title: ERK5 kinase activity is dispensable for cellular immune response and proliferation

city: La Jolla

first: Helge

last: Weissig

state: CA

address: 11025 N. Torrey Pines Rd.

department: Bioinformatics

institute: ActivX Biosciences, Inc.

summary: Unlike other members of the MAPK family, ERK5 contains a large C-terminal domain with transcriptional activation capability in addition to an N-terminal canonical kinase domain.  Genetic deletion of ERK5 is embryonic lethal and tissue-restricted deletions have profound effects on erythroid development, cardiac function and neurogenesis.  In addition, depletion of ERK5 is anti-inflammatory and anti-tumorigenic.  Small molecule inhibition of ERK5 has been shown to have promising activity in cell and animal models of inflammation and oncology.  Here we report the synthesis and biological characterization of potent, selective ERK5 inhibitors.  In contrast to both genetic depletion/deletion of ERK5 and inhibition with previously reported compounds, inhibition of the kinase with the most selective of the new inhibitors had no anti-inflammatory or anti-proliferative activity.  The source of efficacy in previously reported ERK5 inhibitors is shown to be off-target activity on bromodomains (BRDs), conserved protein modules involved in recognition of acetyl-lysine residues during transcriptional processes.  It is likely that phenotypes reported from genetic deletion or depletion of ERK5 arise from removal of a non-catalytic function of ERK5.  The newly reported inhibitors should be useful in determining which of the many reported phenotypes are due to kinase activity, and delineate which can be pharmacologically targeted.

overall_design: Two cellular models with reported ERK5-regulated signaling were used: Pam3CSK4-stimulated HUVECs as a model of inflammation, and EGF-stimulated HeLa cells as an established cell model of ERK5 regulation.  Cells were pre-incubated with DMSO vehicle, AX15836 (ERK5 inhibitor), AX15839 (dual ERK5/BRD inhibitor), or I-BET762 (BRD inhibitor), then stimulated with agonist.  Cellular responses were verified by immunoassays and western blots using replicate wells in the same experiment.

first: Emme

last: Lin

first: Christopher

last: Amantea

first: Tyzoon

middle: K

last: Nomanbhoy

first: Junichi

last: Ishiyama

first: Yi

first: Shyama

last: Sidique

first: Bei

last: Li

first: John

last: Kozarich

first: Jonathan

last: Rosenblum


title: Strand-oriented RNAseq of LNCaP prostate cancer cells in culture for 48 h in the absence of androgen

status: Public on Sep 08 2016

city: São Paulo

first: Sergio

last: Verjovski-Almeida

state: São Paulo

address: Av. Vital Brasil 1500

country: Brazil

institute: Instituto Butantan

type: Expression profiling by high throughput sequencing

summary: The goal of this study was to use NGS RNAseq deep-sequencing in order to characterize the complement of polyadenylated mRNAs and lncRNAs expressed in LNCaP, a prostate cancer cell line. RNA-seq data were processed as aggregates of the two biological replicates to increase resulting transcriptome coverage. Trimmed reads were mapped with TopHat v.2.0.12 and Bowtie v.2.2.3, and a custom GTF file to guide transcriptome assembly. This custom GTF file was built by using the human transcriptome annotation GTF file downloaded from Ensembl Project web-site (http://www.ensembl.org/) and modified to include all lncRNAs reported in Cabili et al, Genes & Development 2011.

overall_design: polyA+ RNA profiles of LNCaP prostate cancer cell line grown in culture for 48 h in the absence of androgen were generated by paired-end deep sequencing, in duplicate, using Illumina HiSeq2000.

first: Felipe

last: Beckedorff

first: Murilo

middle: S

last: Amaral

first: Lucas

middle: F

last: Silva


title: Unique Broad Histone Lysine 4 Methylation Domains in Mouse Oocytes and Dynamic Regulation during Maternal to Zygotic Transition

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: The maternal to zygotic transition (MZT) involves the transfer of genome regulation from the oocyte to the embryo and is essential for the formation of totipotent embryos. However, regulatory mechanisms are still poorly understood despite recent progress in mapping the dynamics in RNA transcripts and DNA methylation1-9. Previous studies suggest that dynamic histone modifications may play important roles in MZT10-12, however direct measurements of chromatin states has been hindered by technical difficulties in profiling histone modifications from small quantities of cells. We have developed a micro-scale chromatin immunoprecipitation and sequencing (μChIP-seq) method and used it to profile histone H3 lysine methylation (H3K4me3) and acetylation (H3K27ac) genome-wide in the mouse oocyte, 2- cell and 8-cell stage embryo. Strikingly, we show that ~22% of the oocyte genome is associated with broad H3K4me3 domains that are anti-correlated with DNA methylation. Most H3K4me3 signal is rapidly lost and constricted to TSS regions in 2-cell embryos, concomitant with the onset of major zygotic genome activation (ZGA). We provide evidence that these broad H3K4me3 domains are established by Mll2 and actively removed by Kdm5a and Kdm5b, and likely play instrumental roles in MZT by defining regions of DNA demethylation in oocytes and the 2-cell embryo. Furthermore, broad H3K4me3 domains specify H3K27ac patterns in the early embryo and ZGA genes are generally related to broad H3K4me3 domains, suggesting a fundamental role in MZT. Our results provide insights into how the developmental program can be set up in the oocyte and transferred to the zygotic genome.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Examination of two different histone modifications in mouse oocytes, 2-cell and 8-cell stage embryos. Two biological replicates were performed for each cell type and histone modificaitons.
Examination of H3K4me3 histone modification by ChIP-seq, and DNA methylation by WGBS in mouse P12 and P15 immature oocytes. Two biological replicates were performed for each cell type and histone modificaitons. Four and six biological replicates were performed for each of WGBS for P12 and P15, respecively. Furthermore, RNA-seq was carried out to assess RNA expression in 2-cell embryos that were depleted in KDM5A and KDM5B, also various control and untreated 2-cell embryos were assessed.

middle: A

last: Dahl

first: Bing

last: Ren

first: Arne

last: Klungland


title: Gene expression analysis of human adenomas.

city: Houston

first: Jian

last: Chen

state: TX

address: 1515 Holcombe Boulevard - Unit 1466

country: USA

institute: The University of Texas M. D. Anderson Cancer Center

summary: Gene expression profiling was carried out in 7 matched colon adenoma samples and normal mucosa to characterize the molecular mechanisms relevant to the etiology ofadenoma and human colorectal carcinoma development.

overall_design: Whole-transcriptome RNA sequencing of the 7 matched colon adenoma samples and normal mucosas.

first: Lopa

last: Mishra


title: Chromatin maps of human ASXL1, FOXK1 and O-GlcNAc

city: Basel

first: Christian

last: Beisel

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

summary: Polycomb group (PcG) proteins are major determinants of gene silencing and epigenetic memory in higher eukaryotes. Acting in multimeric protein complexes, these factors control structure and function of chromatin. We used a robust affinity purification mass spectrometry (AP-MS) approach to systematically map the PcG protein interactome in a single human cell line. Importantly, we uncovered the topology map of the human PR-DUB de-ubiquitination complexes, which comprise the O-linked N-acetylglucosamine transferase OGT1 and a number of transcription factors.  Here we provide genome-wide chromatin maps of identified PR-DUB1 subunits ASXL1, FOXK1 and the OGT1 catalyzed modification O-GlcNAc based on ChIP-seq.

overall_design: Our data set comprises 3 ChIP-seq samples plus 2 input control samples using chromatin from Flp-In HEK293 T-REx cells  cells which was immunoprecipitated using antibodies against ASXL1, FOXK1 and O-GlcNAc.

first: Federico

last: Comoglio


title: Vitamin D Promotes Protein Homeostasis and Longevity via the Stress Response Pathway Genes SKN-1, IRE-1, and XBP-1

status: Public on Sep 07 2016

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: Vitamin D is a secosteroid that has multiple regulatory roles including the regulation of bone and calcium homeostasis. Deficiency of 25-hydroxyvitamin D, the major circulating form of vitamin D, is associated with an increased risk of age-related chronic diseases including Alzheimer’s disease, Parkinson’s disease, cognitive impairment, and cancer. In this study, we utilized Caenorhabditis elegans to examine the mechanism by which vitamin D influences aging. We found that Vitamin D3-induced lifespan extension requires the stress response pathway genes SKN-1, IRE-1, and XBP-1. Vitamin D3 induced expression of SKN-1 target genes, but not canonical targets of IRE-1/XBP-1. Vitamin D3 suppressed an important molecular pathology of aging, that of widespread protein insolubility, and prevented the toxicity caused by human β-amyloid. Our observation that vitamin D3 improves protein homeostasis and slows aging highlights the importance of maintaining appropriate vitamin D serum levels, and may explain why such a wide variety of human age-related diseases are associated with a vitamin D deficiency.

overall_design: The experimental design consisted of contrasting gene expression data derived from RNA extracted from pools of synchronized aged worms. L4 worms were placed on either vehicle (DMSO) or Vitamin D (100uM) for 44 hours prior to extraction. A pool of 50 worms was considered a single biological replicate. For the Vitamin D treated group, there were 6 independent biological replicates, and were compared with a group of untreated (vehicle) wild-type N2 animals, also using 6 biological replicates.

first: Karla

last: Mark

first: Mark

last: Lucanic

first: Gordon

middle: J

last: Lithgow


title: ChIP-Seq of Histone Deacetylases and Cell Cycle-Regulators in Multiple Myeloma cells

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Transcription of oncogenes is regulated by histone deacetylases and cyclins.  Some of these proteins are targetable with small molecules.  This series contains ChIP-Seq targeting transcriptional regulators from a cell line model of multiple myeloma.

first: Lars

last: Anders


title: Tbr2 and Neurog2 transcription factor binding sites in E14.5 WT cerebral cortices

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: To date, speculations on the molecular roles of Tbr2 transcription factor during specification, maintenance and differentiation of cortical specific Intermediate Neural Progenitors are coming from the analysis of loss- and gain-of-function experiments. However since its capacity to bind the DNA to extert its function we did Chromatin Immuno-Precipitation followed by deep sequencing to profile its target on the genome. We performed this approach directly in vivo to respect the physiological and peculiar enviroment of its action during cortical development. Moreover we did the same approach for Neurogenin 2 proneural gene. Interestingly the vast majority of the Neurog2 peaks are in common with Tbr2 dataset suggesting a co-operation between the two factors confirmed by biochemical and functional assays. Finally we compared Tbr2 dataset with the DNA regions bound by the H3K27me3 histone demethylase Jmjd3 (NCBI:Kdm6b) obtained by others. Interestingly we were able to find regions in common linked to important genes for neuronal differentiation.

