title: Gene expression profiles of hypophysectomized male mouse liver treated with growth hormone and male and female livers from intact mice

first: David

summary: This SuperSeries is composed of the SubSeries listed below, and is part of a larger study, where we investigated the impact of a single pulse of GH given to hypophysectomized mice on local liver chromatin accessibility [DNase hypersensitive site analysis], transcription rates [hnRNA analysis], and gene expression [quantitative PCR and RNA-Seq] determined 30, 90 or 240 min later. The STAT5-dependent but sex-independent early GH response genes Igf1 and Cish showed rapid, GH pulse-induced increases in chromatin accessibility and gene transcription, reversing the effects of hypophysectomy. Rapid increases in liver chromatin accessibility and transcriptional activity were also induced in hypophysectomized male mice for some (Ces2b, Ugt2b38) but not for other liver STAT5-dependent male-biased genes (Cyp7b1). Moreover, in pituitary-intact male mice, Igf1, Cish, Ces2b and Ugt2b38 all showed remarkable cycles of chromatin opening and closing, and associated cycles of induced gene transcription, which closely followed each endogenous pulse of liver STAT5 activity. Thus, the endogenous rhythms of male plasma GH pulsation dynamically open and then close liver chromatin at discrete, localized regulatory sites in temporal association with transcriptional activation of Igf1, Cish and a subset of STAT5-dependent male-biased genes.

overall_design: Refer to individual Series


title: RNA-sequencing of human AML cells expressing high and low levels of CD99

status: Public on Feb 24 2017

city: New York

first: Stephen

middle: Shiu-Wah

last: Chung

state: NY- NEW YORK

address: 1275 York Avenue, Box 443

department: Leukemia Service

country: USA

institute: Memorial Sloan Kettering Cancer Center

type: Expression profiling by high throughput sequencing

summary: We FACS purified human AML cells based on CD99 expression and performed RNA-sequencing, demonstrating in CD99 high expression AML cells significant enrichment for hematopoietic stem cell and leukemic stem cell gene expression signatures.

overall_design: FACS purification of two populations (CD99 high and CD99 low) from eight primary AML specimens.

middle: S

first: Wenhuo

last: Hu

first: Christopher

middle: Y

last: Park


title: Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

type: Methylation profiling by high throughput sequencing

summary: Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during ageing and extends lifespan in diverse species including rodents and rhesus monkeys. However the mechanisms by which DR interacts with the ageing process to improve health at old age are poorly understood. DNA methylation could play an important role in mediating the effects of DR, because it is sensitive to the effects of nutrition and can affect gene expression memory over time. Here we have profiled genome-wide changes in DNA methylation, gene expression and lipidomics in response to DR and ageing in mouse liver. DR strongly retarded age-related changes in DNA methylation. With ageing, DNA methylation became confined to genic elements and was associated with reduced gene expression, particularly of genes involved in lipid metabolism.

overall_design: Total RNA and whole genome DNA-methylation profiles of liver tissue extracted from 5 months (young) and 26 months (old) dietary-restricted (DR) and control-fed (AL) F1 hybrid mouse strain (C3B6F1) were generated by deep sequencing using Illumina sequencing

first: Hahn

last: Oliver

first: Grönke

last: Sebastian

first: Stubbs

middle: M

last: Thomas

first: Ficz

last: Gabriella

first: Hendrich

first: Krueger

last: Felix

first: Andrews

last: Simon

first: Zhang

last: Qifeng

first: Wakelam

middle: J

last: Michael

first: Beyer

last: Andreas

first: Reik

last: Wolf

first: Partridge

last: Linda


title: Transcriptional response of human endocervical epithelial A2EN cells to infection with wild-type or CpoS-deficient Chlamydia trachomatis L2/434/Bu

city: Durham

first: Raphael

middle: H

last: Valdivia

state: NC

address: 207 Research Drive

department: Department of Molecular Genetics and Microbiology

institute: Duke University

summary: In a forward genetic screen we identified a Chlamydia trachomatis L2/434/Bu mutant that causes rapid apoptotic and necrotic death of infected host cells. This phenotype could be linked to the loss of the inclusion membrane protein CpoS. We observed a reduction in cell death when infections were carried out in the presence of cycloheximide or actinomycin D, suggesting that the engagement of cell death depends on host transcription and protein synthesis. We applied RNA-Seq to study the transcriptional response of human endocervical epithelial (A2EN) cells to infection with wild-type or CpoS-deficient bacteria. At 6 hpi the transcriptional profiles of cells infected with the two strains were similar to each other and to the transcriptome of uninfected cells. However, by 18 hpi the transcriptional profile of cells infected with the mutant was strongly altered, with 400 host genes being upregulated greater than two-fold. Among those differentially expressed genes, we observed an enrichment of immunity-related genes, including in particular cytokine genes and interferon-stimulated genes. Overall these data demonstrate that the CpoS-deficient mutant induces an exacerbated interferon response.

overall_design: mRNA profiles of uninfected human A2EN cells, A2EN cells infected with wild-type C. trachomatis L2/434/Bu, and A2EN cells infected with CpoS-deficient  C. trachomatis L2/434/Bu were analyzed at 6 hpi and at 18 hpi. The experiment was conducted in triplicate resulting in a total number of 18 samples.

first: Barbara

last: Sixt

first: Robert

last: Bastidas

first: Ryan

last: Finethy

last: Baxter

first: Victoria

middle: K

last: Carpenter

first: Guido

last: Kroemer

first: Jörn

last: Coers


title: RNAseq and ribosome profiling of yeast cells grown under methionine restriction condition.

city: San Francisco

first: Jiashun

last: Zheng

department: Biochemistry and Biophysics

institute: UCSF

summary: We characterize the translational and transcriptional programs induced by MetR and investigate the potential mechanisms through which methionine regulates gene expression, using the budding yeast S. cerevisiae as the model organism. Using ribosomal profiling and RNA-seq, we systematically compared the translational and transcriptional profiles of cells growing in the normal and methionine restricted media. We observed a broad spectrum of gene expression changes in response to MetR, including hundreds of genes whose transcript level and/or translational efficiency changed significantly. These genes fall into specific functional classes that are informative of the physiological state of the cell under MetR. Analysis of ribosome loading patterns of genes with increased translational efficiency suggested mechanisms both similar and different from the canonical model of translational regulation by general amino acid starvation. Analysis of the genes with decreased translational efficiency added support to the thiolation model of translational regulation by methionine. Since MetR extends the lifespan of many species, the list of genes we identified in this study can be good candidates for studying the downstream effectors of lifespan extension.

overall_design: The initial cell culture was incubated in 300 ml SD medium overnight to an OD600 0.8~1.0, then diluted by five fold using fresh SD media and incubated for another 4 hours under 30oC to an OD600 0.8~1.0. The sample was then divided equally into two aliquots. Cells were separated from the media by spin-down at 3000 g for 5 minutes and re-suspended in SD and MetR media respectively. All samples were incubated for another hour before harvesting. All the steps were carried out at 30°C. Raw sequences were obtained from Illumina Hiseq 2000.

first: Ke

last: Zou

first: Hao

last: Li


title: Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [RNA-seq]

status: Public on Feb 25 2017

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

summary: In mammals, DNA methylation occurs mainly at 5mC of CpG dinucleotides. The methylation on the promoter leads to the suppression of gene expression, while the functional role of gene body DNA methylation in highly expressed genes has yet to be clarified. Here, we show that the Dnmt3b-dependent intragenic DNA methylation protects the gene body from RNA Polymerase II (RNA Pol II) spurious entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that loss of Dnmt3b leads to an increase of the RNA Pol II engagement within gene bodies and spurious intragenic transcription initiation events. Furthermore, inhibition of RNA Pol II spurious entry depends on the enzymatic activity of the Dnmt3b recruited by H3K36me3. Thus, elongating RNA Pol II triggers an epigenetic crosstalk that involves SetD2, H3K36me3, Dnmt3b, and DNA methylation to ensure gene transcription initiation fidelity with implications for intragenic hypomethylation in cancer.

overall_design: Genome-wide analysis of Dnmt3b role in mouse ESCs using RNA-seq.

first: Salvatore

last: Oliviero


title: ASXL1 Interacts with the Cohesin Complex to Maintain Chromatid Separation and Gene Expression for Normal Hematopoiesis [RNA-Seq]

city: Miami

first: Peng

last: Zhang

state: FL

address: 1011 NW 15th Street

institute: University of Miami Miller School of Medicine

summary: ASXL1 is frequently mutated in a spectrum of myeloid malignancies with poor prognosis. Loss of Asxl1 leads to myelodysplastic syndrome-like disease in mice, however, the underlying molecular mechanisms remain unclear. Here, we report that ASXL1 interacts with the cohesin complex, which has been shown to guide sister chromotid segregation and to regulate gene expression. Loss of Asxl1 impairs the cohesin function as reflected by an impaired telophase chromatid disjunction in hematopoietic cells. ChIP-seq data revealed that ASXL1, RAD21 and SMC1A share 93% of genomic binding sites at promoter regions in lineage-cKit+ (LK) cells. We have showed that loss of Asxl1 reduced the genome binding of RAD21 and SMC1A, and altered the expression of ASXL1/cohesin target genes in LK cells. Our study underscores the ASXL1-cohesin interaction as a novel means to maintain normal sister chromatid separation and to regulate gene expression in hematopoietic cells.

overall_design: The DEG genes' relation with the changes of ASXL1 peaks and Cohesin peaks changes

first: Zhaomin

first: Feng-Chun

last: Yang


title: ASXL1 Interacts with the Cohesin Complex to Maintain Chromatid Separation and Gene Expression for Normal Hematopoiesis [ChIP-Seq]

type: Genome binding/occupancy profiling by high throughput sequencing


title: Whole transcriptome sequencing of the human thyroid primary cells with knock-down of the FOXE1 gene

city: Columbus

first: Yanqiang

last: Wang

state: Ohio

address: 12th w street

institute: The Ohio State University

summary: FOXE1 gene (also known as thyroid transcription factor 2) has been reported to be essential for thyroid gland development and the maintenance of thyroid differentiated status. Current knowledge of FOXE1 regulated genes is mostly based on the expression and functional studies using cell line models. Here we report gene expression profiles of human thyroid primary cells on Day 5 treated with FOXE1 siRNA or nontarget siRNA. The primary cells were generated from fresh nontumorous thyroid tissues obtained from thyroid cancer patients. A number of new dysregulated genes of FOXE1 were discovered, including THBS1 and IGFBP3, which have not been reported as FOXE1 regulated genes before. This study reveals a novel role of FOXE1 in downstream gene regulation and provides a new explanation of FOXE1’s function in thyroid cancer.

overall_design: Profiling of 3 human thyroid primary cells (generated from 3 different patient samples) transfected with FOXE1 siRNA (75pmol) or with nontarget siRNA (75pmol) was performed using RNA-seq. Cells were cultured for 24h after transfection and then lysed prior to RNA isolation, DNase treatment, purification and RNA-seq library construction. SRA Study accession number is SRP076757 and BioProject accession number is PRJNA326158.

