title: Selective induction of homeostatic Th17 cells in the murine intestine by cholera toxin interacting with the microbiota

city: Cambridge

first: Raivo

last: Kolde

address: 415 Main St

institute: Broad Institute

summary: Th17 cells play a role as an inflammation mediator in a variety of autoimmune disorders, including inflammatory bowel disease (IBD) and thus are widely considered to be pathogenic. However, Th17 cells are present in the normal intestine and show a homeostatic phenotype, i.e., they participate in the maintenance of intestinal homeostasis rather than inducing inflammation. We observed an enlarged Th17 population in the small intestine of C57BL/6.IgA-/- mice compared to wild-type mice, which was further amplified with cholera toxin (CT) immunization without causing intestinal inflammation. The increased Th17 induction and the correspondingly 10-fold higher CTB-specific serum IgG response in C57BL/6.IgA-/- mice after CT immunization was microbiota dependent and was associated with increased segmented filamentous bacteria (SFB) in the small intestine of C57BL/6.IgA-/- mice. Oral administration of vancomycin greatly dampened both CT immunogenicity and adjuvanticity, and the differential CT responses in IgA-/- and wild-type mice disappeared after intestinal microbiota equalization. Using gnotobiotic mouse models, we found that CT induction of homeostatic intestinal Th17 responses was supported not only by SFB but also by other commensal bacteria. Furthermore, transcriptome analysis using IL-17AhCD2 reporter mice revealed a similar gene expression profile in CT-induced intestinal Th17 cells and endogenous intestinal Th17 cells at homeostasis, with upregulated expressions of a panel of immune regulatory genes, which was distinctly different from the gene expression profile of pathogenic Th17 cells. Taken together, we identified a non-pathogenic signature of intestinal homeostatic Th17 cells, which are actively regulated by the commensal microbiota and can be selectively stimulated by CT.

overall_design: Transcriptome analysis of CD4+hCD2+ cells of CT Immunized IgA-/- mice, CD4+hCD2+ cells of IgA-/- mice, CD4+CD25- cells from spleen of WT B6 mice, naïve CD4+CD25-, Th17 with IL-23+IL-1b.

first: Qing

last: Zhao

first: Elson

middle: O

last: Charles


title: Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

status: Public on Aug 31 2017

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

type: Expression profiling by high throughput sequencing

summary: Transcription is a highly regulated process, and stress-induced changes in gene transcription have been shown to play a major role in responses and adaptation to stress. Numerous emerging genome-wide studies reveal prevalent transcription beyond known protein-coding gene loci, generating a variety of new classes of RNAs, most of unknown function. One such class, termed downstream of gene (DoG)-containing transcripts, was reported to result from transcriptional readthrough upon osmotic stress in human cell lines. However, how widespread the readthrough phenomenon is, and what its causes and consequences are, remain elusive. Here we present a systematic genome-wide mapping of transcriptional readthrough, using deep nuclear RNA-seq, comparing heat shock, osmotic and oxidative stress in NIH3T3 mouse fibroblast cells. We observe massive induction of transcriptional readthrough under all stress conditions, with significant, yet not complete overlap of readthrough-induced loci between different conditions. Importantly, our analyses suggest that stress-induced transcriptional readthrough is not a random failure process, but is rather differentially induced across different conditions. Additionally, analyzing public Pol-II occupancy data further supported our findings of stress-induced readthrough. We explore potential regulators and find a role for HSF1 in the induction of a subset of heat shock-induced readthrough transcripts. Furthermore, we examine genomic features of readthrough transcription, and observe a unique chromatin signature typical of DoG-producing regions, suggesting that readthrough transcription is associated with the maintenance of an open chromatin state.

overall_design: RNA profiles of NIH3T3 (mouse embryonic fibroblasts) cells after three stress treatments and control were generated by deep sequencing, in two replicates using Illumina HiSeq 2000.

first: Anna

last: Vilborg


title: Gene expression in GBM with Cav3.2 inhibition

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

country: USA

institute: Signature Science, LLC

summary: Glioblastoma stem cells (GSCs) have been implicated in tumor initiation, progression and resistance to therapy. We investigated the expression, function, mechanisms of action and therapeutic targeting of T-type calcium channels (Cav3.2) with the FDA approved and repurposed drug mibefradil in glioblastoma (GBM), and GSCs. We found that Cav3.2 is highly expressed in human GBM specimens and enriched in GCSs.  Analyses of TCGA and REMBRANDT databases confirmed the upregulation of Cav3.2 in a subset of tumors (TCGA) and showed that overexpression is associated with worse prognosis. Mibefradil and Cav3.2 knockdown inhibited the growth, survival and stemness of GSCs and sensitized them to temozolomide (TMZ) chemotherapy.  To investigate the mechanisms of action of Cav3.2 in GSC, we performed proteomic and transcriptomic screenings followed by functional rescue experiments. Inhibition of Cav3.2 altered cancer signaling pathways and gene transcription. Among other, inhibition of Cav3.2 suppressed GSC growth through inhibition of pro-survival pathways AKT/mTOR, and induction of apoptosis through upregulation of survivin, BAX and cleavage of caspase 9 and PARP.  Inhibition of Cav3.2 induced a decrease in the expression of oncogenes including PDGFA, PDGFB and TGFB1 and an increase in the expression of tumor suppressors including TNFRSF14 and HSD17B14. In vivo oral administration of Cav3.2 blocker mibefradil significantly inhibited GSC-derived xenograft growth, prolonged animal survival and sensitized the tumors to TMZ.  Our study represents the first comprehensive characterization of Cav3.2 in GBM tumors and GSC. The findings establish Cav3.2 inhibition with the repurposed FDA-approved drug mibefradil as a new strategy for GBM therapy.

overall_design: Examination of gene expression after inhibition of Cav3.2 in GBM stem cells

first: Roger

last: Abounader

first: Ying

last: Zhang

first: Nichola

last: Cruickshanks


title: Identification of transcriptional biomarkers by RNA-sequencing for improved detection of ß2-agonists abuse in goat skeletal muscle

city: Beijing

first: Luyao

address: No.12 Southern Street of Zhongguancun

department: Chinese Academy of Agricultural Sciences

country: China

summary: RNA-sequence is applied to reveal gene expression frofiles of β2-agonist in capra hircus

overall_design: One control sample and three treatment samples as replicates

first: Yang

last: Shuming

first: Zhao

last: Luyao


title: Differential requirement for functional telomeres in neurons

city: Bethesda

first: Eros

last: Lazzerini Denchi

state: MD

address: 9000 Rockville Pike building 37, room 2144B

institute: National Cancer Institute

summary: RNAseq was perfomed in control and TRF2-DCVX-cre mice to evaluate the effect of telomere dysfunction in gene expression in neurons

overall_design: Hippocampus and Contex of 3 months old mice were isolated to perform RNAseq. Two cohorts were used: WT and TRF2-DCX-cre

first: Anastasia

last: Labonova


title: Dynamic DNA methylation reconfiguration during seed development and germination (RNA-seq)

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

summary: The life cycle of flowering plants ends and begins with seeds. Unlike animals, plants can pause their life cycle as dormant seeds during this transition. DNA methylation is involved in the regulation of gene expression and genome integrity. Reprogramming erases and re-establishes DNA methylation during development in animals. Knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To better understand epigenetic reconfiguration in the embryo, which forms the plant body, we compared dry and germinating seed time-series methylomes to publicly available seed development methylomes. Time-series whole genome bisulfite sequencing (WGBS) revealed extensive gain of CHH methylation during seed development and drastic loss of CHH methylation during germination. These dynamic changes in methylation mainly occur within transposable elements. Active DNA methylation during embryogenesis depends on both RNA-directed DNA methylation and heterochromatin formation pathways whereas global demethylation during germination occurs in a passive manner. However, an active DNA demethylation pathway is initiated during late embryogenesis, which contributes to the endosperm specific methylation patterns.This study provides new insights into dynamic DNA methylation reprogramming events during seed development and germination and suggests possible mechanisms of regulation. The observed sequential methylation/demethylation cycle suggests an important role of DNA methylation in seed dormancy.

overall_design: RNA-seq from from dry and germinating seed of Arabidopsis

first: Joseph

middle: R

last: Ecker


title: Dynamic DNA methylation reconfiguration during seed development and germination (MethylC-seq)

type: Methylation profiling by high throughput sequencing

overall_design: MethylC-seq from dry and germinating seed of Arabidopsis


title: Generation of RORγt+ antigen-specific T regulatory 17 (Tr17) cells from Foxp3+ precursors in autoimmunity

city: Seoul

first: BYUNG-SEOK

last: KIM

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: SEOUL NATIONAL UNIVERSITY

summary: Th17 cells are potent mediators in autoimmune diseases and RORγt is required for their development. Recent studies have shown that RORγt+ Treg cells in the gut regulate intestinal inflammation by inhibiting effector T cell function. In the current study, we report that RORγt+ Treg cells were also found in lymph nodes following immunization. Not only distinct from intestinal RORγt+ Treg in their transcriptomes, peripheral RORγt+ Treg cells were derived from Foxp3+ thymic Treg cells, in an antigen-specific manner. Development of these RORγt+ Treg cells, coined as T regulatory 17 (Tr17) cells, depended on IL-6/Stat3 signaling. Tr17 cells showed suppressive activity against antigen-specific effector T cells in vitro. In addition, Tr17 cells efficiently inhibited myelin-specific Th17 cell-mediated CNS auto-inflammation in a passive EAE model. Collectively, our study demonstrates Tr17 cells as effector Treg cells that potentially restrict autoimmunity.

overall_design: Examination of mRNA profiles of RORγt+ Tr17 cells in draining lymph nodes of immunized mice by deep sequencing, using SOLiD v4

first: Byung-Seok

last: Kim

first: Seon

middle: H

last: Chang

first: Chen

last: Dong


title: Hippocampus-dependent learning and memory deficits by abnormalities in presynaptic plasticity in LSD1 knock-in mice

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

institute: Kyung Hee University

summary: We examined the molecular and cellular mechanism for memory deficit in LSD1 knock-in mice.

overall_design: Compare gene expression profiles between wild-type and LSD1 knock-in mutant using RNA-Seq (Illumina platform: Hi-Seq 2000)

first: Chae-Seok

last: Lim

first: HyeJin

last: Nam

first: Jaehyun

first: Dongha

first: Jaeun

last: Choi

first: SukJae

middle: J

last: Kang

first: Somi

first: Chuljung

last: Kwak

first: Kyu-Won

last: Shim

first: Siyong

first: Hyoung-Gon

last: Ko

first: Yong-Seok

first: Sung-Hee

last: Baek

first: Bong-Kiun

last: Kaang


title: Transcriptomic  analysis  reveals  inflammasome-dependent  mechanism  for early neutrophil response to Mycobacterium Marinum

