title: Specificity, propagation and memory of pericentric heterochromatin in mouse fibroblasts: H3S10p

city: Heidelberg

first: Jan-Philipp

last: Mallm

address: Im Neuenheimer Feld 267

institute: DKFZ

summary: ChIP-seq of H3S10p in synchronized and asynchronous ESCs and RNA-seq of ESCs after inhibition of AURKB

overall_design: ChIP-seq of H3S10p and RNA-seq for ESCs treated with ZM-447439

first: J

middle: P

first: K

last: Rippe


title: Genome-wide maps of H3K36me3 in metastatic renal cell carcinoma and isogenic renal cell carcinoma cell lines

status: Public on Jun 19 2015

city: Rochester

first: Jeff

last: Nie

state: MN

address: 200 First St. SW

country: USA

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of H3K36me3 ChIP sequencing in SETD2 genotyped samples

overall_design: Examination of H3K36me3 in SETD2 wild-type, mutant renal cell carcinoma and SETD2 isogenic cell lines

first: Thai

middle: H

last: Ho

first: Huihuang

last: Yan


title: Apc restoration promotes cellular differentiation and reestablishes crypt homeostasis in colorectal cancer

status: Public on Jun 18 2015

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

type: Expression profiling by high throughput sequencing

summary: The Adenomatous Polyposis Coli (APC) tumor suppressor is mutated in the vast majority of human colorectal cancers (CRC) and leads to deregulated Wnt signaling. To determine whether Apc disruption is required for tumor maintenance, we developed a mouse model of CRC whereby Apc can be conditionally suppressed using a doxycycline-regulated shRNA. Apc suppression produces adenomas in both the small intestine and colon that, in the presence of Kras and p53 mutations, can progress to invasive carcinoma. In established tumors, Apc restoration drives rapid and widespread tumor-cell differentiation and sustained regression without relapse. Tumor regression is accompanied by the re-establishment of normal crypt-villus homeostasis, such that once aberrantly proliferating cells reacquire self-renewal and multi-lineage differentiation capability. Our study reveals that CRC cells can revert to functioning normal cells given appropriate signals, and provide compelling in vivo validation of the Wnt pathway as a therapeutic target for treatment of CRC

overall_design: Analysis of RNA isolated from colon polyps that presented in shAPC or shAPC/Kras mice as compared to shRenilla (neutral) mouse colon mucosa

first: Lukas

last: Dow

first: Kevin

last: O'Rourke

first: Scott

last: Lowe


title: RNA sequencing of ATCC 17978hm Acineotbacter baumannii strain and CpdA mutant

status: Public on Jun 21 2015

city: Bedford Park

first: Uwe

middle: Horst

last: Stroeher

state: South Australia

address: Carpark 8

department: School of Biological Sciences

country: Australia

institute: Flinders University

summary: Difference in RNA expression levels between Acinetobacter baumannii cells expressing high and low levels of cyclic AMP

overall_design: Total RNA obtained from Acineotbacter baumannii bacterial cells in Log phase gown in MH broth culture, isolated RNA in triplicate from three expreiment. cpdA::Tn mutant and 17978hm strain compared. Assessing increased levels of cAMP within the cell

first: Sarah

middle: K

last: Giles

first: Melissa

last: Brown


title: Age- and Obesity Induced Decline of Brown Fat Function as Consequence of Impaired miR-328 Dependent Silencing of Bace1

status: Public on Jun 17 2015

city: Koeln

first: Gertrud

last: Steger

address: Fuerst-Pueckler-Str. 56

department: Institute for Virology

country: Germany

institute: Universitaet zu Koeln

summary: Activated brown adipose tissue contributes to control of energy and glucose homeostasis in rodents and humans. Defining cell-autonomous processes underlying BAT differentiation and activation may thus reveal novel therapeutic targets for obesity and type 2 diabetes mellitus intervention. Here we show that ageing- and obesity-associated demises in BAT function coincide with down-regulation of mature microRNAs in BAT in the presence of reduced expression of the critical microRNA processing enzyme Dicer1. To mimic this partial down-regulation of microRNA processing in obesity and ageing, we inactivated one allele of Dicer1 selectively in BAT of mice. BAT- restricted heterozygosity of Dicer1 caused glucose intolerance in lean mice and aggravated diet-induced-obesity (DIO)-evoked deterioration of glucose homeostasis. Using combinatorial analyses of altered microRNA-expression in BAT during in vitro preadipocyte commitment and mouse models of progeria, longevity and DIO, we identified 23 microRNAs dysregulated among these conditions. Of these, we identified miR-328 as a novel regulator of BAT differentiation. miR-328 over-expression promotes BAT-differentiation and impairs muscle progenitor commitment, while reducing miR-328 expression blocks BAT specification. We validated the ß-Secretase Bace1 as a target of miR-328, which is consequently over-expressed in BAT of obese and premature ageing mice. Reducing Bace1 expression enhances brown adipocyte, while impairing myogenic differentiation in vitro. In vivo small-molecule Bace1 inhibition in obese mice delayed DIO-induced weight gain, ameliorated obesity-associated deterioration of glucose metabolism and improved insulin sensitivity. Collectively, these experiments reveal reduced Dicer1-miR-328-Bace1 axis in presence of generalized impairment of microRNA processing in ageing and obesity as a novel determinant of ageing- and obesity-associated decline in BAT function. This may define in vivo Bace1-inhibition as an innovative therapeutic approach to not only target age-related neurodegenerative diseases but at the same time improving age-related impairment of BAT-function and metabolism.

overall_design: C57BL/6 mice ( 4 weeks of age) were treated with a calory-rich, high-sugar high-fat diet (HFD) for a course of 4 weeks. Then groups were stratified and one group continued to receive HFD (BAT13-15) or HFD supplemented with an experimental small-molecule Bace 1 inhibitor (BAT17, 33, 35).

first: Matteo

last: Oliverio

first: Elena

last: Schmidt

first: Jan

last: Mauer

first: Cathy

last: Baitzel

first: Nils

last: Hansmeier

first: Sajjad

last: Khani

first: Sandra

last: Konieczka

first: Susanne

last: Brodesser

first: Trieu-My

last: Van

first: Deniz

last: Bartsch

first: Hella

middle: S

last: Brönneke

first: Markus

last: Heine

first: Hans

last: Hilpert

first: Emilio

last: Tarcitano

first: George

middle: A

last: Garinis

first: Peter

last: Frommolt

first: Jörg

last: Heeren

first: Marcelo

last: Mori

first: Jan-Wilhelm

last: Kornfeld

first: Jens

last: Brüning


title: Genetic disruption of COX-1 inhibits multiple oncogenic pathways

status: Public on Jun 22 2015

city: Nashville

first: Dineo

last: Khabele

address: 1161 21st Avenue South

institute: Vanderbily University

summary: We performed RNA sequencing in isogenic models of COX-1 proficient (OV3/SCR) and COX-1 deficient (OV3/COX1KD) OVCAR-3 ovarian cancer cells. COX-1 knockdown was associated with a coordinated anti-oncogenic phenotype, with growth, angiogenesis, migration/invasion, and epithelial-mesenchymal transition among the pathways down-regulated.

overall_design: RNA sequencing was performed at Vanderbilt Technologies for Advanced Genomics (VANTAGE) using Illumina HiSeq 2500.


title: Differential expression between Sh2b3 knockout and wild type mice

city: Framingham

first: Daniel

last: Levy

state: MA

address: 73 Mt. Wayte Avenue, Suite 2

department: Framingham Heart Study

institute: NHLBI

summary: To validate the predicted Sh2b3 derived gene regulatory subnetwork using integrative network approach  in human population study, we examined the gene expression levels of whole blood in WT (wild-type) and Sh2b3-/- mice by RNA sequencing, and identified the differentially expressed genes.

overall_design: RNA sequencing whole blood samples from 4 WT and 4 Sh2b3-/- mice.

first: Meena

last: Madhur

first: Paul

last: Courchesne

first: Tianxiao

last: Huan


title: Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein， regulates plant flowering by targeted alternative polyadenylation

status: Public on Jun 30 2015

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

country: China

summary: Alternative polyadenylation (APA) is a widespread mechanism for gene regulation and has been implicated in flowering, but the molecular basis governing the choice of a specific poly(A) site during the vegetative-to-reproductive growth transition remains unclear. Here we characterize HLP1, an hnRNP A/B protein as a novel regulator for pre-mRNA 3’ end processing in Arabidopsis. Genetic analysis reveals that HLP1 suppresses Flowering Locus C (FLC), a key repressor of flowering in Arabidopsis. Genome-wide mapping of HLP1-RNA interactions indicates that HLP1 binds preferentially to A-rich and U-rich elements around cleavage and polyadenylation sites, implicating a role in 3’-end formation. We show significantly enriched binding of HLP1 to transcripts involved in RNA metabolism and flowering. Comprehensive profiling of the poly(A) site usage reveals that HLP1 mutations cause thousands of poly(A) site shifts. A distal-to-proximal poly(A) site shift in the flowering regulator FCA, a direct target of HLP1, further leading to up-regulated FLC and delayed flowering. Our results elucidate that HLP1 is a novel factor involved in 3’ end processing and controls reproductive timing via targeted APA.

overall_design:
Investigate the role of HLP1 in Alternative Polyadenylation
Contributed by: The Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences

first: Yong

last: Zhang

first: Lianfeng

last: Gu

first: Xiaofeng

last: Cao


first: Jeff

last: Nie

summary: RNA sequencing of SETD2 isogenic renal cell carcinoma cell lines.

overall_design: Examination of RNA expression in SETD2 isogenic cell lines

first: Thai

last: Ho

first: Jinfu

first: Huihuang

last: Yan


title: A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

city: Cambridge

first: John

middle: Edward

last: Froberg

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

summary: The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform identification of direct RNA interacting proteins? (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of interactors, including cohesins, condensins, topoisomerases, RNA helicases, chromatin remodelers and modifiers, which synergistically repress Xi transcription. Inhibiting two or three interactors destabilizes silencing. While Xist attracts some interactors, it repels architectural factors. Xist evicts cohesins from the Xi and directs an Xi-specific chromosome conformation. Upon deleting Xist, the Xi acquires the cohesin-binding and chromosomal architecture of the active X. Our study unveils many layers of Xi repression and demonstrates a central role for RNA in the topological organization of mammalian chromosomes. The RNA-seq data sets generated in this study provide a resource for examining the effects of knockdowns of various Xist-interacting proteins on gene expression. The ChIP-seq data sets provide a comprehensive set of data examining CTCF and cohesion binding the X-chromosome, and the effects of deleting Xist on CTCF and cohesion binding. The Hi-C data is an allele-specific contact map of the X-chromosome higher-order chromatin structure in mouse.