first: Albert

last: de la Chapelle


title: Early Chronological Aging in Human Adipose-Derived Stem Cells Marked by Distinct Transcriptional Regulation Compared to Differentiated Cells

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

summary: Aging is a complex process characterized by a progressive decline in physiological integrity that leads to impaired cellular and tissue function.  Adult stem cells play a critical role in organismal health and aging. Their age-related deterioration contributes to a reduced homeostatic and regenerative capacity. Notably, most studies of stem cell aging focus on the mechanisms of replicative aging in stem cells with high cellular turnover. Yet, the therapeutic potential of stem cells with low cellular turnover, such as adipose-derived stem cells (ASC), is increasingly recognized as potentially superior. The mechanism of aging in low turnover stem cells is thought to differ from those with high turnover and to more closely reflect chronological aging. The latter, however, is exceedingly difficult to study in slowly replicating primary human stem cells and thus remains poorly understood.  Here, we employ our unique model of chronological aging in primary human ASCs to examine genome-wide transcriptional networks in early chronological aging using RNA-seq analyses.  Our findings demonstrate that the transcriptome of aging ASCs is more stable than that of age-matched fibroblasts. Limited transcriptional modifications in aging ASCs reveal more active transcriptional profiles of cell cycle genes and translation initiation genes when compared with aging differentiated cells.  Accordingly, nascent protein synthesis, measured by incorporation of op-puromycin, is increased in ASCs from older individuals, concurrent with a decreased phosphorylation at ser-51 of eIF2, a mechanism of inhibiting translation initiation.  A shortened G1 phase observed in the old ASCs could be linked to the increased protein synthesis activity, potentially resulting in more active cell proliferation.  This effect, however, is not detected in aging fibroblasts.  The altered regulation of cell cycle in aging ASCs could allow a more active cell proliferation to meet an increase demand to preserve tissue and organ functions.  These observations are consistent with data supporting the maintenance of ASC integrity in aging human adipose tissue and reveal early chronological aging mechanisms in ASCs that are inherently different from other cell types.

overall_design: Examination of the transcriptome with RNA-seq in stem cells and fibroblasts

first: Xiaoyin

last: Shan

first: Cleresa

last: Roberts

first: Eun Ji

last: Kim

first: Arianna

last: Brenner

first: Ivona

last: Percec


title: Comparative transcript profiling of fertile and sterile flower buds from multiple-allele-inherited male sterility in Chinese Cabbage (Brassica campestris L. ssp. pekinensis)

status: Public on Feb 23 2017

city: Shenyang

first: xue

last: zhou

state: Liaoning

address: No. 120, Dongling Road, Shenhe District

department: Department of Horticulture

country: China

institute: Shenyang Agricultural University

summary: We studied the causes of sterility underlying multiple-allele-inherited male sterility in Chinese cabbage by identifying differentially expressed genes (DEGs) related to pollen sterility between fertile and sterile flower buds. In this work,we performed transcriptome analysis of mRNA isolated from fertile and sterile buds using Illumina HiSeq 2000 platform sequencing. Approximately 80% of ~229 million high quality paired-end reads were uniquely mapped to the reference genome. In sterile buds, 699 genes were significantly up-regulated and 4,096 genes were down-regulated. Among the DEGs, 28 pollen cell wall-related genes, 53 transcription factor genes, 45 phytohormone-related genes, 20 anther and pollen-related genes, 212 specifically expressed transcripts (SETs), and 417 DEGs located in linkage group R07 were identified. Six transcription factor genes BrAMS, BrMS1, BrbHLH089, BrbHLH091, BrAtMYB103, and BrANAC025, were identified as putative sterility-related genes. The weak auxin signal that is regulated by BrABP1 may be one of the key factors causing pollen sterility observed here. Moreover, several significantly enriched GO terms “cell wall organization or biogenesis” (GO:0071554), “intrinsic to membrane” (GO:0031224), “integral to membrane” (GO:0016021), “hydrolase activity, acting on ester bonds” (GO:0016788) and one significantly enriched pathway “starch and sucrose metabolism” (ath00500) were obtained in this work. qRT-PCR and in situ hybridization validated that our RNA-seq transcriptome analysis was accurate and reliable. This study will lay the foundation for elucidating the molecular mechanism(s) underlying sterility, and provide valuable information for studying multiple-allele-inherited male sterility in Chinese cabbage line ‘AB01’.

overall_design: Fertile and sterile flower buds of the GMS line ‘AB01’ were generated by deep sequencing, using Illumina Hiseq 2000 platform; each treatment had three biological replicates.

first: Hui

last: Feng

first: Xue

last: Zhou


title: EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas

status: Public on Feb 28 2017

city: Copenhagen

first: Faizaan

last: Mohammad

state: Choose A State

address: Ole Maaloøs vej 5 Fourth Floor

country: Denmark

institute: BRIC

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: ASXL1 Interacts with the Cohesin Complex to Maintain Chromatid Separation and Gene Expression for Normal Hematopoiesis


title: γH2AX-ChIP-Seq in cells depleted for the telomeric protein TRF2

city: Nice

first: Olivier

last: Croce

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

summary: We show the enrichment of yH2AX in BJ-HELT cells when the telomeric protein TRF2 is downregulated (siTRF2 minus siControl). We generated genome-wide maps of the enriched profile of reads and found an accumulation of yH2AX reads at the pericentromeric regions of chromosomes and at large regions of chromosomes 3, 8, 11 and 16.

overall_design: Identification of yH2AX-rich regions after TRF2 inhibition

first: Aaron

last: Mendez-Bermudez

first: Eric

last: Gilson


title: Expression data from HUVEC

city: Hong Kong

first: Alice

middle: Sze Tsai

last: Wong

address: 4S-14 Kadoorie Biological Sciences Building, University of Hong Kong, Pokfulam Road

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

summary:
The expression profile of HUVEC in response to IgG or HECD-1 treated exosomes
We used data from this array to identify differentiatly expressed genes.

overall_design: RNA extracted form HUVEC treated with IgG / HECD-1 exosomes, processed for Affymetrix microarray analysis.

first: Maggie

last: Tang


title: Gene expression profile (RNA-seq) of hypophysectomized male mouse liver treated with a single pulse of growth hormone (GH)

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: We investigated the effects of a single pulse of growth hormone on the transcriptional activation of STAT5 target genes in hypophysectomized male mouse liver. This GEO series is part of a larger study, where we investigated the impact of a single pulse of GH given to hypophysectomized mice on local liver chromatin accessibility [DNase hypersensitive site analysis], transcription rates [hnRNA analysis], and gene expression [quantitative PCR and RNA-Seq] determined 30, 90 or 240 min later. The STAT5-dependent but sex-independent early GH response genes Igf1 and Cish showed rapid, GH pulse-induced increases in chromatin accessibility and gene transcription, reversing the effects of hypophysectomy. Rapid increases in liver chromatin accessibility and transcriptional activity were also induced in hypophysectomized male mice for some (Ces2b, Ugt2b38) but not for other liver STAT5-dependent male-biased genes (Cyp7b1). Moreover, in pituitary-intact male mice, Igf1, Cish, Ces2b and Ugt2b38 all showed remarkable cycles of chromatin opening and closing, and associated cycles of induced gene transcription, which closely followed each endogenous pulse of liver STAT5 activity. Thus, the endogenous rhythms of male plasma GH pulsation dynamically open and then close liver chromatin at discrete, localized regulatory sites in temporal association with transcriptional activation of Igf1, Cish and a subset of STAT5-dependent male-biased genes.

overall_design: Liver RNA was isolated from untreated hypophysectomized male mice and from hypophysectomized male mice treated with a single pulse of GH and euthanized 30, 90 or 240 minutes later. 8 Individual RNA samples were pooled to make 2 biological replicates per condition for RNA-seq analysis.

first: Jeannette

last: Connerney

first: Dana

last: Lau-Corona

first: Andy

last: Rampersaud


title: Next gen RNA sequencing of canine hemangiosarcoma

city: Minneapolis

first: Nuri

middle: Alpay

last: Temiz

state: MN

address: 2231 6th St SE

department: Masonic Cancer Center

institute: University of Minnesota

summary: Transcriptome analysis of hemangiosarcoma samples were performed to assess EGFR and PLAUR/uPAR expression profiles  and compare to human tumors from TCGA.  Abstract  Sarcomas differ from carcinomas in their mesenchymal origin. Therapeutic advancements have come slowly so alternative drugs and models are urgently needed. These studies report a new drug for sarcomas that simultaneously targets both tumor and tumor neovasculature. eBAT is a bispecific angiotoxin consisting of truncated, deimmunized Pseudomonas exotoxin fused to epidermal growth factor (EGF) and the amino terminal fragment (ATF) of urokinase. Here, we study the drug in an in vivo “ontarget” companion dog trial since eBAT effectively kills canine hemangiosarcoma (HSA) and human sarcoma cells in vitro. We reasoned the model has value due to the common occurrence of spontaneous sarcomas in dogs and a limited lifespan allowing for rapid accrual and data collection. Splenectomized dogs with minimal residual disease were given one cycle of eBAT followed by adjuvant doxorubicin in an adaptive dose-finding, phase I- II study of 23 dogs with spontaneous, stage I-II, splenic HSA. eBAT improved 6-month survival from <40% in a comparison population to ~70% in dogs treated at a biologically active dose (50 μg/kg). Six dogs were long-term survivors, living >450 days. eBAT abated expected toxicity associated with EGFR-targeting, a finding supported by mouse studies. Urokinase plasminogen activator receptor (uPAR) and EGFR are targets for human sarcomas, so thorough evaluation is crucial for validation of the dog model. Thus, we validated these markers for human sarcoma targeting in the study of 212 human and 97 canine sarcoma samples. Our results support further translation of eBAT for human patients with sarcomas and perhaps other EGFR-expressing malignancies.

overall_design: Dog hemangiosarcomas sequenced using HiSeq 2000

first: Jaime

middle: F

last: Modiano

middle: A


title: The methylome of Alu repeats in human stem cells

city: Badalona

first: Miguel

middle: A.

