title: Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape.

first: Gavin

last: Kelsey

address: Babraham Research Campus

institute: The Babraham Institute

summary: We have performed deep RNA-Seq and de novo transcriptome assembly at different stages of mouse oogenesis. This revealed thousands of novel non-annotated genes as well as alternative promoters for ~10% of reference genes expressed in oocytes, a large fraction of which coincide with transposable elements of the MaLR and ERVK families. We defined the oocyte DNA methylation landscape as composed of large-scale hyper- and hypo-methylated domains. Correlation with our transcriptome assembly revealed that transcription correlates accurately with DNA methylation and potentially account for ~85-90% of the DNA methylome.

overall_design: RNA-Seq in mouse oocytes at different stages of folliculogenesis

first: Lenka

last: Veselovska

first: Heba

last: Saadeh

first: Sebastien

last: Smallwood


title: Impact of flanking chromosomal sequences on localization and silencing by the ncRNA XIST

status: Public on Sep 02 2015

city: Vancouver

first: Carolyn

last: Brown

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed RNA-seq and ChIP-seq on clones of human cell lines carrying an inducible XIST transgene on 1p, 8p, or 12q to study the effects of allelic silencing in cis

overall_design: Total gene expression and allelic changes were examined in HT1080 clones carrying an inducible XIST transgene on 1p, 8p, or 12q after induction by doxycycline. A replicate was done for the 8p clone treated with DOX. An additional 1p clone integrated with an empty vector, and an 1p, 8p, and 12q clone without induction were included as controls. ChIP was performed on the 8p clone to investigate the changes in H3K27 acetylation and trimethylation.

first: Danny

last: Leung

first: Christine

last: Yang


title: Impact of Jmjd3 and Utx histone demethylases on Histone H3 lysine 27 trimethylation (H3K27Me3)  in mature CD4 SP thymocytes

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

country: USA

institute: NIH

summary: While histone H3 lysine 27 trimethylation (H3K27Me3) is associated with gene silencing, whether H3K27Me3 demethylation affects transcription and cell differentiation in vivo has remained elusive. To investigate this, we conditionally inactivated the two H3K27Me3 demethylases, Jmjd3 and Utx, in non-dividing intrathymic CD4+ T cell precursors.  We show that both enzymes redundantly promote H3K27Me3 removal at, and expression of, a specific subset of genes involved in terminal thymocyte differentiation, especially S1pr1, encoding a sphingosine-phosphate receptor required for thymocyte egress.

overall_design: Floxed alleles of the genes encoding Utx and Jmjd3 (Kdm6a and Kdm6b, respectively) were deleted in  double positive (DP) thymocytes carrying a CD4 Cre transgene. Genome-wide H3K27Me3 ChipSeq was performed on (i) pre-selection (CD69lo) DP thymocytes from wild-type mice carrying an endogenous polyclonal TCR repertoire, (ii) mature (TCRhi CD24lo) CD4 SP thymocytes from wild type (Wt), Jmjd3KO, UtxKO and dKO mice carrying an endogenous polyclonal TCR repertoire and (iii)  mature (Va2hi CD24lo) CD4 SP thymocytes from wild type and dKO mice carrying the OTII TCR transgene.

first: Sugata

last: Manna

first: Jong

middle: K

last: Kim

first: Yongmei

last: Zhao

first: Jyoti

last: Shetty

first: Bao

last: Tran

first: Rémy

last: Bosselut


title: Survival and Diversity of Human Homologous Dietary MicroRNAs in Conventionally Cooked Top Sirloin and Dried Bovine Tissue Extracts

city: Palmyra

first: Joseph

last: Dever

state: WI

address: 1200 W Royal Lee Dr.

institute: Standard Process

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the human homologous microRNA profiles in food-grade, bovine-sourced sirloin, heart and adrenal tissue (raw, cooked, and laboratory-prepared pasteurized, freeze-dried extracts)

overall_design: Deep miRNA sequencing of sirloin (raw and cooked), heart tissue (raw, cooked, and pastuerized, freeze-dried extracts) and adrenal tissue (raw, cooked, and laboratory-prepared pasteurized, freeze-dried extracts), 3 replicates each process group

middle: T

first: Amber

middle: L

last: Thompson


title: Decreased TFR/TFH ratio in SIV-infected rhesus macaques may contribute to accumulation of TFH cells in chronic infection

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: T follicular helper cells (TFH) are critical for the development and maintenance of germinal centers (GC) and humoral immune responses. During chronic HIV/SIV infection TFH accumulate, possibly as a result of antigen persistence. The HIV/SIV-associated TFH expansion may also reflect lack of regulation by suppressive follicular regulatory CD4+ T-cells (TFR). TFR are natural regulatory T-cells (TREG) that migrate into the follicle and, similarly to TFH, up-regulate CXCR5, Bcl-6, and PD1. Here we identified TFR as CD4+CD25+FoxP3+CXCR5+PD1hiBcl-6+ within lymph nodes of rhesus macaques (RM) and confirmed their localization within the GC by immunohistochemistry. RNA sequencing showed that TFR exhibit a distinct transcriptional profile with shared features of both TFH and TREG, including intermediate expression of FoxP3, Bcl-6, PRDM1, IL-10, and IL-21. In healthy, SIV-uninfected RM, we observed a negative correlation between frequencies of TFR and both TFH and GC B-cells as well as levels of CD4+ T-cell proliferation. Following SIV infection, the TFR/TFH ratio was reduced with no change in the frequency of TREG or TFR within the total CD4+ T-cell pool. Finally, we examined whether higher levels of direct virus infection of TFR were responsible for their relative depletion post-SIV infection. We found that TFH, TFR and TREG sorted from SIV- infected RM harbor comparable levels of cell-associated viral DNA. Our data suggests that TFR may contribute to the regulation and proliferation of TFH and GC B-cells in vivo and that a decreased TFR/TFH ratio in chronic SIV infection may lead to unchecked expansion of both TFH and GC B-cells.

overall_design: TFR, TFH, TREG and bulk CD4 cells were sorted from spleens of 5 uninfected and 5 infected RM.

first: Ankita

last: Chowdhury

first: Perla

middle: M

last: Estrada Del Rio

first: Greg

first: Ronald

middle: P

last: Trible

first: Rama

middle: R

last: Amara

first: Ann

last: Chahroudi

first: Gustavo

last: Reyes-Teran

first: Steven

middle: E

last: Bosinger

first: Guido

last: Silvestri


title: Next Generation Sequencing  Analysis of Wild Type and Hypomorphic Nkx2-5 mutant heart Transcriptomes

city: London

first: Laurent

last: Dupays

address: The Ridgeway, Mill Hill

country: United Kingdom

institute: The Francis Crick Institute

summary: We report the transcriptome analysis of E11.5 mouse embryonic heart presenting a reduction in Nkx2-5 expression compare to wild-type littermate.

overall_design: Transcriptome analysis of 3 different E11.5 hypomorphic hearts against 3 controls littermate hearts.


title: RNA-Seq of the rat pineal transcriptome, with in-vivo and in-vitro samples, under various treatment and surgical conditions

city: Rockville

first: Stephen

middle: William

last: Hartley

address: 5625 Fishers Lane

department: Cancer Genetics and Comparative Genomics Branch

institute: NHGRI, NIH

summary: Pineal function follows a 24-hour schedule, dedicated to the conversion of night and day into a hormonal signal, melatonin. In mammals, 24-hour changes in pineal activity are controlled by a neural pathway that includes the central circadian oscillator in the suprachiasmatic nucleus and the superior cervical ganglia (SCG), which innervate the pineal gland. In this study, we have generated the first next-generation RNA sequencing evidence of neural control of the daily changes in the pineal transcriptome. We found over 3000 pineal transcripts that are differentially expressed (p <0.001) on a night/day basis (70% of these genes increase at night, 376 with fold change >4 or <1/4), the majority of which had not been previously identified as such. Nearly all night/day differences were eliminated by neonatal removal or decentralization of the SCG, confirming the importance of neural input for differential night/day changes in transcript abundance. In contrast, very few non-rhythmic genes showed evidence of changes in expression due to the surgical procedure itself, which is consistent with the hypothesis that post neonatal neural stimulation is not required for cell fate determination and maintenance of phenotype. Many of the transcripts that exhibit marked differential night/day expression exhibited similar changes in response to in vitro treatment with norepinephrine, the SCG neurotransmitter which mediates pineal regulation. Similar changes were also seen following treatment with an analog of the norepinephrine second messenger, cyclic AMP.

overall_design: For the in vivo data, there were 8 biological conditions: day and night time points for each of four surgical groups: Control (Ctrl) Sham-surgery (Sham), Decentralized (DCN), and Ganglionectomized (SCGX). Samples were pooled into three biological replicates for each biological condition. For the in vitro data there were 3 biological conditions: Untreated control (CN), DBcAMP-treated (DB), and Norepinephrine-treated (NE). For the pineal enrichment comparison, three samples (i.e. no biological replicates) were used: pineal-day, pineal-night and mixed-tissue. For the mixed tissues sample, the following tissues from three rats sacrificed at ZT7 were used: cortex, cerebellum, midbrain, hypothalamus, hindbrain, spinal cord, retina, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, adrenal gland. Total RNA was extracted from each tissue, and then equal amounts of each of the 15 tissues were combined for the final pooled sample.

middle: W

last: Coon

first: Luis

last: Savastano

first: James

last: Mullikin

first: David

last: Klein

first: Cong

last: Fu


title: Comparative histone modification profiling revealed developmentally regulated acetylation on upstream promoters of C4 genes and potential C4 regulators

status: Public on Sep 03 2015

city: Hannover

first: Christoph

last: Peterhansel

address: Herrenhaeuser Strasse 2

department: Botany

country: Germany

institute: Leibniz-Universitaet-Hannover

summary: We analysed genome-wide histone H3 lysine 4 trimethylation and histone H3 lysine 9 acetylation, two modifications typically associated with active genes, in meristematic cells at the base and expanding cells in the maturing zone of the maize (Zea mays) leaf. These data were compared to transcript levels of associated genes. Our data revealed that for individual genes fold-changes in histone modification and transcript abundance were much better correlated than absolute intensities. When focusing on regulated modification sites, we identified secondary upstream H3 lysine 9 acetylation peaks (SUPs) on upstream promoter regions of approximately 6% of all acetylated genes. SUPs showed stronger regulation than the previously described acetylation peaks at transcription initiation sites, were more often found on genes that were upregulated towards the maturing zone than on downregulated genes, and were significantly enriched on photosynthetic genes. We identified SUPs on all genes encoding enzymes of the C4 cycle. Moreover, SUPs were enriched in four lists of candidate C4-associated genes that were derived from previous transcriptomic studies. Based on these data, we used highly regulated SUPs as an epigenetic mark to identify new genes potentially involved in C4 metabolism. This approach also allowed the identification of ethylene response elements as highly enriched cis-acting elements in SUP regions. Our data suggest co-evolution of epigenetic promoter elements during the establishment of C4 photosynthesis.