overall_design: RNA-seq in 3 control and 10 knockdown cell lines. ChIP-seq for CTCF, Rad21 and Smc1a in wild-type fibroblasts and Xist-deletion fibroblasts. Hi-C in wild-type and Xist-deletion fibroblasts.

first: J

middle: E

first: C

middle: Y

last: Wei

first: B

last: Kesner

middle: T

last: Lee


title: Acute TNF-induced repression of cell identity genes is mediated by NFkB-directed redistribution of cofactors from super-enhancers

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: The proinflammatory cytokine tumor necrosis factor (TNF) plays a central role in low-grade adipose tissue inflammation and development of insulin resistance during obesity. In this context, nuclear factor kappa-light-chain-enhancer of activated B cells (NFkB), is directly involved and required for the acute activation of the inflammatory gene program. Here we show that the major transactivating subunit of NF?B, v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA), is also required for acute TNF-induced suppression of adipocyte genes. Notably, this repression does not involve RELA binding to the associated enhancers but rather loss of cofactors and enhancer RNA (eRNA) selectively from high occupancy sites within super-enhancers. Based on these data we have developed models that with high accuracy predict which enhancers and genes are repressed by TNF in adipocytes. We show that these models are applicable to other cell types where TNF represses genes associated with super-enhancers in a highly cell type-specific manner. Our results propose a novel paradigm for NF?B-mediated repression, whereby NF?B selectively redistributes cofactors from high occupancy enhancers, thereby specifically repressing super-enhancer-associated cell identity genes.

overall_design: Genome-wide assesment of the acute transcriptional response to TNF in human SGBS adipocytes using RNA- ChIP- and DHS-seq. Total RNA-seq and RNAPII-ChIP seq for vehicle and TNF treated adipocytes are available under GSE60462

first: Søren

last: Fisker Schmidt

first: Bjørk

last: Ditlev Larsen

first: Anne

last: Loft

first: Ronni

last: Nielsen

first: Jesper

last: Grud Skat Madsen


title: Chromatin signature identifies monoallelic gene expression across mammalian cell types (ChIP-seq)

city: Boston

first: Sebastien

last: Vigneau

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Monoallelic expression of autosomal genes (MAE) is a widespread epigenetic phenomenon which is poorly understood, due in part to current limitations of genome-wide approaches for assessing it. Recently, we reported that a specific histone modification signature is strongly associated with MAE, and demonstrated that it can serve as a proxy of MAE in human lymphoblastoid cells (Nag et al. Elife. 2013 Dec 31;2:e01256). Here, we use murine cells to establish that this chromatin signature is conserved between mouse and human, and is associated with MAE in every tested cell type. Our analyses reveal extensive conservation in the identity of MAE genes between the two species. By applying MAE chromatin signature analysis to a large number of cell and tissue types, we show that the MAE state remains consistent during terminal cell differentiation and is predominant among cell-type specific genes, suggesting a link between MAE and specification of cell identity.

overall_design: Chromatin immunoprecipitation with antibodies specific for histone modifications H3K27me3 and H3K36me3 and subsequent high-throughput sequencing were performed on fixed chromatin from a B-lymphoid clonal cell line, derived from 129S1/SvImJ x CAST/EiJ F1 mice and immortalized with Abelson murine leukemia virus.

first: Nag

last: Anwesha

first: Vigneau

last: Sébastien

first: Savova

last: Virginia

first: Zwemer

middle: M

last: Lillian

first: Gimelbrant

last: Alexander


title: Migration-related phenotypic divergence is associated with epigenetic variation in rainbow trout

city: Davis

first: Melinda

last: Baerwald

state: California

address: 1 Shields Avenue

institute: University of California-Davis

type: Methylation profiling by high throughput sequencing

summary: Migration is essential for the reproduction and survival of many animals, yet little is understood about its underlying molecular mechanisms. We used the salmonid Oncorhynchus mykiss to gain mechanistic insight into smoltification, which is a morphological, physiological, and behavioral transition undertaken by some juveniles that culminates in a seaward migration. This species is experimentally tractable and, unlike common model species, displays intra- and inter-population variation in migration propensity. Migratory individuals can produce non-migratory progeny and vice versa, indicating a high degree of phenotypic plasticity. One potential way that phenotypic plasticity might be linked to variation in migration-related life history tactics is through epigenetic regulation of gene expression. To explore this, we quantitatively measured genome-scale DNA methylation in fin tissue using reduced representation bisulfite sequencing of F2 siblings produced from a cross between steelhead (migratory) and rainbow trout (non-migratory) lines. We identified 57 differentially methylated regions (DMRs) between smolt and resident O. mykiss juveniles. DMRs were of high magnitude, ranging from 20-62% differential methylation between life history types, and over half of the gene-associated DMRs were in transcriptional regulatory regions. Many of the DMRs encode proteins with activity relevant to migration-related transitions (e.g. circadian rhythm pathway, nervous system development, protein kinase activity). This study provides the first evidence of a relationship between epigenetic variation and life history divergence associated with a migration-related transition in any species.

overall_design: Comparing global DNA methyldation profiles (via RRBS) of resident and smolt O. mykiss siblings using caudal fin tissue.

middle: R


title: Transcriptome Analysis of Avicel Utilization by Thermomyces lanuginosus

first: Shan

last: Li

address: No.38 Xueqing Road, Haidian Distric

institute: Novogene institute

summary: Thermomyces lanuginosus is a thermophilic fungus whose genome encodes many carbohydrate-active enzymes involved in Avicel degradation. This study examined and compared the transcriptomes of T. lanuginosus during cultivation on Avicesl or glucose. We identified approximately 4485 genes that showed expression differences when T. lanuginosus was cultured on Avicel compared to glucose. Functional annotation of up-regulated genes showed enrichment for proteins predicted to be involved in Avicel degradation, but also many genes encoding proteins of unknown function. Our study represents the first analysis of transcriptomes, with biologic replicates, generated by RNA-seq technology. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of 2-day old Thermomyces lanuginosus were generated by deep sequencing,in duplicate, using Illumina GAIIx.

first: D

first: Z

last: Geng


title: Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics [ChIP-Seq]

city: Chicago

first: Irene

last: Gallego Romero

state: IL

address: 920 E 58th St, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: Comparative genomics studies in primates are extremely restricted due to our limited access to samples from non-human apes. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To begin demonstrating the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating that the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude.

sample_organism:
Pan troglodytes
Homo sapiens

overall_design: We used ChIP-seq to characterize the genome-wide distribution of two types of histone modifications (H3K27me3 and H3K27ac) in three of our chimpanzee iPSCs and compared them to histone modification data from three human iPSC lines from the Roadmap Epigenomics project:

first: Bryan

middle: J

last: Pavlovic

last: Hernando-Herraez

first: Xiang

last: Zhou

first: Michelle

middle: C

last: Ward

first: Nicholas

last: Banovich

first: Courtney

middle: L

last: Kagan

first: Jonathan

last: Burnett

first: Constance

last: Huang

first: Amy

last: Mitrano

first: Claudia

middle: I

last: Chavarria

first: Inbar

middle: F

last: Ben-Nun

first: Yingchun

first: Karen

last: Sabatini

first: Trevor

last: Leonardo

first: Mana

last: Parast

first: Tomas

last: Marques-Bonet

first: Louise

last: Laurent

first: Jeanne

last: Loring

first: Yoav

last: Gilad


title: Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells

city: LYON cedex

first: Robert

last: Dante

address: Centre Léon Bérard 28, rue Laennec

department: Tumoral escape

country: France

institute: Cancer Research Center of Lyon

type: Genome binding/occupancy profiling by genome tiling array

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Replication fork progression during re-replication requires the DNA damage checkpoint and double-strand break repair

first: Terry

middle: L.

last: Orr-Weaver

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

type: Genome variation profiling by genome tiling array


title: Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells (1)

summary: DNA methylation is thought to induce a transcriptional silencing through the combination of two mechanisms: the repulsion of transcriptional activators that do not recognize their binding sites when methylated, and the recruitment of transcriptional repressors that specifically bind methylated DNA. Methyl CpG Binding Domain proteins MeCP2, MBD1 and MBD2 belong to the latter category. However, the exact contribution of each protein in the DNA methylation dependent transcriptional repression occurring during development and diseases remains elusive. Here we present MBD2 ChIPseq data generated from the endogenous protein in an isogenic cellular model of human mammary oncogenic transformation. In immortalized or transformed cells, MBD2 was found in one fourth of methylated regions and associated with transcriptional silencing. Depletion of MBD2 induces upregulations of genes bound by MBD2 and methylated in their transcriptional start site regions. MBD2 was partially redistributed on methylated DNA during oncogenic transformation, independently of DNA methylation changes. Genes downregulated during this transformation preferentially gained MBD2 binding sites on their promoter. Depletion of MBD2 in transformed cells induced the upregulation of some of these repressed genes, independently of the strategy used for the abrogation of oncosuppressive barriers. Our data confirm that MBD2 is a major interpret of DNA methylation, and show an unreported dynamic in this interpretation during oncogenic transformation.

overall_design: Methylated DNA precipitation (MeDP) and Endogenous MBD2 Chromatin Immunoprecipitation (MBD2 ChIP) followed by hight-througput sequencing in HMEC-hTERT and HMLER cells.