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

summary: Next Generation Sequencing of Unmethylated Alu (NSUMA) interrogation of more than 130,000 individual Alus for differential methylation with concomitant analysis of copy number variations applied to the study of hypomethylation in human stem cells and during differentiation.

overall_design: hESC, colorectal cancer cell lines, iPSC, keratinocyte derived cell lines

first: Mireia

last: Jordà

first: Berta

last: Martín

first: Sergi

last: Lois

first: Izaskun

last: Mallona

first: Anna

last: Díez-Villanueva

first: MJ

last: Barrero


title: Next gen RNA sequencing of canine lymphoma

summary: Transcriptome analysis of lymphoma samples were performed to assess EGFR and PLAUR/uPAR expression profiles and compare to human tumors from TCGA. Abstract  Sarcomas differ from carcinomas in their mesenchymal origin. Therapeutic advancements have come slowly so alternative drugs and models are urgently needed. These studies report a new drug for sarcomas that simultaneously targets both tumor and tumor neovasculature. eBAT is a bispecific angiotoxin consisting of truncated, deimmunized Pseudomonas exotoxin fused to epidermal growth factor (EGF) and the amino terminal fragment (ATF) of urokinase. Here, we study the drug in an in vivo “ontarget” companion dog trial since eBAT effectively kills canine hemangiosarcoma (HSA) and human sarcoma cells in vitro. We reasoned the model has value due to the common occurrence of spontaneous sarcomas in dogs and a limited lifespan allowing for rapid accrual and data collection. Splenectomized dogs with minimal residual disease were given one cycle of eBAT followed by adjuvant doxorubicin in an adaptive dose-finding, phase I- II study of 23 dogs with spontaneous, stage I-II, splenic HSA. eBAT improved 6-month survival from <40% in a comparison population to ~70% in dogs treated at a biologically active dose (50 μg/kg). Six dogs were long-term survivors, living >450 days. eBAT abated expected toxicity associated with EGFR-targeting, a finding supported by mouse studies. Urokinase plasminogen activator receptor (uPAR) and EGFR are targets for human sarcomas, so thorough evaluation is crucial for validation of the dog model. Thus, we validated these markers for human sarcoma targeting in the study of 212 human and 97 canine sarcoma samples. Our results support further translation of eBAT for human patients with sarcomas and perhaps other EGFR-expressing malignancies.

overall_design: Dog lymphomas sequenced using HiSeq 2000


title: The LIM protein AJUBA promotes colorectal cancer cell survival through suppression of JAK1/STAT1/IFIT2 network

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary:
Background and Aims: The LIM protein AJUBA participates in the regulation of cell adhesion, mitosis, DNA damage, cell differentiation, proliferation, migration and gene transcription, yet its roles in tumor development and progression are poorly defined. The aim is to determine the role of AJUBA in colorectal tumorigenesis.
Methods:  We performed data mining in Oncomine databases and immunohistochemistry (IHC) assays on 67 paired colorectal cancer (CRC) samples; we manipulated the AJUBA expression in SW-1116 and Caco-2 cells using specific shRNA and overexpression plasmids and performed assays for cell viability, cell cycle and apoptosis; we performed RNA-seq and qRT-PCR assays to identify genes regulated by AJUBA; we performed western blot, co-immunoprecipitation assays to study the interaction of AJUBA and JAK/STAT;
Results: We discovered that AJUBA is highly expressed in CRC and promotes CRC cell growth in culture and in xenograted mice via an inhibition of apoptosis by repression of the IFIT2 gene. AJUBA specifically binds the FERM domain of JAK1 to dissociate JAK1 from the IFNγ recepter, resulted in inhibition of STAT1 phosporylation and concomitantly its nuclear translocation.  Clinically, the level of AJUBA in CRC specimens is negatively correlated with the levels of IFIT2 and pSTAT1.
Conclusion: Ajuba functions as a specific suppressor of the Interferon-activated JAK1/STAT1 signaling to promote colorectal cancer development via an inhibition of Interferon induced apoptosis.

overall_design: RNA-seq assays to identify genes regulated by AJUBA in SW-1116 cancer cell lines. SW-1116-AJUBA OE and SW-1116-Vector cells were used for sequencing.

first: Zhaoyuan

last: Hou

first: Hao

last: Jia

first: Zhiguang

last: Li

first: Xuehong

last: Zhang


title: Canine tumors

overall_design: Refer to individual Series


title: Bayesian bisulphite sequencing analysis reveals changes in macrophage DNA methylation in glomerulonephritis

city: Singapore

first: Enrico

last: Petretto

address: 8 College Road, Level 8

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke‐NUS Graduate Medical School

summary: DNA methylation is one of the key epigenetic modifications involved in gene regulation. While whole-genome bisulfite sequencing (WGBS) allows the genome-wide quantification of DNA methylation at the single-base pair resolution, the contribution of DNA methylation in disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to accurately detect differentially methylated regions (DMRs) from WGBS data, and employ ABBA to map DNA methylation changes in disease. ABBA enables the genome-wide modeling of single-base resolution DNA methylation data, automatically adapting to different correlation structures in CpG methylation across the genome without requiring user-defined parameters and accounts for covariates and non-genetic confounding factors. First, we demonstrate the approach by an extensive simulation study and benchmarked ABBA against recently proposed alternative methods. We show the better performance of ABBA across a range of relevant parameters, including sequencing depth, number of replicates and noise level originating from incomplete bisulfite conversion. Second, we generated WGBS data from primary macrophages derived from an experimental rat model of glomerulonephritis and control rats, and employed ABBA to identify DMRs (>1,000 at 5% FDR) genome-wide that were associated with disease susceptibility. Investigation of the DMRs revealed differential DNA methylation localized to the promoter of the Ifitm3 gene and comparisons with existing DMR detection methods shows the enhanced interpretability of the results provided by ABBA. Additional ChIP-seq and RNA-seq analyses in the same experimental system showed differential transcription factor binding at the Ifitm3 promoter by JunD (an established determinant of glomerulonephritis) and consistent differential expression of Ifitm3. Taken together, these data suggest a role for DNA methylation alteration of the Ifitm3 gene in the pathogenesis of glomerulonephritis, and provide a proof of concept of using ABBA for differential methylation analysis of WGBS data.

overall_design: Whole-genome bisulfite sequencing of primary bone marrow-derived macrophages (BMDMs) from two rat strains (WKY and Lewis) were generated using the HiSeq 2000 platform. Four biological replicates per strain were used

first: Owen

last: Rackham

first: Sarah

last: Langley

first: Thomas

last: Oates

first: Eleni

last: Vradi

first: Nathan

last: Harmston

first: Prashant

last: Srivastava

first: Jacques

last: Behmoaras

first: Petros

last: Dellaportas

first: Leonardo

last: Bottolo


title: Next-gen RNA sequencing of dog osteosarcoma tumors

first: Nuri

last: Temiz

summary: Trascriptome analysis of osteosarcoma samples were performed

overall_design: Tumor samples were obtained from Rottweilers and Golden Retrievers with proper consents,  cell lines were derived from privious primary tumors and sequenced using Illumina HiSeq 2000

first: David

last: Largaespada

first: Jaime

last: Modiano

first: Subbaya

last: Subramanian

first: Logan

middle: G

last: Spector

first: Aaron

last: L. Sarver


title: Cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer-Independent (4C-seq)

city: Saint Louis

first: Eugene

last: Oltz

state: Missouri

address: 660 Euclid Ave, Campus Box 8118

department: Pathology & Immumonolgy

institute: Washington University in St Louis

summary: Alterations in distal regulatory elements that control gene expression underlie many diseases, including cancer. Epigenomic analyses of normal and diseased cells have produced correlative predictions for connections between dysregulated enhancers and target genes involved in pathogenesis. However, with few exceptions, these predicted cis-regulatory circuits remain untested. Here, we dissect cis-regulatory circuits that lead to overexpression of NEK6, a mitosis-associated kinase, in human B cell lymphoma. We find that only a minor subset of predicted enhancers is required for NEK6 expression. Indeed, an annotated super-enhancer is dispensable for NEK6 overexpression and for maintaining the architecture of a B cell-specific regulatory hub. A CTCF cluster serves as a chromatin and architectural boundary to block communication of the NEK6 regulatory hub with neighboring genes. Our findings emphasize that validation of predicted cis-regulatory circuits and super-enhancers is needed to prioritize transcriptional control elements as therapeutic targets.

overall_design: Interaction profiles for subclones harboring NEK6 CE1 or CS2-4 wild-type and deletion alleles of GM12878 were generated by deep sequencing, using Illumina Hi-Seq 2500.

first: Jacqueline

middle: E

last: Payton

first: Yue

last: Huang


title: Cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer-Independent


title: Cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer-Independent (RNA-seq)

overall_design: Expression profiles of NEK6 SE1 wild-type and deletion subclones of GM12878 were generated by deep sequencing, using Illumina Hi-Seq 2500.


title: Transcription control by the ENL YEATS domain in acute leukemia [RNA-seq]

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Recurrent chromosomal translocations involving the mixed lineage leukemia gene (MLL) give rise to highly aggressive acute leukemia associated with poor clinical outcomes. The preferential involvement of chromatin-associated factors in MLL rearrangements belies a dependency on transcriptional control. To identify new targets for therapeutic development in MLL, we performed a genome-scale CRISPR-Cas9 knockout screen in MLL-AF4 leukemia.  Among validated targets, we identified the transcriptional regulator, ENL, as an unrecognized dependency particularly indispensable for proliferation. To explain the mechanistic role for ENL in leukemia pathogenesis and the dynamic role in transcription control, we pursued a chemical genetic strategy utilizing targeted protein degradation. ENL loss suppresses transcription initiation and elongation genome-wide, with pronounced effects at genes featuring disproportionate ENL load. Importantly, ENL-dependent leukemic growth was contingent upon an intact YEATS epigenomic reader domain. These findings reveal a novel dependency in acute leukemia and a first mechanistic rationale for disrupting YEATS domains in disease.

overall_design: RNA-seq in MV4;11 (Cas9; ENL-FKBP(F36V); ENL -/-) cells with dTAG-13 and EPZ-5676 treatment

first: Michael

last: Erb


title: Transcription control by the ENL YEATS domain in acute leukemia [ChIP-seq]

overall_design: ChIP-seq samples in MV411 and MOLM13 acute leukemia cell lines.


title: Epithelial membrane protein 2 (EMP2) deficiency alters placental angiogenesis mimicking features of human intrauterine growth restriction.

city: LA

first: Madhuri

last: Wadehra

address: 675 Charles Young Dr. South/ 4726 MRL

department: Pathology and Lab Medicine

institute: UCLA

summary: Epithelial membrane protein-2 (EMP2) is a tetraspan protein predicted to regulateplacental development.  Highly expressed in secretory endometrium and trophectoderm cells, previous studies suggest that it may regulate implantation by orchestrating the surface expression of integrins and other membrane proteins. In order to confirm the role of EMP2 in pregnancy, mice lacking EMP2 (Emp2-/- ) were generated.  These animals are fertile but have reduced litter sizes. Moreover, their placentas exhibit dysregulation in pathways related to neoangiogenesis, coagulation, and oxidative stress, and have increased fibrin deposition and altered vasculature.  Given that these findings often occur due to placental insufficiency resulting in an oxygen-poor environment, expression of hypoxia-inducible factor-1 alpha (HIF-1α) was examined. Emp2-/- animals have reduced HIF-1α expression within cells of trophoblast origin. However, they appear to have a compensatory increase in uterine NK (uNK) cells, demonstrating a unique interplay between uNK cells and trophoblasts modulated through EMP2. To determine if these results translated to human pregnancy, placentas from normal, term deliveries or those complicated by intrauterine growth restriction (IUGR) were stained for EMP2.  EMP2 was significantly reduced in both villous and extravillous trophoblast populations in IUGR placentas. Experiments in vitro using human trophoblast cells lines indicate that EMP2 modulates angiogenesis by altering HIF-1a expression. Our results reveal a novel role for EMP2 in regulating trophoblast function and vascular development in conditions of altered oxygen availability in mice and humans and suggest it may be a novel biomarker for placental insufficiency.

