title: Expanded identification and characterization of mammalian circular RNAs

first: Stephen

last: Eichhorn

department: Biology

summary: The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression. However, the global properties of circRNAs are not well understood. We developed a computational pipeline to identify circRNAs and quantify their relative abundance from RNA-seq data. Applying this pipeline to a large set of non-poly(A)-selected RNA-seq data from the ENCODE project, we annotated 7,112 human circRNAs that were estimated to comprise at least 10% of the transcripts accumulating from their loci. Most circRNAs are expressed in only a few cell types and at low abundance, but they are no more cell-type–specific than are mRNAs with similar overall expression levels. Although most circRNAs overlap protein-coding sequences, ribosome profiling provides no evidence for their translation. We also annotated 635 mouse circRNAs, and although 20% of them are orthologous to human circRNAs, the sequence conservation of these circRNA orthologs is no higher than that of their flanking linear exons. The previously proposed miR-7 sponge, CDR1as, is one of only two circRNAs with more miRNA sites than expected by chance, with the next best miRNA-sponge candidate deriving from a primate-specific zinc-finger gene, ZNF91. These results provide a new framework for future investigation of this intriguing topological isoform while raising doubts regarding a biological function of most circRNAs.

overall_design:
Examination of 9 samples in 1 cell type
Note: The ENCODE data we used are under GEO SuperSeries GSE26284 (all samples labeled "_cell_total"). But they were not used in the processing of the U2OS data.

first: Junjie

middle: U

last: Guo

first: Vikram

last: Agarwal

first: Huili

first: David

last: Bartel


title: Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms [RNA-Seq]

status: Public on Jul 08 2014

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

country: USA

institute: UCSD

type: Expression profiling by high throughput sequencing

summary: Human pluripotent stem cells hold great potential for regenerative medicine, but available cell types have important limitations. While embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the "gold standard" of pluripotency, they are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) are prone to epigenetic and transcriptional aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming or secondary to the reprogramming method, we generated a genetically matched collection of human IVF-ESCs, iPSCs, and ESCs derived by somatic cell nuclear transfer (SCNT; NT-ESCs), and subjected them to genome-wide genetic, epigenetic and transcriptional analyses. SCNT-based reprogramming is mediated by the full complement of oocyte cytoplasmic factors, thus closely recapitulating early embryogenesis. NT-ESCs and iPSCs derived from the same somatic donor cells contained comparable numbers of de novo copy number variations (CNVs), suggesting that the two reprogramming methods may not differ significantly in mutagenic or selective pressure. On the other hand, the DNA methylation and transcriptome profiles of NT-ESCs corresponded very closely to those of IVF-ESCs, while iPSCs differed markedly from IVF-ESCs and harbored residual DNA methylation patterns typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal candidates for cell replacement therapies.

overall_design: Duplicate cDNA libraries of two IVF-ESCs, three sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, and the parental fibroblast line were sequenced using Illumina HiSeq 2000. The sequence reads were mapped to hg19 reference genome and hits that passed quality filters were analyzed for differential expression.


title: DNA Topoisomerase 1a Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis [RNA-Seq]

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

country: China

institute: shenzhen university

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-directed DNA methylation (RdDM) is a transcriptional silencing mechanism mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1a (TOP1a) was able to de-repress LUCL by reducing its DNA methylation and H3K9 dimethylation (H3K9me2) levels. Further studies with Arabidopsis top1a mutants showed that TOP1a promotes RdDM by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at transposable elements (TEs).

overall_design: 5 small RNA libraries were sequenced

first: Thanh

middle: T

last: Dinh

first: Xuemei

last: Chen


title: Differential expression analysis for RNA-seq data between cardiac progenitor and uncommitted cells at day 4.75

status: Public on Jul 09 2014

city: San Francisco

first: Gladstone

last: Bioinformatics

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

summary: We report the differential expression between cardiac progenitor and uncommitted cells at day 4.75

overall_design: RNASeq analysis in mESCs and day 4.75 progenitor cells

first: Benoit

middle: G

last: Bruneau

first: Walter

middle: P

last: Devine

first: Matthew

middle: R

last: George

first: Joshua

middle: D

last: Wythe


title: Sequencing and genome-wide mapping of 146 bp mono-nucleosomal DNA from human and bovine sperm

city: Giessen

first: Birgit

last: Samans

address: Heinrich-Buff-Ring 26-28

country: Germany

institute: University of Giessen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The phenomenon of nucleosome retention in mammalian sperm chromatin is still not clarified yet. The goal of our study was to characterize the binding sites of sperm nucleosomes in the human and bovine genomes, and through this, to clarify whether nucleosome retention in sperm underlies rules of great generality and has a biological function. Comparing two mammalian systems we found that nucleosomes remain mainly in centromeres and in non-coding intergenic and intron regions. In contrast, coding DNA, promoter regions and transcription start and end sites, especially in homeobox genes and in the majority of genes with relevance for organ development and morphogenesis, were nucleosome-free.

sample_organism:
Homo sapiens
Bos taurus

platform_organism:
Homo sapiens
Bos taurus

overall_design: 146 bp mono-nucleosomal DNA was isolated and purified from sperm samples of two fertile bulls (bos taurus), one fertile man and a pool of four fertile donors; each DNA sample was deep sequenced using Illumina GAIIx and genome-wide mapped on respective genome; nucleosome-binding sites were analyzed in a genome-wide comparative manner.

first: U

last: Schagdarsurengin

first: B


title: Mycobacterium tuberculosis transcriptional responses to acidic pH and carbon source

status: Public on Jul 07 2014

city: East Lansing

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: The purpose of this study was to examine how Mtb integrates acidic pH and available carbon sources as environmental cues to regulate its metabolism and growth rate. RNA-seq transcriptional profiling of M. tuberculosis growing at acidic or neutral pH, in pyruvate or glycerol, was examined.  These studies identified carbon source-dependent and -independent pH-dependent adaptations.

overall_design: Mtb strain CDC1551 was grown in standing T-75 flasks in 40 mL of medium seeded an initial OD of 0.1.  We examined medium in four conditions pH 7.0 10 mM glycerol, pH 5.7 10 mM glycerol, pH 7.0 10 mM pyruvate, pH 5.7 10 mM pyruvate.  Following 3 days of incubation at 37C, RNA was isolated from the bacterial cultures and used for RNA-seq.

first: Jacob

middle: J

last: Baker

first: Benjamin

middle: K

last: Johnson

middle: B


title: Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis [RNA-Seq]

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

summary: The c-myc proto-oncogene product, Myc, is a transcription factor that binds thousands of genomic loci. Recent work suggested that rather than up- and down-regulating selected groups of genes, Myc targets all active promoters and enhancers in the genome (a phenomenon termed "invasion") and acts as a general amplifier of transcription. However, the available data did not readily discriminate between direct and indirect effects of Myc on RNA biogenesis. We addressed this issue with genome-wide chromatin immunoprecipitation and RNA expression profiles during B-cell lymphomagenesis in mice, in cultured B-cells and fibroblasts. Consistent with long-standing observations, we detected general increases in total RNA or mRNA copies per cell (hereby termed "amplification") when comparing actively proliferating cells with control quiescent cells: this was true whether cells were stimulated by mitogens (requiring endogenous Myc for a proliferative response) or by deregulated, oncogenic Myc activity. RNA amplification and promoter/enhancer invasion by Myc were separable phenomena that could occur without one another. Moreover, whether or not associated with RNA amplification, Myc drove the differential expression of distinct subsets of target genes. Hence, while having the potential to interact with all active/poised regulatory elements in the genome, Myc does not directly act as a global transcriptional amplifier. Instead, our results imply that Myc activates and represses transcription of discrete gene sets, leading to changes in cellular state that can in turn feed back on global RNA production and turnover.

overall_design: Total RNA profiling of gene expression upon Myc regulation in two different cell types by Illumina sequencing

first: Arianna

last: Sabo

first: Theresia

last: Kress

first: Mattia

last: Pelizzola

first: Stefano

last: de Pretis

first: Bruno

last: Amati


title: RNA-seq analysis of vorinostat-resistant HCT116 cells following gene knockdown of potential vorinostat-resistance candidate genes

city: East Melbourne

first: Katrina

middle: Joy

last: Falkenberg

state: Victoria

address: St Andrews Place

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Potential vorinostat-resistance candidate genes were identified using RNA interference screening in vorinostat-resistant HCT116 cells (HCT116-VR) using a synthetic lethal approach.  In order to understand the mechanisms by which these genes contributed to vorinostat response, transcriptomic analysis was conducted on HCT116-VR cells and those with siRNA-mediated knockdown of each of the vorinostat resistance candidate genes.

overall_design: There are 45 samples in total, from triplicate independent biological experiments of 15 samples each.  The negative control to which all gene knockdowns are compared is the mock transfection control (mock).

first: Cathryn

middle: M

last: Gould

first: Ricky

middle: W

last: Johnstone

first: Kaylene

last: Simpson


title: DNA Topoisomerase 1α Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis [Bisulfite-Seq]

first: Lei

last: Gao

type: Methylation profiling by high throughput sequencing

summary: RNA-directed DNA methylation (RdDM) is a transcriptional silencing mechanism mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9 dimethylation (H3K9me2) levels. Further studies with Arabidopsis top1α mutants showed that TOP1α promotes RdDM by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at transposable elements (TEs).

overall_design: ten bisufite libraries were sequenced

first: Thanh

last: Dinh

first: Xuemei

last: Chen


status: Public on Jul 06 2014

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: RNA Sequencing of E14.5 mouse cortical neurospheres in response to Fezf2 over-expression

overall_design: 2 replicates each of GFP-transfected or Fezf2/GFP-transfected E14.5 mouse cortical neurospheres. Paired-end sequencing 101bp.

