title: Oct4 ChIP-Seq at G1 and G2/M phase of cell cycle in mouse embryonic stem cells

city: Seoul

first: Jihoon

last: Shin

address: Biomedical Science Building, 103 Daehakro, Jongro-gu

institute: Seoul National University College of Medicine

summary: We mapped the genome-wide occupancy of Oct4 at G2/M (nocodazole-treated cells) and G1 phase (release of nocodazole-treated cells) in E14 mouse embryonic stem cells.

overall_design: Examination of Oct4 occupancy at different cell cycle.

first: Hong-Duk

last: Youn


title: PLZF & SALL4 ChIP-seq in undifferentiated spermatogonia

status: Public on Apr 19 2016

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

country: USA

institute: University of Texas at San Antonio

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cultured THY1+ spermatogonia were used to reveal the genomic targets of PLZF and SALL4 in undifferentiated spermatogonia.

overall_design: Three replicate preparations of DBA/2 mouse THY1+ spermatogonia were used for independent ChIP of PLZF and SALL4, NGS and MACS-based peak calling.

first: Dawn

last: Lovelace

first: Zhen

last: Gao

first: Yuntao

last: Song

first: Jianhua

last: Ruan


title: ChIP-seq analysis of AF9 and TET2 enrichment in day 12 neural cells

city: Shanghai

first: Naihe

last: Jing

state: Shanghai

address: 320 Yueyang road

country: China

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: AF9 and TET2 were enriched in neural gene loci

overall_design: Examination of AF9 and TET2 distributions in day 12 differentiated cells

first: Yunbo

last: Qiao

first: Xiongjun

last: Wang

first: Ran


title: Genome-wide mapping of H4Ac in Legionella pneumophila-infected human macrophages

status: Public on Apr 18 2016

city: Berlin

first: Annalisa

last: Marsico

address: Ihnestraße 63-73

department: Computational Biology

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: In this study we infected human blood-derived macrophages with L. pneumophila and used immunoprecipitation followed by sequencing (ChIP-Seq) to screen gene promoters for the activating histone 4 acetylation mark. We found about 500 genes with induced acetylation upon infection, including several pro-inflamatory and inflamatory factors and non-coding RNAs. In particular, we assess the functional consequences of tumor necrosis factor alpha-induced protein 2 (TNFAIP2), a factor not yet characterized in the pathology of L.pneumophila, on bacterial replication.

overall_design: Examination of one histone modification H4Ac in blood-derived macrophages with and without Legionella infection. Total input DNA was used as control in both conditions.

last: Caffrey


title: DIP-seq analysis of 5mC and 5hmC distributions in hESCs and day 12 neural cells

type: Methylation profiling by high throughput sequencing

summary: 5mC and 5hmC were specifically distributed in undifferentiated hESCs and neural cells.

overall_design: Examination of 5mC and 5hmC distributions in hESCs and neural progenitor cells


title: RNA-seq analysis of gene expression patterns during hESC neural differentiation

type: Expression profiling by high throughput sequencing

summary: Thousands of genes expression patterns were displayed.

overall_design: Examination of gene expression patterns during hESC neural differentiation every 2 days

first: Yuanyuan

last: Li


title: hESC neural differentiation

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

overall_design: Refer to individual Series


title: Myc-dependent gene activation and repression in oncogene-addicted liver tumors (RNA-seq)

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

summary: Tumors driven by activation of the transcription factor Myc generally show oncogene addiction. However, the gene-expression programs that depend upon sustained Myc activity in those tumors remain unknown. We have addressed this issue in a model of liver carcinoma driven by a reversible tet-Myc transgene, combining gene expression profiling with the mapping of Myc and RNA Polymerase II on chromatin. Switching off the oncogene in advanced carcinomas revealed that Myc is required for the continuous activation and repression of distinct sets of genes, constituting no more than half of those deregulated during tumor progression, and an even smaller subset of all Myc-bound genes. We further showed that a Myc mutant unable to associate with the co-repressor protein Miz1 is defective in the initiation of liver tumorigenesis. Altogether, our data provide the first detailed analysis of a Myc-dependent transcriptional program in a fully developed carcinoma, revealing that the critical effectors of Myc in tumor maintenance must be included within defined subsets (ca. 1,300 each) of activated and repressed genes.

overall_design: RNAseq samples of control liver (n=11), tet-Myc tumors (n=16), tet-Myc tumors with short-term Myc inactivation (n=8), tet-MycVD tumors (n=11)

first: Theresia

middle: R

last: Kress

middle: J

first: Bruno

last: Amati


title: Myc-dependent gene activation and repression in oncogene-addicted liver tumors


title: Innate-like functions of natural killer T cell subsets result from highly divergent gene programs [single_cell_RNA-seq]

city: La Jolla

first: Pandurangan

last: Vijayanand

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: Natural killer T (NKT) cells have immune stimulatory or inhibitory effects on the immune response that are context-dependent.  This may be attributed in part to the existence of functional NKT cell subsets; however, these functional subsets have only been characterized on the basis of differential expression of a few transcription factors and cell surface molecules.  Here we have analyzed purified populations of thymic NKT cell subsets at both the transcriptomic and epigenomic levels, and by single-cell RNA sequencing.  Our data indicate that despite their similar antigen specificity, the functional NKT cell subsets are highly divergent populations characterized by many gene expression and epigenetic differences.  Therefore the thymus imprints innate-like NKT cells with novel combinations of properties, including differences in proliferative capacity, homing, and effector functions that were not previously anticipated.

overall_design: Analysis of single cell transcriptomic heterogeneity in mouse Vα14 iNKT thymocyte subsets (NKT1, NKT2, NKT17 and NKT0). Samples were generated from individual experiment using a pool of thymocytes prepared from five five-week old C57BL/6J females. NKT cells subtypes were isolated from thymuses and directly sorted by flow cytometry into lysis buffer (96 well plate single cell sort). The preparation of samples occurred in 2 different batches (both having a equal representation of the different cell populations).

first: Isaac

last: Engel

first: Grégory

last: Seumois

first: Lukas

last: Chavez

first: Ashu

last: Chawla

first: Brandie

last: White

first: Dennis

last: Mock

first: Mitchell

last: Kronenberg


title: Myc-dependent gene activation and repression in oncogene-addicted liver tumors (ChIP-seq)

overall_design: ChIPseq samples of Myc (n=13), RNA Pol II (n=11), H3K4me3 (n=11), H3K27ac (n=11)


title: Innate-like functions of natural killer T cell subsets result from highly divergent gene programs [bulk_RNA-seq]

overall_design: Transcriptomic analysis of mouse Vα14 iNKT thymocyte subsets (NKT1, NKT2 and NKT17) by microscaled RNA-Seq. Samples were generated from three individual experiments using a pool of thymocytes prepared from five five-week old C57BL/6J females. NKT cells subtypes were isolated from thymuses and directly sorted by flow cytometry into lysis buffer (Trizol LS).


title: Innate-like functions of natural killer T cell subsets result from highly divergent gene programs


title: Gene expression profiling of D. melanogaster strains with varied resistance and tolerance to L. monocytogenes infection

city: Stanford

first: Alexander

last: Louie

address: 299 Campus Dr

department: Microbiology and Immunology

institute: Stanford University

summary: We sequenced the mRNA of four D. melanogaster strains (w1118:BL6326, PBacCG2247:BL18050, PBacPCMT:BL18398, and RAL359:BL28131) during L. monocytogenes infection to determine the changes in gene expression dynamics responsible for resistance and tolerance phenotypes.

overall_design: Examination of mRNA levels in groups of 20 adult males at 12 timepoints throughout infection and recovery. Flies were injected with 1000CFU of L. monocytogenes. On day 3 and onwards, flies were maintained on ampicillin supplemented food.

first: David

last: Schneider


title: An evolutionarily conserved DNA-encoded logic shapes CpG island formation

city: Oxford

first: Hannah

middle: Katherine

last: Long

state: Oxfordshire

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: DNA methylation is an epigenetic modification of the vertebrate genome that contributes to transcriptional repression, imprinting, and X-chromosome inactivation. While the majority of the genome is blanketed in DNA methylation, regions known as CpG islands (CGIs) remain remarkably refractory to this modification. CpG islands are associated with roughly two thirds of gene promoters, are evolutionarily conserved, and play central roles in gene regulation, yet how they are protected from DNA methylation remains enigmatic. Based on the conserved nature of CpG islands, we have exploited genomic approaches and a transchromosomic model system to ask if DNA sequence is sufficient to specify the hypomethylated state at CpG islands when a human chromosome is newly introduced into mouse. Interestingly, this approach revealed that promoter-associated CGIs remain immensely refractory to DNA methylation regardless of the host species, in fitting with their conservation across vertebrate species and revealing that DNA sequence is a central driver in this outcome. In contrast, the methylation state of distal elements is highly variable between species and is host nucleus dependent. These alterations in methylation state at distal elements are defined by DNA nucleotide frequency and occupancy of DNA binding transcription factors, uncovering a widespread role for these features in defining the how this aspect of the epigenome forms away from gene promoters. These central principles are further supported by transplantation of mouse DNA sequences into the evolutionarily distant zebrafish genome, revealing the existence of a highly conserved and DNA encoded logic that shapes the vertebrate epigenome.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: Bio-CAP was used to identify hypomethylated  regions of DNA in the transchromosomic mouse model Tc1, which contains an almost entire copy of human chromosome 21, and wildtype Tc0 mice in liver and testis tissues, and in zebrafish embryos in which mouse BAC DNA has been introduced into the genome.

middle: K

first: Robert

last: Klose


title: miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species

city: Montpellier Cedex 5

first: Stephane

last: Jouannic

address: 911 Avenue Agropolis BP 64501

department: UMR DIADE

country: France

institute: IRD

type: Non-coding RNA profiling by high throughput sequencing

summary: Rice was domesticated independently in Asia and Africa, leading to two distinct but closely related crop species, Oryza sativa and Oryza glaberrima, respectively. The two domestications lead to morphological changes, in which a higher branching complexity of the panicles, influencing seed production and crop yield. Although much emphasis was placed on changes in transcriptional regulation during rice domestication and improvement, no large-scale study of small RNA regulation changes during domestication has been reported so far. To analyze whether rice domestication has altered the expression of small RNAs, we performed deep sequencing of small RNA transcriptomes from early developmental stages of panicles from 10 genotypes of the cultivated African species and 10 genotypes of its wild-relative O. barthii. Our study shows a drastic expression change of the 21-nucleotide smallRNA population. A total of 29% of these smallRNAs are overexpressed in panicles of O. barthii vs. O. glaberrima, corresponding mainly to 21-nucleotide phased siRNAs (or phasiRNAs). We also show that these changes are associated with a differential expression of a known regulator of phased siRNAs, miR2118 during early panicle development. Finally, these changes are associated to a heterochronic alteration of phasiRNAs and miR2118 expression pattern, during panicle development with a delayed expression in the domesticated species. Our study suggests a major reshaping of the regulation network from a specific class of small RNA during African rice domestication.

