title: p53 Enables Self Renewal of Nephron Progenitor Cells

city: New Orleans

first: Yuwen

address: 1430 Tulane Ave SL37 RM5534

department: Pediatrics

institute: Tulane University

summary: p53 limits the self-renewing ability of a variety of stem cells. Here, contrary to its classical role in restraining cell proliferation, we demonstrate a divergent function of p53 in maintenance of self-renewal of the nephron progenitor population in the embryonic mouse kidney. p53-null nephron progenitor cells (NPC) exhibit progressive loss of the self-renewing progenitor niche in the cap mesenchyme, identified by Cited1 and Six2 expression, and loss of cap integrity. Nephron endowment is regulated by NPC availability and their differentiation to nephrons. Quantitatively, the Six2p53-/- cap has 30% fewer Six2GFP+ cells. While the apoptotic index is unchanged the proliferation index is significantly lower, in accordance with cell cycle analysis data showing less mutant Six2p53-/-;GFP+ cells in S and G2/M phases in comparison to Six2p53+/+;GFP+ cells. The mutant kidneys also show nephron deficit and decreased Fgf8 expression. To investigate the underlying changes in gene expression in the cap mesenchyme that contribute to the Six2p53-/- phenotype, we utilized RNA-Seq for transcriptome comparison.  Top biological processes affected by p53 loss are development and morphogenesis, cell adhesion/migration, cell survival and metabolism. Cells from the mutant CM showed increased cellular ROS levels as well as deregulated expression of energy metabolism and mitochondrial genes suggesting metabolic dysfunction. Adhesion defects are visualized by decreased immunostaining of adhesion marker NCAM, and may possibly contribute to the differentiation defect as well.  Altogether our data suggest a novel role for p53 in enabling self-renewal of the NPC and preservation of the progenitor niche, and thus regulating nephron endowment.

overall_design: mRNA profiles of wild-type (WT) and conditional p53 knockout (KO) of Six2+ mouse nephron progenitor cells (NPC) at embryonic day 15.5

first: Jiao

last: Liu

first: Marilyn

first: Zubaida

last: Saifudeen


title: Stretch-Enhancers Delineate Disease-Associated Regulatory Nodes in T Cells

status: Public on Feb 18 2015

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

country: USA

institute: National Institutes of Health

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: T Cell stretch-enhancers are vulnerable to Jak inhibitor tofacitinib

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Treatment of T cells with the Janus kinase (JAK) inhibitor, tofacitinib, disproportionately altered the expression of RA risk genes with stretech-enhancer (SE) structures.

first: Yasuko

last: Furumoto

first: Kan

last: Jiang

first: Yuka

last: Kanno

first: Rahul

last: Roychoudhuri

first: Nicholas

middle: P

last: Restifo

first: Francis

last: Collins

first: Vittorio

last: Sartorelli

first: John

middle: J

last: O'Shea


title: c-Myc Transcriptionally Amplifies Sox2 Target Genes to Regulate Self-Renewal in Multipotent Otic Progenitor Cells [RNA-Seq]

city: Boston

first: David

last: Corey

state: MA

address: 220 Longwood Ave.

department: Neurobiology

institute: Harvard Medical School

summary: An immortalized multipotent otic progenitor (iMOP) cell was generated by transient expression of c-Myc in Sox2-expressing otic progenitor cells. The procedure activated endogenous c-Myc expression in the cells and amplified existing Sox2-dependent transcripts to promote self-renewal. Downregulation of c-Myc expression following growth factor withdrawal resulted in a molecular switch from self-renewal to otic differentiation.

overall_design: Progenitor cells  from embryonic inner ear that form otospheres were infected with a c-Myc retrovirus to promote self-renewal

first: Kelvin

last: Kwan

first: Jun

last: Shen


title: Paraoxonase 2 Serves a Proapopotic Function in Mouse and Human Cells in Response to the Pseudomonas aeruginosa Quorum-Sensing Molecule N-(3-oxododecanoyl)-Homoserine Lactone.

status: Public on Feb 14 2015

city: Berkeley

first: Terry

middle: E

last: Machen

state: CA

address: 231 LSA

department: Molec/Cell Bio

institute: Univ California-Berkeley

summary: Pseudomonas aeruginosa use quorum-sensing molecules, including N-(3-oxododecanoyl)-homoserine lactone (C12), for intercellular communication. C12 activated apoptosis in mouse embryo fibroblasts (MEF) from both wild type (WT) and Bax/Bak double knock-out mice (WT MEF and DKO MEF that were responsive to C12, DKOR MEF): nuclei fragmented; mitochondrial membrane potential (∆ψmito) depolarized; Ca2+ was released from the endoplasmic reticulum (ER), increasing cytosolic [Ca2+] (Cacyto); caspase 3/7 was activated. DKOR MEF had been isolated from a nonclonal pool of DKO MEF that were non-responsive to C12 (DKONR MEF). RNAseq analysis, qPCR and western blots showed that WT and DKOR MEF both expressed genes associated with cancer, including paraoxonase 2 (PON2), while DKONR MEF expressed little PON2. Adenovirus-mediated expression of human PON2 in DKONR MEF rendered them responsive to C12: ∆ψmito depolarized, Cacyto increased and caspase 3/7 activated. Human embryonic kidney 293T (HEK293T) cells expressed low levels of endogenous PON2, and these cells were also less responsive to C12. Overexpression of PON2, but not PON2-H114Q (no lactonase activity) in HEK293T cells caused them to become sensitive to C12. Because [C12] may reach high levels in biofilms in lungs of cystic fibrosis (CF) patients, PON2 lactonase activity may control ∆ψmito, Ca2+ release from the ER and apoptosis in CF airway epithelia. Coupled with previous data, these results also indicate that PON2 uses its lactonase activity to prevent Bax- and Bak-dependent apoptosis in response to common proapoptotic drugs like doxorubicin, staurosporine but activates Bax- and Bak-independent apoptosis in response to C12.

overall_design: Gene expression profiling of mouse embryo fibroblasts from WT and Bax/Bak double knock-out mice (C12 responsive and non-reponsive cell lines).

first: C

last: Schwarzer

first: F

last: Zu

first: T

last: Morita

first: A

middle: G

last: Whitt

middle: M

last: Neely

last: Li


title: Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals

status: Public on Feb 16 2015

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Microbiologie and Infectiologie

country: Canada

institute: Université de Sherbrooke Centre of Excellence in RNA Biology

type: Non-coding RNA profiling by high throughput sequencing

type: Expression profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Reduced insulin secretion in WFS1-deficient mice may be related to downregulation of Trpm5

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

summary: Wolfram syndrome, an autosomal recessive disorder characterized by juvenile-onset diabetes mellitus and optic atrophy, is caused by mutations in the WFS1 gene. WFS1 encodes an endoplasmic reticulum resident transmembrane protein. The Wfs1-null mice exhibit progressive insulin deficiency and diabetes. The aim of the present study was to describe the insulin secretion and transcriptome of pancreatic islets in WFS1-deficient mice. WFS1-deficient (Wfs1KO) mice had considerably less pancreatic islets than heterozygous (Wfs1HZ) or wild-type (WT) mice. Wfs1KO pancreatic islets secreted less insulin after stimulation with 2 and 10 mM glucose and with tolbutamide solution compared to WT and Wfs1HZ islets, but not after stimulation with 20 mM glucose. Differences in proinsulin amount were not statistically significant although there was a trend that Wfs1KO had an increased level of proinsulin. After stimulation with 2 mM glucose solution the proinsulin/insulin ratio in Wfs1KO was significantly higher than that of WT and Wfs1HZ. RNA-seq from pancreatic islets found melastatin-related transient receptor potential subfamily member 5 protein gene (Trpm5) to be downregulated in WFS1-deficient mice. Functional annotation of RNA sequencing results showed that WFS1 deficiency influenced significantly the pathways related to tissue morphology, endocrine system development and function, molecular transport network. These findings suggest an interactive role of WFS1 and TRPM5 in insulin secretion.

overall_design: 12 samples: three genotypes, 4 individuals in each genotype

first: Marilin

last: Ivask

first: Alison

last: Hugill

first: Mario

last: Plaas

last: Kõks


title: FBXW7 modulates stress response by post-translational modification of HSF1

city: New York

first: Nikos

last: Kourtis

address: 550 First Avenue

institute: NYU School of Medicine


title: Identification of active transcriptional regulatory elements with GRO-seq

status: Public on Feb 19 2015

city: Ithaca

first: Charles

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

summary: Transcriptional regulatory elements (TREs), including enhancers and promoters, determine the transcription levels of associated genes.  We have recently shown that global run-on and sequencing (GRO-seq) with enrichment for 5'-capped RNAs reveals active TREs with high accuracy.  Here, we demonstrate that active TREs can be identified by applying sensitive machine-learning methods to standard GRO-seq data.  This approach allows TREs to be assayed together with gene expression levels and other transcriptional features in a single experiment.  Our prediction method, called discriminative Regulatory Element detection from GRO-seq (dREG), summarizes GRO-seq read counts at multiple scales and uses support vector regression to identify active TREs.  The predicted TREs are more strongly enriched for several marks of transcriptional activation, including eQTL, GWAS-associated SNPs, H3K27ac, and transcription factor binding than those identified by alternative functional assays.  Using dREG, we survey TREs in eight human cell types and provide new insights into global patterns of TRE function.

overall_design:
We analyzed GRO-seq or PRO-seq data from eight human cell lines.

