title: Integration of transcriptomic and proteomic analyses reveals new insights into the response of grape leaves to high temperature

first: Lijun

last: Wang

address: No.20 Nanxincun, Xiangshan, Beijing 100093, China

institute: IBCAS

summary: Heat stress is one of the primary abiotic stresses that limit crop production . Grape is a popular cultivated fruit with high economic value throughout the world, and whose growth and development is often influenced by high temperature. Alternative splicing (AS) is a widespread mechanism increasing transcriptome complexity and proteome diversity. We conducted high temperature treatments (35oC, 40oC and 45oC) on grapevines (Vitis vinifera), and assessed proteomic and transcriptomic （especially AS）changes in leaves. We found that nearly 70% of the genes were alternatively spliced under high temperature. Intron retention (IR), exon skipping (ES) and alternative donor/acceptor sites were markedly induced under different high temperatures. IR was the most abundant up- and down-regulated AS event; moreover, IR events at 40 and 45oC were far higher than those at 35oC. These  results indicated AS, especially IR, is an important posttranscriptional regulatory during grape leaf responses to high temperature. Proteomic analysis showed that protein levels of the RNA binding proteins SR45, SR30, and SR34, and the nuclear ribonucleic protein U1A in grape leaves gradually rose as ambient temperature increased. The results also revealed why AS events occurred more frequently under high temperature in grape leaves. After integrating transcriptomic and proteomic data, we found that HSPs and some important transcript factors such as MBF1c and HSFA2 were mainly involved in heat tolerance in grape through up-regulating transcriptional and translational levels, and were especially modulated by AS. The results provide the first simultaneous evidence for grape leaf responses to high temperature at transcriptional, posttranscriptional and translational levels.


title: Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [RNA]

status: Public on Mar 07 2017

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

type: Expression profiling by high throughput sequencing

summary: We report high-throughput profiling of gene expression from whole zebrafish ventricles. We profile mRNA in uninjured ventricles and those undergoing regeneration 14 days after genetic ablation. This study provides a framework for understanding transcriptional changes during adult models of regeneration.

overall_design: Examination of gene expression in cardiomyocytes under different states of proliferation.

first: Joseph

middle: A

last: Goldman

first: Guray

last: Kuzu

first: Nutishia

last: Lee

first: Jaclyn

last: Karasik

first: Matthew

last: Gemberling

first: Ravi

last: Karra

first: Amy

last: Dickson

first: Fei

last: Sun

middle: J

last: Foglia

first: Kenneth

middle: D

last: Poss


title: Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [H33]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report high-throughput profiling of transgenic histone H3.3 in zebrafish cardiomyocytes. The replacement histone H3.3 is deposited at sites of nucleosome turnover including regions of active chromatin. We profile H3.3 in uninjured cardiomyocytes, those undergoing regeneration 14 days after genetic ablation and those proliferating 7 days after Nrg1 stimulated hyperplasia. This study provides a framework for understanding chromatin transitions during adult models of regeneration.

overall_design: Examination of H3.3 occupancy in cardiomyocytes under different states of proliferation.


title: Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes [H3K27Ac]

summary: We report high-throughput profiling of acetylation of lysine 27 on histone H3 from whole zebrafish ventricles. The H3K27Ac mark has been shown to be present at active enhancer elements and including regions of active chromatin. We profile H3K27Ac in uninjured cardiomyocytes and those undergoing regeneration 14 days after genetic ablation. This study provides a framework for understanding chromatin transitions during adult models of regeneration.

overall_design: Examination of H3K27Ac occupancy in uninjured cardiomyocytes and those undergoing regeneration 14 days after genetic ablation


title: Transcriptome of new DGCR8_KO mouse embryonic stem cells generated by paired CRISPR/Cas9 approach

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study was to obtain the trasncriptome of DGCR8_KO mESCs to compare it with the transcriptome of WT mESCs (deposit separately).

overall_design: mRNA profiles of DGCR8_KO mouse embryonic stem cells were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.


title: Transcriptional profiling of NMB0419 mutant of Neisseria meningitidis MC58

city: London

first: Ming-Shi

last: Li

state: Greater London

address: Norfolk Place

department: Medicine/Paediatrics

country: United Kingdom

institute: Imperial College London

summary: Neisseria meningitidis is an obligate commensal colonising the human nasopharynx and occasionally invades the bloodstream causing life-threatening meningitis and septicaemia. The gene NMB0419 on the genome of N. meningitidis MC58 encodes a putative Sel1-like repeat (SLR) containing protein, which has been implicated in mediating meningococcal invasion of epithelial cells. We prepared RNA samples from N. meningitidis MC58 (WT) and its isogenic mutant of NMB0419 grown to log phase in in-vitro culture. The RNA samples were subjected to RNA sequencing. The resulting transcriptomes were compared to determine the genes that differentially expressed in NMB0419 mutant.

overall_design: RNA samples werer prepared from three biological replicates for NMB0419 mutant strain and wild type (WT) MC58 strain and were subjected to paired comparison between NMB0419 mutant and WT strain.

first: J

middle: S

last: Kroll


title: Transcriptome of new Dicer_KO mouse embryonic stem cells generated by paired CRISPR/Cas9 approach

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study was to obtain the trasncriptome of Dicer_KO mESCs to compare it with the transcriptome of WT mESCs (deposit separately).

overall_design: mRNA profiles of Dicer_KO mouse embryonic stem cells were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.


title: Recurrent TRIO fusion in non-translocation-related sarcomas

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

country: France

institute: Cancer Research Center of Toulouse

summary: We used NGS on a cohort of complex genetics sarcomas to study their transcriptomes (RNA-seq technology), looking for recurrent and specific gene fusions. We identified multiple TRIO fusions with different partners in our cohort. No TRIO fusions were reported in negative-control cells (normal tissues) and in simple genetics sarcomas.

overall_design: We performed RNA-seq on 117 various sarcomas. Samples include ERCC Spike-ins. 6 samples contains TRIO fusions.

first: Lucile

last: Delespaul


title: 3D structures of individual mammalian genomes reveal principles of nuclear organization

city: Barcelona

first: Andre

last: Faure

address: Dr. Aiguader 88

department: EMBL-CRG Systems Biology Unit

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: The folding of genomic DNA from the beads-on-a-string like structure of nucleosomes into higher order assemblies is thought to be critically linked to nuclear processes, but it is unclear to what degree it is a cause or consequence of function. We have calculated the first 3D structural models of entire mammalian genomes using data from a new chromosome conformation capture protocol that allows us to first image and then process single cells. This has allowed us to study the folding of chromosomes down to a sub-100 kb scale. We show that the structures of individual topological-associated domains, chromosomes, and the way they pack together, varies very substantially from cell-to-cell. However, in all cells we find a consistent large-scale organization of compartments, with active enhancers and promoters clustering near inter-chromosomal interfaces, suggesting that nuclear processes such as transcription may drive chromosome and genome folding.

overall_design: ChIP-seq, RNA-seq and nuclear RNA-seq in haploid and diploid mouse embryonic stem cells

first: Ernest

last: Laue


title: Identification of early and late responder genes during cell reprogramming of mouse fibroblasts into induced pluripotent stem cells

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

summary: Our recent approach to induction of pluripotent stem cells from fibroblasts using protein extract from mouse ESCs could overcome the potential tumorigenicity risks associated with random retroviral integration. Here we examine the epigenetic modifications and transcriptome in two kinds of iPSCs and a partially reprogrammed iPSC (iPSCp) generated from adult cardiac and skin fibroblasts independently to assess any perturbations of transcription program during reprogramming.

overall_design: The histone H3K4me3 and H3K27me3 profiles were obtained from ESC, two kinds of iPSCs and a partially reprogrammed iPSC (iPSCp) generated from adult cardiac and skin fibroblasts.

first: Jihwan

last: Park

first: Yoo-Wook

last: Kwon

first: Chang-Pyo

last: Hong

first: Seonghye

last: Seo

first: Moon

middle: K

last: Choe

first: So-I

last: Shin

first: Jae

last: Paek

first: Hyo-Soo

last: Kim


title: Tamoxifen-associated endometrial tumors expose differential enhancer activity for Estrogen Receptor alpha [ChIP-Seq]

status: Public on Mar 06 2017

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: Netherlands Cancer Institute

summary: Tamoxifen, a small molecule inhibitor that binds the Estrogen Receptor alpha (ERα), blocks breast cancer progression while increasing the risk for endometrial cancer. In this study, we assessed genome-wide ERα-chromatin interactions in surgical specimens of endometrial tumors from patients who were previously treated for breast cancer with tamoxifen, and endometrial tumors from patients who were treated without tamoxifen. We compared ERα and signal at differential ERα sites in endometrial tumors of nine patients who received tamoxifen with endometrial tumors with six patients who never used tamoxifen. In addition, we performed H3K27ac (a marker for activity) ChIPs on the above mentioned endometrial tumors, and assed this signal at differential ERα sites. Compared to endometrial tumors of non-users, tamoxifen-associated endometrial tumors exposed higher H3K27ac intensities at ERα sites that are enriched in tamoxifen-associated endometrial tumors. Four tamoxifen-associated endometrial tumors that we used in our analysis have been previously published as Tumor A, B, D, and E in GSE81213.

overall_design: Era and H3K27ac ChIP-Seq

first: Marjolein

last: Droog

first: Ekaterina

last: Nevedomskaya

first: Yongsoo


title: Integrin-b4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells

city: Cambridge

first: Brian

last: Bierie

address: 455 Main St

institute: Whitehead Institute

summary: We report the gene expression profiles of normal epithelial and carcinoma cell populations that differ in their relative levels of integrin-beta 4 expression. ITGB4 high, mesenchymal subtype, triple-negative breast cancer cells were found to be more epithelial than related ITGB4 low cells.

overall_design: RNA-seq was used to compare the expression of mesenchymal-like carcinoma cell subtypes isolated from polyclonal cell populations. Isolated cell populations that had high levels of ITGB4 were found to be more epithelial than those with low levels, despite the fact that they were within the mesenchymal-like cell state spectrum.

first: Robert

last: Weinberg


title: Transcriptome of WT mouse embryonic stem cells

first: Constance

last: Ciaudo

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study was to obtain the trasncriptome of WT mESCs to compare it with the transcriptome of RNAi mutant mESCs (deposit separately).

overall_design: mRNA profiles of mouse embryonic stem cells (E14) were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.


title: Integration of Shh and Fgf signaling in controlling Hox expression in cultured limb cells [ChIP-seq]

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

summary: During embryonic development, fields of progenitor cells form complex spatial structures through dynamic interactions with external signaling molecules. However, how complex signaling inputs are integrated to yield appropriate gene expression responses is poorly understood. For instance several critical signals have been well characterized in the early limb bud, including Sonic hedgehog (Shh) and Fibroblast growth Factor 8 (Fgf8). While the former is expressed in the distal posterior mesenchyme where it acts as the mediator of anterior to posterior (AP) patterning, the latter is produced by the apical ectodermal ridge (AER) at the distal tip of the limb bud and directs the outgrowth and the proximal to distal (PD) organization of the limb. Here we use cultured limb mesenchyme cells to try and assess the response of the target Hoxd genes to these two factors.  We find that they act synergistically and that both factors are required to get activation of Hoxd13 in limb mesenchymal cells. However, the analysis of the enhancer landscapes flanking the HoxD cluster reveals that the bimodal regulatory switch observed in vivo is not fully achieved under these in vitro conditions, suggesting the requirement for other factors.

