title: Identifying FancC-dependent transcriptional signatures in mature B cells

city: Cincinnati

first: Mathieu

last: Sertorio

address: 3333 Burnett Avenue

department: Exp Hem and Cancer Bio

institute: Cincinnati Children's Hospital Medical center

summary: We report the first RNA-Seq experiments profiling of FancC deficiency in B cells.

overall_design: RNA-Seq of FancC-dependent gene signatures in mouse mature B cells

first: Qishen

last: Pang


title: The human cellular nucleic acid binding protien binds G-rich elements close to translation initiation sires and promotes translation. [RNA-Seq]

status: Public on Jan 08 2016

city: Wuerzburg

first: Sanjay

middle: Kumar

last: Gupta

state: Bavaria

address: Biozentrum, Am Hubland

department: Dept of Biochemistry

country: Germany

institute: University of Wuerzburg

type: Expression profiling by high throughput sequencing

summary: CNBP is a eukaryote-conserved nucleic-acid binding protein required in mammals for embryonic development. It contains seven CCHC-type zinc-finger domains and was suggested to act as a nucleic acid chaperone, as well as a transcription factor. Here, we identify all CNBP isoforms as cytoplasmic messenger RNA (mRNA)-binding proteins. Using Photoactivatable Ribonucleoside Enhanced Cross-linking and Immunoprecipitation, we mapped its binding sites on RNA at nucleotide-level resolution on a genome-wide scale and find that CNBP interacted with 3961 mRNAs in human cell lines, preferentially at a G-rich motif close to the AUG start codon on mature mRNAs. Loss- and gain-of-function analyses coupled with system-wide RNA and protein quantification revealed that CNBP did not affect RNA abundance, but rather promoted translation of its targets. This is consistent with an RNA chaperone function of CNBP helping to resolve secondary structures, thus promoting translation.

overall_design: CNBP protein knockdown and RNA-seq

middle: K

first: Markus

last: Hafner

first: Stefan

last: Juranek


title: The human cellular nucleic acid binding protien binds G-rich elements close to translation initiation sires and promotes translation. [PAR-CLIP]

overall_design: CNBP PAR-CLIP


title: Validation of THS-seq method, and comparison of published ENCODE DNase-seq data, self-generated ATAC-seq data and published ATAC-seq data, and THS-seq data for quantitation of chromatin accessibility.

status: Public on Jan 09 2016

city: La Jolla

first: Kun

last: Zhang

state: CA

address: 9500 Gilman Drive, MC0412, PFBH402

department: Bioengineering

country: USA

institute: University of California San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin accessibility captures the binding status of protein factors to chromosomes in vivo, and has been considered a highly informative proxy for functional protein-DNA interactions. Existing DNase I and Tn5 transposase based assays generally require tens of thousands to millions of fresh cells. Applying Tn5 tagmentation to single cells yields very sparse maps. Here we present a transposome hypersensitive sites sequencing assay (THS-seq) for highly sensitive characterizations of chromatin accessibility.

overall_design:
Validation of THS-seq method, and comparison of DNase-seq, ATAC-seq and THS-seq methods for quantitation of chromatin accessibility.

GSE47753, GSM1155957 GM12878_ATACseq_50k_Rep1, data downsampled to 8,351,125 reads for analysis: pub_SRR891268_ATAC-seq_50k_cells_Rep1_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155958 GM12878_ATACseq_50k_Rep2, data downsampled to 8,351,125 reads for analysis: pub_SRR891269_ATAC-seq_50k_cells_Rep2_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155959 GM12878_ATACseq_50k_Rep3, data downsampled to 8,351,125 reads for analysis: pub_SRR891270_ATAC-seq_50k_cells_Rep3_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155960 GM12878_ATACseq_50k_Rep4, data downsampled to 8,351,125 reads for analysis: pub_SRR891271_ATAC-seq_50k_cells_Rep4_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155961 GM12878_ATACseq_500_Rep1, data downsampled to 8,351,125 reads for analysis: pub_SRR891272_ATAC-seq_500_cells_Rep1_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155962 GM12878_ATACseq_500_Rep2, data downsampled to 8,351,125 reads for analysis: pub_SRR891273_ATAC-seq_500_cells_Rep2_downsampled_dfilter_peaks.bed.gz
raw data files were merged, alignment with bowtie 1.3 using parameters,  bowtie -n1 -k1 --best --chunkmbs 10240 --strata -l32 -m1 -p4 --nomaqround --sam, followed by clonal read removal for the final data file for further analysis. GSM816665, raw data obtained from UCSC genome browser, https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeOpenChromDnase: wgEncodeOpenChromDnaseGm12878RawData_merged_unique_dfilter_peaks.bed.gz
raw data files were merged, alignment with bowtie 1.3 using parameters,  bowtie -n1 -k1 --best --chunkmbs 10240 --strata -l32 -m1 -p4 --nomaqround --sam, followed by clonal read removal for the final data file for further analysis. GSM864360, raw data obtained from UCSC genome browser, https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeOpenChromFaire: wgEncodeOpenChromFaireGm12878RawData_merged_unique_dfilter_peaks.bed.gz
raw data files were merged, alignment with bowtie 1.3 using parameters,  bowtie -n1 -k1 --best --chunkmbs 10240 --strata -l32 -m1 -p4 --nomaqround --sam, followed by clonal read removal for the final data file for further analysis. GSM736496, GSM736620, raw data obtained from UCSC genome browser, https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeUwDnase: wgEncodeUwDnaseGm12878RawData_merged_unique_dfilter_peaks.bed.gz

first: Brandon

middle: C

last: Sos


title: Genome-wide profiling of the functional DNA methylation landscape at base-pair resolution in human cancer types [BS-seq]

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

type: Methylation profiling by high throughput sequencing

summary: Whole genome bisulphite sequencing of 13 human cancer samples and 9 normal controls. The main goal is to find the Diffrenetial methylated regions (DMR) at Genome wide level in different tissues and cancer types

overall_design: Sequencing of bisulfite converted DNA human cancer samples and normal control tissue types.

first: Holger

last: Heyn


title: Tumor suppressor role of Ezh2 in an NRASQ61K driven model of Early T-cell Precursor Acute Lymphoblastic Leukemia (RNA-Seq)

status: Public on Jan 07 2016

city: Aurora

first: Tobias

last: Neff

state: CO

department: Pediatric Oncology

institute: University of Colorado Denver AMC

summary:
Purpose: To characterize transcriptional changes associated with homozygous inactivation the Polycomb Repressive Complex 2 (PRC2) lysine methyltransferase Ezh2 in a mouse model of earlt T-cell precursor ALL (ETP-ALL)
Methods: We sequenced mRNA from NRASQ61K transformed murine LSK-cells co-transduced with a self-inactivating Cre-vector. Cells were sorted for Cre-expression (lox-stop-loxRosa26-YFP) or expression of an inert control vector (GFP) and differentiated on OP9DL1 stroma with and without a functional Ezh2 gene.
Results: Inactivation of Ezh2 in this model leads to accelerated leukemia development. Resulting gene expression changes are complex and include enrichment of genes associated with immature hematopoietic cells, Ras signaling and Cytokines and their cognate receptors.
Conclusions: Inactivation of Ezh2 in our model leads to accentuated expression of early hematopoietic gene expression programs and  to accentuated growth and survival signaling.

overall_design: Examination of mRNA levels between Ezh2ff and Ezh2ko in vivo, Ezh2ff and Ezh2ko in vitro.

first: Etienne

last: Danis


title: Long non-coding RNA expression profiles in cold-induced injury of mouse livers

city: Luzhou

first: Bo

last: Li

state: Sichuan Province

address: Taiping Street No. 25, Jiangyang District

department: Department of Hepatobiliary Surgery

country: China

institute: the Affiliated Hospital of Luzhou Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: Hepatic injury provoked by cold storage is a major problem affecting liver transplantation, as exposure to cold induces apoptosis in hepatic tissues. Long noncoding RNAs (lncRNAs) are increasingly understood to regulate apoptosis, but the contribution of lncRNAs to cold-induced liver injury remains unknown. Using RNA-seq, we determined the differential lncRNA expression profile in mouse livers after cold storage and found that expression of the lncRNA TUG1 was significantly down-regulated. Over-expression of TUG1 attenuated cold-induced apoptosis in mouse hepatocytes and liver sinusoidal endothelial cells LSECs, in part by blocking mitochondrial apoptosis and ER stress pathways. Moreover, TUG1 attenuated apoptosis, inflammation and oxidative stress in vivo in livers subjected to cold storage. Over-expression of TUG1 also improved hepatocyte function and prolonged hepatic graft survival rates in mice.  These results suggest that the lncRNA TUG1 exerts a protective effect against cold-induced liver damage by inhibiting apoptosis in mice, and suggests a potential role for TUG1 as a target for the prevention of cold-induced liver damage in liver transplantation.

overall_design: Cold-storaged liver lncRNA profiles of male inbred C57BL/6 mice 8-12 week of age and weighing 25 to 30 g were generated by high-throughput, high-sensitivity HiSeq 2500 sequencing platform .

first: Song

last: Su

first: Xianming

last: Xia


title: Tumor suppressor role of Ezh2 in an NRASQ61K driven model of Early T-cell Precursor Acute Lymphoblastic Leukemia (ChIP-Seq)

summary:
Purpose: To characterize changes in genome-wide H3K27me3 associated with homozygous inactivation the Polycomb Repressive Complex 2 (PRC2) lysine methyltransferase Ezh2 in a mouse model of earlt T-cell precursor ALL (ETP-ALL)
Methods: We performed Chip-seq for the H3K27me3 Chromatin mark on Ezh2ff and Ezh2ko cells NRASQ61K leukemias.
Results: Inactivation of Ezh2 in this model leads to accelerated leukemia development. Resulting gene expression changes are complex and include enrichment of genes associated with immature hematopoietic cells, Ras signaling and Cytokines and their cognate receptors.  Genes that lose K27me3 in Ezh2ko vs. Ezh2ff cells (ChIP-Seq) are enriched by GSEA in Ezh2ko vs Ezh2ff cells.
Conclusions: Inactivation of Ezh2 in our model leads to accentuated expression of early hematopoietic gene expression programs, to accentuated growth and survival signaling and to transcriptonal enrichment of PRC2 targets.

overall_design: ChIP-Seq for H3K27me3 using Ezh2ff and Ezh2ko NRASQ61K leukemias harvested from leukemic mice and expanded on OP9DL1 cells.