overall_design: Comparative analysis of H3K9ac, H3K4me3 and the transcription between two developmental zones within one maize leaf.

first: Renke

last: Perduns

first: Ina

last: Horst-Niessen


title: Transcriptomic analysis of cellulolytic fungus Penicillium oxalicum and its sporogenesis related genes deletion strains

status: Public on Sep 01 2015

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

country: China

institute: shandong university

summary: RNA-seq was used to compare differential gene expressions for Penicillium oxalicum wild type strain (M12) and sporognesis related genes knock out strains.The goals of this study are to construct the sporogenesis regulation pathway of Penicillium oxalicum.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and nine mutant strains (flbA knoutout strain, flbB knoutout strain, flbC knoutout strain, flbD knoutout strain, flbE knoutout strain,wetA knoutout strain, abaA knoutout strain,stuA knoutout strain, swi6 knoutout strain)

first: Yinbo

last: Qu

first: Yuqi

last: Qin

first: Xiujun

last: Zhang


title: Partial loss of Rpl11 in adult mice recapitulates Diamond-Blackfan anemia (DBA) and promotes lymphomagenesis

city: Edinburgh

first: Lucía

last: Morgado

address: Edinburgh Bioquarter, 5 Little France Drive

institute: University of Edinburgh

summary: Diamond-Blackfan anemia (DBA) is characterized by anemia and cancer susceptibility, and is caused by mutations in ribosomal genes, including Rpl11. Here, we report that Rpl11-heterozygous embryos are not viable, and homozygous deletion of Rpl11 in adult mice results in death within a few weeks, accompanied by bone marrow aplasia and intestinal atrophy. Importantly, deletion of a single Rpl11 allele in adult mice results in anemia associated to decreased erythroid progenitors and defective erythroid maturation. These phenotypes are also present in mice transplanted with inducible heterozygous Rpl11 bone marrow, indicating a cell-autonomous role of RPL11 in erythropoiesis. Additionally, fibroblasts lacking one or both Rpl11 alleles show defective p53 activation upon ribosomal stress or DNA damage. Furthermore, fibroblasts and hematopoietic tissues from heterozygous Rpl11 mice present higher basal cMYC levels. Accordingly, heterozygous Rpl11 mice are highly susceptible to radiation-induced lymphomagenesis. We conclude that Rpl11-deficient mice recapitulate DBA disorder, including cancer predisposition.

overall_design: RNAseq profiles of bone marrow hematopoietic progenitors cells from WT (Rpl11+/+:: Tg.UbC-CreERT2) and LOX (Rpl11+/lox::Tb.Ub-CreERT2) mice, n=4 independent animals per genotype

first: Lucia

last: Morgado-Palacin

first: Gianluca

last: Varetti

first: Susana

last: Llanos

first: Gonzalo

last: Gómez-López

first: Dolores

last: Martinez

first: Manuel

last: Serrano


title: Oncogenic MYC induces a dependency on the spliceosome in human cancer

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

summary: c-MYC (MYC) overexpression or hyperactivation is one of the most common drivers of human cancer. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. Like other classic oncogenes, hyperactivation of MYC leads to collateral stresses onto cancer cells, suggesting that tumors harbor unique vulnerabilities arising from oncogenic activation of MYC. Herein, we discover the spliceosome as a new target of oncogenic stress in MYC-driven cancers. We identify BUD31 as a MYC-synthetic lethal gene, and demonstrate that BUD31 is a splicing factor required for the assembly and catalytic activity of the spliceosome. Core spliceosomal factors (SF3B1, U2AF1, and others) associate with BUD31 and are also required to tolerate oncogenic MYC. Notably, MYC hyperactivation induces an increase in total pre-mRNA synthesis, suggesting an increased burden on the core spliceosome to process pre-mRNA. In contrast to normal cells, partial inhibition of the spliceosome in MYC-hyperactivated cells leads to global intron retention, widespread defects in pre-mRNA maturation, and deregulation of many essential cell processes. Importantly, genetic or pharmacologic inhibition of the spliceosome in vivo impairs survival, tumorigenicity, and metastatic proclivity of MYC-dependent breast cancers. Collectively, these data suggest that oncogenic MYC confers a collateral stress on splicing and that components of the spliceosome may be therapeutic entry points for aggressive MYC-driven cancers.

overall_design: Examination of intron rentention in MYC-ER HMECs, in 4 conditions

first: Thomas

middle: F

last: Westbrook

middle: A


title: Differential Gene Expression between MCF10A and MCF7 cells

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: These RNA-seq data were generated to correlate with genomic interaction data in a related Hi-C analysis.  MCF10A is a normal-like mammary epithelial cell line and MCF7 is a transformed estrogen responsive breast cancer cell line derived from a metastatic site; both are commonly used in models of breast cancer progression.  Analysis revealed a set of genes related to repression of WNT signalling that were both up-regulated in MCF7 and located in genomic regions that had transitioned from closed to open structure in MCF7.

overall_design: RNA-seq of MCF10A and MCF7 cells. 3 replicates each.  Sequencing was strand-specific and conducted on ribo-depleted RNA.

first: Terri

last: Messier

first: Rasim

last: Barutcu

first: Coralee

last: Tye

first: Joe

last: Boyd

first: Deli

last: Hong

first: Janet

last: Stein

first: Jane

last: Lian

first: Gary


title: Identification of NKX2-5 transcriptional targets in the mouse embryonic heart

first: Laurent

last: Dupays

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

overall_design: Refer to individual Series


title: Genome-wide maps of Nkx2-5 in E11.5 mouse embryonic heart

summary: We report the identification of genome-wide binding site of the cardiac transcription factor Nkx2-5 during mouse heart development.

overall_design: Examination of Nkx2-5 binding in wild-type mouse in duplicate.


title: ERR-gamma links adaptive neuronal metabolism to spatial learning and memory

city: La Jolla

first: Ruth

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute


title: RNA sequencing of ILK-deficient hair follicle bulge stem cells

city: Münster

first: Sara

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

summary: We sequenced mRNA from FACS purified hair follicle bulge stem cells from 21 d old control and ILK-deficient mice, 3 biological replicates each

overall_design: Examination of mRNA levels in control and ILK-deficient hair follicle bulge stem cells


title: Differential expression of GFP+ and RFP+ TriPyMT cells

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

summary: Tri-PyMT cell is a breast tumor cell line established from Tri-PyMT (MMTV-PyMT/fsp1-Cre/Rosa26-RGFP) primary breast tumors. The cells switch from RFP+ to GFP+ during epithelial to mesenchymal transition (EMT). Differential expressed genes between EMT and non-EMT tumor cells will reveal interesting targets for anti-EMT approaches.

overall_design: Tri-PyMT cells were culture in medium with serum (10%FBS). Cells were treated with or without 4-hydroperoxy-cyclophosphamide (4µM) for 7 days and sorted by flow cytometry into RFP+ and GFP+ subpopulations for RNA extraction and subsequent RNA-Seq analysis.

first: Kari

last: Fischer

first: Vivek

last: Mittal


title: An Alternative Splicing Event Amplifies Evolutionary Differences Between Vertebrates

city: Toronto

first: Serge

last: Gueroussov

state: Ontario

address: 160 College Street, Room 1030

department: Molecular Genetics

institute: University of Toronto

summary: Alternative splicing (AS) generates extensive transcriptomic and proteomic complexity. However, the functions of species- and lineage-specific splice variants are largely unknown. Here, we show that mammalian-specific skipping of exon 9 of PTBP1 alters its splicing regulatory activities and affects the inclusion levels of numerous exons. During neurogenesis, skipping of exon 9 reduces PTBP1 repressive activity so as to facilitate activation of a brain-specific AS program. Engineered skipping of the orthologous exon in chicken cells induces a large number of mammalian-like AS changes in PTBP1 target exons. These results thus reveal that a single exon skipping event in an RNA binding regulator directs numerous AS changes between species. The results further suggest that these changes contributed to evolutionary differences in the formation of vertebrate nervous systems.

sample_organism:
Gallus gallus
Homo sapiens

platform_organism:
Gallus gallus
Homo sapiens

overall_design: This study contains two sets of samples: (Set 1) mRNA profiling of human 293 cells subjected to four different conditions in two biological replicates: non-targetting control siRNA, PTBP1 and PTBP2 siRNA, PTBP1 and PTBP2 siRNA with overexpression of full-length human PTBP1, PTBP1 and PTBP2 siRNA with overexpression of exon-excluded human PTBP1. (Set 2) mRNA profiling of chicken DT40 cells with 3 genotypes in two bioligcal replicates: wildtype cells, cells with PTBP1 exon 8 (orthologous to human PTBP1 exon 9) deleted in one allele, and cells with PTBP1 exon 8 deleted in both alleles.

first: Manuel

last: Irimia

first: Benjamin

middle: J

last: Blencowe


title: SK-N-SH Hi-C

first: David

last: Gorkin

state: California

address: 9500 Gilman Dr. CMM-East 2071

institute: Ludwig Institute for Cancer Research

summary: Hi-C was performed on SK-N-SH cells to study 3-dimensional chromatin architecture.

overall_design: Two biological replicates were performed, each with roughly 25x10^7 cells.

first: Inkyung

last: Jung

first: Bing

last: Ren

first: Daniele

last: Canzio

first: Tom

last: Maniatis


title: Selective Death in Spinal Muscular Atrophy: Genome-Wide RNA-Seq Using Purified Patient-Derived Motor Neurons

city: cambridge

middle: G

last: Hendrickson

state: MA

address: 7 divinity ave

institute: Harvard University

summary: Spinal Muscular Atrophy (SMA) is well-known to be caused by mutations in the gene Survival of Motor Neuron 1 (SMN1). Because this gene is ubiquitously expressed, it remains poorly understood why motor neurons (MNs) are one of the most affected cell types. To begin to address this question, we carried out RNA-sequencing studies using fixed, antibody-labeled and purified MNs produced from control and SMA patient-derived induced pluripotent stem cells (iPSCs). We found SMA-specific changes in MNs, including hyper-activation of the endoplasmic reticulum (ER) stress pathway and enhanced apoptosis. Functional studies demonstrated that inhibition of ER stress improves overall MN health and survival in vitro even in MNs with low SMN levels. In SMA mice, we show that systemic delivery of an ER stress inhibitor that crosses the blood-brain-barrier led to preservation of MNs in the spinal cord and prolonged survival of these mice. Therefore, our study implies that selective activation of ER stress underlies MN death in SMA. Moreover, the approach we have taken would be broadly applicable to studying disease-prone human cells in heterogeneous cultures.