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

summary: The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood.  In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum, by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA-seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, wu:fb15h11 (NLRC3 ortholog) and il1β. Crispr/Cas9-mediated knockdown of caspase b, which mediates its effects by the proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterium infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial response to mycobacterial infection in neutrophils. Further perturbation of the IEGs revealed egr3 as a key transcription factor regulating il1β transcription.

overall_design: We report the design of a binary approach in zebrafish that allows for profiling of the initial response of neutrophils to Mycobacterium Marinum by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context allowing for RNA-seq analysis of the active transcriptome.

first: Amy

last: Kenyon

first: Daria

last: Gavriouchkina

first: Jernej

last: Zorman

first: Giorgio

last: Napolitani

first: Vincenzo

last: Cerundolo


title: Principles for the regulation of multiple developmental pathways by a versatile transcriptional factor, BLIMP1(ChIP-Seq)

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcription factors (TFs) regulate biological events depending on cellular contexts, precise mechanisms for which are elusive.  BLIMP1 has been shown to play key roles in many developmental processes, canonically as a transcriptional repressor that targets to proximities of promoters.  Here, we systematically and quantitatively characterized genomic binding patterns of BLIMP1 across four distinct, developing cell types; photoreceptor precursors, embryonic intestinal epithelium, plasmablasts, and primordial germ cells (PGCs).  BLIMP1-binding sites are highly enriched in genomic regions proximal to transcription start sites (TSSs), majority of which are shared among cell types and are highly occupied by BLIMP1, whereas only a small number of associated genes are regulated consistently among cell types.  In contrast, BLIMP1 weakly binds to more distal, cell type-specific sites with divergent recognition sequences, which account for gene regulations much more efficiently in proportion to the magnitude of expression level changes, with notably similar impacts per site among cell types.  Various TF motifs contained in the cell type-specific binding sites exhibit only moderate impacts on transcription dynamics and BLIMP1-occupancy levels.  On the other hand, germ cells uniquely involve the shared binding sites in the specification, and grossly maintain the binding pattern in late PGCs, accounting for vast majority of the repressive targets.  Furthermore, we identified new sequence motifs strongly bound to BLIMP1 especially in the late PGCs, GGGAAA repeats, a few of which are located around key regulators of gametogenesis.  These findings provide a foundation for understanding the genomic regulation of BLIMP1 across developmental processes.

overall_design: 13 EGFP-BLIMP1 ChIP-seq samples in 7 cell types: d2PGCLC (2 replicates), d6PGCLC (2 replicates), E12.5 male and female PGC (E12.5_PGC_M and E12.5_PGC_F, respectively, 1 replicate each), intestinal epithelium (emIE, 2 replicates), Photoreceptor precursor (PRP, 2 replicates), Plasmablast (PB, 2 replicates).,  E12.5 male PGC input (E12.5_PGCM, input, 1 replicate)

first: Tadahiro

last: Mitani

first: Hiroshi

last: Ohta

first: Tomonori

last: Nakamura

first: Chika

last: Yamashiro

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou

first: Kazuki

last: Kurimoto


title: Principles for the regulation of multiple developmental pathways by a versatile transcriptional factor, BLIMP1

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

overall_design: Refer to individual Series


title: Transcriptome sequencing indentifies novel BMP5 downstrem genes and network in HT-29 cells

city: Xi'an

first: Erfei

last: Chen

address: 229# North Taibai Road

institute: Northwest University

summary: Although BMP5 belongs to BMPs(TGF-β)/Smad signaling pathway, the downstream network induced by BMP5 is far from clear. Our transcriptome sequencing results discovered a novel pathway BMP5 transduces through, the Jak-STAT signaling.

overall_design: mRNA profiles of HT-29 (control) and BMP5-expressing HT-29 cells were generated by deep sequencing, in triplicate, using Ion  Proton.

first: Jin

last: Yang


title: Akt Activation Mediates Acquired Resistance to Fibroblast Growth Factor Receptor Inhibitor BGJ398

city: Columbus

first: Eric

last: Samorodnitsky

state: Ohio

address: 460 West 12th Avenue, Room 595

department: Comprehensive Cancer Center

institute: The Ohio State University

summary: Activation of fibroblast growth factor receptor (FGFR) signaling through mutations, amplifications, or fusions involving FGFR1, 2, 3, or 4 are seen in multiple tumors including lung, bladder, and cholangiocarcinoma. Currently, several clinical trials are evaluating the role of novel FGFR inhibitors in solid tumors. As we move forward with FGFR inhibitors clinically, we anticipate emergence of resistance with treatment. Consequently, we sought to study the mechanism(s) of acquired resistance to FGFR inhibitors using annotated cancer cell lines. We identified cancer cell lines that have activating mutations in FGFR1, 2, or 3, and treated them chronically with the selective FGFR inhibitor, BGJ398. We observed resistance to chronic BGJ398 exposure in DMS114 (small cell lung cancer, FGFR1 amplification), and RT112 (urothelial carcinoma, FGFR3 fusion/amplification) cell lines based on viability assays. Reverse phase protein array (RPPA) analysis showed increased phosphorylation of Akt (T308 and S473) and its downstream target GSK3 (S9 and S21) in both the resistant cell lines when compared to matching controls. Results of RPPA were confirmed using immunoblots. Consequently, the addition of an Akt inhibitor (GSK2141795) or siRNA was able to restore sensitivity to BGJ398 in resistant cell lines. These data suggest a role for Akt pathway in mediating acquired resistance to FGFR inhibition.

overall_design: Observing mechanisms of resistance to BGJ398 in DMS114 and RT112 cell lines

first: Jharna

last: Miya


title: Transcriptome profiling of primary monocytes from XLA patients

city: Kuala Lumpur

first: Amir Feisal

last: Merican

state: Kuala Lumpur

address: University of Malaya

department: Institute of Biological Science

country: Malaysia

institute: University of Malaya

summary: In this project we report the transcriptome profiles of X-linked Agammaglobulinema (XLA), an inherited form of Primary Immunodeficiency Diseases (PIDs),  using high-depth RNA-Seq technology .

overall_design:
Total RNAs were extracted from CD14-Positive Monocytes cells of 3 XLA patients.
Transcriptome profiling by high throughput RNA sequencing

first: Hoda

last: Mirsafian

first: Adiratna

middle: M

last: Ripen

first: Saharuddin

middle: B

last: Mohamad

first: Amir

middle: F


title: Principles for the regulation of multiple developmental pathways by a versatile transcriptional factor, BLIMP1 (RNA-Seq)

first: Yukihiro

overall_design: 26 3' RNAseq samples in 13 cell types: d2PGCLC (2 replicates), E16.5_Embryonic intestinal epithelium (E16.5_emIE, 2 replicates), P3_Embryonic intestinal epithelium (P3_emIE, 2 replicates), P14_Embryonic intestinal epithelium (P14_emIE, 2 replicates), P0_Photoreceptor precursor_GFP+ (P0_PRP_GFP+, 2 replicates), P4_Photoreceptor precursor_GFP+ (P4_PRP_GFP+CD73-, 2 replicates), P4_Photoreceptor precursor_CD73+ (P4_PRP_CD73+, 2 replicates), P6_Photoreceptor precursor_CD73+ (P6_PRP_CD73+, 2 replicates), P10_Photoreceptor precursor_CD73+ (P10_PRP_CD73+, 2 replicates), B cell (B cell, 2 replicates), Blast (Blast, 2 replicates), Pre-plasmablast (prePB, 2 replicates), Plamsablast (PB, 2 replicates)


title: The emergence, evolution, and diversification of the miR390-TAS3-ARF pathway in land plants

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

department: Horticulture

institute: South China Agricultural University

summary: In plants, miR390 directs the production of tasiRNAs from TRANS-ACTING SIRNA 3 (TAS3) transcripts to regulate AUXIN RESPONSIVE FACTOR (ARF) genes, transcription factors critical for auxin signaling; these tasiRNAs are known as tasiARFs. This pathway is highly conserved, with the TAS3 as the only one noncoding gene present almost ubiquitously in land plants. To understand the evolution of this miR390-TAS3-ARF pathway, we characterized homologs of these three genes from thousands of plant species, from bryophytes to angiosperms. Both miR390 and TAS3 are present and functional in liverworts, confirming their ancestral role to regulate ARFs in land plants. We found the lower-stem region of MIR390 genes, critical for accurate DCL1 (DICER-LIKE 1) processing, is conserved in sequence in seed plants. We propose a model for the transition of functional tasiRNA sequences in TAS3 genes occurred at the emergence of vascular plants, in which the two miR390 target sites of TAS3 genes showed distinct pairing patterns in different plant lineages. Based on the cleavability of miR390 target sites and the distance between target site and tasiARF we inferred a potential bidirectional processing mechanism exists for some TAS3 genes. We also demonstrated a tight mutual selection between tasiARF and its target genes, and characterized unusual aspects and diversity of regulatory components of this pathway. Taken together, these data illuminate the evolutionary path of the miR390-TAS3-ARF pathway in land plants, and demonstrate the significant variation that occurs in the production of phasiRNAs in plants, even in the functionally important and archetypal miR390-TAS3-ARF regulatory circuit.

overall_design: study the evolution of miR390-TAS3-ARF pathway

first: Jing

last: Xu

first: Blake

middle: C

last: Meyers


title: RNA sequencing reveals resistance of TLR4 ligand-activated microglial cells to inflammation mediated by the selective jumonji H3K27 demethylase inhibitor

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

institute: Hanyang Univ.

summary: Persistent microglia activation is associated with the production and secretion of various pro-inflammatory genes, cytokines and chemokines, which may initiate or amplify neurodegenerative diseases. A novel synthetic histone 3 lysine 27 (H3K27) demethylases JMJD3 inhibitor, GSK-J4, was proven to exert immunosuppressive activities in macrophages. However, a genome-wide search for GSK-J4 molecular targets has not been undertaken in microglia. To study the immuno-modulatory effects of GSK-J4 on a transcriptomic level, triplicate RNA sequencing and quantitative real-time PCR analyses were performed with resting, GSK-J4, LPS and LPS+GSK-J4 challenged primary microglial (PM) and BV-2 microglial cells. Among the annotated genes, transcriptional sequencing of microglia that were treated with GSKJ4 revealed a selective effect on LPS induced gene expression in which the induction of cytokines/chemokines, interferon-stimulated genes, and prominent (transcription factors) TFs as well as previously unidentified genes that are important in inflammation was suppressed. Furthermore, we show that GSK-J4 controls important inflammatory genes targets by modulating STAT1, IRF7, and H3K27me3 level at their promoter site. These unprecedented results demonstrate the histone demethylases inhibitor GSK-J4 could have therapeutic applications for neuroinflammatory diseases.

overall_design: Examination of the effects LPS on GSKJ4-treated PM microglial cells, were generated by deep sequencing on an Illumina HiSeq 2000 (101 cycles PE lane).

first: Young-Gyu

first: Jin-Choul


title: ATAC-seq analysis of the chromatin landscape during in vitro differentiation of murine trophoblast stem cells