sample_organism:
Oryza glaberrima
Oryza barthii

platform_organism:
Oryza glaberrima
Oryza barthii

overall_design: Examination of panicle-associated smallRNA populations from Oryza glaberrima and Oryza barthii

first: Stefan

first: Hélène

last: Adam

first: Yves

last: Vigouroux

first: Kim-Nhung

last: Ta

first: Stéphane

last: de Mita

first: Alain

last: Ghesquière

first: François

last: Sabot


title: Genome-wide transcription start site mapping of Bradyrhizobium japonicum free-living cells and bacteroids -  a rich resource to identify new transcripts, proteins and to study gene regulation

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary:
Background: During the symbiosis with legumes, Bradyrhizobium japonicum cells infect roots where they induce the formation of root nodules and differentiate into intracellular nitrogen-fixing bacteroids. We used differential RNA-seq (dRNA-seq) for the genome-wide detection of transcriptional start sites (TSSs) in B. japonicum USDA 110 cells grown free-living or as bacteroids in soybean root nodules.
Results: A newly developed TSS recognition procedure based on machine learning allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4,329 in bacteroids and 2,766 in both living conditions. Using a proteogenomics approach, we provide evidence for the translation of 107 new transcripts including 14 with TSSs in annotated genes. In addition, we provide evidence for 178 shorter or longer proteins, 109 of them with TSS support. Based on our TSS map and a new de novo promoter prediction algorithm, we identified promoter motifs mainly used in nodules (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). The data is made available in a generic feature format (GFF) file along with an updated and extended genome annotation comprising promoters, TSSs and terminators. The value of such a TSS and promoter map beyond the identification of novel transcripts and ORFs is illustrated by the experimental analysis of an antisense RNA, which is a by-product of transcriptional interference in a gene encoding a cytochrome P450 highly expressed in nodules.
Conclusions: The genome-wide TSS and promoter map along with the extended genome annotation represents a very useful resource for detailed analyses of gene regulation and further systems biology studies on B. japonicum in symbiosis with soybean.

overall_design: dRNA-seq analysis of total RNA from exponentially growing B. japonicum USDA in oxic, liquid cultures (free-living cells) and from soybean root nodules

first: Jelena

last: Čuklina

first: Julia

last: Hahn

first: Maxim

last: Imakaev

first: Ulrich

last: Omasits

middle: U

first: Nikolay

last: Ljubimov

first: Melanie

last: Goebel

first: Gabriella

last: Pessi

first: Hans-Martin

last: Fischer

first: Christian

middle: H

last: Ahrens

first: Mikhail

middle: S

last: Gelfand

first: Elena

last: Evguenieva-Hackenberg


title: MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Chromatin accessibility plays a fundamental role in gene regulation. One mechanism to regulate accessibility is nucleosome placement, which is often measured by quantifying protection of DNA from enzymatic digestion. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC, quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both location of nucleosomes and accessibility to MNase in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares behavior of nucleosomes to that of non-histone proteins. We find that enhancers, promoters and other regulatory regions have changes in accessibility that do not correlate with changes in nucleosome occupancy. Moreover, we show that high nucleosome occupancy does not necessarily preclude high accessibility, revealing novel principles of chromatin regulation.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: MNase-seq profiles for different concentrations obtained for fly, mouse and human samples

first: Jakub

last: Mieczkowski

first: April

last: Cook

first: Sarah

last: Bowman

first: Britta

last: Mueller

first: Burak

last: Alver

first: Sharmistha

last: Kundu

first: Aimee

middle: M

last: Deaton

first: Jennifer

last: Johnson

first: Erica

last: Larschan

first: Peter

last: Park

first: Robert

middle: E

last: Kingston

middle: Y


title: Divergence of Transcription Regulation and the Function of a Conserved Elongation Factor in Budding and Fission Yeast

status: Public on Apr 16 2016

city: Ithaca

first: Gregory

middle: Thomas

last: Booth

state: New York

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

summary: Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet mechanistic details of this evolution remain elusive.  By comparing the transcriptional landscape of distantly related budding and fission yeast, we catch a glimpse of divergence in gene regulation. Using an adapted Precision Run-On sequencing (PRO-seq) approach, we have mapped the positions of RNA polymerase (RNA Pol II) active sites genome-wide in S. pombe and S. cerevisiae at base-pair resolution. We further mapped preferred sites of transcription initiation in each organism, exposing the origins of nascent transcription.  Performing PRO-seq in strains lacking Spt4, a highly conserved elongation factor subunit, results in globally elevated levels of transcribing Pol II within genes in both species. Messenger RNA abundance, however, does not reflect the increases in RNA Pol II density, indicating a possible global elongation rate defect.  Unexpectedly, we identify a novel pause in early elongation, specific to S. pombe, which requires Spt4, suggesting regulatory potential similar to promoter-proximal pausing in mammals.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Examination transcriptional landscapes in S. cerevisiae and S. pombe and the changes that result from the deletion of Spt4.

middle: T

first: John

last: Lis


title: Transcriptome profiling of purified mouse platelets

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary:
Purpose: The aim of this study is to determine the relative expresson levels of mRNA transcripts in wild type platelets
Methods: Total RNA was extracted and purified from purified platelets from BALB/c male mice (3 independent samples). Platelet purification was performed as described in Josefsson EC et al, Journal of Experimental Medicine (2011) 208:2017-31. Total RNA (100 ng) was used to generate sequencing libraries for whole transcriptome analysis following Illumina’s TruSeq RNA v2 sample preparation protocol. Completed libraries were sequenced on HiSeq 2000 with TruSeq SBS Kit v3- HS reagents (Illumina) as 100 bp paired-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Reads were aligned to the mouse reference genome mm10 and counts for known genes were obtained using the Rsubread package (version 1.18.0) (Liao et al. 2013; Liao et al. 2014).

overall_design: Total RNA was extracted and purified from purified platelets from BALB/c male mice (3 independent samples per population).

first: Stephane

last: Chappaz


title: Assessing transcriptomes of mouse cumulus cells, mural granulosa cells, and cumulus-oocyte complexes

status: Public on Apr 15 2016

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: Transcriptomes of mouse mural granulosa cells were sequenced to identify transcripts expressed in mural granulosa cells of ovaries.  Moreover, transcriptomes of cumulus cells were compared between those of young (2 month-old) and old mice (10 month-old) to assess the effects of ageing on cumulus cells.  In addition, transcriptomes of cumulus-oocyte complexes were compared between DBA/2 and (C57BL/6 x DBA/2)F1 mice to assess the strain differences.

overall_design: RNA-seq of cumulus cells, mural granulosa cells, and cumulus-oocyte complexes

first: Kurenai

last: Kawasaki

first: Jun-ichi

last: Sumitomo

first: Katsuyuki

last: Shiroguchi

middle: A

first: Koji

last: Sugiura


title: The SUMO E3 ligase-like proteins PIAL1 and PIAL2 interact with MOM1 and form a novel complex required for transcriptional silencing

city: Beijing

first: Yongqiang

last: Li

address: 7 Science Park Rd., ZGC life science park

institute: NIBS


title: The SUMO E3 ligase-like proteins PIAL1 and PIAL2 interact with MOM1 and form a novel complex required for transcriptional silencing [RNA-seq]

summary:
The mechanism by which MORPHEUS'MOLECULE1 (MOM1) contributes to transcriptional gene silencing remained elusive since the gene was first identified and characterized (Amedeo et al., 2000). Here, we report that two PIAS (PROTEIN INHIBITOR OF ACTIVATED STAT)-type SUMO E3 ligase-like proteins PIAL1 and PIAL2 function redundantly to mediate transcriptional silencing at MOM1 target loci. PIAL1 and PIAL2 physically interact with each other and with MOM1 to form a high-molecular-weight complex. In the absence of either PIAL2 or MOM1, the formation of the high-molecular-weight complex was disrupted. We identified a previously uncharacterized IND (interacting domain) in PIAL1 and PIAL2, and demonstrated that IND directly interacts with MOM1.
The CMM2 (conserved MOM1 motif 2) domain of MOM1 was previously shown to be required for the dimerization of MOM1. We demonstrated that the CMM2 domain is also required for the interaction of MOM1 with PIAL1 and PIAL2. We found that although PIAL2 has a SUMO E3 ligase activity, the activity is dispensable for PIAL2 in transcriptional silencing. This study suggests that PIAL1 and PIAl2 act as components of the MOM1-containing complex to mediate transcriptional silencing at heterochromatin regions.

overall_design: Compare the mRNA profiles of 10-day-old seedlings materials of mutants (mom1, nrpe1, pial1/2, pial2 and mom1pial2) to wild type Col-0 by Illumina sequencing.

first: Xin

last: He

first: Yong

middle: F

last: Han

middle: Q


title: Aging-related virtually naïve memory T (TVNM) cells: a new stage in T cell response to persistent infections in humans

city: New York

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

summary: We conducted RNA-Seq on T cell subsets sorted from five donors to identify a transcriptional signature associated with virtually naïve memory T cells.

overall_design: We sorted various T cell subsets from five donors including TEMRAs, naïve T cells, effector memory T cells, central memory T cells, and virtually naïve memory T cells and used a template-switching-based library construction protocol to faciliate low-input RNA-Seq from tens to hundreds of thousands of cells in each subpopulation.


title: The SUMO E3 ligase-like proteins PIAL1 and PIAL2 interact with MOM1 and form a novel complex required for transcriptional silencing [Bisulfite-seq]

overall_design: Whole genome methylation maps of 3 mutants (pial1/2, nrpe1, mom1) were generated using bisulfite-seq (BS-seq).


title: Identification of microRNAs with the potential role in progression of thioacetamide-induced liver fibrosis in mouse

first: Jae-Sang

last: Hong

state: Seoul

address: building life science and biotech west building L204

country: South Korea

institute: Korea University

summary: We applied Solexa deep sequencing technology to identify which miRNAs were regulated in thioacetamide-induced fibrotic liver tissue

overall_design: Control liver tissue vs. Thioacetamide (TAA)-introduced liver tissue with biological replicates

first: Do-Hoon

last: Lee

first: Ye

middle: W

last: Yook

first: Yu

last: Jang

first: Jong-Hoon

last: Kim

first: Young


title: Human Induced Pluripotent Stem Cells Recapitulate Breast Cancer Patients’ Predilection to Doxorubicin-Induced Cardiotoxicity

city: Chicago

first: Paul

last: Burridge

state: IL

address: 320 E Superior St Searle 8-525

department: Pharmacology

institute: Northwestern

summary: Doxorubicin (Adriamycin) is an anthracycline chemotherapy agent effective in treating a wide range of malignancies1 with a well-established dose-response cardiotoxic side-effect that can lead to heart failure2-4. Even at relatively low cumulative doses of 200–250 mg/m2, the risk of cardiotoxicity is estimated at 7.8% to 8.8%4,5. Doxorubicin-induced cardiotoxicity (DIC) can range from asymptomatic reductions in left ventricular ejection fraction (LVEF) to highly symptomatic heart failure6,7. At present, it is not possible to predict which patients will be affected by DIC or adequately protect patients who are at risk for suffering this devastating side-effect8. Here we demonstrate that patient-specific human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) can recapitulate individual patients’ predilection to DIC at the single cell level. hiPSC-CMs derived from breast cancer patients who suffered clinical DIC are consistently more sensitive to doxorubicin toxicity, demonstrating decreased cell viability, mitochondrial/metabolic function, calcium handling, and antioxidant pathway gene expression, along with increased reactive oxygen species (ROS) production compared to hiPSC-CMs from patients who did not experience DIC. Together, our data indicate that hiPSC-CMs are a suitable platform for identifying and verifying the genetic basis and molecular mechanisms of DIC.

