title: Genome-wide analysis of embryonic gene epression in the absence of Prox1 compared to wild type

city: Newark

first: Melinda

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary: Overview:  We report here that gene expression in E13.5 wild type (WT) mouse lenses differs from the lenses of mice that conditionally lack the Prox1 transcription factor in the lens of their eyes (Prox1 cKO) as assayed by high throughput RNA sequencing (RNAseq).  The methodology outlined herein is similar to a previous RNAseq experiment from our lab (Manthey et al., 2014a)(Geo ascension: GSE 49949), and the filtering and processing criteria for this experiment was published as well.(Manthey et al., 2014b).  The mammalian lens is notable for its biased gene expression, where 90% of the observed protein is expressed by just 50 genes.  RNAseq was employed to sequence past these highly expressed lens structural genes and report the relative abundance of both high and low expression genes.   In this study we demonstrated that 642 genes were differentially expressed in the lenses of Prox1 cKOs as compared to WT lenses.  These data were analyzed using the DAVID biostatical analysis package and we found that the expression of lens specific proteins, as well as cytoskeletal genes and genes that regulated the cytoskeleton were expressed at lower levels in Prox1 cKOs.  This analysis showed that the expression of genes encoding extracellular matrix components and their regulators, as well as cell adhesion increased in Prox1 cKO lenses when compared to WTs.    Description of Filtering Criteria:  Our initial analysis identified 5,492 genes that were differentially expressed in Prox1 cKO lenses as compared to WTs as computed by Pair-wise qCML method exact tests with a Benjamini Hochberg false discovery rate correction greater than the threshold of P < 0.05.  As we described previously, there is significant variation in gene expression between inbred C57Bl/6 <har> and mice with a mixed background below a threshold of 2.5 fold.  For this reason we filtered out all genes whose differential expression was less than 2.5 fold.  We also wanted to filter out genes that were expressed at such low levels that they were unlikely to impact cellular function.  We restricted our list to those genes that were expressed at greater than 2 Reads per Kilobase per million reads (RPKM) in either WT or Prox1 cKO samples, a value which corresponds to approximately 1 mRNA molecule per cell.  The application of these filtering criteria resulted in narrowing our list to 642 genes that were likely to impact the Prox1 cKO lens phenotype.      Manthey, A. L., Lachke, S. A., FitzGerald, P. G., Mason, R. W., Scheiblin, D. A., McDonald, J. H. and Duncan, M. K. (2014a) 'Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development', Mech Dev 131: 86-110.  Manthey, A. L., Terrell, A. M., Lachke, S. A., Polson, S. W. and Duncan, M. K. (2014b) 'Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis', Genom Data 2: 369-374.

overall_design: RNA-Seq comparison of C57Bl/6 <har> wild type controls and Prox1 conditional knockout lenses at E13.5

first: Dylan

last: Audette

middle: K


title: Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

status: Public on Feb 05 2016

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

country: China

institute: Zhejiang University

type: Expression profiling by high throughput sequencing

summary: N1-Methyladenosine (m1A) is a prevalent post-transcriptional RNA modification, yet little is known about its abundance, topol- ogy and dynamics in mRNA. Here, we show that m1A is prevalent in Homo sapiens mRNA, which shows an m1A/A ratio of ~0.02%. We develop the m1A-ID-seq technique, based on m1A immunoprecipitation and the inherent ability of m1A to stall reverse tran- scription, as a means for transcriptome-wide m1A profiling. m1A-ID-seq identifies 901 m1A peaks (from 600 genes) in mRNA and noncoding RNA and reveals a prominent feature, enrichment in the 5' untranslated region of mRNA transcripts, that is dis- tinct from the pattern for N6-methyladenosine, the most abundant internal mammalian mRNA modification. Moreover, m1A in mRNA is reversible by ALKBH3, a known DNA/RNA demethylase. Lastly, we show that m1A methylation responds dynamically to stimuli, and we identify hundreds of stress-induced m1A sites. Collectively, our approaches allow comprehensive analysis of m1A modification and provide tools for functional studies of potential epigenetic regulation via the reversible and dynamic m1A methylation.

overall_design: Identification of m1A sites in human embryonic kidney cells. Comparisons of m1A profiles of wild type HEK293T with ALKBH3 knock out cell line reveals the ALKBH3 specific sites. Stress inducible m1A sites are also identified by comparing the profiles of untreated cells with stress treated cells.

first: Xiaoyu

last: Li

first: Chengqi

last: Yi


title: Genome-wide analysis of ADP-ribosylation by ADPr-ChAP reveals its association with chromatin after oxidative stress

status: Public on Feb 04 2016

city: Zurich

first: Michael

middle: O.

last: Hottiger

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin ADP-ribosylation regulates important cellular processes.  However, the exact location and magnitude of chromatin ADP-ribosylation are largely unknown.  A robust and versatile method for assessing chromatin ADP-ribosylation is therefore crucial for further understanding its function.  Here, we present a chromatin affinity precipitation method based on the high specificity and avidity of two well-characterized ADP-ribose binding domains to map chromatin ADP-ribosylation at the genome-wide scale and at specific loci.  Our ADPr-ChAP method revealed that in cells exposed to oxidative stress, ADP-ribosylation of chromatin scaled with histone density, with highest levels at heterochromatic sites and depletion at active promoters.  Furthermore, in growth factor-induced adipocyte differentiation, increased chromatin ADP-ribosylation was observed at PPARγ target genes, whose expression is ADP-ribosylation-dependent.  In combination with deep-sequencing and conventional ChIP, the established ADPr-ChAP provides a valuable resource for the bioinformatic comparison of ADP-ribosylation with other chromatin modifications and for addressing its role in other biologically important processes.

overall_design: Chromatin of untreated and H2O2-treated samples was pulled down with wild-type and R163A-mutant WWE domain. We performed ChAP followed by DNA-sequencinq of sheared chromatin from untreated cells enriched with wild-type RNF146 WWE domain to define the location of ADP-ribosylation in untreated cells, using the binding mutant as negative control. In addition, as oxidative stress is known to induce chromatin ADP-ribosilation, we include ChAP followed by DNA-sequencinq of sheared chromatin from H2O2-treated cells enriched with wild-type RNF146 WWE or the binding mutant.

first: Giody

last: Bartolomei

first: Mario

last: Leutert

first: Massimiliano

last: Manzo

first: Tuncay

last: Baubec

middle: O


title: Inverse relationship between microRNA-155 and -184 expression with increasing conjunctival inflammation during ocular Chlamydia trachomatis infection

city: london

first: Tamsyn

middle: Ruth

last: Derrick

address: keppel street

country: United Kingdom

institute: london school of hygiene and tropical medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Trachoma, a preventable blinding eye disease, is initiated by ocular infection with Chlamydia trachomatis (Ct). MicroRNA (miR) are post-transcriptional regulators of gene expression and play a major role in health and disease. We have investigated the miR profile during C. trachomatis infection of epithelial cells in vitro and in vivo during follicular trachoma with current C. trachomatis infection. Small RNA sequencing was carried out on human epithelial cells infected in vitro and on samples from five children with follicular trachoma with current Ct infection and five children with no evidence of clinical trachoma or infection. In vitro two strains of ocular Ct that differ in virulence, A2497 and isogenic plasmid-free A2497 were used to infect epithelial cell lines.  RNAseq results were confirmed by qPCR in six in vitro biological replicates and in 163 clinical samples. Differential miR expression was not detected in isolated epithelial cells infected in vitro at 48 hours post infection. HCjE cells, a conjunctival epithelial cell line, have markedly different miR background expression compared to Hep2 cells. The differing miR profiles of Hep2c and HCjE suggest caution should be used when extrapolating data from Hep2 cells to a tissue-specific clinical scenario. In follicular trachoma, miR-155, miR-150, miR-142, miR-181b, miR-181a, miR-342 and miR-132 were up-regulated during current Ct infection. MiR-4728 and miR-184 were down-regulated in follicular trachoma independent of Ct infection. In follicular trachoma, miR expression reflects development and regulation of the immune response during current Ct infection and a prolonged period of wound healing following Ct clearance.

overall_design: (1) miRNA sequencing of conjunctival swab samples from five individuals with trachomatous disease and five normal healthy control individuals. (2) miRNA sequencing of two cell lines (HCjE and Hep2) with three biological repeats of each of the following conditions: mock-infected, Chlamydia trachomatis strain A2497P- infected, and Chlamydia trachomatis strain A2497 infected

first: Anna

middle: R

last: Last

first: Sarah

middle: E

last: Burr

first: Chrissy

middle: H

last: Roberts

first: Meno

last: Nabicassa

first: Eunice

last: Cassama

first: Robin

middle: L

last: Bailey

first: David

middle: C

last: Mabey

first: Matthew

middle: J

last: Burton

first: Martin

last: Holland


title: Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells

status: Public on Feb 03 2016

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

country: France

institute: INSERM

summary: Differentiated macrophages can self-renew in tissues and expand long-term in culture, but the gene regulatory mechanisms that accomplish self-renewal in the differentiated state have remained unknown. Here we show that in mice, the transcription factors MafB and c-Maf repress a macrophage-specific enhancer repertoire associated with a gene network controlling self-renewal. Single cell analysis revealed that, in vivo, proliferating resident macrophages can access this network by transient down-regulation of Maf transcription factors. The network also controls embryonic stem cell self-renewal but is associated with distinct embryonic stem cell-specific enhancers. This indicates that distinct lineage-specific enhancer platforms regulate a shared network of genes that control self-renewal potential in both stem and mature cells.

overall_design: Chromatin marks H3K4me1, H3K27Ac, and transcription factors P300, PU.1, MafB and Flag-MafB were assessed by ChIP-Seq  in 3 different macrophage subtypes.

first: M

last: Sieweke

first: E

last: Soucie

first: A

last: Sidow


title: mRNA sequencing of Arabidopsis thaliana pdx3 mutants

status: Public on Feb 02 2016

city: Geneva

first: Teresa

middle: B.

last: Fitzpatrick

state: Geneva

address: 30, Quai Ernest Ansermet

department: Department of Botany and Plant Biology

institute: University of Geneva

summary: Arabidopsis mutants in the PMP/PNP oxidase PDX3 show abberant growth and development.RNA sequencing reveals strong induction of stress-related genes in pdx3, particularly those associated with biotic stress.

overall_design: Whole rosettes (21- days old) of three biological replicates of wild-type and pdx3-3 (SALK_054167C) and pdx3-4 (GK-260E03) mutants, all ecotype Col-0, were sequenced and a differential gene expression analysis was performed.