overall_design: 3 samples, one input chromatin, one ChIP for Tbr2 and one ChIP for Neurog2

first: Alessandro

last: Sessa

first: Daniela

last: Drechsel

first: Francois

last: Guillemot

first: Vania

last: Broccoli


title: Comparison of immune cells between mice strains

status: Public on Sep 09 2016

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

summary: A number of macrophage and macrophage-like cells are responsible for immune response to challenges. Despite their shared role, these immune cells differ in the inflammatory response and impact on physiology and behavior.  The purpose of this study was to  profile mRNA levels (transcriptome) to better understand differences between immune cells under homeostasis using two mouse strains.

overall_design: total RNA samples were obtained from 12 mice per strain and immune cell type and were subjected to paired-end RNA sequencing


title: Proteomic and genomic characterization of a yeast model for Ogden syndrome [RNA-seq and Ribo-seq]

city: Woodbury

first: Gholson

last: Lyon

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Laboratory

summary: Naa10 is a Nα-terminal acetyltransferase that, in a complex with its auxiliary subunit Naa15, co-translationally acetylates the α-amino group of newly synthetized proteins as they emerge from the ribosome. Roughly 40-50% of the human proteome is acetylated by Naa10, rendering this an enzyme with one of the most broad substrate ranges known. Recently, we reported an X-linked disorder of infancy, Ogden syndrome, in two families harboring a c.109T>C (p.Ser37Pro) variant in NAA10. In the present study we performed in-depth characterization of a yeast model of Ogden syndrome. Stress tests and proteomic analyses suggest that the S37P mutation disrupts Naa10 function and reduces cellular fitness during heat shock, possibly due to dysregulation of chaperone expression and accumulation. Microarray and RNA-seq revealed a pseudo-diploid gene expression profile in ΔNaa10 cells, likely responsible for a mating defect. In conclusion, the data presented here further support the disruptive nature of the S37P/Ogden mutation and identify affected cellular processes potentially contributing to the severe phenotype seen in Ogden syndrome.

overall_design: RNA-seq, microarray

first: Max

last: Dörfel


title: A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells (batch 4)

city: CAMBRIDGE

first: Meromit

last: Singer

state: MASSACHUSETTS

address: 415 main st, ROOM 6031

institute: Broad Institute of MIT and Harvard

summary: Reversing the dysfunctional T cell state that arises in cancer and chronic viral infections is the focus of therapeutic interventions; however, current therapies are effective in only some patients and some tumor types. To gain a deeper molecular understanding of the dysfunctional T cell state, we analyzed population and single-cell RNA profiles of CD8+ tumor-infiltrating lymphocytes (TILs) and used genetic perturbations to identify a distinct gene module for T cell dysfunction that can be uncoupled from T cell activation. This distinct dysfunction module is downstream of intracellular metallothioneins that regulate zinc metabolism and can be identified at single-cell resolution. We further identify Gata-3, a zinc-finger transcription factor in the dysfunctional module, as a regulator of dysfunction, and use CRISPR/Cas9 genome editing to show that it drives a dysfunctional phenotype in CD8+ TILs. Our results open novel avenues for targeting dysfunctional T cell states, while leaving activation programs intact.

overall_design: CD8 TILs from WT and MTKO mice were sequenced at single-cell resolution


title: RNA-seq of human HeLa cell

city: beijing

first: sj

middle: sj

last: Y

state: beijing

address: xueqing road

department: bioinfo

country: China

institute: jianghai

summary: To study the effects of overexpression CD38 in Hela cell

overall_design: 2 simples

first: Jie

last: Shen


title: A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells (batch 1)


title: Using AmpliSeq we have performed quantitative analysis of 20,803 genes in Negative control precursor-miR (NC-Pre-miR) and pre-miR-17 transfected Rheumatoid arthritis Synovial Fibroblasts (RASFs)

city: Spokane

first: Salahuddin

last: Ahmed

state: WA

address: 412 E Spokane Falls Blvd, PBS411

department: Pharmaceutical Sciences

institute: Washington State University

summary:
Purpose: The goals of this study are to determine the effect of microRNA-17 overexpression on 20,803 human genes in RASFs using Ion ProtonTM System platform. Human RASFs from two RA patients were transfected with pre-miR-17 or NC-pre-miR for 48 h and total RNA was prepared using miRNeasy kit (Qiagen). Total RNA integrity was checked using an Agilent Technologies 2100 Bio analyzer (Santa Clara, CA). 10 ng of high quality RNA was used to make cDNA for amplification with the Ion AmpliSeq Transcriptome Human Gene Expression kit (ThermoFisher Scientific).  The cDNA was subjected to 12 cycles of amplification with panel primers and barcoded with adapters as recommended.  Resulting sequencing libraries were quantified by qPCR using SYBR FAST master mix from KapaBiosystems (Wilmington, MA).  Sets of eight libraries were balanced, pooled and sequencing beads produced on an Ion Chef.  Sequencing was performed on an Ion P1 semi-conductor sequencing chip using an Ion Proton™ System (ThermoFisher Scientific, Grand Island, NY). Data was collected and primary analysis performed using Torrent Suite software version 5.0.3. Reads were mapped to the panel and expression values determined. R Software version R-3.2.3 was used to generate heatmap.
Among the panel of 20,803 genes, the expression of 15,067 genes as shown in the representative heat map was observed in pre-miR-17 and NC-pre-miR transfected RASFs. A total of 664 significantly modulated genes (301 upregulated and 363 downregulated) using Student ‘t’ test were further utilized for the IPA analysis. The result of IPA predicted the protein ubiquitin pathway as a major canonical pathway affected by the differentially regulated genes. Interestingly, IPA analysis generated an interactome that showed connectivity among various ubiquitin ligases, NF-ԟB family, AP-1/cJun, 20S and 26S proteasome system.
Conclusion: Our results clearly shows the major pathways affected by miR-17 overexpression in RASFs were Protein ubiquitination related.

overall_design: mRNA profiles of pre-miR-17 and NC-pre-miR transfected RASFs were generated by AmpliSeq, in duplicate, using Ion Proton™ System.

first: Nahid

last: Akhtar

first: Anil

last: Singh


title: MODD mediates deactivation and degradation of OsbZIP46 to negatively regulate ABA signaling and drought resistance in rice

city: Wuhan

first: Ma

last: Siqi

address: No.1,Shizishan Street

institute: Huazhong Agricultural Uinveristy

summary: Responses to drought in rice are regulated by transcription factor OsbZIP46 via ABA signaling. This work characterizes a protein MODD that negatively regulates OsbZIP46 activity and stability through HDAC-related chromatin remodeling and OsPUB70-mediated ubiquitination, respectively, to fine tune ABA signaling and drought resistance.

overall_design: Examination of mRNA levels in modd mutants and wild type plants under normal condition.

first: S

last: Ma

first: N

last: Tang

first: L

last: Xiong


title: A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells (batch 2)


title: Cytokine-independent detection of antigen-specific germinal center T follicular helper (Tfh) cells in immunized non-human primates using a live cell Activation Induced Marker (AIM) technique

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: A range of current candidate AIDS vaccine regimens are focused on generating protective HIV neutralizing antibody responses. Many of these efforts rely on the rhesus macaque animal model. Understanding how protective antibody responses develop and how to increase their efficacy are both major knowledge gaps. Germinal centers (GC) are the engines of antibody affinity maturation. GC T follicular helper (GC Tfh) CD4 T cells are required for GCs. Studying vaccine-specific GC Tfh cells after protein immunizations has been challenging, as antigen-specific GC Tfh cells are difficult to identify by conventional intracellular cytokine staining (ICS). Cytokine production by GC Tfh cells may be intrinsically limited in comparison to other T helper effector cells, as the biological role of a GC Tfh cell is to provide help to individual B cells within the GC, rather than secreting large amounts of cytokines bathing a tissue. To test this idea, we developed a cytokine-independent method to identify antigen-specific GC Tfh cells. RNAseq was performed using TCR stimulated GC Tfh cells to identify candidate markers based on differentially expressed genes and other criteria. Validation experiments determined CD25 (IL2Ra) and OX40 to be highly upregulated activation induced markers on the surface of GC Tfh cells after stimulation. In comparison to ICS, the activation induced marker (AIM) assay identified > 10-fold more antigen-specific GC Tfh cells in HIV Env protein immunized macaques (BG505 SOSIP). Additionally, the AIM assay detected antigen-specific CXCR5+ and CXCR5- CD4 T cells in peripheral blood. Thus, AIM demonstrates that antigen-specific GC Tfh cells are intrinsically stingy producers of cytokines, which is likely an essential part of their biological function.

overall_design: Total RNA obtained from GC Tfh cells from 3 rhesus macaque lymph node cell samples stimulated with Staphylococcal Enterotoxin B compared with 2 unstimulated cell samples.

first: Colin

last: Havenar-Daughton

first: Shane

last: Crotty

first: Greg

first: Nirav

last: Patel


title: A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells (part 2)

overall_design: CD8 TILs sorted on PD1 and Tim3 to subpopulations were analyzed from two batches: batch 1: 2 WT and 2 MTKO mice , batch 2: 2 WT and 3 MTKO mice.


title: A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells (batch 3)


title: Vascular specific H3K27me3 and H3K4me3 profile in the Arabidopsis root

status: Public on Sep 06 2016

city: Davis

first: Gina

middle: Marie

last: Turco

address: University of California, Davis

institute: UC Davis

summary: We isolated Vascular specific root protoplast using the pWOL:GFP marker line  (Birnbaum et al., 2003) and Fluorescence Activated Cell Sorting (FACS). FACS-treated root protoplast from wild type plants (Col0) were used as control. The GFP positive protoplast from the pWOL:GFP line and WT protoplast were used for a ChIP-seq experiment using H3K27me3 and H3K4me3 antibodies.

overall_design: Examination of root vascular specific H3K27me3 and H3K4me3 deposition

first: Miguel

last: de Lucas

first: Siobhan

last: Brady


title: RNA-seq analysis of IMQ-treated wt and Trex2-/- skin

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

summary: TREX2 is a keratinocyte specific 3’-deoxyribonuclease that participates in the maintenance of skin homeostasis upon damage. This transcriptome analysis identified multiple genes and pathways deregulated by TREX2 loss in the IMQ-induced psoriasis-like model in mouse skin.

overall_design: mRNA sequencing of 5 biological replicates of skin from wild-type mice treated with Imiquimod and 6 of Trex2 knockout mice treated with Imiquimod

first: Joan

last: Manils

first: Arnau

last: Viña-Vilaseca

first: Tanya

last: Vavouri

first: Concepció

last: Soler


title: Unexpected role of interferon-g in regulating neuronal connectivity and social behavior