first: Simona

last: Lodato

first: Bradley

last: Molyneaux

first: Emanuela

last: Zuccaro

first: Hsu-Hsin

first: Wen

last: Yuan

first: Alyssa

last: Meleski

first: Emi

last: Takahashi

first: Shaun

last: Mahony

first: John

middle: L

last: Rinn

first: David

last: Gifford

first: Paola

last: Arlotta


title: Molecular mechanism underlying increased ischemic damage in the ALDH2*2 genetic polymorphism using a human iPSC model system

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

summary: We investigated the ALDH2*2 genetic polymorphism and its underlying mechanisms for the first time in a human model system of induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) generated from individuals carrying the most common heterozygous form of the ALDH2*2 genotype. We showed that the ALDH2*2 mutation confers elevated levels of reactive oxygen species (ROS) and toxic aldehydes such as 4HNE, thereby inducing cell cycle arrest and activation of apoptotic signaling pathways, especially during ischemic injury. ALDH2 exerts control of cell survival decisions via modulation of oxidative stress levels. This regulatory circuitry was found to be dysfunctional in the loss-of-function ALDH2*2 genotype, causing upregulation of apoptosis in cardiomyocytes following ischemic insult. These results reveal a novel function of the metabolic enzyme ALDH2 in modulation of cell survival decisions.

overall_design: Molecular mechanism of increased ischemic damage in cardiomyocytes of ALDH2*2 genotype.

first: Antje

last: Ebert


title: Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis [ChIP-Seq]

first: Marco

last: Morelli

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Mapping c-Myc, RNAPII and H3K4me3, H3K4me1 and H3K27ac in four different models of Myc regulation
Note: GEO Sample GSM894093 was used as input sample to generate processed data files P493.Myc.NoMyc.bed, P493.Myc.LowMyc.bed, P493.Myc.HighMyc.bed, P493.Myc.t1h.bed, P493.Myc.t24h.bed, P493.Pol2.NoMyc.bed, P493.Pol2.t24h.bed

first: Arianna

last: Sabo

first: Theresia

last: Kress

first: Mattia

last: Pelizzola

first: Bruno

last: Amati


title: Co-regulated gene expression downstream of a single transcription factor controls the acquisition of corticospinal motor neuron identity

city: University Park

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: The neocortex contains an unparalleled diversity of neuronal subtypes responsible for complex behavior. Each cortical neuron has distinct traits, which are developmentally acquired under the control of batteries of neuron subtype-specific and pan-neuronal genes. The cis-regulatory logic that orchestrates the coordinated regulation of each unique combination of genes is not known for any class of neurons of the neocortex. We report that Fezf2, a transcription factor able to induce defining features of corticospinal motor neurons (CSMN), associates with the proximal promoters and regulates expression of series of CSMN signature genes. Fezf2 targets are functionally relevant as demonstrated by the finding that Fezf2 governs expression of the axon guidance receptor EphB1 to execute the ipsilateral extension of the corticospinal tract. Our data indicate that co-regulated expression of neuron subtype-specific gene batteries by a common transcription factor is one component of the regulatory logic responsible for the establishment of CSMN identity.

overall_design: Fezf2 binding is characterized in neurospheres using ChIP-seq targeted against 3Flag-tagged Fezf2. Two types of control experiments were performed: mock IP and GFP-3Flag ChIP-seq. All experiments were performed in biological duplicate.

first: Simona

last: Lodato

first: Bradley


title: Role of Polycomb group proteins in the DNA damage response – a reassessment

city: London

first: Gordon

last: Peters

address: 44 Lincolns Inn Fields

country: United Kingdom

institute: CRUK London Research Institute

summary: We have investigated whether components of Polycomb repressive complex 1 (PRC1) are recruited to double-strand breaks (DSBs) generated by inducible expression of the AsiSI restriction enzyme in normal human fibroblasts.  Using chromatin immunoprecipitation and deep sequencing (ChIP-seq), which detects PRC1 proteins at common sites throughout the genome, we did not find evidence for recruitment of PRC1 components to AsiSI-induced DSBs.  In contrast, the S2056 phosphorylated form of DNA-PKcs and other DNA repair proteins were detected at a subset of AsiSI sites that are predominantly at the 5’ ends of transcriptionally active genes. Our data question the idea that PcG protein recruitment provides a link between DSB repairs and transcriptional repression.

overall_design: Single chromatin preparations from treated and untreated cells (+/- OHT), immunoprecipitated with two antibodies (pDNA-PKcs and MEL18) were sequenced as technical replicates, along with the corresponding input DNAs

first: Hollie

last: Chandler

first: Harshil

last: Patel

first: Richard

last: Palermo

first: Sharon

last: Brookes

first: Nik

last: Matthews


title: Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis

overall_design:
This SuperSeries is composed of the SubSeries listed below.
Refer to individual Series


title: Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis [DNAse-Seq]

overall_design: Mapping Dnase hypersensitive sites in MycER fibroblasts.

first: Pranami

last: Bora


title: DNA Topoisomerase 1α Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis

first: Lei

last: Gao

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

overall_design: Refer to individual Series


title: MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein

status: Public on Jul 17 2014

first: Carol

last: Gross

institute: UCSF

summary: In enteric bacteria, the transcription factor σE maintains membrane homeostasis by inducing expression of proteins involved in membrane repair and of two small, regulatory RNAs (sRNAs) that downregulate synthesis of abundant membrane porins. Here, we describe the discovery of a third σE-dependent sRNA, MicL, transcribed from a promoter located within the coding sequence of the cutC gene. MicL is synthesized as a 308 nt primary transcript that is processed to an 80 nt form. Both forms possess features typical of Hfq-binding sRNAs, but surprisingly only target a single mRNA, which encodes the outer membrane lipoprotein Lpp, the most abundant protein of the cell. We show that the copper sensitivity phenotype previously ascribed to inactivation of the cutC gene is actually derived from the loss of MicL and elevated Lpp levels. This observation raises the possibility that other phenotypes currently attributed to protein defects are due to deficiencies in unappreciated regulatory RNAs. We also report that σE activity is sensitive to Lpp abundance and that MicL and Lpp comprise a new σE regulatory loop that opposes membrane stress. Together MicA, RybB and MicL allow σE to repress the expression of all abundant outer membrane proteins in response to stress.

overall_design: 12 samples mRNA-seq data, 2 samples ribosome profiling data.  For mRNA-seq data, samples were gathered at the indicated time (in min) after induction of either vector (WT), long (MicL), and short (MicL-S) forms of MicL.

first: Monica

middle: S

last: Guo

first: Taylor

last: Updegrove

first: Emily

last: Gogol

first: Svetlana

last: Shabalina

first: Gisela

last: Storz


title: The G Protein-coupled Receptor P2Y14 Influences Insulin Release and Smooth Muscle Function in Mice

status: Public on Jul 11 2014

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Medical Faculty

institute: Leipzig University

summary: UDP-sugars were identified as extracellular signaling molecules, assigning a new function to these compounds in addition to their well defined role in intracellular substrate metabolism and storage. Previously regarded as an orphan receptor, the G protein-coupled receptor (GPCR) P2Y14 (GPR105) was found to bind extracellular UDP and UDP-sugars. Little is known about the physiological functions of this GPCR. To study its physiological role we used a gene-deficient (KO) mouse strain expressing the bacterial LacZ reporter gene to monitor the physiological expression pattern of P2Y14. We found that P2Y14 is mainly expressed in pancreas and salivary glands and in subpopulations of smooth muscle cells of the gastrointestinal tract, blood vessels, lung and uterus. Among other phenotypical differences KO mice showed a significantly impaired glucose tolerance following oral and intraperitoneal glucose application. An unchanged insulin tolerance suggested altered pancreatic islet function. Transcriptome analysis of pancreatic islets showed that P2Y14 deficiency significantly changed expression of components involved in insulin secretion. Insulin secretion tests revealed a reduced insulin release from P2Y14-deficient islets highlighting P2Y14 as a new modulator of proper insulin secretion.

overall_design: 10 samples from pancreatic islets isolated from wildtype mice; 10 samples from pancreatic islets isolated from P2Y14-knockout mice

first: Jaroslawna

last: Meister

first: Diana

last: Le Duc

first: Albert

last: Ricken

first: Ralph

last: Burkhardt

first: Joachim

last: Thiery

first: Helga

last: Pfannkuche

first: Tobias

last: Polte

first: Johannes

last: Grosse

last: Schoneberg

first: Angela

last: Schulz


title: Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies

status: Public on Jul 05 2014

city: Baoshan

first: Botao

last: Zhao

state: Shanghai

address: 333 Nanchen Rd

department: college of life science

institute: Shanghai University

summary: We report the miRNA profiling in MEF cells, ES cells and three Pluripotent Stem Cells obtained by three different reprogramming approaches from MEF cells based on Solexa sequencing. iPS cells are reprogrammed by four factors (OSKM) from MEF cells. NT-ESCs were established by reprogramming MEF cells into ESCs using nuclear transfer. NT-iPSCs were established to reflect the combination of nuclear transfer and iPS technologies. iPSCs, NT-ESCs, and NT-iPSCs were exactly derived from the same MEF cells. The results indicate NT-ESCs give expression to the unique miRNAs other than both ESCs and iPSCs while pluripotent cells acquire or retain the pluripotent specific miRNAs compared with MEF. Furthermore, the comparison of different reprogramming cells suggests that several miRNAs have key roles in distinctly developmental potential reprogrammine cells.

overall_design: Small RNA profiles of MEF, ES, iPS, NT-ES and NT-iPS cells were generated by Solexa sequencing. MEF and ES cells were performed in triplicate. iPS, NT-ES and NT-iPS cells were sequenced in duplicate.