overall_design: Comparision of the effect of 1uM doxorubicin for 24 h on gene expression in hiPSC-CM derived from 6 patients


title: RNA-Sequencing of C57BL-6 thymocytes

city: Montreal

first: Krystel

last: Vincent

state: Quebec

address: 2950, chemin de la Polytechnique, Marcelle-Coutu Pavilion

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: Thymocytes were extracted from a pool of three 8-12 week old C57BL-6 female mice. Cells were separated from stroma by gently crushing the thymi in between 2 microslides. RNA from thymocytes was extracted using the Trizol reagent and protocol, and analysed using the Illumina HiSeq 2000.

overall_design: Transcriptomic analysis of a single replicate of thymocytes from a pool of three 8-12 week old C57BL-6 female mice, using the Illumina HiSeq 2000

first: Céline

last: Laumont

first: Claude

last: Perreault


title: RNA-sequencing of single whole cells and nuclei from mouse dentate granule cells

first: Fred

last: Gage

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

summary: Single-cell sequencing methods have emerged as powerful tools for identification of heterogeneous cell types within defined brain regions. Application of single-cell techniques to study the transcriptome of activated neurons can offer insight into molecular dynamics associated with differential neuronal responses to a given experience.  Through evaluation of common whole-cell and single-nuclei RNA-sequencing (snRNA-seq) methods, here we show that snRNA-seq faithfully re-capitulates transcriptional patterns associated with experience-driven induction of activity, including immediate early genes (IEGs) such as Fos, Arc, and Egr1. SnRNA-seq of mouse dentate granule cells reveals  large-scale changes in the activated neuronal transcriptome after brief novel environment exposure, including induction of MAPK pathway genes . In addition, we observe a continuum of activation states, revealing a pseudo-temporal pattern of activation from gene expression alone. In summary, snRNA-seq of activated neurons enables the examination of gene expression beyond IEGs,allowing for novel insights into neuronal activation patterns in vivo.

overall_design: Examination of 1) 82 whole-cell (WC) dentate granule cells from a PTZ- or saline-treated mouse, and 2) 23 single-nuclei (SN) from dentate granule cells of a homecage (HC) mouse or 96 nuclei from a mouse exposed to a novel environment (NE)

first: Ben

last: Lacar

first: Sara

last: Linker

first: Baptiste

last: Jaeger


title: Regulation of Vascular Smooth Muscle Cell Dysfunction Under Diabetic Conditions By miRNA-504

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: Diabetes promotes pro-atherogenic and pro-inflammatory phenotype of VSMC associated with vascular complications. Emerging evidence shows that miRNAs play key roles in VSMC, but their role in diabetes induced effects is unclear. We profiled novel diabetes induced miRNAs in VSMC from diabetic mice and examined their role in VSMC dysfunction. High throughput small RNA-sequencing identified 135 differentially expressed miRNAs in VSMC from type 2 diabetic db/db mice (db/dbVSMC) versus non-diabetic db/+ mice. Several of these miRNA were known to regulate VSMC functions. We further focused on miR-504, because it was highly upregulated in db/dbVSMC, but its function in VSMC is unknown. We demonstrated that miR-504 and its host gene Fgf13 were upregulated in VSMC and in vivo in aortas from db/db mice. Bioinformatics analysis predicted that miR-504 targets, including a signaling adaptor Grb10 and a transcription factor Egr2, could regulate growth factor signaling.  We experimentally verified that miR-504 targets Grb10 and Egr2, and it enhanced ERK1/2 activation, proliferation and migration in VSMC. Silencing Grb10 by small interfering RNA also enhanced ERK1/2 activation, inflammatory gene expression and migration. Whereas, Egr2 silencing downregulated anti-inflammatory SOCS1 and increased inflammatory genes. Furthermore, treatment with high-glucose and palmitic acid upregulated miR-504, inhibited Grb10 and enhanced inflammatory genes in VSMC. Diabetes mis-regulates expression of several miRNAs including miR-504 involved in VSMC functions. Changes in miRNAs are sustained in non-diabetic conditions suggesting involvement of miRNA dependent mechanisms in metabolic memory implicated in vascular complications. Targeting such mechanisms could offer novel therapies strategies.

overall_design: Vascular smooth muscle cells (VSMC) were isolated from the thoracic aortas of 10-12 week old male type 2 diabetic db/db mice and control db/+ mice. Total RNA was extracted from VSMC cultures to profile differentially expressed miRNAs in VSMC from diabetic db/db mice versus control db/+ mice.

first: Marpadga

last: Reddy

first: Zhuo

first: Natarajan

last: Rama


title: BRD4 connects enhancer remodeling to senescence immune surveillance (ChIP-Seq)

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University

summary: Cellular senescence is a homeostatic program associated with tumor suppression, wound healing, and certain age related pathologies. Senescent cells display a repressive chromatin configuration thought to stably silence proliferation-promoting genes, while at the same time activate an unusual form of immune surveillance involving a secretory program referred to as the senescence-associated secretory phenotype (SASP). Here we demonstrate that senescence also involves a global remodeling of the enhancer landscape with recruitment of the chromatin reader BRD4 to newly activated super-enhancers adjacent to key SASP genes. Transcriptional profiling and functional studies indicate that BRD4 is required for the SASP and downstream paracrine signaling. Consequently, BRD4 inhibition disrupts immune cell-mediated targeting and elimination of premalignant senescent cells in vitro and in vivo. Our results identify a critical role for BRD4-bound super-enhancers in senescence immune surveillance and in the proper execution of a tumor-suppressive program.

overall_design: Chip-seq for H3K27Ac and BRD4 in proliferating, quiescent or senescent (HrasV12) human fibroblasts (IMR90)

first: Jae-Seok

first: Nilgun

last: Tasdemir

first: Ana

last: Banito

first: Direna

last: Alonso-Curbelo

first: Scott

last: Lowe


title: BRD4 connects enhancer remodeling to senescence immune surveillance (RNA-seq)

overall_design: Analysis of RNA isolated from human fibroblasts (IMR90) in proliferating, quiescent or senescent (HrasV12) conditions upon knockdown of Brd4, p65, p53, p53/RB, p16/21 or Vehicle and JQ1 treatment


title: BRD4 connects enhancer remodeling to senescence immune surveillance

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

overall_design: Refer to individual Series


title: RNA sequencing of olfactory bulb projection neurons in neurotensin-GFP (NTS-GFP) mice at different developing time points

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Characterize the spatiotemporal dynamics of gene expression in neurons in developing olfactory bulb

overall_design: Comparison of transcriptome profiles of GFP+ and GFP- cells derived from olfactory bulb of NTS-GFP at different developmetal time points (E13, E15, E17 and P0).

first: Fumiaki

last: Imamura

first: Mingfeng

last: Li

first: Anna

middle: C

last: Salzberg

first: Nenad

last: Sestan

first: Charles

last: Greer


title: Allele-specific binding analysis of rs242561 by NRF2 ChIP tagmentation sequencing

status: Public on Apr 14 2016

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

summary: We identified a SNP rs242561, located within a regulatory region of the MAPT gene (encoding microtubule-associated protein Tau). It was consistently occupied by NRF2/sMAF in multiple ChIP-seq experiments, and its strong-binding allele increased transactivation, and accorded higher mRNA levels in cell lines and human brain. To confirm the allele-specific binding, we conducted ChIP tagmentaion sequencing experiment in human lymphoblastoid cell line GM12763 which is heterozygous for rs242561. NRF2 ChIP DNA was isolated from GM12763 cells treated with Sulforaphane  (SFN)  in triplicates. The region containing rs242561 was amplified using primers, Fwd 5’-AGCCTTCCCTGTCCTTGATT-3’, Rev 5’-GGACCGAGCTTCCAGTCTAA-3’, and tagmentated using Tn5-based transposition for library construction.  Libraries were sequenced on Illumina MiSeq.

overall_design: NRF2 ChIP tagmentation sequencing of a 241bp intron region in MAPT gene using GM12763 treated with sulforaphane

first: Michelle

middle: R

last: Campbell

first: Ma

last: Wan

first: Douglas

last: Bell


title: Functional characterization of DNA methylation in the oligodendrocyte lineage [RNASeq_Dnmt1cKO_OPC]

first: Sarah

last: Moyon

address: 85 St Nicholas Terrace

department: Neuroscience

institute: CUNY ASRC

summary: Oligodendrocytes derive from progenitors (OPC) through the interplay of epigenetic and transcriptional events. By integrating high-resolution methylomics, RNA-sequencing and multiple transgenic lines, this study defines the role of DNMT1 in developmental myelination. We detected hypermethylation of genes related to cell cycle and neurogenesis during differentiation of OPC, and yet, genetic ablation of Dnmt1 resulted in inefficient OPC expansion and severe hypomyelination associated with ataxia and tremors in mice. This phenotype was not caused by lineage switch or massive apoptosis, but was characterized by a profound defect of differentiation, associated with massive changes in exon-skipping and intron-retention splicing events, and by the activation of an endoplasmic reticulum stress response. Therefore, loss of Dnmt1 in OPC is not sufficient to induce a lineage switch, but acts as an important determinant of the coordination between RNA splicing and protein synthesis, necessary for myelin formation.

overall_design: mRNA profiles of P5 mouse Olig1+/+;Dnmt1flox/flox;Pdgfra-GFP and Olig1cre/+;Dnmt1flox/flox;Pdgfra-GFP sorted OPC were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2500.

first: S

first: J

middle: L

last: Huynh

first: D

last: Dutta

first: Z

last: Fan

last: Ma

last: Yoo

first: R

last: Lawrence

first: M

last: Wegner

first: G

last: John

first: B

last: Emery

first: C

last: Lubetzki

middle: J

last: Franklin

last: Zhu

last: Dupree

first: P

last: Casaccia


title: CXXC finger protein 1 is critical for T cell intrathymic development through regulating H3K4 trimethylation [ChIP-Seq]

city: Guangzhou

first: Lai

last: Wei

address: 54 S. Xianlie Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

summary: T cell development in the thymus is largely controlled by an epigenetic program involving in both DNA methylation and histone modifications. Previous studies have identified Cxxc1 as a regulator of both cytosine methylation and histone 3 lysine 4 trimethylation (H3K4me3). However, it is unknown whether Cxxc1 plays a role in thymocyte development. Here we show that T cell development in the thymus is severely impaired in Cxxc1-deficient mice. Furthermore, we identify genome-wide Cxxc1 binding sites and H3K4me3 modification sites in wild-type and Cxxc1-deficient thymocytes. Our results demonstrate that Cxxc1 directly controls the expression of key genes important for thymocyte survival such as RORγt and for TCR signaling including Zap70 and CD8, through maintaining the appropriate H3K4me3 on their promoters. Importantly, we show that RORγt, a direct target of Cxxc1, can rescue the survival defects in Cxxc1-deficient thymocytes. Our data strongly support a critical role of Cxxc1 in thymocyte development.