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

summary: We identified an enrichment in IFN-gamma dependent genes in the prefrontal cortex of group housed mice compared to single housed mice.

overall_design: Mice were house either grouped or single for 6 days. Mice were euthanized and brains were removed. The prefrontal cortex was disected and prepared for RNA-seq analysis.

first: Anthony

last: Filiano

first: Jonathan

last: Kipnis


title: Tbr2 and Neurog2 occupancy and transcriptional profiling of control and Tbr2 knockout E14.5 cerebral cortices

first: Luca

last: Massimino

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

overall_design: Refer to individual Series


title: The bromodomain protein BRD4 regulates splicing during heat shock

city: Berlin

first: Michal

middle: Ruth

last: Schweiger

address: Ihnestrasse 63-73

department: Lehrach

country: Germany

institute: Max Planck Institute For Molecular Genetics

summary: During heat stress cyto-protective genes including heat shock proteins are transcriptionally up-regulated and post-transcriptional splicing is inhibited. In contrast, co-transcriptional mRNA-splicing is maintained. These factors closely resemble the proteotoxic stress response during tumor development. The bromodomain protein BRD4 has been identified as an integral member of the oxidative stress as well as of the inflammatory response. Furthermore, there is evidence for BRD4's role in splicing regulation; Using RNA-Seq analyses we indeed found a significant increase in splicing inhibition, in particular intron retentions, during heat treatment in BRD4-deficient cells, but not under normal conditions. Subsequent experiments revealed that heat stress leads to the recruitment of BRD4 to nuclear stress bodies, to the interaction with the heat shock factor 1 (HSF1) and to the transcriptional up-regulation of non-coding Sat III RNA transcripts. These findings implicate BRD4 as a central regulator of splicing during heat stress. Since BRD4 is a potent target for anti-cancer therapies, our data linking BRD4 to the splicing machinery and the heat stress response - give additional insight into the mode of action of BRD4 inhibitors.

overall_design: WI38 cells have been treated by heatshock and anti BRD4 siRNA and combination.

first: Michelle

last: Hussong

first: Christian

last: Kaehler

first: Martin

last: Kerick

first: Alexandra

last: Franz

first: Bernd

last: Timmermann

first: Jörg

last: Issensee

first: Tim

last: Hucho

first: Sylvia

last: Krobitsch

middle: R


title: The Smaug RNA-binding protein is essential for microRNA synthesis during the Drosophila maternal-to-zygotic transition

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Metazoan embryos undergo a maternal-to-zygotic transition (MZT) during which a subset of maternal gene products is eliminated and the zygotic genome becomes transcriptionally active. RNA-binding proteins (RBPs) and the microRNA-induced silencing complex (miRISC) – of which Argonaute 1 (AGO1) is a key component in Drosophila – target maternal mRNAs for degradation. The Drosophila Smaug, Brain tumor (BRAT) and Pumilio (PUM) RBPs direct the degradation of maternal mRNAs. Here we elucidate Smaug’s roles in regulation of miRNAs and miRISC during the MZT.
Results: By global analysis of small RNAs at several stages during the MZT, we show that the vast majority of all miRNA species encoded by the Drosophila genome (85%) are expressed during the MZT. Whereas a subset of these miRNAs is loaded into oocytes by the mother and stays at constant levels during the MZT, dozens of miRNA species are either newly synthesized or re-expressed in the early embryo. Loss of Smaug has a profound effect on miRNAs but little effect on piRNAs or siRNAs. Smaug is required for production of new miRNAs during the MZT; Smaug-bound AGO1 reflects the constellation and abundance of the miRNAs present in early embryos; and Smaug is required for the increase in AGO1 protein levels that occurs during the MZT. As a consequence of low miRISC activity in smaug mutants, maternal mRNAs that are normally targeted for degradation by zygotic miRNAs fail to be cleared. BRAT and PUM share target mRNAs with miRISC during the MZT while the miR-309 miRNA family coregulates targets of BRAT but not PUM.
Conclusions: Smaug controls the MZT through direct targeting of a subset of maternal mRNAs for degradation and, indirectly, through production and function of miRNAs and miRISC, which control clearance of a distinct subset of maternal mRNAs. BRAT and/or PUM function together with miRISC during the latter process. With respect to miRISC-dependent transcript degradation, Smaug is required (1) for the synthesis of miRNAs, (2) for synthesis and stabilization of AGO1, and (3) for action of AGO1 in association with its bound miRNAs. In smaug mutants a large number of maternal mRNAs persist and the MZT fails.

overall_design: Examination of miRNA expresssion at different time points in wild type and smuag mutant early embryos .

first: Hua

last: Luo

first: Xiao

last: Li

first: Julie

middle: M

last: Claycomb


title: A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells

first: Meromit

last: Singer


title: Next generation sequencing analysis of epididymal adipose tissue (III)

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: We analyze the contribution of alternative splicing to the transcriptional complexity in adipose tissue and the development of diet-induced obesity.

overall_design: We use Next generation sequencing analysis of eWAT from control and Nova1 and Nova2-deficient mice fed with a high fat diet.

first: Santiago

last: Vernia

first: Yvonne

first: Roger

last: Davis


title: Next generation sequencing analysis of epididymal adipose tissue (II)

overall_design: We use Next generation sequencing analysis of eWAT from control and Nova1 and Nova2-deficient mice fed with a control diet


title: Proteomic and genomic characterization of a yeast model for Ogden syndrome

first: Gholson

last: Lyon


title: Next generation sequencing comparing effects of vehicle, PTH, and YKL-05-093 in Ocy454 cells

city: Boston

first: Marc

last: Wein

address: 15 Fruit Street

department: Massachusetts General Hospital, Department of Medicine

institute: Harvard Medical School

summary: Purpose: The goals of this study are to compare the effects of vehicle, PTH, and YKL-05-093 on gene expression by NGS-derived RNA-sequencing

overall_design: Methods: Ocy454 cells were grown at 37C for 14 days . Cells were then treated with vehicle, PTH (1 nM), or YKL-05-093 (0.5 uM) for 4 hours. Total RNA was isolated using Qiagen Rneasy columns, and submitted for NGS library generation and sequencing. All experiments performed in duplicate.


title: Brain transcriptome of honeybees (Apis mellifera) infected by Nosema ceranae and/or Black Queen Cell Virus

city: Avignon

first: Cédric

last: Alaux

address: Domaine Saint-Paul

department: UMR 406 Abeilles et Environnement

country: France

institute: INRA

summary: Experimental infection of (2 days old) adult honey bee workers (30 bees per replicates, 3 replicates per treatments, from 3 different colonies (one colony per cage for each treatment)) with 10^9 genome equivalent of Black Queen Cell Virus (BQCV) in 10µl of sugar solution and/or 10^5 fresh Nosema ceranae spores (control bees were given a similar bee extract in PBS, without pathogen). Bees were kept in cages of 30 bees in incubator (30°C/50%RH). At day 13 p.i., bees were flash frozen, and stored at -80°C.

overall_design: Brain mRNA profiles of 15 old bees were generated by deep sequencing, in triplicates except for bees infected by both Nosema ceranae and Black Queen Cell Virus (duplicates)

first: Vincent

last: Doublet

first: Yves

last: Le Conte

first: Cynthia

last: McDonnell

first: Robert

last: Paxton


title: Next generation sequencing analysis of epididymal adipose tissue (I)

overall_design: We use Next generation sequencing analysis of mice fed with a control chow diet or a high fat diet.


title: Circadian Epigenomic Control of Skeletal Muscle Fuel Metabolism by HDAC3

city: Philadelphia

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

institute: University of Pennsylvania

summary: We address the function of HDAC3 in skeletal muscle metabolism

overall_design: We performed HDAC3 ChIP-seq, RNA-seq, and GRO-seq in mouse muscles at different times of the day and compared between WT and HDAC3-depleted muscles.

first: Zheng

last: Sun

first: Manashree

last: Damle


title: A distinct gene module uncouples dysfunction from activation in tumor-infiltrating T cells (part 1)

overall_design: naïve and activated CD8 T cells


title: Genome-wide landscape and functional necessity of heart enhancers

city: Berkeley

first: Diane

last: Dickel

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

summary:
Analysis of the transcriptional changes in the heart resulting from the loss of cardiac enhancers.
As there remains a limited understanding of the phenotypic consequences of enhancer mutations, we examined the impact of loss of function mutations by deleting two enhancers near heart disease genes in mice.  In both cases, we observed loss of target gene expression, as well as cardiac phenotypes consistent with heart disease in humans, highlighting the functional importance of enhancers for normal heart function, as well as the potential contribution of enhancer mutations to heart disease.

overall_design: Hearts were dissected from wild-type and enhancer-null mice (either embryonic or adult) and processed for deep RNA-seq analysis.

first: Yoko

last: Yuzawa


title: RNA-Seq of Lgr6 positive and negative cells in mouse mammary gland

city: London

first: Axel

last: Behrens

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick Institute

summary: Lgr6-positive cells have been shown to label stem/progenitors cells in several tissues including tongue and skin. However their role in mammary gland has never been investigated. Here we used Lgr6-eGFP-IRES-CreER2 mice to isolate and characterize Lgr6-positive population in mammary gland of 5-week old female mice.

overall_design: Examination of transcriptional differences between Lgr6 positive and negative cells

first: Leander

last: Blaas

first: Fabio

last: Pucci

first: Hendrik

last: Messal

first: Agneta

last: Andersson

first: Edgar

last: Ruiz

first: Bradley

last: Spencer-Dene

first: Alexandra

last: Musch

first: Richard

last: Mitter

first: Leena

last: Bhaw

last: Stone

first: Dorothee

last: Bornhorst

first: Abdul

last: Sesay

first: Jos

last: Jonkers

first: Gordon

last: Stamp

first: Ilaria

last: Malanchi

first: Rune

last: Toftgård


title: A pre-mRNA Alternative Splicing Program Promotes Adipose Tissue Thermogenesis

first: Dr Yvonne

last: Edwards


title: Desiccation Tolerance of Arabidopsis thaliana seeds

city: Irapuato

first: Sandra

middle: Isabel

last: Gonzalez-Morales

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera León

department: LANGEBIO

country: Mexico

institute: CINVESTAV

summary: Desiccation tolerance (DT) allowed seed plants to conquer ecosystems with long periods of limited water availability. This adaptive features allows seeds to remain dried for very long times without losing their ability to germinate. There is little information about all the signaling components required to achieve DT and on how transcription factors (TFs) modulate global DT processes. We performed RNA-seq experiment and carbohydrates profiles of lec1, lec2, fus3 and abi3, as well as their corresponding wild types, at three stages of seed development 15, 17 and 21 DAF (day after open flower) belonging to the seed desiccation period. A complex experimental design approach and regulatory networks prediction were used to identify differentially expressed genes specifically involved in DT process.