overall_design: total RNA collected from ES cell and patient ES cell derived spinal motor neurons

first: Shi-Yan

last: Ng


title: Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved insulin secretion by pancreatic β cells

city: Jerusalem

first: Dana

last: Avrahami Tzfati

address: Ein-Kerem

department: Developmental Biology and cancer research

country: Israel

institute: Hadassah Hebrew University School of medicine

type: Methylation profiling by high throughput sequencing

summary: Aging at the cellular level is driven by changes in gene activity and epigenetic state that are only partially understood. We performed a comprehensive epigenomic analysis of the pancreatic β cell, key player in glucose homeostasis and diabetes, in adolescent and very old mice. Globally, we observe a general methylation drift resulting in an overall more leveled methylome, suggesting that the maintenance of highly differential methylation patterns becomes compromised with advanced age. Importantly, we discover targeted changes in the methylation status of β cell proliferation and function genes that go against the global methylation drift, are specific to β cells, and correlate with repression of the proliferation program and activation of metabolic regulators. These targeted alterations frequently occur at distal cis-regulator elements, and are associated with specific chromatin marks and transcription factor occupancy in young β cells. Strikingly, we find the insulin secretory response to glucose much improved in mature β cells in mice, as predicted by the changes in methylome and transcriptome and in contrast to the decline in function observed in aged human β cells. Thus, aging of terminally differentiated cells in mammals is not always coupled to functional decline.

overall_design: RNA-seq was done on 3 biological replicas from old and three from young beta cells. each sample originated from a pool of 5-10 mic.e H3K27me3 ChIP-seq was done with two replicas for old mice (pool of 4-7 mice) and the rest of the ChIPseq (H3K4me1, H3K27ac and young H3K27me3) was sone with one sample (pool of few mice). BIS-seq was done on one sample from a pool of 10 young mice and one sample of a pool of old mice (18-22 months old)

last: Avrahami

first: Changhong

last: Li

first: Jia

last: Zhang

first: Jonathan

last: Schug

first: Ran

first: Shilpa

last: Rao

first: Michael

last: Stadler

first: Lukas

last: Burger

first: Dirk

last: Schübeler

last: Glaser

first: Klaus

middle: H

last: Kaestner


title: Decay-initiating endoribonucleolytic cleavage by RNase Y is kept under tight control via sequence preference and sub-cellular localisation

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

summary: Bacteria depend on efficient RNA turnover to rapidly alter gene expression, essentially for responding to changing conditions. Nevertheless, remarkably few details are known about the rate-limiting steps in targeting and decay of RNA. The membrane-anchored endoribonuclease RNase Y is a virulence factor in Gram- positive pathogens. We have obtained a global picture of RNase Y sequence specificity using RNA-seq and the novel transcriptome-wide EMOTE method. Ninety- nine endoribonucleolytic sites produced in vivo were precisely mapped, notably inside six out of seven genes whose half-lives increase the most in an RNase Y deletion mutant, and additionally to three separate transcripts encoding degradation ribonucleases, including RNase Y itself, suggesting a regulatory network. We show that RNase Y is required to initiate the major degradation pathway of a defined sub-set of transcripts that are inaccessible to other ribonucleases, but is prevented from promiscuous activity by membrane confinement and sequence preference for guanosines.

overall_design: Rnase Y activity in S. aureus is analysed on a genome wide scale under two perspectives: a RNA decay timecourse with mRNA-seq; and exact position of cleavage with an EMOTE assay (Exact Mapping Of Trancripts Ends)

first: Vanessa

last: Khemici

first: Patrick

last: Linder

first: Peter

last: Redder


title: Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 (RNA-Seq)

city: Berkeley

first: James

last: Craig

address: 341A Koshland Hall

department: Plant & Microbial Biology

institute: UC Berkeley

summary: abstract: The plant cell wall is composed of many complex polymers, and its deconstruction requires an equally complex orchestration of a wide array of enzymes.  In Neurospora crassa, clr-1, clr-2 and xlr-1 have been identified as the key transcription factors involved in cell wall breakdown.  In order to define their regulons, we performed ChIPseq upon these three transcription factors.  CLR-1, CLR-2 and XLR-1 each bind to the most highly and differentially expressed gene populations, which include the cellulases for the CLRs and the hemicellulases for XLR-1.  CLR-1 also bound to its regulon under non-inducing conditions; however, this did not translate into gene expression.  Motif analysis of the bound genes revealed conserved DNA binding motifs, with the CLR-2 motif matching that of its closest yeast homolog, GAL4.  Co-immunoprecipitation studies were able to show that CLR-1 and CLR-2 act as homodimers.  Finally, we report on a conserved XLR-1 point mutation that is sufficient to drive hemicellulase expression under non-inducing conditions.  Understanding how these transcription factors work in concert to break down plant biomass can inform decisions on how to best engineer future fungal strains for decreased enzyme costs.

overall_design: RNAseq and ChIPseq was performed upon knockout mutants and wild type strains growing on various carbon sources to determin the role of the transcription factors CLR-1, CLR-2, and XLR-1 in plant cell wall degradation

first: Sam

last: Coradetti

first: Trevor

last: Starr

first: N

last: Glass


title: RNA sequencing of C. elegans lsm-1(tm3585) mutants at L3 stage

city: Hospitalet de Llobregat

first: Julián

last: Cerón

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals, planta 3

department: Cancer and Human Molecular Genetics

country: Spain

institute: IDIBELL

summary: Transcriptome analysis of a population of wild type animals and lsm-1 mutants at L3 stage

overall_design: lsm-1(tm3585) mutants were backcrossed three times with wild type N2 animals. lsm-1 mutants and N2 animals were grown for 26 hours at 25C from a synchronized L1 population.

first: Eric

last: Cornes


title: Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1


title: NeuroD2 ChIP-SEQ from embryonic cortex

city: Helsinki

first: Gulayse

last: Ince Dunn

state: Finland

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Program

country: Finland

institute: University of Helsinki

summary: NeuroD2 targets were identified from embryonic day 14.5 cerebral cortex tissue.

overall_design: The cerebral cortex (dorsal telencelphalon) from E14.5 mouse embryos was dissected and ChIP-SEQ was performed using three separate antibodies against NeuroD2.


title: Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network

city: Luxembourg

first: Lasse

last: Sinkkonen

address: 162a, Avenue de la Faiencerie

department: Life Sciences Research Unit

country: Luxembourg

institute: University of Luxembourg

summary: The reconstruction of cell type- and patient-specific metabolic models from easily and reliably measurable features such as transcriptomics data will be increasingly important at the age of personalized medicine. Current reconstruction methods suffer from high computational effort and arbitrary threshold setting. Moreover, understanding the underlying epigenetic regulation might allow the identification of putative intervention points within metabolic networks. Genes under high regulatory load from multiple enhancers or super-enhancers are known key genes for disease and cell identity. However, their role in regulation of metabolism and their placement within the metabolic networks has not been studied. Here we present FASTCORMICS, a fast and robust workflow for the creation of high-quality metabolic models from transcriptomics data. FASTCORMICS is devoid of arbitrary parameter settings and due to its low computational demand allows cross-validation assays.. Applying FASTCORMICS, we have generated models for 63 primary human cell types from microarray data, revealing significant differences in their metabolic networks. To  understand the cell type-specific regulation of the alternative metabolic pathways we built multiple models during differentiation of primary human monocytes to macrophages and performed ChIP-Seq experiments for histone H3 K27 acetylation (H3K27ac) to map the active enhancers in macrophages. Focusing on the metabolic genes under high regulatory load from multiple enhancers or super-enhancers, we found these genes to show the most cell type-restricted and abundant expression profiles within their respective pathways. Importantly, the high regulatory load genes are associated to reactions enriched for transport reactions and other pathway entry points, suggesting that they are critical regulatory control points for cell type-specific metabolism. By integrating metabolic modelling and epigenomic analysis we have identified high regulatory load as a common feature of metabolic genes at pathway entry points such as transporters within the macrophage metabolic network. Analysis of these control points through further integration of metabolic and gene regulatory networks in various contexts could be beneficial in multiple fields from identification of disease intervention strategies to cellular reprogramming.

overall_design: ChIP-Seq was performed with chromatin from macrophages differentiated in vitro for 11 days from primary human CD14+ monocytes isolated from the blood of three different anonymous male donors. For each donor one ChIP sample using an antibody against H3K27ac and one input sample were sequenced. Please see the individual samples for further details.

first: Elisabeth

last: John

first: Merja

last: Heinäniemi


title: Regulation of protein translation during mitosis

city: San Francisco

first: Marvin

last: Tanenbaum

state: ca

address: Genentech Hall, MC 2200, Room N316,   600 16th street

department: CMP

institute: UCSF

summary: Entry into and exit from mitosis is driven by precisely-timed changes in protein abundance, and involves transcriptional regulation and protein degradation. However, the role of translational regulation in modulating cellular protein content during mitosis remains poorly understood. Here, using ribosome profiling, we show that translational, rather than transcriptional regulation is the dominant mechanism for modulating protein synthesis at mitotic entry. The vast majority of regulated mRNAs are translationally repressed, which contrasts previous findings of selective mRNA translational activation at mitotic entry. One of the most pronounced translationally repressed genes in mitosis is Emi1, an inhibitor of the anaphase promoting complex (APC), which is degraded during mitosis. We show that Emi1 degradation is insufficient for full APC activation and that simultaneous translational repression is required. These results provide a genome-wide view of protein translation during mitosis and suggest that translational repression may be used to ensure complete protein inactivation

overall_design: Ribosome profiling and mRNA-seq from 3 time points in the cell cycle

first: Noam

last: Stern-Ginossar

first: Jonathan

middle: S

last: Weissman

first: Ronald

middle: D

last: Vale


title: Neurons that underlie Drosophila melanogaster reproductive behaviors: detection of a large male-bias in gene expression in fruitless-expressing neurons