overall_design: Day 13.5 placental tissue was isolated from Emp2+/+ and Emp2-/- animals and snap-frozen. Total RNA from each tissue was extracted using theRNAeasy kit (Qiagen. 3 samples per group were subjected to Illumina sequencing using the UCLA Pathology and Laboratory Medicine Core.  Libraries for RNA-seq were prepared with KAPA Stranded RNA-Seq Kit.

first: Carmen

last: Williams

first: Alison

last: Chu

first: Wendy

middle: N

last: Jefferson

last: Casero

first: Deepthi

last: Sudhakar

first: Claire

middle: P

last: Hogue

first: Nevil

last: Khurana

first: Priya

last: Patel

first: Peggy

last: Sullivan

first: Elizabeth

last: Padilla-Banks

first: Shabnam

last: Mohandessi

first: Carla

last: Janzen


title: Transcription control by the ENL YEATS domain in acute leukemia


title: ENL Links Histone Acetylation to Oncogenic Gene Expression in AML

city: Grand Rapids

first: Hong

last: Wen

state: Michigan

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: Cancer cells are characterized by aberrant epigenetic landscapes and often exploit the chromatin machinery to activate oncogenic gene expression programs1. The recognition of modified histones by “reader” proteins constitutes a key mechanism underlying these processes; therefore targeting such pathways holds clinical promise, as exemplified by the recent development of BET bromodomain inhibitors2,3. We recently identified the YEATS domain as a novel acetyllysine-binding module4, yet its functional importance in human cancer remains unknown. Here we show that the YEATS domain-containing protein ENL, but not its paralog AF9, is required for disease maintenance in a variety of acute myeloid leukaemias (AML). CRISPR-Cas9 mediated depletion of ENL led to anti-leukemic effects, including increased terminal myeloid differentiation and suppression of leukaemia growth in vitro and in vivo. Biochemical and crystal structural studies in vitro and ChIP-seq analyses in leukaemia cells revealed that ENL binds to acetylated histone H3, and colocalizes with H3K27ac and H3K9ac on the promoters of actively transcribed genes that are essential for leukaemias. Disrupting the interaction between the YEATS domain and histone acetylation via structure-based mutagenesis reduced RNA polymerase II recruitment on ENL target genes, thus leading to suppression of oncogenic gene expression programs. Importantly, disruption of ENL’s functionality further sensitized leukaemia cells to BET inhibitors. Together, our study identifies ENL as a histone acetylation reader that regulates oncogenic transcriptional programs in AML and suggests that displacement of ENL from chromatin is a promising epigenetic therapy alone or in combination with BET inhibitors for AML

overall_design: ENL_Flag, POL2, POL2S2P, H3K9ac, H3K27ac, H3K79me2, H3K79me3 ChIP-seq for MOLM13, MV411, HeLa and OCI-AML2 cells.

first: Yuanxin

last: Xi

first: Liling

last: Wan

first: Jie

last: Lyu


title: Mapping Gene Expression in Excitatory Neurons During Hippocampal Late-Phase Long-term Potentiation

city: Los Angeles

first: Patrick

last: Chen

address: 615 Charles E. Young Dr. S.

department: Biological Chemistry

summary: The long-lasting changes in synaptic connectivity that underlie long-term memory require new RNA and protein synthesis for their persistence. To elucidate the temporal pattern of gene expression that gives rise to long-lasting, learning-related neuronal plasticity, we profiled RNAs in mouse hippocampal CA3-CA1 slices following induction of late phase long-term potentiation (LTP), analyzing differential expression (DE) specifically within pyramidal excitatory neurons by Translating Ribosome Affinity Purification RNA sequencing (TRAP-seq). We detected time-dependent changes in up- and down-regulated ribosome-associated mRNAs over the two hours following LTP induction, with minimal overlap of DE transcripts between time points. TRAP-seq revealed greater numbers and amplitudes of LTP-induced changes than RNA-seq of all cell types in the hippocampus. Transcripts that were DE by TRAP-seq but not RNA-seq were enriched in mRNAs encoding cytoskeletal and cell adhesion proteins, while RNA-seq identified DE in many non-neuronal mRNAs. Together our results highlight the importance of considering both the time course and the cell-type specificity of activity-dependent gene expression during memory formation.

overall_design: RNA-seq and TRAP-seq were performed on RNA isolated from acute hippocampal slices following a chemical LTP induction, which utilizes forskolin followed by elevated levels of Ca2+/K+ in 0 Mg2+ artificial cerebral spinal fluid. We crossed the RiboTag line of mice with a Camk2a-cre line to generate mice heterozygous for both cre and RiboTag, which expresses an HA-tagged ribosomal protein L22 in excitatory neurons. Total RNA from all cell-types and TRAP RNA from excitatory neurons was isolated from the same hippocampal slice homogenate at 30 min, 60 min, and 120 min following LTP induction from LTP induced slices as well as time-matched vehicle-treated control slices. Both LTP and basal slices were generated from the same animals on the same day, with slices from each animal evenly distributed between basal and LTP. Thus, each basal replicate has a corresponding LTP treated replicate.

first: Riki

last: Kawaguchi

first: Giovanni

last: Coppola

first: Kelsey

last: Martin


title: TFAP2A ChIP-seq in human primary melanocytes

city: Iowa City

first: Robert

last: Cornell

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

summary: Mutations in the gene encoding transcription factor TFAP2A result in pigmentation anomalies in model organisms and premature hair graying in humans. However, the pleiotropic functions of TFAP2A and its redundantly-acting paralogs have made the precise contribution of TFAP2-type activity to melanocyte differentiation unclear. Defining this contribution may help to explain why TFAP2A expression is reduced in advanced-stage melanoma compared to benign nevi. To identify genes with TFAP2A-dependent expression in melanocytes, we profile zebrafish tissue and mouse melanocytes deficient in Tfap2a, and find that expression of a small subset of genes underlying pigmentation phenotypes is TFAP2A-dependent, including Dct, Mc1r, Mlph, and Pmel. We then conduct TFAP2A ChIP-seq in mouse and human melanocytes and find that a much larger subset of pigmentation genes is associated with active regulatory elements bound by TFAP2A. These elements are also frequently bound by MITF, which is considered the “master regulator” of melanocyte development. For example, the promoter of TRPM1 is bound by both TFAP2A and MITF, and we show that the activity of a minimal TRPM1 promoter is lost upon deletion of the TFAP2A binding sites. However, the expression of Trpm1 is not TFAP2A-dependent, implying that additional TFAP2 paralogs function redundantly to drive melanocyte differentiation, which is consistent with previous results from zebrafish. Paralogs Tfap2a and Tfap2b are both expressed in mouse melanocytes, and we show that mouse embryos with Wnt1-Cre-mediated deletion of Tfap2a and Tfap2b in the neural crest almost completely lack melanocytes but retain neural crest-derived sensory ganglia. These results suggest that TFAP2 paralogs, like MITF, are also necessary for induction of the melanocyte lineage. Finally, we observe a genetic interaction between tfap2a and mitfa in zebrafish, but find that artificially elevating expression of tfap2a does not increase levels of melanin in mitfa hypomorphic or loss-of-function mutants. Collectively, these results show that TFAP2 paralogs, operating alongside lineage-specific transcription factors such as MITF, directly regulate effectors of terminal differentiation in melanocytes. In addition, they suggest that TFAP2A activity, like MITF activity, has the potential to modulate the phenotype of melanoma cells.

overall_design: TFAP2A ChIP-seq was conducted in a human primary melanocytes purified from discarded neonatal foreskin samples.  TFAP2A enriched chromatin was compared to an IgG "enriched" negative control.

first: Eric

last: Van Otterloo

first: Hannah

last: Seberg


title: tRNA-derived small RNAs target transposable element transcripts

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Eukaryotic organisms have evolved a series of mechanisms to regulate transposable element (TE) expression based on RNA silencing. In plants, the initial step in the recognition of TE transcripts relies on microRNAs, but this is unlikely to take place in the pollen grain where natural reactivation of TE transcription occurs but microRNAs accumulate to low levels. We investigated small non-coding RNA accumulation in plants and found conserved tRNA-derived RNA fragment (tRF) accumulation in the pollen grain or analogous reproductive structure in a variety of plant species.
Results:Analysis of tRF biology in Arabidopsis revealed that tRFs are regulated by the chromatin modifier DDM1, have a microRNA-like biogenesis pathway, and specifically target TE mRNAs. In addition, we provide evidence that tRF targeting is involved in the production of secondary small RNAs derived from TE transcripts, which initiate a cascade of RNAi and TE silencing.
Conclusion:that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.

overall_design: Examination of pollen and flower bud small RNAs from wild type, single or double mutant combinations, many of which have biological replicates. In addition, IP purificaton of the AGO1 protein followed by sequencing of the incorporated small RNAs.

first: R

last: Slotkin

last: Martinez-Arias


title: Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation

status: Public on Feb 22 2017

city: Stanford

first: Howard

last: Chang

state: California

address: 269 Campus Drive

institute: Stanford University

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


title: Empirical comparison of reduced representation bisulfite sequencing and Infinium Beadchip reproducibility and coverage of DNA methylation in humans

first: Alexandra

last: Binder

address: 650 Charles Young Drive, South

department: Department of Epidemiology

institute: University of California Los Angeles

summary: We empirically examined the strength of rapid multiplexed reduced representation bisulfite sequencing (rmRRBS) and Illumina’s Infinium Beadchip. rmRRBS required less input DNA, offered more flexibility in coverage, and interrogated more CpG loci at a higher regional density. The Infinium covered slightly more protein coding, cancer-associated and mitochondrial-related genes, both platforms covered all known imprinting clusters, and rmRRBS covered more microRNA genes than the HumanMethylation450 but fewer than the MethylationEPIC. rmRRBS did not always interrogate exactly the same CpG loci, but genomic tiling improved overlap between different libraries.

overall_design: For the current work, we used frozen peripheral blood from 10 Caucasian males normative aging study participants who were between the ages of 55 and 80 years at the time of blood draw.

first: John

last: Hutchinson


title: Pancreatic alpha and beta-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: We performed a parallel analysis of the molecular properties of α- and β-cell oscillators, using a mouse model expressing three reporter genes: one labeling α-cells, one specific for β-cells, and a third monitoring circadian gene expression. Diurnal transcriptome analysis in separated α- and β-cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. This study represents the first parallel large-scale circadian in vivo transcriptome analysis in separated α- and β-cells.

