title: p190 RhoGAP mediates contact inhibition of cell proliferation by repressing YAP1-mediated gene transcription

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Recently, ARHGAP35 encoding p190A RhoGAP was unexpectedly found to rank among the 20-30 most frequently mutated genes in human cancer.  The spectrum of mutations in ARHGAP35 is consistent with that of a tumor suppressor, but the underlying mechanisms are not well understood.  In this work we sought to elucidate functions for p190A RhoGAP (p190A) and its isoform p190B RhoGAP (p190B) that might confer tumor suppressor capacities in epithelial cells.  We establish an essential role for p190A and p190B to mediate contact inhibition of cell proliferation (CIP).  Both p190A and p190B localize in part to adherens junctions, which is consistent with a role in CIP.  Using an unbiased approach, we determine that p190A and p190B repress expression of a cassette of genes that are modulated by the Hippo pathway.  Moreover, we demonstrate that p190A and p190B promote activation of LATS kinases and inhibit translocation of the Hippo transducer YAP to the nucleus.  Next, we validate that expression of an activated form of YAP induces a gene signature with significant similarities to that of cells depleted of p190A and p190B expression.   Furthermore, we establish that p190A and p190B promote CIP by repressing YAP-TEAD-mediated gene transcription.  Collectively, our results demonstrate that p190 RhoGAPs serve as activators of the Hippo pathway, which is widely implicated in CIP.   Our work suggests that ARHGAP35 belongs to group of tumor suppressor genes, including AJUBA, CDH1, and NF2, with gene products that localize to cell-cell junctions and modulate the activity MST/LATS complex.

overall_design: TR-T10 cells, as well as retroviral and lentiviral 293 packaging cells, were all propagated in DMEM supplemented with 10% FBS. To permit inducible knockdown of p190A and or p190B expression, TR-T10 cells were transduced with retrovirus encoding p190A shRNA or p190B shRNA and cells then selected in hygromycin (p190A shRNA) or puromycin (p190B shRNA).  To generate TR-T10 cells with combined knockdown of p190A and p190B, p190B-kd cells were transduced with retrovirus encoding p190A shRNA and cells were selected in hygromycin.  To induce knockdown of gene expression, cells were plated at subconfluent density and cultured for 3 days in the presence of 4 µg/ml of doxycycline.  Cells were then harvested and replated at subconfluent or confluent density for another 3-5 days prior to experimentation. TR-T10 or p190A+B-kd cells with inducible expression of YAP5SA or YAP5SA+S94A were generated by lentiviral transduction and selected with 3 mg/ml G418. In cells with p190A+B-kd, expression of YAP5SA or YAP5SA+S94A is linked to knockdown p190A and p190B, as both are under control of the TetR.

first: Scott

last: Frank

first: Giorgio

middle: G

last: Galli

first: André

last: Bernards

first: Fernando

middle: D

last: Camargo

first: Morten

last: Frödin

first: Steen

middle: H

last: Hansen


title: RNA-seq experiments of systemic colonization of oilseed rape by Leptosphaeria maculans

status: Public on Dec 30 2016

city: Thiverval Grignon

first: Julie

last: Gervais

address: Avenue Lucien Brétignières

department: BIOGER

country: France

institute: INRA

type: Expression profiling by high throughput sequencing

summary:
Leptosphaeria maculans, causal agent of stem canker disease, colonises oilseed rape (Brassica napus) in two stages: a short and early colonisation stage corresponding to cotyledon or leaf colonisation, and a late colonisation stage during which the fungus colonises systemically and symptomlessly the plant during several months before stem canker appears. To date, determinants of the late colonisation stage are poorly understood; L. maculans may either successfully escape plant defences leading to the stem canker development, or the plant can develop an “adult-stage” resistance reducing canker incidence.
To get insight into these determinants, we performed an RNA-seq pilot project comparing fungal gene expression in infected cotyledons and in symptomless and necrotic stems. Despite the low fraction of fungal material in infected stems, enough fungal transcripts were detected and a large portion of fungal genes were expressed, thus validating the feasibility of the approach. Our analysis showed that all avirulence genes previously identified are under-expressed during stem colonisation compared to cotyledon colonisation. A validation RNA-seq experiment was then done to investigate the expression of candidate effector genes during systemic colonisation. 307 "late" effector candidates, under-expressed in the early colonisation stage and over-expressed in the infected stems, were identified. Finally our analysis revealed a link between regulation of expression of effectors and their genomic location: the late effector candidates, putatively involved in the systemic colonisation, are located in gene-rich genomic regions, whereas the "early" effector genes, over-expressed in the early colonisation stage, are located in gene-poor regions of the genome.

sample_organism:
Brassica napus
Plenodomus lingam

platform_organism:
Brassica napus
Plenodomus lingam

overall_design:
Two RNA-seq-projects:
A pilot project RNA-seq with deep sequencing of L. maculans mRNA during early and late colonisation stages of oilseed rape, using Illumina HiSeq2000.
A validation RNA-seq experiment, with two biological replicates per condition, focused on two infection stages, infected cotyledons and early symptomless stem colonisation, as well as in vitro growth condition as a control.

first: Clémence

last: Plissonneau

first: Juliette

last: Linglin

first: Michel

last: Meyer

first: Karine

last: Labadie

first: Corinne

last: Cruaud

first: Isabelle

last: Fudal

first: Thierry

last: Rouxel

first: Marie-Hélène

last: Balesdent


title: Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats [smallRNA-seq]

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

country: USA

institute: Excet, Inc. / USACEHR

type: Non-coding RNA profiling by high throughput sequencing

summary: Chlorpyrifos (CPF) is an organophosphorus pesticide (OP), and one of the most widely used pesticides in the world. Metabolites of CPF and other OPs continue to be identified in the majority of human samples, even in countries such as the United States where OP use is declining (Arcury et al., 2010). The effects of repeated occupational and environmental exposures to OPs are poorly understood, although human and animal studies consistently identify neurotoxicity as the primary endpoint of concern.  Thus, occupational exposures to sublethal doses of CPF are consistently associated with problems in cognitive abilities, such as learning and memory but the biological mechanism(s) underlying this association remain speculative.  To identify potential mechanisms of CPF neurotoxicity, we employed a rat model that simulated documented CPF exposures in Egyptian agricultural workers. We quantified mRNA expression profiles in the CA1 region of the hippocampus of adult male Long Evans (LE) rats administered CPF at 3 or 10 mg/kg/d (s.c.)  for 21 days. Despite significant inhibition of cholinesterase activity by the end of the 21 d exposure period, the CPF-exposed rats displayed minimal signs of cholinergic toxicity. Distinct hippocampal mRNA and miRNA signatures were associated with CPF exposure. Toxicogenomics-based evidence identified increased expression of neuropeptide genes in the hippocampi of CPF-exposed rats, which have been shown to activate receptor-mediated signaling pathways involved in cell survival. The analysis of small non-coding RNA profiles suggested the possibility that miR132/212-mediated homeostatic regulatory pathways may also be activated by repeated exposures to CPF. These findings identify potential molecular effects that may contribute to neurobehavioral deficits.

overall_design: Adult male Long Evans rats were repeatedly exposed to subclinical doses of chlorpyrifos or vehicle control (peanut oil) for 21 consecutive days (study days 1-21). Two CPF formulations (3 or 10 mg/kg b.w./day) or an equal volume of the vehicle were administered daily by subcutaneous injection, approximately 24 h apart. On the study day 21, animals were euthanized and hippocampus tissues were collected for biochemical and transcriptomic analyses. The global RNA profiles of all test animals were obtained using the Affymetrix GeneChip microarrays. The Illumina sequencing technologies were employed to analyzed comprehensive profiles of mRNAs and small RNAs from the rats exposed to 10 mg/kg/day CPF or the unexposed control rats.

first: Young

middle: S

last: Lee

first: John

middle: A

last: Lewis

first: Naissan

last: Hussainzada

first: Pamela

middle: J

last: Lein

first: David

last: Jackson

first: Jonathan

last: Stallings


title: Toxicogenomic Characterization of Molecular Mechanisms Contributing to Chlorpyrifos Neurotoxicity in Adult Male Rats [RNA-seq]


title: Whole genome bisulfite sequencing of hdp1-1 and hdp2-1and other relative mutants (all with 35S-SUC2 transgene)

status: Public on Dec 29 2016

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

type: Methylation profiling by high throughput sequencing

summary: Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in 35S-SUC WT, hdp1-1 and hdp2-1, mbd7, idm1, and hdp2mbd7 double mutants

overall_design: 6 samples examined: 35S-SUC2 WT, hdp1-1, hdp2-1, mbd7, idm1, and hdp2mbd7 double mutants  ( all with 35S-SUC2 transgene)

first: Cheng-Guo

last: Duan

first: Xingang

last: Wang

first: Kai

last: Tang

first: Shaojun

last: Xie


title: RNA-seq of human adipose tissue following n-3 PUFA supplementation and evoked endotoxemia

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

summary: Dietary consumption of long-chain omega-3 polyunsaturated fatty acids (n-3 PUFA) may protect against cardiometabolic disease through modulation of systemic and adipose inflammation. However, it is often difficult to detect the subtle effects of n-3 PUFA on inflammatory biomarkers in traditional intervention studies. We aimed to identify novel n-3 PUFA modulated gene expression using unbiased adipose transcriptomics during evoked endotoxemia in a clinical trial of n-3 PUFA supplementation. We analyzed adipose gene expression using RNA sequencing in the fenofibrate and omega-3 fatty acid modulation of endotoxemia (FFAME) trial of healthy individuals at three timepoints: before and after n-3 PUFA supplementation (n=8; 3600mg/day EPA/DHA) for 6weeks compared with placebo (n=6), as well as during a subsequent evoked inflammatory challenge (lipopolysaccharide 0.6ng/kg i.v.). As expected, supplementation with n-3 PUFA vs. placebo alone had only modest effects on adipose tissue gene expression. In contrast, the transcriptomic response to evoked endotoxemia was significantly modified by n-3 PUFA supplementation, with several genes demonstrating significant n-3 PUFA gene-nutrient interactions. These data highlight potential mechanisms whereby n-3 PUFA consumption may enhance the immune response to an inflammatory challenge.

