title: RNA-seq Analysis of VRF1 and VRF2-dependent Genes in the mycelia of Magnaporthe oryzae 70-15

summary:
Purpose: The goals of this study are to find out the genes regulated directly or indirectly by C2H2 transcription factors Vrf1 and Vrf2 by RNA-seq and to evaluate the similarities and differences in gene regulation mechanisms of Vrf1 and Vrf2 in the rice blast fungus
Methods: Mycelial mRNAs of the wild type strain 70-15, Δvrf1 and Δvrf2 incubated in H2O at 25˚C for 4 h, in triplicate independently for each strain, were extracted and isolated by RNeasy Plant mini kit (QIAGEN) and AMPure XP beads (Beckman). RNA-sequencing libraries were constructed using NEBNext RNA sample preparation kit (NEB). Samples were sequenced in a 1 x 100 nt way on Illumina Hiseq2500 instrument using TruSeq PE Cluster Kit v3 - cBot - HS (Illumina) and TruSeq SBS Kit v3-HS (Illumina).The M. oryzae genome database (MG8) (www.broadinstitute.org) was used as a reference gene database. Genome-wide transcript levels of genes were quantified in fragments per kilobase of exon model per million mapped reads (FPKM) (Trapnell 2010). Gene Ontology (GO) enrichment analyses for differentially expressed genes were performed using hypergeometric test with topGO, and p-values were adjusted with Bonferroni for multiple testing (Alexa 2006). And we selected FDR < 0.05 as enrichment terms.
Results and Conclusions: We identified 401 genes regulated by VRF1 and 1045 genes by VRF2 through RNA-seq.

overall_design: Mycelial mRNA profiles of wild type strain 70-15 (WT), Δvrf1 and Δvrf2 incubated in H2O for 4 h were generated, in biologic triplicate, by Illumina Hiseq2500 in a 1 x 100 nt way

first: Li

middle: L

last: Zhang


title: Sex-specific chromatin accessibility profiling in human PBMCs

status: Public on Apr 11 2016

city: Stanford

first: Stephen

last: Montgomery

address: 300 Pasteur Lane

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We used ATAC-seq to profile the chromatin accessibility differences between sexes. We investigated the chromatin states of the PBMCs of twenty individuals, with an equal distribution of males and females, controlled for age (18-45 years old) and ethnicity (Caucasian).

overall_design: We examined chromatin accesibility using ATAC-seq in the PBMCs of twenty individuals.

first: Kimberly

last: Kukurba


title: FOXN3 regulates hepatic glucose utilization

status: Public on Apr 10 2016

city: Salt Lake City

first: Santhosh

last: Karanth

state: UT

address: 15 North 2030 East, Rm No. 3460

department: Molecular Medicine Program

institute: University of Utah School of Medicine

type: Expression profiling by high throughput sequencing

summary: We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 (in the liver) and non-transgenic siblings

overall_design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings

first: Jonathon

middle: T

last: Hill

first: Amnon

last: Schlegel


title: Analyzing the Transcriptomes of Two Quorum-Sensing Controlled Transcription Factors,   RcsA and LrhA, Important for Pantoea stewarti Virulence

city: Blacksburg

first: Alison

middle: Kernell

last: Burke

state: VA

address: 970 Washington St SW

department: Biological Sciences

institute: Virgina Tech

summary:
The Gram-negative proteobacterium Pantoea stewartii subsp. stewartii causes wilt disease in corn plants.  Wilting is primarily due to bacterial exopolysaccharide (EPS) production that blocks water transport in the xylem during the late stages of infection.  EsaR, the master quorum-sensing (QS) regulator in P. stewartii, modulates EPS levels.  At low cell densities EsaR represses or activates expression of a number of genes in the absence of its acyl homoserine lactone (AHL) ligand.  At high cell densities, binding of AHL inactivates EsaR leading to derepression or deactivation of its direct targets. Two of these direct targets are the
key transcription regulators RcsA and LrhA, which in turn control EPS production and surface motility/adhesion, respectively.  In this study, RNA-Seq was used to further examine the physiological impact of deleting the genes encoding these two second-tier regulators.  Quantitative reverse transcriptase PCR (qRT-PCR) was used to validate the regulation observed in the RNA-Seq data. A GFP transcriptional fusion reporter confirmed the existence of a regulatory feedback loop in the system between LrhA and RcsA.  Plant virulence assays carried out with rcsA and lrhA deletion and complementation strains demonstrated that both
transcription factors play roles during establishment of wilt disease in corn. These efforts further define the hierarchy of the QS-regulated network controlling plant virulence in P. stewartii.

overall_design: RNA-Seq on three strains harvested and sequenced in duplicate.  Two mutant strains compared to the wild type strain to monitor changes in expression

middle: K

first: Duy

middle: A

last: Duong

first: Roderick

middle: V

last: Jensen

first: Ann

middle: M

last: Stevens


title: Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Chemical inhibition of Histone Deacetylases 1 and 2 induces fetal hemoglobin through activation of Gata2

city: Boston

first: Jeff

last: Shearstone

state: MA

address: 70 Fargo Street

department: Biology

institute: Acetylon Pharmaceuticals

summary: This SuperSeries is composed of the SubSeries GSE60791 and GSE60792.


title: Chronic haloperidol effects on gene expression in mouse [RNA-seq]

city: chapel hill

first: Yunjung

last: Kim

state: North Carolina

address: 120 Mason farm road

institute: UNC at Chapel Hill

summary: We evaluate the effects of chronic administration of antipsychotic haloperidol versus placebo in male, 8-week old, C57BL/6J mice.

overall_design: We used RNA-seq to study gene expression changes after haloperidol treatment in striatum samples of 28 mice (16 haloperidol-treated mice, 12 placebo-treated mice).


title: HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells

city: Durham

first: Christopher

last: Frank

state: NC

address: 101 Science Dr.

institute: Duke University

summary: We used the myelogenous leukemia line K562 as a model of HDACi-induced differentiation to investigate chromatin accessibility (DNase-seq) and expression (RNA-seq) changes associated with this process. We identified several thousand specific regulatory elements (~10% of total DHS sites) that become significantly more or less accessible with sodium butyrate or suberanilohydroxamic acid (SAHA) 72-hour treatments. Most of the differential DNase-hypersensitive (DHS) sites display hallmarks of enhancers; including being enriched for non-promoter regions, associated with nearby gene expression changes, and capable of increasing luciferase reporter expression in K562 cells. Differential DHS sites were enriched for key hematopoietic lineage transcription factor motifs, including SPI1 (PU.1), a known pioneer factor. We found PU.1 becomes up-regulated and increases binding at opened DHS sites by ChIP-seq with HDACi treatment, but show that increased PU.1 protein levels alone are sufficient for only modest increases in chromatin accessibility. PU.1 knockdown by shRNA failed to block the HDACi-induced chromatin accessibility and expression changes in K562, suggesting factors other than PU.1 are responsible for establishment of active enhancers in the HDACi induced differentiation process.

overall_design: K562 +/- NaBut for 72 hr. contains 3 replicates for Dnase-seq and RNA-seq. K562 +/- SAHA for 72 hr. contains 3 replicates for Dnase-seq and 2 replicates for RNA-seq. PU.1 overexpression in K562 cells followed by 2 replicates of Dnase-seq. PU.1 depletion in K562 cells followed by 72 hr. SAHA treatment contains 2 replicates per shRNA (2 shRNAs used). PU.1 ChIP-seq in K562 contains 3 replicates for SAHA treatment plus input controls.

first: Dinesh

last: Manandhar

first: Raluca

last: Gordân

first: Gregory

middle: E

last: Crawford


title: Chronic haloperidol effects on gene expression and chromatin accessibility in mouse brain


title: Chronic haloperidol effects on open chromatin accessibility in mouse [DNase-seq]

overall_design: We used DNase-seq to study chromatin landscape changes after haloperidol treatment in striatum samples of 7 mice (3 haloperidol-treated mice, 4 placebo-treated mice).


title: The SET Domain Proteins SUVH2 and SUVH9 Are Required for Pol V Occupancy at RNA-Directed DNA Methylation Loci

status: Public on Apr 09 2016

city: Beijing

first: Yongqiang

last: Li

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

summary:
Small RNA-induced transcriptional silencing at transposable elements and other DNA repeats is an evolutionarily conserved mechanism in plants, fungi, and animals. In Arabidopsis thaliana, an RNA-directed DNA methylation pathway is involved in transcriptional silencing. Noncoding RNAs produced by the plant-specific DNA-dependent RNA polymerase V are required for RNA-directed DNA methylation. A chromatin-remodeling complex was previously demonstrated to be required for the occupancy of DNA-dependent RNA polymerase V at RNA-directed DNA methylation loci.
Our results suggest that two putative histone methyltransferases are inactive in their enzymatic activity and act as adaptor proteins to facilitate the recruitment of DNA-dependent RNA polymerase V to chromatin by associating with the chromatin-remodeling complex. In combination with previous studies, we propose that the inactive histone methyltransferases bind to methylated DNA, thereby linking DNA methylation to Pol V transcription at RNA-directed DNA methylation loci.

overall_design: Compare the mRNA profiles of 2-week-old seedlings materials of mutants (nrpe1, suvh2suvh9 and dms3) to wild type Col by Illumina suquencing;

first: Xin

middle: J

last: He

first: Zhang

middle: W

last: Liu


title: Integrin signaling regulates YAP/TAZ to control skin homeostasis

city: London

first: Barry

last: Thompson

state: London

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: The Francis Crick Institute

summary: The skin is a squamous epithelium that is continuously renewed by a population of basal layer stem/progenitor cells and can heal wounds. Here, we show that the transcription regulators YAP and TAZ localise to the nucleus in the basal layer of skin and are elevated upon wound healing. Skin-specific deletion of both YAP and TAZ in adult mice slows proliferation of basal layer cells, leads to hair loss and impairs regeneration after wounding. Contact with the basal extracellular matrix and consequent integrin-Src signalling is a key determinant of the nuclear localisation of YAP/TAZ in basal layer cells and in skin tumours. Contact with the basement membrane is lost in differentiating daughter cells, where YAP and TAZ become mostly cytoplasmic. In other types of squamous epithelia and squamous cell carcinomas, a similar control mechanism is present. By contrast, columnar epithelia differentiate an apical domain that recruits CRB3, Merlin (also known as NF2), KIBRA (also known as WWC1) and SAV1 to induce Hippo signalling and retain YAP/TAZ in the cytoplasm despite contact with the basal layer extracellular matrix. When columnar epithelial tumours lose their apical domain and become invasive, YAP/TAZ becomes nuclear and tumour growth becomes sensitive to the Src inhibitor Dasatinib.

