title: Prevalence, evolution and cis-regulation of diel transcription in Chlamydomonas reinhardtii

status: Public on Oct 25 2014

city: East Lansing

first: Nicholas

middle: Louis

last: Panchy

state: MI

address: 1066 Bouge St., Room 2275

department: Genetics

institute: Michigan State University

summary: Biological rhythms in response to both endogenous (circadian) and exogenous (e.g. diel) cycles, with a period of ~24 hours, are a prominent feature of many living systems. In green algal species, knowledge on the extent of diel rhythmicity of genome wide gene expression, its evolution, and its cis-regulatory mechanism is limited. In this study, we identified cyclically expressed genes under diel conditions in Chlamydomonas reinhardtii and found that ~50% of the 17,114 annotated genes exhibited cyclic expression. The cyclic expression patterns indicate a clear succession of biological processes during the course of a day. Among 237 functional categories enriched in cyclically expressed genes, >90% were phase-specific, including photosynthesis, cell division and motility processes. By contrasting cyclic expression between C. reinhardtii and Arabidopsis thaliana putative orthologs, we found significant but weak conservation in cyclic gene expression patterns. On the other hand, within C. reinhardtii cyclic expression was preferentially maintained, particularly amongst older duplicates, and the evolution of phase between paralogs is limited to relatively minor shifts in time. Finally, to better understand the cis regulatory basis of diel expression, putative cis-regulatory elements were identified that could predict the expression phase of a subset of the cyclic transcriptome. Our findings demonstrate both the prevalence of as well as the complex regulatory circuitry required to control cyclic expression in a green algal model, highlighting the need to consider diel expression in studying algal molecular networks and in future biotechnological applications.

overall_design: Total RNA sequences extracted every 3 hours between ZT (Zeitgeber Time, hours since last doawn) 0 and ZT21 from two biological replicates of C. reinhardtiis dw15.1

first: Christoph

last: Benning

first: Eva

last: Farre

first: Shin-Han

last: Shiu


title: University of Manitoba/MGCB2 C thermocellum RNA-seq Experiment

status: Public on Oct 26 2014

city: Winnipeg

first: Richard

last: Sparling

state: MB

address: 418 Buller Building

department: Microbiology

country: Canada

institute: University of Manitoba

type: Expression profiling by high throughput sequencing

summary: Determine overall gene expression profiles; RNA expression observed in stationary relative to exponential phase cells of strain Clostridum thermocellum (ATCC 27405) grown on cellobiose; Comparative RNA expression of 3 Clostridium thermocellu strains (DSM 1237, 2650, and 4150) grown to mid exponential phase on cellobiose; Verify whether observed differences in fermentation end-product ratios are reflected in differences in RNA expression profiles. RNA-seq data will be compared with the same experiments performed with proteomic experiments; Compare gene expression across relative strains.

overall_design: Each test condition was provided as 2 biological replicates for primary strain and 1 replicate for comparing strain

first: David

middle: B

last: Levin

first: Thomas

last: Rydzak

first: Brian

middle: W

last: Fristensky

first: Xiangli

last: Zhang

first: Graham

middle: G

last: Alvare

first: Natalie

middle: K

last: Björklund


title: RNA-Seq Analysis in purified iPS cell-derived neuronal samples

status: Public on Oct 24 2014

city: New York

first: Aiqun

last: Li

state: NY

address: 3960 Broadway

department: Research Institute

country: USA

institute: The New York Stem Cell Foundation

summary: We characterized the gene expression differences in mDA neurons from all PD (Parkinson's disease) cases (6 independent samples) and controls (8 independent samples), identifying 1,028 differentially expressed genes making up the PD expression signature. Strikingly, MAOB gene was identified as significantly differentially expressed (p = 0.046). The heat map clearly differentiates cases from controls, where interestingly most differentially expressed genes had lower expression in PD cases compared to controls. In the clustering, the RNA expression pattern of the control (C2) with a family history of PD located close to the PD expression signature suggested a susceptibility to PD.

overall_design: RNA was isolated from FAC-sorted cells of 14 samples (biological duplicates for each cell line, 7 cell lines in total) using RNeasy Micro Kit (QIAGEN). Quality control of the RNA was carried out with the Agilent Bio-analyzer, Qubit 2.0 at the MPSR of Columbia University. 100 ng of RNA with RIN ≥ 9 were used for generating mRNA-focused libraries using TruSeq RNA Sample Preparation Kit v2 and sequencing on an Illumina 2000/2500 V3 Instrument offered by the Columbia Genome Center.

first: Chris

middle: M

last: Woodard

middle: A

last: Campos

first: Scott

last: Noggle


title: The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia

status: Public on Oct 27 2014

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

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

overall_design: Refer to individual Series


title: Rapidly induced fucosylation of intestinal epithelium sustains host-commensal symbiosis during sickness.

city: San Francisco

first: Peter

middle: James

last: Turnbaugh

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

summary: Systemic infection induces conserved physiological responses that include both resistance and ‘tolerance of infection’ mechanisms. Among these responses, temporary anorexia associated with an infection is often beneficial. It poses, however, a problem for the trillions of microbes residing in the gastrointestinal tract, as they also experience reduced substrate availability. We hypothesized that under anorectic conditions caused by infection, the host might activate protective mechanisms to support the gut microbiota during the acute phase of the disease. Here, we report that systemic exposure to Toll-like receptor (TLR) ligands causes rapid α1,2-fucosylation of the small intestine epithelial cells (IEC). The process requires sensing of TLR agonists and production of IL-23 by dendritic cells, activation of innate lymphoid cells and expression of α1,2-Fucosyltransferase-2 (Fut2) by IL-22-stimulated IECs. Fucosylated proteins are shed into the lumen and fucose is utilized by microbiota, as shown using reporter bacteria and by transcriptional profiling of the gut microbiome.  Fucosylation also reduces the expression of bacterial virulence genes within the commensal gut microbiome and improves host tolerance of the mild pathogen Citrobacter rodentium. Thus, rapid IEC fucosylation appears to be a protective mechanism that utilizes the host’s resources to maintain host-microbial interactions during pathogen-induced stress.

overall_design: RNA-Seq analysis of the murine gut microbiome following LPS exposure. Fut2-/- (B6.129X1-Fut2tm1Sdo/J) mice were backcrossed greater than 7 generations to BALB/c. Fut2-/- (KO) and Fut2+/- (Het) animals were analyzed.

middle: J


title: Analysis of exosome RNA from co-culture of cancer cell and stroma cell

city: Philadelphia

first: Andy

last: Minn

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

summary: How stroma communicates with cancer to influence treatment response is poorly understood. We show that stromal fibroblasts protect breast cancer (BrCa) against radiation and chemotherapy through an exosome-mediated anti-viral pathway and NOTCH3. Stroma increases RAB27B and transfers exosomes to BrCa. RNA within exosomes, comprised largely of non-coding transcripts and transposable elements, stimulates the pattern recognition receptor RIG-I through a 5’-triphosphate motif to activate STAT1. BrCa NOTCH3 is activated in parallel by stromal JAG1 and cooperates with STAT1 to enhance transcriptional responses of NOTCH target genes and to expand therapy resistant tumor-initiating cells. Computational modeling using primary human and mouse BrCa supports the interaction of anti-viral/NOTCH3 pathways in controlling NOTCH target genes and treatment resistance, particularly in basal subtype tumors. Gamma secretase inhibitors reverse stromal protection and abrogate radiation resistance in vivo. Thus, stroma orchestrates an intricate cross-talk with BrCa by utilizing exosomes to coax anti-viral signaling that expands therapy resistant cells through druggable pathways.

overall_design: RNA profile of ceullar RNA and exosome of co-culture of breast caner cell line 1833 and stroma cell line MRC5.

first: Mirjam

middle: C

last: Boelens

first: Tony

last: Wu

first: Barzin

middle: Y

last: Nabet

first: Bihui

last: Xu

first: Yu

last: Qiu

first: Taewon

last: Yoon

first: Diana

last: Azzam

first: Christina

last: Twyman

first: Brianne

middle: Z

last: Wiemann

first: Hemant

last: Ishwaran

first: Petra

last: ter Brugge

first: Jos

last: Jonkers

first: Joyce

last: Slingerland


title: RUNX1 transcription factor genome-wide occupancy in EML cells

city: La Jolla

first: Kentson

last: Lam

address: 3855 Health Sciences Drive

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of sequencing technology for high-throughput profiling of RUNX1 transcription factor occupancy in mouse EML cells. RUNX1 antibody was use for chromatin immunoprecipitation followed by high-throughput sequencing to reveal RUNX1 genome occupancy in hematopoietic stem/progenitor cells.

overall_design: Examination of RUNX1 transcription factor occupancy in EML cells.

first: Dong-Er

last: Zhang


title: Global ChIP-seq Normalization Reveals Epigenome Modulations

status: Public on Oct 30 2014

city: Watertown

first: Eric

last: Olson

state: MA

address: 480 Arsenal Street

institute: Syros Pharmaceuticals

summary: Epigenomic profiling by ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems, such as human disease, yet the lack of an empirical methodology to normalize amongst experiments has limited the usefulness of this technique. Here we describe a “spike-in” normalization method that allows the quantitative comparison of histone modification status across cell populations using defined quantities of a reference epigenome. We demonstrate the utility of this method in measuring epigenomic changes following chemical perturbations and show how control normalization of ChIP-seq experiments enables discovery of disease-relevant changes in histone modification occupancy.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: ChIP-Seq of histone modifications H3K79me2 and H3K4me3 in human samples treated with EPZ-5676 with/without reference epigenome spike-in.

first: Matthew

last: Guenther

first: Mei

last: Chen

first: David

last: Orlando

middle: R


title: Exosome Transfer from Stromal to Breast Cancer Cells Regulates Therapy Resistance Pathways

first: Andy

last: Minn


title: RNA-seq data from MCF-7 cells (breast cancer model) treated with soy extracts

city: Columbia

first: Charles

middle: Michael

last: Greenlief

state: MO

address: 601 S. College Ave.

