title: Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [RNA-Seq Human]

last: Hendrickson

overall_design: We ectopically overexpressed human DUX4  in human pluripotent stem cells (iPSCs). A codon-altered DUX4 (or luciferase control) transgene was cloned into a doxcycline-inducible lentivirus (pCW57.1) and stably integrated. Cells surviving drug-selection were then induced with doxycycline for 14 or 24hrs (two replicates/condition). RNA was collected and 100bp libraries were prepped and sequenced in single-end format.

first: Bradley


title: The BET protein BRD2 cooperates with CTCF to enforce transcriptional and architectural boundaries

status: Public on Mar 31 2017

city: Philadelphia

first: Gerd

middle: A

last: Blobel

state: PA

address: 3615 Civic Center Blvd, ARC 315

department: Pediatrics/Hematology

country: USA

institute: University of Pennsylvania	Children's Hospital of Philadelphia

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: H3K4 Methylation-Mediated Memory of an Active Transcriptional State Impairs Nuclear Reprogramming

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

country: United Kingdom

institute: Genomic Services QIAGEN

type: Expression profiling by high throughput sequencing

summary: Xenopus eggs can induce the reversal of differentiation processes of somatic cells. Yet, the egg is not fully efficient in reprogramming a differentiated nucleus, as certain genes retain a memory of gene expression of their somatic cell of origin. This is thought to be a reason for the low success rate of current cloning and reprogramming strategies. While previous studies addressed extensively the mechanisms that maintain an inactive state of genes (OFF-memory), we investigated the importance of memory of an active transcriptional state (ON-memory) in maintaining cell fate identity and on resistance to reprogramming. We find that donor cell-type specific ON-memory gene-expression in the wrong cell-type of nuclear transfer (NT)-embryos is as common as OFF-memory gene-expression. When compared to properly reprogrammed genes, we find that ON-memory genes show an elevated level of the active histone mark H3K4me3 in endoderm donor cells. Importantly, we show that a reduction of H3K4 methylation level in donor cells decreases the extent of ON-memory gene expression, globally improves transcriptional reprogramming, and enhances the development of NT-embryos. Therefore, our study reveals that H3K4 methylation safeguards endoderm cell identity and acts as a major barrier for efficient reprogramming in NT-embryos. Furthermore, our results suggest that efficient cell fate reprogramming not only relies on the erasure of epigenetic modifications conferring OFF-memory but also crucially depends on the removal of H3 lysine 4 methylation-mediated memory of an active state of gene expression.

overall_design: 73 samples, single-ended RNA-seq libraries from neurula stage 18 or 21 endoderm and gastrula stage 11 ectoderm samples; 2 single-ended ChIP-seq libraries from endoderm cells of neurula (stage 21) embryos with antibody for H3K4me3, 2 replicates for each histone modification pull-down.

first: Eva

last: Hörmanseder

first: George

middle: E

last: Allen

first: Charles

middle: R

last: Bradshaw

first: Magdalena

last: Figlmüller

first: Jerome

last: Jullien

first: John

middle: B

last: Gurdon


title: Transcriptomic analysis of ovaries from ducks with high and low egg production

city: Yangzhou

first: tao

middle: zhi

last: yun

address: Cangjie road NO.58

country: China

institute: jinagsu lnstitute of Poultry Science

summary: Gene expression differences between the ovaries of Jingding duck with high and low egg production were assessed using the RNA-Seq technology. A total of 843 differentially expressed genes were identified. These genes have known or potential roles in regulation the egg production. Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to egg production of ducks.

overall_design: Ducks ovary mRNA profiles of high egg production and low egg production were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Lihui

last: Fang


title: Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [RNA-Seq Mouse siRNA]

city: Salt Lake City

first: Peter

middle: G

state: UT

address: 2000 Circle of Hope Dr.

department: HHMI/Oncological Sciences

institute: University of Utah

summary: To better understand transcriptional regulation during human oogenesis and pre-implantation embryonic development, we defined stage-specific transcription, which revealed cleavage stage as highly distinctive.  We present multiple lines of evidence that two cleavage-specific homologs, mouse mDUX and human DUX4, each activate hundreds of cleavage-specific endogenous genes (e.g. ZSCAN4, ZFP352, KDM4E) and retroviral elements (MERVL/HERVL-family).  Remarkably, mDux expression converts mouse ESCs into two-cell embryo-like (2C-like) cells by binding to MERVL promoters/enhancers and restoring the chromatin landscape (via ATACseq) to the pattern of mouse two-cell embryos

overall_design: We used siRNAs to transiently deplete mESCs of Chaf1a alone and in combination with mouse Dux (mDux). After two consecuitive days of depletion, RNA was collected (2 biological replicates/condition) for sequencing.  125bp libraries were prepped and sequenced in paired-end format.  All sequencing was done on the Illumina HiSeq 2500 platform. Chaf1a silencer select siRNA (and negative control siRNA) was purchased from Life Technologies (s77588). mDux siRNAs (si308 and si309) were synthesized as siRNA pools using Giardia Dicer as described below. Briefly, primers were designed to amplify two ~400bp fragments of the endogenous mDux locus from genomic mouse DNA and add T7 handles. mDux (si308) 5'-AACTCCTCCTCCTTGATCAACTG -3', 5'-CTTCTCTCTGTGGCCAAAAGC-3'. mDux (si309)  5'-CTTCTGCAGAGAGTCCCAGAC-3',  5'-GGCAGATCAGGTGTTGTGTC-3'. Purified PCR products were then used as template for in vitro transcription using the MEGAscript® T7 Transcription Kit (ThermoFischer, AM1334). Template DNA was then degraded and the ssRNA was allowed to anneal before dicing. Diced siRNAs were purified using the PureLinkTM Micro-to-Midi Total RNA purification Kit (Invitrogen, 12183-018) with modifications. siRNA concentration was measured with the Qubit® RNA HS Assay Kit (ThermoFisher,  Q32852).

first: Jessie

last: Dorais

first: Edward

middle: J

last: Grow

first: Jennifer

middle: L

last: Whiddon

first: Jong-Won

last: Lim

first: Candice

last: Wike

middle: D

last: Weaver

first: Christian

last: Pfluegar

first: Benjamin

last: Emery

first: Aaron

last: Wilcox

first: David

last: Nix

first: Matthew

last: Peterson

first: Stephen

last: Tapscott

first: Douglas

last: Carrell

last: Cairns


title: Epigenome comparisons reveal linkage between gene expression and developmental remodeling of chromatin domain topology

city: Bethesda

first: Bruce

middle: Hamilton

last: Howard

state: MD

address: 9000 Rockville Pike

department: Intramural Program

institute: NIH/NICHD

summary: We describe a new approach to ChIP-seq analysis in which conservation of nucleosome-scale H3K27me3 topology, rather than coverage, is quantified; RNA-seq results are related to the new ChIP-seq approach.

overall_design: Examination of histone H3K27me3 modification profiles in human monocytes and dendritic cells, and linkage of histone mark profiles to RNA-seq data

middle: H

first: Tazuko

last: Hirai

first: Valya

last: Russanova


title: BRD2 cooperates with CTCF to enforce transcriptional and architectural boundaries

first: Gerd

last: Blobel

summary: BET (bromodomain and extraterminal motif) proteins are pharmacologic targets for the treatment of diverse diseases, yet the roles of individual BET family members remain unclear. We find that BRD2 colocalizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. To test a role for BRD2 in chromatin architecture we performed HiC in uninduced G1E-ER4 cells (-GATA1), and compared it to HiC in BRD2-depleted G1E-ER4 cells

overall_design: HiC in the G1E-ER4 cell line in the uninduced (-GATA1) condition, comparing unedited control cells to two independent G1E-ER4-derived cell lines in which BRD2 was depleted to undetectable levels using CRISPR/Cas9 (C8 = BRD2 KO cell line #1, D = BRD2 KO cell line #2).

first: Sarah

middle: C

last: Hsu

first: Thomas

last: Gilgenast

last: Phillips-Cremins


title: Gene bivalency at Polycomb domains regulates cranial neural crest positional identity [ATAC-seq]

city: Basel

first: Filippo

middle: M.

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: The cranial neural crest cells are pluripotent cells that provide head skeletogenic mesenchyme and are crucial for craniofacial patterning. Here, we analyzed the in vivo chromatin landscapes of mouse cranial neural crest subpopulations. Early postmigratory neural crest subpopulations contributing to distinct mouse craniofacial structures displayed similar chromatin accessibility patterns, yet differed transcriptionally. Accessible promoters and enhancers of differentially silenced genes carried H3K27me3/H3K4me2 bivalent chromatin marks embedded in large Ezh2-dependent Polycomb domains, indicating transcriptional poising. These postmigratory bivalent regions were already present in neural crest premigratory progenitors. At Polycomb domains, H3K27me3 antagonized H3K4me2 deposition, which was restricted to accessible sites. Thus, bivalent Polycomb domains provide a chromatin template for the regulation of cranial neural crest cell positional identity in vivo contributing novel insights into the epigenetic regulation of face morphogenesis.

overall_design: RNAseq, ChIPseq (single H3K27me3, H3K4me2 and H3K27ac ChIPseq; sequential H3K27me3/H3K4me2 ChIPseq) and ATACseq profiling of cranial neural crest cell (NCC) progenitors (E8.5) and postmigratory subpopulations (FNP, Mx, Md, PA2; E10.5 and E11.5) of wildtype, Ezh2-conditional knockout, Hoxa2-temporal knockout and Hoxa2-overexpression genotypes.

first: Maryline

last: Minoux

first: Sjoerd

last: Holwerda

first: Antonio

last: Vitobello

first: Taro

last: Kitazawa

first: Hubertus

last: Kohler

first: Michael

last: Stadler

middle: M

last: Rijli


title: Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [ChIP-Seq Mouse]

first: Peter

last: Hendrickson

overall_design: We ectopically overexpressed and HA-tagged mouse DUX (mDux) in mESCs by treating stable cells (TRE::3xHA-mDux; MERVL::EGFP) with doxycycline for 24hrs. Cells were then lysed to extract chromatin for immunoprecipitation. 125bp libraries were prepped and sequenced in paired-end format. All sequencing was done on the Illumina HiSeq 2500 platform.

first: Jessie

last: Dorais

first: Edward

last: Grow

first: Jennifer

last: Whiddon

first: Jong-Won

last: Lim

first: Candice

last: Wike

first: Bradley

last: Weaver

first: Christian

last: Pfluegar

first: Benjamin

last: Emery

first: Aaron

last: Wilcox

first: David

last: Nix

last: Peterson

last: Tapscott

last: Carrell


title: Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal- Niche Interactions

