inflammation identifies novel blood and adipose lincRNA signatures of cardio-metabolic diseases

status: Public on Jan 02 2014

city: New York

first: Chenyi

last: Xue

state: NY

country: USA

institute: Columbia University

type: Non-coding RNA profiling by high throughput sequencing

summary: Inappropriate or sustained activation of innate immunity is a pathologic feature of several common cardio-metabolic disorders. Little is known, however, about transcriptomic modulation during inflammatory stress in disease-relevant human tissues. We applied deep RNA sequencing (RNA-seq) during low-dose experimental endotoxemia (LPS) in healthy humans to interrogate, in an unbiased manner, inflammatory tissue-level transcriptome responses of relevance to complex cardio-metabolic diseases. We utilized adipose and blood samples from three individuals who underwent a standardized inpatient endotoxemia protocol. Our comprehensive analysis revealed substantial, highly tissue- and subject-specific LPS-modulated changes in the expression of protein-coding genes and linc-RNAs as well as alternative splicing (AS). We also confirmed adipocytes and macrophages as potential cell sources of selective LPS-modulated linc-RNAs and AS events. Finally, we defined disease relevance of a subset of findings in obese adipose tissue and through interrogation of overlap with genome-wide association study loci for cardio-metabolic traits. Our findings provide novel insights into tissue-level genomic regulation, not detectable through analysis of DNA variations alone, of relevance to common cardio-metabolic diseases.

overall_design: Using RNA-seq data to study LPS-modulated changes in lincRNA expression for adipose and blood of a healthy individual.

first: Yichuan

last: Liu

first: Jane

last: Ferguson

first: Rachel

last: Ballantyne

first: Ian

last: Silverman

first: Jacklyn

last: Serfecz

first: Sager

last: Gosai

first: Brian

last: Gregory

first: Mingyao

last: Li

first: Muredach

last: Reilly


title: Selective suppression of endothelial cytokine production by progesterone receptor

status: Public on Jan 01 2014

state: CA

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Long-range bidirectional transcription is a general feature of developmental gene promoters in mammals (ChIP-Seq 2)

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

summary: Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand-specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristics of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription.

overall_design: Runx1 ChIP-seq in CD4+,CD8+ double-positive (DP) mice thymocytes using single-end sequencing on AB SOLiD Systems.

first: Cyrille

last: Lepoivre

first: Mohamed

last: Belhocine

first: Aurélie

first: Aurélien

last: Griffon

first: Marc

middle: A

last: Garibal

first: Joaquin

last: Zacarias-Cabeza

first: Frederick

last: Koch

first: Romain

last: Fenouil

first: Beatrice

last: Loriod

first: Hélène

last: Holota

first: Jean

last: Imbert

first: Marta

last: Gut

first: Ivo

middle: C

last: Andrau

first: Denis

last: Puthier

first: Salvatore

last: Spicuglia


title: Long-range bidirectional transcription is a general feature of developmental gene promoters in mammals


title: Long-range bidirectional transcription is a general feature of developmental gene promoters in mammals (ChIP-Seq 1)

summary: Recent studies have revealed a myriad of non-coding transcripts in different organisms. For instances, the presence of short bidirectional transcripts is a hallmark of active promoters in mammals, while upstream non-coding transcripts can be detected at most expressed genes in conditions where the RNA degradation machinery is inhibited. Here, we used RNA-seq with very high sequencing depth to characterize strand specific transcripts from primary mouse tissues. We found that a substantial fraction of gene promoters sustain expression of long non-coding antisense transcripts. These transcripts have an average size of 6 kb, have features of mature transcripts, but remain associated with the chromatin. We named this new class of non-coding RNAs Long Upstream Antisense Transcripts (LUAT). Strikingly, the LUAT and coding gene pairs are usually co-regulated, with the associated genes often/generally coding for transcriptional regulators functioning during development and cell differentiation. Indeed, these bidirectional promoters share several characteristic of developmental gene promoters, including large CpG islands and high degree of conservation, and display symetrical GC skews. Finally, we found that bidirectional promoters have enlarged platforms of Pol II initiation, associated with an intensified rate of early transcriptional elongation. We concluded that promoters of developmental regulators are characterized by a specialized mechanism of Pol II transcription, whereby Pol II poising is directly coupled to relaxed bidirectional transcription.

overall_design: H3K79me2 ChIP in CD4+,CD8+ double positive thymocytes from C57BL/6 mice was studied, using  Illumina sequencer

first: Marc-Antoine

first: Jean-Christophe


title: Investigation of breast cancer-associated mutations in RND1 gene

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

type: Genome variation profiling by high throughput sequencing

summary: We identified the Rho family GTPase Rnd1 as a candidate breast tumor suppressor by using bioinformatics analysis in conjunction with iRNA silencing. Upon silencing of Rnd1, normal mammary epithelial cells underwent a complete EMT but eventually became senescent, suggesting that they had experienced an oncogenic insult. Expression of c-Myc rescued the Rnd1-depleted cells from senescence by suppressing p27Kip and it enabled their neoplastic conversion. The resulting cells were able to grow in soft agar and to form invasive, multi-acinar structures in 3D Matrigel. Silencing of Rnd1 promoted disruption of epithelial adhesion and polarity in xenograft models. In contrast, expression of Rnd1 inhibited tumor development. Mechanistic studies revealed that Rnd1 suppresses Ras signaling and prevents the EMT by activating the Ras-GAP domain of Plexin B1. Finally, analysis of clinical samples and cancer cell lines provided evidence that gene deletion, epigenetic silencing, and missense mutations contribute to inactivate RND1 in a subset of human breast cancers. These results indicate that Rnd1 promotes epithelial adhesion and polarity and suppresses oncogenesis by restraining unscheduled activation of Ras.

overall_design:
genomic DNA from 96 breast cancer tissues and 8 normal mammary tissues were extracted and subjected to SOLID deep sequencing for exons of the RND1 gene to identify tumor-associated mutations with the amino acid exchanges
There were two separate SOLID runs (0136 and 0270), on the same 96 tumors. The pools are indicated by "A1", "A2", "B1", etc.

first: Masahiro

last: Ohara

first: Morihito

last: Okada

first: Adriana

last: Heguy

first: Olg

last: a Aminova

first: Agnese

last: Viale

first: Nick

last: Socci

first: Tomoyo

first: Filippo

last: Giancotti


title: Physiological Vascular Permeability Requires Induction of Endothelial NR4A1 by Progesterone Receptor

first: Lauren

last: Goddard


title: Long-range bidirectional transcription is a general feature of developmental gene promoters in mammals (RNA-Seq 2)

first: Aurelie

last: Bergon

overall_design: Expression of noncoding RNA transcripts in CD4-,CD8- double negative thymocytes from Rag2-/- mice was studied by strand-specific, ribosomal-depleted RNA-seq experiment, using  Illumina sequencer

first: Cyrille

last: Lepoivre

first: Mohamed

last: Belhocine

first: Aurélie

first: Aurélien

last: Griffon

last: Garibal

first: Joaquin

last: Zacarias-Cabeza

first: Frederick

last: Koch

first: Romain

last: Fenouil

first: Beatrice

first: Hélène

first: Jean


title: Physiological Vascular Permeability Requires Induction of Endothelial NR4A1 by Progesterone Receptor [RNA-Seq]

summary: Vascular permeability is frequently associated with inflammation and it is triggered by chemokines and by a cohort of secreted permeability factors, such as VEGF.  In contrast, here we showed that the physiological vascular permeability that precedes implantation is directly controlled by progesterone receptor (PR) and it is independent of VEGF. Both global and endothelial-specific deletion of PR block physiological vascular permeability in the uterus while misexpression of PR in the endothelium of other organs results in ectopic vascular leakage. Integration of genome-wide transcriptional profile of endothelium and ChIP-sequencing revealed that PR induces a NR4A1 (Nur77/TR3) specific transcriptional program that broadly regulates vascular permeability in response to progesterone.  This program triggers concurrent suppression of several junctional proteins and leads to an effective, timely and venule-specific regulation of vascular barrier function. Silencing NR4A1 blocks PR-mediated permeability responses indicating a direct link between PR and NR4A1. These results reveal a previously unknown function for progesterone receptor on endothelial cell biology with consequences to physiological vascular permeability and implications to the clinical use of progestins and anti-progestins on blood vessel integrity.

overall_design: Examination of PR target genes in human umbilical vein endothelial cells (HUVECs) using RNA-seq (PR infected only -PR only and PR infected followed by ligand treatment-PR+P)

middle: M

first: Thomas

middle: J

last: Murphy

first: Tonis

last: Org

first: Josephine

last: Enciso

first: Minako

middle: K

last: Hashimoto-Partyka

first: Carmen

last: Warren

last: Sanchez

first: Nancy

last: Allen

first: Peter

last: Tontonoz

first: Hanna

last: Mikkola

first: M

last: Iruela-Arispe


title: Long-range bidirectional transcription is a general feature of developmental gene promoters in mammals (RNA-Seq 1)

first: Aurelie

last: Bergon

overall_design: Expression of noncoding RNA transcripts in CD4-,CD8- double negative thymocytes from Rag2-/- mice was studied by strand-specific, ribosomal-depleted RNA-seq experiment, using  paired-end sequencing on AB SOLiD System 4.0

first: Cyrille

last: Lepoivre

first: Mohamed

first: Aurélie

first: Marc-Antoine

last: Loriod

last: Holota

last: Imbert

first: Marta

last: Gut

first: Ivo

first: Jean-Christophe

last: Andrau

first: Denis

last: Puthier

first: Salvatore

last: Spicuglia


title: Physiological Vascular Permeability Requires Induction of Endothelial NR4A1 by Progesterone Receptor [ChIP-Seq]

first: Lauren

last: Goddard

overall_design: Examination of PR binding sites in HUVEC cells using ChIP-seq (non-infected-negative control, PR infected followed by ligand treatment-PR+P or vehicle PR)

first: Thomas

last: Murphy

first: Tonis

last: Org

first: Josephine

last: Enciso


title: Identification of miRNAs and Their Target Genes in Peach (Prunus persica L.) Using High-Throughput Sequencing and Degradome Analysis

city: Nanjing

first: Zhihong

last: Gao

state: Jiangsu

address: No. 1, Weigang

department: College of Horticulture

country: China

institute: Nanjing Agricultural University

summary: MicroRNAs play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. We identified 117 conserved miRNAs and 186 novel miRNA candidates in peach by deep sequencing and 19 conserved miRNAs and 13 novel miRNAs were further evaluated for their expression by RT-qPCR. The number of gene targets that were identified for 26 conserved miRNA families and 38 novel miRNA candidates, were 172 and 87, respectively. Some of the identified miRNA targets were abundantly represented as conserved miRNA targets in plant. However, some of them were first identified and showed important roles in peach development. Our study provides information concerning the regulatory network of miRNAs in peach and advances our understanding of miRNA functions during tissue development.

