title: RNA Seq analysis in flatworm following 6, 12, or 18 day treatment with RNAi against Pax5, Sox8, or Zfp1, relative to unc22 to identify transcriptional targets.

summary: Epidermis is essential for animal survival, providing both a protective barrier and cellular sensor to the external environment. Interestingly, the epidermes of different species show broad morphological and functional diversity yet it is unclear whether this diversity came from modification of an existing gene regulatory network or de novo innovation of new genes. Here we identify the transcriptional regulators underlying the differentiation program of planarian epidermal lineage. We classify Smed-p53 as the most upstream molecule in this transcriptional cascade, suggesting a potentially conserved role for this gene in epidermal differentiation similar to TP63 in vertebrates. Moreover, we find that homologs of Sox and Pax family transcription factors, Smed-soxP-3 and Smed-pax-5, act cooperatively to activate the expression of epidermal markers. Together, these data show that planarian epidermal differentiation is regulated by a combination of conserved elements (p53/p63), recruitment of a non-conventional transcription module (soxP-3/pax-5), and novel genes (prog); they also suggest that specialized adpatations, such as epidermal mucus-secretion, arise from complex changes to gene networks.

overall_design: Examine gene expression profiles of adult flatworms after 6, 12, or 18 days of treatment with RNAi against either Pax5, Sox8, Zfp, or an unc22 non-targeting control. The experiment was performed in quadruplicate resulting in 48 samples.


title: Transcriptome analysis of 6 hours post fertilization mecp2-null versus wild type zebrafish embryos

status: Public on Sep 01 2016

city: La Jolla

first: Michiel

last: van der Vaart

state: CA

address: 9500 Gilman Dr

country: USA

institute: UCSD

type: Expression profiling by high throughput sequencing

summary: RNA sequencing was performed on RNA isolated from groups of 6 hpf wild type and mecp2-null embryos (n=3 biological replicates per condition with 30 embryos pooled per replicate). DESeq2 analysis was performed using https://usegalaxy.org/

overall_design: Whole embryo mRNA profile of 30 pooled mecp2-null or wild type 6 hpf zebrafish embryos, in triplicate, using the Illumina HiSeq4000 platform

first: David

last: Traver


title: Detection of metabolic activity in dormant conidia of Aspergillus niger and use of growth inhibitors to study transient developmental changes.

city: Nottingham

first: Michaela

last: Novodvorska

address: University Park

department: School of Life Sciences

country: United Kingdom

institute: Nottingham University

summary: The early stages of development of Aspergillus niger conidia during outgrowth were explored by combining genome-wide gene expression analysis (RNAseq), proteomics, Warburg manometry and uptake studies. Resting conidia were shown to be metabolically active as low levels of oxygen uptake and the generation of carbon dioxide were detected, suggesting that low-level respiratory metabolism occurs in conidia for maintenance. Upon triggering of spore germination, generation of CO2 started immediately. For a short period, which coincided with mobilisation of the intracellular polyol, trehalose, there was no increase in uptake of O2 indicating that trehalose was metabolised by fermentation. Data from genome-wide mRNA profiling showed the presence of transcripts associated with fermentative and respiratory metabolism in resting conidia. Following triggering of conidial outgrowth, there was a clear switch to respiration after 25 min, confirmed by cyanide inhibition. No effect of SHAM on respiration suggests electron flow via cytochrome c oxidase. Glucose entry into spores was not detectable before 1 h after triggering germination. Sub-inhibitory levels of sorbic acid delayed both the turnover of trehalose and the uptake of glucose. Oxygen uptake was also then inhibited, delaying the onset of respiration and extending the period of fermentation.

overall_design: Duplicate samples from each time point: dormant conidia MN_T0 (MN_T0A + MN_T0B), conidia germinated for one hour MN_T1 (T1 MN_T1A + MN_T1B) and conidia germinated for one hour in the presence of 1mM of sorbic acid MN_T1SA (MN_T1SA_A + MN_T1SA_B)

first: Malcolm

last: Stratford

first: Martin

middle: J

last: Blythe

first: Raymond

last: Wilson

first: Richard

middle: G

last: Beniston

middle: B

last: Archer


title: A Scalable Epitope Tagging Approach for High Throughput ChIP-seq Analysis

city: Kowloon

first: Jian

last: Yan

address: 83 Tat Chee Ave

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq comparison between CRISPR editing cells using epitope antibody and non-editing cells using endogeneous TF antibody

first: Bing

last: Ren

first: Xiong

last: Xiong

first: Huiming

last: Zhao


title: A highly sensitive and robust method for genome-wide 5hmC profiling of rare cell populations

city: Chicago

first: Dali

last: Han

state: IL

address: 5801 South Ellis Avenue

department: Department of Chemisty

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

summary: Investigations of 5-hydroxymethylcytosine (5hmC) in biologically and clinically samples and models with low cell numbers have been hampered by the low sensitivity and reproducibility using current 5hmC mapping approaches. Here, we develop a selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells (nano-hmC-Seal). Using this technology, we profiled the dynamics of 5hmC across different stages of mouse hematopoietic differentiation. Additionally, applying nano-hmC-Seal to the hematopoietic multipotent progenitor cells in an acute myeloid leukemia (AML) mouse model, we identified leukemia-specific, differentially hydroxymethylated regions that harbor previously reported and as-yet-unidentified functionally relevant factors. The change of 5hmC patterns in AML strongly correlates with the altered gene expression on a global scale. Together, our new approach offers a highly sensitive and robust method to study and detect DNA methylation dynamics from in vivo model and clinical samples.

overall_design: Selective 5hmC chemical labeling approach using tagmentation-based library preparation in order to profile nanogram levels of 5hmC isolated from ~1,000 cells

first: Xingyu

last: Lu

first: Alan

middle: H

last: Shih

first: Ross

middle: L

last: Levine

first: Chuan

last: He


title: High conservation in transcriptomic and proteomic response of white sturgeon to equipotent concentrations of 2,3,7,8-TCDD, PCB 77, and benzo[a]pyrene

city: Saskatoon

first: Jon

middle: A

last: Doering

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology Centre

country: Canada

institute: University of Saskatchewan

summary: Adverse effects associated with exposure to dioxin-like compounds (DLCs) are mediated primarily through activation of the aryl hydrocarbon receptor (AHR). However, little is known about the cascades of events that link activation of the AHR to apical adverse effects. Therefore, this study used high-throughput, next-generation molecular tools to investigate similarities and differences in whole transcriptome and whole proteome responses to equipotent concentrations of three agonists of the AHR, 2,3,7,8-TCDD, PCB 77, and benzo[a]pyrene, in livers of a non-model fish, the white sturgeon (Acipenser transmontanus). A total of 926 and 658 unique transcripts were up- and down-regulated, respectively, by one or more of the three chemicals. Of the transcripts shared by responses to all three chemicals, 85% of up-regulated transcripts and 75% of down-regulated transcripts had the same magnitude of response. A total of 290 and 110 unique proteins were up- and down-regulated, respectively, by one or more of the three chemicals. Of the proteins shared by responses to all three chemicals, 70% of up-regulated proteins and 48% of down-regulated proteins had the same magnitude of response. Among treatments there was 68% similarity between the global transcriptome and global proteome. Pathway analysis revealed that perturbed physiological processes were indistinguishable between equipotent concentrations of the three chemicals. The results of this study contribute towards more completely describing adverse outcome pathways associated with activation of the AHR.

overall_design: Compared transcriptomic as well as proteomic responses to 3 different agonists of the aryl hydrocarbon receptor (AHR) at equipotent doses.

first: Song

last: Tang

first: Hui

last: Peng

first: Bryanna

last: Eisner

first: Jianxian

last: Sun

first: John

last: Giesy

first: Steve

last: Wiseman

first: Markus

last: Hecker

first: Sarah

last: Patterson

first: Jenna

last: Zee

first: Shawn

last: Beitel


title: Mouse embryonic lung FOXF1 ChIP-seq analysis

city: Houston

first: Pawel

last: Stankiewicz

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: FOXF1 targets in embryonic day 18.5 mouse lungs were determined using FOXF1 immunoprecipitation followed by sequencing.

overall_design: FOXF1 binding sites in two biological replicates of pooled E18.5 wildtype mouse lungs (n=3) were to a 2% input control sample.

first: Avinash

last: Dharmadhikari

first: Krzysztof

last: Gogolewski

first: Anna

last: Gambin


title: Integrative genomics outlines a biphasic glucose response and a ChREBP-RORγ axis regulating proliferation in β-cells

status: Public on Sep 06 2016

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Glucose is an important regulator of pancreatic β-cell function. In addition to the acute stimulation of insulin secretion, glucose stimulates long-term adaptive changes in gene expression that can either promote or antagonize the proliferative potential and function of β-cells. The glucose-sensing transcription factor carbohydrate response element binding protein (ChREBP) has been shown to promote both β-cell proliferation and dysfunction; however, the molecular mechanisms underlying these pleiotropic effects of ChREBP and glucose are not well understood. Here, we have generated time-resolved profiles of enhancer and transcriptional activity in response to glucose in the INS-1E pancreatic β-cell line. Our data outline a biphasic response with a first wave during which metabolic genes are activated, and a second wave where cell cycle genes are induced and β-cell identity genes are repressed. We show that ChREBP directly activates first wave genes, whereas repression and activation of second wave genes by ChREBP is indirect. By integrating motif enrichment within late-regulated enhancers with expression profiles of the associated transcription factors, we identify multiple putative regulators of the second wave, including RAR-related orphan receptor (ROR) γ, which we demonstrate is a novel direct ChREBP target gene. Importantly, we show that RORγ activity is necessary for full glucose-induced proliferation of both INS-1E and primary rat β-cells.

overall_design: Genome-wide assesment of the  transcriptional response to glucose in INS-1E β-cells using RNA- ChIP- and DNase-seq

first: Søren

middle: F

last: Schmidt


title: The global tissue-specific RNA transcription dysregulation effects in the third generation after embryonic exposure to the widely used herbicide atrazine are mediated via inherited histone trimethylation [RNA-Seq]