overall_design: 24 samples in duplicates (time course design)

first: Volodymyr

last: Petrenko

first: Camille

last: Saini

first: Laurianne

last: Giovannoni

first: Cedric

last: Gobet

first: Daniel

last: Sage

first: Michael

last: Unser

first: Mounia

last: Heddad Masson

first: Guoqiang

last: Gu

first: Domenico

last: Bosco

first: Frédéric

last: Gachon

first: Jacques

last: Philippe

first: Charna

last: Dibner


title: Small RNA sequencing of serum collected from mice before and after manifestation of tumor

city: Ghent

first: Alan

last: Van Goethem

address: De Pintelaan 185

country: Belgium

institute: Ghent University

summary: To investigate the effectiveness of performing 5' tRNA half depletion, we evaluated the association of tumor burden on circulating miRNAs present in mouse serum. Three nude mice (NCr) were orthotopically injected with SH-SY5Y human neuroblastoma cells. Serum samples were collected one week before cell injection and two weeks after injection, when mice had palpable tumors. We performed 5' tRNA half depletion using biotinylated probes and streptavidin beads and prepared small RNA libraries using the TruSeq Small RNA Library Prep kit. By depleting the 5' tRNA halves in the serum-derived RNA samples, we were able to detect 3 times more differentially expressed miRNAs when comparing serum from mice carrying orthotopically engrafted tumors with serum from healthy control mice. We detected 34 differentially expressed miRNAs, of which six are unique to humans, 13 unique to mice and 15 have complete conservation between the two species.

overall_design: Serum samples from three mice were collected both before and two weeks after tumor cell injection. RNA from each serum sample was divided into two and either depleted for tRNA-halves or not.


title: An electrical pulse stimulation protocol to study acute epigenetic response to muscle cell contraction uncovers acute hydroxymethylation of the exercise-responsive gene Nr4a3 [RNA-Seq]

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

institute: Copenhagen University

summary: Physical exercise triggers numerous positive adaptations through the regulation of genes controlling muscle structure and function. Epigenetic factors like DNA methylation participate in transcriptional activation by allowing the recruitment of the transcription machinery to gene promoters. Exercise induces dynamic DNA demethylation at gene promoters, but the contribution of the demethylation precursor hydroxymethylcytosine is unknown. Given the evanescent nature of  hydroxymethylcytosine, a model of muscle contraction amenable to collection of repeated and acute time series is requested to determine if contraction-induced demethylation is preceded by increased hydroxymethylcytosine levels. Here, we aimed to establish an acute skeletal muscle contraction model that could, at least partly, mimic the effect of acute exercise on gene expression, in order to investigate the effect of muscle contraction in DNA demethylation and hydroxymethylation. We refined an Electrical Pulse Stimulation (EPS) protocol in C2C12 myotubes that we benchmarked to the nuclear receptor subfamily 4 group A member 3 (Nr4a3) gene, a gene selected for having the highest increase in expression in response to acute exercise in humans. Using targeted bisulfite sequencing, we found that a region of the Nr4a3 promoter is rapidly demethylated 60 minutes after EPS and subsequently re-methylated after 120 minutes. Of interest, hydroxymethylation of the differentially methylated region of Nr4a3 promoter after EPS was elevated at 0 minutes and reached lowest levels at 60 minutes after EPS. We established a cell culture-based protocol to mimic acute transcriptional responses to exercise and provide insight into the mechanism by which exercise-responsive genes are demethylated after muscle contraction

overall_design: Ten human subjects sampled pre and post exercise

first: Pattarawan

last: Pattamaprapanont

first: Christian

last: Garde

first: Odile

last: Fabre

first: Romain

last: Barrès


title: An electrical pulse stimulation protocol to study acute epigenetic response to muscle cell contraction uncovers acute hydroxymethylation of the exercise-responsive gene Nr4a3 [Bisulfite-Seq]

overall_design: Triplicate C2C12 cells in control or EPS stimulated condition at time points 0min, 30min, 60min, 120min, 180min and 240min


title: Small RNA sequencing of serum-derived RNA for the evaluation of 5' tRNA halves depletion protocols

summary: 5' tRNA halves are abundantly present in small RNA libraries prepared from serum samples, thereby limiting the detection of other small RNA species. In this study, we developed and compared two protocols for the selective depletion of 5' tRNA halves in RNA isolated from murine serum samples. To evaluate the efficacy of both protocols on small RNA sequencing, we performed the two 5' tRNA halves depletion protocols on total RNA isolated from a serum pool collected from healthy mice. Each RNA sample was divided into three and the resulting fractions were either depleted using beads or RNase H, or used as a control. The experiment was performed in triplicate. Upon depletion, libraries were prepared using TruSeq Small RNA Library Preparation kit. For both protocols, very high depletion efficiencies were observed, with more than 99% of the targeted tRNA-types being depleted. This resulted in a more than 6-fold increase in mapped miRNA reads and 60% more detected mature miRNAs when performing small RNA sequencing on murine serum samples. Importantly, we observed no considerable effects on the relative expression values of miRNAs.

overall_design: Serum samples from healthy mice were combined together into a total of 3 serum pools. The RNA extracted from each pool was divided into three and the resulting fractions were either depleted using beads or RNase H, or used as a control.


title: An electrical pulse stimulation protocol to study acute epigenetic response to muscle cell contraction uncovers acute hydroxymethylation of the exercise-responsive gene Nr4a3

overall_design: Refer to individual Series


title: Evaluation of three small RNA library preparation kits on serum-derived RNA

summary: We evaluated the effect of the small RNA library preparation method on 5' tRNA-halves and miRNA abundance in libraries prepared from serum RNA using three commercially available small RNA library preparation kits (TruSeq small RNA library preparation kit v2 (Illumina), TailorMix miRNA sample preparation kit v2 (Seqmatic) and the NEBNext Multiplex Small RNA library prep kit (New England Biolabs)). RNA isolated from 100 µl of serum collected from healthy mice was used as input for the preparation of a small RNA library in duplicate and libraries were single end sequenced.

overall_design: Serum samples from healthy mice were used to evaluate three different small RNA library preparation kits. Each kit was evaluated in duplicate.


title: Transcriptomics of environmental enrichment and cocaine using quantitative next generation sequencing

city: Galveston

first: Thomas

middle: Arthur

last: Green

state: TX

address: 301 University dr.

department: Pharmacology and Toxicology

institute: University of Texas Medical Branch

summary: Environmental enrichment produces a protective addiction phenotype in animal models. Gene transcription is thought to mediate this protective phenotype and has a profound influence on neuronal plasticity and psychiatric disorders. Understanding the molecular and genetic mechanisms underlying environmental enrichment may lead to novel targets for pharmacotherapeutics to treat cocaine addiction. We investigated the differential regulation of transcript levels using RNA sequencing of the rat nucleus accumbens after environmental enrichment/isolation and cocaine/saline self-administration. New functional pathways were also identified for cocaine modulation and environmental enrichment.

overall_design: mRNA profiles were generated from the nucleus accumbens from enriched or isolated rats that self-administered cocaine or saline for 2 weeks, by RNA sequencing using illumina Hiseq1000.

first: Heidi

last: Spratt

first: Bruce

last: Luxon

first: Yafang

last: Zhang

first: Fanping

last: Kong

first: Dingge

last: Li

first: Elizabeth

last: Crofton

last: Wood

first: Steven

last: Widen


title: Transcriptional profiling of Regulatory T-cells isolated from neonatal skin and skin draining lymph nodes (SDLNs)

city: San Francisco

first: Tiffany

middle: C

last: Scharschmidt

address: 513 Parnassus Ave, 1201B

department: Dermatology

institute: University of California, San Francisco

summary:
Purpose: The goals of this study were to identify preferential gene expression signatures that are unique to Tregs in neonatal skin relative to peripheral Tregs
Methods: Tregs from telogen skin and SDLNs were purified by cell sorting (using the Treg GFP reporter mouse line Foxp3-DTR/GFP) to generate mRNA transcription profiles.
Results: Transcriptional profiling revealed a unique neonatal skin Treg signature relative to SDLN Tregs
Conclusion: Our study represents the first detailed analysis of the neonatal skin Treg transcriptome.

overall_design: mRNA profiles of skin and SDLN Tregs isolated from 13 day old Foxp3-DTR/GFP mice.

first: Michael

middle: D

last: Rosenblum


title: Microenvironmental cues co-regulate pancreatic cancer metabolism and histone acetylation

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: To investigate the paracrine effects of stromal elements on cancer cells, we developed a “stromal” culture system, which incorporates structural and diffusible stroma-derived elements into homotypic cultures amenable to functional genomics and metabolomics.  We show that microenvironmental cues co-regulate cancer metabolism and gene expression.  Stromal inputs broadly influence histone acetylation in the cancer epigenome, coinciding with induction of genes implicated in anabolic metabolism and inflammation. The gene expression and metabolic changes induced by stromal factors overlap with those previously identified following oncogenic Kras, suggesting functional complementarity between cell-autonomous and microenvironmental pathways.  We implicate the BET family of epigenetic readers as key transducers of stromal inputs to drive alterations in gene expression and suggest paracrine epigenome regulation as a conduit through which stromal signals drive metabolic and immune adaptation to a challenging tumor microenvironment.

overall_design: Comparison of histone acetylation marks H3K9ac and H3K27ac in MIAPaCa2 cells cultured under 3D stromal and astromal conditions

first: Mara

last: Sherman

first: Ronald

middle: M

last: Evans


title: Regulated inflammation and lipid metabolism in colon mRNA expressions of obese germfree mice responding to Enterobacter cloacae B29 combined with the high fat diet

city: shanghai

first: menghui

last: zhang

address: 800 dongchuan road

institute: shanghai jiaotong university

summary: Increased evidences demonstrated that gut microbiota targeted diet intervention can alleviate obesity and related metabolic disorders. The underlying mechanism of interactions among diet, microbiota and host still remains unclear. Enterobacter cloacae B29, an endotoxin-producing strain dominated in the gut of a morbidly obese volunteer (weight 174.8 kg, BMI 58.8 kg m-2) was isolated and transplanted to germfree mice. Using deep mRNA sequencing technology, we compared different gene expression profiles in the colon samples of the germfree mice before and after treated with B29 and/or high fat diet (HFD) and identified 279 differential expressed genes in total, including up-regulated genes Apoa4, Ido1, Cyp4a10, and down-regulated genes Cyp2e1, Cyp26b1, Akr1b7, Adipoq, Cyp1a1, Apoa1, Npc1l1, Tff2, Apoc1, Ctla2a, Mttp, Lpl. Fifty-nine GO biological processes and five KEGG pathways, particularly the Peroxisome proliferator-activated receptors (PPARs) signaling pathway, were significantly enriched in response to HFD+B29, which were mainly relevant to inflammation and the metabolism of lipid, lipoprotein and sterols. These functional changes were consistent with the developed obesity, insulin-resistance, and aggravated inflammatory conditions of the HFD+B29 mice. This work provides insight into the gene expression changes in response to HFD+B29, helping to understand the mechanism of the interactions among HFD, B29 and the germfree mice.