overall_design: To identify more conserved and peach-speciﬁc miRNAs and their target genes and to understand further the mechanism of miRNA-regulated target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three different tissues for deep sequencing.

first: Xiaoyan

last: Luo

first: Ting

last: Shi

first: Zongming

last: Cheng

first: Zhen

last: Zhang

first: Zhaojun

last: Ni


title: Genome-wide ATAF1 binding sites in Arabidopsis thaliana

city: Copenhagen

first: Michael

middle: Krogh

last: Jensen

state: N

address: Ole Maaloesvej 5

department: Biology

country: Denmark

institute: University of Copenhagen

summary: Using a transgenic line expressing HA-tagged ATAF1 uncovered >400 ChIP-seq peaks in ATAF1-HA plants compared to Col-0 wild-type plants. Only a small sub-set of the candidate peaks could be verified using ChIP-qpcr or EMSA. Among the verified peaks we uncovered the key ABA biosynthetic gene NCED3 as a target of ATAF1

overall_design: ChIP was performed using anti-HA antibodies on wild-type Col-0 plants and plants expressing HA-tagged ATAF1


title: A differential polarization of Th1, Th2 and Treg immune response determines resistance and susceptibility of sheep breeds to Teladorsagia circumcincta infection

city: Dublin

first: Albin

middle: Mostaque

last: Ahmed

address: Veterinary Science Centre, UCD, Belfield

department: Veterinary Medicines

country: Ireland

institute: University College Dublin

summary: Gastrointestinal nematode (GIN) is a major economic and health concern is sheep farming. Sheep breeds such as Texel are relatively resistant to GIN than the Suffolk. With the objective to understand the underlying genetic mechanism of resistance and susceptibility at the transcriptomic level, two groups of animal from both the breed were artificially (orally) infected with 30,000 L3 larvae of prominent GIN Teladorsagia circumcincta. Subgroups of animals from each breed were slaughtered on day 0, 3, 7, 14 and 21 of post infection (p.i.). Transcriptomic profiling of abomasal lymph node was performed using RNA-seq. The perturbations in gene expression profiles in both the breeds were evident and Texel showed a more tightly regulated immune response than the Suffolk.  The number of differentially expressed (DE) genes between the breeds was highest (437) on un-infected control (day 0) and lowest (173) on day 7 p.i.. Pathway analysis of DE genes identified 3 significant pathways, which involved only more highly expressed genes of Suffolk breed on day 0 and only more highly expressed genes of Texel (with one exception) on day 7 p.i.. The Th1, Th2 and Treg response was evident in response to GIN in Texel and was synchronized, while in Suffolk Th1 response was reduced after infection and pronounced Th2 and Treg was not evident. The study suggests maximum level of transcriptional activity in both breeds on day 7 p.i. and there was a shift of transcriptional activity from Suffolk on day 0 to Texel on day 7 p.i.. Suffolk had a reduced Th1 response with less pronounced Th2 and Treg immune response, while Texel had an active and synchronized Th1/Th2/Treg immune response in response to GIN infection.

overall_design: Abomasal lymph node tissue was taken from control (n=10) and experimentally infected (with T. circumcincta) lambs (n=36) from Texel and Suffolk breed on day 0, 3, 7, 14 and 21 post infection.

first: Torres

last: Sweeney

first: Barbara

last: Good

first: James

middle: P

last: Hanrahan

first: Orla

last: Keane

first: Paul

last: McGettigan

first: Bojlul

last: Bahar

first: Jai

last: Mehta

first: Amanda

last: Lohan

first: John

last: Browne

first: Bryan

last: Markey


title: High-throughput Illumina sequencing of bisulfite transformed genomic DNA from Arabidopsis thaliana wild-type, msh1 mutant and MSH1-epiF3 lines

city: Lincoln

first: Ying-Zhi

last: Xu

state: NE

address: 1901 Vine St.

department: Center for Plant Science Innovation

institute: University of Nebraska

type: Methylation profiling by high throughput sequencing

summary: Arabidopsis msh1 mutants display developmental reprogramming (dr) phenotypes, include reduction in growth, enhanced branching, and delayed maturation and flowering time. MSH1-epi lines were derived by crossing MSH-dr lines with Col-0 wild type, followed by selection for homozygous MSH1/MSH1 F2 plants and serial self-pollination. MSH1-epiF3 plants displayed phenotypic variation in plant growth, showing enhanced growth, larger rosette diameter, thicker floral stems and earlier flowering time. We carried bisulfite sequencing and uncover the methylome changes accompany the heritable MSH1-epi phenotypes that condition dramatic variation in plant growth.

overall_design: 3 samples examined: wild type, Msh1-epiF3, msh1 mutant

first: Sally

last: Mackenzie


title: RNA-Seq analysis of neurons derived from induced pluripotent stem cells reprogrammed from dental pulp

city: Bronx

first: Herb

last: Lachman

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

summary: In this study, we investigated its suitability for disease modeling by carrying out gene expression profiling, using RNA-seq, on neurons derived from iPSCs made from dental pulp extracted from deciduous teeth (T-iPSCs) and fibroblasts (F-iPSCs).

overall_design: Comparison of expression profiles of iPSC derived from dental pulp and skin-fibroblast

first: Herbert

first: Deyou

last: Zheng


title: MBD-Seq of the V/SVZ and the CP at E16

city: Tokyo

first: Itsuki

last: Ajioka

address: 1-5-45 Yushima, Bunkyo-ku

department: Center for Brain Integration Research

country: Japan

institute: Tokyo Medical and Dental University

summary: Cell differentiation and proliferation are mutually exclusive. Although differentiating neurons are recognized as post-mitotic non-dividing cells, some Rb- and Rb family (Rb, p107, and p130)-deficient differentiating neurons proliferate and form tumor. Here, we found that the acute inactivation of all Rb family in differentiating cortical excitatory neurons caused radial migration defect and S-phase progression but not cell division, whereas that in cortical progenitors caused the cell division of the differentiating neurons generated from Rb –/–; p107 –/–; p130 –/– (Rb-TKO) progenitors. Genome-wide DNA methylation analysis revealed that proximal promoters tended to become methylated during differentiation in vivo. DNA demethylation by DNA methyltransferase inhibitor allowed the acutely inactivated Rb-TKO differentiating neurons to undergo G2/M-phase progression. Our finding illustrate that cortical excitatory neurons epigenetically lose their proliferative potency after neurogenesis.

overall_design: 1 sample of the V/SVZ tissue and the CP tissue

first: Mio

last: Oshikawa


title: Deciphering the genetics of mammalian limb growth

city: Edinburgh

first: Pedro

last: Coutinho

address: western general hospital, crewe rd

department: MRC IGMM

country: United Kingdom

institute: University of Edinburgh

summary:
We have used DGE-SAGE, a digital transcriptomics tool, to determine the expression profile of E14.5 mouse forelimbs and hindlimbs. The forelimb, hindlimb developmental lag combined with the analysis of these datasets allow us a better insight into the dynamics of the limb growth genetic network, in particular the characterisation of genes that are differentially expressed and are putative modulators of limb growth and or candidates for limb malformation syndromes.
Conclusions: The datasets and results presented in this study allow us to extend the current knowledge of the limb development and constitute an extremely relevant resource for research into the genetics of organ growth and thus ontogenesis.

overall_design: DGE-SAGE expression profiles for E14.5 mouse forelimb and hindlimb

first: Richard

last: Baldock


title: Transcriptome Sequencing of the RamA Regulon

city: Belfast

first: Amy Jayne

last: McKnight

address: Lisburn Road

institute: Queen's University of Belfast

summary: We report the use of Illumina based transcriptome sequencing to determine the RamA Regulon in K. pneumoniae. This study has identified both genes and small RNAs that are upregulated in the presence of RamA.

overall_design: Comparison of genetically modified mutants; TS67 (delta ramA) and TS68 (delta ramR, ramA overexpresser)

first: A

first: Thamarai

last: Schneiders


title: V/SVZ (ventricular/subventricular zone) tissue and CP (cortical plate) tissue at E16


title: Examining the genetic basis for visceral leishmaniasis disease: Comparison of distinct Leishmania donovani isolates that cause cutaneous and visceral leishmaniasis in Sri Lanka

status: Public on Dec 31 2013

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

summary: Among the most central questions in Leishmania research is why some species remain in the skin dermis at the site of infection by the sand fly vector whereas other species migrate to visceral organs where they cause fatal visceral leishmaniasis. Although L. donovani is the species typically responsible for visceral leishmaniasis, an atypical L. donovani strain is the etiologic agent for cutaneous leishmaniasis in Sri Lanka.  To identify molecular determinants for visceral disease, we have analysed the phenotype and genotype of two L. donovani clinical isolates from Sri Lanka where one isolate was derived from a cutaneous leishmaniasis patient (CL) and the other from a visceral leishmaniasis patient (VL). These isolates cause dramatically different pathology when introduced into mice; notably the CL isolate has lost the ability to survive in visceral organs while the VL isolate was highly virulent in visceral organs of BALB/c mice. Whole genome sequencing of the CL and VL isolates revealed that these genomes were very similar as there were no gene deletions and few individual gene amplifications.  Indels resulting in frame shifts and loss/gain of stop codons resulted in 13 distinct pseudogenes present in each of the CL and VL isolates. There were 154 non-synonymous SNPs specific to the CL isolate and 193 non-synonymous SNPs specific to the VL isolate. Genome wide gene expression analysis revealed several transcript level differences, including the A2 virulence gene resulting in higher expression of A2 proteins in the VL isolate than in the CL isolate.  Genotypic variations relevant to pathology and tropism in Leishmania can be interrogated by reverse genetics. Experimentally increasing A2 expression in the CL isolate through gene transfer significantly increased it’s ability to survive in the spleen of BALB/c mice and conversely, down-regulating A2 expression in the VL isolate abrogated attenuated its survival in BALB/c mice. These observations reveal that there are relatively few genetic differences between the CL and VL isolates apart from the A2 genes, but collectively these have profound effects on human disease and experimentally infected mice.