title: Identification of differentially expressed microRNAs between the fenpropathrin resistant and susceptible strains in Tetranychus cinnabarinus

city: Chongqing

first: Yichao

address: Tiansheng street

institute: Southwest University

summary:
Purpose: The present study provides the firstly large-scale characterization of miRNAs in Tetranychus cinnabarinus and the comparison between fenpropathrin resistant and susceptible strains gives a clue on study how miRNA involving in fenpropathrin resistance

Methods: Using Illumina sequencing to identify the differentially expressed miRNAs between the fenpropathrin resistant and susceptible strains of Tetranychus cinnabarinus

Results: 12 miRNAs that were expressed significantly differently were identified between thethe fenpropathrin resistant and susceptible strains of Tetranychus cinnabarinus

overall_design:
Total RNA obtained from 500  female adults aged 3-5 days post emergence from fenpropathrin resistant and susceptible strains of Tetranychus cinnabarinus,two biological repeats for each strain
Raw sequencing read data were submitted to SRA: SRP067789

first: Lin

last: He


title: Tumor suppressor role of Ezh2 in an NRASQ61K driven model of Early T-cell Precursor Acute Lymphoblastic Leukemia

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

overall_design: Refer to individual Series


title: Subtelomeric p53 Binding Prevents Accumulation of DNA Damage at Human Telomeres

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Telomeres and tumor suppressor protein TP53 (p53) function in genome protection, but a direct role of p53 at telomeres has not yet been described.  Here, we have identified non-canonical p53 binding sites within the human subtelomeres that suppress the accumulation of DNA damage at telomeric repeat DNA.  These non-canonical subtelomeric p53 binding sites conferred transcription enhancer-like functions that include an increase in local histone H3K9 and H3K27 acetylation and stimulation of subtelomeric transcripts, including telomere-repeat containing RNA (TERRA).   p53 suppressed formation of telomere-associated γH2AX and prevented telomere DNA degradation in response to DNA damage stress.  Our findings indicate that p53 provides a direct chromatin-associated protection to human telomeres, as well as other fragile genomic sites.  We propose that p53-associated chromatin modifications enhance local DNA repair or protection to provide a previously unrecognized tumor suppressor function of p53.

overall_design: p53 binding was analyzed by ChIP-Seq in HCT116 cells treated with camptothecin or untreated control.

first: Paul

middle: M

last: Lieberman

first: Steve

middle: B

last: McMahon


title: Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus

city: Chicago

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

institute: Northwestern University

summary: Higher order chromatin structure establishes domains that organize the genome and coordinate gene expression.  However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood.  The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms. CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus.  We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-regulatory elements and siRNA-mediated depletion of architectural proteins to determine the relative contribution of structural elements and enhancers to the higher order structure and expression of the CFTR locus.  We found the boundaries of the CFTR TAD are conserved among diverse cell types and are dependent on CTCF and cohesin complex. Removal of an upstream CTCF-binding insulator alters the interaction profile, but has little effect on CFTR expression. Within the TAD, intronic enhancers recruit cell-type selective transcription factors and deletion of a pivotal enhancer element dramatically decreases CFTR expression, but has minor effect on its 3D structure.

overall_design: Examination of open chromatin region in Caco2 (colorectal adenocarcinoma cells), HBE (primary human bronchial epithelial cells), and primary adult human epididymis cells

first: Rui

last: Yang


title: Expression profile of Pseudomonas aeruginosa  ΔgcsR PAO1 using RNA-Seq

city: Syracuse

first: Christopher

middle: T

last: Nomura

state: New York

address: 1 Forestry Dr.

department: Chemistry

institute: SUNY-ESF

summary: The TyrR-like enhancer-binding protein GcsR (or PA2449) was shown to regulate the expression of genes required for glycine metabolism. In order to define the regulon of GcsR we compared the transcriptome of a gcsR deletion mutant of P. aeruginosa PAO1 with that of the wild-type using RNA-Seq.

overall_design: Strains were grown under glycine rich conditions (peptone broth) and their transcriptomes were compared using RNA-Seq.

first: Zaara

last: Sarwar


title: Mapping binding sites of SIN3 isoforms across the Drosophila genome.

city: Detroit

first: Lori

middle: Ann

last: Pile

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

summary: SIN3 associates with RPD3 and other accessory proteins to form the SIN3 histone modifying complex. A single Sin3A gene encodes multiple SIN3 isoforms, of which SIN3 187 and SIN3 220 are predominant. Previous studies from our laboratory and others have indicated that SIN3 isoforms play non-redundant roles during fly development, however, the genes regulated by SIN3 isoforms are not known. We mapped the genome-wide binding sites of SIN3 isoforms in Drosophila. We established stable S2 cell lines that express either HA-tagged SIN3 187 or SIN3 220. The binding profiles revealed that the majority of the binding sites of SIN3 isoforms are overlapping. Our data revealed that SIN3 isoforms localize to euchromatic regions of the genome and enrichment of SIN3 isoforms are generally concentrated around the transcription start sites of genes. In addition, the extent of SIN3 binding confirmed previous findings indicating that SIN3 is a global transcriptional regulator.

overall_design: Genome-wide binding analysis of SIN3 187 and SIN3 220 in Drosophila. Using chromatin prepared from cell lines expressing either of the isoforms, we performed chromatin immunoprecipitation on chromatin prepared from cells that expresses either of the isoforms using an antibody against HA (ChIP). We coupled our ChIP with high resolution deep sequencing (ChIP-seq) to identify genomic targets of SIN3 isoforms.

first: N

last: Saha

first: L

middle: A


title: Single cell transcriptomics analysis of induced pluripotent stem cell-derived cortical neurons reveals frequent dual layer identity

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Induced pluripotent stem cell (iPSC)-derived cortical neurons present a powerful new model of neurological disease. Previous work has established that differentiation protocols produce cortical neurons but little has been done to characterise these at cellular resolution. In particular, it is unclear to what extent in vitro two-dimensional, relatively disordered culture conditions recapitulate the development of in vivo cortical layer identity. Single cell multiplex RT-qPCR was used to interrogate the expression of genes previously implicated in cortical layer or phenotypic identity in individual cells. Unexpectedly, 22.7% of neurons analysed frequently co-expressed canonical fetal deep and upper cortical layer markers, and this co-expression was also present at the level of translated protein. By comparing our results to available single cell RNA-seq data from human fetal and adult brain, we observed that this co-expression of layer markers was also seen in primary tissue. These results suggest that establishing neuronal layer identity in iPSC-derived or primary cortical neurons using canonical marker genes transcripts is unlikely to be informative.

overall_design:
Single cell RNA-seq of 16 iPSC-derived cortical neurons.
This dataset was used for normalization purposes for GSE67835.

middle: E

first: Zameel

last: Cader


title: Genome-wide profiling of the functional DNA methylation landscape at base-pair resolution in human cancer types

first: Manel

last: Esteller

type: Methylation profiling by genome tiling array

first: Holger

last: Heyn


title: Post-licensing specification of eukaryotic replication origins by facilitated Mcm2-7 sliding along DNA

city: New York

first: Iestyn

last: Whitehouse

address: 1275 York Avenue

department: Molecular Biology

institute: Sloan-Kettering Institute

summary: Eukaryotic genomes are replicated from many origin sites that are licensed by the loading of inactive double hexamers of the replicative DNA helicase, Mcm2-7. How eukaryotic origin positions are specified remains elusive. Here we show that, contrary to the bacterial paradigm, eukaryotic origins are not irrevocably defined by selection of the loading site for the replicative helicase, but can shift in position after helicase loading. Using purified proteins, we show that DNA translocases, including RNA polymerase, can push budding yeast Mcm2-7 double hexamers along DNA. Displaced Mcm2-7 double hexamers support DNA replication initiation distal to the loading site in vitro. In yeast cells that are defective for transcription termination, collisions with RNA polymerase induce a shift in origin positions that correlates with the direction of transcription. These results reveal a eukaryotic origin specification mechanism that departs from the classical replicon model, helping eukaryotic cells to negotiate transcription-replication conflict.

overall_design:
4 samples: one replicate for WT at 37C, two replicates for rat1-1 at 37C, and one replicate for rat1-1 at 24C. All are single-end sequenced via Ion Torrent PGM methodology.
rat1 = Nuclear 5' to 3' single-stranded RNA exonuclease; involved in RNA metabolism (http://www.yeastgenome.org/locus/S000005574/overview).
4 ChIP seq samples and their duplicates are submitted. rat1-1 ORC ChIP at 24C and 37C; rat1-1 MCM ChIP at 24C and 37C.

first: Julien

last: Gros

first: Charanya

last: Kumar

first: Gerard

last: Lynch

first: Tejas

last: Yadav

first: Dirk

last: Remus


title: GATA-1 and heme regulate the erythroid cell transcriptome.

city: Madison

first: Kyle

last: Hewitt

state: Wisconsin

address: 1111 Highland Ave.

institute: University of Wisconsin

summary: Alas2 gene encodes the rate-limiting enzyme in heme biosynthesis. CRISPR/Cas9-mediated ablation of two Alas2 intronic cis-elements strongly reduced GATA-1-induced Alas2 transcription, heme biosynthesis, and GATA-1 regulation of other vital constituents of the erythroid cell transcriptome. Bypassing Alas2 function in Alas2 cis-element-mutant (double mutant) cells by providing its catalytic product 5-aminolevulinic acid (5-ALA) rescued heme biosynthesis and the GATA-1-dependent genetic network. We discovered a GATA factor- and heme-dependent circuit that establishes the erythroid cell transcriptome.

overall_design: G1E-ER-GATA-1 WT and double mutant cells were examined. Untreated WT, beta-estradiol-treated WT, beta-estradiol-treated double-mutant, and beta-estradiol/5-ALA-treated double-mutant cells were subjected to RNA-seq.

first: Nobuyuki

last: Tanimura

first: Colin

middle: N

last: Dewey

first: Emery

middle: H

last: Bresnick


title: MicroRNAs are involved in the regulation of ovary development in the pathogenic blood fluke Schistosoma japonicum

city: SHANGHAI

first: GUOFENG

last: CHENG

address: #518,ZIYUE ROAD

institute: CAAS

summary: We report on the small RNA profiles of Schistosoma japonicum (S. japonicum) miRNAs using small RNA deep sequencing in the key stages of male-female pairing, gametogenesis, and egg production.