overall_design: Adipose tissue RNA from 14 healthy subjects (before and after supplementation with n-3 PUFA or placebo) was sequenced by Illumina HiSeq 2000 with poly-A selection

first: Jane

last: Ferguson

first: C


title: DNA Methylation and Gene Expression Regulation Associated with Vascularization in Sorghum bicolor

city: Davis

first: Gina

middle: Marie

last: Turco

state: CA

address: University of California, Davis

institute: UC Davis

summary: Plant secondary cell walls constitute the majority of plant biomass and are an important source of biomaterials. Secondary cell walls are particularly prominent in xylem cells present in the vascular tissue. Although the process of vascularization has been extensively studied in the dicot Arabidopsis thaliana, remarkably little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome data using laser capture microdissection in the developing vascular and non-vascular tissues of the sorghum root. Many sorghum genes with enriched expression in developing vasculature were orthologous to genes previously associated with vascular development in other species. However, a number of transcription factor families, including NAC domain, MYB and ARF varied in their complement of vascular expressed genes to a considerable degree in sorghum compared to Arabidopsis and/or maize. Differential expression of genes associated with DNA methylation and chromatin modification were identified between vascular and non-vascular cell types, implying that changes in DNA methylation may be a feature of sorghum root vascularization. To profile DNA methylation in these tissues, sodium bisulfite sequencing of laser capture microdissected tissue was performed. DNA methylation was enriched in genic regions of genes demonstrating higher expression in non-vascular tissues. Methylation in genic and intergenic regions varied by tissue type and gene expression level. Furthermore, genes involved in cell elongation showed differences in methylation levels concomitant with expression between non-vascular and vascular tissue types suggesting a novel mode by which root growth in distinct tissues may be modulated. Our results provide both a genetic and epigenetic framework for studying vascularization and secondary cell wall development in sorghum.

overall_design: Eight samples of paired-end reads were analyzed across four tissue types, four samples for RNASeq and four for bisulfite sequencing of Sorghum bicolor (L.) Moench (BTx623) 3 day old seedlings. Whole root, whole shoot, vascular and nonvascular samples were analyzed with three replicates per tissue type for both RNASeq and bisulfite sequencing.

middle: M

first: Kaisa

last: Kajala

first: Govindarajan

last: Kunde-Ramamoorthy

first: Chew-Yee

last: Ngan

first: Andrew

last: Olson

first: Shweta

last: Deshphande

first: Barbara

last: Waring

first: Scott

last: Stelpflug

first: Patricia

last: Klein

first: Shawn

last: Kaeppler

first: Doreen

last: Ware

first: Chia-Lin

last: Wei

first: J

middle: P

last: Etchells

first: Siobhan

last: Brady


title: CD74 role in transcription regulation [RNA-seq]

status: Public on Dec 28 2016

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

summary: CD74 activation was previously shown to affect gene transcription. The goal of this study was to reasarch its role as a transcriptor regulator. CD74 was activated in primary CLL cells obtained from patients for 2 and 8 h. mRNA was then extracted, and mRNA-seq was conducted.

overall_design: mRNA seq was done for CD74 ot IgG activated cells 2 and 8 h following activation in triplicated

first: Idit

last: Shachar

first: Naama

last: Gil-Yarom

first: Lev

last: Shvidel


title: The flightless I protein is involved in the genome-wide mRNA post-transcriptional regulation in lung carcinoma cells

city: Guangzhou

first: Kezhi

last: Chen

state: Guangdong

address: Huangpu Avenue

department: Institute of life and health engineering

country: China

institute: Jinan University

summary: We report the function of Flightless I involved in the overall nuclear export, and genome-wide translation of mRNAs in H1299 cells. By using high-throughput transcriptome and translatome sequencing combined with cell fractionation, we generated genome-wide transcriptome and translatome maps of lung carcinoma cells and normal cells. We find that flightless I protein could modulate the genome-wide translation and mRNA traffiking, suggesting that the post-transcriptional regulation of mRNA might be a major mechanism of action for Flightless I.

overall_design: Examination of mRNA expression, ribosome-nascent chain complex (RNC) expression and mRNA traffiking in overexpressed-FLII H1299cells and knockdown-FLII HBE cells.

first: Cuihua

last: Wang

first: Gong

last: Zhang

first: Langxia

last: Liu


title: Neotenic phenomenon in gene expression in the skin of Foxn1 deficient (nude) mice– projection for regenerative skin wound healing

city: Olsztyn

last: Gawrońska-Kozak

address: ul. Tuwima 10

department: Institute of Animal Reproduction and Food Research

country: Poland

institute: Polish Academy of Sciences

summary: Uninjured skin of adult C57BL/6J mice and mouse fetuses at 18 day of embryonic development (E18), as the models of reparative healing, and Nude and E14, as the models of regenerative healing, were characterized for their gene expression profiles by next-generation high-throughput DNA sequencing. The comparisons of gene expression profiles indicated that there were more similarities within each model of healing (Nude was more similar to E14 and B6 was more similar to E18). The analysis revealed that Nude and E14 showed in common the up-regulation of genes associated with tissue remodeling, cytoskeletal rearrangements, wound healing and immune response and the down-regulation of genes coupled to differentiation.  Gene expression profiles of regenerative adult Nude mice display features of an attenuated skin development resembling that of E14 mice, thus the Nude mouse may be considered as a unique example of neoteny among mammals. The similar expression profiles of genes in the skin of both Nude and E14 mice are direct or indirect consequences of FOXN1 deficiency. FOXN1 appears to regulate the balance between cell proliferation and differentiation and its lack creates a pro-regenerative environment.

overall_design: Skin (C57BL/6J, Nude, E14, E18) and epidermis (C57BL/6J, Nude) mRNA profile were generated by sequencing using the SOLiD™ 3 System.

first: Anna

last: Kur-Piotrowska

first: Marta

last: Kopcewicz

last: Grabowska

first: Leslie

last: Kozak

first: Pawel

last: Sachadyn

last: Gawronska-Kozak


title: Gene expression signatures for lens in Msx2CKO mice and wildtype mouse.

city: Shenyang

first: ziyan

last: yu

state: Liaoning

address: 11 Xinhua Road

institute: China  Medical University

summary: For a deeper understanding of the possible mechanism, we performed RNA microarray analysis with lens isolated from Msx2WT and Msx2CKO mice of P1.The results showed there were 3412 DEGs with more than 2 fold expression change in the Msx2CKO lens, 1815 genes were  up-regulated and 1597 genes were down-regulated.

overall_design: Total RNA was extracted from lens isolated from Msx2cko and Msx2wt mice at P1 using RNeasy micro kit (Cat#74004,  QIAGEN, GmBH, Germany), and Msx2wt lens were used as control. Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).The microarrays were carried out by Shanghai  biotechnology corporation using One-Color Microarray-Based Gene Expression Analysis, and subsequent analyses conducted  using SAS statistical software online (http://sas.ebioservice.com/).

first: Jiangyue

last: Zhao

first: Ziyan

last: YU


title: CD74 role in transcription regulation [ChIP-seq]

last: Friedlander

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CD74 activation was previously shown to affect gene transcription. The goal of this study was to research its role as a transcriptor regulator. CD74 was activated in primary CLL cells obtained from patients for 1 h. The cells were then fixed using DSG and formaldhyde, and ChIP-seq was conducted.

overall_design: ChIP-seq was done for CD74 activated or non activated CLL cells with Ab for CD74 (4 replicates), CD74 activated H3K4Me2 (2 replicates), CD74 non-activated H3K4Me2 (2 replicates), H3K4Me3 (2 replicates), H3K27Ac (2 replicates).

last: Shachar


title: The lncRNA genomic landscape of oligodendrocytes reveals myelination control by a lncOL1/Suz12 complex in the CNS [RNASeq_lncOL1]

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: Long noncoding RNAs (lncRNAs) are emerging as important regulators of cellular functions, but their roles in myelination in the CNS remain undefined. Through de novo transcriptome reconstruction at multiple stages, we establish dynamic expression profiles of lncRNAs during oligodendrocyte lineage progression and uncover a cohort of oligodendrocyte-enriched lncRNAs. Co-expression network analysis reveals a cohort of lncRNAs is linked to protein-coding genes associated with oligodendrocyte maturation. We identify a conserved chromatin-associated oligodendrocyte-restricted lncRNA, lncOL1. Overexpression of lncOL1 promotes oligodendrocyte differentiation in the developing brain, whereas genetic inactivation of lncOL1 causes defects in myelination and remyelination in the CNS. We further show that lncOL1 interacts with Suz12, a component of polycomb repressive complex 2, to promote oligodendrocyte differentiation in part through Suz12-mediated silencing of a differentiation inhibitory network that antagonizes OL maturation. Together, our findings demonstrate lncRNAs as a key layer of the genetic circuitry that controls CNS myelination and myelin repair.

overall_design: Uncover differentially expressed genes in primary oligodendrocytes upon depletion of lncOL1

first: Danyang

last: He


title: RNA-seq data for hdp1-1 and hdp2-1 mutants

first: Jian-Kang

last: Zhu

summary: Using RNA-seq data to provide expression profiling for 35S-SUC WT, hdp1-1 and hdp2-1

overall_design: Six samples (two replicates for each genotype) examined: WT, hdp1-1 and hdp2-1

first: Cheng-Guo

last: Duan

first: Xingang

last: Wang

first: Kai

last: Tang

first: Shaojun

last: Xie


title: The lncRNA genomic landscape of oligodendrocytes reveals myelination control by a lncOL1/Suz12 complex in the CNS

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: A Pair of Transposon-derived Proteins Function in A Histone Acetyltransferase Complex for Active DNA Demethylation


title: CD74 role in transcription regulation

first: Gilgi


title: Identification of chilling responsive microRNAs and their targets in vegetable soybean (Glycine max L.)

city: Hangzhou

first: Xu

last: shengchun

address: Deshengzhonglu

department: Institute of Vegetables

institute: Zhejiang Academy of Agricultural Sciences

summary: Chilling stress is a major factor limiting the yield and quality of vegetable soybean    (Glycine max L.) on a global scale. Systematic identification and function analysis of    miRNA under chilling stress could be helpful to clarify the molecular mechanism of    chilling resistance. In the present study, two independent small RNA libraries from leaves    of vegetable soybean were constructed, and sequenced with the high-throughput Illumina    Solexa system. A total of 434 known miRNAs and three novel miRNAs were identified.    Moreover, the expression patterns of these miRNAs have been verified by qRT-PCR    analysis. Furthermore, we identified their gene targets by high-throughput degradome    sequencing and validated using 5'-RACE. A total of 898 transcripts were targeted by 54    miRNA  families  attributed  to  five  categories.  More  importantly,  we  identified  55    miRNAs that differentially expressed between chilling stress and the control. The targets    of  these  miRNAs  were  enriched  in  oxidation-reduction,  signal  transduction,  and    metabolic  process  functional  categories.  The  qRT-PCR  confirmed  that  there  was  a    negative relationship among the miRNAs and their targets under chilling stress. Our work    provides comprehensive molecular evidence for the possible involvement of miRNAs in    the process of chilling-stress responses in vegetable soybean.

overall_design: 24h chilling treatment and control were collected to extract total RNA to do small RNA sequencing and pooled to do degradome sequencing.

