title: High fat diet-induced changes of mouse hepatic transcription and enhancer activity can be reversed by subsequent weight loss

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: In this setup we have used RNA-seq, DHS-seq, and H3K27ac ChIP-seq to identify changes in transcription, chromatin landscape and enhancer activity in livers of mice fed a high fat diet (HFD) and mice returned from HFD to Chow.

overall_design: Global gene expression analysis, DHS-seq and H3K27ac ChIP-seq in livers of 7 week old mice fed chow or  HFD. Furthermore, we have performed global gene expression analysis and H3K27ac ChIP-seq in 12 week old mice initially fed HFD then returned to chow or continued chow diet.

first: Majken

last: Siersbæk

first: Lyuba

last: Varticovski

first: Shutong

last: Yang

first: Songjoon

last: Baek

first: Ronni

last: Nielsen

first: Susanne

last: Mandrup

first: Gordon

last: L Hager

first: Jay

last: H Chung


title: Seasonal gene expression in a migratory songbird

status: Public on Dec 15 2016

city: Durham

first: Rachel

middle: A

last: Johnston

state: NC

address: 130 Science Dr, Rm 108 Biological Sciences

department: Evolutionary Anthropology

country: USA

institute: Duke University

type: Expression profiling by high throughput sequencing

summary: We sequenced mRNA from brain samples of 20 captive Swainson's thrushes. 10 were from California, belonging to the coastal subspecies, and 10 were from Alaska, belonging to the inland subspecies.

overall_design:
Gene expression level analysis of Swainson's thrushes maintained in captivity for >1 year. The study treatments were: non-migratory inland (N = 4), non-migratory coastal (N = 6), migratory inland (N = 6), migratory coastal (N = 4).
This Series includes 19 Samples.  This Series does not include migratory inland Sample t22 (it was not included in any analyses because its overall expression was an outlier to the remaining dataset).


title: Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis [ATAC-Seq]

city: san francisco

first: Yen-Sin

last: Ang

state: CALIFORNIA

address: 1650 Owens Street

institute: Gladstone Institute, UCSF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heterozygous mutations in GATA4 cause congenital heart defects and cardiomyopathy through unknown mechanisms. To gain insights into the open chromatin status during human cardiac development due to GATA4 heterozygosity, we performed ATAC-seq of  wildtype and GATA4-G296S diseased cardiac progenitors.

overall_design: ATAC sequencing of wildtype and diseased pluripotent stem cell derived cardiomyocytes

first: Deepak

last: Srivastava


title: Examination of microRNA expression in pre- and post-treatment plasma samples of 3 patients

city: Beijing

first: Weidong

last: Han

address: #28 Fuxing Road, HaiDian District

department: School of Life Sciences

country: China

institute: Chinese PLA General Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Drug resistance often tempers the clinical benefit of chemotherapy in human malignant tumors. The potential chemosensitization of low-dose decitabine has been evident both preclinically and in previous phase I trials. Emerging data showed that miRNAs play an important role as a prognostic factor for cancer survival. Given that the biopsy tumor tissue was often not available, especially for patients with relapsed or refractory cancer, plasma RNA provided a valuable source for biomarker development. In order to establish predictive biomarker signature for the clinical efficacy of the decitabine-primed chemotherapy, we evaluated the expression of plasma miRNAs via high throughput microRNA sequencing. We performed miRNA-seq on a training set of 2 partial response (PR) patients and 1 progressive disease (PD) patients, and revealed preliminary data that plasma miRNA expression signature may serve as putative predictive markers of the low-dose decitabine primed chemotherapy. The clinical responses were assessed in a blinded manner according to the Response Evaluation Criteria in Solid Tumors (RECIST) v1.1.

overall_design: miRNA-seq of plasma from cancer patients before (day0) and after (day28) decitabine-primed chemotherapy for two patients with partial response (PR) and one patient with progressive disease (PD).

first: Qian

last: Mei


title: Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis [RNA-Seq]

summary: Heterozygous mutations in GATA4 cause congenital heart defects and cardiomyopathy through unknown mechanisms. To gain insights into the trancriptome perturbations during human cardiac development due to GATA4 heterozygosity, we performed RNA-seq of isogenic wildtype and GATA4-G296S diseased cardiac progenitors (CPCs) and cardiomyocytes (CMs).

overall_design: Transcriptome profiling of total RNA isolated from 26 wildtype or  diseased pluripotent stem cell derived cell types.


title: Next Generation Sequencing Facilitates Quantitative Analysis of ZH11 and OsNF-YB1 RNAi plants Transcriptomes

status: Public on Dec 16 2016

city: Shanghai

first: Jingjng

last: Xu

address: 300, Fenglin road

institute: SIPPE

summary: Analysis of gene expression level. The hypothesis tested in the present study was that OsNF-YB1 is specifically expressed in aleurone layer of developing endosperm and suppressed expression of OsNF-YB1 results in a reduced grain-filling rate and small grains. Of the down-regulated genes, the enrichment of transmembrane transport and ATP biosynthetic process is consistent with the decreased grain-filling rate.

overall_design: Aleurone layer mRNA profiles of 8 DAF ZH11 and OsNF-YB1 RNAi plants were generated by deep sequencing, using Illumina Hiseq 2500 (Oryza sativa).

first: Jingjing

first: Hongwei

last: Xue


title: MNase-sensitive complexes in yeast: nucleosomes and non-histone barriers

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

summary: Micrococcal nuclease (MNase) is commonly used to map nucleosomes genome-wide, but nucleosome maps are affected by the degree of digestion. It has been proposed that many yeast promoters are not nucleosome-free but occupied by easily digested, unstable, “fragile” nucleosomes. We analyzed the histone content of all MNase-sensitive complexes by MNase-ChIP-seq and Sonication-ChIP-seq. We find that yeast promoters are predominantly bound by non-histone protein complexes, with little evidence for fragile nucleosomes. We do detect MNase-sensitive nucleosomes elsewhere in the genome, including transcription termination sites. However, they have high A/T-content, suggesting that MNase sensitivity does not indicate instability, but the preference of MNase for A/T-rich DNA, such that A/T-rich nucleosomes are digested faster than G/C-rich nucleosomes. We confirm our observations by analyzing ChIP-exo, chemical mapping and ATAC-seq data from other laboratories. Thus, histone ChIP-seq experiments are essential to distinguish nucleosomes from other DNA-binding proteins that protect against MNase.

overall_design: We mapped MNase-sensitive complexes in budding yeast by comparing protected DNA fragments at different levels of digestion (MNase titration). We used MNase-ChIP-seq and Sonication-ChIP-seq to detect histones H4 and H2B in order to distinguish between MNase-sensitive nucleosomes and non-histone complexes.

middle: V

first: Josefina

last: Ocampo

first: David

middle: J

last: Clark


title: SHARPIN regulates collagen architecture and ductal invasion in the developing mouse mammary gland

city: Turku

first: Emilia

last: Peuhu

address: Medisiina D5, Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of turku

summary: Primary mammary gland stromal fibroblasts from pubertal SHARPIN-deficient cpdm/cpdm -mice and their littermate controls

overall_design: mRNA seq data from 3 wt and 3 Sharpincpdm mouse mammary gland stromal fibroblast cell samples

first: Johanna

last: Ivaska


title: Genome-wide mapping of 5-hydroxymethyluracil in eukaryote parasite Leishmania

city: Cambridge

first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

summary:
5-hydroxymethyluracil (5hmU) is a thymine base modification found in genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we developed a method for the genome-wide mapping of 5hmU-modified loci based on a chemical tagging strategy for the hydroxymethyl group. We applied the method to generate genome-wide maps of 5hmU in parasitic protozoan Leishmania, where 5hmU forms enzymatically via hydroxylation of thymine. In the genus, another thymine modification 5-(β-glucopyranosyl) hydroxymethyluracil (base J) plays key roles during transcription. To elucidate relationships between 5hmU and base J, we also mapped base J loci by introducing a chemical tagging strategy for the glucopyranoside residue.
Results:
Observed 5hmU peaks were highly consistent among technical replicates, confirming the robustness of the method. 5hmU were particularly enriched in strand switch regions, telomeric regions and intergenic regions. Over 90% of 5hmU-enriched loci overlapped with base J-enriched loci, which occurred mostly within strand switch regions. We also identified loci comprising 5hmU but not base J. These 5hmU-specific loci were enriched with motifs consisting of a stretch of thymine bases and associated with higher RNA levels.
Conclusions:
By chemically detecting 5hmU we provide the first genome-wide map of 5hmU, which will help addressing the emerging interest in the role of 5hmU. The presence of 5hmU-specific loci may suggest that 5hmU has unique roles.

sample_organism:
Leishmania donovani
Leishmania major

platform_organism:
Leishmania donovani
Leishmania major

overall_design:
BaseJ and 5hmU mapped by pull-down and sequencing in Leishmania parasites. Each pull down repeated in 2 or 3 technical replicates. RNA expression in L. major was quantified by RNA-Seq on total RNA in three replicates.
Please note that for RNA-Seq the raw data (fastq files) have been processed as described in the Data processing step section (to investigate RNA expression throughout the genome, not just in annotated genes). Therefore, we did not quantify transcript expressions as normally done for mammalian genomes. The data processing description includes a link to a github repository with the details of the analysis described in the manuscript in preparation. This repository is currently private but it will be made public upon publication of the associated manuscript.

first: Fumiko

last: Kawasaki

first: Robyn

last: Hardisty

last: McInroy

first: Pieter

last: van Delft

first: Shankar

last: Balasubramanian


title: Artemisinins target GABAA receptor signaling and impair alpha cell identity

city: Boston

first: Jin

last: Li

address: Blackfan 3

institute: BIDMC

summary: Type 1 diabetes is characterized by the destruction of pancrea  tic beta cells, and generating   new  insulin-producing  cells  from  other  cell  types is a  major  aim  of  regenerative  medicine. One  promising  approach  is transdifferentiation  of  developmentally  related  pancreatic  cell types  including  glucagon-producing  alpha  cells.  In  a  genetic  model,  loss  of  the  master regulatory  transcription  factor  Arx   is sufficient  to  induce  the  conversion  of  alpha  cells  to   functional  beta-like  cells.  Here  we  identify  artemisinins  as  small  molecules  that  functionally   repress Arx by causing its translocation to the cytoplasm. We   show that the protein gephyrin   is  the  mammalian  target  of  these  antimalaria  drugs, and  that  enhancement  of  GABAA receptor  signaling  contributes  to  the  mechanism of  action of  these  molecules  in  pancreatic   transdifferentiation.  Our  results  in  zebrafish,  rodents  and  primary  human  pancreatic  islets indicate that gephyrin is a novel druggable target for the regeneration of pancreatic beta cell mass from alpha cells.