overall_design: mRNA profiles of control siRNA transfected and YAP1 siRNA transfected cells were generated by deep sequencing, in triplicate, using an Illumina HiSeq 2500 instrument in two human cell lines, A431 and HaCAT. Complimentary to that, mRNA profiles of cells transfected with empty vector or a  constitutively active YAP1 mutant protein (YAP-S5A) in two human cell lines, A431 and HaCAT.

first: Ahmed

last: Elbediwy

first: Zoe

middle: I

last: Vincent-Mistiaen

first: Bradley

last: Spencer-Dene

first: Richard

last: Stone

first: Stefan

last: Boeing

first: Stefanie

last: Wculek

first: Julia

last: Cordero

first: Ee

middle: H

last: Tan

first: Rachel

last: Ridgway

first: Val

middle: G

last: Brunton

first: Erik

last: Sahai

first: Holger

last: Gerhardt

first: Axel

last: Behrens

first: Ilaria

last: Malanchi

first: Owen

last: Sansom


title: Gene expression profiles in growth-inhibition rice seedling implanted by the low-energy N+ beam

city: Luoyang

first: Huiyuan

last: Ya

state: Henan

address: 71# Longmen Road

department: Life science Department

institute: Luoyang Nornal University

summary: Knowledge of genes expression related to the growth-inhibition biological effects induced by low-energy N+ in plant. This study investigated the differentially expressed genes (DEGs) related to  the growth-inhibition biological effects induced by low-energy N+ in plant by RNA-seq. Ion fluences (40Kev, curren intensity=3mA) of 1×1017N+/cm2，2×1017N+/cm2，4×1017N+/cm2，6×1017N+/cm2，8×1017N+/cm2  were used in the ion-implanted experiments. Biological effects with growht-inhibition were arised from the samples implanted by the ion fluences of 6×1017N+/cm2，8×1017N+/cm2  because of the inhibition of seedling height and root length. We sequenced mRNA from these damaged rice seedlings and others. We identified 776 transcripts as reliable DEGs at the growth inhibition sample campared with the control.The pathway enrichment analysis of these 776 DEGs showed that pathway of photosynthesis - antenna proteins was down-regulated. Meanwhile transcription factor analysis showed that genes related to  AUX/IAA were also down-regulated. This study were contributed to a better understanding of molecular events responsible for adaption to the implantation of low-energy ion beam in plant.

overall_design: Examination of mRNA levels in  rice seedlings were sampled after 96 hours-cultivated rice seeds implanted by N+ beam with different fluences

first: Qiufang

last: Chen

first: Weidong

last: Wang

first: Yanwei

last: Cheng

first: Gongyong

last: Qin

first: Gulei

last: Jin


title: Peripheral Blood Mononuclear Cells (PBMC) Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis (JIA)

status: Public on Apr 08 2016

city: BUFFALO

first: JAMES

last: JARVIS

state: NY

address: 875 ELLICOTT STREET 8026

department: PEDIATRIC

institute: UNIVERSITY AT BUFFALO

summary:
Aim: To discovery biomarkers in JIA base on gene expression from RNA sequencing on PBMC
Method: Paired-end Ilumina sequencing to capture gene expression of PBMC from JIA individuals and healthy controls
Results:sample heterogeneity makes RNA sequencing on PBMC unsuitable as a first-step method for screening biomarker candidates in JIA

overall_design: RNA sequencing on PBMC of 3 independent cohorts consist of JIA patients and healthy controls

first: Lai

middle: P

last: Wong

first: Kaiyu

last: Jiang

first: Yanmin

first: Teresa

last: Hennon

first: Lucy

last: Holmes

first: Carol

last: Wallace

first: James

last: Jarvis


title: Chronic haloperidol effects on open chromatin accessibility in mouse [ATAC-seq]

first: Yunjung

last: Kim

overall_design: We used ATAC-seq to study chromatin landscape changes after haloperidol treatment in striatum samples of 14 mice (7 haloperidol-treated mice, 7 placebo-treated mice).


title: The Forkhead box transcription factor FOXM1 is required for the maintenance of cell proliferation and protection against oxidative stress in human embryonic stem cells

city: Hong Kong

first: Kwok Ming

last: YAO

address: L3-69, Laboratory Block, 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: Human embryonic stem cells (hESCs) exhibit unique cell cycle structure, self-renewal and pluripotency. The Forkhead box transcription factor M1 (FOXM1) is critically required for the maintenance of pluripotency in mouse embryonic stem cells and mouse embryonal carcinoma cells, but its role in hESCs remains unclear. Here, we show that FOXM1 expression was enriched in undifferentiated hESCs and was regulated in a cell cycle-dependent manner with peak levels detected at the G2/M phase. Expression of FOXM1 did not correlate with OCT4 and NANOG during in vitro differentiation of hESCs. Importantly, knockdown of FOXM1 expression led to aberrant cell cycle distribution with impairment in mitotic progression but showed no profound effect on the undifferentiated state. Interestingly, FOXM1 depletion sensitized hESCs to oxidative stress. Moreover, genome-wide analysis of FOXM1 targets by ChIP-seq identified genes important for M phase including CCNB1 and CDK1, which were subsequently confirmed by ChIP and RNA interference analyses. Further peak set comparison against a differentiating hESC line and a cancer cell line revealed substantial difference in the genomic binding profile of FOXM1 in hESCs. Taken together, our findings provide the first evidence to support FOXM1 as important regulator of cell cycle progression and defense against oxidative stress in hESCs.

overall_design: Examination of genomic binding profile of FOXM1 in human embryonic stem cells by ChIP-seq, using Illumina HiSeq 2000

first: Chun

last: Kwok

first: Yiming


title: Whole transcriptome sequencing identifies increased CXCR2 expression in PNH granulocytes

city: Shenzhen

first: Wangmin

last: Qiao

address: Building NO.7, BGI Park, No.21 Hongan 3rd Street, Yantian District

institute: BGI

summary: To clarify the selective advantage of the GPI-AP- cells in paroxysmal nocturnal hemoglobinuria (PNH)  patients, RNA-seq was applied to examine functional effects of the PIG-A mutation in human granulocytes.

overall_design: RNA seq, 2 PNH patiant's GPI-AP-  granulocyte,2 PNH patiant's GPI-AP+  granulocyte, 3 Healthy granulocyte

first: Kohei

last: Hosokawa

first: Sachiko

last: Kajigaya

first: Keyvan

last: Keyvanfar

first: Yanling

last: Xie

first: Angelique

last: Biancotto

first: Danielle

last: Townsley

first: Xingmin

last: Feng

first: Neal

middle: S

last: Young


title: The transcriptional repressor Gfi1 inhibits the induction of Th1 program in activated CD4 T cells

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University


title: ChIP-seq of erythroid progenitors treated with vehicle or the HDAC1/2-selective inhibitor ACY-957

first: Jeff

last: Shearstone

summary: Establish the DNA binding profiles of HDAC1, HDAC2 and Gata2 in erythroid progenitors derived from human CD34+ bone marrow cells.  Determine the effects of HDAC1/2 inhibition on the DNA binding profiles of Gata2.

overall_design: 5 samples in total. Cells have either been treated with vehicle or ACY-957 (an HDAC1/2 selective inhibitor) prior to immunoprecipitation. Sample 1 is chromatin from vehicle treated cells immunoprecipitated with anti-HDAC1 antibody. Sample 2 is chromatin from vehicle treated cells immunoprecipitated with anti-HDAC2 antibody. Sample 3 and 4 are chromatin from vehicle treated or ACY-957 treated cells immunoprecipitated with anti-Gata2, respectively. Sample 5 is the input sample, which is a mix of non-immunoprecipitated chromatin from vehicle treated and ACY-957 treated cells.

first: Jeffrey

middle: R

first: Olga

last: Golonzhka

first: Apurva

last: Chonkar

first: David

last: Tamang

first: John

last: van Duzer

first: Simon

last: Jones

first: Matthew

middle: B

last: Jarpe


title: CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq

city: Haifa

first: Naftalie

last: Senderovich

state: International

address: Technion city, Faculty of biology

country: Israel

institute: Technion - Israel Institute of Technology

summary: Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, a modified version of our CEL-Seq method, with three-fold higher sensitivity, lower costs, and less hands-on time. We also implemented CEL-Seq2 on Fluidigm’s C1 system, thereby providing its first single-cell, on-chip barcoding method, and detected gene expression changes accompanying the progression through the cell cycle in mouse fibroblast cells. We also compare with Smart-Seq to demonstrate CEL-Seq2’s increased sensitivity relative to other available methods. Collectively, the improvements make CEL-Seq2 uniquely suited to single-cell RNA-Seq analysis in terms of economics, resolution, and ease of use

sample_organism:
Caenorhabditis elegans
Mus musculus

platform_organism:
Caenorhabditis elegans
Mus musculus

overall_design: Single mouse dendritic and fibroblast cells were analysed for comaprison of CEL-Seq2 to CEL-Seq and Smart-Seq on C1. C. elegans totat RNA was used to calibrate and optimze the new CEL-Seq2 protocol.

first: Tamar

last: Hashimshony

first: Itai

last: Yanai


title: In silico lineage tracing through single cell transcriptomes identifies a neural stem cell population in planarians

city: Portland

first: Bret

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: Background: The planarian, Schmidtea mediterranea, is a master regenerator with a large adult stem cell compartment. The lack of transgenic labeling techniques in this animal have hindered the study of lineage progression and has made understanding the mechanisms of tissue replacement during regeneration a challenge. However, recent advances in single cell transcriptomics and analysis methods may allow for the discovery of novel cell lineages as differentiation progresses from stem cell to terminally differentiated cell. Here we apply Waterfall analysis and single cell transcriptomics to identify adult stem cells belonging to specific cellular lineages and identify novel candidate genes for future in vivo lineage studies. Results: Single-cell-RNA-deep sequencing (scRNAseq) of 168 purified single stem and progeny cells from the planarian head was used to identify a molecularly distinct, neural stem cell population (νNeoblasts). Hierarchical clustering revealed 10 distinct subgroups and pseudotime analysis with Waterfall predicted a neural lineage trajectory as well as a novel alternative lineage. Previously undescribed neural lineage genes identified in silico were characterized in vivo and were shown to have neural expression patterns. Using the predicted νNeoblast markers, we demonstrate that a novel piwi-2+piwi-1lo stem cell population exists adjacent to the brain and immediately takes up BrdU. Conclusions: scRNAseq coupled with in silico lineage analysis offers a new approach for studying lineage progression in planarians. The lineages identified here were extracted from a highly heterogeneous dataset with minimal prior knowledge of planarian lineages, demonstrating that lineage purification by transgenic labelling is not a prerequisite for this approach. The identification of the νNeoblast lineage demonstrates the usefulness of the planarian system for computationally predicting cellular lineages in an adult context coupled with in vivo verification.