department: Department of Chemistry

institute: University of Missouri

summary: The MCF-7 were infected with either control adenovirus expressing B-galactosidase (Ad) or adenovirus expressing ERB (AdERbeta) for 72 h.  For knockdown of the endogenous ERa in MCF-7 cells, cells were treated with siRNA for 24h (AdERbeta+SiERalpha).  Then cells were treated with Veh (0.1% EtOH), 10 nM E2 or 1 uM BEs (botanical extracts) for 24h.

overall_design: Duplicate samples run; treatment after knockdown included a control treatment (V), estradiol (E2) or botanical extracts; genistein (Gen), S-equol, liquiritigenin (Liq)

first: Michael

first: Benita

middle: S

last: Katzenellenbogen


title: rd10 transcriptome analysis

city: Los Angeles

first: Philip

last: Uren

address: 1050 Childs Way, RRI201

institute: University of Southern California

summary: Retinitis pigmentosa (RP) is a photoreceptor disease that affects approximately 100,000 people in the United States. There are currently very limited treatment options and the prognosis for most patients is progressive vision loss. Unfortunately, the understanding of the molecular underpinnings of RP initiation and progression is still poorly understood. However, the development of animal models of RP, coupled with high-throughput sequencing, has provided an opportunity to study the underlying cellular and molecular changes of this disease. Using RNA-Seq, we present the first retinal transcriptome analysis of the rd10 murine model of retinal degeneration.

overall_design: RNA-Seq on whole-retina samples from rd10, wild-type and GFP-expressing mouse retina. Three biological replicates of each.

first: Alan

last: Horsager


title: Whole transcriptome profiling of the rat pineal gland during development from embryonic day 21 to adult

city: Bethesda

first: Steven

last: Coon

state: MD

address: 49 Convent Drive Room 6A83

department: NICHD/PDEGEN

institute: NIH

summary: The transcriptome of the rat pineal gland is highly dynamic, with many hundreds of genes changing more than two-fold on a 24-hr daily rhythm, as revealed earlier using Affymetrix GeneChip analysis. Several key transcription factors and enzymes are known to change dramatically during development of the pineal gland. Studies on a small number of genes indicate that the onset of rhythmic expression generally occurs later in development. This study characterizes this temporally dynamic transcriptome using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs and coding transcripts not represented on the Affymetrix chips.

overall_design: The rat pineal transcriptome was sequenced in samples from four ages, from embryonic day 21 through adult. At each age, samples were taken at mid-day and mid-night. Data were collected to describe the changes in the developing pineal transcriptome and to identify transcripts that exhibit day/night differences in expression at each age.

middle: L

first: Cong

last: Fu

first: Samuel

last: Clokie

first: Peter

last: Munson

first: Praveen

middle: F

last: Cherukuri

last: Sugden

first: James

last: Mullikin

last: Klein


title: Age-associated loss of lamin-B leads to systemic inflammation and gut hyperplasia

status: Public on Oct 23 2014

city: Baltimore

first: Yixian

last: Zheng

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

summary: Aging of immune organs, termed as immunosenescence, is suspected to promote  systemic inflammation and age-associated disease. The cause of immunosenescence and  how it promotes disease, however, has remained unexplored. We report that the  Drosophila fat body, a major immune organ, undergoes immunosenescence and mounts  strong systemic inflammation that leads to de-regulation of immune deficiency (IMD)  signaling in the midgut of old animals. Inflamed old fat bodies secrete circulating  peptidoglycan recognition proteins that repress IMD activity in the midgut, thereby  promoting gut hyperplasia. Further, fat body immunosenecence is caused by ageassociated  lamin-B reduction specifically in fat body cells, which then contributes to  heterochromatin loss and de-repression of genes involved in immune responses. As  lamin-associated heterochromatin domains are enriched for genes involved in immune  response in both Drosophila and mammalian cells, our findings may provide insights into  the cause and consequence of immunosenescence during aging.

overall_design: 17 samples from the fat body, the midgut, or the whole gut with different ages or RNAi treatment. 6 of the samples were wildtype young control. For each experiment, we had two or three biological replicates.

first: Haiyang

first: Xiaobin


title: Comparison of gene expression profiles in three Clostridium thermocellum strains: DSM 1237, 2360 and 4150

first: Richard

last: Sparling

last: Levin

first: Thomas

last: Rydzak

first: Brian

last: Fristensky

first: Xiangli

last: Zhang

first: Graham

last: Alvare

first: Natalie

last: Björklund


title: Role of YbeY in Yersinia enterocolitica O:3

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

summary: In order to detect genes that are directly or indirectly affected by the inactivation of the ybeY gene the transcriptomes of the WT and ybeY bacteria grown at 22°C and 37°C were determined. The two temperatures were chosen since temperature is an important cue regulating the virulence genes. When comparing the WT and ybeY mutant strain transcriptomes of bacteria grown at 22°C we found changes in the expression of 350 genes in the ybeY bacteria, out of which 121 (34.6%) were up-regulated and 229 (65.4%) down-regulated. At 37°C 334 genes in the ybeY bacteria showed changes, out of which 48 (14.4%) were up-regulated and 286 (85.6%) down-regulated. Expression of 92 genes was changed at both temperatures, of these 92 genes, 12 were up- and 80 down-regulated.

sample_organism: Yersinia enterocolitica subsp. palearctica Y11

overall_design: Bacterial RNA profiles of wild type and ybeY- strains were generated using deep sequencing, in duplicates, under two growth temperatures (22°C and 37°C).

first: Katarzyna

last: Leskinen

first: Pirkko

last: Mattila


title: Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver [ChIP-seq]

city: Charlottesville

first: Irina

last: Bochkis

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia

summary: Aging is accompanied by physiological impairments, which, in insulin-responsive tissues, including the liver, predispose individuals to metabolic disease. However, the molecular mechanisms underlying these changes remain largely unknown. Here, we analyze genome-wide profiles of RNA and chromatin organization in the liver of young (3 months) and old (21 months) mice. Transcriptional changes suggest that de-repression of the nuclear receptors PPARα, PPARγ, and LXRα in aged mouse liver leads to activation of targets regulating lipid synthesis and storage, whereas age-dependent changes in nucleosome occupancy are associated with binding sites for both known regulators (forkhead factors and nuclear receptors) and for novel candidates associated with nuclear lamina (Hdac3 and Srf) implicated to govern metabolic function of aging liver. Winged-helix factor Foxa2 and nuclear receptor co-repressor Hdac3 exhibit reciprocal binding pattern at PPARα targets contributing to gene expression changes that lead to steatosis in aged liver.

overall_design: Genome-wide location analysis (ChIP-Seq) of Foxa2 and Hdac3  from young (3 months) and old (21 months) mouse livers

first: Aviv

last: Regev


title: The Drosophila Tis11 protein and its effects on mRNA expression in flies

city: Durham

first: Perry

last: Blackshear

address: 101 Alexander Dr.

institute: NIEHS

summary: Insects generally express one tristetraprolin family member, proteins that in mammals promote mRNA decay. The Drosophila protein, Tis11, can promote mRNA decay in cells, and its deficiency in flies results in major changes in mRNA levels. Tis11 deficiency in Drosophila results in accumulation of potentialtarget transcripts. Tis11 can affect post- transcriptional gene expression in adult flies by regulating mRNA decay.

overall_design: Examination of gene expression differences between  wild-type, Tis11-knockout, and Tis11-mutated  flies

last: Blachshear

first: Youn-Jeong

last: Choi

first: Wi

last: La

first: Elizabeth

middle: D

last: Gersch

first: Weichun

last: Huang

first: Gerald

last: Wilson

first: Robert

last: Fedic

first: Deborah

last: Stumpo

first: Lalith

last: Perera

first: Brandy

last: Brewer

last: Mason


title: Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor (ChIP-seq)

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Small cell lung cancer (SCLC) is an aggressive disease with high mortality. The identification of effective pharmacological strategies to target SCLC biology represents an urgent need. Using a high-throughput cellular screen of a diverse chemical library we observe that SCLC is sensitive to transcription-targeting drugs, and in particular to THZ1, a newly identified covalent inhibitor of cyclin-dependent kinase 7 (CDK7).  We find that expression of super-enhancer associated transcription factor genes including MYC family proto-oncogenes and neuroendocrine lineage-specific factors are highly vulnerability to THZ1 treatment. We propose that downregulation of these transcription factors contributes, in part, to SCLC sensitivity to transcriptional inhibitors and that THZ1 represents a novel treatment paradigm for targeted SCLC therapy.

overall_design: ChIP-Seq for H3K27ac in small cell lung cancer lines

first: Camilla

last: Christensen

first: Nicholas

last: Kwiatkowski

first: Brian

last: Abraham

first: Julian

last: Carretero

first: Fatima

last: Al-shahrour

first: Tinghu

last: Zhang

first: Edmond

last: Chipumoro

first: Grit

last: Hurter-Sprie

first: Esra

last: Akbay

first: Abigail

last: Altabef

first: Jianming

first: Takeshi

last: Shimamura

first: Marzia

last: Capalletti

first: Jakob

middle: B

last: Reibel

first: Jillian

last: Cavanaugh

first: Peng

last: Gao

first: Yan

last: Liu

first: Signe

last: Michaelsen

first: Hans

last: Poulsen

first: Amir

last: Aref

first: David

last: Barbie

first: James

middle: E

last: Bradner

first: Rani

last: George

first: Nathanael

last: Gray

first: Kwok

last: Wong


title: Nucleosome positioning under perturbation conditions in yeast

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: We report nucleosome poisitioning under pertubation conditions such as heat shock, CHD1 deletion, and SET2 deletion

overall_design: Mono-nucleosome DNA was prepared from wild type strain under normal or heat shock conditions, or CHD1 or SET2 deletion strain. The mono-nucleosome DNA was mapped.