first: Youxin

last: Jin


title: The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

summary: Histone variants play crucial roles in gene expression, genome integrity and chromosome segregation. However, to what extent histone variants control chromatin architecture remains largely unknown.  Here, we show that the previously uncharacterized histone variant H2A.W plays a crucial role in condensation of heterochromatin. Genome-wide profiling of all four types of H2A variants in Arabidopsis shows that H2A.W specifically associates with heterochromatin. H2A.W recruitment is independent of heterochromatic marks H3K9me2 and DNA methylation. Genetic interactions show that H2A.W acts in synergy with CMT3 mediated methylation to maintain genome integrity. In vitro, H2A.W enhances chromatin condensation through a higher propensity to make fiber-to-fiber interactions via its conserved C-terminal motif. In vivo, elimination of H2A.W causes decondensation of heterochromatin and conversely, ectopic expression of H2A.W promotes heterochromatin condensation. These results demonstrate that H2A.W plays critical roles in heterochromatin by promoting higher order chromatin condensation. Since similar H2A.W C-terminal motifs are present in other variant found in mammals and other organisms our findings impact our understanding of heterochromatin condensation in a wide variety of eukaryotic organisms.

overall_design: Two mRNA-seq samples, two bisulfite-seq samples, six ChIP-seq samples.

first: Ramesh

last: Yelagandula


title: Identification of gene regulation patterns underlying both E2- and tamoxifen-stimulated cell growth through global gene expression profiling in breast cancer cells [MCF-7]

status: Public on Jul 18 2014

city: Washington

first: V

middle: Craig

last: Jordan

state: DC

address: 3800 Reservoir Road NW

department: Lombardi Comprehensive Cancer Center

institute: Georgetown University

summary: A c-Src inhibitor blocks estrogen (E2)-induced stress and converts E2 responses from inducing apoptosis to growth stimulation in E2-deprived breast cancer cells. A reprogrammed cell line, MCF-7:PF, results with features of functional estrogen receptor (ER) and over-expression of insulin-like growth factor-1 receptor beta (IGF-1Rβ). We addressed the question of whether the selective ER modulator 4-hydroxytamoxifen (4-OHT) could target ER to prevent E2-stimulated growth in MCF-7:PF cells. Selected expression of mRNA was measured through real-time RT-PCR. Global gene expression was analyzed by microarray and RNA-seq analysis. Unexpectedly, both 4-OHT and E2 stimulated cell growth in a concentration-dependent manner. Global gene expression analysis showed a remarkable overlap in genes regulated in the same direction by E2 and 4-OHT. Pathway enrichment analysis of the 280 genes commonly deregulated by 4-OHT and E2 revealed functions mainly related to membrane, cytoplasm, and metabolic processes. Further analysis of 98 up-regulated genes by both 4-OHT and E2 uncovered a significant enrichment in genes associated with membrane remodeling, cytoskeleton reorganization, cytoplasmic adapter proteins, cytoplasm organelles proteins, and related processes. 4-OHT was more potent than E2 to up-regulate some membrane remodeling molecules, such as EHD2, FHL2, HOMER3 and RHOF. In contrast, 4-OHT acted as an antagonist to inhibit expression of the majority of enriched membrane-associated genes in wild-type MCF-7 cells. Long-term selection pressure has changed the cell population responses to 4-OHT. Membrane-associated signaling is critical for 4-OHT-stimulated cell growth in MCF-7:PF cells. This study provides a rationale for the further investigation of targeted therapy for tamoxifen resistant patients.

overall_design: Wild-type MCF-7 cells were treated with vehicle control (0.1% ethanol), E2 (10-9 mol/L) and 4-OHT (10-6 mol/L) respectively for 24 hours.

first: Ping

last: Fan

first: Heather

middle: E

last: Cunliffe

first: Obi

last: Griffith

first: Fadeke

last: Agboke

first: Pilar

last: Ramos

first: Joe

last: Gray

first: Virgil

middle: C


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and dKO round spermatids Transcriptomes

status: Public on Jul 03 2014

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived WT and dKO round spermatids transcriptome profiling (RNA-seq)
Methods: Adult WT and dKO round spermatids mRNA profiles mice were generated by deep sequencing, in dulplicate. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and dKO round spermatids, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Adult wild type (WT) and dKO mouse round spermatids were generated by deep sequencing, in dulplicate, using Illumina GAIIx.

first: Rebecca

last: Smith

first: Chong

last: Tang

first: Tian

last: Yu


title: RNA seq analysis of day of pregnancy 14 ovine conceptuses

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: RNA seq analysis was conducted to determine gene expression in the day 14 ovine conceptus. This was used in conjunction with the day 14 PPARG ChIP-seq analysis to identify genes bound by PPARG which were also expressed or not expressed in the day 14 conceptus. Understanding changes in gene expression during early pregnancy is critical to improving fertility and reproductive efficiency in ruminants.

overall_design: RNA seq analysis of 4 conceptuses from 4 individual Day 14 pregnant columbia/rambouillet crossbred ewes

first: Kelsey

last: Brooks

first: Gregory

last: Burns


title: Endogenous small-noncoding RNAs and their roles in cold response and stress acclimation in Cassava

city: Saint Louis

first: Weixiong

last: Zhang

address: Campus Box 1045 One Brookings Drive

institute: Washington university in St Louis

summary: Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. In order to understand sncRNAs’ roles in plant cold response and stress acclimation, we studied miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate cold stresses, that underwent further severe cold stress after cold acclimation at moderate stress, and that grew under the normal condition. We also included Castor bean (Ricinus communis) to understand conservation of sncRNAs. In addition to known miRNAs, we identified dozens of novel miRNAs as well as ta-siRNA-yielding and nat-siRNA-yielding loci in Cassava and Castor bean, respectively. Among the expressed sncRNAs, many sncRNAs were differentially expressed under cold stresses. Our study provided the results on gene regulation by sncRNAs in cold acclimation of Euphorbiaceous plants and the role of sncRNA-mediated pathways affected by cold stress and stress acclimation in Cassava.

sample_organism:
Manihot esculenta
Ricinus communis

platform_organism:
Manihot esculenta
Ricinus communis

overall_design: Examination of small RNA populations in Cassava cultivar SC124 under the normal condition (NC), gradual cold acclimation (CA), cold shock (CS) and stress acclimation Cold stress after cold acclimation (CCA).

first: Changying

last: Zeng

first: Jing

last: Xia

first: Zheng

last: Chen


title: Analysis of conceptuses from day 14 pregnancy rambouillet cross ewes


title: PPARG regulated genes in the day 14 ovine conceptus

summary: PPARG ChIP seq analysis was conducted to determine genes bound by and potentially regulated by PPARG in the developing ovine conceptus. Determination of gene regulation by prostaglandins through PPARG helps to improve our understanding of early pregnancy events and provides a basis for strategies to improve fertility and reproductive efficiency in ruminants.

overall_design: PPARG ChIP seq analysis of 4 conceptuses from 4 individual Day 14 pregnant columbia/ramboulette crossbred ewes


title: Epigenomic analysis of primary human T cells reveals novel enhancers associated with Th2 memory differentiation and asthma susceptibility (3 cell types)

city: La Jolla

first: Anna

last: Gerasimova

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4+ T cells that produce Th2 cytokines (Th2 cells). By mapping genome-wide histone modification profiles of T cell subsets isolated from peripheral blood of healthy and asthmatic individuals, we identified enhancers with known and potential roles in the normal differentiation of human Th1 and Th2 cells.  In addition, we discovered disease-specific T cell enhancers that differ between healthy and asthmatic individuals.

overall_design: Examination of H3K4me2 histone modifications in 3 human cell types in 11 healthy and 12 asthmatic individuals .

first: Pandurangan

last: Vijayanand

first: Grégory

last: Seumois

first: Bjoern

last: Peters

first: Lukas

last: Chavez


title: Reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay in  mouse derived lymphoblastic cell line (D10.G4.1 cells, ATCC)

summary: To estimate the reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay we performed the genome-wide correlation analysis of H3K4me2 enrichment patterns from 7 independent standard ChIP-Seq assays (2 million D10 cells), and micro-scaled ChIP-Seq 100,000 cells sample –(N=12), 10,000 cells sample–(N=3), and 1000 cell sample – (N=4)

overall_design: Examination of H3K4me2 histone modifications in mouse derived lymphoblastic cell line (D10.G4.1 cells, ATCC).


title: Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [ChIP-seq_differentiation]

city: Copenhagen

first: Kristian

last: Helin

address: Ole Maaloes Vej 5

country: Denmark

institute: BRIC - University of Copenhagen

summary: Polycomb group (PcG) proteins are required for normal differentiation and development, and their activity is found deregulated in cancer. PcG proteins are involved in gene silencing, however, whether they initiate or maintain transcriptional repression is a subject of debate. Here, we show that knockout of the Polycomb repressive complex 2 (PRC2) does not lead to significant gene expression changes in mouse embryonic stem cells (mESCs), and that it is dispensable for initiating silencing of target genes during differentiation. Transcriptional inhibition in mESCs is sufficient to induce genome-wide ectopic PRC2 recruitment to endogenous PcG target genes found in other tissues. PRC2 binding analysis shows that it is restricted to nucleosome-free CpG islands (CGIs) of un-transcribed genes. Our results show that it is the transcriptional state that governs PRC2 binding, and we propose that it binds by default to non-transcribed CGI genes to maintain their silenced state and to protect cell identity.

overall_design: Suz12 ChIP-seq experiments before and after in vitro differentiation (72h) of Mus musculus Suz12 knock-out and wild-type E14 Embryonic Stem Cells respectively.

first: Eva

last: Riising

first: Itys

last: Comet

first: Benjamin

last: Leblanc


title: Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [ChIP-seq_Input]

overall_design: Input from ChIP-seq experiment in Mus musculus wild-type E14 Embryonic Stem Cells.


title: Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [RNA-seq_differentiation]

overall_design: RNA-seq time-course experiments during in vitro differentiation (0h, 24h, 48h and 72h) of Mus musculus wild-type E14 and Suz12 knock-out Embryonic Stem Cells with two biological replicates per condition.