overall_design: Four groups(n=6) of germfree mice treated with: NCD+LB, NCD+B29, HFD+LB, HFD+B29

first: Huiying

last: Yan

last: Fei

first: Guojun

last: Wu

first: Chenhong

first: Liping

last: Zhao

first: Menghui


title: Combinatorial DNA methylation codes at repetitive elements [RNA-Seq]

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

summary: DNA methylation is an essential epigenetic modification, present in both unique DNA sequences and repetitive elements, but its exact function in repetitive elements remains obscure. Here, we describe the genome-wide comparative analysis of the 5mC, 5hmC, 5fC and 5caC profiles of repetitive elements in mouse embryonic fibroblasts and mouse embryonic stem cells. We provide evidence for distinct and highly specific DNA methylation/oxidation patterns of the repetitive elements in both cell types, which mainly affect CA repeats and evolutionary conserved mouse-specific transposable elements including IAP-LTRs, SINEs B1m/B2m and L1Md-LINEs. DNA methylation controls the expression of these retro-elements, which are clustered at specific locations in the mouse genome. We show that TDG is implicated in the regulation of their unique DNA methylation/oxidation signatures and their dynamics. Our data suggest the existence of novel epigenetic code for the most recently acquired evolutionary conserved repeats that could play a major role in cell differentiation.

overall_design: Transcriptome (RNA-seq) analyses of shRNA treated MEFs (control, shSCR or Tdg knockdown, shTDG).

first: Abdulkhaleg

last: Ibrahim

first: Stéphanie

last: Le Gras

first: Amandine

last: Velt

first: Isabelle

last: Stoll

first: Bernard

last: Jost

first: Christian

last: Bronner

first: Stefan

last: Dimitrov

first: Ali

last: Hamiche


title: De novo transcriptomic profiling of halotolerant microalga Dunaliella salina (Chlorophyta) in response to reciprocal alteration of salinities.

city: Zhoushan

first: Jianhua

last: Liu

state: Zhejiang

address: 10 Tiyu Road, Room 502

department: Ocean Research Centre of Zhoushan

institute: Zhejiang University

summary: The unicellular microalga Dunaliella salina is one of the halotolerant and cell wall-less green  microalgae in Dunaliella genus. The ability of halotolerance in Dunaliella is attributed to the  accumulation of glycerol. Both sugar made by photosynthesis and starch serve as carbon sources for  glycerol biosynthesis. Quantitative PCR-based analyses concluded no apparent transcriptional  regulation of glycerol, carbon fixation, and starch metabolisms upon salinity stresses. To examine  whether or not transcriptional regulation is involved at the transcriptomic level, we assembled a de  novo deep sequencing transcriptome. By using a pathway-based approach, we show that low- and  high-salt (i.e., 0.5M versus 2M NaCl) adapted cells share a common transcriptomic profile and that  subsets of ESTs associated with energy metabolisms are less affected upon salinity stress. We find  that enzymes involved in glycerol, carbon fixation, and starch metabolisms are encoded by multiple  EST isoforms. We show that EST isoforms encoding dihydroacetone reductase in glycerol  metabolism, phosphoglycerate kinase in carbon fixation, and beta-amylase and fructobiphosphate  aldolase in starch metabolism display a correlated transcriptional level change to the alteration of  glycerol and starch contents upon salinity stresses. Taken together, our results demonstrate that some  enzymes involved in glycerol, carbon fixation, and starch metabolisms are regulated at the  transcriptional level upon salinity stresses. Furthermore, our analyses indicate that energy  metabolisms are not drastically affected upon salinity stresses, consistent with its ability to adapt to a  wide range of salinities.

overall_design: 18 biological samples, each condition in triplicates

first: Zhenyu

last: Xu


title: Next generation sequencing reveals increased glycolysis and biomass production rate in mammary gland tumors of mice chronically exposed to insulin analogue

city: Leiden

first: Bas

last: ter Braak

state: Zuid-Holland

address: Einsteinweg 55

department: Toxicology

country: Netherlands

institute: Leiden University/LACDR

summary: For up to 70 weeks we  subcutaneuously injected two hundered p53R270HWAPCre mice to different insulin-like molecules (regular insulin, insulin glargine, insulin X10 (of AspB10), IGF1 or vehicle solution). Due to the mammary gland specific p53 mutation the p53R270HWAPCre mice will develop spontanously human like mammary gland tumors in about a year. We found that frequent injections to insulin like molecules decreased the mammary gland tumor latency time in this model. Next we mRNA seqeunced tumors to reveal the underlying mechanisms for the increased tumor progression. For the next generation experiment we isolated mRNA from 50 tumors (10 tumors of each stimulation group) and sequenced with the IonTorrent (40 mil reads, on average 100 bp reads)

overall_design: RNA expression profiles of 50 mammary gland tumors were analyzed, 10 tumors per treatment group (chronic insulin, glargine, x10, IGF1 or vehicle exposure)

first: Bob

last: van de Water

first: Jan

middle: W

last: van der Laan

first: Kris

last: Siezen

first: Pooja

last: Rao

first: Charlotte

last: Voorhoeve

first: Eytan

last: Ruppin


title: RNA-seq of small RNA in Ammopiptanthus mongolicus to investigate drought and cold adaptation

city: Beijing

first: Fei

last: Gao

address: 27 Zhongguancun South Street

institute: Minzu University of China

summary: Ammopiptanthus mongolicus is an ecologically important desert plant. To understand the role of miRNA genes in draught and cold stress adaptation, RNA-seq of small RNA in Ammopiptanthus mongolicus was performed.

overall_design: To identify microRNAs and other small RNA in A. mongolicus, we generated five small RNA libraries using RNA isolated from drought stressed-roots (DT_R) and unstressed roots (CK_R), and RNA isolated from drought stressed-leaves (DT_L), cold stressed-leaves (CT_L)  and unstressed leaves (CK_L). These small RNA libraries were then sequenced by the high throughput Illumina /Solexa sequencing platform.

first: Yijun

last: Zhou


title: Improved prediction of endogenous HLA-associated   epitopes based on mono-allelic mass spectrometry   profiling

status: Public on Feb 21 2017

city: Boston

first: Catherine

middle: J

last: Wu

address: 450 Brookline Ave.

institute: Dana Farber Cancer Institute

summary: LC-MS/MS-based identification of HLA-peptides is poised to provide a deep understanding of the rules underlying antigen presentation. However, a key obstacle limiting the utility of MS data is the ambiguity arising from the co-expression of multiple HLA alleles. Here, we introduce a  strategy for profiling the HLA ligandome one allele at a time. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing a novel spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of novel binding motifs, and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression. We trained neural network prediction algorithms with our large dataset (>24,000 peptides) and outperformed algorithms trained on datasets of peptides with measured affinities. We thus demonstrate a scalable strategy for systematically learning the rules of endogenous antigen presentation.

overall_design: RNA transcript expression was quantified to in order to assess its contribution to Class I peptide prediction

first: Michael

middle: S

last: Rooney


title: Combinatorial DNA methylation codes at repetitive elements

first: Christophe

last: Papin

summary:
DNA methylation is an essential epigenetic modification, present in both unique DNA sequences and repetitive elements, but its exact function in repetitive elements remains obscure. Here, we describe the genome-wide comparative analysis of the 5mC, 5hmC, 5fC and 5caC profiles of repetitive elements in mouse embryonic fibroblasts and mouse embryonic stem cells. We provide evidence for distinct and highly specific DNA methylation/oxidation patterns of the repetitive elements in both cell types, which mainly affect CA repeats and evolutionary conserved mouse-specific transposable elements including IAP-LTRs, SINEs B1m/B2m and L1Md-LINEs. DNA methylation controls the expression of these retro-elements, which are clustered at specific locations in the mouse genome. We show that TDG is implicated in the regulation of their unique DNA methylation/oxidation signatures and their dynamics. Our data suggest the existence of novel epigenetic code for the most recently acquired evolutionary conserved repeats that could play a major role in cell differentiation.

This SuperSeries is composed of the SubSeries listed below.


title: Functional opsin retrogene in nocturnal moth

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: RNA was isolated from first instar larvae, fifth instar larvae and adults using the TRIzol (Invitrogen) reagent by following the company manual. Poly(A) mRNA was isolated from 20 µl total RNA using Oligo (dT) magnetic beads and then was broken into short fragments (about 200bp) in the presence of fragmentation buffer at 94 °C for 5 min. The mRNA samples were used to construct the cDNA libray with mRNA-Seq assay, which was performed by Novogene (Beijing, China).The libraries were sequenced using HiSeq2000 or HiSeq4000 (Illumina) in paired-end mode, creating reads with a length of 101 bp (HiSeq2000) or 151 bp (HiSeq4000).

overall_design: Examination of opsin genes expression levels at different stages

first: Kongming

first: Pengjun

first: Haijun

last: Xiao


title: Transcriptome analysis of a stem rust resistance locus on wheat chromosome 7AL

city: Canberra

first: Linda

last: Tabe

state: ACT

address: PO Box 1600

department: Agriculture and Food

country: Australia

institute: CSIRO

summary:
Aim:To characterise a recently discovered stem rust resistance locus on wheat chromosome 7AL. Transcriptome analysis by RNA-sequencing, in association with microscopic observations,  was used to compare responses to the Puccinia graminis f. sp. tritici pathogen of the susceptible line Columbus, and two independent backcrossed resistant lines containing the locus, Columbus-NS765 and Columbus-NS766.
Results: Microscopic observations of infected leaves revealed that the resistance conferred by the 7AL resistance locus was initiated by two days post-inoculation, upon the entry of the stem rust fungus into the plant through the stoma. Death of guard and epidermal cells adjacent to the fungal points of entry was observed to be clearly more frequent in resistant lines than in the susceptible genotype, suggesting that the resistance response is similar in all genotypes, but enhanced in the resistant lines. Transcriptomic analysis, combined with assignment of genes to wheat chromosomes, revealed a disporportionately high number of differentially expressed genes were located on chromosomes 7AL and 6A. A number of genes annotated as cysteine-rich receptor-like kinases were located on chromosome 7AL. Closer investigation indicated that the encoded proteins were in fact putative receptor-like cytoplasmic kinases (RLCKs). One of the putative RLCK genes contained a SNP marker previously shown to co-segregate with the 7AL resistance locus. The large number of differentially expressed genes on chromosome 6A indicated the presence of a large introgression on this chromosome that co-segregated with stem rust resistance in the two independent resistant lines, but its role in the resistance response is currently unclear.
Conclusions: This study represents the first transcriptome analysis of responses to stem rust in wheat, and the first investigation of the resistance conferred by the newly-discovered wheat 7AL stem rust resistance locus. Microscopy showed the resistance response was associated with pre-haustorial cell death. Results of the RNA-seq, which has the resolution to discriminate between homeologous wheat genes, along with assignment of differentially expressed genes to wheat chromosomes, suggested putative receptor-like cytoplasmic kinases linked to the 7AL locus as candidate resistance genes for further investigation.