overall_design: Examination of different miRNAs between males and females in Schistosoma japonicum

first: Guofeng

last: Cheng


title: Transcriptome analysis upon SIN3 or dKDM5/LID knockdown or both under normal  and paraquat induced stress conditions in Drosophila S2 cultured cells

first: Lori

last: Pile

summary: SIN3 the scaffold protein of a histone deacetylase complex interacts with a histone demethylase KDM5 (little imaginal discs - LID) in Drosophila. Reduction of SIN3 or dKDM5/LID both result in similar phenotypes during cell proliferation and wing development. To identify underlying transcriptional changes that may contribute to these phentypic defects we performed whole genome expression analysis in Drosophila cultured cells upon RNAi-mediated knockdown of Sin3A, lid or both. We identified a large number of genes regulated by SIN3, dKDM5/LID or both. While many common genes were regulated by SIN3 and dKDM5/LID an enrichment for genes involved in stress tolerance pathways was observed. Additional RNAseq analysis of expression changes upon knockdown of Sin3A, lid or both under paraquat mediated oxidative stress conditions identified significant changes in genes involved in cell cycle related processes.

overall_design: Drosophila S2 cells were treated with dsRNA targetting Sin3A, lid and both or GFP as control under normal or oxidative stress conitions induced by treatment with paraquat. mRNA profiling of these samples were performed by deep sequencing using Illumina Hiseq2500.Three biological replicates were performed.

first: Ambikai

last: Gajan

first: Mengying

last: Liu

first: Nirmalya

last: Saha


title: Hepatic transcriptome profiling of liver-specific Xbp1 knockout mice fed a high fat diet

first: Richard

last: Green

state: IL

address: Tarry 15, 303 E. Chicago Av.

summary: Xbp1 is an important regulator of unfolded protein response and lipid metabolism. Its dyregulation has been associcated in human NASH. Feeding a high fat diet with fructose/sucrose to mice causes progressive, fibrosing steatohepatitis. This study is to use RNA-Seq to identify differentially expressed genes in hepatic Xbp1 deficient mice livers fed with a high fat diet compared to controls.

overall_design: Hepatic Xbp1 deficient mice or flox controls were fed either regular chow or a high fat diet (n=4). Samples from each cohort were pooled into two replicates.


title: Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [ChIP-Seq]

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Triple negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which there is no targeted therapy. Here we report the preferential and high sensitivity of TNBCs to BET bromodomain inhibitors such as JQ1 manifested by cell cycle arrest in early G1, apoptosis, and induction of markers of luminal epithelial differentiation in vitro and in vivo. The sensitivity of TNBC and other tumor types to BET inhibition establishes a rationale for clinical investigation, and a motivation to understand mechanisms of resistance. After engendering acquired resistance to BET inhibition in previously sensitive TNBCs, we utilized integrative approaches to identify a unique mechanism of epigenomic resistance to this epigenetic therapy. Resistant cells remain dependent on BRD4, confirmed by RNA interference. However, TNBC cells adapt to BET bromodomain inhibition by re-recruitment of unmutated BRD4 to super-enhancers, now in a bromodomain-independent manner. Proteomic studies of resistant TNBC identify hyper-phosphorylation of BRD4 and strong association with MED1. Together, these studies provide a rationale for BET inhibition in TNBC and argue for combination strategies to anticipate clinical drug resistance.

overall_design: ChIP-seq in parental and JQ1 resistant triple negative breast cancer (TNBC) in response to DMSO or JQ1 treatment

first: Shaokun

last: Shu

first: Charles

middle: Y

last: Lin

first: Housheng

last: He

first: James

last: Bradner


title: SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing [CLIP-Seq]

city: Heidelberg

first: Renate

last: Voit

address: Im Neuenheimer Feld 581

department: Division Molecular Biology of the Cell

institute: German Cancer Research Center

summary: SIRT7 is an NAD+-dependent protein deacetylase with important roles in ribosome biogenesis and cell proliferation. Previous studies have established that SIRT7 is associated with RNA polymerase I, interacts with pre-rRNA and promotes rRNA synthesis. Here we show that SIRT7 is also associated with snoRNAs that are involved in pre-rRNA processing and rRNA maturation. Knockdown of SIRT7 impairs U3 snoRNA-dependent early cleavage steps that are necessary for generation of 18S rRNA. Mechanistically, SIRT7 deacetylates U3-55k, a core component of the U3 snoRNP complex, and reversible acetylation of U3-55k modulates the association of U3-55k with U3 snoRNA. Deacetylation by SIRT7 enhances U3-55k binding to U3 snoRNA, which is a prerequisite for pre-rRNA processing. Under stress conditions, SIRT7 is released from nucleoli, leading to hyperacetylation of U3-55k and attenuation of prerRNA processing. The results reveal a multifaceted role of SIRT7 in ribosome biogenesis, regulating both transcription and processing of rRNA.

overall_design: CLIP-seq was performed in Flag-SIRT7-293T cells.

first: Sifan

last: Chen

first: Maximilian

middle: F

last: Blank

first: Aishwarya

last: Iyer

first: Bingding

last: Huang

first: Lin

last: Wang

first: Ingrid

last: Grummt


title: Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [Chem-Seq]

overall_design: Chem-Seq in parental and JQ1 resistant triple negative breast cancer (TNBC)


title: Maternal DNA methylation regulates early trophoblast development

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

summary: Critical roles for DNA methylation in embryonic development are well established, but less is known about the roles of DNA methylation during trophoblast development, the extraembryonic lineage that gives rise to the placenta. Here we dissected the role of DNA methylation in trophoblast development by performing mRNA and DNA methylation profiling of Dnmt3a/3b-null trophoblast. We find that most gene deregulation is explained by an erasure of maternal methylation in the oocyte, but partially independent of loss of imprinting of the trophoblast-essential Ascl2 gene. Our results reveal that maternal DNA methylation controls multiple differentiation and physiological processes in trophoblast via both imprinting-dependent and -independent mechanisms.

overall_design: mRNA-seq and WGBS-seq of maternal Dnmt3a/3b-null trophoblast; mRNA-seq of maternal Ascl2 KO trophoblast

first: Miguel

last: Branco

first: Michelle

last: King

first: Aaron

last: Bogutz

first: Louis

last: Lefebvre

first: Simon

last: Cook

first: Wendy

last: Dean

first: Myriam

last: Hemberger

first: Wolf

last: Reik


title: Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

first: Jenny

address: 16 Divinity Ave

institute: Harvard

summary: Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation. We present slncky, a computational lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-sequencing data and further uses evolutionary constraint to prioritize lncRNAs that are likely to be functionally important. Our automated filtering pipeline is comparable to manual curation efforts and more sensitive than previously published computational approaches. Furthermore, we develop a sensitive alignment pipeline for aligning lncRNA loci and propose new evolutionary metrics relevant for analyzing sequence and transcript evolution. Our analysis reveals that evolutionary selection acts in several distinct patterns, and uncovers two notable classes of intergenic lncRNAs: one showing strong purifying selection on RNA sequence and another where constraint is restricted to the regulation but not the sequence of the transcript.

sample_organism:
Homo sapiens
Mus musculus
Mus musculus castaneus
Rattus norvegicus

overall_design: To study a comprehensive and comparable set of lncRNAs expressed in the pluripotent state, we analyzed RNA-Seq data from pluripotent cells derived from several strains and species, and grown in two physiological conditions. First we derived “naïve” ES cells (ESCs) from each of three different mice strains: 129SvEv, NOD, and Mus musculus castaneus (cast) mouse, a wild mouse subspecies originally from Thailand, as well as naïve induced pluripotent stem (iPS) cells from rat and human. Next, to facilitate comparisons across pluripotent cells from different species, we also cultured mouse and rat cells in “primed” epiblast stem cell (EpiSC) culture conditions, since human iPS cells in culture are much more similar molecularly and functionally to mouse primed EpiSCs rather than to a ground state naïve ESCs. We polyA selected RNA from each cell type and deeply sequenced on HiSeq2500

first: Alexander

last: Shishkin

first: Xiaopeng

last: Zhu

first: Sabah

last: Kadri

first: Itay

last: Maza

first: Jacob

last: Hanna

first: Aviv

last: Regev

first: Manuel

last: Garber


title: Comparison of alternative decapping enzymes to map transcription start sites genome-wide

status: Public on Jan 06 2016

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

institute: EMBL Heidelberg

summary: The production of Tobacco Acid Pyrophosphatase (TAP), an enzyme commonly used for the removal of the 5’cap of eukaryotic mRNAs, has been recently discontinued. Here we performed a comparison of current alternatives for the mapping of 5’cap mRNAs and the associated transcription start sites in Sacharomyces cerevisiae. Specifically we compared TAP with Cap-clip and a Decapping Pyrophosphohydrolase. Our results suggest that Cap-clip is a good alternative for TAP.

overall_design: We used two biological replicates of S. cerevisiae that was grown to exponential phase (OD600 ~1) in rich media (YPAD). Samples where processed until the dephosphorylation step (CIP treatment). After that each sample was split in 4 aliquots: TAP treatment, Cap-Clip treatment, Decapping Pyrophosphohydrolase treatment or no treatment (negative control). From that step all samples are processed in parallel.

first: Vicent

last: Pelechano

first: Lars

last: Steinmetz


title: Coordinated control of senescence by lncRNA UCA1 and a novel CAPERα/TBX3 co-repressor

city: Danville

first: anne

last: moon

address: 100 North Academy Ave

institute: Geisinger CLinic

summary: Coordination of a complex series of transcriptional, structural and signaling events culminates in cellular senescence, a crucial tumor suppressor mechanism. We have discovered a repressor complex composed of TBX3 and CAPERa which functions upstream of the RB and p53 effector pathways and is required to prevent senescence of primary cells and in mouse embryos. TBX3/ CAPERa directly binds and represses transcription and chromatin structure of genes in multiple senescence pathways and the LncRNA UCA1, which we have identified as a novel tumor suppressor. The TBX3/ CAPERa  complex is physically disrupted in oncogene induced senescence, providing a new molecular mechanism for derepression of prosenescence pathways in this system. Our results provide new insight into the oncogenic properties of TBX3, and are the first demonstration of CAPERa and UCA1 function in vivo.

overall_design: mRNA Seq based gene differential expression analysis of two sample types (TBX3, Caper) relative to control and two sample types (pCDNA3.1, UCA1) relative to each other.

first: Pavan

last: Kumar

first: Uchenna

last: Emechebe

first: Richard

last: Smith

first: Sarah

last: Franklin

first: Barry

last: Moore

first: Mark

last: Yandell

first: Stephen

middle: L

last: Lessnick

first: Anne

last: Moon


title: Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

status: Public on Jan 05 2016

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

institute: Ohio University

summary: In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome anno- tation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions.