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

summary: Human fetal germ cells (FGCs) are precursors to sperm and eggs and are crucial for maintenance of the species. However, the developmental trajectories and heterogeneity of human FGCs remain largely unknown. Here, we performed single-cell RNA-seq analysis of over 2000 FGCs and their gonadal niche cells in female and male human embryos spanning several developmental stages. We found that the female FGCs undergo four distinct sequential phases characterized by mitosis, retinoic acid signaling, meiotic prophase, and oogenesis. Male FGCs develop through stages of migration, mitosis and cell cycle arrest. Individual embryos of both sexes simultaneously contain several subpopulations, highlighting the asynchronous and heterogeneous nature of FGC development. Moreover, we observed reciprocal signaling interactions between FGCs and their gonadal niche cells, including activation of BMP and Notch signaling pathways. Our work provides key insights into crucial features of human FGCs during their highly ordered mitotic, meiotic, and gametogenetic processes in vivo.

overall_design: Here we performed single cell RNA-seq analysis for 2,167 individual PGCs as well as their gonadal niche cells, covering the developmental stages from 4 to 26 weeks after gestation in both female and male human embryos

first: Li

last: Li

first: Liying

last: Yan

first: Jie

last: Qiao

first: Fuchou

last: Tang


title: Molecular reprogramming of granulocyte/macrophage progenitor (GMP) clusters upon induction of BCR/ABL oncogene

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: Single cell RNA Seq and bioinformatic analysis are used to study what processes are important for the molecular reprogramming of GMPs once mice develop chronic myelogenous leukemia-like (CML-like) myeloproliferative neoplasm (MPN) upon induction of BCR/ABL oncogene.

overall_design: Single cell RNA sequencing of GMP cells from mice upon induction of BCR/ABL oncogene

first: Aurélie

last: Hérault

first: Mikhail

last: Binnewies

first: Stephanie

last: Leong

first: Fernando

last: Calero-Nieto

first: Si

middle: Y

last: Zhang

first: Yoona

last: Kang

first: Xiaonan

last: Wang

first: Eric

last: Pietras

first: S

last: Chu

first: Keegan

last: Barry-Holson

first: Scott

last: Armstrong

first: Berthold

last: Göttgens

first: Emmanuelle

last: Passegué


title: Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [ATAC-Seq]

first: Peter

last: Hendrickson

overall_design: We ectopically overexpressed mouse DUX (mDux) in mESCs by treating stable, clonal, cells (TRE::3xHA-mDux; MERVL::EGFP) with doxycycline for 24hrs. Cells were then subjected to FACS to separate GFP-positive and GFP-negative populations (~30,000 cells/replicate; 2 replicates per condition) for ATAC-sequencing. 125bp libraries were prepped and sequenced in paired-end format. All sequencing was done on the Illumina HiSeq 2500 platform.

first: Jessie

last: Dorais

first: Jennifer

last: Whiddon

first: Edward

last: Grow

first: Candice

last: Wike

first: Jongwon

last: Lim

first: Christian

last: Pfluegar

first: David

last: Nix

first: Benjamin

last: Emery

first: Krisitin

last: Murphy

first: Matthew

last: Peterson

first: Stephen

last: Tapscott

first: Douglas

last: Carrell

first: Bradley

last: Cairns


title: Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [RNA-Seq Mouse]

overall_design: We ectopically overexpressed mouse DUX (mDux) in mESCs. For transient mDux expression, a codon altered mDux transgene (or control) was transiently expressed in mouse embryonic stem cells (mESCs) for 24 hours. RNA was collected (2 replicates/condition) and 50bp libraries were prepped and sequenced in single-end format. Additionally, the same mDux transgene with a 3xHA-tag was cloned into a doxcycline-inducible lentivirus (pCW57.1) and stably integrated into mESCs containing a MERVL::EGFP reporter. Single cell clones (TRE::3xHA-mDux; MERVL::EGFP) were drug -selected and expanded. For unsorted RNA seq, TRE::3xHA-mDux; MERVL::EGFP mESCs (2 replicates) were induced with doxycycline for 24hrs (control: 2 replicates without induction) before extracting RNA. For sorted RNA-seq, TRE::3xHA-mDux; MERVL::EGFP mESCs (2 replicates) were induced with doxycycline for 24hrs and then subjected to FACS to sort GFP-positive and GFP-negative populations before extracting RNA. For stable RNA-seqs, 125bp libraries were prepped and sequenced in paired-end format.  All sequencing was done on the Illumina HiSeq 2500 platform.


title: The BET protein BRD2 cooperates with CTCF to enforce a transcriptional boundary

first: Gerd

last: Blobel

summary: Role of the bromodomain and extraterminal motif (BET) protein BRD2 in CTCF chromatin occupancy, tested by CRISPR/Cas9-mediated depletion of BRD2 in GATA1-null erythroblasts expressing an inducible GATA1-ER fusion (G1E-ER4). Pharmacologic inhibitors of the BET (bromodomain and extraterminal motif) family of proteins are being explored for the treatment of various diseases, including cancer, yet the individual functions of BET proteins remain unclear. Here we find that BRD2 co-localizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. CTCF recruits BRD2 to co-bound sites, whereas BRD2 is dispensable for CTCF occupancy. Genome editing at a CTCF/BRD2 co-occupied site reveals a functional boundary element that upon perturbation results in transcriptional misregulation. Single-molecule RNA FISH reveals that either site-specific CTCF loss or BRD2 depletion increases the correlation in expression of two genes flanking the boundary. Together these findings indicate that BRD2 supports chromatin boundary activity in a CTCF-dependent manner and suggest that pharmacologic BET inhibitors influence gene expression in part by perturbing chromatin domain boundary function.

overall_design: GATA1-null erythroblasts expressing GATA1 as a GATA1-ER fusion protein (G1E-ER4) were induced to differentiate by the addition of 100nM estradiol for 24 hours. CTCF occupancy was assessed in wild type G1E-ER4 cells and compared to occupancy in 2 independent G1E-ER4 clonal sub-lines which were engineered with CRISPR/Cas9 to express no detectable BRD2 (C8 = BRD2 KO#1, D = BRD2 KO#2).

first: Sarah

last: Hsu

first: Belinda

last: Giardine


title: Transcriptome analysis of tissue macrophages

status: Public on Apr 10 2017

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

summary: RNA-seq analysis of cardiac, renal, and liver macrophages. CD11b+F4/80+Ly6C-Ly6G- tissue resident macrophages were isolated from the heart, kidney, and liver of mice. Isolated RNA was subjected to RNA-seq to identify differentially expressed transcripts.

overall_design: RNA-seq was done to analyze transcriptomes of cardiac macrophages, liver Kupffer cells, and renal macrophages isolated from adult mice in the steady state.

first: Manabe

last: Ichiro

first: Nakayama

last: Yukiteru

first: Katsuhito

last: Fujiu

first: Munehiko

last: Shibata


title: Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing and Translation Events during T Cell Responses

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time-courses of 4sU-Seq, RNA-Seq, ribosome profiling and RNA polymerase II (RNAPII) ChIP-Seq during T cell activation, we illustrate genome-wide temporal dynamics for ~10,000 genes. This approach reveals immediate-early as well as posttranscriptionally-regulated genes, but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNAPII, primarily mediates transcriptional changes. This coincides with a genome-wide temporary slowdown in cotranscriptional splicing, even for polyadenylated mRNAs that are localized at the chromatin. Subsequent splicing optimization correlates with increasing Ser-2 phosphorylation of the RNAPII carboxy-terminal domain (CTD) and activation of the positive transcription elongation factor complex (pTEFb). Thus, rapid de novo recruitment of RNAPII dictates the course of events during T cell activation, in particular transcription, splicing and consequently translation.

overall_design: Analysis of temporal dynamics of transcription, splicing and translation in real-time resolution during the activation of T effector cells by RNAseq, 4sU-Seq and Ribosome Profiling

first: Kathrin

last: Davari

first: Johannes

last: Lichti

last: Gallus

first: Franziska

last: Greulich

first: N. Henriette

last: Uhlenhaut

first: Matthias

last: Heinig

first: Elke

last: Glasmacher


title: Kinetics of RNA polymerase 2 recruitment and H3K36me3 deposition after stimulation of murine T-cells

city: Freising

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

summary: Activation of immune cells results in extremely rapid functional changes, yet it remains enigmatic how this is accomplished. By combining time-courses of RNA-polymerase-II (RNAPII) Chip-Seq, 4sU-Seq, RNA-Seq and ribosome profiling during Th1 activation we provide a genome-wide view on temporal dynamics for ~10.000 genes. Gene responses vary in time and magnitude and allow the identification of unknown immediate early (IEG) and posttranscriptionally regulated genes. However, >90% are regulated transcriptionally with coupled changes in translation. Surprisingly, not poised, but rather re-positioned RNAPII correlates with transcriptional changes and coincides with fluctuations in cotranscriptional splicing, which lags behind at first. Unspliced transcripts remain here at the chromatin, but are already poly-adenylated. Later splicing readjusts, correlating with progressive Ser-2 phosphorylation of the CTD domain of RNAPII and activation of the elongation-complex pTEFb. Thus, rapid re-positioning of RNAPII and regulating the phosphorylation state of its CTD dictates almost all events during immune responses, including post-transcriptional processes.

overall_design: ChIP-Seq of total RNA-Pol2 and H3K36me3 after 30min and 2h of T-cell stimulation compared to non-restimulated (NR) T-cells

first: Nina

first: Christian

first: Mathias


title: Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons

first: Peter

last: Hendrickson

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Next-generation sequencing analysis of transcriptom in gemcitabine resistant pancreatic cancer cells

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: Next-generation sequencing was applied to compare the transcriptom of 1) SW1990 human pancreatic cancer cell lines and its gemcitabine-resistant derivative established with long-term exposure in medium containing 100 nM gemcitabine; 2) TRA-1-81+ cells and TRA-1-81- cells isolated from SW1990 human pancreatic cancer cell line.

overall_design: mRNA profiles were generated with SW1990 cell lines and its derivatives by deep sequencing, using Illumina-HiSeq2500.

first: Lei

last: Tan


title: Regulation of Lipids is Central to Replicative Senescence

city: Buffalo

first: Omer

last: Gokcumen

address: 639 Cooke Hall

department: Biological Sciences

institute: University at Buffalo

summary: Cellular replicative senescence, a state of permanent cell-cycle arrest that occurs following an extended period of cell division in culture, has been linked to organismal aging, tissue repair and tumorigenesis. In this study, we comparatively investigated the global lipid profiles and mRNA content of proliferating and senescent-state BJ fibroblast cells. We found that both the expression levels of lipid-regulating genes, as well as the abundance of specific lipid families, are actively regulated. We further found that 19 polyunsaturated triacylglycerol species showed the most prominent changes during replicative senescence. We argue that diversion of polyunsaturated fatty acids to glycerolipid biosynthesis could be responsible for the accumulation of specific triacylglycerols. This, in turn, could be one of the cellular mechanisms to prevent lipotoxicity under increased oxidative stress conditions observed during replicative senescence. Collectively, our results place regulation of specific lipid species to a central role during replicative senescence.