first: Maite

last: Colinas

middle: B


title: The Polycomb protein BMI1 induces an invasive gene expression signature in melanoma that promotes metastasis and chemoresistance.

city: Cambridge

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

country: USA

institute: MIT

summary: The epigenetic regulator BMI1 is upregulated in many human malignancies and has been implicated in cell migration, but the impact on autochthonous tumor progression is unexplored. Our analyses of human expression data show that BMI1 levels increase with progression in melanoma. We find that BMI1 expression in melanoma cells does not influence cell proliferation or primary tumor growth. In contrast, BMI1 levels are a key determinant of melanoma metastasis, whereby deletion impairs and overexpression enhances dissemination. Remarkably, BMI1’s pro-metastatic effect reflects enhancement of all stages of the metastatic cascade including invasion, migration, extravasation, adhesion and survival. Additionally, downregulation or upregulation of BMI1 induces sensitivity or resistance to BRAF inhibitor. Consistent with these pleiotropic effects, we find that BMI1 promotes widespread gene expression changes that encompass key hallmarks of the melanoma invasive signature,  including activation of TGFβ, non-canonical Wnt, EMT and EGF/PDGF pathways. Importantly, for both primary and metastatic melanoma samples, this BMI1-induced signature identifies invasive subclasses of human melanoma and predicts poor patient outcome. Our data yield key insights into melanoma biology and establish BMI1 as a compelling drug target whose inhibition would suppress both metastasis and chemoresistance.

overall_design: Three replicates of A375 BMI1 or GFP overexpressing cells.

first: Roberta

last: Ferretti

first: Arjun

first: Molly

last: McNamara

first: Jacqueline

middle: A

last: Lees


title: Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

status: Public on Feb 06 2016

city: East Lansing

first: Benli

last: Chai

state: Michigan

address: 567 Wilson Road Rm 2225 A

department: Center for Microbial Ecology

institute: Michigan State University

summary: Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.

overall_design: Four E.coli strains, laboratory strain K12 (MG1655),  a commensal model strain (IAI1), a soil-isolated strain (TW11588-Clade IV), and a freshwater-isolated strain (TW09308—Clade V) were used. Each strain was grown on a minimal growth medium (Ihssen and Egli, 2004) in three treatment modes: chemostat, batch, and starvation. Cells from batch culture were collected when reaching steady-state. For starvation, the medium flow was stopped during steady-state and bacteria were collected after 4 h.

first: Marius

last: Vital

first: Bjørn

last: Østman

first: James

last: Cole

first: Konstantinos

middle: T

last: Konstantinidis

middle: M

last: Tiedje


title: 5C Chromatin interactions in the Igh locus in B cell progenitors

city: Chicago

first: Amy

last: Kenter

address: 835 South Wolcott

department: Microbiology and Immunology

summary: These tracks include chromatin interaction data produced using the 5C (chromatin conformation capture carbon copy) method by the Kenter Lab located at the University of Illinois College of Medicine, Chicago, IL. These tracks show looping interactions across the Igh locus using alternating forward and reverse primer design scheme.  The 3C method uses formaldehyde crosslinking to covalently associate interacting chromatin segments in intact cells.  The cells are then lysed and chromatin is digested with the Hind III restriction enzyme. The digested fragments are ligated under dilute conditions to promote intra-molecular ligation. A genome-wide interaction library of ligation products corresponding to all possible chromatin interactions is produced by this method. In 5C assays, over 12,000 potential ligation products specific to the Igh locus are detected by PCR using multiplexed primer pairs. These studies have revealed three conserved topological sub-domains. Each topological folds encompasses a major VH gene family. The Pax5 transcription factor organizes the topological sub-domain that spans the VHJ558 gene family.  In the absence of Pax5, the distal J558 VH genes fail to associate with the proximal VH genes, thus providing an explanation for reduced VHJ558 gene rearrangements in Pax5-deficient pro-B cells.  We propose that Igh locus contraction is the cumulative effect of several independently controlled chromatin sub-domains that provide the structural infrastructure to coordinate optimal antigen receptor assembly (Montefiori et al. 2015).  We also note that the configuration of the 3’ end of the Igh locus spanning the CH region genes assumes a developmental stage specific configuration in pro-B cells that appreas to skew class switch recombination to specific isotypes.  This 3D spatial configuration is lost in resting splenic B cells that are capable of class switch recombination to all isotypes (Kumar et al. 2013).

overall_design:
The aim of this study was to create a comprehensive map of chromatin interactions spanning the entire 2.9 Mb Igh locus in murine embryonic fibroblasts (MEF), pro-B cells and resting splenic B cells.  5C primers follow an alternating pattern and were designed at HindIII restriction sites using the 5C primer design tools that are available online  (http://my5C.umassmed.edu) (Lajoie et al., 2009) and were previously reported (Kumar et al., 2013).  In this experimental scheme, 112 forward primers and 113 reverse primers were designed for all possible HindIII restriction fragments. This design allowed for the interrogation of many (but not all) restriction fragments, thus an unbiased interaction map across the locus and for potentially identifying new regulatory elements.  An alternating scheme of forward and reverse primers was also included for a gene desert on chromosome 5 using 24 forward and 25 reverse 5C primers for a total of 525 potential cis interactions. Primers settings were: U-BLAST: 3; S-BLAST: 80: 15-MER: 800; MIN_FSIZE: 1000; MAX_FSIZE: 15,000; OPT_TM: 65; OPT_PSIZE: 30. Several primers with somewhat relaxed parameters were included to provide a more complete coverage of the Igh locus. Currently, data for two biological replicates have been generated for murine embryonic fibroblasts (MEF), progentior B cells and resting splenic B cells spanning the murine Igh locus and a gene desert on chromosome 5 using high-throughput paired-end sequencing in the Illumina GAII platform. The 5C looping interactions that are detected in both the biological replicates are considered significant.
------------------------
Extremely long range chromatin loops link topological domains to facilitate a diverse  antibody repertoire   Lindsey Montefiori, Robert Wuerffel, Damian Roqueiro, Bryan Lajoie, Changying Guo, Tatiana Gerasimova, Supriyo De, William Wood, Kevin G. Becker, Job Dekker, Jie Liang, Ranjan Sen, and Amy L. Kenter, Cell Reports in press, 2015.
Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny.  Kumar, S., Wuerffel, R., Achour, I., Lajoie, B., Sen, R., Dekker, J., Feeney, A.J., Kenter, A.L., Genes Dev. 2013 Nov 15;27(22):2439-44. doi: 10.1101

first: Ranjna

last: Sen

first: Robert

last: Wuerffel


title: Effect of estrogen and selective estrogen receptor modulators on a mouse model of fallopian tube epithelia, an ovarian cancer precursor

status: Public on Feb 08 2016

first: Joanna

last: Burdette

state: IL

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

summary: The fallopian tube epithelium is one of the potential sources of high-grade serous ovarian cancer (HGSC). The use of estrogen only hormone replacement therapy increases ovarian cancer risk. Despite estrogen’s influence in OVCA, selective estrogen receptor modulators (SERMs) typically demonstrate only a 20% response rate. This low response could be due to a variety of factors including the loss of estrogen receptor signaling or the role of estrogen receptor signaling in different potential cell types of origin. The response of fallopian tube epithelium to SERMs is not known, and would be useful when determining therapeutic options for tumors that arise from this cell type, such as high-grade serous cancer. Using normal murine derived oviductal epithelial cells (mouse equivalent to the fallopian tube) estrogen receptor expression was confirmed and interaction with its ligand, estradiol, triggered mRNA and protein induction of progesterone receptor (PR).  The SERMs 4-hydroxytamoxifen, raloxifene and desmethylarzoxifene, functioned as estrogen receptor antagonists in the oviductal cells. Cellular proliferation and migration assays suggested that estradiol does not significantly impact cellular migration and increased proliferation in CD1, but not in FVB derived cell lines. Further, using RNAseq, the oviduct specific transcriptional genes targets of estrogen and 4-hydroxytamoxifen signaling were determined and validated. The RNA-seq revealed enrichment in proliferation, anti-apoptosis, calcium signaling and steroid signaling processes. Finally, the ER and PR receptor status of a panel of HGSC cell lines was investigated highlighting the need for better models of estrogen responsive HGSC cell lines.

overall_design: Murine oviductal epithelial cells from the FVB background were hormone starved for 48 hours (with a media change after 24 hours), then treated in triplicate with solvent control (DMSO) (0.1%), 1 nM 17-betaestradiol or 100 nM 4-hydroxytamoxifen for 24 hours. Following treatment, RNA was was isolated, libraries were prepped and sequenced using the Illumina HiSeq 2500 platform.

first: Georgette

last: Moyle-Heyrman

first: David

last: Davis

first: Matthew

last: Schipma


title: The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-Folate Therapy in Breast Cancer [ChIP-Seq]

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

country: Canada

institute: Université Laval

summary:
Reprogramming of cellular metabolism plays a central role in fuelling malignant transformation, and AMPK as well as the PGC-1α/ERRα axis are key regulators of this process. Intersection of gene expression and binding event datasets in breast cancer cells shows that activation of AMPK significantly increases the expression of PGC-1α/ERRα and promotes the binding of ERRα to its cognate sites. Unexpectedly, the data also reveal that ERRα, in concert with PGC-1α, negatively regulates the expression of several one-carbon metabolism genes resulting in substantial perturbations in purine biosynthesis. This PGC-1α/ERRα-mediated repression of one-carbon metabolism promotes the sensitivity of breast cancer cells and tumors to the anti-folate drug methotrexate. These data implicate the PGC-1α/ERRα axis as a core regulatory node of folate cycle metabolism and further suggest that activators of AMPK could be used to modulate this pathway in cancer.
We used microarrays to detail the global programme of gene expression following AMPK activation by AICAR in BT474 breast cancer cells.

overall_design: BT474 breast cancer cells were treated for 24h with vehicle or the AMPK activator AICAR and RNA was then purified for microarray analysis. Experiments were performed in duplicate for each condition.

last: Papadopoli


title: Humanized PRDM9 Mouse Testis H3K4me3 and DMC1 ChIP-seq

city: Berkeley

first: Nicolas

last: Altemose

state: CA

address: 327 Stanley Hall

department: Bioengineering

institute: University of California, Berkeley

type: Genome variation profiling by high throughput sequencing

summary: We report testis H3K4me3 and DMC1 enrichment at DSB hotspots in various mice to examine differences between infertile hybrid mice and mice that have been humanized at PRDM9, which have rescued fertility. We find that infertile mice have an excess of "asymmetric" DSB hotspots, where both H3K4me3 and DMC1 reads tend to originate from only one homologue. At these hotspots, we see an excess of DMC1 relative to H3K4me3, consistent with delayed DSB repair at these sites. See Davies et al. Nature 2016 for a complete summary.

