title: Identification of a portal vessel-associated fetal liver hematopoietic stem cell niche

first: Jalal

middle: Ahmed

last: Khan

state: New York

address: 1301 Morris Park Ave

department: 1Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Icahn School of Medicine

summary: Whereas the cellular basis of the hematopoietic stem cell (HSC) niche in the bone marrow has been characterized, the nature of the fetal liver (FL) niche is not yet elucidated. We show that Nestin+NG2+ pericytes associate with portal vessels, forming a niche promoting HSC expansion. Nestin+NG2+ cells and HSCs scale during development with the fractal branching patterns of portal vessels, tributaries of the umbilical vein. After closure of the umbilical inlet at birth, portal vessels undergo a transition from Neuropilin-1+Ephrin-B2+ artery to EphB4+ vein phenotype, associated with a loss of peri-portal Nestin+NG2+ cells and emigration of HSCs away from portal vessels. These data support a model in which HSCs are titrated against a peri-portal vascular niche with a fractal-like organization enabled by placental circulation.

overall_design: Characterization of the transcriptome of fetal liver and adult bone marrow niche using RNA-seq

first: Paul

last: Frenette


title: Brg1 Coordinates Multiple Processes During Retinogenesis and is a Tumor Suppressor in Retinoblastoma [ChIP-seq]

status: Public on Dec 02 2015

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

country: USA

institute: St Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Retinal development requires precise temporal and spatial coordination of cell cycle exit, cell-fate specification, cell migration and differentiation.  When this process is disrupted, retinoblastoma, a developmental tumor of the retina, can form. Epigenetic modulators are central to precisely coordinating developmental events, and many epigenetic processes have been implicated in cancer. Studying epigenetic mechanisms in development is challenging because they often regulate multiple cellular processes; therefore, elucidating the primary molecular mechanisms involved can be difficult. Here we explore the role of Brg1 in retinal development and retinoblastoma by using molecular and cellular approaches. Brg1 regulated retinal size by controlling cell cycle length, cell cycle exit, and cell survival during development. Brg1 was not required for cell-fate specification but was required for photoreceptor differentiation and cell adhesion/polarity programs that contribute to proper retinal lamination during development. The combination of defective cell differentiation and lamination led to retinal degeneration in Brg1-deficient retinae. Despite the hypocellularity, premature cell cycle exit, increased cell death, and extended cell cycle length, retinal progenitor cells persisted in Brg1-deficient retinae, thereby making them more susceptible to retinoblastoma. ChIP-seq analysis provided insight into the underlying molecular mechanisms of these complex Brg1-regulated cellular processes during retinal development.

overall_design: Histone marks and BRG1 in mouse BRG1 -/- retinae from mice were compared to controls at distinct time points in embryonic and post-natal development

first: Issam

last: Al-Diri

first: Itsuki

last: Ajioka

first: Beisi

last: Xu

first: Jiakun

last: Zhang

first: Xiang

last: Chen

first: Claudia

last: Benavente

first: Dianna

last: Johnson

first: Jennifer

last: Akiyama

first: Len

last: Pennacchio

first: Michael

last: Dyer


title: Dynamic Changes in Histone Modifications Precede de novo DNA Methylation in Oocytes

city: Cambridge

first: Gavin

last: Kelsey

address: Babraham Research Campus

country: United Kingdom

institute: The Babraham Institute

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: Erasure and subsequent re-instatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly understood, but a number of post-translational modifications of histones are implicated in antagonizing or recruiting the de novo DNA methylation complex. In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in non-dividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Using a chromatin immunoprecipitation and genome-wide sequencing (ChIP-Seq) protocol optimized for low cell numbers and novel techniques for isolating primary and growing oocytes, profiles were generated for histone modifications implicated in promoting or inhibiting DNA methylation. CGIs destined for DNA methylation show reduced protective H3K4me2 and H3K4me3 in both primary and growing oocytes, while permissive H3K36me3 increases specifically at these CGIs in growing oocytes. Methylome profiling of oocytes deficient in H3K4 demethylases KDM1A or KDM1B indicated that removal of H3K4 methylation is necessary for proper methylation establishment at CGIs. This work represents the first systematic study performing ChIP-Seq in oocytes, and shows that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events.

overall_design: ChIP-Seq in duplicate of four histone modifications in primary and growing oocytes, bisulfite sequencing in triplicate of mature oocytes lacking KDM1A/LSD1 or KDM1B/AOF1, RNA-Seq of mature oocytes lacking KDM1B/AOF1, and RNA-Seq of primary E18.5 oocytes.

first: Kathleen

middle: R

last: Stewart

first: Lenka

last: Veselovska

first: Jeesun

last: Kim

first: Jiahao

last: Huang

first: Heba

last: Saadeh

first: Shin-ichi

last: Tomizawa

first: Sébastien

middle: A

last: Smallwood

first: Taiping


title: Next Generation Sequencing Facilitates Quantitative Analysis of Tetranychus urticae and Its Sibling Species Tetranychus cinnabarinus Transcriptomes

city: Chongqing

first: Lu

last: Wencai

address: 216 Tiansheng Road

country: China

institute: Southwest University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of differentially expressed genes (DEG) between the treated samples of mites.The goal of the study is to elucidate the invasion mechanism that results in the continuous expansion of Tetranychus urticae that has occurred in China.
Methods:Transcriptome profiling by RNA sequencing is becoming  an attractive method as it facilitates rapid generation, identification  and quantification of large number of transcripts,  even in the species where no prior genome sequence information  is available.
Results:the expression of 10 P450(cytochrome P450 monooxygenases), 6 GST(glutathione S-transferases), 13 CCE(carboxy/cholinesterases) and other novel candidate genes was higher (>2-fold) in T. urticae than in T. cinnabarinus as detected by using the digital gene expression (DGE) method.

sample_organism:
Tetranychus urticae
Tetranychus cinnabarinus

overall_design: T .cinnabarinus and T. urticae, which were exposed to abamectin, fenpropathrin and tebufenpyrad, and preexposed mites were used for constructing RNA-seq libraries. The experiment was performed with three biological replicates, resulting in total of 24 RNA-seq libraries for sequencing.

first: He

last: Lin


title: Myocardin-related transcription factors are required for cardiac development and function

city: Dallas

first: Eric

middle: N

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

summary: Myocardin-Related Transcription Factors A and B (MRTF-A and MRTF-B) are highly homologous proteins that function as powerful coactivators of serum response factor (SRF), a ubiquitously expressed transcription factor essential for cardiac development. The SRF/MRTF complex binds to CArG boxes found in the control regions of genes that regulate cytoskeletal dynamics and muscle contraction, among other processes. While SRF is required for heart development and function, the role of MRTFs in the developing or adult heart has not been explored.  Through cardiac-specific deletion of MRTF alleles in mice, we show that either MRTF-A or MRTF-B is dispensable for cardiac development and function, whereas deletion of both MRTF-A and MRTF-B causes a spectrum of structural and functional cardiac abnormalities. Defects observed in MRTF-A/B null mice ranged from reduced cardiac contractility and adult onset heart failure to neonatal lethality accompanied by sarcomere disarray.  RNA-seq analysis on neonatal hearts identified the most altered pathways in MRTF double knockout hearts as being involved in cytoskeletal organization. Together, these findings demonstrate redundant but essential roles of the MRTFs in maintenance of cardiac structure and function and as indispensible links in cardiac cytoskeletal gene regulatory networks.

overall_design: P0 Heart mRNA profiles of wild-type (WT) and MRTFA/B double knockout animals were generated in duplicate using DeepSeq using Illumina HiSeq 2500

first: Rhonda

last: Bassel-Duby


title: Persistent Requirement and Alteration of the Key Targets of PRDM1 during Primordial Germ Cell Development in Mice

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

summary: Primordial germ cells (PGCs) are the foundation of totipotency and vital for reproduction and heredity. PGCs in mice arise from the epiblast around Embryonic Day (E) 7.0, migrate through the hindgut endoderm, and colonize and proliferate in the embryonic gonads until around E13.5 prior to their differentiation either into pro-spermatogonia or oogonia. PRDM1, a transcriptional repressor, plays an essential role in PGC specification that includes robustly repressing a somatic mesodermal program. Using an inducible conditional knockout system, we show here that PRDM1 is critically required throughout PGC development. When Prdm1 was deleted in migrating PGCs at E9.5/E10.5 or in male gonadal PGCs at E11.5, PGCs were eliminated by apoptosis from around E10/5/E11.5 or E13.5, respectively. When Prdm1 was deleted in female gonadal PGCs at E11.5, PGCs progressed into the first meiotic prophase in an apparently normal fashion, but the oogonia exhibited an aberrant pachytene phenotype, undergoing abrupt apoptosis from around E16.5. The escape of a fraction of PGCs (~10%) from the Prdm1 deletion was sufficient to recover fairly normal germ-cell pools both in male and female adults. The key targets of PRDM1 in migrating/gonadal PGCs, including genes for development, apoptosis, and pro-spermatogonial differentiation, showed only a modest overlap with those upon PGC specification and were enriched with histone H3 lysine 27 tri-methylation (H3K27me3). Our findings provide a critical insight into the mechanism for maintaining the transcriptional integrity of PGCs.

overall_design: Examination of Prdm1 conditional knock-out primordial germ cells

first: Chika

last: Yamashiro

first: Takayuki

last: Hirota

first: Kazuki

last: Kurimoto

first: Tomonori

last: Nakamura

first: So

last: Nagaoka

first: Hiroshi

last: Ohta

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: RNA Seq in wild type and zfs1 deficient C. albicans

status: Public on Dec 04 2015

city: Durham

first: Melissa

last: Wells

state: NC

address: 111 TW Alexander Drive

department: LST

institute: NIEHS

summary: Members of the tristetraprolin (TTP) family of CCCH tandem zinc finger proteins bind to AU-rich regions in the 3'-untranslated regions (UTR) of target mRNAs, leading to their deadenylation and accelerated decay.  Family members in S. cerevisiae influence iron metabolism, whereas the family member in S. pombe leads to defects in cell-cell interactions.  In the important human fungal pathogen Candida albicans, deep sequencing of transcripts in mutants deficient in the analogous protein, Zfs1p, revealed 156 transcripts whose levels were significantly increased by at least 1.5-fold.  Of these, 113 (72%) contained at least a single predicted TTP family member binding site in their 3’UTR.  In contrast, 102 transcripts were significantly down-regulated by 1.5-fold or more, and only 5 (5%) of these contained potential binding sites.  Sequences of the proteins encoded by the putative Zfs1p targets were highly conserved among other Candida species, while the predicted Zfs1p binding sites in these mRNAs progressively “disappeared” with increasing evolutionary distance from the parental species.  The C. albicans results support the concept that the biochemical functions of the TTP family members in fungal organisms are highly conserved, yet each species appears to have evolved its own set of transcripts that are regulated by this mechanism.