overall_design: ChIP-seq analysis of H3K27ac in cultured distal-anterior mesenchymal cells from chick forelimb buds at HH21.

first: N

first: Y

last: Atsuta

first: C

last: Tabin

first: D

last: Duboule


title: Integration of Shh and Fgf signaling in controlling Hox expression in cultured limb cells [4C-seq]

overall_design: 4C-seq analysis of Hoxd11 and Hoxd13 3D interactions in wt chick limbs, Ozd mutant limbs or cultured wt limb mesenchymal cells

first: G

last: Andrey

first: A

middle: R

last: Rodrigues


title: Small RNA and AGO1 CLIP-seq libraries of female Aedes aegypti fat body

city: Riverside

first: Alexander

last: Raikhel

state: CA

address: 338 Entomology Building

department: Entomology

institute: University of California-Riverside

type: Non-coding RNA profiling by high throughput sequencing

summary: In this work, we aimed to explore miRNA expression and potential targets in the female fat body of the Ae. aegypti mosquito, as well as their changes as a result of blood meal. The fat body is the metabolic center of the insect organism, playing a key role in reproduction. Therefore, understanding of regulatory networks controlling its functions is critical, and the role of miRNAs in the process is largely unknown. Small RNA library analyses revealed four unique miRNA clusters sequentially expressed during the post blood meal (PBM) phase, drawing connections to waves of upstream hormonal signals and gene expression in the same period. To link the miRNA identities with specific downstream targets, transcriptome-wide mRNA 3' UTR interaction sites were experimentally determined at 72 h post eclosion (PE) and 24 h PBM by means of AGO1 CLIP-seq. Hence, the presented manuscript comprehensively elucidated miRNA expression and target dynamics in female mosquito fat body, providing a solid foundation for future functional studies of miRNA regulation during the gonadotrophic cycle.

overall_design: Three independent biological replicates of fat body small RNA libraries at 72 h PE, 6 h PBM, 24 h PBM, 36 h PBM and 48 h PBM. Three independent biological replicates of fat body AGO1 CLIP-seq libraries at 72 h PE and 24 h PBM.

first: Xiufeng

last: Zhang


title: A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor

first: Marco

middle: Paolo

last: Licciardello

address: 15 Cotswold Road

institute: The Institute of Cancer Research

summary: Approved drugs are invaluable tools to study biochemical pathways and further characterization of these compounds may lead to repurposing of single drugs or combinations. Here, we describe a collection of 308 small molecules representing the diversity of structures and molecular targets of all FDA-approved chemical entities. The CeMM Library of Unique Drugs (CLOUD) covers prodrugs and active forms at pharmacologically relevant concentrations and is ideally suited for combinatorial studies. We screened pairwise combinations of CLOUD drugs for impairment of cancer cell viability and discovered the synergistic interaction between flutamide and phenprocoumon (PPC). The combination of these two drugs modulates the stability of the androgen receptor (AR) and resensitizes AR mutant prostate cancer cells to flutamide. Mechanistically, we show that the AR is a substrate for γ-carboxylation, a post-translational modification inhibited by PPC. Collectively, our data suggest that PPC might be repurposed to tackle resistance to antiandrogens in prostate cancer patients.

overall_design: Two biological replicates were produced for each condition. Drug treatment was compared to vehicle-treated cells.

middle: P

first: Anna

last: Ringler

first: Patrick

last: Markt

first: Freya

last: Klepsch

first: Charles-Hugues

last: Lardeau

first: Sara

last: Sdelci

first: Erika

last: Schirghuber

first: André

middle: C

last: Müller

first: Michael

last: Caldera

first: Anja

last: Wagner

first: Rebecca

last: Herzog

first: Thomas

last: Penz

last: Schuster

first: Bernd

last: Boidol

first: Gerhard

last: Dürnberger

first: Yasin

last: Folkvaljon

first: Pär

last: Stattin

first: Vladimir

last: Ivanov

first: Jacques

last: Colinge

first: Christoph

last: Bock

first: Klaus

last: Kratochwill

first: Joerg

last: Menche

first: Keiryn

middle: L

last: Bennett

first: Stefan

last: Kubicek


title: Effect of BCL11B knockdown on transcriptome of human T-cell precursors

city: Duarte

first: chintan

last: parekh

state: California

address: 1500 east duarte

department: Pediatrics

institute: Children's Hospital Los Angeles

summary: To investigate the role of BCL11B in the initial stages of human thymopoiesis, we  performed loss of function (knockdown) studies in an in vitro human thymopoiesis model (cord blood CD34+ cells co-cultured on OP9DLL1 stromal cell line).  Gene expression profiling by RNA-Seq demonstrated that BCL11B knockdown resulted in downregulation of T-lineage genes and upregulation of stem cell, myeloid and NK genes, indicating BCL11B is required for the establishment of a T-lineage commitment transcriptional program.

overall_design: Cord blood CD34+ cells were transduced with a BCL11B knockdown or scrambled control shRNA lentivral vector containing a GFP reporter.  GFP+ cells were isolated by fluorescence activation cell sorting (FACS) at 48 hours post transduction and cultured on OP9DLL1 stroma in the presence of  FLT3 ligand (5 ng/ ml) and IL-7 (5 ng/ ml). On day 14 of co-culture, CD45+GFP+CD7+CD1a- and CD45+GFP+CD7+CD1a+ T-cell precursors were isolated from control and knockdown co-cultures by FACS and analyzed by RNA-Seq to determine the effect of BCL11B knockdown on the transcriptome of T-cell precursors. N=3 experiments, each done with a different pool of cord blood donors.

first: C

last: Parekh


title: Analyses of heterochromatin distributions in the mutatnts defective in an RNAi-heterochromatin positive feedback loop in Tetrahymena [ChIP]

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

institute: Institute of Human Genetics, CNRS

summary: In the ciliated protozoan Tetrahymena, an RNAi-mediated feedback loop is important for assembling heterochromatin on the sequences that are removed from the somatic genome by programmed DNA elimination. Because heterochromatin is formed exclusively on the eliminated sequences, some mechanism must inhibit this feedback loop at the boundaries of the eliminated sequences. In this study, we show that the HP1-like protein Coi6p, its interaction partners Coi7p and Lia5p, and the histone demethylase Jmj1p are crucial for confining the formation of heterochromatin to the eliminated sequences.

overall_design: 26 to 32-nt small RNAs from verious mutants or from immuno precipitated with Argonaute proteins were analyzed by high-throughput sequencing

first: Jan

middle: H

last: Suhren

first: Tomoko

last: Noto

first: Kensuke

last: Kataoka

first: Shan

last: Gao

first: Yifan

last: Liu


title: BCL11B DNA binding sites in progenitor and differentiated populations in the human thymus

summary: To define binding targets during thymopoiesis on a genome wide scale, we performed ChIP-Seq for BCL11B on two cell types isolated from the human thymus: the CD34+ progenitors and the more differentiated CD34- cells

overall_design: ChIP-Seq for BCL11B binding was done on CD34+ and CD34- cells isolated from human thymus (n=2 biological replicates per cell type)


title: Human blood CD1c⁺ dendritic cells encompass CD5-high and CD5-low subsets that differ significantly in phenotype, gene expression and functions

city: Beijing

first: Xiaoyang

last: Jin

state: -- Please, Select --

address: 15 Datun Road, Chaoyang District

country: China

institute: Institute of Biophysics, CAS

summary: There are three major dendritic cell (DC) subsets in both human and mouse, plasmacytoid DCs (pDCs) and two types of conventional DCs (cDCs), cDC1s and cDC2s. cDC2s are important for polarizing CD4+  naive T cells into different subsets including Th1, Th2, Th17, Th22 and regulatory T cells (Tregs). In mice, cDC2s can be further divided into phenotypically and functionally distinct subgroups. However, subsets of human cDC2s have not been reported.  In the present study, we showed that human blood CD1c+ conventional DCs (cDC2s) can be further separated into two subpopulations according to their CD5 expression status. Comparative transcriptome analyses showed that the CD5high DCs expressed higher levels of cDC2-specific genes, including IRF4, which is essential for the cDC2 development and its migration to lymph nodes. In contrast, CD5low DCs preferentially expressed monocyte-related genes, including the lineage-specific transcription factor MAFB. Furthermore, compared with CD5low subpopulation, CD5high subpopulation showed stronger migration toward CCL21 and overrepresentation among migratory DCs in lymph nodes. Additionally, the CD5high DCs induced naïve T-cell proliferation more potently than the CD5low DCs. Moreover, CD5high DCs induced higher levels of IL-10-, IL-22- and IL-4-producing T-cell formation, whereas CD5low DCs induced higher levels of IFN-γ-producing T-cell formation. Thus, we show that human blood CD1c+ cDC2s encompass two subsets that differ significantly in phenotype, gene expression, and functions. We propose that these two subsets of human cDC2s could potentially play contrasting roles in immunity or tolerance.

overall_design: The mRNA profiles of two human blood CD1c+ conventional DCs (cDC2s) subpopulations, in triplicate.

first: Xiangyun

last: Yin

first: Haisheng

last: Yu

first: Jingyun

last: Li

first: Hao

last: Guo

first: Quanxing

last: Shi

first: Zhao

first: Yong

last: Xu

first: Xuefei

last: Wang

first: Rong

first: Shouli

first: Liguo

last: Zhang


title: Integration of Shh and Fgf signaling in controlling Hox expression in cultured limb cells

first: Nayuta

last: Yakushiji-Kaminatsui

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

overall_design: Refer to individual Series


title: Analyses of RNAi-heterochromatin positive feedback loop in Tetrahymena

first: Kazufumi


title: Analyses of scnRNAs in the mutatnts defective in an RNAi-heterochromatin positive feedback loop in Tetrahymena [scnRNA]

summary: In the ciliated protozoan Tetrahymena, an RNAi-mediated feedback loop is important for assembling heterochromatin on the sequences that are removed from the somatic genome by programmed DNA elimination. Because heterochromatin is formed exclusively on the eliminated sequences, some mechanism must inhibit this feedback loop at the boundaries of the eliminated sequences. In this study, we show that the HP1-like protein Coi6p, its interaction partners Coi7p and Lia5p, and the histone demethylase Jmj1p are crucial for confining the production of small RNAs to the eliminated sequences.