first: Vishwanath


title: Targeting Transcriptional Addictions in Small Cell Lung Cancer with a Covalent CDK7 Inhibitor

first: Richard

last: Young


title: Genome-wide RNA tomography in the zebrafish embryo

city: Utrecht

first: Jan Philipp

last: Junker

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. While genome-wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes, they are unable to yield spatially resolved information in embryos or tissues. Microscopy-based approaches, using for example in situ hybridization, can provide spatial information about gene expression, but are limited to analyzing one or a few genes at a time. Here, we present a method where we combine traditional histological techniques with low-input RNA sequencing and mathematical image reconstruction to generate a high-resolution genome-wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. We also demonstrate that our technique is suitable for spatially-resolved differential expression analysis in wildtype and Gli3 mutant mouse forelimbs. Importantly, our method enables searching for genes that are expressed in specific spatial patterns without manual image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: To generate spatially-resolved RNA-seq data for zebrafish embryos (shield stage, 10 somites, 15 somites, 18 somites) and mouse forelimbs (E10.5), we cryosectioned samples, extracted RNA from the individual sections, and amplified and barcoded mRNA using the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012) with a few modifications. Libraries were sequenced on Illumina HiSeq 2500 using 50bp paired end sequencing. Selected zebrafish libraries were sequenced on MiSeq 250bp paired-end to improve 3' annotations.

first: J

middle: P

first: E

last: Noël

first: V

last: Guryev

first: K

last: Peterson

first: G

last: Shah

last: Huisken

first: A

last: McMahon

last: Berezikov

last: Bakkers

last: van Oudenaarden


title: White Cells Facilitate Opposite- and Same-Sex Mating of Opaque Cells in Candida albicans

city: Beijing

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology

summary: Modes of sexual reproduction in eukaryotic organisms are highly diversified. The human fungal pathogen Candida albicans undergoes a phenotypic switch from the white to the opaque phase in order to become mating-competent. In this study, we report that functionally and morphologically differentiated white and opaque cells show a coordinating behavior in the process of mating. Although white cells are mating-incompetent, they are induced to produce sexual pheromones when treated with opposite pheromones or interacted with opaque cells of an opposite mating type. In a co-culture system, pheromones released by white cells induce opaque cells to form mating projections and thus facilitate both opposite- and same-sex mating of opaque cells. Deletion of genes encoding the pheromone precursor proteins and inactivation of the pheromone response signaling pathway (Ste2-MAPK-Cph1) impair the promoting role of white cells (MTLa) in sexual mating of opaque cells. White and opaque cells communicate via a paracrine pheromone signaling and thus create an environment conducive to sexual mating. This coordination behavior of the two different cell types may be a trade-off strategy between sexual and asexual lifestyles in C. albicans.

overall_design: total RNA profiles of white cell treated with pheromone

first: Guanghua

last: Huang

first: Li

last: Tao

first: Chengjun

last: Cao


title: Maternal high-fat diet and obesity compromise fetal hematopoiesis

city: Portland

first: David

last: Ellison

state: OR

address: 3181 SW Sam Jackson Park Rd CR145

institute: Oregon Health and Science University

summary: Objective  Recent evidence indicates that the adult hematopoietic system is susceptible to diet-induced lineage skewing.  It is not known whether the developing hematopoietic system is subject to metabolic programming via in utero high fat diet (HFD) exposure, an established mechanism of adult disease in several organ systems. We previously reported substantial losses in offspring liver size with prenatal HFD. As the liver is the main hematopoietic organ in the fetus, we asked whether the developmental expansion of the hematopoietic stem and progenitor cell (HSPC) pool is compromised by prenatal HFD and/or maternal obesity.    Methods  We used quantitative assays, progenitor colony formation, flow cytometry, transplantation, and gene expression assays with a series of dietary manipulations to test the effects of gestational high fat diet and maternal obesity on the day 14.5 fetal liver hematopoietic system.  Results  Maternal obesity, particularly when paired with gestational HFD, restricts physiological expansion of fetal HSPCs while promoting the opposing cell fate of differentiation. Importantly, these effects are only partially ameliorated by gestational dietary adjustments for obese dams. Competitive transplantation reveals compromised repopulation and myeloid-biased differentiation of HFD-programmed HSPCs to be a niche-dependent defect, apparent in HFD-conditioned male recipients. Fetal HSPC deficiencies coincide with perturbations in genes regulating metabolism, immune and inflammatory processes, and stress response, along with downregulation of genes critical for hematopoietic stem cell self-renewal and activation of pathways regulating cell migration.   Conclusions  Our data reveal a previously unrecognized susceptibility to nutritional and metabolic developmental programming in the fetal HSPC compartment, which is a partially reversible and microenvironment-dependent defect perturbing stem and progenitor cell expansion and hematopoietic lineage commitment.

overall_design: Examination of differentially expressed genes between gestational day 15 (+/- 0.5 days) C57BL/6 mouse fetal livers from diet-induced (60% fat diet) obese or control female mice.

first: Ashley

middle: N

last: Kamimae-Lanning

first: Stephanie

last: Krasnow

first: Natalya

last: Goloviznina

first: Quinn

last: Roth-Carter

first: Peter

last: Levasseur

first: Sophia

last: Jeng

first: Shannon

middle: K

last: McWeeney

last: Kurre

first: Daniel

last: Marks


title: Genome-wide expression profiles in young and old mouse liver [RNA-seq]

first: Irina

last: Bochkis

overall_design: Genome-wide expression profiles (RNA-Seq) from young (3 months) and old (21 months) mouse livers

first: Aviv

last: Regev


first: Vishy

last: Iyer

summary: We report the genome-wide Chd1 co-occupancy with early transcription elongation factors

overall_design: ChIP-seq for Chd1 and elongating RNA polymerase II

first: Vishwanath


title: Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver

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

overall_design: Refer to individual Series


title: Nucleosome occupancy profiles in young and old mouse liver [MNase-Seq]

overall_design: Genome-wide nucleosome profiles  (MNase-Seq) from young (3 months) and old (21 months) mouse livers


title: ERK signaling regulates opposing functions of JUN family transcription factors in prostate cancer cell migration

city: Bloomington

last: Hollenhorst

state: Indiana

address: 1001 E 3rd St

department: Medical Sciences

institute: Indiana University

summary: Knockdowns of c-JUN and JUND had opposite effects on PC3 prostate cell migration. We predicted that c-JUN and JUND control the same set of cell migration genes, but in opposite directions. To test this hypothesis, mRNA with expression changes in c-JUN and JUND knockdown PC3 cell lines were compared to mRNA levels in control (luciferase knockdown) PC3 cells by RNA-seq.

overall_design: mRNA profiles of luciferase knockdown (WT),  c-Jun knockdown, and Jun-D knockdown in PC3 cells were generated using deep sequencing, in triplicate, using Illumina HiSeq. Knockdowns were stable shRNA expression from a lentiviral construct selected with puromycin.

first: Nagarathinam

last: Selvaraj

first: Justin

middle: A

last: Budka


title: RNA-seq from primary skin fibroblasts, derived of matched pairs of middle and late donor age

city: Duarte

first: Marc

last: Jung

address: 1500 East Duarte Street

department: Biology

institute: City Of Hope

summary:
Aging signatures developed from a longitudinal study design are dominated by reduced transcription of genes involved in protein synthesis
Aging is a multifactorial process where the impact of singular components still remains unclear. Furthermore, previous studies were focused on measuring specific traits such as DNA -methylation and used categorical group-wise designs, unable to capture intra-individual signature changes. Here we have developed a new method for a longitudinal, age-related analysis combining the merits of a pair-wise design with the statistical power of gene set enrichment analysis. We present an integrated analysis, including transcriptional changes and genome-wide epigenetic changes in DNA- methylation, H3K4- and H3K27- histone methylation in promoter regions.  We tested our method on a rare collection of paired skin fibroblast samples from male middle age to old age transitions and obtained functional, age-related clusters. By using a set of only ten individuals, we could demonstrate a high overlap of functional terms to previously established tissue-independent age signatures including extracellular matrix, apoptosis and oxidative stress. Importantly, we identify protein translation-related processes as the main cluster of age-driven, specific down regulation.

overall_design: Evaluation of transcriptional changes in matched sample pairs of primary skin fibroblasts from middle and old age.

first: Xiaoying

last: Zhang

first: Seung-Gi

last: Jun

first: Grigory

last: Gogoshin

first: Andrei

last: Rodin

first: Gerd

last: Pfeifer


title: Aging signatures developed from a longitudinal study design are dominated by reduced transcription of genes involved in protein synthesis.

type: Methylation profiling by genome tiling array


title: Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for Osteoporosis Risk [methylome]

status: Public on Oct 22 2014

city: Chang sha

first: shishi

last: min

state: Hunan

address: Lu shan  road

department: College of life sciences

institute: Hunan Normal University

type: Methylation profiling by high throughput sequencing

summary: In this study, we analyzed transcriptome gene expression microarray, epigenomic miRNA microarray and methylome sequencing data simultaneously in PBMs from 5 high hip BMD subjects and 5 low hip BMD subjects. Through integrating the transcriptomic and epigenomic data, firstly we identified BMD-related genetic factors, including 9 protein coding genes and 2 miRNAs, of which 3 genes (FAM50A, ZNF473 and TMEM55B) and one miRNA (hsa-mir-4291) showed the consistent association evidence from both gene expression and methylation data, and 3 genes (TMEM55B, RNF40 and ALDOA) were confirmed in the meta-analysis of 7 GWAS samples and GEnetic Factors for OSteoporosis consortium (GEFOS-2) GWAS results. Secondly in network analysis we identified an interaction network module with 12 genes and 11 miRNAs including AKT1, STAT3, STAT5A, FLT3, hsa-mir-141 and hsa-mir-34a which have been associated with BMD in previous studies. This module revealed the crosstalk among miRNAs, mRNAs and DNA methylation and showed four potential regulatory patterns of gene expression to influence the BMD status, including regulation by gene methylation, by miRNA and its methylation, by transcription factors and co-regulation by miRNA and gene methylation. In conclusion, the integration of multiple layers of omics can yield more in-depth results than analysis of individual omics data respectively. Integrative analysis from transcriptomics and epigenomic data improves our ability to identify causal genetic factors, and more importantly uncover functional regulation pattern of multi-omics for osteoporosis etiology.

first: Jigang

first: Lijun

last: Tan

first: Chao

last: Xu

first: Hao

last: He

first: Qing

last: Tian

first: Yu

last: Zhou

first: Chuan

last: Qiu

first: Xiang

last: Chen

first: Hong

middle: W

last: Deng


title: Barley leaf dark-induced senescence

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

summary: Time-course transcriptional profiling of senescing barley leaves. In this model, the senescence process was induced by continued incubation of the seedlings in darkness. Plant samples for the expression analysis were collected before senescence induction (Day 0) and after 3,7 and 10 days of incubation in the dark. The goal was to find the genes differentially expressed during the senescence process . Additionally, a list of the genes with the invariant expression was generated as a resource for selecting references suitable for qPCR or ddPCR experiments.