overall_design: Strains were grown in YPD media to approximately OD600=0.75 and total RNA was harvested from four biological replicates each of WT and 2 independent isolates of the zfs1 deletion.

middle: L

first: Perry

middle: J

last: Blackshear

first: Onica

last: Washington

first: Stephanie

last: Hicks

first: Clarissa

last: Nobile

first: Nairi

last: Hartooni

first: Gerald

middle: M

last: Wilson

first: Beth

middle: E

last: Zucconi

first: Weichun

last: Huang

first: Leping

last: Li

first: David

middle: C

last: Fargo


title: RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at age of 12 weeks)

status: Public on Dec 03 2015

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
The RNA-seq data contain 3 tissues (brain, liver, skin) of N.furzeri GRZ

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 15 samples: 5 biological replicates per tissue

first: Marco

last: Groth

first: Mario

last: Baumgart

first: Steffen

last: Priebe

first: Andreas

last: Dix

first: Reinhard

last: Guthke

first: Matthias

last: Platzer

first: Alessandro

last: Cellerino


title: Molecular distinctions between proprioceptors supplying Tibialis anterior (TA) and Gastrocnemius (GS) muscles

city: New York

first: Sebastian

last: Poliak

state: NY

address: 701 West 168st

department: Neuroscience and Biochemistry and Molecular Biophysics

institute: Columbia University

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

overall_design: Refer to individual Series


title: Affymetrix exon array and iCLIP analysis of SAFB1 function

status: Public on Dec 01 2015

city: Bristol

first: James

last: Uney

address: Medical School, University Walk

department: School of Clinical Sciences

institute: University of Bristol

type:
Expression profiling by array
Other


title: The effect of in vitro cultivation on the transcriptome of adult Brugia malayi

city: Ste-Anne-de-Bellevue

first: Timothy

middle: G.

last: Geary

state: Quebec

address: 21,111 Lakeshore Rd

department: Parasitology

country: Canada

institute: McGill University

summary: We examined the global transcriptomic profile of B. malayi females at four different time points (6 biological replicates per time point) over 5 days in culture. Focusing on genes that are differentially expressed at various time points, we observed a general perturbation of the expression profile between dissection from the host and receipt after shipment.  The expression of a few genes remained changed at the end of the experiment, after 5 days under controlled conditions; in particular, genes encoding cuticle collagens were prominently represented and strongly overexpressed.

overall_design: Transcriptomic changes over 4 different timepoints: upon jird extraction, upon arrival, 48 hours in culture, 5 days in culture (6 biological replicates per time point).

first: Cristina

last: Ballesteros

first: Lucienne

last: Tritten

first: Maeghan

last: O’Neill

first: Erica

last: Burkman

first: Weam

middle: I

last: Zaky

first: Jianguo

last: Xia

first: Andrew

last: Moorhead

first: Steven

last: Williams

middle: G


title: Production of functional small interfering RNAs by human Dicer

first: Edward

middle: Matthew

last: Kennedy

address: Department of Molecular Genetics and Microbiology, Box 3025

department: Molecular Genetics and Microbiology

institute: Duke University

type: Non-coding RNA profiling by high throughput sequencing

summary: While RNA interference (RNAi) functions as a potent antiviral innate immune response in plants and invertebrates, mammalian somatic cells appear incapable of mounting an RNAi response and few small interfering RNAs (siRNAs) can be detected. To examine why siRNA production is inefficient, we have generated double knockout human cells lacking both Dicer and PKR. Using these cells, which tolerate dsRNA expression, we show that mutant forms of human Dicer lacking the amino-terminal helicase domain can process dsRNAs to produce high levels of siRNAs that are readily detectable by Northern blot and that can effectively and specifically inhibit the expression of cognate mRNAs. However, even these more active Dicer mutants produce only modest levels of viral siRNAs in infected cells that are insufficient to inhibit viral replication. We conclude that the production of siRNAs from viral dsRNAs is likely inefficient due to the poor accessibility of viral dsRNAs to Dicer.

sample_organism:
Homo sapiens
Human poliovirus 1 strain Sabin

overall_design: Small RNA profiling of Dicer-deficient human NoDice(4-25) and NoDice(4-25)ΔPKR cells expressing full-length (WT) human Dicer or N-terminal Dicer truncations (F1, N1, N3) and their ability to process endogenous, ectopically-expressed, and viral double-stranded RNAs into small interfering RNAs (siRNAs).

first: Adam

middle: W

last: Whisnant

first: Anand

middle: V

last: Kornepati

first: Hal

middle: P

last: Bogerd

first: Bryan

last: Cullen


title: Next Generation Sequencing Investigation of altered transcripts in presence of dominant-negative transcription factor

city: La Jolla

first: Gene

last: Yeo

state: CA

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

institute: UCSD

summary:
Purpose:The goals of this study was to determine alterations in expression levels of transcripts downstream of a dominant-negative transcription factor.  Quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods was used to confirm the altered expression of targets.
Methods: Striatal mRNA profiles of 11-month-old wild-type (WT) and Nestin-Cre X PPAR delta E411P mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.  Western blots, and immunofluorescence was also used to confirm if altered mRNA levels translated to changes at the protein level.
Results: Using data analysis workflow, we mapped sequence reads for each sample to the mouse genome (build mm9) and identified transcripts in the striatum of WT and PPARdelta E411P mice.
Conclusions: Our study found multiple transcripts altered in the striatum of the Nestin-Cre x PPAR delta E411P mice as compared to WT striatum, as generated by RNA-SEQ in biologic replicates.

overall_design: Striatal mRNA profiles of 11-month-old wild type (WT) and Nestin-Cre X PPAR delta E411P mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Albert

last: La Spada


title: The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons

city: Madison

first: Patricia

last: Kiley

state: WI

address: 420 Henry Mall, Room 1135 Biochemistry Building

department: Biomolecular Chemistry

institute: University of Wisconsin - Madison

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

sample_organism: Escherichia coli str. K-12 substr. MG1655


title: The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons [ChIP-seq]

summary: As descirbed in the manuscript "The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons" we mapped the locations of Fur DNA binding in E. coli K12 under aerobic or anaerobic growth conditions and anerobic iron deficient growth conditions.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: We performed ChIP-Seq to map the locations of Fur DNA binding in E. coli K12 under aerobic or anaerobic growth conditions and anerobic iron deficient growth conditions.

first: Nicole

last: Beauchene

first: Kevin

middle: S

last: Myers

first: Dongjun

last: Chung

first: Dan

last: Park

first: Allison

last: Weisnicht

first: Sunduz

last: Keles


title: The Ski2-family helicase Obelus regulates Crumbs alternative splicing and cell polarity

first: Jennifer

last: Zallen

address: 1275 York Avenue

department: Developmental Biology

institute: Sloan Kettering Institute

summary: We identified Obelus, a conserved Ski2-family DExD/H-box helicase in a screen for Drosophila mutants with defects in epithelial polarity and junctional organization. To identify the functional targets of Obelus we used RNA sequencing and compared the transcriptional and splicing profiles of staged wild-type embryos with obe1/obe2 and obe2/Df(3R)Exel6174 (obe2/Df) mutant embryos.

overall_design: Comparing the mRNA expression profiles from late stage 5/early stage 6 Drosophila embryos from Oregon-R (wild type), obe2/Df, obe1/obe2 in triplicate, using Illumina HiSeq2500.

first: Athea

last: Vichas


title: Early signs of neurodegeneration in dopaminergic neurons observed in a Drosophila model of Parkinson’s disease

city: Cologne

first: Julia

last: Hoffmann

address: Joseph-Stelzmann-Str. 9b

department: Partridge

institute: MPI for Biology of Ageing

summary: Parkinson’s disease (PD) is the most common neurodegenerative movement disorder characterized by a progressive loss of dopamine-containing neurons in the Substantia nigra and the presence of so-called Lewy bodies. The mechanisms underlying disease initiation and development are poorly understood and causative therapies are currently not available. In order to gain insights into the molecular signatures of affected neurons during early stages of Parkinson’s disease, we utilized a Drosophila Parkinson model. We applied the pesticide rotenone to induce Parkinson-like phenotypes in the fly and isolated dopamine containing neurons of animals at a presymptomatic disease stage in order to elucidate their transcriptomic characteristics. In these rotenone treated neurons several gene ontologies, including regulation of cell death, were significantly enriched. Moreover, numerous signaling pathways known to be relevant for cell survival were apparently deregulated in these neurons. While the activities of the MAPK/EGFR- and TGF-β-signaling pathways were enhanced, the performance of the Wnt-pathway was dampened, which may be of central importance for their increased propensity to undergo apoptosis. Thus, further studies involving these pathways may provide new insights into the molecular events underlying pathogenesis and may lead to the identification of new targets for neuroprotective interventions.

overall_design: We used rotenone to induce Parkinsonism in the fly and combined this with a cDNA microarray analysis of DA neurons that were isolated using a magnetic bead based approach.

first: Flora

last: Stephano

first: Stella

last: Nolte

first: Samar

last: El-Kholy

first: Iris

last: Bruchhaus

first: Christine

last: Fink

first: Thomas

last: Roeder


title: E2F1 ChIP-Seq on mouse hepatocytes overexpressing E2F1

city: lausanne

first: Pierre-Damien

last: Denechaud

address: Rue du Bugnon 7

department: Physiology

country: Switzerland

institute: UNIL

summary: E2F transcription factors are known regulators of the cell cycle, proliferation, apoptosis and differentiation. We reveal an essential role for E2F1 in liver through the regulation of glycolysis and lipogenesis. E2F1 deficiency leads to a decreased in glycolysis and de novo synthesis of fatty acids in hepatocytes. ChIP-Seq was performed to determine direct tagets of E2F1 in hepatocytes. We highlight that E2F1 directly binds the promoters of genes implicated in metabolic process and notably key lipogenic genes to control these pathways.