first: Guillaume

last: Devailly

first: Mélodie

last: Grandin

first: Laury

last: Perriaud

first: Pauline

last: Mathot

first: Jean-Guy

last: Delcros

first: Anne-Pierre

last: Morel

first: Alain

last: Puisieux

first: Patrick

last: Mehlen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Altered Expression of miRNAs and piRNAs in the Testes of Mtdh exon 3-deficient Mice

city: Iowa City

first: xiangbing

last: meng

state: IA

address: 375 Newton Road

institute: University of Iowa

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: To identify the correlation of the expression of testicular miRNAs and piRNAs with the infertility of Mtdh exon 3 deficient mice
Methods: Total RNAs from individual testis of two WT mice and three homozygous Mtdh exon 3-depleted mice were used to prepare the miRNA sequencing library. After the completed libraries were quantified with an Agilent 2100 Bioanalyzer, the DNA fragments in the libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ and sequenced for 36 cycles on Illumina HiSeq 2000 according to the manufacturer’s instructions. Image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8.0). Subsequently, 3’ adapter sequences were trimmed from clean reads (reads that passed Solexa CHASTITY quality filter) and any reads shorter than 15nt were discarded. Next the 3’-adapter-trimmed-reads (≥ 15nt) were aligned to the latest known human reference miRNA precursor set (Sanger miRBase 19) using Novoalign (v2.07.11). Reads (counts < 2) were discarded when calculating miRNA expression. In order to characterize the isomiR variability, any sequences that matched the miRNA precursors in the mature miRNA region ±4nt (no more than one mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. For piRNAs, the 3’-adapter-trimmed reads (length ≥ 15nt) were aligned to the latest piRNA set in piRNAbank using Novoalign software (v2.07.11). Expression of each piRNA was defined as the mapped tag counts.
Results: Reduced expression of miRNAs was detected in homozygous Mtdh exon 3-deficient testes (Table I). As shown in tables II and III, piRNA expression levels were dysregulated, with some being reduced and others increased in homozygous Mtdh exon 3-deficient testes compared to WT mice.
Conclusions: Our study represents the first detailed analysis of Mtdh deficiency on the expression of small noncoding RNAs, generated by RNA-seq technology. We conclude that Mtdh is correlated to the expression of small non-coding RNAs including miRNAs and piRNAs at testis of mouse.

overall_design: Examine expression of miRNAs and piRNAs at testes of wild type and Mtdh deficent mice

first: Xiangbing

last: Meng

first: Shujie

last: Yang

first: Kimberly

last: Leslie


title: Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells (2)

overall_design: RNAseq of untreated HMEC-hTERT cells, siCtrl, siMBD2 or DAC treated HMLER cells, siCtrl or siMBD2 treated HME-ZEB1-RAS and HME-shP53-RAS cells, in duplicates.


title: Identification of lineage-specific cis-regulatory modules associated with variation in transcription factor binding and chromatin activity using Ornstein-Uhlenbeck models

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

summary: Whole-chromatin profile (FAIRE-seq) in three Drosophila species (D. melanogaster, D. pseudoobscura and D. virilis) in eye-antennal imaginal discs at the stage of third instar wandering larvae.

sample_organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila virilis

overall_design: By the use of Ornstein-Uhlenbeck methods, we assess the evolutionary forces acting on regulatory elements (cis-level) on chromatin activity across Drosophila eye-antennal imaginal discs at the stage of third instar larvae.

first: Marina

last: Naval-Sánchez

first: Delphine

last: Potier

first: Gert

last: Hulselmans

first: Valerie

last: Christiaens


title: Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

city: Baltimore

first: Alisa

last: Mo

state: MD

address: 725 N. Wolfe St. PCTB805

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: We developed an affinity purification approach to isolate tagged nuclei in mice (similar to INTACT; [Deal R.B. and Henikoff S. A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell 18,1030-1040. (2010)]) and used it to characterize genome-wide patterns of transcription, DNA methylation, and chromatin accessibility in 3 major neuron classes of the neocortex (excitatory pyramidal neurons, parvalbumin (PV)-positive GABAergic interneurons, and vasoactive intestinal peptide (VIP)-positive GABAergic interneurons). By combining cell purification and integrative analysis, our findings relate the phenotypic and functional complexity of neocortical neurons to their underlying transcriptional and epigenetic diversity.

overall_design: RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq for histone modifications using INTACT-purified nuclei from the mouse neocortex

first: Eran

last: Mukamel

first: Fred

middle: P

last: Davis

first: Chongyuan

last: Luo

first: Sean

last: Eddy

first: Joseph

last: Ecker

first: Jeremy

last: Nathans


title: Characterizing the Chemoresistant Ovarian Cancer Population using the Heterogeneous PDX

city: Birmingham

first: Charles

last: Landen

state: AL

address: 619 19th St S

department: Obstetrics and Gynecology

institute: University of Alabama at Birmingham

summary: The patient-derived xenograft (PDX) model retains the heterogeneity of patient tumors, allowing a means to not only examine efficacy of a therapy across a population, but also study crucial aspects of cancer biology in response to treatment. Herein we describe the development and characterization of an ovarian-PDX model in order to study the development of chemoresistance. We demonstrate that PDX tumors are not simply composed of tumor-initiating cells, but recapitulate the original tumor’s heterogeneity, oncogene expression profiles, and clinical response to chemotherapy. Combined carboplatin/paclitaxel treatment of PDX tumors enriches the cancer stem cell populations, but persistent tumors are not entirely composed of these populations. RNA-Seq analysis of treated PDX tumors compared to untreated tumors demonstrates a consistently contrasting genetic profile after therapy, suggesting similar, but few, pathways are mediating chemoresistance. The pathways most significantly altered included Protein Kinase A signaling, GNRH signaling, and sphingosine-1-phosphate signaling. Pathways and genes identified by this methodology represent novel approaches to targeting the chemoresistant population in ovarian cancer

overall_design: 6 pairs of Patient-Derived Xenografts (PDX) were ananlyzed using RNA-seq for a total of 12 samples. Each pair consists of a treated and untreated PDX of ovarian cancer. Treated Ovarian cancer PDXs were treated with 4 weeks of a combination of carboplatin and taxol. RNA was isolated and converted to cDNA. RNA-seq was conductred on the Illumina HiSeq 2000 with 50 bp paired end sequencing

middle: N

first: Zachary

last: Dobbin


title: AE9aId1fl/flCreER cells

status: Public on Jun 16 2015

city: Miami

first: Lan

last: Wang

address: 1501 NW 10TH AVE BRB 701

institute: University of Miami

summary: AE9aId1fl/flCreER cells treated with the control vehicle, CBD or 4-OHT

overall_design: We treated AE9aId1fl/flCreER leukemia with 0.1 μM 4-hydroxytamoxifen (4-OHT) for 48 hours or the Id1 inhibitor CBD (at 15 µM) for 16 hours, and isolated RNA for RNA-seq analysis.

first: Stephen

middle: D

last: Nimer


title: Altered epigenetic programming links intestinal inflammation to colon cancer (RNA-seq)

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

summary: This study uses whole-transcriptome sequencing to characterize the transcriptomes of the AOM/DSS mouse model. In this model, mice are treated with dextran sodium sulfate (DSS) to induce colitis. When this treatment is preceded by injections of the weak carcinogen azoxymethane (AOM) the mice develop intestinal tumors. Our results identify sets of differentially expressed genes which are correlated with methylation changes of the corresponding genes.

overall_design: Whole transcriptome analysis of Mus musculus. Three conditions were sequenced and analyzed, the first is an untreated control, the second corresponds to inflammation induced by applying DSS, the third to cancer induced by inflammation and application of AOM. The control condition as well as the AOM-induced cancer condition were analyzed using three replicates, the second condition using 4 replicates.

first: F

last: Lyko

first: Y

last: Bergman


title: Discrete Functions of Rev-erba Couple Metabolism to the Clock

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania


title: Altered epigenetic programming links intestinal inflammation to colon cancer


title: Discrete Functions of Rev-erba Couple Metabolism to the Clock [HTS]

summary: Circadian and metabolic physiology are intricately intertwined, as illustrated by Rev-erb , a transcription factor (TF) that functions both as a core repressive component of the cell autonomous clock and as a regulator of metabolic genes.  Here we show that Rev-erb  modulates the clock and metabolism by different genomic mechanisms. Clock control requires Rev-erb  to bind directly to the genome at its cognate sites, where it competes with activating ROR TFs. By contrast, Rev-erb  regulates metabolic genes primarily by recruiting the HDAC3 corepressor to sites to which it is tethered by cell type-specific transcription factors.  Thus, direct competition between Rev-erb  and ROR TFs provides a universal mechanism for self-sustained control of molecular clock across all tissues, whereas Rev-erb  utilizes lineage-determining factors to convey a tissue-specific epigenomic rhythm that regulates metabolism tailored to the specific need of that tissue.

overall_design: Biological replicates were uploaded in separated files and indicated in the file names.

first: Yuxiang

last: Zhang

first: Matthew

last: Emmett

first: Manashree

last: Damle

first: Zheng

last: Sun

first: Dan

last: Feng

last: Armour

first: Jarrett

last: Remsberg

first: Jennifer

last: Jager

first: Raymond

last: Soccio

first: David

last: Steger

first: Mitchell

last: Lazar


title: Genowide-wide analysis of scc2-4 binding.

city: Kansas City

first: Musinu

last: Zakari

state: Missouri

address: 1000E 50th Street

institute: Stowers Institute for Medical Research

summary: The evolutionarily conserved cohesin complex is crucial for holding sister chromatids together from the time of DNA replication until their segregation during the metaphase to anaphase transition. Human diseases associated with with mutations in the cohesin network are termed "cohesinopathies". Scc2 is required for loading cohesin onto DNA prior to DNA replication. Cornelia de Lange syndrome (CdLS), a developmental disorder characterized by growth and intellectual impairment is caused by mutations in Scc2. How mutations in Scc2 gives rise to these developmental defects is currently unknown, as overt defects in chromosome segregation are not observed in CdLS patients. One hypothesis is that, reduced binding of Scc2 causes gene misregulation. To further explore this idea ChIP-seq was performed using an scc2-4 mutant. We observed from the analysis, we observe reduce binding of Scc2 to Pol II transcribed genes (snoRNAs, ribosomal protein genes) and pol II transcribed genes (tRNAs). Studies are currently underway to examine the biological implications of this observation.