overall_design: There are two parts in the transcriptional study on mouse cell lines in this project. One part is on Min6-ARX inducible cells with different induction time of Dox. This is done in three different clones. The other part is on alpha-TC1 cells. This is done in one concentration of Artemether, one time point and two biological repeats.

first: Stefan

last: Kubicek


title: In fetal testis, SOX9 acts on transcription and splicing of its targets genes through binding to genomic regions with conserved signatures

city: Montpellier

first: Francis

last: Poulat

address: 141 rue de la Cardonille

department: Genetic and Development

country: France

institute: IGH CNRS-UM UMR9002

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

sample_organism:
Bos taurus
Mus musculus

platform_organism:
Bos taurus
Mus musculus

overall_design: Refer to individual Series


title: Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis [ChIP-Seq]

first: Yen-Sin

last: Ang

summary: Heterozygous mutations in GATA4 cause congenital heart defects and cardiomyopathy through unknown mechanisms. To gain insights into the genome-wide localization perturbations during human cardiac development due to GATA4 heterozygosity, we performed ChIP-seq of  wildtype and GATA4-G296S diseased cardiomyocytes.

overall_design: ChIP sequencing of GATA4, TBX5, MED1, H3K4me3, H3K36me3, H3K27ac, H3K27me3, plus input, from 75 wildtype or diseased pluripotent stem cell derived cardiomyocytes

first: Deepak

last: Srivastava


title: The arf10/16 double mutant has a differential transcriptional program in response to Al stress

city: Qingdao

first: Zhong-Bao

last: Yang

state: Shandong

address: 72# Binhai Road

department: School of Life Science

institute: Shandong University (Qingdao)

summary: To reveal how ARF10 and ARF16 regulate Al-induced root-growth inhibition, a transcriptome analysis was carried out by comparing without and with Al-exposed arf10/16 double mutant line and WT through RNA sequencing. The present transcriptomic analysis has revealed that many of the differentially transcribed genes associated with cell wall modification were regulated by transcription factors ARF10 and ARF16. The implication is that the auxin-regulated Al-induced inhibition of root growth arises from auxin signalling-regulated cell wall structure or component modification.

overall_design: Total RNA obtained from control (non-treated roots) and Al-exposed roots. Six day old plants were treated with and without Al treatment for 24 h, then total RNA was isolated using the RNeasy® Plant Mini Kit (QIAGEN), and then Illumina sequencing was performed.

first: Xiaoyu

last: Geng

first: Chunmei

last: He

first: Rong

last: Wang

first: Walter

last: Horst

first: Zhaojun

last: Ding


title: Large-scale mapping of gene regulatory logic reveals 5 context-dependent repression by transcriptional 65 activators

status: Public on Dec 14 2016

first: Lucas

last: Carey

state: Bejijng

address: 5 Yiheyuan Road

department: Center for Quantitative Biology

institute: Peking University

summary: Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA sequence, TF concentration, and gene expression output, we have conducted in budding yeast a large-scale measurement of the activity of thousands of designed promoters at six different levels of TF. We observe that maximum promoter activity is determined by TF concentration and not by the number of sites. Surprisingly, the addition of an activator binding site often reduces expression. A thermodynamic model that incorporates competition between neighboring binding sites for a local pool of TF molecules explains this behavior and accurately predicts both absolute expression and the amount by which addition of a site increases or reduces expression. Taken together, our findings support a model in which neighboring binding sites interact competitively when TF is limiting but otherwise act additively.

overall_design: We used a previously described library of 6500 promoters driving YFP expression(Sharon et al. 2012). The pooled library was grown in synthetic media with varying amino acid concentrations and gene expression driven by each promoter was measured as previously described (Sharon et al. 2014).

middle: B

first: David

last: van Dijk

first: Eilon

last: Sharon

first: Eran

last: Segal


title: In fetal testis, SOX9 acts on transcription and splicing of its targets genes through binding to genomic regions with conserved signatures [RNA-seq]

summary: In mammals, male fate is under the control of the master transcriptional regulator, SOX9: in its presence, somatic precursor cells of the embryonic gonads differentiate into Sertoli cells, the main organizers of testicular differentiation. Therefore, analyzing target genes of this transcription factor allows understanding mechanisms of cellular commitment at the genomic level. With the use of ChIP-seq in murine and bovine wild-type testes combined with RNAseq from mouse testes lacking SOX9, we identified SOX9 target genes in the mammalian fetal gonad. SOX9 in murine and bovine fetal testes binds to a large set of genes conserved among mammals, including those with well-established roles in testis and ovary development. RNAseq analysis shows that testis and ovary display sex specific RNA splicing and that SOX9 mediates both target gene transcription and differential splicing. Regions bound by SOX9 are predominantly 5’ proximal or intra-genic, and display a specific genomic features that we call "Sertoli cell signatures" or SCS. The SCS is conserved among mammals and comprises multiple binding motifs for the Sertoli reprogramming factors SOX9, GATA4 and DMRT1; indeed, independent DMRT1 ChIP-seq confirms the enrichment of the SCS. Bioinformatic analysis of SCSs regions predicts novel regulatory mechanisms prompting functional validation. For example, we detected SCS in target genes of the nuclear factor TRIM28 and we show experimentally that SOX9 and TRIM28 proteins interact in fetal testis.

overall_design: examination of the role of the transcription factor SOX9 in the fetal testis

first: Massilva

last: Rahmoun

first: Rowena

last: Lavery

first: Sabine

last: Laurent-Chaballier

first: Nicolas

last: Bellora

first: Gayle

middle: K

last: Philip

first: Moïra

last: Rossito

first: Eric

last: Pailhoux

first: Florence

last: Cammas

first: Jessica

last: Chung

last: Bagheri-Fam

first: Mark

last: Murphy

first: Vivian

last: Bardwell

last: Zarkower

first: Brigitte

last: Boizet-Bonhoure

first: Philippe

last: Clair

first: Vincent

last: R Harley


title: Histone methyltransferase PRDM16 in tumor suppression

city: Ann Arbor

first: Yali

last: Dou

state: MI

address: 1301 Catherine Street

department: Pathology Department

institute: University of Michigan

summary: PRDM16 is highly enriched in adult stem cells and plays a crucial role in multiple developmental processes. Here we demonstrate that PRDM16 is a histone H3K4 methyltransferase and this activity is essential for PRDM16 to function as a tumor suppressor. We show that PRDM16, through its regulation of transcription factor GFI1b, antagonizes the functions of MLL fusion proteins by repressing HOXA gene expression and therefore, specifically suppresses the transformation capability of MLL-AF9, MLL-AF6 and MLL-ENL. Furthermore, overexpression of PRDM16, but not the inactive PRDM16 mutant, blocks MLL mediated leukemogenesis while PRDM16 depletion significantly shortens the disease latency in vivo. We also show that PRDM16 activity is dynamically required at the pre-leukemic stage, but not in fully transformed leukemia, depicting a little known sequence of events necessary for clonal expansion during cancer evolution. Given the importance of PRDM16 and the loss of PRDM16 methyltransferase activity in an array of human malignancies, our findings provide broad insights for PRDM16-dependent physiological and pathological processes.

overall_design:
Compare MLL-AF9+PRDM16 contransduction with MLL-AF9+PRDM16mut cotransduction;
Compare E2A-HLF+PRDM16 contransduction with E2A-HLF+PRDM16mut cotransduction;
Compare MLL-AF9 stable leukemia cell +PRDM16 with MLL-AF9 stable leukemia+PRDM16mut;
Two replicates in each condition

first: Bo

last: Zhou

first: Jingya

last: Wang

first: Yuqing

last: Sun


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

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
To better understand molecular mechanisms of human pancreatic development associated with GATA6 haploinsufficiency, we performed RNA-seq analysis to characterize the biological processes affected by GATA6 heterozygous mutation.
We identified 542 differential expression genes in the mutants, of which 310 were downregulated. Gene ontology analysis showed that top downregulated transcription factors were associated with developmental process.

overall_design: Examination of two wild-type and two GATA6-/+ HUES8 lines at the PP1 stage using the first-generation pancreatic differentiation protocol

first: Zhong-Dong

last: Shi

first: Danwei

last: Huangfu


title: Transcriptomic analysis of wild type and Del(Hotair)-/- mouse tissues

city: Lyon

first: Anamaria

last: Necsulea

address: 43 Bd. du 11 Novembre 1918

department: Laboratoire de Biométrie et Biologie Evolutive

institute: CNRS, Université Claude Bernard Lyon 1

summary: Despite decades of interest, the mechanisms that control Hox gene expression are not yet fully understood. It was recently proposed that Hotair, a lncRNA transcribed from the HoxC cluster, regulates HoxD gene expression via Polycomb targeting and thus is important for correct skeletal development. However, genetic manipulations of the locus led to conflicting results regarding the roles of Hotair. Here, we analyze the molecular and phenotypic consequences of deleting the Hotair locus in vivo. In contradiction with previous findings, we show that deleting Hotair has no detectable effect on HoxD gene expression in vivo. We could not observe any morphological alteration in mice lacking the Hotair locus. However, we find a significant impact of deleting Hotair on the expression of neighboring genes Hoxc11 and Hoxc12. Our results do not support an RNA-dependent role for Hotair in vivo, but argue in favor of a DNA-dependent effect of Hotair deletion on the transcriptional landscape in cis.

overall_design: We micro-dissected wild type and Del(Hotair)-/- E12.5 embryos into 6 segments: forelimbs (FL), hindlimbs (HL), genital tubercle (GT), trunk section corresponding to the lumbar/sacral region (T1); trunk section corresponding to the sacral/caudal region (T2) and trunk section corresponding to the caudal region (T3). We generated strand-specific RNA-seq data for each segment, in two biological replicates and we performed differential expression analyses for each tissue. Furthermore, we analyzed the impact of deleting the Hotair locus on the local transcriptional landscape, in the HoxC cluster.

first: Ana

middle: R

last: De Carvalho Amândio Lhopitallier

first: Denis

last: Duboule


title: Gene expression profile of hedgehog-responsive stromal cells in mouse PB-MYC prostate tumor and normal prostate

first: Zhaohui

last: Yang

address: 430 East 67th Street

summary: We report the application of RNA-sequencing for high-throughput profiling of gene expression in hedgehog-responsive stromal cells in normal mouse prostate and mouse prostate tumors. By using the Gli1-GFP knock-in reporter mouse line, we isolated the subset of mouse prostate stromal cells undergoing hedgehog signaling to compare the transcriptomes between PB-MYC prostate tumor and normal prostate in mice at the age of about 45 weeks.

overall_design: The mRNA profiles of hedgehog-responsive stromal cells in 45-week old wild type (WT) prostates and PB-MYC prostate tumors were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 2000.