overall_design: we performed 2 independents replicates. Each replicate is the combination of 2 independents ChIP experiments

first: PD

first: L

last: Fajas Coll


title: Loss of the yeast SR protein Npl3 alters gene expression due to transcription readthrough

city: Edinburgh

first: Rebecca

middle: Katharine

last: Holmes

state: Midlothian

address: Max Born Crescent

department: Wellcome Trust Centre for Cell Biology

institute: Edinburgh University

summary: Yeast Npl3 is a highly abundant RNA binding protein, related to metazoan SR proteins, with reported functions including transcription elongation, splicing and RNA 3’ end processing. To identify direct targets and functions for Npl3, we used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites. Npl3 binds diverse RNA species, at sites indicative of roles in both early pre-mRNA processing and 3’ end formation on mRNAs and ncRNAs. Consistent with this, tiling array and RNAPII binding data revealed 3’ extended mRNA and snoRNA transcripts in the absence of Npl3. This reflected transcriptional readthrough by RNAPII, and extension and stabilization of cryptic unstable transcript (CUT) long noncoding RNAs. Transcription readthrough was widespread, often resulting in down-regulation of neighboring genes. We conclude that Npl3 is required for the formation of a termination-competent RNA, affecting both coding and noncoding RNAs.

overall_design: We assessed the role of Npl3 in transcription termination, by examining the RNA binding profile of Npl3, Nab3 and Rpo21in WT yeast, as well as Nab3 and Rpo21 in npl3∆ yeast. We have included replicates of each sample as well as an untagged 'BY' negative control

first: Alex

last: Tuck

first: Chenchen

last: Zhu

first: Hywel

last: Dunn-Davies

first: Grzegorz

last: Kudla

first: Sandra

last: Clauder-Munster

first: Sander

last: Granneman

first: Lars

last: Steinmetz

last: Guthrie

first: David

last: Tollervey


title: Site-specific methylation and acetylation of lysine residues in the C-terminal domain (CTD) of RNA polymerase II

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

country: Italy

institute: EMBL

summary: Dynamic modification of the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII) regulates transcription-coupled processes in eukaryotes. The CTD in mammals is composed of 52 heptad-repeats with the consensus sequence Y1-S2-P3-T4-S5-P6-S7. Repeats in the distal part of CTD deviate from the consensus sequence and have frequently replaced serine at position 7 by lysine residues (K7). Mass spectrometry analysis revealed modification of K7 residues in heptad-repeats 39, 42, and 47/49 by acetylation and in heptad-repeats 38, 39, 40, 42, and 47/49 by mono-, di-, or trimethylation. Notably, acetylated as well as di- and tri-methylated K7 residues were found exclusively in phosphorylated CTD peptides, while mono-methylated K7 residues occurred also in non-phosphorylated CTD peptides. Methylation of K7 residues was further studied with the monoclonal antibody (mAb) 1F5, which recognizes mono- and di-methylated K7 in CTD. ChIP experiments revealed high levels of K7 methylation at the transcriptional start site of genes. The low levels of K7 methylation in the body of genes results from impairment of epitope recognition in hyper-phosphorylated CTD by mAb 1F5. In agreement with this notion, phosphatase treatment of hyper-phosphorylated CTD or treatment of cells with kinase inhibitor flavopiridol restored the reactivity of mAb 1F5 towards methylated K7 residues in CTD. We conclude that methylation and acetylation of K7 residues further expand the mammalian CTD code and potentially contribute to regulation of gene expression.

overall_design: This study was performed in a human Raji cell line. It contains ChIP-seq data for CTD Lysine mono- and di-methylated (one replicate). Other samples used in this study can be found at GSE52914.

first: Kirsten

last: Voss

first: Ignasi

last: Forné

first: Nicolas

last: Descostes

first: Corinna

last: Hintermair

first: Roland

last: Schüller

first: Martin

last: Heidemann

first: Andrew

last: Flatley

first: Muhammad

last: Maqbool

first: Axel

last: Imhof

first: Marta

last: Gut

first: Ivo

first: Elisabeth

last: Kremmer

first: Jean-Christophe

last: Andrau

first: Dirk

last: Eick


title: Copper homeostasis at the host vibrio interface: lessons from intracellular vibrio transcriptomics

city: Montpellier

first: Guillaume

last: Charriere

address: Place Eugene Bataillon

department: UMR 5244 IHPE

country: France

institute: Universite de Montpellier

summary:
Recent studies revealed that several vibrio species have evolved the capacity to survive inside host cells. However, it is still often ignored if intracellular stages are required for pathogenicity. Virulence of Vibrio tasmaniensis LGP32, a strain pathogenic for Crassostrea gigas oysters, depends on entry into hemocytes, the oyster immune cells. To identify the mechanisms involved in LGP32 resistance to the hemocyte killing machinery and phagocytosis-dependent cytotoxicity, we used a global comparative RNAseq approach early after vibrio entry into hemocytes (1h after phagocytosis). Transcripts of intracellular LGP32 were obtained from hemocyte monolayers and their relative level of expression was compared to that of transcripts of extracellular LGP32 obtained from vibrios kept in SSW alone.
LGP32 was grown at 20°C in Zobell medium for 10h and washed twice in SSW by centrifugations (10min, 1000g, 20°C). Bacteria were then600 of 0.5 (1.10^9 cfu/mL equivalent). Hemolymph was collected from the adductor muscle of oysters using a 2 mL syringe with a 23-G needle. Freshly collected hemolymph was dispensed in a 6-well plate to obtain monolayers of 6 × 106 hemocytes per well. One hour after plating, vibrios were added at a multiplicity of infection of 100:1, and plates were centrifuged for 5min at 400g for binding synchronization. After 1h of co-incubation, wells were washed extensively three times with SSW to remove extracellular bacteria and 500 µl Trizol reagent (Invitrogen) was added to every well for total RNA extraction. The efficiency of vibrios internalization in hemocytes was verified by microscopy showing that about 40% of hemocytes internalized about 50 to 70 bacteria, with rare bacteria remaining extracellular.  As a control, washed bacteria were incubated in triplicates in SSW for 1h and resuspended in Trizol after centrifugation. RNA from three independent experiments of LGP32 phagocytosis by hemocytes were extracted using the Trizol reagent protocol (Life Technologies). RNA concentration was measured using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc.) and RNA quality was monitored by agarose gel electrophoresis and a 2100 Bioanalyzer (Agilent Technologies Inc.).  The bioanalyzer analysis showed that bacterial RNAs represented approximately 10% of the total RNA in the intrahemocyte samples. Accordingly, control samples were prepared by mixing total RNA extracted from LGP32 incubated in SSW with C. gigas hemocyte RNA with a ratio of 1:9.
For each sample, 7 µg of starting material was treated with DNaseI (4 U) (Ambion’s DNA-free™) following the manufacturer instructions. Samples were then enriched in bacterial RNA using the MICROBEnrich™ Kit (Ambion) and bacterial rRNA were then removed by the MICROBExpress™Kit (Ambion) following the manufacturer instructions. Because the MICROBEnrich™ Kit is based on oligonucleotides that are designed to capture rRNAs from mammal species, it is not fully efficient to remove invertebrate rRNAs. Accordingly, we performed a further depletion step using a 5’-phosphate-dependent exonuclease (Terminator, Epicentre), that degrades processed transcripts, following instructions from the manufacturer. For cDNA sequencing, for each sample, a directional cDNA library was constructed and sequenced on an illumina Hiseq 1000, in paired-end reads of 2x100bp. 3 samples were multiplexed per lane giving ~ 60 x 10^6 reads per sample. Out of 50-60 M reads obtained from the RNA-seq, 1.2 M reads from the SSW samples and 2.3 M reads from the intrahemocyte samples were successfully mapped onto the genome of LGP32.

overall_design: 6 biological samples (12 paired-end fastq files) in 2 experimental conditions (triplicates) :  control and intra oyster hemocytes bacteria.

first: Delphine

last: Destoumieux-Garzon


title: RNA accumulation profiles generated by RNA-Seq in mutants of Schizosaccharomyces pombe exosome exonucleases Rrp6 and Dis3

city: Stony Brook

first: Janet

last: Leatherwood

address: 343 Life Sciences Building

department: Microbiology

institute: Stony Brook University

summary:
We studied the differences in RNA accumulation profiles of an rrp6-null mutant and compared it to RNA accumulation in rrp6 catalytic mutants as well as dis3 mutants using RNA-Seq. Rrp6 and Dis3 are exosome exoncleases, therefore this study was used to determine their target RNAs
We examined 3' end RNA processing changes by RNA-Seq in wild type, rrp6Δ and rrp6-cat mutants. Libraries were made by 3' adapter ligation

overall_design:
polyA selected RNA abundance measurements in wild type and exosome exonuclease mutants rrp6Δ, rrp6-cat, dis3-4 (ts mutant at 23°C and 30°C), rrp6-cat dis3-4 (ts mutant at 23°C and 30°C) double mutant using paired-end Illumina sequencing of stranded libraries
3' end adapter ligated total RNA from wild type, rrp6Δ and rrp6-cat mutants was used to make stranded RNA-Seq libraries and sequenced by paired-end Illumina sequencing

first: Kaustav

last: Mukherjee


title: Genetic and epigenetic variation among inbred littermates: identification of metastable epialleles in the mouse

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

summary: Genomic DNA was extracted from the livers of 5 22week old male mice, bisulfite converted and sequenced to ~30x coverage. The mice were obtained from two litters from an inbred agouti viable yellow colony. The individuals were isogenic but differed in their coat phenotype with one having a yellow coat, one a psuedoagouti coat and the remaining were phenotypically C57/BL6. The resulting DNA metylation profiles were investigated for individual differences in DNA methylation, including the identificaiton of novel metastable epialleles.

overall_design: Whole genome bisulfite sequencing of liver DNA from five inbred male mice

first: Harald

last: Oey

first: Emma

last: Whitelaw


title: High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns and functions in Arabidopsis and rice

first: Xuehua

last: Zhong

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

summary: We generated genome-wide high-resolution maps of H4K16ac and H3K23ac in Arabidopsis thaliana and Oryza sativa.

sample_organism:
Arabidopsis thaliana
Oryza sativa

platform_organism:
Arabidopsis thaliana
Oryza sativa

overall_design: For wild-type Arabidopsis and rice plants, ChIP-seq was performed with H4K16ac and H3K23ac antibodies.

first: Li

last: Lu


title: Molecular distinctions between proprioceptors supplying Tibialis anterior (TA) and Gastrocnemius (GS) muscles [RNA-Seq]

first: Sebastian

last: Poliak

summary: Muscle-specific populations of proprioceptive sensory neurons form selective connections with spinal motor neurons, implying the existence of molecular distinctions between proprioceptor subpopulations. Here, we compare the gene expression profiles of proprioceptors that supply an antagonistic muscle pair functioning at a single hindlimb joint.