overall_design: We sequence total RNA from 3 early PD and 3 senesent human BJ cell lines to detect the expressional differences between early PD and senescent cells.

first: Darleney

last: Lizardo

first: Yen-Lung

last: Lin

first: Ekin

last: Atilla-Gokcumen


title: Molecular reprogramming of granulocyte/macrophage progenitor (GMP) clusters

first: Evangelia

last: Diamanti

overall_design: Refer to individual Series


title: Molecular reprogramming of granulocyte/macrophage progenitor (GMP) clusters upon 5-Fluorouracil (5-FU) treatment

summary: Single cell RNA Seq and bioinformatic analysis are used to study what processes are important for the molecular reprogramming of GMPs after 5-FU treatment. Samples were collected at different time points (0, 8, 10, 12 and 14 days post treatment)

overall_design: Single cell RNA sequencing of GMP cells upon 5-FU treatment

first: Aurélie

last: Hérault

first: Mikhail

last: Binnewies

first: Stephanie

last: Leong

first: Fernando

last: Calero-Nieto

first: Si

last: Zhang

first: Yoona

last: Kang

first: Xiaonan

last: Wang

first: Eric

last: Pietras

first: S

last: Chu

first: Keegan

last: Barry-Holson

first: Scott

last: Armstrong

first: Berthold

last: Göttgens

first: Emmanuelle

last: Passegué


title: Sodium butyrate ameliorates aSyn-induced transcription deregulation and DNA damage

city: Göttingen

first: Ashish

last: Rajput

state: Niedersachsen

address: Von-Siebold-Straße 3A

department: Research Group for Computational Systems Biology

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Alpha-synuclein (aSyn) is widely portrayed as the main culprit on Parkinson’s Disease (PD) pathophysiology. However, the precise molecular function of the protein remains elusive. Recent evidence suggests that aSyn may play a role on transcription regulation, possibly by modulating the acetylation status of histones. Our study aimed to evaluate the impact of wild-type (WT) and mutant A30P aSyn on gene expression, in a dopaminergic neuronal cell model, and decipher potential mechanisms behind aSyn-induced transcriptional deregulation. We performed RNA-sequencing in Lund Human Mesencephalic (LUHMES) cells expressing endogenous (control) or increased WT or A30P aSyn levels. Compared to control, LUHMES cells expressing aSyn exhibited robust changes in the expression of several genes, including downregulation of major genes involved in DNA repair. Expressing WT aSyn, unlike A30P aSyn, led to increased DNA damage and phosphorylated p53 levels. In our dopaminergic neuronal cell model, aSyn expression promoted lower histone 3 acetylation levels. Excitingly, treatment with sodium butyrate, a histone deacetylase inhibitor (HDACi), was able to rescue WT aSyn-induced DNA damage, possibly via upregulation of genes involved in DNA repair. Overall, our findings provide compelling, pioneer evidence for a novel mechanism associated with aSyn neurotoxicity in dopaminergic cells, which could be ameliorated with a HDACi. Prospective studies will be crucial to further validate these findings and its relevance to our knowledge of PD.

overall_design: RNA from Lund Human Mesencephalic (LUHMES) cells was used to assess the impact of alpa-synuclein (aSyn) on cellular transcription. For this purpose, three different cell lines were generated. Briefly, proliferating LUHMES cells were infected with equimolar amounts of lentiviral particles encoding for: IRES-GFP (samples set C); full-length human wild-type (WT) aSyn (SNCA, NM_000345), WT aSyn-IRES-GFP (samples set E) or familial mutant A30P aSyn, A30P aSyn-IRES-GFP (samples set A). Positive green fluorescent cells were selected by fluorescence activated cell sorting. Three independent replicates were generated for each cell line. Total RNA from differentiated LUHMES cells, at differentiation day 8, was extracted and purified using the RNeasy mini kit (Qiagen), according to the instructions of the manufacturer.

first: Isabel

last: Paiva

first: Raquel

last: Pinho

first: Magali

last: Hennion

first: Vincenzo

last: Capece

first: Cemil

last: Kerimoglu

first: Pauline

last: Wales

first: Ellen

last: Gerhardt

first: Éva

last: Szegő

first: Maria

last: Pavlou

first: André

last: Fischer

first: Stefan

last: Bonn

first: Cristina

last: Rego

first: Tiago

middle: F

last: Outeiro


title: Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

first: Federico

last: Gaiti

address: 413 East 69th St.

institute: Weill Cornell Medicine

summary: We deep sequence DNA associated with immunoprecipitated chromatin containing histones with specific post-translational modifications (PTMs) to identify transcriptionally active or repressed regions of the genome of the sponge Amphimedon queenslandica.

overall_design: We carried out chromatin immunoprecipitation (ChIP) on sexually reproducing Amphimedon adults and larvae using antibodies against specific histone H3 PTMs that have been used to define chromatin states in model bilaterians. The antibodies used target the following histone H3 PTMs: (i) monomethylated lysine 4 (H3K4me1), associated with distal cis-regulatory elements such as enhancers; (ii) trimethylated lysine 4 (H3K4me3), enriched in active promoters; (iii) trimethylated lysine 36 (H3K36me3), found with actively transcribed regions; (iv) trimethylated lysine 27 (H3K27me3), enriched in Polycomb-silenced regions; and (v) acetylated lysine 27 (H3K27ac), which occurs around activated regulatory regions. We also used an antibody against total histone H3. An antibody against unphosphorylated Ser2 residues of RNA polymerase II (RNAPII 8WG16) C-terminal domain also was included.

first: Katia

last: Jindrich

first: Selene

last: Fernandez-Valverde

first: Kathrein

last: Roper

first: Bernard

last: Degnan

first: Milos

last: Tanurdzic


title: A genome-wide screen identifies competitive growth advantage for human epidermal stem cells with activated YAP

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

summary:
We performed genome-wide pooled RNAi screens for genes that confer a clonal growth advantage or disadvantage on epidermal stem- and cutaneous squamous cell carcinoma (SCC) cells
What we know from our cell biology is that a shRNA underrepresented at t=14 targets a gene that confers growth advantage.

overall_design: Genome-wide screening of 2 primary cell lines using Decode shRNA library.  Genomic DNA purified from cells at t=0 and after cells were cultured for two weeks (t=14).

first: Gernot

last: Walko

first: Sam

last: Woodhouse

middle: O

last: Pisco

first: Fiona

last: Watt


title: Interleukin 4 induces apoptosis of acute myeloid leukemia cells in a Stat6-dependent manner

city: Lund

first: Pablo

last: Peña-Martínez

address: Klinikgatan 28

department: Clinical Genetics

country: Sweden

institute: Lund University

summary: Acute myeloid leukemia (AML) is associated with poor prognosis, and there is a strong need to develop new therapeutic strategies to improve treatments. We performed a cytokine screen with 114 recombinant proteins to identify selective negative regulators of primitive murine AML cells relative to normal bone marrow cells. The top candidate identified was interleukin 4 (IL4), as it showed the most selective inhibition of leukemia cell growth. Stimulating leukemia cells ex vivo with IL4 and transplanting the cells into mice resulted in reduced leukemia burden and prolonged survival compared with controls. In contrast, IL4 did not inhibit the function of normal hematopoietic stem and progenitor cells in long-term bone marrow repopulation assays. Moreover, we found that IL4 treatment of leukemia cells induced Stat6 phosphorylation, and that leukemia cells with Stat6 knocked out using CRISPR/Cas9-genetic engineering were partially resistant to IL4 stimulation, revealing Stat6 as a critical mediator of the IL4 effect. To evaluate whether IL4 has in vivo therapeutic efficacy, we expressed IL4 ectopically in leukemia cells in vivo and also injected IL4 into leukemic mice; both strategies resulted in the suppression of the leukemia cell burden and increased survival. Further analysis revealed that IL4 treatment induces apoptosis in the leukemia cells. Importantly, IL4 exposure also inhibited the growth and survival of primary AML patient cells. In summary, these findings demonstrate that IL4 selectively inhibits AML cells in a Stat6-dependent manner, thus revealing IL4 as a candidate therapeutic agent in AML. IL4 (ProSpec, East Brunswick NJ, USA) was resuspended following the provider guidelines and stored in aliquotes at -80 °C. Mouse MLL-AF9 leukemia cells were provided by Dr. Benjamin Ebert (Brigham and Women’s Hospital, Boston MA, USA). The murine leukemia cells were cultured in SFEM (StemCell Tech) supplemented with 1% penicillin/streptomycin at 37 °C with 5% CO2.

overall_design: Mouse MLL-AF9 leukemia cells were grown in 20 ng/mL IL3 with or without IL4 (100 ng/mL) for 18 hours.


title: Gene transcription in ovine fetal perirenal adipose tissue.

city: Saint Lucia, Brisbane

first: Tony

last: Vuocolo

state: Queensland

address: 306 Carmody Road

country: Australia

institute: CSIRO

summary: Next Generation Sequencing (NGS) was used to measure the levels of  gene transcription in perirenal adipose tissue in late gestation sheep fetuses (~ 2 weeks before birth). Through the discovery of SNP in the population, allele specific expression was identified.

overall_design: mRNA profiles of perirenal adipose tissue from sheep fetuses at 132 days of gestation (132 d post conception (dpc); term =150±3d)   were generated by deep sequencing using Illumina HiSeq2000 sequencing platform. Samples from 18 animals  were analysed.

first: Ross

last: Tellam


title: Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [RNA-Seq]

first: Peter

last: Hendrickson

summary: To better understand transcriptional regulation during human oogenesis and pre-implantation embryonic development, we defined stage-specific transcription, which revealed cleavage stage as highly distinctive.  We present multiple lines of evidence that two cleavage-specific homologs, mouse mDUX and human DUX4, each activate hundreds of cleavage-specific endogenous genes (e.g. ZSCAN4, ZFP352, KDM4E) and retroviral elements (MERVL/HERVL-family).  Remarkably, mDux expression converts mouse ESCs into two-cell embryo-like (2C-like) cells by binding to MERVL promoters/enhancers and restoring the chromatin landscape (via ATACseq) to the pattern of mouse two-cell embryos

overall_design: We derived and analyzed transcriptomes from seven stages of developing human oocytes and embryos. The blastocyst stage embryos were dissected into inner cell mass (ICM) and trophectoderm lineages and processed independently. Cells from each stage were pooled and RNA was extracted. Two stranded libraries were prepared from each stage. Each library was then split and amplied for 12 or 14 PCR cycles, resulting in four technical replicates per developmental stage. 12 and14 cycle replicates from the same library prep were merged after sequencing

first: Jessie

middle: A

last: Dorais

first: Jennifer

last: Whiddon

first: Edward

last: Grow

first: Candice

last: Wike

first: Jongwon

last: Lim

first: Christian

last: Pfluegar

first: David

last: Nix

first: Benjamin

last: Emery

first: Krisitin

last: Murphy

first: Matthew

last: Peterson

first: Stephen

last: Tapscott

first: Douglas

last: Carrell

first: Bradley

last: Cairns


title: Gene bivalency at Polycomb domains regulates cranial neural crest positional identity [RNA-seq]

first: Filippo

last: RIJLI

overall_design: RNAseq, ChIPseq (single H3K27me3, H3K4me2 and H3K27ac ChIPseq; sequential H3K27me3/H3K4me2 ChIPseq) and ATACseq profiling of cranial neural crest cell (NCC) progenitors (E8.5) and postmigratory subpopulations (FNP, Mx, Md, PA2; E10.5 and E11.5) of wildtype, Ezh2-conditional knockout, Hoxa2-temporal knockout and Hoxa2-overexpression genotypes.