first: Alexandra

last: Joyner


title: In fetal testis, SOX9 acts on transcription and splicing of its targets genes through binding to genomic regions with conserved signatures [ChIP-seq]

first: Francis

last: Poulat

overall_design: examination of the role of the transcription factor SOX9 in the fetal testis: ChIP-seq

first: Massilva

last: Rahmoun

first: Rowena

last: Lavery

first: Sabine

last: Laurent-Chaballier

first: Nicolas

last: Bellora

first: Gayle

last: Philip

first: Moïra

last: Rossito

first: Eric

last: Pailhoux

first: Florence

last: Cammas

first: Jessica

last: Chung

first: Stefan

last: Bagheri-Fam

first: Mark

last: Murphy

last: Bardwell

first: David


title: Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis

first: Yen-Sin

last: Ang


title: Mapping of DHT-responsive or -independent AR-binding sites induced by activated Src in prostate cancer cell lines [ChIP-seq]

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: Building on the observation that metastatic, castration-resistant prostate cancer (CRPC) correlates with activation of Src-family tyrosine kinases, we showed that the expression of activated Src renders LNCaP androgen-independent.  Here, we report on RNA-seq and/or AR ChIP-seq analyses of LNCaP, LNCaP[Src], VCaP, 22Rv1 cells grown in the presence or absence of 10 nM DHT for 16h, or LuCaP35.1 tumors grown in androgen-supplemented vs. castrated mice (androgen-dependent vs. castration-resistant). We identify an 11-gene Src-induced signature found only in CRPC in response to DHT, and moreover, the differentail expression of a subset (DPP4, BCAT1, CNTNAP4, CDH3) correlates with earlier PC metastasis onset and poorer survival.

overall_design: AR ChIP-seq using N-20 Ab to chromatin, followed by production of paired-end NGS libraries and sequencing.  9 samples are seqeucned for V-CaP cell line, Ln-CaP cell line and Ln-CaP with Src-527F cell line.  Each cell line has 3 samples, they are  DHT treated, Control, and input.

first: Irwin

middle: H

last: Gelman


title: Gata6 promotes hair follicle matrix progenitor cell renewal by genome maintenance via Edaradd/NF-κB

city: Ithaca

first: Alex

address: 260 Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

summary: Cell proliferation is essential to rapid tissue growth and repair, but is inherently associated with considerable genome damage that cells must efficiently prevent or fix to prevent cell cycle arrest. Here, we implicate the transcription factor Gata6 in regulation of adult mouse hair follicle regeneration where it controls the renewal of the rapidly proliferating epithelial (matrix) progenitors and hence the extent of production of terminally differentiated lineages. We find that Gata6 protects against DNA damage associated with proliferation, thus preventing cell cycle arrest and apoptosis. Furthermore, we show that Gata6 stimulates the Eddarad/NF-kB pathway, important for DNA-damage repair and stress response in general, and for hair follicle growth in particular. Finally, we find Edaradd essential, downstream of Gata6 for cell survival and proliferation. Our data add to recent evidence in embryonic stem and neural progenitor cells, suggesting a model whereby developmentally regulated transcription factors protect from DNA damage associated with proliferation occurring at key stages of rapid tissue growth. Our data may aid in understanding why Gata6 is a frequent target of amplification in cancers.

overall_design: Gene expression profiling by mRNA-seq to identify differentially expressed genes in wild type (WT) and Gata6 induced knockout (iKO) mouse epidermal keratinocytes

first: Ying

last: Zhang

first: Tudorita

last: Tumbar


title: A specific dsRNA-binding protein complex selectively sequesters endogenous Inverted-Repeat siRNA precursors and inhibits their processing.

city: Strasbourg

first: Patrice

last: Dunoyer

state: Alsace

address: 12 rue du général Zimmer

department: Ibmp

institute: CNRS

summary: In plants, several dsRNA-binding proteins (DRBs) have been shown to play important roles in various RNA silencing pathways, mostly by promoting the efficiency and/or accuracy of Dicer-like proteins (DCL)-mediated small RNA production. Among the DRBs encoded by the Arabidopsis genome, we recently identified DRB7.2 whose function in RNA silencing was unknown. Here, we show that DRB7.2 is specifically involved in siRNA production from endogenous inverted-repeat (endoIR) loci. This function requires its interacting partner DRB4, the main cofactor of DCL4, and is achieved through specific sequestration of endoIR dsRNA precursors, thereby repressing their access and processing by the siRNA-generating DCLs. The present study also provides multiple lines of evidence showing that DRB4 is partitioned into, at least, two distinct cellular pools fulfilling different functions, through mutually exclusive binding with either DCL4 or DRB7.2. Collectively, these findings revealed that plants have evolved a specific DRB complex that modulates selectively the production of endoIR-siRNAs. The existence of such a complex and its implication regarding the still elusive biological function of plant endoIR-siRNA will be discussed.

overall_design: small RNA profiles of wild type (WT) and drb7.2-/- Arabidopsis flowers from two biological replicates were generated by deep sequencing, using Illumina HiSeq 2500 v4.

first: Thomas

last: Montavon

first: Yerim

last: Kwon

first: Aude

last: Zimmermann

first: Philippe

last: Hammann

first: Timothée

last: Vincent

first: Valérie

last: Cognat

first: Fabrice

last: Michel


title: In vivo cleavage map illuminates the central role of RNase E in coding and noncoding RNA pathways

city: Irvine

first: Lei

last: Li

state: CA

address: University of California, Irvine

institute: University of California, Irvine

summary: Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. Our results suggest a prominent biogenesis pathway for bacterial regulatory small RNAs, whereby RNase E acts together with the RNA chaperone Hfq to liberate stable 3’-fragments from various precursor RNAs. Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small RNA precursor for interaction with a mRNA target. In vivo, the processing is required for target regulation. Our findings reveal a general maturation mechanism for a major class of post- transcriptional regulators.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: 8 total RNA samples from Salmonella WT and rne-3071(rne-TS) strains grown at 28°C with and without heat treatment (44°C) for 30min, in duplicate.

first: Yanjie

last: Chao

first: Dylan

last: Girodat

first: Konrad

middle: U

last: Förstner

first: Nelly

last: Said

first: Colin

last: Corcoran

first: Kai

last: Papenfort

first: Richard

last: Reinhardt

first: Hans-Joachim

last: Wieden

first: Ben

last: Luisi

first: Jörg

last: Vogel


title: Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced off-target effects

city: Yangling

first: Yuanpeng

last: Gao

state: Shaanxi

address: 3 Taicheng Road

department: College of Veterinary Medicine

institute: Northwest A&F University

summary: In this study, using chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq), we identified the main binding sites of catalytically inactive Cas9 (dCas9) protein in bovine fetal fibroblast cells (BFFs) in an unbiased manner.

overall_design: In the present study, chromatin immunoprecipitation was performed on catalytically inactive double mutant (D10A and H840A) Cas9 (dCas9)(Mali et al. 2013a; Yang et al. 2013) protein binding site detection in bovine fetal fibroblast cells (BFFs), followed by sequencing (ChIP-seq); we found that single Cas9 nickase (Cas9n)(Cong et al. 2013; Ran et al. 2013a)-mediated single-strand break (SSB) had the potential to restrict repair to the homology-directed repair (HDR) pathway.

first: Yong

last: Zhang


title: Iron-Heme-Bach1 Axis Is Involved In Erythroblast Adaptation To Iron Deficiency

city: Fukuoka

first: Yukihiro

last: Inoguchi

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

type: Methylation profiling by high throughput sequencing

summary: Iron plays the central role in the oxygen transport by the erythrocyte as a constituent of heme and hemoglobin. The importance of iron and heme also resides in their regulatory roles during erythroblast maturation. The transcription factor Bach1 may be involved in their regulatory roles since it is inactivated by direct binding of heme. To address whether Bach1 is involved in the responses of erythroblasts to iron status, low iron conditions that induced severe iron deficiency in mice were established. Under iron deficiency, extensive gene expression changes and mitophagy disorder were induced during maturation of erythroblasts. Bach1 mice showed more severe iron deficiency anemia in the developmental phase of mice and a retarded recovery once iron was replenished when compared with wild-type mice. In the absence of Bach1, the expression of globin genes and Hmox1 (encoding heme oxygenase-1) was de-repressed in erythroblasts under iron deficiency, suggesting that Bach1 represses these genes in erythroblasts under iron deficiency to balance the levels of heme and globin. Moreover, an increase in genome-wide DNA methylation was observed in erythroblasts of Bach1–/– mice under iron deficiency. These findings reveal the principle role of iron as a regulator of gene expression in erythroblast maturation and suggest that the iron-heme-Bach1 axis is important for a proper adaptation of erythroblast to iron deficiency to avoid toxic aggregates of non-heme globin.

overall_design: Gene expression profiles were determined by microarry (GSE77694) and DNA methyomes were determined by WGBS.

first: Masahiro

last: Kobayashi

first: Hiroki

last: Kato

first: Hiroshi

last: Hada

first: Kenji

last: Ichiyanagi

first: Akihiko

last: Muto

first: Ari

last: Itoh-Nakadai

first: Tohru

last: Fujiwara

first: Naohisa

last: Tomosugi

first: Hiroyuki

last: Sasaki

first: Hideo

last: Harigae

first: Kazuhiko

last: Igarashi


title: Nuclear RNAi Contributes to the Silencing of Off-target Genes and Repetitive Sequences in Caenorhabditis elegans

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

institute: University of Science & Technology of China

summary: Small RNAs recognize, bind, and regulate other complementary cellular RNAs. The introduction of small RNAs to eukaryotic cells frequently results in unintended silencing of related, but not identical, RNAs: a process termed off-target gene silencing. Off-target gene silencing is one of the major concerns during the application of small RNA-based technologies for gene discovery and the treatment of human disease. Off-target gene silencing is commonly thought to be due to inherent biochemical limitations of the RNAi machinery. Here we show that, following the introduction of exogenous sources of dsRNA, the nuclear RNAi pathway, but not its cytoplasmic counterparts, is the primary source of off-target silencing in C. elegans. In addition, we show that during the normal course of growth and development the nuclear RNAi pathway regulates repetitive gene families. Therefore, we speculate that RNAi off-target effects might not be “mistakes” but, rather, an intentional and genetically programmed aspect of small RNA-mediated gene silencing, which might allow small RNAs to silence rapidly evolving parasitic nucleic acids. Finally, reducing off-target effects by manipulating the nuclear RNAi pathway in vivo might improve the efficacy of small RNA-based technologies. (The Zhou X, Xu F, Mao H, Ji J, Meng Y, Feng X, and Shouhong Guang (2014) Nuclear RNAi Contributes to the Silencing of Off-Target Genes and Repetitive Sequences in Caenorhabditis elegans. Genetics 2014 May;197(1):121-32. doi: 10.1534/genetics.113.159780.)