overall_design: Four RNAseq data sets in total.  Each sample was generated by pooling three independent biological replicate RNA preps

first: Andy

last: Weiss

first: William

last: Broach

last: Wiemels

first: Austin

last: Mogen

first: Kelly

last: Rice

first: Lindsey

last: Shaw


title: Suppression of Transcriptional Drift Extends C. elegans Lifespan by Postponing the Onset of Mortality

city: La Jolla

first: Michael

last: Petrascheck

address: 10550 N. Torrey Pines Rd

department: Chemical Physiology

institute: TSRI

summary: Longevity mechanisms increase lifespan by counteracting the effects of aging. However, whether longevity mechanisms counteract the effects of aging continually throughout life, or whether they act during specific periods of life, preventing changes that precede mortality is unclear. Here, we uncover transcriptional drift, a phenomenon that describes how aging causes genes within functional groups to change expression in opposing directions. These changes cause a transcriptome-wide loss in mRNA stoichiometry and loss of co-expression patterns in aging animals, as compared to young adults. Using Caenorhabditis elegans as a model, we show that extending lifespan by inhibiting serotonergic signals by the antidepressant mianserin attenuates transcriptional drift, allowing the preservation of a younger transcriptome into an older age. Our data are consistent with a model in which inhibition of serotonergic signals slows age-dependent physiological decline and the associated rise in mortality levels exclusively in young adults, thereby postponing the onset of major mortality.

overall_design:
In this study set out to measure aging in the transcriptome by determining drift-variance changes with age in C.elegans. We set up three different cohorts of water or mianserin treated animals. The title of each cohort indicates the treatment (e.g. h2o or mia), the concentration (mia2, mia10, mia50), the day when the treatment was started (e.g. d1= day 1 of adulthood) and the day when the sample was collected (e.g. d10= day 10 of adulthood).
cohort #1: Celegans was treated with water or mianserin (50uM) on day 1 and RNA was harvested on day1 (water only), d3, d5 and day 10 (file titles: h2o d1/d1, h2o d1/d3, h2o d1/d5, h2o d1/d10, mia50 d1/d3,  mia50 d1/d5, mia50 d1/d10)
cohort #2: Celegans was treated with mianserin (50uM) starting on day 3, and day 5, RNA was harvested on day 5 or 10 (file titles: mia50 d3/d10, mia50 d5/d10, mia50 d3/d5)
cohort #3: Celegans was treated with mianserin 2 uM and 10 uM Mianserin on day 1 and Rna harvested on day 5 (file titles: mia2 d1/d5, mia10 d1/d5)

first: Ryan

last: Thompson


title: Transcriptomic Analysis of the Hippocampus from Six Inbred Strains of Mice Suggests Basis for Sex-Specific Susceptibility and Severity of Neurological Disorders

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

summary: Identifying sex differences in gene expression within the brain is critical for determining why multiple neurological and behavioral disorders differentially affect males and females. Several are more common or severe in males (e.g., autism and schizophrenia) or females (e.g., Alzheimer’s disease and depression). We analyzed transcriptomic data from the mouse hippocampus of six inbred strains (129S1/SvImJ, A/J, C57BL/6J, DBA/1J, DBA/2J and PWD/Ph), to provide a perspective on differences between male and female gene expression. Our data show that: 1) significant gene expression differences in males versus females varies substantially across the strains, 2) 12 genes exist that are differentially expressed across the inbred strains (termed core genes), and 3) there are >2,600 significantly differentially expressed genes (DEGs) among the strains (termed non-core genes). We found that DBA/2J uniquely has a substantial majority (89%) of DEGs that are more highly expressed in females than males; 129/SvImJ is the most strongly male-biased with a majority (69%) of DEGs that are more highly expressed in males. To gain insight into the sex-biased DEGs, we examined gene ontology, pathway and phenotype enrichment and found significant enrichment in phenotypes related to abnormal nervous system morphology and physiology, among others. In addition, several pathways are enriched significantly, including Alzheimer’s disease (AD), with 32 genes implicated in AD, 8 of which are male-biased. Three of the male-biased genes have been implicated in a neuroprotective role in AD. Our transcriptomic data provide new insight into understanding the possible genetic bases for sex-specific susceptibility and severity of brain disorders.

overall_design: Hippocampal mRNA from adult males and females of six inbred strains of mice were analyzed by RNA sequencing of 3 biological replicates using an Illumina HiSeq 2500

first: Surjyendu

last: Ray

first: Crystal-Dawn

last: Badger

first: Joseph

last: Bundy

first: Michelle

last: Arbeitman

middle: S

last: Nowakowski


title: EBNA3 proteins regulate EBNA2 binding to distinct RBPJ genomic sites

first: Eric

last: Johannsen

address: 1111 Highland Ave

department: Department of Medicine

institute: UW-Madison

summary: We report the application of ChIP Seq to study the Epstein Barr Virus Nuclear Antigen EBNA3A, EBNA3B, EBNA3C, an essential transcriptional regulator involved in the transformation of Resting B Lymphocytes to the immortalized Lymphoblast Cell Lines.

overall_design: Examination of EBNA3A, EBNA3B and EBNA3C protein genome binding in LCLs.

first: Anqi

last: Wang

first: Rene

last: Welch

first: Bo

last: Zhao

first: Tram

last: Ta

first: Sündüz

last: Keleș


title: Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [RNA-Seq]

first: Kornelia

last: Polyak

overall_design: RNA-Seq in parental and JQ1 resistant triple negative breast cancer (TNBC) in response to DMSO or JQ1 treatment over time

first: Shaokun

last: Shu

first: Charles

last: Lin

first: Housheng

last: He

first: James

last: Bradner


title: Response and resistance to BET bromodomain inhibitors in triple negative breast cancer

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

overall_design: Refer to individual Series


title: A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array


title: A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing [sRNA-seq]

summary: Co-transcriptional RNA processing and surveillance factors mediate heterochromatin formation in fission yeast. In addition to RNAi, RNA elimination machinery including MTREC (Mtl1-Red1 core) and the exosome are involved in facultative heterochromatin assembly, however, the exact mechanisms remain unclear. Here we show that RNA elimination factors cooperate with the conserved exoribonuclease Dhp1/Rat1/Xrn2, which couples pre-mRNA 3’-end processing to transcription termination, to promote premature termination and facultative heterochromatin formation at meiotic genes. Dhp1 also affects termination of transcripts at genes that are targets of RNAi-mediated heterochromatin assembly. Moreover, Dhp1 facilitates constitutive heterochromatin formation and silencing at centromeric and mating-type loci. Remarkably, we find that Dhp1 interacts with the Clr4/Suv39h methyltransferase complex and acts directly to nucleate heterochromatin. Our results uncover a novel role for 3’-end processing and termination machinery in gene silencing through premature termination and suggest that non-canonical termination by Dhp1 and RNA elimination factors is linked to heterochromatin assembly. These findings have important implications for understanding mechanisms of gene silencing in higher eukaryotes.

overall_design: Sequencing and analysis of small RNA in two S. pombe mutants

first: Venkata

middle: R

last: Chalamcharla

first: H

last: Diego Folco

first: Jothy

last: Dhakshnamoorthy

middle: I


title: Next-generation sequencing for the fat mass and obesity-associated protein (FTO) binding mRNA

city: Taoyuan

first: Chao-Yung

address: 5 Fu-Hsing street

department: Cardiology

country: Taiwan

institute: Chang Gung Memorial Hospital

summary:
Purpose: The goals of this study are to investigate the mRNAs that bind to the FTO protein in the white fat tissue from mice.

Methods: 1. White fat from CAG promoter driven transgenic Flag-tagged FTO mice were extracted with RNA protected. 2. Flag-FTO proteins were immunoprecipitated with control IP using IgG. 3. The immunoprecipitated RNAs were deep sequenced and analyzed.

Results: We focused on the mRNAs which have functions related to lipid metabolism and homeostasis.

overall_design: Immunoprecipitated RNAs profiles from Flag-FTO IP and IgG IP were generated by deep sequencing.

first: Chao


title: Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as a therapeutic strategy to target the IRF4 network in multiple myeloma (ChIP-Seq)

first: Barbara

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

summary: Pharmacological inhibition of chromatin co-regulatory factors represents a clinically validated strategy to modulate oncogenic signaling through selective attenuation of gene expression. Here, we demonstrate that CBP/EP300 bromodomain inhibition preferentially abrogates the viability of multiple myeloma cell lines. Phenotypic effects are preceded by the direct transcriptional suppression of the lymphocyte-specific transcription factor IRF4 and the subsequent down-regulation of the IRF4 transcriptional program. Ectopic expression of IRF4 antagonizes the phenotypic effects of CBP/EP300 bromodomain inhibition and prevents the suppression of the IRF4 target c-MYC. These findings suggest that CBP/EP300 bromodomain inhibition represents a viable therapeutic strategy for targeting multiple myeloma and other lymphoid malignancies dependent on the IRF4 network.

overall_design: A total of 13 ChIP-seq samples were sequenced.  Samples were treated with control (DMSO) or test compound (2.5 uM SGC-CBP30 or 0.25uM CPI267203) for 6 hours.  Signal from input samples was included to subtract background signal from each ChIP-seq sample.  Antibodies used were against p300, H3K18ac, H3K27ac, or BRD4.

first: Andrew

last: Conery

first: Richard

middle: C

last: Centore

first: Charlie

last: Hatton

first: Robert

last: Sims III


title: Single-cell transcriptomics reveals unique features of human pancreatic islet cell subtypes

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: We report the single-cell RNA-seq based identification of 6 known human islet cell types (alpha cells, beta cells, delta cells, pp cells, acinar cells and duct cells) based on the expression of known marker genes. We further assess cell type specific gene expression and suggest novel marker genes for several cell types.

overall_design: Transcriptional dissection of human pancreatic islets of one donor using single-cell RNA-seq

first: Jin

last: Li

first: Johanna

last: Klughammer

first: Matthias

last: Farlik

first: Thomas

last: Penz

first: Andreas

last: Spittler

first: Charlotte

last: Barbieux

first: Ekaterine

last: Berishvili

first: Stefan

last: Kubicek


title: Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as a therapeutic strategy to target the IRF4 network in multiple myeloma


title: NANOG metabolically reprograms tumor-initiating stem-like cells in oxidative phosphorylation and fatty acid metabolism