overall_design: ChIP-Seq analysis of Cxxc1 and H3K4me3 in WT and Cxxc1-deficient mice

first: Lie

last: Wang


title: mRNA-seq of satellite cells cultured and expanded in F10 conventional medium, T cell conditional medium, and cytokine cocktail

city: Shanghai

first: Xin

last: Fu

address: 320 Yueyang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: Like most adult stem cells, culturing and expansion of satellite cells (muscle stem cells) are difficult, that prevents the utilization of satellite cells in cell-based therapies. Here, we reveal that T cells infiltrated into the injury site upon acute inflammation are able to promote muscle stem cell proliferation, expansion, and maintain their injury reparation abilities in vivo. Four cytokines, IL-1α, IL-13, TNF-α, and IFN-γ, were identified as the effective components secreted by T cells to faciliate satellite cell propagation

overall_design: Comparison of mRNA expression profile of satellite cells between different treatment in different sample

first: Yuning

first: Ping

last: Hu


title: CXXC finger protein 1 is critical for T cell intrathymic development through regulating H3K4 trimethylation


title: Identification of the long, edited dsRNAome in LPS-stimulated bone marrow-derived macrophages (BMDMs)

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: Endogenous double-stranded RNA (dsRNA) is intricately regulated in mammals to prevent aberrant activation of host inflammatory pathways by cytosolic dsRNA binding proteins. We define the endogenous dsRNA repertoire in mouse BMDMs during the inflammatory response to bacterial lipopolysaccharide. Editing by adenosine deaminases that act of RNA (ADAR) enzymes was quantified temporally using RNA-Seq data from activated mouse macrophages to identify 342 Editing Enriched Regions (EERs), indicative of highly structured dsRNA. Nearly all mouse EERs were present in 3’UTRs. A comparison of EERs from mouse and human revealed significant conservation of EERs between mouse EER- associated genes and homologous human genes. In addition, using publicly available data and experimental validation, a significant proportion of EERs were shown to accumulate in the nucleus, a strategy that is thought to prevent aberrant activation of proinflammatory cascades in the cytoplasm. Finally, the significant conservation of EERs and the enhancement of structured regions in human suggests an increasingly important role for these regions in human biology.

overall_design: RNA-Seq of total RNA and immunoprecipitated dsRNA isolated from bone marrow-derived macrophages from C57BL/6 mice after activation with bacterial lipopolysacharide for 0, 6, or 12 hours.

middle: G

first: Brenda

last: Bass


title: Endometrial Expression of Steroidogenic Factor 1 Promotes Cystic Glandular Morphogenesis

city: Houston

first: Francesco

last: DeMayo

state: Texas

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: We report the whole genome binding profile of Steroidogenic Factor 1

overall_design: ChIP-seq in murine endometrium

first: Franscesco

first: Yasmin

last: Vasquez


title: Transcriptome profiling of A. thaliana expressing auxin degradation resistant IAA26-P108H-GFP from the IAA26 native promoter

city: College Park

first: James

middle: N

last: Culver

state: MD

address: 4291 Fieldhouse Dr.

department: Plant Science and Landscape Architecture

institute: University of Maryland, College Park

summary: The goal of this study was to compare the transcriptional profile (RNA-seq) of seven-week-old auxin resistant pIAA26::IAA26-P108H-GFP transgenic plants to non-transformed control plants to identify candidate genes and pathways regulated by IAA26.

overall_design: RNA-seq analysis was performed with A. thaliana ecotype Shahdara seven-week-old leaves from auxin resistant pIAA26::IAA26-P108H-GFP transgenic plants or non-transformed controls.  Four fully expanded leaves were collected from each test plant and total RNA from four to six individual test plants was pooled for each of the three biological replicates.  Sequencing was carried out on an Illumina HiSeq 1500 platform using rapid run mode with 50 nt single end reads.

first: Tamara

middle: D

last: Collum


title: Physical interaction between mutant calreticulin and the thrombopoietin receptor is required for transformation of hematopoietic cells

city: Heidelberg

first: Javier

last: Perales-Paton

state: Baden-Württemberg

address: Im Neuenheimer Feld 267

department: Faculty of Medicine

institute: Heidelberg University

summary: Somatic mutations in calreticulin (CALR) are present in approximately 40% of patients with myeloproliferative neoplasms (MPN). However, the mechanism by which mutant CALR is oncogenic is unknown. Here, we demonstrate that a megakaryocytic-specific MPN phenotype is induced when mutant CALR is over-expressed in mice and that the thrombopoietin receptor, MPL is required for mutant CALR driven transformation. Whole transcriptome analysis reveals enrichment of STAT signatures in mutant CALR transformed cells and JAK2 inhibitor treatment abrogates STAT activation. Employing extensive mutagenesis-based structure-function analysis we demonstrate that the positively charged amino acids within the mutant CALR C-terminus are required for cellular transformation through facilitating physical interaction between mutant CALR and MPL. Together, our findings elucidate a novel mechanism of cancer pathogenesis.

overall_design: Transcriptomes derived from BA/F3-MPL cells transformed with human wild-type CALR, human mutant CALR 52bp del, or Empty vector, at time zero (t0) and 24 hours (t24) after IL3-withdrawal culture were generated by deep sequencing, two replicas, by HiSeq2000.

first: Shannon

last: Elf

first: Nouran

last: Abdelfattah

first: Edwin

last: Chen

last: Perales-Patón

first: Emily

last: Rosen

first: Amy

last: Ko

first: Fabian

last: Peisker

first: Natalie

last: Florescu

first: Silvia

last: Giannini

first: Ofir

last: Wolach

first: Elizabeth

last: Morgan

first: Julie-Aurore

last: Losman

first: Rebekka

middle: K

last: Schneider

first: Fatima

last: Al-Shahrour

first: Ann

last: Mullally


title: RNA profiling by deepSAGE sequencing in the cortex of a migraine mouse model after induction of cortical spreading depression

city: Leiden

first: Else

last: Eising

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

summary: Familial Hemiplegic Migraine type 1 (FHM1) is a rare monogenic subtype of migraine with aura caused by mutations in CACNA1A that encodes the a1A subunit of voltage-gated CaV2.1 calcium channels. Transgenic knock-in mice that carry the human FHM1 R192Q missense mutation (“FHM1 R192Q mice”) exhibit an increased susceptibility to cortical spreading depression (CSD), the mechanism underlying migraine aura. Here we analysed gene expression profiles from isolated cortical tissue of FHM1 R192Q mice 24 hours after experimentally induced CSD in order to identify molecular pathways affected by CSD. Gene expression profiles were generated using deep Serial Analysis of Gene Expression sequencing. Our data reveal a signature of inflammatory signalling upon CSD in the cortex of both mutant and wild-type mice. However, only in the brains of FHM1 R192Q mice specific genes are up-regulated in response to CSD that are implicated in interferon-related inflammatory signalling. Our findings show that CSD modulates inflammatory processes in both wild-type and mutant brains, but that an additional unique inflammatory signature becomes expressed after CSD in a relevant mouse model of migraine.

overall_design: Cortical RNA expression analysis using deepSAGE sequencing of wild-type (C57BL/6J) or transgenic R192Q FHM1 mice (n=6 per experimental group) 24 hours after sham surgery or the induction of 7 cortical spreading depression episodes

first: Reinald

last: Shyti

last: Tolner

first: Arn

middle: M

last: van den Maagdenberg


title: Mapping Replication Stress-Dependent Transcriptional Events Dependent on ATM or ATMIN by RNA-seq

city: Vienna

first: Abdelghani

last: Mazouzi

address: Lazarettgasse Lazarettgasse 14, AKH BT 25.3, 7.105

country: Austria

institute: CeMM

summary: The cellular response to replication stress requires the DNA-damage responsive kinase ATM and its co-factor ATMIN, however the roles of this signaling pathway following replication stress are unclear. RNA-seq and subsequent differential expression analyses were utilized to identify the functions of ATM and ATMIN in response to replication stress induced by Aphidcolin (APH).

overall_design: Mouse Embryonic Fibroblasts (MEFs) deleted for ATM or ATMIN were treated with 1µM APH or DMSO as a control. Two different wild-type MEF cell lines (wtATM, wtATMIN) served as controls. RNA-seq was performed in duplicates, in a total of 32 samples, with an average of  31.1M aligned readsobtained  per group,with 15.5M reads obtained per replicate.

first: Doris

last: Chen

first: Joanna

last: Loizou


title: Functional characterization of DNA methylation in the oligodendrocyte lineage [RNASeq_development]

first: Sarah

last: Moyon

summary: Myelination in the CNS is modulated by interplay between transcription factors and recruitment of chromatin modifying enzymes. Using a network built from genome-wide DNA methylation and transcriptomic profiling of sorted oligodendrocyte lineage cells that integrates oligodendrocyte-specific ChIP-Seq data, we defined a crucial role of DNA methylation in coordinating the transition between progenitor cell cycle arrest and oligodendrocyte differentiation. We further identified DNA methyltransferase 1 (DNMT1) as key regulator of oligodendrocyte survival at this transition point, as we detected severe and extensive developmental hypomyelination only in Olig1cre/+;Dnmt1flox/flox but not in Olig1cre/+;Dnmt3aflox/flox mice  or in Cnpcre/+;Dnmt1flox/flox. This phenotype was characterized by decreased expression of genes regulating myelination and lipid metabolism – despite the hypomethylation observed at these genetic loci  – and upregulation of cell cycle and DNA-damage pathways. Therefore DNMT1 is a nodal point regulating proliferation, survival, and differentiation in the oligodendrocyte lineage, and is critical for cell number regulation in the developing brain.

overall_design: mRNA profiles of FAC-sorted P2 Pdgfra::GFP and P18 Plp1-GFP purified cell samples from mouse brains were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.

first: S

first: J

last: Huynh

last: Yoo

first: D

last: Ma

first: P

last: Naik

last: Dutta

first: R

last: Lawrence

first: G

last: John

first: B

last: Emery

first: C

last: Lubetzki

last: Franklin

last: Dupree

last: Fan

last: Zhu

last: Casaccia


title: Functional characterization of DNA methylation in the oligodendrocyte lineage


title: Functional characterization of DNA methylation in the oligodendrocyte lineage [ERRBS]

overall_design: Genome wide DNA methylation profiles of FAC-sorted P2 Pdgfra::GFP and P18 Plp1-GFP purified cell samples from mouse brains were generated by ERRBS analysis, in duplicate, using Illumina HiSeq 2000.