Please note that this study comprises new sample data plus reanalysis of old Sample data submitted by another user. Existing PRO-seq or GRO-seq data was combined as detailed in the GSE66031_readme.txt.
See GSM1613181 and GSM1613182 Sample records for data processing information.


title: Direct regulation of T cell exhaustion by NFAT

status: Public on Feb 13 2015

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute


title: Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans

city: Stanford

first: Can

last: Cenik

address: 300 Pasteur Dr, Alway Building Rm M344

department: Genetics

institute: Stanford University

summary: Elucidating the extent and consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding and chromatin have been explored, little is known about global variation in translation and its genetic determinants among humans. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA levels, translation, and protein abundance suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences.  Finally, we identify genetic differences that specifically modulate ribosome occupancy - many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation.

overall_design: Ribosome profiling and RNA sequencing experiments from human lymphoblastoid cells

first: Elif

last: Sarinay Cenik

first: Gun

middle: W

last: Byeon

first: Fabian

last: Grubert

first: Sophie

middle: I

last: Candille

first: Damek

last: Spacek

first: Jason

middle: A

last: Reuter

first: Bilal

last: Alsallakh

first: Hagen

last: Tilgner

first: Hua

last: Tang

first: Emiliano

last: Ricci

first: Carlos

middle: L

last: Araya

first: Michael

last: Snyder


title: Direct regulation of T cell exhaustion by NFAT [RNA-Seq]

summary: During persistent antigen stimulation, CD8+ cytolytic T cells (CTL) show a gradual decrease in effector function, or “exhaustion”, which impairs the immune response to tumors and infections. Here we show that NFAT, a transcription factor with an established role in T cell activation, in parallel controls a second transcriptional program conferring the characteristic features of CD8+ T cell exhaustion, including upregulation of genes encoding inhibitory cell surface receptors and diminished TCR signaling. Expression of an engineered NFAT1, which induces this negative regulatory program in the absence of the effector program, interferes with the ability of CD8+ T cells to protect against Listeria infection or attenuate tumor growth in vivo. NFAT elicits this second program of gene expression in large part by binding to a subset of the sites occupied by NFAT during a typical effector response, suggesting that a balance between the two pathways determines the outcome of TCR signaling.

overall_design: Understanding the role of CA-RIT-NFAT1 in T cells

first: Gustavo

last: Martinez

first: Renata

last: Pereira

first: Anjana

last: Rao


title: Genome-wide maps of RNAPII Ser5(P) in HEK 293T cells after treatment with 5-aza-CdR

city: Bronx

first: Maria-Paz

last: Ramos

state: New York

address: 1301 Morris Park Ave, Price 314

institute: Albert Einstein College of Medicine

summary: DNA methylation can be abnormally regulated in human disease and associated with effects on gene transcription that appear to be causally related to pathogenesis.  The potential to use pharmacological agents that reverse this dysregulation is therefore an attractive possibility.  To test how 5-aza-2’-deoxycytidine (5-aza-CdR) influences the genome therapeutically, we exposed non-malignant cells in culture to the agent and used genome-wide assays to assess the cellular response.  We found that cells allowed to recover from 5-aza-CdR treatment only partially recover DNA methylation levels, retaining an epigenetic “imprint” of drug exposure.  We show very limited transcriptional responses to demethylation of not only protein-coding genes but also loci encoding non-coding RNAs, with a limited proportion of the induced genes acquiring new promoter activation within gene bodies.  The data revealed an uncoupling of DNA methylation effects at promoters, with demethylation mostly unaccompanied by transcriptional changes.  The limited panel of genes induced by 5-aza-CdR resembles those activated in other human cell types exposed to the drug, and represents loci targeted for Polycomb-mediated silencing in stem cells, suggesting a model for the therapeutic effects of the drug.  Our results do not support the hypothesis of DNA methylation having a predominant role to regulate transcriptional noise in the genome, and indicate that DNA methylation acts only as part of a larger complex system of transcriptional regulation.  The targeting of 5-aza-CdR effects with its clastogenic consequences to euchromatin raises concerns that the use of 5-aza-CdR has innate tumorigenic consequences, requiring its cautious use in diseases involving epigenetic dysregulation.

overall_design: Examination of RNAPII Ser5(P) localization by ChIP-seq in HEK 293T cell after treatment with 5-aza-CdR.

first: N

last: Wijetunga

first: Andrew

middle: S

last: McLellan

first: Masako

last: Suzuki

first: John

last: Greally


title: HEK 293T cells RNA-seq data treated with 5-aza-2-deoxycytidine

overall_design: mRNA profile of 5 different samples of HEK 293T cells treated with 5-aza-CdR


title: RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation

city: Tucson

first: Ramin

last: Yadegari

state: Arizona

address: 1140 E. South Campus Dr.

department: Plant Sciences

institute: University of Arizona

summary: Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the gene regulatory networks that control endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments, and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene co-expression network analysis identified co-expression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a co-expression module highly correlated with the basal endosperm transfer layer (BETL) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types.

overall_design: RNAs from ten compartments of the maize kernel including the central starchy endosperm (CSE), conducting zone (CZ), aleurone (AL), basal endosperm transfer layer (BETL), embryo-surrounding region (ESR), nucellus (NU), pericarp (PE), placenta-chalazal region (PC), the vascular region of the pedicel (PED), and the embryo (EMB) were isolated at 8 days after pollination (DAP) using laser-capture microdissection and sequenced using an Illumina HiSeq 2000 platform.

first: Junpeng

last: Zhan

first: Dhiraj

last: Thakare

first: Chuang

last: Ma

first: Alan

last: Lloyd

first: Neesha

last: Nixon

first: Angela

last: Arakaki

first: William

last: Burnett

first: Kyle

middle: O

last: Logan

first: Dongfang

last: Wang

first: Xiangfeng

first: Gary

middle: N

last: Drews


title: HEK 293T cells HELP-tagging cytosine methylation data treated with 5-aza-2-deoxycytidine

first: Maria-Paz

type: Methylation profiling by high throughput sequencing

overall_design: Cytosine methylation profile of 4 different samples of HEK 293T treated with 5-aza-CdR


title: DNA demethylation by 5-aza-2'-deoxycytidine is imprinted targeted to euchromatin and has limited transcriptional consequences


title: Highly parallel identification of sequence preferences for eukaryotic C2H2 zinc finger domains using a bacterial 1-hybrid assay

status: Public on Feb 17 2015

city: Montreal

first: Hamed

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

institute: McGill University

summary: The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs), each of which typically binds a DNA nucleotide triplet within a larger binding site.  Frequent recombination and diversification of their DNA-contacting residues suggests that these zinc fingers play a prevalent role in adaptive evolution.  Very little is known about the function and evolution of the vast majority of C2H2-ZFs, including whether they even bind DNA.  Using the bacterial 1-hybrid (B1H) system, we determined DNA-binding motifs for thousands of individual natural C2H2-ZFs, and correlated them with the C2H2-ZF specificity residues.

overall_design:
We generated 47,072 variants of the DNA-binding domain of the well-characterized three-C2H2-ZF protein Egr1, in which the third C2H2-ZF ('F3') was replaced with a natural C2H2-ZF.  We screened this library using the bacterial 1-hybrid (B1H) system to assess the relative preference of each protein for 200 of the 256 possible NNN NGG GCG variants of the optimal Egr1 binding site, GCG TGG GCG, each in duplicate. Each sample might have been sequenced multiple times, in which case multiple raw and processed data files are indicated.
This data represent bacterial 1-hybrid assays using three different "Original Library Samples", OLS-A, OLS-B, and OLS-C. The 'characteristics:OLS' indicates which OLS was used as the initial material for each of the assays.
The processed data contains unique ID given to each sequence in the library and its abundance count. The 'OLS.info.xlsx' file contains the mapping of these IDs to different sequences.

first: Sanie

last: Mnaimneh

first: Kathy

last: Lam

first: Timothy

middle: R

last: Hughes


title: HuR- dependent regulation of mRNA splicing is essential for the B cell antibody response

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs


title: HuR- dependent regulation of mRNA splicing is essential for the B cell antibody response [iCLIP-Seq]

summary: Post-transcriptional regulation of mRNA by the RNA binding protein HuR is required in B cells for the germinal centre reaction and for the production of class-switched antibodies in response to T-independent antigens. Transcriptome-wide examination of RNA isoforms, abundance and translation in HuR-deficient B cells, together with direct measurements of HuR-RNA interaction,  revealed that HuR-dependent mRNA splicing affects hundreds of transcripts including the dihydrolipoyl succinyltransferase (Dlst), a subunit of the aketoglutaratedehydrogenase (aKGDH) enzyme. In the absence of HuR, defective mitochondrial metabolism results in high levels of reactive oxygen species and B cell death. Our study shows how post-transcriptional processes control the balance of energy metabolism required for B cell proliferation and differentiation.

overall_design: iCLIP analysis of HuR:RNA interaction in LPS-activated splenic B cells from C57BL/6 mice.  Three biological replicates were sequenced using Illumina Genome Analyzer Iix platform.

first: Manuel

middle: D

last: Diaz-Muñoz

first: Sarah

last: Bell

first: Kirsten

last: Fairfax

first: Elisa

last: Monzon-Casanova

first: Adam

middle: F

last: Cunningham

first: Mar

last: Gonzalez-Porta

first: Simon

last: Andrews

first: Victoria

last: Bunik

first: Kathi

last: Zarnack

first: Tomaz

last: Curk

first: Dimitris

last: Kontoyiannis

first: Jernej

last: Ule

first: Martin

last: Turner


title: Direct regulation of T cell exhaustion by NFAT [ChIP-Seq]

first: Tarmo

last: Äijö

overall_design: Determination of NFAT1 binding sites in CD8 T cells in vitro

first: Gustavo

last: Martinez

first: Renata

last: Pereira

first: Anjana

last: Rao


title: HuR- dependent regulation of mRNA splicing is essential for the B cell antibody response [RNA-Seq]

first: Felix

last: Krueger

overall_design: Sequencing analysis of B cell transcriptome using Illumina TruSeq mRNA sample prep kit and Illumina platform. RNA was isolated from ex-vivo or LPS-activated (48h) splenic B cells from HuRflox/flox x mb1wt control or HuRflox/flox x mb1cre mice. 3-4 biological replicates per genotype and condition.

first: Manuel

last: Diaz-Muñoz


title: Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MeDIP-seq)

city: St. Louis

first: Hyung Joo

last: Lee

state: MO

address: 4515 McKinley Avenue

department: Department of Genetics

institute: Washington University School of Medicine

summary: DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis.

overall_design: MeDIP profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.