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

country: France

institute: Université de Rennes 1

summary: We report the effect of histone trimethylation on transgenerational inheritance. We exposed outbred pregnant CD1 mice to herbicide atrazine and progeny of these mice were crossed for a three generations. First (F1) and third (F3) generation of males were analyzed by using genome-wide sequencing analysis. We analyzed the RNA expression level in liver, brain (hypothalamus) and testis in F3 generation males. The testis samples of F1 and F3 generations’ males were analyzed by ChIP-seq using antibody against H3K4me3. We find that subset of H3K4me3 marks altered in F1 was also detected in F3 males progeny. This subset is enriched in genes of stem cell differentiation. We found that embryonic exposure to atrazine globally affects the RNA transcription in testis: we found the tissue-specific transcription deregulation, increased number transcripts with altered transcription start site, alternatively spliced and polyadenylated mRNA transcripts in a F3 generation males. This study provides a new knowledge of mechanisms of transgenerational inheritance exposed to toxic compounds.

overall_design: RNA-seq performed from testis, liver and hypothalamus tissues of F3  generation males in three biological replicates per condition.

last: Hao

first: Fatima

last: Smagulova


title: ChIP-seq. analysis of pan-histone 3 acetylation in Romidepsin treated TCam-2

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Universitätsstr. 1

department: Urology

country: Germany

institute: University Hospital Düsseldorf

summary: ChIP-seq. analysis of TCam-2 16 h after 10 nanomolar Romidepsin application. DMSO treated cells were used as controls. For ChIP, an antibody against histone H3 pan-acetylation was used. These data are part of the article 'The Histone Deacetylase Inhibitor Romidepsin Efficiently Targets Cisplatin-resistant Germ Cell Cancer Cells via Downregulation of the SWI/SNF-Complex Member ARID1A' (Nettersheim et al., 2016).

overall_design: TCam-2 cells treated for 16h with romidepsin or the solvent were fixed by formaldehyde solution and further processed by Active Motif, including DNA shearing by sonication, chromatin-immunoprecipitaion, library generation and sequencing (NextSeq 500, Illumina). Pooled input DNA of each sample including spike-in Drosophila DNA was used as controls and for normalization. The 75-nt sequence reads were mapped against the genome using BWA algorithm. Duplicate reads were removed. Only peaks that align with no more than 2 mismatches and map uniquely to the genome were used for further analysis. Intervals / peaks were identified by the MACS peak finding algorithm (cutoff p-value 1x10-7) including ENCODE blacklist filtering

first: Hubert

last: Schorle


title: Conserved imprinting associated with unique epigenetic signatures in the Arabidopsis genus

city: Cambridge

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: In plants, imprinted gene expression occurs in endosperm seed tissue and can be associated with differential DNA methylation between maternal and paternal alleles. Imprinting is theorized to have been selected for because of conflict between parental genomes in offspring, but most studies of imprinting have been conducted in Arabidopsis thaliana, an inbred primarily self-fertilizing species that should have limited parental conflict. We examined embryo and endosperm allele-specific expression and DNA methylation genome-wide in the wild outcrossing species Arabidopsis lyrata. Here we show that the majority of A. lyrata imprinted genes exhibit parentally-biased expression in A. thaliana, suggesting that there is evolutionary conservation in gene imprinting. Surprisingly, we discovered substantial interspecies differences in methylation features associated with paternally expressed imprinted genes (PEGs). Unlike A. thaliana, the maternal allele of many A. lyrata PEGs was hypermethylated in the CHG context. Increased maternal allele CHG methylation was associated with increased expression bias in favor of the paternal allele. We propose that CHG methylation maintains or reinforces repression of maternal alleles of PEGs. These data suggest that while the genes subject to imprinting are largely conserved, there is flexibility in the epigenetic mechanisms employed between closely related species to maintain monoallelic expression. This supports the idea that imprinting of specific genes is a functional phenomenon, and not simply a byproduct of seed epigenomic reprogramming.

overall_design: Examination of total gene expression, parent-of-origin specific allelic bias, or DNA methylation in  embryo, endosperm, flower bud or seedcoat tissue from Arabidopsis lyrata accessions MN47 (MN), Karhumaki (Kar or KA), and crosses between them. High-throughput Illumina poly-A-selected mRNA-seq was used to identify imprinted genes in A. lyrata, and high-throughput Illumina whole genome bisulfite-sequencing was used to examine DNA methylation. mRNA-seq samples are designated MMxFF_T# where MM is the mother of the cross (either MN for MN47 or KA for Kar), FF is the father, T is the tissue (E for embryo, N for endosperm, S for seedcoat, b for buds), and # is the replicate numbers.  Samples obtained from bisulfite sequencing follow the same naming but have suffix _BS and indicate cytosine methylation context (CpG, CHG, or CHH). For KAxMN bisulfite sequencing, additional files MMxFF_T#_BS_P_C.txt follow the same naming scheme but contain context-specific methylation data (C) from reads that mapped preferentially to one parent strain (P).

first: Maja

last: Klosinska

first: Colette

last: Picard


title: Compromised oocyte quality and assisted reproduction contribute to sex-specific effects on offspring outcomes and epigenetic patterning

city: Montreal

first: Jacquetta

last: Trasler

state: Quebec

address: 1001 Decarie Boul, Block E, ES1.4380

department: Pharmacology & Therapeutics; Human Genetics

institute: McGill University

summary: Clinical studies have revealed an increased incidence of growth and genomic imprinting disorders in children conceived using Assisted Reproductive Technologies (ART), and aberrant DNA methylation has been implicated. We propose that compromised oocyte quality associated with female infertility may make embryos more susceptible to the induction of epigenetic defects by ART. DNA methylation patterns in the preimplantation embryo are dependent on the oocyte-specific DNA methyltransferase 1o (DNMT1o), levels of which are decreased in mature oocytes of aging females. Here, we assessed the effects of maternal deficiency in DNMT1o (Dnmt1∆1o/+) in combination with superovulation and embryo transfer on offspring DNA methylation and development. We demonstrated a significant increase in the rates of morphological abnormalities in offspring collected from Dnmt1∆1o/+ females only when combined with ART. Together, maternal oocyte Dnmt1o deficiency and ART resulted in an accentuation of placental imprinting defects and the induction of genome-wide DNA methylation alterations, which were exacerbated in the placenta compared to the embryo. Significant sex-specific trends were also apparent, with a preponderance of DNA hypomethylation in females. Among genic regions affected, a significant enrichment for neurodevelopmental pathways was observed. Taken together, our results demonstrate that oocyte DNMT1o-deficiency exacerbates genome-wide DNA methylation abnormalities induced by ARTs in a sex-specific manner and plays a role in mediating poor embryonic outcome.

overall_design: Reduced representation bisulfite sequencing of E11.5 embryonic tissue (whole embryo and placenta) obtained from naturally mating, or ART matings wildtype or heterozygote for Dnmt1o

first: L

last: Whidden

first: J

last: Martel

first: S

last: Rahimi

middle: R

last: Chaillet

first: D

last: Chan

middle: M


title: A network including TGFβ/Smad4, Gata2 and p57 regulates proliferation of mouse hematopoietic stem/progenitor cells

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

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

overall_design: Refer to individual Series


title: Targeting Non-proteolytic Protein Ubiquitination for the Treatment of Diffuse Large B Cell Lymphoma (Affy SNP6.0 Arrays)

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

summary: Chronic active B cell receptor (BCR) signaling, a hallmark of the ABC subtype of diffuse large B cell lymphoma (DLBCL), engages the CARD11-MALT1-BCL10 (CBM) adapter complex to activates IkappaB kinase (IKK) and the classical NF-kappaB pathway. Here we show that the CBM complex includes the E3 ubiquitin ligases cIAP1 and cIAP2, which are essential mediators of BCR-dependent NF-kappaB activity in ABC DLBCL. cIAP1/2 attach K63-linked polyubiquitin chains on themselves and on BCL10, resulting in the recruitment of IKK and the linear ubiquitin chain ligase LUBAC, which is essential for IKK activation. SMAC mimetic drugs target cIAP1/2 for destruction, and consequently suppress NF-kappaB and selectively kill BCR-dependent ABC DLBCL lines, supporting their clinical evaluation in patients with ABC DLBCL.

overall_design:
Four ABC DLBCL tumor biopsy samples and one ABC DLBCL cell line (YM) (n=5) were analysed for copy number gains using the Affymetrix Genome-Wide Human SNP 6.0 Array.

CEL files are being made available through dbGaP


title: A network including TGFβ/Smad4, Gata2 and p57 regulates proliferation of mouse hematopoietic stem/progenitor cells [ChIP-seq]

summary:
Transforming growth factor-β (TGFβ) is a potent inhibitor of hematopoietic stem cell (HSC) proliferation. However, the precise mechanism for this effect is unknown. Here, we have identified the transcription factor Gata2, previously described as an important regulator of HSC function, as an early and direct target gene for TGFβ-induced Smad signaling in hematopoietic stem and progenitor cells (HSPCs). Interestingly, TGFβ-induced Gata2 upregulation is critical for subsequent transcriptional activation of the TGFβ signaling effector molecule p57 and resulting growth arrest of HSPCs. Importantly, both Gata2 and p57 are abundantly expressed in freshly isolated highly purified HSCs, demonstrating the relevance of this circuit in HSC regulation within the HSC niche. Our results connect key molecules involved in HSC self-renewal and reveal a functionally relevant network regulating proliferation of primitive hematopoietic cells.
To identify TGFβ targets downstream of Gata2, we carried out a ChIP-Seq experiment on TGFβ-induced Lhx2 cells. Interestingly, there was a large overlap between the GATA2-bound genes and genes differentially expressed after 2h TGFβ induction.

overall_design: One sample of 1x10^8 cells (treated with 10 ng/ml TGFβ for 2h) was sequenced.

first: Matilda

last: Billing

first: Emma

last: Rorby

first: Alex

last: Tipping

first: John

last: Brown

first: Marjo

last: Salminen

first: Goran

last: Karlsson

first: Tariq

last: Enver

first: Stefan


title: Alterations to the Synaptic Transcriptome in Response to Ethanol-Induced Behavioral Sensitization in DBA/2J Mice