overall_design: Cells from the heads of 30 animals were FACS sorted to obtain 96 single X1s and 72 single X2s and cDNA was prepared from poly-A+ mRNA for each cell using Smartseq2 and deep sequenced to a depth of 5M reads, as illustrated in Figure 1A of the manuscript. cDNA from two X1 and 1 X2 bulk tube controls of 200 cells each was prepared using the same protocol and sequenced to a depth of 10-20M reads each.

first: Alyssa

last: Molinaro


title: Transcription profiling of zebrafish fin regeneration

city: Madison

first: Junsu

last: Kang

state: WI

address: 1111 Highland Avenue, Room 4451, WIMR II, Kang lab, CRB

department: Department of Cell and Regenerative Biology

institute: University of Wisconsin - Madison

summary: We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins

overall_design: Examination of whole fin transcriptional profiles from regenerating fins (2 pools of 10 fins) and uninjured fins (2 pools of 10 fins)

first: Gregory

last: Nachtrab

first: Kenneth

last: Poss


title: Gene signature in sessile serrated polyps identifies colon cancer subtype

first: Integrative

last: Bioinformatics

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

summary: RNA sequencing analysis of gene expression in serrated colon polyps, uninvolved colon and control colon

overall_design: 86 colon RNA sequencing datasets (21 sessile serrated adenomas/polyps, 10 hyperplastic polyps, 10 adenomatous polyps, 21 uninvolved colon, 20 control colon and 4 colon cancer)

first: Priyanka

last: Kanth

first: Curt

last: Hagedorn

first: Don

last: Delker


title: Characterization of chromatin accessibility through the DNaseI hypersensitivity assay in breast cancer cells treated with either Dex or E2

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: The estrogen receptor (ER), glucocorticoid receptor (GR), and forkhead box protein 1 (FoxA1) are significant factors in breast cancer progression.  FoxA1 is well-established as a pioneer factor for steroid receptor recruitment to chromatin.  Here we show that ER and GR have the ability to alter the genomic response of FoxA1 to specific binding sites within the genome.  These findings alter the classical understood mechanism of FoxA1 establishing a dynamic transcription factor that can be regulated by hormones.

overall_design: We examined the ER and GR mediated affects on FoxA1 binding patterms

first: Erin

last: Swinstead

first: Gordon

middle: L

last: Hager


title: Transcription factor ATF4 directs basal and select gene expression in the unfolded protein response and cholesterol metabolism in liver

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: IN

address: 635 Barnhill Dr

department: Biochemistry and Molecular Biology

institute: IU School of Medicine

summary: We report the physiological role of ATF4 within mouse liver, under basal and ER stress conditions.  With three mice per group, and approximately 30 million reads per sample, we obtained genome-wide role of ATF4 within the liver.  We find ATF4 is responsible for a small subset of ER stress genes, and larger than previously thought basal subset.

overall_design: Examination of the loss of ATF4 basally and during 6 hour Tunicamycin induced ER stress

first: Michael

last: Fusakio

first: Jeffrey

last: Willy

first: Yongping

last: Wang

first: Emily

middle: T

last: Mirek

first: Rana

last: Al Baghdadi

first: Christopher

last: Adams

first: Tracy

last: Anthony


title: Modulation of tissue repair by regeneration enhancer elements.

first: Ravi

last: Karra

address: 464 Nanaline Duke, 307 Research Drive

department: Cell Biology

institute: Duke

summary: We compared transcriptional and chromatin profiles of regenerating zebrafish hearts following genetic ablation with profiles from uninjured zebrafish hearts.

overall_design:
Examination of whole heart transcriptional profiles from ablated hearts (2 pools of 10 hearts) and uninjured hearts (2 pools of 10 hearts).

Examination of differential H3K27Ac marks following genetic ablation of cardiomyocytes (regenerating hearts) and uninjured hearts.


title: 4sUDRB-seq of human PA1 cells, undifferentiated H9 cells and H9 differentiated FB neurons

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: We have optimized the metabolic tagging of newly transcribed RNAs by 4-thiouridine (4sU) to identify newly-transcribed (nascent) circRNAs from human PA1 cells, undifferentiated H9 cells and H9 differentiated FB neurons.

overall_design: Ribo-4sUDRB-seq for characterizing nascent circRNA biogenesis.

first: Ling-Ling

last: Chen

first: Yang

last: Zhang

first: Hua-Hong

last: Fang

first: Jun

first: Wei

last: Xue


title: Epigenomic profiling reveals the key function of histone H3K9 methylation during tumor transformation process

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

summary: To understand transcriptome and epigenome profilings alteration during breast cancer initiation and development, we constructed a in vitro breast cancer transformation model. And then, we use mRNA-Seq to uncover differential expression genes during breast cancer transformation process. For epigenomic profilings, we specificly analysis genome wide H3K9me2, H3K9me3,H3K4me3 and H3K27me3 modifications using ChIP-Seq. We found that H3K9 di and tri methylation decrease both in vitro breast cancer cell transformation model and in vivo clinical samples. Further more, we found KDM3A, a demethylase for H3K9 mono and di methylation, increase during the breast cancer model transformation process and clinical samples. KDM3A deficiency impairs the growth of those transformed cell lines and its overexpression promotes tumor formation.

overall_design: To study the underlying mechanisms of breast cancer transformation, we utilized a cell based cell transformation model. Large T antigen, TERT and HRAS(V12) were transfected into purchased primary breast cell, respectively. Four cell lines were used for the following study, named as HMC-p6 (breast primary cell passage 6), HMC-L (breast primary cell with stable large T expression), HMC-LT (breast primary cell with large T and TERT) and HMC-LTR (breast primary cell with large T, TERT and HRAS (V12)). HMC-p6 cell is a normal breast primary cell, and we proved HMC-LTR is a cancer cell by using colony formation and nude mouse tumor formation assay. And then, we performed mRNA-Seq and ChIP-Seq in those four cell lines using standard Illumina TruSeq Kit as the manufaturer's suggested. For KDM3A function analysis, we performed knockdown of KDM3A in L.T and L.T.R by using shRNA and siRNA, respectively.  NC stands for negative control, briefly, for shRNA we used shGFP as control and for siRNA we used negative control RNA.

first: Quan-Yi

last: Zhao


title: A SAM oligomerization domain shapes the genomic binding landscape of the LEAFY transcription factor

city: Grenoble

first: Francois

last: Parcy

address: 17, av. des Martyrs

country: France

institute: CNRS

summary: Multicellular organisms develop new structures by initiating specific gene regulatory programs through coordinated changes at the transcriptional and chromatin levels. Master transcription factors orchestrate such global changes but the underlying molecular mechanisms remain unclear. Here we focus on LEAFY (LFY), a key regulator of flower development in angiosperms. The resolution of the crystallographic structure of its N-terminal domain shows that it forms an unanticipated Sterile Alpha Motif (SAM) domain. This domain drives LFY oligomerization, which we establish to be essential for LFY floral switch function. Combining in vitro and in vivo experiments, we demonstrate that oligomerization facilitates LFY binding to DNA regions with multiple binding sites. Moreover, genome-wide analyses reveal an additional prominent role for the oligomerization domain: it confers upon LFY the capacity to bind to closed chromatin regions. This novel property, combined with its previously demonstrated capacity to recruit chromatin remodelers, indicates that LFY controls floral fate by acting as a plant pioneer transcription factor.

overall_design: A. thaliana LEAFY oligomerization ChIP-seq vs. control, 2 replicates.

first: Camille

last: Sayou

first: Max

last: Nanao

first: Marc

last: Jamin

first: David

last: Posé

first: Emmanuel

last: Thévenon

first: Laura

last: Grégoire

first: Gabrielle

last: Tichtinsky

first: Grégoire

last: Denay

first: Félix

last: Ott

first: Marta

last: Llobet Peirats

first: Markus

last: Schmid

first: Renaud

last: Dumas

first: François


title: Pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation [ChIP-seq]

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin.  Yet the nucleosomal configuration of such open chromatin and the basis for chromatin opening is unclear.  Here we combine low and high levels of MNase digestion along with core histone ChIP-seq to assess the presence of nucleosomes at enhancers and promoters in mouse liver. We find that the pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and helping other transcription factors bind.  MNase-accessible nucleosomes, bound by transcription factors, are retained substantially more at liver-specific enhancers than promoters and tissue-ubiquitous enhancers.  Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.

overall_design: This study assesses genome-wide binding of the transcription factors FoxA3, HNF4a, and CEBPb along with linker histone H1 in WT mice and in FoxAflox;Alfp-Cre mutant mice lacking both FoxA1 and FoxA2. ChIP-seq signal is adjusted by input to account for local sonication efficiency biases. All ChIPs and the input were assessed using two biological replicates in each genetic background.

first: Makiko

last: Iwafuchi-Doi

first: Greg

first: Akshay

last: Kakumanu

first: Jason

middle: A

last: Watts

first: Shaun

last: Mahony

first: B

middle: F

last: Pugh

first: Dolim

last: Lee

first: Klaus

last: Kaestner

first: Kenneth

last: Zaret


title: Identification of Soybean Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to  Aphid Infestation

city: Kansas City

first: Ning

last: Zhang

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary: The soybean aphid, a plant sap sucking insect, is an important soybean pest in the USA causing significant yield losses. The Rag2  gene of soybean provides resistance to soybean aphid biotypes I and II. Transcriptomic  analyses were performed on near isogenic lines (NILs) with the Rag2 allele for aphid resistance or rag2 for susceptibility at the Rag2 locus. Soybeans were infested with soybean aphids and leaves were collected at 0, 4, 8, 24, and 48 hours after infestation.  RNA were extracted and a high throughput RNA-seq approach was used to examine mRNA expression in Rag2 and rag2 soybean leaves. The expression of ~43,000 genes was detected in both the Rag2 and rag2 leaves. Statistical analysis identified 2361 genes significantly regulated between the resistant and susceptible lines at different times after aphid infestation. Genes found up-regulated in the Rag2 line were annotated as involved in the cell wall, secondary and hormone metabolism, as well as in stress, signaling and transcriptional responses. Genes found up-regulated in the rag2 line were annotated as involved in photosynthesis and carbon metabolism. Interestingly, mRNAs of 2 genes (unknown and mitochondrial protease) located within the Rag2 locus were expressed significantly higher in the  resistant genotype. The expression of the putative NBS-LRR resistant gene present in the Rag2 locus was not different between the two soybean lines. However, another NBL-LRR gene located just at the border of the Rag2 locus was and, therefore, may be involved in the differential resistance to aphid infestation exhibited by the two NIL genotypes analyzed.

overall_design: A total of 20 samples was analyzed. Two soybean genotypes, 5 time points and 2 biological replicates per condition were used.