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

institute: University of Warwick

summary: Our goal was to survey changes in chromatin accessibility during early trophoblast differentiation and assess its releationship with transcriptional changes.

overall_design: ATAC-seq was performed on 75,000 cells of two independent wild type trophoblast stem cell lines after 0 and 48 hours of in vitro differentiation.

first: A

last: Mould

first: E

last: Bikoff

last: Robertson


title: Metallibacterium scheffleri: Genetic data reveal a versatile metabolism

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

country: Germany

institute: Max Rubner-Institute

summary: This study describes the physiological properties of a wide spread acidophilic microorganism. Metallibacterium scheffleri DKE6 was described as an acid tolerant, heterotrophic g-proteobacterium living in an acidic biofilm. Casein was reported to be the only growth substrate of the organism. Nevertheless, using a combination of proteomic, genomic and transcriptomic approaches as well as microbiological assays we could identify a rather versatile metabolism. The detected casein hydrolysis was corroborated by the detection of proteases in the supernatant of the organism but also via transcriptome studies. Genomic analysis identified amino acid auxotrophies, which were revealed to be the reason for the observed growth deficiency with other substrates in the absence of casein. Supported by the detection three glycolytic pathways it was verified that glucose could serve as a growth substrate in the presence of amino acids as building blocks. Additionally, genes for sulfur and hydrogen oxidation were found and sulfate formation could be shown during growth with tetrathionate. The organism is acid tolerant. Still, growth with amino acids is accompanied by the release of ammonium and the subsequent increase of the medium pH. The distribution of other Metallibacterium species demonstrates also an adaption to diverse environments with varying pH values. Growth in biofilms or sediments seems to be a preferred habitat . We hypothesize that this supports the ability of the organism to raise the pH in its environment via ammonium production.

overall_design: RNA from two biological duplicates under identical conditions was sequenced. Each duplicate sample was obtained by pool three independent cultures that were harvested in exponential phase.

first: Sibylle

last: Bartsch

first: André

last: Gensch

first: Simon

last: Stephan

last: Dötsch

first: Johannes

last: Gescher


title: Transcriptome sequencing of Propionibacterium acidipropionici with different PA tolerance and production

status: Public on Sep 01 2017

city: Wuxi

first: Ningzi

last: Guan

state: Jiangsu

address: No.1800 Lihu street

institute: Propionibacterium acidipropionici

summary: We reported that analysis of acid tolerance mechanism in Propionibacterium acidipropionici at gene expression level. Genome shuffling was performed on P. acidipropionici to improve the acid tolerance of the strain. Wild type strain P. acidipropionici CGMCC 1.2230 and acid-tolerant mutant P. acidipropionici WSH1105 were compared to find key genes involved in acid tolerance of P. acidipropionici during fermentation. Results provide important information on acid response of P. acidipropionici, such as genes encoded ABC-transporters, proteins involved in amino acids metabolism and propionic acid synthesis.

overall_design: The mRNA of wild type (1.2230) and acid-tolerant mutant (WSH1105) strains, collected exponential growth phase under pH 7.0 and 5.5, were generated by deep sequencing using Illumina Miseq.

first: Long

last: Liu


title: Targeting Phospholipase D4 attenuates kidney fibrosis by modulating immune system and activating proteases

city: Boston

first: Zach

last: Herbert

state: MA

address: 450 Brookline Ave

department: Molecular Biology Core Facilities

institute: Dana-Farber Cancer Institute

summary: Phospholipase D4 (PLD4), a single pass transmembrane glycoprotein, is amongst the most highly upregulated genes in mice kidneys subjected to chronic progressive fibrosis1. Here we characterized the expression pattern of PLD4 and found it to be over expressed in the proximal and distal tubular epithelial cells of mice and human kidneys following fibrosis. Subcellularly, PLD4 was localized to the endoplasmic reticulum, golgi apparatus and mitochondria and was confirmed to interact with Calmegin, Lectin, Mannose Binding 2 and Suppressor of Lin-12-Like Protein 1. Mechanistically, we show that PLD4 facilitates fibrogenesis by modulating innate and adaptive immune system thereby promoting TGF-β signaling pathway. Moreover, PLD4 induces the expression of α1-antitrypsin protein (AAT, a serine protease inhibitor) that results in subsequent down-regulation of Neutrophil Elastase (NE), thereby leading to the accumulation of extracellular proteins and scar tissue formation. Genetic silencing of PLD4 protected mice from development of fibrosis initiated by either Folic acid (FA) treatment or unilateral ureteral obstruction (UUO). Furthermore, therapeutic targeting of PLD4 using specific siRNA also protected the mice from kidney fibrosis via the same mechanisms. These results suggest that inhibition of PLD4 is sufficient to activate protease-mediated degradation of extracellular matrix and reversal of fibrosis thereby highlighting new therapeutic strategies.

overall_design: mRNA profiles in the kidneys of PLD4-/- and PLD4+/+ mice at baseline and following UUO at days 5 and 10 with 4 replicates using Illumina NextSeq500

first: Vishal

last: Vaidya


title: UPF1 knockdown in differentiating human myoblasts

city: Seattle

first: Qing

last: Feng

state: WASHINGTON

address: 1100 Fairview Ave. N., Fred Hutchinson Cancer Research Center

department: Public Health and Basic Science devisions

institute: FRED HUTCH CANCER RESEARCH Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Human myoblast cell line 54-1 is transfected with either a srambled control siRNA or siRNA against UPF1. Two days after transfection, cell were induced to differentiate by changing grow meida to differentiation media. 2 days after induction of differentiation, cells are collected for extraction of RNA.

first: R

last: Bradley

first: Q


title: Dynamic DNA methylation reconfiguration during seed development and germination

first: Taiji

last: Kawakatsu


title: Paf1 modulates Piwi/piRNA silencing capacity in Drosophila

city: BOSTON

first: NELSON

last: LAU

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

summary: To test whether the RNA Polymerase II factor PAF1 affects PIWI silencing, we examined the transcriptome expression levels in Drosophila OSS cells following siRNA knockdown of these factors.

overall_design: The total RNAs from OSS cells were extracted after siRNA knockdown of GFP negative control, PAF1, PIWI, and a double knockdown of both PAF1 and PIWI.  The RNAs were then converted into strand-specific sequencing libraries with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina.

first: Nelson

last: Lau

first: Josef

last: Clark

first: Reazur

last: Rahman


title: Ebola virus glycoprotein variant with increased infectivity for human cells dominated the 2013-2016 outbreak

city: Worcester

first: Alper

last: Kucukural

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

summary: The unprecedented magnitude of the 2013-2016 Makona Ebola virus (M-EBOV) epidemic likely resulted from multiple epidemiologic factors that set it apart from previous outbreaks. Nonetheless, genetic adaptations that distinguish M-EBOV from previous isolates may also have contributed to the scale of the epidemic. Of particular interest is a M-EBOV glycoprotein (GP) variant, GP-A82V, that was first detected at the inflection point of the 2013-2016 outbreak - when the number of cases increased exponentially - and which completely supplanted the earlier M-EBOV sequence. We found that, as compared with the earlier strain, GP-A82V increased the ability of M-EBOV to fuse with and infect cells of primate origin, including human blood dendritic cells, without altering innate immune signaling in target cells. Residue 82 is located at the NPC1-binding site on M-EBOV GP and the increased infectivity of GP-A82V was restricted to cells from species in which the NPC1 orthologue bears primate-defining residues at the critical interface. We utilized HIV-derived lentiviral vectors pseudotyped with founder and A82V containing M-EBOV GPs to explore the potential that this modification alters how human monocyte-derived dendritic cells (MDDCs) respond to EBOV GP stimulation.

overall_design: We generated stocks of lentiviral vector bearing one the following three M-EBOV GPs: founder, A82V, and A82V/T230A. These viral stocks were used to challenge MDDCs from two healthy, anonymous human donors. Stimulated MDDCs were harvested at 1, 2, 4, and 6 hours after viral addition. Gene expression in M-EBOV GP challenged MDDCs was compared to a unstimulated control.

first: Wilhem

middle: E

last: Diehl

first: K

last: Kim

first: Parick

last: McDonel

first: Manuel

last: Garber

first: Jeremy

last: Luban


title: MicroRNAs Expression Profiles Differ between Primary Myofiber of Lean and Obese Pigs breeds

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

summary:
Purpose:  MicroRNAs (miRNAs) are non-coding small miRNA ~22 nucleotides in length and play a vital role in muscle development by binding to messenger RNAs (mRNAs). Large White (LW, a lean type pig) and Meishan pigs (MS, a Chinese indigenous obese breed) have significant postnatal phenotype differences in growth rate, muscle mass and meat quality, and theses difference are programmed during prenatal muscle development.To shed directly light on the miRNA transcriptome difference in prenatal muscles between these two distinct pig breeds.
Methods: skeletal musle miRNA profiles of Meishan pig and large white pig were generated by deep sequencing, in triplicate, using Illumina Hiseq2000 . The sequence reads that passed quality filters were analyzed at the mature miRNA level . qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: We measure the myofiber phenotypes of LW and MS at developmental stages of 35, 55 and 90 days post-conception (dpc). Results shows that the myogenesis process is more intense in MS than in LW at 35 dpc. To investigate the role of miRNAs involved in regulating muscle development at earlier stages of myogenesis and decipher the miRNAs transcriptome difference between LW and MS, here, the miRNAomes of longissimus dorsi muscle collected at 35 dpc from female LW and MS were analyzed by deep sequencing. Overall, we identified 1147 unique miRNAs comprising 434 known miRNAs, 239 conserved miRNAs and 474 candidate miRNAs. Expression analysis of the 10 most abundant miRANs in every library indicated that functional miRNAome may be smaller and tend to be highly expressed. These set of miRNA may play house keeping roles that were involved in myogenesis. A total of 87 miRNAs were significantly differentially expressed between LW and MS (reads > 1000, P < 0.05). Gene ontology (GO) and KEGG pathway enrichment analysis revealed that the differentially expressed miRNAs (DE miRNAs) were associated mainly with muscle contraction, WNT, mTOR, and MAPK signaling pathways. In addition, the expression patterns of myomiRs (miR-1,-133,-206) at three prenatal stages (35,55 and 90 dpc) were determined using qRT-PCR, Notably, ssc-miR-133 was significantly more highly expressed in LW pig skeletal muscle at all prenatal stages compared with its expression in LW pig skeletal muscle. We concluded that the higher expression levels of miR-133 in MS, possibly regulated by myoD, are potential strategies for improvement of myogenesis in earlier prenatal stages.
Conclusions: our results add new information to existing data on porcine miRNAs and be helpful to investigate the dominant (main functional) muscle-related miRNAs sets in different pig breeds. In addition, this study provide a profound knowledge on the role of miRNAs in prenatal muscle development, which could provide great reference value for pork quality improvement.

overall_design: sketetal musle miRNA profiles of Meishan pig and Large white pig  were generated by deep sequencing, in triplicate , using Illumina Hiseq2000 .