overall_design: To better understand the endogenous roles of the nuclear RNAi pathway, and to ask if nuclear RNAi drives off-target silencing during the normal course of growth and development, we immunoprecipitated NRDE-3 from the FLAG::GFP::NRDE-3 strain and deep sequenced the associated small RNAs from embryo lysates. eri-1(mg366);dpy-13(e458);FLAG::GFP::NRDE-3 fed dpy-13 RNAi was included as a control. We used a small RNA-cloning method compatible with cloning monophosphorylated and triphosphorylated small RNAs (i.e., 22G-RNAs). Small RNAs were isolated, pretreated with calf intestinal alkaline phosphatase to remove phosphate groups, treated with polynucleotide kinase to add a monophosphate group to the 5’-ends, and subjected to deep sequencing using the Illumina platform. Small RNAs were aligned to the C. elegans transcriptome (WS243 assembly) using Bowtie2 software with the default parameters, and the number of small RNAs targeting each gene was counted.


title: THZ1 targeting CDK7 suppresses STAT transcriptional activity and sensitizes T-cell lymphomas to BCL2 inhibitors

first: Tharu

middle: M

last: Fernando

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

summary: Peripheral T-cell lymphomas (PTCL) are aggressive diseases with poor response to chemotherapy and dismal survival. Identification of effective strategies to target PTCL biology represents an urgent need. Here we report that PTCL are sensitive to transcription-targeting drugs, and, in particular, to THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7). The STAT-signaling pathway is highly vulnerable to THZ1 even in PTCL cells that carry the activating STAT3 mutation Y640F. In mutant cells, CDK7 inhibition decreases STAT3 chromatin binding and expression of highly transcribed target genes like MYC, PIM1, MCL1, CD30, IL2RA, CDC25A and IL4R. In surviving cells, THZ1 decreases the expression of STAT-regulated anti-apoptotic BH3 family members MCL1 and BCL-XL sensitizing PTCL cells to BH3 mimetic drugs. Accordingly, the combination of THZ1 and the BH3 mimetic obatoclax improves lymphoma growth control in a primary PTCL ex vivo culture and in two STAT3-mutant PTCL xenografts, delineating a potential targeted agent-based therapeutic option for these patients.

overall_design: OCI-Ly13.2 cells were treated with 500 nM THZ-1 or vehicle for 3 h or 6 h in triplicate. Total RNA was harvested from cells and used for expression profiling via RNA-seq.

first: Leandro

last: Cerchietti


title: Combination scaffolds of salmon fibrin, hyaluronic acid, and laminin for human neural stem cell tissue engineering

city: Los Angeles

first: Giovanni

last: Botten

state: California

address: 6525 MRL 675 Charles E. Young Dr. South

department: Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

summary: A goal of this project is to evaluate the integrin mRNA expression in human neural stem/progenitor cells (hNSPC) using high-throughput sequencing technologies. We found high levels of mRNA expression for the  β1, α7, α3, α6, β5, αV, α5, and α9 integrins. This suggests that hNSPCs may express integrin receptors that can bind fibrinogen and laminin proteins.

overall_design: mRNA profiles of hNSPCs from three different passages (12, 15, and 17) were generated by deep sequencing using Illumina HiSeq 2500.

first: Janahan

last: Arulmoli

first: Lisa

last: Flanagan


title: Characterization of a TUTase/nuclease complex required for Drosophila gametogenesis

status: Public on Dec 13 2016

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

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

summary: Total RNAs were cloned from wt, Dis3L2 and Tailor mutant testis tissues to study the role of Tailor and Dis3L2 TUTase/nuclease complex

overall_design: Replicated total RNA samples from Dis3L2 and Tailor single mutant, and Dis3L2/Tailor double mutant and WT (w1118) testes

first: Eric

last: C. Lai


title: miRNA-seq of lung in two kinds of pig breeds after PCV2 injection

city: Beijing

first: Liyuan

last: Wang

state: China

address: No.2 of Yuanmingyuan West Road, Haidian District

department: Animal Sciencie and Technology

institute: China Agricultura University

summary: Postweaning multisystemic wasting syndrome in pigs has devastated the swine industry since the 1990s. Porcine circovirus type 2 (PCV2) is the primary cause of this disease. MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in regulating gene expression, especially at the post-transcription level. The expression profiles of miRNAs have been reported in porcine reproductive and respiratory syndrome, porcine parvovirus, and other pig diseases; however, the miRNA expression profiles in pigs infected with PCV2 have not been reported so far. The Laiwu pig (a Chinese indigenous pig breed) has different meat quality, adipogenesis, and disease-resistance from western commercial pig breeds. In this study, four small RNA libraries were constructed from the lung tissue of uninfected and infected Laiwu and Yorkshire/Landrace crossbred (YL) pigs. High-throughput sequencing and bioinformatics were used to determine the abundance and differential expression of miRNAs in the four libraries

overall_design: miRNA-seq of four groups as PCV2 infected Laiwu pig (Lw-i), uninfected Laiwu pig (Lw-un), infected western commercial (YL-i) and uninfected western commercial pigs (YL-un)


title: Temporal anaylsis of mRNA from pannicle tissue from field grown rice

city: Raleigh

first: Jigar

last: Desai

address: 128 Polk Hall

department: Biochemistry

institute: NCSU

summary: A IR64 variety of rice was grown in a field plot at the International Rice Research Institute (IRRI) in the Philippines. The data ganied from the expremint provides infromation of the daily trnascriptional changes occur in panicle tissue during an important developmental period.

overall_design: When the plants reached 50% flowering  panicle tissue was harvest at ~3 hour intervals for 24 hours. There are 8 timepoints with 4 replicates at each timepoint for a total of 32 samples.

first: Ryan

middle: C

last: Sartor

first: Lovely

last: Lawas

first: Krishna

last: SV

first: Colleen

last: Doherty


title: Neonatal Transplantation Confers Maturation of PSC-Derived Cardiomyocytes Conducive to Modeling Cardiomyopathy

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

summary: Pluripotent stem cell-derived cardiomyocytes (PSC-CMs) were transplanted into rats for one month to determine the change in morphology, structure, and function. Single cell RNA seq analysis was performed to compared the transcriptome of in vivo matured PSC-CMs to adult rat cardiomyocytes and in vitro cultured PSC-CMs.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: single cell RNA seq of 3 cell types

first: Kwon

last: Chulan

first: Cho

last: Gunsik


title: An Estradiol-Inducible Promoter Enables Fast, Graduated Control of Gene Expression in Fission Yeast

city: Worcester

first: Nick

last: Rhind

state: MA

address: 364 Plantation St.

department: Biochemistry and Molecular Pharmalology

institute: UMass Med School

summary: The fission yeast Schizosaccharomyces pombe lacks a diverse toolkit of inducible promoters for experimental manipulation.  Available inducible promoters suffer from slow induction kinetics, limited control of expression levels and/or a requirement for defined growth medium.  In particular, no S. pombe inducible promoter systems exhibit a linear dose response, which would allow expression to be tuned to specific levels.  We have adapted a fast, orthogonal promoter system with a large dynamic range and a linear dose response, based on _-estradiol-regulated function of the human estrogen receptor, for use in S. pombe.  We show that this promoter system, termed Z3EV, turns on quickly, can reach a maximal induction of 20 fold, and exhibits a linear dose response over its entire induction range, with few off target effects.  We demonstrate the utility of this system by regulating the mitotic inhibitor Wee1 to create a strain in which cell size is regulated by _-estradiol concentration.  This promoter system will be of great utility for experimentally regulating gene expression in fission yeast.

overall_design: RNA-seq for asynchronous S. pombe cells, +/- beta-estradiol, in biological triplicate

first: Makoto

last: Ohira

first: David

middle: G

last: Hendrickson

first: R

middle: S

last: McIsaac

first: Nicholas


title: Dynamic changes in chromatin accessibility in CD8+ T cells responding to viral infection

city: La Jolla

first: James

last: Scott-Browne

address: 9420 Athena Circle

institute: La Jolla Institute

summary: In response to acute infection, naive CD8+ T cells expand, differentiate into effector cells and then contract to a long-lived pool of memory cells after pathogen clearance. During chronic infections or in tumors, CD8+ T cells acquire an “exhausted” phenotype. Here we present genome-wide comparisons of chromatin accessibility and gene expression from endogenous CD8+ T cells responding to acute and chronic viral infection using ATAC-seq and RNA-seq. Acquisition of effector, memory or exhausted phenotypes was associated with stable changes in chromatin accessibility away from the naive T cell state. Regions differentially accessible between functional subsets in vivo were enriched for binding sites of transcription factors known to regulate these subsets, including E2A, BATF, IRF4, T-bet and TCF1. Exhaustion-specific accessible regions were enriched for consensus binding sites for NFAT and Nr4a family members, indicating that chronic stimulation confers a unique accessibility profile on exhausted cells.

overall_design: Chromatin accessibility with ATAC-seq and gene expression with RNA-seq for CD8 T cell subsets after in vivo response to viral infection or after in vitro culture (total 44 samples)


title: Characterization of meningeal type 2 innate lymphocytes and their response to CNS injury

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

summary: The meningeal space is occupied by a diverse repertoire of innate and adaptive immune cells. CNS injury elicits a rapid immune response that affects neuronal survival and recovery, but the role of meningeal inflammation in CNS injury remains poorly understood. Here we describe group 2 innate lymphoid cells (ILC2s) as a novel cell type resident in the healthy meninges that is activated following CNS injury. ILC2s are present throughout the naïve mouse meninges, though are concentrated around the dural sinuses, and have a unique transcriptional profile relative to lung ILC2s. After spinal cord injury, meningeal ILC2s are activated in an IL-33 dependent manner, producing type 2 cytokines. Using RNAseq, we characterized the gene programs that underlie the ILC2 activation state. Finally, addition of wild type lung-derived ILC2s into the meningeal space of IL-33R-/- animals improves recovery following spinal cord injury. These data characterize ILC2s as a novel meningeal cell type that responds to and functionally affects outcome after spinal cord injury, and could lead to new therapeutic insights for CNS injury or other neuroinflammatory conditions.

overall_design: ILC2s were isolated from 10 week C57/Bl6 mice with and without spinal cord injury (1 day post injury). 5 mice were pooled per group, with meninges dissected, digested, and FACs sorted (CD45+/DAPI-/Lin–/St2+/Thy1+) directly into RNA lysis buffer.

first: Sachin

middle: P

last: Gadani

first: Igor

last: Smirnov

first: Ashtyn

middle: T

last: Smith

first: Jonathan

last: Kipnis


title: Transcriptional responses of Rhizopus microsporus host and non-host isolates to physical interaction with Burkholderia endobacteria of the host

first: Olga

last: Lastovetsky

address: 334 Plant Science Building, 236 Tower Rd, Cornell University

summary: The goal of this study was to identify fungal gene expression changes during early stages of symbiosis establishment with its Burkholderia endosymbionts. Results: Leveraging this RNA-seq dataset we identified fungal genes utilized for symbiosis establishment with bacteria.