first: Stephen

last: Johnson

first: Ting

last: Wang


title: Gene Expression in AJ and AcB60 mice following Salmonella infection

status: Public on Feb 12 2015

first: Sean

last: Beatty

state: Quebec

address: 3649 Promenade Sir-William-Osler

summary: Analysis of differential genome-wide gene expression within the splenic homogenate of A/J and AcB60 mice, both naïve mice and those infected with Salmonella Typhimrium

overall_design: Total RNA was islolated from the splenic homogenate of naïve A/J and AcB60 mice, as well as mice infected with 1000 CFUs of Salmonella Typhimuirum and sacrified 3, 5, and 7 days post-infection

middle: C

first: Danielle

last: Malo


title: Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos


title: Chromatin dynamics and gene regulation by GR

first: Songjoon

last: Baek

address: 41 Library Drive

department: CCR

institute: NCI / NIH


title: Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

city: Leuven

first: Kristofer

last: Davie

state: Flemish-Brabant

address: Herestraat 49 Bus 602

department: Center for Human Genetics / VIB Center for Brain and Disease Research

country: Belgium

institute: KU Leuven

summary: Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes.

overall_design: FAIRE-Seq in Drosophila wild type eye-antennal imaginal discs (2 wt strains); ATAC-Seq in Drosophila wild type eye-antennal imaginal discs (3 wt strains) ; FAIRE-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late);  ATAC-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila eye discs with Unpaired over-expression (2 biological replicates); CTCF ChIP-seq in Drosophila eye discs; ChIP-seq input in Drosophila eye discs

first: Jelle

last: Jacobs

first: Delphine

last: Potier

first: Valerie

last: Christiaens

first: Stein

last: Aerts


title: Cohesin regulates gene expression through spatial clustering of enhancer elements

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary: H3K27Ac ChIP-seq in wild type and cohesin-deficient thymocytes

overall_design: Rad21 was deleted in CD4+ CD8+ double positive (DP) thymocytes by crossing a Rad21 floxed allele with a Cd4-driven Cre transgene. DP positive thymocytes were FACS-sorted from control and Rad21-/- littermates, which were then used to perform chromatin immunoprecipitation for histone H3 acetylated on lysine 27 (H3K27Ac).

first: Matthias

last: Merkenschlager


title: Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos (MRE-seq)

overall_design: MRE profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.


title: Long-term expandable SOX9+ chondrogenic ectomesenchymal cells from human pluripotent stem cells

status: Public on Feb 15 2015

city: Houston

first: Naoki

last: Nakayama

state: Texas

address: 7000 Fannin, Suite 1200

department: Institute of Molecular Medicine

institute: the University of Texas Health Science Center at Houston

summary:
Purpose: We have succeeded in the generation and long-term expansion of SOX9-expressing CD271+PDGFRa+CD73+ chondrogenic ectomesenchymal cells from the PAX3/SOX10/FOXD3-expressing MIXL1-CD271hiPDGFRaloCD73- neural crest-like progeny of human pluripotent stem cells in a chemically defined medium supplemented with Nodal/Activin/TGFb inhibitor (SB) and FGF2 (hereafter called FSB). When “primed” with TGFb, such cells efficiently formed translucent cartilage particles, which were completely mineralized in 12 weeks in immunocompromized mice. Under the FSB condition, ectomesenchymal cells were expandable without loss of chondrogenic potential for at least 16 passages, maintained normal karyotype for at least 10 passages, which any conditions deviated from it (e.g. FGF2 alone or SB alone) failed to support. In order to address the molecular basis of such effects of FSB, a series of RNA-seq experiments were carried out.
Methods: We generated and compared the transcriptome profiles of human ectomesenchymal cells expanded under FSB  with those cultured under FSB first then under FGF2 alone (F).  As a control, we also generated transcriptome of ectomesenchymal cells expanded from the begining under F conditions. RNA-sequencing libraries were prepared using a SureSelect Strand Specific RNA Library Preparation kit (Agilent technologies, Santa Clara, CA). Sequencing was performed on an Illumina HiSeq 1500 using a TruSeq Rapid SBS kit (Illumina, San Diego, CA) in a 50-base single-end mode. Sequenced reads were mapped against the human reference genome (GRCh37), using TopHat v2.0.12 (http://ccb.jhu.edu/software/tophat/index.shtml). Expression levels were calculated as fragments per kilobase of exon per million mapped fragments (FPKMs) using Cufflinks v2.1.1 (http://cole-trapnell-lab.github.io/cufflinks).
Results: Ectomesenchymal cells maintained under FSB conditions preferentially expressed genes representing embryonic progenitors (SOX4/12, LIN28A/B, MYCN), cranial mesenchymes (ALX1/3/4) and chondroprogenitors (SOX9, COL2a1) of the neural crest origin (SOX8/9, NGFR, NES). In contrast, those cultured under FSB then F, still expressed SOX4/11/12, but lost LIN28, MYCN, ALX1/3/4, NGFR, COL2a1 expression. Interestingl it enhances expresion ofTGFβ-inducible genes such as THBS1/2 and DCN  and osteogenesis-related genes such as  COL1a1/2 and RUNX1/2.
Conclusions: The CD271+CD73+ ectomesenchymal cells accumulated under FSB conditions possess an mRNA profile of proliferating primitive neural crest/ectomesenchymal cells, although they lacked SOX10 expression, which is critical for neural and melanocytic lineage commitment. Transition from FSB to F conditions supressed the proliferation-related genes expression and enhanced the ossification/mineralization, vasculogenesis/angiogenesis, and cardiac myogenesis-related gene expression. Thus, suppression of TGFβ signaling by SB does not seem to freeze the developmental stage of the hPSC-derived neural crest during expansion. Such suppression may instead simply support the high proliferative potential of the cells as well as the expression of SOX9 (and COL2a1), and thereby maintain chondrogenic activity. SOX9 expression initiated at the specification and pre-migratory stages is transient in trunk neural crest but persists in cranial neural crest. The chondrogenic CD271+CD73+ ectomesenchymal cells that maintain SOX9 transcription and translation may therefore represent proliferating cranial neural crest, with a slight commitment to non-neural lineages.

overall_design: Examination of human ES-derived neural crest-like progenies expanded in 3 different culture media. Each group contains three biological replicates.

first: Hirotsugu

last: Oda


title: Changes in DNaseI hypersensitivity upon ultradian (pulsed) hormone stimulation [Dnase-seq]

summary: We report changes in DNaseI accessibility genome-wide upon treatment with corticosterone (Cort) for 20 minutes, treatment with Cort for 20 minutes followed by hormone withdrawal for 40 minutes, 60 minutes continuous stimulation with Cort, as well as Mock treatments for the aforementioned conditions.

overall_design: We examine DNaseI accessibility genome-wide upon following treatments: 0' Cort, 20' Cort, 60' Cort Pulsed, 60' Cort Constant, as well as Mock treatments simulating 0' Cort, 20' Cort, 60' Cort Pulsed, 60' Cort Constant.

first: Diana

last: Stavreva

first: Gordon

last: Hager

first: Myong-Hee

last: Sung


title: GR and Pol II interactions with regulatory elements in response to ultradian (pulsed) hormone stimulation [ChIP-seq]

summary: We report changes in GR and Pol II binding profiles genome-wide upon treatment with corticosterone (Cort) for 20 minutes, treatment with Cort for 20 minutes followed by hormone withdrawal for 40 minutes, 60 minutes continuous stimulation with Cort, and  60 minutes continuous stimulation with Dexamethasone (Dex).

overall_design: We examine GR binding upon following treatments: 0' Cort, 20' Cort, 60' Cort Pulsed, 60' Cort Constant; Pol II binding upon following treatments: 0' Cort, 20' Cort, 60' Cort Pulsed, 60' Cort Constant, 60' Dex Constant;  Pol II binding upon Mock treatments simulating 0' Cort, 20' Cort, 60' Cort Pulsed, 60' Cort Constant; CTCF binding profile of untreated cells.


title: Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (RNA-seq)

status: Public on Feb 11 2015

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Maize anthers, the male reproductive floral organs, express two classes of phased, small interfering RNAs (phasiRNAs). RNA profiling from ten sequential cohorts of staged maize anthers plus mature pollen revealed that 21-nt phased siRNAs (21-phasiRNAs) from 463 loci appear abruptly after germinal and initial somatic cell fate specification and then diminish, while 24-nt phased siRNAs (24-phasiRNAs) from 176 loci coordinately accumulate during meiosis and persist as haploid gametophytes differentiate into pollen. RNA sequencing of anther developmental mutants, together with in situ RNA hybridization detection of phasiRNA biogenesis factors, demonstrated that 21-phasiRNAs and 24-phasiRNAs are independently regulated. Furthermore, 21-phasiRNAs require epidermal cells while 24-phasiRNAs require functional tapetal cells.  Maize phasiRNAs and mammalian PIWI-interacting RNAs (piRNAs) illustrate convergent evolution of small RNAs to support male reproduction.

overall_design: Examination of maize phasiRNAs by high throughput sequencing for RNA-seq, small RNA and PARE profiling.

first: Jixian

last: Zhai

first: Han

last: Zhang

first: Siwaret

last: Arikit

first: Kun

last: Huang

first: Virginia

last: Walbot


title: Multiple Arkadia/RNF111 structures coordinate its Polycomb body association and transcriptional control

city: La Jolla

first: Huaiyu

last: Sun

address: 10010 North Torrey Pines Road

department: Molecular and Cell Biology Laboratory

institute: Salk Institute for Biological Studies

summary: The RING domain protein Arkadia/RNF111 is a ubiquitin ligase in the transforming growth factor beta (TGFβ) pathway. We previously identified Arkadia as a small ubiquitin-like modifier (SUMO)-binding protein with clustered SUMO-interacting motifs (SIMs) that together form a SUMO-binding domain (SBD). However, precisely how SUMO interaction contributes to the function of Arkadia was not resolved. Through analytical molecular and cell biology, we found that the SIMs share redundant function with Arkadia's M domain, a region distinguishing Arkadia from its paralogs ARKL1/ARKL2 and the prototypical SUMO-targeted ubiquitin ligase (STUbL) RNF4. The SIMs and M domain together promote both Arkadia's colocalization with CBX4/Pc2, a component of Polycomb bodies, and the activation of a TGFbeta pathway transcription reporter. Transcriptome profiling through RNA sequencing showed that Arkadia can both promote and inhibit gene expression, indicating that Arkadia's activity in transcriptional control may depend on the epigenetic context, defined by Polycomb repressive complexes and DNA methylation [Sun, Liu, and Hunter (2014) Mol Cell Biol 34(16):2981-2995].