overall_design: Examination of adult testis H3K4me3 and DMC1 enrichment in different mice. This Series contains a re-analysis of Sample GSM869781 submitted by another user. The dmc1hotspots_B6.PRDM9bb* processed data files are linked as supplementary files at the foot of this Series record.

first: Simon

last: Myers

first: Edouard

last: Hatton

first: Peter

last: Donnelly


title: Quantification of RNA editing in MEF cells of different genetic backgrounds with and without interferon treatment

city: Stanford

first: Gokul

last: Ramaswami

address: 300 Pasteur Drive Alway M305

institute: Stanford University

summary: We report the application of mmPCR-seq to mouse embryonic fibroblasts. We quantified RNA editing at 557 different loci using a microfluidic multiplex PCR method coupled with deep sequencing.

overall_design: RT-PCR amplification of 557 loci from 6 MEF lines with and without interferon treatment to quantify RNA editing levels.

first: Charles

last: Samuel


title: Genome-wide map of SOX2 occupancy in human ES cells (hESCs) and hESC derived neural progenitor cells (hNPCs)

city: Shanghai

first: Ying

last: Jin

address: 225 South Chongqing Road

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

summary: To compare the genome wide binding profiles of SOX2 in hESCs and hNPCs, we carried out SOX2 ChIP-seq in the two cell types and dissected the the cell type and stage dependent regulatory groups of SOX2, thus providing important information for the mechanism underlying SOX2's dynamic functions in hESCs and hNPCs.

overall_design: Comparative analysis of SOX2 genome-wide occupancy in hESCs and hNPCs

first: Chenlin

last: Zhou


title: Effect of Bmal1 post-natal knockout on liver gene expression: time-series

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

summary: Gene expression in the liver has been studied extensively in normal mice, but not in mice with circadian disruption. We use a tamoxifen-inducible Lox/Cre KO mouse strain with the most important clock gene knocked out, BMAL-1. The aim of this experiment was to study the effect of circadian disruption on gene expression in the liver by comparing conditional Bmal1 KO mice with WT mice using RNA-seq. All mice were housed under 12h:12h LD conditions with free access to food and water. Seven days after the last dose of tamoxifen, mice were kept under constant darkness for 36 h and then sacrificed. Four mice per genotype were sacrificed in darkness every 4h for 20h (6 time points). Illumina TruSeq RNA Sample Prep v2 was used for library construction and samples were sequenced on an Illumina HiSeq 2000. RNA-seq data were aligned by STAR, and data were normalized with a resampling strategy (https://github.com/itmat/Normalization).

overall_design: Time-series liver mRNA profiles of 4- to 6-month-old male wild type (WT) and Bmal1 knockout (KO) mice were generated by sequencing, four mice per genotype per timepoint, using Illumina HiSeq 2000.

first: Guangrui

last: Yang

first: Georgios

last: Paschos

first: Tilo

last: Grosser

first: Garret

last: FitzGerald

first: Lihong

last: Chen


title: Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components

city: Kansas City

first: Gaye

last: Hattem

state: Missouri

address: 1000 E. 50th Street

department: Proteomics

institute: Stowers Institute

summary: The Saccharomyces cerevisiae R2TP protein complex consists of Rvb1, Rvb2, Pih1 and Tah1. The R2TP complex has been implicated in various cellular processes such as assembly of snoRNP complex, RNA polymerase II complex, apoptosis and PIKK signaling. The involvement of R2TP in assembling various complexes seems to be in part due to Pih1 and Tah1, which serve as adapter/recruiter proteins. Here, we have performed high resolution RNA-seq. analyses to identify differential expression levels between wild type and PIH1 and TAH1 deletion strains of Saccharomyces cerevisiae that can help in unraveling other functions of Pih1 and Tah1. Both wild type and deletion strains contained TAP (tandem affinity purification) tag at the C-terminal end of either RVB1 or RVB2.

overall_design: 3 biological replicates were performed for each strains

first: Mahadevan

last: Lakshminarasimhan

first: Mike

middle: P

last: Washburn


title: Defining the molecular mechanisms underlying immunological memory in T cells (DNase-Hypersensitivity)

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

summary: Immunological memory is a defining feature of animal development, allowing rapid responses to repeat infections, yet the very basis of T cell-dependent memory remains poorly understood. Here we demonstrate that the critical steps in the acquisition of T cell memory occur not after completion of T cell differentiation but during the initial activation phase of naïve T cells, when extensive chromatin remodelling reprograms immune response genes towards a stably maintained primed state. During this process, inducible factors including AP-1 create hundreds of DNase I hypersensitive sites (DHSs), allowing the recruitment of ETS1 and RUNX1 to sites that were previously inaccessible. Significantly, these DHSs remain temporally and mitotically stable long after cessation of AP-1 activation, and function to maintain regions of active chromatin in the vicinity of genes that regulate immune responses. This priming enables increased accessibility and the accelerated induction of other inducible regulatory elements in previously activated T cells.

overall_design: Examination of DNAseI hypersensitivity patterns in naïve, blast, memory T-cells with or without PMA activation via DNase-Seq study.

first: Sarah

last: Bevington

first: Piper

last: Jason

first: Bertrand

last: Elizabeth

first: Lalli

last: Naveen

first: Sascha

last: Ott

first: Constanze

last: Bonifer

last: Cockerill


title: Defining the molecular mechanisms underlying immunological memory in T cells (ChIP-Seq)

overall_design: Examination of epigenetic patterns in naïve, blast, memory T-cells with or without PMA activation via ChIP-Seq study.

first: Peter


title: Defining the molecular mechanisms underlying immunological memory in T cells

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

overall_design: Refer to individual Series


title: Novel functional microRNAs from virus-free and infected Vitis vinifera plants under water stress.

city: Bari

first: Vitantonio

last: Pantaleo

address: Via Amendola 165/a

country: Italy

institute: Institute for Sustainable Plant Protection

summary: Size fractionated small RNA from total RNA extracts of Vitis vinifera leaves  were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit Please see www.illumina.com for details of the sequencing technology.

overall_design: Short RNA fractionation and characterization

first: Giorgio

last: Gambino


title: mRNA sequencing of the global effect of SOX2 on gene expression in hESC and hESC derived NPCs.

first: Ying

last: Jin

summary: Global transcriptome analysis reveals that SOX2 regulates a common group safeguarding stem cell identity in hESCs and hNPCs, and also distinct functional groups regulating diverse cell type dependent developmental processes in hESCs and hNPCs, sheding light on the mechanism underlying SOX2's dynamic function in the two related stem cell types.

overall_design: To analyze the global effect of SOX2 on gene expression in hESC and hNPC, we analyzed the gene expression profiles upon SOX2 KD in hESC and hNPC. Due to the compensation effect of SOX3 in hESC, we used non-targeting siRNA (siNT) and two sets of siRNAs targeting both SOX2 and SOX3 (siSOX2/3-1 and siSOX2/3-2)  to knock down both SOX2 and SOX3 in hESC and compared the gene expression profile between siNT and siSOX2/3 by RNA-seq. We also compared the gene expression profiles in hNPC treated with siNT and two SOX2 siRNAs (siSOX2-1 and siSOX2-2) by RNA-seq.

first: Chenlin

last: Zhou


title: A study of alterations in DNA epigenetic modifications (5mC and 5hmC) and gene expression influenced by simulated microgravity in human lymphoblastoid cells [meDIP-seq]

city: West Lafayette

first: Joseph

last: Irudayaraj

state: IN

address: 225 S. University Street

department: Bindley Bioscience Center

institute: Purdue University

type: Methylation profiling by high throughput sequencing

summary: Here, in this study we systematically examined the patterns of DNA methylation and hydroxy-methylation with its functional implications in gene regulation for the cultured TK6 lymphoblastoid cells upon exposure to micro-gravity conditions. theThe results reported here indicate that simulated microgravity alters methylation  patterns in a limited way  and subsequently the expression of genes involved in stress response like ATF3, FBXO17, MAP3K13 and VCL in TK6 cells.

overall_design: Examination of 2 different DNA modifications with 2 replicates each for 1 cell type

first: Basudev

last: Chowdhury

first: Zhiping

last: Wang

first: Arun

last: Seetharam

first: Jyothi

last: Thimmapuram

first: Yunlong

last: Liu

first: Amy

last: Lossie


title: A study of alterations in DNA epigenetic modifications (5mC and 5hmC) and gene expression influenced by simulated microgravity in human lymphoblastoid cells [RNA-seq]

summary: Here, in this study we systematically examined the patterns of DNA methylation and hydroxy-methylation with its functional implications in gene regulation for the cultured TK6 lymphoblastoid cells upon exposure to micro-gravity conditions. The results reported here indicate that simulated microgravity alters methylation  patterns in a limited way  and subsequently the expression of genes involved in stress response like ATF3, FBXO17, MAP3K13 and VCL in TK6 cells.

overall_design: Examination of RNA-seq with 2 replicates each for 1 cell type


title: Time course RNA-Seq of Innate Lymphoid Cells in Early Acute HIV Infection

city: Durban

first: Alasdair

last: Leslie

address: 719 Umbilo Road

country: South Africa

institute: African Health Research Institute

summary: We apply RNA-seq to limited populations of Innate Lymphoid Cells type 2 and type 3 (ILC2s and ILC3s, respectively) in human individuals infected with acute HIV in the FRESH study. We measured the whole transcriptome of ILC2s and ILC3s in both untreated (n=2) and ART treated (n=2) individuals over the course of infection, in order to compare these populations at key points during infection, namely: viral detection, peak viremia, and weeks past peak viremia (6-7 weeks post detection). Lacking true biological replicates, HIV- patients in the same study (n=9) were used as replicates to conduct Differential Expression (DE) analysis between time points in both ILC2s and ILC3s on a patient by patient basis. In untreated patients, ILC2s and ILC3s differentially expressed genes associated with apoptosis and cell death between peak viremia and viral detection, while ART treated patients' ILC2s and ILC3s demonstrated a mitigated response. Comparing 6-7 weeks after detection with peak viremia revealed a relative decrease in genes associated in cell death in untreated patients, while ART treated patients showed varied responses where several DE genes were associated with immune response.

overall_design: RNA-seq of two Innate Lymphoid Cell populations in 2 HIV+ untreated patients, 2 HIV+ ART treated patients, and 9 HIV- patients (control, replicates).