first: Laurent

last: Brechenmacher

first: Tran

last: Nguyen

first: Tae-Hwan

last: Jun

first: Dong

last: Xu

first: Rouf

last: Mian

first: Gary

last: Stacey


title: Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers [MNase-Seq]

first: Gregory

summary: In higher eukaryotes, enhancers and promoters share many properties, including binding of transcription factors, existing in open chromatin, and bidirectional transcription.  Yet the structural features that distinguish enhancers and promoters are unclear.  Genome-wide micrococcal nuclease (MNase) studies previously interpreted MNase hypersensitivity to indicate that active enhancers and promoters are nucleosome-free, yet other studies found histone variants and post-translational modifications at active enhancers.  We find that prior MNase genomic studies have an overdigestion bias and that low-level MNase digestion, coupled with mapping core histones, reveals two classes of MNase-hypersensitive sites:  at active promoters, which are nucleosome depleted, and at tissue-specific enhancers, which retain core histones and co-bound transcription factors substantially more than promoters.  Hypersensitivity of active enhancer nucleosomes may reflect their preferential exposure in chromatin and can be maintained by pioneer transcription factors such as FoxA.  These findings unveil fundamental differences in the chromatin structure of active enhancers and promoters.

overall_design: MNase-seq: for each of our two conditions (high vs low MNase concentration) we include two biological replicates with three sequencing samples (technical replicates) per biological replicate. All data was collected from adult mouse liver.


title: Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers [ChIP-Seq]

overall_design: We include two biological replicates for each of H2B and H3 and one sample for each of FoxA2, H3K4me2 and input.  All data was collected from adult mouse liver.

first: Makiko


title: HEXIM1 is induced by DHODH inhibition to suppress melanoma [ChIP-Seq]

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Recent evidence suggests that leflunomide, a DHODH inhibitor, disrupts neural crest development and melanoma pathogenesis via inhibiting transcription elongation. Here, we provide evidence that a transcriptional regulator, HEXIM1, is upregulated in response to leflunomide. HEXIM1 is assembled into the 7SK snRNP complex to sequester and inhibit the kinase P-TEFb. P-TEFb triggers elongation by phosphorylating RNA polymerase II and pausing factors. Knockdown of hexim in zebrafish rescues the effects of leflunomide. HEXIM1 expression is low in human melanoma. In addition, HEXIM1 overexpression can suppress melanoma onset in zebrafish. Increased HEXIM1 expression, in response to low nucleotides triggered by DHODH inhibition, sequesters P-TEFb away from melanoma pathogenesis, proliferation and cell cycle genes based on GRO-seq and ChIP-seq analyses. This reduces productive elongation at genes that maintain the tumorigenic state. Our study illustrates that HEXIM1 is a tumor suppressor that responds to cell stress, consequently inhibiting productive elongation of proliferative genes in melanoma.

overall_design: ChIP-seq analysis of HEXIM1 and CDK9 chromatin binding in human A375 melanoma cells treated with either DMSO or 25uM A771726 for 48 hrs.

first: Justin

last: Tan

first: Song

last: Yang

first: Zi

last: Fan

first: Yi

last: Zhou

first: Richard

last: Young


title: HEXIM1 is induced by DHODH inhibition to suppress melanoma [Gro-Seq]

overall_design: 2 DMSO control, 2 Leflunomide treated and 2 A771726 treated replicates.

first: Violaine

last: Saint-André

first: Celeste

last: Greer

first: Yoon

last: Kim

first: Tae


title: Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers [ChIP-exo]

last: Donahue

overall_design: We include two biological replicates for FoxA2, and also two biological replicates for IgG, our control. All data was collected from adult mouse liver.

last: Iwafuchi-Doi

first: Greg

first: Jason

last: Watts

first: Shaun

last: Mahony

first: B

last: Pugh

first: Dolim

last: Lee

first: Klaus

last: Kaestner

first: Kenneth

last: Zaret


title: Regulatory T cell modulation by CBP/EP300 bromodomain inhibition

city: Cambridge

first: Barbara

middle: M

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

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

overall_design: Refer to individual Series


title: Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers

first: Gregory


title: Transcriptional regulators compete with nucleosomes post-replication

status: Public on Apr 07 2016

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Every nucleosome across the genome must be disrupted and reformed when the replication fork passes, but how chromatin organization is re-established following replication is unknown. To address this problem, we have developed Mapping In vivo Nascent Chromatin with EdU and sequencing (MINCE-seq) to characterize the genome-wide location of nucleosomes and other chromatin proteins behind replication forks at high temporal and spatial resolution. We find that the characteristic chromatin landscape at Drosophila promoters and enhancers is lost upon replication. The most conspicuous changes are at promoters that have high levels of RNA polymerase II (RNAPII) stalling and DNA accessibility and show specific enrichment for the BRM remodeler. Enhancer chromatin is also disrupted during replication, suggesting a role for transcription factor (TF) competition in nucleosome re-establishment. Thus, the characteristic nucleosome landscape emerges from a uniformly packaged genome by the action of TFs, RNAPII and remodelers minutes after replication fork passage.

overall_design: Using MINCE-seq, we mapped the newly replicated and maturing chromatin landscape at promoters and enhancers. There are 24 samples, 12 input-pulldown pairs. Three of these pairs are biological replicates.

first: Srinivas

last: Ramachandran

first: Steven


title: Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - HepG2/K562 cells]

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: RNA binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNAs. As defects in protein-RNA recognition lead to human disease, UV-crosslinking and immunoprecipitation (CLIP) of ribonuclear complexes followed by deep sequencing (-seq) is critical in constructing protein-RNA maps to expand our understanding of RBP function. However, current CLIP protocols are technically demanding and involve low complexity libraries that yield squandered sequencing of PCR duplicates and high experimental failure rates. To enable truly large-scale implementation of CLIP-seq, we have developed an enhanced CLIP methodology (eCLIP) that features a decrease of ~10 cycles of requisite amplification with a concomitant >60% decrease in discarded PCR duplicate reads, while maintaining the ability to identify RNA binding with single-nucleotide resolution. By simplifying the generation of paired IgG and size-matched input controls, eCLIP also dramatically improves specificity in discovery of authentic binding sites. To demonstrate that eCLIP enables large-scale and robust profiling of RBPs, 102 eCLIP experiments in biological duplicate for a diverse collection of 74 RBPs in HepG2 and K562 cells were completed (available at https://www.encodeproject.org). We establish that eCLIP is comparable in amplification and sample requirements to ChIP-seq, and enables integrative analysis of diverse RBPs to reveal factor-specific profiles, common artifacts for CLIP experiments and RNA-centric perspectives of RBP activity.

overall_design: eCLIP-seq in HepG2 and K562 Cells

first: Eric

last: Van Nostrand

first: Gabriel

last: Pratt

first: Alexander

last: Shishkin

first: Chelsea

last: Gelboin-Burkhart

first: Mark

last: Fang

first: Balaj

last: Sundararaman

last: Blue

first: Thai

last: Nguyen

first: Christine

last: Surka

first: Keri

last: Elkins

first: Rebecca

last: Stanton

first: Frank

last: Rigo

first: Mitchell

last: Guttman


title: G9a-Mediated Methylation of ERα Links the PHF20/MOF Histone Acetyltransferase Complex to Hormonal Gene Expression

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

summary: The euchromatin histone methyltransferase 2 (EHMT2, aka G9a) methylates histone H3K9 to repress gene expression, but it also acts as a coactivator for some nuclear receptors.  The molecular mechanisms underlying this activation remain elusive.  Here we show that G9a functions as a bona fide coactivator of the endogenous estrogen receptor α (ERα) in breast cancer cells in a histone methylation-independent manner. G9a dimethylates ERα protein at lysine 235 both in vitro and in cells. Dimethylation of ERαK235 (ERαK235me2) is recognized by the Tudor domain of PHF20, which in turn recruits the MOF histone acetyltransferase (HAT) complex to ERα target gene promoters to deposit histone H4K16 acetylation promoting active transcription. Together, our in vitro and in vivo data establish the molecular mechanism by which G9a functions as an ERα coactivator. Along with the PHF20/MOF complex, G9a links the crosstalk between ERα methylation and histone acetylation governing the epigenetic regulation of hormonal gene expression.

overall_design: G9a KD RNA-seq and PHF20 KD RNA-seq with and without E2 treatment

first: Xi

last: Zhang

first: Danni

last: Peng

first: Chao

last: Yuan


title: Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival [eCLIP-Seq]

first: Gene

last: Yeo

summary: Human pluripotent stem cells (hPSCs) require precise control of post-transcriptional RNA networks to maintain proliferation and survival. Using a recently developed enhanced UV crosslinking and immunoprecipitation (eCLIP) approach, we identify RNA targets of the IMP/IGF2BP family of RNA-binding proteins in hPSCs. At the broad region- and binding site-level IMP1 and IMP2 show reproducible binding to a large and overlapping set of 3'UTR-enriched targets. RNA Bind-N-Seq applied to recombinant full-length IMP1 and IMP2 reveals CA-rich motifs that are enriched in eCLIP-defined binding sites. We observe that IMP1 loss in hPSCs recapitulates IMP1 phenotypes, including a reduction in cell adhesion and an increase in cell death. For cell adhesion, in hPSCs we find IMP1 maintains levels of integrin mRNA, specifically regulating RNA stability of ITGB5. Additionally, we show IMP1 can be linked to hPSC survival via direct target BCL2. Thus, transcriptome-wide binding profiles identify hPSC targets modulating well-characterized IMP1 roles.

overall_design: eCLIP-seq was performed in biological replicate for IGF2BP1/IMP1 and IGF2BP2/IMP2, as well as one replicate each for IGF2BP3/IMP3, RBFOX2, and an IgG control. Each sample has a size-matched input control for analysis

first: Anne

last: Conway

last: VanNostrand

first: Stefan

last: Aigner

first: Melissa

last: Wilbert

first: Balaji

last: Sundaraman

first: Peter

last: Freese

first: Nicole

last: Lambert

first: Shashank

last: Sathe

first: Tiffany

middle: Y

last: Liang

first: Anthony

last: Essex

first: Severine

last: Landais

first: Christopher

last: Burge

first: D

last: Jones


title: Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival


title: Enhanced CLIP uncovers IMP protein-RNA targets in human pluripotent stem cells important for cell adhesion and survival [RNA-Seq]

middle: E

first: Eric

first: Gabriel

last: Pratt


title: A Surveillance System of Active Enhancers by a RACK7-histone Demethylase Complex