overall_design: To determine the role of Arkadia in TGFβ signaling at the transcriptome level, the profiles of TGFβ-stimulated gene expression were examined in Ark+/+ (Ark_WT), Ark-/- (Ark_null), and Arkadia (WT and sim mutant)-reconstituted Ark-/- MEFs. RNA sequencing was carried out using poly(A)-enriched RNA samples from unstimulated cells and cells treated with TGFβ for 1h, 4h, or 16h as indicated. Two batches of sequencing data for a total of 16 independent samples were submitted.

first: Tony

last: Hunter


title: HuR- dependent regulation of mRNA splicing is essential for the B cell antibody response [Ribo-Seq]

first: Felix

last: Krueger

overall_design: Sequencing analysis of ribosome protected RNA fragments in ex vivo or LPS-activated splenic B cells was performed using ARTseq™ Ribosome Profiling Kit - Mammalian (Epicentre, RPHMR12126) and Illumina platform. Splenic B cells come from HuRf/f control or HuR cKO mice. 4-5 biological replicates per genotype and condition.

first: Manuel

last: Diaz-Muñoz

first: Sarah

last: Bell

first: Kirsten

last: Fairfax

first: Elisa

last: Monzon-Casanova

first: Adam

last: Cunningham

first: Mar

last: Gonzalez-Porta

first: Simon

last: Andrews

first: Victoria

last: Bunik

first: Kathi

last: Zarnack

first: Tomaz

last: Curk

first: Dimitris

last: Kontoyiannis

first: Jernej

last: Ule

first: Martin

last: Turner


title: Macrophage epoxygenase determines a pro-fibrotic transcriptomesignature

status: Public on Feb 10 2015

first: Jacques

last: Behmoaras

address: Du Cane road

department: Centre for Complement and Inflammation Research (CCIR),

institute: Imperial College

summary: Epoxygenases belong to the cytochrome P450 family and they generate epoxyeicosatrienoic acids (EETs) known to have anti-inflammatory effects but little is known about their role in macrophage function. By high-throughput sequencing of RNA (RNA-seq) in primary macrophages derived fromrodents and humans, we establish the relative expression of epoxygenases in these cells. Zinc-finger nuclease-mediated targeted gene deletion of the major ratmacrophage epoxygenaseCyp2j4 (orthologue of human CYP2J2),resulted inreduced EET synthesis. Cyp2j4-/-macrophages have relatively increased PPARγ levels and show a pro-fibrotic transcriptome,displayingover-expression of a specific subset of genes (260 transcripts) primarily involved in extracellular matrix, with fibronectin being the most abundantly expressed transcript.Fibronectin expression is under the control of epoxygenase activity in human and rat primary macrophages. In keeping with the invitro findings, Cyp2j4-/- rats show up-regulation of type I collagen following unilateral ureter obstruction (UUO) of the kidney and quantitative proteomics analysis (LC-MS/MS) showed increased renal type I collagen and fibronectin protein abundance resulting from experimentally induced crescentic glomerulonephritis in these rats. Taken together, these results identify the rat epoxygenase Cyp2j4 as a determinant of a pro-fibrotic macrophage transcriptome that could have implications in various inflammatory conditions depending on macrophage function.

overall_design: Gene expression profile generated for macrophages in wild type and Cyp2j4 KO WKY rats

first: Prashant

last: Srivastava


title: Spatiotemporal and cell-type dependent phasiRNA biogenesis in maize male reproduction (PARE)

first: Blake

last: Meyers

overall_design: Examination of maize phasiRNAs by high throughput sequencing for RNA-seq, small RNA, and PARE profiling

first: Jixian

last: Zhai

first: Han

last: Zhang

first: Siwaret

last: Arikit

first: Kun

last: Huang

first: Virginia

last: Walbot


title: Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

summary: Approximately 75% of the human genome is transcribed, the majority of which does not encode protein. However, most noncoding RNA (ncRNA) is rapidly degraded after transcription, and relatively few have established functions, questioning the significance of this observation. Here we show that esBAF, a SWI/SNF family nucleosome remodeling factor, suppresses transcription of ncRNAs from approximately 57,000 nucleosome-depleted regions (NDRs) throughout the genome of mouse embryonic stem cells (ESCs). We show that esBAF functions both to keep NDRs nucleosome-free and to promote elevated nucleosome occupancy adjacent to NDRs. Reduction of adjacent nucleosome occupancy upon esBAF depletion is strongly correlated with ncRNA expression, suggesting that flanking nucleosomes form a barrier to pervasive transcription. Upon forcing nucleosome occupancy near an NDR using a nucleosome-positioning sequence, we find that esBAF is no longer required to silence transcription. These data reveal a novel role for esBAF in suppressing pervasive transcription from open chromatin regions in ESCs.

overall_design: Examine nucleosome occupancy (MNase-Seq) and transcript production (CapSeq and RNA-Seq) in EGFP KD and Smarca4 KD ESCs

first: Weifeng

last: Gu

first: Benjamin

last: Carone

last: Landry

first: Oliver

last: Rando

first: Craig

last: Mello

first: Thomas

last: Fazzio


title: Epigenome analysis of serum cell-free circulating DNA in progression of HBV-related Hepatocellular carcinoma

city: San Diego

first: Shicheng

last: Guo

address: 8730 Costa Verde

institute: MCRI, SHSCI, GHH, UCSD

summary:
Purpose:  Aberrantly methylated DNA are hallmarks for many cancers, HCC included. Tumor shed its DNA into circulation stream, and serum DNA methylation analysis is a less-invasive and accessable way to judge the primary tumor status. The goals of this study are to compare DNA methylation profiling in serum cell-free DNA from different stages of HCC progression including healthy control, chronic HBV carrier, HBV-related liver Cirrhosis and HCC, to establish HCC development-related aberrnat DNA methylation patterns.
Methods: MBD methylCap/seq was carried out to screen differentially methylated CpG islands in serum cell-free DNA on four different stage of HBV-related HCC development. MSP and multiplex-BSP validation was performed using independent serum DNA or tumor and adjacent tissues.
Results: Using a MBD methylCap/seq platform, we produced 33- to 37- million raw reads per sample and mapped them, in about half of the raw reads, to human genome(build h19) in the serum cf DNA of healthy control, HBV carrier, HBV cirrhosis and HCC. The mapped reads formed 180k to 260k peaks per sample, with 160 k common peaks shared by four samples. After subtraction of the common peaks, there left 51k, 107k and 78 k DMRs representing hypermethylations, in HBV carrier, HBV cirrhosis and HCC, respectively. We define those DMRs as early, middle and late when these DMRS occurred and maintained in HBV carrier, HBV cirrhosis and HCC, which including 27k, 24k and 19k DMRs, corresponding to 1,416, 1,337, 1,006 genes. GO analysis of them revealed gene categories and pathways associated with tumorogenenisis related process
Conclusions: Our study represents the first detailed analysis of serum cf-DNA methylation profiling in the progression of HBV related HCC development. The processed data analysis here offers a comprehensive evaluation of DNA methylation in serum cf DNA. We conclude that MBD methylCap/seq based methylation profiling would benefit epigenetic research in HCC.

overall_design: Serum cell-free DNA fragment enrichment according to their methylation strength by MBD MethylCap/deep sequencing, using illumina GAIIx.

first: Jian

last: Yu

first: Yangxing

last: Zhao

first: Hongyu

first: Jingfeng

last: Sun


title: Cistromic and epigenomic changes in Prdm16 knock-out brown adipose tissue

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Prdm16 is a transcription factor that drives a complete program of brown adipocyte differentiation, but the mechanism by which Prdm16 activates gene transcription remains unknown. Utilizing ChIP-seq teqhnique, we found that Prdm16 binds to chromatin at/near many brown fat-selective genes in BAT. Interestingly, Prdm16-deficiency dramatically reduced the binding of Med1 to Prdm16-target sites. Indeed, Prdm16 binds and recruits Med1 to BAT-enriched genes and the loss of Prdm16 caused a fundamental change in chromatin architecture at key BAT-selective genes and also reduced transcirptional activity. Moreover, Prdm16, through its interaction with Med1, defines and regulates the activity of super-enhancers that drive the expression of cell identity genes. Together, these data demonstrate that Prdm16 drives gene transcription by recruiting Med1 to control chromatin architecture and super-enhancers.

overall_design: Brown adipose tissues were collected from Prdm16 knockout and wiletype 9-month-old mice and ChIP-seq was performed for Prdm16, PolII, Med1, and H3K27ac.

first: Matthew

last: Harms

first: Suzanne

last: Shapira

first: Yugong

last: Ho

first: Jeff

last: Ishibashi

first: Sona

last: Rajakumari

first: Kyoung-Jae

last: Won

first: Patrick

last: Seale


title: A unique chromatin complex occupies young alpha-satellite arrays of human centromeres

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Using high-resolution chromatin immunoprecipitation (ChIP) of centromere components and clustering of sequence data we find that specific dimeric alpha-satellite units shared by multiple individuals dominate functional human centromeres.

overall_design: We have analyzed the chromatin landscape of the human genome using paired-end MNase-seq

first: Jitendra

last: Thakur

first: Steven


title: RNA-Seq Versus Oligonucleotide Array Assessment of Dose-Dependent TCDD-elicited Hepatic Gene Expression in Mice

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

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

overall_design: Refer to individual Series


title: The Genetic Architecture of Gene Expression Levels in Wild Baboons

city: Durham

first: Jenny

last: Tung

state: NC

address: 125 Science Drive

institute: Duke University

summary: Primate evolution has been argued to result, in part, from changes in how genes are regulated. However, we still know little about gene regulation in natural primate populations. We conducted an RNA sequencing (RNA-seq)-based study of baboons from an intensively studied wild population. We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substantial evidence for, and surprising power to detect, genetic effects on gene expression levels in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes; interestingly, genes with eQTL significantly overlapped between baboons and a comparable human eQTL data set. Our results suggest that genes vary in their tolerance of genetic perturbation, and that this property may be conserved across species. Further, they establish the feasibility of eQTL mapping using RNA-seq data alone, and represent an important step towards understanding the genetic architecture of gene expression in primates.

overall_design: 63 samples (1 per individual) from a wild population of baboons to understand genetic contributions to population variance in gene expression levels

first: Xiang

last: Zhou

first: Susan

last: Alberts

last: Stephens

first: Yoav

last: Gilad


title: RNA-Seq Versus Oligonucleotide Array Assessment of Dose-Dependent TCDD-elicited Hepatic Gene Expression in Mice [RNA-Seq]

summary: Dose-dependent hepatic gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure as well as compare the performance of RNA-Seq and Agilent oligonucleotide microarrays for detection and identificatioin of differentially expressed genes.