first: Henrik

middle: N

last: Kloverpris

first: Samuel

middle: W

last: Kazer

first: Alex

middle: K

last: Shalek

first: Bruce

middle: D

last: Walker

first: Thumbi

last: Ndung'u


title: The helix-loop-helix protein ID2 governs NK cell fate by tuning their sensitivity to interleukin-15

status: Public on Feb 01 2016

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary: The inhibitor of DNA binding 2 (Id2) is essential for NK cell development with its canonical role in this pathway being to antagonize E-proteins, silencing E-box gene expression and subsequent commitment to the T and B cell lineages. However, how E-box genes prevent NK cell development and homeostasis remains enigmatic. Here we identify a key role for Id2 in regulating the threshold for IL-15 receptor signaling and homeostasis of NK cells by repressing multiple E-protein target genes including Socs3. Deletion of Id2 in mature NK cells was incompatible with their homeostasis due to impaired IL-15 receptor signaling. Id2-null NK cells displayed impaired IL-15 mediated JAK1/STAT5 phosphorylation, compromised metabolic function and enhanced apoptosis. Remarkably, Id2-null NK cell homeostasis could be fully rescued in vivo by IL-15 receptor stimulation and partially rescued by genetic ablation of Socs3. During normal NK cell maturation we observed an inverse correlation between the expression levels of E-protein target genes and Id2. These results shift the current paradigm on the role of Id2, indicating that it is not only required to antagonize E-proteins during NK cell commitment, but constantly required to titrate E-protein activity to regulate NK cell fitness and responsiveness to IL-15.

overall_design: Transcriptional profiling of wild type and Id2-null natural killer (NK) cells using RNA sequencing

first: Rebecca

last: Delconte

first: Gabrielle

last: Belz

first: Sebastian

last: Carotta

first: Nicholas

last: Huntington


title: Targeted proteolysis of the histone H3 tail facilitates epigentic reporgramming during differentiation

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

summary: Though limited proteolysis of the histone H3 N-terminal tail (H3NT) is frequently observed during mammalian differentiation, however the specific genomic sites targeted for H3NT proteolysis and their functional significance of H3NT cleavage remain unknown.We used genome wide RNA-seq approaches to an established cell model of osteoclast differentiation. We discovered that H3NT proteolysis is selectively targeted near transcription start sites of a small group of genes and that most of these H3NT-cleaved genes are epigenetically regulated during osteoclastogenesis.We have identified that the principal H3NT protease of osteoclastogenesis is matrix metalloproteinase 9 (MMP-9). We next studied genomewide mRNA expression in MMP9 knockout cells and its effect in the epigenetic reprogramming of gene pathways required for proficient osteoclastogenesis.

overall_design: Differential expresssion profile of transcripts in wt and MMP9 knockout cells

first: Kyunghwan

last: Kim

first: Jin-Man

first: Sunyoung

last: Lee

first: Tobias

middle: S

last: Ulmer

first: Wange

last: Lu

first: Judd

last: Rice

first: Woojin

last: An


title: The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-Folate Therapy in Breast Cancer

first: Etienne

last: Audet-Walsh


title: Effects of Freeze-Thawing and Intravenous Infusion on Mesenchymal Stromal Cell Gene Expression

city: Rotterdam

first: Martin

last: Hoogduijn

address: 's-Gravendijkwal 230

country: Netherlands

institute: Erasmus MC

summary: Mesenchymal stromal cells (MSC) are increasingly used as an investigative therapeutic product for immune disorders and degenerative disease. Typically, MSC are isolated from human tissue, expanded in culture and cryopreserved until usage. The safety and efficacy of MSC therapy will depend on the phenotypical and functional characteristics of MSC. The freeze-thawing procedure may change these characteristics. Furthermore, the microenvironment that the cells encounter after administration may impact the properties of MSC. It has been demonstrated that the large majority of MSC localize to the lungs after intravenous infusion, making this the site to study the effects of the in vivo milieu on administered MSC. In the present study we investigated the effect of freeze-thawing and of the mouse lung microenvironment on human adipose tissue-derived MSC. The effect of freeze-thawing on the whole genome expression profile of MSC was small and did not exceed inter-donor differences. There were no major changes in the expression of hemostatic regulators on transcriptional level, but significantly increased expression of procoagulant tissue factor on the surface of thawed adipose MSC, correlating with increased procoagulant activity of thawed cells after blood exposure in vitro and after infusion to mice. Exposure for 2h to the lung microenvironment had a major effect on MSC gene expression and affected several immunological and metabolic pathways. This indicates that MSC undergo functional changes shortly after infusion and this may influence the efficacy of MSC to modulate inflammatory responses. The results of this study demonstrate that MSC rapidly alter in response to the local milieu and that disease specific conditions may shape MSC after administration.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 3 groups, n=3 per group + 1 negative control

first: Samantha

middle: F

last: de Witte

first: Franka

last: Luk

first: Mirjam

last: van den Hout - van Vroonhoven

first: Lech

last: Ignatowicz

first: Rusan

last: Catar

first: Tanja

last: Strini

first: Sander

last: Korevaar

first: Wilfred

last: van Ijcken

first: Michiel

middle: G

last: Betjes

first: Marcella

last: Franquesa

first: Guido

last: Moll

first: Carla

last: Baan


title: Differential RNA-seq analysis comparing APC-defective and APC-restored SW480 colorectal cancer cells

city: Parkville

first: Oliver

last: Sieber

state: VIC

address: 1G Royal Parade

institute: Walter and Eliza Hall Insitute of Medical Reseach

summary: Identify genes that are differentially regulated as a consequence of restoration of full-length functional APC in a colorectal cancer cell lines.

overall_design: Examine mRNA expression level changes between SW480 (APC defective) and SW480+APC (SW480 cells with restored functional APC) cells, whilst accounting for any non-specific expression changes by comparison to SW480+control vector.

first: Lauren

last: King

first: Christopher

last: Love

first: Maree

last: Faux

first: Antony

last: Burgess


title: Transcriptional regulation of the innate immune reponse by the MITF/TFE3 family

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

summary: To understand the activation of the MITF/TFE transcription factors in effective defense against pathogens we examined the genome wide distribution of TFE3 in control and activated mouse macrophages. It was determined that TFEB and TFE3 collaborate with each other to promote efficient autophagy induction, increased lysosomal biogenesis, and transcriptional upregulation of proinflammatory cytokines and key mediators of the inflammatory response.

overall_design: 4 samples were analyzed: Background Control, Control, Starvation, LPS

first: Rosa

last: Puertollano

first: Heba

last: Diab


title: Targeted proteolysis of the histone H3 tail facilitates epigenetic reprogramming during differentiation

first: Vasu

last: Punj

summary: Though limited proteolysis of the histone H3 N-terminal tail (H3NT) is frequently observed during mammalian differentiation, however the specific genomic sites targeted for H3NT proteolysis and their functional significance of H3NT cleavage remain unknown.We used genome wide  Chip-seq (ChIPac-Seq) approaches  to an  established cell model of osteoclast differentiation. We discovered that H3NT proteolysis is selectively targeted near transcription start sites of a small group of genes and that most of these H3NT-cleaved genes are epigenetically regulated during osteoclastogenesis.We also discovered that the principal H3NT protease of osteoclastogenesis is matrix metalloproteinase 9 (MMP-9).Abrogation of H3NT proteolysis impaired osteoclastogenic gene activation concomitant with defective osteoclast differentiation. In summary our  results support the necessity of MMP-9-dependent H3NT proteolysis in the epigenetic reprogramming of gene pathways required for proficient osteoclastogenesis.

overall_design: Genome wide study on the effect of H3NT (histone H3 N-terminal tail) cleavage using a ChIPac_seq.

first: Kyunghwan

last: Kim

first: Jin-Man

first: Sunyoung

last: Lee

first: Tobias

last: Ulmer

first: Wange

last: Lu

first: Judd

middle: C

last: Rice

first: Woojin

last: An


title: RNAseq data from in vitro-stimulated (6 hours) murine nfkb2fl/flCD19-Cre and CD19-Cre splenic B cells purified by magnetic cell separation (CD40)

city: New York

first: Ulf

last: Klein

state: NY

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University

summary: RNAseq analysis of CD40 in vitro-stimulated (6 hours) murine nfkb2fl/flCD19-Cre (furtheron designated as REL) and CD19-Cre (furtheron designated as WT) splenic B cells identifies genes regulated by the transcription factor NF-kB2 in activated B cells.

overall_design: Splenic B cells from 12-week old relfl/flCD19-Cre and CD19-Cre littermate mice were isolated by magnetic cell separation from splenic mononuclear cells and stimulated in vitro for 6 hours with anti-CD40 and anti-IgM. RNA was isolated and submitted for RNA-sequencing on an Illumina HiSeq2000 instrument for 30 million single-ended reads.

first: Nilushi

last: De Silva


title: Integrated stress response regulation by the MITF/TFE3 transcription factor family

summary: To reestablish homeostasis and mitigate stress, cells must activate a series of adaptive intracellular signaling pathways. To understand the activation of the MITF/TFE transcription factors in response to ER stress we exposed mouse embryonic fibroblasts to starvation and tunicamycin (used to induce ER stress).

overall_design: 4 samples were analyzed: Background Control, Control, Starvation, Tunicamycin


title: RNAseq data from in vitro-stimulated (6 hours) murine nfkb2fl/flCD19-Cre and CD19-Cre splenic B cells purified by magnetic cell separation (BAFF)

summary: RNAseq analysis of BAFF in vitro-stimulated (6 hours) murine nfkb2fl/flCD19-Cre (furtheron designated as REL) and CD19-Cre (furtheron designated as WT) splenic B cells identifies genes regulated by the transcription factor NF-kB2 in BAFF-stimulated B cells.

overall_design: Splenic B cells from 12-week old relfl/flCD19-Cre and CD19-Cre littermate mice were isolated by magnetic cell separation from splenic mononuclear cells and stimulated in vitro for 6 hours with BAFF. RNA was isolated and submitted for RNA-sequencing on an Illumina HiSeq2000 instrument for 30 million single-ended reads.


title: RNA-seq from L4 animals treated with RNAi against gfp (control), ham-3, and swsn-2.2

city: Hospitalet de Llobregat

first: Julián

last: Cerón

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals, planta 3

department: Cancer and Human Molecular Genetics

country: Spain

institute: IDIBELL

summary: Transcriptome analysis of a population of control gfp(RNAi) animals and  worms in which ham-3 or swsn-2.2 were partially inactivated by RNAi.

overall_design: Animals in all samples were synchronized at L1 stage, grown at 25C for 36 hours, and then harvested at L4 stage.