overall_design: 6 Samples in total, 3 each from VL and CL causing isolates were analyzed by Splice Leader RNASeq. These three samples from each of the isolates were grown to form one of the following three lifestages, Promastigotes, Macrophage derived Amastigotes, Axenic Amastigotes.

first: Wen-Wei

last: Zhang

first: Laura-Isobel

last: McCall

first: Andrew

last: Haydock

first: Shalindra

last: Ranasinghe

first: Renu

last: Wickremasinghe

first: Peter

last: Myler

first: Greg

last: Matlashewski


title: Distinct properties of cell type-specific and shared transcription factor binding sites

city: Huntsville

first: Jason

last: Gertz

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

summary: Most human transcription factors bind a small subset of potential genomic sites and often use different subsets in different cell types.  To identify mechanisms that govern cell type-specific transcription factor binding, we used an integrative approach to study estrogen receptor α (ER).  We found that ER exhibits two distinct modes of binding.  Shared sites, bound in multiple cell types, are characterized by high affinity estrogen response elements (EREs), inaccessible chromatin and a lack of DNA methylation, while cell-specific sites are characterized by a lack of EREs, co-occurrence with other transcription factors and cell type-specific chromatin accessibility and DNA methylation.  These observations enabled accurate quantitative models of ER binding that suggest tethering of ER to one-third of cell-specific sites.  The distinct properties of cell-specific binding were also observed with glucocorticoid receptor and for ER in primary mouse tissues, representing an elegant genomic encoding scheme for generating cell type-specific gene regulation.

overall_design: ChIP-seq of transcription factors in mouse tissues

last: Myers


title: EZH2 controls mammary differentiation independently of its methyltransferase activity through controlling genomic STAT5 access

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

summary: Mammary development is characterized by the proliferation and progressive differentiation of alveolar epithelium during pregnancy, culminating in lactation. These processes are largely controlled by hormones through transcription factors. We now explore the contributions of histone methyltransferases, which establish H3K27me3 marks, in the temporally-regulated differentiation of mammary epithelium. Loss of EZH2, but not EZH1, resulted in precocious mammary differentiation, which was facilitated by STAT5 binding to specific target genes and their activation. Mammary stem cells were not compromised in the absence of EZH2. Genome-wide H3K27me3 patterns remained intact in the absence of EZH2. Mammary-specific loci were devoid of H3K27me3 marks in mammary progenitor and mature cells, suggesting no regulatory role for this repressive mark. Lastly, the combined absence of EZH1 and EZH2 inhibited the formation of alveoli. Taken together, EZH2 controls temporally-restricted differentiation of mammary epithelium through H3K27me3-independent mechanisms.

overall_design:
mRNA-seq and ChIP-seq in MMTV-Cre (Control), E1-/- (E1KO), E1+/-;E2f/f;control (E1+/-E2KO) and Ezh2f/f;control (E2KO) mammary gland tissues or MECs (purified mammary epithelial cells).
H3K27me3 and STAT5 ChIP-seqs in mammary tissues at p13; H3K4me3 ChIP-seq in MECs (mammary epithelial cells) at p13; RNA-seqs at mature virgin (with/without prolactin injection), p13 and p18 mammary tissues.

first: Kyung

middle: H

last: Yoo

first: Tim

last: Hensel

first: Gertraud

middle: W

last: Robinson

first: Lothar

last: Hennighausen


title: Nucleosome Positioning and Histone Modifications Define Relationships between Regulatory Elements and Nearby Gene Expression in Breast Epithelial Cells

first: Suhn

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: We report the application of FAIRE seq and ChIP seq in breast cancer cell line, MDAMB231.

overall_design: Examination of FAIRE and ChIP assay in MDAMB231

first: S

first: G

last: Coetzee


title: Global miRNA expression status of human hematopoietic stem–progenitor cells modulates myelopoiesis

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: We investigated how suppression of the most upstream microRNA–processing RNase, Drosha, affects the differentiation of human CD34+ hematopoietic stem–progenitor cells (HSPCs). We hypothesized that knock-down of Drosha would alter blood lineage development by modulating the expression of microRNAs. Lentiviral delivery to HSPCs of a short-hairpin targeting Drosha resulted in a viable phenotype with promotion of myeloid, and especially monocytic, maturation and suppression of apoptosis. Our results show that Drosha deficiency triggered a parallel upregulation of components of the RNAi machinery, including DGCR8, Dicer and Ago2. Deep sequencing analyses revealed global miRNA deficiency after Drosha short-hairpin treatment with relative maintenance of mature miR-223 expression. Restoration of miR-223 to normal levels after Drosha knock-down further enhanced monocytic maturation concomitant with the modulation of myeloid transcription factors that promoted monocytic differentiation. Our results support a miRNA accentuation model in which relative enhancement of miR-223 increases levels of PU.1 thereby promoting monocytic differentiation.

overall_design: CD34+ HSPCs were isolated from umbilical cord blood and transduced with an empty lentivector (EV) or a lentivector encoding a short-hairpin RNA targeting the pri-miRNA–processing enzyme, Drosha (shDrosha). EV and shDrosha transduced HSPCs were grown in liquid culture promoting myelopoiesis and sampled on days 0 and 7 for total RNA collection. Total RNA was size fractionated to enrich for the small RNA population and deep sequenced using ABI's SOLiD 4.0 platform.

first: Krist

middle: T

last: Azizian

first: John

last: Rossi


title: Ribosome profiling of wild-type and loc1- cells in S. cerevisiae

city: Boston

first: Suzanne

last: Komili

state: MA

address: 44 Binney St.

institute: Harvard University

summary: We performed ribosome profiling of wild-type and loc1- cells.  We found that approximately 1500 genes exhibit increased translational efficiencies in the absence of Loc1, indicating that Loc1 is required for their translational repression.

overall_design: Examination of translational efficiencies by comparing ribosome footprints and mRNA abundances in two different cell lines.

first: Dale

last: Muzzey

first: Frederick

last: Roth


title: Functional genomic characterization of germinal cells in larval Schistosoma mansoni

city: Urbana

first: James

last: Collins

address: 601 S. Goodwin

institute: University of Illinois at Urbana Champaign

summary:
RNA-seq experiments to identify gene expression changes following miracidia to sporocyst transformation in Schistosoma mansoni.

Schistosomes infect hundreds of millions of people in the developing world. Transmission of these parasites relies on a stem cell-driven, clonal expansion of larvae inside a molluscan intermediate host. How this novel asexual reproductive strategy relates to current models of stem cell maintenance and germline specification is unclear. Here, we demonstrate that this proliferative larval cell population (germinal cells) shares some molecular signatures with stem cells from diverse organisms, in particular neoblasts of planarians (free-living relatives of schistosomes). We identify two distinct germinal cell lineages that differ in their proliferation kinetics and expression of a nanos ortholog. We show that a vasa PL10 homolog is required for proliferation and maintenance of both populations; whereas, argonaute2 and a fibroblast growth factor receptor-encoding gene are required only for nanos-negative cells. Our results suggest that an ancient stem cell-based developmental program may have enabled the evolution of the complex life-cycle of parasitic flatworms.

overall_design: Total RNA was purified from ~10,000 freshly hatched miracidia or sporocysts 48 h post-transformation.

first: Bo

last: Wang

first: Phillip

last: Newmark


title: A haploid gene-trap mutant collection enables functional genetics in human cells

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

summary: Recently, gene-trap mutagenesis in near haploid human cells has been used to disrupt genes and identify novel host-pathogen interactions and elucidate mechanisms of drug action. Building on this technology, we here report the generation of a human gene-trap mutant collection of individual clones, which currently covers over a quarter of the expressed genome.

overall_design: Strand specific RNA-Seq of ribosomal RNA depleted total cellular RNA to measure transcript abundance and to detect fusion transcripts in KBM7 cells at standard culture conditions.

first: T

last: Bürckstümmer

first: F

last: Nijman


title: Evidence for the independent evolution of "functional progesterone withdrawal" in primates and guinea pigs: a comparative transcriptomic study

city: west Haven

first: Mauris

middle: Chukwudebelu

last: Nnamani

state: CT

address: 300 heffernan drive B31-ABC/rm269

department: Systems Biology institute, EEB

institute: Yale University

summary: Cervix remodeling (CRM) is a critical process in preparation for parturition. Early cervix shortening is a powerful clinical predictor of preterm birth, and thus understanding how CRM is regulated is important for the prevention of prematurity. Humans and other primates differ from most other mammals by the maintenance of high levels of systemic progesterone concentrations and thus differ dramatically from most model species. Humans have been hypothesized to perform functional progesterone withdrawal (FPW), but the mechanisms of FPW are not known. Guinea pigs are similar to humans as they also maintain high progesterone concentrations through parturition. The aim of this study is to document gene expression during pregnancy in the guinea pig uterine cervix in order to assess whether guinea pig can be used as a model for human FPW

overall_design: Total RNA obtained from isolated cervical tissues from non-pregnant and two genstation stages (mid-term, and late-term but not in labor).

first: Roberto

last: Romero

first: Günter

last: Wagner

first: Silvia

last: Plaza


title: Genome-wide analyses of Loc1, Puf6, and Khd1

type: Genome binding/occupancy profiling by array

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

overall_design: Refer to individual Series


title: Integrating microRNA and mRNA expression profiling in Symbiodinium, the dinoflagellate symbiont of reef-building corals (mRNA)

city: Kiel

first: Till

last: Bayer

address: Düsternbrookerweg 20

department: Marine Ecology

country: Germany

institute: GEOMAR Helmholtz Centre for Ocean Research

summary: Animal and plant genomes produce numerous small RNAs (smRNAs) regulating gene expression affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3'UTRs of 12,858 mRNAs and 53 plant-like target sites in 51,917 genes. We assembled a transcriptome of 58,649 genes and determined differentially expressed genes (DEGs) between treatments. Heat stress was found to produce a much larger number of DEGs than other treatments. Analysis of DEGs also revealed that minicircle-encoded photosynthesis proteins seem to be common targets of transcriptional regulation. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.