last: Shengchun


title: The lncRNA genomic landscape of oligodendrocytes reveals myelination control by a lncOL1/Suz12 complex in the CNS [RNASeq_DH]

overall_design: Profile lncRNA dynamics during oligodendrocyte differentiation and maturation


title: Trithorax-group protein ASH1 defines novel H3K36me3/H3K9me3 bivalent domains

city: Chiyodaku

first: Yujiro

last: Tanaka

state: Tokyo

address: 2-3-10 Kandasurugadai

department: School of Biomedical Science

country: Japan

institute: Tokyo Medical and Dental University

summary: A Trithorax-group (TrxG) protein ASH1 selectively dimethylates histone H3 lysine 36 (H3K36) and is required for expression of Hox genes. Genome-wide targets and molecular functions of ASH1, however, have remained elusive. Here we report ChIP-seq analysis of ASH1 targets in the human genome using a leukemia cell line K562. We identified 4,596 ASH1 binding sites, 2,502 of which are in the coding region, mostly in a proximity of promoters. Remaining half of the ASH1 binding sites are in the intergenic region. Analysis of histone methyation patterns revealed that a majority of ASH1 bidning sites are closely associated not only with trimethylated H3K36 (H3K36me3) but also with H3K9me3, shedding light for the first time to H3K36/H3K9 double methylation domains. Of note, an H3K9 methyltransferase SETDB1 is enriched in the ASH1 bidning sites, whereas EZH2 but not SUZ12 of the Polycomb Repression Complex 2 (PRC2) is present in bivalent domains. In addition, a small subset of ASH1 targets bear H3K4me3 and colocalize with RNA polymerase II. These select targets are highly enriched for regulators of gene expression, such as CXXC1, WHSC2/NELFA, and a battery of zinc finger proteins, suggesting that ASH1 might acts as a master regulator of gene expression.

overall_design:
Two biological replicates using different batches of affinity purified rabbit polyclonal antibodies against the C-terminal 18 amino acids of human/mouse ASH1.
Anti-ASH1 antibodies were made in-house: batch #1 (Tanaka et al. Gene 397:161-168, 2007) and batch #3.


title: The lncRNA genomic landscape of oligodendrocytes reveals myelination control by a lncOL1/Suz12 complex in the CNS [ChIPSeq]

overall_design: Analysis of Suz12 genomic occupancy in oligodendrocyte lineage cells

first: Chuntao


title: Deptor transcriptionally regulates Endoplasmic Reticulum homeostasis in Multiple Myeloma cells.

status: Public on Dec 27 2016

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

institute: Italian National Cancer Institute "Regina Elena"

summary: We performed a RNA-seq analysis by using mRNA from KMS27 cells transfected with siRNA Deptor or siRNA negative control.

overall_design: The raw FASTQ files are available under SRA project SRP072090, bioproject PRJNA315795. There are two samples: control and silenced for Deptor, loaded in triplicate.

first: Valeria

last: Catena

first: Tiziana

last: Bruno

first: Francesca

last: De Nicola

first: Frauke

last: Goeman

first: Simona

last: Iezzi

first: Cristina

last: Sorino

first: Giovanni

last: Cigliana

first: Aristide

last: Floridi

last: Blandino

first: Maurizio

last: Fanciulli


title: SOX9 Drives WNT Pathway Activation in Prostate Cancer

city: Boston

first: Fen

last: Ma

state: MA

address: 3 Blackfan Circle

department: Hem/Onc

institute: BIDMC


title: ChIP-seq data for HDP2 transgenic line

first: Jian-Kang

last: Zhu

summary: Data for genome-wide binding of HDP2

overall_design: Use ChIP-seq to study the genome-wide binding of HDP2 in HDP2 transgenic line

first: Cheng-Guo

last: Duan

first: Xingang

last: Wang

first: Kai

last: Tang


title: Single cell transcriptomic profiling of mouse pancreatic progenitors

city: Philadelphia

first: Diana

middle: Elena

last: Stanescu

state: PA

address: 3400 Civic Center Blvd

department: IDOM

institute: University of Pennsylvania

summary: We report the transcriptome of single pancreatic cells at embryonic day e13.5

overall_design: Single cells mRNA of wild-type mouse pancreata at embryonic day 13.5

middle: E

first: Doris

last: Stoffers


title: RNA-seq of breast in 3-week and 6-week age native Pekin and Cherry Valley Pekin ducks

city: Beijing

first: Liyuan

state: China

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

department: Animal Sciencie and Technology

institute: China Agricultura University

summary: Muscle development and lipid deposition are complex processes regulated by a coordinated expression profile of genes. Pekin ducks displayed a significant difference from Cherry Valley duck in muscle fiber development and IMF contents. Genetic comparisons between these two breeds would contribute to the exploration of mechanisms underlying the phenotypic differences. In the present study, breast tissues of Pekin (BD) and Cherry Valley (CD) ducks were used for RNA-seq in two different time points (3 and 6-week) to investigate the transcriptome basis. A total of 16705 genes from duck breast muscle were detected as positively expressed genes (RPKM>0.1) and 2273 genes were regarded as novel genes. Differentially expressed genes (DEGs) in BD3 VS CD3 were regarded as muscle development-related genes as CD3 grown faster than BD3 in muscle fibers. DEGs in BD6 VS CD6 were regarded as lipid-related genes as a much higher IMF contents in BD6 than CD6 while no differences observed in 3-week. DEGs obtained from BD3 VS BD6 and CD3 VS CD6 were also analyzed as relative genes here. In all, 9 genes (MAT1A, KAZALD1, SHROOM3, KLHL6, MYH13, ALDOA, TNNT2, PDLIM3 and PFKM) were validated as muscle development correlated candidate genes, and another 11 genes (DHCR24, CNTFR, ANGPTL4, BCL6, HIP1, TRIB1, ADORA1, C1QTNF2, CD36, PRKAG2 and ACSL1) were regarded as lipid correlated genes in duck. What’s more, functional analysis confirmed that the immune reaction, ECM and energy metabolism also correlated with muscle development and lipid deposition closely. The present study not only enlarged the duck genetic information pool but also provided a dozen of candidate genes related to muscle development and lipid deposition, which laid a firm foundation for the further studies on molecular mechanisms in duck.

overall_design: RNA-deep sequencing of breast muscle in 3-week and 6-week age native Pekin duck and Cherry Valley Pekin duck under Hi-seq 2000

first: Hao

last: Zhang


title: Cripto is essential to capture mouse epiblast stem cell and human embryonic stem cell pluripotency

city: Naples

first: ALESSANDRO

last: FIORENZANO

state: Naples

address: Castellino 111

department: IGB institute CNR

institute: I.G.B. Institute, CNR

summary: We reported RNA-seq transcriptome profiling of WT and Cripto KO ESC→EpiSC transition using the Illumina HiSeq platform. Whole-genome expression revealed that epiblast associated-genes were all severely reduced in absence of Cripto compare to WT. Interestingly, besides a set of common genes deregulated in both WT and Cripto KO ESC→EpiSC transition, we identified two different sets of genes that were uniquely deregulated. We find a large cluster of genes coding for components of the five respiratory electron transport complexes, which are involved in mitochondrial oxidative phosphorylation, downregulated only in WT ESC→EpiSC transition, while their expression was unvaried in Cripto KO. Moreover the RNAseq analysis reveals a set of genes that were uniquely upregulated in Cripto KO, such as Hox genes and trophoectodermal markers.  RNAseq data and validation both at RNA and protein level provide new evidences that Cripto is required for the metabolic reprogramming that occurs in the conversion of mouse ESCs into EpiSCs, preserving ESC lineage restriction.

overall_design: RNA-seq  profiling of WT and Cripto KO ESCs and EpiSCs using the Illumina HiSeq platform

first: Gabriella

last: Minchiotti

first: Alessandro

last: Fiorenzano


title: A transcriptomics approach to compare transcriptomes of individual methylotrophs from Lake Washington sediment in artificial communities and in pure cultures.

status: Public on Dec 26 2016

city: Seattle

first: Sascha

last: Krause

state: Washington

address: 616 NE Northlake Place

department: Microbiology

institute: University of Washington

summary: We established simple synthetic microbial communities in a microcosm model system to determine the mechanisms that underlay cross-feeding in microbial methane-consuming communities. Co-occurring strains from Lake Washington sediment were used that are involved in methane consumption, a methanotroph and two non-methanotrophic methylotrophs.

sample_organism:
Methylobacter tundripaludum
Methylotenera mobilis

overall_design: RNAseq profiles of methanotrophs and non-methanotrophic methylotrophs in pure culture and in two species mixtures. Duplicate samples (total N = 10) were submitted for transcriptomics analysis to GENEWIZ (Seattle, USA). 1 x 50 bp were sequenced in single-read configuration in Rapid Run mode on a HiSeq 2500 System.

first: Timothy

last: Johnson

first: Yasodara

last: Karunaratne

first: Yanfen

last: Fu

first: David

last: Beck

first: Ludmila

last: Chistoserdova

first: Mary

last: Lidstrom


title: Genome-wide quantitative core promoter activity maps reveal a wide range of sequence-intrinsic transcription initiation strengths

city: Vienna

first: Alexander

last: Stark

address: Dr Bohr-Gasse 7

country: Austria

institute: Research Institute for Molecular Pathology (IMP), Vienna Biocenter VBC

summary: Gene expression is controlled by enhancers that activate transcription from the core promoters of their target genes. Although a key function of core promoters is to convert enhancer activities into gene transcription, whether and how strongly they activate transcription in response to enhancers has not been systematically assessed on a genome-wide level. Here we describe self-transcribing active core promoter sequencing (STAP-seq), a method to determine the responsiveness of genomic sequences to enhancers, and apply it to the Drosophila melanogaster genome. We cloned candidate fragments at the position of the core promoter (also called minimal promoter) in reporter plasmids with or without a strong enhancer, transfected the resulting library into cells, and quantified the transcripts that initiated from each candidate for each setup by deep sequencing. In the presence of a single strong enhancer, the enhancer responsiveness of different sequences differs by several orders of magnitude, and different levels of responsiveness are associated with genes of different functions. We also identify sequence features that predict enhancer responsiveness and discuss different core promoters are employed for the regulation of gene expression.

overall_design: STAP-seq was performed in S2 cells (using zfh1, sgl, ham, ncm, ssp3 enhancers) and OSC cells (using tj enhancer).

first: Cosmas

last: Arnold

first: Muhammad

last: Zabidi

first: Michaela

last: Pagani

first: Martina

last: Rath

first: Katharina

last: Schernhuber

first: Tomáš

last: Kazmar


title: SOX9 Drives WNT Pathway Activation in Prostate Cancer [ChIP-seq]

first: Fen

last: Ma

summary: SOX9 is critical for prostate development and is implicated in prostate cancer, we used SOX9 ChIP-seq in combination with transcriptome profiling to identify genes and pathways it regulates in normal or neoplastic epithelium.

overall_design: Chromatin was immunoprecipitated by SOX9 antibody in the TMPRSS2-ERG fusion positive prostate cancer cell line VCaP with high basal SOX9 expression and submitted for high throughput sequencing in parallel with input control.