title: Genomic variation and adaptation in fragmented landscapes

status: Public on Jul 04 2014

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

summary: We have compared allelic and gene expression variation using individual-based RNA-seq data from four regional populations of the Glanville fritillary butterfly (Melitaea cinxia) in northern Europe. Two of the populations represent fragmented habitat and two continuous habitat. Based on sequence information, we constructed genealogy for four populations. Based on gene expression, we found 1841 genes to be differentially expressed between two different landscape types. Our results demonstrate genomic adaptations to living in fragmented landscapes, which are likely to be related to phenotypic life-history adaptations that have been documented for many species.

overall_design: RNA-seq from thorax, 174 individuals from four populations.

first: Jouni

last: Kvist

first: Suvi

last: Ikonen

first: Virpi

last: Ahola

first: Petri

last: Auvinen

first: Lars

last: Paulin

first: Patrik

last: Koskinen

first: Liisa

last: Holm

first: Minna

last: Taipale

first: Jussi

first: Jukka

last: Siren

last: Corander

first: Mikko

last: Frilander

first: Rainer

last: Lehtonen

first: Ilkka

last: Hanski


title: Heterochromatin-associated interactions of Drosophila HP1 with dADD1, HIPP1, and repetitive RNAs

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

summary: We report chromatin-associated protein and RNA interactions of HP1a, indentified by BioTAP-XL mass spectrometry and sequencing. We identify an extensive list of both known and novel HP1a-interacting proteins from Drosophila S2 cells and from whole organisms across embryonic, larval and adult stages.

overall_design: BioTAP-XL protocol was used to identify HP1a interacting proteins through mass-spectrometry analysis. ChIP-seq-like pulldown/input samples were generated using BioTAP-XL to validate genomic distribution of the HP1a-BioTAP contructs, and the newly identified interacting proteins (CG8290 and CG3680); To examine the RNAs associated with the HP1a complexes, the RNA fraction of the BioTAP-XL pulldowns was analyzed using Illumina-based RNA-seq protocols, as well as Helicos direct RNA sequencing.

first: Mitzi

middle: I

last: Kuroda

first: Art

last: Alekseyenko

middle: V


title: Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide

first: Kristian

last: Helin

overall_design: Refer to individual Series


title: Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [ChIP-seq_drugs]

overall_design: Suz12, H3K27me3 and RNAPII ChIP-seq experiments before and after transcriptional inhibition with either DRB (0h, 6h and 12h) or Triptolide (0h, 3h and 9h) treatment of Mus musculus wild-type E14 Embryonic Stem Cells with up to two biological replicates per condition.

first: Eva

last: Riising

first: Itys

last: Comet

first: Benjamin

last: Leblanc


title: DNMT3L promotes quiescence in postnatal spermatogonial progenitor cells

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

summary: We analyzed transcriptome profiles of postnatal germ cells and demonstrated that DNMT3L is important for spermatogonial stem/progenitor cell development

overall_design: Examination of wild-type and Dnmt3l knockout smaples in postnatal male germ cells

first: Hung-Fu

last: Liao

first: Wendy

last: Chen

first: Yu-Hsiang

first: Tzu-Hao

last: Kao

first: Chien-Yueh

last: Lee

first: Yu-Chiao

last: Chiu

first: Qian-Jia

first: Yen-Tzu

last: Tseng

first: Yung-Hao

last: Ching

first: Kenichiro

last: Hata

first: Winston

middle: T

last: Cheng

first: Mong-Hsun

last: Tsai

first: Hiroyuki

last: Sasaki

first: Hong-Nerng

last: Ho

first: Yen-Hua

last: Huang

first: Shinn-Chih

last: Wu

first: Pauline

last: Yen


title: Genome-wide analysis of SUMOylation effects on androgen receptor (AR) binding in HEK293 cells (ChIP-seq)

city: Kuopio

first: Päivi

last: Sutinen

address: Yliopistonranta 1 E

department: School of Medicine

institute: University of Eastern Finland

summary: Androgen receptor (AR) plays an important regulatory role during prostate cancer development. AR’s transcriptional activity is regulated by androgenic ligands, but also by post-translational modifications. To study the role of the AR SUMOylation in genuine chromatin environment, we compared androgen-regulated gene expression and AR chromatin occupancy in PC-3 prostate cancer and HEK293 cell lines stably expressing wild-type (wt) or SUMOylation site-mutated AR (AR-K386R,K520R). Our genome-wide gene expression analyses reveal that the SUMOylation modulates the AR function in a target gene and pathway selective manner. The transcripts that are differentially regulated by androgen and SUMOylation are linked to cellular movement, cell death, cellular proliferation, cellular development and cell cycle. In line with these data, SUMOylation mutant AR cells proliferate faster and are more sensitive to apoptosis. Moreover, ChIP-seq analyses show that the SUMOylation modulates the chromatin occupancy of AR on many loci in a fashion that parallels with their differential androgen-regulated expression. De novo motif analyses show that other transcription factor-binding motifs are differentially enriched at the wtAR- and the AR-K386R,K520R-preferred genomic binding positions. Taken together, our data indicate that SUMOylation does not simply repress the AR activity, but it regulates AR’s interaction with the chromatin and the receptor’s target gene selection.

overall_design: Androgen receptor (AR) genomic binding was studied in wild-type AR (wtAR) or SUMOylation-deficient AR (AR-K2R) stably expressing cells HEK293 cells, in biological dublicates. Cells were treated 40 min either with 10 nM R1881 or EtOH (vehicle) and input was used as control (FRT_input GSM1176703).

first: Marjo

last: Malinen

first: Sami

last: Heikkinen

first: Jorma

last: Palvimo


title: Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [RNA-seq_PcG-KO]

first: Kristian

last: Helin

overall_design: RNA-seq experiments with Mus musculus E14TG2a (E14-WT), Ezh2[fl/fl] (Ezh2-WT), Ezh2[-/-] (Ezh2-KO), Suz12[-/-] (Suz12-KO), Ring1A[-/-];Ring1B[-/-] (Ring1A+B-DKO) Embryonic Stem Cells with three biological replicates per condition.

first: Eva

last: Riising

first: Itys

last: Comet

first: Benjamin

last: Leblanc

first: Xudong


title: Gene expression (RNA-Seq) analysis of primary human T cells reveals novel genes associated with Th2 memory differentiation and asthma susceptibility

first: Anna

last: Gerasimova

summary: A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4+ T cells that produce Th2 cytokines (Th2 cells). By comparing gene expression profiles of T cell subsets isolated from peripheral blood of healthy and asthmatic individuals, we identified genes with known and potential roles in the normal differentiation of human Th1 and Th2 cells.

overall_design: Examination of gene expression in 3 human cell types in healthy and asthmatic individuals.

first: Pandurangan

last: Vijayanand

first: Grégory

last: Seumois

first: Bjoern

last: Peters

first: Lukas

last: Chavez


title: Regulation of Ptch1 expression in the limb

city: Los Angeles

first: Kevin

last: Peterson

address: 1425 San Pablo St.

department: Department of Stem Cell Biology and Regenerative Medicine

institute: Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine

summary: Ptch1 is a critical negative feedback regulator of the Hedgehog signaling and is upregulated in response to pathway activation. How tissue specific responses are mediated remains unknown. Here, we performed ChIP-seq analysis for epitope-tagged endogenous Gli3 protein to identify limb-specific binding regions within the 500 kb region surrounding Ptch1.

overall_design: ChIP was carried out using an endogenously FLAG-tagged Gli3 protein.

first: Andrew

middle: P

last: McMahon


title: mRNA-Seq and microRNA-Seq whole-transcriptome analysis of rhesus monkey ESC neural differentiation revealed the potential rosette neural stem cell regulators

first: Yuqi

last: Zhao

address: 2000 Terasaki Life Sciences Bldg 610 Charles E. Young Drive East

department: Department of Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: Rosette neural stem cells (R-NSCs) represent early stage of neural development and possess full neural differentiation and regionalization capacities. R-NSCs are considered as stem cells of neural lineage and have important implications in study of neurogenesis and cell replacement therapy. However, the molecules regulating their functional properties remain largely unknown. Rhesus monkey is ideal model to study human neural degenerative diseases and plays intermediate translational roles as therapeutic strategies evolve from rodent systems to human clinical applications. In this study, we derived R-NSCs from rhesus monkey embryonic stem cells (rESCs) and systematically investigated the unique expressions of mRNAs, microRNAs, and signaling pathways by genome-wide comparison of the mRNA and microRNA profilings of ESCs, R-NSCs at early (R-NSCP1) and late passages (R-NSCP6) and neural progenitor cells (NPCs). Apart from the R-NSCP1 specific protein-coding genes and microRNAs, we identified several pathways including Hedgehog and Wnt highly activated in R-NSCP1. The possible regulatory interactions among the microRNAs, protein-coding genes and signaling pathways were proposed. Besides, many genes with alternative splicing switch were identified at R-NSCP1. These data provided valuable resource to understand the regulation of early neurogenesis and to better manipulate the R-NSCs for cell replacement therapy.

overall_design: mRNA and miRNA profiles for four stages in rhesus embryonic stem cell neural differentiation, eight samples in all

first: Shuang

last: Ji

first: Jinkai

last: Wang

first: Jingfei

last: Huang

first: Ping

last: Zheng


title: Stress acclimation in Cassava

first: Weixiong

last: Zhang

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


title: Genome wide profiling of MBD2 binding

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: We show that in vivo MBD2 is mainly recruited to CpG island promoters that are highly methylated. We also report that MBD2 binds to a subset of CpG island promoters that are characterized by the presence of active histone marks and RNA polymerase II (Pol2). At such sites, MBD2 binds downstream of the transcription start site. Active promoters bound by MBD2 show low to medium gene expression levels and H3K36me3 deposition suggesting a putative role for MBD2 in blocking polymerase II (Pol2) elongation at these promoters.

overall_design: To gain further insight into the function of and epigenetic regulation by MBD2 we generated a tagged version of the protein and stably expressed it in the MCF-7 cell line. We mapped genome wide binding of MBD2 by ChIP sequencing (ChIP-seq) and together with base resolution whole genome bisulfite sequencing (WGBS) we were able to determine the methylation content and the role of methylation density at MBD2 enriched regions. We further dissected MBD2 binding properties, taking advantage of a large set of ChIP-seq data including active histone marks, RNA polymerase II (POL2) and strand specific RNA-seq.