overall_design: Examining genome-wide binding of scc2-4 mutant

first: Rhonda

last: Egidy

first: Christopher

middle: W

last: Seidel

last: Gerton


title: Next Generation RNAseq of neonatal hearts one day post surgery comparing sham, apical resection or apical resecection plus vagotomy treatments

first: Caitlin

last: O'Meara

address: 65 landsdowne street

department: Medicine

institute: Brigham and Women's hospital

summary: We report global RNA expression profiles in whole heart ventricle tissue from postnatal day 2 mice that had undergone surgery 24 hours prior to collection.

overall_design: Heart ventricle mRNA profiles were generated from CD-1 neonatal mice by deep sequencing, in triplicate, on the Illumina HiSeq 2500.

first: Donald

last: Bryant


title: Expression profiling and Pol II occupancy of HeLa cell line treated with CDK9 inhibitor

city: emeryville

first: Zhenhai

last: Gao

address: 4560 Horton street

institute: Novartis Institute for Biomedical Research


title: RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships RDIP-seq)

status: Public on Jun 15 2015

city: Bronx

first: Julie

last: Nadel

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

summary: Mapping of RNA:DNA hybrids in human cells reveals a number of characteristics of these non-canonical  nucleic  acid  structures.    A  directional  sequencing  approach  reveals  the  RNA component of the RNA:DNA hybrid to be purine-rich, indicating a thermodynamic contribution to the stability of these structures.  The RNA:DNA hybrids are enriched at loci with decreased DNA methylation  and  increased  DNase  hypersensitivity,  and  within  larger  domains  with characteristics of heterochromatin formation.  Studies of chromatin at RNA:DNA hybrids shows the  presence  of  the  ILF2  and  ILF3  transcription  factors,  supporting  a  model  of  certain transcription factors binding preferentially to the RNA:DNA conformation.  Overall, there is little to indicate a dependence for RNA:DNA hybrids forming co-transcriptionally, with results from the ribosomal DNA repeat unit instead supporting a model of RNA generating these structures in trans.  The results of the study indicate heterogeneous functions of these genomic elements and new insights into their formation and stability in vivo.

overall_design: Investigation of locatization of RNA in RNA:DNA hybrids genome-wide in HEK293T and IMR-90 cells through RNA:DNA hybrid immunorprecipitation strand-specific sequencing

middle: A

first: John

last: Greally


title: EBV BART MicroRNAs Target Multiple Pro-apoptotic Cellular Genes to Promote Epithelial Cell Survival

city: Durham

first: Dong

last: Kang

state: North Carolina

address: BOX 3025 213 Research Drive, Duke University

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Here, we report a systematic effort to identify pro-apoptotic mRNA targets for the EBV miR-BART miRNAs. We demonstrate that at least five of the 22 miR-BART pre-miRNAs have anti-apoptotic activity and we identify seven pro-apoptotic cellular mRNA targets, six of them novel, that contribute significantly to the observed anti-apoptotic phenotype. Together, these data represent a substantial increase in our understanding of the role of the miR-BART miRNAs in promoting EBV infection and latency.

overall_design: Use of deep sequencing to identify all the miRNAs expressed in C666 cells and PAR-CLIP to comprehensively profile EBV miRNA targets in C666 cells.

first: Rebecca

last: Skalsky

first: Bryan

last: Cullen


title: Massively parallel quantification of the regulatory effects of non-coding genetic variation

last: Vockley

state: NC

address: 101 science drive rm 2193

summary: We report a novel high-throughput method to empirically quantify individual-specific regulatory element activity at the population scale. The approach combines targeted DNA capture with a high-throughput reporter-gene expression assay. As demonstration, we have measured the activity of more than 100 putative regulatory elements from 95 individuals in a single experiment. We found that, in agreement with previous reports, most genetic variants have weak effects on distal regulatory element activity. Because haplotypes are typically maintained within but not between assayed regulatory elements, the approach can be used to identify likely causal regulatory haplotypes that contribute to human phenotypes. Finally, we demonstrate the utility of the method to functionally fine map causal regulatory variants in regions of high linkage disequilibrium identified by expression quantitative trait loci (eQTL) analyses.

overall_design:
104 candidate regulatory elements from 95 individuals were resequenced using Illumina custom amplicon sequencing. We then cloned the resulting DNA fragments into a massively parallel reporter assay to quantify allele-specific regulatory activity from that population.
SNP-fdr.txt contains output of significance evaluation
haplotype.fasta.gz contains the reference used to generate alignment files

first: Cong

last: Guo

first: William

middle: H

last: Majoros

first: Michael

last: Nodzenski

first: Denise

last: Scholtens

first: M

middle: G

last: Hayes

last: Lowe

first: Timothy

last: Reddy


title: Small RNA Solexa sequencing of mouse CD11c+Ia high and CD11c+Ia low cells

city: Shanghai

first: Xiaoping

last: Su

address: 800 Xiangyin Road

institute: National Key Laboratory of Medical Immunology & Institute of Immunology

summary: We applied Illumina massively parallel signature sequencing to identify miRNomes in CD11c+Ia high and CD11c+Ia low cells.The miRNomes of these DC subsets will contribute to investigate the significance of miRNAs in DC immunobiology.

overall_design: Examination of miRNome in CD11c+Ia high and CD11c+Ia low cells . All two mouse cell types.

first: Xuetao

last: Cao


title: Altered epigenetic programming links intestinal inflammation to colon cancer (Bisulfite-seq)

first: Guenter

last: Raddatz

summary: This study uses whole-genome bisulfite sequencing to characterize the methylomes of the AOM/DSS mouse model at single-base resolution. In this model, mice are treated with dextran sodium sulfate (DSS) to induce colitis. When this treatment is preceded by injections of the weak carcinogen azoxymethane (AOM) the mice develop intestinal tumors. Our results identify hypermethylated DMVs as a prominent feature of the colitis methylome that is conserved in intestinal adenocarcinomas. Further analyses reveal a subset of DMV-associated genes, expressed in normal intestinal epithelial cells, that were silenced and hypermethylated in inflamed and cancerous intestinal cells. Together, these findings provide strong support for the hypothesis that inflammatory signals induce a higher risk for cancer development by manipulating the epigenome. .

overall_design: Whole genome methylation analysis of M. musculus. Three conditions were sequenced analyzed, the first is an untreated control, the second corresponds to inflammation, the third to cancer induced by inflammation. All three conditions were analyzed using three replicates.

first: F

last: Lyko

first: Y

last: Bergman


title: Regulating Interleukin-2 activity with engineered receptor signaling clamps

city: Bethesda

first: Peng

last: Li

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Interleukin-2 (IL-2) is a pleiotropic cytokine that regulates lymphocyte function by signaling through heterodimerization of the IL-2Rβ and γc receptor subunits. Previously, we engineered an IL-2 “superkine” (H9) with enhanced affinity for IL-2Rβ. Here, we describe next-generation IL-2 variants that function as “receptor signaling clamps.” They retain high-affinity for IL-2Rβ, thereby inhibiting binding of endogenous IL-2, but their engagement of γc is weakened, thereby attenuating IL-2Rβ-γc heterodimerization. These IL-2 analogues act as partial agonists and can differentially affect lymphocytes poised at distinct activation thresholds. Moreover, one of these variants potently antagonized IL-2 and IL-15 signaling and function better than blocking antibodies against IL-2Rα or IL-2Rβ. Furthermore, this mutein prolonged survival in a model of graft versus host disease and blocked spontaneous proliferation of smoldering adult T-cell leukemia (ATL) T cells ex vivo. This receptor-clamping approach may be a general mechanism-based strategy for engineering cytokine partial agonists for therapeutic immunomodulation.

overall_design: Genome-wide transcription factors binding of STAT5 and mRNA-Sequencing of gene expression profiles in human pre-activated CD8+ T cells.

first: Suman

last: Mitra

first: Aaron

last: Ring

first: Shoba

last: Amarnath

first: Wei

last: Ju

first: Jamie

middle: B

last: Spangler

first: Suzanne

last: Fischer

first: Jangsuk

last: Oh

first: Rosanne

last: Spolski

first: Kipp

last: Weiskopf

first: Holbrook

last: Kohrt

first: Jason

middle: E

last: Foley

first: Sumati

last: Rajagopalan

first: Eric

middle: O

last: Long

first: Daniel

last: Fowler

first: Thomas

last: Waldmann

last: Garcia

first: Warren

last: Leonard


title: Small RNA Solexa sequencing of mouse hematopoietic progenitor and dendritic cell samples

first: Xiaoping

last: Su

summary: We applied Illumina massively parallel signature sequencing to identify miRNomes in hematopoietic stem cells, bone morrow-derived immature DCs, mature DCs, and IL-10 and NO-producing regulatory DCs.The miRNomes of these DC subsets will contribute to investigate the significance of miRNAs in DC immunobiology.

overall_design: Examination of the miRNome in hematopoietic stem cells, bone morrow-derived immature DCs, mature DCs, and IL-10 and NO-producing regulatory DCs. All four mouse cell types.

first: Xuetao

last: Cao


title: The cohesin loader Scc2 regulates key regulatory genes critical for development

first: Musinu

last: Zakari

summary: The evolutionarily conserved cohesin complex is crucial for holding sister chromatids together from the time of DNA replication until their segregation during the metaphase to anaphase transition. Human diseases associated with with mutations in the cohesin network are termed "cohesinopathies". Scc2 is required for loading cohesin onto DNA prior to DNA replication. Cornelia de Lange syndrome (CdLS), a developmental disorder characterized by growth and intellectual impairment is caused by mutations in Scc2. How mutations in Scc2 gives rise to these developmental defects is currently unknown, as overt defects in chromosome segregation are not observed in CdLS patients.This has led to the hypothesis that developmental disorders in CdLS patients are a result of dysregulated gene expression. To examine the transcriptional program of Scc2 mutants called scc2-4, RNA sequencing was performed. Analysis of gene expression program shows upregulation of genes involved in ribosome biogenesis and downregulation of genes needed for oxidative phosphorylation. Studies are currently underway to investigate how scc2-4 mutation causes gene misregulation. The answer(s) could provide insight into the molecular etiology of CdLS.