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Medicine Biomedical Sciences

institute: Florida State University

summary: Male and female reproductive behaviors in Drosophila melanogaster are vastly different, but the neurons that express sex-specifically spliced fruitless transcripts (fru P1) underlie these behaviors in both sexes. How this set of neurons can generate such different behaviors between the two sexes is an unresolved question. A particular challenge is that fru P1-expressing neurons comprise only 2-5% of the adult nervous system, and so studies of adult head tissue or whole brain may not reveal crucial differences. Translating Ribosome Affinity Purification (TRAP) identifies the actively translated pool of mRNAs from fru P1-expressing neurons allowing a sensitive, cell-type-specific assay. Genes with TRAP mRNAs that are detected in both sexes are four times as likely to be male biased (1,210) as female biased (331) in fru P1-expressing neurons. This suggests a potential mechanism to generate dimorphism in behavior. The male-biased genes may direct male behaviors by establishing cell fate in a similar context of gene expression observed in females. These results suggest a possible global mechanism for how distinct behaviors can arise from a shared set of neurons.

overall_design: Libraries were prepared from five independent biological replicates, from TRAP adult heads samples from males and females, and the mRNA input from adult heads from males and females. For each experimental condition, approximately 1,000 flies that were 8 to 24 hours post-eclosion were used.

first: Nicole

last: Newell

first: Felicia

last: New

first: Justin

last: Dalton

first: Lauren

last: McIntyre


title: The microRNA-212/132 cluster regulates B cell development and apoptosis by targeting SOX4

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: MicroRNAs have emerged as key regulators of B cell fate decisions and immune function. Deregulation of several microRNAs in B cells leads to the development of autoimmune disease and cancer in mice. We demonstrate that the microRNA-212/132 cluster (miR-212/132) is induced in B cells in response to B cell receptor signaling. Enforced expression of miR-132 results in a block in early B cell development at the pre-pro-B cell to pro-B cell transition and induces apoptosis in primary bone marrow B cells. Importantly, loss of miR-212/132 results in increased B cell output under non-homeostatic conditions. We find that miR-212/132 regulates B lymphopoiesis by targeting the transcription factor SOX4. Co-expression of SOX4 with miR-132 rescues the defect in B cell development from over-expression of miR-132 alone. In addition, we show that the expression of miR-132 in cells that are prone to spontaneous B cell cancers can have a protective effect on cancer development. We have thus uncovered a novel regulator of B cell lineage specification that may potential applications in B cell cancer therapy

overall_design: RNA-seq of wild-type and microRNA-212/132 knock-out B-cells after IgM stimulation

first: Arnav

last: Mehta

middle: K

first: David

last: Baltimore


title: Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

city: Cuernavaca

first: Damien

last: Formey

state: Morelos

address: Avenida de la Universidad

department: Center for Genomic Science

country: Mexico

institute: UNAM


title: Novel DICER-LIKE1 siRNAs Bypass the Requirement for DICER-LIKE4 in Maize Development

city: Cold Spring Harbor

first: Marja

last: Timmermans

address: 1 Bungtown Rd

department: Plant Biology

institute: Cold Spring Harbor Laboratory

summary: Dicer enzymes function at the core of RNA silencing to defend against exogenous RNA, or as an endogenous mechanism of gene regulation. Plant DICER-LIKE4 (DCL4) performs dual functions, acting in antiviral defense, as well as in development via the biogenesis of tasiR-ARFs. These small RNAs play an essential role in the grasses and act to spatially define the expression domain of AUXIN RESPONSE FACTOR3 (ARF3) transcription factors. However, contrary to tasiR-ARFs’ essential function in development, DCL4 proteins exhibit strong evidence of recurrent adaptation typical of host factors involved in antiviral immunity. Here, we address how DCL4 balances its role in development with pressures to diversify in response to viral attack. We show that, in contrast to other tasiR-ARF biogenesis mutants, dcl4 null alleles condition an uncharacteristically mild phenotype, correlated with normal expression of select arf3 targets. Loss of DCL4 activity yields a class of 22-nt tasiR-ARF variants associated with the processing of arf3 transcripts into 22-nt secondary siRNAs by DCL1. Our findings uncover the presence of a novel DCL1-dependent siRNA pathway that bypasses the otherwise adverse developmental effects of DCL4 mutations. This novel pathway is predicted to have important implications for DCL4’s role in antiviral defense by reducing the selective constraints on DCL4 and allowing it to diversify in response to viral suppressors.

overall_design: Examination of small RNAs isolated from dcl4, dcl1 and double mutants in imbibed kernels of maize

first: Katherine

last: Petsch

first: Oliver

last: Tam

first: Molly

last: Hammell


title: Genome wide analysis of androgen-regulated transcripts

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed RNA sequence analysis in AR positive prostate cancer cell line, LNCaP. In addition, we used hormone-refractory prostate cancer model cells, Bicalutamide-resistant (BicR) to explore the differences of androgen signaling in prostate cancer progression.

overall_design: Short RNA sequence analysis of androgen-regulated miRNAs in two prostate cancer cells

first: Satoshi

last: Inoue


title: Estrogen Receptor Beta Impacts Hormone-Induced Alternative mRNA Splicing in Breast Cancer Cells

city: Baronissi

first: Antonio

last: Rinaldi

state: SA

address: Via Salvatore Allende, 1

department: Faculty of Medicine and Surgery

country: Italy

institute: University of Salerno

summary: Estrogens play an important role in breast cancer (BC) development and progression, where the two isoforms of the estrogen receptor (ERα and ERβ) are generally co-expressed and mediate the effects of these hormones in cancer cells. ERβ has been suggested to exert an antagonist role toward the oncogenic activities of ERα, and for this reason it is considered an oncosuppressor. As clinical evidence regarding a prognostic role for this receptor subtype in hormone-responsive BC is still limited and conflicting, more knowledge is required on the biological functions of ERβ in cancer cells. We described previously the ERβ and ERα interactomes of BC cells, identifying specific and distinct patterns of protein interactions for the two receptors. In particular, we identified factors involved in mRNA splicing and maturation as important components of both ERα and ERβ pathways. Guided by these findings, we investigated here in depth the differences in the early transcriptional events and RNA splicing patterns induced in ERα vs ERα+ERβ cells, by expressing ERβ in ERα+ human BC MCF-7 cells. High-throughput mRNA sequencing was then performed in both cell lines after stimulation with 17b-estradiol, and the results obtained were compared.

overall_design: We investigated here in depth the differences in the early transcriptional events and RNA splicing patterns induced in ERα vs ERα+ERβ cells, by expressing ERβ in ERα+ human BC MCF-7 cells. High-throughput mRNA sequencing was then performed in both cell lines after stimulation with 17b-estradiol, and the results obtained were compared.

first: Dougba

last: Dago

first: Claudio

last: Scafoglio

first: Domenico

last: Memoli

first: Giorgio

last: Giurato

first: Giovanni

last: Nassa

first: Maria

last: Ravo

first: Francesca

last: Rizzo

first: Roberta

last: Tarallo

first: Alessandro

last: Weisz


title: Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing [degradome-seq]

first: Damien

last: Formey

summary:
Background: MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21 and no phasiRNAs have been identified for the legume model Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs of this organism and, particularly, new protagonists of the symbiotic nodulation events.
Results: We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs, known to play crucial roles in the well-establishment of nodules, and novel miRNAs specific of the common bean suggesting a specific action of these sequences. In parallel, we identified 125 loci that potentially produce phased small RNAs and 47 of them present all the characteristics to be triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study.
Conclusions: We provide here a set of new small RNAs, which contribute to the broader scene of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we draw up here the probable functional regulation associated with the sRNAome and particularly in N2-fixing symbiotic nodules.

overall_design: Degradome sequencing from Phaseolus vulgaris seedling

first: Ramanjulu

last: Sunkar

first: Yong-Fang

last: Li


title: Genome wide analysis of androgen-regulated miRNAs

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed short RNA sequence analysis in AR positive prostate cancer cell line, LNCaP. In addition, we used hormone-refractory prostate cancer model cells, Bicalutamide-resistant (BicR) to explore the differences of androgen signaling in prostate cancer progression.


title: Hi-C study of the E. coli MG1655 chromosome

city: Konstanz

first: Jörg

last: Hartig

address: Universitätsstraße 10

department: Chemistry

institute: Universität Konstanz

summary: We performed Hi-C analysis of Escherichia coli MG1655 cells in exponential and stationary growth phase. We could detect long-range interactions predominantly in the Ori domain of the chromosome. Interestingly, the use of a new type of control revealed that these interactions are mostly crosslinking independent.

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

overall_design: 6 samples from exponential phase growth in M9 medium; 6 samples from stationary phase growth in M9 medium; for each growth condition, 3 samples were with crosslinking and 3 samples were without.

first: Philipp

last: Voss

first: Stefanie

last: Wagner

first: Martin

last: Horn

first: Michele

last: Felletti

first: Michael

last: Zinsmaier

last: Berthold


title: Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing [smallRNA-Seq].

overall_design: Small RNA sequencing from 5 Phaseolus vulgaris tissues

first: Luis Pedro

last: Iñiguez

first: Pablo

last: Pélaez

first: Federico

last: Sanchez

first: José Luis

last: Reyes

first: Georgina

last: Hernandez


title: Identification of direct target genes of the Neurospora crassa essential plant biomass deconstruction transcription factors CLR-1, CLR-2 and XLR-1 (ChIP-Seq)

first: James

last: Craig

overall_design: RNAseq and ChIPseq upon knockout mutants and sild type growing on various carbon sources to determin the role of the transcription factors: CLR-1, CLR-2, and XLR-1 in plant cell wall degradation

first: Sam

last: Coradetti

first: Trevor

last: Starr

first: N

middle: L

last: Glass


title: DNA methylation at transcription start sites blocks TBP binding and transcription onset by RNApolII

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: DNA methylation at transcription start sites blocks TBP binding and transcription onset by RNApolII [ChIPbisSeq]

summary: We report the application of ChIP bisulfite sequencing (ChIPbisSeq) to establish the methylation state of DNA bound to RNApol2 phosphorylated in Ser5 (RNAPol2Ser5) in the mouse cortex. We first profiled the RNAPol2Ser5 binding using regular ChIPSeq from 45 million raw read pairs (31 million unique pairs were aligned to the genome). Then we used bisulfite converted DNA immunoprecipitated with an antibody against RNAPol2Ser5 (87 million raw read pairs, 38 million unique read pairs aligned to the genome) to map RNAPol2Ser5 sites and to establish the methylation state at these sites.

overall_design: Examination of methylation state at RNAPol2Ser5 binding sites in the mouse cortex.