overall_design: TA and GS muscles in a Pv::YFP reporter line were injected at p0  with ctb-555; retrogradely labeled  proprioceptors were manually isolated at p1 and pooled to form 25-30 neuron samples.

first: Amy

last: Norovich

first: Thomas

last: Jessell


title: Multifunctional role of the transcription factor Blimp1 in coordinating plasma cell differentiation

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Blimp1 is an essential regulator of plasma cells. Here we studied its functions in early plasmablast differentiation by identifying regulated Blimp1 target genes. Blimp1 promoted plasmablast migration and adhesion by controlling many genes involved in these processes. It repressed several transcription factor genes and Aicda, thus silencing B-cell-specific gene expression, antigen presentation and class switch recombination in plasmablasts. It also directly activated genes, leading to increased expression of the plasma cell regulator IRF4 and proteins involved in immunoglobulin secretion. Blimp1 strongly induced immunoglobulin gene transcription by controlling the activity of Igh and Igk 3’ enhancers and regulated the posttranscriptional switch of expression from the membrane-bound to secreted immunoglobulin heavy-chain by activating Ell2. Notably, Blimp1 recruited chromatin-remodeling and histone-modifying complexes to regulate its target gene. Hence, many essential functions of plasma cells are under Blimp1 control.

overall_design: 40 samples in total: A) 16 RNA-Seq samples in 5 cell types: Activated B cells (Act B cell, 2 replicates), Pre-Plasmablasts (Pre-PB, 3 genotypes, 2-4 replicates each), Plasmablasts (PB, 2 replicates), Plasma cells (2 replicates), Mature B cells (2 replicates); B) 19 ChIP-Seq samples in 3 cell types: Act B cell (IRF4,  H3K9ac, H3K4me2, H3K4me3, 1 replicate each; H3K27me3, 2 genotypes, 2 and 1 replicates), Pre-PB (IRF4, 1 replicate; H3K27me3, 2 genotypes, 1 replicate each), PB ( PU.1, IRF4, H3K9ac, H3K4me2, H3K4me3, 1 replicate each;  Blimp1, H3K27me3, 2 replicates each); C) 5 ATAC-Seq samples in 3 cell types: Act B cell (2 genotypes, 1 replicate each), Pre-PB (2 genotypes, 1 replicate each), PB (1 replicate).

first: Martina

last: Minnich

first: Hiromi

last: Tagoh

first: Peter

last: Bönelt

first: Elin

last: Axelsson

first: Maria

last: Fischer

first: Beatriz

last: Cebolla

first: Alexander

last: Tarakhovsky

first: Stephen

last: Nutt

first: Markus

last: Jaritz

first: Meinrad

last: Busslinger


title: Mouse Hotchon ChIRP-seq

city: Porltand

first: Herman

middle: Scott

last: Stadler

state: OR

address: 3101 SW Sam Jackson Park Rd

institute: Shriners Hospital

summary: The goal of this study was to determine the genome-wide localization of the lncRNA Hotchon in murine limb mesenchyme

overall_design: Four samples were characterized.  Two samples, Limb Even and Limb Odd used limb mesenchyme which expressed the lncRNA Hotchon.  The Limb Even sample was hybridized with the Even Hotchon probe set, The Limb Odd sample was hybridized with the Odd Hotchon probe set.  Two additional samples from a mouse glial cell line that does not express the lncRNA Hotchon were used as controls and hybridized with either the Hotchon Odd or Hotchon Even probe set.

first: H


title: let-7 controls cancer stemness through ARID3B

city: Taipei

first: Tsai-Tsen

last: Liao

state: State...

address: No.201, Sec.2, Shih-Pai Rd. Peitou, Taipei, Taiwan, 11221, R.O.C

country: Taiwan

institute: Institute of Clinical Medicine

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

overall_design: Refer to individual Series


title: SAFB1 iCLIP in SHSY-5Y cells

first: James

last: Uney

address: Medical School, University Walk

institute: University of Bristol

summary: We used iCLIP to investigate the RNA interactions of the RNA binding protein SAFB1

overall_design: SH-SY5Y neuroblastoma cells were UV-crosslinked to mediate the formation of protein-RNA complexes. SAFB1 iCLIP was performed with partial RNase I digestion and following SDS-PAGE analysis of immunoprecipitated SAFB1 the cross-linked RNA was extracted, reverse-transcribed and PCR-amplified before being subjected to high-throughput sequencing using Illumina HiSeq 2500.

first: Caroline

last: Rivers


title: Genome-wide characterization of ARID3B binding sites and KDM4C in ARID3B-knockout OECM1 cells

summary: In this study we assayed for genome-wide localization of ARID3B and KDM4C enrichment in control and ARID3B-knockout OECM1 cells. The expression of the embryonic stem cell (ESC) signature in cancer cells indicates the coordinated regulation of the stemness genes in cancer stem cells, which are responsible for cancer initiation and dissemination. let-7 family microRNAs are crucial regulators for stem cell differentiation. In cancer cells, let-7 suppresses cancer stemness through targeting different oncogenes such as c-Myc, RAS, and HMGA2. However, most let-7 target genes are oncogenes rather than stemness factors, and the mechanism of let-7-repressed stemness is unclear. Here we demonstrate that let-7 supresses the formation of AT-rich interacting domain 3B (ARID3B) complex through targeting the expression of ARID3B, the interacting partner ARID3A, and importin 9. ARID3B complex recruits histone demethylase 4C (KDM4C) to the regulatory region of stemness genes for reducing histone 3 lysine 9 trimethylation, resulting in an open configuration of the chromatin of stemness genes. In cancer tissues, ARID3B expression correlates with the nuclear ARID3A expression and a worse prognosis. This result highlights the role of let-7 in regulating stemness through histone modifications.

overall_design: The Cas9/gRNA target sites containing20 bp gRNA sequence plus the PAM sequence (NGG) using Jack Lin’s CRISPR/Cas9 gRNA finder tool. The gRNA using for knockout ARID3B was predicted by blasting with human genomic and transcript sequences using the NCBI/blastn suite for the detection of potential off-targets.

first: Yang

last: Muh-Hwa

first: Liao

last: Tsai-Tsen


title: Selective coregulator function for different steroid receptors and restriction of steroid receptor chromatin occupancy by Hic-5

city: Los Angeles

first: Dai-Ying

last: Wu

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

institute: University of Southern California

summary: We investigate the relationship between GR and Hic5 and identify classes of genes that respond differently when cells are induced with hormone and when Hic5 is knocked down.

overall_design: GR ChIP-seq with and without depletion of Hic5

first: Rajas

last: Chodankar

first: Michael

middle: R

last: Stallcup


title: Establishment of tractable human iPSC-based models for the study and targeting of glioma initiation (ChIP-Seq)

first: Robert

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

summary: Gliomas can originate upon transformation of adult Neural Progenitor Cells (NPCs) to Tumor Initiating Cells (TICs). Studies on human Glioma TICs (GTICs) have focused on the use of primary tumors from which GTICs could be isolated. Therefore investigations on the driver events underlying NPC transformation and human glioma initiation remain limited to the use of human embryonic material. Here we report on the development of strategies for the modeling of human gliomagenesis based on the use of human induced Pluripotent Stem Cells (hiPSCs). Transformation of hiPSC-derived NPCs (iNPCs) by defined genetic alterations led to the establishment of tractable human GTIC models suitable for studying the early steps of gliomagenesis as well as for screening studies. Dysregulation of PI3K, MAPK and p53 signaling in iNPCs led to the acquisition of functional GTIC properties. In vivo transplantation led to the formation of highly aggressive, infiltrative and heterogeneous tumors upon limited dilutions and secondary transplantation, faithfully recapitulating gliomagenesis. Metabolic modulation by chemical approaches compromised GTIC viability. Pilot screening of 101 anti-cancer compounds identified 3 molecules specifically targeting transformed iNPCs and primary GTICs. Together, our results demonstrate the potential of hiPSCs for the functional testing of putative driver mutations underlying human tumorigenesis and pave new avenues for the development of personalized cancer therapeutics.

overall_design: Five samples were subjected to ChIP-Seq for both Sox2 and H3K4me3, wild-type neural progenitor cells, neural progenitor cells with P53 knockdown, neural progenitor cells with P53 knockdown and inhibition of the PI3K and MAPK signaling pathways, neural progenitor cells with the  inhibition of the PI3K and MAPK signaling pathways, and Glioma Stem Cells (Glioma Tumor Initiating Cells).

first: Louise

last: Laurent

first: Ignacio

last: Sancho-Martinez

first: Juan

last: Belmonte


title: Combining ChIP-Seq and RNA-Seq data in early placental development to study trophoblast invasion [RNA-Seq]

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

summary: The placenta is an understudied organ that has a critical role in mammalian development. In early placental development, the essential process of trophoblast invasion establishes adequate blood flow between mother and fetus.  Despite its importance, little is known about the genomic regions responsible for regulating trophoblast invasion.  In order to identify enhancers that are important for regulating the process, we carried out ChIP-Seq for an enhancer-associated mark at two time points during early placental development.   Combining these data with RNA-Seq data and protein interaction data allowed us to construct a gene-enhancer network describing trophoblast invasion.

overall_design: RNA-Seq at two time points in early placenta development (e7.5 an e9.5).  There are 3 biological replicates per time point.  Samples were pooled and sequenced on two lanes.


title: Identification of miRNome of cancer stem cells in head-and-neck squamous cell carcinoma.