overall_design: Examining gene expression in 3 biological replicates of scc2-4 relative to wt by Ilumina sequencing

first: Jennifer

last: Gerton

first: Allison

middle: R

last: Peak

first: Chris

last: Seidel


title: Analysis of WRKY33 binding sites and WRKY33-dependent gene expression in Arabidopsis thaliana upon Botrytis cinerea 2100 inoculation

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

institute: Max Planck Institute for Plant Breeding Research

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

overall_design: Refer to individual Series


title: Role of Pou3f1 during mouse pluripotent stem cell neural fate commitment

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

institute: Chinese Academy of Sciences


title: The E3 SUMO ligase Mms21 controls ribosome biogenesis

status: Public on Jun 13 2015

state: MO

department: Genomics

institute: Stowers Institute

summary: The budding yeast E3 SUMO ligase Mms21, a component of the Smc5-6 complex, regulates sister chromatid cohesion, DNA replication, and DNA repair. We identify a role for Mms21 in ribosome biogenesis. The mms21RINGD mutant exhibits reduced rRNA production, nuclear accumulation of 60S and 40S ribosomal proteins, and elevated Gcn4 translation. Genes involved in ribosome biogenesis and translation are down-regulated in the mms21RINGD mutant.

overall_design: Examining gene expression profile of mms21RINGD mutant compared to wild-type by RNA Seq using Ilumina sequencing

first: Dong-Hwan

last: Kim


title: RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships (RNA-seq)

first: Julie

last: Nadel

overall_design: Investigation of expression data genome-wide in HEK293T and IMR-90 cells through RNA-seq, including rRNA

first: John

middle: M

last: Greally


title: WRKY33-dependent expression of Arabidopsis genes upon Botrytis cinerea 2100 inoculation

summary: The Arabidopsis thaliana mutant wrky33 is highly susceptible to the necrotrophic fungus Botrytis cinerea. Comparing the expression profiles of B. cinerea-infected wrky33 and WT plants we identified 2765 differentially expressed genes dependent on WRKY33, of which 1675 were up-regulated in the mutant (termed WRKY33-repressed genes) and 1090 were down-regulated in the mutant. Combined with ChIP-seq data 318 genes were identified as direct functional targets of WRKY33 at 14 h post inoculation with spores of Botrytis cinerea 2100.

overall_design: Comparison of altered gene expression in Arabidopsis WT and wrky33 mutant plants 14 hours post inoculation with Botrytis cinerea 2100.

first: Shouan

last: Liu

first: Rainer

last: Birkenbihl

first: Imre

last: Somssich


title: Transcriptomic analysis of the estrogenic effect of soy protein isolate in rat uterus

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: There are concerns regarding possible reproductive toxicity from consumption of soy including an increased risk of endometriosis and endometrial cancer. We used global uterine gene expression profiles in adult ovariectomized (OVX) female rats assessed by RNAseq to examine the estrogenicity of soy protein isolate (SPI) and the potential for feeding SPI to alter estrogen signaling in the uterus. Rats were fed AIN93G diets made with casein (CAS) or SPI from postnatal day (PND) 30. Rats were OVX on PND 50 and infused with 17 beta-estradiol (E2) or vehicle. E2 increased uterine wet weight (P<0.05) and significantly altered expression of 2084 uterine genes. In contrast, SPI feeding had no effect on uterine weight and only altered expression of 177 genes. Overlap between E2 and SPI genes was limited to 69 genes (3%). GO analysis indicated significant differences in uterine biological processes affected by E2 and SPI and little evidence for recruitment of ER alpha  to the promoters of ER-responsive genes after SPI feeding. The major E2 up-regulated uterine pathways were cancer pathways and extracellular organization. SPI feeding up-regulated uterine PPAR signaling and fatty acid metabolism.  The combination of E2 and SPI feeding resulted in significant regulation of 715 fewer genes relative to E2 alone.  In a separate experiment, the combination of E2 and SPI reversed the ability of E2 to induce uterine proliferation in response to the carcinogen dimethybenz(a)anthracene (DMBA). These data suggest SPI does not act as a weak estrogen in the uterus but appears to be a selective estrogen receptor modulator (SERM) interacting with a small sub-set of E2-regulated genes and to be anti-estrogenic in the presence of endogenous estrogens.

overall_design: Rat uterus mRNA of ovariectomized adult female rats subject to four different diets (Caseine, Caseine + E2, Soy and Soy+E2 )  were sequenced, in triplicate, in an Illumina GAIIx sequencer.

first: Martin

last: Ronis


title: Analyses of Early- and Late-scnRNAs of Tetrahymena

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

institute: Institute of Human Genetics, CNRS

summary: In this study, we demonstrated that there is a novel, unanticipated mechanism regulating programmed DNA elimination: a genome-wide trans-recognition network for IES identification. In this mechanism, Early-scnRNAs produced from Type-A IESs in the MIC identify not only the IESs from which they are derived but also other IESs in trans to trigger the cis-spreading of Late-scnRNA production in the IESs. This cis-spreading of Late-scnRNA production requires heterochromatin formation . Furthermore, these Late-scnRNAs can recognize other IESs in trans. This “chain reaction” of Late-scnRNA production by the trans-recognition network most likely provides strong robustness in DNA elimination by buffering cell-to-cell variability in the initial Early-scnRNA populations.

overall_design: 26 to 32-nt small RNAs from various mutants or from immuno precipitated with Argonaute proteins were analyzed by high-throughput sequencing

first: Tomoko

last: Noto

first: Kensuke

last: Kataoka

first: Jan

last: Suhren


title: WRKY33 binding sites in Arabidopsis upon Botrytis cinerea 2100 inoculation

summary: The Arabidopsis thaliana mutant wrky33 is highly susceptible to the necrotrophic fungus Botrytis cinerea. We identified by ChIP-seq >1680 high-confidence WRKY33 binding sites associated with 1576 genes within the Arabidopsis genome, with all of them being dependent on rapid activation of WRKY33 expression by Botrytis cinerea strain 2100. Genome-wide transcriptional analysis defined 318 genes as direct functional targets at 14 h post inoculation. Comparison between resistant wild-type Columbia-0 and susceptible wrky33 mutant plants revealed that expression of 75% of all WRKY33 regulated targets were down-regulated upon infection, indicating that WRKY33 predominately acts as a repressor. However, WRKY33 appears to possess dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. Our genome-wide analysis confirmed known WRKY33 targets involved in ethylene and jasmonic acid hormone signaling and phytoalexin biosynthesis, but also uncovered a previously unknown role of abscisic acid (ABA) biosynthesis in the complex regulatory circuitry affecting resistance towards Botrytis.

overall_design: Analysis of transgenic plants expressing WRKY33-HA under its native promoter post inoculation with spores of Botrytis cinerea 2100


title: MPE-seq, a New Method for the Genome-wide Analysis of Chromatin Structure

city: La Jolla

first: Haruhiko

last: Ishii

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

summary: In this study we developed MPE-seq, a method for the genome-wide characterization of chromatin that involves the digestion of nuclei with methidiumpropyl-EDTA-Fe(II) [MPE-Fe(II)] followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. We also performed MNase-seq as a comparison. We further performed ChIP-seq using chromatin samples obtained by MPE-Fe(II) or MNase digestion of nuclei.

overall_design: Nuclei from J1 mouse embryonic stem cells were treated with MPE-Fe(II) or MNase. The isolated DNA was sequenced by Illumina HiSeq sequencers. Some of the digested chromatin was studied by performing ChIP-seq using antibodies against histone H2B or H3.

first: James

middle: T

last: Kadonaga

first: Bing

last: Ren


title: Small-RNA asymmetry is directly driven by mammalian Argonautes

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

summary: Asymmetric selection of single-stranded guide RNAs from double-stranded RNA (dsRNA) precursors is crucial for RNA silencing-mediated gene regulation. However, the precise mechanisms for small RNA asymmetry remain unclear, especially since asymmetric selection can still occur under depletion of putative asymmetry sensors, Drosophila R2D2 and mammalian Dicer. Here we report direct contribution of mammalian Argonaute 2 (Ago2) to microRNA (miRNA) asymmetry. Ago2 selects strands with 5´-uridine/adenosine and thermodynamically unstable 5´-ends in parallel through its two sensor regions, which contact 5´-nucleobase and 5´-phosphate(s) of the prospective guide strands, respectively. Consistently, miRNA asymmetry shows characteristic digital-analog superposed patterns reflecting 5'-end nucleotide identity and thermodynamic stability. Furthermore, we demonstrate that cancer-associated miRNA variations reprogram asymmetric selection. Finally, our study presents a model of this universal principle that will aid a comprehensive understanding of miRNA function and therapeutic reinvention of RNA silencing in precision medicine.

overall_design: Immunoprecipitation of WT or mutant Ago2 in mouse ES cells (Ago-null background) and small RNA sequencing

first: T

last: Ueno

first: H


title: Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells

status: Public on Jun 12 2015

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston


title: RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

first: Julie

last: Nadel


title: DNA elimination analysis of scnRNA production-defective Tetrahymena

summary: Analysis of genome-wide IES elimination of Late-scnRNA accumulation-defective cells inducates that Early-scnRNAs are sufficient to induce DNA elimination for a majority of IESs, whereas Late-scnRNAs are important for DNA elimination of some, mainly Type-B, IESs.

overall_design: new MACs of exconjugants were isolated from different mutants at 36 hpm, and the genomic DNA was analyzed by high-throughput sequencing


title: Histone H3.3 maintains genome integrity during mammalian development

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

institute: University of North Carolina at Chapel Hill

summary: Histone H3.3 is a highly conserved histone H3 replacement variant in metazoans, and has been implicated in many important biological processes including cell differentiation and reprogramming. Germline and somatic mutations in H3.3 genomic incorporation pathway components, or in H3.3 encoding genes, have been associated with human congenital diseases and cancers, respectively. However, the role of H3.3 in mammalian development remains unclear. To address this question, we generated H3.3 null mouse models through classical genetic approaches. We found H3.3 plays an essential role in mouse development. Complete depletion of H3.3 leads to developmental retardation and early embryonic lethality. At the cellular level, H3.3 loss triggers cell cycle suppression and cell death. Surprisingly, H3.3 depletion does not dramatically disrupt gene regulation in the developing embryo. Instead, H3.3 depletion causes dysfunction of heterochromatin structures at telomeres, centromeres and pericentromeric regions of chromosomes leading to mitotic defects. The resulting karyotypical abnormalities and DNA damage lead to p53 pathway activation. In summary, our results reveal that an important function of H3.3 is to support chromosomal heterochromatic structures, thus maintaining genome integrity during mammalian development.