overall_design: Symbiodinium cultures were treated with nine different conditions: cold shock, cold stress, heat stress, heat shock, hyposalinity, hypersalinity, dark stress, dark cycle and control.

first: Sebastian

last: Baumgarten

first: Christian

middle: R

last: Voolstra


title: The RON receptor tyrosine kinase promotes metastasis by triggering epigenetic reprogramming through the thymine glycosylase MBD4 (Bisulfite-Seq)

city: Salt Lake City

first: Stephanie

last: Cunha

state: Utah

address: 2000 Circle of Hope

department: Oncological Science

institute: Huntsman Cancer Institute, University of Utah

summary: Metastasis is the major cause of death in cancer patients, yet the genetic/epigenetic programs that drive metastasis are poorly understood. Here, we report a novel epigenetic reprogramming pathway that is required for breast cancer metastasis. Concerted differential DNA methylation is initiated by activation of the RON receptor tyrosine kinase by its ligand, macrophage stimulating protein (MSP). Through PI3K signaling, RON/MSP promotes expression of the G:T mismatch-specific thymine glycosylase MBD4. RON/MSP and MBD4-dependent aberrant DNA methylation results in misregulation of a specific set of genes. Knockdown of MBD4 reverses methylation at these specific loci, and blocks metastasis. We also show that the MBD4 glycosylase catalytic residue is required for RON/MSP-driven metastasis. Analysis of human breast cancers using a set of specific genes that are regulated by RON/MSP through MBD4-directed aberrant DNA methylation revealed that this epigenetic program is significantly associated with poor clinical outcome. Furthermore, inhibition of Ron kinase activity with a new pharmacological agent prevents activation of the RON/MBD4 pathway and blocks metastasis of patient-derived breast tumor grafts in vivo.

overall_design: Examination of 3 cell types.

first: Alana

last: Welm


title: Integrating microRNA and mRNA expression profiling in Symbiodinium, the dinoflagellate symbiont of reef-building corals (smRNA)


title: Integrating microRNA and mRNA expression profiling in Symbiodinium, the dinoflagellate symbiont of reef-building corals


title: Widespread Transcription beyond mRNA 3’ Ends Yields Abundant Regulatory RNAs

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary: Through RNA-seq analyses of nascent transcripts, we found large numbers of RNA transcripts that extend beyond the 3’ ends of protein-coding genes; we refer to these extended transcripts as geRNAs. These findings demonstrate that transcription of most human protein-coding genes does not terminate within close proximity to poly(A) signals; rather, it terminates at sites far beyond these signals (up to 50 kb).

overall_design: Examination of different RNA species in HelaS3 cells by strand-specific RNA-seq. The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.

middle: S

first: Gong

middle: G

last: Xue

first: Chang-zheng

last: Chen


title: Deep transcriptome sequencing of rhizome and shoot in Sorghum propinquum

city: beijing

first: ting

last: zhang

state: beijing

address: zhongguancun south street 12

institute: Chinese Acadamy of agricultural science

summary: Our study provides the first comprehensive insight into the comparative transcriptome between shoot and rhizome in sorghum propinquum. Using the deep RNA sequencing technique, more than 70% of genes were identified to be expressed. Comparative analysis revealed that a strong difference in gene expression patterns between shoot and rhizome organs, especially a set of organ-specific TF genes and cis-elements were determined, implying a unique complicated molecular network controlling shoot or rhizome growth and development. Furthermore, this data set including a deep coverage of the subterranean rhizome transcriptome, provided essential information for future molecular genetic dissection of rhizome formation.

overall_design: A S. propinquum vegetative clone (unnamed accession) with abundant tillering and strong rhizomes cultured in the greenhouse was used in this experiment. Two organs, shoots and rhizomes, at active tillering stage were collected and flash frozen in liquid nitrogen.

first: Ting

last: Zhang

first: Xiuqin

last: Zhao

first: Wensheng

last: Wang

first: Liyu

first: Xiaoyue

last: Liu

first: Ying

last: Zong

first: Linghua

last: Zhu

first: Daichang

last: Yang

first: Binying

last: Fu

first: Zhikang

last: Li


title: Gene expression data from CD11b-positive myeloid cells infiltrating tumors after local irradiation

first: Haiqing

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

summary: Analysis of global gene expression in myeloid cells infiltrating tumors after irradiation. Cell death induces recruitment of myeloid cells into irradiated tumors thereby stimulating tumor recurrence. Results provide insights into molecular mechanisms regulating tumorigenic functions of myeloid cells in tumors re-growing after radiation therapy.

overall_design: Samples were collected at day 4 from irradiated tumors in WT, TLR9KO and Stat3KO (MxCre/Stat3flox). There were total 11 samples with  3-4 replicates of each sample type.

first: Marcin

last: Kortylewski

first: Chan

last: Gao

first: Anna

last: Kozlowska


title: Tau promotes neurodegeneration through global chromatin relaxation

first: Bess

last: Frost

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Brigham and Women's Hospital

summary: We performed H3K9me2-based ChIP-seq to identify regions of the Drosophila genome that are H3K9me2-depleted due to transgenic neuronal expression of human mutant tau.

overall_design: Examination of H3K9me2 histone methylation in 10 day old control and tau transgenic Drosophila heads.

first: Martin

last: Hemberg

first: Mel

last: Feany


title: Comprehensive investigation of miRNAs enhanced by analysis of sequence variants, expression patterns, AGO loading and target cleavage

city: NEWARK

first: Dong-Hoon

last: Jeong

state: DE

address: 15 Innovation Way

institute: University of Delaware

summary: MicroRNAs (miRNAs) are a class of small RNAs which typically function by guiding cleavage of target messenger RNAs. They have been shown to play major roles in a variety of plant processes including development, and responses to pathogens and environmental stresses. To identify new miRNAs and regulation in Arabidopsis thaliana, 27 small RNA libraries were constructed and sequenced from various tissues, stresses and small RNA biogenesis mutants, resulting in 95 million genome-matched sequences. The use of rdr2 to enrich the miRNA population greatly enhanced this analysis and led to the discovery of 44 new miRNAs arising from both known and new precursors. Parallel Analysis of RNA Ends (PARE) data provide evidence that the majority guide target cleavage. The inclusion of novel stress/tissue conditions, such as submergence-stressed flowers, enabled identification of new stress regulation of both miRNAs and their targets, all of which were validated in wild type plants. By combining small RNA expression analysis with ARGONAUTE (AGO) immunoprecipitation data and global target cleavage data from PARE, a much more complete picture of Arabidopsis miRNAs was obtained. This combinatorial approach led to the discovery of AGO loading and target cleavage biases, which gave important insights into tissue-specific expression patterns, pathogen responses and the role of sequence variation among closely related miRNA family members.

overall_design:
Examination of various tissues, stresses and small RNA biogenesis mutants in Arabidopsis by high-throughput sequencing for small RNA profiling.

We have used AGO-IP and PARE data from the published data, which were downloaded from NCBI GEO with the following accession number.

AGO-IP from GSM253622, GSM707682, GSM642335, GSM642336, GSM512703, GSM512702, GSM707683, GSM707684, GSM707685, GSM149080, GSM253623, GSM304283, GSM642337, GSM642338, GSM253624, GSM415788, GSM707686, GSM707687, GSM707688, GSM707689, GSM415787, GSM149081, GSM253625, GSM415789, GSM415790, GSM304285, GSM415791, GSM415792

PARE sequencing data from xrn4 flowers were obtained from Gene Expression Omnibus with accession number GSM280227.

first: Pamela

last: Green

first: Dong

first: Shawn

last: Thatcher


title: Methylome of CD4+ T cell subsets

city: Braunschweig

first: Stefan

last: Floess

address: Inhoffenstr. 7

department: Experimental Immunology

institute: Helmholtz-Centre for Infection Research

summary: We compared the methylated and non-methylated regions in the genome of ex vivo-isolated naive CD4+ T cells, Th1 cells, Th17 cells and regulatory T cells by methyl-CpG binding domain protein sequencing (MBD-seq). Naive T cells and Th1 cells share more methylated regions than naive T cells and Th17 cells or Th1 and Th17 cells. However, analysis of the non-methylated regions revealed the highest similarity between Th1 and Th17 cells. Another aim was the analysis of the Th17 lineage on the basis of the methylome. We searched for regions absent in the methylome of Th17 but present in naive T cells, Th1 cells and regulatory T cells.  Here, we identified differential methylation in the loci of Il17a, Chn2, Dpp4 and Dclk1.

overall_design: CD4+ T effector cells were prepared ex vivo, stimulated with PMA/Ionomycin, subjected to a comercially available cytokine secretion kit (IL-17A and IFNg), stained by adding fluorescence-labeled antibodies against CD3, CD4 and CD45RB and sorted by flow cytometry. We sorted naive CD4+ T cells (CD3+CD4+CD45RB_high), Th1 cells (CD3+CD4+CD45RB_low_IFNg+IL17A-), Th17 cells (CD3+CD4+CD45RB_low_IFNg-IL17A+) and regulatory T cells (CD3+CD4+CD25++).

first: Bi-Huei


title: Whole RNA-seq on clones of GM12878 lymphoblastoid clones DF1 and DF2

first: Virginia

last: Savova

address: 450 Brookline Ave.

institute: DFCI

summary: Analysis of Allelic bias in clonal lymphoblastoid cells. Abstract: In mammals, numerous autosomal genes are subject to mitotically stable monoallelic expression (MAE), including genes that play critical roles in a variety of human diseases. Due to challenges posed by the clonal nature of MAE, very little is known about its regulation; in particular, no molecular features have been specifically linked to MAE. Here we report an approach that distinguishes MAE genes in human cells with great accuracy: a chromatin signature consisting of chromatin marks associated with active transcription (H3K36me3) and silencing (H3K27me3) simultaneously occurring in the gene body. The MAE signature is present in ~20% of ubiquitously expressed genes and over 30% of tissue-specific genes across cell types. Notably, it is enriched among key developmental genes that have bivalent chromatin structure in pluripotent cells. Our results open a new approach to the study of MAE that is independent of polymorphisms, and suggest that MAE is linked to cell differentiation.