overall_design: Time-course experiment, two-color, common reference design. All of the data were obtained from material collected in three independent, time-separated leaf senescing experiments (biological replicates). In each replicate, samples from senescing leaves (3 Days, 7 Days, 10 Days) were compared to samples collected before the senescence induction (Day 0). 3 biological replicates.Cy5-labeled samples of interest (Day 0, Day 3, Day 7 and Day 10 from each biological replicate) were each hybridized against a Cy3-labeled common reference (RNA pool of all samples) on a total of 12 microarrays.

first: Anna

last: Samelak-Czajka

first: Michal

last: Goralski

first: Ewa

last: Sobieszczuk-Nowicka

first: Marek

last: Figlerowicz


title: SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy

city: Basel

first: Friedrich

last: Metzger

address: Grenzacherstr.

country: Switzerland

institute: F. Hoffmann-La Roche

summary: Characterization of the selectivity of SMN splicing modifiers in SMA type I fibroblasts by RNASeq

overall_design: In total 12 samples were analyzed, divided into four distinct groups (treated with SMN-C3 @ 500 nM; controls for SMN-C3; treated with SMN-C1 @ 100 nM; controls for SMN-C1) containing 3 replicates each.

first: Amal

last: Dakka

first: Anirvan

last: Ghosh

first: Anthony

last: Turpoff

first: Anuradha

last: Bhattacharyya

first: Bansri

last: Furia

first: Chang-Sun

last: Lee

first: Chien-Ping

last: Ko

first: Daniel

last: Haehnke

first: Ellen

middle: M

last: Welch

first: Gary

last: Karp

first: Guangming

first: Hasane

last: Ratni

first: Hongyan

last: Qi

first: Irene

last: Gerlach

first: Jana

last: Narasimhan

first: Jesse

last: Mull

first: Jiyuan

last: Ma

first: John

last: Babiak

first: Joseph

last: Colacino

first: Josephine

last: Sheedy

first: Karen

last: Ling

first: Kathleen

last: McCarthy

first: Lee

last: Rubin

first: Loren

last: Eng

first: Luca

last: Santarelli

first: Manaswini

last: Sivaramakrishnan

first: Marla

last: Weetall

first: Martin

last: Ebeling

first: Matthew

middle: G

last: Woll

first: Maureen

last: Lynes

first: Nanjing

last: Zhang

first: Neil

last: Almstead

first: Nicole

last: Risher

first: Nikolai

last: Naryshkin

first: Panayiota

last: Trifillis

first: Paulo

last: Fontoura

first: Priya

last: Vazirani

first: Roland

last: Schmucki


title: Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for Osteoporosis Risk

first: shishi

last: min

platform_organism:
Homo sapiens
synthetic construct


title: Plant microRNA profiling of Honeysuckle and Honeysuckle Decoction

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary: Influenza A viruses (IAVs), particularly H1N1, H5N1 and H7N9, pose a substantial threat to public health worldwide. Here, we report that MIR2911, a honeysuckle (HS)-encoded atypical microRNA, directly targets IAVs with a broad spectrum. MIR2911 is highly stable in HS decoction, and continuous drinking or gavage feeding of HS decoction leads to a significant elevation of the MIR2911 level in mouse peripheral blood and lung. Bioinformatics prediction and a luciferase reporter assay showed that MIR2911 could target various IAVs, including H1N1, H5N1 and H7N9. Synthetic MIR2911 significantly inhibited H1N1-encoded PB2 and NS1 protein expression but did not affect mutants in which the MIR2911-binding nucleotide sequences were altered. Synthetic MIR2911, extracted RNA from HS decoction and HS decoction all significantly inhibited H1N1 viral replication and improved viral infection-induced mouse weight loss but did not affect infection with a mutant virus in which the MIR2911-binding nucleotide sequences of PB2 and NS1 were altered. Importantly, the inhibitory effect of HS decoction on viral replication was abolished by an anti-MIR2911 antagomir, indicating that the physiological concentration of MIR2911 in HS decoction could directly and sufficiently suppress H1N1 viral replication. MIR2911 also inhibited H5N1 and H7N9 viral replication in vitro and in vivo. Strikingly, administration of MIR2911 or HS decoction both dramatically reduced mouse mortality caused by H5N1 infection. Our results demonstrate that MIR2911 is the first active component identified in Traditional Chinese Medicine to directly target various IAVs and may represent a novel type of natural product that effectively suppresses viral infection.

overall_design: Screening and profiling of known plant microRNA in HS and HS decoction

first: Xihan

last: Li


title: Vanillin derivatives triggers oxidative stress and inhibit mitochondrial functions in Cryptococcus neoformans

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary:
Purpose: The purpose of this study is to define the mechanism of antifungal action of the vanillin derivative, o-vanillin, against Cryptococcus neoformans
Methods: mRNA profiles of C. neoformasn cells cultured with or without o-vanillin were generated by RNA-Seq, using Illumina GAIIx. The sequence reads that passed quality filters were mapped to reference genome and the normalized RPKM values were calculated by CLC Genomics Workbench.
Results: o-vanillin significantly altered global transcript profiles, induces oxidative stress, and interferes mitochondrial functions in C. neoformans.
Conclusions: o-vanillin can be considered as the effective antifungal drug candidate.

overall_design: mRNA profiles of the cells grown in the presence or absence of o-vanillin were generated by RNA-Seq using Illumina GAIIx.

first: Jin

middle: H

last: Kim

first: Han-Ok

last: Lee

first: Jeongmi

first: Jongsik

last: Chun

first: Jaehyuk

last: Choi

first: Younghoon

first: Won

last: Jung


title: Aberrant DNA methylation in rhabdomyosarcoma

city: Seattle

first: Scott

middle: J.

last: Diede

state: WA

address: 1100 Fairview Avenue North, Mailstop c3-168

institute: Fred Hutchinson Cancer Research Center

summary: Many pediatric malignancies are embryonal in nature, and one hypothesis for the origin of embryonal tumors is that they arise from a defect in differentiation, either by an inability to terminally differentiate or a reversion to a pluripotent state. There is emerging evidence that epigenetic regulation plays an important role in the transition from embryonic stem cell to a more committed cell fate, utilizing both de novo DNA methylation and poised ‘bivalent’ chromatin domains (H3K27me3 and H3K4me3) to abolish pluripotency and gain lineage- and cell-type-specific characteristics as a cell differentiates. Thus inappropriate epigenetic silencing by aberrant DNA methylation of bivalent genes required for differentiation could lead to the uncontrolled cell growth observed in cancer. Our broad hypothesis is that aberrant DNA methylation in cancer is targeted to a non-random subset of critical pathways used in normal development. This dysregulation of the normal epigenetic program used in development promotes cellular proliferation and provides a mechanism to block differentiation in pediatric cancers, such as rhabdomyosarcoma.

overall_design: Examination of DNA methylation in fourteen human rhabdomyosarcoma patient samples using RRBS. In addition, RRBS was used to examine DNA methylation in one human rhabdomyosarcoma cell line (RD) forced to terminally differentiate by expression of the forced heterodimer MyoD~E12 (MDE). Lastly, RRBS was used to examine DNA methylation changes during normal differentiation in one primary human normal myoblast cell line

middle: J

first: Zizhen

last: Yao

first: Erin

last: Rudzinski

first: Douglas

last: Hawkins

first: Stephen

last: Tapscott


title: High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture (NGS)

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: Eukaryotic genomes are folded into a hierarchy of three-dimensional structures that impact nuclear functions, including transcription, replication, and repair1-3. Studies in Drosophila and mammals have revealed megabase-sized topologically associated domains (TADs) within chromosomes, which in turn are spatially restricted within the nucleus4-8.  However, little is known about local physical constraints that drive higher-order folding of chromosomes. Here we performed Hi-C analysis of the fission yeast Schizosaccharomyces pombe to explore genome organization at high resolution. S. pombe comprises a small genome ideal for examining structural features of chromatin folding, and contains fundamental components present in higher eukaryotes. Large domains of heterochromatin coat centromeres and telomeres and recruit cohesin, a ring-like protein complex that binds sister chromatids and mediates long range looping of interphase chromosomes. Our analyses reveal a highly ordered chromosome organization, consistent with a Rabl configuration, which is dependent on constraints imposed at centromeres and telomeres. We find that local chromatin compaction and cohesin recruitment to centromeres mediated by heterochromatin is required for maintaining global genome territorial restraint. In addition to larger complex domains, we also observed locally interacting regions of chromatin ~50 kilobases long, which organize chromosome arms into structures referred to as “globules”. Globule boundaries are enriched in cohesin and convergent gene orientation. The role of cohesin in maintaining globule domains is independent of its role in sister chromatid cohesion, as globule domains are also a feature of G1 chromosome architecture. Defect in cohesin disrupts globule domains and results in an altered chromosome organization at larger scales, including the loss of chromosome territories. Disruption of globules also affects functional annotation of the genome, leading to impairment of borders between neighboring transcriptional units. Our analyses reveal key features of chromatin organization and folding and show that distinct mechanisms uniquely impact the hierarchy of genome organization to protect genome integrity and to coordinate nuclear functions.

overall_design: Comparison of HiC contact maps under various conditions reveal fundamental principles of genome organization

first: Sameet

last: Mehta

first: Mizuguchi

last: Takeshi


title: PRC2 loss amplifies Ras-driven transcription and confers sensitivity to BRD4-based therapies [ChIP-seq]

status: Public on Oct 21 2014

city: Boston

first: Thomas

last: De Raedt

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Harvard Medical School -  Brigham Women's Hospital

summary: The polycomb repressive complex 2 (PRC2) exerts oncogenic effects in many tumour types1. However, loss-of-function mutations in PRC2 components occur in a subset of haematopoietic malignancies, suggesting that this complex plays a dichotomous and poorly understood role in cancer2,3. Here we provide genomic, cellular, and mouse mod- elling data demonstrating that the polycomb group gene SUZ12 func- tions as tumour suppressor in PNS tumours, high-grade gliomas and melanomas by cooperating with mutations in NF1. NF1 encodes a Ras GTPase-activating protein (RasGAP) and its loss drives cancer by activating Ras4. We show that SUZ12 loss potentiates the effects of NF1 mutations by amplifying Ras-driven transcription through effects on chromatin. Importantly, however, SUZ12 inactivation also triggers an epigenetic switch that sensitizes these cancers to bromodomain inhib- itors. Collectively, these studies not only reveal an unexpected con- nection between the PRC2 complex, NF1 and Ras, but also identify a promising epigenetic-based therapeutic strategy that may be exploited for a variety of cancers.