first: Xin

last: Yuan

first: Steven

last: Balk


title: Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

city: Stanford

first: William

last: Greenleaf

address: 279 Campus Drive, Beckman Center B257

department: Genetics

institute: Stanford University


title: Variable chromatin secondary structures in live cells revealed by radiation-induced spatially correlated DNA cleavage mapping [RICC-Seq]

summary: Chromatin structure at the length scale encompassing nucleosome-nucleosome interactions is thought to play a crucial role in regulating transcription and access to DNA. However, this chromatin secondary structure remains poorly understood compared to the primary structure of single nucleosomes or the tertiary structure of long-range looping interactions. Here we report the first genome-wide map of chromatin conformation in human cells at the 1-3 nucleosome (50-500 bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq). Unbiased analysis of RICC-seq DNA fragments in 1 Mb windows reveals a similar fragment length profile across the genome, with regional enrichment of characteristic fragments spanning tri-nucleosome units in heterochromatin. We observe differences in nucleosome-nucleosome contacts among euchromatin, H3K27me3-marked heterochromatin, and H3k9me3-marked heterochromatin. After calibrating RICC-seq signal to 3D distances, we show that compact 2-start helical fiber structures with stacked alternating nucleosomes are consistent with RICC-seq fragmentation patterns from H3K9me3-marked heterochromatin, while non-compact zig-zags and other extended structures are preferred in open chromatin. Our data support a model of heterochromatin condensation in native, intact nuclei consistent with longitudinal compaction of two-start helical fibers.

overall_design: This data set includes three biological replicates of primary RICC-seq experiments, one size-selected RICC-seq experiment, one crosslinked RICC-seq experiment, and one ATAC-seq experiment. Each RICC-seq data set consists of one experimental library (300 gy) and two types of controls (0 gy (no irradiation) and purified DNA from lysed cells). The number of technical replicates for each condition varies between experiments.

first: Viviana

middle: I

last: Risca

first: Sarah

last: Denny

first: Aaron

middle: F

last: Straight


title: Variable chromatin secondary structures in live cells revealed by radiation-induced spatially correlated DNA cleavage mapping [ATAC-Seq]

overall_design: This data set includes eight technical replicates of ATAC-seq performed on a human foreskin fibroblast cell line.


title: Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD

status: Public on Dec 25 2016

first: Tingting

last: Li

address: 38 Xueyuan Rd

department: Medical informatics

institute: Peking University

summary: Long non-coding RNAs are important regulators of diverse biological prosesses. Here, we report on functional identification and characterization of a novel long intergenic noncoding RNA with MyoD-regulated and skeletal muscle-restricted expression that promotes the activation of the myogenic program, and is therefore termed Linc-RAM (Linc-RNA Activator of Myogenesis). Linc-RAM is transcribed from an intergenic region of myogenic cells and its expression is upregulated during myogenesis. Notably, in vivo functional studies show that Linc-RAM knockout mice display impaired muscle regeneration due to differentiation defect of satellite cells. Mechanistically, Linc-RAM regulates expression of myogenic genes by directly binding MyoD, which in turn promotes the assembly of the MyoD-Baf60c-Brg1 complex on the regulatory elements of target genes. Collectively, our findings reveal the functional role and molecular mechanism of a lineage-specific Linc-RAM as a regulatory lncRNA required for tissues-specific chromatin remodeling and gene expression.

overall_design: We first investigated the global effect of Linc-RAM on gene expression by RNA-Seq analysis during myogenic differentiation using RNAs isolated from differentiating C2C12 myoblasts in which Linc-RAM was either stably overexpressed or knocked down.

first: Dahai

last: Zhu

first: Yong

last: Zhang


title: Chromosome loop control of oncogenic MYC produces a common vulnerability in diverse cancers [ChIP-seq]

status: Public on Dec 24 2016

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: The majority of human cancers become highly dependent on a deregulated MYC oncogene, thus identifying a common mechanism underlying MYC regulation could provide valuable targets for therapy. We show here that diverse tumor-specific super-enhancers acquired throughout the 3Mb MYC insulated neighborhood functionally interact with a single conserved site occupied by CTCF protein in the MYC promoter. CRISPR-mediated deletion analysis shows that this common CTCF site is required for super-enhancer looping to the MYC promoter, high MYC expression and rapid cell proliferation in multiple cancers. Targeted methylation of the MYC enhancer anchor by a dCAS9-DNMT3A-3L fusion protein abrogates CTCF binding with consequent loss of MYC expression, suggesting a common vulnerability and a novel approach for therapeutic targeting of aggressive cancers.

overall_design: Evaluation of CTCF or  H3K27Ac ChIP-seq in three cell types

first: Jurian

last: Schuijers


title: Chromosome loop control of oncogenic MYC produces a common vulnerability in diverse cancers

overall_design: Refer to individual Series


title: HNRNPL RIP-seq in LNCaP prostate cancer cells

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

summary: RNA immunoprecipitation coupled with next generation sequencing (RIP-seq)  was used to map the HNRNPL-RNA interactome in LNCaP cells.

overall_design: Analysis of RIP-seq and total RNA data enabled the identification of the HNRNPL binding sites in the LNCaP cell transcriptome.

first: Teng

last: Fei

first: Chen

last: Yiwen

first: Shirley

last: Liu

first: Brown

last: Myles


title: Global binding of isoforms of Wilms' Tumor gene 1 and H3K4me3 in K562 cells

city: Lund

first: Linnea

last: Järvstråt

state: Scania

address: Klinikgatan 26

department: Department of Hematology and Transfusion Medicine

country: Sweden

institute: Lund University

summary: Background: Wilms' tumor gene 1 (WT1) acts as an oncogene in acute myeloid leukemia (AML). A naturally occurring alternative splice event between zinc fingers three and four, removing or retaining three amino acids (KTS), is believed to change the DNA binding affinity of WT1. Altered balance between WT1 -KTS and WT1 +KTS expression associates with poor prognosis in AML. Methods: We characterized the DNA binding patterns of biotin-tagged WT1 -KTS and WT1 +KTS in K562 cells by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Results: We discovered that WT1 -KTS preferentially binds near transcription start sites (TSS) and in enhancers, whereas WT1 +KTS binds within gene bodies. Additionally, we observed a significant overlap between WT1 -KTS and WT1 +KTS target genes, despite the binding sites being distinct. Motif analysis showed enrichment of two TRANSFAC derived motif matrices within peaks for both isoforms, and enrichment of several previously published WT1 motifs which, however, differed between isoforms. Additional analyses showed that WT1 -KTS and WT1 +KTS target genes are transcribed to a higher extent than non-targets, and involved in cell proliferation, cell death, and development. Conclusions: Our results provide the first evidence that WT1 -KTS and WT1 +KTS bind principally different regions of the genome, yet share target genes. Our results indicate isoform-specific regulation of processes related to cell proliferation and differentiation, consistent with the involvement of WT1 in AML.

overall_design: Streptavidin capture of biotinylated WT1 –KTS (two replicates), biotinylated WT1 +KTS (three replicates) and background K562-BirA cells (three replicates; background control). H3K4me3 immunoprecipitation in cells containing biotinylated WT1 –KTS (three replicates) and in cells containing biotinylated WT1 +KTS (two replicates).

first: Tove

last: Ullmark


title: Transcripts enriched in microsome fraction in ribosome-independent manner

city: Kyoto city

first: Takanari

last: Umegawachi

state: Kyoto

address: Sakyo-ku

institute: Kyoto Institute of Technology

summary: To identify the transcripts fractionated into microsome fraction in ribosome-independent manner, we isolate rough microsome fraction by sucrose density gradient ultracengrifugation, then the rough microsome fraction is centrifugated following treatment with puromycine and EDTA in high-salt buffer to remove ribosomes. The pellet and surpernatant are named naked microsome fraction (NM) and stripped ribosome fraction (SR), respectively.  By calculating the ratio of the level of each mRNA in NM and SR, we identify the enriched transcripts in NM.

overall_design: Transcript profiles of subcellular fractions from S2-DRSC Drosophila cultured cell

first: Hideki

last: Yoshida

first: Hiromu

last: Koshida

first: Momoko

last: Yamada

first: Yasuyuki

last: Ohkawa

first: Tetsuya

last: Sato

first: Mikita

last: Suyama

first: Henry

last: Krause

first: Masamitsu

last: Yamaguchi


title: Endoplasmic reticulum as a hub organizing microRNAs and a subset of endogenous siRNAs in Arabidopsis [Ribo-Seq and RNA-Seq]

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

summary: Endoplasmic reticulum (ER) was implicated as the site of microRNA (miRNA)-mediated translational repression in plants. Here, we examined the ER- and rough ER- associated small RNAome, transcriptome and translatome. We found that nearly all cellular transcripts were present on membrane-bound polysomes (MBPs), and miRNAs and a small set of endogenous siRNAs were particularly enriched on MBPs. The MBP- enriched miRNAs and siRNAs associated with, and were recruited to membranes by, their effector protein ARGONAUTE1 (AGO1). AGO1 associated with ER in a partly RNA-independent manner. Reduced membrane association of 22-nt miRNAs, which trigger the biogenesis of phased, secondary siRNAs (phasiRNAs) from their target transcripts, was accompanied by decreased production or loss of phasing of phasiRNAs. The phasiRNA precursor transcripts, previously thought to be noncoding, were associated with MBPs in a manner that supported phasiRNA production. These findings point to the ER as a hub that hosts and organizes endogenous small RNAs in plants.

overall_design: Ribo-Seq and mRNA-Seq libraries from RNA extracted from membrane bound polysome fractions (One biological replicate)

first: Xuemei

first: Lin


title: Transcriptome profiles of virgin and mated Callosobruchus maculatus seed beetles

status: Public on Dec 23 2016

city: Uppsala

first: Göran

last: Arnqvist

address: Norbyvägen 18D

department: Ecology and Genetics

institute: Uppsala University

summary:
Objective: Sexually dimorphic phenotypes arise largely from sex-specific gene expression, which has mainly been characterized in sexually naïve adults. However, we expect sexual dimorphism in transcription to be dynamic and dependent on factors such as reproductive status. Mating induces many behavioral and physiological changes distinct to each sex and is therefore expected to activate regulatory changes in many sex-biased genes.
Methods: Using RNA-seq we first characterized sexual dimorphism in gene expression, for the first time in Callosobruchus maculatus seed beetles. We then examined how females and males respond to mating and how it affects sex-biased expression, both in more sex-limited (abdomen) and sex-shared (head and thorax) tissues.
Results: Mating responses were largely sex-specific and, as expected, females showed more numerous changes compared to males. Of the sex-biased genes present in virgins, 16%  (1,041 genes) in the abdomen and 17% (243 genes) in the head and thorax altered their relative expression between the sexes. Sex-bias status changed in 2% of the genes in the abdomen and 4% in the head and thorax following mating. Mating responses involved de-feminization of females and, to a lesser extent, de-masculinization of males relative to their virgin state: mating decreased rather than increased dimorphic expression of sex-biased genes.