overall_design: Poly A purified total RNA was used for library construction using a method described by Parkhomchuk et. al. NAR 2009. The library was strand-specific but the pipeline for data analysis does not assume the library is strand-specific.

first: Anwesha

last: Nag


title: Whole Genome sequencing of a normal karyotype AML cell line

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

country: Canada

institute: University of Montreal

summary:
Normal Karyotype acute myeloid leukemia (NK-AML) represents approximately 50% of all cases of AML which patients develop.  Most AML cell lines are highly abnormal and therefore not good models for investigating NK-AML biology
a novel AML cell line, CG-SH, was recently estabished and here we characterize the gene expression and mutations present through high-throughput sequencing of RNA and genomic DNA using a HiSeq 2000

overall_design: The overall design of the experiment was to characterize, at single base pair resolution, all of the genetic defects present in a novel normal karyotype cell line, CG-SH

first: Magalie

last: Celton

first: Geraldine

last: Gosse

first: Audrey

last: Forest


title: Expression profiling of Grosmannia clavigera (Gc) under various conditions

city: Vancouver

first: Ye

last: Wang

state: BC

department: Department of Wood Science

institute: University of British Columbia

summary: Gc, a Mountain pine beetle associated pathogen, can survive from highly abundant pine chemicals ( e.g terpenes) and use some unflavored compound’s as carbon source.  using RNA_Seq, we analyzed the transcriptome of Gc when it grew on limonene, mannose  oliver-oil, oleic acid as carbon source, as well as when it survived from high concentration of limonene or heptane. We profiled the expression of some interesting genes ( ABC transporters, P450s)  potentially involved in the tree-pathogen interaction.  An ABC-G group transporter gene (GcABC-G1) was one of the most highly induced genes and characterized as a mono-terpene specific efflux transporter with genetic and molecular tools. RNA- seq also indicated Gc utilize limonene and oleic acid through the same beta-oxidation  pathway. However the degradation of limonene is more complex and multiple pathways contributed to the survival/utilization.

overall_design: mRNA was extracted from Gc mycelium under various conditions and cDNA libraries were generated for pair-end sequencing. The 70-100bp illumina sequence read was mapping to reference genome and RNA-Seq was carried out in CLC genomic work bench.

first: Andrew

last: Mungall

first: Joerg

last: Bohlmann

first: Colette

last: Breuil


title: Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis

city: Beijing

first: Xu

last: Yanhong

address: No. 151,Malianwa North Road, Hai Dian District

institute: The Institute of Medicinal Plant Development

summary: Agarwood is an expensive resinous heartwood derived from the wounded Aquilaria plants. To identify the primary genes that maybe related to agarwood formation, we sequenced 2 cDNA libraries generated from healthy and wounded A. sinensis (Lour.) Gilg. A total of 89,137 unigenes with an average length of 678.65 bp were obtained, and they were annotated in detail at bioinformatics levels. Of those associated with agarwood formation, 30 putatively encoded enzymes in the sesquiterpene biosynthesis pathway, a handful of transcription factors, and protein kinases related to wound signal transduction. Three full-length cDNAs of sesquiterpene synthases (ASS1-3) were cloned and expressed in Escherichia coli, and enzyme assays revealed that they are active enzymes, with the major products being δ-guaiene. A methyl jasmonate (MJ) induction experiment revealed that the expression of ASS was significantly induced by MJ, and the production of sesquiterpenes was elevated accordingly. The expression of some transcription factors and protein kinases, especially MYB4, WRKY4, MPKK2 and MAPK2, was also induced by MJ and coordinated with ASS expression, suggesting they maybe positive regulators of ASS. This study provides extensive transcriptome information for Aquilaria spp. and valuable clues for elucidating the mechanism of wound-induced agarwood sesquiterpenes biosynthesis and their regulation.

overall_design: healthy and wounded stems of three-year-old A. sinensis trees

first: Yanhong

last: Xu

first: Jianhe

last: Wei


title: Study the effect of PARP-14 and its activity on Th2 differentiation

city: Indianapolis

first: Purvi

last: Mehrotra

state: IN

address: 1044 West Walnut Street, R4-279

department: Pediatric Pulmomology

institute: Indiana School of medicine

overall_design: ChIP seq was performed on Th2 differentiated cells isolated from PARP-14 +/+ and PARP-14 -/- treated with or without PJ34

first: Jonathan

last: Riley


title: Chromatin immunoprecipitation of MADS29 to find the cis regulatory regions and targets of this transcription factor

city: New Delhi

first: Sanjay

last: Kapoor

address: Benito Huarez MArg

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi, South Campus

summary: A ChIP-seq analysis revealed 378 targets of OsMADS29, which include genes involved in cytokinin metabolism and auxin signaling, carbohydrate metabolism, transporters and a large number of transcription factors, reflecting on its functional diversity.

overall_design: Chromatin Immunonoprecipitation of MADS29 using antiMADS29 antibody was done using rice 9 DAP seed tissue with total input chromatin and mock immunoprecipitated chromatin as controls

first: Saraswati

last: Nayar


title: New microRNAs in Drosophila

city: Ann Arbor

first: Yang

last: Lyu

state: Michigan

address: 109 Zina Pitcher Place

institute: University of Michigan

summary: MicroRNAs (miRNA) are small, endogenous RNAs that regulate the expression of mRNAs posttranscriptionally. Evolutionarily new miRNAs, like new protein-coding genes, are dominantly expressed in reproductive organs. To dissect the evolutionary dynamics of new miRNAs in Drosophila spp, we sequenced small RNAs from two species of Drosophila, including four samples from reproductive organs and one sample from imaginal discs / CNS. miRNA expression profile shows vast majority of new miRNAs are specifically expressed in testes and/or ovaries, suggesting a role of sexual selection for new miRNA evolution.

sample_organism:
Drosophila pseudoobscura
Drosophila simulans

overall_design: Five small RNA samples, mainly from reproductive organs of D. simulans and D. pseudoobscura were analyzed. The small RNAs were sequenced by Illumina HiSeq 2000. After triming the adapters, the 18-30 nt sequences were extracted for further study.

first: Y

last: Shen

first: H

last: Li

last: Chen

first: L

last: Guo

last: Zhao

first: E

last: Hungate

first: S

last: Shi

first: C

middle: I

last: Wu

first: T

last: Tang


title: Analysis of Fetal liver cells from hnRNP L KO mice

first: Brian

last: Wilhelm

summary: The regulation of post-transcriptional modifications of pre-mRNA by alternative splicing is important for cellular function, development and immunity. To investigate the role of hnRNP L in this process, we have generated conditional hnRNP L knockout mice carrying floxed alleles in order to generate a specific defect in hnRNP L activity.  We have previously characterized defects present in the thymocytes of hnRNP L -/- mice and the current study extends the analysis to examine the effects in fetal liver cells.  Overall these cells exhibit a very different phenotype from thymocytes characterized by significant cell death and a potential block in proliferation.  Further functional studies were performed to better characterize these effects.

overall_design: RNA-seq from fetal liver cells of WT mice compared to KO (hnRNP L) mice

first: Tarik

last: Möröy

first: Marie-Claude

last: Gaudreau


title: A genome-wide and dose-dependent inhibition map of androgen receptor binding by small molecules reveals its regulatory program upon antagonism

city: San Diego

first: Zhou

last: Zhu

address: 10646 Science Center Drive (CB4)

institute: Pfizer Worldwide Research & Development

summary: The androgen receptor plays a critical role throughout the progression of prostate cancer and is an important drug target for this disease.  While chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-Seq) is becoming an essential tool in studying transcription and chromatin modification factors, it has rarely been employed in the context of drug discovery.  Here we report the first publicly available genome-wide and dose-dependent inhibition landscape of AR binding by drug-like small molecules including correlation with binding strength using ChIP-Seq.  Integration of sequence analysis, transcriptome profiling, cell viability assays and in vivo tumor inhibition studies enabled us to establish a direct cistrome-activity relationship for two novel potent AR antagonists.  By selectively occupying the strongest binding sites, AR signaling remains active even when low androgen levels are low, a scenario characteristic of first-line androgen ablation therapy.  Coupled cistrome and transcriptome profiling upon small molecule antagonism led to the identification of not only key direct downstream effectors of AR but also their mode of regulation:  unbiased pathway mapping revealed that AR is a key modulator of steroid metabolism by forming a tightly controlled feedback loop with other nuclear receptor family members.  Furthermore, we found AR has an extensive role in negative gene regulation and estrogen (related) receptor likely mediates its function as a transcriptional repressor.  In conclusion, our study provides a global and dynamic view of AR’s regulatory program upon antagonism, which may serve as a molecular basis for deciphering and developing AR therapeutics.

overall_design:
GSM814034-GSM814044: Compartative study of the mRNA profiles of VCaP cells treated with small molecule inhibitor of AR and those treated with AR-siRNA

GSM817346-GSM817354: Comparative study of AR binding in VCaP cells (1) in the presence and absence of the synthetic AR agonist metribolone (R1881) and (2) in the presence of R1881 and small molecule inhibitors of AR

first: Manli

first: Wenyue

last: Hu

first: Heather

last: Estrella

first: Jon

last: Engebretsen

first: Tim

last: Nichols

first: David

last: Briere

first: Natilie

last: Hosea

first: Gerrit

last: Los

first: Paul

last: Rejto

first: Andrea

last: Fanjul


title: Genome-wide parent-of-origin DNA methylation analysis [Methyl-seq]

status: Public on Dec 28 2013

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

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

department: PEBC

country: Spain

institute: IDIBELL

summary: Genomic imprinting is a form of epigenetic regulation that results in expression of either the maternally or paternally inherited allele of a subset of genes. Imprinted loci contain differentially methylated regions (DMRs) where cytosine methylation marks one of the parental alleles, providing cis-acting regulatory elements that influence the allelic expression of surrounding genes, however to date the total number of imprinted loci within the human genome is unknown. To characterize known imprinted DMRS and identify novel imprinted loci we have performed whole-genome bisulphite sequencing and high-resolution DNA methylation array analysis of healthy tissues.