overall_design: Five biological replicates for each dose (0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30) of TCDD and sesame oil vehicle

first: Kelly

last: Fader

first: Timothy

last: Zacharewski


title: ALS-causative mutations in FUS/TLS confer gain- and loss-of-function by altered association with SMN and U1-snRNP

first: Xiang-Dong

last: Fu

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: The RNA-binding protein FUS/TLS, mutation in which is causative of the fatal motor neuron disease ALS, is demonstrated to directly bind to the U1-snRNP and SMN complexes. ALS-causative mutations in FUS/TLS are shown to abnormally enhance their interaction with SMN and reduce interaction with U1-snRNP. Correspondingly, global RNA analysis reveals a mutant-dependent loss of splicing activity, with ALS-linked mutants failing to reverse changes caused by loss of wild-type FUS/TLS. Furthermore, a common FUS/TLS mutant-associated RNA splicing signature is identified in ALS patient fibroblasts. Taken together, our studies establish potentially converging disease mechanisms in ALS and spinal muscular atrophy, with ALS-causative mutants acquiring properties representing both gain (dysregulation of SMN) and loss (reduced RNA processing mediated by U1-snRNP) of function.

overall_design: RNA-mediated oligonucleotide Annealing, Selection, and Ligation with Next-Generation sequencing (RASL-seq) method was used for analyzing alternative splicing changes. Oligonucleotide probes are designed to anneal to the exon-exon junctions. The probe library was assembled to assess 5530 unique alternative splicing events, most of which were exon inclusion or skipping, with a minority for alternative 5’- or 3’- splice sites. The splicing changes were compared among groups of reducing FUS/TLS or SMN levels, or expressing various FUS mutations to determine the loss versus gain of FUS/TLS function on splicing regulation.

first: Shuying

last: Sun

first: Shuo-Chien

last: Ling

first: Jinsong

last: Qiu

first: Claudio

middle: P

last: Albuquerque

first: Yu

first: Seiya

last: Tokunaga

first: Hairi

last: Li

first: Haiyan

first: Anh

last: Bui

first: Gene

last: Yeo

first: Eric

last: Huang

first: Kevin

last: Eggan

first: Huilin

first: Clotilde

last: Lagier-Tourenne

first: Don

last: Cleveland


title: Epigenome in brown and white adipose tissue

first: Hee-Woong

last: Lim

summary: PR (PRD1-BF1-RIZ1 homologous) domain-containing 16 (PRDM16) drives a brown fat differentiation program, but the mechanisms by which PRDM16 activates brown fat-selective genes have been unclear. Through chromatin immunoprecipitation (ChIP) followed by deep sequencing (ChIP-seq) analyses in brown adipose tissue (BAT), we reveal that PRDM16 binding is highly enriched at a broad set of brown fat-selective genes. Importantly, we found that PRDM16 physically binds to MED1, a component of the Mediator complex, and recruits it to superenhancers at brown fat-selective genes. PRDM16 deficiency in BAT reduces MED1 binding at PRDM16 target sites and causes a fundamental change in chromatin architecture at key brown fat-selective genes. Together, these data indicate that PRDM16 controls chromatin architecture and superenhancer activity in BAT.

overall_design: H3K27ac/H3K4me1 histone modification and PolII transcription profiles in mouse brown and white adipose tissues. H3 ChIP-seq as a control for histone modification.

first: David

last: Steger

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells [ChIP-Seq]

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

summary: DNA methylation is catalysed by DNA methyltransferases (DNMTs) and is necessary for a correct embryonic development. On the other hand, the DNA demethylation is mediated by the Ten Eleven Translocation (Tet) proteins through oxidation of 5-methyl cytosine (5mC) to 5-hydroxyl (5hmC), 5-formyl (5fC) and 5-carboxyl (5caC) cytosine, and by the Thymine-DNA glycosylase (TDG) that excises the 5fC and 5caC. In embryonic stem cells (ESCs), gene promoters are maintained in an hypomethylated state, but the dynamics of this phenomenon still remains unknown. Here we present a genome-wide approach, named methylation-assisted bisulfite sequencing (MAB-Seq) that enables single-base resolution mapping of 5fC and 5caC and measuring of their relative abundance. Application of this method to mouse ESCs exposed the presence of 5fcaC residues on the hypomethylated promoters of the expressed genes, revealing an active DNA demethylation mechanism since the loss of TDG leads to an increase of 5fC/5caC. We also show that TDG is actually bound on these regions and that co-localizes and interacts with Tet1. We moreover demonstrate, by reduced representation of bisulfite sequencing (RRBS), that active promoters are actually demethylated by a Tet-dependent mechanism and that Dnmt1 and Dnmt3a are responsible of this DNA methylation. Our work shows the whole-genome map of 5fC and 5caC at single base resolution in ESCs, it demonstrates in detail the DNA methylation dynamics occurring on expressed gene promoters and identifies the key players of this mechanism. Furthermore, we provide a new tool (MAB-Seq) that can be broadly used in all biological contexts for epigenetics study involving identification and quantification of 5fC and 5caC at single base resolution.

overall_design: Methylation-assisted bisulfite sequencing (MAB-Seq) of E14 embryonic stem cells (ESCs), Biotag ChIP-Seq of Tdg and Reduced representation Bisulfite Sequencing (RRBS) in E14 ESCs.

first: Danny

last: Incarnato

first: Salvatore

last: Oliviero


title: Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells [MAB-Seq]


title: Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells [RRBS]


title: Age-dependent gene and protein expression following transection of neonatal spinal cord of Monodelphis domestica (South American Grey Short-tailed opossum)

city: Melbourne

first: Norman

last: Saunders

state: VIC

address: Grattan Street, Parkville

department: Pharmacology and Therapeutics

institute: University of Melbourne

summary: In the present study we investigated the genome and the proteome in the segment of cord rostral to the site of injury following a complete spinal cord transection in opossums at an age when axonal growth across a lesion and substantially normal locomotor development occur (postnatal day 7, P7) and compared this with an older age when no axon growth can be seen, but nevertheless a demonstrable body weight-bearing locomotion is present (P28, Wheaton et al, 2011).

overall_design: 7 RNA-seq samples, consisting of 2 biological replicates of controls at day 8, 1 control sample at day 29, and 2 biological replicates each from injured animals at days 8 and 29.

first: Natassya

last: Noor

first: Katarzyna

last: Dziegielewska

first: Benjamin

last: Wheaton

first: Shane

last: Liddelow

last: Steer

first: C

last: Ek

first: Mark

last: Habgood

first: Matthew

last: Wakefield

first: Helen

last: Lindsay

first: Jessie

last: Truettner

first: Robert

last: Miller

first: A

last: Smith

first: W

last: Dietrich


title: Single base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals the actual promoter DNA methylation dynamics in embryonic stem cells

last: Neri


title: Rare Allele of A Novel Histone H4 Acetyltransferase Enhances Grain Weight, Yield and Plant Biomass Presumably Through the Regulation of Transcription

city: Nagoya

first: Tomoyuki

last: Furuta

state: Aichi

address: Furo-cho

country: Japan

institute: Nagoya university

summary: Grain weight is an important crop yield component; however, its underlying regulatory mechanisms are largely unknown. Here, we identify a grain-weight quantitative trait locus (QTL) encoding a new-type GNAT-like protein that harbors intrinsic histone acetyltransferase activity (OsglHAT1). Our genetic and molecular evidences pinpointed the QTL-OsglHAT1’s allelic variations  to a 1.2-kilobase region upstream of the gene body, which is consistent with its function as a positive regulator of the traits. Elevated OsglHAT1 expression enhances grain weight and yield by enlarging spikelet hulls via increasing cell number and accelerating grain filling, and increases global acetylation levels of histone H4. OsglHAT1 localizes to the nucleus, where it likely functions through the regulation of transcription. Despite its positive agronomical effects on grain weight, yield and plant biomass, the rare allele elevating OsglHAT1 expression has so far escaped human selection. Our findings reveal the first example, to our knowledge, of a QTL for a yield component trait being due to a chromatin modifier that has the potential to improve crop high-yield breeding.

overall_design: Two replicates of Nipponbare as control, three replicates of GW6a-4.6 substitution lines and three replicates of OsglHAT1-OE transgenic lines.

first: Takamasa

last: Suzuki


title: microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach

status: Public on Feb 09 2015

city: Buenos Aires

first: Natalia

last: Macchiaroli

address: Paraguay 2155, 13th floor

country: Argentina

institute: IMPaM

summary: microRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as development and metabolism. Here, we perform a comprehensive analysis of miRNAs in the zoonotic parasite E. canadensis G7, one of the causative agents of the neglected disease cystic echinococcosis. Small RNA libraries from protoscoleces and cyst walls of E. canadensis G7 and protoscoleces of E. granulosus sensu stricto G1 were sequenced using Illumina technology. As a result, we found transcriptional evidence of 37 miRNAs thus expanding the miRNA repertoire of E. canadensis G7. Differential expression analysis showed significant regulated miRNAs between life cycle stages of E. canadensis G7. We confirmed the remarkable loss of conserved miRNA families in E. canadensis, reflecting their low morphological complexity and high adaptation to parasitism. This study will provide valuable information for better understanding the complex biology of this parasite and could help to find new potential targets for therapy and/or diagnosis.

sample_organism:
Echinococcus granulosus
Echinococcus canadensis

overall_design: Small RNA libraries from protoscoleces and cyst walls of E. canadensis G7 and protoscoleces of E. granulosus sensu stricto G1 were sequenced using Illumina technology. For each sample type, two libraries were constructed from two independent samples in order to have biological replicates.