first: Maryline

last: Minoux

first: Sjoerd

last: Holwerda

first: Antonio

last: Vitobello

first: Taro

last: Kitazawa

first: Hubertus

last: Kohler

first: Michael

last: Stadler

last: Rijli


title: Gene bivalency at Polycomb domains regulates cranial neural crest positional identity

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


title: Crosstalk between Streptococcus mutans and Aggregatibacter actinomycetemcomitans in dual-species biofilms.

city: Braunschweig

first: Szymon

middle: Piotr

last: Szafranski

address: Inhoffenstr. 7

department: Research Group Microbial Communication

institute: Helmholtz Centre for Infection Research

summary: We performed comparative analysis of transcriptomes of S. mutans in single biofilms and in mixed-biofilms with A. actinomycetemcomitans. We also compared the transcriptomic profiles of A. actinomycetemcomitans in single biofilms and A. actinomycetemcomitans in mixed biofilms with S. mutans. Finally we looked at the changes in gene expression in both organisms in time.

sample_organism:
Aggregatibacter actinomycetemcomitans
Streptococcus mutans

overall_design: RNAseq of single species biofilms (S. mutans, A.act.) - 8 and 24 h, dual-species biofilms (S.mutans with A.act.) - 4, 6, 8,10, 12, and 24 h. All in duplicate. Using Illumina HiSeq.

middle: P

first: Juergen

last: Tomasch

first: Zhi-Luo

last: Deng

last: Jarek

first: Sabin

last: Bhuju

first: Manfred

last: Rohde

first: Helena

last: Sztajer

first: Irene

last: Wagner-Doebler


title: Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis

status: Public on Mar 30 2017

city: Novosibirsk

first: Petr

last: Laktionov

address: Lavrenitev ave 8/2

country: Russia

institute: Institute of molecular and cellular biology SD RAS


title: Interruption of Hepatic Glucagon Signaling Reveals a Hepatic-α-Islet Cell Axis Where L-Glutamine Stimulates α-Cell Proliferation

city: Nashville

first: Danielle

last: Dean

state: TN

address: 7465 MRBIV, 2215 Garland Avenue

department: Division of Diabetes, Endocrinology, and Metabolism

institute: Vanderbilt University Medical Center

summary: Decreasing glucagon action lowers blood glucose and may be a useful therapeutic approach for diabetes. However, interrupted glucagon signaling in mice leads to hyperglucagonemia and α-cell hyperplasia. We show using islet transplantation, mouse and zebrafish models, an in vitro islet culture assay that a hepatic-derived, circulating factor in mice with interrupted glucagon signaling stimulates α-cell proliferation, which was dependent on mTOR signaling and the FoxP transcription factors. α-cells of transplanted human islets also proliferated in response to this signal in mice. A combination of liver transcriptomics and serum fractionation with proteomics/metabolomics found changes in hepatic gene expression relating to amino acid catabolism predicting the observed increase in serum amino acid levels. Amino acid concentrations that mimicked the levels in mice with interrupted glucagon signaling, specifically L-glutamine, stimulated α-cell proliferation. These results indicate a hepatic-α-islet cell axis where glucagon regulates serum amino acid availability and L-glutamine regulates α-cell proliferation via mTOR-dependent nutrient sensing.

overall_design: Ten days of GCGR mAb treatment increased the percentage of proliferating α-cell approximately 14-fold while Gcgr-/- mice also have increased α-cell proliferation (Dean et al., unpublished; Longuet et al., 2013). Therefore, we used these two models for liver transcriptomics. Mice were fasted for 6 hours prior to tissue collection. For RNA isolation, approximately 100mg punches of liver tissue were stored in RNAlater (Ambion) according to the manufacturer’s instructions until isolation using RNeasy Mini kit with DNase I (Qiagen Hilden, DE) digestion. RNA purity and quantity were determined by Bioanalyzer. Transcriptome expression was determined as described previously (Reinert et al, 2014; Brissova et al., 2014).

first: Alvin

last: Powers

first: E


title: Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [DamID]

summary: To investigate the mechanisms of gene regulation during Drosophila spermatogenesis, we obtained genome-wide binding profiles of the proteins involved in gene regulation during drosophila spermatogenesis using germline-specific DamID-Seq approach.

overall_design: DamID-Seq protein binding profiling of Comr, Can, CG9879, Mip40 in germline cells of WT Drosophila testes. We also performed DamID profiling of Mip40 and Polycomb at the different developmental stages of male germ cells, using testes of bam-, aly- and can-mutants. For every experiment Dam-alone control was performed. Experiments were performed in replicates.

first: Stanislav

middle: E

last: Romanov

first: Daniil

last: Maksimov

first: Dmitry

last: Koryakov

first: Stepan

middle: N

last: Belyakin


title: microRNA microarray of Sinperca chuatsi's skeletal muscle

city: Changsha

first: zhang

last: fangliang

state: hunan

address: Changsha City Kaifu District

institute: Changsha University

summary: Contains 90 Sinperca chuatsi miRNAs identified in fast and slow muscle fibers, and 60 miRNAs showed significantly different levels of expression.

overall_design:
In this experiment, six Samples are analyzed with 3 replicates are included.The miRNA microarrays were used to analyze miRNA expression patterns in the white muscle and red muscle (LC-Bio Hangzhou, China). Chip hybridizations were performed overnight on a μParaflo microfluidic chip using a microcirculation pump (Atactic Technologies). Based on mature miRNA sequences of zebrafish downloaded in miRBase Release 19.0 (http://microrna.sanger.ac.uk/), 246 probes were designed to detect S. chuatsi miRNAs on microarray chips. In addition, the arrays contained 95 probes complementary to the miRNA in S. chuatsi, positive control probes for zebrafish 5s rRNA, and negative controls for normalizing data with low-density signals. Sufficient RNA was extracted to hybridize in triplicate with three biological repeats to ensure microarray reproducibility. After hybridization, signals were detected using tag-specific Cy3 and Cy5 dyes. Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Devices, Sunnyvale, CA, USA) and digitized by Array-Pro image analysis software (Media Cybernetics, Bethesda, MD, USA). Finally, hybridization signals were detected and quantified, and data were analyzed by first subtracting the background and then normalizing the signals with a cyclic LOWESS filter (Locally-weighted Regression).
Please note that the  experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as though they are single channel (Cy3 and Cy5 signals are calculated). Therefore there are total 3 raw data files for 6 samples, and the corresponding raw data file is indicated in the sample description field.

first: FangLiang

last: Zhang

first: WuYing

last: Chu

first: JianShe


title: Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [RNA-Seq]

summary: To investigate the mechanisms of gene regulation during Drosophila spermatogenesis, we performed RNA-Seq gene expression profiling in testes from Drosophila males, bearing mutations that affect spermatogenesis.

overall_design: RNA-Seq gene expression profiling in bam-, comr-, can-, mip40-, CG9879-, bam-/mip40-mutant and wild-type testes of Drosophila melanogaster. We generated biological replicate for each sample, thus we obtained 14 RNA-Seq gene expression profiles.


title: MicroRNAs 146a/b-5p, 425-3p and 24-3p are markers of antidepressant response and regulate MAPK/Wnt-system genes

city: Montreal

first: Juan Pablo

last: Lopez

state: Quebec

address: 6875 La Salle Blvd

department: Human Genetics

country: Canada

institute: McGill University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Antidepressants (ADs) are the most common treatment for major depressive disorder (MDD). However, only about 30% of patients experience adequate response after a single AD trial, and this variability remains poorly understood. Here, we investigated microRNAs (miRNAs) as biomarkers of AD response using small RNA-sequencing in paired samples from MDD patients enrolled in a large, randomized placebo-controlled trial of duloxetine collected before and eight weeks after treatment.
Results: Our results revealed differential expression of miR-146a-5p, miR-146b-5p, miR-425-3p and miR-24-3p according to treatment response. These results were replicated in two independent clinical trials of MDD, a well-characterized animal model of depression, and post-mortem human brains. Furthermore, using a combination of bioinformatics, mRNA studies and functional in vitro experiments, we showed significant dysregulation of genes involved in MAPK/Wnt signaling pathways.
Conclusions: Together, our results indicate that these miRNAs are consistent markers of treatment response and regulators of the MAPK/Wnt systems.

overall_design: MicroRNAs as biomarkers of antidepressant response

first: Juan

first: Gustavo

last: Turecki

first: Jean-François

last: Théroux


title: Nuclear Pores provide a scaffold for induced enhancer promoter contacts

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We found that in addition to promoters, multiple Nups bind enhancers and insulators in the Drosophila genome. We identified a functional role for Nup98 in mediating enhancer-promoter looping at ecdysone-inducible genes. These genes were found to be stably associated with nuclear pores before and after activation. Interestingly, although changing the levels of Nup98 disrupted induced enhancer-promoter contact, it did not affect transcriptional activation. Instead, loss of Nup98-mediated enhancer-promoter contact affected the primed response to subsequent transcriptional activation or transcriptional memory. In support of the enhancer-looping role, we found Nup98 to gain and retain physical interactions with several architectural proteins upon stimulation with ecdysone.

overall_design: Characterization of Nup98 occupancy by ChIP-Seq in drosophila embryonic S2 cells. Drosophila brains were also dissected from 3rd instar larvae and ChIP-Seq were performed using Nup93, Elys, Nup98, H3K27ac and H3K27m3 antibodies. Control S2 cells and Nup93 and Elys knockdown cells were used to test antibodies specificity.

first: Pau

last: Pascual-Garcia

first: Maya

last: Capelson


title: Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [ChIP-Seq]

first: Petr

summary: To investigate the mechanisms of gene regulation during Drosophila spermatogenesis, we studied the effects of comr and can mutations on the chromatin of the cells in Drosophila testes by H3K27me3 ChIP-Seq.