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

institute: National Yang Ming Chiao Tung University

summary: Accumulating evidence suggests that cancer cells possess characters reminiscent of those of normal counterparts. Unveiling small RNAs responsible for cell stemness, diseases progression and progress will eventually lead to the development of novel therapeutic approaches.

overall_design: Expression profiles of FadU cells and its cancer spheres expanded under stem cell medium cultivation were generated for identifying key miRNAs.

first: Hsei-Wei

last: Wang


title: 4C-seq analysis of the BX-C in S2 cells and cells expressing wild type or SAM mutant Polyhomeotic

city: Montreal

first: Nicole

last: Francis

address: 110 Ave des Pins Ouest

institute: IRCM/University of Montreal

summary: 4C-seq analysis using three viewpoint sequences in the Drosophila Bithorax Complex of Hox genes. 4C contacts were compared among S2 cells and those expressing wild type or SAM mutant Ph.

overall_design: Two replicates from each cell line for each of three viewpoints were carried out. 6 samples per lane were sequenced.


title: RNA-seq of C.elegans treated with bcat-1 RNAi and controls

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
Worms were treated with bcat-1 RNAi

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 6 samples: 3 replicates for bcat-1 RNAi treatment; 3 replicates for controls

first: Marco

last: Groth

first: Steffen

last: Priebe

first: Johannes

last: Mansfeld

first: Matthias

last: Platzer

last: Ristow


title: Combining ChIP-Seq and RNA-Seq data in early placental development to study trophoblast invasion [ChIP-Seq]

overall_design: Examination of a histone mark, H3k27Ac at two time points in early placenta development (e7.5 and e9.5).  There are 2 replicates per time point.  Input DNA is used as a control for each time point and replicate.


title: Genome-wide DNA methylation map reveals widespread epigenetic variation in healthy individuals (RRBS)

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

country: New Zealand

institute: University of Otago

summary: Using neutrophils from a cohort of normal individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation.

overall_design: Here we generated single-nucleotide resolution DNA methylation maps from neutrophils isolated from a cohort of healthy individuals, using Reduced Representation Bisulphite Sequencing (RRBS).

first: Peter

middle: A

last: Stockwell

first: Euan

last: Rodger

first: Ian

last: Morison


title: Transcriptome profiling of Gossypium hirsutum in response to NO by high-throughput tag-sequencing

city: YangLing

last: Huang

state: Shaanxi

address: NO. 3. WeiHui Road

department: College of Agronomy

institute: Northwest Agriculture & Forestry University

summary: Nitric oxide(NO) is emerging as an important signaling molecule with diverse physiological functions in plants, leading to a necessity to discover the downstream genes and signal transduction network modulated by NO. In the current study, changes in gene expression in response to NO were studied in upland cotton(Gossypium hirsutum) using Solexa/Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing method. After mapping to an integrated reference sequence database, we obtained about 30,000 genes per library, and yielded 2,393 differential expressed genes in total.

overall_design: Plants 3 hours after treatment with Mock(A), 100μM SNP(B), 250μM SNP(C), and 10μM cPTIO(D) were used for RNA extraction and library construction. To investigate the reliability and reproducibility of the sequencing method, another library was constructed for 250μM SNP(CR), forming a technical replicate.

first: Shu-xun

last: Yu


title: Combining ChIP-Seq and RNA-Seq data in early placental development to study trophoblast invasion


title: Genome-wide DNA methylation map reveals widespread epigenetic variation in healthy individuals (RNA-Seq)

summary: Using neutrophils from a cohort of normal individuals, we generated transcriptomic profile of 4 individuals.

overall_design: Here we generated gene expression profile of neutrophil cells of 4 normal individuals.This data was integreated with DNA methylation profiles of same individuals.

middle: J

first: Elizabeth

last: Duncan


title: RNA-seq of Danio rerio and Mus musculus skin for three different age groups

summary:
Background: Comparison of temporal gene expression profiles.
The RNA-seq data comprises 3 age groups: 2, 15 and 30 months for mouse skin; 5, 24 and 42 months for zebrafish skin.
Illumina 50bp single-stranded single-read RNA sequencing

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design: 15 samples for mouse: 5 biological replicates for 2 months, 6 biological replicates for 15 months and 4 biological replicates for 30 months; 20 samples for zebrafish: 9 biological replicates for 5 months, 6 biological replicates for 24 months and 5 biological replicates for 42 months

first: Christiane

last: Frahm

first: Madlen

last: Guenther

first: Otto

last: Witte

first: Nils

last: Hartmann

first: Christoph

last: Englert


title: Polysome-seq of YBX heterozygous testes

status: Public on Nov 30 2015

city: Bar Harbor

last: Snyder

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: RNA sequence analysis of mRNP and polysome occupancy in single and compound Ybx2/3 heterozygotes revealed loss of translational repression almost exclusively in the compound Ybx2/3 heterozygotes.

overall_design: RNA-sequencing of total RNA, the mRNP, and polysome fractions from wildtype, single YBX heterozygous, and compound YBX heterozygous adult testes

first: Robert

last: Braun

middle: M


title: Complementarity and redundancy of IL-22-producing innate lymphoid cells

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

summary: Homeostasis of the gut microbiota is pivotal to the survival of the host. Intestinal T cells and Innate Lymphoid cells (ILCs) control the composition of the microbiota and respond to its perturbations. Interleukin 22 (IL-22) plays a pivotal role in the immune control of gut commensal and pathogenic bacteria and is secreted by a heterogeneous population of intestinal T cells, NCR- ILC3 and NCR+ILC3. Expression of NCR by ILC3 is believed to define an irreversible effector ILC3 end-state fate in which these cells are key to control of bacterial infection via their production of IL-22. Here we identify the core transcriptional signature that drives the differentiation of NCR- ILC3 into NCR+ ILC3 and reveal that NCR+ILC3 exhibit more plasticity than originally thought, as NCR+ ILC3 can revert to NCR- ILC3. Contrary to the prevailing understanding of NCR+ ILC3 genesis and function, in vivo analyses of mice conditionally deleted of the key ILC3 genes Stat3, Il22, Tbet and Mcl1 demonstrated that NCR+ ILC3 were not essential for the control of colonic infections in the presence of T cells. However, NCR+ ILC3 were mandatory for homeostasis of the caecum. Our data identify that the interplay of intestinal T cells and ILC3 results in robust complementary fail-safe mechanisms that ensure gut homeostasis.

overall_design: Transcriptional profiling of wild-type and T-bet knockout innate lymphoid cells (ILC3) using RNA sequencing

first: Lucille

last: Rankin

first: Sabrina

last: Carpentier

first: Cyril

last: Seillet

first: Gordon

middle: K

last: Smyth

first: Gabrielle

middle: T

last: Belz

first: Eric

last: Vivier


city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

institute: Nagoya University

summary: MicroRNA-31 regulates endothelial-to-mesenchymal transition and associated secretory phenotype induced by TGF-β.

overall_design: RNA-seq analysis in MS-1 endothelial cells treated with TGF-beta and/or miR-31 inhibitors.

first: T

last: Ueno

first: H


title: RNA splicing alteration on glioblastoma and normal neural stem cells

city: Cleveland

first: Christopher

middle: G.

last: Hubert

state: OH

address: 9500 Euclid Ave.

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic

summary: We identified PHF5A as a functional synthetic-lethal hit in glioblastoma stem cells compared to normal neural stem cells. We wanted to perform analysis of RNA isoforms present in glioblastoma or normal neural stem cells with or without PHF5A depletion. We performed shRNA knockdown of PHF5A or used non-silencing shRNA as a control, selected infected cells with puromycin, and isolated RNA for sequencing.

overall_design: We analyzed RNA from either normal neural stem cells or two different glioblastoma specimens aster either control knockdown, or two different shRNA sequences against the PHF5A gene transcript.

first: Patrick

last: Paddison

last: Bradley


title: In utero exposure of rats to high-fat diets perturbs gene-expression profiles and cancer susceptibility of prepubertal mammary glands

city: Cincinnati

first: Mario

last: Medvedovic

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Human studies suggest that high-fat diets (HFD) increase the risk of breast cancer. The 7,12 dimethylbenz[a]anthracene (DMBA)-induced mammary carcinogenesis rat model is commonly used to evaluate the effects of lifestyle factors such as HFD on mammary-tumor risk. Past studies focused primarily on the effects of continuous maternal exposure on the risk of offspring at the end of puberty (PND50). We assessed the effects of prenatal HFD exposure on cancer susceptibility in prepubertal mammary glands and identified key gene networks associated with such disruption. During pregnancy, dams were fed AIN93G-based diets with high (39% Kcal) olive oil, butterfat, or safflower oil. The control group received AIN-93G with 10% Kcal soy oil. Female offspring were treated with DMBA on PND21. However, a significant increase in tumor volume and a trend of shortened tumor latency were observed in rates with HFD exposure against the controls (p=0.067 and 0.048 respectively). Large-volume tumors harbored carcinoma in situ. Transcriptome profiling identified 43 differentially expressed genes in the mammary glands of the HFD group as compared with control. Rapid hormone signaling was the most dysregulated pathway. The diet also induced aberrant expression of Dnmt3a, Mbd1, and Mbd3, suggesting potential epigenetic disruption. Collectively, these findings provide the first evidence supporting susceptibility of prepubertal mammary glands to DMBA-induced tumorigenesis that can be modulated by dietary fat that involves aberrant gene expression and epigenetic dysregulation.

overall_design: Rats were treated prenatally with control (AIN) or high fat butter (HFB) diet from gestation day 1 to  PND 23. The newborns were exposed only to AIN from postnatal day 0 and day 21.  One snap frozen mammary gland from each litter and six from each group (CTL vs HFB) were collected for RNAseq analyses.

first: Vinothini

last: Govindarajaha

first: Yuet-Kin

last: Leung

first: Jun

last: Ying

first: Robin

last: Gear

middle: L

last: Bornschein

first: Shuk-Mei

last: Ho


title: Genome-Wide Transcriptional Regulation Mediated By Biochemically Distinct Forms of SWI/SNF

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

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

overall_design: Refer to individual Series


title: Combinatorial Regulation Mediated by Biochemically Distinct Forms of SWI/SNF [RNA-Seq]

summary: The precise makeup of chromatin remodeling complexes is important for determining cell type and cell function. The SWI/SNF chromatin remodeling complex is made up of multiple subunits that can be filled by mutually exclusive proteins. Inclusion or exclusion of these proteins has profound functional consequences, yet we currently understand little about the direct functional relationship between these biochemically distinct forms of remodeling complexes. Here we combine chromatin immunoprecipitation, transcriptome analysis, and transcription factor binding information from the ENCODE project to determine the functional relationship between three biochemically distinct forms of SWI/SNF. We find widespread overlap in transcriptional regulation and the genomic binding of the three ARID (AT-Rich Interacting Domain) subunits of SWI/SNF. Despite the numerous similarities in their transcriptional regulation and the co-factors bound with each ARID we identify several novel interaction modalities. Previous work has found examples of competition or subunit switching at individual loci, and we find this functional relationship is widespread, and in these cases gene expression changes following loss of one ARID depend on the function of another ARID. We also identify a previously unknown cooperative interaction between ARID1B and ARID2 in the repression of a large number of genes. Together these data help untangle the complicated combinatorial relationships between a highly heterogenous chromatin remodeling family.