title: Transcriptome analysis in a radiosensitive and a radioresistant cell line after ionizing radiation

status: Public on Apr 13 2016

city: Bellaterra

first: Mireia

last: Borràs-Fresneda

address: s/n

country: Spain

institute: Universitat Autònoma de Barcelona

summary: Differential gene expression profiling was performed in two lymphoblastoid cell lines with different radiosentivitity, one radiosensitive (RS) and another radioresistant (RR), after different post-irradiation times. A greater and a prolonged transcriptional response after irradiation was induced in the RS cell line. Functional analysis showed that 24 h after irradiation genes involved in DNA damage response, negative regulation of the cell cycle and apoptosis were still differentially up-regulated in the RS cell line but not in the RR cell line.

overall_design: Sham-irradiated and irradiated (2 Gy) cell cultures of the RS and the RR cell line were incubated at 37ºC for 4 and 24 h and 14 days. After that, RNA was extracted and sequenced with QuantSeq technology

first: M

last: Barquinero

last: Gomolka

last: Hornhardt

first: U

last: Rössler

last: Armengol

first: L

last: Barrios


title: Next Generation Sequencing Compares Effects of microRNA-9 perturbation in control and SZ hiPSC NPCs

first: Kristen

last: Brennand

address: 1425 Madison Ave, 9-20B

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary:
To follow-up findings that miR-9 was abundantly expressed in control NPCs, significantly down-regulated in a subset of SZ NPCs, and that miR-9 levels/activity, neural migration and diagnosis were strongly correlated, we tested the effect of manipulating miR-9 at cellular, proteomic and transcriptomic levels. Unexpectedly, proteomic- and RNAseq-based analysis revealed that these effects were mediated primarily by small changes in expression of indirect miR-9 targets, rather than large changes in direct miR-9 targets; these indirect targets are enriched for migration-associated genes. Together these data indicate that aberrant levels and activity of miR-9 may be one of the many factors that contribute to SZ risk, at least in a subset of patients.

Methods: We compared global transcription of forebrain NPCs from two control and two SZ patients with manipulated miR-9 levels by RNAseq.

Results:  Although RNAseq analysis revealed large inter-individual heterogeneity, we were able to resolve several functional consistencies in the effects of our miR-9 perturbations: i) the change in miR-9 activity was consistent with the inhibitory role of miR-9, ii) the gene expression fold-change of miR-9 target genes (between each perturbation and its corresponding control, summarized by the first principal component) was correlated (r=0.95, p=3.92e-04) with miR-9 fold change and iii) the differentially expressed (DE; p <0.01) gene list resulting from miR-9 perturbation (paired t-test) was enriched for miR-9 targets (1.53-fold, p=1.2e-5).

Conclusions: We integrated the miR-9 perturbation RNAseq data with our existing RNAseq datasets contrasting control and SZ hiPSC NPC expression from our cohort 1 (six controls, four patients), to ask whether there was any relationship between the “SZ NPC signature” and “miR-9 perturbation” datasets; we observed that the DE (p-value <0.01) in “SZ NPC signature” is enriched for DE (fdr<0.01) in “miR-9 perturbation” (the overall enrichment is 2.31-fold (p=9.39e-09)); there is significant correlation between DE fold-change in these two datasets (overall genes r=0.188; p<10e-50). Effects were mediated primarily by small changes in expression of indirect miR-9 targets, rather than large changes in direct miR-9 targets; these indirect targets are enriched for migration-associated genes

overall_design: Biological duplicates of passage-matched NPCs from 1 control (female) and 1 SZ patient (female) were transduced with either RV-GFP or RV-miR-9-GFP; GFP-positive NPCs were purified by fluorescent activated cell sorting (FACS) and expanded for two passages. In parallel, passage-matched NPCs from 2 controls (1 male, 1 female) and 2 SZ patients (1 male, 1 female) were transiently transfected with either scrambled or miR-9 LNA probes. In both instances, miR-9 perturbation was confirmed by qPCR.

first: Gang

last: Fang


title: Replication-coupled nucleosome assembly and positioning by ATP-dependent chromatin remodeling enzymes

first: Iestyn

last: Whitehouse

address: 1275 York Avenue

institute: Sloan-Kettering Institute

summary: We have previously shown that Okazaki fragments in Saccharomyces cerevisiae are sized according to the chromatin repeat. Here we demonstrate that nucleosome positioning is rapidly established on newly synthesized DNA. Using deep sequencing, we demonstrate that ATP-dependent chromatin remodeling enzymes, Isw1 and Chd1, collaborate with histone chaperones, such as CAF-1 and Rtt106, to remodel nucleosomes, as they are loaded. Importantly, we find that nucleosome positioning is ultimately specified by select sequence-specific DNA-binding factors, which serve as physical cues for chromatin remodeling. Our results provide a mechanistic understanding of how chromatin structures are replicated in vivo, and show that chromatin structure at gene promoters is rapidly established after DNA replication.  Altogether, our data provide evidence for coordinated “loading and remodeling” of nucleosomes behind the replication fork, in collaboration with packing of nucleosomes against a barrier.

overall_design: 7 samples, including a wild type, are included. All are single-end sequenced via Ion Torrent PGM methodology.

first: Tejas

last: Yadav


title: Epigenomic landscapes of human primary pancreatic cell types

city: Stanford

first: Seung

last: Kim

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

summary: Intensive efforts are focused on identifying regulators of human pancreatic islet cell growth and maturation to accelerate development of therapies for diabetes. After birth, islet cell growth and function are dynamically regulated; however, establishing these age-dependent changes in humans has been challenging. Here we describe a multimodal strategy for isolating pancreatic endocrine and exocrine cells from children and adults to identify age-dependent gene expression and chromatin changes on a genomic scale. These profiles revealed distinct proliferative and functional states of islet alpha-cells or beta-cells, and histone modifications underlying age-dependent gene expression changes. Expression of SIX2 and SIX3, transcription factors without prior known functions in the pancreas and linked to fasting hyperglycemia risk, increased with age specifically in human islet beta-cells. SIX2 and SIX3 were sufficient to enhance insulin content or secretion in immature beta-cells. Our work provides a unique resource to study human-specific regulators of islet cell maturation and function.

overall_design: For this study we purified primary human pancreatic cells from juvenile and adult donors and analyzed the chromatin landscape using ChIP-Seq assays.

first: Hatice

middle: E

last: Arda

first: Jennifer

last: Tsai


title: Regulation of gene expression during the onset of ligninolytic oxidation by Wolfiporia cocos on colonized wood

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

summary: Certain wood decay basidiomycetes, collectively referred to as brown-rot fungi rapidly depolymerize cellulose while leaving behind the bulk of cell wall lignin as a modified residue. The mechanism(s) employed are unclear, but considerable evidence implicates the involvement of diffusible oxidants, particularly hydroxyl radical. Toward a better understanding of this process, we have examined the transcriptome and secretome of Wolfiporia cocos when cultivated on media containing glucose, purified crystalline cellulose, aspen (Populus grandidentata) or lodgepole pine (Pinus contorta) as sole carbon source. Compared to glucose, 39, 331 and 357 genes exhibited 4-fold increases in transcript levels in cellulose, aspen and lodgepole pine, respectively. Mass spectrometry identified peptides corresponding to 64 glycoside hydrolase (GH) proteins and, of these, 17 corresponded to transcripts upregulated on one or both woody substrates. Most of these genes were broadly categorized as hemicellulases or chitinases. Consistent with an important role for ·OH in cellulose depolymerization, high transcript levels and upregulation were observed for genes involved in iron homeostasis, iron reduction and extracellular peroxide generation. These patterns of regulation differ markedly from the closely related brown rot fungus, Postia placenta, and expand the number of enzymes potentially involved in the oxidative depolymerization of cellulose.

overall_design: Medium containing glucose, microcrystalline cellulose, ground aspen or ground lodgepole pine was inoculated with W. cocos. RNA was purified from cultures. Single read 100 bp Illumina runs were performed.


title: Small RNAs from Drosophila melanogaster WT and Tailor mutant S2 cells and ovaries

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

institute: John Curtin School of Medical Research, The Australian National University

summary: Small RNAs were cloned from wt and tailor mutant cells or ovary tissues to study the role of Tailor in miRNA uridylation

overall_design: Small RNA samples from GFP-KD and Tailor-KD S2 cells and WT (w1118) and Tailor KO ovaries

first: Fuqu

last: Hu

first: Eric

last: Lai


title: Signaling couples hair follicle stem cell quiescence with reduced histone H3K4/K9/K27me3 for proper tissue homeostasis

first: Jayhun

last: Lee

state: TX

address: 6431 Fannin St. MSE R222

department: Microbiology and Molecular Genetics

institute: The University of Texas Health Science Center at Houston

summary: Mechanisms of plasticity to acquire different cell fates are critical for adult stem cell (SC) potential, yet are poorly understood. Reduced global histone methylation is an epigenetic state known to mediate plasticity in cultured embryonic SCs and T cell progenitors. We used mouse hair follicle stem cells (HFSCs) at two different hair cycle stages (early anagen and late catagen) to compare the genome-wide changes in the levels of histone modification marks H3K4me3, H3K9me3, and H3K27me3.

overall_design: Hair follicle stem cells from Early Anagen (EA-HFSCs) and Late Catagen (LC-HFSCs), and their non-HFSCs counterparts (nEA-HFSCs and nLC-HFSCs), were FACS-isolated for Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) analysis of H3K4me3, H3K9me3, and H3K27me3.

first: Tudorita

last: Tumbar


title: Mapping of nascent RNA in MLL2 F/F and FC/FC MEF cells

city: South Mimms

first: Theo

last: Kantidakis

address: Blanche Lane

department: Clare Hall Laboratories

institute: Francis Crick Institute

summary: Global Run-On has been performed in MLL2 F/F and FC/FC MEF cells. The aim of the experiment is to test how the lack of MLL2 affects nascent RNA transcription.

overall_design: Four samples were analyzed - 2 independent replicates. The experiments were performed using immortalized mouse embryonic fibroblasts (MEF) in which both MLL2 alleles were targeted by the loxp system (F/F cells). Tamoxifen treatment of the F/F cells for 24 hours results in the excision of both MLL2 alleles (FC/FC cells).

first: Theodoros

first: Jesper

last: Svejstrup


title: Mutation of cancer driver MLL2 results in transcription stress and genome instability

type: Genome variation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Mutations in histone and other genes in MLL2-impaired human and mouse cells

summary: We used human or mouse MLL2-impaired cells (including a human DSET MLL2 cell line,) as well as their parental controls, and measured mutations in histones and a few other genes that were affected in our gH2AX ChIP-Seq experiments. We found that cells lacking or having impaired MLL2 were presenting statistically signifficant, higher levels of mutations at the tested genes as compared to their parental controls.