overall_design: Methods: Host (ATCC 52813) and non-host (ATCC 11559) isolates of R. microsporus were growth alone or in the presence of Burkholderia endobacteria isolated from the host isolate. Fungal mycelia were harvested at a timepoint when the fungal colony has just begun to come into physical contact with the bacteria. Total RNA was extracted, rRNA depleted with RiboZero, and sequenced on the Illumina Hi-Seq 100bp-paired end reads platform

first: Teresa

middle: E

last: Pawlowska


title: A novel compound that blocks HIV-1 replication inhibits the splicing regulatory function of SRSF10

status: Public on Dec 19 2016

city: Heidelberg

first: Benjamin

middle: Andrew

last: Story

address: Meyerhofstrasse 1

department: Genomics

country: Germany

institute: European Molecular Biology Laboratory (EMBL)

summary:
Purpose: We have identified a new compound (1C8) that inhibits HIV-1 replication and that displays very low cellular toxicity. Here, we assess the molecular mechanisms of action of 1C8. Following transcription of the HIV-1 genome, its primary transcript is processed to produce dozens of distinct mRNAs through the alternative use of splice sites.
Results: 1C8 decreases the activity of SRSF10, a cellular protein that controls the selection of splice sites in HIV-1 transcripts. 1C8 decreases the phosphorylation of SRSF10, and this change is associated with alterations in the interaction of SRSF10 with HIV-1 transcripts and factors that control splice site selection. Thus, 1C8 represents a novel compound with properties that are potentially useful for treating HIV-1 infection.

overall_design: Examination of RNA-seq to investigate alternative splicing changes between control and 4 different concentrations of a drug that 1C8. 4 replicates were sequenced for each condition.

first: Lulzim

last: Shkreta

first: Marco

last: Blanchette

first: Johanne

last: Toutant

first: Emmanuelle

last: Wilhelm

first: Brendan

last: Bell

first: Alan

last: Cochrane

first: Peter

last: Cheung

first: P

last: Harrigan

last: Grierson

first: Benoit

last: Chabot


title: A kinase-phosphatase switch transduces environmental information into a bacterial cell cycle circuit

city: Stockholm

first: Kristina

last: Jonas

address: Svante Arrheniusväg 20 C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

summary: The bacterial cell cycle has been extensively studied under standard growth conditions. How it is modulated in response to environmental changes remains poorly understood. Here, we demonstrate that the freshwater bacterium Caulobacter crescentus blocks cell division and grows to filamentous cells in response to stress conditions affecting the cell membrane. Our data suggest that stress switches the membrane-bound cell cycle kinase CckA to its phosphatase mode, leading to the rapid dephosphorylation, inactivation and proteolysis of the master cell cycle regulator CtrA. The clearance of CtrA results in downregulation of division and morphogenesis genes and consequently a cell division block. Upon shift to non-stress conditions, cells quickly restart cell division and return to normal cell size. Our data indicate that the temporary inhibition of cell division through the regulated inactivation of CtrA constitutes a growth advantage under stress. Taken together, our work reveals a new mechanism that allows bacteria to alter their mode of proliferation in response to environmental cues by controlling the activity of a master cell cycle transcription factor. Furthermore, our results highlight the role of a bifunctional kinase in this process that integrates the cell cycle with environmental information.

overall_design: RNA-sequencing was performed to determine gene expression changes induced by salt stress (100 mM NaCl), ethanol stress (4% EtOH) or by loss of DivL function. RNA abundance in wild type cultures grown for 30 and 60 min in the presence of 100 mM NaCl or 4% ethanol (EtOH) was compared to the untreated wild type control. To analyze gene expression changes induced by loss of DivL function, a divLts mutant strain was grown for 60 min at the restrictive temperature of 37C and RNA abundance was compared to wild type cells grown at 37C.

last: Heinrich


title: Early life antibiotic treatment enhances the pathogenicity of CD4+ T cells curing intestinal inflammation

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

summary: Comparison between splenic naïve CD4 T cells from antibiotic treated and non-treated C57BL/6 mice 8-10 weeks after birth. The antibiotic treatement occurred for the first 3 weeks of life until weaning.

overall_design: 3 Control samples, 3 Cocktail treated samples

first: Sebastian

last: Scheer

first: Alex

first: Tiago

last: Medina


title: RNA sequencing of E11.5 Control and Prmt5cKO forelimbs

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

summary: We preformed RNA sequencing on control and Prmt5cKO embryos at E11.5 to determine differentially expressed genes resulting from a loss of Prmt5.

overall_design: We generated three control and two Prmt5cKO biological replicates for RNA sequencing

first: Jacqueline

last: Norrie


title: DNA methylation inheritance across generations

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

summary: Cytosine DNA methylation regulates the expression of eukaryotic genes and transposable elements. Methylation is copied by DNA methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Trans-generational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of trans-generational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells – the cell types that comprise pollen – with mutations in the DRM, CMT2 and CMT3 methyltransferases.

overall_design: We isolated sperm and vegetative nuclei from pollen of Col-0, and cmt2, cmt3, drm1 drm2 (d1d2), and h1.1 h1.2 (h1) mutant Arabidopsis thaliana plants, respectively. DNA is extracted from the isolated nuclei and used for bisulfite-sequencing.

first: Ping-Hung

last: Hsieh

first: Shengbo

last: He

first: Toby

last: Buttress

first: Hongbo

last: Gao

first: Matthew

last: Couchman

first: Robert

middle: L

last: Fischer

first: Daniel

last: Zilberman


title: TADs emerge as a functionally, but not structurally privileged scale in the hierarchical folding of chromosomes

status: Public on Dec 12 2016

city: Milano

first: Yinxiu

last: Zhan

address: Via Adamello 16

country: Italy

institute: European Institute for Oncology

summary: Understanding how regulatory sequences interact in the context of chromosomal architecture is a central challenge in biology. Chromosome conformation capture revealed that mammalian chromosomes possess a rich hierarchy of structural layers, from multi-megabase compartments to sub-megabase topologically associating domains (TADs), and further down to sub-TAD loop domains. TADs appear to act as regulatory microenvironments by constraining and segregating regulatory interactions across discrete chromosomal regions. However, it is unclear whether other (or all) folding layers share similar properties, or rather TADs constitute a privileged folding scale with maximal impact on the organization of regulatory interactions. Here we present a novel parameter-free algorithm (CaTCH) that identifies hierarchical trees of chromosomal domains in Hi-C maps, stratified through their reciprocal physical insulation which is a simple and biologically relevant property. By applying CaTCH to published Hi-C datasets, we show that previously reported folding layers appear at different insulation levels. We demonstrate that although no structurally privileged folding level exists, TADs emerge as a functionally privileged scale defined by maximal enrichment of CTCF at boundaries, and maximal cell-type conservation. By measuring transcriptional output in embryonic stem cells and neural precursor cells, we show that TADs also maximize the likelihood that genes in a domain are co-regulated during differentiation. Finally, we observe that regulatory sequences occur at genomic locations corresponding to optimized mutual interactions at the scale of TADs. Our analysis thus suggests that the architectural functionality of TADs arises from the interplay between their ability to partition interactions and the genomic position of regulatory sequences.

overall_design: The hybrid mouse ESC line F1-21.6 (129Sv-Cast/EiJ), previously described in (Jonkers et al., 2009), were grown on mitomycin C-inactivated MEFs in ES cell media containing 15% FBS (Gibco), 10-4 M b-mercaptoethanol (Sigma), and 1000U/ml of leukaemia inhibitory factor (LIF, Chemicon). Mouse ES cells were differentiated into neural progenitor cells (NPC) as previously described (Conti et al., 2005; Splinter et al., 2011). Total RNAs were prepared by Trizol extraction from the mouse ESC line, and for one NPC clone derived from it. Two biological replicates were collected for ESCs and NPCs. After ribosomal RNA depletion with Ribo-Zero (Illumina),  RNA-seq libraries were prepared using ScriptSeq v2 kit (Illumina) following the manufacturer’s instructions. Libraries were prepared in two technical replicates per biological replicate. 50 bp single-end sequencing was performed on Illumina HiSeq 2000 instruments according to manufacturer’s instructions.

first: Luca

last: Mariani

first: Iros

last: Barozzi

first: Egga

last: Schulz

first: Nils

last: Bluthgen

last: Stadler

first: Guido

last: Tiana

last: Giorgetti


title: Functional mutations form at CTCF-cohesin binding sites in melanoma due to uneven nucleotide excision repair across the motif

city: Sydney

first: Rebecca

last: Poulos

state: NSW

address: Level 2 ACP UNSW Australia

institute: UNSW Australia

summary: CTCF binding sites are frequently mutated in cancer, but how these mutations accumulate and whether they broadly perturb CTCF binding is not well understood. We report that skin cancers exhibit a highly-specific asymmetric mutation pattern within CTCF motifs attributable to ultraviolet irradiation and differential nucleotide excision repair (NER). CTCF binding site mutations form independent of replication timing and are enriched at sites of CTCF/cohesin complex binding, suggesting a role for cohesin in stabilizing CTCF-DNA binding and impairing NER. Performing CTCF ChIP-seq in a melanoma cell-line, we show CTCF binding site mutations to be functional by demonstrating allele-specific reduction of CTCF binding to mutant alleles. While topologically-associating domains with mutated CTCF anchors in melanoma contain differentially-expressed cancer-associated genes, CTCF motif mutations appear generally under neutral selection. However, the frequency and potential functional impact of such mutations in melanoma highlights the need to consider their impact on cellular phenotype in individual genomes.

overall_design: Chromatin immunoprecipiation sequencing (ChIP-seq) against CTCF in malignant melanoma cell-line COLO829, together with IgG background control. 2 replicate experiments performed. Replicates for CTCF ChIP sequenced separately. IgG ChIP from second replicate experiment sequenced.