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

summary: Alcoholism is a complex neurological disorder characterized by loss of control in limiting intake, and progressive compulsion to seek and consume ethanol. Prior studies have suggested that the characteristic behaviors associated with escalation of drug use are caused, at least in part, by ethanol-evoked changes in gene expression affecting synaptic plasticity. Implicit in this hypothesis is a dependence on new protein synthesis and remodeling at the synapse. It is well established that mRNA can be transported to neuronal distal processes, where it can undergo localized translation that is regulated in a spatially restricted manner in response to stimulation. It is unknown whether such modulation of the synaptic transcriptome might contribute to ethanol-induced synaptic plasticity. Using ethanol-induced behavioral sensitization as a model of neuroplasticity, here we investigated whether repeated exposure to ethanol altered the synaptic transcriptome, contributing to synaptic plasticity underlying a subsequent increase in the ethanol-evoked locomotor response. A synaptoneurosome preparation was utilized to enrich for RNAs trafficked to the synapse versus the proximal cellular fraction. Two complementary methods of genomic profiling, RNA-Seq and microarrays, were used to survey the synaptic transcriptome of DBA/2J mice subjected to ethanol-induced behavioral sensitization. Strikingly, a large number of genes regulated by acute ethanol showed adaptation to repeated ethanol exposure with sensitization. Genomic profiling showed distinct functional classes in RNA found to be enriched in the synaptoneurosome faction, consistent with their role in synaptic function. A subset of ethanol-responsive genes significantly enriched at the synapse were related to biological functions such as protein folding and extra-cellular matrix components, suggesting a role for local regulation of synaptic protein function by ethanol. In contrast, RNA classes regulated by ethanol in the cell soma included an over-abundance of RNA-binding and trafficking proteins, perhaps reflecting increased demand for dendritic RNA localization. These experiments document that both acute and repeated ethanol produce specific alterations in the complement of RNA at the synapse and lay the foundation for further investigations into the role of the synaptic transcriptome in behavioral adaptations to ethanol.

overall_design: 24 samples were analyzed from 3 treatment groups and 2 cell fractions with 4 biological replicates for each treatment/cell fraction.Cell fractionation was carried out on tissue from a frontal pole dissection of DBA2/J mice, isolating a cytosolic (S2) and synaptoneurosomal (P2) fraction. Treatment groups describe chronic treatment (10 daily injections) and treatment used on test day (single injeciion), producing saline-saline (SS), saline-ethanol (SE) and ethanol-ethanol (EE) groups. Analysis of RNA-seq compared similar treatments across cell fractions or different treatments within a cell fraction.

first: Megan

last: O'Brien


title: Chromatin immunoprecipitation and RNA-seq analysis in purified quiescent yeast cells to identify the genomic RNA polymerase II and histone H3 methylation occupancy profiles and the quiescent cell transcriptome.

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: A defining characteristic of quiescent cells is their low level of gene activity compared to growing cells.  Using a yeast model for cellular quiescence, we compared the genome-wide profiles of multiple histone modifications between growing and quiescent cells, and correlated these profiles with the presence of RNA polymerase II and its transcripts.  Quiescent cells retained several forms of histone methylation normally associated with transcriptionally active chromatin and had many transcripts in common with growing cells. Quiescent cells also contained high levels of RNA polymerase II, but only low levels of the canonical initiating and elongating forms of the polymerase.  The data suggest that the transcript and histone methylation marks in quiescent cells were either inherited from growing cells or established early during the development of quiescence and then retained in this non-growing cell population.  This might ensure that quiescent cells can rapidly adapt to a changing environment to resume growth.

overall_design: RNA-seq analysis was performed in yeast Log-phase cells and purified Quiescent yeast cells and the transcriptomes in each were compared. The RNA data was correlated with genomic RNA polymerase II and histone H3 methylation occupancy profiles in the log and quiescent cells.

first: Conor

middle: P

last: Young

first: Cory

last: Hillyer

first: Darren

last: Fitzpatrick

first: Nikifor

last: Konstantinov

first: Jacqueline

middle: S

last: Welty

first: Scott

last: Ness

first: Margaret

last: Werner-Washburne

first: Alastair

last: Fleming

first: Mary

last: Osley


title: Tumor hypoxia causes DNA hypermethylation by reducing TET activity (TAB-Seq)

city: Heverlee

first: Bernard

last: thienpont

address: Herestraat 49

department: Vesalius Research Center

country: Belgium

institute: VIB

summary: Hypermethylation of tumor suppressor gene (TSG) promoters confers growth advantages to cancer cells, but how these changes arise is poorly understood. Here, we report that tumor hypoxia reduces the activity of oxygen-dependent TET enzymes, which catalyze DNA de-methylation through 5-methylcytosine oxidation. This occurs independently of hypoxia-associated alterations in TET gene expression, basal metabolism, HIF activity or nuclear reactive oxygen species, but directly depends on oxygen shortage. Hypoxia-induced loss of TET activity increases hypermethylation at gene promoters in vitro, while also in patients, gene promoters are markedly more methylated in hypoxic than normoxic tumors. Affected genes are frequently involved in DNA repair, cell cycle regulation, angiogenesis and metastasis, indicating cellular selection of hypermethylation events. Overall, up to 50% of the tumor-associated hypermethylation is ascribable to hypoxia across various cancer types. Accordingly, spontaneous murine breast tumors become hypermethylated when rendered hypoxic through vessel pruning, whereas vessel normalisation rescues this effect. Tumor hypoxia thus acts as a novel regulator underlying DNA methylation.

overall_design: Shallow tet-assisted-bisulfite-sequencing of tumors with a normalized or truncated vasculature to assess global differences in 5hmC levels


title: Dynamic and specificity of CUC transcription factors during leaf development : Towards a high-resolution Gene Regulatory Network model

city: evry

first: remi

last: bounon

state: essonne

address: 2 avenue Gaston Crémieux

department: BAP

institute: INRA

summary:
Define the regulatory network involved in leaf development
3-weeks old plants grown in short condition from each genotype (cuc2-3, WT and CUC2gm-4 lines) were dissected and meristem tissue and young leaf primordia were collected and snap frozen in liquid nitrogen. Total RNA were extracted using miRVANA kit following manufacturers instructions. 3 biological repeats were performed for each genotype.

overall_design: mRNA seq on wild-type Col0 and two CUC mutants knock out.

first: Arnaud

last: Nicolas

first: Sandrine

last: Balzergue

first: Rémi

last: Bounon

first: Véronique

last: Brunaud

last: Zakia

first: Etienne

last: Delannoy

first: Marie-Laure

last: Martin-Magniette


title: Tumor hypoxia causes DNA hypermethylation by reducing TET activity (Bisulfite-Seq)

overall_design: bisulfite-seq of MCF7 cells grown under hypoxic and normoxic conditions. Submission includes data on 2 independent SeqCap Epi-enriched BSseq experiments, each containing a biological replicate grown under hypoxic conditions (0.5% oxygen), and a replicates grown under normoxic conditions.


title: Targeting Non-proteolytic Protein Ubiquitination for the Treatment of Diffuse Large B Cell Lymphoma (Agilent Arrays)

first: Louis

last: Staudt

overall_design: Samples from four ABC DLBCL cell lines (HBL1, TMD8, OCILY3, and OCILY10) were exposed to 2.5 uM birinapant for 2, 4, 6, and 24 hours (n=16). Samples from 2 ABC DLBCL cell lines (HBL1 and TMD8) were transduced with shRNA and induced with doxycycline for 3 and 4 days (n=4).


title: Histone gene regulation in normal and tumor cells

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki


title: Construction and characterization of synthetic microRNA cluster for multiplex RNA interference in mammalian cells

city: Beijing

first: Zhen

last: Xie

state: Beijing

address: Qinghua yuan street, Haidian district

department: Department of Automation

country: China

institute: Tsinghua University

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA interference (RNAi) technology is widely used in basic and translational research. By mimicking natural primary microRNA (pri-miRNA) cluster, multiple engineered hairpins can be transcribed as a single transcript from the same Pol-II promoter, enabling multiplex RNAi in mammalian cells 1-5. However, constructing synthetic miRNA cluster is still time-consuming, and the processing and function of miRNA cluster are incompletely understood. Here, we identified a miRNA precursor architecture that allowed precise miRNA maturation. We established a hierarchical cloning method for efficient construction of synthetic miRNA cluster harboring up to 18 miRNA precursors. We demonstrated that maturation and function of individual miRNA precursors were independent on their positions in the cluster. We then analyzed the integration efficiency of miRNA clusters with varying number of miRNA precursors by using CRISPR/Cas9 mediated integration, piggyBac transposon system, and lentiviral system. This synthetic miRNA cluster system provides an important tool for multiplex RNAi in mammalian cells.

overall_design: Different kinds of synthetic miRNAs or miRNA clusters, including the same synthetic miRNA precursor embedded in a series of derivative backbones, 18 synthetic miRNA precursors, miRNA precursors with various stem lengths and miRNA clusters carrying different numbers of different pri-miRNA hairpins, were expressed in HEK293 cells. The microRNA maturation pattern of individual miRNA precursors was detected by small RNA sequencing.

first: Tingting

last: Wang


title: Cell type-specific chromatin states differentially prime squamous cell carcinoma tumor-initiating cells for epithelial to mesenchymal transition [ATAC-seq]

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

institute: ULB

summary: Epithelial to mesenchymal transition (EMT) in cancer cells has been associated with metastasis, stemness and resistance to therapy. The reason why some tumors undergo EMT and other not might reflect intrinsic properties of their cell of origin, although this possibility is largely unexplored. By targeting the same oncogenic mutations to discrete skin compartments, we show cell type-specific chromatin and transcriptional states differentially prime tumors to EMT.  Squamous cell carcinomas (SCCs) derived from intrafollicular epidermis (IFE) are generally well-differentiated, while hair follicle (HF) stem cell-derived SCCs frequently exhibit EMT, efficiently form secondary tumors, and possess increased metastatic potential.  Transcriptional and epigenomic profiling revealed IFE and HF tumor-initiating cells possess distinct chromatin landscapes and gene regulatory networks associated with tumorigenesis and EMT that correlate with accessibility of key epithelial and EMT transcription factor binding sites.  These findings highlight the importance of chromatin states and transcriptional priming in dictating tumor phenotypes and EMT.

overall_design: Accessible chromatin regions were profiled using ATAC-seq, enriched peak regions were used to infer transcription factor binding sites.

first: M

last: Latil

first: B

last: Beck

first: S

last: Boumhadi

first: L

first: A

last: Brisebarre

first: R

last: Yi

first: C


title: microRNA profiling of Sprague Dawley organs

city: Indianapolis

first: Aaron

middle: Thomas

last: Smith

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly

summary: We performed deep sequencing of the miRNAs present in ~20 toxicologically relevant tissues in Sprague Dawley rats and used three independent analysis of the data to determine which miRNAs are tissue specific and tissue enriched.

overall_design: We performed deep sequencing of miRNAs in 21 organs from 5 male Sprague Dawley rats and 23 organs from 5 female Sprague Dawley rats.

middle: T

first: Craig

last: Fisher

first: John

middle: N

last: Calley


title: Genome-wide analysis of enhancers in Drosophila DV patterning

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

summary:
The submitted data have been utilized in the following two papers:

"Drosophila poised enhancers are generated during tissue patterning with the help of repression" (Koenecke et al 2016, Genome Research):
Histone modifications are frequently used as markers for enhancer states, but how to interpret enhancer states in the context of embryonic development is not clear. The poised enhancer signature, involving H3K4me1 and low levels of H3K27ac, has been reported to mark inactive enhancers that are poised for future activation. However, future activation is not always observed and alternative reasons for the widespread occurrence of this enhancer signature have not been investigated. By analyzing enhancers during dorsal-ventral (DV) axis formation in the Drosophila embryo, we find that the poised enhancer signature is specifically generated during patterning in the tissue where the enhancers are not induced, including at enhancers that are known to be repressed by a transcriptional repressor. These results suggest that, rather than serving simply as an intermediate step before future activation, the poised enhancer state may mark enhancers for spatial activation during tissue patterning. We discuss the possibility that the poised enhancer state is more generally the result of repression by transcriptional repressors.

"Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis" (Koenecke and Johnston et al 2016, Genome Biol):
Background: Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification and morphogenesis during development. Histone acetylation such as H3K27ac is an excellent marker for active enhancers, but it is challenging to obtain precise locations for enhancers as the highest levels of this modification flank the enhancer regions. How to best identify tissue-specific enhancers in a developmental system de novo with a minimal set of data is still unclear.
Results: Using DV patterning as a test system, we develop a simple and effective method to identify tissue-specific enhancers de novo. We sample a broad set of candidate enhancer regions using data on CBP co-factor binding or ATAC-seq chromatin accessibility, and then identify those regions with significant differences in histone acetylation between tissues. This method identifies hundreds of novel DV enhancers and outperforms ChIP-seq data of relevant transcription factors when benchmarked with mRNA expression data and transgenic reporter assays. These DV enhancers allow the de novo discovery of the relevant transcription factor motifs involved in DV patterning and contain additional motifs that are evolutionarily conserved and for which the corresponding transcription factors are expressed in a DV-biased fashion. Finally, we identify novel target genes of the regulatory network, implicating morphogenesis genes as early targets of DV patterning.
Conclusions: Taken together, our approach has expanded our knowledge of the DV patterning network even further and is a general method to identify enhancers in any developmental system, including mammalian development.

overall_design: ChIP-seq for histone modifications and transcription factors was peformed in Drosophila wild-type embryos as well as embryos of DV mutants Tl10b, Tlrm9/rm10 and gd7. RNA-seq was performed with the DV mutants and differential gene expression was determined among them. ATAC-seq was performed with wild-type embryos.

first: Nina

last: Koenecke

first: Jeff

last: Johnston

first: Samuel

last: Meier

first: Björn

last: Gärtner

first: Qiye

last: He

first: Malini

last: Natarajan


title: Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis

city: Harbin

first: Jing

last: Hu

state: Heilongjiang

address: 157 Baojian Road

department: College of Bioinformatics Science and Technology

institute: Harbin medical university

summary: Schizophrenia (SZ) and bipolar disorder (BD) are severe neuropsychiatric disorders with serious impact on patients, together termed “major psychosis”. Recently, long intergenic non-coding RNAs (lincRNAs) were reported to play important roles in mental diseases. However, little was known about their molecular mechanism in pathogenesis of SZ and BD. Here, we performed RNA sequencing on 82 post-mortem brain tissues from three brain regions (orbitofrontal cortex (BA11), anterior cingulate cortex (BA24) and dorsolateral prefrontal cortex (BA9)) of patients with SZ and BD and control subjects, generating over one billion reads. We characterized lincRNA transcriptome in the three brain regions and identified 20 differentially expressed lincRNAs (DELincRNAs) in BA11 for BD, 34 and 1 in BA24 and BA9 for SZ, respectively. Our results showed that these DELincRNAs exhibited brain region-specific patterns. Applying weighted gene co-expression network analysis, we revealed that DELincRNAs together with other genes can function as modules to perform different functions in different brain regions, such as immune system development in BA24 and oligodendrocyte differentiation in BA9. Additionally, we found that DNA methylation alteration could partly explain the dysregulation of lincRNAs, some of which could function as enhancers in the pathogenesis of major psychosis. Together, we performed systematical characterization of dysfunctional lincRNAs in multiple brain regions of major psychosis, which provided a valuable resource to understand their roles in SZ and BD pathology and helped to discover novel biomarkers.

overall_design: RNA sequencing of 82 brain samples including each of 19 from BA9 and BA24 and 44 from BA11. We performed RNA sequencing on three brain regions namely the BA11 (part of orbitofrontal cortex), BA24 (part of anterior cingulate) and BA9 (part of dorsolateral prefrontal cortex) from SZ and BD patients and psychiatrically normal individuals.In summary, there were 44 BA11 samples from 16 SZ, 16 BD and 12 control subjects, and 19 BA24 and 19 BA9 samples from the same subjects including 6 SZ, 7 BD and 6 controls.

first: Jinyuan

last: Xu

first: Lin

last: Pang


title: Active Demethylation of Both Maternal and Paternal Genomes in Mouse Zygotes

first: Xianlong

last: Li

address: 5, Yiheyuan Rd., Haidian District

department: Biodynamic Optical Imaging Center, College of Life Sciences

institute: Peking University

summary: The epigenomes of mammalian sperm and oocytes, characterized by gamete-specific 5-methylcytosine (5mC) patterns, are reprogrammed in early embryogenesis to establish full developmental potential. It is broadly accepted that the paternal genome is actively demethylated in the zygote while the maternal genome undergoes passive demethylation thanks to DNA replication over the subsequent cleavage divisions. Here we reveal that both maternal and paternal genomes undergo widespread active and passive demethylation in the pronuclear zygote before the first mitotic division. Whereas the passive demethylation requires DNA replication, the active demethylation relies on enzymatic oxidation of 5mC, as deletion of the DNA dioxygenase, Tet3, but not the inhibition of replication, blocks the active demethylation. At actively demethylated loci, 5mCs appear to be processed to unmodified cytosines in a manner independent of the DNA glycosylase TDG. These observations suggest the occurrence of genuine active demethylation in both parental genomes following fertilization.

overall_design: An extra supportive Tet3 knock-out female pronuclear sample related to experiment Series GSE56650.

first: Fan

last: Guo

first: Dan

last: Liang

first: Tong

first: Ping

last: Zhu

first: Hongshan

first: Xinglong

last: Wu

first: Lu

last: Wen

first: Tian

last: Gu

first: Boqiang

first: Colum

last: Walsh

first: Jin

first: Fuchou

last: Tang

first: Guo


title: Tumor hypoxia causes DNA hypermethylation by reducing TET activity (RNA-Seq)

first: Bernard

last: thienpont

overall_design: RNAseq of MCF7 cells grown under hypoxic and normoxic conditions. Submission includes data on 5 independent RNAseq experiments, each containing biological replicates grown under hypoxic conditions (0.5% oxygen), and under normoxic conditions.


title: Tumor hypoxia causes DNA hypermethylation by reducing TET activity

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Tumor hypoxia causes DNA hypermethylation by reducing TET activity (DIP-Seq)

overall_design: mDIPseq and hmDIPseq of MCF7 cells grown under hypoxic and normoxic conditions. Submission includes data on 4 independent DIPseq experiments, each containing 2 biological replicates grown under hypoxic conditions (0.5% oxygen), and 2 biological replicates grown under normoxic conditions.


title: Characterization of Paf1 complex occupancy in mouse myoblasts and myotubes under control conditions or Phf5a knockdown

status: Public on Aug 31 2016

city: New York

first: Alexandros

last: Strikoudis

state: NY

address: 550 First Avenue, Smilow 1303

department: Pathology

institute: NYU Medical Center

summary: Phf5a regulates occupancy of Paf1 complex in mouse myotubes. In this study we assayed for genome-wide localization of Leo1 subunit of the Paf1 complex in mouse myoblasts or myotubes under conditions of shControl or shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in significant decrease of Leo1 binding to its targets in myotubes.

overall_design: Ten million cells were used for the ChIP and precipitated using 5 micrograms of respective antibodies. Original reference: Zhu B. et al. (2005) "The human PAF complex coordinates transcription with events downstream of RNA synthesis"


title: Gene expression profiling using RNA-sequencing in mouse embryonic stem cells under control conditions or Phf5a knockdown

summary: Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed gene expression profiling using RNA-sequncing in mouse ESCs under conditions of self-renewal, Phf5a knockdown and Paf1 knockdown. These results revealed that Phf5a and Paf1 regulate similar gene expression signatures in mouse ESCs.

overall_design: RNA was extracted from 10 million self-renewing, Phf5a knockdown or Paf1 knockdown treated ESCs using Trizol extraction (Invitrogen) according to the manufacturer’s protocol following Poly-A selection which was then used for library preparation. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Gene expression analysis was performed for matched shControl versus shPhf5a or shPaf1 knockdown in each biological replicate.


title: RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

summary: Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.

overall_design: Identification of blue light and red light regulated genes by deep sequencing in biological duplicates. qRT-PCR was performed to verify the RNA-seq results.

first: Mehmet

last: Tardu

first: Ugur

last: Dikbas

first: Ibrahim

last: Baris

last: Kavakli


title: Histone genes transcription regulators binding in human cancer (U2OS) and normal (hTERT-RPE1) cells

first: Maria

last: Sokolova

summary: The regulation of replication-dependent histone genes by CASP8AP2 and NPAT is likely direct, based on ChIP-seq. CASP8AP2 and NPAT ChIP-Seq peaks were enriched near transcription start sites (TSSs) of replication-dependent, but not replication-independent histone genes on chromosomes 1, 6 and 12 in both cell lines. HINFP ChIP-Seq peaks were enriched near transcription start sites (TSSs) of replication-dependent histone genes H4 and H2B and replication-independent histone genes H1FX and H1F0 in both cell lines. Another histone gene regulator, E2F1 also bound to TSSs of many histone genes mainly replication-independent.