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A Surveillance System of Active Enhancers by a RACK7-histone Demethylase Complex (RNA-Seq II)

summary: Primed enhancers are marked by histone H3K4 mono-methylation (H3K4me1), and the conversion to active enhancers involves acetylation of histone H3K27 (H3K27Ac). However, whether active enhancers are regulated remains unclear. Here we report a biochemical complex consisting of a potential chromatin reader (RACK7) and a histone demethylase (KDM5C) that occupies many active enhancers in a breast cancer cell line. Loss of RACK7 or KDM5C results in hyperactive enhancers marked by H3K4me3 and H3K27Ac, and characterized by an increased eRNA transcription and elevated expression of nearby genes.  Loss of RACK7 or KDM5C also leads to increased cell invasion and migration, and enhanced tumor growth. We propose that RACK7/KDM5C functions as an enhancer “brake” to ensure appropriate enhancer activities in the cell. Our findings provide important insight into histone H3K4 methylation dynamics at enhancers and reveal a molecular mechanism that controls the activities of active enhancers, which when compromised, can contribute to tumorigenesis.

overall_design: nascent RNA-seq of parental and RACK7-KO cells

first: Hongjie

last: Shen

first: Fei

last: Lan


title: A Surveillance System of Active Enhancers by a RACK7-histone Demethylase Complex (ChIP-Seq I)

overall_design: ChIP-seq data of RACK7, KDM5C and histone modifications in parental and RACK7-KO ZR-75-30 cells.


title: The interplay between a protein and an mRNA antagonist controls CsrA-mediated regulation of flagella genes in Campylobacter jejuni

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary: This study investigates the CsrA regulon of the food-borne pathogen Campylobacter jejuni. Direct RNA binding targets of CsrA in two strains of C. jejuni, NCTC11168 and 81-176, were determined using RIP-seq.

sample_organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

sample_organism: Campylobacter jejuni subsp. jejuni 81-176

overall_design: Identification of CsrA binding sites in two C. jejuni strains using RIP-seq

first: Gaurav

last: Dugar

first: Sarah

last: Svensson

first: Thorsten

last: Bischler

first: Richard

last: Reinhardt

first: Cynthia

last: Sharma


title: Comparative analysis of human and mouse transcriptomes of Th17 cell priming.

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

summary: Uncontrolled Th17 cell activity is associated with cancer and autoimmune and inflammatory diseases. To validate the potential relevance of mouse models of targeting the Th17 pathway in human diseases we used RNA sequencing to compare the expression of coding and non-coding transcripts during the priming of Th17 cell differentiation in both human and mouse. In addition to already known targets, several transcripts not previously linked to Th17 cell polarization were found in both species. Moreover, a considerable number of human-specific long non-coding RNAs were identified that responded to cytokines stimulating Th17 cell differentiation. We integrated our transcriptomics data with known disease-associated polymorphisms and show that conserved regulation pinpoints genes that are relevant to Th17 cell-mediated human diseases and that can be modelled in mouse. Substantial differences observed in non-coding transcriptomes between the two species as well as increased overlap between Th17 cell-specific gene expression and disease-associated polymorphisms underline the need of parallel analysis of human and mouse models. Comprehensive analysis of genes regulated during Th17 cell priming and their classification to conserved and non-conserved between human and mouse facilitates translational research, pointing out which candidate targets identified in human are worth studying by using in vivo mouse models.

overall_design: Altogether 114 (57 human and 57 mouse) samples were analyzed representing 3 biological replicates of timeseries data (0, 0.5, 1, 2, 4, 6, 12, 24, 48 and 72 hours) of Th17 polarized cells and control Th0 cells

first: Soile

last: Tuomela

first: Helena

last: Ahlfors

first: Viveka

last: Öling

first: Verna

last: Salo

first: Ubaid

last: Ullah

first: Zhi

last: Chen

first: Saara

last: Hämälistö

first: Subhash

middle: K

last: Tripathi

first: Tarmo

last: Äijö

first: Omid

last: Rasool

first: Hayssam

last: Soueidan

first: Lodewyk

last: Wessels

first: Brigitta

last: Stockinger

first: Harri

last: Lähdesmäki

first: Riitta

last: Lahesmaa


title: A large microRNA cluster on chromosome 19 is a transcriptional hallmark of WHO type A and AB thymomas

status: Public on Apr 06 2016

first: Milan

last: Radovich

state: Indiana

address: 980 W. Walnut St, Room C312

institute: Indiana University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Thymomas are one of the most rarely diagnosed malignancies. To better understand its biology and to identify therapeutic targets, we performed next-generation RNA sequencing.  The RNA was sequenced from 13 thymic malignancies and 3 normal thymus glands. Validation of microRNA expression was performed on a separate set of 35 thymic malignancies. For cell-based studies, a thymoma cell line was used. Hierarchical clustering revealed 100% concordance between gene expression clusters and WHO subtype. A substantial differentiator was a large microRNA cluster on chr19q13.42 that was significantly overexpressed in all A and AB tumors and whose expression was virtually absent in the other thymomas and normal tissues. Overexpression of this microRNA cluster activates the PI3K/AKT/mTOR pathway. Treatment of a thymoma AB cell line with a panel of PI3K/AKT/mTOR inhibitors resulted in marked reduction of cell viability. A large microRNA cluster on chr19q13.42 is a transcriptional hallmark of type A and AB thymomas. Furthermore, this cluster activates the PI3K pathway, suggesting the possible exploration of PI3K inhibitors in patients with these subtypes of tumor. This work has led to the initiation of a phase II clinical trial of PI3K inhibition in relapsed or refractory thymomas.

overall_design: 13 thymic malignancies and 3 Normal Thymus RNA-Sequenced in triplicate


title: ATXN7L3 And ENY2 Coordinate Activity Of Multiple H2B Deubiquitinases Important For Cellular Proliferation And Tumor Growth [ChIP-Seq]

city: Smithville

first: Sharon

middle: Roth

last: Dent

state: Texas

address: 1808 Park Road 1C

institute: Univ Texas M.D. Anderson Cancer Center

summary: We report that the H2B deubiquitinating enzymes USP22, USP27x and USP51 have both unique and overlapping target loci.

overall_design: Comparing H2Bb1 (K120) distribution profiles of MCF7 cells stably expressing shRNA targeting ATXN7L3, USP22, USP27X or USP51 and cells expressing non-targeting shRNA.

first: Boyko

last: Atanassov

first: Yue

last: Lu


title: ATXN7L3 And ENY2 Coordinate Activity Of Multiple H2B Deubiquitinases Important For Cellular Proliferation And Tumor Growth


title: ATXN7L3 And ENY2 Coordinate Activity Of Multiple H2B Deubiquitinases Important For Cellular Proliferation And Tumor Growth [RNA-Seq]

summary: We report that H2B deubiquitinating enzymes USP22, USP27x and USP51 have both unique and overlapping target loci.

overall_design: Comparing gene expression profiles of MCF7 cells stably expressing shRNA targeting either USP22, USP27X or USP51 and cells expressing non-targeting shRNA.


title: Nrf2 bindng in C2C12 myotubes

city: Sendai

first: Akira

last: Uruno

state: Miyagi

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

institute: Tohoku University Graduate School of Medicine

summary: Nrf2 (NF-E2-related-factor-2) contributes to the maintenance of glucose homeostasis in vivo. Nrf2 suppresses blood glucose levels by protecting pancreatic β-cells from oxidative stress and improving peripheral tissue glucose utilization. To elucidate the molecular mechanisms by which Nrf2 contributes to the maintenance of glucose homeostasis, we generated skeletal muscle (SkM)-specific Keap1-knockout (Keap1MuKO) mice that express abundant Nrf2 in SkM and then examined Nrf2-target gene expression in this tissue. In Keap1MuKO mice, blood glucose levels were significantly downregulated, and the levels of glycogen branching enzyme (Gbe1) mRNA, along with those of glycogen branching enzyme (GBE) protein, were significantly upregulated in mouse SkM. Consistent with this result, chemical Nrf2-inducers promoted Gbe1 mRNA expression in both mouse SkM and C2C12 myotubes. Chromatin-immunoprecipitation analysis demonstrated that Nrf2 binds the Gbe1 upstream promoter regions. In Keap1MuKO mice, muscle glycogen content was strongly reduced, and forced GBE expression in C2C12 myotubes promoted glucose uptake. Therefore, our results demonstrate that Nrf2-induction in SkM increases GBE expression and reduces muscle glycogen content, resulting in improved glucose tolerance.

overall_design: Chromatin occupancy of Nrf2 under CDDO-Im-treated condition were generated by deep sequencing, in dupliplicate

first: Fumiki

last: Katsuoka

first: Yoko

last: Yagishita

first: Masayuki

last: Yamamoto


title: A Surveillance System of Active Enhancers by a RACK7-histone Demethylase Complex (ChIP-Seq II)

first: Yang

last: Shi

first: Hongjie

last: Shen

first: Fei

last: Lan


title: Transcriptome Profile of CYC2 K.O. and WT during meiosis in Tetrahymena thermophila

city: Hefei

first: Xiaoyuan

last: Song

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

institute: University of Science and Technology of China

summary: Meiotic recombination is carried out through a specialized pathway for the formation and repair of DNA double-strand breaks (DSBs) made by the Spo11 protein. The present study shed light on the functional role of Cyclin, CYC2, in Tetrahymena thermophila which has transcriptionally high expression level during meiosis process. Knocking out the CYC2 gene results in arrest of meiotic conjugation process at 2.5–3.5 h after conjugation initiation, before the meiosis division starts, and in company with the absence of DSBs. To investigate the underlying mechanism of this phenomenon, a complete transcriptome profile was performed between wild-type strain and CYC2 knock-out strain. Functional analysis of RNA-Seq results identifies related differentially expressed genes (DEGs) including SPO11 and these DEGs are enriched in DNA repair/mismatch repair (MMR) terms in homologous recombination (HR), which indicates that CYC2 could play a crucial role in meiosis by regulating SPO11 and participating in HR.

overall_design: We performed mRNA profiling on both wild-type strains and CYC2-knocking out strains at four different stages during meiosis prohase of Tetrahymena thermophila.

first: Qianlan

last: Xu

first: Ruoyu

last: Wang


title: Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing [RNA-seq]

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: Genetic ablation of the maintenance methyltransferase Dnmt1 induces widespread demethylation and transcriptional activation of CpG-rich IAP (intracisternal A particle) proviruses. Here, we report that this phenomenon is not simply a consequence of loss of DNA methylation. By exploiting conditional deletions of Dnmt1 and Np95, each of which is essential for maintenance methylation, we find that while IAPs are indeed de-repressed in Dnmt1-ablated embryos and embryonic stem cells (ESCs), these proviruses remain silenced in Np95-ablated cells, despite similar kinetics of passive demethylation. Paradoxically, transient IAP activation in Dnmt1-ablated ESCs requires the presence of NP95. We subsequently show that in the absence of NP95, the H3K9 methyltransferase SETDB1 maintains IAP silencing; while in the absence of DNMT1, prolonged binding of NP95 to hemimethylated DNA perturbs SETDB1-dependent H3K9me3 deposition. Taken together, these observations reveal that following acute loss of Dnmt1, H3K9 methylation-dependent IAP silencing is disrupted by aberrant NP95 binding to hemimethylated DNA.