first: Jason

middle: W

last: Wong

first: Julie

last: Thoms

first: John

last: Pimanda


title: Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

department: Immunology

country: Israel

institute: Weizmann Institute

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

overall_design: Refer to individual Series


title: Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells [ChIP-Seq]

summary: Aire is a transcriptional regulator that induces promiscuous expression of thousands of tissue-restricted antigen (TRA) genes in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs regulating its own expression remain elusive. We used Affymetrix microarrays to analyze the gene expression patterns of Aire expressing cells (mature mTECs and Thymic B cells) and compared them to control counterparts, namely immature mTECs, cortical Thymic epithelial cells and splenic B cells of tissue-restricted antigen (TRA) genes in medullary thymic epithelial cells (mTECs). While the target genes of Aire are well characterized, the transcriptional programs regulating its own expression remain elusive. We’ve used Assay for transposase-accessible chromatin using sequencing (ATAC-Seq) on the different thymic epithelial cell populations to assess chromatin accessibility around the Aire locus in these cells. Moreover, we’ve used the indexing-first chromatin immunoprecipitation (iChIP) technique to assess the occupancy of the Irf8 transcription factor in the Aire locus

overall_design: Mature EpCAM+MHC-II high mTECs, Immature EpCAM+MHC-II low mTECs, and EpCAM+Ly51+ cTECs were flow-sorted from thymi isolated from thymi of C57BL/6 6weeks old mice. These cells were then subjected to ATAC-Seq. typically 10 thousand cells were used per replicate.  Mature EpCAM+MHC-II high mTECs and Immature EpCAM+MHC-II low mTECs were flow-sorted and pooled from thymi isolated from thymi of C57BL/6 6weeks old mice and iChIP using Irf8-specific antibody was then performed. Typically 250 thousand cells were used per replicate.

first: J


title: Chromatin immunoprecipitation and ATAC-Seq data from meduallar thymic epithelial cells [ATAC-Seq]

overall_design: Mature EpCAM+MHC-II high mTECs, Immature EpCAM+MHC-II low mTECs, and EpCAM+Ly51+ cTECs were flow-sorted from thymi isolated from thymi of C57BL/6 6weeks old mice. These cells were then subjected to ATAC-Seq. typically 10 thousand cells were used per replicate.


title: Integrated analyses identify phenotype specific BMP4 signaling in breast cancer [Dnase-seq]

city: Tampere

first: Tommi

middle: Tapani

last: Rantapero

address: Biokatu 8

department: BioMediTech

institute: University of Tampere

summary: Bone morphogenetic protein 4 (BMP4) plays an important role in cancer pathogenesis. In breast cancer, it reduces proliferation and increases migration in a cell line-dependent manner. To characterize the transcriptional mediators of these phenotypes, we performed RNA-seq and DNase-seq analyses after BMP4 treatment in MDA-MB-231 and T-47D breast cancer cells that respond to BMP4 with enhanced migration and decreased cell growth, respectively.

overall_design: We characterized the Dnase I hypersensitive sites BMP4 treated and non-treated MDA-MB-231 and T-47D cells using Dnase-seq

first: Minna

last: Ampuja

first: Alejandra

last: Rodríquez-Martinez

first: Maaria

last: Palmroth

first: Emma-Leena

last: Alarmo

first: Matti

last: Nykter

first: Anne

last: Kallioniemi


title: Integrated analyses identify phenotype specific BMP4 signaling in breast cancer


title: Genome-wide Identification of Neuronal Activity-regulated Genes in Drosophila [Elav_ChR2]

city: Waltham

first: Xiao

last: Chen

address: 415 South St

department: Biology

institute: Brandeis University

summary: We identified ARGs in a genome-wide manner, in fly brains as well as in sorted neurons; they included dopaminergic neurons (DA) and a subset of circadian-related neurons (PDF+ neurons).

overall_design: Elav-GAL4;UAS-ChR2-XXL or Elav-GAL4 flies stimulated with 30-second blue LED and mRNA isolated and sequenced 0, 15, 30, 60 min after.

first: Michael

last: Rosbash


title: Genome-wide Identification of Neuronal Activity-regulated Genes in Drosophila [KCl]

overall_design: KCl stimulation of dissected brains and mRNA isolated and sequenced 0, 15, 30, 60 min after.


title: Genome-wide Identification of Neuronal Activity-regulated Genes in Drosophila [DA_PDF]

overall_design: TH-GAL4 (DA neurons)/PDF-gal4 (PDF+ cells);UAS-TrpA1 or TH-GAL4 flies stimulated with temperature shift and mRNA isolated and sequenced 0 or 60 min after.


title: Genome-wide Identification of Neuronal Activity-regulated Genes in Drosophila


title: Single-cell epigenomic variability reveals functional cancer heterogeneity

city: Stanford

first: Howard

last: Chang

address: 269 Campus Drive

department: Dermatology

institute: Stanford University

summary:
Background: Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity, but is difficult to detect and assess functionally.

Results: We develop a strategy to bridge the gap between measurement and function in single-cell epigenomics. Using single-cell chromatin accessibility and RNA-seq data in K562 leukemic cells, we identify the cell surface marker CD24 as co-varying with chromatin accessibility changes linked to GATA transcription factors in single cells. Fluorescence-activated cell sorting of CD24 high vs. low cells prospectively isolated GATA1 and GATA2 high vs. low cells. GATA high vs. low cells express differential gene regulatory networks, differential sensitivity to the drug imatinib mesylate, and differential self-renewal capacity. Lineage tracing experiments show that GATA/CD24hi cells have the capability to rapidly reconstitute the heterogeneity within the entire starting population, suggesting that GATA expression levels drive a phenotypically relevant source of epigenomic plasticity.

Conclusion: Single-cell chromatin accessibility can guide prospective characterization of cancer heterogeneity. Epigenomic subpopulations in cancer impact drug sensitivity and the clonal dynamics of cancer evolution.

overall_design: Cells were maintained at 37° C and 5% CO2 at recommended density and were  harvested at mid-log phase. After harvest, K562 cells were stained with CD24-PE (BD Biosciences) antibody and sorted using a BD FACSAriaII for CD24-high and CD24-low expressing cells. 50 000 sorted cells for each replicate were washed, lysed, and tagmented using the standard ATAC-seq protocol (Buenrostro et al., 2013). Libraries were  purified using Qiagen MinElute columns and quality was checked using Bioanalyzer. High-Throughout Sequencing was performed on a NextSeq Illumina machine using the NextSeq 500 kit. Settings were 75x75 cycles, paired end.

first: Ulrike

last: Litzenburger

middle: D

last: Buenrostro

middle: Y

first: Ying

last: Sheng

first: William

middle: J

last: Greenleaf

first: Nathan

last: Sheffield

first: Beijing

last: Wu

first: Arwa

last: Katheria


title: Genome-wide Identification of Neuronal Activity-regulated Genes in Drosophila [Elav_TrpA1]

overall_design: Elav-GAL4;UAS-TrpA1 or Elav-GAL4 flies stimulated with temperature shift and mRNA isolated and sequenced 0, 15, 30, 60 min after.


title: Genome-wide Identification of Neuronal Activity-regulated Genes in Drosophila [Elav_TrpA1_ATAC]

overall_design: Elav-GAL4;UAS-TrpA1 or Elav-GAL4 flies stimulated with temperature shift and chromatin DNA isolated and sequenced 0 and 30 min after.


title: Integrated analyses identify phenotype specific BMP4 signaling in breast cancer [RNA-seq]

last: Rantapero

overall_design: We characterized mRNA levels from BMP4 treated and non-treated MDA-MB-231 and T-47D cells using RNA-seq


title: Direct Induction of Neural Progenitor Cells Transiently Passes Through a Partially-reprogrammed State

status: Public on Dec 11 2016

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road NO.1239

institute: Tongji University

summary: During giNPC induction process, cell samples were harvested at various induction days including named Day1, Day4, Day7, Day10, Day14, Day17 and Day21. Meanwhile, samples from primary neurosphere-like cluster (named pre-NPCs), established giNPC cell line at passage 6 (named giNPCs P6), Brain-NPCs as well as Teratoma were also collected. Total RNA was isolated from cell pellets by Trizol reagent and RNA-Seq library were generated using KAPA Strandard mRNA-Seq Kits according to the manufacturer's recommendations.

overall_design: mRNA profiles of 11 cell types, generated by deep sequencing in duplicate, using HiSeq 2000. Paired-end 100-bp sequencing was applied.

first: Rui

first: Wenchao

last: Xiu


title: Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures

city: Las  Cruces

first: Elba

last: Serrano

state: NM

address: NMSU Foster Hall Biology Box 30001-3AF

institute: NMSU

summary: Biomaterial scaffolds have the potential to enhance neuronal development and regeneration. Understanding the genetic responses of astrocytes and neurons to biomaterials could facilitate the development of synthetic environments that enable the specification of neural tissue organization with engineered scaffolds.  In this study, we used high throughput transcriptomic and imaging methods to determine the impact of a hydrogel with no known bioactive epitopes, Puramatrix™, on human glial cells in vitro. Parallel studies were undertaken with cells grown in a monolayer environment on tissue culture polystyrene. When the Normal Human Astrocyte (NHA) cell line is grown in a hydrogel matrix environment, the glial cells adopt a structural organization that resembles that of neuronal-glial cocultures, where neurons form clusters that are distinct from the surrounding glia.  Statistical analysis of next generation RNA sequencing  data  uncovered a  set  of  genes  that are  differentially  expressed  in  the  monolayer  and  matrix  hydrogel  environments.   Functional  analysis  demonstrated  that  hydrogel-upregulated  genes  can  be  grouped  into  three  broad  categories:  neuronal differentiation  and/or  neural  plasticity, response  to  neural  insult,  and  sensory  perception.  Our results demonstrate that hydrogel biomaterials have the potential to transform human glial cell identity, and may have applications in the repair of damaged brain tissue

overall_design: RNA sequencing of normal human astrocytes (Lonza) from 2 biological donors that were cultured for 5 days either with the peptide hydrogel Puramatrix or on tissue culture polystyrene

first: V

middle: B

last: Knight


title: Gene expression changes upon Mll1 knockout in NUP98-HOXA9 transformed murine LSKs

city: New York

first: Scott

last: Armstrong

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

summary: We report Illumina next generation RNA sequencing (RNAseq) of NUP98-HOXA9 in vitro transformed murine LSKs upon genetic deletion of Mll1. These gene expression data illustrate that Mll1 regulates Hoxa, Hoxb and Meis1 expression in NUP98-HOXA9 transformed murine BM cells.

overall_design: RNAseq comparing Mll1 homozygous knockout cells to Mll1 flox/flox control

first: Haiming

last: Xu


title: Ikaros-regulated genes in a mouse model of BCR-ABL1+ acute lymphoblastic leukemia

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary: To examine Ikaros tumor suppressor mechanisms, we have utilized inducible RNAi to dynamically restore endogenous Ikaros expression in BCR-ABL1+ B-ALL driven by its knockdown (Ikaros knockdown), and compared these tumors to tumors driven by BCR-ABL1 alone (control). Restoration of Ikaros causes rapid regression of tumor cells in vivo, significantly prolonging tumor transplant recipient survival. Using both transgenic and retroviral approaches, we conducted expression analysis of B-ALL by RNA-Seq and have identified a series of Ikaros-regulated genes within established tumor cell in vivo. Comparison of Ikaros-activated and Ikaros-repressed genes with human B-ALL expression data shows a set of conserved Ikaros target genes, some of which are associated with patient outcome (namely, CTNND1, IFITM3 and EMP1).