overall_design: Virgin and mated male and female expression data generated from abdomen and combined head and thorax, using Illumina HiSeq 2500 technology. Each sample type was replicated three times and each replicate was sequenced on two lanes.

first: Elina

last: Immonen

first: Ahmed

last: Sayadi

first: Helen

last: Bayram


title: Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis [RNA-Seq]

summary: The endoplasmic reticulum (ER) was implicated as the site of microRNA (miRNA)-mediated translation repression in plants. Here, we examined the ER- and rough ER-associated small RNAome, transcriptome and translatome. We found that almost all cellular transcripts were present on membrane-bound polysomes (MBPs), and miRNAs were enriched in membranes and on MBPs. miRNAs were recruited to membranes by their effector protein AGO1, whereas AGO1 associated with membranes and, partly ribosomes, in an RNA-independent manner. Most strikingly, 22 ntmiRNA isoformsand a set of 22 ntsiRNAs, were enriched in the membrane fraction and onMBPs, where they trigger phasedsecondary siRNAproduction from target transcripts. Loss of membrane association of the 22 nt small RNAs resulted in the loss of phasing in secondary siRNA production.These findings point to the ER as a hub that hosts and organizes endogenous small RNAs in plants.

overall_design: Examination of mRNA in 4 cell fractions of Col-0 seedlings with 3 biological replicates

last: Chen


title: Aging, microglia and cytoskeletal regulation are key factors in the pathological evolution of the APP23 mouse model for Alzheimer’s disease

city: Wilrijk (Antwerp)

first: Peter Paul

last: De Deyn

state: Antwerpen

address: universiteitsplein 1

country: Belgium

institute: University of Antwerp

summary:
Aging is a key factor in Alzheimer's disease, but it's correlation with the pathology and pathological factors like amyloid-beta remains unclear
In our study we aimed to provide an extensive characterisation of age-related changes in the gene expression profile of APP23 mice and controls and correlate these changes to pathological and symptomatic features of the model
We found a clear biphasic expression profile with a developmental and aging phase. The second phase, particularly, displays aging features and similarties with the progression of Alzheimer pathology in human patients
Processes involved in microglial activation, lysosomal processing, neuronal differantion and cytoskeletal regulation appear key factors in this stage.
Interestingly, the changes in the gene expression profile of APP23 mice also seem to occur in control animals, but at a later age. The changes appear accelerated and/or exacerbated in APP23 mice.

overall_design: mRNA profiles of APP23 mice and wild-type control littermates aged 1.5, 6, 18 or 24 months. For all the age groups, samples of 3 mice of each genotype were analyzed

first: Leen

last: Janssen

first: Marissa

middle: L

last: Dubbelaar

first: Inge

middle: R

last: Holtman

first: Jelkje

last: de Boer-Bergsma

first: Bart

last: Eggen

first: Erik

middle: W

last: Boddeke

first: Peter

first: Debby

last: Van Dam


title: Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis [ncRNA-Seq]

overall_design: Examine the sRNA preference and changes of 12 samples with various biological replicates of different cell fractions in WT, ago1-27 and ago1-36 seedlings


title: Testicular adenosine to inosine RNA editing in the mouse

city: Bar Harbor

first: Elizabeth

last: Snyder

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Adenosine to inosine (A-to-I) RNA editing occurs in a wide range of tissues and cell types and can be catalyzed by one of two adenosine deaminase acting on double stranded RNA enzymes, ADAR and ADARB1. Editing can impact both coding and non-coding regions of RNA, and in higher organisms, has been proposed to function in adaptive evolution. Neither the prevalence of A-to-I editing nor the role of either ADAR or ADARB1 has been examined in the context of germ cell development in mammals. Computational analysis of whole testis and cell type specific RNA-sequencing data followed by molecular confirmation demonstrated that A-to-I RNA editing occurs in both the germ line and in somatic Sertoli cells in two targets, Cog3 and Rpa1. Expression analysis demonstrated both Adar and Adarb1 were expressed in both Sertoli cells and in a cell-type dependent manner during germ cell development. Conditional ablation of Adar did not impact testicular RNA editing in either germ cells or Sertoli cells.  Additionally, Adar ablation in either cell type did not have gross impacts on germ cell development or male fertility. In contrast, global Adarb1 knockout animals demonstrated a complete loss of A-to-I RNA editing in spite of normal germ cell development. Taken together, these observations demonstrate ADARB1 mediates A-to-I RNA editing in the testis and these editing events are dispensable for male fertility in an inbred mouse strain in the lab.

overall_design: 6 wildtype late juvenile whole testes


title: Gene expression analysis of HdhQ111 mice in a Pin1 knock-out background

city: Novara

first: Francesca

last: Persichetti

state: Italy

address: via Solaroli 17

department: Scienze della Salute

institute: Universita' del Piemonte Orientale

summary: we report additional phenotypes of mHtt mice that are modified in Pin1 knock-out mice

overall_design: RNAs from the striatum of three mice of 12 months of age were purified for each of the genotypes (PinWT/HttWT; PinKO/HttWT; PinWT/HttKI; PinKO/HttKi)  to carry out gene expression profiling

first: Elena

last: Agostoni


title: Short Read Sequencing Data of the Transcriptome of the Rheumatoid Arthritis Rat Model Treated with Acupuncture (HiSeq 2000, miRNA, batch 1)

city: Rome

first: Christine

last: Nardini

address: Via dei Taurini 9

institute: PICB

summary: We report the application of Illumina Hiseq2000 sequencing technology for high-throughput miRNA profiling of the rheumatoid arthritis (RA) rat model induced by collagen type II (CIA),  with acupuncture and placebo treatments.

overall_design: The experiment is designed as 2 arms: epidermal needle manipulation (AP/MEC) and placebo (PLA, used as control) on CIA induced rheumatoid arthritis (RA) rats. Muscle tissue samples sampling was carried out before any therapy in RA rats (RA_T0), and after at 1 hour and 34 days of therapeutic treatments for both AP and PLA. From all the 10 blood collected samples (2 replicates for each group, for each timepoint), total RNA were extracted. Finally, purified RNA were analyzed using illumina hiseq 2000).

first: Valentina

last: Devescovi

first: Yuanhua

last: Liu


title: S-Nitrocysteine (CysNO) responsive genes transcriptome profiling modulates diverse regulatory pathways in Oryzea sativa

city: Daegu

first: Sang-Uk

last: Lee

address: 80 Daehakro, Bukgu

country: South Korea

institute: Kyungpook National University

summary: To understand the nitric oxide induced signaling mechanism in crop plants.

overall_design: 5mM CysNO treatment to seedling plant, Transcriptome profiling

first: Bong-Gyu

last: Mun

first: Chan-Ju

first: Byung-Wook

last: Yun


title: Transcriptome of aerobically/anaerobically grown Actinobacillus succinogenes strain 130Z on fumarate/glucose

status: Public on Dec 22 2016

city: Seoul

first: kucsbl

last: submitter

state: Seoul

address: Anamdong 5-ga, Seongbuk-gu

department: Department of Biotechnology

institute: Korea University

overall_design: Four types of growth conditions, aerobic growth on glucose, anaerobic growth on glucose, aerobic growth on fumarate with glycerol and anaerobic growth on fumarate with glycerol, were used. In triplicate. Sequencing was performed with Illumina Miseq.

first: Hyeok-jin

last: Ko

first: Byeonghyeok

last: Park


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and H3.3 Knockdown neural stem cell Transcriptomes

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression. The goals of this study are to compare the different transcripts between control or Histone H3.3 knockdown in the neural stem cells.

overall_design: Methods:Neural stem cell isolated from E12 mice and cultured in vitro. RNA used for global transcriptome analysis were extracted from the different lentivirus infected neural stem cells and sequenced by Hiseq 2500. Significantly differentially expressed genes were identified when we compared Normalized Reads Count between groups with p < 0.05 and |Log2FoldChange| > 1.

first: Wenlong

last: Xia


title: Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis

first: Chenjiang

last: You

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


title: Reconstitution of the RNAi response in human cells using drosophila gene products

city: Durham

first: Edward

middle: Matthew

last: Kennedy

state: NC

address: Department of Molecular Genetics and Microbiology, Box 3025

department: Molecular Genetics and Microbiology

institute: Duke University

summary: While mammalian somatic cells are incapable of mounting an effective RNA interference (RNAi) response to viral infections, plants and invertebrates are able to generate high levels of functional short interfering RNAs (siRNAs) of viral origin that can effectively control many infections. In Drosophila, the RNAi response is mediated by the Dicer 2 enzyme (dDcr2) acting in concert with two co-factors called Loqs-PD and R2D2. To examine whether a functional RNAi response could be reconstituted in human somatic cells by expression of these insect proteins, we expressed dDcr2, in the presence or absence of Loqs-PD and/or R2D2, in a previously described human cell line, NoDice/ΔPKR, that lacks functional forms of both the human Dicer (dcr) and EIF2AK2 (pkr) gene. Upon expression of dDcr2, Loqs-PD and R2D2 in these human cells, we observed the production of ~21-nt long siRNAs, derived from a co-transfected double stranded RNA (dsRNA) expression vector, that were loaded into the human RNA-induced silencing complex (RISC) and were able to significantly reduce the expression of a cognate indicator gene. We conclude that it is possible to at least partly rescue the ability of mammalian somatic cells to express functional siRNAs by using gene products of invertebrate origin.

overall_design: Combinations of Drosophila Dicer2 and cofactors were transfected into 425-PKR cells to determine whether they were sufficient for genesis of siRNAs in mammalian cells.

first: Anand

middle: V

last: Kornepati

first: Hal

last: Bogerd

first: Bryan

last: Cullen


title: Transcriptome profiling of P-granule-depleted or P-granule mutant gonads versus control gonads over time

city: Santa Cruz

first: Susan

last: Strome

state: CA

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

summary: The germ cells of multicellular organisms protect their developmental potential through specialized mechanisms.  A shared feature of germ cells from worms to humans is the presence of non-membrane-bound ribonucleoprotein organelles called germ granules.  Depletion of germ granules in Caenorhabditis elegans (i.e., P granules) leads to sterility and in some germlines expression of the neuronal transgene unc-119::gfp and the muscle myosin MYO-3.  Thus, P granules are hypothesized to maintain germ cell totipotency by preventing somatic development, although the mechanism by which P granules carry out this function is unknown.  In this study, we performed transcriptome and single molecule RNA-FISH analyses of dissected P-granule-depleted gonads at different developmental stages.  Our results demonstrate that P granules are necessary for adult germ cells to down-regulate spermatogenesis RNAs and to prevent the accumulation of numerous soma-specific RNAs.  P-granule-depleted gonads that express the unc-119::gfp transgene also express many other genes involved in neuronal development and concomitantly lose expression of germ cell fate markers.  Finally, we show that removal of either of two critical P-granule components, PGL-1 or GLH-1, is sufficient to cause germ cells to express UNC-119::GFP and MYO-3 and to display RNA accumulation defects similar to those observed after depletion of P granules.  Our data identify P granules as critical modulators of the germline transcriptome and guardians of germ cell fate.