overall_design:
The experiments were performed using human and mouse cells. For the human cells, the parental HCT116 cells were used as control. Two different MLL2 KO clones (KO19 and KO34) and a DSET MLL2 cell line were employed. For the mouse cells, the F/F cells were used, in which both MLL2 alleles are targeted by loxp. Tamoxifen treatment for 24 hours results in the excision of both MLL2 alleles (FC/FC cells). F/F cells were treated with tamoxifen (FC/FC) or vehicle (DMSO, F/F) for 24 hours. Half of the cells were then harvested and used as controls (T0), while the other half were cultured for another 30 days (T30). Mutations after 30 days (T30) of tamoxifen/vehicle treatment were measured compared to the T0 controls. In all cases, two different pools of primers were employed. All histone genes available to target with high coverage were studied, in either human or mouse cells. For the human cells, 32 histone (HIST1H1A HIST1H1B HIST1H1C HIST1H1D HIST1H1E HIST1H1T HIST1H2AC HIST1H2AD HIST1H2AG HIST1H2AH HIST1H2AI HIST1H2AJ HIST1H2AK HIST1H2BF HIST1H2BG HIST1H2BH HIST1H2BI HIST1H2BJ HIST1H2BK HIST1H2BN HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H4B HIST1H4F HIST1H4J HIST2H2AC) and 6 other genes (BTG2 SGK1 MDM2 CDKN1A EGR1 RPLP0) were targeted. For the mouse cells, 21 histone (HIST1H1A HIST1H1B HIST1H1C HIST1H1D HIST1H1E HIST1H1T HIST1H2AK HIST1H2BQ HIST1H3B HIST1H3C HIST1H3F HIST1H4F HIST1H4J HIST1H4N HIST1H4N HIST2H2AA1 HIST2H2AA1 HIST2H2AA2 HIST2H2AA2 HIST2H2AC HIST2H2BB) and 6 other genes (BTG2 SGK1 MDM2 CDKN1A EGR1 RPLP0) were targeted.
Processed data to be submitted to appropriate variation archive.


title: Allorecognition, via TgrB1 and TgrC1, mediates the transition from unicellularity to multicellularity in the social amoebae Dictyostelium discoideum

first: Gad

last: Shaulsky

address: One Baylor Plaza

department: Molecular and Human Genetics

summary: The social amoeba Dictyostelium discoideum integrates into a multicellular organism when individual starving cells aggregate and form a mound. The cells then integrate into defined tissues and develop into a fruiting body that consists of a stalk and spores. Aggregation is initially orchestrated by waves of extracellular cyclic adenosine monophosphate (cAMP) and previous theory suggested that cAMP and other field-wide diffusible signals mediate tissue integration and terminal differentiation as well. Cooperation between cells depends on an allorecognition system comprised of the polymorphic adhesion proteins TgrB1 and TgrC1. Binding between compatible TgrB1 and TgrC1 variants ensures that non-matching cells segregate into distinct aggregates prior to terminal development. Here, we have embedded a small number of cells with incompatible allotypes within fields of developing cells with compatible allotypes. We found that compatibility of the allotype encoded by the tgrB1 and tgrC1 genes is required for tissue integration, as manifested in cell polarization, coordinated movement, and differentiation into prestalk and prespore cells. Our results show that the molecules that mediate allorecognition in D. discoideum also control the integration of individual cells into a unified developing organism and this acts as a gating step for multicellularity.

overall_design: Total 12 samples were used for this analysis. 3 developmental timepoints were analyzed with 2 biological replication. And same 3 developmental timepoint of references (5 RNA mix) with 2 biological replication.

first: Shigenori

last: Hirose

first: Balaji

last: Santhanam

first: Mariko

last: Katoh-Kurasawa

first: Adam

last: Kuspa


title: Evidence for two protein coding transcripts at the Igf2as locus

status: Public on Apr 12 2016

city: Zürich

first: Martin

middle: H

last: Braunschweig

address: Reckenholzstrasse 191

country: Switzerland

institute: Agroscope

summary: The insulin-like growth factor 2 antisense (Igf2as) gene is part of the Ins-Igf2-H19 imprinted gene cluster. The function of the paternally expressed Igf2as is still elusive.In our previous work, we showed that Igf2as transcripts were located in the cytoplasm of C2C12 mouse myoblast cells, associated with polysomes and polyadenylated suggesting that Igf2as is protein coding. In the present work, the protein coding capacity of Igf2as was investigated. We demonstrate for the first time the existence of a polypeptide translated from an Igf2as construct. Furthermore, an RNA-Seq analysis was performed using RNA prepared from skeletal muscles of newborn wild-type and ∆DMR1-U2 mice to further elucidate the function of Igf2as transcripts. We found no evidence for a regulatory role of Igf2as in the imprinted gene cluster. Interestingly, the RNA-Seq analysis indicated that Igf2as plays a role in the energy metabolism, the cell cycle, histone acetylation and muscle contraction pathways. Our Igf2as investigations further elucidated that there are two distinct Igf2as transcripts corresponding to two putative ORFs.

overall_design: Skeletal muscle tissue from four wild-type and four ∆DMR1-U2 female newborn mice were selected and mRNA expression compared in a RNA-Seq experiment.

first: Carolina

last: Duart-Garcia

first: Philippe

last: Plattet

first: Rémy

last: Bruggmann

first: Cedric

last: Simillion

first: Irene

last: Keller

first: Göran

last: Andersson


title: A global profiling of  gene expression in chilling stress in rice

city: Beijing

first: jingyu

last: zhang

address: Xiangshan Nanxincun 20 #

department: Plant Biology

institute: Institute of Botany, CAS

summary: RNA-Seq was performed to study the change of gene expression before and after chilling treatment  in rice. Different change patterns were identified. We have provided a complete view of  transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants.

overall_design: The mRNA profiles of 15-day-old rice seedlings with and without chilling treatment  (4 °C for 33 h)  were generated by deep sequencing using  Illumina Hiseq 2000 platform.

first: Jingyu

last: Zhang


title: Genome wide profiling of the RNAPII, γH2AX, H3K4Me1, H3K4M2 and H3K4Me3 in MLL2 F/F and FC/FC MEF cells

first: Theo

summary: We investigated the RNAPII and γH2AX occupancy genome wide by ChIP-Seq in MLL2 F/F and FC/FC80 MEF cells. We found that a week after MLL2 excision (FC/FC cells), a group of genes present higher levels of γH2AX and RNAPII near the TSS, as compared to the control (F/F cells).  H3K4Me1, H3K4M2 and H3K4Me3 levels near the TSS were also studied.

overall_design: There is a total of 52 samples. 3 independent replicates for each experiment were performed. H3, H2AX and IgG ChIPs were used for normalisation or as controls.The experiments were performed using immortalised mouse embryonic fibroblasts (MEF) in which both MLL2 alleles were targeted by the loxp system (F/F cells). Tamoxifen treatment of the F/F cells for 24 hours results in the excision of both MLL2 alleles (FC/FC cells).


title: CXXC finger protein 1 is critical for T cell intrathymic development through regulating H3K4 trimethylation [RNA-Seq]

first: Lai

last: Wei

address: 54 S. Xianlie Road

institute: Sun Yat-sen University

summary: T cell development in the thymus is largely controlled by an epigenetic program involving in both DNA methylation and histone modifications. Previous studies have identified Cxxc1 as a regulator of both cytosine methylation and histone 3 lysine 4 trimethylation (H3K4me3). However, it is unknown whether Cxxc1 plays a role in thymocyte development. Here we show that T cell development in the thymus is severely impaired in Cxxc1-deficient mice. Furthermore, we identify genome-wide Cxxc1 binding sites and H3K4me3 modification sites in wild-type and Cxxc1-deficient thymocytes. Our results demonstrate that Cxxc1 directly controls the expression of key genes important for thymocyte survival such as RORγt and for TCR signaling including Zap70 and CD8, through maintaining the appropriate H3K4me3 on their promoters. Importantly, we show that RORγt, a direct target of Cxxc1, can rescue the survival defects in Cxxc1-deficient thymocytes. Our data strongly support a critical role of Cxxc1 in thymocyte development.

overall_design: RNA-Seq analysis of WT and Cxxc1-deficient mice

first: Lie

last: Wang


title: Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing

city: Chicago

first: Guan-Zheng

last: Luo

address: 929 E 57th St

department: Chemistry

institute: UChicago

summary: To interrogate single-base resolution 6mA sites in the genome-wide, we develop DA-6mA-seq (DpnI-Assisted N6-methylAdenine sequencing), an optimized sequencing method taking advantage of restriction enzyme DpnI, which exclusively cleaves methylated adenine sites. We find DpnI also recognizes other sequence motifs besides the canonical GATC restriction sites, largely expanding the application range of this method. DA-6mA-seq requires less starting material and lower sequencing depth than previous methods, but achieves higher sensitivity, providing a good strategy to identify 6mA in large genome with a low abundance of 6mA. We rebuild the 6mA maps of Chlamydomonas by DA-6mA-seq and then apply this method to another two eukaryotic organisms, Plasmodium and Penicillium. Further analysis reveals most 6mA sites are symmetric at various sequence contexts, suggesting 6mA may function as a new heritable epigenetic mark in eukaryotes.

sample_organism:
Chlamydomonas reinhardtii
Penicillium chrysogenum
Plasmodium falciparum

overall_design: A new sequencing method is developed to detect 6mA in eukaryotes

first: Chuan

last: He


title: Identification of the long, edited dsRNAome of LPS-stimulated immune cells

first: Matthew

last: Blango

address: Adolf-Reichwein-Str. 23

institute: Leibniz Institute for Natural Product Research and Infection Biology


title: Innate-like functions of natural killer T cell subsets result from highly divergent gene programs [ChIP-seq]

city: La Jolla

first: Pandurangan

last: Vijayanand

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: Natural killer T (NKT) cells have immune stimulatory or inhibitory effects on the immune response that are context-dependent.  This may be attributed in part to the existence of functional NKT cell subsets; however, these functional subsets have only been characterized on the basis of differential expression of a few transcription factors and cell surface molecules.  Here we have analyzed purified populations of thymic NKT cell subsets at both the transcriptomic and epigenomic levels, and by single-cell RNA sequencing.  Our data indicate that despite their similar antigen specificity, the functional NKT cell subsets are highly divergent populations characterized by many gene expression and epigenetic differences.  Therefore the thymus imprints innate-like NKT cells with novel combinations of properties, including differences in proliferative capacity, homing, and effector functions that were not previously anticipated.

overall_design: Genome wide chromatin accessibility analysis using H3K27Ac ChIP-Seq  datasets in mouse Vα14 iNKT thymocyte subsets (NKT1, NKT2 and NKT17).  Samples were generated from three individual experiments using a pool  of thymocytes prepared from five five-week old C57BL/6J females. NKT  cells subtypes were isolated from thymuses and directly sorted by flow cytometry and fix adequately for chromatin immunoprecipitation  downstream experiments.