overall_design: We performed depletion of ARID subunits (ARID1A , n=5; ARID1B, n=3, ARID2, n=5) of SWI/SNF using siRNA or a Non-Targeting control (N=6) and performed expression analysis using polyA+ selected RNA and a strand-specific dUTP incorporation library protocol.

first: Terry

last: Magnuson


title: Establishment of human iPSC-based models for the study and targeting of glioma initiating cells

city: La Jolla

first: Robert

middle: E

last: Morey

institute: UCSD


title: Space environmental factor impacts upon murine colon microbiota and mucosal homeostasis

city: College Station

first: Nancy

middle: D.

last: Turner

state: TX

address: 2253 TAMU

department: Nutrition & Food Science

institute: Texas A&M University

summary: We report how high and low linear energy transfer (LET) radiation, microgravity, and elevated dietary iron affect colon microbiota (determined by 16S rDNA pyrosequencing) and colon function. Three independent experiments were conducted: 1) fractionated low LET γ radiation (137Cs, 3 Gy, RAD), high Fe diet (IRON) (650 mg/kg diet), and a combination of low LET γ radiation and high Fe diet (IRON+RAD) in male Sprague-Dawley rats; 2) high LET 38Si particle exposure (0.050 Gy), 1/6 G partial weight bearing (PWB), and a combination of high LET38Si particle exposure and PWB in female BalbC/ByJ mice; and 3) 13 d spaceflight in female C57BL/6 mice. For each experiment, the colon was resected and feces removed for microbial sequencing analysis on a Roche 454 Genome Sequencer  FLX Titanium instrument (Microbiome Core Facility, Chapel Hill NC) using the GS FLX Titanium XLR70 sequencing reagents and protocols. Analysis of amplicon sequencing data was carried out using the QIIME pipeline. Low LET radiation, high iron diet, and spaceflight increased Bacteroidetes and decreased Firmicutes. Low LET radiation, high Fe diet, and spaceflight did not significantly affect diversity or richness, or elevate pathogenic genera. Spaceflight increased Clostridiales and decreased Lactobacillales, and similar trends were observed in the experiment using a ground-based model of microgravity, suggesting altered gravity may affect colonic microbiota. Microbiota characteriztion in these models is a first step in understanding the impact of the space environment on intestinal health.

sample_organism:
mouse gut metagenome
rat gut metagenome

platform_organism:
mouse gut metagenome
rat gut metagenome

overall_design: Phylogenetic characterizaiton of fecal microbiota from a total of 49 mouse and rat fecal samples (18 and 31 samples, respectively, no replicates)

middle: D

first: Lauren

last: Ritchie

first: M

last: Azcarate-Peril


title: RNA- and ChIP-seq analysis of cytokine treated islets

city: Vancouver

first: Brad

last: Hoffman

state: BC

institute: University of British Columbia

summary:
Purpose: In the early phases of T1D development exposure of β-cells to IFNγ, IL-1β, and TNFα  is thought to induce β-cell dysfunction and the expression of chemokines and cytokines. These changes are mediated in part by post-translational histone modifications within cis-regulatory regions. The purpose of this study was to determine if prevention of these epigenetic changes can alter cytokine induced gene expression changes.
Methods: Pancreatic islets were isolated from both male and female CD1 mice by collagenase digestion and were picked by hand. Hand-picked islets were cultured for four days with 1.6ng/ml IFNγ, 0.25ng/ml IL-1β and 0.16ng/ml TNFα (cytokine) or were left untreated (nocytokine). For RNA-seq islets were collected and processed for NGS using the Illumina TruSeq library prep kit. Chromatin immunoprecipitation (ChIP) was performed using 3μg of anti-H3K4me1 (Abcam) with islets from at least 10 adult ICR mice (8-10 weeks old) exposed to 1.6ng/ml IFNγ, 0.25ng/ml Il-1β and 0.16ng/ml TNFα for four days. DNA from 4 separate ChIP experiments was pooled for library construction and sequencing using the Illumina platform.
Results: Comparison of gene expression levels between untreated and cytokine-treated islets resulted in the identification of 205 genes that showed an IFNγ, Il-1β, and TNFα-induced chromatin state change (from repressed or inactive to H3K4me1 enriched, i.e. the de novo regions), or increased H3K4me1 enrichment, that were associated with genes with up-regulated expression in response to IFNγ, Il-1β, and TNFα, and 111 genes with reduced H3K4me1 and down-regulated expression in response to IFNγ, Il-1β, and TNFα.
Conclusions: Our study confirms that exposure of islets to pro-inflammatory cytokines induces the expression of chemokines and that these changes are the result of a switch from an inactive to an active chromatin state. Further we show that disruption of the trithorax group complex inhibits the upregulation of pro-inflammatory gene expression.

overall_design: Isolated islets were cultured with or without IFNγ, IL-1β, and TNFα for four days and processed for RNA- and ChIP-seq.

first: Bryan

last: Tennant


title: Transcriptome analysis of SiHa cells

first: Jennifer

last: Webster-Cyriaque

state: NC

address: 385 S. Columbia St.

department: Dental Research

institute: University of North Carolina at Chapel Hill

summary: This study assessed the transcriptional profile of SiHa cells. SiHa is a cervical cancer cell line with integrated HPV16, and was used as a model to study human gene expression in the context of integrated virus. Gene expression in SiHa, calculated by Cufflinks, was scored in windows around the locations of known viral integrations in patients or cell lines to determine if there was an association between gene expression and viral integration. We found that SiHa gene expression was higher near loci of integration for HPV18 vs. HPV16, cervical tissues vs. head and neck cancers, and cervical cancers vs. in vitro integrations. This study provides insight into the factors that may influence where viruses integrate in the human genome.

overall_design: Gene Expression in untreated SiHa cells.

first: Danielle

last: Cunningham

first: Janet

last: Doolittle-Hall


title: Human Embryo Single Cell Transcriptome Analysis

city: Stanford

first: Livia

middle: Zarnescu

last: Yanez

state: California

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

summary: We sorted 2PN stage human embryos by predicted viability using a noninvasive measurement we previously developed. We then performed RNA-seq on each embryo (which was a single cell) and looked for differences in expression between viable and nonviable embryos.

overall_design: We sequenced the transcriptomes of 22 human zygotes (2PN stage) embryos, of which 11 were predicted nonviable and 11 were predicted viable. We excluded 5 which had no siblings in this data set. From the remaining 17 embryos, we analyzed the set of genes that was differentially expressed between those predicted viable and those predicted nonviable.

middle: Z

first: Jinnuo

last: Han

first: Barry

middle: B

last: Behr

first: Renee

last: Reijo Pera

first: David

last: Camarillo


title: Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

city: Utrecht

first: Geert

last: Geeven

state: Utrecht

address: Uppsalalaan 8

department: Biomedical Genomics

country: Netherlands

institute: Hubrecht Institute

summary: Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure. We find that depletion of histone H1 changes the epigenetic signature of thousands of potential regulatory sites across the genome. Many of them show cooperative loss or gain of multiple chromatin marks. Epigenetic alterations cluster to gene-dense topologically associated domains (TADs) that already showed a high density of corresponding chromatin features. Genome organization at the three-dimensional level is largely intact, but we find changes in the structural segmentation of chromosomes specifically for the epigenetically most modified TADs.

overall_design: We have used a combination of genome-wide approaches including DNA methylation, histone modification and DNaseI hypersensitivity profiling as well as Hi-C to investigate the impact of reduced cellular levels of histone H1 in embryonic stem cells on chromatin folding and function.

first: Arthur

middle: I

last: Skoultchi

first: Wouter

last: de Laat


title: Transcriptome of Stabilin-1 siRNA transfected human monocytes

city: Turku

first: Kati

last: Elima

address: Tykistökatu 6

department: MediCity

country: Finland

institute: University of Turku

summary: Stabilin-1/CLEVER-1 is a multidomain protein present in lymphatic and vascular endothelial cells and in M2 immunosuppressive macrophages. Stabilin-1 functions in scavenging, endocytosis and leukocyte adhesion to and transmigration through the endothelial cells. We have analyzed the putative functions of Stabilin-1 in blood monocytes and found that in healthy individuals 60-80% of both CD14+CD16- and CD14+C16+ monocytes, but not CD14dimCD16+ monocytes, expressed Stabilin-1 on the surface. Microarray and RNAseq analysis was performed to get more insight into the effect of Stabilin-1 expression on human monocytes transcriptome.

overall_design: The transcriptome of human monocytes transfected with Stabilin-1 siRNA was compared to that of control siRNA transfected monocytes

first: Senthil

last: Palani

first: Eeva

last: Ekholm

first: Sirpa

last: Jalkanen

first: Marko

last: Salmi


title: Gfi1 proteins regulate the emergence of HSCs and blood precursors in the  AGM through recruitment of LSD1 [HTS]

city: Manchester

first: Roshana

middle: S

last: Thambyrajah

address: Wilmslow Road

department: Stem Cell Biology

institute: CRUK Manchester

summary: Gfi1:Dam and Gfi1b:Dam binding analysis of sorted hemogenic endothelial cells (TIE2/C-KIT)

overall_design: The cDNAs encoding DAM-GFI1 and DAM-GFI1B fusion proteins or a DAM control were inserted in a Dox inducible HPRT docking site in ainv18 ES cells (Kyba et al, 2002). Following differentiation, HE cell populations were isolated, genomic DNA prepared and digested with DpnI. The methylated DNA fragments were amplified as previously described {Orian et al, 2009, Vogel et al, 2007) and sequenced on a Illumina HiSeq platform

first: Milena

last: Mazan

first: Rahima

last: Patel

first: Victoria

last: Moignard

first: Monika

last: Stefanska

first: Thomas

last: Clapes

first: Tarik

last: Möröy

first: Catherine

last: Robin

first: Shaun

last: Cowley

first: Berthold

last: Göttgens

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud


title: Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging

city: Huddinge

first: Maria

last: Eriksson

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska institutet

summary: Alternative splicing (AS) is a key regulatory mechanism for the development of different tissues; however, not much is known about changes to alternative splicing during aging. Splicing events may become more frequent and widespread genome-wide as tissues age and the splicing machinery stringency decreases. Using skin, skeletal muscle, bone, thymus and white adipose tissue from wild-type C57BL6/J male mice (4 and 18-months-old), we examined the effect of age on splicing by AS analysis of the differential exon usage of the genome. The results identified a considerable number of AS genes in skeletal muscle, thymus, bone and white adipose tissue between the different age groups (ranging from 27-246 AS genes corresponding to 0.3-3.2% of the total number of genes analyzed). For skin, skeletal muscle and bone we included a later age group (28-month-old) that showed the number of alternatively spliced genes increased with age in all three tissues (P<0.01). Analysis of alternatively spliced genes across all tissues by gene-ontology and pathway analysis identified 158 genes involved in RNA processing. Additional analysis of AS in a mouse model for the premature aging disease Hutchinson-Gilford progeria syndrome was performed. The results show that expression of the mutant protein, progerin, is associated with impaired developmental splicing. As progerin accumulates the number of genes with AS increases compared to in wild-type skin. Our results indicate the existence of a mechanism for increased AS during aging in several tissues, emphasizing that AS has a more important role in the aging process than previously known.

