title: Altered Nucleocytoplasmic Proteome and Transcriptome Distributions in an In Vitro Model of Amyotrophic Lateral Sclerosis

city: Seoul

first: Yoon-Ho

last: Hong

address: 28 Yeongeon-dong, Jongno-gu

department: Neurology

institute: Seoul National University College of Medicine

summary: An integrated analysis of the nucleocytoplasmic distribution of the proteome and transcriptome demonstrated multiple candidate pathways including RNA processing/transport and protein synthesis and folding that may be relevant to the pathomechanism of ALS.

overall_design: After subcellular fractionation of motoneuronal cell lines expressing human wild-type or mutant SOD1 (G93A), quantitative mass spectrometry and next-generation RNA sequencing (RNA-seq) were performed for the nuclear and cytoplasmic compartments.

first: Jung-Joon

last: Sung

first: Jin

middle: Y

last: Kim


title: RNA-seq analysis of  transcriptomes of thymus derived tTreg cells and the exFoxp3 precursor cells

status: Public on Mar 01 2017

city: Beijing

first: xuyu

last: zhou

address: 1st West Beichen, Chaoyang

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: To determine the phenotype of the precursor of exFoxp3 cells and find the signals that affect the stability of  tTreg cells, we analysis the  transcriptomes of epigenetic stable thymus derived tTreg cells and the exFoxp3 precursor cells.

overall_design: Transcriptioanl profiles of  tTreg cells (Thy1.1+YFP+) and exFoxp3 precursor cells (Thy1.1+YFP+) cells isolated from Foxp3 ΔCNS1-Cre-R26-YFP transgenic mice were generated by RNA-sequencing.

first: Zhongmei

last: Zhang

first: Xuyu

last: Zhou


title: Selection for transcript diversity in the extremophile Galdieria sulphuraria results in retention of the splicing machinery

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

summary:
Purpose: Red algae show two putative phases of massive genome reduction. RNA-splicing represents an important form of post-transcriptional regulation in eukaryotes. This process generates increased transcriptome and proteome diversity via alternative splicing that can maximize the DNA-encoded genetic diversity embedded within genomes. Why would Spliceosomal Machinery genes and a relatively more complex intron-exon structure be preserved in the compact Galdieria genome? The answer may lie in the fact that RNA-splicing represents an important form of post-transcriptional regulation in eukaryotes. It is hypothesized that his process generates increased transcriptome and proteome diversity via alternative splicing that can maximize the DNA-encoded genetic diversity embedded within genomes.
Methods: The experimental design followed a temperature shift timeline: after two weeks of cultivation at 42°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions the first sampling took place (H-42) and the cultures of G.sulphuraria were swiftly moved to 28°C. After cold treatment at 28°C for 48 hours, a second sampling was performed (C-28.1). The G. sulphuraria was then switched to 46°C for 48 hours, at end of which a third sampling was retrieved (H-46). It again was followed by a cold treatment at 28°C for 48 hours when a fourth sampling was retrieved (C-28.2). Altogether, two 48h timepoints from high temperatures (42°C and 46oC) and two 48h timepoints from cold temperature (28°C) were targeted for sampling.
Results: We show that RNA-splicing provides an avenue for generating transcriptome diversity under strong constraints on genome size and gene number.
Conclusions: We report the relatively high retention of Spliceosomal Machinery genes and the enrichment of intron-exon structures in G. sulphuraria that might be associated with the exceptional transcriptome and proteome diversity of this species. These results suggest that the losses of genes and functions caused by genome reduction might be mitigated by sequence diversity generated by a robust RNA-splicing system. More generally, the strong constraints imposed by genome reduction appear to be ameliorated by processes that operate on the transcriptomic and proteomic levels.

overall_design: mRNA reads of a temperature-shift timecourse were generated by sequencing, using Illumina HiSeq2000, PE-Reads, 2x100bp.

first: Huan

last: Qiu

first: Alessandro

middle: W

last: Rossoni

middle: P

first: Hwan

middle: S

last: Yoon

first: Debashish

last: Bhattacharya


title: Olfactory receptor accessory proteins play crucial roles in receptor gene choice

city: Durham

first: Kentaro

last: IKEGAMI

address: 213 Research Drive

country: USA

institute: Duke University

summary: Mice with olfactry accessory protein RTP1 and RTP2 knocked out show severe bias in their olfactory receptor repertoire. Surprisingly, even though RTP1,2(-/-) animals have fewer OSNs, we discovered ~8% of the ORs are expressed in larger numbers than the wild type.

overall_design: RNA-Seq in RTP1/2 dKO vs wild type mice olfactory epithelium

first: Hiroaki

last: Matsunami

first: Ruchira

last: Sharma

last: Ikegami


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

city: Lausanne

first: Francois

last: Mange

state: VAUD

address: Genopode building

department: Center for Integrative Genomic

country: Switzerland

institute: University of Lausanne

type: Genome binding/occupancy profiling by high throughput sequencing

summary: RNA polymerase III (pol III) synthesizes short non-coding RNAs, many of which, including tRNAs, Rpph1 RNA, Rn5s rRNA, and Rmrp RNA, are essential for translation. Accordingly, pol III activity is tightly regulated with cell growth and proliferation by factors such as MYC, RB1, TRP53, and MAF1. MAF1 is a repressor of pol III transcription whose activity is controlled by phosphorylation; in particular, it is inactivated through phosphorylation by mTORC1 kinase, a sensor of nutrient availability. Pol III regulation is thus sensitive to environmental cues, yet a diurnal profile of pol III transcription activity is so far lacking. Here we document pol III occupancy of its target genes in mouse liver during the diurnal cycle and show that pol III occupancy rises before the onset of the night, stays high during the night, when mice normally ingest food and when translation is increased, and decreases in daytime. By comparing diurnal pol III occupancy in wild-type mice, arrhythmic mice owing to inactivation of the Arntl gene, mice fed at regular intervals during both night and day, and mice lacking the Maf1 gene, we show that whereas higher pol III occupancy during the night reflects a MAF1-dependent response to feeding, the rise of pol III occupancy before the onset of the night reflects a circadian clock-dependent response. Thus, pol III transcription during the diurnal cycle is regulated both in response to nutrients and by the circadian clock, which allows anticipatory pol III transcription.

overall_design: To characterize RNA polymerase III occupancy in our mice models, liver were collected from control mice, constantly fed mice, Arntl KO mice, and Maf1 KO mice every 4 hours during 2 consecutive days. Chromatin was isolated and an antibody directed against one of the RNA polymerase III subunit (RPC4) was used to perform the immunoprecipitation step. DNA fragments were then sequenced and enrichment in Pol III loci was calculated.

first: François

first: Viviane

last: Praz

first: Eugenia

last: Migliavacca

first: Ian

middle: M

last: Willis

first: Frédéric

last: Schütz

first: Nouria

last: Hernandez


title: The Arcuate Estrogenome: Estrogen Response Element-dependent and -independent Signaling of ERα

city: NEW BRUNSWICK

first: Troy

middle: A.

last: Roepke

state: NJ - New Jersey

address: 84 LIPMAN DR

department: Animal Sciences

institute: Rutgers University

summary: We used three genotypes of mice: 1) wild-type, 2) KIKO (knock in/knock out), which lack a functional ERE-binding domain, and 3) ERKO (total ERα knockout) to determine ERE-dependent and -independent signaling of E2 in the arcuate nucleus of mice.

overall_design: Examination of three genotypes (WT, KIKO, ERKO) in two treatments (oil and E2)

first: Jennifer

middle: A

last: Yang

first: Hillary

last: Stires

first: William

last: Belden


title: A genome-wide study reveals a pathway for small RNA-mediated recognition of UV-induced DNA lesions

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: ChIP-seq of ER and RUNX2 in MCF7 breast cancer cell lines

city: New York City

first: MacIntosh

middle: Grant

last: Cornwell

state: NY

department: School of Medicine

institute: New York University

summary:
We performed ChIP-seq on MCF7 cells in an effort to discern differential binding patterns between wild type MCF7s and MCF7s that have acquired resistance to Tamoxifen and Estrogen deprivation. Furthermore, we also performed an HAtag ChIP on a DOX inducible RUNX2 overexpression MCF7 cell line.
We also performed RNA-seq on MCF7 cells to determine transciptional changes after acquisition of Tamoxifen resistance, and also transciptional changes in a DOX inducible RUNX2 overexpression model.

overall_design: ER and HAtag ChIP on MCF7 cells, RNAseq on MCF7 cells

first: Rinath

last: Jeselsohn

first: Matthew

last: Pun


title: A genome-wide study reveals a pathway for small RNA-mediated recognition of UV-induced DNA lesions (CPDs)

summary: This study reports that the DNA DAMAGE-BINDING PROTEIN 2 (DDB2) and ARGONAUTE 1 (AGO1) form a chromatin-bound complex, which facilitates recognition of photo-lesions.

overall_design: Immunoprecipitation of photolesions (CPDs) after UV exposure


title: A genome-wide study reveals a pathway for small RNA-mediated recognition of UV-induced DNA lesions (smallRNAs)

overall_design: siRNAs populations after UV exposure


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

city: Cologne

first: Yulia

last: Kargapolova

address: Robert-Koch-Straße 21

department: CMMC

institute: Cologne University


title: Genome-wide analysis of histone modifications in Jurkat cells upon ELF-MF exposure

city: Basel

first: Primo

last: Schaer

address: Mattenstrasse 28

department: Department of Biomedicine

institute: University of Basel

summary: To address whether ELF-MF influences the epigenetic landscape in the T cell lymphoma cell line Jurkat , we exposed Jurkat cells in the exponential growth phase to ELF MF or a sham control for 72 h, applying intermittently (5’ on/10’ off) a 50 Hz sine ELF-MF at a flux density of 1 mT. Additionally, cells were treated with the histone deacetylation inhibitor trichostatin A (TSA) at a subtoxic dose of 10 nM.  Genome-wide profiling of active and repressive histone modifications did not reveal significant alterations. However, ELF-MF exposure has an influence on the robustness of the epigenetic landscape in leukaemic cells. Our data suggests that ELF-MF has a stochastic effect on the epigenetic landscape of individual cells.

overall_design: H3K4me2 and H3K27me3 profiles from Jurkat cells before the exposure experiment (t0), ELF-MF and sham exposed for 72 h, and cells treated with the histone deacetylate inhibitor trichostatin A (10 nM TSA) analyzed by deep sequencing in douplicates of pools of three biological replicates each.