overall_design: Transcriptome profiles of 3 replicates of L4 P-granule RNAi gonads, 3 replicates of L4 control gonads, 3 replicates of Day 1 Adult P-granule RNAi gonads grown at 24°C

first: Andrew

middle: K

last: Knutson

first: Thea

last: Egelhofer

first: Andreas

last: Rechtsteiner


title: Selective packaging of cellular microRNAs into HIV-1 virions inhibits infectivity

summary: We analyzed the incorporation of cellular microRNAs (miRNAs) into highly purified HIV-1 virions and observed that this largely, but not entirely, mirrored the level of miRNA expression in the producer CD4+ T cells. Specifically, of the 58 cellular miRNAs detected at significant levels in the producer cells, only five miRNAs were found at a 2 to 4-fold higher level in virions than predicted based on random sampling. Of note, these included two miRNAs, miR-155 and miR-92a, reported previously to at least weakly bind HIV-1 transcripts. To test whether miRNA binding induces virion incorporation, we introduced artificial miRNA target sites into the HIV-1 genome and observed a 10 to 40-fold increase in the packaging of the cognate miRNA into virions, leading to the recruitment of up to 1.6 copies into each virion. Importantly, this high level of incorporation significantly inhibited HIV-1 virion infectivity. We conclude that target sites for cellular miRNAs can inhibit RNA virus replication at two distinct steps, i.e., during infection and during viral gene expression, thus explaining why a range of different RNA viruses appear to have evolved to restrict cellular miRNA binding to their genome.

overall_design: This dataset inludes total small RNA libraries for CEM-SS cells and purified HIV-1 virions produced in these cells.  Two replicates for each sample

first: Adam

last: Whisnant


title: Comparison of Transcriptomics of Mouse Skin Derived Precursors (SKPs) and Dermal Fibroblasts by RNA-Seq

city: chengdu

first: li

last: li

state: sichuan

address: wai nan guo xue xiang #37

department: dermatology

institute: west china hospital

summary: Skin-derived precursors (SKPs) from dermis possess the capacities of self-renewal and multipotency. In vitro and in vivo studies demonstrated that they can differentiate into fibroblasts. However, little is known about the molecular mechanism of the differentiation of SKPs into fibroblasts in vitro. To elucidate the genes involved in the process, transcriptome profiling of SKPs and fibroblasts was analyzed and compared using RNA-Seq. A total of 2659 differentially expressed genes (DEGs) were identified by RNA-Seq, which provided abundant data for further analysis. Gene Ontology enrichment analysis revealed that genes related to cell differentiation, cell proliferation, protein binding, transporter activity and membrane were significantly enriched. A novel gene 1700009N14Rik related to cell differentiation was significantly up-regulated. The most significantly up-regulated genes Wnt4, Wisp2 and Tsp-1 and the down-regulated genes Retn, Slitrk1, Klk6, Agtr2, Ivl, Msx1, IL15, Atp6v0d2, Kcne1l and Thbs4 might play important roles in the transition of SKPs to fibroblasts. KEGG analysis showed that DEGs were significantly enriched in the TGF-β signaling pathway, Wnt signaling pathway and Notch signaling pathway, which have been previously proven to regulate the differentiation and self-renewal of various stem cells. These identified DEGs and pathways could facilitate further investigations of the detailed molecular mechanisms, making it possible to take advantage of the potential therapeutic applications of SKPs in skin repair in the future.

overall_design: Examination of 2 cell types (SKPs and fibroblasts).

first: Yujie

last: Mao

first: Lidan

last: Xiong

first: Siyu

last: Wang

first: Jianqiao

last: Zhong

first: Rongying

last: Zhou

first: Li

last: Li


title: RNA-seq analysis of retinoic acid treated mouse neuromesodermal progenitors

city: La Jolla

first: Gregg

last: Duester

address: 10901 N. Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Bipotent neuromesodermal progenitors (NMPs) residing in the caudal epiblast drive coordinated body axis extension by generating both posterior neuroectoderm and presomitic mesoderm. Retinoic acid (RA) is required for body axis extension, however the early molecular response to RA signaling is poorly defined, as is its relationship to NMP biology. As endogenous RA is first seen near the time when NMPs appear, we used WNT/FGF agonists to differentiate embryonic stem cells to NMPs which were then treated with a short 2-h pulse of 25 nM RA or 1 µM RA followed by RNA-seq transcriptome analysis. Differential expression analysis of this dataset indicated that treatment with 25 nM RA, but not 1 µM RA, provided physiologically relevant findings. The 25 nM RA dataset yielded a cohort of previously known caudal RA target genes including Fgf8 (repressed) and Sox2 (activated), plus novel early RA signaling targets with nearby conserved RA response elements. Importantly, validation of top-ranked genes in vivo using RA-deficient Raldh2-/- embryos identified novel examples of RA activation (Nkx1-2, Zfp503, Zfp703, Gbx2, Fgf15, Nt5e) or RA repression (Id1) of genes expressed in the NMP niche or progeny. These findings provide evidence for early instructive and permissive roles of RA in controlling differentiation of NMPs to neural and mesodermal lineages.

overall_design: 3 samples were analyzed in duplicate: DMSO control (2 hours), 25 nM retinoic acid (2 hours), 1 µM retinoic acid (2 hours)

first: Thomas

last: Cunningham


title: Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder

city: Wien

first: Christoph

last: Dotter

address: Zimmermannplatz 10

institute: St. Anna Children’s Cancer Research Institute (St. Anna CCRI)

summary: Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to decreased levels of brain BCAAs, abnormal mRNA translation and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function.

overall_design: RNA-sequencing of cerebellum from 3 wildtype mice and 3 Slc7a5 KO mice

first: Dora

middle: C

last: Tarlungeanu

first: Gaia

last: Novarino


title: Transcription dynamics prevents RNA-mediated genomic instability through SRPK2-dependent DDX23 phosphorylation

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

summary: Genomic instability is frequently caused by nucleic acids structures formed during transcription termed R-loops. Despite their harmful potential, mechanisms that sense, signal and suppress these structures remain elusive. Here we report that oscillations in transcription dynamics are a major sensor of R-loops. We show that pausing of RNA polymerase II (RNA Pol II) initiates a signaling cascade whereby the serine/arginine protein kinase 2 (SRPK2) phosphorylates the DDX23 helicase culminating in the suppression of R-loops. We show that in the absence of either SRPK2 or DDX23, accumulation of R-loops leads to massive genomic instability revealed by high levels of DNA double-strand breaks (DSBs). Importantly, we found DDX23 mutations in several cancers and detected homozygous deletions of the entire DDX23 locus in 10 (17%) adenoid cystic carcinoma samples. Our results unravel molecular details of a novel link between transcription dynamics and RNA-mediated genomic instability that may play important roles in cancer development.

overall_design: To map the genomic occupancy of splicing factors SRPK1 and SRPK2, ChIP-seq was performed in MCF10A cells.

first: Sreerama

last: Sridhara

first: Silvia

last: Carvalho

first: Lina

last: Gallego-Paez

first: Maria

last: Carmo-Fonseca

first: Sérgio

last: de Almeida


title: Transcriptome Profiling of Human Primary Monocytes

city: Kuala Lumpur

first: Amir Feisal

last: Merican

state: Kuala Lumpur

address: University of Malaya

department: Institute of Biological Science

country: Malaysia

institute: University of Malaya

summary: We profiled the gene expression pattern of human primary monocyte, an essential component of the innate immune system, from healthy subjects using RNA-Seq analysis

overall_design: Total RNAs were extracted from classical (CD14++CD16−) monocytes of 6 healthy subjects. Deep poly-adenylated paired-end RNA-Seq was conducted on extracted RNAs.

first: Hoda

last: Mirsafian

first: Adiratna

last: Ripen

first: Thamilvaani

last: Manaharan

first: Saharuddin

middle: B

last: Mohamad

first: Amir


title: Changes in gene expression and RNA editing in Adar2-WT and Adar2-KO Mouse embryonic Fibroblasts (MEFs)

city: Urbana

first: Prasanth

last: Kannanganattu

state: IL

address: 601S Goodwin Avenue

department: Cell and Developmental Biology

institute: UIUC

summary:
Purpose: Measure gene expression and RNA editing changes in Adar-WT and Adar2-KO MEFs
Methods: Performed PolyA+ RNA-seq (single end, one sample each) of Adar2-WT and Adar2-KO MEFs
Results: Observed changes in editing and gene expression of several genes
Conclusion: Adar2 influences gene expression and editing of transcripts

overall_design: Gene expression and editing profiles of Adar2-WT and Adar2-KO were generated by PolyA+ RNA-seq (single end, one sample each), using Illumina HiSeq 2500

first: Kannanganattu

last: Prasanth


title: Genome models integrating chromatin contacts and nuclear lamin-genome interactions reveal implications of laminopathy-causing lamin mutations on genome architecture

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Processes shaping the 3-dimensional (3D) human genome remain elusive. We present Chrom3D, a user-friendly 3D whole-genome modeling software that dynamically simulates the radial positioning of topological domains (TADs) in the nucleus. We integrate Hi-C and lamin-associated domain (LAD) information to generate high-resolution ensembles of models that recapitulate single-cell TAD distribution. Chrom3D reveals dynamic TADs and TADs constitutively placed at the nuclear periphery or nuclear interior. TAD stability in these compartments is consistent with differences in TAD gene density and expression level. A- and B-type lamins as radial constraints differentially skew LAD distribution towards the nuclear interior or periphery. Predictions of radial LAD placement in model ensembles are validated by quantitative imaging. Chrom3D models reveal unexpected features of LAD regulation in the nuclear interior in cells from laminopathy patients with a LMNA mutation. Integration of radial positioning constraints in 3D genome models enables the study spatial gene regulation in disease contexts.