first: Jan

first: Tomoko

first: Kensuke


title: Effect of BCL11B overexpression on transcriptome of T-cell acute lymphoblastic leukemia (T-ALL) cells

first: chintan

last: parekh

summary: To investigate the effects of BCL11B on T-cell differentiation, we  performed gain of function studies in cells with a T-lineage differentiation arrest, namely T-ALL cells. Gene expression profiling by RNA-Seq demonstrated that BCL11B overexpression induced transcriptional changes consistent with T-cell differentiation as early as 72 hours after transduction, indicating a rapid regulatory effect of BCL11B on the T-lineage transcriptional program and supporting an important role for BCL11B in human T-cell differentiation.

overall_design: T-ALL cells were transduced with a BCL11B-GFP expression vector (overexpressing cells) or an empty GFP vector (control cells). GFP+ cells were isolated by fluorescence activation cell sorting (FACS) at 72 hours post transduction and analyzed by RNA-Seq to determine the effect of BCL11B on the transcriptome of T-ALL cells.

first: C

last: Parekh


title: BCL11B


title: SALL4 ensures oocytes maturation by modulating DNA methylation and histone modifications (RNA-Seq)

city: Shanghai

first: Shaorong

address: No. 1239, Siping Road

institute: Tongji University

summary: Splat-like 4 (Sall4) plays important roles in maintaining pluripotency of embryonic stem cells and in various developmental processes. Here, we find that the SALL4 null oocytes fail to undergo maturation to form fully-grown oocytes (FGOs) and subsequent meiosis resumption. We further discover that the loss of maternal SALL4 causes failure in establishment of DNA methylation. Moreover, we demonstrate that SALL4 modulates H3K4me3 and H3K27me3 modifications by regulating the expression of Kdm5b, Kdm6a and Kdm6b. Taken together, SALL4 plays pivotal roles in oocyte epigenetic maturation.

overall_design: In this study, we have 19 RNA-seq data and 18 RRBS data. As for RNA-seq, secondary follicle (SF) stage WT oocyte group have 2 replicates, and SF stage oocyte group have 3 replicates. Early antral follicle (EAF) stage Sall4 KO or WT oocyte group both have 3 replicates. In the microinjection experiments, the control group have 5 replicates, and the experimental group have 3 replicates. As for RRBS, SF WT group have 7 replicates, and SF Sall4 KO group have 5 replicates. EAF WT group have 4 replicates, and EAF Sall4 KO group have 2 replicates.

first: Kai

first: Xia

last: Chen

first: Hui

last: Yang

first: Yiwen

first: Yuanlin

last: He

first: Chenfei

first: Hua

last: Huang

first: Baodong

first: Wenqiang

first: Jingyi

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Kun

first: Linfeng

first: Zhenzhen

last: Hou

first: Hong

first: Hailin

first: Jing

first: Hengyu

last: Fan

first: Fengchao

first: Yawei

first: Jiayu


title: Determination of key transcriptional changes in VhlF/FPbrm1F/FKsp-Cre kidney tumors

city: New York

first: Jeffrey

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: To investigate whether transcriptional aberrations might be responsible for the formation of kidney tumors in VhlF/FPbrm1F/FKsp-Cre animals, RNA-Seq was performed on kidney tumors and age-matched WT renal cortices.

overall_design: VhlF/FPbrm1F/FKsp-Cre kidney tumors were compared with the normal kidneys to determine the transcriptional outputs that may be important to cause tumors

first: Amrita

middle: M

last: Nargund

first: James

last: Hsieh


title: Vhl and Pbrm1 double deletion effect on kidney


title: RNA-seq characterization of downstream effects of upregulating SMN2 via down-regulating PRC2 or blocking the PRC2:SMN-AS1 interaction with a mixmer oligonucleotide

first: Caroline

middle: J.

last: Woo

state: Massachusetts

address: 200 Sidney Street

institute: RaNA Therapeutics Inc.

summary: To determine how targeting the disruption of PRC2:SMN-AS1 interactions might affect PRC2 targets globally, we performed RNA-sequencing after transfection of a PRC2:SMN-AS1 targeting mixmer oligo, RN-0005, an antisense gapmer oligonucleotide targeting SUZ12, a subunit of the PRC2 complex, or mock in SMA fibroblasts. Via RT-qPCR, treatment with either the mixmer oligo or the SUZ12 gapmer for 2 and 3 days results in significant increases of SMN mRNA levels compared to transfection control samples. We sequenced total RNA from 12 GM09677 fibroblast samples split into two day or three day treatments (6 samples each). Within each set of six samples, there were 2 mock control replicates, 2 mixmer replicates, and 2 SUZ12kd-gapmer replicates. By controlling for time and looking at the two treatments versus mock samples, we identified the genes that change when knocking down PRC2 systemically with a gapmer versus more specifically blocking PRC2 activity with a mixmer oligo targeting the SMN2-AS1 lncRNA.

overall_design: Mock, RN-0005 mixmer, and the SUZ12-KD gapmer treated SMA fibroblasts were sequenced. For each of the treatments, there were two time points with each time point having two replicates for a total number of 4 samples per condition. Gene expression differences were identified for the contrasts of RN-0005 vs. mock and SUZ12-KD vs. mock after fitting to a linear model blocking for time.

first: John

middle: F

last: Brothers


title: Transcriptome of NaCl-treated Limonium bicolor Leaves to Reveal How Many Genes Control Salt Secretion

city: Jinan

first: Baoshan

last: Wang

state: Shandong

address: No.88 East Wenhua Road, Jinan 250014, Shandong, China

department: College of Life Sciences

institute: Shandong Normal University

summary: Limonium bicolor, a typical recretohalophyte living in saline land, excretes excessive salt to the environment through salt glands in the epidermis for avoiding salt stress. The aim of this study was to screen genes involved in salt secretion by high-throughput RNA sequencing. A model was established to illustrate the candidate genes regulating salt secretion of salt gland. These genes will shed light on molecular mechanism of salt secretion of salt gland in plant.Normalized cDNA libraries of L. bicolor were constructed using mature leaves treated with 200 mM NaCl (with the highest salt secretion) and the control. Illumina paired-end platform was utilized to yield 2×100 bp independent reads. After de novo assembly, unigenes were aligned to the non-redundant (Nr) protein database and differentially expressed genes were enriched by GO annotations. Candidate genes were further verified by L. bicolor mutants with abnormal salt secretion.19,498 genes were targeted in Nr database and 5,768 were differentially expressed mapping to Arabidopsis, 2,269 up-regulated and 3,519 down-regulated under NaCl treatment compared with the control. Genes related to ion transport, vesicle, reactive oxygengen species scavenging, abscisic acid-dependent signal pathway and transcription factors were found high expression under NaCl treatment, of which 55 genes were likely involved in salt secretion and also confirmed by salt-secretion mutants.The present report identified candidate genes which are highly associated with salt secretion of L. bicolor salt gland. A salt transporting pathway was illustrated to explain how Na+ excreted outside by salt gland in L. bicolor. This data provides a useful reference source for salt secretion study of recretohalophytes.

overall_design: The control and NaCl-treated leaves were used as samples to analyze the transcriptome changes under salt treatment.

first: Fang

last: Yuan

first: Mingju

last: Lv

last: Sui

first: Bingying

last: Leng

first: Xinguang

last: Zhu


title: ChIP-exo of human KRAB-ZNFs transduced in HEK 293T cells and KAP1 in hES H1 cells

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

institute: EPFL

summary: Encoded in the hundreds by the human genome, KRAB-containing zinc finger proteins (KRAB-ZFPs) constitute a rapidly evolving family of transcription factors with largely undefined functions. Here, by a combination of phylogenetic and genomic approaches, we retrace the evolutionary history of KRAB-ZFP genes and define the genomic targets of their human products. Through in silico analysis of 207 vertebrate genomes and chromatin immunoprecipitation / deep sequencing characterization of 257 human KRAB-ZFPs, we identify the root of the family in an early Devonian ancestor of tetrapods, describe its diversity amongst these species, and reveal that the majority of its human members primarily recognize transposable elements. Furthermore, by dissecting the timeline and modalities of interactions between human KRAB-ZFPs and their targets, we provide evidence strongly suggesting that these proteins, rather than just engaged in an evolutionary arms race against transposable elements, exploit these invaders as regulatory platforms for the benefit of the host.

overall_design: We transduced HEK 293T cells with doxycyclin-inducible plasmids encoding for human KRAB-ZFPs fused with 3 HA tags at the C-terminus. We next performed ChIP-exo and prepared a barcoded Illumina library for each sample - these library were pooled and sequenced 12 per lane on an Illumina Hiseq 2500 to a minimum depth of around 15 million 100 bp single-end reads. Reads were mapped to the GRC h37 g1k assembly of the human genomes and peaks were identified using MACS - the resulting peak list was further filtered according to various criteria designed to minimize the presence of artifacts. We used a total input derived from random sampling from all samples in the study, as it was found to perform better than either the standard total input or the exonuclease treated total input. We also performed ChIP-exo on endogenous KAP1 from H1 embryonic stem cells using the same overall design.

first: Michael

last: Imbeault

first: Pierre-Yves

last: Helleboid

first: Didier

last: Trono


title: Effect of glucocorticoid steroid regimens on murine dystrophic muscle

status: Public on Mar 04 2017

city: Chicago

first: Mattia

last: Quattrocelli

state: IL

address: 303 E. Superior St.

department: Center for Genetic Medicine

institute: Northwestern University

summary: The goal of this study is to compare the effect of weekly and daily steroid regimens (prednisone) on transcriptional regulation of candidate genes for muscle repair and atrophic response in mdx mice (n=5 mice/group).

overall_design: Total RNA was isolated from ~30mg muscle tissue (quadriceps muscles from treated and control DBA/2J-mdx male 6 month-old mice) with the RNeasy Protect Mini Kit as per manufacturer’s instructions. RNA was quantitated at the Qubit fluorometer and quality-controlled at a 2100 Bioanalyzer. Libraries were prepared from approximately 1ug RNA/sample by means of TruSeq Stranded Total RNA Library Prep Kit. Libraries were sequenced through the Illumina NextSeq 500 System (high-throughput, paired-end 150bp fragment sequencing. Reads from each sample were aligned with TopHat v2.1.0 to the mm10 genome assembly (grcm38, version 78). Transcripts were assessed and raw read counts per gene were quantified with HTseq.  Reads Per Kilobase of transcript per Million mapped reads (RPKM) and fold-changes between groups were calculated using EdgeR from the Bioconductor package. Differentially expressed genes were identified by adjusted P-value <0.05.

first: Andy

last: Vo

first: Elizabeth

last: McNally


title: PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Maintenance of chromatin homeostasis involves proper delivery of histone variants to the genome. The interplay between different chaperones regulating the supply of histone variants to distinct chromatin domains remains largely undeciphered. We report a role of promyelocytic leukemia (PML) protein in the routing of histone variant H3.3 to chromatin and in the organization of megabase-size heterochromatic PML-associated domains that we call PADs. Loss of PML alters the heterochromatic state of PADs by shifting the histone H3 methylation balance from K9me3 to K27me3. Loss of PML impairs deposition of H3.3 by ATRX and DAXX in PADs but preserves the H3.3 loading function of HIRA in these regions. Our results unveil an unappreciated role of PML in the large-scale organization of chromatin and demonstrate a PML-dependent role of ATRX/DAXX in the deposition of H3.3 in PADs. Our data suggest that H3.3 loading by HIRA and ATRX-dependent H3K27 trimethylation constitute mechanisms ensuring maintenance of heterochromatin when the integrity of these domains is compromised.