overall_design: ChIP-Seq of H3K27me3 histone modification in comr- and can-mutant testes of Drosophila melanogaster. We processed two biological replicates of every sample and corresponding input specimen.

first: Olga

middle: V

last: Posukh


title: Effect of BET bromodomain inhibition with JQ1 in stressed human derived iPS cardiomyocytes

first: Saptarsi

last: Haldar

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

summary: Gene expression profile of endothelin-1 (ET-1) stressed human derived iPS cardiomyocytes (from Cellular Dynamics) with or without the BET bromodomain inhibitor JQ1

overall_design: Human derived iPS cardiomyocytes from Cellular Dynamics were cultured according to manufacturers protocol with a 4 day serum starvation following by pre-treatment with either JQ1 ( ) or DMSO for 3 hours then stimulation with endothelin-1

first: Qiming

last: Duan

first: Sarah

last: McMahon

first: Madeleine

last: Lemieux

first: Priti

last: Anand


title: BET bromodomain inhibition

overall_design: Refer to individual Series


title: Gene expression profile during cardiac stress induced by transverse aortic constriction (TAC) and myocardial infarction (MI) with or without BET protein inhibitor JQ1 in mouse hearts

summary: Purpose: to reveal cardiac stress-inducible genes that are attnuated by BET inhibition

overall_design:
Method: Adult C57Bl/6 mice (male, 10 wks) were subjected to sham surgery and received vehicle injection for 6 weeks starting post-op week 4.
Method: Adult C57Bl/6 mice (male, 10 wks) were subjected to TAC surgery with a 27 gauge needle. Starting at the beginning of post-op week 4, JQ1 at 50 mg/kg/d was adminstrated via I.P. injections and continue for another 6 weeks.
Method: Adult C57Bl/6 mice (male, 10 wks) were subjected to Permanent Ligation of the Left Anterior Descending Coronary Artery. Beginning from post-op day 6, JQ1 at 25 mg/kg/d or vehcle was given via I.P. for 6 days and then increased to 50 mg/kg/d for additional 16 days.


title: Untangling the Role of H3K9 Methylations in Transgenerational Small RNA Inheritance

city: Tel-Aviv

first: Itamar

last: Lev

address: Dr George Wise

country: Israel

institute: Tel-Aviv University

summary: In C.elegans, disruption of the chromatin landscape produces transgenerational effects, such as inherited increase in lifespan and gradual loss of fertility. Inheritance of histone modifications can be induced by double strand RNA-derived heritable small RNAs. We show that the mortal germline phenotype which is typical to met-2 mutants, defective in H3K9 methylation, depends on HRDE-1, an argonaute that carries small RNAs across generations, and is accompanied by accumulated transgenerational misexpression of heritable small RNAs. We discovered that MET-2 inhibits small RNA inheritance, and as a consequence, induction of RNAi in met-2 mutants leads to permanent RNAi responses that do not terminate even after more than 30 generations. We found that potentiation of heritable RNAi in met-2 animals results from global hyperactivation of the small RNA inheritance machinery. Thus, changes in histone modifications can give rise to drastic transgenerational epigenetic effects, by controlling the overall potency of small RNA inheritance.

overall_design: C. elegans worms were grown in 20 degrees and fed either on dsRNA producing bacteria or control empty-vector bearing bacteria. The inheritance of the RNAi response was followed in the subsequent generations which were grown on plates seeded with standard OP-50 bacteria. RNA was extracted from one day adult worms.

last: lev

first: Uri

last: Seroussi

first: Hila

last: Gingold

first: Sarit

last: Anava

first: Oded

last: Rechavi


title: Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [ChIP-seq_round2]

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

summary: Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. However, the genome-wide requirement for Spt5 in transcription has not been extensively studied. To address this issue, we have comprehensively analyzed the consequences of Spt5 depletion on transcription by RNAPII in Schizosaccharomyces pombe using four genome-wide approaches: ChIP-seq, NET-seq, 4tU-seq, and RNA-seq. Our results demonstrate that, in the absence of Spt5, RNAPII accumulates at a high level over the first ~500 bp of transcription units, suggesting that Spt5 is globally required to elongate past a barrier to transcription. This possibility is strongly supported by results showing that Spt5 is required for a normal level of RNA synthesis. In addition to these effects on sense-strand transcription, Spt5 depletion results in widespread convergent antisense transcription that initiates at approximately the same position as the sense-strand barrier. While the role of these antisense transcripts is unknown, the two that were tested control the distribution of RNAPII. Our results also show that Spt5 represses divergent antisense transcription, explaining why it has not been previously observed in S. pombe. Taken together, our results reveal a global and critical role for Spt5 in multiple classes of transcription by RNAPII.

overall_design: Four ChIP experiments (anti-Pol II, S2P, S5P, and Spt5) in biological duplicate, with three strains (Spt5-degron, Spt5-untagged, and Spt5-tagged), and three conditions (treatment with DMSO, with NAA+T, no treatment)

first: Ameet

last: Shetty

first: Scott

last: Kallgren

first: Burak

last: Alver

first: Fred

last: Winston


title: Mutations in Argonaute5 Illuminate Epistatic Interactions of the K1 and I Loci Leading to Saddle Seed Color Patterns in Glycine max

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: The soybean (Glycine max) seed coat has distinctive, genetically programmed patterns of pigmentation and the recessive k1 mutation can epistatically overcome the dominant I and i-i alleles, which inhibit seed color by producing small interfering RNAs (siRNAs) targeting chalcone synthase (CHS) mRNAs. Small RNA sequencing of dissected regions of immature seed coats demonstrated that CHS siRNA levels cause the patterns produced by the i-i  and i-k alleles of the I locus, which restrict pigment to the hilum or saddle region of the seed coat, respectively. To identify the K1 locus, we compared RNA-Seq data from dissected regions of two Clark isolines having similar saddle phenotypes mediated by CHS siRNAs but different genotypes (homozygous i-k K1 versus homozygous i-i k1). By examining differentially expressed genes, mapping information, and genome resequencing, we identified a 129-bp deletion in Glyma.11G190900 encoding Argonaute5 (AGO5), a member of the Argonaute family. Amplicon sequencing of several independent saddle pattern mutants from different genetic backgrounds revealed independent lesions affecting AGO5, thus establishing Glyma.11G190900 as the K1 locus. Non-functional AGO5 from k1 alleles leads to altered distributions of CHS siRNAs, thus explaining how the k1 mutation reverses the phenotype of the seed coat regions from yellow to pigmented, even in the presence of the normally dominant I or i-i  alleles.

overall_design: Immature seed coats of 100-200 mg with chimeric pigmented phenotypes of Clark 8 (i-k, K1) or Clark 18a (i-i, k1) were separated into the regions destined to become either the black saddle region or the yellow sections.  Extracted mRNAs were subjected to high throughput sequencing and analyzed for expression analyses to determine the genetic differences conferred by the K1 locus or the differences in expression in different dissected regions of the seed coat.

first: Young

middle: B

last: Cho


title: RNA-seq of Drosophila 0-2 hr embryos Rnase R

city: Singapore

first: Jun Wei

last: Pek

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: We report the identification of Rnase R resistent stable intronic sequence RNAs (sisRNAs) in Drosophila.

overall_design:
RNA was obtained from 0-2 hr embryos and subjected to deep sequencing.
----------------------------------------
Authors state "We screened by manual inspection on the genome browser after mapping the reads to the genome" and "We managed to obtain 6 candidates with this approach".

first: Jun

middle: W


title: Functions of UHRF1 in the regulation of DNA methylation in retinoblastoma

city: Guangzhou

first: Qi

last: Zhao

state: Guangdong

address: No. 651, Dongfengdong Road

department: Medical Oncology

institute: Sun Yat-sen University Cancer Center

type: Methylation profiling by high throughput sequencing

summary: UHRF1 (ubiquitin-like with PHD and ring finger domains 1) is an epigenetic regulator that is involved in the regulation of DNA and histone methylation and many other cellular events. The UHRF1 is frequently found to be overexpressed in various human cancers, and its overexpression has been associated with pro-tumorigenic effects such as inhibition of apoptosis and high metastatic potential. However, the molecular mechanisms underlying these pro-tumorigenic effects of UHRF1 overexpression in cancers still remain unclear. Retinoblastoma (Rb) is an intraocular tumor which arises from developing retina by biallelic inactivation of Rb1 gene. In this study, we uncovered that the UHRF1 is highly expressed in retinoblastoma, and genomes of retinoblastoma have differential DNA methylation patterns compared to those of normal retina, characterized by global hypomethylation and promoter hypermethylation at key tumor suppressor genes. Given the well-documented functions of UHRF1 in the regulation of DNA methylation, we hypothesized that the overexpressed UHRF1 may contribute to the aberrant DNA methylation in retinoblastoma genomes. To test our hypothesis, we profiled the genome-wide methylation patterns in normal retina and Y79 retinoblastoma cell line by MeDIP-seq, and then investigated how the methylation patterns in Y79 are affected by down-modulation of UHRF1. For identification of differentially methylated regions between the control and UHRF1 knockdown Y79 cells, we analysed three independent sets of sequencing data to unambiguously determine the effects of UHRF1 down-modulation on the methylome of Y79 retinoblastoma cells.

overall_design: PRJNA348780; SRP091683;Genome-wide methylation profiling of human normal retina and Y79 retinoblastoma cell line by MeDIP-seq; Identification of differentially methylated regions (DMR) between control and UHRF knockdown Y79 cells by MeDIP-seq using three independent biological replicates

first: JongKyong

last: Kim

first: Guangyan

last: Kan


title: MiRNA Profiling of Gastrointestinal Stromal Tumors by Next Generation Sequencing

city: Kiel

first: Simonas

last: Juzenas

address: Am Botanischen Garten 11

department: Institute of Clinical Molecular Biology

institute: Christian-Albrechts-University of Kiel

summary: Gastrointestinal stromal tumors (GISTs) have an impaired gene expression. As microRNAs (miRNAs) are involved in post-transcriptional regulation of gene expression we performed the first high-throughput miRNA profiling of 15 paired GIST formalin-fixed and paraffin-embedded samples (tumor and adjacent normal tissue) using small RNA sequencing approach.