first: Marcela

last: Cucher

first: Magdalena

last: Zarowiecki

first: Lucas

last: Maldonado

first: Laura

last: Kamenetzky

first: Mara

last: Rosenzvit


title: Correction of human phospholamban R14del mutation associated with cardiomyopathy using targeted nucleases and combination therapy [Exome-Seq]

city: NEW YORK

first: FRANCESCA

last: STILLITANO

address: 1470 Madison Avenue

department: CARDIOVASCULAR RESEARCH

institute: Mount Sinai School of Medicine

type: Genome variation profiling by high throughput sequencing

summary:
Phospholamban R14del mutazion (PLN-R14del) has been identified in a large family pedigree in which heterozygous carriers exhibited inherited dilated cardiomyopathy (DCM) and death by middle age. To better understand the causal link between the mutations in PLN and DCM pathology, we derived induced pluripotent stem cells from a DCM patient carrying the PLN R14del mutation. We showed that iPSC-derived cardiomyocytes recapitulated the DCM-specific phenotype and demonstrated that either TALEN-mediated genetic correction or combinatorial gene therapy resulted in phenotypic rescue. Our findings offer novel insights into the pathogenesis caused by mutant PLN and point to the development of potential new therapeutics of pathogenic genetic variants associated with inherited cardiomyopathies.
Submitter confirms there are no patient privacy concerns with these data.

overall_design: iPSCs were derived from a female patient carrying a heterozygous mutation (R14del) in the PLN gene. Tree samples were analyzed: R14del-CMs (clone L2), corrected R14del-CMs (clone L2GC1) and corrected R14del-CMs (clone L2GC2)

first: Ioannis

last: Karakikes

first: Francesca

last: Stillitano

first: Mathieu

last: Nonnenmacher

first: Jens

last: Hansen

first: Roger

last: Hajjar


title: Correction of human phospholamban R14del mutation associated with cardiomyopathy using targeted nucleases and combination therapy


title: Effects of physiological and synthetic IAP antagonism on c-IAP dependent signaling

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Cellular inhibitor of apoptosis proteins 1 and 2 (c-IAP1/2) play central roles in signal transduction mediated by numerous receptors that participate in inflammatory and immune responses. In certain pathways, such as activation of NF-kB, their degradation is a major regulatory event and is physiologically induced by activation of receptors. Additionally, a number of synthetic compounds have been developed that also target the c-IAPs and induce their degradation. However, the extent of a synthetic IAP antagonist’s ability to mirror the transcriptional program by a physiological signal remains unclear. Here we take a systems approach to compare the transcriptional programs triggered by activation of CD30, a well-characterized receptor previously shown to induce the degradation of the c-IAPs, to SM-164, a synthetic IAP antagonist that specifically triggers c-IAP degradation. Employing a technique that allows the specific analysis of newly transcribed RNA, we have generated comparative transcriptome profiles for CD30 activation and SM-164 treatment. Analysis of these profiles revealed that the genes regulated by each stimulus were not completely shared, indicating novel functions of IAP antagonists and consequences of c-IAP1/2 degradation. The data identified a role for c-IAP1/2 in the regulation of the ribosome and protein synthesis, which was subsequently confirmed by biological assays. These findings expand our knowledge of the roles of c-IAP1/2 in signaling and provide insight into the mechanism of synthetic IAP antagonists, furthering our understanding of their therapeutic potential.

overall_design: This submission contains two different experiments. In experiment 1, cells were exposed to drug treament (DMSO or SM-164) for 3 hours. In experiment 2, cells were exposed to an adherent layer of CHO cells either expressing or not CD30L. Each treatment in each experiment was conducted once, leading to a total of 4 samples.

first: Andrew

last: Kocab

first: Artur

last: Veloso

first: Michelle

middle: T

last: Paulsen

first: Colin

last: Duckett


title: Correction of human phospholamban R14del mutation associated with cardiomyopathy using targeted nucleases and combination therapy [RNA-Seq]

state: NY

summary: Phospholamban R14del mutazion (PLN-R14del) has been identified in a large family pedigree in which heterozygous carriers exhibited inherited dilated cardiomyopathy (DCM) and death by middle age. To better understand the causal link between the mutations in PLN and DCM pathology, we derived induced pluripotent stem cells from a DCM patient carrying the PLN R14del mutation. We showed that iPSC-derived cardiomyocytes recapitulated the DCM-specific phenotype and demonstrated that either TALEN-mediated genetic correction or combinatorial gene therapy resulted in phenotypic rescue. Our findings offer novel insights into the pathogenesis caused by mutant PLN and point to the development of potential new therapeutics of pathogenic genetic variants associated with inherited cardiomyopathies.

overall_design: iPSCs were derived from a female patient carrying a heterozygous mutation (R14del) in the PLN gene. Tree samples were analyzed: Cardiomyocytes derived from PLN-R41del iPSC cells (R14del-CM); R14del-CMs infected with AAV6-EGFP-miR-PLN and R14del-CMs infected with AAV6-EGFP-miR-luc used as a negative control


title: Small RNA profiling of two important cultivars of banana and overexpression of miRNA156 in transgenic banana plants

status: Public on Feb 07 2015

city: Mumbai

first: T

last: Ganapathi

state: Maharashtra

address: Trombay

department: Nuclear Agriculture & Biotechnology Division

country: India

institute: Bhabha Atomic Research Centre, Mumbai

sample_organism:
Musa acuminata AAA Group
Musa AAB Group

platform_organism:
Musa acuminata AAA Group
Musa AAB Group


title: Decoding the regulatory network of early blood development from single-cell gene expression measurements.

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: Reconstruction of the molecular pathways controlling organ development has been hampered by a lack of methods to resolve embryonic progenitor cells. Here we describe a strategy to address this problem that combines gene expression profiling of large numbers of single cells with data analysis based on diffusion maps for dimensionality reduction and network synthesis from state transition graphs. Applying the approach to hematopoietic development in the mouse embryo, we map the progression of mesoderm toward blood using single-cell gene expression analysis of 3,934 cells with blood-forming potential captured at four time points between E7.0 and E8.5. Transitions between individual cellular states are then used as input to develop a single-cell network synthesis toolkit to generate a computationally executable transcriptional regulatory network model of blood development. Several model predictions concerning the roles of Sox and Hox factors are validated experimentally. Our results demonstrate that single-cell analysis of a developing organ coupled with computational approaches can reveal the transcriptional programs that underpin organogenesis.

overall_design: Transcriptome analysis in populations of 50 cells from each of 5 mouse embryos at primitive streak, neural plate and head fold stages of development

first: Victoria

last: Moignard

first: Steven

last: Woodhouse

first: Laleh

last: Haghverdi

first: Josh

last: Lilly

first: Yosuke

last: Tanaka

first: Adam

last: Wilkinson

first: Florian

last: Buettner

first: Iain

last: Macaulay

first: Wajid

last: Jawaid

first: Shin-Ichi

last: Nishikawa

first: Nir

last: Piterman

first: Valerie

last: Kouskoff

first: Fabian

last: Theis

first: Jasmin

last: Fisher

first: Berthold

last: Göttgens


title: Whole Transcriptome RNA-seq Analysis: the Tumorigenesis and Metastasis of Melanoma

city: Bejing

first: Shaobin

last: Wang

address: No.7 Beitucheng West Road, Chaoyang District,

country: China

institute: Beijing institute of Genomics

summary: To better understand the tumorigenesis and metastasis of human metastatic melanoma(MM) , we analyzed the transcriptomes of three cell lines that represent the three distinct stages of MM pathogenesis: the normal stage (HEMn), the onset of MM (A375), and the metastasis stage (A2085). Using the next generation sequencing (NGS) technology, we detected unsymmetrical expression of genes particularly in Chr9, 12, and 14 among three cell lines, an indication of the involvement of these genes in the tumorigenesis and metastasis of MM. These genes were assigned into 41 categories by their expression patterns and their biological functions were subsequently analyzed by Ingenuity Pathway Analysis software. In the top category associated with cancer, HIF1A, IL8, TERT, ONECUT1 and FOXA1 had direct interaction with the transcription factors or cytokines known to be involved in the tumorigenesis or metastasis in other malignant tumors. Our findings suggest that pathway about cytokines regulation in macrophages may play a more prominent role in the pathogenesis of MM. This study provides not only new targets for downstream mechanistic studies in the tumorigenesis and metastasis of MM, but also a new strategy to study the progression of other malignant cancers.

overall_design: Compare the transcriptome of 3 cell lines of human melanocyte/melanoma

first: Xiangdong

last: Fang

first: Songnian

last: Hu


title: Discovery of cis-spliced chimeric RNAs between adjacent genes in human prostate cells

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

summary: Total RNA extracted from prostate cancer LNCaP cells transfected with siRNA against CTCF(siCTCF), or negative control siRNA (si-)were processed, and sequenced by two different companies using Illumina Hi-seq 2000 platform to generate RNA sequencing with two output sequences: paired-end 50bp and 101bp in read length. Nearly 100 million and 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts.

overall_design: Discovering fusion genes from siCTCF and si- in LNCaP cells.

first: Hui

last: Li


title: The chromatin-modifying enzyme Ezh2 is critical for the maintenance of regulatory T cell identity after activation

city: SAN FRANCISCO

first: GAURAV

last: CHOPRA

state: CA

address: 513 PARNASSUS AVE, HSW 1102

department: DIABETES CENTER

institute: UNIVERSITY OF CALIFORNIA - SAN FRANCISCO (UCSF)

summary: Regulatory T cells (Tregs) are essential for maintaining proper immune homeostasis. Extracellular signals (e.g. TCR, CD28, IL-2R) are necessary for the generation and maintenance of Tregs, but how these signals are integrated to control the gene expression patterns of Tregs is less clear. Here we show that the epigenetic regulator, Ezh2, was induced by CD28 costimulation and Ezh2 activity was elevated in Tregs as compared to conventional CD4+ T cells. Deletion of Ezh2 in mouse Tregs led to a progressive autoimmune disease because Tregs were compromised after activation, losing proper control of essential Treg lineage genes and adopting a gene expression pattern similar to Foxp3-deficient ‘Tregs.’ Lineage-tracing of Ezh2-deficient Tregs in vivo confirmed that the cells were destabilized selectively in activated Treg populations, which led to a significant loss of Tregs in non-lymphoid tissues. These studies reveal an essential role for Ezh2 in the maintenance of Treg “identity” during cellular activation and differentiation.

overall_design: RNAseq of sorted populations of CD62Lhi or CD62Llo Tregs for both Ezh2-HET (Foxp3YFP-Cre/Foxp3WT;Ezh2fl/+ female mice) and Ezh2-KO (Foxp3YFP-Cre/Foxp3WT;Ezh2fl/fl female mice) were generated, in triplicate for each condition, using Illumina HiSeq 2500 single-end 50bp sequencing platform.