overall_design: HeLa cells (American Type Culture Collection; CCL-2) were cultured in MEM containing Glutamax (Gibco), 1% non-essential amino acids and 10% fetal calf serum. Fibroblasts (abbreviated as "HSF" in the sample lists)  were cultured in DMEM/F12/10% fetal calf serum, 10 ng/ml epidermal growth factor, 24 ng/ml basic fibroblast growth factor and 1% Penicillin-Streptomycin. Cultures were at passage 5-7 when used.   The dataset contains LMNA ChIP-seq data for 3 control normal  fibroblast samples (CTL-1, CTL-2, CTL-3) and 4 patient fibroblast samples all with the same LMNA p.R482W mutation (FPLD-p1, FPLD-p2, FPLD-p3, FPLD-p4). Chromatin from these samples was prepared by sonication (Bioruptor, Diagenode) after formaldehyde-crosslinking (15 min), and ChIPed using anti-lamin A/C antibodies (50 microgram antibody per 10e7 cells). ChIP DNA was eluted and isolated by phenol-chloroform isoamylalcohol extraction. The data also contains RNA -seq samples for the aforementioend 7 samples. The data also contain ChIP-sq samples from HeLa cells overexpressing Flag-tagged versions of LMNA wild-type (wt) and mutants (Flag-LMNA(R388P); Flag-LMNA(L647R)). For these samples, HeLa cells were transfected with the wt, R388P and L647R LMNA constructs; 24 h after transfection, cells were cross-linked with formaldehyde for 15 min, chromatin fragmented by sonicatioin (Bioruptor; Diagenode) and analysed by ChIP using anti-Flag antibodies (20 microgram antibody per 10e7 cells). ChIP DNA was eluted and isolated by phenol-chloroform isoamylalcohol extraction. For all ChIP samples, Illumina libraries were prepared from 12 ng DNA and sequenced on an Illumina HiSeq2500. The data also contains RNA -seq samples for the aforementioend 3 "CTL" and 4 "FLPD" samples. Total RNA was isolated using the Ambion TRIzol® Reagent RNA extraction kit (Life Technologies), quality checked using a BioAnalyzer 2100 and processed for library preparation. RNAseq libraries were prepared according to the Illumina protocol, and sequenced on an Illumina HiSeq2500 at the Norwegian Sequencing Center.

first: Jonas

last: Paulsen

first: Monika

last: Sekelja

first: Akshay

last: Shah


title: Single Cell Transcriptomics Reveals Multi-Dimensional Heterogeneity in Early Hematopoietic Precursors

city: New Haven

first: Sherman

last: Weissman

state: CT

address: 1 Gilbert street

institute: Yale University

summary: Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) are at the apex of the hematopoietic hierarchy. The relationship among HSC and MPPs, their heterogeneity and regulation are challenging subjects of continuing study. We performed single-cell RNA-seq on HSC and their immediate progeny MPP1 cells and compared results with bulk RNA-seq data from 18 hematopoietic populations, literature compilations of cell cycle-related genes, lineage specific genes, and putative quiescence genes. HSC and MPP1 were separated into several distinct subsets including actively cycling, quiescent and a putative hibernating subset. The quiescent cells preferentially expressed lymphoid precursor genes, while in actively cycling cells, the relative level of genes specific for individual lineages were differently correlated with stages of cell cycle. Granulocytic/monocytic and megakaryocytic precursor mRNA levels rose in early G1 phase, while erythroid specific expression showed selective augmentation at the G2/M phase. Stimulation of erythropoiesis shifted most HSCs into the active cell fraction without a disproportionate increase in the expression of early erythroid genes. Most transcription factors of the hematopoietic lineages were randomly expressed in a number of the early precursor cells but certain transcription factor mRNAs were detected only in very few cells. The latter genes may act as valves controlling the flow of differentiation. In summary we detect multi-level heterogeneity of the earliest hematopoietic precursor cells, demonstrate novel lineage specific cell cycle effects on the expression of precursor genes, and find that key regulatory genes for stages of differentiation can be identified from their silencing in stem cells.

overall_design: RNA samples from HSC, MPPs (both from normal and bled mice) and the other early precursors were obtained. Gene expression of those cells were analyzed with single cell- and bulk RNA-seq.

first: Jennifer

last: Yang

first: Yoshiaki

last: Tanaka

first: Xinghua

last: Pan

first: Montrell

last: Seay


title: Next Generation Sequencing Facilitates Quantitative Analysis of Piscor (control) and Nap1l1-shRNA expressed neural stem cell Transcriptomes

status: Public on Dec 21 2016

first: Jianwei

last: Jiao

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression. The goals of this study are to compare the different transcripts between control or Nap1l1 knockdown

overall_design: Methods:Neural stem cell isolated from E12 mice and cultured in vitro. RNA used for global transcriptome analysis were extracted from the lentivirus infected neural stem cells and sequenced by Hiseq 2500. Significantly differentially expressed genes were identified when we compared Normalized Reads Count between groups with p < 0.05 and |Log2FoldChange| > 1.

first: Huimin

last: Qiao


title: Gene expression profiling of pre-HPCs derived from CML-iPSCs

city: Bunkyo-City

first: Masashi

last: Miyauchi

state: Tokyo

address: 7-3-1 Hongo

department: Department of Hematology and Oncology

institute: Graduate School of Medicine,  The University of Tokyo

summary: Properties of cancer stem cells (CSC) involved in drug-resistance and relapse have significant effect on clinical outcome. Although tyrosine kinase inhibitors (TKIs) have dramatically improved survival of patients with chronic myelogenous leukemia (CML), TKIs have not fully cure CML due to TKI-resistant CML stem cells. Moreover, the relapse after discontinuation of TKIs has not been predicted in CML patients with best TKI-response. In our study, pre-hematoopoietic progenitor cells (pre-HPCs), a model of CML stem cells derived from CML-iPSCs identified a novel antigen of TKI-resistant CML cells. Even in the fraction reported as TKI-sensitive, the antigen+ cells showed TKI-resistance in CML patients. In addition, residual CML cells in patients with optimal TKI-response were concentrated in the antigen+ population.

overall_design: Imatinib induced gene expression in pre-HPCs from CML-iPSCs and normal-iPSCs and differentiated cells (DCs) from CML-iPSCs was measured at 6 hours after exposure to doses of 2.5 microM.  Three independent experiments were performed using different clones for each experiment.


title: A Homeostatic Shift Facilitates Endoplasmic Reticulum Proteostasis through Transcriptional Integration of Proteostatic Stress Response Pathways [ChIP-seq]

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

summary: Eukaryotic cells maintain protein homeostasis through the activity of multiple basal and inducible systems, which function in concert to allow cells to adapt to a wide range of environmental conditions. Although the transcriptional programs regulating individual pathways have been studied in detail, it is not known how the different pathways are transcriptionally integrated such that a deficiency in one pathway can be compensated by a change in an auxiliary response. One such pathway that plays an essential role in many proteostasis responses is the ubiquitin-proteasome system, which functions to degrade damaged, unfolded, or short half-life proteins. Transcriptional regulation of the proteasome is mediated by the transcription factor Nrf1. Using a conditional knockout mouse model, we found that Nrf1 regulates protein homeostasis in the endoplasmic reticulum (ER) through transcriptional regulation of the ER stress sensor ATF6. In Nrf1 conditional-knockout mice, a reduction in proteasome activity is accompanied by an ATF6-dependent downregulation of the endoplasmic reticulum-associated degradation machinery, which reduces the substrate burden on the proteasome. This indicates that Nrf1 regulates a homeostatic shift through which proteostasis in the endoplasmic reticulum and cytoplasm are coregulated based on a cell's ability to degrade proteins.

overall_design: Three individual samplings of wild-type MEFs immortalized with SV40 large T antigen. MEFs were treated with 10 μM of MG132 for 6 hr. ChIP-seq was performed using antibody to Nrf1.

first: Liam

last: Baird

first: Tadayuki

last: Tsujita

first: Ryo

last: Funayama

first: Takeshi

last: Nagashima

first: Keiko

last: Nakayama

first: Masayuki

last: Yamamoto


title: MRTF activates TEAD-YAP target gene expression

city: Cambridge

first: Tackhoon

last: Kim

state: Massachusetts

address: 500 Technology Square, NE47-221

institute: MIT

summary: Yes Associated Protein (YAP) and Myocardin Related Transcription Factor (MRTF) play similar roles and crosstalk in directing the transcriptional responses to chemical and physical extracellular cues. However the mechanism by which the two proteins crosstalk has been unclear. Here, we show MRTF family proteins bind YAP via a conserved PPXY motif that interacts with the YAP WW domain. This interaction allows MRTF to recruit NcoA3 to the TEAD-YAP transcriptional complex and potentiate its transcriptional activity. We show this interaction of MRTF and YAP is critical for LPA-induced cancer cell invasion in vitro and breast cancer metastasis to the lung in vivo. We also demonstrate the significance of MRTF-YAP binding in mechanotransduction by showing that the nucleo-cytoplasmic shuttling of MRTF induced by changes in the actin cytoskeleton constitutes the LATS-independent regulation of YAP activity. Our results provide clear evidence of crosstalk between MRTF and YAP independent of the LATS kinases that normally act upstream of YAP signaling and suggest a mechanism by which extracellular stimuli can coordinate physiological events downstream of YAP.

overall_design: To examine the impact of MRTFB overexpression on TEAD-YAP target genes, we overexpressed G-actin binding deficient MRTFB mutants (MRTFB dN) that are otherwise wildtype, YAP binding deficient (dPY), SRF binding deficient (YA), both-binding deficient (YA/dPY) in MCF-10A cells by retroviral infection and performed RNA sequencing experiment. We were able to identify genes whose expressions are activated by MRTFB overexpression, and genes whose expressions are depedent on MRTF-YAP or MRTF-SRF binding.

first: Daehee

last: Hwang

first: Jeong-Hwan

first: Jong-Hwan

first: Seon-Young

first: Dae-Sik

last: Lim


title: Proteogenomics-based identification of the repertoire of human MHC class I-associated peptides

city: Montreal

first: Diana

middle: Paola

last: Granados

state: Quebec

address: C.P. 6128, succursale Centre-ville

department: Medecine

country: Canada

institute: IRIC

summary: We have develop a proteogenomics-based approach for identification of human MHC class I-associated peptides, including those deriving from polymorphisms, mutations and non-canonical reading frames

overall_design:
RNA-seq of human EBV-infected B lymphoblasts derived from peripheral blood mononuclear cells from volunteers

Please note that GSM1641204 and GSM1641205 are reanalyzed and duplicated sample records of GSM1186811 and GSM1186812, respectively, for the convenient retrieval of the complete raw data from SRA

first: Claude

last: Perreault


title: Expression data for WT(Col0) and double mutants for AtTric1 (At3g49560) and AtTric2 (At5g24650) in Arabidopsis

city: Bundoora

first: Reena

last: Narsai

address: 5 Ring road

country: Australia

institute: La trobe University

summary: Transcriptomic differences in leaves and seedlings of double mutants for AtTric1 (At3g49560) and AtTric2 (At5g24650) compared to WT plants.

overall_design:
WT(Col0), double mutants for AtTric1 (At3g49560) and AtTric2 (At5g24650) were collected under normal, high light and low light conditions.
contributor: Plant Energy Biology


title: Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus

city: Livermore

first: Dan

last: Park

address: 7000 East Ave

department: BBTD

institute: Lawrence Livermore National Lab

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

sample_organism:
Caulobacter vibrioides
Caulobacter vibrioides NA1000

overall_design: Refer to individual Series


title: Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus [RNA-seq]

summary: Despite the well-known toxicity of uranium (U) to bacteria, little is known about how cells sense and respond to U.  The recent finding of a U-specific stress response in Caulobacter crescentus has provided a foundation for studying the mechanisms of U- perception in bacteria.  To gain insight into this process, we used a forward genetic screen to identify the regulatory components governing expression of the urcA promoter (PurcA) that is strongly induced by U.  This approach unearthed a previously uncharacterized two-component system, UzcRS, which is responsible for U-dependent activation of PurcA.  UzcRS is also highly responsive to zinc and copper, revealing a broader specificity than previously thought.  Using ChIP-seq, we found that UzcR binds extensively throughout the genome in a metal-dependent manner and recognizes a non-canonical DNA binding site.  Coupling the genome-wide occupancy data with RNA-seq analysis revealed that UzcR is a global regulator of transcription, predominately activating genes encoding proteins that are localized to the cell envelope; these include metallopeptidases, multidrug resistant efflux (MDR) pumps, TonB-dependent receptors and many proteins of unknown function.  Collectively, our data suggest that UzcRS couples detection of U, Zn and Cu with a novel extracytoplasmic stress response.