overall_design: MiRNA profiling of paired (tumor and adjacent normal tissue) GIST formalin-fixed and paraffin-embedded samples

first: Jurgita

last: Skieceviciene


title: Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection

city: Davis

first: Payam

last: Vahmani

state: California

address: One Shields Avenue

department: Department of Animal Science

institute: University of California Davis

summary: Here, we integrated genome-wide genotype, gene expression and phenotype (viremia level (VL) and weight gain (WG)) data to identify genetic variations and genes that are associated with variation in pigs’ response to PRRSV infection. RNA-seq analysis of peripheral blood samples collected just prior to experimental challenge (day 0) and at 4, 7, 10 and 14 days post infection from 44 pigs revealed 6430 differentially expressed genes after infection. We mapped genetic variations that are associated with inter-individual differences in expression at each day and found evidence of cis expression quantitative trait loci (cis-eQTL) for 1201 genes. Associations between cis-eQTL markers and phenotypes using 383 pigs indicated that host genotype-dependent reduced expression of GBP5, CD1D, PAK1, and USP18 contribute to higher VL or lower WG in response to PRRSV infection. We also validated that cis-eQTLs of these candidate genes for host response to PRRSV infection generally acted by a mechanism involving allele-specific expression.

overall_design:
Sixteen pigs (8 AA and 8 AB individual at the WUR marker) were selected from the PHGC3 trial. Twenty-eight pigs (18 AA, 9 AB and 1 BB individuals at the WUR marker) were selected from the PHGC5 trial. After a seven-day acclimation period, pigs were challenged orally with PRRSV isolate NVSL 97-7985 and followed for 42 days post infection (dpi). RNA-Seq was performed using Illumina HiSeq on whole blood samples obtained from each individual at 0, 4, 7, 10, and 14 dpi. For individuals from the PHGC5 trial, RNA-Seq was performed on whole blood samples collected at 2 additional time-points: 21 and 28 dpi. The PHGC5 RNA-Seq data is represented here.
Please note that the PHGC3 RNA-Seq data has been submitted directly to SRA [SRA accession: SRP069349].

first: Hua

last: Bao

first: Arun

last: Kommadath

first: Igseo

last: Choi

first: Joan

middle: K

last: Lunney

first: James

last: Reecy

first: Jack

last: Dekkers

first: Graham

middle: S

last: Plastow

first: Paul

last: Stothard


title: Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [RNA-seq]

first: Peter

last: Park

overall_design: Six pairs of biological replicates: with and without Spt5 C-terminal region, before and after treatment to deplete Spt5 transcript and protein, and before and after the same treatment on a control strain with wild-type spt5 gene.

first: Ameet

last: Shetty

first: Scott

last: Kallgren

first: Burak

middle: H

last: Alver

first: Fred

last: Winston


title: Potato virus Y HCPro suppression of antiviral silencing in Nicotiana benthamiana plants correlates with its ability to bind in vivo to small RNAs of 21 and 22 nucleotides in length of viral sequence

city: Madrid

first: Francisco

middle: Javier

last: del Toro

state: Madrid

address: Ramiro de Maeztu, 9

department: Enviromental Biology

country: Spain

institute: Centro de Investigaciones Biologicas (CSIC))

summary: We have investigated short and small RNAs (sRNAs) that were bound to a biologically active hexahistidine-tagged Potato virus Y (PVY) HCPro suppressor of silencing, expressed from a heterologous virus vector in Nicotiana benthamiana plants, and purified under non-denaturing conditions.  We found that RNAs in purified preparations were differentially enriched in sRNAs of 21 and to a much lesser extent of 22 nucleotides (nt) in length and of viral sequence (vsRNAs) when compared to those found in a control plant protein background bound to the nickel resin in the absence of HCPro, or in a purified alanine substitution HCPro mutant (HCPro mutB) control that lacked suppressor of silencing activity.  In both controls, sRNAs were composed almost entirely by molecules of plant sequence, indicating that the resin-bound protein background had no affinity for vsRNAs, and also that HCPro mutB failed to bind to vsRNAs.  Therefore, PVY HCPro suppressor activity correlated with its ability to bind to 21 and 22 nt vsRNAs.  HCPro constituted at least 54 % of the total protein content in purified preparations and we were able to calculate its contribution to the 21 and the 22 nt pool of sRNAs present in the purified samples and its binding strength relative to the background.  We also found that in the 21 nt vsRNAs of the HCPro preparation 5´ terminal adenines were overrepresented relative to the controls, but not in vsRNAs of other sizes or of plant sequence.

overall_design: To analyze sRNA populations, three separate deep sequencing events were performed: The first one analysed the sRNAs present in the plants infected with either PVX or PVX-P1-6x-HCPro used as input for the purification. For that, total RNAs were extracted from ~25 g of infected tissue in both cases. 30 µg of total RNA were sent straight for sequencing of sRNAs (18 to 30 nt in legth). Total RNAs were isolated with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the instruction of the manufacturers. The second one analyzed the short RNAs of 18 to over 120 nt that were present in the purified control and HCPro samples of the first purification experiment. For that, 1.5 ml aliquots from the purified elution samples obtained from tissues infected with either PVX or PVX-P1-6x-HCPro were used to obtain 9.61 and 13.38 ng of gel-eluted RNAs from the control and HCPro samples, respectively: total RNAs from the purified samples were fractioned by electrophoresis in 10%-PAGE containing 8M urea. The gel region resolving ~12 nt to ~500 nt in size was sliced with a razor and RNAs were eluted from the gel with 0.3 M NaCl, and resulting precipitated with 1 µl of glycogen (20 µg/µl) (Roche, Basel, Switzerland) and 1 volume of isopropanol. The third massive sequencing analyzed the sRNAs of 18 to 30 nt present in the Ni2+-NTA column-purified HCPro mutB and HCPro samples of the second purification experiment. For that, 1.5 ml aliquots from the purified elution samples obtained from tissues infected with either PVX-P1-6x-HCPro mutB or PVX-P1-6x-HCPro were used to obtain 597 and 339 ng of total RNAs for sequencing, respectively.

first: Livia

last: Donaire

first: Emmanuel

last: Aguilar

last: Tenllado

first: Bong-Nam

last: Chung

first: Tomás

last: Canto


title: Foxh1 marks the embryonic genome prior to the activation of the mesendoderm gene regulatory program

city: Irvine

first: Rebekah

middle: M

last: Charney

address: 4410 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: We examined the binding dynamics of the maternal TF Foxh1 over a time course of germ layer development. Foxh1 binding was compared to the onset of zygotic transcription (RNA pol II), binding of the co-repressor Tle, Nodal signaling (Smad2/3) and the zygotic endoderm TF Foxa.

overall_design: ChIP-seq analysis of transcription factors Foxh1 and Foxa, RNA Polymerase II and the co-repressor TLE, during zygotic gene activation and germ layer development. Includes biological replicates and stage-matched input controls. Five Samples from GSE53652 are included in this study. The reanalyzed processed data for these Samples are on the Series record.

first: Ken

last: Cho


title: Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [ChIP-seq_round1]

overall_design: Four pairs of biological replicates: with and without Spt5 C-terminal region, and before and after treatment to deplete Spt5 transcript and protein.


title: Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription

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


title: A metabolic function for phospholipid and histone methylation

city: Pittsburgh

first: Zheng

last: Kuang

address: 4400 Fifth Avenue

institute: Carnegie Mellon University

summary: S-adenosylmethionine (SAM) is the methyl donor for biological methylation modifications that regulate protein and nucleic acid functions. Here we show that methylation of a phospholipid, phosphatidylethanolamine (PE), is the major consumer of SAM in budding yeast. The induction of phospholipid biosynthetic genes is accompanied by induction of the enzyme that hydrolyzes S-adenosylhomocysteine (SAH), a product and inhibitor of methyltransferases. Beyond its function for the synthesis of phosphatidylcholine (PC), the methylation of PE facilitates the turnover of SAM for the synthesis of cysteine and glutathione. Strikingly, cells that lack PE methylation accumulate SAM, which leads to hypermethylation of histones and the major phosphatase PP2A, dependency on cysteine, and sensitivity to oxidative stress. Without PE methylation, particular sites on histones then become methyl sinks to enable the turnover of SAM. These findings reveal an unforeseen metabolic function for phospholipid and histone methylation intrinsic to the life of a cell.

overall_design: Two biological replicates of wild type and cho2Δ cells in YPL media, in SL media after 1 hour and in SL media after 3 hour were collected for sequencing.

first: Cunqi

last: Ye

first: Benjamin

last: Sutter

first: Yun

last: Wang

last: Tu


title: Allele-Specific Non-CG Methylation Marks Domains of Active Chromatin in Mouse Brain

city: San Diego

first: Eran

last: Mukamel

state: United States

address: 9500 Gilman Dr.

department: Cognitive Science

institute: University of California-San Diego

summary: We examined genome-wide, base-resolution, allele-specific methylation and expression in the prefrontal cortex using a mouse model of deterministic X-inactivation, where the paternal allele was always inactivated. Our findings elucidate the role methylation may play in chromatin regulation under X-inactivation and genomic imprinting.

overall_design: MethylC-seq, RNA-seq from the mouse frontal cortex

first: Christopher

middle: L

last: Keown

first: Joel

last: Berletch

first: Rosa

last: Castanon

first: Joseph

middle: R

last: Nery

first: Christine

last: Disteche

last: Ecker


title: RNA-seq of Odora cells exposed to zinc gluconate

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Zinc is both an essential and potentially toxic metal. It is widely believed that oral zinc supplementation can reduce the effects of the common cold; however, there is strong clinical evidence that intranasal (IN) zinc gluconate (ZG) gel treatment for this purpose causes anosmia, or the loss of the sense of smell, in humans. Using the rat olfactory neuron cell line, Odora, we investigated the molecular mechanism by which zinc exposure exerts its toxic effects on olfactory neurons. Following treatment of Odora cells with 100 and 200 μM ZG for 0-24 h, RNA-seq and in silico analyses revealed up-regulation of pathways associated with zinc metal response, oxidative stress, and ATP production. We observed that Odora cells recovered from zinc-induced oxidative stress, but ATP depletion persisted with longer exposure to ZG. ZG exposure increased levels of NLRP3 and IL-1β protein levels in a time-dependent manner, suggesting that zinc exposure may cause an inflammasome-mediated cell death, pyroptosis, in olfactory neurons.