first: Melissa

last: Manser

first: Mohamad

last: Sater

first: Christoph

last: Schmid

first: Faiza

last: Noreen

first: Manuel

last: Murbach

first: David

last: Schurmann

last: Schar


title: Genome-wide analysis of histone modifications during neutrophilic granulopoiesis following ELF-MF exposure

summary: To address whether ELF-MF influences the epigenetic landscape in differentiating haematopoietic cells, we performed an in vitro haematopoietic differentiation under powerline-simulating ELF-MF exposure (50 Hz, 1 mT, 5’ on/10’ off) in comparison to sham exposure (50 Hz, 7 µT, 5’ on/10’ off) or no exposure. We differentiated CD34+ cells (allcells, CB008F, lot: CBC121009M) isolated from human cord blood into the neutrophilic lineage, and performed ChIP combined with next generation sequencing for the histone modifications H3K4me2 and H3K27me3 before (t0) and after 5 days (t5) of differentiation. Genome-wide profiling of active and repressive histone modifications did not reveal significant alterations. However, ELF MF exposure has an influence on the robustness of the epigenetic landscape during global chromatin programming of granulopoiesis. Our data suggests that ELF MF has a stochastic effect on the epigenetic landscape of individual cells.

overall_design: H3K4me2 and H3K27me3 profiles from CD34+ cells, sham and ELF-MF exposed neutrophilic progenitors after 5 days of differentiation in duplicates and not-exposed neutrophlic progenitors after 5 days (one replicate) analyzed by deep sequencing.


title: miRBShunter: a pipeline to identify miRNA binding sites from Ago2-CLIP data by de novo motif finding

city: Nice

first: Silvia

last: Bottini

address: 299, chemin de la ginestiere

summary: The proposed method uses enriched de novo motifs on the peak sequences of Ago2-CLIP to determine miRNA-RNA heteroduplex for either canonical or non-canonical miRNA-binding sites. miRNA-RNA heteroduplex are ranked based on a duplex score. Since the quality of the peak detection is of pivotal importance for the final output of the proposed method, we also provide an illustrative comparative evaluation of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, for four publicly available Ago2-datasets and one previously unpublished in-house Ago2-dataset in stem cells. The experimental validation was carried out on the in-houseAgo2 dataset by gene reporter assay.

overall_design: Ago2 HITS-CLIP in P19 cell in triplicates.

first: Nedra

last: Hamouda-Tekaya

first: Bogdan

last: Tanasa

first: Laure-Emmanuelle

last: Zaragosi

first: Pascal

last: Barbry

first: Valerie

last: Grandjean

first: Emanuela

last: Repetto

first: Michele

last: Trabucchi


title: Transcriptome analysis for KDM6A mutated urothelial bladder carcinoma and EZH2 inhibitor treated KDM6A mutated urothelial bladder carcinoma

city: Singapore

first: Xiaoran

last: Chai

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Purpose:  The goals of this study are to compare 1. The transcription profile in KDM6A wildtype and KDM6A mutated urothelial bladder carcinoma. 2. The transcriptional changes in KDM6A mutated urothelial bladder carcinoma upon EZH2 inhibitor treatment.

overall_design:
Transcriptome profiling of KDM6A wildtype and KDM6A mutated urothelial bladder carcinoma were generated by deep sequencing, 10 cases in each group, using Hiseq2000.
Transcriptome profiling of EZH2 inhibitor-treated KDM6A wildtype and KDM6A mutated urothelial bladder carcinoma were generated by deep sequencing, in triplicate, using Hiseq2000.

first: L

middle: D

last: Ler

first: B

middle: T

last: Teh


title: Transcriptomic study of rice crowns from genotypes differing in tolerance to Zn deficiency

city: Tsukuba

first: Amrit Kaur

last: Nanda

state: Ibaraki

address: 1-1 Ohwashi

department: Crop Livestock and Environment

country: Japan

institute: Japan International Research Center for Agricultural Sciences

summary: The transcriptome of crown tissue from several Zn-efficient and Zn-inefficient rice genotypes, exposed or not to Zn deficiency, was investigated using RNA sequencing. By grouping data from different genotypes within each efficiency group, we were able to 1) identify several well-known and novel Zn transporters involved in Zn retranslocation from the crown to the shoot and roots in response to Zn deficiency; 2) determine that Zn deficiency triggers the conversion of soluble sugars into starch; and 3) detect several candidate genes possibly conferring Zn efficiency.

overall_design: The crowns of three Zn-efficient and three Zn-inefficient rice genotypes were harvested after 8 days of treatment, with or without Zn, and RNA was extracted and sequenced as paired-end for 150 bp. RNA sequencing reads were aligned against the Nipponbare reference genome and differentially expressed genes between treatments and efficiency groups were detected.

first: Amrit

middle: K

first: Vincent

last: Pujol

first: Matthias

last: Wissuwa


title: A label-retaining but unipotent cell population resides in biliary compartment of mammalian liver.

city: Tartu

first: Viljar

last: Jaks

state: Tartumaa

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

summary: Cells with slow proliferation kinetics that retain the nuclear label over long time periods – the label-retaining cells (LRCs) – represent multipotent stem cells in a number of adult tissues. Since the identity of liver LRCs (LLRCs) had remained elusive we utilized a genetic approach to reveal LLRCs in normal non-injured livers and characterized their regenerative properties in vivo and in culture. We found that LLRCs were located in biliary vessels and participated in the regeneration of biliary but not hepatocyte injury. In culture experiments the sorted LLRCs displayed an enhanced self-renewal capacity but a unipotent biliary differentiation potential. Transcriptome analysis revealed a unique set of tumorigenesis- and nervous system-related genes upregulated in LLRCs when compared to non-LRC cholangiocytes. We conclude that the LLRCs established during the normal morphogenesis of the liver do not represent a multipotent primitive somatic stem cell population but act as unipotent biliary progenitor cells.

overall_design: Transcriptome comparison of label-retaining biliary epithelial cells and non-label-retaining biliary epithelial cells (cells with GFP expression were compared to the cells without GFP). Illumina HiSeq 2000 was used to analyze 8 RNA samples from 4 mice.


title: Inactivation of Ezh2 upregulates Gfi1 and drives aggressive Myc-driven Group 3 medulloblastoma

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital


title: Regulation of KMT2D by PI(3)K/AKT signalling orchestrates oestrogen receptor mediated transcriptional activation in breast cancer [ChIP-seq]

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

summary: We aim to elucidate the mechanisms of how PI3K inhibition is promoting oestrogen receptor (ER) activation and ER dependency in breast cancer.

overall_design: Genome-wide analysis of ER, FOXA1 TF upon treatment with the PI3K inhibitor (BYL719).

first: Eneda

last: Toska


title: Inactivation of Ezh2 upregulates Gfi1 and drives aggressive Myc-driven Group 3 medulloblastoma [RNA-Seq]

summary: The most aggressive of four medulloblastoma (MB) subgroups are cMYC-driven Group 3 (G3) tumors, some of which overexpress EZH2, the histone H3K27 trimethylase of polycomb repressive complex-2. Yet, engineered deletions of Ezh2 in G3 MBs by gene editing nucleases accelerated tumorigenesis, whereas Ezh2 re-expression reversed attendant histone modifications and slowed tumor progression. Candidate oncogenic drivers upregulated following Ezh2 deletion included Gfi1, a proto-oncogene frequently activated in human G3 MBs. Gfi1 disruption antagonized the tumor promoting effects of Ezh2 loss; conversely, Gfi1 overexpression collaborated with Myc to bypass effects of Trp53 inactivation in primary cerebellar neuronal progenitors thereby driving MB progression. Although negative epigenetic regulation of Gfi1 by Ezh2 may restrain MB development, Gfi1 activation can bypass these effects.

overall_design: Mouse tumorspheres  from a  p53-/-;p18-/- or WT mixed background that is over-expressing Myc   are transfected with a CAS9 vector to knockout Ezh2, or over express Ezh2, or overexpress Ezh2 to rescue a Ezh2 KO , or a vector that over expresses Gfi1

first: BaoHan

last: Vo

first: Chunliang

last: Li

first: Marc

last: Morgan

first: Ilan

last: Theurillat

first: Shaela

last: Wright

first: Judith

last: Hyle

first: Stephanie

last: Smith

first: Yiping

last: Fan

first: Yong-Dong

last: Wang

first: Gang

last: Wu

first: Brent

last: Orr

first: Paul

last: Northcott

first: Ali

last: Shilatifard

first: Charles

middle: J

last: Sherr

first: Martine

middle: F

last: Roussel


title: Regulation of KMT2D by PI(3)K/AKT signalling orchestrates oestrogen receptor mediated transcriptional activation in breast cancer [ATAC-seq]

first: Hatice

last: Osmanbeyoglu

overall_design: Genome-wide analysis of chromatin accessibility upon treatment with the PI3K inhibitor (BYL719).


title: Regulation of KMT2D by PI(3)K/AKT signalling orchestrates oestrogen receptor mediated transcriptional activation in breast cancer


title: Parvovirus B19 NS1 protein induces cell cycle arrest at G2 phase

city: Kansas City

first: Jianming

last: Qiu

state: KS

address: 3901 rainbow blvd

department: Microbiology

institute: University of Kansas Medical Center

summary: We construct two stable UT7/Epo-S1 cell lines which could be inducible expressing B19 NS1 and NS1 TAD2 domain mutation proteins. After treated with or without doxycycline induction, we extract the total RNA for RNA-seq analysis.

overall_design: UT7/Epo-S1 cells were transduced by lentiviruses inducible expressing NS1 or NS1mTAD2. Two days post-transduction, puromycin was added at a concentration of 0.5 μg/ml, then cells were cultured in presence of puromycin for 3 to 4 passages to select the lentivirus transduced cells.  UT7/Epo-S1 cells stably expressing NS1 (NS1-S1) and NS1mTAD2 (NS1mTAD2-S1) were cultured under similar conditions as normal S1 cells except for the addition of 5 mg/ml doxycycline (Dox) for inducing the expression of NS1 and NS1mTAD2 proteins, respectively. Total RNA of the two cell lines treated with or without Dox were extracted and for further RNA-seq analysis.

first: Peng

last: Xu

first: Min

last: Xiong


title: Glucocorticoid Receptor: MegaTrans Switching Mediates Repression of ERα-Regulated Transcriptional Program [ChIP-Seq]

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

summary: The mechanisms underlying GR-dependent inhibition of ERα-regulated gene activation programs at the global genomic level have been poorly understood. We found the binding of GR in trans on ERα-activated enhancers results in gene and enhancer repression by disassembling the MegaTrans Complex.

overall_design: All ChIP-Seq experiments were designed to elucidate the mechanism involving GR-mediated repression of ERα-Regulated Transcriptional Program

first: Feng

last: Yang


title: Glucocorticoid Receptor: MegaTrans Switching Mediates Repression of ERα-Regulated Transcriptional Program [Gro-Seq]

overall_design: All GRO-Seq experiments were designed to understand the effects of different ligands (E2, Dex or combine together) treatments to MCF7 cells, to evaluated the two signal cross-talk.


title: Glucocorticoid Receptor: MegaTrans Switching Mediates Repression of ER?-Regulated Transcriptional Program


title: Benomyl toxicity links histone H3 lysine 4 methylation to cell cycle control