first: Dongting

last: He

first: Daiwen

last: Chen


title: Next generation sequencing based analysis of the embryonic (E15.5) transcriptome of wild type and β1-integrin-cKO lenses

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary: β1-integrin is the major β-integrin subunit expressed in both lens epithelial and fiber cells. Our previous research indicated that β1-integrin is essential for the maintenance of lens epithelial integrity and survival in late embryonic lens development (Simirskii et al, 2009). Lack of β1-integrin in the lens will lead to severe micropthalmia and lack of lens in adult mice. In order to study the mechanisms involved, high throughput RNA sequencing (RNAseq) was performed to determine the genes that are differentially expressed between  E15.5 wild type (WT) lenses and lenses that lack β1-integrin expression due to the action of MLR10 CRE (β1-cKO). The methodology used here is similar to the other RNAseq experiments that were previously performed in our lab (Manthey et al., 2014a and Audette et al, 2015) (Geo accession: GSE 49949 and GSE69940) . Meanwhile, the filtering criteria and processing procedures were also published (Manthey et al., 2014b).  Compared to WT, 120 genes were found to be differentially expressed in β1-cKO lenses. Moreover, bioinformatics tools (DAVID (the database for Annotation, Visulization and Integrated Discovery), and PANTHER (Protein Analysis through Evolutionary Relationship) classification system) as well as manual literature searching was applied for further data analysis. It showed that genes involved in EMT and stress-responses were differentially expressed in β1-cKO compared to that of WT.   Description of filtering criteria:  To identify the differentially expressed genes, pair-wise qCML method exact tests with a Benjamini Hochberg false discovery rate correction greater than the threshold of P<0.05 was applied, which identified 5120 genes. As previously described (Manthey et al., 2014b), most of the genes differentially expressed between inbred C57Bl/6 <har> and mice with a mixed background were below a threshold of 2.5 fold change. Therefore, all differentially expressed genes with a less than 2.5 fold change were filtered out. Further, genes whose expression level were not high enough to be biologically significant were also filtered out, based on the RPMK (Reads per Kilobase per million reads) value. Any gene in the final list has RPKM greater that 2 in either WT or β1-cKO samples, a value that corresponds to approximately 1 mRNA molecule per cell. By applying a combination of these filtering criteria, 120 differentially expressed genes were found, which could potentially elucidate the molecular connections between conditional deletion of β1-intergrin from the lens and the observed phenotypic abnormalities.    Manthey, A. L., Lachke, S. A., FitzGerald, P. G., Mason, R. W., Scheiblin, D. A., McDonald, J. H. and Duncan, M. K. (2014a) 'Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development', Mech Dev 131: 86-110.  Manthey, A. L., Terrell, A. M., Lachke, S. A., Polson, S. W. and Duncan, M. K. (2014b) 'Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis', Genom Data 2: 369-374.

overall_design: RNA-Seq comparison of C57Bl/6 <har> wild type controls and β1-integrin conditional knockout lenses at E15.5, three biological replicates were used in each group

first: Anne

last: Terrell

first: Yichen

last: Wang

middle: K


title: Polycomb-mediated axial patterning requires nucleosome compaction

first: Robert

last: Kingston

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital


title: Polycomb-mediated axial patterning requires nucleosome compaction [ChIP-seq]

summary: We determined the genome-wide binding profiles of wild type and compaction mutant CBX2 (denoted as 'KRA') in mouse embryonic stem cells (mESCs) by ChIP-seq.

overall_design: CBX2 ChIP in two mESC lines.

first: Mei

middle: S

first: Andrej

last: Savol

first: Peggy

middle: I

first: Ruslan

last: Sadreyev


title: Polycomb-mediated axial patterning requires nucleosome compaction [RNA-seq]

summary: We determined by RNA-seq gene expression changes in mESCs following the induced expression of WT-, KRA- or DEA-CBX2 variants in Cbx2 null cells.

overall_design: We generated mRNA profiles from 5 mESC lines (2 WT, 2 KRA, 1 DEA) treated with doxycycline to express similar levels of CBX2, and, from a 6th condition where one of the KRA mESC lines was treated with more doxycycline. Each sample was compared to its own control, which is no doxycycline treatment, to determine the effect of induced CBX2 on gene expression changes. Each sample (with and without doxycycline treatment) was performed with 2 or 3 biological replicates.

last: Lau


title: TET2 loss and the lymphoma-associated RHOA mutation cooperate to disrupt CD4+ T cell function through inactivation of FOXO1

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: Angioimmunoblastic T cell lymphoma (AITL) represents a distinctive form of peripheral T cell lymphoma with a dismissal prognosis. Recent exome sequencing in AITL patients revealed frequent coexistence of somatic mutations in the RHO GTPase (RHOAG17V) and the 5-methylcytosine oxidase TET2. Here we demonstrated that Tet2 loss and RhoAG17V cooperatively caused abnormal CD4+ T cell proliferation and differentiation by perturbing FoxO1 gene expression and its subcellular localization, an abnormality that is also detected in AITL tumor samples. Re-expression of FoxO1 attenuated aberrant immune responses induced by genetic lesions in both Tet2 and RhoA. Our findings suggest that mutational cooperativity between epigenetic factors and GTPases in adult CD4+ T cells may account for immunoinflammatory responses that are commonly associated with AITL.

overall_design: Determine the differential expressed genes between WT, Tet2-/-, RhoAG17V, Tet2-/-RhoAG17V mutant CD4+ T cells.

first: Yun

last: Huang

first: Deqiang

last: Sun


title: ChIP-seq analysis of Blimp1 in day 2 differentiated mouse trophoblast stem cells.

first: Andrew

last: Nelson

summary: Our goal was to survey genomic binding of Blimp1 in differentiating trophoblast giant cells in order to identify direct transcriptional target genes.

overall_design: ChIP-seq was performed using a mouse anti-Blimp1 ascites fluid on 4x10^7 of each of two wild type differentiated TS cell clones, and one differentiated mutant clone as a negative control.

first: A

middle: W

last: Mould

first: E

last: Bikoff

last: Robertson


title: Gene expression profiling of drought tolerant and sensitive Brassica rapa accessions under control and osmotic stress conditions

city: Giessen

first: Birgit

last: Samans

address: Heinrich-Buff-Ring 26-28

institute: University of Giessen

summary: In this study genome-wide gene expression profiling was used to analyze mechanisms of drought tolerance in Brassica rapa. Using an Illumina Mi-Seq platform we sequenced RNA from shoot tissues of drought tolerant and drought sensitive B. rapa genotypes in control conditions and after application of osmotic stress. Differentially expressed genes between the different conditions and genotypes were used to identify drought relevant gene networks.

overall_design: Two accessions of Brassica rapa with previously-identified contrasting drought responses were exposed to osmotic stress in a hydroponic growth system. Polyethylene glycol (PEG) simulated osmotic stress applied to half of the plants of each accession when plants had 4-5 true leaves while the other half remained with Murashige and Skoog (MS) medium as control for PEG. Total RNA isolated from shoot tissue was used for RNA-sequencing. For each genotype and condition three biological replicates were taken at 4h, 8h and 12h after stress treatment.  cDNA libraries were prepared with the TruSeq Stranded Total RNA with Ribo-ZeroTM Plant kit from Illumina. Sequencing was carried out on each library to generate 150 bp PE reads using an Illumina Mi-Seq platform. The transcriptome reads were mapped to the B. rapa cv. Chiifu reference genome v1.5 (Wang et al., 2011) allowing 3 mismatches, then normalised and quantified as FPKM values using the spliced aligner TopHat/Cufflinks (http://ccb.jhu.edu/software/tophat/index.shtml,http://cole-trapnell-lab.github.io/cufflinks/).

first: Samans

last: Birgit

first: Guo

last: Yiming


title: Transcriptome analysis of metronidazole-induced sensory neuron ablation in zebrafish

city: St. Louis

first: Mark

last: Voigt

state: MO

address: 1402 S Grand Blvd

department: Pharmacology and Physiology

institute: Saint Louis University

summary: Damage to and/or loss of sensory neurons can result in debilitating neuropathies that often have a dramatic impact on quality of life. The cellular mechanisms involved in the response of neurons and glia to such pathological insults are poorly understood. Investigation has shown that peripheral glia play critical roles in both the degenerative and regenerative processes that are involved in the responses to peripheral nerve damage. The vast majority of studies have focused primarily on myelinating Schwann cells], with the result that very little is known regarding how the non-myelinating glia that ensheath axons and neuronal somas respond to nerve damage. This is a significant knowledge gap, given that over 80% of cutaneous fibers are unmyelinated, that they transduce such important modalities as itch, pain, temperature, touch and pressure, and that they are affected in many prevalent peripheral neuropathies. It is the goal of this study to shed light on the genetic programs involved in the responses of non-myelinating glia roles to nerve degeneration. We utilized RNA-seq to identify genes that were differentially expressed in the larval head during the process of sensory neuron ablation and axon degeneration in both wild-type larvae and in larvae that do not have peripheral glia (foxd3 mutants) using a selective, conditional approach. Overall, the information regarding differential gene expression in these conditions will provide a basis for further investigation into the cellular processes that underlie pathophysiological responses of neurons and glia to sensory nerve damage.

overall_design: mRNA levels were determined using biological triplicate samples from five sets of samples. Three sets from wild-type: control, 2 hrs of metronidazole treatment and 5 hrs of metronidazole treatment. And two sets from foxd3 mutants: control and 5hrs of metronidazole treatment.

first: Jane

middle: A

last: Cox

first: Bo

last: Zhang

first: Holly

last: Pope


title: EZH2 inhibition as a targeted therapy for H3K27M mutant pediatric gliomas [RNA-Seq]

city: Copenhagen

first: Faizaan

last: Mohammad

state: Choose A State

address: Ole Maaloøs vej 5 Fourth Floor

country: Denmark

institute: BRIC

summary: Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive brain tumour that is located in the pons and primarily affects children. Whole-exome sequencing studies have identified recurrent driver mutations in H3F3A and HIST1H3B, leading to the expression of histone H3 in which lysine 27 is substituted with methionine (H3K27M) in nearly 80% of DIPGs. H3K27M inhibits Polycomb Repressive Complex 2 (PRC2) activity by binding to its catalytic subunit EZH2 and although DIPGs with H3K27M mutation show global loss of H3 with trimethylated lysine 27 (H3K27me3), several genomic loci are still H3K27me3 positive. Here, we describe a new mouse DIPG model in which H3K27M potentiates tumourigenesis. Using this model and primary patient-derived DIPG cell lines, we show that H3K27M expressing tumours require PRC2 for proliferation. Furthermore, we demonstrate that small molecule EZH2 inhibitors abolish in vitro and in vivo tumour cell growth through a mechanism involving induction of the tumour suppressor protein p16INK4A. In agreement with this, we show that tumour cells with inactivated p16INK4A function do not respond to EZH2 inhibitors. By analysing genome-wide H3K27me3 enrichment profile in mouse DIPG model, we highlight distinct features of the loci that lose or retain H3K27me3 in H3K27M expressing cells. Taken together these results show that residual PRC2 activity is required for the proliferation of H3K27M positive DIPGs, and we propose a therapeutic strategy for these tumours using EZH2 inhibitors and expression of p16INK4A as a marker for stratifying potential responding tumours.