overall_design: In order to identify mechanisms involved in the acquisition of DT during seed development, we designed a comparative transcriptomic analysis between the seed desiccation intolerant (DI) mutants lec1-1, abi3-5 and fus3-3, the desiccation tolerant mutant lec2-1 and the desiccation tolerant weak allele of abi3 (abi3-1) with their respective wild type controls. This analysis should allow to identify genes that are differentially expressed in the desiccation intolerant mutants respect to tolerant mutants and WT controls.

middle: I

first: Luis

middle: H

last: Estrella


title: Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neural Stem Cell Model Systems

city: New Haven

first: Nenad

last: Sestan

address: 333 Cedar Street, SHM C-316C

institute: Yale University School of Medicine

summary:
Purpose: Use single cell RNA-seq technology on neural epithelial stem cell culture to understand the composition and transcriptome property of the model system. The culture system was then used to study ZIKV infection.
Methods: Single cell RNA-seq and bioinformatic analysis on NES cells in culture and single cells from  5-6 post conception week (pcw), 16 pcw, as well as 19-20 pcw human fetal neocortex.
Results: We find that NES cells are highly similar to RGCs and neural progenitor cells in terms of their gene expression profile. Both NES cells and neural stem cells/progenitors from fetal neocortex expressed canonical marker genes of proliferating and differentiating neuronal cells.
Conclusions: We successfully established the NCX-NES cell culture as an experimental system for the study of neural stem cells and used it to study ZIKV infection

overall_design: Single cell RNA-seq of over 1,000 cells of NCX-NES cell culture and fetal brain.  All of the cells in this dataset are non-ZIKV-infected.

first: Zhen

last: Li

first: Mingfeng


title: Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy

city: Warsaw

first: Katarzyna

last: Lukasiuk

address: 3 Pasteur Street

department: Department of Molecular and Cellular Neurobiology

country: Poland

institute: Nencki Institute of Experimental Biology Polish Academy of Sciences


city: Kuopio

first: Asla

last: Pitkänen

address: P.O.B. 1627 (Neulaniementie 2)

department: Department of Neurobiology

country: Finland

institute: University of Eastern Finland


title: Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (Amygdala stimulation – MBD-seq)

summary: Explore DNA methylation in focal amygdala stimulation model of epilepsy and its relationship to gene expression.

overall_design: Examination of methylation changes in stimulated rats compared to sham operated animals in focal amygdala stimulation model of epilepsy.

first: Konrad

last: Dębski

first: Anna

last: Bot

first: Ishant

last: Khurana

first: Harikrishnan

last: Kaipananickal

first: Mark

last: Ziemann

first: Antony

last: Kaspi

first: Assam

last: El-Osta


title: Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice

status: Public on Sep 05 2016

city: Cambridge

first: Martin

last: Turner

address: Babraham Hall

department: Lymphocyte Signalling and Development

institute: Babraham Institute


title: Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (Amygdala stimulation – mRNA-seq)

overall_design: Examination of expression changes in stimulated rats compared to sham operated animals in focal amygdala stimulation model of epilpesy.


title: Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (TBI – MBD-seq)

summary: Explore DNA methylation in traumatic brain injury model of epilepsy and its relationship to gene expression.

overall_design: Examination of methylation changes in stimulated rats compared to sham operated animals in traumatic brain injury model of epilepsy.

last: Pitkanen

first: Noora

last: Puhakka


title: Identification of microRNAs and transcript targets in Jatropha seeds

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

institute: Universidade Federal do Rio Grande do Sul

summary: MicroRNAs or miRNAs are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received much attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library from mature seeds and three mRNA libraries, from three different stages of seed development, were generated by deep sequencing in order to identify and characterize miRNAs and pre-miRNAs of J. curcas. Computation analysis allowed the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs), as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense and also lipid metabolism. Some of pre-miRNA and miRNA targets have different abundance among the three stages of seed development. A search for sequences that produce siRNA was performed indicating that J. curcas siRNAs play a role in nuclear functions, transport, catalytic process and diseases resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing and contributes to understand the function of these miRNAs.

overall_design: microRNA identification in a mature seed library of Jatropha curcas by deep sequencing (Illumina HiSeq2000).

first: Vanessa

middle: V

last: Galli

first: Ana

last: Körbes

first: Frank

last: Guzman

first: Rogério


title: Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation

city: Newcastle Upon Tyne

first: Konstantinos

last: Stellos

state: England

address: Central Parkway, Centre for Life

department: Faculty of Medical Sciences

institute: Newcastle University

summary: Adenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by a family of adenosine deaminase acting on RNA (ADAR) enzymes, is important in the epitranscriptomic regulation of RNA metabolism. However, the role of A-to-I RNA editing in vascular disease is unknown. Here we show that cathepsin S mRNA (CTSS), which encodes a cysteine protease associated with angiogenesis and atherosclerosis, is highly edited in human endothelial cells. The 3′ untranslated region (3′ UTR) of the CTSS transcript contains two inverted repeats, the AluJo and AluSx+ regions, which form a long stem–loop structure that is recognized by ADAR1 as a substrate for editing. RNA editing enables the recruitment of the stabilizing RNA-binding protein human antigen R (HuR; encoded by ELAVL1) to the 3′ UTR of the CTSS transcript, thereby controlling CTSS mRNA stability and expression. In endothelial cells, ADAR1 overexpression or treatment of cells with hypoxia or with the inflammatory cytokines interferon-γ and tumor-necrosis-factor-α induces CTSS RNA editing and consequently increases cathepsin S expression. ADAR1 levels and the extent of CTSS RNA editing are associated with changes in cathepsin S levels in patients with atherosclerotic vascular diseases, including subclinical atherosclerosis, coronary artery disease, aortic aneurysms and advanced carotid atherosclerotic disease. These results reveal a previously unrecognized role of RNA editing in gene expression in human atherosclerotic vascular diseases.

overall_design:
1) Evaluation of transcriptome expression and RNA editing sites (A-to-G and T-to-C nucleotide mismatches) in poly(A) RNA-seq data derived from endothelial cell transcriptome after ADAR1 or ADAR2 knockdown (n=2 biological replicates per condition, total n=8 biological samples).
2) Evaluation of transcriptome expression and RNA editing sites (A-to-G and T-to-C nucleotide mismatches) in total-RNA-seq data derived from peripheral blood mononuclear cells (n=12 total biological samples; n=4 replicates per condition).
3) Evaluation of transcriptome expression and RNA editing sites (A-to-G and T-to-C nucleotide mismatches) in total-RNA-seq data derived from endothelial cell transcriptome under basal and hypoxic conditions (n=2 biological replicates per condition, total n=4 biological samples).
4) Evaluation of RNA editing sites (A-to-G and T-to-C nucleotide mismatches) in total RNA-seq data derived from endothelial cell transcriptome under basal and hypoxic conditions after ADAR1 knockdown (n=3 replicates per condition, total n=12 biological samples).
5) HuR iCLIP RNA-sequencing data derived from HUVEC HuR iCLIP after ADAR1 knockdown (scrambled control and siADAR1, n=1 per condition, total n=2 biological samples).

first: Stefanie

last: Dimmeler


title: Response of C2C12-hN1∆ECD to DAPT washout

status: Public on Sep 04 2016

city: Pasadena

first: Nagarajan

last: Nandagopal

state: CA

address: 1200 E. California Blvd, M/C 114-96

institute: California Institute of Technology

summary: C2C12 cells expressing constitutively active hN1∆ECD were activated by complete DAPT washout for 1h or 6h, or left in 10 uM DAPT

overall_design: 2 Samples and 1 Control

first: Michael

middle: B

last: Elowitz


title: Steinernema carpocapsae Breton small RNA sequencing insect in vitro simulation system, from "The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle"

city: Edinburgh

first: José

middle: Roberto

last: Bermúdez-Barrientos

state: Lothian

address: Charlotte Auerbach Rd

department: Institute of Immunology & Infection

institute: The University of Edinburgh

summary: We report small RNA sequencing of the entomopathogenic nematode Steinernema carpocapsae. The nematodes were grown in liquid culture in homogenates of pig kidney/fat and infective juveniles were gathered. Then Galleria mellonella insect haemolymph was added to simulate insect infection, control nematodes weren't added haemolymph. Nematodes were collected after two hours after haemolymph addition.

overall_design: infective juveniles S. carpocapsae were incubated with and without haemolymph, three replicates

first: Alejandra

last: Rougon-Cardoso

first: Mitzi

last: Flores-Ponce

first: Hilda

last: Ramos-Aboites

first: Christian

middle: E

last: Martinez-Guerrero

first: You-Jin

last: Hao

first: Luis

last: Cunha

first: Jonathan-Alejandro

last: Rodríguez-Martínez

first: Cesaré

last: Ovando-Vázquez

first: Cei

last: Abreu-Goodger

first: Norberto

last: Chavarria-Hernández

first: Nelson

last: Simões

first: Rafael

last: Montiel-Duarte


title: Transcriptome profiling of 5 human adenocarcinoma cell lines

status: Public on Sep 02 2016

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 compare the transcriptome profiles of a limited number of lung cancer cell lines with the intention of selecting the two most similar cell lines for a mixture experiment (GSE64098).
Methods - Cell Culture: Five lung adenocarcinoma cell lines (H2228, NCI-H1975, HCC827, H838 and A549) from a range of passages (2-4) were grown on 2 separate occasions in RPMI media (Gibco) supplemented with Glutamax and 10\% fetal calf serum to a 70\% confluence. To replicate common experimental conditions cell lines were treated with 0.01\% Dimethyl sulfoxide (Sigma), which is commonly used as a vehicle in drug treatment experiments. After 6 hours of treatment, cells were collected, snap-frozen on dry ice and stored at -80 degree C until required.
Methods - RNA preparation: Total RNA was extracted from between half a million and million cells using Total RNA Purification Kit (Norgen Biotek) according to the kit instructions. RNA quality and concentration were assessed using Nanodrop and Tapestation RNA ScreenTape (Agilent) respectively.
Methods - RNA-seq: 1 ug of total RNA from each sample were used for RNA-seq library preparation using TruSeq Total Stranded RNA with Ribozero (Illumina) according to manufacturer's instructions. Completed libraries were sequenced on HiSeq 2000 with TruSeq SBS Kit v3- HS reagents (Illumina) as 100 bp single end reads at the Australian Genome Research Facility (AGRF), Melbourne. We obtained on average 28 million for each sample (range from 25 to 29 million). Reads were aligned to the human reference genome hg19 using the Rsubread package (version 1.16.1) (Liao et al. 2013). Single reads were then summarized into gene-level counts using FeatureCounts in the reverse-stranded mode (Liao et al. 2014).