first: Renaud

last: Massart

first: Matthew

last: Suderman


title: Genome wide analysis of androgen-regulated transcriptional startsites

first: Ken-ichi

last: Takayama

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed CaP analysis of gene expression (CAGE) analysis in AR positive prostate cancer cell line, LNCaP. In addition, we used hormone-refractory prostate cancer model cells, Bicalutamide-resistant (BicR) to explore the differences of androgen signaling in prostate cancer progression.

overall_design: CAGE analysis of androgen-regulated transcripts in two prostate cancer cells

first: Satoshi

last: Inoue


title: Genome wide analysis of androgen-receptor binding sites and epigenetic condition in prostate cancer

summary: Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. To investigate the AR signaling, we performed ChIP sequence analysis in AR positive prostate cancer cell line, LNCaP. In addition, we used hormone-refractory prostate cancer model cells, Bicalutamide-resistant (BicR) to explore the differences of androgen signaling in prostate cancer progression.

overall_design: ChIP sequence analysis of AR binding sites and epigenetic condition in two prostate cancer cells


title: T cell UTX promotes Tfh-mediated clearance of persistent virus infection

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

institute: University of North Carolina at Chapel Hill

summary: Epigenetic changes, including histone methylation, control T cell differentiation and memory formation, though the enzymes that mediate these processes are not clear. We show that UTX, a histone H3 lysine 27 (H3K27) demethylase, promotes the generation of T follicular helper (Tfh) cells, a CD4+ T cell subset essential for B cell antibody generation and clearance of chronic viral infections. Mice with T cell specific UTX deletion (UTX TKO mice) had fewer Tfh cells, showed defective germinal center formation, lacked virus-specific IgG production, and were unable to resolve chronic lymphocytic choriomeningitis virus infection. In UTX TKO T cells, decreased expression of IL-6R±, and other Tfh-related loci, was associated with increased H3K27 methylation. Additionally, Turner Syndrome subjects, who are predisposed to chronic ear infections, have reduced UTX expression in immune cells and decreased Tfh frequency. Thus, we identify a critical link between UTX in T cells and immunity to infection.

overall_design: Mice were infected with chronic LCMV and sorted for Tfh on day 21 pi (sorted for: CD4+CXCR5+CD62Llo T cell).  ChIP-Seq and RNA-Seq on WT and Utx KO cells.

first: Kevin

last: Cook

first: Karl

middle: B

last: Shpargel

first: Fatima

last: Whitfield-Larry

first: Bridget

last: Conley

first: Denise

last: Allard

first: Julia

last: Rager

first: Rebecca

middle: C

last: Fry

first: Marsha

last: Davenport

first: Terry

last: Magnuson

first: Jason

last: Whitmire

first: Maureen

last: Su


title: Epigenome signatures during gastric carcinogenesis based on next generation sequencing

city: Daejeon

first: Hee-jin

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB


title: Genome-wide maps of DNA methylation state in rice embryo and endosperm

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development.

overall_design: Rice embryo and endosperm were selected for DNA extraction and methylacytosine immunoprecipetation combined with Illumina sequencing. We sought to obtain the genome-wide DNA methylation profilings of embryo at 3,6,9 days after pollination(DAP) and endosperm at 2,3,6,9 DAP. To that end, we hand-selected embryo at 3,6,9 DAP and endosperm at 2,3,6,9 DAP according to morphological criteria.

first: Hong-Wei

last: Xue


title: Epigenome signatures during gastric carcinogenesis based on next generation sequencing analysis [MBD-Seq]

summary: Because gastric cancer cells already had genetic and epigenetic alterations which can affect the gastric carcinogenesis, we tried to characterize genetic and epigenetic changes during gastric carcinogenesis. To do this, we performed MBD sequencing and RRBS sequencing.

overall_design: MBD and RRBS sequencing of gastric mucosa, intestinal metaplasia, and gastric cancer cells from one patient were generated by NGS using Illumina GAII.

first: Yong

first: Hee-Jin

first: Su-Jin

last: Baek


title: Epigenome signatures during gastric carcinogenesis based on next generation sequencing analysis [Bisulfite-Seq]


title: The Wright Stuff: Reimagining Path Analysis Reveals Novel Components of the Sex Determination Hierarchy in Drosophila Melanogaster

first: Michelle

last: Arbeitman

summary: The Drosophila sex determination hierarchy consists of a splicing cascade with sex-specific transcription directing somatic sexual dimorphism. Our understanding of this pathway, and many others, is incomplete. Here we pioneer an approach to expand our knowledge of gene regulatory networks (GRNs) by leveraging natural genetic variation. This approach is generalizable to any natural population, including humans. Two studies from Drosophila female head tissue were used – the DSPR collection (alleles from 15 natural variants) and F1-hybrid collection (alleles from heterozygotes of 75 isogenic lines crossed to w1118) – in a structural equation model (SEM) analysis. We expanded the sex hierarchy GRN by adding novel links among genes in the pathway and by adding novel genes to the pathway. A link from fruitless (fru) to Sex-lethal (Sxl) was found in both populations, which is supported by the presence of fru binding sites in the Sxl locus. The splicing factors male-specific lethal 2 and Rm62 were correctly identified as downstream targets of Sxl. There were 754 additional candidate genes for an expanded sex hierarchy GRN. These candidates were enriched for genes with sex-biased splicing and many components of the spliceosome were placed in the GRN. As with other population-genetic analyses, the number of alleles limits the number of observable interactions. Network expansion was only clear in the F1-hybrid population, which has an average of twice as many alleles as the DSPR population. Independent studies of doublesex and transformer mutants support many novel connections, including evidence for a link between the sex hierarchy and metabolism, with the inclusion of Insulin-like receptor in the sex hierarchy GRN.

overall_design: RNA sequencing was performed on mRNA derived from adult male or female heads, for a total of 9 samples. These samples included females that produce the male isoform of dsx [w/+;DsxD/dsxm+r15 (XX)], and two dsx mutants: females [w/+; dsxm+r15/dsxd+r3 (XX)] and males [w;dsxm+r15/dsxd+r3 (XY)]. Two wild type genotypes (Berlin and Canton-S) were sequenced at the same time, but have previously been published as part of GSE50515. There were at least 3 replicates from biological samples.

first: J

middle: M

last: Fear

first: M

middle: P

last: Salomon

middle: E

last: Dalton

last: Tower

first: S

middle: V

last: Nuzhdin

first: L

last: McIntyre


title: RNASeq analysis of Salmonella B cell infection model

city: San Diego

first: Marcus

last: Jones

address: 4120 Torrey Pines Road

institute: JCVI

summary: We report the transcriptome analysis of S. enterica 14028 during infection of murine B cells. Mice spleens were infected with Salmonella enterica 14028. Mouse spleens were harvested and cells FACS sorted into various immune cells containing bacteria. Short reads were mapped to the S. enterica 14028 genome.

overall_design: Mice were infected with S. enterica strain 14028. Spleens were collected, homogenized and cells FACS sorted. Total RNA was extracted using the Ambion mirVana RNA isolation kit. Purified RNA was depleted of rRNA utilizing the epicentre ribozero metabacteria and eukaryotic kits.

first: Heffron

last: Fred

first: Yoon

last: Hyunjin

first: Jones

last: Marcus


title: Netrin-1 facilitates somatic cell reprogramming by limiting Dcc pro-apoptotic activity.

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

summary: The generation of induced pluripotent stem (iPS) cells holds great promise in regenerative medicine. However, the relative flaws in the understanding of the molecular mechanisms promoting or limiting reprogramming still hinder the efficient generation of high quality iPS cells.  Whereas modulation of the initial Oct4, Sox2, Klf4 and c-Myc (OSKM) cocktail with new transcription factors has been extensively documented, comparatively little is known about soluble molecules promoting the process, even if such recombinant factors could be highly valuable for therapeutic applications. In this study we developed a large-scale identification method to uncover novel programmed cell death (PCD)-related mechanisms limiting somatic cell reprogramming to pluripotency (SCRP). We identified Netrin-1 and its dependence receptor Dcc (Deleted in Colorectal Carcinoma), previously described for their respective survival/death functions both in normal and oncogenic contexts, as novel key SCRP modulators. We show that the early phase of SCRP is accompanied with a strong Netrin-1 deficiency, due to the improper epigenetic regulation of the Ntn1 promoter by OSKM. Mechanistically, we demonstrate that such Netrin-1 imbalance induces apoptosis mediated by the dependence receptor Dcc in a p53-independent manner. Correction of the Netrin-1/Dcc equilibrium by gain-of-ligand and loss-of-receptor experiments constrains apoptosis and improves reprogramming. As a consequence, we propose a novel iPS derivation protocol including a sequential treatment with recombinant Netrin1 that greatly facilitates the generation of mouse and human iPS cells.

overall_design: RNA-sequencing of mouse embryonic fibroblasts (passage 2 and passage 4), mouse pre-iPS cells (passage 5 and passage 25), 1 clone of control iPS (passage 5 and passage 25) and 2 independent clones of  "Netrin-1 derived" iPS cells (passage 5 and passage 25). For this analysis, mouse iPS cell lines were grown in KSR+LIF media.

first: Suzy

last: Markossian

first: Benjamin

last: Ducarouge

first: Olivier

last: Féraud

last: Gibert

first: Isabelle

last: Durand

first: Nicolas

last: Gadot

first: Annelise

last: Bennaceur-Griscelli

first: Jean-Yves

last: Scoazec

first: Frederic

last: Flamant

first: Jesus

last: Gil

first: Agnes

last: Bernet

first: Patrick

last: Mehlen


title: Global analysis of androgen-signaling reveals the function of miRNAs for the epigenomic regulation in prostate cancer cells

first: Ken-ichi

last: Takayama


title: piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

status: Public on Aug 31 2015

city: Vienna

first: Kirsten-André

middle: A

last: Senti

state: Wien

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

summary: PIWI-clade Argonaute proteins silence transposon expression in animal gonads. Their target specificity is defined by bound ~23-30nt piRNAs that are processed from single-stranded precursor transcripts via two distinct pathways. Primary piRNAs are defined by the endo-nuclease Zucchini, while biogenesis of secondary piRNAs depends on piRNA-guided transcript cleavage and results in piRNA amplification. Here, we analyze the inter-dependencies between these piRNA biogenesis pathways in the developing Drosophila ovary. We show that secondary piRNA-guided target slicing is the predominant mechanism that specifies transcripts—including those from piRNA clusters—as primary piRNA precursors and that defines the spectrum of Piwi-bound piRNAs in germline cells. Post-transcriptional silencing in the cytoplasm therefore enforces nuclear, transcriptional target silencing, which ensures the tight suppression of transposons during oogenesis. As target slicing also defines the nuclear piRNA pool during mouse spermatogenesis, our findings uncover an unexpected conceptual similarity between the mouse and fly piRNA pathways.