overall_design: RNA-seq for Np95, Dnmt1 and Setdb1 wt, single conditional KO (cKO) and double cKO ES cells; RRBS-seq for Dnmt1 and Np95 single and double cKO ESCs; Myc-tagged NP95, DNMT1 ChIP-seq; and wt and Np95wt and cKO H3K9me3 ChIP-seq.

first: Haruhiko

last: Koseki

first: Matthew

last: Lorincz

first: Jafar

last: Sharif


title: Uncoupling X chromosome number from sex determination separates contribution of sex and X dose to sex-biased gene expression in C. elegans

city: New York

first: Sevinc

last: Ercan

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

summary: The difference in X chromosome copy number creates a potential difference in X chromosomal gene expression between males and females. In many animals, dosage compensation mechanisms equalize X chromosome expression between sexes. Yet, X chromosome is also enriched for sex-biased genes due to differences in the evolutionary history of the X and autosomes. The manner in which dosage compensation and sex-biased gene expression exist on the X chromosome remains an open question. Most studies compare gene expression between two sexes, which combines expression differences due to X chromosome number (dose) and sex.  Here, we uncoupled the effects of sex and X dose in C. elegans and determined how each process affects expression of the X chromosome compared to autosomes.  We found that in the soma, sex-biased expression on the X chromosome is almost entirely due to sex because the dosage compensation complex (DCC) effectively compensates for the X dose difference between sexes. In the germline where the DCC is not present, X chromosome copy number contributes to hermaphrodite-biased gene expression. These results suggest that X dose contributes to sex-biased gene expression based on the level of dosage compensation in different tissues and developmental stages.

overall_design: RNA-Seq profiles of C. elegans XO hermaphrodite and XX male L3 larvae and adults

first: Maxwell

last: Kramer

first: Kranz

last: Anna-Lena


title: New insight into a host-pathogen interaction unveiled by transcriptomics response of the global insect pest Plutella xylostella to a fungal pathogen

city: Hangzhou

first: Chu

last: ZhenJian

state: Zhejiang

address: Yuhangtang Road 388

department: College of Life Science

institute: Zhejiang University

summary: A genomic insight into how an insect pest responds to the infection of a fungal insect pathogen, such as Beauveria bassiana, is critical for alternative strategy of insect pest contol based on fungal insecticides but has not been well probed. Here we constructed three pairs of digital expression libraries (transcriptomes) of Plutella xylostella (global lepidopteran pest) larvae 24, 36 and 48 hours post treatment of infection (hptI) and control (hptC) to reveal the host response to B. bassiana infection at genomic level. The paired libraries comprised 2144, 3200 and 2967 differentially expressed genes (DEGs) of P. xylostella at 24, 36 and 48 hptI/hptC, respectively. These DEGs were enriched in various immune pathways activated by the fungal infection, such as the pathways of complement and coagulation cascades, protein digestion and absorption, and drug metabolism - cytochrome P450. We found that 24 hptI was critical either for the cuticular penetration of B. bassiana or for the initial activation of the host defense system. The host immune response peaked at 36 hptI so that multiple defense mechanisms were activated against the fungal entry into the host hemocoel. At 48 hptI, many host genes involved in immunity and metabolism were downregulated, suggesting a success of fungal localization in the host hemocoel by overcoming the host defense reaction. Finally, we revealed that several fungal pathways could play important roles in the host-pathogen interaction, such as antioxidant activity, peroxidase activity and proteolysis. Up to 1636 fungal genes were co-expressed at the three time points, and 116 of them encode putative secretion proteins. Our results provide a novel insight into the pathogen-insect interaction and help to probe molecular mechanisms involved in the control of P. xylostella by B. bassiana.

first: Zhen-Jian

last: Chu

first: Yu-Jun

first: Sheng-Hua

last: Ying

first: Xiao-Wei

first: Ming-Guang

last: Feng


title: RNA sequencing of e15.5 pancreas from Wild Type, Blinc1-/- and Blinc+/- mice.

city: Aurora

first: Lori

last: Sussel

state: CO

address: 1775 Aurora Ct.

institute: University of Colorado

summary: We report the transcriptome changes that result of the genomic deletion of one or two alleles of an islet-specific long non-coding RNA (Blinc1) in isolated pancreas from e15.5 mouse embryos.

overall_design: Pancreas from e15.5 embryos were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq.

first: Luis

last: Arnes


title: Genoma-wide analysis of pro- and anti-inflammatory activation states in embryonic stem cell-derived microglia

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

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

overall_design: Refer to individual Series


title: Regulatory T cell modulation by CBP/EP300 bromodomain inhibition [ChIP-seq]

first: Barbara

last: Bryant

state: MA

summary: Genome-wide chromatin H3K27ac, H3K18ac and H3K4me3 occupancy changes in response to CBP inhibitor treatment in Treg cells using ChIP sequencing (ChIP-seq).

overall_design: Expression profiling by ChIP-seq of Treg cells treated with DMSO or CBP inhibitor

first: Srimoyee

last: Ghosh

first: Jose

last: Lora

first: Robert

last: Sims

first: Melissa

last: Chin

first: Hon-Ren

last: Huang

first: Andres

last: Salmeron

first: Pranal

middle: J

last: Dakle

first: Deanna

last: Mele

first: Charlie

last: Hatton


title: GATA3 restrains Notch signaling activity and represses NK cell development to induce human T cell commitment following Notch-induced T-lineage specification (ChIP-Seq)

city: Ghent

first: Inge

last: Van de Walle

address: De Pintelaan 185, blokA 4th floor

country: Belgium

institute: UGent

summary: The stepwise conversion of multipotent precursors into committed T-cell progenitors depends on several transcriptional regulators, but the interplay between these factors is still obscure. This is particularly true in human since the core early Notch signalling pathway also supports NK cell development and requires tight regulation for efficient T-lineage commitment and differentiation. Here, we show that GATA3, in contrast to TCF1, induces T-lineage commitment following NOTCH1-induced T-lineage specification through direct regulation of at least 3 distinct processes: repression of NK-cell fate, activation of T-lineage genes to promote further differentiation, and downmodulation of Notch signalling activity. GATA3-mediated repression of the NOTCH1 target gene DTX1 hereby is essential to induce T-lineage commitment at the expense of NK cell differentiation. Thus, human T-lineage commitment is dependent on the precise collaboration of several transcriptional regulators that integrate through both positive and negative regulatory loops.

overall_design: ChIP-sequencing data was generated for GATA3 in human thymocytes

first: Kaat

last: Durinck

first: Wouter

last: Van Loocke

first: Sagar

last: Damle

first: Pieter

last: Van Vlierberghe

first: Frank

last: Speleman

first: Ellen

last: Rothenberg

first: Tom

last: Taghon


title: A Surveillance System of Active Enhancers by a RACK7-histone Demethylase Complex (RNA-Seq I)

city: Shanghai

first: Yang

last: Shi

overall_design: mRNA-seq of parental and RACK7-KO ZR-75-30 cells

first: Hongjie

last: Shen

first: Fei

last: Lan


title: Regulatory T cell modulation by CBP/EP300 bromodomain inhibition [RNA-seq]

first: Barbara

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

summary: Genome-wide gene expression changes in response to CBP inhibitor treatment in Treg cells using RNA sequencing (RNA-seq).

overall_design: Expression profiling by RNA-seq of Treg cells treated with DMSO or CBP inhibitor

first: Srimoyee

last: Ghosh

first: Jose

last: Lora

first: Robert

last: Sims

first: Melissa

last: Chin


title: Histone Lysine ß-hydroxybutyrylation ChIP-seq and RNA-seq analysis of mouse liver during starvation

city: Chicago

first: Yingming

last: Zhao

state: IL

address: 929 East 57th St. W410

department: The Ben May Department for Cancer Research

institute: University of Chicago


title: Metabolic Regulation of Gene Expression by Histone Lysine ß-hydroxybutyrylation [RNA-seq]

summary: We identified a new type of histone mark-lysine ß-hydroxybutyrylation (Kbhb). This ketone body derived histone mark (Kbhb) was dramatically induced in livers during starvation. To charactize histopne Kbhb: 1) We mapped genomic distributions of histone Kbhb marks (H3K9bhb, H3K4bhb and H4K8bhb) by ChIP-seq in mouse liver. 2) We examined the response of histone Kbhb mark to starvation by carrying out ChIP-seq experiments for H3K9bhb in both "starved" and "fed" mouse liver. 3) We also examined differentially-expressed genes during starvation by carrying out RNA-seq experiments in both "starved" and "fed" mouse liver. By integrating analyses of ChIP-seq and RNA-seq data, we tried to get a correlation between H3K9bhb mark and gene expression in response to starvation. Sequencing was performed on the HiSeq2000 (Illumina).

overall_design: RNA-seq of mouse liver cells both in "starved" and "fed" conditions.

first: Di

last: Zhang

first: Dongjun

last: Chung


title: Tissue specific demethylation is required for proper B-cell differentiation and function

city: Jerusalem

first: Howard

last: Cedar

address: Ein Kerem Campus

institute: The Hebrew University

summary: Many studies have demonstrated that somatic cell differentiation during development is accompanied by extensive demethylation of specific sites relevant to each cell type.  Although the mechanism of this process has not yet been elucidated, it is likely to involve the conversion of 5mC to 5hmC by Tet enzymes [Ziller, 2013 #5787].  In this paper, we show that a Tet2/Tet3 conditional knockout at early stages of B-cell development largely prevents lineage-specific programmed demethylation events. This lack of demethylation affects the expression of nearby B-cell lineage genes, probably by inhibiting enhancer activity, thus causing defects in B- cell differentiation.  Our studies represent the first demonstration that tissue-specific demethylation may be necessary for proper development in vivo.

overall_design: DNA methylation profile of different developmental stages of B-cells isolated from wild-type or Tet2/Tet3 single and double knock out. The data was generated using the RRBS protocol followed by deep sequncing. RNAseq was performed on these samples as well.

first: Shari

last: Orlanski

first: Verena

last: Labi

first: Yitzhak

last: Reizel

first: Adam

last: Spiro

first: Michal

last: Lichtenstein

first: Rena

last: Levin-Klein

first: Sergei

last: Koralov

first: Yael

last: Skversky

first: Klaus

last: Rajewsky

first: Yehudit

last: Bergman


title: Histone variants and modification in T-47D cells

city: Perth

first: Zhaoyu

last: Li

state: Western Australia

address: QE II, M block, 225C

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

summary: To investigate the impact of histone variants and modification on gene regulation, we report high-throughput profiles of six histone markers, H2A.Z, H3K4me2, H3K9me3, H3K27me3, H3K27ac, and H3K36me3, by ChIP-Seq in T-47D breast cancer cells. Libraries were sequenced with the Illumina HiSeq 2000 analyzer for 50 bp paired-end reads and over 20 million uniquely aligned reads were collected for each histone marker.