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

summary: Stem cell markers such as NANOG have been implicated in various cancers; however, the functional contribution of NANOG to cancer pathogenesis has remained unclear. In the present study, we show that Toll-like receptor 4 (TLR4) signaling phosphorylates E2F1 to transactivate NANOG. Down-regulation of Nanog significantly reduces tumor development. In the search for the NANOG-dependent mechanisms underlying growth of tumor-initiating stem-like cells (TICs), NANOG ChIP-seq identifies the genes associated with mitochondrial metabolic pathways.

overall_design: Genome wide Identification of Nanog binding partners in tumor initating stem cells

first: Chia-Lin

last: Chen

first: Dinesh

last: Kumar

first: Jun

last: Xu

first: Linda

last: Sher

first: Sonja

last: Hess

first: Keigo

last: Machida


title: Cytokine-mediated differentiation reflects genome-wide loss of a uSTAT transcriptional program

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

summary: uSTAT transcriptional program

overall_design: HPC7 cells were fixed with either 1% formaldehyde for 10 mins. Chromatin was isolated, sonicated for 7 mins (30 sec on, 30 sec off), and specific antibodies were used to pull down the transcription factors of insterest after a pre-clearing step. Chromatin was washed, de-crosslinked, amplified, size selected by gel purification and sequenced.

first: Rebecca

last: Hannah

first: Hyun

middle: J

last: Park

first: Juan

first: Simon

last: Biddie

first: Ana

last: Leal-Cervantes

first: Veronika

last: Sexl

first: Berthold

first: Anthony

last: Green


title: Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

city: Exeter

first: Nick

last: Owens

state: Exeter

address: Barrack Road

institute: University of Exeter Medical School

summary:
Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development where rapid changes in gene expression dictate cell fate decisions. By ultra-high frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by 8 orders of magnitude. Ordering genes by expression dynamics, we find temporal synexpression predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.

Gene expression proﬁles may be visualized at http://genomics.crick.ac.uk/apps/profiles/

overall_design: High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing.

middle: D

first: Ira

last: Blitz

first: Maura

last: Lane

first: Ilya

last: Patrushev

first: John

last: Overton

first: Michael

last: Gilchrist

first: Ken

middle: W

last: Cho

first: Mustafa

middle: K

last: Khokha


title: Next generation sequencing of A375 melanoma cell line revealed a complex regulatory network when IGFBP5 overexpressed

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

summary: IGFBP5, a critical regulators of insulin-like growth factors, has been reported to be involved in many kinds of carcinogenesis and cancer metastases. The role of IGFBP5 in human malignant melanoma (MM), however, remains largely unknown. In this study, we demonstrated that IGFBP5 was aberrantly expressed in human melanoma cells and cancer tissues. Overexpression of IGFBP5 dramatically inhibited the proliferation, migration and invasion of human melanoma cells, whereas knockdown of IGFBP5 by shRNA resulted in the opposite effects, enhanced the cell proliferation, migration and metastasis. In addition, IGFBP5 overexpression suppressed the growth and metastasis of melanoma xenograft tumor in vivo and IGFBP5 overexpression inhibited epithelial–mesenchymal transition (EMT) phenotype and stem cell property of tumor cell, with decreased expression of HIF1α, E-cadherin and stem cell markers NANOG, SOX2, OCT4, KLF4 and CD133. Moreover, IGFBP5 exhibited its growth inhibitory activity through inhibition of extracellular signal-regulated Kinase (ERK) and P38-MAPK signaling pathway. Taken together, our findings indicate that IGFBP5 acts as tumor suppressor roles in MM through the modulation of ERK1/2 and P38-MAPK signaling pathway as well as EMT procession and cell stemness, suggesting IGFBP5 as a novel target for human melanoma diagnosis and therapy.

overall_design: mRNA profiles of IGFBP5 over expression (OE) in A375 and A375 cell line were generated using Ion torrent

first: Xiangdong

last: Fang


title: Genome-wide binding profiles of an artificial zinc finger protein with or without a KLF3 functional domain

city: UNSW Sydney

first: WOOI FANG

last: LIM

state: NSW

address: School of Biotechnology and Biomolecular Sciences

department: BABS

country: Australia

institute: University of New South Wales

summary:
Transcription factors are often regarded as having two distinct components: a DNA binding domain (DBD) to allow binding to the regulatory region of a target gene and a trans-acting functional domain (FD) to modulate gene expression. Recently, it is becoming clear that the DBDs of transcription factors alone are incapable of providing sufficient specificity to account for the highly complex genomic structures in eukaryotes. Other regions, outside of the DBD, may play a role in transcription factor DNA binding specificity in vivo.
In order to test this hypothesis, we examined a model zinc finger transcription factor, Krüppel-like factor 3 (KLF3) with a FD that recruits partner proteins for its repressive activity and a three zinc finger DBD. Previously, we showed that deletion of the entire KLF3 FD reduced DNA binding across the genome. This implied the importance of the FD for in vivo DNA binding specificity. In the current study, we fused the KLF3 FD onto an unrelated, but well characterised Artificial Zinc Finger (AZF) targeting a standard target gene, VEGF-A.  We compared the genomic DNA binding profile of this chimeric KLF3 construct, termed KLF3FD-AZF, to that of the AZF alone. Chromatin Immunoprecipitation followed by next generation sequencing was used to assess genomic wide DNA-binding of these AZFs. Remarkably, in these gain-of-function experiments, we again observed that the KLF3 FD is critical for in vivo DNA binding specificity. The addition of KLF3 FD increased the number of binding sites by more than two fold compared to the AZF alone. KLF3 FD also directed more binding to the promoter regions. Further investigations of these acquired sites identified a substantial portion of these sites as the known endogenous KLF3 bound regions, whilst others contain sequences that are similar but not identical to the predicted AZF target sequence.
These results clearly demonstrate that the specific localisation of this model transcription factor to target genes is not solely dependent on the DBD and that the regions outside of this domain may also play an important role.

overall_design: ChIP-Seq experiments were performed on four HEK293 cell lines, two each stably expressing AZF or KLF3FD.AZF or KLF3FD only (two biological replicates). Input samples were included as controls.

first: Wooi

last: Lim

first: Jon

last: Burdach

first: Alister

middle: P

last: Funnell

first: Richard

last: Pearson

first: Kate

last: Quinlan

first: Merlin

last: Crossley


title: Spatial gene expression gradients underlie prominent heterogeneity of CA1 pyramidal neurons

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

summary: Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types.  This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but may also be further hampered by prominent within-class variability.  Here, we considered a well-defined, canonical neuronal population – hippocampal CA1 pyramidal cells – and systematically examined the extent and spatial rules of transcriptional heterogeneity.  Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous expression gradients, producing a profile consistent with a multifarious continuum of cells.  This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits.

overall_design: Hippocampal RNA profiles were generated by deep sequencing on Illumina HiSeq 2500, with three biological replicates per population

first: Nelson

last: Spruston


title: Next Generation Sequencing of PKD2 mutant mice kidneys

city: Dallas

first: Ronak

last: Lakhia

state: Texas

address: 5323 Harry Hines

institute: UTSW

summary: This Study sought to understand the differential gene expression profile of Pkd2 mutant mice kidneys in the setting of miR-21 deletion

overall_design: 4 Wild type mice, 3 Pkd2 Knockout mice and 3 Pkd2-miR-21 knockout mice were analyzed

first: Vishal

last: Patel


title: Transcriptional effects of I-PpoI induced DNA double strand breaks in mouse lymphocytes

status: Public on Jan 04 2016

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

summary: DNA double-strand breaks (DSBs) and their repair can cause extensive epigenetic changes. As a result, DSBs have been proposed to promote transcriptional and, ultimately, physiological dysfunction via both cell-intrinsic and cell-non-autonomous pathways. Studying the consequences of DSBs in higher organisms has, however, been hindered by a scarcity of tools for controlled DSB induction. Using a mouse model for both tissue-specific and temporally controlled DSB formation, we investigated the transcriptional response to break repair.

overall_design: Transcriptional profiling of lymphocytes in spleen and thymus by RNA-Seq, with and without I-PpoI knock-in.

first: Jyeongkyu

last: Kim

first: Andy

last: Tran

last: Sinclair

first: Philipp

last: Oberdoerffer


title: The apoptotic network and expression of BH3-containing proteins predict phenotypic response to BET bromodomain inhibitors

first: Barbara

middle: M

last: Bryant

summary: Small molecule inhibitors of the bromodomain and extraterminal (BET) family of proteins are in clinical trials for a variety of cancers, but patient selection strategies are limited.  This is due in part to the heterogeneity of response following BET inhibition (BETi), which includes differentiation, senescence, and cell death in subsets of cancer cell lines.  To elucidate the dominant features defining response to BETi, we carried out phenotypic and gene expression analysis of both treatment naïve cell lines and engineered tolerant lines.  We found that both de novo and acquired tolerance to BET inhibition are driven by the robustness of the apoptotic response and that genetic or pharmacological manipulation of the apoptotic signaling network can modify the phenotypic response to BETi.  We further identify that ordered expression of the apoptotic genes BCL2, BCL2L1, and BAD significantly predicts response to BETi.  Our findings highlight the role of the apoptotic network in response to BETi, providing a molecular basis for patient stratification and combination therapies.

overall_design: Gene expression profiling of A375 melanoma cells or NOMO-1 AML cells treated with DMSO or the BET inhibitor, CPI203.  Also, gene expression profiling of the respective derived BETi-tolerant cells treated with DMSO or CPI203.

first: Andrew

last: Conery

last: Centore

first: Kerry

last: Spillane

first: Nicole

middle: E

last: Follmer

first: Charlie

last: Hatton

first: Patricia

last: Greninger

first: Arnaud

last: Amzallag

first: Cyril

last: Benes

first: Jennifer

middle: A

last: Mertz

first: Robert

last: Sims


title: Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent [RNA-Seq]

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: Nrf2(A502Y) mutant failed to recognize cis-element required for induction of Nrf2 target genes.To examine whether Nrf2(A502Y) supports expression of a distinct gene set from that supported by Nrf2, RNA-Seq analysis was performed. We compared gene expression profiles in peritoneal macrophages from Nrf2+/+ and Nrf2AY/AY mice between basal and DEM (which is an electorophilic stress agent promoting Nrf2 induction)-treated conditions.

overall_design: mRNA profiles of wild type (WT) and Nrf2AY/AY (AY) mutant macrophages under basal and DEM-treated condition were generated by deep sequencing, in triplicate.