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: The PAT-seq approach was utilised to determine the gene expression changes over the cell-cycle of wildtype and delta-set1 yeast strains. The cell were synchronised by alpha-factor arrest and cell-cycle release

overall_design: Analysis gene expresson across the S. cerevisiae cell cycle.

first: Bernhard

last: Dichtl

last: Harrrison

middle: H


title: Transcriptome of Zfp36l1-deficient MZ B cells, WT MZ B cells and WT FO B cells.

city: Cambridge

first: Martin

last: Turner

address: Babraham Hall

department: Lymphocyte Signalling and Development

country: United Kingdom

institute: Babraham Institute

summary: Purpose: to identify the effects on the transcriptome of deleting ZFP36L1 in MZ B cells

overall_design:
Method (MZ B cells): RNAseq libraries were prepared from 5ng RNA isolated from sorted ex-vivo MZ B cells. Total RNA samples were sent to Aros Applied Biotechnology A/S and were prepared using the Clontech SMARTer kit. Libraries were sequenced (100bp paired end) on the Illumina Hiseq.
Method (FO B cells): RNAseq libraries were prepared from RNA isolated from sorted ex-vivo FO B cells. Total RNA samples were sent to Aros Applied Biotechnology A/S and were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina). Libraries were sequenced (100bp single end) on the Illumina Hiseq.

first: Rebecca

last: Newman

first: Helena

last: Ahlfors


title: Cell responses to dysregulated VZV-induced cell-cell fusion

city: Stanford

first: Stefan

last: Oliver

state: California

address: 300 Pasteur Drive, Grant Rm S366

department: Pediatrics

institute: Stanford University School of Medicine

summary: The highly conserved herpesvirus glycoprotein complex, gB/gH-gL, mediates membrane fusion during virion entry and cell-cell fusion.  Varicella-zoster virus (VZV) characteristically forms multi-nucleated cells, or syncytia, during the infection of human tissues but little is known about this process.  The cytoplasmic domain of VZV gB (gBcyt) has been implicated in cell-cell fusion regulation because a gB[Y881F] substitution causes hyperfusion.  The gBcyt regulation is necessary for VZV pathogenesis as the hyperfusogenic mutant gB[Y881F] is severely attenuated in human skin xenografts.  In this study, gBcyt regulated fusion was investigated by comparing melanoma cells infected with wild type-like VZV or hyperfusogenic mutants.  The gB[Y881F] mutant exhibited dramatically accelerated syncytia formation in melanoma cells caused by fusion of infected cells with many uninfected cells, increased cytoskeleton reorganization and rapid displacement of nuclei to dense central structures when compared to pOka using live cell confocal microscopy.  VZV and human transcriptomes were concurrently investigated using RNA-seq to identify viral and cellular responses induced when the gBcyt regulation was disrupted by the gB[Y881F] substitution.  The expression of four vital VZV genes, ORF61 and glycoproteins, gC, gE and gI, was significantly reduced at 36 hours post infection for the hyperfusogenic mutants.  Importantly, hierarchical clustering demonstrated an association of differential gene expression with dysregulated gBcyt-mediated fusion.  A subset of Ras GTPase genes linked to membrane remodeling were upregulated in cells infected with the hyperfusogenic mutants.  These data implicate the gBcyt in the regulation gB fusion function that, if unmodulated, triggers cellular processes leading to hyperfusion that attenuates VZV infection.

sample_organism:
Homo sapiens
Human alphaherpesvirus 3

platform_organism:
Homo sapiens
Human alphaherpesvirus 3

overall_design: Biological duplicates from 3 time points (12, 24 and 36 hours post infection) of uninfected MeWo cells or MeWo cells infected with varicella-zoster virus strain pOka or mutants gB[Y881F], gB[Y920F] or gB[Y881/920F]

middle: L

first: Ann

last: Arvin


title: Transcriptomic response of Podospora anserina to bacterial and fungal non self

city: Bordeaux

first: Mathieu

last: Paoletti

address: 1 rue Camille Saint Saëns

department: IBGC

institute: CNRS

overall_design: Transfer of P. anserina onto plates seeded with two different bacterial species, for two different times, and to vegetative incompatibility conditions. Comparisons are made to P. anserina transcriptome after transfer to a bacteria free medium


title: Transcriptome of GFP-ZFP36L1 expressing and WT FO B cells

summary: Purpose: to identify the effects on the transcriptome of overexpressing ZFP36L1 in FO B cells

overall_design: Method: RNAseq libraries were prepared from RNA isolated from sorted ex-vivo FO B cells. Total RNA samples were sent to Aros Applied Biotechnology A/S and were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina). Libraries were sequenced (100bp paired end) on the Illumina Hiseq.


title: Inactivation of Ezh2 upregulates Gfi1 and drives aggressive Myc-driven Group 3 medulloblastoma [ChIP-Seq]

first: David

last: Finkelstein

overall_design: Mouse tumorspheres from a p53-/-;p18-/- or WT mixed background that is over-expressing Myc  are transfected with a CAS9 vector to knockout Ezh2, or over express Ezh2, or overexpress Ezh2 to rescue a Ezh2 KO , or a vector that over expresses Gfi1

first: BaoHan

last: Vo

first: Chunliang

last: Li

first: Marc

last: Morgan

first: Ilan

last: Theurillat

first: Shaela

last: Wright

first: Judith

last: Hyle

first: Stephanie

last: Smith

first: Yiping

last: Fan

first: Yong-Dong

last: Wang

first: Gang

last: Wu

first: Brent

last: Orr

first: Paul

last: Northcott

first: Ali

last: Shilatifard

last: Sherr


title: Distinct roles of Brd2 and Brd4 in potentiating the transcriptional program for Th17 cell differentiation

city: New York

first: Martin

middle: J.

last: Walsh

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

summary: We analyzed the ChIP-seq data of Brd2 and Brd4 in Th17 cells. We find that Brd2 and Brd4 have distinct genome-wide deposition in Th17 cells, further experiments reveal tht Brd2 faciliates TF-complex formation in enhancers, enhancer-promoter interaction while Brd4 enhances transcriptional elongation.

overall_design: ChIP-seq study of Brd2, Cohesin and Brd4 in Th17 cells. Additional samples include Nipbl, Smc1, Smc3 ChIP-seq samples. The Th17 cells are differentiated for 48hrs and ChIP with the corresponding antibodies and ChIP-seq libraries are made. Additional samples are intended to determine the global occupancy of cohesin proteins.

first: KL

last: Cheung

first: G

last: Lu

first: T

last: Shen

first: F

last: Zhang

first: A

last: Vincek

last: Jaganathan

first: R

first: CH

last: Chen

last: Plotnikov

first: H

last: Zhu

first: E

last: Rusinova

last: Zhou

first: J

last: Yang

first: L

last: Peng

first: M

last: Ohlmeyer

first: W

middle: B

last: Xiong


title: NeuroD2 ChIP-SEQ from postnatal cortex

city: Helsinki

first: Gulayse

last: Ince Dunn

state: Finland

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Program

country: Finland

institute: University of Helsinki

summary: NeuroD2 targets were identified from postnatal day 0 cerebral cortex tissue.

overall_design: The cerebral cortex (dorsal telencelphalon) from P0 mouse pup was dissected and ChIP-SEQ was performed using three separate antibodies against NeuroD2.

middle: I

last: Dunn


title: Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice

city: Milano

first: Fabio

last: Fornara

address: Via Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

summary: Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between between long and short day model species.

overall_design: In this study, we explored the effects of drought stress applied to rice plants grown under specific photoperiods and during floral commitment, when plants switch from vegetative to reproductive growth. It is a 2x2 factorial design with the four conditions: 1) normal water regime plants in long day, 2) normal water regime plants in short day, 3) plants under 13 days of drought stress in long day, 4) plants under 13 days of drought stress in short day.

first: Francesca

last: Galbiati

first: Remo

last: Chiozzotto

first: Franca

last: Locatelli

first: Alberto

last: Spada

first: Annamaria

last: Genga


title: Time course transcriptional profiles of the Arabidopsis thaliana response to flg22 infiltration for all combinatorial genotypes of the alleles dde2-2, ein2-1, pad4-1, and sid2-2.

city: St Paul

first: Fumiaki

last: Katagiri

state: Minnesota

address: 1500 Gortner Ave

department: Dept of Plant and Microbial Biology

institute: Univ of Minnesota

summary: Plant immunity protects plants from numerous potentially pathogenic microbes. The biological network that controls plant inducible immunity must function effectively even when network components are targeted and disabled by pathogen effectors. Network buffering could confer this robustness by allowing different parts of the network to compensate for loss of each other’s functions. Networks rich in buffering rely on interactions within the network, but these mechanisms are difficult to study by simple genetic means. Through a network reconstitution strategy, where we disassemble and stepwise reassemble the plant immune network that mediates Pattern-Triggered-Immunity, we have resolved systems-level regulatory mechanisms underlying the Arabidopsis transcriptome response to the immune stimulant flagellin-22 (flg22). These mechanisms show widespread evidence of interactions among major sub-networks—the components that we call sectors—in the flg22-responsive transcriptome. Many of these interactions result in network buffering. Resolved regulatory mechanisms also show unexpected patterns for how the jasmonate (JA), ethylene (ET), phytoalexin-deficient 4 (PAD4), and salicylate (SA) signaling sectors control the transcriptional response to flg22. We demonstrate that many of these mechanisms are hidden from the traditional genetic approach of single-gene null-mutant analysis. As potential pathogenic perturbations to the network, null-mutant effects can be buffered by the immune network as well.

overall_design:
We profiled the Arabidopsis thaliana response to flg22 infiltration in the wild type (Col-0), as well as 4 single-gene mutants, 6 double-gene mutants, 4 triple-gene mutants, a quadruple-gene mutant for the null-mutant alleles dde2-2, ein2-1, pad4-1, and sid2-2, as well as a control genotype, fls2, which has a null-mutation in the flg22 receptor gene. Profiles were collected through a detailed time course 0, 1, 2, 3, 5, 9, and 18 hrs after infiltration. 0 hrs samples were untouched. Three biological replicates were profiled for each genotype:time combination. Each biological replicate was collected from the pooled tissue of 4 independent biological experiments. In each of these experiments, 3 leaves, leaf stages 7-9, of 31-32 days old plants were infiltrated with 1uM flg22 and collected at the indicated timepoint. Thus each biological replicate contained the tissue of 4*3 = 12 leaves. In total, 357 separate samples were sequenced: 17 genotypes * 7 time points * 3 biological replicates = 357. Internal barcodes—the first 4-8 bases of the sequence—were used to multiplex stranded mRNA Tag-Seq libraries (1) for sets of 16 samples each into a single lane of an Illumina Genome Analyzer IIX flowcell. References. 1.  Rallapalli G, Kemen EM, Robert-Seilaniantz A, Segonzac C, Etherington GJ, Sohn KH, et al. EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics. BMC Genomics. 2014 Jan;15:341.