first: Iris

last: Ertl

last: Madrigal


title: Effect of Bmal1 pre-natal knockout on liver gene expression: time-series

first: Georgios

last: Paschos

address: 10-102 Translational Research Center, 3400 Civic Center Boulevard, Building 421

department: Pharmacology

institute: University of Pennsylvania, School of Medicine

summary: We use a conventional (pre-natal) Bmal1 KO (cKO) mouse strain to investigate the effect of circadian disruption on gene expression in the liver by comparing cKO mice with wild type (WT) mice using RNA-Seq. All mice were housed under 12h:12h LD conditions with free access to food and water. Three mice per genotype were sacrificed every 4 h for 20 h (6 time points). Illumina TruSeq Stranded mRNA Sample Prep Kit Set A was used for library construction and samples were sequenced on an Illumina HiSeq 2500. RNA-seq data were aligned by STAR, and data were normalized with a resampling strategy (https://github.com/itmat/Normalization).

overall_design: Time-series liver mRNA profiles of 6.4- to 13.9-week-old male and female wild type (WT) and Bmal1 knockout (KO) mice were generated by sequencing, three mice per genotype per timepoint, using Illumina HiSeq 2500.

first: Guangrui

last: Yang

first: Gregory

middle: R

last: Grant

first: Tilo

last: Grosser

first: Garret

last: FitzGerald


title: Core pathway mutations induce de-differentiation of murine astrocytes into glioblastoma stem cells that are sensitive to radiation, but resistant to temozolomide

city: Chapel Hill

first: Ryan

last: Miller

state: North Carolina

address: 6109B Neuroscience Research Building

institute: University of North Carolina - Chapel Hill

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

overall_design: Refer to individual Series


title: SATB2 expression increased anchorage-independent growth and cell migration in human bronchial epithelial cells

city: Tuxedo

first: Max

last: Costa

address: 57 Old Forge Road

department: Environmental Medicine

institute: New York University School of Medicine

summary: The special AT-rich sequence-binding protein 2 (SATB2) is a protein that binds to the nuclear matrix attachment region of the cell and regulates gene expression by altering chromatin structure.  We show that ectopic expression of SATB2 in normal human bronchial epithelial cell-line BEAS2B  increased anchorage-independent growth and cell migration,RNA sequencing analyses of SATB2 regulated genes revealed the enrichment of those involved in cytoskeleton, cell adhesion and cell-movement pathways.

overall_design: Total RNA samples from 2 vector transfected clonesand 2 SATB2 transfected were converted into cDNA libraries using a Tru-seq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA). Reads were aligned to Ensemble gene model (Homo_sapiens.GRCh37.71.gtf) using HTseq (0.6.1.p.1)

first: Feng

last: Wu

first: Ashley

last: Jordan

first: Thomas

last: Kluz

first: Steven

last: Shen

first: Hong

last: Sun

first: Laura

last: Cartularo


title: A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [zebrafish RNA-Seq]

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: We report gene expression data for FACS sorted zebrafish crestin_1kb:EGFP + cells collected at 15 somite stage (SS).

overall_design: crestin_1kb:EGFP + embryos were homogenized, filtered, and sorted using FACS into PBS, collecting ~5,500 EGFP (+) cells and 100K EGFP (-) cells with a single sample for each.

first: Charles

last: Kaufman

first: Song


title: A study of alterations in DNA epigenetic modifications (5mC and 5hmC) and gene expression influenced by simulated microgravity in human lymphoblastoid cells

first: Joseph

last: Irudayaraj


title: A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [human cell line RNA-seq]

summary: We report gene expression data for human melanoma cell lines using RNAseq.

overall_design: RNAseq was performed on 8 melanoma cell lines and one normal human melanocyte cell line.  All done as single replicates, except for two biological replicates of A375.


title: A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [zebrafish ChIP-seq]

summary: We report the distribution of H3K27Ac histone marks in a zebrafish melanoma cell line and a zebrafish primary melanoma tumor with the aim of identifying super-enhancer regions and regions of interest.  We also report sox10 ChIP-Seq on the same zebrafish melanoma cell line.

overall_design: Examination of H3K27Ac chromatin marks and sox10 binding in one zebrafish melanoma cell line.  Examination of H3K27Ac chromatin marks in one freshly isolated zebrafish primary melanoma tumor.


title: A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [human cell line ChIP-seq]

summary: We report the distribution of H3K27Ac histone marks in multiple human melanoma cell lines with the aim of identifying super-enhancer regions and regions of interest.  Also performed ChipSeq for H3K4Me1 to identify active enhancers in a representative human melanoma cell line, A375.

overall_design: Examination of H3K27Ac chromatin mark in 6 human melanoma lines. Examination of H3K4Me1 in one human melanoma cell line.


title: Core pathway mutations induce de-differentiation of murine astrocytes into glioblastoma stem cells that are sensitive to radiation, but resistant to temozolomide (RNA-seq)

summary: Introduction:  Glioma stem cells isolated from human glioblastomas are resistant to radiation and cytotoxic chemotherapy and may drive tumor recurrence. Treatment efficacy may depend on the presence of glioma stem cells, expression of DNA repair enzymes such as methylguanine methyltransferase (MGMT), or transcriptome subtype. Methods:  To model genetic alterations in the core signaling pathways of human glioblastoma, we induced conditional Rb knockout, Kras activation, and Pten deletion mutations in cortical murine astrocytes.  Serial neurosphere culture, multi-lineage differentiation, and orthotopic transplantation were used to assess whether these mutations induced de-differentiation of cortical astrocytes into glioma stem cells.  Efficacy of radiation and temozolomide was examined in vitro and in an allograft model in vivo.  The effects of radiation on transcriptome subtype was examined by expression profiling. Results:  G1/S-defective, Rb knockout astrocytes gained unlimited self-renewal and multi-lineage differentiation capacity, in both the presence and absence of Kras and Pten mutations.  Only triple mutant astrocytes formed serially-transplantable glioblastoma allografts.  Triple mutant astrocytes and allografts were sensitive to radiation, but expressed Mgmt and were resistant to temozolomide.  Radiation induced a shift in transcriptome subtype of glioblastoma allografts from proneural to mesenchymal. Conclusion:  A defined set of core signaling pathway mutations induces de-differentiation of cortical murine astrocytes into glioma stem cells.  This non-germline genetically engineered mouse model mimics human proneural glioblastoma on histopathological, molecular, and treatment response levels.  It may be useful in dissecting the genetic and cellular mechanisms of treatment resistance and developing more effective therapies.

overall_design: Investigation of chromatin accessibility in astrocytes and glioblastoma cell lines

first: Jeremy

last: Simon

first: Ralf

last: Schmid

first: C


title: The glutathione-disrupted biofilm of clinical Pseudomonas aeruginosa strains: enhanced antibiotic affect and a novel biofilm transcriptome

city: Sydney

first: Jim

last: Manos

state: NSW

address: Camperdown

institute: University of Sydney

summary: Pseudomonas aeruginosa infections for individuals with Cystic Fibrosis (CF), result in high morbidity and mortality, with premature death often occurring. These infections are complicated by the formation of biofilms in the sputum. Antibiotic therapy is stymied by antibiotic resistance of the biofilm matrix, making novel anti-biofilm strategies highly desirable. Within the P. aeruginosa biofilm, the redox factor pyocyanin enhances biofilm integrity by intercalating with extracellular DNA. The antioxidant glutathione (GSH) reacts with pyocyanin to disrupt intercalation. This study investigated GSH disruption by assaying the physiological effects of GSH and DNase I on  biofilms of clinical CF isolates grown in artificial CF sputum media (ASMDM+). Confocal scanning laser microscopy showed that 2mM GSH alone or combined with DNase I significantly disrupted the immature (24 hour) biofilms of Australian Epidemic Strain (AES) isogens AES-1R and AES-1M. GSH alone greatly disrupted the mature (72 hour) biofilm of AES-1R, resulting in significant differential expression of 587 genes, as evidenced by RNA-sequencing. Upregulated systems included cyclic diguanylate and pyoverdine biosynthesis, the Type VI secretion system, nitrate metabolism and translational machinery. Physiochemical biofilm disruption with GSH revealed a metabolically active cellular physiology distinct from either mature or dispersed biofilm physiology. RNA-seq results were validated by biochemical assay and qPCR. Biofilms of a range of CF isolates disrupted with GSH and DNase I were significantly more susceptible to ciprofloxacin, and increased antibiotic effectiveness was achieved at 10mM GSH. This study demonstrated that GSH alone or with DNase I represent effective anti-biofilm treatments when combined with appropriate antibiotics.

overall_design: Examination of the effects of 2mM glutathione (GSH) on the mature (72 hour) biofilms of P. aeruginosa strain AES-1R. 2 replicates control (1× PBS treated) 2 replicates 2mM GSH treated. RNA harvest 8 hours post-treatment.

first: William

last: Klare

first: Theerthankar

last: Das

first: Amaye

last: Ibugo

first: Edwina

last: Buckle

first: Mike

last: Manefield


title: A Dual Molecular Analog Tuner for Dissecting Mammalian Protein Function

first: avinash

last: waghray

address: 185 Cambridge Street, CPZN Room 4254A

department: Center for Regenerative Medicine

institute: Massachussets General Hospital

summary: Loss-of-function studies are fundamental for dissecting gene function. Yet, methods to rapidly and effectively perturb genes in mammalian cells are scarce. We present a novel system, deliverable with only two lentiviral vectors, which enables simultaneous control over two different proteins in the same cell. By harnessing the plant auxin and jasmonate hormone-induced degradation pathways, combined with RNA interference, this system allows constitutive depletion of two endogenous proteins and their replacement with two exogenous proteins whose degradation is rapidly and reversibly induced by external ligands, representing a dual analog molecular tuner. Focusing on NANOG, CHK1 and NOTCH1 in embryonic stem cells and p53 in cancer cells we have validated the efficiency, rapidity, reversibility, titratability and multiplicity of the engineered tuners, and demonstrated their potential to facilitate previously-unfeasible experimental approaches and to generate novel biological insights.

overall_design: For mRNA-Seq preparation, coronatine/DMSO treated cells were collected.