first: Isaac

last: Engel

first: Grégory

last: Seumois

first: Lukas

last: Chavez

first: Ashu

last: Chawla

first: Brandie

last: White

first: Dennis

last: Mock

first: Mitchell

last: Kronenberg


title: Age-dependent pancreatic gene regulation reveals mechanisms governing human β-cell function

first: Seung

last: Kim


title: Age-dependent gene expression changes in human islets

summary:
We report the transcriptomic profiling of islet cell subtypes obtained from young and old human donors.
We report the transcriptomic profiling of Endo-ßH1C cells expressing SIX3, SIX2 or GFP.

overall_design:
Profiling FACS-purified human pancreatic islet cells by RNA-Seq.
We analyzed the gene expression changes in Endo-ßH1C cells expressing SIX3, SIX2 or GFP using RNA-Seq.

first: H

last: Arda

first: Jennifer

last: Tsai


title: A Novel Role of Polycomb in Positive Transcription Regulation by Modulating H4K20me1

first: Gang

state: Shanghai

address: 320 Yue Yang Road

institute: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Polycomb group (PcG) proteins were originally shown to play central roles in maintaining heritable gene suppression during the normal development of higher eukaryotes. However, recent studies in Drosophila and mammals imply a potential positive role of PcG proteins in gene transcription with unknown mechanism. Here, for the first time we report Pc-mediated, E(z)/H3K27me3-dependent positive transcription regulation of Ci and Sens, two key transcription factors involved in body plan during normal development. Further mechanistic studies showed that Pc regulates Sens expression by regulating H4K20me1 at Sens locus. More importantly, this mechanism applies to other genes involved in the developmental process. In summary, we report a novel and general transcription regulation mechanism, that is, Pc-mediated, E(z)/H3K27me3-dependent positive transcription regulation by modulating H4K20me1 during development.

overall_design: H4K20me1 ChIP-seq dataset was generated in wide type Drosophila third instar larvae wing discs. RNA-seq datasets were generated for wide type, Polycomb RNAi samples.

first: Xiangdong

last: Lv

first: Zhijun

last: Han

first: Hao

last: Chen

first: Xiaofeng

last: Yang

first: Zhao

last: Zhang

first: Bo

first: Yuanxin

last: Xia

first: Yi

last: Lu

first: Chenyu

last: Pan

first: Lin

last: Fu

first: Hui

first: Feifei

last: Mao

first: Min

last: Wu

first: Zhaocai

last: Zhou

first: Dangsheng

last: Li

first: Lei

first: Hai

last: Jiang

first: Yun

last: Zhao


title: The dynamic regulatory genome of Capsaspora owczarzaki and the origin of animal multicellularity

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

institute: Centre for Genomic Regulation

summary: We carried out multiple functional genomic assays in Capsaspora owczarzaki, the unicellular relative of animals with the largest known gene repertoire for transcriptional regulation. We show that changing chromatin states, differential lincRNA expression and dynamic cis-regulatory sites are associated with life cycle transitions in Capsaspora.

overall_design: ChIP-seq of four different histone modifications and ATAC-seq; both in 3 different temporal cell types.

first: Iñaki

last: Ruiz-Trillo


title: Single-muscle-cell transcriptome profiling along the planarian anteroposterior axis

city: Cambridge

first: Peter

last: Reddien

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: How positional information instructs adult tissue maintenance is poorly understood. Planarians undergo whole-body regeneration and tissue turnover, providing a model for adult positional information studies. Genes encoding secreted and transmembrane components of multiple developmental pathways are predominantly expressed in planarian muscle cells. Several of these genes regulate regional identity, consistent with muscle harboring positional information. Here, single-cell RNA-sequencing of 115 muscle cells from distinct anterior-posterior regions identified 44 regionally expressed genes, including multiple Wnt and ndk/FGF receptor-like (ndl/FGFRL) genes. Two distinct FGFRL-Wnt circuits, involving juxtaposed anterior FGFRL and posterior Wnt expression domains, controlled planarian head and trunk patterning. ndl-3 and wntP-2 inhibition expanded the trunk, forming ectopic mouths and secondary pharynges, which independently extended and ingested food. fz5/8-4 inhibition, like that of ndk and wntA, caused posterior brain expansion and ectopic eye formation. Our results suggest that FGFRL-Wnt circuits operate within a body-wide coordinate system to control adult axial positioning.

overall_design:
Single-cell RNA-seq on cells isolated from 10 distinct anteroposterior (AP) regions and expressed muscle markers was used to identify muscle regionally expressed genes (mRGs).
Non-dividing single cells from 10 consecutive regions along the AP axis were isolated by fluorescence activated cell sorting (FACS), and the resulting single-cell cDNA libraries were screened by qRT-PCR for expression of planarian muscle markers troponin or collagen before sequencing. Principal component analysis (PCA) on the 177 single cells sequenced that expressed >1000 unique transcripts (>2 read count) was performed using highly variable transcripts. Two significant principal components that separated cells by expression of muscle markers (PC1<0) and expression of neoblast markers (PC2<0) were identified. PCA and troponin expression confirmed the identity of 115 muscle cells, and these 115 cells were used in all subsequent analyses.
Single-cell differential expression (SCDE, (Kharchenko et al. 2014)) analyses of three different anterior-versus-posterior region comparisons (anterior(regions 1, 2, 3; n=23 cells) versus posterior (regions 8, 9, 10; n=38 cells); head (region 1; 11 cells) versus post-pharyngeal (regions 7, 8, 9; n=35 cells); pre-pharyngeal (regions 2, 3, 4; n=22 cells) versus tail (region 10; n=12 cells)) identified transcripts of 99 genes as differentially expressed at p<0.005 (|Z| > 2.58). Whole mount in situ hybridization to visualize gene expression patterns verified 44 genes as regionally expressed (mRGs) (35/44 with p<0.005 in any of anterior-versus-posterior SCDE analyses).

first: M

last: Scimone

first: Lauren

last: Cote

first: Travis

last: Rogers


title: Study of Topoisomerase I in human

city: Bethesda

first: Damian

last: Wojtowicz

address: 8600 Rockville Pike; Rm 8N811N

institute: NCBI/NLM/NIH

summary: We report a mechanism through which the transcription machinery directly controls topoisomerase 1 (TOP1) activity to adjust DNA topology throughout the transcription cycle. By comparing TOP1 occupancy using ChIP-Seq, versus TOP1 activity using TOP1-Seq, a method reported here to map catalytically engaged TOP1, TOP1 bound at promoters was discovered to become fully active only after pause-release. This transition coupled the phosphorylation of the carboxyl-terminal-domain (CTD) of RNA polymerase II (RNAPII) with stimulation of TOP1 above its basal rate, enhancing its processivity. TOP1 stimulation is strongly dependent on the kinase activity of BRD4, a protein that phosphorylates Ser2-CTD and regulates RNAPII pause-release. Thus the coordinated action of BRD4 and TOP1 overcame the torsional stress opposing transcription as RNAPII commenced elongation, but preserved negative supercoiling that assists promoter melting at start sites. This nexus between transcription and DNA topology promises to elicit new strategies to intercept pathological gene expression.

overall_design: Examination of RNAPII and BRD4 by ChIP-Seq, Topoisimerase I by ChIP-Seq and Top1-Seq, and transcriptome expression by RNA-Seq in human colon cancer cells HCT116 (wt, wt+CPT, wt+JQ1, kiTop, kiTop1+JQ1, and siTop1).

first: Laura

last: Baranello

first: Fedor

last: Kouzine

first: Kairong

last: Cui

first: Ka

middle: Y

last: Chan-Salis

first: Ballachanda

last: Devaiah

first: Dinah

last: Singer

first: Yves

last: Pommier

first: B

last: Pugh

first: Teresa

last: Przytycka

first: Brian

last: Lewis

first: Keji

first: David

last: Levens


title: Dysregulation of miRNA-9 in a subset of schizophrenia patient-derived neural progenitor cells

status: Public on Apr 11 2016

city: New York

first: Kristen

last: Brennand

address: 1425 Madison Ave, 9-20B

institute: Icahn School of Medicine at Mount Sinai


title: DNA methylation landscape of fat deposit and fatty acid composition variation in obese and lean pigs

city: Chengdu

first: Linyuan

last: Shen

state: Sichuan

address: 211# Huiming Road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: Obese and lean type pig breeds show obvious differences in fat deposit and fatty acid composition. However, the underlying diversities in DNA methylation that related to the phenotypic differentiation have not been clarified. Here, we employed Landrace pigs (a leaner, Western breed) and Rongchang pigs (a fatty, Chinese breed) as models to survey genome-wide DNA methylation in the backfat adipose using a methylated DNA immunoprecopitation sequencing approch.We sequenced 6 methylated DNA immunoprecipitation (MeDIP) libraries, generated 38.27 gigabases (Gb) of methylated DNA immunoprecitation sequencing (MeDIP-seq) data from the six samples, representing about 15 times the size of the pig genome. About 88.89% of all reads could be aligned on the pig reference genome (Sus scrofa 10.2) using the SOAP2 software, and about 76.68% of reads had a unique genomic location. There was 483 different methylated regions (DMRs) located in genes promoter region, which are mainly involved in the processes of “olfactory and sensory activity” and “lipid metabolism”. This study provides a solid basis for exploring the epigenetic mechanisms of fat deposit and fatty acid composition, have benefit to promoting human health diet and improving pork quality and production efficiency.

overall_design: The aim of our study is to identify different methylated genes that are linked to the phynotypic of fat deposit and fatty acid composition variation in obese and lean pigs

first: Shunhua

last: Zhang

first: Yudong

last: Xia

first: Xuewei

last: Li

first: Guoqing

last: Tang

first: Yanzhi

last: Jiang

first: Mingzhou

first: Li

last: Zhu


title: Genetic identification of an adipocyte expressed anti-diabetic target in mice selected for resistance to diet-induced obesity

city: Bar Harbor

first: Steven

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Discovery of genetic mechanisms of resistance to obesity and diabetes may illuminate new therapeutic strategies to tackle this escalating global health burden. We used the polygenic Lean mouse model, selected for low adiposity over 60 generations, to identify thiosulfate sulfur transferase (Tst, rhodanese) as a candidate obesity-resistance gene with selectively increased adipocyte expression. Adipose Tst expression correlated with indices of metabolic health across diverse mouse strains. Transgenic overexpression of Tst in adipocytes protected mice from diet-induced obesity and insulin-resistant diabetes. Tst gene deficiency markedly exacerbated diabetes whereas pharmacological TST activation ameliorated diabetes in mice in vivo. TST selectively augmented mitochondrial function combined with degradation of reactive oxygen species and sulfide. In humans, adipose TST mRNA correlated positively with adipose insulin sensitivity and negatively with fat mass. Genetic identification of Tst as a beneficial regulator of adipocyte mitochondrial function may have therapeutic significance for type 2 diabetes.