overall_design: Total RNA was extracted from lung adenocarcinoma cell lines H2228, NCI-H1975, HCC827, H838 and A549 (2 independent samples for each cell line). Total RNA transcriptome from these samples was profiled by RNA-seq.

first: Aliaksei

middle: Z

last: Holik


title: Targeted experimentation to increase functional coverage in omics dataset

status: Public on Sep 03 2016

city: davis

first: Ilias

last: Tagkopoulos

state: CALIFORNIA

address: 2063 kemper hall, 1 shields avenue

institute: university of california at davis

summary: To increase the GO coverage of Ecomics, we investigated which new conditions would lead to the most informative transcriptional profiles. We first transcriptionally profiled and included in the compendium 9 KO experiments that we had identified before as being highly informative for both GO coverage and model performance. We assumed that a GO term is represented in the compendium if the compendium has profiles where one or more genes that include that GO term have been perturbed. We identified the gene rank iteratively under the assumption that all genes of higher rank have been perturbed. Based on the resulting ranked list, we performed transcriptional profiling for the top 16 genetic perturbations (in triplicate; 48 profiles total), which led to an increase in coverage by 19.8% for KEGG, 24.3% for BP and 63.9% for MF.

overall_design: Genome-wide expression profiling of 25 single-gene knockouts for BW25113 and its wild-type grown with either LB or M9 media supplemented with glucose (total 87 samples).

first: Navneet

last: Rai

first: Violeta

last: Zorraquino

first: Minseung

last: Kim


title: The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan (ATAC-Seq)

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

summary: Neutrophils, eosinophils and “classical” monocytes collectively account for ~70% of human blood leukocytes and are among the shortest-lived cells in the body. Precise regulation of the lifespan of these myeloid cells is critical to maintain protective immune responses while minimizing the deleterious consequences of prolonged inflammation. However, how the lifespan of these cells is strictly controlled remains largely unknown. Here, we identify a novel long non-coding RNA (lncRNA) that we termed Morrbid, which tightly controls the survival of neutrophils, eosinophils and “classical” monocytes in response to pro-survival cytokines. To control the lifespan of these cells, Morrbid regulates the transcription of its neighboring pro-apoptotic gene, Bcl2l11 (Bim), by promoting the enrichment of the PRC2 complex at the Bcl2l11 promoter to maintain this gene in a poised state. Notably, Morrbid regulates this process in cis, enabling allele-specific control of Bcl2l11 transcription. Thus, in these highly inflammatory cells, changes in Morrbid levels provide a locus-specific regulatory mechanism that allows for rapid control of apoptosis in response to extracellular pro-survival signals. As MORRBID is also present in humans and dysregulated in patients with hypereosinophilic syndrome, this lncRNA may represent a potential therapeutic target for inflammatory disorders characterized by aberrant short-lived myeloid cell lifespan.

overall_design: Examination of chromatin accessibility in mouse neutrophils.

first: Jonathan

last: Kotzin

first: Sean

middle: P

last: Spencer

first: Sam

last: McCright

first: Dinesh

last: Uthaya Kumar

first: Magalie

last: Collet

first: Walter

middle: K

last: Mowel

first: Ellen

middle: N

last: Elliott

first: Michelle

last: Makiya

first: Margaret

middle: C

last: Dunagin

last: Harman

first: Anthony

middle: T

last: Virtue

first: Stella

last: Zhu

first: Will

last: Bailis

first: Judith

last: Stein

first: Cynthia

last: Hughes

first: Arjun

last: Raj

first: E

last: Wherry

first: Loyal

last: Goff

first: Amy

last: Klion

first: John

middle: L

last: Rinn

first: Adam

last: Williams

first: Richard

last: Flavell

first: Jorge

last: Henao-Mejia


title: The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan

first: Asli

last: Uyar

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

overall_design: Refer to individual Series


title: Widespread natural variation of DNA methylation within angiosperms

city: Athens

first: Robert

middle: J

last: Schmitz

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. By examining these variations in a phylogenetic context it becomes clear that there is extensive variation in mechanisms that govern gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. Extensive variation is observed at all cytosine sequence contexts (CG, CHG and CHH, where H = A, C, T), with the Brassicaceae showing reduced CHG methylation levels and also reduced or loss of CG gene-body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time, in the absence of sexual reproduction. These results show that DNA methylation targeting pathways have diverged functionally and that extant DNA methylation patterns are likely a reflection of the evolutionary and life histories of plant species.

sample_organism:
Cannabis sativa
Theobroma cacao
Cucumis sativus
Populus trichocarpa
Brassica rapa
Malus domestica
Prunus persica
Medicago truncatula
Manihot esculenta
Ricinus communis
Erythranthe guttata
Setaria viridis
Sorghum bicolor
Brachypodium distachyon
Vitis vinifera
Lotus japonicus
Panicum virgatum
Fragaria vesca
Eucalyptus grandis
Eutrema salsugineum
Citrus x clementina
Beta vulgaris
Panicum hallii

overall_design: Bisulfite-seq of leaf tissue from plants representing diverse angiosperms. RNA-seq and small RNA-seq was performed on leaf tissue of a subset of the species.

first: Chad

last: Niederhuth


title: An ectopic CTCF binding element disturbs Vδ usage at the mouse Tcra-Tcrd locus by regulating contact between Vδ and Dδ gene segments

city: Boston

first: Lijuan

last: Zhao

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: Chromatin looping mediated by the CCCTC binding factor CTCF regulates V(D)J recombination at antigen receptor loci. CTCF-mediated looping can influence recombination signal sequence accessibility by regulating enhancer activation of germline promoters. CTCF-mediated looping has also been shown to limit directional tracking of the RAG recombinase along chromatin, and to regulate through-space interactions between recombination signal sequences, independent of the RAG recombinase. However, in all prior instances in which CTCF-mediated looping was shown to influence V(D)J recombination, it was not possible to fully resolve the relative contributions to the V(D)J recombination phenotype of changes in accessibility, RAG-tracking, and RAG-independent long-distance interactions. Here, to assess mechanisms by which CTCF-mediated looping can impact V(D)J recombination, we introduced an ectopic CTCF binding element (CBE) immediately downstream of Eδ in the murine Tcra-Tcrd locus. The ectopic CBE impaired inversional rearrangement of Trdv5 in the absence of measurable effects on Trdv5 transcription and chromatin accessibility. Moreover, although the ectopic CBE limited directional RAG tracking from the Tcrd recombination center, such tracking cannot account for Trdv5-to-Trdd2 inversional rearrangement. Rather, the defect in Trdv5 rearrangement could only be attributed to a reconfigured chromatin loop organization that limited RAG-independent through-space interactions between the Trdv5 and Trdd2 RSSs. We conclude that CTCF can regulate V(D)J recombination by segregating RSSs into distinct loop domains and inhibiting RSS synapsis, independent of any effects on transcription, RSS accessibility and RAG tracking.

overall_design: RAG-initiatd Tcrd D segment rearrangements in developing thymocytes were generated by deep sequencing using illumine Miseq

first: Frederick

middle: W

last: Alt


title: Progenitor Cell Marker Aldehyde Dehydrogenase 1a3 Defines a Subset of Failing Pancreatic Beta Cells in Diabetic Mice

city: New York

first: Youngjung

middle: Rachel

last: Kim

address: 1150 St. Nicholas Ave

department: Medicine

institute: Columbia University

summary: Insulin-producing beta cells become dedifferentiated during diabetes progression. An impaired ability to select substrates for oxidative phosphorylation, or metabolic inflexibility, sets the stage for progression from beta cell dysfunction to beta cell dedifferentiation. In this study, we sought to isolate and functionally characterize failing beta cells, as a preliminary step to identify pathways to reverse dedifferentiation. Using various experimental models of diabetes, we found a striking enrichment in the expression of aldehyde dehydrogenase 1 isoform A3 (ALDH+) as beta cells become dedifferentiated. Flow-sorted ALDH+ islet cells demonstrate impaired glucose-induced insulin secretion, are depleted of Foxo1 and MafA, and include a Neurogenin3-positive subset. RNA sequencing analysis demonstrates that ALDH+ cells are characterized by: (i) impaired oxidative phosphorylation and mitochondrial complex I, IV, and V; (ii) activated RICTOR; and (iii) progenitor cell markers. We propose that impaired mitochondrial function marks the progression from metabolic inflexibility to dedifferentiation in the natural history of beta cell failure.

overall_design: RNA-Sequencing analysis of 2 different cell types in 2 different genotype categories.

middle: R


title: The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan (ChIP-Seq)

overall_design: Examination of 4 different histone modifications in mouse neutrophils.

first: Jonathan

last: Kotzin

first: Sean

last: Spencer

first: Sam

last: McCright

first: Dinesh

last: Uthaya Kumar

first: Magalie

last: Collet

first: Walter

last: Mowel

first: Ellen

last: Elliott

first: Michelle

middle: A

last: Makiya

first: Margaret

last: Dunagin

first: Christian

middle: D

last: Harman

first: Anthony

last: Virtue

first: Stella

last: Zhu

first: Will

last: Bailis


title: Transcriptome Profiling of Rattus norvegicus Embryonic Stem Cells by RNA-Sequencing

city: Columbia

first: Elizabeth

last: Bryda

state: MO

address: 4011 Discovery Ridge

institute: University of Missouri

summary: In order to establish a rat embryonic stem cell transcriptome, mRNA from rESC cell line DAc8, the first male germline competent rat ESC line to be described and the first to be used to generate a knockout rat model was characterized using RNA sequencing (RNA-seq) analysis.

overall_design: 2 biological replicates of RRRC#464 DA-EC8/Rrrc cell line  were sequenced with  50bp paired end reads using Illumina Hi-Seq 2000

first: Nathan

last: Johnson


title: Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (TBI – mRNA-seq)

first: Asla

last: Pitkänen

overall_design: Examination of expression changes in stimulated rats compared to sham operated animals in traumatic brain injury model of epilepsy.

last: Pitkanen

first: Noora

last: Puhakka

first: Ishant

last: Khurana

first: Harikrishnan

last: Kaipananickal

first: Mark

last: Ziemann

first: Antony

last: Kaspi

first: Assam

last: El-Osta


title: HDAC3 modulates enhancer activity to regulate terminal B cell differentiation