first: Akihito

last: Otsuki

first: Suzuki

last: Mikiko

first: Fumiki

last: Katsuoka

first: Kouhei

last: Tsuchida

first: Hiromi

last: Suda

first: Masanobu

last: Morita

first: Ritsuko

last: Shimizu


title: Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as a therapeutic strategy to target the IRF4 network in multiple myeloma (RNA-Seq)

first: Barbara

last: Bryant

overall_design: Through the use of CBP/EP300 bromodomain inhibitors (CBP/EP300i), we demonstrate that MYC expression in BETi-resistant cells is dependent on CBP/EP300 bromodomains and that treatment with CBP/EP300i restores phenotypic sensitivity.

first: Andrew

last: Conery

first: Richard

last: Centore

last: Sims III


title: Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent


title: Pioneer factor FOXA1 defines GATA2- and AR-mediated transcriptional program in prostate cancer

status: Public on Jan 11 2016

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University


title: Integrated metabolomics, transcriptomics and proteomics identifies metabolic pathways affected by Anaplasma phagocytophilum infection in tick cells

city: Ciudad Real

first: Jose

last: De La Fuente

state: Ciudad Real

address: Ronda de Toledo s/n

institute: SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM

summary: Anaplasma phagocytophilum is an emerging zoonotic pathogen that causes human granulocytic anaplasmosis. These intracellular bacteria establish infection by affecting cell function in both the vertebrate host and the tick vector, Ixodes scapularis. Previous studies have characterized the tick transcriptome and proteome in response to A. phagocytophilum infection. However, in the post-genomic era, the integration of omics datasets through a systems biology approach allows network-based analyses to describe the complexity and functionality of biological systems such as host-pathogen interactions and the discovery of new targets for prevention and control of infectious diseases. This study reports for the first time a systems biology integration of metabolomics, transcriptomics and proteomics data to characterize essential metabolic pathways involved in the response of tick cells to A. phagocytophilum infection. The results showed that infection affected protein processing in endoplasmic reticulum and glucose metabolic pathways in tick cells. These results supported tick-Anaplasma co-evolution by providing new evidence of how tick cells limit pathogen infection, while the pathogen benefits from the tick cell response to establish infection. The results suggested that A. phagocytophilum induces protein misfolding to limit the tick cell response and facilitate infection, but requires protein degradation to prevent ER stress and cell apoptosis to survive in infected cells. Additionally, A. phagocytophilum may benefit from the tick cell’s ability to limit bacterial infection through PEPCK inhibition leading to decreased glucose metabolism, which also results in the inhibition of cell apoptosis that increases infection of tick cells. These results support the use of this experimental approach to systematically identify tick cell pathways and molecular mechanisms involved in tick-pathogen interactions

overall_design: Two samples with two replicates each were analyzed. Samples included Ixodes scapularis ISE6 cells uninfected (control) and infected with Anaplasma phagocytophilum human NY18 isolate.

first: Margarita

last: Villar

first: Nieves

last: Ayllón

first: Pilar

last: Alberdi

first: Andrés

last: Moreno

first: María

first: Raquel

last: Tobes

first: Lourdes

last: Mateos-Hernández

first: Sabine

last: Weisheit

first: Lesley

last: Bell-Sakyi

first: José

last: de la Fuente


title: A designed inhibitor of p53 aggregation rescues p53 tumor-suppression in ovarian carcinomas

first: Sanaz

last: Memarzadeh

state: CA - California

address: 555 Westwood Plaza

department: Departments of Obstetrics and Gynecology

institute: University of California, Los Angeles

summary: Half of all human cancers lose p53 function by missense mutations, with an unknown fraction of these containing p53 in a self-aggregated, amyloid-like state. Here we show that a cell-penetrating peptide, ReACp53, designed to inhibit p53 amyloid formation, rescues p53 function in cancer cell lines and in organoids derived from high-grade serous ovarian carcinomas (HGSOC), an aggressive cancer characterized by ubiquitous p53 mutations. Rescued p53 behaves similarly to its wild-type counterpart in regulating target genes, reducing cell proliferation and increasing cell death. Intraperitoneal administration decreases tumor proliferation and shrinks xenografts in vivo. Our data show the effectiveness of targeting a specific aggregation defect of p53 and its potential applicability to HGSOCs.

overall_design: Vehicle vs. ReACp53 treatment in 4 different samples: 2 cell lines (MCF7 w/ WT p53 as negative control and OVCAR3 w/ R248Q p53) and 2 clinical specimens (primary cells from patient #8 w/ WT p53 as negative control and primary cells from patient #1 w/ R248Q p53)

first: Alice

last: Soragni

first: David

last: Eisenberg

first: Jing

last: Lu

first: Matteo

last: Pellegrini


title: Transcriptomic study (RNAseq) of Brachypodium distachyon ecotypes Bd21 and Bd2-3 under submergence stress

city: Tuxtepec, OAX

first: Julian

last: Pena-Castro

state: South America

address: Circuito Central 200

department: Biotechnology

country: Mexico

institute: Universidad del Papaloapan

summary:
Purpose: The goal of this study is to compare the transcriptomes expressed during submergence stress of two Brachypodium distachyon ecotypes with contrasting survival under this stress. Bd21 is a submergence sensitive ecotype with EC50 of 2.5 days and Bd2-3 is a tolerant ecotype with EC50 of 4 days.
Methods (Stress): Brachypodium Bd21 and Bd2-3 plants (14-day-old, 6 leaves stage) were submerged in a water column of 30 cm inside opaque-wall plastic tanks. Light still reached the plants at 40 μE m−2 s−1. Ecotypes were submerged side-by-side in a randomized manner; only plants submerged in the same tank were compared. Controls were grown in plastic tanks without a water column. Submergence stress started at ZT14 (2h before night, long-day regime 16h light, 8h dark). Above ground tissue was collected after 48 h submergence stress in liquid nitrogen and stored at -80ºC in an ultra freezer until further processing. Tissue was ground to powder with mortar, pestle and liquid nitrogen avoiding thawing. Control and submerged total RNA was extracted with TRIzol reagent (Invitrogen, 15596018), purified with Direct-zol RNA mini prep columns (Zymo Research, R2050) and digested in-column with DNAse I (ThermoScientific, #EN0521). RNA integrity and concentration was verified in denaturing 1.0% agarose gels, Nanodrop 2000 (ThermoScientific) and in a Bioanalyzer 2100 (Agilent) with the integrated software 2100 Expert, samples had a RNA Integrity Number (RIN) between 6.4-7.2 characteristic of aerial plant tissue (Babu and Gassman, 2011). Total RNA extracted from control and submerged tissue from three independent experiments consisting each of four individuals were used to construct cDNA indexed libraries and sequenced in a HiSeq2500 (Illumina) at 1x50 format, making a total of 12 sequenced libraries (tolerant and intolerant ecotype, control and submerged, all experimental triplicates) in a 2-lane format. RNA integrity, library construction and sequencing was performed as a service at the Unidad Universitaria de Secuenciación Masiva, Instituto de Biotecnología, Universidad Nacional Autónoma de México (IBT-UNAM).Differential Gene Expression (DGE) analysis was performed with edgeR using a generalized linear model and false discovery rate <0.05 (FDR). To group differentially expressed transcripts a logFC value of 1.5 (up-regulated) or -1.5 (down-regulated) and a FDR <0.05x10-5 were selected. GO analysis of differential transcripts was performed at phytozome.org
Results: We identified commonly up-regulated genes (317) and exclusively up-regulated in Bd2-3 (466) or Bd21 (706). Regarding down-regulation, 330 transcripts were common, an exclusively 851 and 1026 for Bd2-3 and Bd21, respectively. GO analysis indicated that oxidative stress, pathogen responses and nitric oxide homeostasis were the most differential characteristics of tolerant ecotype Bd2-3.
Conclusions: The use of triplicate RNAseq data of transcriptomes expressed in ecotypes with contrasting tolerance to submergence under long-day light regime, allowed us to identify common responsive routes such as SUSY, glycolysis, anaerobic routes (alanine, ethanol, lactate, GABA) and glyoxylate cycle. It also enabled us to discover integrated oxidative stress and NO homeostasis pathways that are differentially expressed in the tolerant ecotype. We expect that this information can be translated to agricultural relevant plants to increase our knowledge and biotechnological possibilities on plant submergence stress.

overall_design: Sequenced libraries (triplicates, HiSeq2500 Illumina, 1x50 format) of aerial tissue (control and 24h submergence stress) of Brachypodium distachyon Bd21 (sensitive) and Bd2-3 (tolerant).

first: Julián

last: Peña-Castro

first: Piyada

last: Juntawong


title: Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans

first: Aleksandra E

last: Kornienko

address: Lazarettgasse 14, AKH BT 25.3, 3rd floor

institute: CeMM  Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary:
Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-specific expression compared to mRNAs. An unexplored factor potentially confounding lncRNA identification is inter-individual expression variability. Here, we characterize lncRNA natural expression variability in human primary granulocytes.

Results: We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from ten healthy individuals, identifying multiple lncRNAs absent from reference annotations, and use this to investigate three known features (higher tissue-specificity, lower expression, and reduced splicing efficiency) of lncRNAs relative to mRNAs. Expression variability was examined in seven individuals sampled three times at one or more than one month intervals. We show that lncRNAs display significantly more inter-individual expression variability compared to mRNAs. We confirm this finding in 2 independent human datasets by analyzing multiple tissues from the GTEx project and lymphoblastoid cell lines from the GEUVADIS project. Using the latter dataset we also show that including more human donors into the transcriptome annotation pipeline allows identification of an increasing number of lncRNAs, but minimally affects mRNA gene number.