Please note that [1] concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively. [2] the readme.txt contains Sample acc, title and processed data column headers indicating which sample each data column belongs to.

first: Rachel

last: Hillmer

first: Kenichi

last: Tsuda

first: Ghanasyam

last: Rallapalli

first: Shuta

last: Asai

first: William

last: Truman

first: Jonathan

last: Jones

first: Chad

last: Myers


title: IDN2 Interacts with RPA and Facilitates DNA Double-Strand Break Repair by Homologous Recombination in Arabidopsis

status: Public on Feb 28 2017

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

summary: Repair of DNA double-strand break (DSB) is critical for the maintenance of genome integrity. We have previously shown that a class of DSB-induced small RNAs (diRNAs) facilitates homologous recombination (HR)-mediated DSB repair in Arabidopsis thaliana. Here we show that INVOLVED IN DE NOVO 2 (IDN2), a double-stranded RNA (dsRNA) binding protein involved in small RNA-directed DNA methylation, is required for DSB repair in Arabidopsis. We find that IDN2 interacts with the heterotrimeric replication protein A (RPA) complex. Depletion of IDN2 or the diRNA-binding ARGONAUTE 2 (AGO2) leads to increased accumulation of RPA at DSB sites and mislocalization of the recombination factor RAD51. These findings support a model in which IDN2 interacts with RPA and facilitates the release of RPA from ssDNA tails and subsequent recruitment of RAD51 at DSB sites to promote DSB repair.

overall_design: Here we examined the DSB repair rate via introducing a well-established DGU.US reporter system in idn2-3, mutant background. This system consists of the DGU.US reporter (R) line containing a unique I-SceI recognition site within the direct repeats and the DSB-triggering (T) line that expresses the endonuclease I-SceI. In the crossed (RxT) line, DSBs are generated at the I-SceI site and the repair of DSBs results in restored expression of β-glucuronidase (GUS). To compare the DSB repair efficiency in a mutant background with that in the corresponding wild-type background, we first crossed both the R line and T line with idn2-3 mutant independently. After F2 segregation, the following progenies were identified by genotyping: those homozygous for either the recombination substrate locus from the R line or the I-SceI expressing locus from the T line in the respective homozygous mutant background (named R/R; idn2-3 (-/-) and T/T; idn2-3 (-/-), respectively) and those in the WT background (named R/R; IDN2 (+/+) and T/T; IDN2 (+/+), respectively). Then, plants R/R; idn2-3 (-/-) were crossed with T/T; idn2-3 (-/-) to obtain RxT; idn2-3 (-/-), whereas the corresponding WT siblings R/R; IDN2 (+/+) were crossed with T/T; IDN2 (+/+) to obtain RxT; IDN2 (+/+). The seeds of these crosses were harvested, sterilized, and sown on MS medium. Thirteen-day-old seedlings were collected for RNA extraction. To evaluate the effects of IDN2 mutation on diRNA production, small RNAs from RxT; IDN2 (+/+) and RxT; idn2-3 (-/-) plants were cloned and sequenced on Illumina Genome Analyzer IIx platform.

first: Mingming

last: Liu

first: Zhaoqing

last: Ba

first: Pedro

last: Costa-Nunes

first: Wei

last: Wei

first: Lanxia

last: Li

first: Yan

first: Jijie

last: Chai

first: Olga

last: Pontes


title: Transcriptome analysis of liver tissue in HBV - associated liver fibrosis mice

city: Beijing

first: Fangming

last: Kan

address: Dongdansantiao

institute: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences

summary:
Purpose:Next-generation sequencing (NGS) were performed to investigate the differentially expressed molecular signature that were associated with HBV-mediated liver fibrosis
Method: four cDNA libraries of separated groups ranging from 1, 3, 6-months post injection were constructed in the HBV (-) and analyzed using RNA-seq.
results: Sequencing of the clean reads resulted in ~29–40 million reads per sample, for a total of ~438 million reads across 12 samples.  Specifically, an average of 16,782, 17,088, 18,701, and 19,364 genes were identified  in the HBV (+) mouse (1, 3, 6-months post injection) and HBV (-) mouse (control groups), respectively.

overall_design: Analysis mRNA profiles of HBV(+) mouse samples from 1, 3, 6-months post injection and HBV(-) mouse samples.

first: Wuping


title: Global transcriptome profiling of triple-negative breast cancer cell lines treated with small-molecules targeting Bromodomain and Extra Terminal (BET) proteins

first: Chao-Yie

last: Yang

state: Tennessee

address: 881 Madison Avenue, Rm559

department: Pharmaceutical Sciences

institute: University of Tennessee HSC

summary: Triple negative breast cancer (TNBC) represents the most clinically challenging subtypes of breast cancer for which targeted therapeutics are still lacking. Bromodomain and Extra Terminal (BET) proteins, including ubiquitously expressed BRD2, BRD3, BRD4 and testis-specific BRDT, are epigenetic “readers” and play a major role in epigenetic regulation of gene transcription. BET proteins have emerged as new therapeutic targets for human cancer and other diseases. Based upon a new class of BET bromodomain (BRD) inhibitor, BETi-211, we have developed a highly selective and potent BET protein degrader, BETd-246. In comparison, BETd-246 is much more potent and effective than the corresponding BET inhibitor BETi-211 in growth inhibition and apoptosis induction in TNBC cell lines, indicating critical differences between these two different BET targeting approaches in their regulation of gene transcription. To understand the mechanisms of actions of BETi-211 and BETd-246 in TNBC, we performed RNA-seq analysis on MDA-MB-157, MDA-MB-231 and MDA-MB-468. These cell lines were treated for 3 h to capture the early transcriptional responses to BETi-211 or BETd-246. RNA-seq analysis reveals that BETd-246 predominantly down-regulates the expression of a large number of genes whereas BETi-211 up- and down-regulates an approximately equal number of genes in TNBC cells. Critically, transcriptomic analysis uncovers that a set of proliferation and survival-related genes, including MCL1 and BRD2, were oppositely regulated by BETd-246 and BETi-211 in these TNBC cell lines.

overall_design: Global gene transcription profiling was performed in MDA-MB-157, MDA-MB-231 and MDA-MB-468 cell lines treated with DMSO, Thalidomide (1000 nmol/L), BETi-211 (1000 nmol/L) or BETd-246 (100 nmol/L) for 3 hours. Independent biological replicates (such as DMSO1 and DMSO2) were analyzed for each cell line under each condition. Both DMSO- and Thalidomide-treated samples were used as controls.

first: Longchuan

last: Bai

first: Hui

last: Jiang

first: Shaomeng

last: Wang


title: The within-host dynamics of infection in trans-generationally primed beetles

city: Nashville

first: Ann

last: Tate

address: 465 21st Ave., MRBIII Room 4270

department: Biological Sciences

institute: Vanderbilt University

summary: We report the temporal dynamics of differential gene expression between primed and unprimed beetles infected with the entomopathogen Bt

overall_design: Tribolium castaneum larvae from mothers who had (primed treatment) or had not (unprimed treatment) been pricked with heat killed Bacillus thuringiensis (Bt) were infected with an LD50 dose of Bt and then sacrificed at 0 hours (uninfected) or 2,6,8,12 hours post infection. This experiment was repeated twice (TS1 or TS2). The extracted RNA was used to prepare mRNA libraries using the Illumina TruSeq v2 kit and sequenced on the Hiseq

first: Peter

last: Andolfatto

first: Andrea

last: Graham


title: A Novel TET1 Based Complex Controls DNA Repair Genes by Modulating H4K16 Acetylation In response to oxidative damage [RRBS]

city: Chong Qing

first: Xianfeng

address: Da ping

department: Department of Gastroenterology, Daping Hospital

institute: Army Medical University (Third Military Medical University)

type: Methylation profiling by high throughput sequencing

summary: TET1, in addition its function as a DNA demethylase, plays important roles in both transcriptional repression and activation. However, the underlying mechanism how TET1 functions in transcriptional regulation remains elusive. Here, by integrative genomic and biochemical studies, we demonstrate that TET1 forms a novel chromatin modifying complex with hMOF, SIRT1, and the scaffold protein SIN3A to specifically regulate DNA repair genes by modulating H4K16 acetylation. Dynamic recomposition of this complex induced by oxidative damage, characterized as dissociation of TET1 and hMOF or increased binding of SIRT1, leads to hypoacetylation of H4K16 to repress the expression of DNA repair genes. Importantly, similar recomposition of this complex was validated in an oncogenic transformation cell line, which further endorsed that the role of this complex was involved in tumorigenesis. Our findings reveal a novel mechanism for TET1 to modulate H4K16ac by chromatin recomposition, with which TET1 regulates the expression of DNA repair genes instead of its well-known role in DNA demethylation.

overall_design: Reduced representation bisulfite sequencing (MspI,~40-220bp size fraction) data for HEK293T cell line with or without H2O2 treatment were generated by deep sequencing, using Illumina Illumina HiSeq 2000.

first: Jianing

last: Zhong

first: Zhongsheng

last: Sun


title: 3alpha-acetonyltabersonine induces glioblastoma apoptosis via the inhibition of DNA damage repair

city: Kunming

first: Junjun

last: Hao

address: 32 Jiaochang Donglu Kunming

institute: Kunming Institute of Zoology

summary: we report the antitumor activity of an indole alkaloid, 3alpha-acetonyltabersonine, which was isolated from Melodinus suaveolens. 3alpha-acetonyltabersonine was found to be cytotoxic to glioblastoma cell line and stem cells at low concentrations.

overall_design: Examination the differental expression of 3alpha-acetonyltabersonine-treated and the control.

first: Yuan


title: Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (anti-PD-L1 vs Control IgG RNA-seq)

city: Los Angeles

first: Roberto

last: Spreafico

state: CA

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

summary: T cell exhaustion is a progressive loss of effector function and memory potential due to persistent antigen exposure, which occurs in chronic viral infections and cancer. Here we investigate the relation between gene expression and chromatin accessibility in CD8+ tumor-infiltrating lymphocytes (TIL) that recognize a model tumor antigen and have features of both activation and functional exhaustion. By filtering out accessible regions observed in bystander, non-exhausted, TIL and in acutely restimulated CD8+ T cells, we define a pattern of chromatin accessibility specific for T cell exhaustion, characterized by enrichment for consensus binding motifs for Nr4a and NFAT transcription factors. Anti-PD-L1 treatment of tumor-bearing mice results in cessation of tumor growth and partial rescue of cytokine production by the dysfunctional TIL, with only limited changes in gene expression and chromatin accessibility. Our studies provide a valuable resource for the molecular understanding of T cell exhaustion in cancer and other inflammatory settings.