overall_design: To examine the impact of histone modification on gene expression regulation in T-47D cells.

first: Gaihua


title: miRNA expression profile of 14 mouse tissues

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

summary: We sequenced 14 mouse tissues' small RNA samples from C57BL/6J mouse and aligned the sequenced reads to miRBase_v16 to profile miRNA expression levels in these 14 tissues.

overall_design: We collect several tissue samples from 10 C57BL/6J mouse. Use high-throughout sequence technology to profile miRNA expression level in each tissue.

first: Dongxia

last: Hou

first: Chao

last: Gao


title: Genome-wide maps of the effect of butanol in P. putida BIRD1

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida BIRD1 in the presence of butanol with the aim to study in more detail the mechanisms involved in butanol response. Our work is the first global transcriptomic analysis done in P. putida BIRD1 in the presence of butanol.

overall_design: P. putida BIRD1 mRNA profiles in the presence of control condition (LB) and butanol (carbon source) or butanol shock.

first: C

last: Molina-Santiago

first: M

last: Cuenca

first: María

last: Gómez-García

first: J

last: Ramos


title: Rabbit limbal epithelial side population (SP) cells and non-SP cells

status: Public on Apr 18 2016

city: Tokyo

first: Sumako

last: Kameishi

address: 2-2, Wakamatsucho, Shinjukuku

department: Advanced Science and Engineering

institute: Graduate School of Waseda University

summary: Corneal epithelial stem cells reside in the limbus that is the transitional zone between the cornea and conjunctiva, and are essential to maintain the homeostasis of corneal epithelium. However, their characterization is poorly understood. Therefore, we constructed gene expression profiles of limbal epithelial SP and non-SP cell using RNA-sequencing. As a result, limbal epithelial SP cells have immature cell phenotypes with endothelial/mesenchymal cell markers, while limbal epithelial non-SP cells have epithelial progenitor cell markers.

overall_design: Examination of rabbit limbal epithelial SP and non-SP cells

first: Umemoto

last: Terumasa

first: Masako

last: Fujita


title: TRIBE : Hijacking an RNA-editing enzyme to identify cell-specific targets of RNA-binding proteins

status: Public on Apr 05 2016

city: Waltham

first: Aoife

last: McMahon

state: Massachusetts

address: 415 South St

institute: Brandeis University

summary: RNA transcripts are bound and regulated by RNA-binding proteins (RBPs). Current methods for identifying in vivo targets of a RBP are imperfect and not amenable to examining small numbers of cells. To address these issues, we developed TRIBE (Targets of RNA-binding proteins Identified By Editing), a technique that couples an RBP to the catalytic domain of the Drosophila RNA editing enzyme ADAR and expresses the fusion protein in vivo. RBP targets are marked with novel RNA editing events and identified by sequencing RNA. We have used TRIBE to identify the targets of three RBPs (Hrp48, dFMR1 and NonA). TRIBE compares favorably to other methods, including CLIP, and we have identified RBP targets from as little as 150 specific fly neurons. TRIBE can be performed without an antibody and in small numbers of specific cells.

overall_design: Three different TRIBE fusion proteins (an RNA-binding protein fused to the catalytic domain of the RNA editing enzyme dADAR) are expressed in cell lines (Drosophila S2 cells) or specific sub-groups of Drosophila neurons. mRNA or nascent RNA is sequenced from cells of interest and compared to sequenced gDNA. RNA editing events are identified as RNA-A-gDNA-G mismatches and indicate the binding position of the TRIBE protein. CLIP was performed for one RBP as validation. Code for RNA editing analysis is available here: https://github.com/rosbashlab/TRIBE

first: Michael

last: Rosbash


title: Control of progenitor cell positioning and organ patterning during embryogenesis

city: Muesnter

first: Katsiaryna

last: Tarbashevich

address: Von-Esmarch Str 56

institute: Institute for Cell Biology

summary: The precise positioning of organ progenitor cells constitutes an essential, yet poorly understood step in organ development and function. Using primordial germ cells and the process of gonadogenesis as an in vivo model, we present the developmental mechanisms facilitating the maintenance of a motile progenitor cell population at the site where the organ develops. We find that the action of repulsive cues coupled with the generation of physical barriers confine the cells to the correct bilateral positions within the embryo. Using computer particle-based simulations we could also demonstrate the role of reflecting barriers, from which cells turn away upon contact, and the importance of proper level of cell-cell interaction for maintaining the tight cell clusters and their correct positioning at the target region. The cellular mechanisms operating during those events were determined using high-resolution live imaging microscopy. This analysis revealed cell polarity change upon interaction with the physical barrier and the establishment of compact clusters that involves increased cell-cell interaction as a result of collapse of cell protrusions and enhanced adhesion. The combination of these developmental and cellular

overall_design: RNA profiling in zebrafish embryos of 7 hpf and 36 hpf in sorted germ cells and randomly sorted somatic cells

first: Erez

last: Raz


title: H3K4me3 ChIP in multiple myeloma MM1S cells in the presence and absence of KDM5-C70

city: Oxford

first: Udo

last: Oppermann

state: Oxfordshire

address: Botnar Research Centre, Nuffield Orthopaedic Centre, Windmill Road

department: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences

institute: University of Oxford

summary: In this experiment we demonstrate the use of an inhibitor of the KDM5 family of histone demethylases, KDM5-C70, on H3K4me3 marks in the multiple myeloma cell line MM1S.  KDM5-C70 increases H3K4me3 in a global fashion across the genome.

overall_design: Examination of H3K4me3 mark across MM1S cells treated with either KDM5-C70 or vehicle control

first: Edward

last: Hookway


title: Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [ESRP KD]

city: Los Angeles

first: Yi

last: Xing

state: CA

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA

summary: Epithelial specific splicing regulatory protein 1 and 2 (ESRP1 and ESRP2) are important regulators of alternative splicing during EMT. To study the alternative splicing events regulated by ESRP1/2 at a genome wide scale, we used lentiviral shRNAs to knockdown ESRP1/2 in H358 cells and performed RNA-seq in biological triplicates.

overall_design: We used lentiviral based shRNAs targeting ESRP1 and ESRP2 to knockdown both regulators in human H358 cells. We harvested total RNA and protein from ESRP1/2 knockdown and control knockdown in biological triplicates. We made cDNA libraries for each replicate and subjected them to RNA-seq.

first: Russ

last: Carstens


title: Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [RBM47 KD]

summary: RBM47 is a RNA binding protein that is known to regulate alternative splicing. To study the genome wide regulatory role of RBM47 in alternative splicing and determine the potential function of RBM47 during EMT, we used lentiviral shRNAs to knockdown RBM47 in H358 cells and performed RNA-seq in biological triplicates.

overall_design: We used lentiviral based shRNAs to knockdown RBM47 in human H358 cells. We harvested total RNA and protein from RBM47 knockdown and control knockdown in biological triplicates. We made cDNA libraries for each replicate and subjected them to RNA-seq.


title: Next generation sequencing of Pseudomonas aruginosa PAO1 in the presence of Free Nitrous Acid stress

city: Brisbane

first: Shuhong

last: Gao

state: QLD

address: Research Road, St Lucia

department: Advanced Water Management Centre

institute: The University of Queensland

summary:
Purpose: Free nitrous acid (FNA) has recently been demonstrated as an antimicrobial agent to a range of microorganisms. However, its antimicrobial mechanism is largely unknown. For this study Pseudomonas aeruginosa PAO1 was selected to gain a systematic understanding of the antimicrobial mechanism of FNA.
Methods: PAO1 was grown under anaerobic denitrifying conditions and when FNA was added (0.1 mg-N/L) growth temporarily stopped. From cultures with and without added FNA, RNA was extracted and the abundance of gene transcripts was detected by sequencing. Transcripts exhibiting ≥2.5 or ≤-2.5 fold abundance change in the presence of FNA were designated as differentially expressed.
Results:In response to FNA, 167 genes showed increased transcription while 424 exhibited deceased transcript levels. Respiration was likely inhibited as denitrification activity was severely decreased. Genes coding for enzymes of the tricarboxylic acid cycle were down regulated, while highly increased transcripts were detected for pyruvate fermentation, indicating a possible survival response to FNA. Moreover, genes coding ribosomal proteins had significantly decreased transcript levels, implicating that protein biosynthesis was severely inhibited by FNA. Whereas, genes encoding proteins functioning to preserve ribosome units under stressful conditions, were up-regulated during FNA exposure.
Conclusion: In this study, we performed genome-wide high throughput RNA sequencing (RNA-Seq) analysis on PAO1 in the absence and presence of a bacteriostatic-level of FNA (0.1 mg N/L). By combining the global activated/suppressed gene profiles and detected physiological responses, we detected the microbial response to FNA exposure and revealed potential antimicrobial mechanisms of FNA on this prevalent opportunistic pathogen and environmentally relevant denitrifier.

overall_design: mRNA profiles of P. aeruginosa PAO1 towards FNA stress were generated by next generation sequencing in triplicate via Illumina 2000.

first: Philip

last: Bond


title: GATA3 restrains Notch signaling activity and represses NK cell development to induce human T cell commitment following Notch-induced T-lineage specification

first: Inge

last: Van de Walle

overall_design: Refer to individual Series


title: The chromatin remodeler ATRX binds to atypical chromatin domains at the 3’ exons of ZNF genes to preserve H3K9me3 enrichment

city: New York

first: Emily

last: Bernstein

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: Here, we report that ATRX co-localizes with the H3K9-methyl transferase SETDB1 (also known as ESET), the co-repressor TRIM28 (also known as KAP1), and the transcription factor ZNF274 at 3’ exons of Zinc Finger Genes (ZNFs) containing an atypical H3K9me3/H3K36me3 chromatin signature. Disruption of ATRX and ZNF274 leads to a significant reduction of H3K9me3, particularly at the 3’ ZNF exons and other atypical chromatin regions, higher percentages of DNA damage, and defects in cell cycle. Taken together, our studies suggest that ATRX binds the 3’ exons of ZNFs to maintain genomic stability through the regulation of their H3K9me3 levels

overall_design: XL-MNase ChIP-seq of ATRX was performed in the erythroleukemic cell line K562 and the Neuroblastoma cell line LAN6. Two independent replicates using different ATRX antibodies were performed in K562. Additionally, Native ChIP-seq of H3K9me3 in LAN6, ATRX WT and ATRX KO K562 cells was performed. Input samples were sequenced as control.