first: Ran

last: Brosh

first: Avinash

last: Waghray

first: Ihor

last: Lemischka


title: Transcriptome analysis of Brassica rapa near-isogenic lines carrying clubroot-resistant and -susceptible alleles in response to Plasmodiophora brassicae during early infection

city: Shenyang

first: Jingjing

last: Chen

state: Liaoning

address: #120  Dongling Road

department: Department of Horticulture

institute: Shenyang Agricultural University

summary: Although Plasmodiophora brassicae is one of the most common pathogens worldwide, the causal agent of clubroot disease in Brassica crops, resistance mechanisms to it are still only poorly understood. To study the early defense response induced by P. brassicae infection, a global transcriptome profiling of the roots of two near-isogenic lines (NILs) of clubroot-resistant (CR BJN3-2) and clubroot-susceptible (BJN3-2) Chinese cabbage (Brassica rapa) was performed by RNA-seq. Among the 42,730 unique genes mapped to the reference genome of B. rapa, 1,875 and 2,103 genes were found to be up- and down-regulated between CR BJN3-2 and BJN3-2, respectively, at 0, 12, 72, and 96 hours after inoculation (hai). Functional annotation showed that most of the differently expressed genes are involved in metabolism, transport, signal transduction, and defense. Of the genes assigned to plant-pathogen interactions, 151 showed different expression patterns between two NILs, including genes associated with pathogen-associated molecular patterns (PAMPs) and effectors recognition, calcium ion influx, hormone signaling, pathogenesis-related (PR) genes, transcription factors, and cell wall modification. In particular, the expression level of effector receptors (resistance proteins), PR genes involved in salicylic acid (SA) signaling pathway, were higher in clubroot-resistant NIL, while half of the PAMP receptors were suppressed in CR BJN3-2. This suggests that there was a more robust effector-triggered immunity (ETI) response in CR BJN3-2 and that SA signaling was important to clubroot resistance. The dataset generated by our transcriptome profiling may prove invaluable for further exploration of the different responses to P. brassicae between clubroot-resistant and clubroot-susceptible genotypes, and it will strongly contribute to a better understanding of the molecular mechanisms of resistance genes of B. rapa against P. brassicae infection.

overall_design: Root mRNA of thirty-day old clubroot-resistant and -susceptible NIL at 0,12 72 and 96 hours after inoculation of P. brassicae by RNA-seq

first: Wenxing

last: Pang

first: Bing

first: Chunyu

last: Zhang

first: Zhongyun

last: Piao


title: Allelic Series of Huntington's Disease Knock-in Mice Reveals Expression Discorrelates

city: Birmingham, AL

first: Peter

last: Detloff

state: AL

address: 720 20th Street South

department: Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: We report a simultaneous comparison of striatal mRNA levels by RNA sequencing mice with graded levels of HD-like abnormalities

overall_design: Examination of 4 different mouse lines

middle: J

first: David

last: Crossman


title: Gene expression profiling in metabolically heterogeneous human lung tumors

city: Dallas

first: Min

last: Ni

state: TX

address: 6000 Harry Hines Blvd

department: Children's Research Institute

institute: UT Southwestern Medical Center

summary: To investigate the impact of genetic and environmental factors that influence cancer cell metabolism in vivo, we conducted intra-operative 13C-glucose infusions in NSCLC patients. We determined that regional glucose metabolism was correlated with tumor perfusion as assessed by pre-surgical dynamic gadolinium enhancement.  Tumors or tumor regions showing high or low perfusion were collected and subjected to RNA-seq analysis.

overall_design: RNA-seq analysis was performed to evaluate gene transcriptional levels in human non-small cell lung cancer (NSCLC) tissues showing high or low perfusion as measured by dynamic contrast-enhanced (DCE) MRI.

first: Brandon

last: Faubert

first: Christopher

last: Hensley

first: Ralph

last: DeBerardinis


title: Core pathway mutations induce de-differentiation of murine astrocytes into glioblastoma stem cells that are sensitive to radiation, but resistant to temozolomide (FAIRE-seq)

first: Ryan

last: Miller

first: Jeremy

last: Simon

first: Ralf

last: Schmid

first: C


title: 7SK-BAF axis controls pervasive transcription at enhancers [icShape]

city: Stanford

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265

institute: Stanford University

summary: Eukaryotic genomes are extensively transcribed, but unfettered transcription alters gene expression and leads to genome damage by several means. Divergent transcription occurs at active enhancers and promoters, distinct classes of cis-regulatory elements critical for precise control of gene expression. A key step in RNA Polymerase II (Pol II) transcription is promoter-proximal pausing, which occurs bidirectionally ~25-60 nucleotides downstream of transcription start sites (TSS). Promoter-proximal pause release is gated by the positive transcription elongation factor b (P-TEFb)-7SK snRNA pathway; release from 7SK allows P-TEFb phosphorylation of Pol II and subsequent elongation. The 7SK small nuclear ribonucleoprotein (snRNP) is thought to reside in the nucleoplasm, but it has been suggested that 7SK could operate physically on chromatin. Notably, while enhancer transcription is one of the earliest steps of gene activation and some enhancer RNAs (eRNAs) participate in gene regulation, far less is known about the control of eRNA transcription. Here we show that 7SK inhibits enhancer transcription by modulating nucleosome position. 7SK occupies enhancers and super enhancers genome-wide, and 7SK is required to limit eRNA initiation and synthesis in a manner distinct from promoter pausing. Clustered elements at super enhancers uniquely require 7SK to prevent convergent transcription of colliding polymerases that lead to DNA damage. 7SK inhibits enhancer transcription by modulating chromatin structure, physically interacts with the BAF chromatin remodeling complex, and is required to recruit BAF to enhancers. In turn, 7SK occupancy at enhancers coincides with Brd4 and is exquisitely sensitive to the bromodomain inhibitor JQ1. Thus, 7SK employs distinct mechanisms to counteract diverse consequences of pervasive transcription that distinguish super enhancers, enhancers, and promoters.

overall_design: Each experiment was performed in at least biological duplicate with input or other controls when appropriate.

first: Brian

last: Do

first: Adam

last: Rubin

first: Eliezer

last: Calo

first: Byron

last: Lee

first: Hannes

last: Kuchelmeister

first: Michael

last: Rale

first: Ci

last: Chu

first: Eric

last: Kool

first: Joanna

last: Wysocka

first: Paul

last: Khavari

first: Howard

middle: Y

last: Chang


title: The effect of developmental transitions on small RNAs in Arabidopsis thaliana shoots

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: We were interested in changes in small RNA abundance changes in response to developmental transitions in Arabidopsis thaliana shoots, with special focus on vegetative phase change. We specifically wanted to separate the temporal changes in gene expression that result from vegetative phase change and those from flowering. Because of the close timing between the juvenile-to-adult and adult-to-reproductive developmental transitions in Arabidopsis grown under long day conditions, we used the late-flowering genotype FRI;FLC developed by the lab of Richard Amasino by introgressing the FRI allele from Sf-2 into the Col-0 genetic background, which is fri;FLC. For the early flowering genotype, we used FRI;flc-3, also developed by the Amasino lab by EMS-mutagenizing FRI;FLC, identifying early flowering mutants, and backcrossing multiple times to eliminate other EMS-induced mutations. The onset of vegetative phase change in FRI;FLC and FRI;flc-3 under our growth conditions was identical, but the progression was slower in FRI;FLC. By sequencing small RNAs from shoot apices at different time points and fully-expanded leaves at different positions on the shoot and comparing the results between the two genotypes, we were able to obtain a clear picture of changes in small RNA abundance in response to vegetative phase change and flowering in Arabidopsis. For the small RNA samples, we performed two replicates using two different indices in the 5'-adapter and ran each replicate pair on the same sequencing lane. For the cotyledon and leaf samples we only performed one replicate using the same index for all samples because we obtained significantly different results with the two adapters used for the shoot apices, preventing us from using them as true replicates.

overall_design: Genome-wide small RNA profiling was done by a home assembled version of Illumina's  2007 small RNA library sample preparation followed by high-throughput sequencing with Illumina's Genome Analyzer II platform.

first: R

last: Poethig

first: Matthew

last: Willmann

first: Kevin

last: McCormick


title: Isolation and characterization of a novel gammaherpesvirus from a microbat cell line

city: Rockville

first: Reed

last: Shabman

state: MD

address: 9704 Medical Center Dr

department: Viral Genomics

institute: J. Craig Venter Institute

summary: While employing deep sequencing and de novo assembly to characterize the mRNA transcript profile of a cell line derived from the microbat Myotis velifer incautus, we serendipitously identified mRNAs encoding proteins with a high level of identity to herpesviruses.  Next generation sequencing and de novo assembly of the viral genome from supernatants from Vero cells yielded a single contig of approximately 130 kilobases with at least 80 ORFs, predicted microRNAs and a gammaherpesvirus genomic organization.  Phylogenetic analysis of the envelope glycoprotein (gB) and DNA polymerase (POLD1) revealed similarity to multiple gammaherpesvirus, including those from as yet uncultured viruses of the Rhadinovirus genus that were obtained by deep sequencing of bat tissues.  Cumulatively, this study provides the first isolation and characterization of a replication competent bat gammaherpesvirus.

sample_organism:
Myotis velifer
Bat gammaherpesvirus 8

platform_organism:
Myotis velifer
Bat gammaherpesvirus 8

overall_design: This is a single RNA sample from a microbat cell line (ATCC CRL-6012).  Total RNA was harvested by Trizol extraction.  One microgram of material was purified by oligo dT to enrich for messenger RNA.  Standard Illumina library construction was performed and the sample was sequenced on the Illumina Genome Analyzer II (76bp single read data).  Following genome assembly and annotation, the dataset was imported into CLC Genomics Workbench (Version 8), where reads were mapped onto the novel Bat Gammaherpesvirus 8 (BGHV8) annotated genome to calculate the RPKM for each annotated CDS.  Mapped reads to this reference genome are provided.

first: Susmita

last: Shrivastava

first: Oliver

last: Attie

first: Ravi

last: Sachidanandam

first: Christopher

last: Basler


title: A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation [ATAC-Seq]

first: Leonard

last: Zon

state: MA

summary: We report the locations of accessible/open chromatin as assayed by ATAC-Seq on two zebrafish melanoma cell lines, zcrest 1 and zcrest 2.

overall_design: ATAC-Seq was performed on two independent zebrafish melanoma cell lines (50K cells per sample), one replicate of each.

first: Charles

last: Kaufman

first: Song

last: Yang


title: Differential expression in LNCaP cells expressing the wild-type androgen receptor (AR-WT) or the ligand-independent AR-V7 splice variant

city: STRASBOURG

first: Félicie

last: COTTARD

address: 1 place de l'Hôpital

institute: INSERM U1113


title: miRNA differential expression in LNCaP cells expressing the wild-type androgen receptor (AR-WT) or the ligand-independent AR-V7 splice variant

summary:
Constitutively active AR variants are truncated proteins lacking the c-terminal region containing the ligand binding domain (LBD) and the activation function 2 (AF-2).
The expression of these AR variants in CRPC was also associated with the resistance to novel therapies such as enzalutamide and abiraterone acetate.
These variants are also involved in tumor progression.