overall_design: Examination of H3, H3.3-3xFlag, H3K9me3, H3K27me3 and PML genomic localization by ChIP-seq, and transcriptome analysis by RNA-seq, in wild-type and PML knock-out MEFs

first: Jane

last: Spirkoski

first: Erwan

last: Delbarre

first: Kristina

last: Ivanauskiene

first: Thomas

last: Küntziger

first: Akshay

last: Shah


title: SLC2525-AS1: a potential lncRNA biomarker for radiotherapy sensitivity of colorectal carcinoma

status: Public on Mar 03 2017

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University


title: Gpr124 is essential for blood-brain barrier integrity in central nervous system disease

city: Stanford

first: Calvin

last: Kuo

address: 265 Campus Drive

department: Medicine

institute: Stanford University School of Medicine

summary: Although blood-brain barrier (BBB) compromise is central to the etiology of diverse central nervous system (CNS) disorders, endothelial receptor proteins that control BBB function are poorly defined.  The endothelial G protein-coupled receptor (GPCR) Gpr124 has been reported to be required for normal forebrain angiogenesis and BBB function in mouse embryos, but the role of this receptor in adults is unknown. Here, conditional Gpr124 knockout (CKO) in the endothelia of adult mice did not affect homeostatic BBB integrity but resulted in BBB disruption and microvascular hemorrhage in mouse models of ischemic stroke and glioblastoma, accompanied by reduced cerebrovascular canonical Wnt/beta-catenin signaling. Constitutive activation of Wnt/beta-catenin signaling fully corrected the BBB disruption and hemorrhage defects of Gpr124 cko mice, with rescue of the endothelial tight junction, pericyte coverage and extracellular-matrix deficits. We thus identify Gpr124 as an endothelial GPCR specifically required for endothelial Wnt signaling and BBB integrity under pathological conditions in adult mice. This finding implicates Gpr124 as a potential therapeutic target for human CNS disorders characterized by BBB disruption.

overall_design: Identification of genes and signaling pathways regulated by Gpr124 and beta-catenin in adult brain endothelial cells.

first: Junlei

last: Chang


title: Whole genome developmental time course of Tn5 transposon accessible chromatin patterns in sea urchin embryos

city: PASADENA

first: Robert

middle: Andrew

last: Cameron

address: Caltech 1200 EAST CALIFORNIA BOULEVARD

department: Biology and Biological Engineering

institute: California Institute of Technology

summary: We have adapted ATAC-seq to sea urchin embryos. As a proof of concept, we documented strong ATAC-seq signals over the locations of a number of previously authenticated, developmentally active, cell type specific cis-regulatory modules. We then used the method to generate a systematic developmental series for embryos from three independent batches, obtained every six hours from blastula stage until completion of embryogenesis at 72h. The independent batches provide internal reproducibility controls.

overall_design: In order to identify sites of active transcription through correlation of Tn5 accessible open chromatin with other genome feature, we collected embryos from three independent matings at 18 hour post fertilization (hpf), 24hpf, 30hpf, 50hpf, 60hpf and 70hpf. The nuclei were isolated and then processed by standard methods for Tn5 transposon binding. The subsequent labelled fragments were read on the Illumina latform and mapped to the genome.

first: Erika

last: Vielmas

first: Parul

last: Kudtarkar

first: Igor

last: Antoshechkin


title: Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate.

first: Edouard

last: Bertrand

address: 1919 Route de Mendes

department: SERANAD

institute: CNRS

summary: The nuclear cap-binding complex (CBC) stimulates processing reactions of capped RNAs, including their splicing, 3'-end formation, degradation, and transport. CBC effects are particular for individual RNA families, but how such selectivity is achieved remains elusive. Here, we analyze three main CBC partners known to impact different RNA species. ARS2 stimulates 3'-end formation/transcription termination of several transcript types, ZC3H18 stimulates degradation of a diverse set of RNAs, and PHAX functions in pre-small nuclear RNA/small nucleolar RNA (pre-snRNA/snoRNA) transport. Surprisingly, these proteins all bind capped RNAs without strong preferences for given transcripts, and their steady-state binding correlates poorly with their function. Despite this, PHAX and ZC3H18 compete for CBC binding and we demonstrate that this competitive binding is functionally relevant. We further show that CBC-containing complexes are short lived in vivo, and we therefore suggest that RNA fate involves the transient formation of mutually exclusive CBC complexes, which may only be consequential at particular checkpoints during RNA biogenesis.

overall_design:
RNA profiles of HeLa cells treated with PHAX, ZC3H18 and control siRNAs were generated by paired-end sequencing, in triplicated samples.
iCLIP experiments were carried out on the CBP20, ARS2, PHAX, and ZC3H18 proteins in HeLa and HEK293 cells. Two replicates per protein were used.

first: Thierry

last: Gostan


title: Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells [RRBS]

city: San Francisco

first: Emmanuelle

last: Passegue

address: 35 Medical Center Way, RMB-1017, Box 0667

department: Department of Medicine, Hem/Onc Division

institute: The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California San Francisco

type: Methylation profiling by high throughput sequencing

summary: Autophagy is critical for protecting HSCs from metabolic stress. Here, we used a genetic approach to inactivate autophagy in adult HSCs by deleting the Atg12 gene. We show that loss of autophagy causes accumulation of mitochondria and an oxidative phosphorylation (OXPHOS)-activated metabolic state, which drives accelerated myeloid differentiation likely through epigenetic deregulations rather than transcriptional changes, and impairs HSC self-renewal activity and regenerative potential. To determine how loss of autophagy affects DNA methylation, we conducted enhanced reduce representation bisulfite sequencing (ERRBS) of purified control and Atg12 conditional knockout HSCs.

overall_design: Atg12flox/flox:Mx1-Cre conditional knockout mice and control Atg12flox/flox mice were injected with poly(I:C) at 4 week of age, and HSCs (Lin-/c-Kit+/Sca-1+/Flk2-/CD150+/CD48-) were isolated from the bone marrow of individual mice 2-3 months later. DNA was extracted from 4 mice per group, and ERRBS was conducted as described in the methods.

first: Theodore

middle: T

last: Ho

first: Matthew

last: Warr

first: Emmalee

last: Adelman

first: Evgenia

middle: V

last: Verovskaya

first: Olivia

last: Lansinger

first: Johanna

last: Flach

first: Maria

middle: E

last: Figueroa

last: Passegué


title: Mir-132/212 shapes age-dependent transcriptome and is required for binocular matching of orientation preference and depth perception.

city: Irvine

first: Christophe

middle: Nicolas

last: Magnan

address: Institute for Genomics and Bioinformatics 236, Info & Computer Science Building 2

institute: University of California, Irvine

summary: We performed RNA sequencing and smallRNA sequencing experiments on visual cortex tissues from three groups of animals: wildtype mice postnatal day 10 (P10-WT), wildtype mice postnatal day 28 (P28-WT), and miR-132/212 null mice postnatal day 28 (P28-KO).

overall_design: The objective of this study was to examine the role of Mir-132/212 in age-dependent transcriptome and binocular matching of orientation preference and depth perception.

first: Raffaele

last: Mazziotti

first: Laura

last: Baroncelli

first: Nicholas

last: Ceglia

first: Gabriele

last: Chelini

first: Grazia

last: Sala

first: Debora

last: Napoli

first: Elena

last: Putignano

first: Davide

last: Silingardi

first: Jonida

last: Tola

first: Paola

last: Tognini

first: J

last: Arthur

first: Pierre

last: Baldi

first: Tommaso

last: Pizzorusso


title: Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells

first: Emmanuelle

last: Passegue


title: SLC25A25-AS1 knockdown data of two colorectal carcinoma cell lines (HT29 and SW480)

first: Xi

last: Chen

summary: We identified that SLC25A25-AS1 was a lncRNA influencing radiation response. Therefore, we aimed to explore more biological roles of SLC25A25-AS1 in this process. Towards this end, we used RNA interference (RNAi)-mediated knockdown of SLC25A25-AS1 in HT29 and SW480 to explore the changes of mRNA expression profiles and explore the phenotype outcomes.

overall_design: A four sample study using total RNA collected from three cell lines (HT29 and SW480) with or without knockdown of SLC25A25-AS1.

first: Xiaowen

last: Xu

first: Xiaomei

last: Hou

first: Zhen

last: Tan

first: Zhiqi

last: Yu

first: Chang

last: Zhang

first: Chuangang

last: Fu

first: Guangwen

last: Cao


title: Short Bowel Syndrome (SBS) has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model

status: Public on Mar 08 2017

city: Los Angeles

first: Tracy

last: Grikscheit

address: 4650 Sunset Boulevard Mailstop#100

summary:
Purpose: Most of the morbidity associated with short bowel syndrome (SBS) are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition (TPN). We hypothesized that acute SBS alone has significant systemic effects, and tested this in a zebrafish SBS model.
Methods: With IACUC approval, adult male wild-type zebrafish underwent SBS (laparotomy, proximal stoma, distal ligation,n=3) or sham (laparotomy alone,n=3) surgery. After 2 weeks, the proximal intestine was harvested, RNA isolated and external RNA controls consortium (ERCC) controls spiked into each sample, sequenced and aligned to reference genome with gene ontology (GO) enrichment analysis performed.  CyclinD1, CyclinB1, SAA1, IFN-gamma, and CYP7A1 gene expression were confirmed by qPCR.
Results: RNA-seq analysis identified 1346 up-regulated genes and 678 down-regulated genes in SBS zebrafish compared to sham. The up-regulated genes were involved in acute phase response signaling, complement system, coagulation, cell proliferation, cellular barrier, production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down-regulated genes were involved in folate synthesis, gluconeogenesis, glycogenolysis, fatty-acid oxidation & activation, and drug & steroid metabolism. CyclinD1 gene expression was 2-fold higher, CyclinB1 2.8-fold higher, SAA1 4.5-fold higher, IFN-gamma 2.1-fold higher, and CYP7A1 25-fold higher in SBS than sham by qPCR.
Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways, some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy.

overall_design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.

first: Kathy

last: Schall

first: Brendan

last: Grubbs

first: Matt

last: Thornton


title: Mutations in EGFR compromise hypoxia associated radiation resistance through impaired repair of replication fork associated DNA double-strand breaks

status: Public on Mar 02 2017

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Gene expression analysis in human bronchial epithelial cells expressing wild type EGFR or activating mutations, L858R or E7646-E750 EGFR in a normoxic environment (21% oxygen) or at 24 hours of exposure to a hypoxic environment (0.1% oxygen). The effect of EGFR mutations on base-line and hypoxia-induced gene expression was determined.