overall_design: Examination of histone genes transcroption regulators binding by ChIP-seq in normal and cancer cell lines

first: Mikko

last: Turunen


title: Expression profiling changes during different albescent stages of 'Anji Baicha' (Camellia sinensis)

city: Hangzhou

first: Chun-Fang

last: Li

state: Zhejiang

address: 9 South Meiling Road

department: Key Laboratory of Tea Biology and Resources Utilization

institute: Tea Research Institute of the Chinese Academy of Agricultural Sciences

summary: The RNA-Seq was used to analyze the expression profiling of genes in different ablescent stages of 'Anji Baicha'

overall_design: Examination of three tea leaf samples in yellow stage, white stage and green stage

first: Liang

last: Chen


title: Voluntary running triggers VGF-mediated oligodendrogenesis to prolong the lifespan of Snf2h-null ataxic mice

city: Ottawa

first: Matias

last: Alvarez-Saavedra

state: Ontario

address: 501 Smyth Road

department: Regenerative Medicine

institute: Ottawa Hospital Research Institute

summary: Exercise enhances cognitive function and slows progressive neurodegenerative disease.  While exercise promotes neurogenesis, oligodendrogenesis and adaptive myelination are also significant contributors to brain repair and brain health. Nonetheless, the molecular details underlying these effects remain poorly understood. Conditional ablation of the Snf2h gene (Snf2h cKO) impairs cerebellar development producing mice with poor motor function, progressive ataxia and death between postnatal day 25 to 45. Here we show that voluntary running induced an endogenous brain repair mechanism that resulted in a striking increase in hindbrain myelination and the long-term survival of Snf2h cKO mice. Further experiments identified the VGF growth factor as a major driver underlying this effect. VGF neuropeptides could promote oligodendrogenesis in vitro, while Snf2h cKO mice treated with full-length VGF-encoding adenoviruses obliterated the requirement of exercise for survival. Together, these results suggest that VGF delivery could represent a therapeutic strategy for cerebellar ataxia and other pathologies of the central nervous system.

overall_design: 4 samples per genotype in biological replicates (8 paired-end libraries)

first: Yves

last: De Repentigny

first: Doo

last: Yang

first: Ryan

last: O'Meara

first: Keqin

last: Yan

first: Lukas

first: Lemuel

last: Racacho

first: Ilya

last: Ioshikhes

first: Dennis

middle: E

last: Bulman

first: Robin

last: Parks

first: Rashmi

last: Kothary

first: David

last: Picketts


title: RNA sequencing from neural ensembles activated during fear conditioning in the mouse temporal association cortex

city: BOSTON

first: Jesse

last: Gray

state: Massachusetts

address: 77 AVENUE LOUIS PASTEUR, NRB room 0356

department: Genetics

institute: Harvard Medical School

summary: The stable formation of remote fear memories is thought to require neuronal gene induction in cortical ensembles that are activated during learning. However, the set of genes expressed specifically in these activated ensembles is not known; knowledge of such transcriptional profiles may offer insights into the molecular program underlying stable memory formation. Here we use RNA-Seq to identify genes whose expression is enriched in activated cortical ensembles labeled during associative fear learning. We first establish that mouse temporal association cortex (TeA) is required for remote recall of auditory fear memories. We then perform RNA-Seq in TeA neurons that are labeled by the activity reporter Arc-dVenus during learning. We identify 944 genes with enriched expression in Arc-dVenus+ neurons. These genes include markers of L2/3, L5b, and L6 excitatory neurons but not glial or inhibitory markers, confirming Arc-dVenus to be an excitatory neuron-specific, layer non-specific activity reporter. Cross comparisons to other transcriptional profiles show that 125 of the enriched genes are also activity-regulated in vitro or induced by visual stimulus in the visual cortex, suggesting that they may be induced generally in the cortex in an experience-dependent fashion. Prominent among the enriched genes are those encoding potassium channels that down-regulate neuronal activity, suggesting the possibility that part of the molecular program induced by fear conditioning may initiate homeostatic plasticity.

overall_design: For the RNA sequencing study, the Arc-dVenus transgenic mice were divided into three different groups. One group (FC, n = 3) went through the FC and received 7 CS (10 sec, 6khz pure tone) and US pairing (1 sec, 0.5mA). Another group (Shock, n = 2) received 7 repetitions of US (1-s footshock, 0.5mA DC; inter-trial interval: 20-180s) without any CSs. The bulk-tissue controls included two mice that were shocked without tones, and one mouse that was fear conditioned. All Arc-dVenus transgenic mice were sacrificed 6hrs after the behavioral procedures.

first: Jinhyung

last: Cho

first: Ben

last: Huang


title: HiChIP: Efficient and sensitive analysis of protein-directed genome architecture

city: Stanford

middle: Alexander

last: Flynn

state: CA

address: 380 Roth Way, Room 265

institute: Stanford University

summary: Three-dimensional genome structure is central to gene control, but current technologies are often impractical for many biological questions due to cell and read number requirements. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the fraction of conformation-informative reads by over 10-fold and lowers input requirement greater than 100-fold to 1 million cells. HiChIP of cohesin reveals multi-scale genome architecture with greater signal to noise than in situ Hi-C. Thus, HiChIP will enable insight into the genome’s three-dimensional structure and regulation in once-inaccessible biological systems.

overall_design:
[HiChIP cohesin] GM and mESC 25m (25 million cell input): 2 biological with 2 technical replicates, mESC 10m, 5m, and 1m: 2 technical replicates
[HiChIP oct4] mESC 25m (25 million cell input): 2 biological with 2 technical replicates

first: Maxwell

last: Mumbach

first: Adam

last: Rubin

first: Chao

last: Dai

first: Paul

last: Khavari

first: William

last: Greenleaf

first: Howard

middle: Y

last: Chang


title: Drosophila TDP-43 RNA-binding Protein Facilitates Association of Sister Chromatid Cohesion Proteins with Genes, Enhancers, and Polycomb Response Elements

city: Saint Louis

first: Dale

last: Dorsett

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

summary: Binding of sister chromatid cohesion and RNA-bindng proteins to chromosomes was measured by ChIP-seq

overall_design: Comparison of binding of sister chromatid cohesion and RNA-binding proteins in untreated (Mock) cells and cells RNAi depleted for sister chromatid cohesion and RNA-binding proteins

first: Amanda

last: Swain


title: TRF2 is recruited to the pre-initiation complex as a testis-specific subunit of TFIIA/ ALF to promote haploid cell gene expression [ChIP-seq]

city: Illkirch

first: Igor

last: Martianov

address: 1 rue Laurent Fries

institute: IGBMC

summary: TRF2 is a paralogue of TATA-box binding protein (TBP) with highest expression in testis. Although Trf2 inactivation in mice leads to arrested spermatogenesis, there is no direct evidence that Trf2 is recruited to chromatin to directly regulate gene expression. We used genetically modified mice where endogenous Trf2 has been modified to carry a TAP-TAG  to perform ChIP-reChIP followed by deep sequencing. We found that Trf2 is recruited to all active promoters as a subunit of TFIIA/ALF complex together with TBP.

overall_design:
TRF2 ChIP-reChIP was done using anti-FLAG immobilized antibody (M2, Sigma) followed by anti-TRF2 antibody (house made) on MNase I digested chromatin from testes of adult Trf2-tag/tag mice. We performed the same ChIP-reChIP procedure on Trf2-/- testes in parallel as a control. TBP ChIP-reChIP was done using anti-TBP ab28175 (Abcam) followed by anti-TBP ab51841 (Abcam) on sonicated chromatin from Trf2tag/tag and Trf2-/- testes. PolII ChIP was performed using anti-PolII antibody (sc-9001X, Santa Cruz) on sonicated chromatin from Trf2tag/tag and Trf2-/- testes. H3K4Me3 ChIP was done using anti-H3K4Me3 antibody (04-745, Millipore) on sonicated chromatin from Wt and Trf2-/- testes.

Please note that the alignment bed files were used to generate heat maps with ChIP-seq data interpretation platform seqMINER (seqMINER: an integrated ChIP-seq data interpretation platform. Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L. Nucleic Acids Res. 2011 Mar;39(6):e35. doi: 10.1093/nar/gkq1287. Epub 2010 Dec 21.). No other (further) processed data as seqMINER illustrates well enough our conclusions.

first: Irwin

last: Davidson


title: MOG KO Tregs versus WT Tregs

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

summary: Transcriptional comparison of WT Tregs versus MOG KO Tregs

overall_design: WT Tregs were compared to Tregs from a whole mouse KO of MOG

first: Ryan

middle: J

last: Martinez


title: RNA-seq analysis of testis transcripts from Wt and Trf2-/- mice [RNA-seq]

summary: TRF2 is a paralogue of TATA-box binding protein (TBP) with highest expression in testis. Although Trf2 inactivation in mice leads to arrested spermatogenesis, there is no direct evidence that Trf2 is recruited to chromatin to directly regulate gene expression. We used genetically modified mice where endogenous Trf2 has been modified to carry a TAP-TAG  to perform ChIP-reChIP followed by deep sequencing. We found that Trf2 is recruited to all active promoters as a subunit of TFIIA/ALF complex together with TBP. To assess the effect of Trf2 inactivation on gene expression we performed RNA-seq on WT and Trf2-/- testes at 21 days of age when haploid cell gene expression is activated.

overall_design: The testes from three 21 day old WT and three Trf2-/- males were taken to prepare total RNAs for deep sequencing.


title: RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes

city: Tarrytown

first: Yurong

last: Xin

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

summary: Pancreatic islet cells are critical for maintaining normal blood glucose levels and their malfunction underlies diabetes development and progression. We used single-cell RNA sequencing to determine the transcriptomes of 1,492 human pancreatic α-, β-, δ- and PP cells from non-diabetic and type 2 diabetes organ donors. We identified cell type specific genes and pathways as well as 245 genes with disturbed expression in type 2 diabetes. Importantly, 92% of the genes have not previously been associated with islet cell function or growth. Comparison of gene profiles in mouse and human α- and β-cells revealed species-specific expression. All data are available for online browsing and download and will hopefully serve as a resource for the islet research community.

overall_design: Single-cell RNA sequencing of human non-diabetic and type 2 diabetic pancreatic islet cells

first: Jesper

last: Gromada


title: TRF2 is recruited to the pre-initiation complex as a testis-specific subunit of TFIIA/ ALF to promote haploid cell gene expression

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

overall_design: Refer to individual Series


title: Methylation and gene expression profiling in Dnmt3a-deficient chronic lymphocytic leukemia and peripheral T-cell lymphoma in mice.