overall_design: RNA-seq from tumor-infiltrating CD8+ T cells in mice treated with anti-PD-L1 or Control IgG


title: Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells

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

overall_design: Refer to individual Series


title: Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (OT-I vs P14 RNA-seq)

overall_design: RNA-seq from tumor-infiltrating OT-I or P14 CD8+ T cells


title: Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (ATAC-seq for in-vivo experiments)

overall_design: Chromatin accessibility by ATAC-seq in CD8+ tumor-infiltrating lymphocytes


title: Gene expression changes in dauer defective strains

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Animals change developmental fates in response to external cues. In the nematode Caenorhabditis elegans, unfavorable environmental conditions induce a state of diapause known as dauer by inhibiting the conserved DAF-2 insulin-like signaling (ILS) pathway through incompletely understood mechanisms. We previously established a role for the C. elegans dosage compensation protein DPY-21 in the control of dauer arrest and DAF-2 ILS. Here we show that dosage compensation acts through the histone H4 lysine 20 methyltransferase SET-4 to promote dauer arrest in part by repressing the X-linked ins-9 gene, which encodes a new agonist insulin-like peptide (ILP) expressed specifically in the paired ASI sensory neurons that are required for dauer bypass. ins-9 repression in dauer-constitutive mutants requires DPY-21, SET-4, and the FoxO transcription factor DAF-16, which is the main target of DAF-2 ILS. In contrast, autosomal genes encoding major agonist ILPs that promote reproductive development are not repressed by DPY-21, SET-4, or DAF-16/FoxO. Our results implicate the dosage compensation machinery as a sensory rheostat that reinforces developmental fates in response to environmental cues by modulating autocrine and paracrine DAF-2 ILS.

overall_design: 35 total samples, 7 strains collected in 5 replicates each. C elegans larvae were grown for 24 hr at 25C (developmental stage L2D in eak-7;akt-1 background). L2D animals were compared to wild type animals and dauer-defective compound mutants deficient in daf-16, dpy-21, set-4 or daf-12.

first: Colin

middle: E

last: Delaney

first: Patrick

last: Hu


title: RNA-Seq analysis of developmental, juvenile, and anhydrobiotic stages of Hypsibius dujardini and Ramazzottius varieornatus

city: Tsukuba

first: Yuki

last: Yoshida

address: 1-2 Owashi

department: NIAS

institute: NARO

summary: Limno-terrestrial tardigrades enter a state called anhydrobiosis when exposed to desiccation, and acquire tolerance against various extreme environments. The anhydrobiotic tardigrade Hypsibius dujardini, is a non-pigmented tardigrade easy to culture and RNAi method have been established, therefore making it a model tardigrade for tardigrade molecular research. Previous genome assemblies of this tardigrade had increased size due to heterozygosity. Here, we have sequenced the genome of H. dujardini using single individual Illumina DNA-Seq data and PacBio long read data, and employed a heterozygosity aware assembly method to assemble a near-complete high quality genome. In order to annotate the genome with gene predictions, we conducted RNA-Sequencing of various stages of developmental, juvenile, adult, and anhydrobiotic stage H. dujardini and Ramazzottius varieornatus, a tardigrade capable of rapid anhydrobiosis entry, and used these data for gene prediction with BRAKER v1.9 or differential gene expression analysis of the active and anhydrobiotic stages.

sample_organism:
Hypsibius dujardini
Ramazzottius varieornatus

overall_design: We obtained RNA-Seq data for the developmental, juvenile, active, and Tun stages of Hypsibius dujardini and Ramazzottius varieornatus, N=3 for each sample.

first: Georgios

last: Koutsovoulos

first: Dominik

last: Laetsch

first: Lewis

middle: R

last: Stevens

first: Sujai

last: Kumar

first: Daiki

last: Horikawa

first: Kyoko

last: Ishino

first: Shiori

last: Komine

first: Masaru

last: Tomita

first: Mark

last: Blaxter

first: Kazuharu

last: Arakawa


title: Identification of synaptic activity-regulated genes in primary mouse hippocampal neurons

city: Heidelberg

first: Carlos

last: Bas Orth

address: Im Neuenheimer Feld 307

department: Anatomy and Cell Biology

institute: Ruprecht-Karls-University Heidelberg

summary: Synaptic activity drives changes in gene expression to promote long-lasting adaptations of neuronal structure and function. One example of such an adaptive response is the buildup of acquired neuroprotection, a synaptic activity- and gene transcription-mediated increase in the resistance of neurons against harmful conditions. A hallmark of acquired neuroprotection is the stabilization of mitochondrial structure and function. We therefore re-examined previously identified sets of synaptic activity-regulated genes to identify genes that are directly linked to mitochondrial function. In mouse and rat primary hippocampal cultures synaptic activity caused an upregulation of glycolytic genes and a concomitant downregulation of genes required for oxidative phosphorylation, mitochondrial biogenesis and maintenance. Changes in metabolic gene expression were induced by action potential bursting, but not by glutamate bath application activating extrasynaptic NMDA receptors. The specific pattern of gene expression changes suggested that synaptic activity promotes a shift of neuronal energy metabolism from oxidative phosphorylation toward aerobic glycolysis, also known as Warburg effect. The ability of neurons to upregulate glycolysis has, however, been debated. We therefore used FACS sorting to show that, in mixed neuron glia co-cultures, activity-dependent regulation of metabolic gene expression occurred in neurons. Changes in gene expression were accompanied by changes in the phosphorylation-dependent regulation of the key metabolic enzyme, pyruvate dehydrogenase. Finally, increased synaptic activity caused an increase in the ratio of L-lactate production to oxygen consumption in primary hippocampal cultures. Based on these data we suggest the existence of a synaptic activity-mediated neuronal Warburg effect that may promote mitochondrial homeostasis and neuroprotection.

overall_design: We compared the mRNA expression profile of primary hippocampal neurons after 4h of basal synaptic activity vs. 4h of action potential bursting. Two independent experiments with independent cell preparations were performed.

last: Bas-Orth

first: Yan-Wei

last: Tan

first: Hilmar

last: Bading


title: The mouse genome displays highly dynamic populations of KRAB-zinc finger protein genes and related genetic units

city: Lausanne

first: Julien

last: Duc

address: Station 19 CH-1015 Lausanne

department: School of Life Science

institute: EPFL

summary: We present a thorough analysis of KZFP genes and related units in the murine genome. We first identified about twice more elements than previously annotated either as KZFP genes or pseudogenes, we then could delineate an organization in clusters distributed throughout the genome, with signs of recombination, translocation, duplication and seeding of new sites by retrotransposition of KZFP genes and related genetic units (KZFP/rGUs). Finally, we could demonstrate that the KAP1-SETDB1 repressor complex tames the expression of KZFP/rGUs within clusters, yet that the primary target of this regulation was not the KZFP/rGUs themselves but enhancers contained in neighboring endogenous retroelements.

overall_design: Analysis of KZFP/rGUs genomic distribution (ChIP-seq), expression profiles (RNA-seq), related transcripts and associated histone modifications (ChIP-seq). Characterization of binding and transcriptional control of KAP1 in KZFP/rGUs clusters via ChIP-seq and RNA-seq.

first: Annamaria

last: Kauzlaric


title: Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors [ChIP-seq]

city: Cincinnati

first: Aaron

middle: M

last: Zorn

state: OH

address: 3333 Burnet Ave

department: Develpomental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how they are integrated in the genome is poorly understood. Here we identified the Xenopus foregut and hindgut progenitor transcriptomes, which are largely conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/b-catenin acts as a genome-wide toggle between foregut and hindgut programs. In addition to b-catenin-Tcf promoting hindgut gene transcription, we unexpectedly observed Wnt-repressed foregut genes associated with b-catenin-binding to DNA lacking Tcf motifs, suggesting a novel direct repression. We define how BMP and Wnt signaling are integrated in the genome with Smad1 and β-catenin co-occupying DNA elements associated with hundreds of key regulatory genes. These results extend our understanding of GI organogenesis and how Wnt and BMP may coordinate genomic responses in other contexts.

overall_design: ChIP of whole embryos, foregut and hindgut explants for 3 different antibodies (b-catenin, Smad1 and p300).

first: Mariana

first: Praneet

last: Chaturvedi

first: Scott

last: Rankin

first: Melissa

last: Macdonald

first: Sajjeev

last: Jagannathan

first: Masashi

last: Yukawa

first: Artem

last: Barski


title: Transcriptomic profiling of mice receiving immunoprophylactic and immunotherapeutic hypoallergen-encoding DNA vaccine

city: HKSAR

first: Christine

middle: Yee Yan

last: Wai

address: Shatin, N.T.

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: RNA-seq analysis was performed to define the changes in gene expression of small intestine samples from mice pre-vaccinated and treated with MEM49-encoding DNA vaccine to elucidate the modulatory mechanism of DNA vaccine.

overall_design: DNA vaccine was constructed by expressing the hypoallergen MEM49 in the plasmid pCI-Neo. Balb/c mice were intradermally injected with 100 mg DNA vaccine prior to or after shrimp tropomyosin sensitization. Non-sensitized mice and sensitized mice receiving PBS or mock plasmid as sham treatment were included as negative and positive controls. Total RNA was extracted from ileum sections of the small intestine from the negative control, positive control group, mice pre-vaccinated with MEM49-encoding DNA vaccine (P-MEM49) and mice treated with MEM49-encoding DNA vaccine (T-MEM49). Samples from three animals from each group were pooled as one replicate and two replicates from each group were used for RNA-sequencing on the Ion-Proton Platform. Subsequent transcriptomic analysis identified significant gene expression changes related to the induction of tolerogenic dendritic cells and regulatory T cells in the DNA vaccine pre-vaccinated and treated mice.

middle: Y

first: Jing

last: Qing

first: Nicki

last: Leung

first: Patrick

middle: S

first: Ka

last: Chu


title: EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas [RNA-Seq mouse tumors]

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 (H3.3) and HIST1H3B (H3.1), leading to the expression of histone H3 in which lysine 27 is substituted with methionine (H3K27M) in nearly 80% of DIPGs1-5. 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 (Refs. 1-8). Here, we describe a 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 that is dependent on the induction of the tumour suppressor protein p16INK4A. Genome-wide enrichment analyses show that the genes that retain H3K27me3 in H3K27M cells are strong polycomb targets and are highly enriched for H3K27me3/PRC2/PRC1 in cells prior to H3K27M expression. Furthermore, we find a highly significant overlap between genes that retain H3K27me3 in the mouse DIPG model and in human primary DIPGs expressing H3K27M. Taken together, these results show that residual PRC2 activity is required for the proliferation of H3K27M positive DIPGs, and inhibition of EZH2 is as a potential therapeutic strategy for the treatment of these tumours.

overall_design: RNA-seq experiments in mouse tumor samples derived from injection of DIPG cells expressing K27M mutant histone H3.3

first: Nicolas

last: Rapin

first: Benjamin

last: Leblanc

first: Kristian

last: Helin


title: EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas [ChIP-Seq mouse cell lines]

overall_design: H3K27me3, Suz12 and Ring1b ChIP-seq experiments in mouse DIPG cells expressing wild-type or K27M mutant histone H3.3 in presence or absence of Ezh2 inhibitor.