first: Roberta

last: Menafra

first: Arie

last: Brinkman

first: Filomena

last: Matarese

first: Gianluigi

last: Franci

first: Stefanie

middle: J

last: Bartels

first: Luan

last: Nguyen

first: Takashi

last: Shimbo

first: Paul

last: Wade

first: Nina

last: Hubner

first: Hendrik

middle: G


title: Epigenomic analysis of primary human T cells reveals novel enhancers associated with Th2 memory differentiation and asthma susceptibility

first: Anna

last: Gerasimova


title: MicroRNA regulation of monocyte inflammatory and metabolic networks in an in vivo infection model

city: Meath

first: Nathan

last: Lawless

address: Grange

country: Ireland

institute: Teagasc


title: Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [iTC-seq_drugs]

first: Kristian

last: Helin

overall_design: in vivo Trancription Capture-sequencing (iTC-seq) time-course experiments during transcriptional inhibition with either DRB (0h, 2h and 5h) or Triptolide (0h, 1h and 2h) treatment of Mus musculus wild-type E14 Embryonic Stem Cells with two biological replicates per condition.

first: Eva

last: Riising

first: Itys

last: Comet

first: Benjamin

last: Leblanc


title: Characterization of miRNomes in acute and chronic myeloid leukemia cells

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

summary: An in-depth analysis of miRNomes in 3 human myeloid leukemia cell lines was carried out to comprehensively identify miRNAs that distinguish acute and chronic myeloid leukemias and relate to myeloid cell differentiation.

overall_design: Characterization the miRNomes in 3 myeloid leukemia cell lines.

first: Songnian

last: Hu

first: Xiangdong

last: Fang


title: MicroRNA regulation of the bovine local and systemic monocyte transcriptional responses to an in vivo Streptococcus uberis challenge

overall_design: Milk and blood isolated CD14+ monocyte cells taken from 5 infected Holstein friesians and 5 control Holstein friesians. Five animal infected with live S. uberis, cells extracted at 0, 12, 24, 36, and 48 hours post infection.

first: Kenneth

last: Bryan

first: Timothy

last: Reinhardt

first: Mike

last: Baker

first: Bruce

last: Pesch

first: Duane

last: Zimmerman

first: Kurt

last: Zuelke

first: Tad

last: Sonstegard

first: Cliona

last: O’Farrelly

first: John

middle: D

last: Lippolis

first: David

last: Lynn


title: Profiling premalignant lesions in lung squamous cell carcinomas identifies mechanisms involved in stepwise carcinogenesis

first: Adam

last: Gower

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary: Lung squamous cell carcinoma (SCC) is thought to arise from premalignant lesions in the airway epithelium, therefore studying these lesions is critical for understanding lung carcinogenesis. We performed RNA sequencing on laser-microdissected representative cell populations along the SCC pathological continuum of patient-matched normal basal cells, premalignant lesions, and tumor cells. We discovered transcriptomic changes and identified genomic pathways altered with initiation and progression of SCC within individual patients. We used immunofluorescent staining to confirm gene expression changes in premalignant lesions and tumor cells, including increased expression of SLC2A1, CEACAM5, and PTBP3 at the protein level and increased activation of MYC via nuclear translocation. Cytoband enrichment analysis revealed coordinated loss and gain of expression in chromosome 3p and 3q regions, respectively, during carcinogenesis. This is the first gene expression profiling of airway premalignant lesions with patient-matched samples that provides insight into the mechanisms of stepwise lung carcinogenesis.

overall_design: Profiling of mRNA expression in laser-microdissected normal airway basal cells, premalignant airway lesions, and lung SCC tumor cells by massively parallel RNA sequencing.

first: Aik

last: Ooi


title: Genome-wide analysis of SUMOylation effects on androgen receptor (AR) binding in PC-3 cells (ChIP-seq)

first: Päivi

last: Sutinen

overall_design: Androgen receptor (AR) genomic binding was studied in wild-type AR (wtAR) or SUMOylation-deficient AR (AR-K2R) stably expressing cells PC-3 cells, in biological dublicates. Cells were treated 1h either with 10 nM R1881 or vehicle and inputs were used as controls.

first: Marjo

last: Malinen

first: Sami

last: Heikkinen

first: Jorma

last: Palvimo


title: MicroRNAs are amplifiers of monocyte inflammatory networks and repressors of metabolism

first: Nathan

last: Lawless


title: Differentiation state-specific mitochondrial dynamic regulatory networks are revealed by global transcriptional analysis of the developing chicken lens.

status: Public on Jul 02 2014

city: Boca Raton

first: Marc

last: Kantorow

state: Florida

address: 777 Glades Rd

institute: Florida Atlantic University

summary: The mature eye lens contains a surface layer of epithelial cells called the lens epithelium that require a functional mitochondrial population to maintain the homeostasis and transparency of the entire lens.  The lens epithelium overlies a core of terminally differentiated fiber cells that must degrade their mitochondria to achieve lens transparency.  These distinct mitochondrial populations make the lens a useful model system to identify those genes that regulate the balance between mitochondrial homeostasis and elimination.  Here we used an RNA sequencing and bioinformatics approach to identify the transcript levels of all genes expressed by distinct regions of the lens epithelium and maturing fiber cells of the embryonic Gallus gallus (chicken) lens.  Our analysis detected over 15,000 unique transcripts expressed by the embryonic chicken lens.  Of these, over 3000 transcripts exhibited significant differences in expression between lens epithelial cells and fiber cells.  Multiple transcripts coding for separate mitochondrial homeostatic and degradation mechanisms were identified to exhibit preferred patterns of expression in lens epithelial cells that require mitochondria relative to lens fiber cells that require mitochondrial elimination.  These included differences in the expression levels of metabolic, autophagy, and mitophagy transcripts between lens epithelial cells and lens fiber cells. These data provide a comprehensive window into all genes transcribed by the lens and those mitochondrial regulatory and degradation pathways that function to maintain mitochondrial populations in the lens epithelium and to eliminate mitochondria in maturing lens fiber cells.

overall_design: Differentiation-state transcriptional analysis of embryonic chicken lenses was performed following microdissection of 100 embryonic day 13 (E13) chicken lenses into four distinct regions that represent a continuum of lens cell differentiation states: lens central epithelium (EC), equatorial epithelium (EQ), cortical fibers (FP), and central fibers (FC).  Further analysis of the transcriptional content of biologically replicate samples was performed by Illumina directional mRNA sequencing and resulting reads mapped by TopHat and assembled with Cufflinks.

first: Daniel

last: Chauss

first: Subhasree

last: Basu

first: Suren

last: Rajakaruna

first: Zhiwei

last: Ma

first: Victoria

last: Gau

first: Sara

last: Anastas

first: Lisa

last: Brennan

first: J

middle: F

last: Hetjmancik

first: A

last: Menko


title: Global characterization of the oocyte-to-embryo transition in C. elegans uncovers a novel mRNA turnover mechanism

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: The oocyte-to-embryo transition (OET) is thought to be mainly driven by post-transcriptional gene regulation. However, expression of both RNAs and proteins during the OET has not been comprehensively assayed. Furthermore, specific molecular mechanisms that regulate gene expression during OET are largely unknown. Here, we quantify and analyze, transcriptome-wide, expression of mRNAs, small RNAs and thousands of proteins in C. elegans oocytes, 1-cell, and 2-cell embryos. This represents a first comprehensive gene expression atlas during the OET in animals. We discovered a first wave of degradation in which thousands of mRNAs are turned over shortly after fertilization. Sequence analysis revealed a statistically highly significant presence of a novel polyC motif in the 3' untranslated regions (3' UTRs) of most of these degraded mRNAs. Transgenic reporter assays showed that this polyC motif is indeed required and sufficient for mRNA degradation after fertilization. We show that orthologs of human poly-C binding-protein specifically bind this motif. Together, our data suggest a mechanism in which the polyC motif and binding partners direct degradation of maternal mRNAs. Our data also indicate that endogenous siRNAs but not miRNAs promote mRNA clearance during the OET.

overall_design: To study the OET in C.elegans we isolated large quantities of  oocytes, 1-cell embryos, 2-cell embryos and sperm. We then sequenced polyA RNA.

first: Marlon

last: Stoeckius

first: Marieluise

last: Kirchner

first: Salah

last: Ayoub

first: Francesca

last: Torti

first: Fabio

last: Piano

first: Margareta

last: Herzog

first: Matthias

last: Selbach

first: Nikolaus

last: Rajewsky


title: Role of LDB1 in the transition from chromatin looping to transcription activation

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Many questions remain about how close association of genes and distant enhancers occurs and how this is linked to transcription activation. In erythroid cells, LDB1 is recruited to the β-globin locus via LMO2 and is required for looping of the β-globin locus control region (LCR) to the active β-globin promoter. We show that the LDB1 dimerization domain (DD) is necessary and, when fused to LMO2 is sufficient, to completely restore LCR-promoter looping and transcription in LDB1 depleted cells. The looping function of the DD is unique and irreplaceable by heterologous dimerization domains. Dissection of the DD revealed distinct functional properties of conserved subdomains. Notably, a conserved helical region (DD4/5) is dispensable for LDB1 dimerization and chromatin looping but essential for transcriptional activation. DD4/5 is required for the recruitment of the co-regulators FOG1 and NuRD complex. Lack of DD4/5 alters histone acetylation and RNA polymerase II recruitment and results in failure of the locus to migrate to the nuclear interior as normally occurs during erythroid maturation. These results uncouple enhancer-promoter looping from nuclear migration and transcription activation and reveal new roles for LDB1in these processes.

overall_design: RNA-seq in LDB1 knockdown, LDB1 delta4/5 construct, LDB1 full-length construct, and control in induced MEL cells; three replicates each.