overall_design: RNA-seq was performed on BCR-ABL1+ B-ALL with inducible Ikaros knockdown (Ikaros knockdown, n=8; transgenic n=5, retroviral n=3) or BCR-ABL1+ alone B-ALL (control, n=4; transgenic n=3, retroviral n=1) cells isolated from untreated and three 3-day Dox-treated mice. Samples were run on HiSeq or NextSeq platform. B-ALL B031 was run in technical duplicate. Extended Dox samples (B027: d7 and d10) and relapse samples for B027, B029 and B035 have also been analyzed in this dataset.

first: Matthew

last: Witkowski

first: Yifang

last: Hu

first: Ross

last: Dickins


title: Nuclear mRNA quality control is bypassed for rapid export of stress responsive transcripts [RNA-Seq]

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Comparative analyses of Mex67 and Npl3 binding to mRNA at normal growth condition (25°C) and upon shift to heat stress (30 min, 42°C).

overall_design: Examination of two biological RNA Co-IP replicates of Mex67, Npl3 and no tag control at 25°C and upon shift to 30 min at 42°C (Heat stress) and subsequent Illumina RNA deep-sequencing

first: Thomas

last: Lingner

first: Alexandra

last: Hackmann

last: Salinas-Riester

first: Heike

last: Krebber


title: Genome-wide maps of NUP98 fusion and MLL1 co-bound targets and their chromatin state in NUP98 fusion transformed cells.

summary: By performing biotin-mediated chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) for two different NUP98 fusions, we defined the genome-wide direct binding sites of NUP98-HOXA9 or NUP98-HOXD13. To test whether NUP98 fusions and Mll1 were recruited to the same region of Hox genes promoters, Mll1 ChIP-seq analysis was carried out in murine NUP98-HOXA9 transformed cells using an anti-Mll1n antibody. In agreement with our results showing that NUP98-HOXA9 interacts with MLL1 in NSL/MLL1 complex, Mll1 binding targets significantly overlap with that of NUP98-HOXA9 at promoter region and gene body region. Given that MOF and MLL1 work in concert to modify H4K16ac and H3K4me3 at promoters, we further test whether H3K4me3 and H4K16ac marks are associated with NUP98-HOXA9-bound targets in murine NUP98-HOXA9 transformed cells by anti-H3K4me3 and anti-H4K16ac ChIP-seq. Our data show that both H3K4me3 and H4K16ac mark presents on NUP98-HOXA9 binding targets at promoters, and this is in line with the coordination role in the activities between MOF-mediated H4K16 acetylation and MLL/SET-mediated H3K4 methylation. In summary, our results confirmed that NUP98-HOXA9 and Mll1 are recruited to the same Hox loci, and this recruitment is associated with activating epigenetic marks, supporting the notion of the association between NUP98 fusions and NSL/Mll1 complex, suggesting that the recruitment of NUP98 fusions to the Hox gene loci maybe through MLL1.

overall_design: To define the binding targets of NUP98 fusion proteins, and the co-bound sites with MLL1. To determine the status of 2 different histone modifications on NUP98 fusion binding targets using NUP98-HOXA9 transfromed mouse bone marrow LSK cells.


title: Transcription profiling of neuronal metabolic reprogramming

city: La Jolla,

first: Tony

last: Hunter

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: we explored the changes in metabolic gene expression during neuronal differentiation from neural progenitor cells (NPC).

overall_design: Examination of transcription profile in NPC and neurons.

first: Xinde

last: Zheng


title: RNA sequencing of WT and MSC KO iTreg cells

status: Public on Dec 10 2016

city: Bethesda

first: Chuan

last: Wu

address: 10 Center Drive, Building 10, RM 4B17

institute: National Cancer Institute

summary: Although the master transcription factors (TFs) are the key to the development of specific T cell subsets, whether additional transcriptional regulators are induced by the same stimuli that dominantly repress development of other T cell lineages has not been fully elucidated. Using Transforming growth factor-b (TGF-b) induced regulatory T cell (iTreg) system, we identify the TF Musculin (MSC) as critical for iTreg development by repression of TH2 transcriptional program. Loss of MSC reduces Foxp3 expression and induces TH2 differentiation even under TGF-b induced iTreg differentiation conditions. MSC mediates this effect by interrupting binding of GATA3 to TH2 locus and reducing intrachromosomal interactions within the Th2 locus. MSC-deficient iTregs are not able to suppress TH2 responses and the Msc–/– mice spontaneously develop gut and lung inflammation with age. Our data indicate that MSC enforces Foxp3 expression and promotes unidirectional induction of iTregs by repressing development of the TH2 developmental program.

overall_design: mRNA profiles of in vitro differentiated iTreg cells from WT and MSC KO mice by deep sequencing.

first: Vijay

last: Kuchroo


title: Calcineurin-dependent lateral transfer of Aspergillus fumigatus through a VASP tunnel during human macrophage cell death enables control of fungal germination

city: London

first: Darius

middle: P H

last: Armstrong-James

address: Faculty of Medicine

department: National Heart and Lung Institute

institute: Imperial College London

summary: We sequenced total RNA from human monocyte derived macrophages (n = 6, healthy donors) pre-treated with calcineurin inhibitor FK506 (10 ng/ml) for 1h and stimulated with live Aspergillus fumigatus swollen conidia (MOI=1) for 1h and 6h.

overall_design: We sequenced total RNA from human monocyte derived macrophages from six healthy donors. For each donor, we had six conditions (Unstimulated control, FK506 pre-treated control, 1 hour stimulation with live Aspergillus fumigatus, 1 hour stimulation with live Aspergillus fumigatus with FK506 pre-treatment, 6 hour stimulation with live Aspergillus fumigatus, 6 hour stimulation with live Aspergillus fumigatus with FK506 pre-treatment. In total we analysed 36 samples (6 healthy donors with 6 conditions).

first: Shichina

last: Kannambath


title: Next Generation Sequencing (NGS) of zebrafish embryos transcriptome by pentachlorophenol (PCP) treatment

first: Ting

address: No. 1239 Road Siping

summary:
Purpose: We report the application of NGS for profiling the impacts of PCP exposure on the transcriptome of zebrafish embryos.
Methods: mRNA profiles of 10 hpf/24 hpf PCP-treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks.
Results: At 24 hpf, 6087 transcripts were affected after 200 μg/l exposure, in which 3593 were up-regulated and 2494 were down-regulated, and 1783 transcripts were affected after 5 μg/l exposure, in which 1031 were up-regulated and 752 were down-regulated.  At 10 hpf, 2970 transcripts were affected after 200 μg/l exposure, in which 1526 were up-regulated and 1444 were down-regulated, and 1366 transcripts were affected after 5 μg/l exposure, in which 521 were up-regulated and 845 were down-regulated.
Conclusions: This study provides a framework for the application of high-throughput RNA sequencing towards characterization of the impacts of PCP on whole zebrafish larval transcriptome.

overall_design: Examination of zebrafish embronic transcriptomes with 2 concentrations and 2 durations of PCP treatments.

first: Jing

last: Zhao


title: CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

city: Oslo

first: Elisa

last: Fiorito

address: Forskningsparken - Gaustadalleen 21

department: Norwegian Centre for Molecular Medicine (NCMM)

country: Norway

institute: University of Oslo (UiO)

overall_design: Refer to individual Series


title: Microglial-specific transcriptome changes following chronic alcohol consumption

city: Austin

first: Gizelle

middle: Marin

last: Robinson

state: TX

address: 2500 Speedway

department: Waggoner Center for Alcohol and Addiction Research

institute: University of Texas at Austin

summary: Microglia are fundamentally important immune cells within the central nervous system (CNS) that respond to environmental challenges to maintain normal physiological processes. Alterations in steady-state cellular function and over-activation of microglia can facilitate the initiation and progression of neuropathological conditions such as Alzheimer’s disease, Multiple Sclerosis, and Major Depressive Disorder. Alcohol consumption disrupts signaling pathways including both innate and adaptive immune responses that are necessary for CNS homeostasis. Unbiased RNA-Seq profiling was used to identify gene expression changes in isolated microglia in response to recurring bouts of voluntary alcohol drinking behavior. Gene coexpression analysis identified a coordinately regulated group of genes, unique to microglia, that collectively are associated with alcohol consumption. Several genes in this group were involved in toll-like receptor signaling and production of the inflammatory cytokine interferon-gamma. Coordinate expression of these genes is not ascertained from an admixture of CNS cell-types, underscoring the importance of examining isolated cellular populations to reveal systematic gene expression changes arising from mature microglia. We identified a distinctive microglial gene expression signature for neuroimmune responses related to alcohol consumption that provides valuable insight into microglia-specific changes underlying the development of substance abuse, as well as related CNS disorders.

overall_design: We examined mRNA from both total homogenate (mixture of all cell types) and microglia from the cortex of control mice and mice that have undergone chronic voluntary ethanol consumption

first: G

middle: R

first: R

last: Mayfield


title: CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions [RNA-seq]

summary: In our work we used high-throughput sequencing methods to get insight in the role of CTCF in ER-mediated gene regulation in luminal breast cancer cells. After assessing genome-wide binding of CTCF, ER, FOXA1 and Lamin B in MCF7 cells treated with estrogen for different time points, we could correlate the interaction to the chromatin with estrogen-induced de novo transcription (from GRO-seq data) and loop formation (from ChIA-PET, Fullwood et al., 2009). We observed that CTCF binding correlates with ER-mediated transcription and its depletion can affect ER-ER loop formation and subsequently gene expression.

overall_design: RNA-seq in MCF7 cells transfected with siRNA targeting CTCF (siCTCF) or control (siNT) and treated for 0h or 3h with 100 nM Estrogen.

first: Yogita

last: Sharma

first: Siv

last: Gilfillan


title: miR-17-92 cluster regulates adult hippocampal neurogenesis, anxiety and depression

status: Public on Dec 09 2016

first: Seung-Nam

last: Kim

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary: Emerging evidence has shown that noncoding RNAs, particularly microRNAs (miRNAs), contribute to the pathogenesis of mood and anxiety disorders, although the molecular mechanisms are poorly understood. Here we show altered levels of miR-17-92 in adult hippocampal neural progenitors have a significant impact in neurogenesis and anxiety- and depression-related behaviors in mice. miR-17-92 deletion in adult neural progenitors causes a decrease, while its overexpression an increase of neurogenesis in the dentate gyrus, through regulating genes in the glucocorticoid pathway, especially serum- and glucocorticoid-inducible protein kinase-1 (Sgk1). miR-17-92 knockout mice show anxiety- and depression-like behaviors, whereas miR-17-92 overexpressing mice exhibit anxiolytic and antidepression-like behaviors. Furthermore, we show that miR-17-92 expression in the adult mouse hippocampus responds to chronic stress, and miR-17-92 rescues proliferation defects, induced by corticosterone, in hippocampal neural progenitors. Our study uncovers a crucial role for miR-17-92 in adult neural progenitors to regulate neurogenesis and anxiety- and depression-like behaviors.