overall_design: 2x3 samples (DMSO and PDJQ treated; WCL, BRD4 and H3K27Ac pulldown)


title: Inactivation of the Budding Yeast Cohesin Loader Scc2 alters Gene Expression both Globally and in Response to a Single DNA Double Strand Break

city: Stockholm

first: Lena

last: Ström

address: Berzelius väg 35

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae


title: Role of Tet3 and DNA replication in zygotic demethylation of both paternal and maternal genomes

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School


title: Inactivation of the Budding Yeast Cohesin Loader Scc2 alters Gene Expression both Globally and in Response to a Single DNA Double Strand Break [ChIP-seq]

summary: Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2, but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding.

overall_design: We investigated Scc1 FLAG tagged binding in WT ans Scc2-4 mutant in absence and presence of a single DNA DSB on Chr. VI

first: Emma

last: Lindgren

first: Sara

last: Hägg

first: Fosco

last: Giordano

first: Johan

last: Björkegren


title: Role of Tet3 and DNA replication in zygotic demethylation of both paternal and maternal genomes [RNA-seq]

summary: With the exception of imprinted genes and certain repeats, DNA methylation is globally erased during pre-implantation development. Recent studies have suggested that Tet3-mediated oxidation of 5-methylcytosine (5mC) and DNA replication-dependent dilution both contribute to global paternal DNA demethylation, but demethylation of the maternal genome occurs via replication. Here we present genome-scale DNA methylation maps for both the paternal and maternal genomes of Tet3-depleted and/or DNA replication-inhibited zygotes. In both genomes, we found that inhibition of DNA replication blocks DNA demethylation independently from Tet3 function, and that Tet3 facilitates DNA demethylation by coupling with DNA replication. For both, our data indicate that replication-dependent dilution is the major contributor to demethylation, but Tet3 plays an important role, particularly at certain loci. Our study therefore both defines the respective functions of Tet3 and DNA replication in paternal DNA demethylation and reveals an unexpected contribution of Tet3 to demethylation of the maternal genome.

overall_design: In this data set, we include RNA-Seq data of mouse 2-cell embryos and blastocysts derived from both wildtype and Tet3-null oocytes

first: Azusa

last: Inoue

first: Jin

last: He

first: Yuting

last: Liu

first: Falong

last: Lu

first: Yi

last: Zhang


title: Identification of miRNAs and their target genes in developing maize ears by deep sequencing

city: Wenjiang,Chengdu

first: hongjun

last: liu

state: Sichuan

address: 211 Huimin Road

institute: Sichuan Agricultural University

summary: In plants, MicroRNAs (miRNAs) are a new class of endogenous small RNAs that play essential regulatory roles in plant growth, development and stress response. Extensive studies of miRNAs have been performed in model plants such as rice, Arabidopsis thaliana and other plants. However, the number of miRNAs discovered in maize is relatively low and little is known about miRNAs involved in the four stages during maize ear development. Here, we use deep-sequencing, miRNA microarray assays and computational methods to identify, proﬁle, and describe conserved and non-conserved miRNAs at four developmental stages. A total of 27 conserved miRNA families were identiﬁed in all four stages, In addition to known miRNAs, we also found 23 new maize-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. We have found that many known and new miRNAs showed temporally expression. Finally, a total of 251 transcripts (140 genes) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.This study led to the confirmation of the authenticity of 27 conserved miRNA families and the discovery of 23 novel miRNAs in maize. In addition, we have identified 130 targets of known and new miRNAs and ta-siRNA using recently developed tools for the global identification of miRNA targets. Identification and characterization of this important class of regulatory genes in maize may improve our understanding of molecular mechanism controlling flower development.

overall_design: The seeds of maize inbred line B73 were first sterilized and germinated in an incubator, then grown in a controlled environment with 28°C/21°C (day/night) under a 16-h day/8-h night photoperiod with a relative humidity of 70%. Ear development can be divided into four stages: the growth point elongation phase, spikelet differentiation phase, the floret primordium differentiation phase and floret organ differentiation phase. Plant materials (ears) were collected as described previously. In brief, ears were manually collected at the four developmental stages according to the plant features (number of visible leaves, leaf age index, and number of unfolded and folded leaves) combined with microscopic observation.

first: Hongjun

first: Cheng

last: Qin

first: Zhen

last: Chen

first: Huangkai

last: Zhou

first: Meng

last: Xu

first: Yaou

first: Haijian

first: Xiujing

first: Yinchao

first: Lujiang

last: Li

first: Haiping

last: Ding

last: Lubberstedt

first: Zhiming

first: Guangtang

last: Pan


title: High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture

first: Shiv

last: Grewal

type: Genome variation profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array


title: EGR2 is Critical for Peripheral Naïve T Cell Differentiation and the T-cell Response to Influenza

first: Peng

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: EGR2 is an early growth response transcription factor that negatively regulates T-cell activation, in contrast to its positive regulation by EGR1. Here, we unexpectedly found that EGR2 promotes peripheral naïve T cell differentiation, with delayed TCR-induced proliferation in naïve T cells from Egr2 conditional knockout (CKO) mice, and decreased production of IFN-γ, IL-4, IL-9, and IL-17A in cells subjected to T helper differentiation. Moreover, genes that promote T-cell activation, including Tbx21 and Notch1, had decreased expression in Egr2 CKO T cells and are direct EGR2 target genes. Following influenza infection, Egr2 CKO mice had delayed viral clearance, more weight loss, and more severe pathological changes in the lung than did WT and Egr1 KO mice, with decreased production of effector cytokines and infiltration of antigen-specific memory-precursor CD8+ T cells but lower numbers of lung-resident memory CD8+ T cells. Thus unexpectedly EGR2 can function as a positive regulator that is essential for naïve T-cell differentiation and in vivo T-cell responses to a viral infection.

overall_design: Genome-wide transcription factors mapping and binding of EGR2 in mouse Total T cells. RNA-Seq is conducted in WT and Egr2-/- mice.

first: Ning

last: Du

first: Hyokjoon

last: Kwon

first: Erin

last: West

first: Jangsuk

last: Oh

first: Wei

last: Liao

first: Zu-Xi

last: Yu

first: Min

last: Ren

first: Warren

last: Leonard


title: Tumor cell-specific inhibition of MYC function using small molecule inhibitors of the HUWE1 ubiquitin ligase

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

summary: Deregulated expression of MYC is a driver of colorectal carcinogenesis, necessitating novel strategies to inhibit MYC function. The ubiquitin ligase HUWE1 (HECTH9, ARFBP1,  MULE) associates with both MYC and the MYC-associated protein MIZ1. We show here that HUWE1 is required for growth of colorectal cancer cells in culture and in orthotopic xenograft models. Using high throughput screening, we identify small  molecule inhibitors of HUWE1, which inhibit MYC-dependent transactivation in colorectal cancer cells, but not in stem and normal colon epithelial cells. Inhibition of HUWE1 stabilizes MIZ1. MIZ1 globally accumulates on MYC target genes and contributes to repression of MYC-activated target genes upon HUWE1 inhibition. Our data show that transcriptional activation by MYC in colon cancer cells requires the continuous degradation of MIZ1 and identify a novel principle that allows for inhibition of MYC function in tumor cells.

overall_design: MIZ1 and MYC ChIPseq experiments in HUWE1 inhibitor-treated Ls174T cells as well as RNAseq experiments in HUWE1- or MIZ1-depleted Ls174T cells after HUWE1 inhibitor treatment. Sequencing was performed on an Illumina Genome Analyzer IIx.

first: Stefanie

last: Peter

first: Jennyfer

last: Bultinck

first: Kevin

last: Myant

first: Laura

last: Jaenicke

first: Susanne

last: Walz

first: Judith

last: Müller

first: Michael

last: Gmachl

first: Matthias

last: Treu

first: Guido

last: Boehmelt

first: Carsten

last: Ade

first: Werner

last: Schmitz

first: Armin

last: Wiegering

first: Christoph

last: Otto

first: Nikita

last: Popov

first: Owen

last: Sansom

first: Norbert

last: Kraut


title: Genome-wide profiling of microRNAs in sweet orange

city: Wuhan

first: Liu

last: Yuanlong

address: Shizishan street NO.1

institute: Huazhong agriculture university

summary: miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs in leaves and flowers of sweet orange. Consequently we identified genome-wide 183 known miRNAs and 38 novel miRNAs.

overall_design: Small RNA sequencing of the leaves and flowers in sweet orange

first: Yuanlong

last: Liu

first: Qiang

last: Xu


title: Genome-wide profiling of microRNAs and their targets in sweet orange

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

overall_design: Refer to individual Series


title: SCBI Wild type and mutant Expression data

status: Public on Oct 20 2014

city: Durham

first: Louis

last: Tisa

state: NH

address: 46 College Rd

department: MCBS

institute: University of New Hampshire

summary: Purpose: To compare RNASeq data of wild type and mutants under standard growth conditions (Stationary Phase)28C for 18 h.  The mutants were found defective in genes encoding the following proteins: an alkaline metalloprotease secretion protein AprE,  GidA,  and a PIN domain protein. RNA-seq analysis provided insight into how inactivation of AprE, GidA and a PIN-domain protein influences global gene expression

overall_design: mRNA profiles of wild type and mutants were generated by deep sequencing and mapped to SCBI genome by CLC Gemonic Workstation.  The transcriptome profiles of the mutants were compared to the wild type.