city: Omaha

first: Rene

last: Opavsky

state: NE

address: 985040 Nebraska Medical Center

institute: University of Nebraska Medical Center

summary: The goal of this study was to identify genome-wide methylation changes and aberrant gene expression profiles that occur upon deletion of Dnmt3a in a mouse model of CLL and PTCL.

overall_design: Deletion of Dnmt3a in the hematopoietic compartment of mice results in the development of chronic lymphocytic leukemia (CLL) and peripheral T cell lymphoma in mice (PTCL). The resulting tumors and appropriate controls were analyzed to identify changes in DNA methylation and gene expression. Specifically, whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS), and RNA-seq analysis was performed on WT B-1a, WT CD8+ T cells, Dnmt3a+/Δ CLL, Dnmt3aΔ/Δ CLL, and Dnmt3aΔ/Δ PTCL. All mice were on the N/FVB background.


title: MYOCD overexpression in HCASMs

city: ny

first: mingyan

last: lin

address: 1925 morris park ave

institute: aecom

summary: To identify novel genes especially lncRNAs linked to vascular smooth muscle cell (VSMC) differentiation, we performed RNA sequencing of adenovirus–MYOCD transduced human coronary artery smooth muscle cells (HCASMs).  Simiilar amount of  empty Adenovirus was used as control.

overall_design: Total RNA was isolated from duplicate HCASMs tranduced with ad-MYOCD or empty control virus and submitted for RNA-Sequencing at the University of Rochester Medical Center Genomics Research Center. Briefly, RNA-Sequencing was done with the polyadenylated RNA component at a depth of 20 million reads per replicate using the Illumina HISeq 2500.

first: Joseph

last: Miano

first: Xiaochun

last: Long


title: Long Non-coding RNA PICSAR Promotes Growth of Cutaneous Squamous Cell Carcinoma by Regulating ERK1/2 Activity

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

institute: University of Turku

summary: Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Long non-coding RNAs (lncRNAs) are involved in various biological processes, and their role in cancer progression is emerging. Whole transcriptome analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=4) revealed overexpression of long intergenic ncRNA (LINC00162) in cSCC cells (GSE66412). We wanted to futher study the RNA expression profile of LINC00162 knockdown cSCC cells. Based on our observations, LINC00162 was named PICSAR (P38 Inhibited Cutaneous Squamous cell carcinoma Associated lincRNA).

overall_design: RNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of lincRNA PICSAR. Total RNAs from negative control and PICSAR siRNA-treated cSCC cell lines (n=3) were extracted. The samples were sequenced using Illumina sequencing.

first: Minna

last: Piipponen

first: Veli-Matti

last: Kähäri


title: Role of Yng2 PHD and CHD-containing Eaf3 subunits of NuA4 on genome wide histone H4K8 acetylation, NuA4 localization and Pol II distribution

city: Lausanne

first: Eric

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

summary: The NuA4 acetyltransferase complex contains two reader modules, an H3K4me3-specific PHD domain within the Yng2 subunit and H3K36me2/3-specific chromodomain in the Eaf3 subunit. The objectives of this study are to evaluate the role these two reader modules on NuA4 genome-wide localization, histone H4K8 acetylation and RNA polymerase II occupancy. We demonstrate here that Yng2 PHD specifically directs H4 acetylation near the transcription start site of highly expressed genes while Eaf3 is important downstream on the body of the genes. Strikingly, the recruitment of the NuA4 complex to these loci is not significantly affected.  Furthermore, RNA polymerase II occupancy is decreased only in conditions where both PHD and chromo domains are lost, and mostly in the second half of the gene coding regions.  Altogether, these results argue that methylated histone reader modules in NuA4 are not important for its recruitment on the promoter or coding regions but rather orient its acetyltransferase catalytic site to the methylated H3-bearing nucleosomes in the surrounding chromatin, allowing proper transcription initiation and elongation.

overall_design: Chromatin immunoprecipitations were performed on myc-epl1 wild-type, yng2-W247A, ∆eaf7 and yng2-W247A ∆eaf7 mutants Saccharomyces cerevisiae strains. NuA4 complex genome wide localization is defined by Myc-Epl1 signal and RNA polymerase II occupancy using a specific antibody against total RNA Pol II. Histone acetylation profile is determined by H4K8 acetylation corrected on total H4 signal.

first: Anne-Lise

last: Steunou

first: Valérie

last: Côté

first: Dorine

last: Rossetto

first: Jacques


title: Characterization of histone modifications in mouse embryonic stem cells under control conditions or Phf5a knockdown

first: Alexandros

last: Strikoudis

summary: Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed for genome-wide localization of H3K4me3, H3K79me2 and H3K36me3 in mouse ESCs under conditions of shControl and shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in the decrease of the elongation marks H3K79me2 and H3K36me3 from the gene bodies of pluripotency genes in ESC, wherease the promoter-associated mark H3K4me3 remains unaffected.

overall_design: Ten million cells were treated with micrococcal nuclease to generate mono-nucleosomes and for the ChIP chromatin was precipitated using 10 micrograms of antibody against H3K4me3 (Millipore, 07-473), H3K79me2 (Active Motif, 39143) and H3K36me3 (Abcam, ab9050).


title: Characterization of Paf1 complex occupancy in mouse embryonic stem cells under control conditions or Phf5a knockdown

summary: Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed for genome-wide localization of Paf1, Leo1 and Cdc73 subunits of the Paf1 complex in mouse ESCs under conditions of shControl and shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in the significant decrease of Paf1 complex binding to its targets in ESCs.

overall_design: Ten million cells were used for the ChIP and precipitated using 5 micrograms of respective antibodies. Original reference: Zhu B. et al. (2005) "The human PAF complex coordinates transcription with events downstream of RNA synthesis"


title: Deep RNA sequencing of the human placental transcriptome

city: Perth

first: Sam

last: Buckberry

state: WA

address: 35 Stirling Highway, Crawley

country: Australia

institute: The University of Western Australia

summary: The goal of this study was to conduct an in-depth analysis of the human placental transcriptome. RNA was extracted from 16 placental samples using TRIzol following the manufacturer’s protocol. All samples were spiked with 96 External RNA Controls Consortium (ERCC) ExFold RNA transcripts. Ribosomal RNAs were depleted from samples using Ribo-Zero Gold and sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation kits. Sequencing was performed on the Illumina Hi-Seq 2500 using a 100bp paired-end protocol. Sequence adapters were trimmed using AdapterRemoval with options --trimns, --minlength 20. Trimmed RNA-Seq reads were aligned to known UCSC hg19 genes and the hg19 genome using Bowtie 2 v2.1.0 and TopHat v2.0.9 with options --library-type=fr-firststrand --mate-inner-dist -20 --mate-std-dev 180. UCSC hg19 reference genome and transcriptome was obtained through Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). Aligned RNA-Seq reads were summarised using the summarizeOverlaps algorithm with the UCSC known genes hg19 GTF file using the the options overlapMode=``Union'', ignoreStrand=FALSE, singleEnd=FALSE, fragments=TRUE to generate a table of unique read counts per gene for each sample. All samples were processed in the same way, with all sequencing libraries created in the same batch and sequenced together.

overall_design: Villous tissue from 16 human placental samples were profiled by total RNA-Seq.

first: Claire

last: Roberts


title: Characterization of RNA Polymerase II occupancy in mouse embryonic stem cells under control conditions or Phf5a knockdown

summary: Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed for genome-wide localization of  Ser-5-phosphorylated RNA polymerase II and Ser-2-phosphorylated RNA polymerase II in mouse ESCs under conditions of shControl and shPhf5a knockdown. These results revealed that downregualtion of Phf5a results in the increase of the initiating form of RNA polymerase II (Ser5-phosphorylated) and in the aberrant loss of the elongating form of RNA polymerase II (Ser2-phosphorylated) of pluripotency genes in ESCs.

overall_design: Ten million cells were used for the ChIP and precipitated using 10 micrograms of antibody  against Ser-5-Phosphoryalted RNA polymerase II (Abcam, ab5131 ) and  against Ser-2-Phosphoryalted RNA polymerase II (Active Motif, clone 3E10)


title: Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana

city: Beijing

first: Jiapei

last: Yuan

address: Tsinghua Yuan

institute: Tsinghua University

summary: We sequenced the poly(A)+ and poly(A)- samples of the roots and shoots from 10-day-old WT seedlings grown under P+ and P- condition. The WT plant refers to Columbia ecotype Arabidopsis seedlings. Each condition has two replicates. After total RNA extraction, ribosomal RNAs were removed using RiboMinus™ Plant Kit repeated two times. The poly(A)+ and poly(A)- constituent were separated with oligo(dT) magnetic beads (Oligotex mRNA Mini Kit, QIAGEN). Using a 2-fold change and a P-value <0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified novel noncoding lncRNAs.

overall_design: We performed a RNA-seq analysis on Columbia WT plants. Total RNAs were extracted from the shoots and roots of 10-day-old P+ and P- WT seedlings (i.e., seedling grown on P-sufficient and P-deficient media). The extracted RNAs were subjected to polyA(+) and polyA(-) RNA purification, library construction and RNA deep sequencing. We used Tophat to map reads to TAIR10 genome and used Cufflinks to assemble transcripts based on 16 datasets of RNA-seq samples.

first: Jia

first: Zhi

last: Lu


title: Genome-wide translational analysis of RAW264 macrophages by ribosome profiling

city: Tokorozawa

first: Hiroaki

last: Sako

country: Japan

institute: Waseda University

summary:
Purpose: The aim is to analyze the translational kinetics of the basal and LPS-stimulated conditions of RAW264 macrophages focusing on ribosome density
Method: RAW264 macrophages were cultured at 3.0 x 10^5 cells/ml in media (DMEM, 2mM Glutamine, 10% FBS, 100 units penicillin and 100µg streptomycin/mL) 24 hours prior to harvest. It was confirmed that the confluency of cells never surpassed 80 ~ 90%.  Cell were harvested in their basal state or LPS stimulated condition (100 ng/ml for 30 min) and ribosome profiling (Ribo-Seq) and high-throughput mRNA sequencing (mRNA-Seq) were conducted. Ribosome protected fragments (RPF) were sequenced and the density was normalized by mRNA abundance.
Result and conclusion: We discovered where in the ribosome translational arrest ocurs and how this happens. Translational stall was striking at A-site and P-site of ribosomal complex. The other arrest site was observed 3 to 5 residues away from the peptidyl transfer center of the exit tunnel, in which ribosomal density and hydrophobicity showed a significant negative correlation.