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

summary: B220+GL7+ (GC) and B220+GL7- (non-GC) B cells were sorted from SRBC-immunized mice deficient for Hdac3 and wild type controls. RNA-sequencing revealed an upregulation of critical regulators of B cell differentiation in Hdac3-deleted animals.

overall_design: 10 days post-immunization with SRBCs, GC and non-GC B cells were sorted and RNA isolated by Trizol extraction for RNA-sequencing. 2 replicates were sequenced for each condition.

first: Kristy

last: Stengel


title: Pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice. [iCLIP]

first: Martin

last: Turner

summary:
Purpose: We aimed to identify the targets of the RNA binding protein ZFP36L1 in thymoctes.
Methods:  Total naïve thymocytes from control or DCKO mice were treated with UV light to crosslink RNA and proteins, then RNA-protein complexes were pulled down with anti-ZFP36L1.  RNA was extracted and used to make cDNS libraries that were then sequenced by MiSeq 150bp single-end read (Sample 1) and HiSeq2500 RapidRun 50bp single-end read (sample 2, 3).
Results: Sample demultiplexing was performed by identification of the 3 known bases of the 7 bases barcode introduced in the 5’ end of the read by the RCLIP primer.  The remaining four random bases were used to remove PCR duplicate reads.  Reads were trimmed to remove any adaptor sequence and barcodes before mapping reads to genome GRCm38 using Bowtie.  After read mapping, the single-nucleotide at position -1 was annotated as unique ZFP36L1 crosslink site.  Identification of highly significant ZFP36L1 binding sites was performed using iCount to assign a FDR to each crosslink site.
Conclusions: We identified ZFP36L1 binding sites in 8675 thymocyte mRNAs.

overall_design: Individual nucleotide resolution cross linking immunoprecipitation (iCLIP) of ZFP36L1-bound RNAs in total naive thymocytes from C57BL/6 mice.

first: Katharina

middle: U

last: Vogel

first: Helena

last: Ahlfors


title: Transcriptome analysis of tetraploid cells identifies Cyclin D2 as a facilitator of adaptation to genome doubling in the presence of p53

status: Public on Sep 01 2016

city: Kansas City

first: Chris

last: Seidel

department: Genomics

institute: Stowers Institute


title: Paternal pachytene piRNAs are not required for fertilization, embryonic development and paternal epigenetic inheritance in mice

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

summary:
Pachytene piRNAs are PIWI-interacting small RNAs abundantly expressed in pachytene spermatocytes and spermatids in adult mouse testes. Both MIWI and MILI-bound pachytene piRNAs have been found enriched in round spermatids. Miwi-null male mice are sterile due to spermiogenic arrest.  In C. elegans, sperm-borne piRNAs appear to have an epigenetic role during fertilization and development because progeny of offspring derived from piRNA-deficient sperm display a progressive fertility loss after several generations. In mice, it remains unknown whether MIWI-bound pachytene piRNA-deficient round spermatids can produce offspring, and whether the progeny of offspring derived from MIWI-bound pachytene piRNA-deficient round spermatids also exhibit transgenerational loss of fertility.  Here, we report that Miwi KO round spermatids could fertilize both wild type (WT) and Miwi KO oocytes through round spermatid microinjection (ROSI), and produce healthy and fertile offspring despite the aberrant pachytene piRNA profiles in those Miwi KO spermatids.  Progeny of ROSI-derived heterozygotes, both male and female, displayed normal fertility for at least three generations when bred with either WT or Miwi KO females. Our data indicate that aberrant MIWI-bound pachytene piRNAs profiles in spermatids do not affect fertilization, early embryonic development, or fertility of the offspring, suggesting a normal pachytene piRNAs profile is not required for paternal transgenerational epigenetic inheritance in mice.
Method: Round spermatids were purified from WT and Miwi KO adult testes using a mini-STA-PUT method[Methods Enzymol 1993; 225:84-113.]，the purity of round spermatids was >90% based on our previous report[ J Biol Chem 2012; 287:25173-25190.]. Small RNA was isolated from round spermatids using the mirVana RNA isolation kit (Ambion) according to the manufacturer’s instructions. RNA quality and quantity were assessed using the Agilent 2100 Bioanalyzer. Small RNA-Seq was performed on an Ion Proton sequencer (Life Technologies). Libraries were prepared using the Ion Total RNA-Seq Kit v2 (Invitrogen) with biological triplicates for WT and Miwi KO samples.
Resutls:Our data indicate that aberrant MIWI-bound pachytene piRNAs profiles in spermatids do not affect fertilization, early embryonic development, or fertility of the offspring, suggesting a normal pachytene piRNAs profile is not required for paternal transgenerational epigenetic inheritance in mice.

overall_design: In Miwi KO males, round spermatid production in the seminiferous tubules proceed up to step 4 (J Anat. 2000 Feb; 196(Pt 2): 217–232. ), which provides us with an opportunity to use steps 1-4 round spermatids to fertilize eggs through round spermatid microinjection (ROSI).  In this study, we aimed to answer the following questions: 1) Is the pachytene piRNA profile altered in Miwi-deficient round spermatids? 2) Are the Miwi-deficient round spermatids competent for fertilization? 3) If so, are the progeny derived from ROSI offspring using Miwi-deficient round spermatids fertile? 4) Does paternal MIWI inactivation in mice phenocopy CSR-1 inactivation in C. elegans and display the “gremlin mortal” epigenetic inheritance? Here, we report that MIWI deficiency leads to altered pachytene piRNAs profiles and Miwi-deficient round spermatids can fertilize the eggs and produce normal offspring.  Unlike C. elegans, the absence of paternal MIWI did not induce epigenetic “germline-mortal” phenotype in mice.

first: Chong

last: Tang


title: RNAseq of pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice.

summary:
Purpose: Conditional knockout of Zfp36l1 Zfp36l2 early in lymphocyte development leads to a bypass of beta-selection and subsequently T cell acute lymphoblastic leukemia. This RNA seq experiment aimed to determine the molecular pathways affected by loss of Zfp36l1 and Zfp36l2, and to deduce direct targets of these RNA binding proteins.
Methods: RNA was isolated from sorted Zfp36l1fl/fl; Zfp36l2fl/fl DN3a (Lineage-negative, CD44-, Kitlow, CD25+, CD98low) and DN3b (Lineage-negative, CD44-, Kitlow, CD25intermediate, CD98+) cells as well as Zfp36l1fl/fl; Zfp36l2fl/fl; CD2cre DN3 (Lineage-negative, CD44-, Kitlow, CD25+) cells with the RNeasy Micro Kit (Qiagen). RNAseq libraries were prepared from 20-200ng RNA using the TruSeq Stranded Total RNA and rRNA Removal Mix – Gold from Illumina. Libraries were sequenced by Hiseq in 100bp single-end reads. The reads were trimmed to remove adapter sequences using Trim Galore then mapped using Tophat (version 2.0.12) to the GRCm38 mouse assembly; reads with an identical sequence to more than one genomic locus were not mapped.  Quality control analysis was carried out with FastQC.  Reads were counted using htseq-count tool and mouse gtf file version 78.
Results:  Differences in the abundance of transcripts between DCKO and control samples were calculated in the R/Bioconductor program DESeq2 (version 1.6.3).  Adjusted P values for differential expression were calculated in DESeq2 using a Benjamini-Hochberg correction: genes with an adjusted p-value of less than 5% were considered significant. Differentially expressed mouse transcripts identified using DESeq2 were analyzed for gene set enrichment using Toppfun.
Conclusions: We identified an enrichment of mRNAs involved in cell cycle progression within Zfp36l1 Zfp36l2 double conditional knockouts.

overall_design: 4 biological replicates of control DN3a, control DN3b and DCKO DN3-like cells were analyzed


title: RNA-Seq analysis RPE1 cells following exposure to Nutlin-3 to identify target genes of p53 [tpo12]

summary: Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell division in polyploid cells is error-prone and produces aneuploid cells.  This study investigates changes in gene expression evoked in acute and adapted tetraploid cells and their impact on cell-cycle progression.  Acute polyploidy was generated by knockdown of essential regulator of cytokinesis Anillin, which resulted in cytokinesis failure and formation of binucleate cells, or by chemical inhibition of Aurora kinases, causing abnormal mitotic exit with formation of single cells with aberrant nuclear morphology.  Transcriptome analysis of these acute tetraploid cells revealed common signatures of activation of the tumor-suppressor protein p53.  Suppression of proliferation in these cells was dependent on p53 and its transcriptional target - Cdk inhibitor p21.  Rare proliferating tetraploid cells can emerge from acute polyploid populations.  Gene expression analysis of single-cell derived, adapted tetraploid clones showed upregulation of several p53 target genes and cyclin D2, the activator of Cdk4/6/2.  Overexpression of cyclin D2 in diploid cells strongly potentiated the ability to proliferate with increased DNA content despite the presence of functional p53.  These results point out that p53-mediated suppression of proliferation of polyploid cells can be averted by increased levels of oncogenes such as Cyclin D2, elucidating a possible route for tetraploidy-mediated genomic instability in carcinogenesis.

overall_design: Cells were exposed to Nutlin-3 or DMSO and assessed for differences in gene expression by RNA Seq in triplicate for a total of 6 samples.

first: Tamara

last: Potapova

first: Andrew

last: Box

first: Giulia

last: Rancati

first: Rong

last: Li


title: RNA-Seq analysis of 4N and 2N RPE1 cells following polyploid induction via cytokinesis failure by siRNA knockdown of Anillin [tpo8]

overall_design: Three biological replicates of cells treated with siRNA against Anillin or a non-targeting control are FACS sorted into 2N or 4N populations and assessed for gene expression differences via RNA Seq for a total of 12 samples.


title: RNA-Seq analysis of 4N and 2N RPE1 cells following polyploid induction via cytokinesis failure or Aurora kinase inhibition [tpo3]

overall_design: Three biological replicates of cells treated with either Aurora inhibitor (ZM447439), CytochalasinD, or untreated are FACS sorted into 2N or 4N populations and assessed for gene expression differences via RNA Seq for a total of 18 samples.


title: RNA-Seq analysis of proliferating 4N and 2N RPE1 cells derived from single cell clones following inhibition of Aurora B to induce polyploidization [tpo10]

overall_design: Three biological replicates of cells derived from isolated 2N and 4N single cells were assessed for differences in gene expression by RNA Seq for a total of 18 samples.