first: Lauren

last: Petersen


title: RNA sequencing of monocytes and microglia from mice with experimental autoimmune encephalomyelitis illustrates a changing phenotype with disease course

city: Ridgefield

first: Jonathan

middle: Daryl

last: Hill

state: CT

address: 900 Ridgebury Road

department: Computational Biology

institute: Boehringer Ingelheim Pharmaceuticals Inc

summary: The role of microglia and infiltrating monocytes in experimental autoimmune encephalomyelitis (EAE) pathogenesis has been controversial. To gain insight into their respective roles, we developed a method for differentiating between microglia and infiltrating monocytes in the CNS using CD44. We used this system to monitor changes in cell number, activation status, and gene expression by RNA sequencing (RNA-Seq) over the course of disease. This in vivo characterization and RNA-Seq dataset improves our understanding of myeloid cell biology in the brain under inflammatory conditions and may lead to strategies to identify therapies for inflammatory pathways active in neuroinflammatory diseases.

overall_design: Pooled samples from 10 mice were analyzed for both microglia and monocytes at distinct timepoints post EAE inducation.  Peritoneal macrophages were isolated and analyzed for five samples, and also in a pool.

first: Nuruddeen

last: Lewis

first: Kathryn

last: Juchem

first: Louise

last: Modis

first: Dimitria

last: Stefanopoulos


title: Genome-wide profiling of microRNAs target transcripts in sweet orange

summary: miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs targets in leaves, flowers and fruit of sweet orange.C onsequently, 55257, 62365 and 19393 degraded mRNA fragments were identified in leaf, flower and fruit, respectively.

overall_design: miRNAs-mediated degraded fragments sequencing of the leaves, flowers and fruit in sweet orange


title: Cooperativity, specificity and evolutionary stability of Polycomb targeting in Drosophila

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

summary: We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species (GSE60428) and HiC analysis in Drosophila melanogaster. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of  PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter

overall_design: HiC experiments in wild type drosophila embryos

first: Bernd

last: Schuettengruber

first: Noa

middle: O

last: Elkayam

first: Tom

last: Sexton

first: Marianne

last: Entrevan

first: Shani

last: Stern

first: Aubin

last: Thomas

first: Eitan

last: Yaffe

first: Hugues

last: Parrinello

first: Amos

last: Tanay

first: Giacomo

last: Cavalli


title: Transcriptome-wide ribonuclease footprinting to identify RNA-protein interaction sites

city: Philadelphia

first: Ian

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

institute: University of Pennsylvania

summary: RNA-binding proteins (RBPs) are intimately involved in all aspects of RNA processing and regulation and are linked to neurodegenerative diseases and cancer. Therefore, understanding the relationship between RBPs and their RNA targets is critical for a broader understanding of post-transcriptional regulation in normal and disease processes.  The majority of approaches to study RNA-protein interactions focus on single RBPs, however there are many hundreds RBPs encoded in the human genome, and each cell type expresses a different catalog of these regulatory molecules, greatly limiting the ability of these single RBP approaches to capture the global landscape of RNA-protein interactions. We and others have developed approaches to globally catalog regions of mRNAs that are bound by proteins in an unbiased manner.  Here we describe a detailed protocol for performing our RNase-mediated protein footprint sequencing approach, termed protein interaction profile sequencing (PIP-seq). In this protocol, RNA-protein interactions are stabilized by cross-linking, and un-bound regions are digested with RNases, leaving only the protein-bound regions intact. To control for RNase insensitive regions, proteins are first denatured and then RNP complexes are subject to RNase treatment. After high-throughput sequencing of remaining fragments, peak calling is performed to identify protein protected sites (PPSs). We describe the application of this protocol to a human embryonic kidney cell line and perform basic quality control, reproducibility and benchmarking analyses.  Finally, we describe the landscape of protein-interactions in HEK293T cells, underscoring the value of this approach.  Future applications of this method to study the dynamics of RNA-protein interactions in developmental processes will help to uncover the role of RBPs in post-transcriptional regulation.

overall_design: Protein interaction profile sequencing (PIP-seq) in HEK293T cells. Three replicates of formaldehyde cross-linked PIP-seq are described

first: Brian

last: Gregory


title: m6A RNA modification controls cell fate transition in mammalian embryonic stem cells

city: Los Angeles

first: Jinkai

last: Wang

address: 650 Charles E. Young Drive South, CHS 33-228

institute: University of California, Los Angeles

summary: N6-methyl-adenosine (m6A) is the most abundant modification on messenger RNAs and is linked to human diseases, but its functions in mammalian development are poorly understood. Here we reveal the evolutionary conservation and function of m6A by mapping the m6A methylome in mouse and human embryonic stem cells. Thousands of messenger and long noncoding RNAs show conserved m6A modification, including transcripts encoding core pluripotency transcription factors. m6A is enriched over 3’ untranslated regions at defined sequence motifs, and marks unstable transcripts, including transcripts turned over upon differentiation. Genetic inactivation or depletion of mouse and human Mettl3, one of the m6A methylases, led to m6A erasure on select target genes, prolonged Nanog expression upon differentiation, and impaired ESC’s exit from self-renewal towards differentiation into several lineages in vitro and in vivo. Thus, m6A is a mark of transcriptome flexibility required for stem cells to differentiate to specific lineages.

overall_design: Examing m6A modification differences in two different cell types

first: Cosmas

middle: C

last: Giallourakis

first: Yi

last: Xing

first: Benoit

last: Molinie


title: Identification and validation of antisense RNAs in Escherichia coli

status: Public on Oct 18 2014

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions

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

overall_design: To detect the complement of transcripts expressed from E. coli, we collected two independent biological replicates (B1 and B2 samples) from MG1655 wild type strain grown to exponential (OD 600 ~0.4) or stationary phase (OD 600 ~2.0) in LB medium (samples LB 0.4 and LB 2.0, respectively) as well as grown to exponential phase (OD 600 ~0.4) in M63 minimal glucose medium (sample M63 0.4). For all six samples, total RNA was extracted and subjected to differential RNA-seq (dRNA-seq) library preparation for primary transcriptome analysis as described previously (Sharma et al., 2010). Specifically, prior to cDNA library construction half of each RNA sample was treated with 5’ terminator exonuclease (+TEX samples), which degrades RNAs containing a 5’-mono-phosphate (5’-P) and, thus, enriching enriches for primary transcripts containing 5’-tri-phosphates (5’-PPP). The other half of each sample was left untreated (-TEX samples) and thus contains both primary transcripts (5’-PPP) and processed RNAs (5’-P).

first: Thorsten

last: Bischler

first: Maureen

last: Thomason

first: Sara

last: Eisenbart

first: Aixia

last: Zhang

middle: U

first: Alexander

last: Herbig

first: Kay

last: Nieselt

first: Cynthia

last: Sharma

first: Gisela

last: Storz


title: A role for non-coding variation in schizophrenia

status: Public on Oct 17 2014

city: New York

first: Panos

last: Roussos

state: NY

address: 1470 Madison Ave

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary: A large portion of common variant loci associated with genetic risk for schizophrenia reside within non-coding sequence of unknown function. Here, we demonstrate promoter and enhancer enrichment in schizophrenia variants associated with expression quantitative trait loci (eQTL). The enrichment is greater when functional annotations derived from human brain are used relative to peripheral tissues. Regulatory trait concordance analysis ranked genes within schizophrenia genome-wide significant loci, based on co-localization of a risk SNP, eQTL and regulatory element sequence. These include physical interactions of non-contiguous gene-proximal and distal elements bypassing the linear genome, which was verified in prefrontal cortex and human induced pluripotent stem cell derived neurons for the L-type calcium channel (CACNA1C) risk locus. Our findings point to a functional link between schizophrenia-associated non-coding SNPs and 3-dimensional genome architecture associated with chromosomal loopings and transcriptional regulation in the brain.

overall_design: Examination of H3K4me3 histone modifications in 3 samples.

first: Schahram

last: Akbarian


title: Transcriptome data of CD34+ human cord blood-derived cell treated with UM171, SR1 or both

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: mRNA profiling of CD34+ human cord blood-derived cell treated with UM171, SR1 or both

overall_design: mRNA profiles of CD34+ human cord blood-derived cell treated with DMSO (control), SR1 [500nM], UM171  [35nM] or combination SR1 [500nM]+ UM171  [35nM] for 30min, 3hr, 12hr, 24hr, 48hr, 72hr were generated by deep sequencing

first: Iman

last: Fares


title: Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell type specificity

status: Public on Oct 16 2014

city: Groningen

first: Barbara

last: Hrdlickova

state: the Netherlands

address: PO Box 30 001

department: of Genetics

institute: University of Groningen, University Medical Center Groningen

summary:
Background: Although genome-wide association studies (GWAS) have identified hundreds of variants associated with risk of autoimmune and immune-related disorders (AID), our understanding of the diseases mechanisms is limited. In particular, more than 90% of the risk variants lie in non-coding regions, and almost 10% of these map to long non-coding RNA transcripts (lncRNAs). LncRNAs are known to show more cell-type specificity than protein-coding genes.
Methods: In this study, we aimed to characterize lncRNAs and protein-coding genes located in loci associated with nine AID which have been well-defined by Immunochip analysis, by transcriptome analysis across seven peripheral blood leukocyte populations (granulocytes, monocytes, NK cells, B-cells, memory-T cells, naive CD4+ and naive CD8+ T-cells) and four cord blood derived T-helper cell populations (precursor, primary, polarized (Th1, Th2) T-helper cells).
Results: We show that lncRNAs mapping to loci shared between AIDs are significantly enriched in immune cell types when compared to lncRNAs from the whole genome (α<0.005). We were not able to prioritize single cell types relevant for specific diseases, but we observed five cell types enriched (α<0.005) in five AID (NK cells for inflammatory bowel disease, juvenile idiopathic arthritis, primary biliary cirrhosis, psoriasis; memory-T and CD8+ T-cells in juvenile idiopathic arthritis, primary biliary cirrhosis, psoriasis, rheumatoid arthritis; Th0 and Th2 cells for inflammatory bowel disease, juvenile idiopathic arthritis, primary biliary cirrhosis, psoriasis, rheumatoid arthritis). Furthermore we show that co-expression analyses of lncRNAs and protein-coding genes can predict the signaling pathways in which these AID-associated lncRNAs are involved.
Conclusions: The observed enrichment of lncRNA transcripts in AID loci implies an important role for lncRNAs in AID etiology and suggests that lncRNA genes should be studied in more detail to correctly interpret GWAS findings. The co-expression results strongly support a model in which the lncRNA and protein-coding genes function together in the same pathways.