overall_design: mRNA and RPF of RAW264 macrophages were deep-sequenced with two independent biological replicates by Ion PGM sequencer


title: Nascent transript profiling upon in mouse embryonic stem cells under control conditions or Phf5a knockdown

city: New York

institute: NYU Medical Center

summary: Phf5a regulates transcription elongation in mouse embryonic stem cells (ESCs), through regulation of the Paf1 complex. In this study we assayed nascent RNA profiling using global run-on sequncing in mouse ESCs under conditions of self-renewal, differentiation and Phf5a knockdown. These results revealed that genes positively regulated by Paf1 in ESCs exibit RNA elongation pausing on their promoters. We used conditions of self-renewal, differentiation, Phf5a knockdown and Paf1 knockdown to monitor nascent transcript expression changes during Phf5a depletion using global run-on RNA sequencing (GRO-seq). These results revealed that Phf5a through the control of Paf1 complex regulates pause release and elongation of pluripoency-associated genes in embryonic stem cells.

overall_design: Nascent RNA was extracted from 10 million self-renewing, differentiated or Phf5a knockdown treated ESCs using Trizol extraction (Invotrogen) according to the manufacturer’s protocol following the global run-on (GRO) reaction and BrUTP labeling. Nascent BrUTP-containing RNA was purified using BrdU beads (Santa Cruz) which was then used for library preparation. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Pause release analysis was performed for each matched shControl versus shPhf5a knockdown in each biological replicate.


title: Tissue-specific DamID profiling of chromatin proteins in Drosophila melanogaster

status: Public on Aug 30 2016

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

summary: Analysis of gene expression regulation typically requires identification of genomic sites where regulatory proteins bind. For this purpose, ChIP and DamID methods applied to cell lines or model organisms are now routinely used, even in selected cell types. In this work, we present modifications to experimental DamID protocol, as well as a custom data processing algorithm that allows to confidently identify genomic sites enriched with the proteins of interest. This algorithm is implemented in Perl and is also available as executable files thereby making DamID analysis relatively straightforward. Finally, we demonstrate how this pipeline performs when fed with real experimental data.

overall_design: Examination of comr chromatin protein binding to chromosomes in wild type adult testes using DamID technique.

first: Petr

last: Laktionov

first: Stepan

last: Belyakin


title: Gene expression of Glut1 transgenic and control iTreg

city: Nashville

first: Jeffrey

middle: C

last: Rathmell

state: Tennessee

address: 1161 21st Avenue South, A-5301 MCN

institute: Vanderbilt University Medical Center

summary: Effector (Teff) and regulatory (Treg) CD4 T cells undergo metabolic reprogramming to support proliferation and immune function. While Phosphatidylinositide 3-kinase (PI3K)/Akt/mTORC1 signaling induces the glucose transporter Glut1 and aerobic glycolysis for Teff proliferation and inflammatory function, mechanisms that regulate Treg metabolism and function remain unclear. We show that TLR signals that promote Treg proliferation increase Glut1, PI3K/Akt/mTORC1 signaling, and glycolysis.  However, TLR-induced mTORC1 signaling also impaired Treg suppressive capacity.  Conversely, FoxP3 opposed PI3K/Akt/mTOR signaling to reduce glycolysis and anabolic metabolism while increasing oxidative and catabolic metabolism.  Importantly, Glut1 expression was sufficient to increase Treg numbers but reduced suppressive capacity and FoxP3 expression.  Thus, inflammatory signals and FoxP3 balance mTORC1 signaling and glucose metabolism to control Treg proliferation and suppressive function.

overall_design: RNAseq of induced Glut1 transgenic and control Treg

first: Aguirre

last: De Cubas


title: Direct interrogation of the role of H3K9 in metazoan heterochromatin function

city: Chapel Hill

first: Taylor

last: Penke

state: NC

address: 3344 Genome Sciences Building, 250 Bell Tower Drive

department: Genetics and Molecular Biology

institute: University of North Carolina Chapel Hill

summary: We replaced the endogenous histones of Drosophila melanogaster with histones containing an H3K9R mutation to interrogate the role of H3K9 in heterochromatin formation and function. We queried heterochromatin formation through Formaldhyde Assisted Isolation of Regulatory Elements coupled with sequencing to examine nucleosome occupancy and Heterochromatin Protein 1a ChIP sequencing to determine the localization of the major reader of H3K9me. We found that regions of pericentromeric heterochromatin exhibit decreased HP1a and nucleosome occupancy in H3K9R mutants. To examine potential consequences of these changes of chromatin architecture, we performed total RNA-seq. In H3K9R mutants we observed increased levels of transposon and pIRNA cluster transcripts; however, the protein-coding transcriptome was similar to controls.

overall_design: FAIRE-seq and total RNA-seq were performed in imaginal wing discs from 3rd instar Drosophila larvae. gDNA-seq samples are input samples for FAIRE-seq. HP1a ChIP-seq was performed from whole 3rd instar larvae. All three experiments were performed on endogenous histone mutants rescued with either a wild-type (HWT) or H3K9R mutant transgenic histone array. Experiments were carried out in duplicate or triplicate.


title: L-MYC Expression Maintains Self Renewal and Prolongs Multipotency of Primary Human Neural Stem Cells

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: These data support the therapeutic development of immortalized LM-NSC008 cells for allogeneic use in brain tumors, TBI and other CNS diseases

overall_design: Comparison of early and late passages of human NSC008, LM-NSC008 and LM-NSC008 Differentiated cells in culture

first: Margarita

last: Gutova


title: Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a

address: 550 First Avenue, Smilow 1303


title: Evolution of insect hindwing morphology: A comparative genomic analysis of targets of Hox protein Ultrabithorax

city: Pune

first: Naveen

last: Prasad

state: Maharashtra

address: Dr Homi Bhaba Road

department: Biology

country: India

institute: IISER Pune

summary: To gain insights into the species-specific events downstream of Ubx, we identified direct targets of Ubx from Apis  by ChIP-seq and compared them with those of Drosophila at the level of both their function and regulation. While the majority of the targets are species-specific, the ontological distribution of all targets was similar amongst the two species. Interestingly, although considerable number of wing-patterning genes are retained as targets of Ubx over the past 300 millions years, many of them are differentially expressed only between wing and haltere in Drosophila and not between forewing and hindwing in Apis . Detailed bioinfomatics analysis and and experimental validation of enhancer sequences suggest that acquisition of binding  sites for additional transcription factors without altering binding per se of Ubx could also contribute to the diversity in Ubx function.

overall_design: We carried out ChIP seq on fore and hind wing buds of Apis mellifera (two replicates each) using polyclonal anti Ubx antibody and pre immune IgG from the same animal.  We identifed peaks in the chipped samples using input DNA as a reference.  All the experiments were carried out on two independent biological replicates.

first: L

last: Shashidhara


title: Extensive Supporting Cell Proliferation and Mitotic Hair Cell Generation by In Vivo Genetic Reprogramming in the Neonatal Mouse Cochlea

city: Shanghai

first: Luo

last: Guo

address: 83# fenyang road, 9# building, room 613

institute: Fudan University

summary: We used RNA sequencing to compare the transcripts of the cochleae from control mice and from mice with β-catenin activation, Notch1 deletion, and β-catenin activation combined with Notch1 deletion in Sox2+ SCs. We identified the genes involved in the proliferation and transdifferentiation process that are either controlled by individual signaling pathways or by the combination of Wnt and Notch signaling.

overall_design: Supporting cell proliferation and mitotic hair cell generation by in vivo genetic reprogramming of Wnt and Notch pathways

first: Huawei

last: Li

first: Wenli

last: Ni

first: Chen

last: Lin

first: Wenyan


title: Next Generation Sequencing Analysis of control and DEHP exposure HepG2 cell Transcriptomes

first: Ning

last: Wei

address: 320 Yueyang RD.

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: we treated the HepG2 cells with low concentration or control solvent for a long time. Then we extracted the RNAs and performed the next generation sequencing. By comparing sequcing data from control and DEHP treated samples, we profiled the gene expression regulated by low concentration exposure.

overall_design: HepG2 cells mRNA profiles of Control and DEHP treated samples were generated by deep sequencing, using ABI Ion Proton.


title: LINC00520 is Induced by Src, STAT3, and PI3K and Plays a Functional Role in Breast Cancer

city: Boston

first: David

last: Hendrickson

address: 725 Parsons

country: USA

institute: Harvard

summary: Long non-coding RNAs (lncRNAs) have been implicated in normal cellular homeostasis as well as pathophysiological conditions, including cancer. Here we performed global gene expression profiling of mammary epithelial cells transformed by oncogenic v-Src, and identified a large subset of uncharacterized lncRNAs potentially involved in breast cancer development. Specifically, our analysis revealed a novel lncRNA, LINC00520 that is upregulated upon ectopic expression of oncogenic v-Src, in a manner that is dependent on the transcription factor STAT3. Similarly, LINC00520 is also increased in mammary epithelial cells transformed by oncogenic PI3K and its expression is decreased upon knockdown of mutant PIK3CA. Additional expression profiling highlight that LINC00520 is elevated in a subset of human breast carcinomas, with preferential enrichment in the basal-like molecular subtype. ShRNA-mediated depletion of LINC00520 results in decreased cell migration and loss of invasive structures in 3D. RNA sequencing analysis uncovers several genes that are differentially expressed upon ectopic expression of LINC00520, a significant subset of which are also induced in v-Src-transformed MCF10A cells. Together, these findings characterize LINC00520 as a lncRNA that is regulated by oncogenic Src, PIK3CA and STAT3, and which may contribute to the molecular etiology of breast cancer.

overall_design: Transcriptome profiling of MCF10A-Src transformation and LINC00520 over expression


title: Gene expression profiling shows that combination of jazQ and phyB-9 mutations promotes additive and enhanced expression of growth- and defense-related genes

city: East Lansing

first: Gregg

last: Howe

address: 612 Wilson Rd

department: Plant Research Laboratory

institute: Michigan State University

summary: The quintuple jaz mutant jazQ and the phytochrome mutant phyB-9 affect plant growth and defense. We used RNA-sequencing to query the transcriptomes of jazQ and phyB-9, as well as the combined jazQ phyB-9 sextuple mutatant, and examined how these mutations alter the expression of growth- and defense-associated genes. The data highlight how jasmonate and light signaling pathways contribute to growth and defense, and how their removal genetically promotes additive responses.