overall_design: Sequencing of bisulfite converted DNA analysis of normal brain (white matter), liver and term placenta tissue

last: Monk


title: NOTCH1/RBPJ complexes drive target gene expression through dynamic interactions with super-enhancers

status: Public on Dec 27 2013

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

summary: The main oncogenic driver in T-lymphoblastic leukemia (T-LL) is NOTCH1, which activates genes by forming chromatin-associated Notch transcription complexes. Gamma-secretase (GSI) inhibitor treatment prevents NOTCH1 nuclear localization, but most genes with NOTCH1 binding sites are insensitive to GSI. Here, we demonstrate that fewer than 10% of NOTCH1 binding sites show dynamic changes in NOTCH1 occupancy when T-LL cells are toggled between the Notch-on and –off states with GSI. Dynamic NOTCH1 sites are functional, being highly associated with Notch target genes, are located mainly in distal enhancers, and frequently overlap with RUNX1 binding. In line with the latter association, we show that expression of IL7R, a gene with key roles in normal T cell development and in T-LL, is coordinately regulated by Runx factors and dynamic NOTCH1 binding to distal enhancers. Like IL7R, most Notch target genes and associated dynamic NOTCH1 binding sites co-occupy chromatin domains defined by constitutive binding of CCCTC binding factor (CTCF), which appears to restrict the regulatory potential of dynamic NOTCH1 sites. More remarkably, the majority of dynamic NOTCH1 sites lie in super-enhancers, distal elements with exceptionally broad and high levels of H3K27ac. Changes in Notch occupancy produces dynamic alterations in H3K27ac levels across the entire breadth of super-enhancers and in the promoters of nearby Notch target genes. These findings link regulation of super-enhancer function to NOTCH1, a master regulatory factor and potent oncoprotein in the context of immature T cells, and delineate a generally applicable roadmap for identifying functional Notch sites in cellular genomes.

overall_design: NOTCH1/RBPJ complexes binding dynamics in human T-LL

first: Hongfang

last: Wang

first: Len

last: Taing

first: X

last: Liu

last: Aster


title: Genome-wide parent-of-origin DNA methylation analysis

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery

city: Cambridge

first: Sebastian

last: Hoersch

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

summary: The identification of cancer drivers is a major goal of current cancer research. Finding driver genes within large chromosomal events is especially challenging because such alterations encompass many genes. Previously, we demonstrated that zebrafish malignant peripheral nerve sheath tumors (MPNSTs) are highly aneuploid, much like human tumors. In this study, we examined 147 zebrafish MPNSTs by massively parallel sequencing and identified both large and focal copy number alterations (CNAs). Given the low degree of conserved synteny between fish and mammals, we reasoned that comparative analyses of CNAs from fish versus human MPNSTs would enable elimination of a large proportion of passenger mutations, especially on large CNAs. Accordingly, we found less than one third of the human CNA genes were co-gained or co-lost in zebrafish, dramatically narrowing the list of candidate cancer drivers for both focal and large CNAs. We conclude that zebrafish-human comparative analysis represents a powerful, and broadly applicable, tool to enrich for evolutionarily conserved cancer drivers. --- This filing comprises data related to GEO entry GSE23666 ("Highly Aneuploid Zebrafish Malignant Peripheral Nerve Sheath Tumors have Genetic Alterations Similar to Human Cancers"), representing a followup study.

overall_design: 147 pairs of zebrafish (Danio rerio) tumor (MPNST) and normal tail control samples

first: GuangJun

last: Zhang

first: Adam

last: Amsterdam

first: Charles

last: Whittaker

first: Eline

last: Beert

first: Julian

last: Catchen

first: Sarah

last: Farrington

first: John

last: Postlethwait

first: Eric

last: Legius

first: Nancy

last: Hopkins

first: Jacqueline

last: Lees


title: Intergenerational genomic DNA methylation patterns in mouse hybrid strains

status: Public on Dec 30 2013

city: Los Angeles

first: Luz

last: Orozco

state: CA

address: 610 Charles Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

overall_design: Reduced representation bisulfite sequencing from mouse liver, using MspI restriction enzyme, and selecting ~100-300bp size fraction.

middle: D

first: Liudmilla

last: Rubbi

first: Lisa

last: Martin

first: Fang

last: Fang

first: Farhad

last: Hormozdiari

first: Nam

last: Che

first: Andrew

last: Smith

first: A

last: Lusis

first: Matteo

last: Pellegrini


title: Analysis of gene expression changes in RN2 acute myeloid leukemia (AML) cells at 24hrs and 48hrs after Ddx5 knockdown.

status: Public on Dec 26 2013

city: Cold Spring Harbor

first: Anthony

last: Mazurek

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Ddx5 inhibition in RN2 cells slows cell proliferation and induces apoptosis within 48-72hrs. The aim of this analysis was to gain insight into how Ddx5 inhibition causes this outcome by analyzing gene expression changes in RN2 cells that occur at early timepoints after Ddx5 inhibition that precedes the timepoint when RN2 proliferation/cell death becomes evident in tissue culture (72hrs after inhibition).

overall_design:
Derivatives of RN2 AML cells were prepared that encode doxycycline-inducible expression of either of two different shRNAs targeting Ddx5 (shDdx5.1322 and shDdx5.2086) or a negative control shRNA that targets Renilla Luciferase (shRen.713).
Six independent cultures of each derivative RN2 cell line (shDdx5.1322, shDdx5.2086, or shRen.713) were treated with doxycycline at timepoint 0 days to induce expression of the indicated shRNA in the RN2 cells. Each shRNA is co-expressed with dsRed in a doxycycline-induced manner and flow cytometry analysis indicated that doxycycline induced expression of dsRed and the shRNA in 70-to-80% of the cells in each culture. RNA was isolated from three independent cultures of each derivative RN2 cell line at either 24hrs and 48hrs after dpxycycline treatment. Therefore this study consists of 18 samples, sequencing results from biological triplicate samples of RN2-shDdx5.1322, RN2-shDdx5.2086, and RN2-shRen.713 at 24hrs post-doxycycline and sequencing results from biological triplicate samples of RN2-shDdx5.1322, RN2-shDdx5.2086, and shRen.713 at 48hrs post-doxycycline.


title: Expressed dsRNA provokes selective sequence-independent PKR response in transient co-transfection experiments

city: Prague 4

first: Radek

last: Malik

address: Videnska 1083

department: Dep. of Epigenetics Regulations

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

summary: In mammals, double-stranded RNA (dsRNA) plays roles in sequence-specific RNA interference, sequence-independent interferon response, and RNA editing by adenosine deaminases. We have previously shown that long hairpin dsRNA expression in cultured cells does not activate the interferon response, it is poorly processed into siRNAs, and it is partially edited. Here, we demonstrate that dsRNA expressed from transiently transfected plasmids strongly inhibits expression of co-transfected reporter plasmids but not expression of endogenous genes or reporters stably integrated in the genome. The inhibition is concentration-dependent and independent of a cell type, transfection method, or dsRNA sequence. The inhibition occurs at the level of translation and is mediated by protein kinase R (PKR). PKR binds the expressed dsRNA, becomes phosphorylated and changes its distribution along polysome fractions. In conclusion, we demonstrate that expression from plasmids is selectively repressed if one of co transfected plasmids produces dsRNA. Our results highlight the importance of proper controls and careful interpretation of co-transfection experiments.

overall_design: HEK293 cells (human origin) were transiently transfected with hairpin dsRNA-expressing (MosIR) and control (pCag) plasmids.

first: Jana

last: Nejepinska

first: Petr

last: Svoboda


title: Direct sequencing of polyadenylation sites in fission yeast S. pombe

city: Boston

first: Ruby

last: Yu

address: 240 Longwood Avenue

department: Cell Biology

institute: Harvard University

summary: We sequenced the 3' ends of polyadenylated transcripts among total RNA in fission yeast wildtype and rdp1∆ cells and mapped the 3'-most nucleotide prior to polyadenylation. We find that mRNA-coding open reading frames have a low number of polyadenylation sites with most of the reads, whereas pericentromeric dg and dh repeats have a high number of polyadenylation sites throughout the transcribed region, mapping to both strands.

overall_design: direct sequencing of polyadenylated 3' ends of RNA (Helicos)

first: Danesh

last: Moazed


title: RNA-seq analysis of differentiating human erythroblasts

status: Public on Dec 25 2013

city: Berkeley

first: Lior

last: Pachter

address: 1081 Evans Hall, Department of Mathematics, University of California at Berkeley

department: Mathematics and Molecular and Cell Biology

institute: UC Berkeley

summary:
Human erythroblasts purified from cord blood were cultured in vitro and FACS-sorted into five highly purified populations representing distinct differentiation stages:  proerythroblasts, early basophilic erythroblasts, late basophilic erythroblasts, polychromatophilic erythroblasts, and orthochromatophilic erythroblasts. The methods for culture and sorting experiments are given in Hu et al. 2013. For each RNA-seq library, RNA was isolated from 1x 106 sorted human erythroblasts using RNeasy Plus Mini kits (Qiagen). Libraries were then prepared using Illumina TruSeqTM RNA kits to obtain 50 nt reads. Collaborators at the New Your Blood Center were responsible for erythroblast culture, FACS purification of erythroblast populations, and acquisition of RNA-seq data. Collaborators at U.C. Berkeley and Lawrence Berkeley National Laboratory performed data analysis and experimental validation of alternative splicing in erythroblasts.
Results: Differentiating erythroblasts execute a dynamic alternative splicing program that is enriched in genes affecting cell cycle, organelle organization, chromatin function, and RNA processing. Alternative splicing plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells.