overall_design: Total RNA obtained from HBEC cells stably expressing WT, L858R or E746-E750 forms of EGFR. All three cell lines were incubated in either aerobic conditions (21% O2/5%CO2) or exposed for 24 hours to a hypoxic environment containing 0.1% O2/5%CO2

first: Mohammad

last: Saki

first: Haruhiko

last: Makino

first: Nozomi

last: Tomimatsu

first: Liang-Hao

first: Jennifer

last: Clark

first: Elaine

last: Gavin

first: Joel

last: Andrews

first: Michael

last: Story

first: Sandeep

last: Burma

first: Chaitanya

last: Nirodi


title: Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells [ERRBS]

first: Emmanuelle

last: Passegue

summary: Autophagy is critical for protecting HSCs from metabolic stress. Here, we used a genetic approach to inactivate autophagy in adult HSCs by deleting the Atg12 gene. We show that loss of autophagy causes accumulation of mitochondria and an oxidative phosphorylation (OXPHOS)-activated metabolic state, which drives accelerated myeloid differentiation likely through epigenetic deregulations rather than transcriptional changes, and impairs HSC self-renewal activity and regenerative potential.

overall_design: Quiescent HSCs HSCs (Lin-/c-Kit+/Sca-1+/Flk2-/CD150+/CD48-) were isolated from BL6 WT mice and activated HSCs were cultured 21 hours in cytokine+ media as described. DNA was extracted from -5 mice per group, and ERRBS was conducted as described in the methods. For cultured HSCs, HSCs were grown in StemPro34 medium (Invitrogen) supplemented with penicillin (50 U/ml)/streptomycin (50 μg/ml) and L-glutamine (2 mM), and with or without the following cytokines (±cyt): SCF (25 ng/ml), Flt3L (25 ng/ml), IL-11 (25 ng/ml), IL-3 (10 ng/ml), GM-CSF (10 ng/ml), Epo (4 U/ml) and Tpo (25 ng/ml) (Peprotech).

first: Theodore

last: Ho

first: Matthew

last: Warr

first: Emmalee

last: Adelman

first: Evgenia

last: Verovskaya

first: Olivia

last: Lansinger

first: Johanna

last: Flach

first: Maria

last: Figueroa

last: Passegué


title: Bisphenol A alternatives can effectively substitute for estradiol in promoting cell growth through estrogen receptor alpha in human breast cancer cells

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

institute: Kings College London

summary:
Plasticizers with estrogenic activity, such as bisphenol A (BPA), have been reported to have potential adverse health effects in humans, especially in fetal and infant stages. Due to mounting evidence and public pressure BPA is being phased out by the plastics manufacturing industry and is being replaced by other bisphenol variants in “BPA-free” products.  We have compared estrogenic activity of 7 bisphenol analogues (BPA; bisphenol S, BPS; bisphenol F, BPF; bisphenol AP, BPAP;  bisphenol AF, BPAF; bisphenol Z, BPZ; bisphenol B, BPB) in human breast cancer cell lines.
We used microarrays to detail the alterations in gene expression profiles associated with MCF-7 cell line exposure to bisphenol A analogues

overall_design: MCF-7 cells treated during a period of 48h with the BPA alternatives and the natural hormone 17β-estradiol were subjected to a full transcriptome profiling using the Affymetrix microarray platform.

middle: J

last: Arno


title: Compartmentalization of DNA damage response between heterochromatin and euchromatin is mediated by distinct H2A histone variants

city: Vienna

first: Zdravko

last: Lorkovic

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

summary: DNA double strand break (DSB) repair depends on the ataxia telangiectasia mutated (ATM) kinase that phosphorylates the conserved C-terminal SQ motif present in the histone variant H2A.X [1-7]. In constitutive heterochromatin of mammals, DSB repair is delayed and relies on phosphorylation of the proteins HP1 and KAP1 by ATM [2, 8-14]. However, KAP1 is not conserved in plants and the HP1 related protein Like-HP1 (LHP1) is not localized at constitutive heterochromatin [15], suggesting that in plants, alternative mechanisms could be responsible for repair of DSBs in heterochromatin. In Arabidopsis, constitutive heterochromatin is marked by H3K9 methylation, and the plant-specific histone variants H2A.W which are distinguished by their C-terminal motif KSPKK and required for heterochromatin compaction [16-18]. We report that the Arabidopsis histone variant H2A.W.7 is confined to heterochromatin and carries a SQ motif that is phosphorylated by ATM. In response to DNA damage, phosphorylation of H2A.W.7 takes place in heterochromatin while H2A.X phosphorylation takes place primarily in euchromatin. We propose that H2A.W.7 evolved in addition to H2A.X to facilitate DNA damage response in highly condensed heterochromatin, thus playing a role similar to KAP1 and HP1 phosphorylation in mammals. These data support the idea of the functional diversification of histone variants and their role in spatial compartmentalization of chromatin related functions in eukaryotes.

overall_design: 2 samples + 1 reference sample (control)

last: Lorković

first: Chulmin

last: Park

first: Malgorzata

last: Goiser

first: Frédéric

last: Berger


title: Embryonic stem cells-derived neural progenitor cells

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
J14 ES cells differentiated into MGE-like cells.
Three groups of single-cell preparations were analyzed: ES cells (undifferentiated), differentiated cells (unsorted, of which less than 10% are GFP+) and GFP+ differentiated cells. These are specified in the "group" sample characteristic, with values "ES", "Unsorted" and "GFP+" respectively.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0007904

first: Jasmine

last: Chen

first: Zora

last: Modrusan


title: Opposing macrophage-polarization programs show extensive epigenomic and transcriptional cross-talk [ChIP_broadly]

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

summary: The M1 and the M2 macrophage polarization programs (activated by IFNγ and IL-4, respectively) lie at the opposite edges of a continuum of activation states but are frequently co-activated during co-infections and in cancer despite controlling divergent functional responses. Whether these two programs are mutually exclusive, how they influence each other, and whether one represents the prevailing response, are all open questions. Co-administration of IFNγ and IL-4 exerted complex inhibitory effects over the M1 and M2 programs at the level of both epigenomic and transcriptional changes. Computational data mining and validation analyses revealed the molecular basis of the differential sensitivity of genes and cis-regulatory elements to the antagonistic effects of the opposite stimulus. For instance, while STAT1 and IRF motifs were associated with robust and IL-4-resistant responses to IFNγ, their coexistence with binding sites for some auxiliary transcription factors such as AP-1, generated vulnerability to IL-4-mediated inhibition. These data provide a core mechanistic framework for the integration of signals that control macrophage activation and the starting point for understanding macrophage responses in complex environmental conditions

overall_design: Analysis of transcriptional and epigenomic changes in mouse macrophages stimulated with different cytokines or their combinations

first: Alessia

last: Curina

first: Marco

last: Genua

first: Serena

last: Ghisletti

first: Marta

last: Simonatto

first: Arianna

last: Sabò

first: Bruno

last: Amati

first: Renato

last: Ostuni

first: Gioacchino

last: Natoli


title: Transcriptome of invasive mucinous adnocarcinoma of the lung and adjacent normal lung tissues from 6 patients based on RNA-seq method

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

summary: In order to identify genes that are highly expressed in human IMA, we performed mRNA-seq analysis using RNAs extracted from 6 human invasive mucinous adenocarcinoma of the lung (IMA) and adjacent normal lung tissues and determined genes differentially expressed in human IMA.

overall_design: RNA samples from invasive mucinous adnocarcinoma of the lung and adjacent normal lung tissues from the 6 patients were obtained, sequenced, and compared.

first: Yutaka

last: Maeda

first: Koichi

last: Tomoshige


title: Gene signature driving invasive mucinous adenocarcinoma of the lung

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

overall_design: Refer to individual Series


title: Opposing macrophage-polarization programs show extensive epigenomic and transcriptional cross-talk [RNA-Seq]


title: Opposing macrophage-polarization programs show extensive epigenomic and transcriptional cross-talk [ChIP_narrow]


title: Altered regulation and expression of genes by BET family of proteins in alveolar macrophages from COPD patients

city: Molndal

first: Elisabeth

last: Israelsson

address: Pepparedsleden 1

department: Translational Biology

country: Sweden

institute: AstraZeneca, IMED RIA

summary: BET proteins (BRD2, BRD3, BRDT and BRD4) belong to the family of bromodomain containing proteins, which form a class of transcriptional co‑regulators.  BET proteins bind to acetylated lysines in the histones of nucleosomal chromatin and function either as co‑activators or co‑repressors of gene expression. An imbalance between HAT and HDAC activities resulting in hyperacetylation of histones has been identified in COPD.  We hypothesized that BET inhibitor (JQ1) treatment of BET protein interactions with hyperacetylated sites in the chromatin will regulate excessive activation of pro-inflammatory genes and survival of key inflammatory drivers, alveolar macrophages (AM) in COPD. Transcriptome analysis of AM from COPD patients indicated up-regulation of macrophage type 1 genes upon LPS stimulation. BET inhibitor JQ1 treatment attenuated expression of multiple genes, including pro-inflammatory cytokines and regulators innate and adaptive immune cells. We demonstrated for the first time that JQ1 regulates differentially LPS-induced cytokine release from AM or peripheral blood mononuclear cells (PBMC) of COPD patients than PBMC of healthy controls. Using BET regulated gene signature, we identified a subset of COPD patients, which we propose to benefit from BET inhibition.  This work demonstrates that the effects of BET inhibition through JQ1 treatment of inflammatory cells has the potential to restore gene expression dysregulated in COPD patients vs healthy controls, and the expression of BET regulated genes is altered in COPD. The findings provide evidence of histone hyperacetylation as a mechanism driving chronic inflammatory changes in COPD.

overall_design: Alveolar macrophages were incubated with JQ1 (10uM) for 1h at 37°C and subsequently challenged with 100ng/ml of LPS from E. coli (serotype 026:B6, Sigma) for 6h or 24 h at 37°C in CO2 incubator. DMSO-treated cells were used as a vehicle control.

first: Nisha

last: Kurian

first: Xiao-Hong

last: Zhou

first: Fanyi

last: Jiang

first: Amy

last: DeMicco

first: Göran

last: Delgren

first: Goran

last: Edenro

first: Miika

last: Ahdesmäki

first: Maryam

last: Clausen

first: Susan

last: Monkley

first: Ib

middle: G

first: Graham

last: Belfield

first: Outi

last: Vaarala

first: Rajneesh

last: Malhotra

first: Lisa

last: Öberg


title: Genes regulated by SPDEF or FOXA3 in A549 lung carcinoma cells [RNA-seq]

first: Minzhe

last: Guo

summary: To identify genes regulated by SPDEF or FOXA3 in A549 lung carcinoma cells, we analyzed the whole-transcriptomic mRNA profiles of A549 cells expressing SPDEF or FOXA3 based on RNA-seq.

overall_design: A549 cells expressing NKX2-1 (Maeda et al., J Clin Invest. (2012) doi: 10.1172/JCI64048) were infected with Control (pGK), SPDEF or FOXA3-expressing lentivirus. For each lentivirus infection, RNA-seq experiments were performed on three biological replicates. Differential expression analyses were performed using DESeq2.