title: Transcription Factors Sp8 and Sp9 Coordinately Regulate Olfactory Bulb Interneuron Development [RNA-Seq]

city: Shanghai

first: Jiwen

address: NO. 138 Yixueyuan Road

institute: Fudan University

summary:
Purpose: To asses changes in gene expression profiles from the P11 no cre littermate control olfactory bulbs and conditional double knockout olfactory bulbs of Dlx5/6-CIE; Sp8 Flox/Flox; Sp9 Flox/Flox (Sp8/Sp9-DCKO) mice.
Methods: Total RNA was isolated and sequenced from the olfactory bulbs of the P11 no cre littermate controls or Sp8/Sp9-DCKO mice in duplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed  which performed fold-change>=2 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of Sp8 and Sp9.
Results: 32 genes were significantly increased and 144 genes were significantly decreased in expression level due to the loss of Sp9 and Sp8 expression.

first: J

first: C

last: Wang

first: Z

last: Zhang

first: Y

last: Wen

first: L

last: An

first: S

last: Wei

first: T

last: Guo

first: G

last: Liu

last: Tao

last: You

first: H

last: Du

first: M

last: He

first: B

last: Chen

first: K

last: Campbell

last: Rubenstein

first: z

last: Yang


title: Metformin alters DNA methylation genome-wide via the H19/SAHH axis

first: Tingting

last: Geng

address: 263 Farmington Avenue

department: Department of Immunology

institute: Uconn Health

summary: To determine whether exposure of endometrial cancer cells to metformin would induce changes in global DNA methylation, ARK2 cells were incubated with metformin for 48 h, followed by genome-scale DNA methylation profiling using platform of an improved version of Reduced Representation Bisulfite Sequencing (RRBS). Metformin treatment led to extensive methylation changes genome-wide compared to control-treated cells. We found 2000 genes became hypermethylated, and 2000 genes became hypomethylated in ARK2 treatment group.

overall_design: ARK2 cells were incubated with metformin for 48 h, cellular genomic DNA was extracted and subjected to genome-scale DNA methylation mapping using the platform of an improved version of Reduced Representation Bisulfite Sequencing (RRBS).

first: Yingqun

last: Huang


title: Transcriptome analyses of EJC haploinsufficient neocortices

city: Durham

first: Debra

last: Silver

state: North Carolina

address: 224 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: RNA sequencing of E10.5 neocortices from control, Magoh, Rbm8a, and Eif4a3 haploinsufficient embryos (generated with Emx1-Cre)

overall_design: neocortical mRNA profiles of embryonic day 10.5 control (Emx1-Cre) and EJC haploinsufficent mutants (Eif4a3, Magoh, and Rbm8a conditional crossed with Emx1-Cre) mice were generated by deep sequencing, in triplicate.


title: KAT6A determines CD8+ T cell diversity via regulation of co-receptors

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: To identify genes specifically expressed in WT or Kat6a knockout CD8+ T cells, the gene expression profiles of T cell subsets from naïve or LCMV WE infected mice were compared.

overall_design: Three wildtype and three Kat6a knockout P14 transgenic mice were infected with LCMV WE for 8 days. Two wildtype and two knockout mice were uninfected. CD8+ T cells were harvested from the spleens of all mice. In the infected cohort, the T cells were further subsetted into KLRG1+ and KLRG1-.

first: Dane

last: Newman

first: Aaron

last: Lun


title: Distinct Roles of H3K27me2 and H3K27me3 States Unveiled By Fate Specification of Embryonic Stem Cells

city: Bethsda

first: Vittorio

last: Sartorelli

state: MD

address: 50 South Dr.

department: NIAMS

institute: NIH

summary: The Polycomb Repressive Complex 2 (PRC2) induces methylation of lysine 27 of histone H3 (H3K27) through its catalytic subunit Ezh2. PRC2-mediated di- and tri-methylation (H3K27me2/me3) have been interchangeably associated with gene repression. However, it remains unclear whether these two degrees of H3K27 methylation have indeed different functions. In this study, we have generated isogenic mouse embryonic stem cells (ESC) with a modified H3K27me2/H3K27me3 ratio. Our findings document a developmental dynamic control in the genomic distribution of H3K27me2 and H3K27me3 at regulatory regions in ESC. They also reveal that modifying the H3K27me2/H327me3 ratio is sufficient for the acquisition and repression of defined cell lineage transcriptional programs and phenotypes, along with influencing induction of the ESC ground state.

overall_design: To establish the role of H3K27me2 and H3K27me3 ratio balance in ES cell differentiation, we constructed a mutant ES cell line by TALEN which carries a hyperactive form of Ezh2 that changes the ratio of H3K27me2 and H3K27me3 . The distribution of H3K27 methylation status (H3K27me1, H3K27me2, H3K27me3) and other histone marks (H3K4me1, H3K27ac) were examined by ChIP-seq (2 replicates each) along with gene expression profiles by RNA-seq (3 replicates each) in wild type ES cells, mutant ES cells,ES cells differentated for 24 hours, ES cells differentiated to embryoid bodies and C2C12 skeletal muscle cell line. To understand the affect of H3K27me2/H3K27me3 ratio change during ES cell ground state transition, RNA expression profiles were examined in ground state wild type and mutant ES cells by RNA-seq (3 replicates)

first: Aster

middle: H

last: Juan

first: Stan

last: Wang

first: Kyung-Dae

last: Ko

first: Hossein

last: Zare

first: Pei-Fang

last: Tsai

first: Xuesong

last: Feng

first: Karinna

middle: O

last: Vivanco

first: Anthony

middle: M

last: Ascoli

first: Gustavo

last: Gutierrez-Cruz

first: Jordan

last: Krebs

first: Simone

last: Sidoli

first: Adam

last: Knight

first: Roger

last: Pedersen

first: Benjamin

last: Garcia

first: Rafael

last: Casellas

first: Jizhong

last: Zou


title: CTCF promotes epithelial ovarian cancer metastasis by broadly controlling the expression of metastasis-associated genes

first: Bo

last: Zhu

address: Institute of Cancer, Xinqiao Hospital, Third Military Medical University

department: Institute of Cancer, Xinqiao Hospital

institute: Third Military Medical University

summary: CCCTC-binding factor (CTCF) is an 11 zinc fingers transcription factor that functions as both an oncogenic and tumor suppressor, depending on the cancer types, through epigenetic regulation. Epigenetic regulation including DNA methylation and histone modifications are critically involved in cancer metastasis. We then hypothesized that CTCF might play a vital role in epithelial ovarian cancer metastasis. Firstly, we found that CTCF expression was elevated in ovarian cancer tissues compared to non-tumor tissues. The elevated expression of CTCF predicts poor prognosis of ovarian cancer patients. Then, we revealed that CTCF knockdown significantly inhibited the migration, invasion and metastasis of ovarian cancer cells, although it had no effect on cell proliferation and tumor growth, which have been demonstrated with both in vitro and in vivo experiments. More importantly, we observed a higher CTCF expression in metastatic lesions than that in primary lesions from ovarian cancer patients. Mechanically, PCR array demonstrated that CTCF might regulate a series of metastasis associated genes, including CTBP1, SERPINE1 and SRC. Finally, we observed positive correlations between CTCF expression and those three genes in epithelial ovarian cancer specimens. In conclusion, this study demonstrates that CTCF is an oncogene in ovarian cancer to promote tumor metastasis through broadly controlling the expression of metastasis-associated genes. Our findings suggest CTCF could be a novel drug target to treat ovarian cancer by interfering with cancer cell metastasis.

overall_design: Examination of CTCF binding site using SKOV3 cell lines

first: Lintao

last: Zhao

first: Shigang

last: Yin


title: Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation and Homeostasis by PTF1A [6-day RNA-Seq]

city: Dallas

first: Galvin

last: Swift

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: U TX Southwestern Medical Center

summary: RNA-seq analysis documented mRNA changes in total pancreatic RNA preparations 6 days after Ptf1a inactivation.

overall_design: pancreas mRNA profiles of Tamoxifen treated adult control mice [Ptf1a(CreER/+)] and Ptf1a conditional knockout mice [Ptf1a(CreER/fl)] were generated by deep sequencing using an Illumina Hiseq 2500.

first: Chinh

last: Hoang

first: Ana

last: Azevedo-Pouly

first: Raymond

last: MacDonald


title: Dose-dependent metabolic reprogramming and differential gene expression in TCDD-elicited hepatic fibrosis

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

summary: We have previously shown that in response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-elicited NAFLD progression, central carbon, glutaminolysis and serine/folate metabolism are reprogrammed to support NADPH production and ROS defenses. To further investigate underlying dose-dependent responses associated with TCDD-induced fibrosis, female C57BL/6 mice were gavaged with TCDD every 4 days (d) for 28d or 92d. RNA-Seq, ChIP-Seq (2hr), and 28d metabolomic (urine, serum, and hepatic extract) analyses were conducted with complementary serum marker assessments at 92d. Additional vehicle and 30 µg/kg treatment groups were allowed to recover for 36d following the 92d treatment regimen to examine recovery from TCDD-elicited fibrosis. Histopathology revealed dose-dependent increases in hepatic fat accumulation, inflammation, and periportal collagen deposition at 92d, with increased fibrotic severity in the recovery group. Serum proinflammatory and profibrotic interleukins-1β, -2, -4, -6, and -10, as well as TNFα and IFNγ, exhibited dose-dependent induction. An increase in glucose tolerance was observed with a concomitant 3.0-fold decrease in hepatic glycogen linked to increased ascorbic acid biosynthesis and proline metabolism, consistent with increased fibrosis. RNA-Seq identified differential expression of numerous matrisome genes including an 8.8-fold increase in Tgfb2 indicating myofibroblast activation. Further analysis suggests reprogramming of glycogen, ascorbic acid, and amino acid metabolism in support of collagen deposition and the use of proline as a substrate for ATP production via the proline cycle. Conclusion: In addition to metabolic reprogramming in support of NADPH production for ROS defense, we demonstrate that glycogen, ascorbic acid, and amino acid metabolism are also reorganized to support remodeling of the extracellular matrix, progressing to hepatic fibrosis in response to chronic injury from TCDD.

overall_design: Three biological replicates for each dose (0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30) of TCDD and sesame oil vehicle. Gavaged every 4 days for 92 days.

first: Kelly

last: Fader

first: Dustin

last: Ammendolia

first: Peter

last: Dornbos

first: Dave

last: Potter

first: Bonnie

last: Sharratt

first: Kazuyoshi

last: Kumagai

first: Jack

last: Harkema

first: Sophia

middle: Y

last: Lunt

first: Timothy

last: Zacharewski


title: Atr maintains chromosomal integrity during postnatal cerebellar neurogenesis

city: Chapel Hill

last: Gershon

state: NC

address: 6109 Neuroscience Research Building

department: Pediatric Hematology Oncology

institute: University of North Carolina at Chapel Hill

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

overall_design: Refer to individual Series


title: The global tissue-specific RNA transcription dysregulation effects in the third generation after embryonic exposure to the widely used herbicide atrazine are mediated via inherited histone trimethylation [ChIP-Seq, 2]