Conclusions: A comprehensive annotation of lncRNAs is known to require an approach that is sensitive to low and tight tissue-specific expression. Here we show that increased inter-individual expression variability is an additional general lncRNA feature to consider when creating a comprehensive annotation of human lncRNAs or proposing their use as prognostic or disease markers.

overall_design: We used PolyA+ RNA-seq data from human primary granulocytes of 10 healthy individuals to de novo annotate lncRNAs and mRNAs in this cell type and ribosomal depleted (total) RNA-seq data from seven of these individuals sampled three times to analyze lncRNA amd mRNA expression variability

first: Aleksandra

first: Christoph

last: Dotter

first: Florian

last: Pauler

first: Denise

last: Barlow


title: MLX transcriptional regulation in muscle cells

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: This study set out to identify MLX transcriptional targets in muscle cells. C2C12 Myoblasts were virally transduced to increase MLX activity, by overexpression of the wild-type protein; and to decrease MLX activity by overexpression of a dominant negative MLX protein and by shRNA induced knockdown of MLX. Transcripts that were significantly and consistently regulated by the different modes of MLX modulation were identified. The largest proportion of these were genes encoding secreted proteins including growth factors, cytokines and extracellular proteins. We therefore conclude that MLX can regulate myokine transcripts.

overall_design: mRNA profiles from C2C12 muscle cells with increased and decreased MLX activity were examined.

first: Liam

last: Hunt

first: Fabio

last: Demontis


title: Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

summary: Parental dietary conditions can influence the metabolic traits of offspring. In mice, paternal consumption of low protein diet alters cholesterol and lipid metabolism of progeny. Here, we examine RNA species expressed in male reproductive tissues of mice. Protein restriction leads to altered levels of multiple small RNAs in mature sperm, as well as throughout the male reproductive tract, with decreased levels of let-7 family members and increased levels of 5’ fragments of tRNA-Gly isoacceptors. Intriguingly, tRNA fragments are scarce in the testis, but their levels increase in sperm during posttesticular maturation in the epididymis. We find that epididymosomes – extracellular vesicles which fuse with sperm during epididymal transit – exhibit RNA payloads closely matching those of mature sperm, and can deliver tRNA fragments to immature sperm in vitro both in mouse and in bull. Finally, we show that tRNA-Gly-GCC fragments play a role in repressing genes associated with the endogenous retroelement MERVL, both in ES cells and in preimplantation embryos. Our results shed light on small RNA biogenesis during post-testicular sperm maturation, and link tRNA fragments to regulation of endogenous retroelements active in the early embryo.

overall_design: E14 mESCs  were transfected with LNA-containing oligos antisense to tRF-GG or GFP-esiRNA as control, then either total RNA was isolated or 80S ribosomes were isolated from Rnase-digested whole cell lysate, and footprints between 26-32nt were collected for ribosome profiling library construction using a kit-free protocol based on Heyer et al. 2015 NAR.

first: Oliver

last: Rando

first: Xinyang

last: Bing


title: Expression profiles of cultured human epididymis cells reveal the functional diversity of caput, corpus and cauda regions.

city: Chicago

first: Ann

last: Harris

state: Illinois

address: 2430 N Halsted

institute: Northwestern University

summary:
Purpose: To compare the transcriptome profiles (RNA-seq) of cultured human epididymis cells and tissue from the caput, corpus and cauda regions of the human epididymis.
Methods: Human epididymis tissue was obtained with Institutional Review Board approval from 3 patients (UC05, UC06, UC09, range: 22 - 36 years) undergoing inguinal radical orchiectomy for a clinical diagnosis of testicular cancer. None of the epididymides had extension of the testicular cancer. The three anatomical regions: caput, corpus and cauda, were separated and segments of each snap frozen. Adult human epididymis epithelial (HEE) cultures were also established from  tissue. RNA was extracted from both tissue and cultured HEE cells and RNA-seq libraries prepared (TruSeq RNA Sample Preparation Kit v2, Low-Throughput protocol, Illumina). Libraries were sequenced on Illumina HiSeq2500 machines. Data were analyzed using TopHat and Cufflinks.
Results: Libraries generated ~19-39 million reads per library from the cells (95-99% mapping to the human genome) and ~14-39 million reads from the tissue samples (84-99% mapped). Raw reads were aligned to the genome with Tophat and gene expression values were processed using Cufflinks as Fragments Per Kilobase per Million mapped fragments (FPKM). FPKM values were subject to principle component analysis, which revealed that though caput, corpus and cauda cell samples respectively from UC05, UC06 and UC09 clustered together. RNA-seq data from the 3 biological replicas (UC05, UC06 and UC09) of caput, corpus and cauda were pooled for further analysis. Cufflinks was used to determine differentially expressed genes (DEGs) between caput, corpus and cauda cells, combined from the 3 donors. The gene expression profiles of corpus and cauda are remarkably similar and both differ from the caput to a similar degree. We identified ~40 genes differentially expressed between corpus and cauda and more than 1600 DEGs between caput and cauda. The DEGs for each comparison (caput and corpus/cauda) were analysed using a gene ontology process enrichment analysis (DAVID, Huang et al., NAR 2009;37:1-13, Huang et al., 2009 Nat Prot 4:44-57).
Conclusions: Here we describe an in depth analysis of the gene expression repertoire of primary cultures of epithelial cells and intact tissues from each region of the adult human epididymis. These data will be valuable to decipher pathways of normal epididymis function and aspects of epididymis disease that cause male infertility.

overall_design: RNA-seq was performed on libraries generated from caput, corpus and cauda-derived cultured cells (passage 2 or 3) from 3 donors and on caput, corpus and cauda tissue from 2 of the same donors. Donor age range: 22 - 36 years.

first: James

last: Browne

first: Rui

last: Yang


title: Genome-wide mapping of Nup98HoxA9- and Crm1-binding sites in ES cell lines.

city: Ibaraki

first: Masahiro

last: Oka

state: Osaka

address: 7-6-8 Saito-Asagi

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

summary: We used ChIP-seq to examine the genome-wide binding of Nup98-HoxA9 and Crm1 in ES cells. Our analysis revealed that Nup98-HoxA9 is highly and preferentially targeted to specific chromatin sites, particularly near Hox cluster regions where the export factor Crm1 is originally prebound.

overall_design: chromatin immunoprecipitation

first: Yoshihiro

last: Yoneda

first: Kazumitsu

last: Maehara

first: Saki

last: Hirata

first: Yasuyuki

last: Ohkawa


title: Comparison of expression profiles of WT and Nrf2AY/AY mutant macrophages under electrophilic stress agent [ChIP-Seq]

first: Masayuki

last: Yamamoto

summary: Nrf2(A502Y) mutant macrophages Nrf2(AY/AY) macrophages were more susceptible to toxicity of xenobiotics. To confirm preferences of binding sequences of Nrf2 and Nrf2A502Y in vivo, we performed ChIP-Seq analyses using an anti-Nrf2 antibody on the DEM-treated peritoneal macrophages derived from Nrf2+/+ and Nrf2AY/AY mice.

overall_design: Chromatin occupancy of wild type (WT) Nrf2 and Nrf2AY mutant under DEM-treated condition were analyzed by deep sequencing, in triplicate

first: Akihito

last: Otsuki

first: Suzuki

last: Mikiko

first: Fumiki

last: Katsuoka

first: Kouhei

last: Tsuchida

first: Hiromi

last: Suda

first: Masanobu

last: Morita

first: Ritsuko

last: Shimizu


title: MAGE-A1 Promotes Proliferation, Migration and Invasion of Human Melanoma Cells through RNA-SEQ Analysis via Affecting C-JUN-IL8-ARHGAP29 Network

first: yadong

last: yang

summary: To define the role of MAGE-A1 in melanoma growth and metastasis, we performed RNA-seq analysis on MAGE-A1 overexpression (OE) and knockdown (KD) models in A375 human melanoma cell line. Our results revealed that overexpression of MAGE-A1 dramatically promoted proliferation, migration, and invasion of human melanoma cells in vitro and down-regulated of MAGE-A1 inhibited tumor cell proliferation and invasion. Furthermore, MAGE-A1 exerts its tumor promoting activity via activating including ERK-MAPK signaling pathway by RNA-seq analysis.

overall_design: mRNA profiles of MAGE-A1 over expression (OE), knockdown (KD),  pcDNA-vector control, and pRNAT-scramble control in A375 cell line were generated using Ion torrent

first: Xiangdong

last: Fang


title: RUNX1B expression distinguishes megakaryocytic and erythroid lineage fate in adult hematopoiesis

city: Manchester

first: Georges

last: Lacaud

address: Wilmslow Road

department: Cancer Research UK Manchester Institute

institute: University of Manchester

summary: The Core Binding Factor (CBF) protein RUNX1 is a master regulator of definitive hematopoiesis, crucial for hematopoietic stem cell (HSC) emergence during ontogeny, which also plays vital roles in adult mice, in regulating the correct specification of numerous blood lineages. Akin to the other mammalian Runx genes, Runx1 has two promoters P1 (distal) and P2 (proximal) which generate distinct protein isoforms. The activities and specific relevance of these two promoters in adult hematopoiesis remain to be fully elucidated. Utilizing a dual reporter model, we demonstrate here that the distal P1 promoter is broadly active in adult hematopoietic stem and progenitor cell (HSPC) populations. By contrast, the activity of the proximal P2 promoter is more restricted and its upregulation, in both the immature Lineage- Sca1high cKithigh (LSK) and bipotential Pre-Megakaryocytic/Erythroid Progenitor (PreMegE) populations, coincides with a loss of erythroid specification. Accordingly, the PreMegE population can be prospectively separated into "pro-erythroid" and "pro-megakaryocyte" populations based on Runx1 P2 activity. Comparative gene expression analyses between Runx1 P2+ and P2- populations indicated that the level of CD34 expression could substitute for P2 activity to distinguish these two cell populations in wild type (WT) bone marrow (BM). Prospective isolation of these two populations will provide the opportunity to further investigate and define the molecular mechanisms involved in megakaryocytic/erythroid (Mk/Ery) cell fate decisions. Moreover, comparison of a RUNX1C null (KO) PreMegE to its WT counterpart demonstrated considerably enhanced erythroid specification at the expense of megakaryopoiesis in the absence of P1-specified RUNX1C expression.

overall_design: mRNA profiles of wild type (WT), Runx1 P2-hCD4+ (P2+), Runx1 P2-hCD4- (P2-) and RUNX1C knockout (KO) bone marrow Pre-Megakaryocyte/Erythroid (PreMegE) progenitors were generated from young adult (12-16 weeks) mice by deep sequencing, in triplicate, using Illumina NextSeq 500.

first: Julia

last: Draper

first: Muhammad

middle: Z

last: Fadlullah

first: Hui

last: Leong

first: Valerie

last: Kouskoff


title: Arabidopsis PHL2 act as the key component of the central regulatory system controlling transcriptional responses to phosphate starvation

status: Public on Jan 03 2016

first: Lichao

last: Sun

state: Beijing

address: Tsinghua University

department: Life of Science

institute: Tsinghua university

summary: We first compared the transcriptomes of the roots of WT seedlings grown under P+ and P- conditions. Using a 2-fold change and a FDR (false discovery rate) of <0.05 as the cut-off for selecting the differentially expressed transcripts, we found that the expression of 581 genes was induced and that the expression of 120 genes was repressed by Pi starvation. We then compared the expression levels of these 581 PSI genes in the WT and phl2. The results showed that the average expression level of these genes was 51% lower in phl2 relative to the WT. If we arbitrarily defined a 30% reduction in the expression level of PSI genes as “a significant reduction”, the expression of 87.6% of PSI genes was significantly reduced in P- phl2 relative to P- WT seedlings. Thus, we conclude that PHL2 is a key component of the central regulatory system controlling transcriptional responses to Pi starvation.