first: Yutaka


title: Single cell RNA expression of mouse embryonic basal forebrain

first: Brad

last: Friedman

summary:
Single-cell RNA-Seq RNA from medial ganglionic eminence at E11.5, E13.5, E15.5 or E17.5.
The ID of this project in Genentech's ExpressionPlot database is PRJ0007389

overall_design: Single-cell RNA-Seq from medial ganglionic eminence at E11.5, E13.5, E15.5 or E17.5.

first: Jasmine

last: Chen

first: Zora

last: Modrusan


title: Opposing macrophage-polarization programs show extensive epigenomic and transcriptional cross-talk

first: Viviana

last: Piccolo


title: Transcriptome of the geldanamycin producer Streptomyces hygroscopicus XM201

city: Shenzhen

first: Xinran

last: Wang

state: Guangdong

address: No.1068 Xueyuan Avenue

department: Center for Synthetic Biochemistry

institute: Shenzhen Institute of Advanced Technology, Chinese Acadamy of Science

summary: For systematically improving geldanamycin yield, we investigated the gene expression profile on the fourth day during geldanamycin fermentation (geldanamycin began to largely accumulated on this day). According to the RNA-seq data, we deduced that the PKS genes gdmAI-AIII are rate-limiting genes for geldanamycin biosynthesis. We also found a strong endogeneous promoter according to the RNA-seq data and the reporter gene. Replacing the native PKS promoter with this strong promoter brought an obvious increase in geldanamycin yield.

overall_design: Exploration of the expression profile of geldnamycin related genes and screening for strong endogeneous promoters.

first: Linquan

last: Bai


title: Global gene expression profiles in male and female single bovine blastocysts

status: Public on Mar 01 2017

city: Daejeon

first: Byungkuk

last: Min

address: 125 Gwahak-ro, Yuseong-gu

department: Development and Differentiation Research Center

institute: KRIBB

summary: X-chromosome reactivation (XCR) in early development was studied using transcriptome data from bovine male and female blastocysts derived by in vitro fertilization (IVF) or somatic cell nuclear transfer (SCNT). X-chromosome genes (X-genes) were upregulated almost twofold higher in female IVF blastocysts compared to that found in males. Since the mean expression levels of autosomal genes were relatively constant in both males and females, the upregulation of X-genes in female IVFs demonstrated a transcriptional sexual dimorphism between the sexes. X-genes were similarly expressed in inner cell mass and trophectoderm cells of female blastocysts, indicating no imprinted inactivation of paternal X in trophectoderm. Whereas the distribution of female-to-male expression ratios for autosomal genes was well balanced in IVFs, the distribution of X-genes was biased towards females such that approximately 80% of X- genes showed an increased level of expression. These observations of XCR and of X and autosomal gene expressions in IVFs were found in SCNTs, although to a lesser extent than that found in IVFs. We found that sham SCNT blastocysts, which underwent the same nuclear transfer procedures but retained their embryonic genome, closely mimicked that found with IVFs, and therefore, demonstrated that embryo manipulation itself did not interrupt XCR. In addition, from a heatmap of X-gene expression, we found a distinctive pattern between the sexes in which female SCNTs differed from male SCNTs and donor cells, but resembled female IVFs. Our findings that female IVFs, and to a lesser extent female SCNTs, undergo XCR, demonstrate that clonal reprogramming of bovine X chromosomes is incomplete and varies not only among local chromosomal regions but also among individual blastocysts.

overall_design: Males or females blastocysts generated by in-vitro fertilization (IVF), somatic cell nuclear transfer (SCNT), or sham-SCNT manipulation along with the donor cells used in the SCNT process.

first: Jung

middle: S

last: Park


title: Genome-wide mapping of NKX2-1 and SPDEF binding sites in A549 lung carcinoma cells by ChIP-seq

summary: ChIP-seq was performed to identify the binding regions of SPDEF and NKX2-1 in A549 lung carcinoma cells expressing NKX2-1 and SPDEF.

overall_design: ChIP-seq experiments were performed in A549 cells infected with lentivirus expressing NKX2-1 and SPDEF on two biological replicates per each transcription factor (TF). Peak regions were identified in all ChIP-seq TF data sets using the peak caller algorithm MACS2 (Zhang et al., Genome Biology, 9(9):R137, 2008).

last: Maeda

first: Koichi

last: Tomoshige


title: Genome-wide functional assessment of enhancer activities in the human genome

first: Kevin

last: White

address: 900 E 57th Street

department: Institute for Genomics and Systems Biology

institute: University of Chicago

summary: We illustrate that modifications to the previously published STARR-seq protocols are capable of  assessing enhancer activity of  whole genomes on mammalian systems using the human prostate cancer cell line, LNCaP. Besides detecting accessible enhancers located in open chromatin regions, we are also able to discover active, inaccessible enhancers in closed chromatin regions. By applying histone deacetylase inhibitor, trichostatin A, genes nearby the previously inaccessible enhancers are up-regulated, indicating the potential for endogenous functionality of these regulatory elements. These results exemplify how  whole genome STARR-seq provides an improved approach to gain a better understanding of the intricacies of transcriptional regulation of high complexity mammalian genomes.

overall_design: Profile enhancer activity of whole human genome in LNCap cells, and investigate the endogenous regulatory potential of active, inaccessible enhancers by examining gene expression and chromatin accessibility before and after trichostatin A treatment.

first: Yuwen

last: Liu

first: Shan

last: Yu

first: Vineet

last: Dhiman

first: Tonya

last: Brunetti

first: Heather

last: Scott


title: Quantification of differential gene expression by multiplexed targeted resequencing of cDNA

city: Nijmegen

first: Kees

last: Albers

address: Geert Grooteplein 10

department: Human Genetics

institute: Radboud University Medical Center

summary: We present an approach for quantification of differential mRNA expression by targeted resequencing of cDNA using single-molecule molecular inversion probes (cDNA-smMIPs), which enable highly multiplexed resequencing of cDNA target regions of ~100 nt and counting of individual molecules. We show that accurate estimates of differential expression can be obtained from molecule counts for hundreds of smMIPs per reaction and that smMIPs are also suitable for quantification of relative gene expression and allele-specific expression. cDNA-smMIPs are a cost-effective tool for hypothesis-driven expression analysis in large numbers of genes (10 to 500) and samples (hundreds to thousands).

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Analysis of differential gene expression using artificial ERCC transcripts and endogeneous transcripts from primary cells and cell lines

first: Alexander

last: Hoischen


title: TDRD6 mediates early steps of spliceosome maturation in primary spermatocytes

city: Dresden

first: Rolf

last: Jessberger

address: Fiedlerstraße 42

department: Institut für Physiologische Chemie, MTZ

country: Germany

institute: Medizinische Fakultät der TU Dresden

summary: Very little is known about splicing and its regulation in germ cells, particularly during meiosis. This paper describes the role of a male germ cell-specific protein, Tudor containing protein 6 (TDRD6), in assembly of the spliceosome in spermatocytes. We show that in spermatocytes, TDRD6 interacts with the key protein methyl transferase of the splicing pathway PRMT5. PRMT5 methylates arginines in substrate proteins. In a methylation dependent manner, TDRD6 also associates with spliceosomal core protein SmB in the absence of RNA, thus before an RNP-type spliceosome has been assembled. In Tdrd6-/- primary spermatocytes, PRMT5's association with SmB and the arginine dimethylation of SmB are much reduced. Abrogation of arginine methylation impaired the assembly of spliceosomes and the presence of the spliceosomal RNA U5 is aberrantly increased. These deficiencies in spliceosome maturation correlated with decreased numbers of Cajal bodies and gems involved in later stages, i.e. nuclear snRNP maturation. To reveal functional consequences of these deficiencies, transcriptome analysis of primary spermatocytes showed high numbers of splicing defects such as aberrant usage of intron and exons as well as aberrant representation of splice junctions upon TDRD6 loss. This study reveals a novel function of TDRD6 in spliceosome maturation and mRNA splicing in spermatocytes.

overall_design: Examination of splicing defects in isolated diplotene cells of 20dpp Tdrd6-/- vs. Tdrd6+/- testes pooled from at least 4 mice by deep sequencing in duplicate using Illumina® HiSeq 2500.

first: Müge

last: Akpınar

first: Mathias

last: Lesche

first: Grigorios

last: Fanourgakis

first: Jun

last: Fu

first: Konstantinos

last: Anasstasiadis

first: Andreas

last: Dahl


title: Whole transcriptome analysis of PBMCs stimulated with either a P. aeruginosa phage PNM lysate or with its bacterial host  P. aeruginosa

city: Gent

first: Jonas

last: Van Belleghem

state: Oost-Vlaanderen

address: De Pintelaan 185

department: Dept. Clinical Chemistry, Microbiology and Immunology (GE06)

country: Belgium

institute: Ghent University

summary: The ability of bacteriophages to kill bacteria is well known, as is their potential use as alternatives to antibiotics. As such, bacteriophages reach high doses locally through infection of their bacterial host in the human body. In this study we assessed the gene expression profile, by means of whole transcriptome analysis, of peripheral blood mononuclear cells (PBMCs) derived from a healthy human donor and stimulated with a Pseudomonas aeruginosa phage PNM lysate, or P. aeruginosa strain 573. The PBMCs were stimulated for 20 h, followed by lysis of the cells and RNA extraction. In total, three stimulations were performed: control sample (i.e. not stimulated), P. aeruginosa phage PNM lysate and P. aeruginosa strain 573. Each stimulation was conducted in triplicate. The transcriptome analysis showed that the phage induce a clear immunological responses. Both pro- and anti-inflammatory genes were up-regulated in the PBMCs in the presence of the phage or its bacterial host. Our results indicate that bacteriophages might play a bigger role in the  immune response then previously described and might have a broader effect than the clearing of bacterial infections alone, such as the suppression of the immune response to benefit their own survival.

middle: D

first: Mario

last: Vaneechoutte


title: Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex

city: Göttingen

first: Björn

last: Schwalb

address: Fassberg 11

institute: MPI

summary: 2 transcription elongation complex

overall_design: Examination of the effect of Paf1C subunit knock-out strains in S. cerevisiae on global transcription.

first: Youwei

last: Xu

first: Patrick

last: Cramer


title: RNA-Seq of Single Lung Circulating Tumor Cells (CTCs) and primary Tumor Cells from an orthotopic lung xenograft model

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: An orthotopic lung xenograft model was used to identify differential expression of lung CTCs in comparison to primary lung tumor cells.

overall_design: Briefly, 300,000 MGH134 (a patient-derived non-small cell lung cancer line [Pubmed ID 25758528]) cells stably expressing luciferase and GFP were introduced into the lung by percutaneous injection. Mice blood samples were collected 7-8 weeks after injection, and CTCs were isolated using the CTC iChip [Pubmed ID 23552373]. Primary tumors were digested into single cells by collagenase and hyaluronidase (Stemcell Technologies). A total of 10 GFP-positive single CTCs and 6 single primary tumor cells were individually micromanipulated using a 10 μm transfer tip on an Eppendorf TransferMan NK 2 micromanipulator. Single cell sequencing was performed under the same procedure as described in [Pubmed ID 26383955].