overall_design:
LNCaP cells were transduced with lentival particles for expression of AR-WT or AR-V7 for 72 hours in complete medium containing 10 nM DHT. Libraries were sequenced using the Illumina Hiseq2500 technology
The goal of this experiment was to delineate differential miRNA levels upon the expression of the AR-V7 in LNCaP cells compared with cells expressing the wild-type AR.

last: Cottard

first: Jocelyn

last: Céraline


title: The identificantion of novel miRNA targets in Arabidopsis thaliana shoots using genome-wide mapping of uncapped and cleaved transcripts (GMUCT) 2.0

summary: We were interested in identifying targets of novel putative miRNAs we identified from small RNA sequencing libraries of Arabidopsis shoots. The small RNA (smRNA) sequencing libraries were made to identify changes in abundance of specific smRNAs in response to developmental transitions in Arabidopsis thaliana shoots, with special focus on vegetative phase change. We specifically wanted to separate the temporal changes in gene expression that result from vegetative phase change and those from flowering. Because of the close timing between the juvenile-to-adult and adult-to-reproductive developmental transitions in Arabidopsis grown under long day conditions, we used the late-flowering genotype FRI;FLC developed by the lab of Richard Amasino by introgressing the FRI allele from Sf-2 into the Col-0 genetic background, which is fri;FLC. For the early flowering genotype, we used FRI;flc-3, also developed by the Amasino lab by EMS-mutagenizing FRI;FLC, identifying early flowering mutants, and backcrossing multiple times to eliminate other EMS-induced mutations. The onset of vegetative phase change in FRI;FLC and FRI;flc-3 under our growth conditions was identical, but the progression was slower in FRI;FLC. By sequencing small RNAs from shoot apices at different time points and fully-expanded leaves at different positions on the shoot and comparing the results between the two genotypes, we were able to obtain a clear picture of changes in small RNA abundance in response to vegetative phase change and flowering in Arabidopsis. We then used the remaining RNA to make genome-wide mapping of uncapped and cleaved transcripts (GMUCT) 2.0 libraries of a subset of our samples. GMUCT 2.0 allows you to identify RNAs that are 1) uncapped and in the process of 5’->3’ exonuclease degradation and 2) miRNA and siRNA-mediated cleavage products. We wanted to use these GMUCT 2.0 libraries to identify targets of novel putative miRNAs discovered by our smRNA sequencing, thereby supporting the idea that these novel putative miRNAs are in fact functional.

overall_design: Genome-wide uncapped and cleaved transcript profiling was done using GMUCT 2.0 library sample preparation followed by high-throughput sequencing with Illumina's TruSeq platform.


title: A new MCM modification cycle regulates DNA replication initiation

first: Xiaolan

last: Zhao

address: 430 East 67th Street, RRL 917D

department: Molecular Biology Program

institute: Memorial Sloan-Kettering Cancer Center

summary: The hexameric DNA helicase MCM (Mcm2-7) is a central regulatory target in eukaryotic replication. Chromatin-bound MCM is kept inactive during G1 phase and subsequently activated in S phase to initiate replication. During this transition, the only known chemical change on the Mcm2-7 proteins is the gain of multi-site phosphorylation that promotes recruitment of co-factors. As replication initiation is tied intimately to multiple biological cues, additional changes on these proteins can provide a second regulatory point. Here we describe a new MCM modification cycle mediated by SUMO that enables a negative regulation of replication initiation. We show that all MCM subunits undergo sumoylation upon loading at origins in G1 phase prior to MCM phosphorylation. Then bulk MCM sumoylation is lost as MCM phosphorylation rises. The pattern of MCM sumoylation suggests a negative role in replication. Indeed, increasing MCM sumoylation delays genome-wide replication initiation. Mechanistically, this is partly due to enhancing the recruitment of a conserved phosphatase that delays MCM phosphorylation and activation. By revealing a new MCM modification cycle and its role in replication, our findings suggest a new model, in which MCM sumoylation counterbalances kinase-based regulation to ensure accurate control of replication initiation.

overall_design: Two sets of samples at are included: 1) set 1 contains 4 reference  samples, collected at 0 min, 15 min, 30 min, 40 min post cdc7-4 release; 2) set 2 contains 4 mutant samples, collected at the same time point as the reference. Whole genome sequencing (Illumina HiSeq) was used to access the copy number change and origin firing in the these samples.

first: Lei

last: Wei

first: Tuo

last: Zhang

first: Jenny

last: Xiang


title: mRNA differential expression in LNCaP cells expressing the wild-type androgen receptor (AR-WT) or the ligand-independent AR-V7 splice variant

overall_design:
LNCaP cells were transduced with lentival particles for expression of AR-WT or AR-V7 for 72 hours in complete medium containing 10 nM DHT. Libraries were sequenced using the Illumina Hiseq2500 technology
The goal of this experiment was to delineate differential gene expression upon the expression of the AR-V7 in LNCaP cells compared with cells expressing the wild-type AR.


title: A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation

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

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Refer to individual Series


title: 7SK-BAF axis controls pervasive transcription at enhancers [GRO-Seq]

first: Ryan

last: Flynn

state: CA

summary: Eukaryotic genomes are extensively transcribed, but unfettered transcription alters gene expression and leads to genome damage by several means. Divergent transcription occurs at active enhancers and promoters, distinct classes of cis-regulatory elements critical for precise control of gene expression. A key step in RNA Polymerase II (Pol II) transcription is promoter-proximal pausing, which occurs bidirectionally ~25-60 nucleotides downstream of transcription start sites (TSS). Promoter-proximal pause release is gated by the positive transcription elongation factor b (P-TEFb)-7SK snRNA pathway; release from 7SK allows P-TEFb phosphorylation of Pol II and subsequent elongation. The 7SK small nuclear ribonucleoprotein (snRNP) is thought to reside in the nucleoplasm, but it has been suggested that 7SK could operate physically on chromatin. Notably, while enhancer transcription is one of the earliest steps of gene activation12 and some enhancer RNAs (eRNAs) participate in gene regulation, far less is known about the control of eRNA transcription. Here we show that 7SK inhibits enhancer transcription by modulating nucleosome position. 7SK occupies enhancers and super enhancers genome-wide, and 7SK is required to limit eRNA initiation and synthesis in a manner distinct from promoter pausing. Clustered elements at super enhancers uniquely require 7SK to prevent convergent transcription of colliding polymerases. 7SK inhibits enhancer transcription by modulating chromatin structure, physically interacts with the BAF chromatin remodeling complex, and is required to recruit BAF to enhancers. Thus, 7SK employs distinct mechanisms to counteract diverse consequences of pervasive transcription that distinguish super enhancers, enhancers, and promoters

middle: A

first: Brian

middle: T

last: Do

first: Adam

last: Rubin

first: Eliezer

last: Calo

first: Byron

last: Lee

first: Michael

last: Rale

first: Ci

last: Chu

first: Joanna

last: Wysocka

first: Paul

last: Khavari

first: Howard

last: Chang


title: Gene expression in TAL1-driven T-cell ALL in response to TAL1-KD, UTX-KD, and GSKJ4 treatment

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary: T-cell Acute Lymphoblastic Leukemia (T-ALL) is a heterogeneous group of hematological tumors composed of distinct subtypes that vary in their genetic abnormalities, gene expression signatures and prognoses. However, it remains unclear whether T-ALL subtypes differ at the functional level, and as such T-ALL treatments are uniformly applied across subtypes leading to variable responses between patients. Here we reveal the existence of a subtype-specific epigenetic vulnerability in T-ALL whereby a particular subgroup of T-ALL characterized by expression of the oncogenic transcription factor TAL1 is uniquely sensitive to variations in dosage and activity of the histone 3 lysine 27 (H3K27) demethylase UTX. Specifically, we identify UTX as a co-activator of TAL1. Furthermore, we demonstrate that UTX, previously described as a tumor suppressor in T-ALL, is in fact a potent oncogene essential for maintaining the leukemic phenotype of TAL1-positive (but not TAL1-negative) T-ALL. Exploiting this subtype-specific epigenetic vulnerability, we designed a novel therapeutic approach based on UTX inhibition through in vivo administration of an H3K27 demethylase inhibitor that is highly effective against TAL1-positive primary human leukemia. These findings provide the first opportunity to develop personalized epigenetic therapy for T-ALL patients.

overall_design: RNA-seq expression analysis (three treatments and matched controls; two replicates of each).

first: Marjorie

last: Brand

first: Aissa

last: Benyoucef

first: Christopher

last: Porter


title: Complete Haplotype Phasing of the MHC and KIR Loci with Targeted HaploSeq

city: La Jolla

first: Anthony

last: Schmitt

state: California

address: 9500 GILMAN DR., BLDG. CMME RM 2071

institute: UC San Diego

summary: Rapid advances in biochemical technologies have enabled several strategies for typing candidate HLA alleles, but linking them into a single MHC haplotype structure remains challenging. Here we have developed a multi-loci haplotype phasing technique and demonstrate its utility towards phasing of MHC and KIR loci in human samples. We accurately (~99%) reconstruct the complete haplotypes for over 90% of sequence variants spanning the 4-megabase region of these two loci. By haplotyping a majority of coding and non-coding alleles at the MHC and KIR loci in a single assay, this method has the potential to assist transplantation matching and facilitate investigation of the genetic basis of human immunity and disease.

overall_design: Complete haplotype phasing of 2 loci (MHC and KIR) in 1 human cell line.

first: Siddarth

last: Selvaraj

first: Bing

last: Ren


title: 7SK-BAF axis controls pervasive transcription at enhancers

first: Ryan

last: Flynn


title: Quantitative transcriptomics of pheromone biosynthetic midgut and fat body tissues in the mountain pine beetle, Dendroctonus ponderoase Hopkins

city: Quebec City

middle: Ian

last: Keeling

state: QC

address: 1055 rue du PEPS

department: Canadian Forest Service

institute: Natural Resources Canada

summary: Bark beetles (Coleoptera: Scolytinae) are pests of many forests around the world.  The mountain pine beetle (MPB), Dendroctonus ponderosae Hopkins, is a significant pest of western North American pine forests.  The MPB is able to overcome the defences of pine trees through pheromone-assisted aggregation that results in a mass attack of host trees.  These pheromones, both male and female produced, are believed to be biosynthesized in the midgut and/or fat body of these insects.  We have used transcriptomics (RNA-seq) to identify transcripts differentially expressed between sexes and between tissues, with juvenile hormone III treatment, which is known to induce pheromone biosynthesis.