first: Gaurav

last: Chopra

first: Michel

last: DuPage

first: Jeffrey

last: Bluestone


title: High throughput sequencing of the small RNAs from banana cv. Rasthali (AAB group)

first: T

last: Ganapathi

summary: Small RNAs comprise a group of non coding RNAs which play significant role in the genetic regulation of growth and development in plants. The most important members of this family are the small inhibiting RNAs (siRNAs) and microRNAs (miRNAs). They are processed by the DICER like proteins in plants and incorporated into the RNA induced silencing complex to silence the cognate mRNAs by sequence specific cleavage. High throughput sequencing strategies have enabled the identification of complete gamut of small RNA sequences present in a plant tissue at a particular point of time enabling the study of their biological significance in different plant tissues. The small RNA profile of each plant shows few plant conserved sequences, few species specific sequences and few novel RNA sequences characteristic of each cultivar. Here we have performed high throughput sequencing of small RNA population derived from leaves of an elite edible Indian cultivar of banana cv. Rasthali (‘Silk’ subgroup with AAB genotype) to identify the microRNAs and other important small RNAs being expressed in the leaves of banana cv Rasthali.

overall_design: Generation of complete small RNA profile of banana cv. Rasthali for comparison with similar databases

first: Siddhesh

middle: B

last: Ghag

first: Upendra

middle: K

last: Shekhawat

first: Thumballi


title: Effect of SF3A1 inhibition on pre-mRNA splicing

city: Denver

first: Scott

last: Alper

state: CO

address: 1400 Jackson St.

department: Integrated Center for Genes Environment & Health

institute: National Jewish Health

summary: We previously found that the SF3A mRNA splicing complex was required for a robust innate immune response; SF3A acts in part by inhibiting the production of a negatively acting splice form of the TLR signaling adaptor MyD88. Here we inhibit SF3A1 using RNAi and subsequently perform an RNAseq study to identify the full complement of genes and splicing events regulated by SF3A in murine macrophages. Surprisingly, SF3A has substantial specificity for mRNA splicing events in innate immune signaling pathways compared to other pathways, affecting the splicing of many genes in the TLR signaling pathway to modulate the innate immune response.

overall_design: RNAseq was used to monitor the effects of SF3A1 siRNA-mediated knockdown in murine macrophages.  Three biological replicates were used for each of the four treatment combinations (with/without siRNA, with/without LPS).  The first replicates for each combination were each sequenced in two runs, which were combined in the analysis.

first: Brian

last: O’Connor

first: Thomas

last: Danhorn

first: Lesly

last: De Arras

first: Roland

last: Marcus

first: Eveline

last: Farias-Hesson

first: Sonia

middle: M

last: Leach


title: High throughput sequencing of the small RNAs from banana cv. Grand Naine (AAA group)

summary: Small RNAs especially small inhibiting RNAs (siRNAs) and microRNAs (miRNAs) play essential role in the regulation of gene expression in plants. These non coding RNAs are processed by the DICER like proteins into 21-24 nucleotides single stranded molecules that guide the activity of RNA induced silencing complex. This complex along with the processed small RNA identifies the cognate mRNA and brings about sequence specific mRNA degradation thereby silencing the gene expression. The small RNA profile is unique for each plant tissue at a given point of time. High throughput sequencing method allows the study of differential expression of these small RNAs. Deep sequencing of small RNAs derived from the leaves of an elite cultivar of banana cv. Grand Naine (‘Cavendish’ subgroup with AAA genotype) was carried out.

overall_design: Generation of complete small RNA profile of banana cv. Grand Naine for comparison with similar databases


title: MethlyC-Seq of nrpd1-3, nrpd1-12, and nrpe1-11

status: Public on Feb 05 2015

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: Using MethylC-Seq to provide single-base resolution of DNA methylation status in  nrpd1-3, nrpd1-12, and nrpe1-11 mutants

overall_design: MethylC-Seq: 3 mutants examined,  nrpd1-3, nrpd1-12, and nrpe1-11

first: Mingguang

last: Lei

first: Kai

last: Tang


title: Parallel Epigenomic and Transcriptomic Responses to Viral Infection in Honey Bees (Apis mellifera)

status: Public on Feb 06 2015

city: University Park

first: David

middle: Asher

last: Galbraith

state: Pennsylvania

address: 19a Chemical Ecology Lab

institute: Penn State University

summary: Here, we examined the transcriptional and epigenetic (DNA methylation) responses to viral infection in honey bee workers.  One-day old worker honey bees were fed solutions containing Israeli Acute Paralysis Virus (IAPV), a virus which causes muscle paralysis and death and has previously been associated with colony loss.  Uninfected control and infected, symptomatic bees were collected within 20-24 hours after infection.  Worker fat bodies, the primary tissue involved in metabolism, detoxification and immune responses, were collected for analysis. We performed transcriptome- and bisulfite-sequencing of the worker fat bodies to identify genome-wide gene expression and DNA methylation patterns associated with viral infection.  There were 753 differentially expressed genes (FDR<0.05) in infected versus control bees, including several genes involved in epigenetic and antiviral pathways. DNA methylation status of 156 genes (FDR<0.1) changed significantly as a result of the infection, including those involved in antiviral responses in humans.  There was no significant overlap between the significantly differentially expressed and significantly differentially methylated genes, and indeed, the genomic characteristics of these sets of genes were quite distinct. Our results indicate that honey bees have two distinct molecular pathways, mediated by transcription and methylation, that modulate protein levels and/or function in response to viral infections.

overall_design: Examination of epigenomic and transcriptomic antiviral responses to Israeli Acute Paralysis Virus in honey bees

first: Christina

last: Grozinger


title: Mouse sinoatrial node transcriptome

city: San Francisco

first: Vasanth

last: Vedantham

address: 505 Parnassus Avenue, M1176D

department: Medicine-Cardiology

institute: University of California, San Francisco

summary:
RNA Sequencing of Mouse Sinoatrial Node Reveals an Upstream Regulatory Role for Islet-1 in Cardiac Pacemaker Cells

Rationale: Treatment of sinus node disease with regenerative or cell-based therapies will require a detailed understanding of gene regulatory networks in cardiac pacemaker cells (PCs).

Objective: To characterize the transcriptome of PCs using RNA sequencing, and to identify transcriptional networks responsible for PC gene expression.

Methods and Results: We used laser capture micro-dissection (LCM) on a sinus node reporter mouse line to isolate RNA from PCs for RNA sequencing (RNA-Seq). Differential expression and network analysis identified novel SAN-enriched genes, and predicted that the transcription factor Islet-1 (Isl1) is active in developing pacemaker cells. RNA-Seq on SAN tissue lacking Isl1 established that Isl1 is an important transcriptional regulator within the developing SAN.

Conclusions: (1) The PC transcriptome diverges sharply from other cardiomyocytes; (2) Isl1 is a positive transcriptional regulator of the PC gene expression program.

overall_design: There are 25 RNA-Sequencing Samples

first: Rahul

last: Deo


title: Genome-wide miRNA profile of MCF7 cells overexpressing wild-type and mutant miR-222

city: New Haven

first: Mei

last: Zhong

address: 10 Amistad Street

department: Stem Cell Center

institute: Yale University

summary: MCF7 cells were infected with retrovirus to overexpress wild-type and mutant miR-222

overall_design: Measure miRNA expression level in MCF7 cells after overexpressing wild-type and mutant miR-222

first: Yanwen

last: Guo

first: Jun

last: Lu


title: The effects of the global loss of DNA methylation on the functional cancer epigenome

city: Los Angeles

first: Fides

last: Lay

address: 615 Charles E Young Drive South, BSRB 457

department: MCDB

institute: UCLA

summary: We compare the global histone modification patterns of HCT116 colon cancer cells with its genetic derivatives DKO1 cells which lack DNMT3B and DNMT1 activity

overall_design: Comparison of histone marks in two cell types

first: Yaping

last: Liu

first: Ben

last: Berman

first: Peter

last: Jones


title: Chromatin profiling reveals novel proteins associated with histone-marked genomic regions

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Our understanding of the functions of DNA elements is limited by the paucity of information about the spectrum of proteins that occupy these genomic regions. Here we describe an approach to identify proteins associated with genomic regions whose chromatin is marked by specific modified histones, which we term chromatin profiling. We used chromatin immunoprecipitation followed by mass spectrometry (ChIP-MS) to identify proteins associated with genomic regions marked by histone H3K27Ac, H3K4me3, H3K79me2 and H3K36me3 in mouse embryonic stem (mES) cells. We identified 385 known and 224 novel candidate proteins associated with these histone-marked genomic segments and confirmed that several of the novel candidates are indeed associated with histone-marked segments of the genome. Future study of the novel candidates, many of which have been implicated in various diseases, should lead to an improved understanding of gene control and its dysregulation in disease.

overall_design: ChIP-seq for nucleosomes with modified histones in mouse embryonic stem cells

first: Xiong

last: Ji

first: Daniel

last: Dadon

first: Brian

last: Abraham


title: MethlyC-Seq of Col-0 background wild-type (WT)

first: Jian-Kang

last: Zhu

summary: Using MethylC-Seq to provide single-base resolution of DNA methylation status in Col-0 WT

overall_design: MethylC-Seq: 1 WT examined, Col-0 WT

first: Mingguang

last: Lei


title: MethlyC-Seq of ros1-13 mutant

summary: Using MethylC-Seq to provide single-base resolution of DNA methylation status in ros1-13 mutant

overall_design: Whole genome methylation maps of ros1-13 (with 35S-SUC2 transgene) was generated using BS-seq

first: Kai

last: Tang


title: Genome-wide miRNA turnover profile after transcription inhibition in HDMYZ cells with biological triplicate

summary: HDMYZ cells were treated with 4ug/ml ActD for 0, 1, 4 and 12 hours. Small RNAs of 15-40 bases were gel-purified from 5 ug total RNA, and subjected to multiplex Illumina small RNA library preparation. Small RNA libraries were sequenced on a HiSeq2000 (Illumina).

overall_design: Measure miRNA expression level at 0, 1, 4, 12 hours post ActinomycinD treatment to examine miRNA turnover pattern.