overall_design: RNA-seq in embryos at E10.5 comparing 3 samples with the following genotype Trp53-/-; H3f3afl/-; H3f3bfl/-; Sox2-CreTg/0 to three samples with the following genotype Trp53-/-; H3f3afl/+; H3f3bfl/+; Sox2-CreTg/0

first: Chuan-Wei

last: Jang

first: Yoichiro

last: Shibata

first: Della

last: Yee

first: Terry

last: Magnuson


title: Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

department: Biological Sciences

institute: Louisiana State University

summary: In this study, we analyzed the DNA methylation levels of 4799 IAP LTRs in three murine cell types: AB2.2 ES cells, somatic cells and a neuroblastoma cell line Neuro2A. According to the results, half of the IAP LTR retrotransposons show constant methylation patterns between the three cell types whereas the remaining half display variable levels of methylation. About half of the variably methylated IAP LTRs tend to be hypomethylated in ES cells, and nearly all of this group are hypomethylated in Neuro2A cells. Interestingly, the observed hypomethylation in both cell types occur in a non-uniform, locus-specific manner and to various degrees of severity, with some of them being easily detectible by COBRA. Overall, this study demonstrates the feasibility of HT-TREBS to study alterations in DNA methylation at retrotransposons in a locus-specific manner in multiple cell types and further suggests the potential utility of this technique in developing epigenetic biomarkers for tracking disease progression.

overall_design: HT-TREBS has been used with the Ion Torrent PGM platform to analyze the DNA methylation of 4799 IAP LTRs in a locus-specific manner in 3 cell types: somatic cells (previously submitted under GEO Accession GSE49222), AB2.2 ES cells and Neuro2A cells

first: Arundhati

last: Bakshi


title: Genomic analysis of the scc2-4 mutant in budding yeast

first: Musinu

last: Zakari

address: 1000E 50th Street

institute: Stowers Institute for Medical Research


title: Dynamics of gene silencing during X inactivation using allele-specific RNA-Seq

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

summary: Background: During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells containing a single X chromosome. We use mouse female Embryonic Stem Cells (ESCs) with nonrandom XCI and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome (Xi) by high-resolution allele-specific RNA-Seq. Results: Induction of XCI by differentiation of female ESCs shows that genes proximal to the X-inactivation center (XIC) are silenced earlier than distal genes, while lowly expressed genes show faster XCI dynamics than highly expressed genes. The active X chromosome shows a minor but significant increase in gene activity during differentiation, resulting in complete dosage compensation in differentiated cell types. Genes escaping XCI show little or no silencing during early propagation of XCI. Using allele-specific RNA-Seq of Neural Progenitor Cells (NPCs) generated from the female ESCs, we identify three regions distal to the XIC that stably escape XCI during differentiation of the female ESCs, as well as during propagation of the NPCs. These regions coincide with Topologically Associated Domains (TADs) as determined in the undifferentiated female ESCs. Also the previously characterized human gene clusters escaping XCI correlate with TADs. Conclusions: Together, the dynamics of gene silencing observed over the Xi during XCI provide further insight in the formation and maintenance of the repressive Xi complex. The association of regions of escape with TADs, in mouse and human, suggests a regulatory role for TADs during propagation of XCI.

overall_design: 19 RNA-Seq profiles of mouse ESCs, EpiSCs and NPCs, mostly from distant crosses to allow allele specific mapping. 1 HiC profile of an undifferentiated mouse female ESC line containing a Tsix mutation. Mainly focusing on X inactivation.

first: Hindrik

last: Kerstens

first: Tahsin

middle: S

last: Barakat

first: Erik

last: Splinter

first: Wouter

last: de Laat

first: Joost

last: Gribnau

last: Stunnenberg


title: Mutational Interference Mapping Experiment (MIME) to identify the binding site of the HIV-1 Pr55Gag protein to the HIV-1 genomic RNA

city: Strasbourg

first: Redmond

last: Smyth

state: Alsace

address: 15 rue Rene Descartes

department: Architecture et Réactivité de L'ARN

institute: IBMC CNRS

summary: During HIV-1 assembly, the structural protein Pr55Gag specifically selects viral genomic RNA by interacting with packaging signals present in the 5’ untranslated region (UTR). Despite a large number of studies, Pr55Gag binding to the genomic RNA remains poorly understood. To precisely define the Pr55Gag binding site we performed Mutational Interference Mapping Experiment on the 5’UTR and the beginning of the gag gene. To do this, we first generated mutant RNA libraries by in vitro transcription of PCR products that had been subjected to two or three sequential rounds of mutagenic PCR. Sequencing showed a mutation rate of 0.6% ensuring that the vast majority of molecules contained at least one mutation. RNA was mixed with His-tagged Pr55Gag, and functional selection was performed using magnetic beads to separate the bound and the unbound RNA populations. RNA was then reverse transcribed, converted into double stranded DNA, and sequenced using the Illumina HiSeq 2000 platform. This platform generates a large number of sequencing reads but with a read length that is shorter than our target sequence (100 nucleotides from each end of the DNA versus 532 nucleotides). We overcame this limitation by randomly fragmenting our DNA into fragments ranging from 100 to 500 nucleotides during library preparation. Using this strategy sequencing data was obtained for all positions of the target, whilst also retaining linkage data for all pairs of nucleotides whose distance does not exceed the largest fragment size. We aligned approximately 170 million sequences to the reference genome, comprising ~9x107 mutations over ~3x1010 base pairs, after quality control steps. We also sequenced cDNA from a non-mutated template, which we used in a mathematical analysis to correct for errors introduced during in vitro transcription, library preparation and sequencing.

overall_design: Mutational Interference Mapping Experiment of Pr55Gag binding to RNA in vitro

first: R

last: Marquet


title: Gene expression changes in control- and shSamd14-infected R1 fetal liver

status: Public on Jun 11 2015

city: Madison

first: Kyle

last: Hewitt

state: Wisconsin

address: 1111 Highland Ave.

institute: University of Wisconsin

summary: Samd14 was discovered as a novel GATA-2 target gene.  Samd14 increased hematopoietic progenitor levels/activity, promoted signaling by a pathway instrumental for  hematopoietic stem/progenitor cell regulation (Stem Cell Factor/c-Kit), and c-Kit rescued Samd14 loss-of-function phenotypes

overall_design: A control shRNA or an shRNA targeting Samd14 was retrovirally introduced to fetal liver ex vivo cultures. Progenitor cells (CD71-, Ter119-) were isolated and analyzed from these cultures

middle: J

first: Colin

last: Dewey


title: FOXM1 binds directly to non-consensus sequences in the human genome

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

summary: The Forkhead transcription factor, FOXM1, is a key regulator of the cell cycle and is over-expressed in most types of cancer. FOXM1, similar to other Forkhead (FKH) factors binds to a canonical FKH motif in vitro. However, genome-wide mapping studies in different cell lines have shown a lack of enrichment of the FKH motif at FOXM1 binding sites suggesting an alternative mode of chromatin recruitment. We have investigated the role of direct versus indirect DNA binding in FOXM1 recruitment by performing ChIP-seq with WT and DNA binding deficient FOXM1. An in vitro fluorescence polarization (FP) assay was used to identify point mutations in the DNA binding domain (DBD) of FOXM1 that inhibit binding to a FKH consensus sequence. Stable cell lines expressing either WT or DBD mutant green fluorescence protein (GFP)-tagged FOXM1 were utilized for genome-wide mapping studies comparing the distribution of the DBD mutant protein to the WT. This showed that interaction of the DBD of FOXM1 with target DNA is essential for recruitment. Moreover, analysis of protein interactome of the WT versus DBD mutant FOXM1 showed that the reduced recruitment is not due to the mutation inhibiting protein-protein interactions. This study showed that a functional DBD domain is essential for FOXM1 chromatin recruitment. Even in FOXM1 mutants that show almost complete loss of binding the protein-protein interactome and pattern of phosphorylation are largely unaffected. These results strongly support a model whereby FOXM1 is specifically recruited to chromatin through co-factor interactions by binding directly to both canonical and non-canonical DNA sequences.

overall_design: 15 samples, 40 bp single-ended ChIP-Seq libraries from cell lines with antibody for FOXM1 or expressing GFP-tagged FOXM1 (GFP-FOXM1), either wild type (GFP-FOXM1 WT) and with 2 different point mutations (GFP-FOXM1-HA and GFP-FOXM1-RA respectively). FOXM1: 2 replicates, samples labelled FOXM1_GTX; FOXM1-GFP WT: 5 replicates, samples labelled GFP and WT_GFP_FOXM1; FOXM1-GFP HA: 3 replicates, samples labelled GFP_FOXM1_HA; FOXM1-GFP RA: 2 replicates, samples labelled GFP_FOXM1_RA; input libraries: 3 different inputs for the respective experiments.

first: Deborah

last: Sanders

first: Michael

middle: V

last: Gormally

first: Dario

last: Beraldi

first: David

last: Tannahill

first: Chris

last: Taylor

first: Shankar

last: Balasubramanian


title: Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [RNA-Seq]

status: Public on Jun 10 2015

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells is sufficient to induce luminal-to-basal phenotypic switch implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells.

overall_design: RNA-Seq in breast cancer cell-lines

first: Reo

last: Maruyama

first: Ying

last: Su


title: Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 3]

overall_design: Examination of histone H3K27Ac modifications in various breast cancer cell lines.


title: Critical role of histone demethylase Jmjd3 in the regulation of CD4+ T cell differentiation