overall_design: To understand the hierarchical order of primary versus secondary piRNA biogenesis in Drosophila ovaries, we sequenced piRNAs bound to total-Piwi, germline-Piwi, Aubergine and Argonaute3 from ovaries of germline specific knockdowns of control, piwi, aub, ago3 single knockdowns and aub/ago3 double knockdowns. To determine changes in Transposable Element (TE) transcription or TE RNA steady state  in perturbed piRNA pathway conditions, we performed Pol2-ChIP-sequencing and polyA bound RNA-sequencing from ovaries of multiple germline knockdown genotypes. We also sequenced genomic DNA from ovaries of control knockdowns to experimentally estimate the TE copy number in our genetic background. Finally, we used CAP-seq from germline specific Piwi depletions to identify the Transcriptional Start Sites (TSS)  in TEs in a deregulated background. Replicates are labeled with R1, R2, R3, R4 where indicated.

first: Daniel

last: Jurczak

first: Ravi

last: Sachidanandam

first: Julius

last: Brennecke


title: 5-hydroxymethylcytosine is linked with expression of brain-specific protein-coding genes but not brain-specific microRNA host genes (RNA-Seq)

city: Copenhagen

first: Sheroy

last: Minocherhomji

state: Copenhagen N

address: Blegdamsvej 3B, Building 18.1

department: Nordea Centre for Healthy Aging, Faculty Of Health Sciences Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: DNA methylation (5mC) is an epigenetic modification classified by the addition of a methyl group (Ch3-) catalysed by DNA methyltransferases (DNMTs) and S-adenosyl methionine (SAM). Recently hydroxymethylation at the same carbon-5 residue of the cytosine base catalysed by the TET (Ten–Eleven Translocation) family of proteins has been shown occur in mouse embryonic stem cells and the brain. 5-hydroxymethylcytosine (5hmC) has been shown to be distributed at a lesser extent in most mammalian tissues with an increased occurrence in Purkinje cells of the mouse brain. Here we assess genome-wide 5hmC distribution relative to 5mC enrichment in the human cerebellum and peripheral blood lymphocytes (PBLs) using high-resolution sequencing by synthesis. We found a significant increase and change in 5hmC distribution in human cerebellum at loci highly expressed in the human brain and postsynaptic density (PSD) compared to PBLs. Minimal changes in 5mC distribution were observed at these same loci and genome-wide in both human cerebellum and PBLs. Using high-throughput RNA-Seq of total RNA from human brain, cerebellum and PBLs we quantified elevated expression of gene products implicated in neuronal activity and having significantly increased 5hmC distribution across their gene bodies only in brain tissue compared to PBLs. Furthermore we show elevated expression of gene loci in the cerebellum to co-localise with increased 5hmC in Purkinje neurons. Our data provide new evidence for 5hmC mediated regulation of gene loci highly expressed in the human brain and PSD and implicated in neuronal activity and development.

overall_design: High-throughput RNA-Seq analysis of total RNA isolated from human cerebellum (Capital Biosciences)

first: Yuan

last: Mang

first: Niels

last: Tommerup

first: Asli

last: Silahtaroglu


title: CETCh-Seq  of Mammalian Transcription Factors

city: Huntsville

first: Eric

last: Mendenhall

state: Alabama

address: 301 Sparkman Dr

department: Biological Sceinces

institute: University of Alabama Huntsville

summary: Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade  antibodies, and the vast majority of commercially available antibodies fail to generate usable  datasets. To ameliorate these technical obstacles, we present a robust methodological  approach for performing ChIP-seq through epitope tagging of endogenous TFs. We used Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-based genome  editing technology to develop CRISPR Epitope Tagging ChIP-seq (CETCh-seq) of DNA-binding  proteins. We assessed the feasibility of CETCh-seq by tagging several TFs spanning a wide  range of endogenous expression levels in the hepatocellular carcinoma cell line HepG2. Our  data exhibit strong correlations between both replicate types as well as with standard ChIP-seq  approaches that use TF antibodies. Notably, we also observed minimal changes to the cellular  transcriptome and to the expression of the tagged TF. To examine the robustness of our  technique, we further performed CETCh-seq in the breast adenocarcinoma cell line MCF7 as  well as mouse embryonic stem cells and observed similarly high correlations. Collectively,  these data highlight the applicability of CETCh-seq to accurately define the genome-wide  binding profiles of DNA-binding proteins, allowing for a straightforward methodology to  potentially assay the complete repertoire of TFs, including the large fraction for which ChIPquality  antibodies are not available.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CRISPR/Cas9 mediated epitope tagging of transcription factors in human cell types

first: E

first: R

last: Myers


title: 5-hydroxymethylcytosine is linked with expression of brain-specific protein-coding genes but not brain-specific microRNA host genes


title: 5-hydroxymethylcytosine is linked with expression of brain-specific protein-coding genes but not brain-specific microRNA host genes [hMeDIP-Seq]

overall_design: Examination of hydroxymethylation (hMeDIP-Seq), hypermethylation (MBD-Seq using a his-MBD2B antibody) and hypomethylation (MRE-Seq using HpaII restriction enzyme digestion) in genomic DNA from human cerebellum and peripheral blood lymphocytes


title: Identification of differentially expressed miRNAs in HCSC cell lines compared with HCC cell lines

city: Shanghai

first: Min

last: Ding

address: Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

summary: Hep3B and Huh7 are two types of human hepatoma cell lines (HCC). In our laboratory, we cultured their stem-like cancer cells (HCSCs), Hep3B-C and Huh7-C. And we have demonstrated that these cells had enhanced stem cell properties, drug resistance, properties of EMT, and stronger tumor-initiating capabilities. To explore functionally crucial miRNAs in HCSCs, 2 samples of HCSCs and 2 samples of HCCs were sequenced by the Illumina Genome Analyzer II. Through differential expression analysis, we finally identified 9 up- and 9 down-regulated miRNAs which were consistently up- and down-regulated in two stem cells compared to the cancer cells.

overall_design: Expression analysis using total RNAs extracted from 2 HCSC cell lines (Hep3B-C and Huh7-C), and 2 HCC cell lines (Hep3B and Huh7).

first: Jiang

last: Li

first: Zi

last: Yan


title: Distinct murine mucosal Langerhans cell subsets develop from pre-DCs and monocytes

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: Langerhans cells (LCs) populate the mucosal epithelium, a major entry portal for pathogens, yet their ontogeny remains unclear. In contrast to skin LCs originating from self-renewing radioresistant embryonic precursors, we found that oral mucosal LCs derive from circulating radiosensitive precursors. Mucosal LCs can be segregated into CD103+CD11blow (CD103+LCs) and CD11b+CD103- (CD11b+LCs) subsets. We further demonstrated that similar to non-lymphoid dendritic cells (DCs), CD103+LCs originate from pre-DCs, whereas CD11b+LCs differentiate from both pre-DCs and monocytic precursors. Despite this ontogenetic discrepancy between skin and mucosal LCs, transcriptomic signature and immunological function of oral LCs highly resemble those of skin LCs but not DCs. These findings, along with their epithelial position, morphology and expression of LC-associated phenotype strongly suggest that oral mucosal LCs are genuine LCs. Collectively, in a tissue-dependent manner, murine LCs differentiate from at least three distinct precursors (embryonic, pre-DCs and monocytic) in steady state

overall_design: The following cells were isolated from mice (2-4 replicates): Lung DCs, mucosal CD103+ LC, mucosal CD11b+ LC, Skin LC. Transcriptome analysis was performed.


title: Identification of differentially expressed mRNAs in HCSC cell lines compared with HCC cell lines

summary: Hep3B and Huh7 are two types of human hepatoma cell lines (HCC). In our laboratory, we cultured their stem-like cancer cells (HCSCs), Hep3B-C and Huh7-C. And we have demonstrated that these cells had enhanced stem cell properties, drug resistance, properties of EMT, and stronger tumor-initiating capabilities. To explore functionally crucial mRNAs in HCSCs, 2 samples of HCSCs and 2 samples of HCCs were sequenced by the Illumina Genome Analyzer II. Through differential expression analysis, we finally identified 115 up- and 402 down-regulated miRNAs which were consistently up- and down-regulated in two stem cells compared to the cancer cells.


title: Epigenomics of neural cells: REST-induced down- and up-regulation of gene expression in a two clone PC12 cell model.

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

summary: Cell epigenomics depends on the marks released by transcription factors operating via the assembly of complexes that induce focal changes of DNA and histone structure. Among these factors is REST, a repressor that, via its strong decrease, governs both neuronal and neural cell differentiation and specificity. REST operation on thousands of possible genes can occur directly or via indirect mechanisms including repression of other factors. In previous studies of gene down- and up-regulation, processes had been only partially investigated in neural cells. PC12 are well known neural cells sharing properties with neurons. In the widely used PC12 populations, low-REST cells coexist with few, spontaneous high-REST PC12 cells. High- and low-REST PC12 clones were employed to investigate the role and the mechanisms of the repressor action. Among 15,500 expressed genes we identified 1,770 target and non-target, RESTdependent genes. Functionally, these genes were found to operate in many pathways, from synaptic function to extracellular matrix. Mechanistically, downregulated genes were predominantly repressed directly by REST; up-regulated genes were mostly governed indirectly. Among other factors, Polycomb complexes cooperated with REST for down-regulation, Smad3 and Myod1 participated in up-regulation. In conclusion, we have highlighted that PC12 clones are a useful model to investigate REST, opening opportunities to development of epigenomic investigation.

overall_design: 4 samples have been analyzed: 2 replicates from wtPC12 clone and 2 replicates from the hrPC12 clones

first: Silvia

last: Bonfiglio

first: Dejan

last: Lazarevic

first: Elia

last: Stupka

first: Davide

last: Cittaro

first: Jacopo

last: Meldolesi

first: Maria

last: Malosio


title: Comparative analysis of drought-responsive transcriptome in soybean lines contrasting for canopy wilting

city: Columbia

first: Trupti

last: Joshi

state: MO

address: 1201 Rollins St.