overall_design: Erythroid differentiation stage-specific transcriptome analysis was performed by RNA-seq analysis of highly purified erythroblast populations

first: Harold

last: Pimentel

first: Marilyn

last: Parra

first: Sherry

last: Gee

first: Dana

last: Ghanem

first: Xiuli

last: An

first: Jie

last: Li

first: Narla

last: Mohandas

first: John

last: Conboy


title: Effects of RNAi protein overexpression in mutant cells on H3K9 dimethylation in fission yeast cells

summary: We test the effects of overexpressing RNAi proteins Dcr1, Rdp1, or Ago1 in wildtype, dcr1∆, ago1∆, or rdp1∆ cells. We find that overexpression does not generally affect H3K9me2 at euchromatic loci, but there are varying effects in H3K9me2 on centromeric heterochromatin.

overall_design: Examination of genome-wide enrichment in H3K9 dimethylation in fission yeast haploid cells

first: Gloria

last: Jih


title: Role of 3' UTR in spreading of siRNAs

summary: We use small RNA sequencing to look for spreading of secondary and tertiary siRNAs along transcripts targeted by ectopic hairpin-derived primary siRNAs. We find that signals within the 3' UTR inhibit siRNA spreading.

overall_design: sequencing of 20-30nt sRNAs from Argonaute immunoprecipitation


title: ChIP-Seq of Transcriptional Components in Colon carcinoma

status: Public on Dec 24 2013

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Discovery of the genome-wide location of proteins using ChIP-Seq has allowed global mapping of the key transcription factors and chromatin regulators that control gene expression programs in various cells. Many DNA-associated processes are targeted for disease therapy. CDK8 is a kinase component of the Mediator co-activator complex and is often over-expressed in colorectal cancer. This study investigates the genome-wide localization of CDK8 in human colorectal cancer cells.

overall_design: Genomic DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against H3K27ac and CDK8 as well as whole-cell extract (WCE) DNA controls.

first: Jessica

last: Reddy


title: ChIP-Seq of Transcriptional Components in Ly1 DLBCL and Colon carcinoma

summary: Discovery of the genome-wide location of proteins using ChIP-Seq has allowed global mapping of the key transcription factors and chromatin regulators that control gene expression programs in various cells. Many DNA-associated processes are targeted for disease therapy. This study investigates the functions of small molecule therapeutics that target DNA-associated processes involved with CDK9 and BRD4.

overall_design: Genomic DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against Brd4, RNA Polymerase II, Med1, H3K27ac, and CDK8 as well as whole-cell extract (WCE) DNA controls

first: Heather

last: Hoke


title: Glucocorticoid Receptor and Androgen Receptor DNA binding in LREX'

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: LREX' are a LnCAP/AR subline with natural expresison of the glucocorticoid receptor.  We used the model to compare the AR and GR cistromes in prostate tissue.

overall_design: We determined the GR cistrone in the presence of Dex (100nM) treatment and the AR cistrome in the presene of DHT (1nM) treatment.

first: Vivek

last: Arora

first: Emily

last: Schenkein

first: Deyou

last: Zheng

first: Charles

middle: L

last: Sawyers


title: The splicing activator DAZAP1 integrates splicing control into MEK/Erk regulated cell proliferation and migration

city: Chapel Hill

first: Zefeng

last: Wang

state: NC

address: 4113 Genetic Medicine

department: Pharmacology

institute: UNC

summary: DAZAP1 was depleted in culterd HEK 293T cells using shRNA and the resulting poly A RNA were isolated  c-DNA library constructed and paired end sequenced on illumina Hi-seq 2000 platform the data was compared to a control shRNA depleted cell

overall_design: Gene expression and splicing switches upon DAZAP1 knockdown

first: Rajarshi

last: Choudhury

first: Sreerupa

last: Roy

first: Yihsuan

last: Tsai

first: Ashutosh

last: Tripathy

first: Lee

middle: M

last: Graves


title: Transcriptomic analyses of Kras induced zebrafish liver cancer

city: Singapore

first: Weiling

address: Science Drive 4

country: Singapore

institute: National University of Singapore

summary: The kras transgenic line was generated by using a mifepristone-inducible transgenic system in combination with a Cre-loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month-post-induction.

overall_design: Transcriptome profiling of Kras tumor sample (6T1 and 6T2) and control samples (6M1 and 6M2) were generated by deep sequencing, using 3' RNA-SAGE on SOLiD system

first: Anh

last: Nguyen

first: Alexander

last: Emelyanov

first: Zhiyuan

last: Gong


title: Disruption of H3K27me3 through loss of EZH1 and EZH2 accelerates progression of hepatosteatosis to fatal liver fibrosis

city: Cheonan

first: Keunsoo

last: Kang

address: Dandae-ro 119

department: Microbiology

institute: Dankook University

summary: Although epigenetic mechanisms, such as specific histone modifications, control common and cell-specific genetic programs, a role for histone modifying enzymes in liver metabolism and disease has not been investigated. This report demonstrates that the combined loss of the histone methyltransferases EZH1 and EZH2 in mouse hepatocytes led to the disruption of H3K27me3 homeostasis by age three months, simple fatty liver by age six months and fatal fibrosis by age 15 months. Global and gene-specific reduction of H3K27me3 marks paralleled a concomitant increase of H3K4me3 marks at genes associated with chronic liver disease. Advanced disease was accompanied by widespread infiltration of immune cells, an increase of activated hepatic stellate cells and collagen deposition. Expression of genes from the cytochrome P450 family that control drug metabolism was already deregulated by age two months and mice were fatally hypersensitive to carbon tetrachloride (CCl4). These genetic experiments, for the first time, illustrate that the simple loss of EZH1/EZH2, which results in the disruption of epigenetic modifications, is sufficient for the progression of fatal liver disease.

overall_design: RNA-seq and ChIP-seq were performed in liver tissues.

first: Woo

last: Bae

first: Ji

last: Yu

first: Kyung

last: Yoo

first: Lothar

last: Hennighausen


title: Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH


title: Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions (Dnase-Seq)

summary: ATP-dependent chromatin remodeling is an essential process required for the dynamic organization of chromatin structure. Here we describe the genome-wide location and activity of three remodeler proteins with diverse physiological functions in the mouse genome: Brg1, Chd4, and Snf2h. The localization patterns of all three proteins significantly overlap with one another and with regions of accessible chromatin. Furthermore, using inducible mutant variants, we demonstrate that the catalytic activity of these proteins contributes to the remodeling of chromatin genome-wide, and that each of these remodelers can independently regulate chromatin reorganization at distinct sites. Most regions require the activity of more than one remodeler to regulate accessibility. These findings provide a dynamic view of chromatin organization, and highlight the differential contributions of remodelers to chromatin maintenance in higher eukaryotes.

overall_design: We examine the genome-wide location and activity of three remodeler proteins (Brg1, CHD4 and Snf2h)

first: Stephanie

last: Morris

first: Gordon

last: Hager

first: Myong-Hee

last: Sung


title: Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions (ChIP-Seq)


title: Smc5/6-Mms21 prevents and eliminates inappropriate recombination intermediates in meiosis

city: Vienna

first: Franz

last: Klein

address: Dr. Bohrg. 9

department: Chromosome Biology

institute: University of Vienna, MFPL

summary: Repairing broken chromosomes via joint molecule (JM) intermediates is hazardous and therefore strictly controlled in most organisms. Also in budding yeast meiosis, where production of enough crossovers via JMs is imperative, only a subset of DNA breaks are repaired via JMs, closely regulated by the ZMM pathway. The other breaks are repaired to non-crossovers avoiding JM formation requiring BLM/Sgs1 helicase. "Rogue" JMs that escaped the ZMM pathway and BLM/Sgs1 are eliminated before metaphase by resolvases like Mus81-Mms4 to prevent chromosome nondisjunction.

overall_design: 7 genome-wide meiotic ChIP-seq sets: 2 meiotic time points Smc6-myc DNA interaction (Smc6-ChIP), 2 meiotic time points Smc6-myc DNA interaction in the absence of induced recombination (Smc6-ChIP, spo11delta), 2 meiotic time points Sgs1-myc DNA interaction (Sgs1-ChIP), and 1 meiotic time point untagged as a negative control. (Corresponds to the main Figures 2 and 6, as well as to Figures S4, S7, in the associated publication.)

first: Martin

last: Xaver

first: Lingzhi

last: Huang

first: Doris

last: Chen


title: Global Target mRNA Specification and Regulation by RNA-Binding Protein ZFP36/Tristetraprolin/TTP [PAR-CLIP]

city: Aurora

first: Neelanjan

last: Mukherjee

state: CO

department: BMG/RBI

institute: University of Colorado School of Medicine

summary: Tristetraprolin/ZFP36/TTP and ELAVL1/HuR are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embyonic kidney cells and examined combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1. Among the targets ZFP36 binds and negatively regulates the mRNA of genes encoding proteins necessary for immune function and cancer, and other RBPs. Using partial correlation analysis, we were able to quantify the association between ZFP36 binding sites and differential target RNA abundance from ZFP36 overexpression independent of effects from confounding features, such as 3’ UTR length. We identified thousands of overlapping ZFP36 and ELAVL1 binding sites, in 1,313 genes. ZFP36 preferentially interacts with and regulates AU-rich sequences while ELAVL1 prefers predominantly U- and CU-rich sequences. RNA target specificity identified by global in vivo ZFP36-mRNA interactions were quantitatively similar to previously reported in vitro binding affinities. ZFP36 and ELAVL1 both bind an overlapping spectrum of RNA sequences, yet with differential relative preferences that dictate combinatorial regulatory potential. Our findings and methodology delineate an approach to untangle the in vivo combinatorial regulation by RNA-binding proteins.

overall_design: FLAG-HA ZFP36

first: Thomas

last: Tuschl

first: Uwe

last: Ohler

first: Perry

middle: J

last: Blackshear


title: Global Target mRNA Specification and Regulation by RNA-Binding Protein ZFP36/Tristetraprolin/TTP

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

overall_design: Refer to individual Series


title: H2A.B and MeDIP sequence result

city: Ann Arbor

first: Yibin

state: MI

address: 1115 w medical drive

institute: university of Michigan

summary: H2A.B is a unique histone H2A variant that shares only 40 ~ 50 % sequence identity with canonical H2A. It has only been identified in mammals and has quickly evolved with remarkable sequence diversity among different species. H2A.B is ubiquitously expressed in most cells and tissues. It is mainly deposited in gene body region. The localization of H2A.B is associated with methylated CpG islands in mouse ES cells. H2A.B facilitates transcription elongation to go through methylated CpG islands in the gene bodies. One typical example is that H2A.B regulates transcription elongation at imprinted loci.