first: Jens

last: Vilstrup Johansen


title: EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas [ChIP-Seq human cell lines]

overall_design: H3K27me3 ChIP-seq experiments in four human DIPG cell lines expressing K27M mutant histone H3.


title: Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors

first: Aaron


title: EZH2 is a potential therapeutic target for H3K27M mutant paediatric gliomas [RNA-Seq - mouse cell lines]

overall_design: RNA-seq experiments in mouse DIPG cells expressing wild-type or K27M mutant histone H3.3 in presence or absence of Ezh2 inhibitor.


title: mRNA microarray in MCAo rat model with IV-hUMSC

city: Seongnam-si

first: Jinkwon

last: Kim

address: Yatap-ro

department: Neurology

country: South Korea

institute: CHA medical University

summary:
To evaluate the change of gene expression at cerebral infarction by the treatment of IV-human umblical cord derived mesenchymal stem cell. RNA was isolated from the ipsilateral hemisphere to MCAo in rats.
At 72 h post-MCAo, the ipsilateral hemisphere subjected to MCAo was used for mRNA microarray. RNA was isolated from the ipsilateral hemisphere to MCAo in rats without MCAo (control group, n=5), rats treated with 1x106 IV-hUMSC (hUMSC group, n=6) and saline (saline group, n=5) at 24h post-MCAo.

overall_design: Gene expression of Rat brain tissue at 72 hours post-MCAo was measured. N: Control=5, Saline group=5, IV-hUMSC=6.

first: Seung-Hun

last: Oh

first: Jihwan

last: Song


title: Genomic integration of Wnt/b-catenin and BMP/Smad1 coordinates the transcriptional program of foregut and hindgut progenitors [RNA-seq]

last: Zorn

overall_design: mRNA profile of foregut and hindgut explants from BMP and Wnt manipulated embryos.

first: Mariana

last: Stevens

first: Praneet

last: Chaturvedi

first: Scott

middle: A

last: Rankin

first: Melissa

first: Sajjeev


title: DNA methylation in mouse liver tissue

status: Public on Feb 27 2017

city: Memphis

first: Khyobeni

last: Mozhui

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

summary: We performed affinity-based enrichment with methyl-CpG binding domain protein followed by high-throughput sequencing (MBD-seq) to assay DNA methylation in mouse liver tissue.

overall_design: Mouse tissue were from two different inbred strains (C57BL/6J and DBA/2J) and from 3 age groups classified as young (4 months), mid (11–12 months) and old (24 months).


title: Bacillus anthracis gene expression upon plantazolicin and Me2-Arg-Az5

city: Urbana

first: Douglas

last: Mitchell

state: IL

address: 1206 W. Gregory Dr. MC-195 Room 3105 IGB

department: Chemistry

institute: University of Illinois at Urbana-Champaign

summary: Subinhibitory concentrations of compound used to assess their influence on the gene expression profile of Bacillus anthracis.

overall_design: Bacillus anthracis cells were treated with 0.25X MIC of compound (Me2-Arg-Az5, plantazolicin) for 10 min. RNA was isolated, sequenced, and analyzed using Rockhopper.

first: Katie

last: Molohon

first: Patricia

last: Blair

first: James

last: Doroghazi


title: Mycelium growth and conidiogenesis of Metarhizium robertsii

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

summary: Digital gene expression profiling analysis of the mycelium growth and conidiogenesis stages of  Metarhizium robertsii

overall_design: Metarhizium robertsii is a well-characterized entomopathogenic fungus that used as an important alternative to chemical insecticides in programs of agricultural pest and disease vector control. Metarhizium conidia are involved in fungal propagation and also are responsible for host infection. RNA interference (RNAi) is a gene silencing mechanism that plays an important role in gene regulation in a number of eukaryotic organisms. However, the physiological role of RNAi remains largely unclear in fungal development. Gene expression analysis was performed on mycelium growth and conidiogenesis stages of M. robertsii wild type and Δdcl2. The analysis revealed that modest changes occur in development or metabolism processes, which could explain the reduction in conidiation in Δdcl2 mutant.

first: Hui-min

last: Meng

first: Bo

last: Huang


title: Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (ATAC-seq for in-vitro experiments)

first: Roberto

last: Spreafico

overall_design: Chromatin accessibility by ATAC-seq for CD8+ T cells restimulated in vitro


title: Identification of a unique gene expression signature in mercury and 2,3,7,8-tetrachlorodibenzo-p-dioxin co-exposed cells

city: Tuxedo

first: Suresh

last: Cuddapah

state: New York

address: 57 Old Forge Road

department: Environmental Sciecne

institute: New York University Langone Medical center

summary: Mercury (Hg) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are major environmental contaminants that commonly co-occur in the environment. Both Hg and TCDD are associated with a number of human diseases including cancers. While the individual toxicological effects of Hg and TCDD have been extensively investigated, studies on co-exposure are limited to a few genes and pathways. Therefore, a significant knowledge gap exists in the understanding of the deleterious effects of co-exposure to Hg and TCDD. Due to the prevalence of Hg and TCDD co-contamination in the environment and the major human health hazards they pose, it is important to obtain a fuller understanding of genome-wide effects of Hg and TCDD co-exposure. In this study, by performing a comprehensive transcriptomic analysis of human bronchial epithelial cells (BEAS-2B) exposed to Hg and TCDD individually and in combination, we have uncovered a subset of genes with altered expression only in the co-exposed cells. We also identified the additive as well as antagonistic effects of Hg and TCDD on gene expression. Moreover, we found that co-exposure impacted several biological and disease processes not affected by Hg or TCDD individually. Our studies show that the consequences of Hg and TCDD co-exposure on the transcriptional program and biological processes could be substantially different from single exposures, thus providing new insights into the co-exposure-specific pathogenic processes.

overall_design: Methods: we performed a comprehensive analysis of the transcriptomes of cells exposed to Hg or TCDD individually and in combination. RNA Seq gene expression comparison done in replicates.

first: Lakshmanan

last: Jagannathan

first: Cynthia

last: Jose


title: The FUS protein participates in circRNA biogenesis

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

institute: "Sapienza" University of Rome

summary: The RNA binding protein FUS exerts its function in several RNA biosynthetic processes; moreover, mutations leading to changes in its expression levels or alterations in cellular compartmentalization have been linked to the pathogenesis of Amyotrophic Lateral Sclerosis.  Here, we describe an additional novel function of FUS, that is the control of back-splicing reactions which lead to circular RNA (circRNA) production. We identified circRNAs expressed in murine ES-derived motoneurons and then compared their levels in control versus FUS-/- cells. We discovered that a considerable number of circRNAs is affected by FUS levels.

overall_design: Analysis of WT and FUS -/- mouse motorneurons. For each condition there is a triplicate of samples. In total 6 samples are analyzed.

first: Stefano

middle: D

last: Modigliani

first: Lorenzo

last: Errichelli

first: Pietro

last: Laneve

first: Ivano

last: Legnini

first: Davide

last: Capauto

first: Alessandro

last: Rosa

first: Riccardo

last: De Santis

first: Rebecca

last: Scarfò

first: Giovanna

last: Peruzzi

first: Lu

last: Lei

first: Elisa

last: Caffarelli

first: Neil

last: Shneider

first: Mariangela

last: Morlando

first: Irene

last: Bozzoni


title: Functional analysis of the Arabidopsis thaliana Pol V largest subunit, NRPE1, carboxy-terminal domain by whole genome bisulfite sequencing

status: Public on Feb 25 2017

city: Bloomington

first: Jered

last: Wendte

state: IN

address: 915 E. 3rd Street

institute: Indiana University

summary: RNA Polymerase V transcription recruits siRNA-Argonaute protein complexes to chromatin, thereby specifying sites of RNA-directed DNA methylation (RdDM) and transcriptional gene silencing in plants. The Pol V largest subunit, NRPE1, has an extensive carboxyl-terminal domain (CTD) that is dispensable for catalytic activity in vitro, yet essential in vivo. A CTD subdomain, DeCL, named for its similarity to a chloroplast protein, DEFECTIVE CHLOROPLASTS AND LEAVES, is required for Pol V function at virtually all loci, similar to mutants defective for Pol V recruitment. Deletions removing three other CTD subdomains affect overlapping subsets of loci, similar to mutants lacking proteins that bind Pol V or its transcripts. A yeast two-hybrid screen for CTD-interactors identified the 3-prime -> 5-prime exoribonuclease, RRP6L1 as an interactor with the DeCL subdomain and the adjacent QS subdomain, named for its numerous glutamine-serine (QS) repeats. These RRP6L1-binding subdomains immediately follow the Argonaute-binding subdomain. Experimental evidence indicates that RRP6L1 trims the 3-prime ends of Pol V transcripts sliced by ARGONAUTE 4 (AGO4), suggesting a model whereby the adjacent CTD subdomains enable the spatial and temporal coordination of AGO4 and RRP6L1 RNA processing activities.

overall_design: NRPE1 constructs with targeted carboxy-terminal domain deletions were assessed for their ability to complement nrpe1-11 mutants. Controls include Col-0 wild-type plants, nrpe1-11 mutant plants, and nrpe1-11 mutants expressing a full length NRPE1 transgene.

first: Craig

last: Pikaard


title: Heterotypic nucleosomes and PRC2 drive DIPG oncogenesis

city: Chicago

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Diffuse intrinsic pontine gliomas (DIPG) are characterized by a heterozygous lysine-to-methionine mutation of histone H3 (H3K27M) that potently reduces Polycomb Repressive Complex 2 (PRC2) methylation of wild-type histone H3K27 (H3K27wt). The role of H3K27M and reduced H3K27wt methylation in DIPG pathogenesis has yet to be determined. Here, we have performed epigenomic profiling of patient-derived H3K27M mutant DIPG cells and demonstrate that H3K27M resides in nucleosomes with H3K27wt acetylation (H3K27ac), and H3K27M-H3K27ac containing nucleosomes co-localize with bromodomain proteins at actively transcribed genes and that PRC2 is excluded from H3K27M occupied regions. With respect to therapeutic implications of these observations, we demonstrate that pharmacologic bromodomain protein inhibition suppresses tumor growth in vivo. In total, our results indicate that H3K27M promotes H3K27ac at the expense of H3K27 methylation, and points to bromodomain protein inhibition as a clinical strategy for treating DIPG.

overall_design: Examination of different histone modifications, histone mutant and chromatin modifiers in 2 different DIPG patient-derived cells. Control cells such as HCT116 were used to test H3K27M antibody specificity

first: Andrea

last: Piunti

first: Elizabeth

middle: T

last: Bartom


title: sRNA expression in the Pol V largest subunit mutant, nrpe1-11

overall_design: The Pol V largest subunit mutant, nrpe1-11, was assessed for sRNA expression across regions that undergo Pol V dependent CHH methylation.