first: David

last: Valle-Garcia

first: Zulekha

last: Qadeer


title: HEXIM1 is induced by DHODH inhibition to suppress melanoma

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

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


title: Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution

city: Cambridge

first: Boyang

last: Zhao

address: 500 Main Street

institute: MIT

summary: In this study, using a murine model of Ph+ acute lymphoblastic leukemia (Ph+ ALL), a combined pharmacological profile and drug selection experimental approach identified distinct stages of tumor clonal evolution with vulnerabilities to sets of small molecules. Through genotypic, phenotypic, signaling, and binding measurements, we identified the mutation V299L in the ABL1 kinase domain as mediator for an on-target ABL1 inhibition and hence the sensitization phenotype. To further rule out any off-target effects, we performed RNA-seq analysis of select derived cell lines. Variant calls suggest that although there were other mutations, the only mutation shared among cell lines with the sensitization phenotype and that went from 0% to 100% variant allele frequency was c.895G>C, leading to BCR-ABL1 V299L. In addition, transcriptional profile does not suggest functional changes in BCR-ABL1 V299L and WT cell lines.

overall_design: RNA-seq of parental murine Ph+ acute lymphoblastic leukemia (Ph+ ALL) cell line and derived cell lines (via dose escalating concentrations of dasatinib or DMSO vehicle control).

first: Douglas

last: Lauffenburger

last: Hemann


title: Effect of Smyd1 conditional knockout on gene expression in skeletal muscle

city: Houston

first: M. David

last: Stewart

state: TX

address: 4800 Calhoun Rd

institute: University of Houston

summary: Transcriptome analysis by RNA-seq of tibialis anterior muscle from control and Smyd1 myocyte-specific conditional knockout mice at 6 weeks of age.  Smyd1 is a methyltransferase specifically expressed in striated muscle and CD8+ T cells.  Smyd1 deficiency resulted in centronuclear myopathy primarily affecting fast-twitch muscle fibers.  These results provide insight into how loss of Smyd1 altered transcriptional programs resulting in centronuclear myopathy.

overall_design: 6 animals per group (control and Smyd1 conditional knockout)

first: M

middle: D


title: Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition


title: Metabolic Regulation of Gene Expression by Histone Lysine ß-hydroxybutyrylation [ChIP-seq]

first: Yingming

overall_design:
ChIP-seq for histone Kbhb marks in both "starved (ST)" and "fed (AL)" mouse liver cells
The anti-H3K4bhb, -H3K9bhb, and -H4K8bhb antibodies were generated from PTM biolabs. The process for generating antibodies were described similarly in  Cell, 2011. 146: p. 1016-1028, Mol Cell, 2015. 58(2): p. 203-15, Nat Chem Biol, 2014. 10(5): p. 365-70, except for using different immunogens.

first: Di

last: Zhang

first: Dongjun

last: Chung


title: Next Generation Sequencing Facilitates Quantitative Analysis of germ cell RA signaling mutant and control THY1+ spermatogonia Transcriptomes

status: Public on Apr 04 2016

first: Zhen

last: Lin

state: Shanghai

address: 320 Yue Yang Road

department: Shanghai  Institute of Biochemistry and Cell Biology

institute: University of Chinese Academy of Sciences

summary:
Purpose: The goal of this sequencing  is to investigate alterations in gene expression that result from impaired retinoid signaling compared with control, and how the RA signaling controls spermatogonia differentiation
Methods: THY1+ spermatogonia mRNA profiles of 4-day-old control and germ cell specific impaired retinoid signaling mice were generated by High-throughput sequencing
Results: Gene ontology (GO) analysis of the genes at the top of the ranked genes indicated enrichment in genes associated with roles in reproduction, transcription and spermatogenesis. In total, we identified 1633 and 742 transcripts (Reads Per Kilobase of transcript per Million mapped reads (RPKM) > 1) that were significantly (p-value < 0.05, > 1.5-fold difference) down- and up-regulated, respectively, in the germ cell mutants compared with the controls. Most importantly, we found that the majority of transcripts of replication-dependent core histone genes, histone cluster 1 (Hist1) were downregulated in germ cell mutants.

overall_design: THY1+ spermatogonia mRNA profiles of 4-day old  germ cell specific impaired retinoid signaling and control mice were generated by deep sequencing, twice, using Illumina HiSeq 2000

first: Yao

last: Chen

first: Li

last: Ma


title: The role of WRKY transcription factors in stress responses

city: Helsinki

first: Mikael

last: Brosché

address: Viikinkaari 1

department: Department of Biosciences

institute: University of Helsinki


title: mRNA sequence data from anterior ovarioles of w1118 virgin females of Drosophila melanogaster

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: Transcriptional profiling of anterior ovarioles (germaria and round previtellogenic egg chambers) of w1118 virgin females of Drosophila melanogaster 1 to 8 days post eclosion.

overall_design: Anterior ovarioles were dissected from w1118 virgin females 1 to 8 days post eclosion. Three independent biological replicates were prepared for each day. Total RNA was isolated from the samples and used for the generation of multiplexed stranded PolyA+ libraries. External RNA controls were added to ovarian polyA+ RNA during library preparation. 76bp single end libraries were sequenced by Illumina Hiseq 2000.

first: Hina

last: Sultana

first: Haiwang

last: Yang


title: H3K36ac is an evolutionary conserved histone modification that marks active genes in plants

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

summary: In eukaryotic cells, DNA is tightly packed in the nucleus in chromatin which has histones as its main protein component. Histones are subject to a large number of distinct post-translational modifications, whose sequential or combinatorial action affects genome function. Here, we report the identification of acetylation at lysine 36 in histone H3 (H3K36ac) as a modification in Arabidopsis thaliana. H3K36ac was found to be an evolutionary conserved modification in seed plants. It is highly enriched in euchromatin and very low in heterochromatin. Genome-wide ChIP-seq experiments revealed that H3K36ac is generally found at the 5’ end of genes. Independently of gene length, H3K36ac covers about 500 bp, about two to three nucleosomes, immediately downstream of the transcriptional start. H3K36ac overlaps with H3K4me3 and the H2A.Z histone variant. The histone acetyl transferase GCN5 and the histone deacetylase HDA19 are required for normal steady state levels of H3K36ac in plants. There is negative crosstalk between H3K36ac and H3K36me3, mediated by the histone methyl transferase SDG8 and GCN5. H3K36ac levels are associated with transcriptional activity but show no linear relation. Instead, H3K36ac is a binary indicator of transcription

overall_design: Characterization of the genome-wide distribution of H3K36ac using ChIP-seq. Analysis of the mechanistic crosstalk in the deposition of acetylation and methylation at H3K36 by ChIP-seq of H3K36ac and H3K36me3 in sdg8-2 and gcn5-1, respectively.

first: Walid

last: Mahrez

middle: S

last: Trejo-Arellano

first: Lars

last: Hennig


title: Anterior Heart Field (AHF)-conditional Mef2c Knockout

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St

institute: J David Gladstone Institutes

summary: We have performed conditional inactivation of mef2c in the anterior heart field (AHF) of mice and observed a phenotypic spectrum of outflow tract anomalies in the conditional mutant hearts.  In an effort to identify misregulated genes in the outflow tracts of the mutants, we have performed RNA-Seq on outflow tract samples dissected from E10.5 mutant and wild-type embryos.

overall_design: There are four wild-type samples and four mutant samples.

last: Black

first: Reuben

last: Thomas


title: Long-range chromosome interactions mediated by cohesin shape circadian gene expression [ChIP-Seq]

first: Yichi

last: Xu

state: NY

address: 1275 York Avenue

institute: MSKCC

summary: Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes. As genome-wide transcription is organized under the high-order chromosome structure, it is unclear how circadian gene expression is influenced by chromosome structure. In this study, we focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor) in circadian rhythm. We analyzed the interactome of a Bmal1-bound enhancer upstream of a clock gene, Nr1d1, by 4C-seq and observed that cohesin binding sites are enriched in the interactome. Integrating circadian transcriptome data and cistrome data, we found that cohesin-CTCF co-binding sites tend to insulate the phases of circadian oscillating genes while cohesin-non-CTCF sites facilitate the interaction between circadian enhancer and promoter. A coarse-grained model integrating the long-range effect of cohesin and CTCF markedly improved our mechanistic understanding of circadian gene expression. This model is subsequently supported by our RNA-seq data from cohesin knockout cells. Cohesin is required at least in part for driving the circadian gene expression by facilitating the enhancer-promoter looping. Taken together, our study provided a novel insight into the relationship between circadian transcriptome and the high-order chromosome structure.

overall_design: Bmal1 ChIP-Seq in WT mouse embryonic fibroblast cells

first: Weimin

last: Guo

first: Ping

last: Li

first: Yan

first: Zenghua

last: Fan

first: Zhihu

last: Zhao

first: Jun

last: Yan


title: Regulation of poly(A) tail and translation during the somatic cell cycle

city: Seoul

first: Jong-Eun

last: Park

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: Poly(A) tails are critical for mRNA stability and translation. However, recent studies have challenged this view, showing that poly(A) tail length and translation efficiency are decoupled in non-embryonic cells. Using TAIL-seq and ribosome profiling, we investigate poly(A) tail dynamics and translational control in the somatic cell cycle. We find dramatic changes in poly(A) tail lengths of cell cycle regulatory genes like CDK1, TOP2A, and FBXO5, explaining their translational repression in M phase. We also find that poly(A) tail length is coupled to translation when the poly(A) tail is <20 nucleotides. However, as most genes have >20 nucleotide poly(A) tails, their translation is regulated mainly via poly(A) tail length-independent mechanisms during the cell cycle. Specifically, we find that terminal oligopyrimidine (TOP) tract-containing transcripts escape global translational suppression in M phase and are actively translated. Our quantitative and comprehensive data provide a revised view of translational control in the somatic cell cycle.

overall_design: HeLa cells were synchronized at S or M phase, and subject to RNA-seq, ribosome profiling and TAIL-seq analysis.

first: Hyerim

last: Yi

first: Yoosik

last: Kim

first: Hyeshik

last: Chang

first: V

middle: N


title: Transcriptome and analysis of Wdr70 deletion by next-generation sequencing

city: Chengdu

first: Cong

last: Liu

address: Ren Ming Nan Lu 3-17

institute: Sichuan University

summary: CRL4 is a family of SCF-like ubiquitin ligase constituted by Cul4-Ddb1-RING finger scaffold and DCAF substrate adaptors. We revealed Wdr70 as a novel DCAF protein that assembles with Cul4-Ddb1 and functions as chromatin remodeling factor in Schizosaccharomyces pombe.Besides its function in DNA repair, CRL4Wdr70 is speculated to regulate gene expression in a  subset of yeast transcriptome. Here we use the next-generation sequencing to show that deletion of Wdr70 gene disturbs the gene expression profile of G2-synchronised yeast cells.

overall_design: Examination of genome-wide gene expression in 2 different yeast strains using Illumina Hiseq2500.

first: Antony

last: Carr

first: Ming

last: Zeng