overall_design: Anterior midgut and fat body mRNA profiles of emerged beetles of both sexes 8 h after juvenile hormone III or acetone control treatment were generated by deep sequencing, in quadruplicate, using Illumina paired-end sequencing.

middle: I

first: Maria

last: Li

first: Harpreet

last: Dullat

first: Hannah

last: Henderson

first: Macaire

middle: M

last: Yuen

first: Joerg

last: Bohlmann


title: Distinct epigenomes in CD4+ T cells of newborns, middle-ages and centenarians.

city: Shanghai

first: Hanqi

last: Yin

state: Shanghai

address: libing road 151

institute: shanghai biochip corporation

summary: To reveal dynamic changes in networks of gene expression and epigenetic regulation during healthy human T cell aging.

overall_design: Peripheral blood was obtained from 90 healthy newborn (0 y), 90 healthy middle-aged (age range from 40 to 55 years) and 90 long-lived subjects (age range from 90 to 110 years). The NB samples came from umbilical cord blood. 90 individuals from each age stage were distributed equally into 3 pools with identical male/female ratios. Peripheral blood mononuclear cells (PBMCs) were isolated from the pooled blood samples using density gradient centrifugation, and CD4+ T cells were isolated by positive selection using CD4 beads.

first: Ming

last: Zhao

first: Jian

last: Qin

first: Yixin

last: Tan

first: Wei

last: Liao

first: Qian

last: Liu

first: Shuangyan

last: Luo

first: Min

last: He

first: Gongping

last: Liang

first: Yajing

last: Shi

first: Qing

last: Zhang

first: Wenjun

last: Cai

first: Guangliang

first: Yin

last: Zhou

first: Jing

last: Wang

first: Mengying

first: Yi

last: Huang

first: Aiyun

first: Haijing

last: Wu

first: Zhiyong

first: Qianjin

last: Lu


title: T-cell ALL in response to TAL1-KD, UTX-KD, and GSKJ4 treatment

first: Theodore

last: Perkins


title: Effect of Asr1 RING mutation on the transcriptome of S. cerevisisae.

status: Public on Jan 31 2016

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

summary: This analysis identified 27 genes that are induced, and 29 that are repressed, by a factor of two or more in Asr1RING mutant cells. Genes in each category did not cluster according to gene ontology or chromosome, but we did notice that 33% of genes in the induced set lie within 50 kb of a telomere. In contrast, for repressed genes, only 7% were similarly telomere-proximal. The induction of subtelomeric gene expression in Asr1RING mutant cells suggests that the Ub-ligase activity of Asr1 may be required for authentic patterns of subtelomeric gene silencing.

overall_design: Transcriptome of WT and Asr1 RING mutant cells grown at log phase in enriched media.

first: William

last: Tansey

first: Tyler

last: McCann


title: Genome-wide analysis identifies Bcl6 repression of the IL-7R/STAT5 axis during T follicular helper (Tfh) cell differentiation

city: Beijing

first: Huiping

address: Tsinghua university

institute: Tsinghua university

summary: T follicular helper (Tfh) cell is a unique T cell subset specialized in promoting germinal center reactions. Bcl6 has been identified as an obligatory transcription factor in Tfh cells; however, the molecular mechanism underlying Bcl6 function still remains unknown. Here, we combined genome-wide Bcl6 occupancy and transcriptome profiling to systemically analyze Bcl6 targets in Tfh cells. We found that Bcl6 exhibits unique binding preferences in Tfh cells from those in Th9, B cells and macrophage and its binding is closely associated with decrease in 5-hydroxymethylcytosine (5hmC). Importantly, Bcl6 directly binds to the IL-7R/CD127 gene and suppresses its expression. Bcl6 also binds the same sequences recognized by signal transducer and activator of transcription (STAT) 5, downstream of IL-7R. Bcl6 promotes CD127loPDhi Tfh cell differentiation; deletion of the Bcl6 gene in T cells results in enhanced IL-7R-STAT5 signaling and substantial expansion of CD127hiPDlo non-Tfh cells. Our study thus systemically examines Bcl6-controlled regulatory networks and provides novel insights into its biological functions in Tfh cells.

overall_design: Examination of Bcl6 binding profile in Tfh cells.

first: Liu

last: Xindong

first: Lu

last: Huiping

first: Wei

last: Lai

first: Dong

last: Chen


title: Genome-wide map of SIX2 and SIX1 binding in human embryonic kidney cortex

city: Los Angeles

first: Andrew

middle: P

last: McMahon

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

summary: Nephron endowment is determined by the self-renewal and induction of a nephron progenitor pool established at the onset of kidney development. In the mouse, the related transcriptional regulators Six1 and Six2 play non-overlapping roles in nephron progenitors. Transient Six1 activity prefigures, and is essential for, active nephrogenesis. In contrast, Six2 maintains later progenitor self-renewal from the onset of nephrogenesis. We compared Six2’s regulatory actions in mouse and human nephron progenitors by chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq). Surprisingly, SIX1 was identified as a SIX2 target unique to the human nephron progenitors. Further, RNA-seq and immunostaining revealed overlapping SIX1 and SIX2 progenitor activity in the 16 week human fetal kidney. Human SIX1 ChIP-seq revealed a similar set of targets to SIX2, and predicted both factors bind DNA through an identical recognition site. In contrast to the mouse where Six2 binds its own enhancers but doesn’t interact with DNA around Six1, both human SIX1 and SIX2 bind homologous SIX2 enhancers and putative enhancers positioned around SIX1. Transgenic analysis of a putative human SIX1 enhancer in the mouse revealed a transient, mouse-like, pre-nephrogenic, Six1 regulatory pattern. Together, these data demonstrate a divergence in SIX-factor regulation between mouse and human nephron progenitors. In the human, an auto/cross-regulatory loop drives continued SIX1 and SIX2 expression during active nephrogenesis. In contrast, the mouse establishes only an auto-regulatory Six2 loop. It is tempting to speculate that differential SIX-factor regulation may contribute to species differences in the duration of progenitor programs and nephron output.

overall_design: Examination of SIX2, SIX1 binding profile in human embryonic kidney cortex and Six2 binding profile in mouse embryonic kidney using ChIP-Seq, with input DNA as negative control.

first: Lori

last: O'Brien

first: Qiuyu

first: Anton

last: Valouev


title: Gene expression data of allodiploid embryonic stem cells.

first: Xiaolong

last: Cui

address: No.1 Beichen West Road

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: RNA-Seq was used to assess the gene expression profiles of 4 allodiploid embryonic stem cell lines and 4 control embryonic stem cell lines. Moreover, single-cell RNA-Seq was used to quantify the transcriptomes of 87 allodiploid single cells.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Comparison of mRNA profiles of 4 allodiploid embryonic stem cell lines to 4 control mouse and rat embryonic stem cell lines using the Illumina HiSeq 2000 platform. Single-cell RNA-Seq was conducted to check the transcriptomes of single allodiploid embryonic and differentiated cells.

first: Xiu-Jie

first: Qi


title: Mastermind-like 3 controls proliferation and differentiation in neuroblastoma (RNA-seq)

city: Amsterdam

first: Prashanth Kumar

last: Bajpe

address: Plesmanlaan 121

department: Molecular Carcinogenesis

institute: Netherlands Cancer Institute

summary: Neuroblastoma cell lines can differentiate upon retinoic acid (RA) treatment, a finding that provided the basis for the clinical use of RA to treat neuroblastoma. However, resistance to RA is often observed, which limits its clinical utility. Using a gain-of-function genetic screen we identify the transcriptional coactivator Mastermind-like 3 (MAML3) as a gene whose ectopic expression confers resistance to RA. We find that MAML3 expression leads to loss of activation of a subset of RA target genes, which hampers RA-induced differentiation. The regulatory DNA elements of this subset of RA target genes show overlap in binding of MAML3 and the retinoic acid receptor, suggesting a role for MAML3 in the regulation of these genes. In addition, MAML3 has RA independent functions, including the activation of IGF1R and downstream AKT signaling via upregulation of IGF2, resulting in increased proliferation. Our results indicate an important role for MAML3 in differentiation and proliferation of neuroblastomas.

overall_design: RNA-seq of SK-N-SH control and MAML3 overexpressing (SD3.23) cells, either untreated (UT) or treated with 1 μM RA (RA).

first: Guus

last: Heynen

first: Ekaterina

last: Nevedomskaya

first: Andreas

last: Schlicker

first: Wilbert

last: Zwart

first: Rene

last: Bernards

first: Prashanth

middle: K


title: H3K27 methylation changes in Jurkat cells in response to TAL1-KD

first: Theodore

last: Perkins

overall_design: H3K27me3 ChIP-seq in two conditions (Wt and TAL1-KD), and one input sample (no replicates).

first: Marjorie

last: Brand

first: Aissa

last: Benyoucef

first: Christopher

last: Porter


title: Mastermind-like 3 controls proliferation and differentiation in neuroblastoma


title: UTX inhibition as selective epigenetic therapy against TAL1-driven T cell acute lymphoblastic leukemia

summary: We performed ChIP-Seq in Jurkat T-ALL cells to identify UTX binding sites across the genome. We then compared UTX binding sites (this study) with  TAL1 binding sites (Data from Palii, 2011 GSE25000), and found a high degree of overlap between TAL1 and UTX in Jurkat T-All cells. Indeed, over 80% of TAL1 binding sites overlap with UTX.

overall_design: Using ChIP-Seq, we identified UTX binding across the genome in Jurkat T-ALL cells. We then compared the binding sites of UTX and TAL1 (Data from Palii, 2011 GSE25000).

first: Carmen

last: Palii

first: Alphonse

last: Chu


title: Mastermind-like 3 controls proliferation and differentiation in neuroblastoma (ChIP-seq)

overall_design: Genome binding of MAML3 and RARalpha in SK-N-SH neuroblastoma cells treated and non-treated with retinoic acid


title: Nephron endowment

first: Andrew


title: RNA-Seq profiles of Drosophila melanogaster S3 cells treated with novel lipid storage inhibitors

city: Bethesda

first: Brian

last: Oliver

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: We performed mRNA transcriptional profiling on Drosophila S3 cells after 4 hours treatment with novel lipid storage inhibitors belonging to three different chemotypes.

overall_design: Profiling of RNA expression after treatment with three pairs of active/inactive compounds or DMSO as a control in triplicates and without treatment in the presence/absence of oleic acid in sextuplicate.

first: Kseniya

last: Golovnina

first: Zhen-Xia

last: Chen

first: Kirsten

last: Tschapalda

first: Mathias

last: Beller