overall_design: AS analysis of RNA sequencing data from 1 young (18-month-old) and 3 old ( 28-month-old) skeletal muscle samples from mice, to validate  AS analysis performed on exon array data in the same samples

last: Källman


title: Deep sequencing analysis of small non-coding RNAs reveals the diversity of microRNAs and piRNAs in the human epididymis.

city: Yantai

first: Yan

last: Li

state: Shandong

address: 20th, Yu Dong Road, Zhifu Area

institute: Shandong  Research  Centre  for  Stem  Cell  Engineering

summary: The epididymis in male reproductive system plays a crucial role in regulating the development of sperm motility and fertilizing capacity. Small non-coding RNAs (sncRNAs), especially microRNAs (miRNAs), can participate in the regulation of various physiological pathways. However, their abundance and whether they are involved in the regulation of gene expression in the human epididymis are unknown. By adopting the Solexa deep sequencing approach, we systematically investigated the sncRNAs in the adult human epididymis. A total of 4,903 unique reads representing 527 known miRNA were discovered. Eighteen novel miRNA genes encoding 23 mature miRNAs were also identified, suggesting a complicated miRNA regulatory network. The expression of some of the novel miRNA was confirmed by qRT-PCR. The presence of Piwi-interacting RNAs (piRNAs) in the library also adds to the diversity of sncRNA population in the human epididymis. This research lays the foundation for the functional study of sncRNAs in huamn reproductive system.

overall_design: The epididymis from a  26-year-old male who is healthy and fertile was deep-sequenced.

first: Haiyan

last: Wang

first: Fengchun

last: Wan

first: Fujun

last: Liu

first: Juan

last: Zhang

first: Shaohua

last: Jin

first: Jianyuan


title: Differential expression of human parthenogenic stem cells, neural stem cells and DA progenitors.

status: Public on Nov 29 2015

first: Robert

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

summary: Neural stem cells (NSC) derived from human parthenogenic stem cells (hpSC) have been observed to show stronger positive functional effects than hpSC-derived dopaminergic neuron precursors (DAP) in treatment of induced Parkinson Disease in animal models. RNAseq of the two types of cells were normalized and analyzed to compare gene expression profiles.

overall_design: cDNA library of hpsC, NSC and DAP triplicates were sequenced using Illumina HiSeq 2000. The sequence reads were mapped to hg19 reference genome and hits that passed quality filters were analyzed for differential expression.

first: Ibon

last: Garitaonandia

first: Rob

first: Chuan

last: Jiang


title: Genome-wide profiling of long non-coding RNAs in Arabidopsis

status: Public on Nov 28 2015

city: Beijing

first: Yijun

last: Qi

address: #7 Science Park Road, Zhongguancun Life Science Park

institute: National Institute of Biological Sciences

summary: We developed a stringent selection pipeline for lncRNA identification, combining high-throughput RNA sequencing and computational approaches. Using this pipeline, we annotated 1,353 lncRNAs in Arabidopsis thaliana. We further found that one fifth of the lncRNAs were associated with Polycomb repressive complex 2 (PRC2). Some PRC2-associated lncRNAs could repress the transcription of their neighboring genes through mediating histone H3 lysine 27 trimethylation.

overall_design: Identification of Arabidopsis lncRNA through high throughput sequencing.

first: Jingrui

first: Yang

last: Wu

first: Yugang

last: Hu

first: Weilong

last: Guo

first: Michael

middle: Q


title: Reversal of MECP2 duplication syndrome using genetic rescue and antisense oligonucleotides

status: Public on Nov 27 2015

city: Houston

first: Yehezkel

last: Sztainberg

address: 1250 Moursond

institute: Baylor College of Medicine


title: Reversal of MECP2 duplication syndrome using genetic rescue and antisense oligonucleotides [ASO time point 2]

summary: MECP2 duplication syndrome, a childhood neurological disorder characterized by autism, intellectual disability, motor dysfunction, anxiety and epilepsy, is caused by a duplication on chromosome Xq28 spanning the MECP2 gene that results in doubling of MeCP2 levels. MECP2 overexpression in mice causes neurobehavioral and electroencephalographic defects similar to those of human patients, but the gross anatomy of the brain remains unaffected. We hypothesized that MECP2 duplication syndrome would be reversible and tested two methods to restore MeCP2 levels to normal: conditional genetic recombination and antisense oligonucleotide therapy. Both approaches rescued molecular, physiological and behavioral features of adult symptomatic mice. Antisense therapy also restored normal MeCP2 levels in lymphoblastoid cells from MECP2 duplication patients, in a dose-dependent manner. Our data indicate that antisense oligonucleotides could provide a viable therapeutic approach for human MECP2 duplication syndrome as well as other disorders involving copy number gains.

overall_design: Hippocampal mRNA profiles of WT, MECP2-TG and MECP2-TG ASO-treated treated mice 8 weeks after the initiation of the treatment, were generated by deep sequencing, in triplicate, using Illumina TruSeq.

first: Ying-Wooi

first: Zhandong

first: Huda

middle: Y

last: Zoghbi


title: Pregnacy-induced regulation of islet proteins

city: Måløv

first: Jeannette

middle: Schlichting

last: Kirkegaard

address: Novo Nordisk park

department: Department of islet and stem cell biology

country: Denmark

institute: Novo Nordisk A/S

summary: We report pregnacy-induced changes at the RNA level using RNAseq

overall_design: Comparison of RNA transcript of islets isolated from 5 control and 5 pregnant animals at gestational day 14.5

first: J

first: S

last: Horn

last: Hoelper

first: P

middle: A

last: Seymour

first: C

last: Rescan

middle: H

last: Nielsen

first: O

last: Madsen

middle: N

last: Jensen

first: M

last: Krüger

last: Grønborg

last: Ahnfelt-Rønne


title: Gfi1 proteins regulate the emergence of HSCs and blood precursors in the  AGM through recruitment of LSD1

first: Roshana

last: Thambyrajah


title: Reversal of MECP2 duplication syndrome using genetic rescue and antisense oligonucleotides [ASO time point 1]

country: USA

overall_design: Hippocampal mRNA profiles of WT, MECP2-TG and MECP2-TG ASO-treated treated mice 4weeks after the initiation of the treatment, were generated by deep sequencing, in triplicate, using Illumina TruSeq.

last: Wan

last: Liu


title: Reversal of MECP2 duplication syndrome using genetic rescue and antisense oligonucleotides [Genetic Rescue Experiments]

overall_design: Hippocampal mRNA profiles of conditional MECP2 overexpression and genetic rescue mice were generated by deep sequencing, in triplicate, using Illumina TruSeq.


title: Characterization and profiling of liver microRNAs in cattle divergently selected for residual feed intake by RNA-sequencing

city: Armidale

first: WIJDAN

last: AL-HUSSEINI

state: NSW

address: UNE

department: Centre for Genetics Analysis and Applications, School of Environmental and Rural Science

institute: University of New England

summary:
MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI) and identify miRNAs related to feed efficiency in beef cattle
Results: Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1). We identified 305 known bovine miRNAs (miRBase v.19). Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378 and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (version 19). We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle
Conclusions: Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI give some insights into liver miRNAs regulating physiological pathways underlying residual feed intake in bovine

overall_design: 2 libraries were constructed from pooled RNA extracted from livers of 13 low-RFI animals and 13 high-RFI animals, sequenced by Illumina genome analyser using single-read cluster generation kit v2

first: Wijdan

last: Al-Husseini

first: Yizhou

last: Chen

first: Cedric

last: Gondro

first: Robert

middle: M

last: Herd

first: John

middle: P

last: Gibson

first: Paul

middle: F

last: Arthur


title: genomic DNA from MEF cells

status: Public on Nov 26 2015

city: Dalian

first: Qingkai

last: Yang

state: Liaoning

address: 9 Western Lvshun South Road

department: 9 Western Lvshun South Road

institute: Institute of Cancer Stem Cell, DaLian Medical University

summary:
Genome wide DNA methylation profiling of WT and Pml KO mEF cells treated W/O Doxorubicin for 24 hours.
TET2 plays critical roles in the regulation of cell identity and inhibition of tumorigenesis through modulating DNA methylation. However, little is known about how TET2 is targeted to specific DNA-binding sites. It was found by us that TET2 is significantly recruited to specific sites by PML. Moreover, TET2 and PML synergistically inhibited cell proliferation. Further study indicated that multi chemotherapies, such as doxorubicin, were able to promote PML-NB, increase 5hmC and result in specific DNA demethylation. Due to the important role of inactivation of tumor suppressors by DNA methylation in cancer, the activity of most therapies depends to an extent on activation of tumor suppressors by demethylation. Consequently, it is not surprising that methylation of tumor suppressors has been reported to diminish in responder patients after end of chemotherapy. Little is known about mechanism of therapy-promoted DNA demethylation, although this therapy-promoted DNA demethylation potentially plays general roles in therapy response, resistance and recurrence. It was also found that knock out of Pml significantly diminished chemotherapy-promoted DNA demethylation. To identify PML-TET2 pathway-regulated genes, WT and Pml knock out MEF cells were treated W/O Doxorubicin. The genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to manufacturer’s instruction. The resultant Genome DNA was cut by Restriction Enzyme. After DNA-end repair and 3’-dA overhang, the 40-220bp fragments were selected and treated with ZYMO EZ DNA Methylation-Gold kit according to manufacturer’s instruction. Then the bisulphite converted DNA from the 4 samples (WT, WT Dox, PML KO and Pml KO Dox) were sequenced using standard Illumina protocol. Standard recommended Illumina scanner setting was carried out in study.