overall_design: 7 immune cell types

first: Sebo

last: Withoff


title: Genome-wide profiling of Zfp335 binding sites in thymocytes

city: Singapore

first: Brenda

middle: Yuyuan

last: Han

address: 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology, A*STAR

summary: The generation of naïve T lymphocytes is critical for immune function yet the mechanisms governing their maturation remain incompletely understood. We have identified a mouse mutant, bloto, that harbors a hypomorphic mutation in the zinc finger protein Zfp335. Mutant blt/blt mice exhibit a naïve T cell deficiency due to an intrinsic developmental defect that begins to manifest in the thymus and continues into the periphery, affecting T cells that have recently undergone thymic egress. Zfp335 binds to promoter regions via a consensus motif, and its target genes are enriched in categories related to protein metabolism, mitochondrial function and transcriptional regulation. Restoring the expression of one target, Ankle2, partially rescues T cell maturation. Our findings identify Zfp335 as a transcription factor and essential regulator of late-stage intrathymic and post-thymic T cell maturation.

overall_design: 4 Zfp335 ChIP-seq samples and 2 input samples with WT vs. blt/blt thymocytes.

middle: Y

first: Shuang

last: Wu

first: Chuan

middle: S

last: Foo

first: Robert

last: Horton

first: Craig

last: Jenne

first: Susan

middle: R

last: Watson

first: Belinda

last: Whittle

first: Christopher

last: Goodnow

first: Jason

last: Cyster


title: mRNA and sRNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation for Allopolyploid Heterosis in Nascent Hexaploid Wheat

city: Beijing

first: Mengdi

last: Liu

address: No.38 Xueqing Road, Haidian District

institute: Novogene institute

summary: Nascent allohexaploid wheat may represent the initial genetic state for the evolution and domestication of common wheat, which arose by combining the AB genomes of tetraploid Triticum turgidum with the D genome from Aegilops tauschii and out-competed its parents in growth vigor and adaptability. To better understand the molecular basis for this success, we performed mRNA and small RNA expression analyses in three tissues of nascent allohexaploid wheat and its following generations, their progenitors, and Chinese Spring, with the assistance of newly released A and D genome sequences. We found that nonadditive expression was rare among protein-coding genes which exhibited profound parental expression level dominance, with genes of total homoeolog expression level in nascent allohexaploid progeny similar to their expression levels in T. turgidum functionally enriched for development and those to Ae. tauschii distinctively for adaptation. In contrast, miRNAs appeared to be sensitive to polyploidization, with nonadditively expressed miRNAs potentially involved in growth vigor and adaptation. Meanwhile, siRNAs may contribute to biased repression of D homoeolog, possibly due to increased siRNA density on transposable element (TE)-associated D homoeologs. Together, our data provide new insights into homoeolog regulatory mechanisms that may be essential to heterosis in nascent hexaploid wheat.

sample_organism:
Triticum aestivum
Triticum turgidum
Aegilops tauschii

overall_design: We performed mRNA and small RNA analyses in three tissues of nascent allohexaploid wheat and its following generations, their progenitors, and Chinese Spring.Among these samples, Samples 1-6 and 26-31, tetraploid progenitors; Samples 7-12 and 32-37, diploid progenitors;  Samples 13-22 and 38-47, following generations; Samples 23-25 and 48-50, Chinese Spring.

first: L

last: Mao

first: D

last: Li

first: J


title: Golden snub-nosed monkey transcriptome data used for gene annotation

status: Public on Oct 19 2014

city: Bei Jing

first: Shilin

last: Tian

address: Xueqing Road

department: genome research

institute: Novogene Bioinformatics Technology CO.ltd

summary: To optimize the golden snub-nosed monkey genome annotation, one RNA library of mixed tissues from one individual were constructed using the Illumina mRNA-Seq Prep Kit.

overall_design: We sequenced mixed tissues using the Illumina HiSeq 2000 platform.

first: Xuming

last: Zhou

first: Boshi

last: Wang

first: Qi

last: Pan

first: Ruiqiang

first: Ming


title: Role of Tet3 and DNA replication in zygotic demethylation of both paternal and maternal genomes [RRBS]

city: Boston

first: Li

last: Shen

address: 200 Longwood Ave

institute: HHMI/Boston Children's Hospital/Harvard Medical School

summary: With the exception of imprinted genes and certain repeats, DNA methylation is globally erased during pre-implantation development. Recent studies have suggested that Tet3-mediated oxidation of 5-methylcytosine (5mC) and DNA replication-dependent dilution both contribute to global paternal DNA demethylation, but demethylation of the maternal genome occurs via replication. Here we present genome-scale DNA methylation maps for both the paternal and maternal genomes of Tet3-depleted and/or DNA replication-inhibited zygotes. In both genomes, we found that inhibition of DNA replication blocks DNA demethylation independently from Tet3 function, and that Tet3 facilitates DNA demethylation by coupling with DNA replication. For both, our data indicate that replication-dependent dilution is the major contributor to demethylation, but Tet3 plays an important role, particularly at certain loci. Our study therefore both defines the respective functions of Tet3 and DNA replication in paternal DNA demethylation and reveals an unexpected contribution of Tet3 to demethylation of the maternal genome.

overall_design: In this data set, we include RRBS data of manually isolated paternal and maternal pronuclei from both WT and Tet3 CKO zygotes with or without aphidicolin treatment

first: Azusa

last: Inoue

first: Jin

last: He

first: Yuting

first: Falong

last: Lu

first: Yi

last: Zhang


title: Identification of MicroRNAs and Their Targets in Tomato Infected with Cucumber Mosaic Virus

city: Hangzhou

first: Junli

last: Feng

address: Hangzhou, Jiaogong Road 149#

institute: Zhejiang Gongshang University

summary: We constructed two independent small RNA libraries from leaves of mock and Cucumber mosaic virus (CMV) infected tomatoes, respectively, and sequenced with a high-throughput Illumina Solexa system. Based on sequence analysis and hairpin structure prediction, a total of 50 known miRNAs (32 families) and 568 potentially candidate miRNAs (PC-miRNAs) were firstly identified in tomato, with 12 known miRNAs and 154 PC-miRNAs supported by both the 3p and 5p strands. Comparative analysis revealed 79 miRNAs (including 15 novel tomato miRNAs) and 40 PC-miRNAs were differentially expressed between the two libraries. Among these virus responsive miRNAs, expression patters of some novel tomato miRNAs and PC-miRNAs in mock and in CMV-Fny infected tomatoes were further validated by qRT-PCR. Moreover, we revealed 563 potential targets for 66 tomato miRNAs by the recently developed degradome sequencing approach, including 124 targets for 7 new tomato miRNAs and 97 targets for 24 PC-miRNAs. Target annotation for the newly identified miRNA and PC-miRNAs indicated that they were involved in multiple biological processes, including transcriptional regulation and virus resistance. Gene ontology analysis of these target transcripts demonstrated that stress response- and photosynthesis-related genes were most affected in CMV-Fny infected tomatoes.

overall_design: Examination of small RNAs and their targets in mock and CMV-Fny infected tomatoes.


title: Transcriptome Analysis of KSHV virions produced from BCBL1 and BAC36 in 293L cells

city: Reno

first: Subhash

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

summary: The objective of this study was to identify the viral transcripts packaged into the virion particles produced from BCBL1 cells as well as virions from 293L cells containing BAC36 BACs

overall_design: RNA from virions were extracted and analyzed by RNA sequencing

first: Pravinkumar

last: Purushothaman


title: Transcriptome Analysis of KSHV during de novo primary infection of human B cells (PBMCs)

summary: The objective of this study was to identify the viral transcripts packaged into the virion particles and the transcription profiles of the viral genome during early infection, till the virus establishes latent infection in human PBMCs

overall_design: Samples from each time points were analyzed and the experiments were done in duplicate.


title: SOX4 genome binding targets  in glioblastoma cell line

city: hangzhou

first: jie

last: liu

address: yuhangtang road 866

institute: zcni

summary: Overexpression of SOX4 in LN229 glioblastoma cells prevents their cell cycle

overall_design: Examination of SOX4 binding profile in prostate cell LN229-SOX4 with LN229-GFP as negative control.

first: Jing

first: Biaoyang

last: Lin


title: Transcriptome Analysis of KSHV during de novo primary infection of endothelial (TIVE) cells

summary: The objective of this study was to identify the viral transcripts packaged into the virion particles and the transcription profiles of the viral genome during early infection, till the virus establishes latent infection in endothelial (TIVE) cells


title: Transcriptome Analysis of KSHV during de novo primary infection of human B-and endothelial-cells

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

overall_design: Refer to individual Series


title: Transcriptome Analysis of BAC36 and ORF59 deleted BAC36 during de novo primary infection of human B cells (PBMCs)

summary: The objective of this study was to identify the transcription profiles of wild type KSHV and ORF59 deleted KSHV (Kaposi's sarcoma-associated herpesvirus) genome during early infection, till the virus establishes latent infection in human PBMCs


title: Establishment of regions of genomic activity during the Drosophila maternal-to-zygotic transition

city: Berkeley

first: Michael

middle: B

last: Eisen

state: CA

address: 379 Stanley Hall, MC 3220

department: MCB

institute: HHMI/Univ. California, Berkeley

summary: A conspicuous feature of early animal development is the lack of transcription from the embryonic genome, and it typically takes several hours to several days (depending on the species) until widespread transcription of the embryonic genome begins. Although this transition is ubiquitous, relatively little is known about how the shift from a transcriptionally quiescent to transcriptionally active genome is controlled. We describe here the genome-wide distributions and temporal dynamics of nucleosomes and post-translational histone modifications through the maternal-to-zygotic transition in embryos of the pomace fly Drosophila melanogaster. At mitotic cycle 8, when few zygotic genes are being transcribed, embryonic chromatin is in a relatively simple state: there are few nucleosome-free regions, undetectable levels of the histone methylation marks characteristic of mature chromatin, and low levels of histone acetylation at a relatively small number of loci. Histone acetylation increases by cycle 12, but it is not until cycle 14 that nucleosome-free regions and domains of histone methylation become widespread. Early histone acetylation is strongly associated with regions that we have previously shown are bound in early embryos by the maternally deposited transcription factor Zelda. Most of these Zelda-bound regions are destined to be enhancers or promoters active during mitotic cycle 14, and our data demonstrate that they are biochemically distinct long before they become active, raising the possibility that Zelda triggers a cascade of events, including the accumulation of specific histone modifications, that plays a role in the subsequent activation of these sequences. Many of these Zelda-associated active regions occur in larger domains that we find strongly enriched for histone marks characteristic of Polycomb-mediated repression, suggesting a dynamic balance between Zelda activation and Polycomb repression. Collectively, these data paint a complex picture of a genome in transition from a quiescent to an active state, and highlight the role of Zelda in mediating this transition.