middle: K

first: Ann

last: Dean

first: Ivan

last: Krivega


title: Effect of LMP7 and MECL1-immunoproteasome subunits deficiency on the transcriptome of mouse bone marrow-derived dendritic cells

city: Montréal

first: Claude

last: Perreault

state: Québec

address: P.O. Box 6128, Downtown Station

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: As regulators of protein degradation, proteasomes regulate practically all cellular functions. It is therefore logical to assume that replacement of the constitutive proteasome (CP) by its IFN-  inducible homolog immunoproteasome (IP) could have far reaching effects on cell function. Accordingly, recent studies have revealed important roles for IPs in immune cells beyond MHC I-peptide processing. Moreover, the expression of IPs in non-immune cells from non-inflamed tissues suggests that the involvement of IPs is not limited to the immune system. We demonstrate here that IP-deficiency affects the transcription of 8104 genes in maturing dendritic cells (DCs). This occurs mainly through non-redundant regulation of key immune-related transcription factors by CPs and IPs. Additionally, IP-deficiency decreases DC's efficiency to activate CD8+ T cells in vivo. Our study reveals that the broad cellular roles of IPs could rely on transcription regulation and, more importantly, illustrates how IP-deficiency could generate MHC I-peptide processing-independent phenotypes.

overall_design: Examination of the transcriptome of WT and immunoproteasome-deficient cells at 4 different time points of dendritic cell maturation, in 4 experimental replicates (total of 32 samples).

first: Danielle

last: de Verteuil

first: Alexandre

last: Rouette

first: Marie-Pierre

last: Hardy

first: Stéphanie

last: Lavallée

first: Assya

last: Trofimov

first: Étienne

last: Gaucher


title: Long-term survival of influenza virus infected club cells drives immunopathology

status: Public on Jul 01 2014

city: New York

first: Benjamin

last: tenOever

state: NY

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

summary: Analysis of mRNA expression of influenza infected and uninfected pulmonary epithelial cells in vivo


title: SUMOylation modulates the transcriptional activity of androgen receptor in a target gene and pathway selective manner.

first: Päivi

last: Sutinen

overall_design: Refer to individual Series


title: An Integrated Approach to Reconstructing Genome-scale Transcriptional Regulatory Networks [ChIP-Seq]

city: Madison

first: Timothy

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

summary: By integrating sequence information from closely related bacteria with a compendium of high-throughput gene expression datasets, a large-scale transcriptional regulatory networks was constructed for Rhodobacter sphaeroides. Predictions from this network were validated in part using genome-wide analysis for 3 transcription factors (PpsR, RSP_0489 and RSP_3341).

overall_design: Genome-wide protein-DNA interaction analysis of 3 transcription factors predicted to be involved in photosynthesis (PpsR), carbon metabolism (RSP_0489) and iron homeostasis (RSP_3341) were used to validate predictions from a large-scale reconstruction of R. sphaeroides transcriptional regulatory network.

first: Saheed

last: Imam


title: RNA Sequencing analysis of Wild Type and HID1 mutant Transcriptomes

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: Seedling photomorphogenesis is a sophisticated developmental process that is controlled by both the transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis noncoding RNA, designated HIDDEN TREASURE 1 (HID1), as a new factor promoting photomorphogenesisin continuous red light (cR). We show that HID1 acts through PHYTOCHROME-INTERACTING FACTOR 3 (PIF3), a bHLH transcription factor known to be a key repressor of photomorphogenesis.

overall_design: Total RNA was isolated from 5-day-old cR-grown WT and hid1(hidden treasure 1)seedlings using RNeasy Plant Mini Kits (Qiagen). Three biological replicates for each sample were subjected to RNA-seq. Poly (A) RNA from 1 μg total RNA was used to generate the cDNA library according to the TruSeq RNA Sample Prep Kit protocol. The library was then sequenced using a HiSeq 2000 system (Illumina). RNA-seq reads were mapped to TAIR10 using Tophat (version 2.0.9) (1). Differentially expressed genes were defined as those that differed by >2-fold with an adjusted P value ≤0.05 that was identified using Cuffdiff software (version 2.0.0)

first: Yuqiu

first: Danmeng

last: Zhu

first: Xingwang

last: Deng


title: A comprehensive survey of degradation and 3′ end modification of plant microRNAs by deep sequencing

city: LIN AN

first: ZHENGJIA

last: WANG

address: 88 NORTH CIRCLE ROAD

institute: ZHEJIANG A & F UNIVERSITY

summary: The degradation and 3′ end modification of plant microRNAs (miRNAs) play crucial roles in regulating miRNA function and stability. However, the process and mechanism of miRNA degradation and 3′ end modification has, to date, been poorly characterized. Here, we report that analysis of the two small RNA libraries constructed from two hickory floral differentiation stages by deep sequencing obtained a large number of truncated miRNAs and miRNAs with 3′ end modifications. The presence of so many truncated miRNAs suggests that plant miRNAs may be degraded through the 5′ to 3′ and 3′ to 5′ ends simultaneously, but the probability of miRNAs being truncated from the 3′ end was higher than from the 5′ end. Single- or double-nucleotide 3′ additions to miRNAs has been observed in many families. In this study, the 3′ addition of adenine to miRNA was the most common, accounting for more than 50% of all miRNA 3′ end modification in both small RNA libraries, followed by uridine addition. This suggests that the 3′ end modification of miRNAs shows a bias towards adenine and uridine in plants. Furthermore, we observed that both truncated miRNA and isomiR expressions associated with mature miRNAs. Our study provides more information regarding the degradation and 3′ end modification of miRNAs in plants.

overall_design: Examination of 2 different female flower buds

first: zhengjia

last: wang


title: Chromosome as oncogenic organizer: functional consequences of structural mutations in breast cancer (RNA-Seq)

city: Bar Harbor

first: Edison

last: Liu

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

summary: Chromosomal structural mutations play an important role in determining the transcriptional landscape of human breast cancers. To assess the nature of these structural mutations, we analyzed a representative sampling of the major types of breast tumor samples for detailed structural mutations using paired-end tag sequencing of long-insert genomic DNA (DNA-PET) with matched transcriptome ascertainment by RNA-seq. Compared with other structural mutations, tandem duplications are enriched around partners of fusion transcripts and demarcate regions of high gene expression. Moreover tandem duplications appear to be early events in tumor evolution by facilitating subsequent downstream amplification and deletion of important adjacent cancer associated genes. In a detailed reconstruction of events in chr17, we found large unpaired-inversions connect a duplicated ERBB2 with neighboring 17q21.3 amplicons while simultaneously deleting the intervening BRCA1 tumor suppressor locus. Using siRNAs in breast cancer cell lines, we showed that the 17q21.3 amplicon harbored a significant number of weak oncogenes that appeared consistently co-amplified in primary tumors. Down-regulation of BRCA1 expression augmented the cell proliferation in human normal mammary epithelial cells. Finally, using in silico approaches, we determined that genes whose expression in breast tumors are associated with either poor or good clinical prognosis appear clustered together in segments of frequent amplification or deletion, suggesting that structural abnormalities induce the loss or gain of blocks of adjacent genes with oncogenic or growth suppressor function. These analyses suggest that structural mutations efficiently orchestrate the gain and loss of cancer gene cassettes that engage many oncogenic pathways simultaneously.

overall_design: RNA sequencing of four primary breast cancer RNA samples (SOLiD, Applied Biosystems).

first: XingYi

last: Woo

first: Francesca

last: Menghi

first: Iry

last: Witham


title: Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Human pluripotent stem cells hold great potential for regenerative medicine, but available cell types have important limitations. While embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the 'gold standard' of pluripotency, they are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) are prone to epigenetic and transcriptional aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming or secondary to the reprogramming method, we generated a genetically matched collection of human IVF-ESCs, iPSCs, and ESCs derived by somatic cell nuclear transfer (SCNT; NT-ESCs), and subjected them to genome-wide genetic, epigenetic and transcriptional analyses. SCNT-based reprogramming is mediated by the full complement of oocyte cytoplasmic factors, thus closely recapitulating early embryogenesis. NT-ESCs and iPSCs derived from the same somatic donor cells contained comparable numbers of de novo copy number variations (CNVs), suggesting that the two reprogramming methods may not differ significantly in mutagenic or selective pressure. On the other hand, the DNA methylation and transcriptome profiles of NT-ESCs corresponded very closely to those of IVF-ESCs, while iPSCs differed markedly from IVF-ESCs and harbored residual DNA methylation patterns typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal candidates for cell replacement therapies.

overall_design: Whole-genome single-base resolution methyl-C sequencing collected from a variety of Human pluripotent cells

first: Ryan

last: O'Neil

first: Yupeng

last: He

first: Matthew

last: Schultz

last: Nery

first: Rosa

last: Castanon


title: Nuclear stability and transcriptional directionality separate functionally distinct RNA species

city: Copenhagen N

first: Robin

last: Andersson

address: Ole Maaloes Vej 5

institute: University of Copenhagen

summary: Sequencing of 5' ends of RNA molecules from control and exosome-depleted HeLa-S3 cells.

overall_design: CAGE library construction from RNA extracted from control and exosome-depleted cells.