overall_design: WT and uzcR mutant strains assayed in the presence and absence of Zn in triplicate

first: Yongqin

last: Jiao


title: Genome-wide maps of N_NUP98 and NUP98-TOP1 and MLL1 co-bound targets and their chromatin state in NUP98 fusion transformed cells.

city: New York

first: Haiming

last: Xu

state: NY

address: 1275 York Avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: By performing biotin-mediated chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) for two different NUP98 fusions, we defined the genome-wide direct binding sites of NUP98-TOP1 or N-NUP98. To test whether NUP98 fusions and MLL1 were recruited to the same region of Hox genes promoters, MLL1 ChIP-seq analysis was carried out in murine NUP98-HOXA9 transformed cells using an anti-MLL1n antibody (MO435). In agreement with our results showing that NUP98 fusions interacts with MLL1 in NSL/MLL1 complex, MLL1 binding targets significantly overlap with that of N-NUP98 or NUP98-TOP1 at promoter region and gene body region.  In summary, our results confirmed that NUP98 fusions and MLL1 are recruited to the same Hox loci, supporting the notion of the association between NUP98 fusions and NSL/Mll1 complex, suggesting that the recruitment of NUP98 fusions to the Hox gene loci maybe through MLL1.

overall_design: To define the binding targets of NUP98 fusion proteins, and the co-bound sites with MLL1 using NUP98 fusion transformed mouse bone marrow LSK cells.

first: Scott

middle: A

last: Armstrong


title: Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus [ChIP-seq]

overall_design: Mapping of UzcR occupancy of in the genome of Caulobacter crescentus NA1000 in PYE following spike-in with or without Zn for 1 hour.  Immunoprecipitated DNA in wild type strain compared to Immunoprecipitated DNA in ΔuzcR strain.


title: RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature

city: Bethesda

first: Coralie

last: Viollet

state: MD

address: 10 Center Dr

institute: NIH/NCI


title: Reversible methylation of m6Am in the 5′ cap controls mRNA stability

city: Heidelberg

first: Jan

last: Mauer

state: BW

address: Im Neuenheimer Feld, 583

country: Germany

institute: BioMed X Innovation Center

summary: Internal bases in mRNA can be subjected to modifications that influence the fate of mRNA in cells. One of the most prevalent modified bases is found at the 5′ end of mRNA, at the first encoded nucleotide adjacent to the 7-methylguanosine cap. Here we show that this nucleotide, N6,2′-O-dimethyladenosine (m6Am), is a reversible modification that influences cellular mRNA fate. Using a transcriptome-wide map of m6Am we find that m6Am-initiated transcripts are markedly more stable than mRNAs that begin with other nucleotides. We show that the enhanced stability of m6Am-initiated transcripts is due to resistance to the mRNA-decapping enzyme DCP2. Moreover, we find that m6Am is selectively demethylated by fat mass and obesity-associated protein (FTO). FTO preferentially demethylates m6Am rather than N6-methyladenosine (m6A), and reduces the stability of m6Am mRNAs. Together, these findings show that the methylation status of m6Am in the 5′ cap is a dynamic and reversible epitranscriptomic modification that determines mRNA stability.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Seq was performed on HEK293T cells transfected with scrambled siRNA, or siRNA targeting FTO or ALKBH5, wild-type HEK293T cells or HEK293T cells with CRISPR-inactivated DCP2, HEK293T cells transfected with FLAG-vector or NES-FTO-vector (both untreated and 6h actinomycin D treated) and wildtype and Fto knockout mouse liver. Furthermore, miCLIP was performed on HEK293T cells as previously described (see GSE63753). For RNA-Seq, 2-3 biological replicates were used for each experiment and condition. For miCLIP, 6 biological replicates were used and combined into a single fastq file.

first: Samie

last: Jaffrey

first: Megerditch

last: Kiledjian


title: A transcription factor pulse can prime chromatin for heritable transcriptional memory

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

institute: Ecole Normale Superieure


title: KSHV Infection Mimics the Hypoxic Response Based on Next-Generation Sequencing [mRNA-Seq]

summary:
Purpose: Kaposi’s sarcoma associated-herpesvirus (KSHV) causes several hyperproliferative disorders, including Kaposi’s sarcoma, primary effusion lymphoma and multicentric Castleman’s disease. KSHV encodes for a number of microRNAs (miRNAs), and KSHV infection can affect the expression of cellular miRNAs. Hypoxia has been shown to induce KSHV reactivation, directly induce several KSHV lytic genes, and also induce the most abundant latent viral protein, LANA.  Also, several KSHV proteins can stabilize and increase the cellular levels of hypoxia-inducible factor (HIF-1α). However, the degree to which hypoxic pathways are utilized by KSHV has yet to be determined.
Methods: We investigated the interplay between hypoxia and KSHV infection by comparing the 31effects of hypoxia and KSHV infection on miRNA and mRNA expression, and by examining the 32effects of hypoxia on uninfected and KSHV-infected cells. This was accomplished using next-33generation sequencing (NGS), qRT-PCR, Taqman assays, and pathway analysis.
Results: NGS analysis of human mRNAs revealed striking similarities (~34%) between the transcriptomic response to hypoxia and the transcriptomic response to KSHV infection. Additionally, hsa-miR-210, a key hypoxia-inducible miRNA with pro-angiogenic and anti-apoptotic properties, was found significantly up-regulated by both KSHV infection and hypoxia using Taqman assays. Finally, KSHV infected cells differed somewhat in their response to hypoxia compared to KSHV-uninfected controls.
Conclusions: These results demonstrate that KSHV harnesses a part of the hypoxic cellular response and induces miR-210 up-regulation. The understanding of how these miRNAs, genes and pathways are regulated by HIF-1α and KSHV infection are essential to a better understanding of the biology of KSHV-associated diseases.

overall_design: 6 samples analyzed. Two experimental conditions: hypoxic uninfected cells (SLK cells) and hypoxic chronically KSHV-infected cells (SLKK cells) (n=3). Two sequencing platforms: microRNA-Seq and mRNA-Seq.

first: Viollet

last: Coralie

first: Yarchoan

last: Robert

first: Ragoussis

last: Jiannis

first: Reczko

last: Martin


title: Notch Activation Confers Enhanced Lymphoid Potential in Murine ESC/iPSC-derived HSC and Reconstitutes Adaptive Immunity In Vivo [RNA-Seq]

city: Baltimore

first: Patrick

last: Cahan

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: Hematopoietic stem cell (HSC) transplantation has the potential to cure blood disorders but is limited by donor availability. Hence innovative approaches to engineer HSC are critically needed. HoxB4 over-expression in mouse embryonic stem cell-derived HSC (ESC-HSC) confers long-term engraftment, yet lacks efficient lymphogenesis. Transcriptome comparison of ESC-HSC versus embryo-derived HSC showed that ESC-HSC are deficient in expression programs activated by Notch. Therefore, we aim to improve ESC-HSC by further providing Notch signals through Notch1 intra-cellular domain transgene activation or by ligand stimulation. Here, we report that Notch-enhanced ESC-HSC (nESC-HSC) confer clonal multipotentiality with robust lymphopoiesis that endows adaptive immunity. Notably, nESC-HSC further evolve to a hybrid cell-type co-expressing gene regulatory networks of hematopoietic stem/progenitor cells and differentiated lineages at single-cell level that accounts for multipotentiality. Our work reveals a proof-of-concept model of HSC engineering by assembling self-renewing factor and lineage-guiding pathway into one product-cell that functionally recapitulate HSC in vivo.

overall_design: The gene expression of murine hematopoietic stem cells, ESC, and HSC-like cells derived from differentiation of embryonic stem cells and subsequently transplanted were determined by single cell RNA-Seq.

first: Yi-Fen

last: Lu


title: Transcriptome sequencing of GRK6 knockout HSCs and CLPs

city: Shanghai

first: Qiumin

last: Le

address: 130 Dong'an Road

institute: Fudan University

summary: WT and GRK6-/- Lin-c-kit+sca-1+ cells (hereafter referred to as HSC) as well as CLP (Lin-c-kit+sca-1+Il-7Ra+) with pooled cDNA library of 13-15 sorted and individually amplified cells from 3-4 mice were sequenced.

overall_design: pooled cDNA libraries from WT and GRK6-/- HSCs and CLPs were sequenced.


title: A protein interaction network of mental disorder factors in neural stem cells

city: Rotterdam

first: Raymond

last: Poot

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: Erasmus MC

summary: Mental disorders (MDs) such as intellectual disability (ID), autism spectrum disabilities (ASD) and schizophrenia have a strong genetic component. Recently, many gene mutations associated with these MDs have been identified by high-throughput sequencing technology. A substantial fraction of these mutations is in genes encoding proteins involved in transcriptional regulation. It is unclear whether different MD-associated transcriptional regulators act in the same gene regulatory network. Such information is important to appreciate the underlying etiology of an MD and the molecular relatedness of different MDs. Physical interaction between transcriptional regulators is a strong predictor for their cooperation in gene regulation. Here, we purified several MD-associated transcriptional regulators from neural stem cells, identified their interaction partners by mass spectrometry and assembled a protein interaction network containing over 200 proteins. The interaction network is enriched for protein factors associated with ID, ASD or schizophrenia and enriched for protein factors encoded by evolutionary constrained genes. Our network thereby provides molecular connections between established MD factors and a discovery tool for novel MD genes. We identified interactions between many transcriptional regulators with a different MD association. We show that network factors preferentially co-localize on the genome and cooperate in the regulation of disease-relevant genes to explain overlapping phenotypes in different syndromes. Our results suggest that the observed transcriptional regulators associated with ID, schizophrenia or ASD are part of the same transcriptional network. We find that the severity of mutations in network factors increased with the severity of the associated MD, suggesting that the level of disruption of a common transcriptional network affects mental disorder outcome.

overall_design: Examination of genome wide binding of Tcf4, Olig2, Npas3 and Smad4. RNA-seq before and after knockdown of Tcf4.

first: Johannes

last: Brandsma

first: Maaike

middle: J

last: Moen


title: Notch Activation Confers Enhanced Lymphoid Potential in Murine ESC/iPSC-derived HSC and Reconstitutes Adaptive Immunity In Vivo