overall_design: Illumina 100bp paired-end RNA-seq was profiled from subcutaneous inguinal fat from 24 female 26-week old mice from four inbred strains (C57BL/6J, NZO/HiLtJ, CAST/EiJ, WSB/EiJ) raised on standard chow or high fat diet (3 biological replicates per strain*diet group).

first: Nicholas

last: Morton

first: Jasmina

last: Beltram

first: Roderick

last: Carter

first: Zoi

last: Michailidou

first: Gregor

last: Gorjanc

first: Clare

last: McFadden

first: Martin

last: Barrios-Llerena

first: Sergio

last: Rodiguez-Cuenca

first: Matthew

last: Gibbins

first: Rhona

last: Aird

first: Jose

last: Moreno-Navarrete

first: Karen

last: Svenson

first: Annalisa

last: Gastaldo

first: Lynne

last: Ramage

first: Gregorio

last: Naredo

first: Maximilian

last: Zeyda

first: Zhao

middle: V

last: Wang

first: Alexander

last: Howie

first: Aila

last: Saari

first: Petra

last: Sipila

first: Thomas

last: Stulnig

first: Vilmundur

last: Gudnasson

first: Christopher

last: Kenyon

first: Jonathan

last: Seckl

last: Walker

first: Scott

middle: P

last: Webster

first: Donald

last: Dunbar

first: Gary

middle: A

last: Churchill

first: Antonio

last: Vidal-Puig

last: Fernandez-Real

first: Valur

last: Emilsson

first: Simon

last: Horvat


title: Dclk1+ mouse pancreatic progenitor cells

first: Timothy

middle: Cragin

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

summary: Dclk1 (Doublecortin like kinase-1) labels a rare population of long-lived and largely quiescent cells in the adult mouse pancreas. The expression of Dclk1+ vs Dclk1- pancreatic cells (mostly acinar) is observed.

overall_design: Dclk1+ vs Dclk1-

first: C

middle: B

last: Westphalen

first: Yoshihiro

last: Takemoto

first: Takayuki

last: Tanaka

first: Marina

last: Macchini

first: Zhengyu

last: Jiang

first: Bernhard

middle: W

last: Renz

first: Xiowei

last: Chen

first: Steffen

last: Ormanns

first: Karan

last: Nagar

first: Yagnesh

last: Tailor

first: Randal

last: May

first: Youngjin

last: Cho

first: Samuel

last: Asfaha

first: Daniel

last: Worthley

first: Yoku

last: Hayakawa

first: Alexandra

last: Urbanska

first: Michael

last: Quante

first: David

last: Wah

first: Joshua

last: Broyde

first: Federico

last: Giorgi

last: Lachmann

first: Prem

middle: S

last: Subramaniam

first: Helen

last: Remotti

first: Gloria

last: Su

first: Richard

last: Friedman

first: Andrea

last: Califano

first: Courtney

last: Houchen

first: Kenneth

last: Olive


title: 82-kDa ChAT and SATB1 ChIP-seq after vehicle or amyloid-beta exposure

city: London

first: Sandeep

last: Gill

state: Ontario

address: 100 Perth Drive

department: Molecular Medicine

institute: Robarts Research Institute

summary: Using chromatin immunoprecipitation and next-generation sequencing (ChIP-seq), we assessed the effects of acute exposure to oligomeric amyloid-beta on 82-kDa ChAT and SATB1 genome association in human SH-SY5Y neural cells, finding that Aβ-exposure increased 82-kDa ChAT and SATB1 association with gene promoters, introns and matrix attachment regions. We found that both SATB1 and 82-kDa ChAT associate with synapse and cell stress related genes after amyloid-beta exposure.

overall_design: Examination of effects of amyloid-beta exposure on 82-kDa ChAT and SATB1 in human SH-SY5Y neural cells

first: R

middle: J

last: Rylett

first: Warren

last: Winick-Ng


title: Rebalancing gene haploinsufficiency in vivo by targeting chromatin

city: Naples

first: Antonio

last: Baldini

address: Via Pietro Castellino 111

institute: CNR Institute of Genetics and Biophysics Adriano Buzzati Traverso

summary: Here we show that the T-box transcription factor encoded by Tbx1 positively regulates monomethylation of histone 3 lysine 4 (H3K4me1) at a significant number of regions that it occupies throughout the genome, often located at the 3' end of target genes. Treatment of cells with Tranylcypromine (TCP), an inhibitor of histone demethylases, rescues the expression of approx. one third of the genes dysregulated by Tbx1 suppression and it rebalances H3K4me1 levels at many Tbx1 occupied sites. In addition, TCP treatment of mouse models of the 22q11.2DS ameliorates substantially the cardiovascular phenotype.

overall_design: Examination of Tbx1 binding profile, H3K4 monomethylation, H3K27 acetylation and transcription profile in P19Cl6 cells during cariomyocytes differentiation and in mouse embyos.

first: Filomena

last: Fulcoli

first: Monica

last: Franzese

first: Xiangyang

last: Liu

first: Zhen

last: Zhang

first: Claudia

last: Angelini


title: Next Generation Sequencing Analysis of Wild Type and SRSF2-/- D11 mice liver Transcriptomes

city: Shanghai

first: Ning

last: Wei

address: 320 Yueyang RD.

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

summary: We generated the liver specific SRSF2 -/- mice, and collected their liver at 11 day after birth and controls. Then, we extracted RNAs and performed next generation sequencing. By comparing sequencing data from WT and SRSF2 -/- samples, we profiled the alternative splicing events and gene expression regulated by SRSF2 during mouse liver development process.

overall_design: D11 liver mRNA profiles of wild type (WT) and  liver specific SRSF2-/- mice were generated by deep sequencing, using Illumina HiSeq2000.

first: Yuanming

last: Cheng


title: RNA-Seq Analysis of VRF1-dependent Genes in the appressoria of Magnaporthe oryzae 70-15

city: Hangzhou

first: Jianping

last: Lu

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

institute: Zhejiang University

summary:
Purpose: The goals of this study are to find out the genes regulated directly or indirectly by C2H2 transcription factors Vrf1 by RNA-seq in the rice blast fungus Magnaporthe oryzae
Methods: Appressorial mRNAs of the wild type strain 70-15 and Δvrf1 conidia incubated in H2O on plastic membranes at 28˚C for 5 h, in triplicate independently for each strain, were extracted and isolated by RNeasy Plant mini kit (QIAGEN) and AMPure XP beads (Beckman). RNA-sequencing libraries were constructed using NEBNext RNA sample preparation kit (NEB). Samples were sequenced on Illimina Nextseq500 SE75 (1*75).The M. oryzae genome database (Version 7) (www.broadinstitute.org) was used as a reference gene database. Genome-wide transcript levels of genes were quantified in fragments per kilobase of exon model per million mapped reads (FPKM) (Trapnell 2010). Gene Ontology (GO) enrichment analyses for differentially expressed genes were performed using hypergeometric test with topGO, and p-values were adjusted with Bonferroni for multiple testing (Alexa 2006). And we selected FDR < 0.05 as enrichment terms.
Results and Conclusions: We identified 2709 genes regulated by VRF1 through RNA-Seq, with 1739 genes down-regulated and 970 genes up-regulated in Δvrf1. Interestingly, a lots of appressorium-specific genes were down-regulated in Δvrf1, suggesting that Vrf1 is a specific transcription factor which regultes the expression of genes in appressorium formation.

overall_design: Appressorial mRNA profiles of the wild type strain 70-15 (WT) and Δvrf1 conidia incubated in H2O on plastic membranes for 5 h were generated, in biologic triplicate.

first: Jian

first: Hui

last: Cao

first: Peng

last: Huang

first: Fu

middle: C

last: Lin


title: The transcriptional repressor Gfi1 inhibits the induction of Th1 program in activated CD4 T cells [ChIP-seq]

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

summary: The transcriptional repressor Gfi1 promotes Th2 cell development and inhibits Th17 and inducible regulatory T cell differentiation.  However, the contribution of Gfi1 to Th1 cell differentiation and Th1-type immune responses has not been clarified yet.  We herein demonstrate that Gfi1 inhibits the activation of Th1 program in CD4 T cells.  The activated Gfi1-deficient naïve CD4 T cells spontaneously develop into Th1 cells in an IL-12- and IFN-g-independent manner.  The increased in vivo Th1-type immune response in Gfi1-deficient mice is confirmed using murine model of nickel allergy and delayed-type hypersensitivity.  The expressions of Th1-related transcription factors including Tbx21, Eomes, Atf3, Runx1, Runx2 and Runx3 are increased in Gfi1-deficient activated CD4 T cells.  Tbx21, Eomes and Runx2 are identified as candidates for direct target of Gfi1.  Gfi1 binds to the Tbx21, Eomes and Runx2 gene loci and represses histone H3K4 methylation levels.  Together, these findings establish a novel role of Gfi1 in inhibiting Th1 cell differentiation and Th1-type immune response.

overall_design: Examination of Gfi1 binding in WT and Gfi1-dficient CD4 T cells

first: Masakatsu

last: Yamashita


title: Simultaneous profiling of transcriptome and DNA methylome from a single cell

city: los angeles

first: Qin

last: An

state: CALIFORNIA

address: Room 6554 Gonda Building, UCLA

department: Department of Human Genetics

institute: ucla

summary: We developed a new single cell sequencing method to simultaneously sequence methylome and transcriptome for mouse DRG neurons

overall_design: Integrative analysis of transcription and methylation at single cell level

first: Youjin

last: Hu

first: Kevin

last: huang

first: Guoping

last: Fan


title: EGFRvIII/STAT3 targets in glioblastoma pathogenesis

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: Next generation sequencing platforms were used to identify STAT3 targets in the background of EGFRvIII expresssion

overall_design: mRNA of 3 EGFRvIII positive brain tumor stem cell lines (BTSC #68, 73, and 90) were compared to an EGFRvIII negative line (#41) to identify EGFRvIII-regulated targets in human BTSC. EGFRvIII-dependent targets in mouse astrocytes were identified by mRNA-seq analyses of EGFRvIII- or MSCV-expressing astrocytes. STAT3-differentially regulated genes in EGFRvIII expressing mouse astrocytes were obtained by subjecting  EGFRvIII,STAT3f/f and EGFRvIII, STAT3-/- astrocytes to mRNA-Seq analyses. Sites of STAT3 occupancy in EGFRvIII expressing astrocytes were identified by ChIP-Seq using a STAT3 antibody or IgG control. We identified OSMR as a direct target of STAT3 in both EGFRvIII-expressing human BTSC and mouse astrocytes. Therefore to identify OSMR-regulated genes, we used a lentiviral mediated RNAi system to knockdown OSMR in EGFRvIII-expressing astrocytes. OSMR-dependent differentially expressed genes were obtained by comparison of OSMR knockdown (KD1 and KD2) astrocytes to control  groups (ShRNA control and Vector control)

first: Arezu

last: Jahani-Asl

first: Michael

last: Rudnicki

first: Azad

last: Bonni