overall_design: Expression profile was analyzed in mouse DIPG cells expressing wild-type or K27M mutant H3.3 in presence or absence of Ezh2 inhibitor using RNA-seq.


title: Tissue overgrowth induced by coexpression of the progenitor genes hth/MEIS1 and tsh/TSHZ results from an imbalance in the estrogen response pathway in Drosophila [RNA-Seq]

city: Marseille

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

country: France

institute: CRCM

summary: Analysis of third instar eye-antennal Drosophila imaginal discs with forced expression of hth, tsh or hth+tsh in the eye using an eye-specific GAL4 driver (optix2.3-GAL4). Forced maintenance of hth+tsh expression (but not of any of the two alone) results in overgrowth and aberrant cell differentiation. Results provide insight into new targets of hth+tsh.

overall_design: RNA-seq gene expression profiling across Drosophila 3rd instar larval wild type eye-antennal discs and genetic perturbations of tsh, hth and tsh-hth together.

first: Marta

last: Neto

first: Marina

last: Naval Sánchez

first: Paulo

last: Pereira

first: Dirk

last: Geerts

first: Stein

last: Aerts

first: Fernando

last: Casares


title: Tissue overgrowth induced by coexpression of the progenitor genes hth/MEIS1 and tsh/TSHZ results from an imbalance in the estrogen response pathway in Drosophila

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

overall_design: Refer to individual Series


title: Pseudomonas stutzeri RCH2 [delta]CzcR Zinc Stress

status: Public on Aug 30 2017

city: Emeryville

first: Megan

middle: Elizabeth

last: Garber

state: CA

address: 5885 Hollis st

department: Department of Energy/ UC Berkeley

institute: ENIGMA

summary: Goal was to characterize the regulon of the CzcR response regulator under zinc stress in Pseudomonas stutzeri RCH2

overall_design: Triplicates of WT and [delta]CzcR Pseudomonas Stutzeri RCH2 we grown to mid-log and were challenged with and without a 50µM concentration of Zinc Chloride. The [delta]CzcR1 sample that did not receive Zn was excluded from analysis.

first: Aindrila

last: Mukhophadhyay


title: EZH2 inhibition as a targeted therapy for H3K27M mutant pediatric gliomas [ChIP-seq]

summary: Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive brain tumour that is located in the pons and primarily affects children. Whole-exome sequencing studies have identified recurrent driver mutations in H3F3A and HIST1H3B, leading to the expression of histone H3 in which lysine 27 is substituted with methionine (H3K27M) in nearly 80% of DIPGs. H3K27M has been shown to inhibit Polycomb Repressive Complex 2 (PRC2) activity by binding to its catalytic subunit EZH2, and although DIPGs with H3K27M mutation show global loss of H3 with trimethylated lysine 27 (H3K27me3), several genes retain H3K27me3. Here, we describe a new mouse DIPG model in which H3K27M potentiates tumourigenesis. Using this model and primary patient-derived DIPG cell lines, we show that H3K27M expressing tumours require PRC2 for proliferation. Furthermore, we demonstrate that small molecule EZH2 inhibitors abolish tumour cell growth through a mechanism involving induction of the tumour suppressor protein p16INK4A. In agreement with this, we show that tumour cells with non-functional p16INK4A do not respond to EZH2 inhibitors. Genome-wide enrichment analyses show that several genes retain H3K27me3 even in the presence of H3K27M. Several of these genes are associated with high levels of H3K27me3 in the absence of H3K27M, whereas regions with low H3K27me3 levels tend to lose H3K27me3 upon H3K27M expression. Furthermore, we find significant overlap between genes that retain H3K27me3 in mouse and human primary DIPGs expressing H3K27M. Taken together, these results show that residual PRC2 activity is required for the proliferation of H3K27M positive DIPGs, and we propose a therapeutic strategy for these tumours using EZH2 inhibitors and expression of p16INK4A as a marker for stratifying potential responding tumours.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: H3K27me3 enrichment profile was analyzed in mouse DIPG cells expressing wild-type of K27M mutant H3.3 in presence or absence of Ezh2 inhibitor. In addition, H3K27me3 enrichment profile was also analyzed in four human DIPG cell lines expressing K27M mutant H3.

first: Benjamin

last: Leblanc

first: Jens

last: Johansen

first: Kristian

last: Helin


title: RNA-Seq Profiling of Intestinal Expression of Xenobiotic Processing Genes in Germ-Free Mice

first: Julia

middle: Yue

last: Cui

state: WA

address: 4225 Rossevelt Way Ne

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: This study aimed to quantify and compare the mRNA abundance of all major XPGs in liver and intestine between conventional (CV) and germ-free (GF) mice using RNA-Seq.  The CV RNA-Seq data were previously uploaded to GEO database by the same research group (GSE79848). All CV and GF mice were age-matched, and were analyzed under the same conditions (diet, water, bedding, and animal facility).

overall_design: mRNA profiles of liver and four sections of intestine of conventional (CV) and germ-free (GF) mice were generated by RNA-Seq, in triplicate, by illumina HiSeq 2000.

first: Joseph

middle: L

last: Dempsey

middle: Y


title: Immune-Responsive Gene 1 expression in myeloid cells prevents neutrophil mediated immunopathology during Mycobacterium tuberculosis infection, in vitro neutrophils data

first: Maxim

middle: N.

last: Artyomov

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Immune-Responsive Gene 1 (Irg1) is a mitochondrial enzyme that produces itaconate under inflammatory conditions principally in cells of myeloid lineage. Cell culture studies suggest that itaconate regulates inflammation through inhibitory effects on cytokine and reactive oxygen species production. To evaluate the functions of Irg1 in vivo, we challenged wild-type (WT) and Irg1 KO mice with Mycobacterium tuberculosis (Mtb) and monitored disease progression. Irg1 KO but not WT mice succumbed rapidly to Mtb, and mortality was associated with increased infection, inflammation, and pathology. Infection of LysM-Cre Irg1 flox, MPR8-Cre Irg1 flox, and CD11c-Cre Irg1 flox conditional knockout mice along with neutrophil depletion experiments revealed a role for Irg1 in alveolar macrophages and LysM+ myeloid cells in preventing neutrophil-mediated immunopathology and disease. RNA-seq analyses suggest that Irg1 and its production of itaconate temper Mtb-induced inflammatory responses in myeloid cells at the transcriptional level. Thus, Irg1 modulates inflammation to curtail Mtb-induced lung disease.

overall_design: Neutrophils were purified from bone marrow of naïve mice by negative selection using magnetic-activated cell sorting beads (Miltenyi). Neutrophil purity (>95%) was assessed by flow cytometry as the percentage of Ly6G+ CD11b+ cells. Neutrophils were cultured in RPMI-1640 supplemented with 1% non-essential amino acids at 37°C, 5% CO2. GFP-Mtb was grown to mid-log phase, washed with PBS, sonicated to disperse clumps, and resuspended in neutrophil culture media. GFP-Mtb then was opsonized prior to infection by mixing with an equal volume of normal mouse sera (Sigma) and incubation at room temperature for 30 min. Neutrophils were mock-infected or infected with opsonized GFP-Mtb at MOI 1 and incubated at 37°C, 5% CO2.

first: Sharmila

last: Nair

first: Jeremy

middle: P

last: Hyunh

first: Vicky

last: Lampropoulou

first: Ekaterina

last: Esaulova

last: Loginicheva

first: Anshu

last: Gounder

first: Adrianus

last: Boon

first: Elizabeth

last: Schwarzkopf

first: Tara

middle: R

last: Bradstreet

first: Brian

middle: T

last: Edelson

middle: N

first: Christina

last: Stallings

first: Michael

last: Diamond


title: Immune-Responsive Gene 1 expression in myeloid cells prevents neutrophil mediated immunopathology during Mycobacterium tuberculosis infection.


title: Immune-Responsive Gene 1 expression in myeloid cells prevents neutrophil mediated immunopathology during Mycobacterium tuberculosis infection, in vivo neutrophil data

overall_design: C57BL/6N (WT) mice were purchased from Charles River. B6.SJL (CD45.1) mice were obtained from Jackson Laboratories. Irg1−/− mice (embryonic stem cells obtained from KOMP (C57BL/6N background), MGI: 103206) were generated at Washington University. Adult mice (6-13 weeks of age) of both sexes were used, and sex was randomized between experiments. Neutrophils were purified by magnetic-activated cell sorting from the bone marrow of naïve mice (negative selection) or the lungs of Mtb-infected mice at 16 dpi (selection for Ly6G+ cells) (Miltenyi).

middle: C


title: Genome-wide maps of chromatin state of Smyd2 binding in renal epithelial cells

city: Kansas City,

first: Xiaogang

last: Li

state: KS

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

summary: To identify potential transcriptional targets of Smyd2, we performed ChIP-sequencing (ChIP-seq) analysis in renal epithelial cells with an anti-Smyd2 antibody. We identified 91 potential Smyd2 target genes in Pkd1 wild type MEK cells and 116 potential Smyd2 target genes in Pkd1 null MEK cells. There were 14 genes identified in both Pkd1 wild type and null MEK cells. Thus, the number of potential Smyd2 target genes in Pkd1 null MEK cells are 116 - 14 = 102 genes

overall_design: Examination of  Smyd2 transcriptional target genes in 2 cell types.

first: Xiaoyan

first: Xia

last: Zhou


title: Clonal Variation of Human Induced Pluripotent Stem Cells for Induction into the Germ Cell Fate

city: Kyoto

first: Yukihiro

last: Yabuta

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: The mechanisms for human germ cell development have remained largely unknown, due to the difficulty in obtaining suitable experimental materials. The establishment of an in vitro system to reconstitute human germ cell development will thus provide a critical opportunity to understand its mechanisms at a molecular level. It has previously been shown that human induced pluripotent stem cells (hiPSCs) are first induced into incipient mesoderm-like cells (iMeLCs), which are in turn induced into primordial-germ cell like cells (PGCLCs) with gene expression properties similar to early migratory PGCs. Here we report that the efficiency of PGCLC induction varies among hiPSC clones, and, interestingly, the clonal variations in PGCLC induction efficiency are reflected in the gene-expression states of the iMeLCs. Remarkably, the expression levels of EOMES, MIXL1 or T in the iMeLCs are positively correlated with the efficiency of subsequent PGCLC generation, while the expressions of CDH1, SOX3 or FGF2 are negatively correlated. These results indicate that the expression changes of these genes occurring during iMeLC induction are key markers indicative of successful induction of PGCLCs, and furthermore, that hiPSC clones have different properties that influence their responsivity to the iMeLC induction. Our study thus provides important insights into the mechanism of hPGC specification as well as the development of a better strategy for inducing human germ cell fate from PSCs in vitro.