overall_design: 5 treatment groups, 3 replicates/group, 1 control group, 3 groups treated with 100 µM zinc gluconate for increasing time (6, 12, and 24 h), 1 group treated with 200 µM zinc gluconate for 6 h

first: Heidi

last: Hsieh

first: Kavitha

last: Vignesh

first: George

last: Deepe

first: Divaker

last: Choubey

first: Howard

middle: G

last: Shertzer

first: Mary

last: Genter


title: RNA-seq Transcriptome Profiling of Tiller Buds in the First Leaf Axil of Phytochrome B mutant (phyB-1) and Wild-type Sorghum from Initiation to Dormancy (phyB-1) and Outgrowth (wild-type)

city: College Station

first: John

last: Mullet

address: 300 Olsen Boulevard

institute: Texas A&M University

summary: Phytochrome B (phyB) enables plants to modify shoot branching or tillering in response to varying light intensities and ratios of red and far-red light caused by shading and neighbor proximity. Tillering is inhibited in sorghum genotypes that lack phytochrome B (58M, phyB-1) until after floral initiation. The growth of tiller buds in the first leaf axil of wild-type (100M, PHYB) and phyB-1 sorghum genotypes is similar until 6 d after planting when buds of phyB-1 arrest growth, while wild-type buds continue growing and develop into tillers. Transcriptome analysis at this early stage of bud development identified numerous genes that were up to 50-fold differentially expressed in wild-type/phyB-1 buds. Up-regulation of terminal flower1, GA2oxidase, and TPPI could protect axillary meristems in phyB-1 from precocious floral induction and decrease bud sensitivity to sugar signals. After bud growth arrest in phyB-1, expression of dormancy-associated genes such as DRM1, GT1, AF1, and CKX1 increased and ENOD93, ACCoxidase, ARR3/6/9, CGA1, and SHY2 decreased. Continued bud outgrowth in wild-type was correlated with increased expression of genes encoding a SWEET transporter and cell wall invertases. The SWEET transporter may facilitate Suc unloading from the phloem to the apoplast where cell wall invertases generate monosaccharides for uptake and utilization to sustain bud outgrowth. Elevated expression of these genes was correlated with higher levels of cytokinin/ sugar signaling in growing buds of wild-type plants.

overall_design: RNA-seq libraries were prepared from tiller buds in the first leaf axil of phyB-1 and wild-type sorghum at 6 DAP (Days After Planting), 7 DAP and 8 DAP

first: Tesfamichael

last: Kebrom


title: Comparative analyses of DMRs

status: Public on Mar 29 2017

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: We clarify the role of the DNA methylation by using microarrays in the shoot apical meristem (SAM) of Populus × euramericana clones dormant or active and submitted to contrasted environments. This work aimed at characterizing: (i) the range of genetic and environmental variations of global DNA methylation and its correlation with biomass production, (ii) mitotically-conserved DMRs in winter-dormant SAM and (iii) common DMRs with their corresponding genes network and their biological role in phenotypic plasticity and stress memory toward natural environment conditions.

overall_design: For each conditions one sample was used


first: Lila

last: Vodkin

overall_design: High-throughput sequencing using Illumina HiSeq 2000 was performed on pigmented and non-pigmented parts of soybean seeds coat separately, with two biological replicates.

first: Young

last: Cho

middle: O


title: Hormonal and stress-response pathways regulate naked mole rat eusociality

city: ShenZhen

first: Jinmin

last: Lian

address: Building No.11, Beishan Industrial Zone, Yantian District

institute: BGI-ShenZhen

summary: Naked mole rats live in eusocial colonies where subordinates help a single dominant female and a few males to breed. We investigated the genome-wide regulatory mechanisms underlying their reproductive division of labor by examining brain and gonad transcriptomes and DNA-methylomes. Subtle expression differences were observed between brains of dominants and subordinates, but differentially expressed genes clustered consistently in a module with similar function for both sexes. Gonadotropin-releasing hormone (GNRH1) was central in this module and linked with stress-response genes such as neuropeptide Y and corticotrophin-releasing hormone. Breeder-subordinate modifications in DNA methylation were substantial in male brains and associated with the GNRH1 module. The GNRH1-regulated estrogen synthesis pathway was completely blocked in subordinate ovaries and sperm-related genes were significantly down-regulated in subordinate testes. Our results indicate that reproductive suppression is based on hormonal- and stress-related control by the dominant female, but with significant differences in molecular mechanisms between males and females.

overall_design: Naked mole rats were housed in our laboratory. Animals were sacrificed, and the tissues immediately frozen and stored in liquid nitrogen. Tissues were obtained from male (n = 2) and female (n = 2) breeders as well as male (n = 2) and female (n = 2) non-breeders (subordinates). We analyzed brains from all eight individuals separately, but female ovaries were only large enough for individual analysis in breeders, whereas subordinate ovaries were so small that 3–5 of them had to be pooled for gene expression analyses. The testes of breeding and non-breeding males were not visually different, but breeder status was known because these males had previously sired pups.

first: Bitao

last: Qiu

first: Qiye

last: Li

first: Pei

last: Zhang

first: Zongji

last: Wang

first: Lijun

last: Jin

first: Sanne

last: Nygaard

first: Yang

last: Zhou

first: Inge

last: Seim

first: Thomas

last: Park

first: Vadim

last: Gladyshev

first: Jacobus

last: Boomsma

first: Guojie


title: The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans (RNA-seq)

city: Cambridge

first: Juan

last: Alvarez-Dominguez

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Enhancer-derived RNAs are thought to contribute locally to their parent enhancers’ functions. Whether large domains of clustered enhancers (super-enhancers, SEs) also produce cis-acting RNAs, however, remains unclear. Unlike typical enhancers, SEs form large spans of robustly transcribed chromatin, amassing capped and polyadenylated RNAs that are sufficiently abundant to sustain trans functions. Here, we show that one such RNA, alncRNA-EC7/Bloodlinc, is transcribed from a SE of the erythroid membrane transporter SLC4A1/BAND3 but diffuses beyond this site. Bloodlinc localizes to trans-chromosomal loci encoding critical regulators/effectors of terminal erythropoiesis and directly binds chromatin-organizing and transcription factors, including the chromatin attachment factor HNRNPU. Inhibiting Bloodlinc or Hnrnpu compromises the terminal erythropoiesis gene program, blocking red cell production, whereas expressing Bloodlinc ectopically stimulates this program and can promote erythroblast proliferation and enucleation in the absence of differentiation stimuli. Thus, Bloodlinc represents a novel type of trans-acting SE RNA that potentiates red blood cell development.

overall_design: RNA-seq of erythroid progenitors purified from E14.5 mouse fetal livers, transduced with shRNAs or overexpression vectors, and collected after 24 hours of ex vivo differentiation, generated by deep sequencing using the Illumina HiSeq2000 platform.


title: Demethylated HSATII DNA and aberrant HSATII RNA foci act as sponges for epigenetic factors in cancer

city: Swarthmore

first: Dawn

last: Carone

state: PA

address: 500 College Ave

department: Biology

institute: Swarthmore College

summary: This study reveals that the millions of satellite II (HSATII) sequences in the human genome can bind and impact distribution of epigenetic regulators, and that this goes awry in cancer.  In many cancers master epigenetic factors form two-types of cancer-specific nuclear bodies, caused by locus-specific deregulation of HSATII DNA and RNA, respectively.  DNA demethylation at the 1q12 mega-satellite, common in cancer, causes PRC1 aggregation into prominent Cancer-Associated Polycomb (CAP) bodies. These loci remain silent, whereas HSATII loci in regions low in PRC1 become de-repressed, reflecting imbalanced distribution of UbH2A on these and other PcG-regulated loci.  Large nuclear foci of HSATII RNA form and sequester copious MeCP2 into Cancer-Associated Satellite Transcript (CAST) bodies.    Hence, HSATII DNA and RNA have an exceptional capacity to “sponge” epigenetic factors into abnormal nuclear bodies in cancer. Results support a new concept that demethylation of “junk” repeats can trigger further epigenetic compromise by compartmentalizing regulatory factors within nuclear structure.

overall_design: Examination of the distribution of ubiquityl Histone H2A in U2OS and Tig-1 fibroblast cells.  Input samples are included as controls.

first: Jeanne

last: Lawrence


title: Functional genomic analysis of the haploinsufficient tumor suppressor, CUX1

city: Chicago

first: Megan

middle: E.

last: McNerney

state: Illinois

address: 900 East 57th Street, KCBD 5128

department: Pathology

institute: The University of Chicago

summary: CUX1 is a homeodomain-containing transcription factor that is conserved, ubiquitous, and essential in vertebrates and invertebrates. CUX1 is mutated or deleted in high-risk myeloid neoplasms and solid tumors, resulting in haploinsufficiency and tumor growth.  Here we provide the first analysis of endogenous, whole genome, CUX1 DNA binding.  We demonstrate that CUX1 binds with transcriptional activators and cohesin at distal enhancers across three different human cell types.  Haploinsufficiency of CUX1 altered the expression of a large number of genes, including cell cycle regulators, with concomitant increased cellular proliferation.  Surprisingly, CUX1 occupancy decreased genome-wide in the haploinsufficient state, and binding site affinity did not correlate with differential gene expression.  Instead, differentially expressed genes had multiple, low-affinity CUX1 binding sites, consistent with an analog model for CUX1 gene regulation.  A machine-learning algorithm determined that chromatin accessibility, enhancer activity, and distance to the transcription start site are features of functional CUX1 DNA binding.  Moreover, CUX1 is enriched at sites of DNA looping, and these loops connect CUX1 to the promoters of target genes.  We propose that CUX1 is an analog transcription factor that regulates target genes through higher order genome architecture.

overall_design: RNA-seq and ChIP-seq of CUX1 in the wildtype and haploinsufficient states in K562 cells


title: Whole exome sequencing of murine derived intestinal tumour organoids [exome-capture]

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

summary:
DNA was isolated from Apcmin/+;KrasLSL-G12D/+;VillinCre;Lgr5DTReGFP (AKVL), Apcmin/+;KrasLSL-G12D/+;VillinCre;Lgr5DTReGFP;p53KO (AKVPL) and Apcmin/+;KrasLSL-G12D/+;VillinCre;Lgr5DTReGFP;p53KO,Smad4KO (AKVPSL) organoids as well as the spleen of the AKVL donor animal
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.

overall_design: Whole exome sequencing of murine derived intestinal organoids containing increasing number of CRC driver mutations was performed to identify potential mutations in coding regions that were introduced by off-target binding of the CRISPR-Cas9 complex.

first: Felipe

last: de Sousa e Melo

first: Antonina

last: Kurtova


title: Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [4tU-seq]

city: Boston

first: Peter

address: 10 Shattuck St

institute: Harvard Medical School

summary: Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. However, the genome-wide requirement for Spt5 in transcription has not been extensively studied. To address this issue, we have comprehensively analyzed the consequences of Spt5 depletion on transcription by RNAPII in Schizosaccharomyces pombe using four genome-wide approaches: ChIP-seq, NET-seq, 4tU-seq, and RNA-seq. Our results demonstrate that, in the absence of Spt5, RNAPII accumulates at a high level over the first ~500 bp of transcription units, suggesting that Spt5 is globally required to elongate past a barrier to transcription. This possibility is strongly supported by results showing that Spt5 is required for a normal level of RNA synthesis. In addition to these effects on sense-strand transcription, Spt5 depletion results in widespread convergent antisense transcription that initiates at approximately the same position as the sense-strand barrier. While the role of these antisense transcripts is unknown, the two that were tested control the distribution of RNAPII. Our results also show that Spt5 represses divergent antisense transcription, explaining why it has not been previously observed in S. pombe. Taken together, our results reveal a global and critical role for Spt5 in multiple classes of transcription by RNAPII.