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

summary: Epigenetic factors have been implicated in the regulation of CD4(+) T-cell differentiation. Jmjd3 plays a role in many biological processes, but its in vivo function in T-cell differentiation remains unknown. Here we report that Jmjd3 ablation promotes CD4(+) T-cell differentiation into Th2 and Th17 cells in the small intestine and colon, and inhibits T-cell differentiation into Th1 cells under different cytokine-polarizing conditions and in a Th1-dependent colitis model. Jmjd3 deficiency also restrains the plasticity of the conversion of Th2, Th17 or Treg cells to Th1 cells. The skewing of T-cell differentiation is concomitant with changes in the expression of key transcription factors and cytokines. H3K27me3 and H3K4me3 levels in Jmjd3-deficient cells are correlated with altered gene expression through interactions with specific transcription factors. Our results identify Jmjd3 as an epigenetic factor in T-cell differentiation via changes in histone methylation and target gene expression.

overall_design: ChIP-seq of histone modification marks H3K4me3 and H3K27me3 in WT and JMJD3 cKO mouse CD4+ T-cells


title: Otx2 controls regional patterning within the MGE and regional identity of the septum [ChIP-Seq]

city: San Francisco

first: John

last: Rubenstein

state: CA

address: 1550 4th Street

department: Psychiatry

institute: UCSF

summary: The Otx2 homeobox transcription factor is essential for gastrulation and early neural development. We generated Otx2 conditional knockout (cKO) mice to investigate its roles in telencephalon development after E9.0. We conducted transcriptional profiling and in situ hybridization to identify genes de-regulated in Otx2 cKO ventral forebrain. In parallel, we used ChIP-seq to identify enhancer elements, OTX2 binding motif, and which de-regulated genes are likely direct targets of Otx2 transcriptional regulation. We found that Otx2 was essential in septum specification; regulation of Fgf signaling in the rostral telencephalon; and medial ganglionic eminence (MGE) patterning, neurogenesis, and oligodendrogenesis. Within the MGE, Otx2 was required for ventral but not dorsal identity; this is the first demonstration of a transcription factor that contributes to regional patterning within the MGE.

overall_design: Microdissected subpallium (septum, MGE, and LGE ) from wildtype E12.5 CD-1 embryos was used in three independentanti-OTX2 ChIP-seq experiments.

first: Renée

last: Hoch

first: Susan

last: Lindtner

first: James

last: Price


title: Androgen Receptor (AR) targets in a cell line from the mouse proximal caput epididymus

first: Katrin

middle: Alice

last: Mooslehner

state: Cambridgeshire

address: Hills Road

department: Paediatrics

institute: Addenbrookes Hospital

summary: Sequence data represent a profile of AR network targets in proliferating and non-proliferating P17 cells without cross linking AR to DNA prior to purification. P17 cells were derived from the mouse epididymal cell line PC1 by genetic modification to express a tagged wild type mouse AR cDNA (N-TAP-mAR). N-TAP-mAR allows purification of multi-protein complexes and their genomic targets with FLAG antibody coupled magnetic beads under native conditions.

overall_design: comparison of AR targets in proliferating versus non-proliferating cells using the PC1 WT cell line (not expressing a tagged AR) as a negative control.

last: Davies


title: Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells [RNA-Seq]

first: Lisha

last: Zhu

summary: We sequenced mRNA from 3 neutrophil cells taken from 3 male adult to generate the gene expression profile of human neutrophil cells

overall_design: Examination of mRNA levels in human neutrophils.

first: Kaiyu

last: Jiang


title: Otx2 controls regional patterning within the MGE and regional identity of the septum

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

overall_design: Refer to individual Series


title: Discovery of novel isoforms of Huntingtin reveals a new hominid-specific exon

city: New York

first: Albert

last: Ruzo

state: NY

address: 1230 York Avenue

department: Laboratory of Stem Cell Biology and Molecular Embryology

institute: The Rockefeller University

summary: Huntington’s disease (HD) is a devastating neurological disorder that is caused by an expansion of the poly-Q tract in exon 1 of the Huntingtin gene (HTT). HTT is an evolutionarily conserved and ubiquitously expressed protein that has been linked to a variety of functions including transcriptional regulation, mitochondrial function, and vesicle transport. This large protein has numerous caspase and calpain cleavage sites and can be decorated with several post-translational modifications such as phosphorylations, acetylations, sumoylations, and palmitoylations. However, the exact function of HTT and the role played by its modifications in the cell is still not well understood. Scrutiny of HTT function has been focused on a single, full length, mRNA.  In this study, we report the discovery of 5 novel HTT mRNA splice isoforms that are expressed in normal and HD-hESC lines as well as cortical neurons differentiated from hESCs. Interestingly, none of the novel isoforms generates a truncated protein. Instead, 4 of the 5 new isoforms specifically eliminate domains and modifications to generate smaller HTT proteins. The fifth novel isoform incorporates a previously unreported additional exon, dubbed 41b, which is hominid-specific and introduces a potential phosphorylation site in the protein. The discovery of this hominid-specific isoform may shed light on human-specific pathogenic mechanisms of HTT, which could not be investigated with current mouse models of the disease.  Furthermore, it provides a new human-specific target for drug screening in Huntington’s disease.

overall_design: We performed RNAseq of human embryonic stem cells in pluripotency conditions to check expression of multiple HTT isoforms.

first: Ali

last: Brivanlou


title: Transcriptional profile of XBP1-deficient ovarian cancer-associated dendritic cells (DCs)

first: Juan

last: Cubillos-Ruiz

institute: Weill Cornell Medicine

summary: ID8-based ovarian tumors were developed for 3 weeks in wild type (WT, N=3) or conditional knockout mice selectively deleting XBP1 in CD11c positive cells (KO, N=3). Tumor-associated DCs were independently sorted via FACS and used for transcriptional profiling.

overall_design: Total RNA from sorted tumor-associated DCs (N=3/genotype) was independently isolated using the miRVANA kit (Life Technologies) and further purified and concentrated using minElute columns (Qiagen). RNA integrity was confirmed using an Agilent Bioanalyzer 2100.

first: Laurie

last: Glimcher


title: Structural basis for retroviral integration into nucleosomes

city: London

first: Peter

middle: P

last: Cherepanov

address: 1 Midland Road

institute: The Francis Crick Institute

summary: Retroviral integration is catalyzed by a tetramer of integrase (IN) assembled on viral DNA ends in a stable complex, known as the intasome. How the intasome interfaces with chromosomal DNA, which exists in the form of nucleosomal arrays, is currently unknown. Here we show that the prototype foamy virus (PFV) intasome is proficient at stable capture of nucleosomes as targets for integration. Single-particle cryo-electron microscopy (EM) reveals a multivalent intasome-nucleosome interface involving both gyres of nucleosomal DNA and one H2A-H2B heterodimer. While the histone octamer remains intact, the DNA is lifted from the surface of the H2A-H2B heterodimer to allow integration at strongly preferred superhelix location (SHL) ±3.5 positions. Amino acid substitutions disrupting these contacts impinge on the ability of the intasome to engage nucleosomes in vitro and redistribute viral integration sites on the genomic scale. Our findings elucidate the molecular basis for nucleosome capture by the viral DNA recombination machinery and the underlying nucleosome plasticity that allows integration.

overall_design: Genomic positions of integration sites of WT and mutant PFV vectors in HT1080 cells were determined using ligation-mediated PCR and next generation sequencing. Integration sites of purified recombinant PFV intasome into deproteinized human genomic DNA were used as a reference dataset.

first: Erik

last: Serrao

first: Alan

last: Engelman


title: Compensatory induction of MYC expression by sustained CDK9 inhibition via a BRD4-dependent mechanism: Pol II occupancy profiling by ChIP-Seq in HeLa cell line in the presence or absence of CDK9 inhibition

city: emeryville

first: Zhenhai

last: Gao

state: California

address: 4560 Horton street

institute: Novartis Institute for Biomedical Research

summary: CDK9 is the kinase subunit of P-TEFb that enables RNA polymerase (Pol) II to transit from promoter-proximal pausing to productive elongation. Although considerable interest exists in CDK9 as a therapeutic target, little progress has been made due to the lack of highly selective inhibitors. Here, we describe the development of i-CDK9 as such an inhibitor that potently suppresses CDK9 phosphorylation of substrates and causes genome-wide Pol II pausing. While most genes experience reduced expression, MYC and other primary response genes increase expression upon sustained i-CDK9 treatment. Essential for this increase, the bromodomain protein BRD4 captures P-TEFb from 7SK snRNP to deliver to target genes and also enhances CDK9’s activity and resistance to inhibition. Because the i-CDK9-induced MYC expression and binding to P-TEFb compensate for P-TEFb’s loss of activity, only the simultaneous inhibition of CDK9 and MYC can efficiently induce growth arrest and apoptosis of cancer cells, suggesting the potential of a combinatorial treatment strategy.

overall_design: ChIP-seq of Pol II in HeLa cells before or after i-CDk9 treatment

first: Guoying

middle: K

last: Yu

first: Carolina

last: Arias

first: Ben

last: Weisburd

first: Alexandre

last: Mercier

first: Huasong

last: Lu

first: Qiang

last: Zhou


title: Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells [ChIP-Seq]

summary: We applied ChIP-Seq on two histone marks: H3K4me1 and H3K27ac in healthy human neutrophils. After peak calling, we obtained the peak regions enriched with H3K4me1 and H3K27ac histone marks and identifed aciive enhancers (H3K27ac+/H3K4me1+) and H3K27ac active enhancers  (H3K27ac+/H3K4me1-) in human neutrophils and checked whether those enhancers are located in the LD blocks of 22 SNPs associtated with Juvenile Idiopathic Arthritis.

overall_design: Identification of active enhancers in human neutrohils


title: Identification of transcripts regulated by CEBPA protein and its P30 isoform in K562

city: Rome

first: Alessandro

last: Fatica

address: P.le Aldo Moro 5

department: Biology and Biotechnology "C. Darwin"

country: Italy

institute: Sapienza University of Rome

summary: To investigate the effect of CEBPA and its mutant isoform P30 on the expression of mRNAs and long non-coding RNAs (lncRNAs), we utilized the K562 AML cell line carrying a stable and Tet-on inducible CEBPA  or P30 allele.

overall_design: Based on the expression of known CEBPA transcriptional targets, we selected RNA extracted from 48 hours of induction (CEBPA or P30)  together with RNA extracted from control-induced cells (CTR).  2 biological replicates for each sample have been utilized.