overall_design: Hippocampal mRNA profiles of 13-week old wildtype and miR-17-92 knockout mice were generated by whole RNA-sequencing, using IlluminaHiSeq1000.

first: Junghee

last: Jin

first: Tao

last: Sun


title: Structure and variation in microbiome from continuous and rotational Pinellia ternata cropping soils

city: yangling

first: zhigui

last: he

institute: Northwest A & F University, College of Life Sciences

summary: We used wheat as rotational crop to assess the influence of continuous cropping on microbiome in Pinellia ternata rhizosphere and the remediation of rotational cropping to the impacted microbiota. Illumina high-throughput sequencing technology was utilized for this method to explore the rhizosphere microbial structure and diversity based on continuous and rotational cropping.

sample_organism:
uncultivated soil bacterium
Pinellia ternata

overall_design: Greenhouse experiment was designed to reveal the difference in microbiome of rotational and continuous cropping soil; details provided in the readme.txt and supporting figure for experimental_design.pdf files.

first: Zhigui

last: He

first: Juan'e

last: Dong


title: Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response

city: LUJAN DE CUYO

first: Marcos

last: Paolinelli

state: Mendoza

address: San Martin 3853

country: Argentina

institute: CONICET-INTA

summary:
Purpose: Lasiodiplodia theobromae is a pathogenic fungus causing Botryosphaeria dieback in grapevine. Heat and drought stress was suggested to promote the disease incidence in recent years, therefore we decided to evaluate the effect of heat on in vitro experiment, adding grapevine wood to simulate the environment in the trunk during in field infection.
Methods: Fungal mRNA was extracted from mycellium collected after 49 hours of growth without stress in the presence of GW (GW_noHS) or in its absence (VS_noHS). Some mRNA were extracted form mycellium collected 10 min after stress (1 hour at 42 C) both in the presence of GW (GW_HS) or in its absence (VS_HS). The cDNA and sequenciation was done according with Illumina HiSeq 2500 recomendations by triplicate. Paired end reads (100bp) were used for de novo assembly through Trinity. Transdecoder was used to predict ORFs. The transcripts functional annotatio was done through BlastX and Blast2GO. Bowtie2 was used to map the reads for each sample to the previously assembled transcritome, a homemade Perl script was used to count the mapped reads and edgeR was employed for differential expression and statistical analysis.
Results: Seventy million reads were asembled to produce 19,860 transcripts, from those 15,981 were predicted to codify for ORFs. Thirty-five % of transcripts did not have any homologue in NCBI NR database, most of those also did not were predicted to codify for ORFs. With the remainning 38 % of transcripts the functional annotation was obtained. Around 90% of reads for each sample were mapped to the de novo assembled transcriptome. Around 2339 genes were differentially expressed when comparing GW_HS vs GW_noHS or vs VS_noHS and GW_noHS vs VS_noHS and VS_HS vs VS_noHS. Hierarchical clustering with functional enrichment were used to predict metabolic pathways with differential regulation. In silico prediction were then verified with RT-qPCR showing linear correlation (r2=0.87) in in vitro experiment. Then trough in planta fungal gene expression helps to verify that phenolic metabolism is important for colonization in grapevine.
Conclusion: A model for fungal response to HS in the presence of GW was proposed. This correspond to the first work to identify nucleotide sequences, measure gene expression and propose pathogenicity factors important for disease establishment in grapevine.

last: Paolinelli-Alfonso

first: Rufina

last: Hernandez-Martínez


title: CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions [ChIP-seq]

overall_design: Examination of CTCF, ER, FOXA1 and Lamin B chromatin binding in MCF7 cells upon estrogen stimulation for 0h, 45min or 3h.


title: Identification of Novel Targets of Diabetic Nephropathy Using RNA-seq

city: Cambridge

first: Anna

last: Salzberg

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

summary: Diabetic nephropathy (DN) is a major complication of type 1 and type 2 diabetes and may lead to kidney failure. Understanding how diabetes regulates transcriptome dynamics in DN is important for understanding the biology of the disease and for guiding development of new treatments. In this study, we identified a set of unique biomarkers and canonical pathways that may hold the key to understanding mechanisms of DN pathobiology with value for clinical translation. Our data suggest that mitochondrial dysfunction, genotoxicity and oxidative stress are principal events in DN and that P78-PEDF, an active PEDF peptide, holds promise for its management.

overall_design: We analyzed the transcriptome of diabetic D2.B6-Ins2Akita/MatbJ mice, a diabetic model of DN, before and after treatment with P78-PEDF. Age-, weight-, and gender-matched diabetic mice and wild-type (wt, DBA/2J background) littermates were treated at 6 wks of age (early treatment) or 12 wks of age (late treatment) for the duration of 6 wks. All animals, including wild-type controls, were implanted with an osmotic mini pump delivering 0.3 ug/g/day P78-PEDF to diabetic groups or vehicle (PBS) to controls (wild-type and diabetic). Four groups of samples were used: 1. Normal mice (wt control), 2. Diabetic mice (diabetic control), 3. Early treatment with P78 (ET), and 4. Late treatment with P78 (LT). For the Diabetic Group, only animals with blood glucose levels > 350 mg/dl were used. Samples were pooled (n=7-13/group) and each group was analyzed using next-generation RNA-seq technology.

first: Joyce

last: Tombran-Tink

middle: C


title: Distinct 5-methylcytosine profiles in poly(A)RNA from mouse embryonic stem cells and the brain

city: Innsbruck

first: Alexandra

last: Lusser

state: Tyrol

address: Innrain 80

department: Molecular Biology

country: Austria

institute: Biocenter Medical University Innsbruck

summary:
Background: Recent work identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation and methylation of carbon 5 in cytosine (m5C). However, knowledge about prevalence and transcriptome-wide distribution of m5C is still extremely limited and thus, studies in different cell types, tissues and organisms are needed to gain insight into possible functions of this modification and interactions with other regulatory processes
Results: We carried out an unbiased global analysis of m5C in total and nuclear poly(A)RNA of embryonic stem cells (ESCs) and brain of the mouse. We show that there are intriguing differences in these samples and cell compartments with respect to degree of methylation, functional classification of methylated transcripts and position bias within the transcript. Specifically, we observe a pronounced accumulation of m5C sites in the vicinity of the translational start codon, depletion in coding sequences and mixed patterns of enrichment in the 3’UTR. Degree and pattern of methylation distinguish transcripts modified in both ESCs and brain from those methylated in either one of the samples. Furthermore, we observed significant enrichment of m5C in the vicinity of the transcriptional start site in lncRNAs. We also present data regarding correlations between m5C and N6-methyladenosine, miRNA target sites and binding sites of RNA binding proteins.
Conclusion: Our study presents the first comprehensive picture of cytosine methylation in the mouse epitranscriptome. These data can serve as a basis for future studies of function and biological significance of m5C in mRNA in mammals.

overall_design: RNA was isolated from mouse embryonic stem cells (ESC) and brains as well as from the nuclei of the respective samples (in triplicates) and RNA-Bisulfite sequencing was performed.

first: Thomas

last: Amort

first: Dietmar

last: Rieder

last: Wille

first: Daria

last: Khokhlova-Cubberley

first: Christian

last: Riml

first: Lukas

last: Trixl

first: Xi-Yu

last: Jia

first: Ronald

last: Micura


title: Genome wide localizatoin of ORCA during G1 phase in U2OS cells and map of methyl-CpG sites in U2OS cells

city: Urbana

first: Supriya

last: Prasanth

state: ILLINOIS

address: 601 S Goodwin Ave

institute: University of Illinois at Urbana-Champaign

summary: ORCA is an ORC associated protein that plays important roles in replication initiation as well as heterochromatin organization. We carried out ORCA ChIP-seq in U2OS cells synchronized at different stage of G1 phase to determine its genome wide localization. To understand the genomic features of ORCA binding regions, we also carried out Methylated DNA IP (MeDIP) followed by deep sequencing in U2OS cells to determine the genome wide localizatoin of methyl-CpG sites in U2OS cells and how ORCA bidning regions co-localize with this important repressive mark.

overall_design: ORCA ChIP-seq was carried out in U2OS cells that were synchronized at early, mid and late G1 phase. MeDIP-seq was performed in U2OS cells.

first: Yating

last: Wang

first: Abid

last: Khan

middle: G

last: Marks

first: Owen

last: Smith

first: Mirit

middle: I

last: Aladjem

first: Rachel

last: Creager

first: David

middle: M

last: MacAlpine


title: Global transcriptional profiling changes upon knockdown of LKB1 in human glioblastoma cell lines

status: Public on Dec 08 2016

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: The experiment was designed to display differential gene expression profiling changes in two human glioblastoma cells upon knockdow of LKB1 tumor suppressor, by using RNAseq technology.

overall_design: LKB1 was first silenced in two glioblastoma cells: U87 and T98 by siRNA-mediated knockdown. Total RNA was extracted from duplicated cancers cells transfected with control siRNA and LKB1 specific siRNA at 72h posttransfection for RNAseq analysis. Differentially expressed genes in LKB1-attenuated glioblastoma cells were identified in comparison to that in glioblastoma cells transfected with control siRNA.

first: Keqiang

last: Zhang

first: Jinghan

first: Jinhui

first: Xiwei

last: Wu

first: Lu

last: Yang

first: Yun

last: Yen


title: Genes encoding cognate receptors for IRI-related recipient cytokines are expressed in donor livers

city: Los Angeles

first: Rebecca

middle: A.

last: Sosa

state: California

address: 1000 Veteran Ave

department: Pathology & Lab Medicine

institute: UCLA

summary:
Purpose: RNAseq was used to look in donor allografts for genes encoding cytokine receptors specific to the cytokines identified to be upregulated in the blood of Orthotopic liver transplantation (OLT)  receipients with ischemia reperfusion injury (IRI)
Methods: Liver mRNA cytokine receptor profiles of allografts taken before and after transplant, demultiplexed with Illumina CASAVA, trimmed with Cutadapt, aligned to hg38 with STAR, counted with featureCounts
Results: We identified expression of genes encoding 10 cognate receptors for the 14 potential cytokines found to be upregulated in IRI+ patients.
Conclusion: Many of the cytokines that are upregulated in the blood of IRI+ OLT recipients have cognate receptors present in donor livers that could allow completed signaling pathways to occur

overall_design: Liver allograft mRNA profiles of pre- and post-reperfusion biopsies from IRI+ and IRI- OLT recipients were generated by deep sequencing using Illumina HiSeq 2000

first: Elaine

middle: F

last: Reed