title: Functional analysis of the RNA polymerase V CTD

overall_design: Refer to individual Series


title: 3'RACE analyses of Pol V transcript 3' end lengths in mutants of the exonuclease RRP6L1

overall_design: 3' RACE targeting Pol V dependent transcripts was conducted in two independent mutants of RRP6L1, rrp6L1-1 and rrp6L1-2. RACE was also conducted in Col-0 wild type and Pol V mutant (nrpe1-11) controls.


title: Combination targeted therapy to disrupt aberrant oncogenic signaling and reverse epigenetic dysfunction in IDH2- and TET2-mutant acute myeloid leukemia

city: New York

first: Cem

last: Meydan

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College


title: Epigenomic rescue of genetically defective Ucp1 expression in subcutaneous fat of C57BL/6 mice [RNA-Seq]

city: Philadelphia

first: Raymond

last: Soccio

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Obesity causes insulin resistance, and PPARγ ligands like rosiglitazone (rosi) are insulin-sensitizing, yet mechanisms remain unclear. High fat diet (HFD) induced obesity has major effects on visceral epididymal adipose tissue (eWAT) of C57BL/6 (B6) mice, and here we report altered activity of gene regulatory elements with changes in PPARγ genome-wide occupancy. Treatment with rosi restored insulin sensitivity, yet surprisingly had little effect on eWAT, leading us to consider the subcutaneous inguinal fat (iWAT). In this depot, rosi markedly induced molecular signatures of brown fat including the key thermogenic gene Ucp1. Obesity-resistant 129S1/SvImJ (129) mice showed this degree of iWAT browning even in the absence of rosi. Remarkably, the 129 Ucp1 locus had increased PPARγ binding and gene expression that was preserved in B6x129 F1 intercross iWAT, with imbalance favoring the 129-derived alleles showing a cis-acting genetic difference. Thus, B6 mice have a genetic defect in Ucp1 expression. However, imbalanced expression favoring 129 over B6 was nearly lost when Ucp1 was activated by rosi, or by iWAT browning in cold-exposed or young mice. These results provide a novel framework for understanding how environmental influences like drugs can rescue genetically determined disease phenotypes by affecting the epigenome.

overall_design: C57BL/6J and 129S1/SvlmJ mice were on LFD or HFD; then treated with rosiglitazone

first: Raymound

first: Yee

last: Foong

first: Zhenghui

last: Li


title: Characterization of molecular functions, pathways and protein classes affected by aging-related changes of miRNA expression in peripheral blood mononuclear cells

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

summary:
Epigenetic drift, an aging-associated change of the epigenome is one of the factors that can influence the rate and course of aging. In fact, even subtle changes of the miRnome can affect cellular functions. Therefore, changes of aging-associated miRNA expression in peripheral blood mononuclear cells (PBMC) of long-lived humans (n=24, mean age 94.8±3.9 years) and healthy, young individuals (n=24, 28.0±4.0 years) was evaluated using next generation sequencing. Twenty three miRNAs had at least 2-fold lower and 9 at least 2-fold higher mean expression in PBMC of long-lived than young study subjects. Expression of select miRNAs was verified by RT-PCR. Target genes were searched for by the MirWalk2 and MirTarBase programs. Next, using bioinformatics tools we analyzed what molecular functions, pathways and protein classes were affected by these miRNAs. Molecular functions, pathways and protein classes were analyzed using the PANTHER Classification System v. 11 database. In total, 12663 target genes have been identified. The largest number of aging-affected miRNAs interacted with mRNA of genes with established role in aging, senescence and/or chronic inflammation such as DISC1 (binding sites for 11 miRNAs), IGF-1R (10), BCL2  (9), MYC (8), TP53 (7), CCND1 (7), CDKN1A (6), CDKN1B (6), FOXO1 (6), XIAP (6), as well as those with a less known or unknown role in these processes such as ZNF460 (13), INPP5B (8), TMEM136 (8), NOTCH2 (8), ZNF652 (8), ACER2 (8), and MAP3K1 (8). Nine molecular functions, 13 pathways and 5 protein classes were indicated as affected by aging-associated miRnome change. Affected molecular functions included signal transducer activity, antigen binding, receptor activity, catalytic activity, binding, nucleic acid binding, G-protein coupled receptor activity, DNA binding, and protein binding. Affected pathways were gonadotropin-releasing hormone receptor pathway, CCKR signaling map, angiogenesis, apoptosis signaling pathway, PDGF signaling pathway, EGF receptor signaling pathway, TGF-β signaling pathway, 5HT2 type receptor mediated signaling pathway, VEGF signaling pathway, integrin signaling pathway, heterotrimeric G-protein signaling pathway-Giα and Gsα mediated pathway, interleukin signaling pathway, and p53 pathway. Protein classes most significantly associated with aging-related change in the miRNA expression were immunoglobulin, nucleic acid binding, defense/immunity protein, transcription factor, and zinc finger transcription factor classes.
In conclusion, aging-related miRnome change affects multiple molecular mechanisms in peripheral blood mononuclear cells, intensifying in this way aging-associated dysfunction of the immune system.

overall_design: Examination of miRNA expression in mononuclear immune system cells from young and long lived donors

first: Magdalena

last: Owczarz

first: Monika

last: Kolanowska

last: Budzinska

last: Puzianowska-Kuznicka


title: Combination targeted therapy to disrupt aberrant oncogenic signaling and reverse epigenetic dysfunction in IDH2- and TET2-mutant acute myeloid leukemia (RRBS)

summary: Genomic studies in acute myeloid leukemias (AML) have identified mutations which drive altered DNA methylation, including TET2 and IDH. Functional studies have shown these mutations contribute to transformation, although how these mutations impact the response to epigenetic therapies is not fully delineated. Here we show AMLs with TET2/IDH2 mutations combined with FLT3ITD mutations are specifically sensitive to 5-Azacytidine or to the IDH2 inhibitor AG-221, respectively. 5-Azacytidine/AG-221 therapies induced a reduction in leukemic blasts and in stem/progenitor expansion, with attenuation of aberrant DNA hypermethylation. These therapeutic benefits were achieved through restoration of differentiation, such that normalized hematopoiesis was derived from mutant cells.  Consistent with these data, at the time of clinical response to 5-Azacytidine or AG-221, most patients had mutant-derived hematopoiesis. By contrast, combined AG-221/5-Azacytidine plus FLT3 inhibition reduced disease burden and reversed epigenetic dysfunction. Our studies suggest combined targeting of signaling and epigenetic pathways can increase therapeutic response in AML.

overall_design: Using ERRBS, we profiled genome-wide DNA methylation patterns of the hematopoietic stem cells (LSK) population in Wild-type, Idh2 R140Q Flt3-ITD, and Tet2-/-;Flt3-IDT mice.  Idh2 R140Q Flt3-ITD mice with AML were treated with either vehicle, AC220 (Quizartinib, a Flt3 inhibitor), AG-221 (the first small molecule in vivo inhibitor of IDH2 to enter clinical trials) as well as the combination therapy with AC220 and AG-221 together. Tet2-/-;Flt3-IDT mice with AML were treated with vehicle, AC220, 5-Azacytidine (Decitabine, hypomethylating agent) or a combination of AC220 and 5-Azacytidine. All experiments were done in 3-6 replicates.

first: Alan

last: Shih

first: Eytan

last: Stein

first: Kaitlyn

last: Shank

first: Francine

last: Garrett-Bakelman

first: Patrick

last: Ward

first: Abbas

last: Nazir

first: Kristina

last: Knapp

first: Jeremy

last: Travins

first: Kim

last: Straley

first: Christopher

last: Mason

first: Camelia

last: Gliser

first: Katharine

last: Yen

last: Thompson

first: Ari

last: Melnick

first: Ross

last: Levine


title: GABP determines the epigenetic status of mutant TERT promoter

city: Singapore

first: Melissa

middle: Jane

last: Fullwood

address: 14 Medical Drive, #12-01

department: Centre for Translational Medicine

institute: Cancer Science Institute of Singapore

summary: Blocking telomerase is recognized as a key anti-cancer mechanism. Unlike in stem cells, levels of telomerase catalytic subunit TERT are limiting in reconstituting telomerase activity in somatic cells. However in some cancers, Tert is transcriptionally reactivated by mutations in its promoter. Given that Tert in stem cells is driven by WT Tert promoter, if we can selectively target Tert reactivation through mutant Tert promoters we can block telomerase activity specifically in cancer cells without toxicity in stem cells. Here we report the epigenetic regulation of Tert promoter comparing WT and mutant promoters. We showed that GABPA homodimerization through long-range interaction stabilizes Gabpa to drive Tert expression. Furthermore, BRD4 specifically activates the C250T mutant promoter via dual mechanism involving GABPA, thereby setting the stage for future therapeutics.

overall_design: We examine 2 biological replicates of each sample including BLM, A375, BLM6 (Crispr-Tert mutant promoter C250T) and BLM14 (Crispr-Tert WT promoter C250C )

first: Semih

last: Akincilar

first: Ekta

last: Khattar

first: Priscilla

last: Boon

first: Bilal

last: Unal

middle: J

first: Vinay

last: Tergaonkar


title: Epigenomic rescue of genetically defective Ucp1 expression in subcutaneous fat of C57BL/6 mice

first: Raymond

last: Soccio

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


title: Combination targeted therapy to disrupt aberrant oncogenic signaling and reverse epigenetic dysfunction in IDH2- and TET2-mutant acute myeloid leukemia (RNA-Seq)

first: Cem

last: Meydan

overall_design: We profiled genome-wide transcription patterns of the hematopoietic stem cells (LSK) population in Wild-type, Idh2 R140Q Flt3-ITD, and Tet2-/-;Flt3-IDT mice.  Idh2 R140Q Flt3-ITD mice with AML were treated with either vehicle or AG-221 (the first small molecule in vivo inhibitor of IDH2 to enter clinical trials). Tet2-/-;Flt3-IDT mice with AML were treated with vehicle or 5-Azacytidine (Decitabine, hypomethylating agent).

first: Alan

middle: H

last: Shih

first: Eytan

last: Stein

first: Kaitlyn

last: Shank

first: Francine

last: Garrett-Bakelman

first: Patrick

last: Ward

last: Nazir

first: Craig


title: Changes in the erythroblast miRNA profile in the bone marrow of a Plasmodium vivax-infected patient

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

country: Brazil

institute: Oswaldo Cruz Foundation - Fiocruz

summary: Human studies of Plasmodium vivax in the bone marrow are scarce. Here, we present a detailed characterization of bone marrow aspirates taken from a P. vivax patient with high parasitaemia on admission and 42 days after treatment. Analysis of miRNAs related to erythropoiesis revealed a distinct series of differentially expressed miRNAs during infection compared to at convalescence. These results suggest that parasites in the bone marrow affect erythropoiesis.