overall_design: We performed a RNA-seq analysis on WT and phl2 plants. Total RNAs were extracted from the roots of P+ and P- WT seedlings (i.e., seedling grown on P-sufficient and P-deficient media) and of P- phl2 seedlings. The extracted RNAs were subjected to RNA deep sequencing. Our RNA-seq analyses showed that among the 581 PSI genes, the expression of 87% is significantly reduced in phl2, demonstrating that PHL2 positively regulates the transcription of a large number of PSI genes at the genomic level

first: Dong

last: Liu


title: High-Throughput mapping of the regulatory DNA

city: Cambridge

first: Nisha

last: Rajagopal

state: Massachusetts

address: 32 Vassar Street

institute: MIT

summary: We introduce the Multiplexed Editing Regulatory Assay (MERA), a high-throughput CRISPR/Cas9-based approach that analyzes the regulatory genome for function in its native context.  By tiling thousands of mutations across ~40 kb of cis-regulatory genomic space and using knock-in GFP reporters to read out gene activity, we obtain quantitative information on the contribution of cis-regulatory regions to gene expression.  In addition, we performed a deep-sequencing strategy to  find basepair-resolution functional motifs involved in regulation of the gene by sequencing thousands of functional and non-functional genotypes at genomic locations perturbed by specific guide RNAs.

overall_design: Design of 3908 gRNAs to perturb regulatory regions associated with the genes Tdgf1,Nanog,Zfp42 and Rpp25 as well as 10 GFP-targetting positive controls. Also, deep-sequencing of genomic regions mutated by 6 selected gRNAs after sorting the electroporated cells into GFP-positive and GFP-negative populations.

first: Sharanya

last: Srinivasan

first: Kameron

last: Kooshesh

first: Yuchun

last: Guo

first: Matt

last: Edwards

first: Budhaditya

last: Banerjee

first: Tahin

last: Syed

first: Bart

last: Emons

first: David

last: Gifford

first: Richard

last: Sherwood


title: Effects of dynamic cytosine methylation on alternative pre-mRNA splicing in T lymphocytes

city: Bethesda

last: Sturgill

summary: Intragenic 5-methylcytosine and CTCF mediate opposing affects on pre-mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5-methylcytosine evicts CTCF, leading to exon exclusion. However, the mechanisms governing dynamic DNA methylation at CTCF binding sites were unclear. In this study, we identify the methylcytosine dioxygenases TET1 and TET2 as active regulators of CTCF-mediated alternative splicing through conversion of 5-methylcytosine to its oxidation derivatives.

overall_design: Transcriptional profiling of human T-lymphocytes in the naïve and activated states was performed by RNA-Seq.  Methylation status (5mC and 5hmC) was assayed by medIP-Seq.  CTCF binding sites were identified by ChIP-Seq.

first: Ryan

last: Marina

first: Morgan

last: Thenoz

first: Marc

last: Bailly

first: Garima

last: Singh

first: Maria

last: Prigge

first: Kyster

last: Nanan

first: Sanjeev

last: Shukla

first: Nazmul

last: Haque

first: Shalini

last: Oberdoerffer


title: Ubiquitin-dependent turnover of MYC promotes loading of the PAF complex on RNA Polymerase II to drive transcriptional elongation (RNA-seq)

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: The MYC transcription factor is an unstable protein and its turnover is controlled by the ubiquitin system. Ubiquitination enhances MYC-dependent transactivation, but the underlying mechanism remains unresolved. Here we show that proteasomal turnover of MYC is dispensable for recruitment of RNA polymerase II (RNAPII), but is required to promote transcriptional elongation at MYC target genes. Degradation of MYC stimulates histone acetylation and recruitment of BRD4 and P-TEFb to target promoters, leading to phosphorylation of RNAPII CTD and the release of elongating RNAPII. In the absence of degradation, the RNA polymerase II-associated factor (PAF) complex associates with MYC via interaction of its CDC73 subunit with a conserved domain in the amino-terminus of MYC ("MYC box I"), suggesting that a MYC/PAF complex is an intermediate in transcriptional activation. Since histone acetylation depends on a second highly conserved domain in MYCs amino-terminus ("MYC box II"), we propose that both domains co-operate to transfer elongation factors onto paused RNAPII.

overall_design: RNA-Seq Experiments were performed in a primary breast epithelial cell line (IMEC).The cell line expressed doxycycline-inducible versions of MYC (WT;Kless,Swap=WTN-KC). Where indicated cells were transfected with siRNAs (siCtrl;siSKP2). Where indicated cells were treaed with the proteasome inhibitor MG132 or EtOH as solvent control. DGE was performed by comparing Dox-treated populations expressing either Dox-inducible MYC or a vector control or comparing Dox-induced cells with EtOH (solvent control) treated cells.

first: Laura

last: Jaenicke

first: Björn

last: von Eyss

first: Anne

last: Carstensen

first: Wenshan

last: Xu

first: Nikita

last: Popov


title: Subtype Specific Addiction of the Activated B Cell Subset of Diffuse Large B Cell Lymphoma to FOXP1

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: Genome wide transcript and target gene profiling reveal that FOXP1 acts directly and indirectly by enforcing known ABC-DLBCL hallmarks, including Chronically Activated B cell receptor Signaling (CABS) and the classical NF-κB survival pathway. Our data further suggest that FOXP1 maintains ABC-subtype distinction by repressing gene expression programs dominant in GCB-DLBCL and support a model in which the normally transitory B cell plasmablast is the target of ABC-DLBCL transformation.

overall_design: ChIP sequenicng was performed for the FOXP1 transcription factor in DLBCL cell lines. Input was sequenced and used as a control.

first: Haley

last: Tucker

first: Vishwanath


title: Ubiquitin-dependent turnover of MYC promotes loading of the PAF complex on RNA Polymerase II to drive transcriptional elongation

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

overall_design: Refer to individual Series


title: Conversion of Fibroblasts into  Functional Trophoblast Stem-like Cells

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

summary: Here we demonstrate the generation of stable induced trophoblast stem cells (iTSCs) from fibroblasts by the transient expression of Gata3, Eomes and Tfap2c.  Transcriptome and methylome analyses and functional assays such as hemorrhagic lesion formation and placenta contribution suggested a high degree of conversion. Careful examination of the reprogramming process indicated that the cells did not go through a transient pluripotent state.

overall_design: Detect and compare different H2A.X deposition patterns in ES cells,MEFs and iTSC and TS cells, with Illumina HiSeq 2000

first: Tao

last: Wu

first: Yosef

last: Buganim


title: Differential gene regulation downstream of murine Tmem173 variants

city: Boston

first: Alexander

last: Poltorak

address: 150 Harrison avenue

institute: Tufts University

summary: We report positional cloning and characterization of a novel Sting allele that fails to activate IFN production in the wild-derived mice of MOLF/Ei strain in response to HSV (Herpes Simplex Virus) and Listeria monocytogenes both in vitro and in vivo. We show that previously uncharacterized mutations in the N-terminal of STING are responsible for low levels of IFN due to failure of MOLF STING to respond to cytosolic STING agonists such as 2’3’cGAMP, 5,6-Dimethylxanthenone-4-acetic acid (DMXAA) or poly(deoxyadenylic-deoxythymidylic) acid (dAdT). Using Next-Generation Sequencing (NGS) for the analysis of DNA-responses in congenic C57BL6.StingMOLF/MOLF (MOLF STING) mouse macrophages, we show that these mutations in MOLF/Ei discriminate in responses between different STING agonists. Macrophages from C57BL6.StingB6/B6¬ (B6 STING), or B6 STING expressing littermates were stimulated as a positive control for STING activation, and STING -/- (STING KO) macrophages served as a negative control.

overall_design:
To examine differential gene regulation downstream of murine Tmem173 (STING) allelic variants. We stimulated macrophages from B6 mice congenic for MOLF STING; macrophages from B6 STING expressing littermates were stimulated as a positive control for STING activation, and STING -/- (STING KO) macrophages served as a negative control.
One replicate of RNA-seq reads after each stimulation provided. Conditions are peritoneal macrophages from B6 congenic mice expressing: B6 STING, MOLF STING, or STING KO stimulated with 2’3’cGAMP, 5,6-Dimethylxanthenone-4-acetic acid (DMXAA), poly(deoxyadenylic-deoxythymidylic) acid (dAdT), or no treatment. This constitutes a total of 12 reads analyzed in this data set.

first: Guy

last: Surpris


title: Transcriptome sequencing of skeletal muscle for PRMT7 knockout mouse

status: Public on Jan 01 2016

city: Madiosn

first: Romeo

last: Blanc

state: WI

address: 1111 Highland Ave, WIMR II, 4th floor, Blanc Lab

department: CRB

institute: University of Wisconsin-Madison

summary: We report that whole body PRMT7-/- adult mice display a significant reduction in in muscle mass. RNA sequencing was performed to identify potential PRMT7 targets. We found that top canonical pathways affected by the loss of PRMT7 includes cell cycle and senescence.

overall_design: RNA was extracted from tibialis anterior muscles harvested from 3 WT and 3 PRMT7 null mice at 8months. RNA sequencing was performed to compare mRNA in skeletal muscles between WT and KO mice.

first: Roméo

first: Gillian

last: Vogel

first: Stéphane

last: Richard

first: Taiping

last: Chen


title: Epigenomic landscape during organ formation in human early embryos

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

summary: Here we present the whole genome ChIP-Seq analyses of a wide variety of histone marks, H3K27ac, H3K4me1, H3K4me3, and H3K27me3 in the brain, heart, and liver, along with the RNA-seq data of these organs of early human embryos 12 weeks after gestation.

overall_design: In total, brain, heart, and liver of early human post-implantation embryos were used, and four histone modifications were detected, including H3K27ac, H3K4me1, H3K4me3 and H3K27me3. Also, the transcriptomes of these three organs were analyzed.

first: Liying

last: Yan

first: Boqiang

last: Hu

first: Fuchou

last: Tang