overall_design: Three pairs of biological replicates before and during treatment to deplete Spt5 transcript and protein.

first: Kerstin

middle: C

last: Maier

first: Carina

last: Demel

first: Patrick

last: Cramer


title: The role of Lgr5 intestinal cancer stem cells in tumour initiation, progression and metastasis

type: Genome variation profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [k27ac]

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

institute: Institute of Molecular Biology, Mainz

summary: To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x105 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.

overall_design: Intestinal epithelial cells from two embryonic stages (E12.5 and E14.5), adult Lgr5+ ISCs and enterocytes were used. For each stage biological duplicates were analyzed.

first: Natalia

last: Soshnikova


title: Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [rnaseq]

summary: To follow the changes in the transcriptional programs accompanying the specification, maintenance and differentiation of the adult ISCs we sequenced whole transcriptomes of embryonic intestinal epithelium progenitors (at E12.5 and E14.5), adult ISCs and their differentiated progenies, the majority of which are absorptive enterocytes. EpCAM positive embryonic gut epithelium was isolated from dissected small intestines using fluorescence activated cell sorting (FACS). Adult ISCs were purified on the basis of GFP fluorescence from crypts of Lgr5GFP-Cre-ERT mice (Barker et al. 2007), whereas enterocytes (EpCAM+ CD45- CD31-) were isolated from villi.

overall_design: Intestinal epithelial cells from two embryonic stages (E12.5 and E14.5), adult Lgr5+ ISCs and enterocytes were used. For each stage biological triplicates were analyzed.


title: Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [k27m3]


title: Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [k4m3]

summary: To determine chromatin changes associated with ISCs specification we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using 2x10e5 FACS purified E12.5 or E14.5 embryonic intestinal epithelial cells, Lgr5+ adult ISCs and enterocytes.


title: Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [h2az]


title: Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells


title: Profiling of AKVPL derived tumors after depletion of Lgr5+ cells

summary:
RNA was isolated from fluorescence activated cell sorted (FACS) CD45 negative, EpCAM positive bulk tumor cells from Apcmin/+;KrasLSL-G12D/+;VillinCre; Lgr5DTReGFP;p53KO (AKVPL) intestinal tumours at different time points after a single dose of vehicle saline or diphteria toxin.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0011163

overall_design: Gene expression profiling of cells from AKVPL murine derived intestinal tumours after Diphteria Toxin (DT) mediated depletion of Lgr5+ cells


title: Profiling of AKVPL vs AKVPSL derived tumor cells  (Mouse)

summary:
RNA was isolated from fluorescence activated cell sorted (FACS) Lgr5-GFP+ and Lgr5-GFP- from aged matched subcutaneously implanted Apcmin/+;KrasLSL-G12D/+;VillinCre; Lgr5DTReGFP;p53KO  (AKVPL) and Apcmin/+;KrasLSL-G12D/+;VillinCre; Lgr5DTReGFP;p53KO;SMAD4KO (AKVPSL) intestinal tumours.
"SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0009421

overall_design: Gene expression profiling of Lgr5+ and Lgr5- tumour cells from AKVPL and AKVPSL murine derived intestinal tumours


title: Dynamic changes in chromatin states during specification and differentiation of adult intestinal stem cells [mbd]

summary: We assessed whether changes in DNA methylation were associated with the regulation of ISC signature genes. Methylated regions of DNA from whole genome were isolated using Methyl Binding Domain pull-down followed by sequencing (MBD-seq). The size of DNA fragments was between 120 to 170 bp, which provides a resolution at nucleosome level.


title: Transcriptomic and epigenetic responses to social challenge and their association with future behavior in honey bees (ChIP-Seq)

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: We studied behavioral, brain transcriptomic and epigenetic responses of honey bees to social challenge. Bees were exposed to two intruders at different intervals. The initial exposure caused two behavioral effects at the individual level: an increase in the intensity of aggression toward a second intruder at 30 and 60 minutes, and an increased probability of responding aggressively toward a second intruder that persisted for two hours. The shorter-lived response was associated with one pattern of gene expression in the mushroom bodies, highlighted by genes related to cytoskeleton remodeling. The longer-lived response was associated with a different pattern; highlighted by genes related to hormones, stress response and transcription factors. Histone profiling revealed few changes in chromatin accessibility in response to social challenge; most differentially expressed genes were “ready” to be activated. These results demonstrate how biological embedding of a social challenge involves changes in the neurogenomic state to influence future behavior.

overall_design: There are a total of 8 sets of pooled samples used in the H3K27Ac ChIP-Seq experiment equally balanced between 3 factors: 4 challenge (X) and 4 control (C); 4 30m and 4 120m; and 4 colony R41 and 4 colony R46.

first: Hagai

middle: Y

last: Shpigler

first: Emma

middle: E

last: Murdoch

first: Amy

last: Cash-Ahmed

first: Christopher

last: Seward

first: Laura

last: Sloofman

first: Sriram

last: Chandrasekaran

first: Saurabh

last: Sinha

first: Lisa

last: Stubbs

first: Gene

last: Robinson


title: Phagocytosis imprints heterogeneity in tissue macrophages

first: Manuel

middle: J

last: Gomez

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: Our study identifies the molecular heterogeneity of the populations of tissue resident macrophages that phagocytose circulating cells in the steady state.

overall_design: Phagocytic macrophages were isolated from bone marrow, large intestine and spleen based on the acquisition, or no acquisition, of DsRed fluorescence derived from phagocytosed DsRed-Tg. The phagocytosed cells originated from DsRed-Tg mice that were conjoined by parabiosis to non-fluorescent mice.

first: A

last: Hidalgo

first: N

middle: A

last: Gonzalez


title: Single-cell RNA-seq reveals hypothalamic cell diversity

first: Xiaoji

last: Wu

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: PCMM

institute: Boston Children's Hospital

summary: We performed single-cell RNA-seq of mouse hypothalamus to reveal the cell diversity of this region.

overall_design: Hypothalamus of mice (kept in normal condition or food deprivation) were dissected for single-cell RNA-seq through Drop-seq technique.

first: Renchao

last: Chen

first: Lan

last: Jiang

first: Yi

last: Zhang


title: Transcriptomic and epigenetic responses to social challenge and their association with future behavior in honey bees (RNA-Seq)

first: Michael

last: Saul

overall_design: There are a total of 180 samples equally balanced between 3 factors: 90 challenge (X) and 90 control (C); 60 30m, 60 60m, and 60 120m; 60 colony R02, 60 colony R03, and 60 colony R21. The control and experimental samples are paired. We excluded a total of 26 samples with a proportion of reads mapping to the Deformed Wing Virus (DWV) genome of ≥ 0.005.


title: Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [NET-seq]

first: Peter

last: Park

overall_design: Two pairs of biological replicates before and after treatment to deplete Spt5 transcript and protein. T0_I was taken from a separate experiment (1) because the other T0 replicate in experiment 2 showed high rate of PCR duplication.

first: Ameet

last: Shetty

first: Scott

middle: P

last: Kallgren

first: Burak

last: Alver

first: Fred

last: Winston


title: Transcriptomic and epigenetic responses to social challenge and their association with future behavior in honey bees

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


title: Maternal obesity induced mouse embryonic defects derive from Stella insufficiency in oocytes

status: Public on Mar 28 2017

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: In order to obtain genome-wide profiles, base-resolution methylomes of zygotes were generated using the bisulfite sequencing (BS-seq) method for small samples. We find that  global loss of DNA methylation during zygotic development in HFD mice. A total of 412 DMRs were identified, of which 294 were hypomethylated (hypo-DMRs; 71.4%) and 118 were hypermethylated (hyper-DMRs; 28.6%) (Fig. 6A and 6B), showing a predominance of hypo-DMRs. Furthermore, we show that hyper-DMRs are significantly depleted from CGI, but enriched in short interspersed elements (SINEs) and non-CGI regions. Strikingly, hypo-DMRs are specifically depleted from SINEs, with a concurrent enrichment in DNA transposons.

overall_design: Examination of DNA methylome in zygotes from normal and HFD mice.

first: Qiang

last: Wang

first: Chao

last: Ren


title: Whole genome sequencing of murine derived intestinal tumour organoids

first: Robert

last: Piskol

overall_design: Low-coverage (5X) whole genome sequencing of murine derived intestinal organoids containing increasing number of CRC driver mutations

first: Felipe

last: de Sousa e Melo

first: Antonina

last: Kurtova


title: Flicr, a long noncoding RNA modulating Foxp3 expression and autoimmunity (ATAC-Seq)

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

summary: ATAC-seq profiles of Tregs isolated from spleen and LN in Flicr WT and KO mice

overall_design: DAPI-CD4+TCRb+ CD25hi (top 50%) Tregs were single sorted from the spleen and LN  of male NOD mice and ATAC-seq was performed

first: David

last: Zemmour

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Enhancer and transcriptomic changes in skeletal muscles in response to physical exercise

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

summary: We address the transcriptomic changes in skeletal muscle after bouts of exercise

overall_design: We performed RNA-seq and GRO-seq in mouse after treadmill running in both WT and HDAC3-depleted skeletal muscles.

first: Zheng

last: Sun

first: Manashree

last: Damle


title: Histone acetyltransferase OsGCN5 palys an important role in establishing programs of cell proliferation of crown root meristem

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: Shoot-borne crown roots are the major root system in cereals. Previous work has shown that the Wuschel-related homeobox gene WOX11 is necessary and sufficient to promote rice crown root emergence and elongation. Here, we show that WOX11 recruits the ADA2-GCN5 histone acetyltransferase (HAT) module to activate downstream target genes in crown root meristem. OsGCN5 and OsADA2 are highly expressed in root meristem. Knockdown of OsGCN5 and OsADA2 affects crown root initiation and elongation. Here we sought to find the downstream genes of OsGCN5 in rice crown root tip.

overall_design: Genome-wide analysis of root transcriptome of OsGCN5 RNAi and corresponding wild type.

first: S

last: Zhou

first: D

middle: X


title: PyMT 4 stages tumor progression RNA-seq

city: bronx

first: ying

last: cai

state: New York

address: 1300 morris park ave

institute: Albert Einstein College of Medicine

summary: We sequenced mammary gland samples of MMTV-PyMT mouse from 4 stages (hyperplasia at week 6, adenoma/MIN at week 8, early carcinoma at week 10, and late carcinoma with lung metastasis at week 12) during tumor progression.

overall_design: We sacrificed 3 PyMT mice and 3 FVB control mice at each of the 4 stages, extracted RNA and performed sequencing.

first: Ying

last: Cai

first: Ruben

last: Nogales-Cadenas

first: Quanwei

last: Zhang

first: Jhih-rong

last: Lin

first: Wen

first: Kelly

last: O'Brien

first: Zhengdong