overall_design: RNAseq analysis of human induced pluripotent stem cells (hiPSC) and incipient mesoderm-like cells (iMeLC).

first: Shihori

last: Yokobayashi

first: Keisuke

last: Okita

first: Masato

last: Nakagawa

first: Tomonori

last: Nakamura

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: TRAP sequencing of D1 and D2 spiny projection neurons from young and old mice and ribosome profiling in NIH-3T3 cells

city: Cambridge

first: Peter

last: Sudmant

address: 77 Massachusetts Ave

institute: MIT

summary: Particular brain regions and cell populations exhibit increased susceptibility to aging-related stresses. Here, we describe the age-specific and brain-region-specific accumulation of ribosome-associated 3' UTR RNAs that lack the 5' UTR and open reading frame. Our study reveals this phenomenon impacts hundreds of genes in aged D1 spiny projection neurons of the mouse striatum and also occurs in the aging human brain. Isolated 3' UTR accumulation is tightly correlated with mitochondrial gene expression and oxidative stress, with full-length mRNA expression that is reduced but not eliminated and with production of short 3' UTR-encoded peptides. Depletion of the oxidation-sensitive Fe-S cluster ribosome recycling factor ABCE1 induces the accumulation of 3' UTRs, consistent with a model in which ribosome stalling and mRNA cleavage by No-Go decay yields isolated 3' UTR RNAs protected by ribosomes. Isolated 3' UTR accumulation is a hallmark of brain aging, likely reflecting regional differences in metabolism and oxidative stress.

overall_design: sequencing of TRAP isolated cell-type specific mRNA from D1 and D2 spiny projection neurons in aged and young mice. 4 Biological replicates per condition. Additional experiments from ribosome profiling of NIH-3T3 cells treated with paraquat, siRNAs to ABCE1 and a control siRNA

middle: H


title: Role of OSGIN1 in Mediating Smoking-induced Autophagy in the Human Airway Epithelium [RNA-Seq]

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Enhanced autophagy is recognized as a component of the pathogenesis of smoking-induced airway disease. Based on the knowledge that enhanced autophagy is linked to oxidative stress and the DNA damage response, both of which are linked to smoking, we used microarray analysis of the small airway epithelium to identify smoking up-regulated genes known to re-spond to oxidative stress and the DNA damage response. This analysis identified OSGIN1 as significantly up-regulated by smoking in both the large and small airway epithelium (1.8-fold, p<0.01, 2.1-fold, p<10-4, respectively), an observation confirmed by an independent small airway microarray cohort, TaqMan PCR and RNAseq. Genome-wide correlation of RNAseq analysis of airway basal/progenitor cells isolated from healthy subjects (n=17) showed a direct correlation of OSGIN1 mRNA levels to multiple classic autophagy genes, including, LC3B, P62, WIPI1 and ATG13 (all rho>0.7, p<0.01). In vitro cigarette smoke extract exposure of nonsmoker primary airway basal/progenitor cells was accompanied by a dose-dependent up-regulation of OSGIN1 and autophagy induction. Lentivirus-mediated enhanced expression of OSGIN1 in human primary basal/progenitor cells induced puncta-like staining of LC3B and up-regulation of LC3B mRNA and protein and P62 mRNA expression level in a dose and time-dependent manner. OSGIN1-induction of autophagosome / amphistome / autolysosome formation was confirmed by co-localization of LC3B with P62 or CD63 (endosome marker) and LAMP1 (lysosome marker). Induction of autophagy by OSGIN1 is accompanied with heightened oxidative stress. Together, these observations support the concept that smoking-induced up-regulation of OSGIN1 is at least one link between smoking-induced stress and enhanced-autophagy in the human airway epithelium.

overall_design: Airway epithelium transcriptome analysis suggested that OSGIN, an oxidative response and cell death induction gene, was up-regulated by cigarette smoking and might be involved in autophagy regulation. In vitro study demonstrated that smoking can increase OSGIN1 expression and enhanced-expression of OSGIN1 led to autophagy, which is accompanied with heightened oxidative stress.

first: Guoqing

last: Wang

first: Haixia

first: Mohammed

last: Al-Hijji

first: Xuemei

last: Ou

first: Jacqueline

last: Salit

first: Matthew

last: Walters

first: Michelle

last: Staudt

first: Robert

middle: J

last: Kaner

first: Ronald

middle: G

last: Crystal


title: A memory of early life physical activity is retained in bone marrow of adult rats but does not prevent reversal to obese phenotype

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary: Studies have reported opposing effects of high-fat diet and mechanical stimulation on lineage commitment of the bone marrow stem cells. Yet, how the bone marrow modulates its gene expression in response to the combined effects of mechanical loading and a high-fat diet has not yet been addressed. We investigated whether early-life voluntary physical activity can modulate the effects of a high-fat diet on body composition, bone phenotype and bone marrow gene expression in male Sprague Dawley rats. We show that early-life high-fat diet positively affected body weight, total fat percentage and bone mass indices. In the bone marrow, early-life high-fat diet resulted in adipocyte hypertrophy and a pro-inflammatory and pro-adipogenic gene expression profile. Crucially, the bone marrow of the rats that undertook wheel exercise while on a high-fat diet retained a memory of the early-life exercise. This memory lasted at least 60 days after the cessation of the voluntary exercise and was manifest by: 1) the bone marrow adipocyte size of the exercised rats not exhibiting hypertrophy; and 2) genes associated with mature adipocyte function being down-regulated. Our results are consistent with the marrow adipose tissue having a unique and long-lasting response to high-fat feeding in the presence or absence of exercise.

overall_design: Eighty male SD rats were randomised at weaning into : chow-fed group (C-SED) or a high-fat fed group. The high-fat fed group was further divided into three sub-groups: the high-fat sedentary (HF-SED) group,  the high-fat late-exercise (HF-LEX) group,   and the high-fat early-exercise (HF-EEX) group. At day 120-123, the animals were culled and total RNA was extracted from the bone marrow of the femur. The RNA was sequenced using Illumina Hiseq4000 technology. Differential gene expression analysis was carried out using Tuxedo suite of bioinformatic tools.

first: Dharani

middle: M

last: Sontam

first: Mark

last: Vickers

first: Elwyn

last: Firth


title: Loss of CTCF reveals basic properties of post-mitotic epigenomes and induces heart failure [HiC-seq]

city: Los Angeles

first: Tom

last: Vondriska

address: 650 Charles E Young Dr, BH553

institute: UCLA

summary: Understanding the principles of endogenous chromatin structure has key implications for epigenetic therapy. To determine the mechanisms of genome structure-function in post-mitotic cells, genome-wide chromatin conformation capture was performed in cardiac myocytes, a non-dividing, differentiated cell responsible for cardiac contraction. Cardiac-specific CTCF knockout mice demonstrated that loss of CTCF had minimal effect on topologically associating domains; however, it selectively altered boundary strength and A/B compartmentalization, with gene expression changes mimicking those in heart failure. Loss of CTCF (or subjecting wild-type mice to clinically relevant pressure overload stress) remodeled long-range chromatin looping to alter 3D proximity of enhancers and disease causing genes. Depletion of CTCF was sufficient to induce heart failure in mice and human heart failure patients receiving mechanical unloading to attenuate disease progression show increased CTCF expression. These findings establish CTCF in the maintenance of chromatin looping and identify global chromatin remodeling as a causative factor in heart failure.

overall_design:
Control, CTCF knockout, and pressure overload Hi-C experiments in isolated cardiac myocytes
Please note that each sample represents combined replicates and processed data was generated from the combined samples.

first: Thomas

first: Manuel

last: Garrido

first: Douglas

last: Chapski


title: Loss of CTCF reveals basic properties of post-mitotic epigenomes and induces heart failure [ChIP-seq]

overall_design: Control, CTCF knockout, and pressure overload ChIP-seq experiments in isolated cardiac myocytes


title: Polycomb Responds to Low Levels of Transcription

last: Ptashne

address: 1275 York Ave

department: Molecular Biology Program

institute: Sloan Kettering Institute

summary: How is Polycomb (Pc), a eukaryotic negative regulator of transcription, targeted to specific mammalian genes? Our genome-wide analysis of the Pc mark H3K27me3 in murine cells revealed that Pc is preferentially associated with CpG island promoters of genes that are transcribed at a low level and less so with promoters of genes that are either silent or more highly expressed. Studies of the CpG island promoter of the Kit gene demonstrate that Pc is largely absent when the gene is silent in myeloid cells, as well as when the gene is highly expressed in mast cells. Manipulations that increase transcription in the former case, and reduce it in the latter, increase Pc occupancy. The average negative effect of Pc, we infer, is about 2-fold. We suggest possible biological roles for such negative effects and propose a mechanism by which Pc might be recruited to weakly transcribed genes.

overall_design: Five different cell types with five different antibodies.

first: Georgina

last: Berrozpe

first: Gene

middle: O

last: Bryant

first: Katherine

last: Warpinski

first: Dan

last: Spagna

first: Santosh

last: Narayan

first: Shivangi

last: Shah


title: Loss of CTCF reveals basic properties of post-mitotic epigenomes and induces heart failure


title: SWI-SNF-like fetal gene reprogramming dynamically regulates epicardial progenitor activity

city: Oxford

first: Joaquim

middle: Miguel

last: Vieira

address: South Parks Road

department: Department of Physiology, Anatomy & Genetics

institute: University of Oxford

summary: Epicardium-derived cells (EPDCs) contribute cardiac cell types during development and in adulthood respond to Thymosin β4 (Tβ4) and myocardial infarction (MI) by reactivating a fetal gene program to promote neovascularization and cardiomyogenesis.  The mechanism for epicardial gene activation remains elusive.  Here we reveal that SWI/SNF chromatin-remodeling complexes restored embryonic potential upon MI.  BRG1, the essential ATPase subunit of SWI/SNF, physically interacted with Tβ4 and was recruited by CCAAT/enhancer-binding protein β (C/EBPβ) to discrete regulatory elements in the Wilm’s tumor 1 (Wt1) locus. BRG1-Tβ4 co-operative binding promoted transcription of Wt1 as the master regulator of embryonic EPDCs and Wt1as, an antisense lncRNA produced from within intron 1, which increased Wt1 mRNA stability through heteroduplex formation.  ChIP-seq revealed global BRG1 binding which was enhanced by Tβ4 at key embryonic epicardial loci downstream of Wt1.  These findings reveal novel essential functions for chromatin-remodeling and antisense RNA in the embryonic programming of EPDCs during cardiac development and repair.

overall_design: ChIP-seq study using the Illumina platform NextSeq 500. Chromatin immunoprecipitation of BRG1 was performed in biological duplicates using PBS- and Tβ4-primed, -injured adult murine hearts collected four days after MI.

first: Daria

last: Gavriouchkina

first: Tatjana

last: Sauka-Spengler

first: Paul

last: Riley


title: Mesenteric lymph node stromal cell-derived extracellular vesicles contribute to peripheral de novo induction of Foxp3+ regulatory T cells.