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

institute: Université de Rennes 1

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

overall_design: Examination of H3K4me3 in spermatocytes and spermatids

last: Hao

first: Fatima

last: Smagulova


title: Molecular mechanisms of transcriptional regulation by the nuclear zinc-finger protein Zfat in T cells

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

summary: ZFAT is a nuclear protein that harbors putative DNA-binding domains. Studies in mice have shown that ZFAT plays a critical role in survival and differentiation in T cells. However, molecular mechanisms whereby ZFAT regulates gene expression programs in T cells remain poorly unknown. We here identify the direct target genes of ZFAT in thymocytes through combination of chromatin immunoprecipitation with sequencing and transcriptional profiling.

overall_design: ChIPseq data were obtained for a zinc-finger transcription factor, ZFAT, and histone modifications (H3K9me3 and H3K9ac/K27ac) to further elucidate the functions of ZFAT in thymocytes.

first: Shuhei

last: Ishikura

first: Toshiyuki

last: Tsunoda

first: Senji

last: Shirasawa


title: The transcriptional outputs of AP2 and AG in floral development at the genomic scale

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

summary: To determine whether AP2 and AG have antagonistic effects on transcription, The gene expression profiles of Ler, ag-11, ag-11 ap2-35 and ag-11 ap2-43 were examined using RNA-seq.

overall_design: Inflorescences containing stage 7 and younger flowers were used, and three biological replicates were performed.

first: Xuemei

last: Chen

first: Zhigang

last: Huang


title: Atr maintains chromosomal integrity during postnatal cerebellar neurogenesis [RNA-Seq]

summary: Microcephaly and medulloblastoma result from mutations that compromise genomic stability. We report that Atr, which is mutated in the microcephalic disorder Seckel syndrome, is required to maintain chromosomal integrity during postnatal cerebellar neurogenesis. Atr deletion in cerebellar granule neuron progenitors (CGNPs) induced proliferation-associated DNA damage, p53 activation, apoptosis, and cerebellar hypoplasia. Co-deletions of either Bax and Bak or p53 prevented apoptosis in Atr-deleted CGNPs, but failed to fully rescue cerebellar growth. Atr-deficient CGNPs showed impaired cell cycle checkpoint function and continued to proliferate, accumulating chromosomal abnormalities. RNA-Seq demonstrated that the transcriptional response to Atr-deficient proliferation was p53-driven. Acute Atr inhibition in vivo by nanoparticle-formulated VE-822 reproduced the disruptions seen with Atr deletion. Our data show that p53-driven apoptosis and senescence, and non-apoptotic cell death redundantly limit growth in Atr-deficient progenitors. These overlapping mechanisms that suppress growth in Atr-disrupted CGNPs may be exploited for treatment of CGNP-derived medulloblastoma using Atr inhibition.

overall_design: RNA-Seq on total RNA from P3 mouse cerebella of Math1-Cre;Atr-loxP/loxP;Bax-loxP/loxP;Bak--/- (n=5), Math1-Cre;Bax-loxP/loxP;Bak--/- (n=4), Math1-Cre;Atr-loxP/loxP;p53-loxP/loxP (n=5), and Math1-Cre;p53-loxP/loxP (n=3), all run in 2 lanes

first: Patrick

last: Lang

first: Jeremy

last: Simon

first: Joel

middle: S

last: Parker


title: A sliding-bulge structure at the Dicer processing site of pre-miRNA regulates alternative Dicer processing to generate 5’-isomiRs (miR-203)

city: El Paso

first: Haoquan

last: wu

state: Texas

address: 5001 El Paso Dr

department: Biomedical Scienes

institute: Texas Tech Health Sciences Center El Paso

summary: 5’-isomiRs expand the repertoire of miRNA targets. However, how they are generated is not well understood. Here, we showed that, for some miRNAs in mammalian cells, 5’-isomiRs are generated by alternative Dicer processing by using miRNA offset RNAs (moRs) to determine Drosha cleavage sites in cells. In addition, we showed that in miR-203, alternative Dicer processing is regulated by a conserved sliding-bulge structure at the Dicer processing site, which allows the pre-miRNA molecule to fold into two different structures that are processed differently by Dicer. So far no RNA motif that slides to change conformation and alter a protein–RNA interaction has been reported. Thus, our study revealed a novel RNA motif that regulates 5’-isomiR generation in some miRNAs. It might also contribute to regulating protein–RNA interactions in other biological processes, since it takes only one point mutation to generate the sliding bulge, and there are a large number of different RNAs in the cell.

overall_design: Mutants as well as the wild type of pri-miR-203 were designed. They were constructed into pLL3.7 and transfected into 293FT cells. The small RNAs were then profiled with deep sequencing. Three independent profiling exprements (replicates) were included in the dataset. RNA sample from each mutant of each replicate was barcoded, multicomplexed and sequenced in a single run of illumina Miseq sequencing.

first: Hongming

last: Ma

last: Wu


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

overall_design: Examination of H3K4me3 in F1 generation (exposed to atrazine) and F3 generation (not exposed) testis tissue performed in two biological replicates per condition.


title: A sliding-bulge structure at the Dicer processing site of pre-miRNA regulates alternative Dicer processing to generate 5’-isomiRs (pre-miR-203)


title: RNA Seq analysis of neoblasts from Schmidtea mediterranea treated with RNAi against zfp1, p53, or unc22 to identify factors involved in neoblast differentiation.

first: Chris

last: Seidel

summary: Epidermis is essential for animal survival, providing both a protective barrier and cellular sensor to the external environment. Interestingly, the epidermes of different species show broad morphological and functional diversity yet it is unclear whether this diversity came from modification of an existing gene regulatory network or de novo innovation of new genes. Here we identify the transcriptional regulators underlying the differentiation program of planarian epidermal lineage. We classify Smed-p53 as the most upstream molecule in this transcriptional cascade, suggesting a potentially conserved role for this gene in epidermal differentiation similar to TP63 in vertebrates. Moreover, we find that homologs of Sox and Pax family transcription factors, Smed-soxP-3 and Smed-pax-5, act cooperatively to activate the expression of epidermal markers. Together, these data show that planarian epidermal differentiation is regulated by a combination of conserved elements (p53/p63), recruitment of a non-conventional transcription module (soxP-3/pax-5), and novel genes (prog); they also suggest that specialized adpatations, such as epidermal mucus-secretion, arise from complex changes to gene networks. This experiment aims to identify regulators involved in epidermal differentiation at the neoblast stage by using RNA Seq to examine transcriptional changes in neoblasts (X1 population) isolated from animals treated with zfp-1 or p53 dsRNA.

overall_design: Examine gene expression profiles of FACS sorted X1 stem cell population from adult flatworms after 6, 9, and 13 days of treatment with RNAi against either zfp1, p53, or an unc22 non-targeting control. The experiment was performed in quadruplicate, with one discarded as an outlier for low sequence yield, resulting in 35 samples.

first: Li-Chun

last: Cheng

first: Alejandro

last: Alvarado


title: Heritability and Reversibility of DNA Methylation Induced by in vitro Grafting between Brassica juncea and B. oleracea

city: Hangzhou

first: Liping

address: Yuhangtang road No.866

department: Vegetable science

institute: Zhejiang University

summary: We found that compared with the expression of siRNAs in leaves of TTT, 3284, 4789, and 6208 unique siRNAs were significantly up-regulated, and 3420, 3850, and 4245 unique siRNAs were significantly down-regulated in GS1, GS3, and GS5, respectively through the high-throughput sequencing of small RNAs

sample_organism:
Brassica juncea
Brassica juncea x Brassica oleracea

overall_design: Small RNA sequencing were performed in tuber mustard (TTT) and selfed progenies GS1, GS3, GS5 (GS=grafting-selfing, n=generations) of TTC [LI-LII-LIII, LI=outer layer of shoot apical meristem (SAM), LII=middle layer, LIII=inner layer, T=tuber mustard, C=red cabbage] was created by in vitro grafting between tuber mustard and red cabbage. Two biological replicates per sample combined 3 plants each

first: Liwen

last: Cao


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

first: Chunxiang

last: HAO


title: The cell type and dynamic complexity of the planarian epidermis is determined by both conserved and derived transcriptional regulators.


title: RNA Seq analysis of gene expression in Planaria at 24, 48, 72, and 96 hours after exposure to 6k rad of gamma irradiation.

summary: Epidermis is essential for animal survival, providing both a protective barrier and cellular sensor to the external environment. Interestingly, the epidermes of different species show broad morphological and functional diversity yet it is unclear whether this diversity came from modification of an existing gene regulatory network or de novo innovation of new genes. Here we identify the transcriptional regulators underlying the differentiation program of planarian epidermal lineage. We classify Smed-p53 as the most upstream molecule in this transcriptional cascade, suggesting a potentially conserved role for this gene in epidermal differentiation similar to TP63 in vertebrates. Moreover, we find that homologs of Sox and Pax family transcription factors, Smed-soxP-3 and Smed-pax-5, act cooperatively to activate the expression of epidermal markers. Together, these data show that planarian epidermal differentiation is regulated by a combination of conserved elements (p53/p63), recruitment of a non-conventional transcription module (soxP-3/pax-5), and novel genes (prog); they also suggest that specialized adpatations, such as epidermal mucus-secretion, arise from complex changes to gene networks. The purpose of this experiment is to identify genes associated with neoblasts (stem cells). Worms are exposed to 6k rad of gamma radiation, allowed to recover for 24, 48, 72, or 96 hours, and compared to the pre-cursor un-exposed population by RNA Seq to identify genes with decreased expression following radiation exposure.

overall_design: Examine gene expression in adult flatworms at 0, 24, 48, 72, or 96 hours after exposure to 6k rad of gamma irradiation. The experiment was performed in triplicate resulting in 15 samples.


title: Analysis of transcriptomes of naive CD4+ T cells, polarized under Th17 cell skewing conditions for 24h in presence or abscence of CK2 Inhibitor

city: Mainz

first: Tobias

last: Bopp

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center Mainz

summary: The goal of this study was to elucidate the transcriptional changes evoked by CK2 inhibition in developing Th17  cells

overall_design: Messenger RNA profiles of naive CD4+ T cells, FACS-purifed from spleens of C57BL6 mice and stimulated with plate-bound anti-CD3 and anti-CD28 for 24h under Th17 polarizing conditions in presence or abscence of CK2 inhbititors DMAT (1.5µM) or CX4945 (1µM) were generated by sequencing using Illumina MiSeq

first: Alexander

last: Ulges