overall_design: Analysis of Col-0 (wildtype), jazQ, phyB-9, and jazQ phyB-9 (four genotypes), with three biological replicates per genotype - 12 total samples.

first: Campos

middle: L

last: Marcelo


title: Total RNA sequencing of HCT116 cells with vitamin C, 5-Aza-CdR and combination treatment compared to untreated cells I

city: Grand Rapids

first: Peter

middle: A

last: Jones

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: Total RNA sequenceing method was used to compare the differential expression of genes in HCT116 cells with vitamin C, 5-Aza-CdR and combination treatment compared to untreated cells

overall_design: Examination of total RNA expressed after cells with vitamin C, 5-Aza-CdR and combination treatment compared to untreated cells

first: Minmin

last: Liu


title: Total RNA sequencing of HCT116 cells with vitamin C, 5-Aza-CdR and combination treatment compared to untreated cells II


title: Double-stranded RNA sequencing of HCT116 cells with 5-Aza-CdR and combination treatment compared to untreated cells

summary: double stranded RNA was prepared using J2 antibody pull-down

overall_design: Examination of double stranded RNA expressed after cells with 5-Aza-CdR and combination treatment compared to untreated cells


title: MSL2 reads DNA shape to distinguish X from autosome for dosage compensation (MLE RNAi in S2 cells experiments)

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary:
The rules according to which transcription factors selectively bind only a small subset of genomic sites from a vast pool of similar sequences are not understood. One of the most challenging tasks in DNA recognition is posed by dosage compensation systems that require the unequivocal distinction between a sex chromosome and all autosomes. In Drosophila melanogaster the male-specific-lethal dosage compensation complex (MSL-DCC) doubles the transcription output of most genes on the X chromosome via chromatin modification, but the nature of this selectivity is not known.
We now found that MSL2, the male-specific organizer of the DCC, uses two distinct DNA interaction surfaces to read out previously identified X chromosomal ‘high affinity sites’. Specificity is provided by the interaction of the CXC domain with a novel, X-specific motif defined by DNA sequence and shape features. By several criteria these ‘PionX sites’ are primary determinants of X chromosome identity.

overall_design: ChIP-Seq of MSL2 in S2 cells treated with control or MLE RNAi

first: Raffaella

last: Villa

first: Tamas

last: Schauer

first: Pawel

last: Smialowski

middle: B

last: Becker


title: MSL2 reads DNA shape to distinguish X from autosome for dosage compensation (SXL RNAi in Kc cells experiments)

overall_design: ChIP-Seq of MSL2 in Kc cells treated with control or SXL RNAi for 3, 6 or 9 days


title: Analyzing the interactions of mRNAs, miRNAs, lncRNAs and circRNAs to predict competing endogenous RNA networks in glioblastoma

city: cheng du

first: Mao

last: Qing

department: neurosurgery

institute: west china hospital, Si chuan university

summary: Cross-talk between competitive endogenous RNAs (ceRNAs) may play a critical role in revealing potential mechanisms of tumor development and physiology. Glioblastoma is the most common type of malignant primary brain tumor, and the mechanisms of tumor genesis and development in glioblastoma are unclear. Here, to investigate the role of non-coding RNAs and the ceRNA network in glioblastoma, we performed paired-end RNA sequencing and microarray analyses to obtain the expression profiles of mRNAs, lncRNAs circRNAs and miRNAs. We identified that the expression of 501 lncRNAs, 1789 mRNAs, 2038 circRNAs and 143 miRNAs were often altered between glioblastoma and matched normal brain tissue. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on these differentially expressed mRNAs and miRNA-mediated target genes of lncRNAs and circRNAs. Furthermore, we used a multi-step computational framework and several bioinformatics methods to construct a ceRNA network combining mRNAs, miRNAs, lncRNAs and circRNA, based on co-expression analysis between the differentially expressed RNAs. We identified that plenty of lncRNAs, CircRNAs and their downstream target genes in the ceRNA network are related to glutamatergic synapse, suggesting that glutamate metabolism is involved in glioma biological functions. Our results will accelerate the understanding of tumorigenesis, cancer progression and even therapeutic targeting in glioblastoma. We hope to inspire researchers to study the role of non-coding RNAs in glioblastoma.

overall_design: RNA sequcence for 3 glioma and paired normal brain tissue

first: Yang

last: Yuan


title: MSL2 reads DNA shape to distinguish X from autosome for dosage compensation

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

overall_design: Refer to individual Series


title: TUT7 Catalyzes the Uridylation of the 3’ End for Rapid Degradation of Histone mRNA

status: Public on Aug 29 2016

first: William

middle: F

last: Marzluff

address: 207 Fordham Hall

institute: The University of North Carolina at Chapel Hill

summary: Using high-throughput sequencing of histone mRNAs and degradation intermediates, we find that knockdown of TUT7 reduces both the uridylation at the 3’ end as well as uridylation pattern at the 3’ end, and only had a small effect on the uridylation in the stemloop uridylation of the major during histone mRNA degradation. Knockdown of 3’ hEXO also altered the uridylation of histone mRNAs, revealing a dynamic equilibrium between 3’ hEXO digestion and TUT7 uridylation, suggesting that TUT7 and 3’ hExo function together in trimming and uridylating histone mRNAs.

overall_design: We sequenced 3' ends of histone mRNAs and degradation intermediates before and after inhibition of DNA replication in HeLa cells using the previously described EnD-seq strategy.

first: Joshua

middle: D

last: Welch


title: sRNA drives epigenetic changes in F1 hybrids

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

institute: csiro

summary: Hybrid Arabidopsis plants undergo epigenetic reprogramming producing decreased levels of 24nt siRNAs and altered patterns of DNA methylation that can affect gene expression.  Driving the changes in methylation are the processes Trans Chromosomal Methylation (TCM) and Trans Chromosomal deMethylation (TCdM).  In TCM/TCdM the methylation state of one allele is altered to resemble the other allele.  These changes in DNA methylation and the associated changes in small RNA levels in the F1 hybrid can be maintained in subsequent generations and affect hundreds of regions in the F2 epigenome.  The inheritance of these altered epigenetic states varies in F2 individuals resulting in individuals with genetically identical loci displaying different epigenetic states and gene expression profiles.  At these regions the change in methylation is associated with the presence of small RNAs.  Loci without any sRNA activity can have altered methylation states, suggesting that a sRNA-independent mechanism may also contribute to the altered methylation state of the F1 and F2 generations.

overall_design: Arabidopsis thaliana accessions C24 and Landsberg erecta (Ler,) were used as parental lines. Reciprocal C24 x Ler, hybrids were generated by hand pollination. For all libraries immature inflorescence was used.  sRNA and mRNA libraries were prepared from total RNA extracted using the Direct-zol RNA mini-prep kit.  RNA was extracted from two biological replicates of pooled C24 and Landsberg erecta material.  For F1 hybrids the RNA was extracted from three individual F1 plants for each reciprocal hybrids.  These individual hybrid plants have been designated F1-A, F1-B, F1-C, F1-D, F1-E, F1-F.  RNA was also extracted from 6 individual F2 plants designated F2-A, F2-B, F2-C, F2-D, F2-E, F2-F.  One of these F2 individuals has been derived from one of the F1 individuals (i.e. F2-A is derived from F1-A).  Methyl-seq libraries were prepared as described in Lister et al, 2008.  6 methyl-seq libraries were prepared from the same  F2 samples used in the RNA-seq analyses (F2-A, F2-B, F2-C, F2-D, F2-E, F2-F).

first: Steve

last: Eichten

first: Michael

last: Groszmann

first: Aihua

last: Wang

first: Hua

last: Ying

first: Elizabeth

last: Dennis

first: W

last: Peacock


title: An essential role for the IL-2 receptor in Treg cell function

first: Takatoshi

last: Chinen

address: 417 East 68th Street

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: Regulatory T (Treg) cells, expressing abundant amounts of the IL-2 receptor (IL-2R), are reliant on IL-2 produced by activated T cells. This feature implied a key role for a simple network based on IL-2 consumption by Treg cells in their suppressor function. However, congenital deficiency in IL-2R results in reduced expression of the Treg lineage specification factor Foxp3, confounding experimental efforts to understand the role of IL-2R expression and signaling in Treg suppressor function. Using genetic gain and loss of function approaches, we demonstrate that IL-2 capture is dispensable for control of CD4+ T cells, but is important for limiting CD8+ T cell activation, and that IL-2R dependent STAT5 transcription factor activation plays an essential role in Treg suppressor function separable from T cell receptor signaling.

overall_design:
Gene expression profiles in Treg cells with or without an expression of an active form of STAT5 were compared by RNA sequencing.
Male 8-wk-old Foxp3Cre-ERT2Rosa26Stat5bCA (STAT5b-CA) and Foxp3Cre-ERT2 (control) mice, nine mice for each experimental group, received a single dose (4 mg) of tamoxifen by oral gavage 4 months before isolation.
Splenic CD4+Foxp3(YFP/GFP)+GITRhiCD25hi Treg and CD4+Foxp3(YFP/GFP)-CD62LhiCD44lo T naive cells were double sorted using a BD FACSAria II cell sorter.
The T cell subsets isolated from three individual mice in the same experimental group (genotype) was pooled into one biological replicate; three biological replicates were generated.
A total of 12 samples, i.e., two genotypes, two cell cypes, and three replicates, was subjected to RNA-seq analysis.
Samples were sequenced on the Illumina HiSeq 2500 to an average depth of 27.5 million 50-bp read pairs per sample.

first: Xiying

last: Fang

first: Alexander

last: Rudensky


title: MSL2 reads DNA shape to distinguish X from autosome for dosage compensation (DIP experiments)

first: Tobias

last: Straub

overall_design: DNA immuno precipitation (DIP) of recombinant MSL2 and mutants after incubation with sheared genomic DNA from various sources

first: Raffaella

last: Villa

last: Schauer

first: Peter


title: A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report

city: Oxford

first: Bass

last: Hassan

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology, Oxford Molecular Pathology Institute

country: United Kingdom

institute: University of Oxford

type: Genome variation profiling by genome tiling array

type: Genome variation profiling by high throughput sequencing


title: Brown adipocyte differentiation modulation by LSD1 inhibitor

first: Wei

last: Qi

address: Jinke Road

institute: China Novartis Institutes for BioMedical Research


title: Normal stroma suppresses cancer cell proliferation via mechanosensitive regulation of JMJD1a-mediated transcription

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

institute: University of Turku