title: Unraveling the Sox4-orchestrated pro-B cell differentiation program: Intricate roles of the RAG and CK1e genes

city: Houston

first: Xiaoping

last: Sun

state: Texas

address: 2130 Westholcombe Blvd, LSP12.3014

department: Laboratory Medicine

institute: The University of Texas MD Anderson Cancer Center


title: Unraveling the Sox4-orchestrated pro-B cell differentiation program: Intricate roles of the RAG and CK1ε genes (ChIP-Seq)

summary: Commitment of hematopoietic stem cells to B lineage precursors and development of B lineage precursors into mature B cells is attained through the coordinated function of multiple signaling networks, which are in turn controlled through stringent functioning of stage-specific transcription factors. Here, we describe the essential role of Sox4, an HMG (high mobility group)-box-containing transactivator, in B cell development. In the absence of Sox4, differentiation from pre-pro B to pro-B, from pro-B fraction B to pro-B fraction C and further to the immature B cell stage was severely impaired. Loss of differentiation was associated with reduced expression of Rag1 and Rag2 and markedly reduced DJ (diverse, joining) and VDJ (variable DJ) recombination at immunoglobulin heavy chain gene loci. We uncovered Sox4-regulated transcriptional circuits and a landscape of Sox4-chromatin interactions in pro-B cells. Sox4 ensured the negative regulation of Wnt signaling, which is critical for self-renewal of hematopoietic stem cells and early progenitors, by inducing one of its downstream effectors, casein kinase 1 epsilon. Our findings suggest that Sox4 orchestrates a unique transcriptional program and coordinates multilevel control in the differentiation of early-stage B cells.

overall_design: One sample of BAP-Sox4 bioChIP DNA and one sample of BAP-Sox4 input chromatin DNA were used.

first: Saradhi

last: Mallampati

first: Yue

last: Lu


title: "Drug-seq": An Approach to Identify the Genomic Targets of Chemicals Identified by Functional Phenotypic Screens

first: MICHAEL

last: ROSENFELD

address: 9500 Gilman Drive

institute: HHMI/UCSD


title: Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers

first: Kemal

middle: Marc

last: Akat

address: 1230 York Avenue

institute: The Rockefeller University


title: Next generation sequencing identifies discrete classes of box C/D snoRNAs featuring different ends and RNA binding protein dependency

city: Sherbrooke

first: Michelle

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

institute: University of Sherbrooke

summary: The paired-end next-generation sequencing of all small RNAs of less than 200 nucleotides in length from four different human cell lines (SKOV3ip1, MCF-7, BJ-Tielf, INOF) allowed us to determine the exact sequence(s) and variations of human box C/D snoRNAs (small nucleolar RNAs), revealing processing patterns of this class of molecules.   Two distinct groups of box C/D snoRNAs were identified based on the position of their ends with respect to their characteristic boxes and the terminal base pairing potential. Short box C/D snoRNAs start sharply 4 or 5 nucleotides upstream of their box C and end 2 or 3 nucleotides downstream of their box D. In contrast, long box C/D snoRNAs start 5 or 6 nucleotides upstream of their box C and end 4 or 5 nucleotides downstream of their box D, increasing the likelihood of formation of a k-turn between their boxes C and D. Sequencing of SKOV3ip1 cells following the depletions of NOP58, a core box C/D snoRNA-binding protein and of RBFOX2, a splicing factor, shows that the short box C/D snoRNA forms are significantly more affected by the depletion of RBFOX2 while the long snoRNA forms, which display more canonical box C/D snoRNA features, are significantly more affected by the depletion of NOP58. Together the data suggest that box C/D snoRNAs are divided into at least two groups of RNA with distinct maturation and functional preferences.

overall_design: Small RNAs (<200 nucleotides) were isolated from different human cell lines that were either untreated or depleted of NOP58 or RBFOX2 using specific siRNAs. The resulting libraries were multiplexed and paired-end sequenced using Illumina HiSeq.


title: "Drug-seq": An Approach to Identify the Genomic Targets of Chemicals Identified by Functional Phenotypic Screens [Drug-seq]

summary: Here we report an approach that has permitted us to uncover the sites and mechanisms of action of a drug, referred to as SD70, initially identified by phenotypic screening for inhibitors of ligand and genotoxic stress-induced translocations in prostate cancer cells. Based on synthesis of a derivatized form of SD70 that permits its application for a ChIP-seq-like approach, referred to as Drug-seq, we were next able to efficiently map the genome-wide binding locations of this small molecule, revealing that it largely co-localized with androgen receptor (AR) on regulatory enhancers. Based on these observations, we performed the appropriate global analyses to ascertain that SD70 inhibits the androgen-dependent AR program, and prostate cancer cell growth, acting, at least in part, by functionally inhibiting the jumonji (JMJ) domain-containing demethylase, KDM4C. Drug-seq represents a powerful strategy for new drug development by mapping genome-wide location of small molecules, a powerful adjunct to contemporary drug development strategies.

overall_design: Drug-seq assay followed by high-throughput sequencing (HT-seq).

first: Chunyu

last: Jin

first: Liuqing

last: Yang

first: Daria

last: Merkurjev


title: Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers [small RNA-seq]

summary: Heart failure is associated with high morbidity and mortality and its incidence increases worldwide. MicroRNAs (miRNAs) are potential markers and targets for diagnostic and therapeutic applications, respectively. We determined myocardial and circulating miRNA abundance and its changes in patients with stable and end-stage heart failure before and at different time points after mechanical unloading by a left ventricular assist device (LVAD) by small-RNA-sequencing. MiRNA changes in failing heart tissues partially resembled that of fetal myocardium. Consistent with prototypical miRNA–target-mRNA interactions, target mRNA levels were negatively correlated to changes in abundance for highly expressed miRNAs in heart failure and fetal hearts. The circulating small RNA profile was dominated by miRNAs, and fragments of tRNAs and small cytoplasmic RNAs. Heart- and muscle-specific circulating miRNAs (myomirs) increased up to 140-fold in advanced heart failure, which coincided with a similar increase in cardiac troponin I protein, the established marker for heart injury. These extracellular changes nearly completely reversed 3 months following initiation of LVAD support. In stable heart failure, circulating miRNAs showed less than 5-fold differences compared to normal, and myomir and cardiac troponin I levels were only captured near the detection limit. These findings provide the underpinning for miRNA-based therapies and emphasize the usefulness of circulating miRNAs as biomarkers for heart injury performing similar to established diagnostic protein biomarkers.

overall_design: Total RNA isolated from human left ventricular myocardium of failing hearts due to dilated or ischemic cardiomyopathy before and after mechanical unloading by a left ventricular assist device, and fetal myocardium compared to non-failing postnatal myocardium was subjected to multiplexed small RNA-sequencing on the Illumina platform. mRNA gene expression data using Illumina HumanHT-12v4 beadarrays for a subset of the myocardial samples is available (GSE52601).

middle: M

first: Thomas

last: Tuschl

first: Paul

last: Schulze


title: CORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development From Human Embryonic Stem Cells

city: Rensselaer

last: Kiehl

address: One Discovery Drive

institute: Neural Stem Cell Institute

summary: Many neurological and psychiatric disorders affect the cerebral cortex, and a clearer understanding of the molecular processes underlying human corticogenesis will provide greater insight into such pathologies. To date, knowledge of gene expression changes accompanying corticogenesis is largely based on murine data. Here we present a searchable, comprehensive, temporal gene expression dataset encompassing cerebral cortical development from human embryonic stem cells (hESCs). Using a modified differentiation protocol and RNA-Seq technology with computational analysis, we identified sets of genes and long non-coding RNAs that significantly change during corticogenesis, and those enriched for disease-associations. Numerous alternatively-spliced genes with varying temporal patterns of expression are revealed, including TGIF1, involved in holoprosencephaly and MARK1, involved in autism. We have created a database (http://cortecon.neuralsci.org) that provides online, query-based access to changes in RNA expression and alternatively spliced transcripts during human cortical development.

overall_design: Nine timepoints (days 0,7,12,19,26,33,49,63,77) covering human corticogenesis from embyronic stem cells.

first: Nathan

last: Boles

first: Joyce

last: van de Leemput

first: Sally

last: Temple

first: Christopher

middle: A

last: Fasano


title: Cross talk between the cell wall integrity and cAMP/protein kinase A pathways in Cryptococcus neoformans

city: St. Louis

first: Maureen

last: Donlin

address: 1100 South Grand

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

summary: Cryptococcus neoformans is a fungal pathogen of immunocompromised people that causes fatal meningitis.   The fungal cell wall is essential to viability and pathogenesis of C. neoformans, and biosynthesis and repair of the wall is primarily controlled by the cell wall integrity (CWI) signaling pathway.  Previous work by us and others have shown that deletion of genes encoding the four major kinases in the CWI signaling pathway, namely PKC1, BCK1, MKK2 and MPK1 results in severe cell wall phenotypes, sensitivity to a variety of cell wall stressors and, for Mpk1, reduced virulence in a mouse model.  Here, we examined the global transcriptional response of gene deletions of BCK1, MKK2 and MPK1 compared to wild-type cells.  We found over 1000 genes were differentially expressed in one or more of the deletion strains, with 115 genes differentially expressed in all three strains, many of which have been identified as genes regulated by the cAMP/protein kinase A (PKA) pathway.  Biochemical measurements of cAMP levels in the kinase deletion stains revealed significantly less cAMP in all of the deletion strains compared to wild-type cells.  The deletion strains also produced significantly smaller capsules than wild type KN99 under capsule inducing conditions, although they shed similar levels of capsule as wild type.  Finally, addition of exogenous cAMP led to reduced sensitivity to cell wall stress and restored surface capsule to near wild-type levels.  Thus, we have direct evidence of cross talk between the CWI and cAMP/PKA pathways that may have important implications for regulation of cell wall and capsule homeostasis.

overall_design: Comparison of three gene deletion strains to wild-type, with 3 biological replicates for each sample.

first: Jennifer

last: Lodge


title: Promoter methylome and integrative transcriptome profiling identify key epigenetics-regulated genes in human HCCs [expression]

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

summary: Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide and has a poor prognosis. Promoters represent an essential regulatory element of gene transcription in human genome. In order to understand the promoter methylation in relation with gene transcription in HCCs, We applied a liquid hybridization capture-based bisulfite sequencing (LHC-BS) approach to examine the promoter methylome of HCCs, for which we customized 150,407 capture probes and enabled coverage of 91.8% of the RefSeq gene promoters within human genome. We found the differential promoter DNA methylation between HCCs and peripheral normal tissues. Then we integrated promoter methylomic and transcriptomic profiling and described gene expression and regulation in HCCs. Lastly, We validated the key genes in larger number of samples and screened candidate genes aberrantly regulated by DNA methylation in human HCCs.