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

summary: Intestinal regulatory T cells (Tregs) are fundamental in peripheral tolerance toward commensals and food-borne antigens. Accordingly, gut-draining mesenteric lymph nodes (mLNs) represent a site of efficient peripheral de novo Treg induction when compared to skin-draining peripheral LNs (pLNs), and we had recently shown that LN stromal cells substantially contribute to this process. Here, we aimed to unravel the underlying molecular mechanisms and generated immortalized fibroblastic reticular cell lines (iFRCs) from mLNs and pLNs, allowing unlimited investigation of this rare stromal cell subset. In line with our previous findings, mLN-iFRCs showed a higher Treg-inducing capacity when compared to pLN-iFRCs. RNA-seq analysis focusing on secreted molecules revealed a more tolerogenic phenotype of mLN- as compared to pLN-iFRCs. Remarkably, mLN-iFRCs produced substantial numbers of microvesicles (MVs) that carried elevated levels of TGF-β when compared to pLN-iFRC-derived MVs, and these novel players of intercellular communication were shown to be responsible for the tolerogenic properties of mLN-iFRCs. Thus, stromal cells originating from mLNs contribute to peripheral tolerance by fostering de novo Treg induction using TGF-β-carrying MVs. This finding provides novel insights into the subcellular/molecular mechanisms of de novo Treg induction and might serve as promising tool for future therapeutic applications to treat inflammatory disorders.

overall_design: Identification of differentially expressed genes in immortalized fibroblastic reticular cells from mesenteric or skin-draining lymph nodes of specific-pathogen-free housed mice.

first: Jochen

last: Huehn

first: Joern

last: Pezoldt

first: Maria

last: Szente-Pasztoi


title: Tissue overgrowth induced by coexpression of the progenitor genes hth/MEIS1 and tsh/TSHZ results from an imbalance in the estrogen response pathway in Drosophila [FAIRE-Seq]

first: Delphine

last: Potier

overall_design: RNA-seq gene expression profiling across Drosophila 3rd instar larval wild type eye-antennal discs and genetic perturbations of tsh, hth and tsh-hth together.

first: Marta

last: Neto

first: Marina

last: Naval Sánchez

first: Paulo

middle: S

last: Pereira

first: Dirk

last: Geerts

first: Stein

last: Aerts

first: Fernando

last: Casares


title: High-resolution Comparative Analysis Reveals a Primitive 3D Genome in Embryonic Stem Cells

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

type:
Other
Third-party reanalysis

summary: The landscape of human epigenome undergoes extensive changes during development, leading to distinct transcription programs in different cell types. It is however still not clear how the high-order genome organization reshapes in cellular differentiation. Using Hi-C, we compared the comprehensive 3D genome maps in human embryonic stem cells (ESCs) and two differentiated cell types at kilobase resolution. Consistent with previous reports, we found that the CTCF protein anchors long-range constitutive interactions that are invariant between different cell types. The most stable DNA contacts in ESC are between a few hundred genomic loci with strongest histone H3 lysine 27 tri-methylation (H3K27me3) binding, which plays a key role maintaining pluripotency by inhibiting key development genes. These repressive 3D chromatin structures are resolved in differentiated cells, accompanied by redistribution of H3K27me3 mark. Most surprisingly, we found that in human ESCs, DNA looping interactions are not enriched at enhancers, suggesting a stochastic nature of DNA looping interactions at ESC enhancers. This is in sharp contrast to differentiated cells, in which a majority of cell type specific DNA looping interactions are at enhancers, regardless of whether the enhancers are co-occupied by CTCF. Taken together, our analysis revealed a primitive enhancer-independent genome architecture in ESCs, which is consistent with the stem cell pluripotency and differentiation plasticity. Most of the stable DNA looping interactions associated with lineage-governing enhancers are created only during cell fate commitment.

overall_design: We performed kilobase-resolution Hi-C analysis at fragment level in H1 hESCs, IMR90 and GM12878 cells. Identified DNA looping interactions are compared to chromatin marks in these cell types.

first: Xiaoxiao

last: Liu

first: Yan

last: Li


title: The genomic distribution of G9a, H3K9me2, H3K27me3 and Mef2c in cardiomyocyte-enriched populations isolated from G9a-KO and Cre mice

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

country: Italy

institute: Humanitas Research Hospital

summary: The role of the histone methyltrasferase G9a (also known as Ehmt2) in the normal heart has not been studied extensively. To identify  the genomic regions bound to G9a in cardiomyocytes (CMs),we first generated a conditional, cardiac-specific KO mouse for this gene using the Cre-Lox approach, crossing G9a flox/flox mice with αMHC-MerCreMer mice (Cre mice were used as controls). Then we performed ChIP-seq for G9a and H3K9me2 – the main histone methylation catalysed by the HMT – on isolated G9a-KO and Cre CMs, and considered the best G9a-bound genomic regions as those that had a loss or decrease of G9a binding as well as a lower level of H3K9me2 in G9a-KO CMs. Since G9a contributes to trimethylation of H3K27 at a set of developmental genes through its interaction with PRC2, we also evaluated whether the loss of G9a had an effect on the distribution of this histone mark. To this end, we performed ChIP-seq for H3K27me3 in Cre CMs and G9a-KO CMs. Finally co-immunoprecipitation assays revealed that G9a interacts with Mef2c, thus to elucidate the function of the G9a–Mef2c interaction in adult cardiomyocytes, we used ChIP-seq to define the genomic distribution of Mef2c in Cre CMs and G9a-KO CMs.

overall_design: ChIP-seq for G9a, H3K9me2, H3K27me2 and Mef2c carried-out with cardiomyocyte-enriched populations isolated from G9a-KO and Cre mice. Two biological replicates were profiled for each antibody type.

first: Roberto

last: Papait

first: Gianluigi

last: Condorelli


title: Loss of CTCF reveals basic properties of post-mitotic epigenomes and induces heart failure [RNA-seq]

first: Tom

last: Vondriska

overall_design:
Control, CTCF knockout, and pressure overload RNA-seq experiments in isolated cardiac myocytes
TAC  (transverse aortic constriction) samples represent mouse with  diseased hearts.

first: Thomas

first: Manuel

last: Rosa-Garrido

first: Douglas

last: Chapski


title: Gene expression profiling of cardiomyocyte-enriched populations isolated from G9a-KO and Cre mice

summary: The role of the histone mehyltrasferase G9a  (also known as Ehmt2) in heart has not been extensively studied.  To identify the genes regulated by G9a in the normal heart, we first generated a conditional, cardiac-specific KO mouse for this gene using the Cre-Lox approach, crossing G9a flox/flox mice with αMHC-MerCreMer mice (Cre mice were used as controls). Then, we sequenced total RNA (Total-RNA-seq) from cardiomyocyte-enriched populations isolated from G9a-KO and Cre mice, and compared the two expression profiles.

overall_design: Profiling of the transcriptome of cardiomyocyte-enriched populations isolated from G9a-KO and Cre mice. Two biological replicates were profiled for each cell type.


title: The genomic distribution and gene expression profiling of cardiomyocyte-enriched populations

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

overall_design: Refer to individual Series


title: Antagonistic regulation of spermatogonial differentiation in zebrafish (Danio rerio) by Igf3 and Amh

city: Bergen

first: Diego

last: Crespo

address: Nordnesgaten 50

department: Reproduction and Developmental Biology

country: Norway

institute: Institute of Marine Research

summary: Fsh-mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here, we study if and how two Sertoli cell-derived Fsh-responsive growth factors, anti-Müllerian hormone (Amh; inhibiting steroidogenesis and germ cell differentiation) and insulin-like growth factor 3 (Igf3; stimulating germ cell differentiation), cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures, Fsh upregulated igf3 transcript levels and down-regulated amh transcript levels; igf3 transcript levels were more rapidly up-regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3-stimulated proliferation of type A (both undifferentiated [Aund] and differentiating [Adiff]) spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development, we examined Amh-induced changes in testicular gene expression by RNA sequencing. The majority (69%) of the differentially expressed genes was down-regulated by Amh, including several stimulators of spermatogenesis, such as igf3 and steroidogenesis-related genes. At the same time, Amh increased the expression of inhibitory signals, such as inha and id3, or facilitated prostaglandin E2 (PGE2) signaling. Evaluating one of the potentially inhibitory signals, we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals, such as Igf3

overall_design: 10 samples in total were analyzed: 5 biological replicates from control testis samples and 5 biological replicates from Amh-treated testis samples (all co-incubated with 11KT)

middle: D

last: Morais

first: Rafael

last: Nóbrega

first: Moline

last: Lemos

first: Henk

last: van de Kant

first: Luiz

last: França

first: Rune

last: Male

first: Jan

last: Bogerd

first: Rüdiger

middle: W

last: Schulz


title: The genomic distribution of G9a, H3K9me2 and H3K27me3  in cardiac hypertrophy.

summary: The role of the histone methyltrasferase G9a (also known as Ehmt2) in the normal heart has not been studied extensively. To identify which  genes were direct targets of G9a  in hypertrophic cardiomyocytes,  we performed ChIP-seq for G9a and H3K9me2 – the main histone methylation catalysed by the HMT – on cardiomyocytes isolated from normal mice (sham) and mice subject to transverse aortic constriction (TAC) for 1 wk, a surgical procedure that causes cardiac hypertrophy following the induction of pressure overload.  We considered the best G9a-bound genomic regions as those in which G9a and H3K9me2 peaks overlapped. Since G9a contributes to trimethylation of H3K27 at a set of developmental genes through its interaction with PRC2,  we also evaluated whether G9a had an effect on the distribution of this histone mark in hypertrophic cardiomyocytes. To this end, we performed ChIP-seq for H3K27me3 in CMs isolated from sham and TAC mice.

overall_design: ChIP-seq for G9a, H3K9me2, H3K27me3 carried-out with cardiomyocyte-enriched populations isolated from mice subiect subject to transverse aortic constriction (TAC) for 1 wk  . Two biological replicates were profiled for each antibody type.


title: The Kinesin KIF1Bβ links neuroblastoma and neurodegenerative disease through anterograde transport of TRKA

city: Solna

first: Susanne

last: Schlisio

address: Nobels vag 3

country: Sweden

institute: Ludwig Institute for Cancer Research Ltd

summary: We recently identified pathogenic KIF1Bb mutations in sympathetic nervous system malignancies that are defective in developmental apoptosis. Here we deleted KIF1Bb in the mouse sympathetic nervous system based on a cre recombination system driven by the dopamine beta hydroxylase (DBH) promoter. We observed impaired sympathetic nervous function and misexpression of genes required for sympathoadrenal lineage differentiation in KIF1Bb deficient sympathetic ganglia.

overall_design: We analyzed superior cervical ganglia from post-natal day 1 mice. We compared ganglia from four wild-type control animals (KIF1Bb fl/fl) with ganglia from four animals with conditional knockout of KIF1Bb (KIF1Bb fl/fl : DBHcre +/-).