first: Yu

last: Zheng

first: David

last: Miyamoto

first: James

middle: P

last: Sullivan

first: Nicola

last: Aceto

first: Nicole

last: Vincent-Jordan

first: Min

last: Yu

first: Murat

last: Karabacak

first: Valentine

last: Comaills

first: Robert

last: Morris

first: Rushil

last: Desai

first: Niyati

first: Erin

last: Emmons

first: Richard

last: Lee

first: Chin-Lee

last: Wu

first: Sridhar

last: Ramaswamy

first: Wilhelm

last: Haas

last: Ting

first: Mehmet

last: Toner

first: Shyamala

last: Maheswaran

first: Daniel

last: Haber


title: pSILAC mass spectrometry reveals ZFP91 as novel IMiD dependent substrate of the CRL4CRBN ligase

first: Eric

last: Fischer

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Thalidomide and its derivatives lenalidomide and pomalidomide (IMiDs) are effective treatments of hematologic malignancies. It was shown that IMiDs impart gain of function properties to the CUL4-RBX1-DDB1-CRBN (CRL4CRBN) ubiquitin ligase that enable binding, ubiquitination and degradation of key therapeutic targets such as IKFZ1, IKZF3 and CSNK1A1. While these substrates have been implicated as efficacy targets in multiple myeloma (MM) and 5q deletion associated myelodysplastic syndrome (del(5q)-MDS), other targets likely exist. Using a pulse-chase SILAC mass spectrometry-based proteomics approach, we demonstrate that lenalidomide induces the ubiquitination and degradation of ZFP91. We establish that ZFP91 is a bona fide IMiD dependent CRL4CRBN substrate and further show that ZFP91 harbors a zinc finger (ZnF) motif, related to the IKZF1/3 ZnF, critical for IMiD dependent CRBN binding. These findings demonstrate that single time point pulse-chase SILAC mass spectrometry-based proteomics (pSILAC-MS) is a sensitive approach for target identification of small molecules inducing selective protein degradation.

overall_design: Total RNAseq of Hct116 cells treated with 30µM Lenalidomide or DMS control for 16 hours. Four biological replicates of each, lenalidomide and DMSO treatment.

first: Jian

last: An

first: Charles

last: Ponthier

first: Ragna

last: Sack

first: Jan

last: Seebacher

first: Michael

middle: B

last: Stadler

first: Katherine

last: Donovan


title: Transcriptomic analysis of reovirus-induced host responses

city: Cambridge

first: Mukund

last: Varma

address: 415 Main Street

institute: Broad Institute


title: Transcriptomic (RNAseq) analysis of reovirus-induced host responses in mesenteric lymph node of interferon alpha/beta receptor (IFNabR) knockout and WT mouse.

summary: Analysis of reovirus-induced host responses at the level of gene expression. Results provide insights into how reovirus infection breaks tolerance to dietary antigens and promotes the development of celiac disease.

overall_design: Total RNA obtained from mesenteric lymph node from WT and IFNabR KO mouse, and subjected to 48 hours stimulation with Reoviruses T1L or T3D-RV compared to Sham.

first: Romain

last: Bouziat

first: Reinhard

last: Hinterleitner

first: Judy

last: Brown

first: Jennifer

last: Stencel-Baerenwald

first: Mine

last: Ikizler

first: Toufic

last: Mayassi

first: Marlies

last: Meisel

first: Sangman

last: Kim

first: Valentina

last: Discepolo

first: Andrea

last: Pruijssers

first: Jordan

last: Ernest

first: Jason

last: Iskarpatyoti

last: Costes

first: Ian

last: Lawrence

first: Brad

last: Palanski

first: Matthew

last: Zurenski

first: Solomiia

last: Khomandiak

first: Nicole

last: McAllister

first: Pavithra

last: Aravamudhan

first: Karl

middle: W

last: Boehme

first: Fengling

last: Hu

first: Janneke

middle: N

last: Samsom

first: Hans-Christian

last: Reinecker

first: Sonia

last: Kupfer

first: Stefano

last: Guandalini

first: Carol

last: Semrad

first: Valérie

last: Abadie

first: Chaitan

last: Khosla

first: Luis

last: Barreiro

first: Ramnik

last: Xavier

first: Aylwin

last: Ng

first: Terence

last: Dermody

first: Bana

last: Jabri


title: Zika virus infection reprograms global transcription of host cells to allow sustained infection

city: La Jolla

first: Tariq

last: Rana

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

summary: Zika virus (ZIKV) is an emerging virus causally linked to neurological disorders, including congenital microcephaly and Guillain–Barré syndrome. There are currently no targeted therapies for ZIKV infection. To identify novel antiviral targets and to elucidate the mechanisms by which ZIKV exploits the host cell machinery to support sustained replication, we analyzed the transcriptomic landscape of human microglia, fibroblast, embryonic kidney, and monocyte-derived macrophage cell lines before and after ZIKV infection.

overall_design: To analyze factors contributing to ZIKV pathogenesis, we selected four human cell lines, microglia, BJ (foreskin fibroblast), 293FT (embryonic kidney), and THP-1 derived macrophages (monocyte-derived macrophage), and inoculated them with ZIKV produced in Vero and BHK cells at a multiplicity of infection of 1.

first: Jason

last: Dang


title: TOP2 synergizes with BAF chromatin remodeling for resolution of facultative heterochromatin

city: Stanford

first: Erik

last: Miller

address: 279 Campus Drive

institute: Stanford University

summary: Resolution and formation of facultative heterochromatin is essential to development, reprogramming, and oncogenesis. The mechanisms underlying these changes are poorly understood due to difficulty with interrogating heterochromatin dynamics and structure in vivo. BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes are known to promote chromatin accessibility. As the function of topoisomerase IIa (TOP2A) is largely dependent on BAF complexes in embryonic stem (ES) cells, we tested whether TOP2 was involved in BAF-mediated resolution of heterochromatin by performing ATAC-seq on ES cells treated with the TOP2 inhibitor ICRF-193, Brg1 (the primary ATPase subunit of esBAF complexes) conditional knockout cells, and Baf53a (a non-catalytic subunit dispensable for in vitro remodeling) conditional knockout cells. We found that TOP2 synergizes with BAF complexes genome-wide to resolve facultative heterochromatin to accessible chromatin at a large number of regulatory elements.

overall_design: We grew two passages of wild-type ES cells on gelatin-coated plates in serum-LIF media and treated them with DMSO or 1 µM ICRF-193 for 24 hours and three passages of cells treated with 1 µM ICRF-193 for 1 hour. We also grew two passages of Brg1 conditional knockout ES cells (Brg1fl/fl; Actin-CreER) and Baf53a conditional knockout ES cells (Baf53afl/-; Actin-CreER), treated them with ethanol or 0.8 µM tamoxifen for 24 hours, and then grew in fresh media without ethanol or tamoxifen for another 48 hours. At the end of the period of ICRF-193 treatment or BAF subunit deletion, we harvested the cells for chromatin accessibility profiling by ATAC-seq.

middle: L

first: Diana

middle: C

last: Hargreaves

first: Cigall

last: Kadoch

first: Chiung-Ying

last: Chang

first: Joseph

last: Calarco

first: Courtney

last: Hodges

last: Buenrostro

first: Kairong

last: Cui

first: William

last: Greenleaf

first: Keji

last: Zhao

first: Gerald

middle: R

last: Crabtree


title: TOP2 synergizes with BAF chromatin remodeling for both resolutions and formation of facultative heterochromatin


title: Targeted Apoptosis of Senescent Cells Restores Tissue Homeostasis in Response to Chemotoxicity and Aging

city: Rotterdam

first: Peter

last: de Keizer

address: Wytemaweg 80

department: Molecular Genetics

institute: Erasmus University Medical Center

summary: The accumulation of irreparable cellular damage restricts healthy lifespan after acute stress or natural aging. Senescent cells are thought to impair tissue function and their genetic clearance can successfully delay features of aging. Identifying how senescent cells avoid apoptosis would allow for the prospective design of anti-senescence compounds to address whether homeostasis can be restored. Here, we identify FOXO4 as a pivot in the maintenance of senescent cell viability. We designed a FOXO4-based peptide which selectively competes for interaction of FOXO4 with p53. In senescent cells, this results in p53 nuclear exclusion and cell-intrinsic apoptosis. Importantly, under conditions where it was well tolerated, the FOXO4 peptide restored liver function after Doxorubicin-induced chemotoxicity. Moreover, in fast aging XpdTTD/TTD, as well as in naturally aged mice the FOXO4 peptide could counteract the loss of fitness, fur density and renal function. Thus, it is possible to therapeutically target senescent cells and thereby effectively counteract senescence-associated loss of tissue homeostasis.

overall_design: mRNA expression levels are compared between IR-induced senescent and proliferating IMR90 cells in triplicate

first: Marjolein

last: Baar

first: Kasper

last: Derks

first: Wilfred

middle: F

last: van IJcken


title: Histone H3Lys4 trimethylation in budding yeast S. cerevisiae for wild type and cnc1Djhd2D yeast mutants

city: Stratford

first: Michael

last: Law

state: NJ

address: 2 Medical Center Dr., #122

department: Molecular Biology

institute: Rowan University

summary: In this study, we measured histone H3Lys4 trimethylation in budding yeast S. cerevisiae for wild type and cnc1Djhd2D yeast mutants. These experiments were performed for yeast cultured to mid-logarithmic phase in non-fermentable carbon.

overall_design: Measurement of histone H3Lys4 3me relative to histone H3 for two different genotypes with biological replicates. NGS was performed twice on each biological replicate resulting in 16 samples total.


title: Core Mediator structure at 3.4 A extends transcription initiation complex model

first: Björn

last: Schwalb

summary: 2 biological replicates of three S. cerevisiae mediator mutant strains and their parent strain were 4tU labeled. After labeled RNA purification, RNA-seq libraries were produced and sequenced.

overall_design: Examination of the effect of mediator subunit mutations in S. cerevisiae on global transcription.

first: Kayo

last: Nozawa

first: Patrick

last: Cramer

first: Thomas

last: Schneider


title: esBAF chromatin remodeling complexes promote spacing of nucleosomes flanking pluripotency factor binding sites

first: Erik

last: Miller

summary: We showed that topoisomerase II synergizes with BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes genome-wide to resolve facultative heterochromatin to accessible chromatin. To study the consequences of this on transcription factors, we performed MNase-seq on light digest of native chromatin in Brg1 conditional knockout embryonic stem (ES) cells. We found that spacing of nucleosomes flanking pluripotency factor binding sites specifically partially collapsed upon Brg1 deletion, indicating that pluripotency factor binding is likely lost.

overall_design: We grew Brg1 conditional knockout ES cells (Brg1fl/fl; Actin-CreER) ES cells on gelatin-coated plates in serum-LIF media, treated them with ethanol or 0.8 µM tamoxifen for 24 hours, and then grew in fresh media without ethanol or tamoxifen for another 48 hours before harvesting the cells for nucleosome profiling by MNase-seq.