first: James

last: Hughes

first: Ivano

last: Legnini


title: Genome-wide binding and mechanistic analyses of Smchd1 mediated epigenetic regulation [ChIP-Seq, MBD-Seq]

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

institute: the university of Adelaide

summary:
Purpose: The aim of this study is (1) to identify the chromatin occupancy of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain; (2) to profile key epigenetic marks H3K4me3, H3K27me3 and DNA methylation in wild type and Smchd1 null NSCs; (3) to identify the chromatin occupancy of Ctcf in wild type and Smchd1 null NSCs.
Methods: Chromatin immunoprecipitation for Smchd1, H3K4me3, H3K27me3 and Ctcf was performed essentially as in (Nelson et al. 2006). Briefly, nuclei were isolated from formaldehyde crosslinked NSCs and chromatin was fragmented by sonication. Chromatin immunoprecipitation was performed with corresponding antibodies for Smchd1, H3K4me3 and H3K27me3. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking. Isolated DNA was used to generate sequencing libraries with Illumina's TruSeq DNA Sample Preparation Kit or Ovation Ultralow system (NuGen) according to manufacturer's instruction. Libraries were pooled and sequenced on the Illumina HiSeq 2000 platform for 100 bp single-end reads. Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.12.4.2, running on the instrument computer. Real-time base calling on the HiSeq instrument computer was performed with the RTA software. Illumina CASAVA1.8 pipeline was used to generate the sequence data. To examine the level of DNA methylation, genomic DNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) and methylated DNA was isolated via binding to the methyl-CpG binding domain of human MBD2 protein coupled beads using the MethylMiner methylated DNA enrichment kit (Life Technologies) according to the manufacturer’s instructions. Isolated DNA was used to generate sequencing libraries as for the ChIP-seq experiment with Illumina’s TruSeq DNA Sample Preparation Kit according to manufacturer's instruction and sequenced on the Illumina HiSeq 2000 platform for 49 bp single-end reads. Sequencing analysis was performed as described for the ChIP-seq experiments.

overall_design: Chromatin occupancy of the epigenetic regulator Smchd1 in neural stem cells (NSCs) derived from E14.5 mouse brain was determined by Smchd1 ChIP-seq. Enrichment of H3K4me3 and H3K27me3 in wild type and Smchd1 null NSCs were assessed by H3K4me3 and H3K27me3 ChIP-seq, respectively.  DNA methylation in wild type and Smchd1 null NSCs was assessed by MBD-seq. Chromatin occupancy of Ctcf in wild type and Smchd1 null NSCs was determined by by Ctcf ChIP-seq.


title: USP7 cooperates with SCML2 to regulate the activity of PRC1

city: New York City

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor Rm 211

institute: NYU School of Medicine / HHMI

summary: In this experiment, we sought to identify the distribution of USP7 on chromatin relative to other PRC1 components

overall_design: ChIP-seq for USP7 in 293T-REx cells

first: Emilio

last: Lecona

first: Varun

last: Narendra


title: Next generation RNA sequencing to identify overexpressed transporter genes in Zymoseptoria tritici field strains

city: Thiverval-Grignon

first: Sabine

last: Fillinger

department: UMR1290 BIOGER

institute: INRA

summary: Septoria leaf blotch is a worldwide threat for wheat and mainly controlled by the application of synthetic fungicides. The fungal pathogen responsible for this disease, Zymoseptoria tritici, was shown as highly adaptable to its host plant, but also to fungicide challenge. Over the past decades it developed resistance to most fungicides due to target site modifications. Recently isolated strains showed cross-resistance to diverse fungicides and to unrelated drugs, suggesting a resistance mechanism that seems rarer in phytopathogenic fungi, known as multidrug resistance (MDR) in other organisms. In this study we show for two Z. tritici MDR strains, MDR6 and MDR7, enhanced prochloraz efflux sensitive to the modulators amitryptiline and chlorpromazine. Efflux was also inhibited by verapamil in the MDR7strain. Transcriptomics revealed several overexpressed transporter genes in both MDR strains, out of which the expression of the MgMFS1 transporter gene was the strongest and constitutively high in tested MDR field strains. Its inactivation in the MDR6 strain abolished resistance to fungicides with different modes of action revealing its involvement in the MDR phenomenon in Z. tritici.

overall_design: A total of four strains were compared, two sensitive (IPO323, S6) and two MDR strains (09-ASA-3apz; 09-CB01) with three replicates each. All strains were grown in liquid YPD medium to exponential growth.

first: Selim

last: Omrane

first: Hind

last: Sghyer

first: Catherine

last: Lanen

first: Colette

last: Audéon

first: Anne-Sophie

last: Walker


title: Semiconductor-based sequencing of genome-wide DNA methylation states

first: Michael

last: Corley

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

summary: Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used  approach to study DNA methylation genome-wide. Here, we present a novel MeDIP-Seq  protocol compatible with the Ion Torrent semiconductor-based sequencing platform that  is scalable and accurately identifies sites of differential DNA methylation. Additionally,  we demonstrate that the high-throughput data derived from MeDIP-Seq on the Ion  Torrent platform provides adequate coverage of CpG cytosines, the methylation states  of which we validated at single-base resolution on the Infinium HumanMethylation450K  Beadchip array. We applied this integrative approach to further investigate the role of  DNA methylation in alternative splicing and to profile 5-mC and 5-hmC variants of DNA  methylation in normal human brain tissue that we observed localize over distinct  genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have  broad utility and add to the current methodologies for profiling genome-wide DNA  methylation states in normal and disease conditions.

overall_design: MeDIP-Seq on Ion Torrent Platform in HCT116 and Human Brain

first: Alika

last: Maunakea


title: Somatic piRNAs in the adult mouse

city: Los Angeles

first: Dario

last: Boffelli

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

summary: Small RNAs were deep sequenced from the liver and spleen of adult mice in an effort to identify somatic piRNAs.  Following sequencing of all small RNAs, known non-coding RNAs were computationally removed from the dataset. The remaining RNAs were then mapped to the genome and analyzed for sequence characteristics (5' base, length) typical of known piRNAs.  To determine if any of the identified small RNAs were MIWI2 dependent, we deep sequenced small RNAs from liver and spleen of MIWI2 KO mice and analyzed them as above.

overall_design: We deep sequenced small RNAs from the liver and spleen of one WT mouse and one MIWI2 knock-out mouse.  We then trimmed sequencing adapters and removed known ncRNAs (rRNA, tRNA, snoRNA, snRNA, miRNA) from the dataset before aligning reads to the mm9 assembly of the mouse genome.

first: Jennifer

last: Yamtich

first: Seok-Jin

last: Heo

first: Joseph

last: Dhahbi

first: David

last: Martin


title: Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [DGE]

first: Kornelia

last: Polyak

state: MA

summary: Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells is sufficient to induce luminal-to-basal phenotypic switch implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells.

overall_design: Digital gene expression profiles of basal-like, luminal and their heterofusion cells were generated by deep sequencing, using Helicos HeliScope.

first: Reo

last: Maruyama

first: Ying

last: Su

first: Noga

last: Bloushtain-Qimron


title: Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [ChIP-Seq 1]

overall_design: Examination of histone H3K27me3 modifications in 6 cell lines


title: c-Jun impedes somatic cell reprogramming by activating mesenchymal core regulators and suppressing pluripotent ones

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

summary: The somatic cell fate can be converted to tumor or pluripotent ones by ectopic expression of transcription factors in vitro and in vivo. Many oncogenic transcription factors are known to mediate both fates as they share similar proliferative and metabolic properties. Paradoxically, we found c-Jun as the first oncogene that appears to specify a somatic fate, oppose the pluripotent one and impede reprogramming. We performed a series of high through out sequencing to understand the way cJun works.

overall_design: To understand how c-Jun drives mESCs differentiating, we obtained c-Jun TetOn mESCs, and performed RNAseq 36h later with dox inducing or not . To understand why c-Jun blocks reprogramming while c-JunDN and Jdp2 can replace Oct4, we overexpressed these factors with KSM during reprogramming and performed RNAseq 3 Days after virus transfection. Moreover, to extend understand how these factors regulate gene expression, we also overexpressed these factors in MEF and performed RNAseq. Further more, to understand how cJun regulates cell fates and gene expression, we overexpressed c-Jun in mouse ESC and performed ChIP-seq. Also, we performed c-JunDN ChIP-seq during somatic cells reprogramming on day 3, to explore the binding sites of c-JunDN.

first: Jiekai

last: Chen

first: Duanqing

last: Pei


title: Transcriptional profiling of BXD dorsal root ganglia

city: Berkeley

first: Takeshi

last: Morita

address: 355 LSA

department: Molecular and Cell Biology

institute: University of California - Berkeley

summary: We sequenced dorsal root ganglia mRNA from 25 BXD recombinant inbred mouse strains to determine their variation in gene expression.

overall_design: Dorsal root ganglia mRNA profiles of recombinant inbred mouse strains

first: Rachel

last: Brem

first: Diana

last: Bautista


title: BATSeq of ESC-FCS/ESC-2i/NSC

status: Public on Jun 09 2015

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

country: Spain

institute: CRG

summary: Single-cell polyadenylation site quantification

overall_design: 48 single cells each of murine embryonic stem cells maintained in FCS+LIF medium ("ESC"), embryonic stem cells maintained in serum free, 2i containing medium ("2i") and neural stem cells ("NSC") were sequenced by BATSeq, a single cell transcriptomic protocol for mapping polyadenylation sites in single cells.

first: Simon

last: Anders

first: Aleksandra

last: Pekowska

first: Aino

middle: I

last: Järvelin

first: Wolfgang

last: Huber

first: Vicente

last: Pelechano

last: Steinmetz


title: Ribosome profiling of E. coli K-12 MG1655 MOPS rich media with 0.2% glucose

city: La Jolla

first: Haythem

last: Latif

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive

institute: University of California San Diego

summary: Ribosome profiling was performed on E. coli wild type cells. All replicates were grown to an OD of ~0.4 in MOPS rich Media with 0.2% glucose supplemented, aerobically in shake flasks. Cultures were treated with chloramphenicol 2 min prior to harvest.

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

overall_design: Two biological replicates

first: Richard

last: Szubin

first: Karsten

last: Zengler

first: Berhnard

last: Palsson