overall_design: We performed genome-wide mapping of histone H3 and 9 types of histone modifications, including H4K5ac, H4K8ac, H3K4me1, H3K4me3, H3K27me3, H3K36me3, H3K9ac, H3K18ac, and H3K27ac by ChIP-seq, in hand-sorted wild-type Drosophila melanogaster embryos at 4 different development time points corresponding to mitotic cycle 7-9, 11-13, 14a-b, and 14c-d, respectively. We also carried out ChIP-seq experiments in zelda mutant embryos after showing that the deposition of histone marks in early embryos strongly correlated with the binding of Zelda in wild-type embryos.

first: Xiao

first: Melissa

last: Harrison

first: Tommy

last: Kaplan


title: Cooperativity, specificity and evolutionary stability of Polycomb targeting in Drosophila

city: Montpellier

first: Bernd

last: Schuettengruber

address: 141, rue de la cardonille

country: France

institute: Institute de Génétique Humaine

summary: We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of  PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter

sample_organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila simulans
Drosophila virilis
Drosophila yakuba

overall_design: ChIP-seq analysis of histone marks and chromatin associated factors across 4-5 Drosophila species

first: Noa

last: Elkayam

first: Tom

last: Sexton

first: Marianne

last: Entrevan

first: Shani

last: Stern

first: Aubin

last: Thomas

first: Eitan

last: Yaffe

first: Hugues

last: Parrinello

first: Amos

last: Tanay

first: Giacomo

last: Cavalli


title: Zinc finger protein Zfp335 is required for formation of the naïve T cell compartment

first: Brenda

last: Han


title: Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: This study uses Whole Transcriptome Shotgun Sequencing (RNA-Seq) data to interrogate the developmental dynamics of the C57BL/6 mouse liver transcriptome. We analyze gene expression patterns in the developing mouse liver over 12 distinct time points from late embryonic stage (2 days before birth) to maturity (60 days after birth). Biological functions deemed significant at different developmental stages are identified and their leverage is mapped over time. Upstream regulators modulating these gene expression patterns are determined and their regulatory networks are described along with putative transcriptional modules associated with gene regulation. Several genes that were alternatively spliced over time were identified. Previously uncharacterized isoforms were found for several genes.

overall_design: We analyze gene expression patterns in the developing mouse liver over 12 distinct time points from late embryonic stage (2 days before birth) to maturity (60 days after birth). Three replicates per time point.

first: Curtis

middle: D

last: Klaassen

first: Xiao-bo

last: Zhong

first: Hong

last: Lu


title: Arid3a modulates the first cell fate decision by direct regulation of both embryonic and extraembryonic gene expression (ChIP-Seq)

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway NMS 4.246

department: Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology

institute: University of Texas at Austin

summary: Arid3a, a transcription factor known for its requirement in B-lymphocyte development, has been recently identified as a member of ES cell pluripotency network. Arid3a is moderately expressed in ES cells, and its expression is gradually increased during differentiation. Since Arid3a shows the highest expression in placenta, we hypothesized that Arid3a may play important roles in TE development. We report that Arid3a is a central regulator of both TE-specific and pluripotency-associated gene expression during ES cell differentiation. While dispensable for self-renewal, we observed that knockdown of Arid3a delays differentiation of ES cells. Induction of Arid3a leads ES cells to promote differentiation, specifically towards TE lineage. Moreover, these Arid3a-overexpressing cells maintained in TE culture media are sufficient to generate functional trophoblast stem-like cells, suggesting roles of Arid3a in TE differentiation. By integrative analyses using the chromosomal targets of Arid3a with expression profiling, we revealed the dual roles of Arid3a, as a direct activator of TE-specific genes and a repressor of pluripotency-associated genes. We further revealed the repressive roles of Arid3a are mediated by histone deacetylases (HDACs). Taken together, our results demonstrate that Arid3a is a critical novel regulator in TE lineage specification.

overall_design: Arid3a ChIP was performed using bioChIP-sequencing. Control ChIP-sequencing was performed using BirA cells. HDAC1 ChIP was performed as native antibody ChIP-sequencing.


title: Arid3a is essential to execution of the first cell fate decision via direct embryonic and extraembryonic transcriptional regulation


title: The Global Landscape of Transcription Initiation During the Caulobacter Cell Cycle [timecourse]

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

summary: The Caulobacter cell cycle includes in an asymmetric cell division that is driven by a core regulatory circuit comprised of 4 transcription factors (DnaA, GcrA, CtrA, and SciP) and a DNA methyltransferase (CcrM).  Using a modified global 5’ RACE protocol we mapped 2,726 transcriptional start sites (TSS) in the 4mb Caulobacter genome and identified 586 cell cycle-regulated TSS.  The core cell cycle circuit directly controls about 55% of cell cycle-regulated TSS by integrating multiple regulatory inputs within at least 322 promoters, providing a large number of transcription profiles from a small number of regulatory factors.  Here, we identified  previously unknown features of the core cell cycle circuit, including antisense TSS within dnaA and ctrA, plus newly identified TSS for ctrA and ccrM.  Altogether, we identified 615 antisense TSS plus 241 genes that are transcribed from multiple TSS. The multiple TSS in the same promoter region often exhibit different cell cycle activation timing, These novel features of the global transcript profile add significant insight to the system architecture of the Caulobacter cell cycle regulatory circuit.

overall_design: Global 5' RACE was performed to measure Transcription Start Site activity at time points of the Caulobacter NA1000 cell cycle

first: Bo

last: Zhou

first: Harley

last: McAdams

first: Lucy

last: Shapiro


title: MicroRNA Marker Based Prognostication of Oral Squamous Cell Carcinoma

first: Angela

last: Yoon

address: 630 West 168th Street, PH15W-1562

institute: Columbia University Medical Center

summary: The aim of our study was to discover a miR marker panel prognostic of 5-year survival in OSCC patients that may be utilized in parallel with the current clinical covariates. We assessed differential expression of miRNAs genome-wide via deep sequencing in 20 tumor tissue samples. We also attempted to identify deregulated miR expression signatures that may serve as the prognostic marker of cancer survival. Selected miR marker-based panel then may serve as a guide for selection of appropriate follow-up chemo/radiation treatment, significantly improving the clinical management of OSCC and the overall survival rate.

overall_design: Identify miRs differentially expressed in the poor prognosis group compared to the good prognosis group

first: Nicolas

last: Robine


title: Swi/Snf dynamics on stress responsive genes is governed by competitive bromodomain interactions.

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: Acetylation of Snf2 regulates Swi/Snf recruitment during stress

overall_design:
ChIP was done for Snf2 in unstressed and stressed condition fro WT, Snf2 K1493R K1497R, Wt delta bromodomain, Snf2 K1493R K1497R delta bromodomain using Snf2 antibodies,
Mnase-seq was done for Snf2 in unstressed and stressed condition fro WT, Snf2 K1493R K1497R

first: Arnob

last: Dutta

first: Jerry

middle: L

last: Workman


title: m6A RNA modification controls cell fate transition in mammalian embryonic stem cells (RNA methylation)

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: Here we determine the map of RNA methylation (m6A) in mouse embrionic stem cells, and Mettl3 knock out cells

overall_design: Examination of m6A modification sites on the transcriptome of mouse Embryonic stem cells and Embryonic Mettl3 knock out cells, using a m6A specific antibody.

first: Pedro

last: Batista

first: Howard

last: Chang


title: Bru-seq nascent RNA sequencing of human and mouse cells: correlation to replication timing and genome instability

city: Ann Arbor

first: Thomas

middle: E.

last: Wilson

state: MI

address: 2065 BSRB, 109 Zina Pitcher

department: Department of Pathology

institute: University of Michigan

summary: Bru-seq nascent RNA sequencing (PubMed ID 23973811) was performed on two primary human fibroblast cell lines, mouse embryonic stem cells, and GM12878 human lymphoblastoid cells. Read data, which include both exon and intron signals, were used to identify transcription unit spans genome-wide, where a transcription unit is roughly correspondent to the longest expressed isoform of a gene. However, because algorithms were not constrained by annotated genes, transcription units need not and often do not correspond precisely to gene boundaries and include extragenic transcription. Transcription units were then compared to separate data sets that comprised induced copy number variants, common fragile sites, and Repli-seq replication timing. The objective was to discover the relationships between transcription unit span and size, local genomic instability, and replication timing. This GEO sample series provides the span and intensity of transcription units called genome-wide in the various samples. Correlations to genome stability and replication timing are provided in the associated manuscript. In addition, one human fibroblast line and the mouse embryonic stem cells had paired samples treated and untreated with low dose aphidicolin. Gene RPKM signal intensities are provided for these samples, although comparing these was not the principal objective of the study.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bru-seq single-read nascent RNA sequencing on human 090 fibroblasts +/- aphidicolin treatment, human UMHF1 fibroblasts (3 replicates), human GM12878 lymphoblastoid cells, and mouse embryonic stem cells+/- aphidicolin treatment.

middle: E

first: Martin

middle: F

last: Arlt

first: So

last: Park

first: Sountharia

last: Rajendran

first: Michele

last: Paulsen

first: Mats

last: Ljungman

middle: W

last: Glover


title: m6A RNA modification controls cell fate transition in mouse embryonic stem cells