overall_design: Illumina Sequencing was performed for 3 biological replicates of seedling leaf RNA from 3 genotypes of Triticum aestivum (1 susceptible and 2 resistant) at 3 time points after inoculation with Puccinia graminis f. sp. tritici, total 27 samples.

first: Vincent

last: Pujol

first: Li

last: Huang

first: Evans

last: Lagudah


title: Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples

first: Alan

last: Van Goethem

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


title: Combinatorial DNA methylation codes at repetitive elements [ChIP-Seq]

overall_design: Pol2 and H3K9me3 ChIP-seq in MEFs.

first: Abdulkhaleg

last: Ibrahim

first: Stéphanie

last: Le Gras

first: Amandine

last: Velt

first: Isabelle

last: Stoll

first: Bernard

last: Jost

first: Christian

last: Bronner

first: Stefan

last: Dimitrov

first: Ali

last: Hamiche


title: OTX2 activity at distal regulatory elements shapes the chromatin landscape of Group 3 medulloblastoma [RNA-seq]

first: Sowmya

last: Iyer

department: Pathology

institute: Massachusetts General Hospital

summary: Medulloblastoma is the most frequent malignant pediatric brain tumor and is divided into at least four subgroups known as Wnt, SHH, Group 3 and Group 4. Here we characterized gene regulation mechanisms in the most aggressive subtype, Group 3 tumors, through genome-wide chromatin and expression profiling. Our results show that most active distal sites in these tumors are occupied by the transcription factor OTX2. Highly active OTX2 bound enhancers are often arranged as clusters of adjacent peaks and are also bound by the transcription factor NEUROD1. These sites are responsive to OTX2 and NEUROD1 knockdown and could also be generated de novo upon ectopic OTX2 expression in primary cells, showing that OTX2 cooperates with NEUROD1 and plays a major role in maintaining and possibly establishing regulatory elements as a pioneer factor. Among OTX2 target genes we identified the kinase NEK2, whose knockdown and pharmacological inhibition decreased cell viability. Our studies thus show that OTX2 controls the regulatory landscape of Group 3 medulloblastoma through cooperative activity at enhancer elements and contributes to the expression of critical target genes.

overall_design:
Primary Group 3 Medulloblastomas tumor samples were analyzed by RNA-seq. Group 3 medulloblastoma cell line (D341) was analyzed by RNA-seq. OTX2 was depleted by infection with lentiviral shRNAs (sh OTX2 and sh GFP control).

Raw data not provided for primary Medulloblastoma  samples due to patient privacy concerns. Submitter states that the raw data for these samples will be submitted to dbGaP.

first: Gaylor

last: Boulay

first: Miguel

last: Rivera


title: OTX2 activity at distal regulatory elements shapes the chromatin landscape of Group 3 medulloblastoma [ATAC-seq]

overall_design:
ATAC-seq for Group 3 medulloblastoma cell line D283 and mesenchymal stem cells. OTX2 was expressed in MSCs with lentiviral expression vectors.

Raw data not provided for primary Medulloblastoma  samples due to patient privacy concerns. Submitter states that the raw data for these samples will be submitted to dbGaP.


title: OTX2 activity at distal regulatory elements shapes the chromatin landscape of Group 3 medulloblastoma [ChIP-seq]

overall_design:
ChIP-seq for of 4 histone modifications (H3K27ac, H3K4me1, H3K4me3 and H3K27me3) in primary Group 3 Medulloblastomas tumor samples, cell lines (D341 and D283) and mesenchymal stem cells (MSC). ChIP-seq for the transcription factors OTX2 and NEUROD1 in Group 3 medulloblastoma cell lines  (D341 and D283) and mesenchymal stem cells (MSC). OTX2 and NEUROD1 were knocked-down with lentiviral shRNA or knocked-out using Cas9 in Group 3 medulloblastoma cell lines. OTX2 and NEUROD1 were expressed in MSCs with lentiviral expression vectors.

Raw data not provided for primary Medulloblastoma  samples due to patient privacy concerns. Submitter states that the raw data for these samples will be submitted to dbGaP.


title: Tracking the embryonic stem cell transition from ground state pluripotency

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: Mouse embryonic stem (ES) cells are locked into self-renewal by shielding from inductive cues. Release from this ground state in minimal conditions offers a system for delineating developmental progression from naive pluripotency. Here we examined the initial transition process. The ES cell population behaves asynchronously. We therefore exploited a short-half-life Rex1::GFP reporter to isolate cells either side of exit from naive status. Extinction of ES cell identity in single cells is acute. It occurs only after near-complete elimination of naïve pluripotency factors, but precedes appearance of lineage specification markers. Cells newly departed from the ES cell state display features of early post-implantation epiblast and are distinct from primed epiblast. They also exhibit a genome-wide increase in DNA methylation, intermediate between early and late epiblast. These findings are consistent with the proposition that naive cells transition to a distinct formative phase of pluripotency preparatory to lineage priming

overall_design: DNA methylation analysis in Rex1-GFP ESCs by whole genome bisulfite sequencing, in triplicate, using the Illumina platform

first: Tuzer

last: Kalkan

first: Nelly

last: Olova

first: Heather

last: Lee

first: Wolf

last: Reik

first: Austin

last: Smith


title: Identification of lipid-binding lncRNAs in triple-negative breast cancer

city: Houston

first: Liuqing

last: Yang

state: Texas

address: 1515 Holcombe Blvd.

department: Molecular and Cellular Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: To comprehensively identify RNA molecules that are naturally associated with cellular lipid components, we isolated lipid fractions and their bound RNAs from triple-negative breast cancer (TNBC) patient tissues. Fresh frozen TNBC tissues and their normal counterparts were subjected to total RNA extraction, or in parallel, to whole cell fractionation via Hydrostatic Pressure Cycling to form a lipid-containing upper phase, a denatured protein-containing lower phase, and an insoluble fraction containing DNA and RNA (PBI Inc.) The RNAs extracted from the lipid fractions were applied to LncRNA Array v3.0 (Arraystar).

overall_design: LncRNA profiling analysis of lipid-bound lncRNAs extracted from paired triple-negative breast cancer tissue and adjacent normal breast tissue by Arraystar Human LncRNA Array v3.0.

first: Aifu

last: Lin

first: Qingsong

last: Hu

first: Chunlai

last: Li

first: Zhen

last: Xing

first: Guolin

last: Ma

first: Cheng

last: Wang

first: Jun

last: Yao

first: Ke

last: Liang

first: Shouyu

first: Peter

middle: K

last: Park

first: Jeffrey

middle: R

last: Marks

first: Yan

last: Zhou

first: Jianwei

first: Mien-Chie

last: Hung

first: Han

first: Zhibin

first: Hongbing

last: Shen

first: David

middle: H

last: Hawke

first: Leng

last: Han

first: Yubin

first: Chunru


title: An atlas and analysis of bovine skeletal muscle long noncoding RNAs

city: Hohhot

first: Xinfeng

last: Liu

address: 24 Zhaojun Road

institute: Inner Mongolia University

summary: In this study, 7188 bovine skeletal muscle lncRNAs were identified by RNA-Seq and a stringent screening procedure in four different muscle tissues. These lncRNAs shared many characteristics with other mammalian lncRNAs, such as the shorter ORF and lower expression level than mRNAs. Furthermore, the chromosomal locations and global expression patterns for these lncRNAs were also described in detail.Our results provided a global expression pattern of lncRNAs specific to bovine skeletal muscle and supplied us important targets for studying the function of lncRNAs in muscle development, which would help to better identify mechanisms underlying muscle development in bovine.

overall_design: Analysis of lncRNA expression profiling for four types of skeletal muscle samples in bovine.

first: Hong

last: Guo


title: RNASeq -/+ UV 8 and 24 hr

city: London

first: Laura

last: Williamson

address: 1 Midland Road

institute: The Francis Crick Institute

summary: The transcription-related DNA damage response was analyzed on a genome-wide scale with great spatial and temporal resolution. Upon UV irradiation, a slowdown of transcript elongation and restriction of gene activity to the promoter-proximal ~25 kilobases is observed. This is associated with a shift from expression of long mRNAs to shorter isoforms, incorporating alternative last exons (ALEs) that are more proximal to the transcription start site. Notably, this includes a shift from a protein-coding ASCC3 mRNA to a shorter transcript isoform of which the RNA, rather than an encoded protein, is critical for the eventual recovery of transcription. The protein-coding ASCC3 isoform counteracts the function of the non-coding isoform, indicating crosstalk between them. Thus, the ASCC3 gene expresses both coding and noncoding transcript isoforms with opposite effects on transcription recovery after UV-induced DNA damage

overall_design: MRC5VA cells were either left untreated or treated with 15J/m2 of UVC irradiation, followed by recovery for 8 or 24 hours. Two biological replicates were performed for each sample.

first: Marco

last: Saponaro

first: Stefan

last: Boeing

first: Philip

last: East

first: Richard

last: Mitter

first: Theodoros

last: Kantidakis

first: Gavin

last: Kelly

first: Anna

last: Lobley

first: Jane

last: Walker

first: Bradley

last: Spencer-Dene

first: Michael

last: Howell

first: Nik

last: Matthews

first: Aengus

last: Stewart

first: Jesper

last: Svejstrup


title: OTX2 activity at distal regulatory elements shapes the chromatin landscape of Group 3 medulloblastoma

first: Sowmya

last: Iyer

overall_design: Refer to individual Series


title: The Sin3a/HDAC co-repressor complex cooperates with Nanog in promoting stem cell pluripotency and somatic cell reprogramming [ChIP-Seq]

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Despite the requirement of Sin3a for survival of early embryos and embryonic stem cells (ESCs), mechanistic action of Sin3a in the maintenance and establishment of pluripotency remains unexplored. Here we report the transcriptional regulatory roles of Sin3a in maintaining ESC pluripotency and in reprogramming somatic cells towards full pluripotency. Sin3a/HDAC complex members were enriched in an extended Nanog interactome and exhibited a predominant transcriptional co-activator role at a global level in ESCs. We also established a critical role for Sin3a in efficient reprogramming of somatic cells towards full pluripotency. Nanog and Sin3a co-localize at almost all of their genome-wide targets in pre-iPSCs, and both factors are required to directly induce a synergistic transcriptional program wherein pluripotency genes are activated and reprogramming barrier genes are repressed. Our results, for the first time, establish positive roles of the Sin3a/HDAC complex in the maintenance and establishment of pluripotency.