first: Stuart

last: Fell


title: Whole-transcriptome profilings between a pair of HCA7-derived KRAS-wildtype cetuximab sensitive and resistant colon cancer cells from 3D culture

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: We report the results of RNA-Seq and small RNA-Seq from a pair of HCA7-derived, KRAS wildtype CC and CC-CR cultured in 3D. A total of 361 genes showed more than a two-fold change in expression (false-discovery rate [FDR] - adjusted p<0.01) between CC-CR and CC; there were 141 transcripts upregulated and 220 transcripts downregulated in CC-CR compared to CC. Small RNA-Seq detected 7 miRNAs upregulated and 24 miRNAs downregulated in CC-CR cells compared to CC cells (fold change>2, FDR<0.01). Differential expression analysis revealed several novel candidates that may contribute to cetuximab resistance. The whole-transcriptome profilings using cetuximab resistance model from 3D culture provide novel candidates for cetuximab resistance and further functional studies might open the door to a novel understanding of how non-mutational mechanisms mediate cetuximab resistance.

overall_design: mRNA and small-RNA profiles of cetuximab sensitive CC and resistant CC-CR from 3D culture were generated by deep sequencing, in triplicate, using Illumina NextSeq 500 sequencer.

first: Robert

last: Coffey

first: Yuanyuan

last: Lu

first: Qi

last: Liu


title: Gene expression changes upon Mof knockout in MLL-AF9 transformed murine LSKs

first: Scott

last: Armstrong

address: 1275 York Avenue

department: Center for Epigenetics

institute: MSKCC

summary: We report Illumina next generation RNA sequencing (RNAseq) of MLL-AF9 in vitro transformed murine LSKs upon genetic deletion of Mof. These gene expression data illustrate that Mof regulates the expression of genes involved in DNA damage response and chromatin stability in MLL-AF9 transformed cells.

overall_design: RNAseq comparing Mof homozygous knockout cells to Mof wild type control

middle: A


title: A new 3D culture system to identify disease-relevant genes in colorectal cancer

first: Shilin

last: Zhao

address: 2200 Pierce Ave, PRB building 571

department: Center for Quantitative Sciences

institute: Vanderbilt University

type:
Other
Expression profiling by array


title: Hair follicles engage in chemosensation: Olfactory receptor OR2AT4 regulates human hair growth

status: Public on Aug 29 2017

city: Muenster

first: Jérémy

last: Cheret

address: Heisenbergstrasse 11

institute: Monasterium Laboratory

summary: Olfactory receptors (OR) regulate physiological cell functions beyond olfaction. Here, we show that human hair follicle (HF) epithelium engages in chemosensation: it expresses OR2AT4, whose stimulation by a synthetic sandalwood odorant (prolongs hair growth (anagen) ex vivo via increased IGF-1 production. Instead, OR2AT4-silencing inhibits hair growth. Thus, human HFs can “smell” and require OR2AT4-mediated signaling to sustain their growth, inviting novel therapeutic hair growth regulation by targeting HF chemosensation.

overall_design: 4 different donors for each experiment (Vehicle untreated vs Sandalore 500μM and Scrambled oligos vs siRNA OR2AT4)

first: JÃ©rÃ©my

last: ChÃ©ret

first: Marta

last: Bertolini

first: Leslie

last: Ponce

first: Teresa

last: Tsai

first: Majid

last: Alam

first: Hanns

last: Hatt

first: Paus

middle: Â

last: Ralf


title: Human adipose transcriptome reveals primate-specific long intergenic noncoding RNAs that modulate adipocyte metabolic function

first: Chenyi

last: Xue

institute: Columbia University

summary: Through deep RNA-seq in human subcutaneous adipose bioposies and established long noncoding RNAs (lincRNAs) annotations, we identified human lincRNAs expressed in all subjects, including subsets of lincRNAs that exhibit differential expression by sex and race. Our comprehensive profiling on subcutaneous adipose lincRNA transcriptome provides great resource to advance novel understanding of genetic regulation in adipose biology.

overall_design: Gluteal subcutaneous adipose from 25 healthy subjects were sequenced by Illumina HiSeq 2000 with poly-A selection.

first: Zhang

last: Xuan

first: Xue

last: Chenyi


title: A new 3D culture system to identify disease-relevant genes in colorectal cancer [Exome-Seq]

summary: It is increasingly appreciated that properties of cultured epithelial cells differ dramatically in 2D compared to 3D, and the latter more faithfully recapitulates in vivo behavior. By studying a battery of human colorectal cancer (CRC) cell lines in type-1 collagen, we have found that HCA-7 cells form colonies with two distinctive and persistent morphological and functional properties. We observed predominantly single-layered polarized cysts (cystic colonies, CC) and a smaller fraction displaying disorganized solid masses (spiky colonies, SC) that were highly invasive in vivo. Despite overall genomic similarity, CC and SC exhibited distinct and dynamic patterns of gene expression in 3D.

overall_design: Identification of SNPs, Indels, and copy number variantions between SC and CC cells. The raw files were uploaded to SRA with accession (SRP066923:PRJNA304768)

first: Cunxi

last: Li

first: Bhuminder

last: Singh

first: Ramona

last: Graves Deal

first: Haiting

last: Ma

first: Alina

last: Starchenko

first: Will

last: Fry

first: Yang

last: Wang

first: Ginger

last: Milne

first: Gregory

last: Ayers

first: Mary

middle: K

last: Washington

first: Tim

last: Yeatman

first: Oliver

last: Mcdonald


title: OCT4 and SOX2 Work as Transcriptional Activators in Reprogramming Human Fibroblasts

first: Mark

last: Ptashne

summary: SOX2 and OCT4, in conjunction with KLF4 and cMYC, are sufficient to reprogram human fibroblasts to induced pluripotent stem cells (iPSCs), but it is unclear if they function as transcriptional activators or as repressors. We now show that, like OCT4, SOX2 functions as a transcriptional activator. We substituted SOX2-VP16 (a strong activator) for wild-type (WT) SOX2, and we saw an increase in the efficiency and rate of reprogramming, whereas the SOX2-HP1 fusion (a strong repressor) eliminated reprogramming. We report that, at an early stage of reprogramming, virtually all DNA-bound OCT4, SOX2, and SOX2-VP16 were embedded in putative enhancers, about half of which were created de novo. Those associated with SOX2-VP16 were, on average, stronger than those bearing WT SOX2. Many newly created putative enhancers were transient, and many transcription factor locations on DNA changed as reprogramming progressed. These results are consistent with the idea that, during reprogramming, there is an intermediate state that is distinct from both parental cells and iPSCs.


title: LCM-seq of resident NG2 glia reprogrammed to neurons in vivo using the transcription factors Ascl1, Lmx1a and Nurr1 (ALN)

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

institute: Stockholm University

summary: Reprogramming resident glia into functional and subtype-specific neurons in vivo by delivering reprogramming genes directly to the brain provides a step forward towards the possibility of treating brain injuries or diseases. Here, we show that neurons reprogrammed using Ascl1, Lmx1a and Nurr1 functionally mature and integrate into existing brain circuitry, and that the majority of the reprogrammed neurons have properties of fast spiking, parvalbumin-containing interneurons.

overall_design: A total of 6 samples were analyzed. Each sample is consists of approximately  33 laser-captured reprogrammed-neurons identified by nuclear GFP and expressing the transcription factors Ascl1, Lmx1a and Nurr1 (ALN).

first: Julio

last: Aguila Benitez

first: Maria

last: Pereira

first: Malin

last: Parmar

first: Daniella

last: Rylander-Ottosson


title: RNA-seq analysis of miRNAs expression in chciken ALV-J-infected primary monocyte-derived macrophages (MDM) and uninfected control.

city: Guangzhou

first: Min

last: Feng

address: wushan road

institute: South China Agricultural University

summary:
Purpose: The goals of this study are to investigate the differentially expressed miRNAs between ALV-J-infected primary monocyte-derived macrophages (MDM) and uninfected control by Illumina deep sequencing.
Methods:Total RNA from two ALV-J-infected MDM (designated: J3h_1, J3h_2, J36h_1 and J36h_2) and two uninfected MDM samples (designated:  NC3h_1, NC3h_2, NC36h_1 and NC36h_2) was isolated by TRIzol following the manufacturer’s instruction at 3 h post infection (hpi) and 36 hpi. RNA samples of two individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Hiseq 2000.
Results:  compared to the uninfected MDM, we identified 13 significant up-regulated miRNAs and 2 significant down-regulated miRNAs in ALV-J infected MDM at 3 hpi, and 6 significant up-regulated miRNAs and 2 significant down-regulated miRNAs in ALV-J infected MDM at 36 hpi.
Conclusions: Our results suggest that DE miRNAs involved in the immune response induced by ALV-J infection in MDM at 3 hpi. In addition, only 25 miRNAs-target DEGs were identified in MDM with ALV-J infection at 36 hpi, and these target DEGs can’t be significantly enriched in any GO terms and KEGG pathway..

overall_design: Chicken miRNAs profiles of ALV-J infected MDM and uninfected MDM were generated by deep sequencing, using  Illumina Hiseq 2000..

first: Xiquan

last: Zhang


title: RNA-seq analysis of mRNAs and lncRNAs expression in chciken ALV-J-infected primary monocyte-derived macrophages (MDM) and uninfected control.

summary:
Purpose: The goals of this study are to investigate the differentially expressed mRNAs and lncRNAs between ALV-J infected MDM and uninfected MDM in chickens by Illumina deep sequencing.
Methods:  Total RNA from two ALV-J-infected MDM (designated: J3h_1, J3h_2, J36h_1 and J36h_2) and two uninfected MDM samples (designated:  NC3h_1, NC3h_2, NC36h_1 and NC36h_2) was isolated by TRIzol following the manufacturer’s instruction at 3 h post infection (hpi) and 36 hpi. RNA samples were subjected to Illumina deep sequencing by Illumina Hiseq 2000.
Results:Compared to the uninfected control, a total of 1568 and 550 up-regulated genes were identified in chicken MDM at 3 hpi and 36 hpi respectively, and 1227 and 397 down-regulated genes were identified at 3 hpi and 36 hpi, respectively.128 and 30 DE lncRNAs were identified in MDM at 3 hpi and 36 hpi, respectively.
Conclusions: Strong immune response induced by ALV-J infection in MDM at 3 hpi. Many genes, lncRNAs  involved in immune response such as PRRs signaling pathway and Jak-STAT signaling pathway at 3 hpi. Specifically, 78 ISGs expression significantly increased in ALV-J-infected MDM at 3 hpi. We speculated that host innate immune response could inhibit ALV-J replication in chicken MDM. These results provide valuable insights into the game of host antiviral immune response and ALV-J infection.

overall_design: Chicken mRNAs and lncRNAs profiles of ALV-J infected MDM and uninfected MDM were generated by deep sequencing, using  Illumina Hiseq 2000.