first: Sarah

last: Elfenbein


title: RNAseq data from wild type and evolved Pseudomonas fluorescens SBW25 strains

city: North Shore City

first: Paul

last: Rainey

address: The Station Crescent

department: NZIAS

country: New Zealand

institute: Massey University

summary: We report mRNA expression data from Pseudomonas fluorescens SBW25 wild type and two evolved strains (Beaumont et al., 2009).  The evolution of one of these strains saw the emergence of colony switching; 1B4 switches rapidly between two different colony phenotypes. These two phenotypes were found to be genetically identical. Thus, in order to gain insight into epigenetic mechanisms of switching, we were interested in identifiying gene expression differences between ancestors and the 1B4 colony phenotypes.

overall_design: Measuring the expression levels of the wildtype (SBW25), the evolved strain 1A4 and the evolved strain 1B4. 1B4 exists in two different phenotypic states (CAP+, CAP-); these were seperated by centrifugation prior to individual analysis. This means there are four datasets in total.

first: Jenna

last: Gallie

first: Eric

last: Libby

first: Frederic

last: Bertels

first: Philippe

last: Remigi

first: Christian

last: Jendresen

first: Gayle

last: Ferguson

first: Nicolas

last: Desprat

first: Marieke

last: Buffing

first: Uwe

last: Sauer

first: Hubertus

last: Beaumont

first: Jan

last: Martinussen

first: Mogens

last: Kilstrup


title: Two-signal requirement for growth-promoting function of Yap

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

summary: The transcriptional coactivator Yap promotes proliferation and inhibits apoptosis, suggesting that Yap functions as an oncogene. Most oncogenes, however, require a combination of at least two signals to promote proliferation.  Here we present evidence that Yap activation is insufficient to promote growth in the otherwise normal tissue. Using a mosaic mouse model, we demonstrate that Yap overexpression in a fraction of hepatocytes does not lead to their clonal expansion, as proliferation is counterbalanced by increased apoptosis. To shift the activity of Yap towards growth, a second signal provided by tissue damage or inflammation is required. In response to liver injury, Yap drives clonal expansion, suppresses hepatocyte differentiation and promotes a progenitor phenotype. These results suggest that Yap activation is insufficient to promote growth in the absence of a second signal thus coordinating tissue homeostasis and repair.

overall_design: Totally sixteen samples

first: Tian

last: Su

first: Tanya

last: Bondar

last: Zhou

first: Cuiling

last: Zhang

first: Hang

last: He

first: Ruslan

last: Medzhitov


title: Pri-miRNA identification by generating a Drosha null/conditional-null mouse model.

city: Volos

first: Artemis

last: Hatzigeorgiou

address: 37 Glavani – 28th October Str

department: Department of Electrical and Computer Engineering

country: Greece

institute: University of Thessaly

summary: We report the ability of the Drosha null/conditional-null mouse model to enable the identification of pri-miRNA transcripts. The conditional-null allele of Drosha phenocopies the null allele both in mESC and in mice, upon conversion to the null state with Cre.

overall_design: Examination of the effects of Drosha deficiency in mouse embryonic stem cells.

first: Aris

last: Economides

first: Peter

last: Yang


title: Retinoid X receptors orchestrate osteoclast differentiation and postnatal bone remodeling [SREBP]

status: Public on Feb 04 2015

city: Pamplona

first: Daniel

last: Alameda

address: Av. de Pío XII, 55

country: Spain

institute: CIMA

summary: Data from SREBP1c binding to the genome was visualized using Genome Browser (UCSC) in order to test its role in Mafb transcriptional regulation

overall_design: SREBP ChIP was performed in thioglycollate-elicited peritoneal macrophages treated as indicated.

first: Nathanael

last: Spann

first: Christopher

last: Glass


title: Retinoid X receptors orchestrate osteoclast differentiation and postnatal bone remodeling

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

overall_design: Refer to individual Series


title: Genome-wide analysis of chromatin occupancy of GATA1 and its short isoform GATA1s (ChIP-Seq)

city: Cincinnati

first: Timothy

middle: Michael

last: Chlon

state: OH

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's

summary: We report ChIP-Seq data for GATA1 and the leukemia-associated short isoform GATA1s in G1ME cells, a Gata1-null cell line with both erythroid and megakaryocytic differentiation potential.  We introduced HA-tagged GATA1 or GATA1s into G1ME cells via retroviral transduction.  The cells were crosslinked at 48h post-transduction, and an HA antibody was used for chromatin immunoprecipitation (ChIP).  ChIP and input samples were sequenced on Illumina GAII or GAIIx high-throughput sequencers.  The data reveal a deficiency of chromatin occupancy by GATA1s, especially at genes involved in erythrocyte differentiation and function.

overall_design: Examinaton of chromatin occupancy of GATA1 and GATA1s  in G1ME cells cultured in TPO.

first: Louis

last: Dore

first: John

last: Crispino


title: Global transcriptome and chromatin occupancy analysis  reveal the short isoform of GATA1 is deficient for erythroid specification and gene expression


title: hsa-miR-503, hsa-miR-103, and hsa-miR-494 genome wide target profiles [RNA-Seq and RIP-Seq]

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: We constructed a genome wide target profile of hsa-miR-503, hsa-miR-103, and hsa-miR-494 by sequencing RNA isolated from Ago2 immunoprecipitations and total RNA samples following transfection of the respective miRNA in mature duplex form

overall_design: Examination of mRNA levels in HeLa cells and Ago2 immunoprecipitations from HeLa cells following miR-503, miR-103, or miR-494 mature duplex or control siRNA transfection

first: Damon

last: Polioudakis

first: Vishwanath


title: Genome-wide Oct4 binding profile in lung cancer A549 cells

city: Tainan

first: Yi-Ching

last: Wang

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

summary: Oct4 stemness gene encoding a transcription factor has been shown to overexpress in cancers. However, precise mechanisms of Oct4 relevant to transcriptional reprogramming leading to somatic cancer progression remain unclear. To address the Oct4-mediated transcriptional program in lung cancer, we integrated genome-wide Oct4 binding profiles from chromatin-immunoprecipitation sequencing and ENCODE datasets. We identified that Oct4 occupied at functional promoter and enhancer regions of genes which play key roles in several signaling pathways involving tumorigenesis.

overall_design: Genome-wide Oct4 binding sites were identified via chromatin immunoprecipitation-sequencing analysis of vecoter control and stably Oct4-overexpressing A549 lung cancer cells. ChIP-seq analyses were performed in duplicated samples using Applied Biosystems SOLiD system.

first: Yen-An

last: Tang

first: H

middle: S

last: Sun


title: Retinoid X receptors orchestrate osteoclast differentiation and postnatal bone remodeling [RXR and PPARg]

summary: Data from nuclear receptors RXR and PPARg binding to the genome was visualized using Genome Browser (UCSC) in order to test their role in Mafb transcriptional regulation

overall_design: RXR and PPARg ChIP was performed in thioglycollate-elicited peritoneal macrophages in basal conditions

first: Mercedes

last: Ricote


title: iRNA-seq: Computational method for genome wide assessment of acute transcriptional regulation from total RNA-seq data

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: RNA-seq is a sensitive and accurate technique to compare steady state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel method, iRNA-seq, for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. To test our method, we have performed total RNA-seq and RNA polymerase II (RNAPII) ChIP-seq profiling of the acute transcriptional response of human adipocytes to TNFα treatment and analyzed these using iRNA-seq in addition to different publically availbale dataset.  Comparison of the results derived from iRNA-seq analyses with results derived using current methods for genome-wide determination of transcriptional activity, i.e. Global Run-On (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides very similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.

overall_design: Genome-wide assesment of the acute transcriptional response to TNFa in human SGBS adiposytes using total RNA-seq data end RNAPII ChIP-seq

first: Jesper

middle: G

last: Madsen

first: Søren

last: Schmidt

first: Bjørk

last: Larsen

first: Anne

last: Loft

first: Ronni

last: Nielsen


title: Pluripotent cell models of Fanconi anemia identify the early pathological defect in human hemoangiogenic progenitors

status: Public on Feb 03 2015

city: Kyoto

first: Megumu

last: Saito

address: 53, Shogoin-Kawahara

institute: Kyoto University

summary: Fanconi anemia (FA) is a disorder of genomic instability characterized by progressive bone marrow failure (BMF), developmental abnormalities and an increased susceptibility to cancer. Although various consequences in hematopoietic stem/progenitor cells have been attributed to FA-BMF, the quest to identify the initial pathological event is still ongoing. To address this issue, we established induced pluripotent stem cells (iPSCs) from fibroblasts of six FA patients with FANCA mutations. An improved reprogramming method yielded iPSC-like colonies from all patients, and iPSC clones were propagated from two patients. Quantitative evaluation of the differentiation ability demonstrated that the differentiation propensity toward the hematopoietic and endothelial lineages is already defective in early hemoangiogenic progenitors. The expression levels of critical transcription factors were significantly downregulated in these progenitors. These data indicate that the hematopoietic consequences in FA patients originate from the early hematopoietic stage, and highlight the potential usefulness of iPSC technology for elucidating the pathogenesis of FA-BMF.

overall_design: The investigation of the RNA-seq analysis of iPSC-derived HAPCs.

first: Naoya

last: Suzuki

first: Akira

last: Watanabe


title: The effects of the global loss of DNA methylation on the functional cancer epigenome (Bisulfite-seq)

first: Fides

last: Lay

summary: We compare the global DNA methylation and nucleosome occupancy patterns of HCT116 colon cancer cells with its genetic derivatives DKO1 cells which lack DNMT3B and DNMT1 activity

overall_design: Simultaneous genome-wide mapping of DNA methylation and nucleosome occupancy of HCT116 and DKO1 cells using NOMe-seq, rep2

first: Yaping

last: Liu

first: Ben

last: Berman

first: Peter

last: Jones


title: Transcription profiling of a S96xSK1 yeast cross and its pool of spores.

city: Munich

first: Daniel

middle: Magnus

last: Bader

address: Feodor-Lynen Str 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilians-University

summary: To dissect local regulation into cis and trans contribution, we measured allelic differential expression in a hybrid cross of two yeast strains and compared it against allelic differential expression in a pool of spores of the same cross.

overall_design: RNA- and DNA-seq of a diploid S. cerevisiae hybrid and its haploid spores.

first: Julien

last: Gagneur