overall_design: Genome binding/occupancy profiling of Nanog and Sin3a in pre-iPSCs for somatic cell reprogramming

first: Arven

last: Saunders

first: Xin

last: Huang


title: Combinatorial DNA methylation codes at repetitive elements [MeDIP-Seq]

first: Christophe

last: Papin

overall_design: Immunoprecipitation of genomic DNA isolated from shRNA treated MEFs (control, shSCR or Tdg knockdown, shTDG) using 5mC, 5hmC, 5fC and 5caC antibodies.

first: Abdulkhaleg

last: Ibrahim

first: Stéphanie

last: Le Gras

first: Amandine

last: Velt

first: Isabelle

last: Stoll

first: Bernard

last: Jost

first: Christian

last: Bronner

last: Dimitrov

first: Ali

last: Hamiche


title: UV_24h_GRO-Seq

first: Laura

last: Williamson

summary: The transcription-related DNA damage response was analyzed on a genome-wide scale with great spatial and temporal resolution. Upon UV irradiation, a slowdown of transcript elongation and restriction of gene activity to the promoter-proximal ~25 kilobases is observed. This is associated with a shift from expression of long mRNAs to shorter isoforms, incorporating alternative last exons (ALEs) that are more proximal to the transcription start site. Notably, this includes a shift from a protein-coding ASCC3 mRNA to a shorter transcript isoform of which the RNA, rather than an encoded protein, is critical for the eventual recovery of transcription. The protein-coding ASCC3 isoform counteracts the function of the non-coding isoform, indicating crosstalk between them. Thus, the ASCC3 gene expresses both coding and noncoding transcript isoforms with opposite effects on transcription recovery after UV-induced DNA damage.

overall_design: Cells were irradiated with UVC (15 J/m2) or left untreated and incubated for 2, 5, 8, 10, 12 or 24 hours, followed by nuclei isolation. Nuclei were processed for GRO-Seq.

first: Marco

last: Saponaro

first: Stefan

last: Boeing

first: Philip

last: East

first: Richard

last: Mitter

first: Theodoros

last: Kantidakis

first: Gavin

last: Kelly

first: Anna

last: Lobley

first: Jane

last: Walker

first: Bradley

last: Spencer-Dene

last: Howell


title: Distal regulation of c-myb expression during IL-6 inudced differentiation in murine myeloid progenitor M1 cells [DHS-seq]

city: Shanghai

first: Junfang

last: Zhang

address: Huchenghuan Road 999

department: College of fishery and life science

institute: Shanghai Ocean University

summary: We report DNAase1 hypersensitive sites located upstream of the c-myb gene,associated with gene expression

overall_design: Examination of DNAase1 hypersensitive sites in 2 cell types.

first: Bingshe

last: Han

first: Linda

last: Wolff


title: Genome-wide maps of H3K27me3 in CD8 T cell subsets

city: Stanford

first: Howard

middle: Y

last: Chang

address: 269 Campus Drive

institute: Stanford University

summary: To understand epigenetic repression mechanisms underlying CD8 T cell differentiation, we performed ChIP-seq of repressive mark H3K27me3 in CD8 T cell subsets.

overall_design: Examination of H3K27me3 histone modification in 4 CD8 T cell subsets.

first: Bingfei

last: Yu

first: Ananda

last: Goldrath


title: Distal regulation of c-myb expression during IL-6 induced differentiation in murine myeloid progenitor M1 cells [4C-seq]

summary: We report genome-wide long-range interactions of the c-myb promoter in M1 cells.

overall_design: Examination of long-range interactions of the c-myb promoter in M1 cells by Circular chromosome conformation capture (4C) method.


title: Distal regulation of c-myb expression during IL-6 induced differentiation in murine myeloid progenitor M1 cells


title: DRB/GRO-Seq -/+ UV

last: Williamson

overall_design: Cells were treated with DRB (100 μM, 3.5 hrs), followed by UVC irradiation (15 J/m2) or left untreated. Cells were washed with PBS to remove DRB immediately after UV irradiation and incubated for 10, 25 or 40 minutes, followed by cell lysis and nuclei isolation. Nuclei were processed for GRO-Seq.

first: Michael

first: Nik

last: Matthews

first: Aengus

last: Stewart

first: Jesper

last: Svejstrup


title: UV-Irradiation Induces a Noncoding RNA that Functionally Opposes the Protein Encoded by the Same Gene

first: Laura


title: Transcriptome of psychrophilic fungus Mrakia psychrophila cultured at different temperature at 4,12,20 degree centigrade

first: Xingzhong

last: Liu

address: NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China

department: The State Key Laboratory of Mycology

institute: Institute Of Microbiology Chinese Academy of Sciences

summary: Mrakia psychrophlila is a psychrophilic fungus widely spread all over the world. The cold adaptation mechanism of Mrakia psychrophila is unknown. Using RNA sequencing, differentially expressed genes of Mrakia psychrophila cultured at 4, 12 and 20 degree centigrade are identified. The result may be benefit for understanding cold adaptation of microorganisms.

overall_design: Examination of differentially expressed genes of psychrophilic fungus cultured at three different temperature. Raw data submitted to SRA: SRP066938

first: Yao

last: Su

first: Xianzhi

last: Jiang

first: Wenping

last: Wu

first: Manman

last: Wang

first: M

middle: I

last: Hamid

first: Meichun

last: Xiang


title: Changes in relative transcript amounts caused by the addition of mitomycin C in Streptococcus pneumoniae

status: Public on Feb 20 2017

city: Oxford

first: Angela

middle: B

last: Brueggemann

address: Peter Medawar Building for Pathogen Research

department: Nuffield Department of Medicine

institute: University of Oxford

summary: Bacteriophages (phages) are widespread in Streptococcus pneumoniae, with most strains carrying phage genomes integrated into the chromosome. RNA sequencing was utilised to explore whether phage gene expression could be detected. The pneumococcal reference strain PMEN3 (Spain9V-3), which contained two full-length phages and one partial phage, was grown in broth culture and mitomycin C was added to facilitate phage induction. PMEN3 culture samples were taken at sequential time points and RNA was extracted and sequenced.

overall_design: Seven 10 ml tubes of brain-heart infusion broth were inoculated with pneumococcal reference strain PMEN3 and incubated at 37°C+5% CO2. An aliquot of 0.5 ml broth was removed and the absorbance at OD600 was measured at each time point from 0-6 h to measure increased bacterial growth. Mitomycin C (Sigma-Aldrich) was added to the broth culture tubes after 3 h of incubation (OD600 ≥0.5). Just prior to the addition of mitomycin C at 3 h and after 4, 5 and 6h of incubation, respectively, broth cultures were removed from the incubator for processing. A 0.5 ml aliquot was used to measure the absorbance and the RNA was stabilised in the remaining 9.5 ml of broth culture by the addition of 19 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was immediately extracted from the samples using the Promega Maxwell® 16 Instrument and LEV simplyRNA Cells purification kit, following the manufacturer’s protocol. RNA extracts were sent to the Oxford Genomics Centre where library preps were made using RNA-Seq Ribozero kits (Illumina, Inc) and sequencing was performed on the MiSeq (Illumina, Inc). The sequenced forward and reverse reads were paired and mapped to reference genomes using Bowtie2 with the highest sensitivity option. Differential gene expression was assessed in Geneious using the DESeq method. Genes with an adjusted P value <0.05 were deemed to be differentially expressed.

first: Caroline

middle: L

last: Harrold

first: Reza

last: Rezaei Javan

first: Andries

last: van Tonder

first: Angus

last: McDonnell

first: Ben

middle: A

last: Edwards


title: Tissue-specific histone variant exchange during transcriptional activation and the link with pre-mRNA splicing factors

first: David

last: Tremethick

address: 131 Garran Rd

department: John Curtin School of Medical Research

institute: Australian National University

summary: ChIP-seq, CLIP-seq,  and mRNA-seq from  mouse hippocampal tissues and testes to study the role of histone variant H2A.B

overall_design: Replicated ChIP-seq, CLIP-seq,  and mRNA-seq samples from mouse hippocampal tissues and testes

first: Brian

last: Parker


title: Pluripotent stem cell disease modeling of GATA6 haploinsufficiency in human pancreatic development

first: Zhong-Dong

last: Shi

state: NY

address: 430E 67th Street

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
To better understand molecular mechanisms of human pancreatic development associated with GATA6 haploinsufficiency, we performed RNA-seq analysis to characterize the biological processes affected by GATA6 heterozygous mutation.
We found majority of top downregulated transcription factors are known to play key roles in pancreatic development and top downregulated genes were enriched with factors involved in developmental processes, with the pancreas being the top affected lineage.

overall_design: Examination of two wild-type lines and two GATA6-/+ lines at the PP2 stage.

first: Danwei

last: Huangfu


title: Identification of hypoxia-induced HIF1A targets in melanocytes reveals a molecular profile associated with poor prognosis for melanoma

city: Bethesda

first: Stacie

last: Loftus

address: 49 Convent Dr

institute: National Human Genome Research Institute


title: Inflammatory cytokines activate unliganded estrogen receptor and alter the sensitivity of breast cancer cells to tamoxifen

city: La Jolla

first: Joshua

last: Stender

state: CA

address: 9500 Gillman

institute: University of California at San Diego

summary: Genome-wide analyses of the transcriptomes and transcription factor recruitment in estrogen receptor breast cancer cells in response to estradiol, IL1b, or TNFa treatments. Also, the role of inflammatory cytokines on affecting tamoxifen sensitivity is analyzed on a genome-wide scale.

overall_design: Transcription factor binding (ERa, p65) and transcriptome analyses were performed in estradiol- and pro-inflammatory cytokine-treated MCF7 cells.

first: Christopher

last: Glass


title: The Sin3a/HDAC co-repressor complex cooperates with Nanog in promoting stem cell pluripotency and somatic cell reprogramming

first: Jianlong


title: Identification of hypoxia-induced HIF1A targets in melanocytes reveals a molecular profile associated with poor prognosis for melanoma [ChIP-seq]

overall_design:
ChIP-seq profiling of HIF1A binding in mouse immortalized melanocyte cell line melan-Ink4a-Arf null cells
contributor: NISC Comparative Sequencing Program

first: Laura

last: Baxter

first: Julia

last: Cronin

first: Temesgen

last: Fufa

first: William

last: Pavan


title: Transcriptome analysis of tomato leafless (lfs) mutants and TIBA-induced pins

status: Public on Feb 19 2017

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: The purpose of this study was to identify genes that are misregulated in tomato pin-like apices. These apices could be induced either by the lfs mutation, or by treatment with the auxin polar transport inhibitor TIBA

overall_design: The tomato lfs mutant was compared to WT and to TIBA-induced pin. Experiment was done in two repeats for each condition.

first: Yossi

last: Capua

first: Yuval

last: Eshed