department: Computer Science

institute: University of Missouri

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of abiotic stress molecular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of contrasting slow wilting lines to quantify transcript abumdance under drought stress condition

overall_design: Methods: The three biological replicates of DS line, Pana (control and drought samples) and DT line, PI 567690 (control and drought samples) leaf sample RNA were multiplexed and sequenced on an Illumina Hi-Seq 2000 platform. The RNA concentration of each sample was approximately 200ng/µl with a quantity of 50 µl.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

first: Silvas

last: Prince

first: Henry

middle: T

last: Nguyen


title: Ribosome profiling in muscle reveals the translation landscape of the giant protein titin

city: Salt Lake City

first: Robert

last: Weiss

state: UT

department: Human Genetics

institute: University of Utah

summary:
Purpose: Ribosome profiling and RNA-Seq were used to map the location and abundance of translating ribosomes on mouse heart and skeletal muscle transcripts.
Methods: Tissue was rapidly harvested and snap-frozen to minimize bias to the pool of translating ribosomes.  RNA was prepared from a single homogenate for each tissue so that starting RNA populations for both libraries were closely matched.  Homogenates were not clarified before RNase digestion to avoid loss of ribosomes associated with large molecular weight complexes, and RNA-Seq libraries were prepared after rRNA subtraction to avoid positional loss of 5’ reads.  Trimmed reads from 50 cycles of Illumina single-end sequencing were mapped onto a non-redundant set of 18,499 mouse protein-coding RefSeq transcripts from the nuclear genome.
Results: Mapped sequence reads to myosin, actin and the giant protein titin together account for ~20% of the total mRNA-derived ribosome protected fragments (RPFs).  We observed large-scale uniformity in the distribution of RPFs on the >30,000 codon titin open reading frame, from which we inferred an in vivo ribosome elongation error rate of ≤10-5.  Ribosome footprints on Ttn mRNA also uncovered a novel 5’ UTR within a phylogenetically conserved intronic element that would produce ~2.35 mDa titin isoform that corresponds to the titin 'T2' band frequently described as a proteolytic artifact.  Local translation efficiency across several >10 kb muscle mRNAs was also uniform, while their global translation efficiencies varied by ~20-fold suggesting initiation rate plays a major role in the translation efficiency of large mRNAs. Evidence for RPFs on 5’ UTRs was widespread with particular enrichment for ribosomes positioned at CUG codons. Comparison of global translation efficiency in cardiac and skeletal muscle revealed novel examples of tissue-specific translational control including synthesis of the myogenic factor Mef2c, and the titin-binding stress response protein Ankrd23.
Conclusions: Our study represents the first detailed analysis of translation in an adult mammalian tissue generated by ribosome profiling technology. Current limitations to using ribosomal profiling in tissues include unknown perturbations to the dynamic state of translation despite rapidly harvested and snap-frozen samples. The uniform 5’ to 3’ coverage observed on individual large mRNAs and the ability to observe footprints on the extremely small phospholamban coding sequence, suggests that initiation and elongation were halted on similar time scales.  More detailed examination of the positional information within CDS region requires further understanding of the bias introduced during the library preparation steps for both RPF-and RNA-Seq, as well as local biases induced as translation is arrested.   Despite these qualifications, this initial view of active translation in muscle tissue highlights the potential for ribosome profiling to monitor the dynamic translation response to exercise, injury or disease pathology in animal models at a level of resolution not easily attainable with other quantitative approaches.

overall_design: Heart and skeletal muscle ribosome-protected fragment and RNA-Seq profiles of 10-week old C57BL/6J male mice were generated by deep sequencing using the Illumina HiSeq 2000.


title: Loss of EZH2 results in precocious mammary gland development and the activation of STAT5-dependent genes

city: Bethesda

first: Sumin

last: Oh

state: MD

address: 9000 Rockville Pkie

department: NIDDK

institute: NIH

summary: Establishment and differentiation of mammary alveoli during pregnancy are controlled by prolactin through the transcription factor STAT5. As pregnancy progresses mammary signature genes are activated in a defined temporal order, which coincides with the recruitment of STAT5 to respective regulatory sequences. This study addressed the question whether the methyltransferase and transcriptional co-activator EZH2 controls the differentiation clock of mammary epithelium. Ablation of Ezh2 from mammary stem cells resulted in precocious differentiation of alveolar epithelium during pregnancy and the activation of mammary-specific STAT5 target genes. This coincided with enhanced occupancy by STAT5, EZH1 and Pol II to these loci. Limited activation of differentiation-specific genes was also observed in mammary epithelium lacking both EZH2 and STAT5, suggesting a modulating but not mandatory role for STAT5. Notably, loss of EZH2 did not result in overt changes in genome-wide and gene-specific H3K27me3 patterns, suggesting that enhanced EZH1 recruitment can compensate for the loss of EZH2. Differentiated mammary epithelia failed to form in the combined absence of EZH1 and EZH2. Transplantation experiments failed to demonstrate a role for EZH2 in the biology of mammary stem and progenitor cells. In summary, while EZH1 and EZH2 serve redundant functions in the establishment of H3K27me3 and formation of mammary alveoli, the presence of EZH2 is required to obtain controlled temporal differentiation of mammary epithelium.

overall_design: mRNA-seq in WT;MMTV-Cre (Control) at p13 and p18, E1-/- (E1KO), Ezh2f/f;MMTV-Cre(E2KO), Stat5f/f;MMTV-Cre(S5KO), and Ezh2f/f;Stat5f/f;MMTV-Cre (E2S5DKO) at p13 mammary tissues. ChIP-seq for H3K27me3, STAT5, EZH1, EZH2 and PolII in mammary tissues at p13

first: Kyung

last: Yoo

first: Tim

last: Hensel

first: Gertraud

middle: W

last: Robinson

first: Keunsoo

last: Kang

first: Lothar

last: Hennighausen


title: Single-cell RNA Seq of hematopoietic stem and progenitor cells

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

institute: CRG

summary: This dataset is part of a study that investigated how the hematopoietic system coordinates the rapid and efficient regeneration of the megakaryocytic lineage during stress scenarios. We found that the phenotypic hematopoietic stem cell (HSC) compartment contains stem-like megakaryocyte-committed progenitors (SL-MkPs), a cell population that shares many features with multipotent HSCs and serves as a lineage-restricted emergency pool for inflammatory insults. This dataset contains single-cell RNA sequencing data of 30 hematopoietic stem and progenitor cells which, in the context of our study, confirmed that MK-specfic transcripts are of highly variable expression in HSCs. The dataset further showed that variations in MK transcript expression in HSCs is not correlated with global transcriptomic rearrangements.

overall_design: Murine bone marrow cells were sorted by Lin-cKit+CD150+CD48- (referred to as cd150+ in the following) and Lin-cKit+CD150- (referred to as cd150- in the following). Transcriptomes of 11 cd150- and 9 cd150+ HSCs were determined using QUARTZ, a single-cell RNASeq protocol

first: Simon

middle: F

last: Haas

last: Steinmetz

first: Andreas

last: Trumpp

first: Marieke

last: Essers


title: Transcriptome comparison between Beagle dogs and Chinese Field dogs after chronic stress exposure in the pituitary-adrenal axis

status: Public on Aug 30 2015

city: Guangzhou

first: Zhenhui

last: Li

address: Tianhe District Wushan road

institute: South China Agricultural University

summary:
Purpose: The transcriptome profiles were compared among groups of chronic stress exposure and control in two different breeds to identify genes and pathways related to response to chronic stress in the pituitary-adrenal axis.
Methods: 6 male adult CFD and 6 Beagles were chosen at random with the similarities in good health, weight and other aspects. Separately, 3 of these two breeds were freely selected for the stress exposure via intermittent electrical stimulation and restraint stress, while the other 3 of these two breeds were non-disposed for normal control.The details for the disposal of dogs were: every morning dogs were restrained and electrical stimulations were exerted with a stable current of 10 mA for 6 s and then with a 6 s interval, lasting for 20 min every day. The duration of disposal was ten days.ll 12 dogs were killed by air embolism in the 11th day. Subsequently, pituitary and adrenal cortex tissues were fast collected and isolated for further high-sequencing.
Results: 8 cDNA libraries were constructed for RNA-seq. A number of reads ranging from 53,295,978 to 65,414,932 was obtained in those 8 groups. About 10,000 genes and transcripts were annotated in each group. Besides,A total of 40, 346, 376, 69, 70, 38, 57, and 71 DEGs were detected in the contrasts of BP1_vs_BP2, CFDP1_vs_CFDP2, BP1_vs_CFDP1, BP2_vs_CFDP2, BAC1_vs_BAC2, CFDAC1_vs_CFDAC2, BAC1_vs_CFDAC1, and BAC2_vs_CFDAC2, respectively.
Conclusions: Our results can contribute to a more comprehensive understanding about the genetic mechanisms of response to chronic stress in adrenal cortex and pituitary.

overall_design: Adrenal cortex and pituitary mRNA profiles of adult Chinese Field Dog and Beagle under chronic stress exposure and normal control, including BAC1 (Beagle adrenal cortex with disposal), BAC2 (Beagle adrenal cortex with non-disposal), BP1 (Beagle pituitary with disposal), BP2 (Beagle pituitary with non-disposal), CFDAC1 (Chinese Field Dog adrenal cortex with disposal), CFDAC2 (Chinese Field Dog adrenal cortex with non-disposal), CFDP1 (Chinese Field Dog pituitary with disposal), CFDP2 (Chinese Field Dog pituitary with non-disposal), were generated by deep sequencing, using Illumina Genome Analyzer IIx.

first: Wei

last: Luo

first: Qinghua

last: Nie


title: H3K4me2 profiling in OCI-Ly1 and OCI-Ly7 cell lines.

status: Public on Aug 28 2015

city: New York

first: Yanwen

last: Jiang

state: NY

institute: Weill Cornell Medical College

summary: Define and compare H3K4me2 enrichment in OCI-Ly1 and OCI-Ly7 cell lines.

overall_design: Using ChIP-seq, we examined the H3K4me2 genomic enrichment locations in two biological replicates in each cell line

first: Ari

last: Melnick

first: Olivier

last: Elemento


title: MLL4 (KMT2D) inactivating mutations lead to focal loss of H3K4me1/2 and deregulated gene expression in B cell lymphomas

summary: We identified KMT2D target loci in OCI-LY7 by ChIPseq.

overall_design: KMT2D ChIPseq was carried out in the LY7 cell line (n=1).