overall_design: WT and Pml knock out MEF cells were treated with  Doxorubicin. The genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to manufacturer’s instruction. The resultant Genome DNA was cut by Restriction Enzyme. After DNA-end repair and 3’-dA overhang, the 40-220bp fragments were selected and treated with ZYMO EZ DNA Methylation-Gold kit according to manufacturer’s instruction. Then the bisulphite converted DNA from the 4 samples (WT, WT Dox, PML KO and Pml KO Dox) were sequenced using standard Illumina protocol. Standard recommended Illumina scanner setting was carried out in study.

first: Chengli

last: Song


title: Downregulation of neuropilin-1 on macrophages modulates antibody-mediated tumoricidal activity

city: Kyoto

first: Kosuke

last: Kawaguchi

address: 54 Kawaharacho Shogoin Sakyo-ku

institute: Kyoto University

summary: We reported that NRP-1 expression on CD4+ T cells was probably induced by NRP-1 transfer from macrophages to T cells. In HER2+ BC, NRP-1 expressing TIIs correlated with better clinical outcomes.

overall_design: Examination of monocytes and monocyte derived macrophages.

first: Eiji

last: Suzuki

first: Masakazu

last: Toi


title: Sex hormones have pervasive effects on thymic epithelial cells

city: Montréal

first: Maude

last: Dumont-Lagacé

state: Quebec

address: 2950 chemin de la polytechnique

institute: IRIC - Université de Montréal

summary: The goal of our study was to evaluate at the systems-level, the effect of sex hormones on thymic epithelial cells (TECs). To this end, we sequenced the transcriptome of cortical and medullary TECs (cTECs and mTECs) from three groups of 6 month-old mice: males, females and males castrated at four weeks of age. In parallel, we analyzed variations in the size of TEC subsets in those three groups between 1 and 12 months of age. We report that sex hormones have pervasive effects on the transcriptome of TECs: the number of differentially expressed genes was 1,440 in cTECs and 1,783 in mTECs. Sexual dimorphism was particularly conspicuous in cTECs. Male cTECs displayed low proliferation rates that correlated with low expression of Foxn1 and its main targets. Furthermore, male cTECs expressed relatively low levels of genes instrumental in thymocyte expansion (e.g., Dll4) and positive selection (Psmb11 and Ctsl). Nevertheless, cTECs were more abundant in males than females. Accumulation of cTECs in males correlated with differential expression of genes regulating cell survival and cell differentiation. Unexpectedly, we observed that female and male sex hormones repressed promiscuous gene expression in mTECs. Since sex hormones did not affect the expression of Aire per se, they must impinge on the activity of unidentified regulator(s) of promiscuous gene expression in mTECs. The sexual dimorphism of TECs highlighted here may be mechanistically linked to the well-recognized sex differences in susceptibility to infections and autoimmune diseases.

overall_design: Cortical and medullary thymic epithelial cells from 6 month-old male, female and castrated male mice were sequenced in 3 replicates (but only 2 replicates for castrated male mTECs).

first: Charles

last: St-Pierre

first: Claude

last: Perreault


title: High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

status: Public on Nov 25 2015

city: Toronto

first: Jason

last: Moffat

state: ON

address: 160 College St

department: CCBR

institute: University of Toronto

summary: The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context- dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. We present a list of 1,580 human core fitness genes and describe their general properties. Moreover, we demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell.  Additional data can be found at tko.ccbr.utoronto.ca

overall_design: RNAseq of five human cell lines with Cas9 knock-ins.

first: Traver

last: Hart

first: Megha

last: Chandrashekhar

first: Michael

last: Aregger

first: Zachary

last: Steinhart

first: Kevin

middle: R

last: Brown

first: Graham

last: MacLeod

first: Monika

last: Mis

first: Michal

last: Zimmermann

first: Amelie

last: Fradet-Turcotte

first: Song

last: Sun

first: Patricia

last: Mero

first: Peter

last: Dirks

first: Sachdev

last: Sidhu

first: Frederick

last: Roth

first: Olivia

last: Rissland

first: Daniel

last: Durocher

first: Stephane

last: Angers


title: Acute loss of TET function results in aggressive myeloid cancer in mice [WGBS]

city: La Jolla

first: Anjana

last: Rao

address: 9420 Athena Circle

department: Signaling and Gene Epression

institute: La Jolla institute

summary: To evaluate the DNA methylation in LSK cells from  the bone marrow of wildtype or  Tet2/3 DKO mice.

overall_design: In order to address the impact of the loss of Tet2/3 proteins in DNA methylation in LSK  cells, we compared by WGBS the methylome of wild and, Tet2/3 DKO LSK cells in bone marrow.

first: Jungeun

last: An

first: Edahi

last: Gonzalez Avalos

first: Lukas

last: Chavez

first: Myunggon

last: Ko


title: Spatial-temporal order of regulation in tomato early fruit development

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: Early fruit development is crucial for crop production in tomato. After fertilization, the ovary undergoes a cell division and a cell expansion stages before maturation. Although the roles of regulatory signals such as hormone and carbohydrate during early fruit development have been studied, the spatial distribution and the sequential initiation of these regulatory signals is still poorly understood. Using the cultivated tomato “Moneymaker” as materials, we analyzed the transcriptome of the ovule and the ovary wall dissected from the different stages of the early developing fruits. These datasets provide us the whole picture about the spatial and temporal signal distribution of fruit formation which has not been studied in such a detailed manner. Our results suggest that the hormone signal was initiated in both ovule and ovary wall after fertilization. After that, the different signals were activated in ovule and ovary wall due to their distinct developmental processes. By analyzing the global expression profiling of hormone related genes, we found that the auxin might be synthesized in both ovule and ovary wall after fertilization. The expression pattern of sugar related genes revealed the different carbohydrate metabolism events occurred in ovule and ovary wall. At last, we identified a gene showed tissue and stage specific expression pattern and localized in previously reported fruit weight locus which might be selected during tomato breeding.

overall_design: RNA-seq of ovule and ovary wall/pericarp tissues in four stages of tomato early developing fruits

first: Shuaibin

last: Zhang

first: Meng

last: Xu

first: Zhenkun

last: Qiu

first: Ketao

last: Wang

first: Yongchen

last: Du

first: Xia

last: Cui


title: Next Generation Sequencing Facilitates Quantitative Analysis of genome-wide binding sites of hnRNP U in BNL CL.2 cells.

city: Shanghai

first: Fang

address: NO. 800 Xiangyin Road

department: Medical Genetics

institute: Second Military Medical University

summary:
Purpose:The aim of this study is to evaluate the characteristics of hnRNP U binding site.
Methods: The chromatin of BNL CL.2 cells was immunoprecipitated with anti-hnRNP U(Abcam) and normal rabbit immunoglobulin G (IgG). The immunoprecipitated DNA was then subjected to various previously constructed sequencing libraries. The libraries were sequenced using the Illumina Hiseq2500. All reads were aligned to the mm9 genome browser using the bowtie with default parameters.
Results: A total number of 12249 peaks that specifically binded by hnRNP U was obtained.
Conclusions: Our study represents the first detailed analysis of genome-wide binding sites of hnRNP U generated by ChIP-seq technology.

overall_design: hnRNP U binding profiling in Mus musculus fetal liver cell line BNL CL.2 cells, and the IgG antibody was used as a negative control

first: Shaobing


title: 5'RNA-seq analysis of soleus, tibialis anterior (TA), diaphragm and left ventricle myocardial tissue from adult wild-type mice.

city: Chicago

first: Andrea

middle: A.

last: Domenighetti

state: IL

address: 345 East Superior St

institute: Northwestern University & Rehabilitation Institute of Chicago

summary: We applied a 5'RNA-seq methodology to assess gene and differential isoform expression in striated muscle tissues extracted from adult wild-type mice.

overall_design: 5'RNA-seq analysis of transcriptomes from mouse soleus, tibialis anterior (TA), diaphragm and left ventricle myocardial tissues. Three biological replicates per tissue were pooled into a single sequencing run. 5'RNA-seq methodology consists of enhanced sequencing of 5' ends and computational assessment of changes at start-sites of genes.

first: Jonathan

last: Seidman


title: Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

city: Seattle

first: Linda

last: Buck

state: Washington

address: 1100 fairview ave North

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Centre

summary: We report RNA sequencing of single olfactory neurons from mouse olfactory epithelium in developmental progression from progenitors to precursors to immature neurons to mature neurons. Most mature neurons expressed only one of ~ 1000 odorant receptor genes (Olfrs) at high levels, whereas many immature neurons expressed low levels of multiple Olfrs.

overall_design: Investigating expression of odorant receptors genes in mouse olfactory sensory neurons during development.

first: Cole

last: Trapnell


title: Transcriptional heterogeneity and lineage commitment in myeloid progenitors [ChIP-seq]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Within the bone marrow, hematopoietic stem cells differentiate and give rise to diverse blood cell types and functions. Currently, hematopoietic progenitors are defined using surface markers combined with functional assays that are not directly linked with the in vivo potential or gene regulatory mechanisms. Here we comprehensively identify myeloid progenitor subpopulations by transcriptional sorting of single cells from the bone marrow. We describe multiple progenitor subgroups showing unexpected transcriptional priming towards seven differentiation fates, but no progenitors with a mixed state. Transcriptional differentiation is correlated with combinations of known and previously undefined transcription factors, suggesting the process is tightly regulated. Histone maps and knockout assays are consistent with the transcriptional states while traditional transplantation experiments are only partially overlapping myeloid transcriptional priming. Our analyses uncover the function of the underlying regulatory mechanisms for several sub groups and establishes a general framework for dissecting hematopoiesis.

overall_design: Bone marrow common myeloid progenitor H3K4me2  profiles were generated by deep sequencing of iChIP libraries on an Illumina NextSeq

first: Amos

last: Tanay

first: Franziska

last: Paul

first: Ya’ara

last: Arkin

first: Amir

last: Giladi


title: Transcriptome-wide identification of Hfq-associated RNAs in Brucella suis by deep sequencing

city: Toulouse

first: Bashir

last: Saadeh

address: 4 Rue Villaudric

institute: CNRS

summary: We report the identification of new noncoding RNAs in Brucella suis 1330 and that are associated to the chaperone protein Hfq

overall_design: Coimmunoprecipitation using Flag-tagged Hfq as bait

first: Clayton

middle: C

last: Caswell

first: Yanjie

last: Chao

first: Philippe

last: Berta

first: Alice

last: Wattam

first: R

last: Martin Roop II

first: David

last: O'Callaghan