overall_design: Characterization of bone marrow aspirates taken from a P. vivax patient with high parasitaemia on admission and 42 days after treatment

first: Marcus

middle: V

last: de Lacerda

first: Hernando

last: del Portillo


title: Untimely expression of gametogenic genes in vegetative cells causes uniparental disomy (RNA-seq)

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: We report gene expression profiling in the fission yeast Schizosaccharomyces pombe. We performed high-throughput sequencing of RNA isolated from wild-type, ago1d, mmi1d and dcr1d strains.

overall_design: RNA expression profiles of Schizosacccharomyces pombe strains containing deletions were compared to the wild type to generate differences in gene expression.

first: H

last: Folco

first: Tomoyasu

last: Sugiyama

first: Venkata

last: Chalamcharla

first: Gobi

last: Thillainadesan

first: Martin

last: Zofall

first: Vanivilasini

last: Balachandran

first: Jothy

last: Dhakshnamoorthy

first: Takeshi

last: Mizuguchi


title: Untimely expression of gametogenic genes in vegetative cells causes uniparental disomy

type: Genome binding/occupancy profiling by genome tiling array


title: Epigenomic rescue of genetically defective Ucp1 expression in subcutaneous fat of C57BL/6 mice [ChIP-Seq]

first: Raymond

last: Soccio

state: PA

first: Raymound


title: Transcript identification and quantification on Mouse Imprinted Region Tiling Array (MIRTA)

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

type: Non-coding RNA profiling by genome tiling array


title: RNA-Seq to compare gene expression to MIRTA tiling arrays

summary: We performed additional sequencing of samples from GSM718982, GSM718983 to increase coverage in order to comapre gene expression by RNA-Seq to MIRTA tiling array expression performed on the same samples.

overall_design: Re-sequencing of samples from GSE22959  (GSM718982, GSM718983) in two technical replicates

first: R

last: Huang

first: F


title: Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [CAPIP-seq]

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

institute: University of Torino

summary: In mammals, DNA methylation occurs mainly at 5mC of CpG dinucleotides. The methylation on the promoter leads to the suppression of gene expression, while the functional role of gene body DNA methylation in highly expressed genes has yet to be clarified. Here, we show that the Dnmt3b-dependent intragenic DNA methylation protects the gene body from RNA Polymerase II (RNA Pol II) spurious entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that loss of Dnmt3b leads to an increase of the RNA Pol II engagement within gene bodies and spurious intragenic transcription initiation events. Furthermore, inhibition of RNA Pol II spurious entry depends on the enzymatic activity of the Dnmt3b recruited by H3K36me3. Thus, elongating RNA Pol II triggers an epigenetic crosstalk that involves SetD2, H3K36me3, Dnmt3b, and DNA methylation to ensure gene transcription initiation fidelity with implications for intragenic hypomethylation in cancer.

overall_design: Genome-wide analysis of Dnmt3b role in mouse ESCs using CAPIP-seq.

first: Salvatore

last: Oliviero


title: Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [ChIP-seq]

overall_design: Genome-wide analysis of Dnmt3b role in mouse ESCs using RNA-seq.


title: Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [ART-seq]

overall_design: Genome-wide analysis of Dnmt3b role in mouse ESCs using ART-seq.


title: Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [BS-seq]

overall_design: Genome-wide analysis of Dnmt3b role in mouse ESCs using BS-seq.


title: Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies


title: RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA

status: Public on Feb 24 2017

city: Madison

first: Gina

last: Gordon

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin Madison

summary:
In this study, we performed RNA-sequencing on an E. coli model system to confirm known sites, identify novel targets, and determine the impact of RNase III cleavage events on transcript degradation and metabolic phenotypes. To find cleavage sites, we compared the abundance of sequencing reads across the transcriptome of a wild-type E. coli and an rnc- deletion mutant. The RNA-sequencing approach provided wider coverage and unprecedented resolution of mRNA abundance at each position in the transcriptome compared to prior studies that used qPCR, Northern blots, or microarrays. In addition to data collected from exponentially growing cells, we observed the effects of RNase III cleavage on transcript degradation by collecting samples in a time course after stopping nascent transcription with rifampicin.

This work was supported by the Department of Energy Grant DE-SC0010329

overall_design: Examination of RNA-seq read coverage between a strain with and without RNase III throughout time after preventing nascent transcription with rifampicin; partial biological replicate of WT

first: Jeffrey

last: Cameron

first: Brian

middle: F

last: Pfleger


title: Intragenic DNA methylation prevents cryptic transcription initiations on gene bodies [DECAP-seq]

overall_design: Genome-wide analysis of Dnmt3b role in mouse ESCs using DECAP-seq.


title: RNAseq changes in human fibroblasts after treatment with E16.5 skin extract

city: Taipei

first: Mai-Yi

last: Fan

address: No1, Sec. 1, Jen - Ai Rd.

country: Taiwan

institute: National Taiwan University

summary: To identify the cellular processes upregulated in fibroblasts after treatment with E16.5 skin extract

overall_design: Fibroblasts mRNA profiles of human with treatments and adult DP were generated by next generation sequencing. SRA Study accession:SRP100585; BioProject accession:PRJNA375952

first: Sung-Jan

last: Lin


title: Cell Cycle Reprogramming for PI3K Inhibition Overrides Relapse-Specific C481S BTK Mutation Revealed by Longitudinal Functional Genomics in Mantle Cell Lymphoma

first: Selina

last: Chen-Kiang

state: NY

address: 1300 York Avenue, C338

country: USA

summary: The RNA-seq data presented in this study include libraries from Mantle Cell Lymphoma (MCL) tumor cells sequentially obtained from patients

overall_design: RNA-Seq on MCL patient samples

first: David

last: Chiron

first: Priyanka

last: Vijay

first: Pedro

last: Blecua

first: Maurizio

last: Di Liberto

first: Christopher

last: Mason


title: Gene expression profiling of Male and Female adult mouse liver using RNA-seq

city: Boston

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: RNA-seq analysis of intact male and female adult mouse liver. This GEO series is part of a larger study, where we investigated the impact of a single pulse of GH given to hypophysectomized mice on local liver chromatin accessibility [DNase hypersensitive site analysis], transcription rates [hnRNA analysis], and gene expression [quantitative PCR and RNA-Seq] determined 30, 90 or 240 min later. The STAT5-dependent but sex-independent early GH response genes Igf1 and Cish showed rapid, GH pulse-induced increases in chromatin accessibility and gene transcription, reversing the effects of hypophysectomy. Rapid increases in liver chromatin accessibility and transcriptional activity were also induced in hypophysectomized male mice for some (Ces2b, Ugt2b38) but not for other liver STAT5-dependent male-biased genes (Cyp7b1). Moreover, in pituitary-intact male mice, Igf1, Cish, Ces2b and Ugt2b38 all showed remarkable cycles of chromatin opening and closing, and associated cycles of induced gene transcription, which closely followed each endogenous pulse of liver STAT5 activity. Thus, the endogenous rhythms of male plasma GH pulsation dynamically open and then close liver chromatin at discrete, localized regulatory sites in temporal association with transcriptional activation of Igf1, Cish and a subset of STAT5-dependent male-biased genes.

overall_design: Liver RNA was isolated from intact male and female mice. RNA samples were pooled to make 3 biological replicates per condition comprised of 12-17 individuals each.

first: Dana

last: Lau-Corona

first: Andy

last: Rampersaud


title: Gene expression profiling (RNA-seq with partial depletion of rRNA) of livers of hypophysectomized male mice treated with a single pulse of growth hormone (GH)

summary: We investigated the effects of a single pulse of growth hormone on the transcriptional activation of STAT5 target genes in hypophysectomized male mouse liver. This GEO series is part of a larger study, where we investigated the impact of a single pulse of GH given to hypophysectomized mice on local liver chromatin accessibility [DNase hypersensitive site analysis], transcription rates [hnRNA analysis], and gene expression [quantitative PCR and RNA-Seq] determined 30, 90 or 240 min later. The STAT5-dependent but sex-independent early GH response genes Igf1 and Cish showed rapid, GH pulse-induced increases in chromatin accessibility and gene transcription, reversing the effects of hypophysectomy. Rapid increases in liver chromatin accessibility and transcriptional activity were also induced in hypophysectomized male mice for some (Ces2b, Ugt2b38) but not for other liver STAT5-dependent male-biased genes (Cyp7b1). Moreover, in pituitary-intact male mice, Igf1, Cish, Ces2b and Ugt2b38 all showed remarkable cycles of chromatin opening and closing, and associated cycles of induced gene transcription, which closely followed each endogenous pulse of liver STAT5 activity. Thus, the endogenous rhythms of male plasma GH pulsation dynamically open and then close liver chromatin at discrete, localized regulatory sites in temporal association with transcriptional activation of Igf1, Cish and a subset of STAT5-dependent male-biased genes.

overall_design: Liver RNA was isolated from hypophysectomized male mice that were untreated, or were treated with a single pulse of GH and euthanized 30, 90 or 240 minutes later. 8 Individual RNA samples were pooled to make 2 biological replicates per condition for RNA-seq analysis.

first: Jeannette

last: Connerney


title: Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model

city: Lausanne

first: Julia

last: DI IULIO

state: Vaud

address: Bugnon 48

country: Switzerland

institute: Institute of Microbiolgy

summary: HIV latency is a major obstacle to curing infection. Current strategies to eradicate HIV aim at increasing transcription of the latent provirus. In the present study we observed that latently infected CD4+ T cells from HIV-infected individuals failed to produce viral particles upon ex vivo exposure to SAHA (vorinostat), despite effective inhibition of histone deacetylases. To identify steps that were not susceptible to the action of SAHA or other latency reverting agents, we used a primary CD4+ T cell model, joint host and viral RNA sequencing, and a viral-encoded reporter. This model served to investigate the characteristics of latently infected cells, the dynamics of HIV latency, and the process of reactivation induced by various stimuli. During latency, we observed persistence of viral transcripts but only limited viral translation. Similarly, the reactivating agents SAHA and disulfiram successfully increased viral transcription, but failed to effectively enhance viral translation, mirroring the ex vivo data. This study highlights the importance of post-transcriptional blocks as one mechanism leading to HIV latency that needs to be relieved in order to purge the viral reservoir.

overall_design: Establishment and maintenance of HIV latency+ reactivation with different agents. RNAseq was performed for both HIV infected and mock infected cells at: Week 0,2,4,6,8 and 10 of latency and at 8, 24 and/or 72 hours post reactivation with vorinostat (SAHA), disulfiram (disu), azacytidine (aza), interleukin-7 (IL-7), anti-CD3/anti-CD28 (antiCD3) or DMSO).

first: Pejman

last: Mohammadi

last: di Iulio

first: Miguel

last: Munoz

first: Raquel

last: Martinez

first: Istvan

last: Bartha

first: Cavassini

last: Matthias

first: Christian

last: Thorball

first: Jacques

last: Fellay

first: Niko

last: Beerenwinkel

first: Angela

last: Ciuffi

first: Amalio

last: Telenti