first: Ana

last: Ortega-Molina

first: Isaac

last: Boss

first: Heng

last: Pan

first: Deqing

last: Hu

first: Ali

last: Shilatifard

first: Hans-Guido

last: Wendel


title: KRAS-Dependent Sorting of miRNAs and other small RNAs to secreted vesicles

city: Nashville

first: Yongchao

last: Dou

state: Tennessee

address: 2525 west end

institute: vanderbilt medical center

summary: Although long thought to act cell autonomously, mutant KRAS colorectal cancer (CRC) cells release protein-laden exosomes that can alter the tumor microenvironment.  We have previously shown that mutant KRAS induces EGFR-ligand trafficking to exosomes and drastically alters exosomal protein contents, leading to activities that contribute to neoplastic growth. We have performed small library RNAseq analysis on cells and matched exosomes from isogenic CRC cell lines differing only in KRAS status to determine whether mutant KRAS regulates the composition of secreted small RNAs. Exosomal small RNA profiles were distinct from cellular profiles, with principle component analysis showing clusters of mutant KRAS cell-derived exosomes distinct from wild type KRAS cell-derived exosomes. Secreted RNA species encompassed several different classes of small RNAs, including ribosomal and tRNA fragments, as well as mature miRNA sequences. miR-10b, was selectively increased in wild type KRAS-derived exosomes, whereas miR-100 was selectively increased in mutant KRAS-derived exosomes.  Ceramide inhibition resulted in accumulation of miR-100 in mutant KRAS cells, suggesting KRAS-dependent miRNA export.  In Transwell cell culture experiments, mutant, but not wild type, KRAS donor cells conferred miR-100-mediated target repression in wild type KRAS recipient cells

overall_design: miRNAseq deep sequencing for both cell and exosome mirnas of Dks-8, DLD-1, and DKO-1 cell lines. The DKs-8 line contains a wild type KRAS alleles, the DLD-1 line contains both wild type and mutant (G13D) KRAS alleles, and the DKO-1 line contains only a mutant KRAS allele.

first: Jeffrey

last: Franklin

first: Diana

middle: J

last: Cha

first: Qi

last: Liu

first: James

last: Higginbotham

first: Alissa

last: Weaver

first: Kasey

last: Vickers

first: Michelle

last: Demory Beckler

first: Nripesh

last: Prasad

first: Shawn

last: Levy

first: Bing

last: Zhang

first: Robert

last: Coffey

middle: G

last: Patton


title: Transcriptome analysis of poplar during leaf spot infection with Sphaerulina spp.

city: Quebec City

first: Adam

last: Foster

address: 8678 rue de la Comtoise

department: CFS

country: Canada

institute: Natural Resources Canada

summary: Diseases of poplar caused by the fungal pathogen Sphaerulina musiva and related species are of growing concern, particular with the increasing interest in intensive popluliculture to meet increasing energy demands. S. musiva is able to cause infection on leaves, resulting in defoliation and canker formation on stems. To gain a greater understanding of the different responses of poplar species to infection with their natural Sphaerulina species, RNA-seq was conducted on leaves of Populus deltoides, P. balsamifera and P. tremuloides infected with S. musiva, S. populicola and a new undescribed species Ston1, respectively. Progression of disease symptoms, pathogen growth and host response were detected. Through the time course of infection, different and species-specific metabolic pathways were activated. In all three species, genes associated with growth and development were down-regulated, while genes involved the phenylpropanoid, terpenoid and flavonoid biosynthesis were up-regulated. Poplar defensive genes were expressed early in P. balsamifera and P. tremuloides, but delayed in P. deltoides, which correlated with the rate of disease symptoms development. This data gives an insight into the large differences in timing and expression of genes between poplar species being attacked with their native associated Sphaerulina pathogen.

sample_organism:
Populus tremuloides
Populus deltoides
Populus balsamifera

first: Gervais

last: Pelletier

first: Philippe

last: Tanguay

first: Armand

last: Séguin


title: Interactions of C4 subtype metabolic activities and transport in maize are revealed through the characterization of dct2 mutants

city: Saint Louis

first: Sarit

last: Weissmann

address: 975 North Warson Rd

country: USA

institute: Donald Danforth Plant Science Center

summary: We sequenced mRNA from from four segments along a developing 9 day old third maize leaf of WT W22 accession and ZmDCT2 KO (in W22 background - dct2-1::Ac) plants, to identify changes in gene expression in dct2-1::Ac as a response to the loss of ZmDCT2 function.

overall_design: The segments were referenced relative to the position of the ligule of leaf 2 as this point represents the source-sink boundary in a wild-type leaf and the transition from shaded leaf tissue to fully light exposed.  Segment -4 was isolated at the base of the leaf blade that is photosynthetically inactive, -1, defined as the sink to source transition zone (just below the point of leaf emergence from the whorl), segment +4, from a fully light exposed and photosynthetically active region in the mid-leaf (maturation zone), and +10, the tip of the leaf and the terminally differentiated tissue

first: Fangfang

last: Ma

first: Koki

last: Furuyama

first: Howard

last: Berg

first: Ying

last: Shao

first: Mitsutaka

last: Taniguchi

first: Doug

last: Allen

first: Thomas

last: Brutnell


title: Genome-wide expression profile of livers from mice fed HFD,SO-HFD or Viv chow [RNAseq]

city: Elk Grove

first: joseph

last: dhahbi

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

summary: Purpose: Aim of the study is to identify changes in hepatic gene expression induced by either a 40kcal% coconut oil rich high fat diet (HFD), a 40kcal% soybean oil plus coconut oil high fat diet (SO-HFD) or a low fat vivarium chow diet (Viv).  Methods: Livers from mice that had been fed one of the above mentioned diets for 35 weeks, were used to make cDNA libraries that were then sent for deep sequencing, using the Illumina TruSeq RNA. Result: Many genes involved in metabolism, lipid binding, transport and storage and many Cyp genes are dysregulated in the two high fat diets as compared to Viv HFDs in SO-HFD mice. Comparing the two HFDs shows more metabolism and disease related genes  dysregulated in SO-HFD vs HFD. Conclusion: A diet high in soybean oil may be more detrimental to metabolic health than a diet high in saturated fats.

overall_design: cDNA isolated from livers from mice fed HFD, SO-HFD or Viv for 35 weeks, were 50bp pair-ended sequenced in triplicate using Illumina TruSeq RNA Sample Prep v2 Kit.

first: J

last: Dhahbi

first: F

last: Sladek


title: Papilio xuthus developmental transcriptomes by RNAseq

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: Papilio xuthus developmental transcriptomes from egg to adult

overall_design: 10 samples from egg to adult

first: Xue

middle: Y

last: Li

first: Ding

middle: D

last: Fan


title: The histone variant H2A.Z is an important regulator of enhancer activity.

city: Sherbrooke

first: Nicolas

last: Gevry

state: Québec

address: 2500 boulevard de l'université

department: Biologie

institute: Université de Sherbrooke

summary: Gene regulatory programs in different cell types are largely defined through cell-specific enhancers activity. The histone variant H2A.Z has been shown to play important roles in transcription mainly by controlling proximal promoters, but its effect on enhancer functions remains unclear. Here, we demonstrate by genome-wide approaches that H2A.Z is present at a subset of active enhancers bound by the estrogen receptor alpha (ERα). We also determine that H2A.Z does not influence the local nucleosome positioning around ERα-enhancers using ChIP-sequencing at nucleosomal resolution and unsupervised pattern discovery. We further highlight that H2A.Z-enriched enhancers are associated with chromatin accessibility, H3K122ac enrichment and hypomethylated DNA. Moreover, upon estrogen stimulation, the enhancers occupied by H2A.Z produce enhancer RNAs (eRNAs), and recruit RNA polymerase II as well as RAD21, a member of the cohesin complex involved in chromatin interactions between enhancers and promoters. Importantly, their recruitment and eRNAs production are abolished by H2A.Z depletion, thereby revealing a novel functional link between H2A.Z occupancy and enhancer activity. Taken together, our findings suggest that H2A.Z acts as an important player for enhancer functions by establishing and maintaining a chromatin environment required for RNA polymerase II recruitment, eRNAs transcription and enhancer-promoters interactions, all essential attributes of enhancer activity.

overall_design: The MNase ChIP-seqs in this study measure the genome-wide binding landscape of H2A.Z, H3K4me1, H3K27ac and H3K4me3 in MCF-7 cells in the absence or presence of E2. Two biological replicates were done for each ChIP-seq experiment and for each condition, as well as, control input.

first: Mylène

last: Brunelle

first: Alexei

last: Nordell Markovits

first: Sébastien

last: Rodrigue

first: Mathieu

last: Lupien

first: Pierre-Étienne

last: Jacques

last: Gévry


title: Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea

city: New Delhi

first: Gopal

last: Joshi

state: Delhi

address: First Floor

department: Department of Botany

country: India

institute: Delhi University

summary:
Purpose: Brassica. juncea is vulnerable to abiotic stresses at specific stages in its life cycle. However, till date no attempts have been made to elucidate the genome-wide changes in the transcriptome of B. juncea subjected to either high temperature or drought stress.  Hence, to gain global insights into genes, transcription factors and kinases regulated by these stresses and to provide basic information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de novo assembly to discover B. juncea transcriptome associated with high temperature and drought.
Results: We constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS) from control, high temperature treated and drought treated seedlings of Brassica juncea. More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPde-novo assembler. A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence. We established a subset of 19110 transcripts, which were differentially regulated by either high temperature and/or drought stress. Furthermore, 886 and 2834 transcripts that code for transcription factors and kinases, respectively, were also identified. Investigation of identified transcription factors revealed that 92 responded to high temperature, 72 exhibited alterations in expression during drought stress, and 60 were commonly associated with both the stresses. Similarly, 217, 259 and 193 kinases were responsive to high temperature, drought or both stresses, respectively.  Maximum number of up-regulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration responsive element-binding (DREB) families respectively. We also identified 239 metabolic pathways, which were perturbed during high temperature and drought treatments. Analysis of gene ontologies associated with differentially regulated genes forecasted their involvement in diverse biological processes.
Conclusions: Our study provides first comprehensive discovery of B. juncea transcriptome under high temperature and drought stress conditions. Transcriptome resources generated in this study will enhance our understanding on the molecular mechanisms involved in defining the response of B. juncea against two important abiotic stresses. Furthermore this information would benefit designing of efficient crop improvement strategies for tolerance against conditions of high temperature regimes and water scarcity.

overall_design: Total three RNA-Seq libraries were prepared and sequenced independently  [B. juncea control (BC), B. juncea high temperature stressed (BHS) and  B. juncea drought stressed (BDS) on Illumina GAIIx sequencer].

first: Ankur

middle: R

last: Bhardwaj

first: Bharti

last: Kukreja

first: Vidhi

last: Malik

first: Priyanka

last: Arora

first: Ritu

last: Pandey

first: Rohit

middle: N

last: Shukla

first: Kiran

last: Bankar

first: Surekha

last: Katiyar-Agarwal

first: Shailendra

last: Goel

first: Arun

last: Jagannath

first: Amar

last: Kumar

first: Manu

last: Agarwal