overall_design: RNA-seq for 8 pairs of HCC tumor and non-tumor liver (NTL) samples.

first: Fei

last: Gao

first: Hanlin


title: "Drug-seq": An Approach to Identify the Genomic Targets of Chemicals Identified by Functional Phenotypic Screens [GRO-seq]

first: MICHAEL

last: ROSENFELD

overall_design: Global Run-On (GRO) assay followed by high-throughput sequencing (GRO-seq).


title: Promoter methylome and integrative transcriptome profiling identify key epigenetics-regulated genes in human HCCs

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


title: Promoter methylome and integrative transcriptome profiling identify key epigenetics-regulated genes in human HCCs [methylation]

summary: Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide and has a poor prognosis. Promoters represent an essential regulatory element of gene transcription in the human genome. In order to understand the promoter methylation in relation with gene transcription in HCCs, we applied a liquid hybridization capture-based bisulfite sequencing (LHC-BS) approach to examine the promoter methylome of HCCs, for which we customized 150,407 capture probes and enabled coverage of 91.8% of the RefSeq gene promoters within the human genome. We found the differential promoter DNA methylation between HCCs and peripheral normal tissues. Then we integrated promoter methylomic and transcriptomic profiling and described gene expression and regulation in HCCs. Lastly, we validated the key genes in a larger number of samples and screened candidate genes aberrantly regulated by DNA methylation in human HCCs.

overall_design: Capture-based whole genome promoter bisulfite-seq for 8 pairs of HCC tumor and non-tumor liver (NTL) samples.

last: Lu


title: An atlas of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2

first: Berit

last: Lilje

address: Ole Maaløes Vej 5

department: Department of Biology, Section for Computational and RNA Biology

summary: Sequencing of 5'ends of RNA molecules from Caco-2 cells +/- TNFa stimulation

overall_design: CAGE library construction from RNA extracted from Caco-2 cells

first: Albin

last: Sandelin


title: ZNF804A transcriptome networks in differentiating human neurons derived from induced pluripotent stem cells

city: Bronx

first: Herb

last: Lachman

address: 1300 Morris Park Ave., F103

department: Psychiatry

institute: Albert Einstein College of Medicine

summary: The goal of this project is to study transcriptome change by knocking down ZNF804A, a schizophrenia and bipolar disorder candidate gene, in early neurons derived from iPSCs.

overall_design: Neural progenitor cells (NPCs) were developed from human induced pluripotent stem cells (iPSCs) and transduced by two independent shRNA vectors targeting ZNF804A, a schizophrenia and bipolar disorder candidate gene. After recovery and selection in puromycin, neuronal differentiation was induced. After 14 days, RNA was recovered and analyzed by RNA-seq. The expression profiles were compared with NPCs that were transduced with scrambled control vectors. This corresponds to controls 1-3 and KD 1-3, which was carried out on a male iPSC line. Scramble 1 and 2 and KD1 and 2 are technical replicates. Scrambled 3 and KD 3 were carried out on an independent NPC culture. For control 4 and KD4, neuronal differentiation was induced, and on day 10 the cells were transduced with the same ZNF804A KD and scrambled control vectors used for scrambled control 3 and KD3. In addition, this last set was carried out on a female iPSC line

first: Herbert

first: Deyou

last: Zheng


title: Profiling changes in gene expression by RNA-Seq during drought and recovery in switchgrass (Panicum virgatum Alamo AP13)

city: Austin

first: Thomas

last: Juenger

address: 2401 Speedway

institute: University of Texas, Austin

summary: In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel light:dark cycles, we profiled gene expression in drought and control treatments under pre-dawn and mid-day conditions. Soil drying resulted in reduced leaf water potential, gas exchange, and chlorophyll fluorescence along with differential expression of a large fraction of the transcriptome (37%). Many transcripts responded differently depending on time of day (e.g. up-regulation pre-dawn and down-regulation mid-day). Genes associated with C4 photosynthesis were down-regulated during drought, while C4 metabolic intermediates accumulated. Rapid changes in gene expression were observed during recovery from drought, along with increased water use efficiency and chlorophyll fluorescence. Our findings demonstrate that drought responsive gene expression depends strongly on time of day and that gene expression is extensively modified during the first few hours of drought recovery. Analysis of covariation in gene expression, metabolite abundance, and physiology among plants revealed non-linear relationships that suggest critical thresholds in drought stress responses. Future studies may benefit from evaluating these thresholds among diverse accessions of switchgrass and other C4 grasses.

overall_design: mRNA profiles of leaf tissue from clonal replicates at various time points during drydown and recovery were generated by deep sequencing 3' mRNA tags using SOLiD.

first: Eli

last: Meyer

first: Michael

last: Aspinwall

first: David

middle: B

last: Lowry

first: Juan

last: Palacio-Mejía

first: Tierney

middle: L

last: Logan

first: Philip

last: Fay


title: Genome-wide analysis of gene expression changes in mouse tongue squamous cell carcinomas induced by 4-nitroquinoline 1-oxide (4-NQO)

first: Xiaohan

last: Tang

address: 1300 York Avenue, Room E-405

institute: Weill Cornell Medical College

summary:
We hypothesized that the expression of many genes are dysregulated during oral cancer carcinogenesis.  We examined genome-wide transcript levels in normal mouse tongues and the tongue squamous cell carcinomas induced by 4-NQO.
The results will provide important information for the diagnosis, prevention, and treatment of human oral cancers, including tongue cancer.

overall_design: Total RNA obtained from normal tongues (not treated with 4-NQO) and tongue squamous cell carcinomas induced by 4-NQO.

first: Xiao-Han

first: Alison

last: Urvalek

first: Kwame

last: Osei-Sarfo

first: Lorraine

last: Gudas


title: The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here we examined the contribution of structural domains in Piwi proteins towards defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5′ uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5’ end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis

overall_design: Immunoprecipitated small RNA were purified from Bmn4 cells for preparation of high-throughput sequencing libraries.

first: Elisa

last: Cora

first: Radha

last: Pandey

first: Jordi

last: Xiol

first: Josh

last: Taylor

first: Ravi

last: Sachidanandam

first: Andrew

last: McCarthy

middle: S


title: Allele-Specific Methylation Occurs at Genetic Variants Associated with Complex Disease

city: Boston

first: John

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

summary: We use targeted bisulfite PCR and next-generation 454 sequencing of multiple amplicons to analyze the association of cis-regulated allele-specific methylation (ASM) with multiple complex disease-associated variants in a population of 82 individuals. We detect ASM at four variants implicated in complex phenotypes such as ulcerative colitis and AIDS progression disease (rs10491434), Celiac disease (rs2762051), Crohn’s disease, IgA nephropathy and early-onset inflammatory bowel disease (rs713875) and height (rs6569648).

overall_design: 82 samples analysed


title: A Role for WDR5 in Integrating Threonine 11 Phosphorylation to Lysine 4 Methylationon Histone H3 and in Prostate Cancer

city: Chicago

first: Grant

middle: D.

last: Barish

state: IL

address: 303 E Superior Street

department: Medicine

institute: Northwestern University

summary: Upon androgen stimulation, PKN1-mediated histone H3 threonine 11 phosphorylation (H3T11P) promotes AR target genes activation. However, the underlying mechanism is not completely understood. Here, we show that WDR5, a subunit of the SET1/MLL complex, interacts with H3T11P and this interaction facilitates the recruitment of the SET1/MLL complex and subsequent H3K4 trimethylation (H3K4me3). Using ChIP-seq, we find that androgen stimulation results in a six-fold increase in the number of H3T11P-marked regions and induces WDR5 colocalization to one third of H3T11P-enriched promoters, thus establishing a genome-wide relationship between H3T11P and recruitment of WDR5. Accordingly, PKN1 knock-down or chemical inhibition severely blocks WDR5 association and H3K4me3 on AR target genes. Finally, WDR5 is critical in prostate cancer cell proliferation, and is hyperexpressed in human prostate cancers. Together, these results identify WDR5 as a critical epigenomic integrator of histone phosphorylation and methylation and a major driver of androgen-dependent prostate cancer cell proliferation.

overall_design: Identification of Histone 3 threonine 11 phosphorylation (H3T11P) marks and WDR5 binding sites in LNCaP cells treated with R1881 ligand (androgen) or solvent control.

first: Ji-Young

last: Kim

first: Mairead

last: Baker

first: Debabrata

last: Chakravarti


title: Hematopoietic stem/progenitor cells HELP-tagging cytosine methylation data (Albert Einstein College of Medicine)

city: BRONX

first: Fabien

last: Delahaye

address: 1300 Morris Park Avenue

department: Genetics

institute: AECOM

summary: Extreme fetal growth is associated with adult disease through a cellular memory of unknown mechanism.  We tested whether heritable epigenetic processes in long-lived CD34+ hematopoietic stem/progenitor cells (HSPCs) showed evidence for re-programming associated with the extremes of fetal growth. Here we show that both extremes of fetal growth are associated with global shifts towards DNA hypermethylation, targeting cis-regulatory elements in proximity to genes involved in glucose homeostasis and stem cell function. A sexually dimorphic response was found, intrauterine growth restriction (IUGR) associated with greater epigenetic dysregulation in males but large for gestational age (LGA) growth affecting females to a greater extent. The findings are consistent with extreme fetal growth interacting with variable fetal susceptibility to influence cellular aging characteristics through epigenetic mechanisms, with the potential for identifying infants at higher risk for chronic disease later in life.

overall_design:
60 HpaII test

Please note that the '*[healthy control]' samples are the same samples represented in the GSE49836, and re-used in this study. They are re-accessioned (for retrieval of the complete raw data from SRA).

first: Francine

middle: H

last: Einstein

first: N

last: Wijetunga

first: Hye

last: Heo

first: Jessica

last: Tozour

first: Yong

last: Zhao

last: Greally