first: Diana

last: Hargreaves

first: Cigall

last: Kadoch

last: Chang

first: Jason


title: Transcriptome analysis of the effect of DAPT in GHMT-induced cardiac reprogramming

city: Dallas

first: Eric

last: Olson

address: 6000 Harry Hines Blvd.

institute: University of Texas Southwestern Medical Center at Dallas

summary: The purpose of this experiment is to anlyze the transcriptomic changes associated with Notch inhibition, by DAPT treatment, during cardiac reprogramming mediated by GHMT (Gata4, Hand2, Mef2c anf Tbx5).

overall_design: RNA-seq was performed on MEFs infected with GHMT (Gata4, Hand2, Mef2c anf Tbx5) and  treated for 15 days with DMSO (vehicle) or DAPT.

first: Maria

last: Abad

first: Hisayuki

last: Hashimoto

first: Huanyu

last: Zhou

last: Morales

first: Beibei

last: Chen

first: Rhonda

last: Bassel-Duby


title: Effect of drugs on transcriptomic profiles

city: Illkirch

first: Frederic

last: Coin

address: 1, rue laurent fries

department: Functional Genomics and Cancer

institute: IGBMC

summary: the goal of this project is to determine the impact on genome-wide RNA expression of two molecules with biomedical applications on cancer

overall_design: Spironolactone (SP) and triptolide (TPL) treatments

first: Frédéric


title: Gene Expression of Breast Cancer Cell Lines Across Biomaterial Platforms

city: Amherst

first: Alyssa

last: Schwartz

address: 686 N pleasant St, Goessmann 159

department: Chemical Engineering

institute: University of Massachusetts Amherst

summary: 2 Breast Cancer Cell lines were seeded onto TCPS, on 2D PEG-PC gels, and encapsulated in 3D PEG-Maleimide  gels as single cells or spheroids to determine transcript level changes based on culture platform

overall_design: Examination of transriptome data of 2 cell lines in several biomaterial platforms

first: Shelly

last: Peyton


title: The Smc5/6 Complex Restricts HBV when Localized to ND10 without Inducing an Innate Immune Response and is Counteracted by the HBV X Protein Shortly after Infection

city: Foster City

first: Li

last: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

summary: RNA-Seq analysis of HBV-infected primary human hepatocyte

overall_design: RNA-Seq was conducted in two independent primary human hepatocyte (PHH) donors. Duplicate samples for each donor were analyzed on day 13 post-infection, with single samples per donor at other time-points (4 hr, 8 hr, 12 hr, 24 hr, day 2, day 3, day 6, day 8, day 10). Cell culture media was changed on days 1, 3, 6, 8 and 10

first: Congrong

last: Niu

first: Christine

middle: M

last: Livingston

first: Rudolf

middle: K

last: Beran

first: Stephane

last: Daffis

first: Dhivya

last: Ramakrishnan

first: Dara

last: Burdette

first: Leanne

last: Peiser

first: Eduardo

last: Salas

first: Hilario

last: Ramos

first: Mei

last: Yu

first: Guofeng

last: Cheng

first: Michel

last: Strubin

first: William

last: Delaney IV

first: Simon

last: Fletcher


title: RNASeq of molecular basis of ancestral vertebrate electroreception

city: San Francisco

first: Duncan

last: Leitch

department: Physiology

institute: University of California - San Francisco

summary: Elasmobranch fishes, including sharks, rays, and skates, use specialized electrosensory organs called Ampullae of Lorenzini to detect extremely small changes in environmental electric fields. Electrosensory cells within these ampullae are able to discriminate and respond to minute changes in environmental voltage gradients through an as-yet unknown mechanism. Here we show that the voltage-gated calcium channel CaV1.3 and big conductance calcium-activated potassium (BK) channel are preferentially expressed by electrosensory cells in little skate (Leucoraja erinacea) and functionally couple to mediate electrosensory cell membrane voltage oscillations, which are important in the detection of specific, weak electrical signals. Both channels exhibit unique properties compared with their mammalian orthologues to support electrosensory functions: structural adaptations in CaV1.3 mediate a low voltage threshold for activation, while alterations in BK support specifically tuned voltage oscillations. These findings reveal a molecular basis of electroreception and demonstrate how discrete evolutionary changes in ion channel structure facilitate sensory adaptation.

overall_design: Examination of gene expression in ampullary cells, ampullary canals, body skin, and liver from one adult Leucoraja erinacea skate prepared from poly A+ RNA using Illumina TruSeq Stranded mRNA Library Prep Kit

first: Nicholas

last: Bellono

first: David

last: Julius


title: Comprehensive analysis of genome-wide transcriptome modification during neuronal differentiation of mouse embryonic stem cells by all-trans retinoic acid

city: Gwanju

first: Lee

last: Sung-gwon

address: Yong-bong ro 77

institute: Chonnam national university

summary: Total RNA from 4 sample which are control and differentiation stage after treated ATRA with 4days (Embryonic body, Embryonic body + ATRA (0D), Embryonic body + ATRA (6D), Embryonic body + ATRA (10D))

first: Sung-gwon

last: Lee

first: Hyun-gwan


title: Cardiac microvascular endothelail cells of EC-KLF2 and/or KLF4 knockout mice at day 6 post-tamoxifen

city: Cleveland

first: Mukesh

last: Jain

state: Ohio

address: 2103 Cornell Road

department: Department of Medicine

institute: Case Western Reserve University

summary: Maintenance of vascular integrity in the adult animal is needed for survival and critically dependent on the endothelial lining, which controls barrier function, blood fluidity, and flow dynamics. However, nodal regulators that coordinate endothelial identity and function in the adult animal remain poorly characterized. Here we show that endothelial KLF2 and KLF4 control a large segment of the endothelial transcriptome thereby affecting virtually all key endothelial functions. Inducible endothelial-specific deletion of Klf2 and/or Klf4 reveals that a single allele of either gene is sufficient for survival, but absence of both (EC-DKO) results in acute death from myocardial infarction, heart failure, and stroke. EC-DKO animals exhibit profound compromise in vascular integrity and profound dysregulation of the coagulation system. Collectively, these studies establish an absolute requirement for KLF2/4 for maintenance of endothelial and vascular integrity in the adult animal.

overall_design: Eight-to-ten-week old mice were intraperitoneally injected with tamoxifen to trigger endothelial-specific gene deletion of KLF2 and/or KLF4. At day 6 post-injection, endothelial cells were isolated from the heart and total RNA was purified.

first: Panjamaporn

last: Sangwung


title: sCLIP – An integrated platform to study RNA-protein interactome(s) in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs [RNA-Seq]

city: Cologne

first: Yulia

last: Kargapolova

address: Robert-Koch-Straße 21

department: CMMC

institute: Cologne University

summary: RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing. sCLIP exploits linear amplification of the immunoprecipitated RNA improving the complexity of the sequencing-library despite significantly reducing the amount of input material and omitting several purification steps. Additionally it permits a radiolabel-free visualization of immunoprecipitated RNA. In a proof of concept, we identify that CSTF2tau binds many previously not recognized RNAs including histone, snoRNA and snRNAs. CSTF2tau-binding is associated with internal oligoadenylation resulting in shortened snRNA isoforms subjected to rapid degradation. We provide evidence for a new mechanism whereby CSTF2tau controls the abundance of snRNAs resulting in alternative splicing of several RNAs including ANK2 with critical roles in tumorigenesis and cardiac function. Combined with a bioinformatic pipeline sCLIP thus uncovers new functions for established RBPs and fosters the illumination of RNA-protein interaction landscapes in health and disease.

overall_design: Sequencing of total RNA from 2 biological replicates for CSTF2tau knockdown experiments were performed. In total 4 samples were analyzed.

first: Michal

last: Levin

first: Karl

last: Lackner

first: Sven

last: Danckwardt


title: sCLIP – An integrated platform to study RNA-protein interactome(s) in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs [CLIP-Seq]

overall_design: Sequencing of CSTF2tau sCLIP (3 biological replicates).


title: Calpain 2 is a Mechanosensitive Link Between Integrin α6 and EGFR

first: Alyssa

last: Schwartz

summary: RNA-Seq Transcriptome analysis of MDA-MB-231s cultured on 2D biomaterials

overall_design: Examination of gene expression across 4 stiffnesses (1,4,8,41 kPa) at 24 hours and 6 days, compared to cells on TCPS

first: Christopher

last: Hall

first: Lauren

middle: E

last: Barney

first: Courtney

last: Babbitt

first: Shelly

last: Peyton


title: RNA-seq analysis of gene expression in adult head of Canton-S and Bully lines

city: boston

first: Edward

last: Kravitz

state: ma

address: 220 longwood avenue

department: neurobiology

institute: Harvard medical school

summary: Goal: Identify genes that are differentially expressed in hyper-aggressive Bully line. We used wildtype Canton-S flies as control. We also explored the effect of developmental temperature on gene expression.

overall_design: Total RNA were extracted from 6-day-old adult heads from Canton-S or Bully lines that were raised at 19C or 25C. A total of 4 samples were obtained. For each sample, 2 independent biological replicates were included.

first: Budhaditya

last: Chowdhury

first: Yick-bun

last: Chan


title: Intergenic non-coding transcription utilises an RNA-based mechanism to drive transcriptional interference

city: Oxford

first: Beth

last: Watts

address: South Parks Road

department: Biochemistry

institute: University of Oxford

summary: Recent studies have revealed that eukaryotic genomes are pervasively transcribed by RNA polymerase II, producing a plethora of non-coding RNAs which frequently overlap protein-coding genes. Despite the fact that overlapping transcription is well known to repress transcription initiation from downstream promoters, the mechanism behind this phenomenon has remained elusive. It was proposed that transcriptional interference relies on the act of transcription rather than the RNA itself to block access of the transcription machinery to downstream promoters. Here, we demonstrate that an RNA and chromatin-dependent mechanism is responsible for transcriptional interference in fission yeast. This relies on co-transcriptional recruitment of the histone deacetylase Clr3 to nascent non-coding RNA, leading to formation of hypoacetylated chromatin and repression of the downstream protein-coding gene. Our findings highlight the unexpected requirement for RNA as well as trans-acting protein factors in mediating the repressive effects imposed on gene expression through overlapping non-coding transcription.

overall_design: Two replicates of Clr3-TAP were analysed for PAR-CLIP together with a no cross-link control. Three replicates of each wild-type and seb1-1 were analysed for RNA-seq.

first: Sina

last: Wittmann

first: Sofia

last: Battaglia

first: Patrick

last: Cramer

first: Lidia

last: Vasiljeva


title: Diurnal regulation of RNA polymerase III transcription is under the control of both feeding-fasting response and circadian clock

city: Lausanne

first: Francois

last: Mange

address: Genopode building

department: Center for Integrative Genomic

institute: University of Lausanne

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

overall_design: Refer to individual Series