overall_design: We found H2A.B enriched in some methylated loci. Using ChIP-seq and MeDIP-seq, we test the correlation of H2A.B and DNA methylation.

first: Xiaochun


title: H2A.B facilitates transcription at methylated CpG Loci


title: Transcription factor occupancy is linked to DNA methylation turnover at active regulatory regions [MeDIP-Seq]

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Genome wide analysis revealed that distal regulatory elements form Low Methylated Regions (LMRs). Even though transcription factor binding is required for LMR formation, we show for the test case CTCF that actual occupancy does not distinguish DNA methylation states. However, in line with a dynamic model of binding and DNA methylation turnover, we find that the product of active demethylation, 5-hydroxymethylcytosine (5hmC), is enriched at LMRs. 5hmC is present at active regulatory regions in stem and somatic cells and as a result a substantial fraction of changes in 5hmC occurs at LMRs. This suggests that transcription factor binding mediates active turnover of DNA methylation as an integral part of reprogramming of regulatory regions.

overall_design: hMeDIP sequencing in mouse embryonic stem cells (ES) and derived neuronal progenitors (NP).

first: Robert

last: Ivanek

first: Angelika

last: Feldmann

first: Rabih

last: Murr

first: Dimos

last: Gaidatzis

first: Lukas

last: Burger

last: Schübeler


title: Deletion of conserved protein phosphatases reverses defects associated with mitochondrial DNA damage in Saccharomyces cerevisiae

status: Public on Dec 23 2013

city: Sariyer

first: Cory

middle: David

last: Dunn

state: Istanbul

address: Rumelifeneri Yolu

department: Molecular Biology and Genetics

country: Turkey

institute: Koç University

summary: Mitochondrial biogenesis is regulated by signaling pathways sensitive to extracellular conditions and to the internal environment of the cell. We found that deletion of protein phosphatase 2A (PP2A) or of protein phosphatase 6 (PP6) diminishes the nuclear transcriptional response associated with mtDNA damage.

overall_design: Six samples were analyzed to determine message RNA levels.

first: Görkem

last: Garipler

first: Nebibe

last: Mutlu

first: Nathan

last: Lack


title: Transcription factor occupancy is linked to DNA methylation turnover at active regulatory regions


title: Determinants of heterochromatic siRNA biogenesis and function

first: Ruby

last: Yu

state: MA

country: USA

first: Danesh

last: Moazed


title: Transcriptome profiling of Arabidopsis using strand-specific RNA-seq

first: Huan

last: Wang

address: 1230 York Avenue

institute: The Rockefeller University

summary: We applied single-end strand-specific RNA-seq experiments to compare the abundance of natural antisense transcripts in Arabidopsis.

overall_design: Examination of 3 wild type (WT) organs, including leaves, inflorescences and siliques.

first: Michelle

last: Kean


title: An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants.

city: basel

first: maria alessandra

last: vigano

department: department of biomedicine

institute: university of basel

summary: Using a stromal cell free system, we described the gene expression and two genome wide epigenetic profiles of a unique population of undifferentiated bone marrow cells selectively driven towards the T cell differentiation pathway

overall_design: Undifferentiated bone marrow cells, transduced with NUP98-HOXB4 fusion protein, in vitro expanded with IL6 and SCF represents the hematopoietic stem cells (HSC); when grown in the presence of  DLL4 (Notch1 ligand) and IL7, they are directed towards the T cell lineage (ProT); these in vitro generated ProT cells injected in a Rag2-/- mouse give rise to mature double positive T cells (DP). 2 replica for each population

first: M

last: Vigano


title: Targeting transcriptional dependencies in cancer using a covalent CDK7 inhibitor

city: Cambridge

first: Richard

last: Young


title: Generation of Rdp1-independent primary siRNAs

summary: We tested whether we could increase the population of Rdp1-independent primary siRNAs in fission yeast by overexpressing the Dcr1 ribonuclease. We found that in addition to generation of centromeric siRNAs, which was expected, Dcr1 overexpression also resulted in generation of genome-wide primary siRNAs, mapping to many open reading frames.

overall_design: sequencing of 20-30nt sRNAs from total RNA


title: smRNAs generated by single-stranded and double-stranded silencers

summary: To investigate possible smRNAs linked to TMM silencing by single-stranded and double-stranded silencers, we determined sequences of smRNAs by the Illumina high-throughput sequencing platform and compared silencing efficiency of different strategies. We found that single-stranded silencer alone could promote the production of smRNAs.

overall_design: smRNA profiles of 2-week-old wide type seedlings (WT) and different silencers were generated by Illumina Genome Analyzer IIx.

first: Shulin

last: Deng

first: Hongzheng

last: Dai

first: Catalina

last: Arenas-Huertero

first: Qi-Wen

last: Niu

first: Nam-Hai

last: Chua


title: The C. elegans CSR-1 argonaute pathway counteracts epigenetic silencing to promote germline gene expression

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: Organisms can develop adaptive sequence-specific immunity by reexpressing pathogen-specific small RNAs that guide gene silencing. For example, the C. elegans PIWI-Argonaute/piwi-interacting RNA (piRNA) pathway recruits RNA-dependent RNA polymerase (RdRP) to foreign sequences to amplify a transgenerational small-RNA-induced epigenetic silencing signal (termed RNAe). Here, we provide evidence that, in addition to an adaptive memory of silenced sequences, C. elegans can also develop an opposing adaptive memory of expressed/self-mRNAs. We refer to this mechanism, which can prevent or reverse RNAe, as RNA-induced epigenetic gene activation (RNAa). We show that CSR-1, which engages RdRP-amplified small RNAs complementary to germline-expressed mRNAs, is required for RNAa. We show that a transgene with RNAa activity also exhibits accumulation of cognate CSR-1 small RNAs. Our findings suggest that C. elegans adaptively acquires and maintains a transgenerational CSR-1 memory that recognizes and protects self-mRNAs, allowing piRNAs to recognize foreign sequences innately, without the need for prior exposure.

overall_design: Examine small RNA population changes in different transgene lines

first: Meetu

last: Seth

first: Masaki

last: Shirayama

first: Weifeng

last: Gu

first: Takao

last: Ishidate

first: Darryl

last: Conte


title: Epstein Barr Virus Nuclear Antigen 3C binds to BATF/IRF4/SPI1 sites and represses CDKN2A by recruiting Sin3A

status: Public on Dec 22 2013

first: Hufeng

last: Zhou

address: 181 Longwood Ave,

department: Department of Microbiology and Molecular Genetics

institute: Harvard Medical School

summary: We report the application of ChIP Seq to study the Epstein Barr Virus Nuclear Antigen 3C, an essential transcriptional regulator involved in the transformation of Resting B Lymphocytes to the immortalized Lymphoblast Cell Lines

overall_design: Examination of viral and cellular transcription factors in 1 type of cell line

first: Sizun

last: Jiang

first: Bradford

last: Willox

first: Amy

last: Holthaus

first: Anqi

first: Tommy

last: Shi

first: Seiji

last: Maruo

first: Eric

last: Johannsen

first: Peter

last: Kharchenko

first: Elliott

last: Kieff

first: Bo

last: Zhao


title: Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain (Bisulfite-seq)

first: Junjie

last: Guo

institute: Whitehead Institute

summary: DNA methylation plays critical roles in the nervous system and has been traditionally considered to be restricted to CpG dinucleotides in metazoan genomes. Here we show that the single-base resolution neuronal DNA methylome from the adult mouse dentate gyrus consists of both CpG (~75%) and CpH (~25%) methylation (H = A/C/T). Neuronal CpH methylation is conserved in human brains, enriched in low CpG-density regions, depleted at protein-DNA interaction sites, and anti-correlated with gene expression. Functionally, both mCpGs and mCpHs can repress transcription in vitro and are recognized by MeCP2 in vivo. Unlike most CpG methylation, CpH methylation is established de novo during neuronal maturation and requires DNMT3A for active maintenance in post-mitotic neurons. These characteristics of CpH methylation suggest a significantly expanded proportion of the neuronal genome under cytosine methylation regulation and provide a new framework for understanding the roles of this key epigenetic modification in neuronal identity, maturation, plasticity and neurological disorders.

overall_design: Two biological replicates (dentate gyrus samples from C57Black6 mice) were analyzed in Bisulfite-seq.


title: Small RNA sequencing in Arabidopsis plants

city: Esch-Belval

first: Patrick

last: May

state: Luxembourg

address: 7, avenue des Hauts-Fourneaux

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

summary: Identification of microRNA expressed in Arabidopsis plants grown at different ambient CO2 concentrations and different ambient temperatures

overall_design: Small RNA sequencing of Arabidopsis wild type ecotype Columbia (Col-0) rossette leaves at bolting stage grown at 430 ± 50ppm and 810 ± 50ppm CO2 concentrations and 22 ± 0.5oC and 28 ± 0.5oC temperatures

first: Qiong

last: Liu

first: Will

last: Liao

first: Michael

middle: Q

last: Zhang


title: Hr78-GFP_W3L_ChIP-seq

status: Public on Dec 21 2013

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
modENCODE_submission_5000
This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: Hr78-GFP; Developmental Stage: L3; Genotype: PBac{y[+]-attP-3B}VK00037; Sex: Unknown; Transgene: Hr78 genomic coding region;  EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene Hr78; Strain Hr78-GFP; Antibody GFP ab290 (target is Green Fluorescent Protein)

first: Kevin

last: White

first: Lijia

last: Ma

first: Matthew

last: Slattery


title: dMyc_S2_cells_ChIP-seq

summary:
modENCODE_submission_5007
This submission comes from a modENCODE project of Kevin White. For full list of modENCODE projects, see http://www.genome.gov/26524648
Project Goal: The White Lab is aiming to map the association of all the Transcription Factors (TF) on the genome of Drosophila melanogaster. One technique that we use for this purpose is chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) utilizing an Illumina next generation sequencing platform. The data generated by ChIP-seq experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male;  EXPERIMENTAL FACTORS: Antibody MycN (target is fly genes:dm); Cell Line S2-DRSC