title: Regulation of DNA replication time is crucial for appropriate gene expression

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary: Eukaryotic genomes are replicated in a reproducible temporal order, however, the physiological significance is poorly understood. We compared replication dynamics in divergent yeast species and identified genomic features with conserved replication times. Histone genes were amongst the earliest replicating loci in all species. We delayed the replication of HTA1-HTB1 and discovered that this halved the histone gene expression. Finally, we show that histone and cell cycle genes in general are exempt from dosage compensation mechanisms. Thus we have uncovered one of the first physiological requirements for regulated replication time and demonstrate a direct link between replication time and gene expression.

sample_organism:
Saccharomyces cerevisiae
Lachancea kluyveri
Zygosaccharomyces rouxii
Nakaseomyces glabratus
Naumovozyma castellii
Kluyveromyces lactis
Henningerozyma blattae

overall_design: Measurement of genome replication time from 6 budding yeast species (Candida glabrata, Naumovozyma castellii, Tetrapisispora blattae, Zygosaccharomyces rouxii, Kluyveromyces lactis, Lachancea kluyveri) and a Saccharomyces cerevisiae strain (triple origin mutant with ARS427.5, ARS428 and ARS429 inactivated). For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase).

first: Carolin

last: Müller


title: Transciptome profiling of NoDice and RNaseIII null cells prior to and after polyIC treatment

status: Public on Jun 28 2017

city: New York

first: Benjamin

last: tenOever

state: NY

address: 1468 Madison Avenue

department: Microbiology

country: USA

institute: Ichan School of Medicine at Mount Sinai

type: Expression profiling by high throughput sequencing

summary:
To assess the impact of endogenous RNaseIII nucleases on the overall transcriptome and the reseponse to dsRNA.
We utilized CRISPR techology to engineer an RNaseIII null cell line using the NoDice 293T parental strain genearated the Cullen lab as the parental cell line.

overall_design: mRNA profiles of 293T, NoDice 293T, and RNaseIII null cells alone or treated with polyIC for 8 hours

middle: R


title: The Gcn4 Transcription Factor Reduces  Protein Synthesis Capacity and Extends Yeast Lifespan

city: Basel

first: Joao

middle: C

last: Guimaraes

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. Chromatin immunoprecipitation reveals Gcn4 binding not only at genes that are activated, but also at genes that are repressed upon Gcn4 overexpression. The promoters of repressed genes contain Rap1 binding motifs. Our data suggest that Gcn4 is a central regulator of protein synthesis under multiple perturbations - including ribosomal protein (RP) gene deletions, calorie restriction, rapamycin treatment - and provide an explanation for its role in longevity and stress response.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Immune escape in breast cancer during in situ to invasive carcinoma transition

city: Boston

first: Muhammad

middle: B

last: Ekram

state: MA

address: 450 Brookline Avenue, DA 740A

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: To dissect mechanisms of immune escape during breast tumor progression, we analyzed the composition of leukocytes in normal breast tissues, ductal carcinomas in situ (DCIS), and HER2+ and triple negative invasive ductal carcinomas (IDC). We found significant tissue and tumor subtype-specific differences in multiple cell types including T cells and neutrophils. Analysis of gene expression profiles of T cells demonstrated enrichment for activated GZMB+MKI67+CD8+ effector T cell signatures in DCIS. TCR clonotypes also showed highest diversity in DCIS. Naïve T cell signatures predominated IDCs, especially triple negative subtypes. TIGIT and PDL1 immune checkpoint proteins showed differential expression between DCIS and IDCs with amplification of CD274 (encoding PDL1) only detected in triple negative IDCs. Our results imply that DCIS progression is limited by an anti-tumor immune response that becomes muted in invasive tumors due to selection for cancer cells and microenvironment that suppress activated T cells or no longer trigger their activation.

overall_design: RNA-Seq: Gene expression analyses in leukocytes sorted from normal breast tissues, ductal carcinomas in situ (DCIS), and HER2+ and triple negative invasive ductal carcinomas (IDC).

first: Carlos

middle: J

last: Gil Del Alcazar

first: Sung

last: Huh

first: Anne

last: Trinh

first: Kornelia

last: Polyak


title: The Gcn4 Transcription Factor Reduces Protein Synthesis Capacity and Extends Yeast Lifespan [ChIP-Seq]

summary: In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. Chromatin immunoprecipitation reveals Gcn4 binding not only at genes that are activated, but also at genes that are repressed upon Gcn4 overexpression. The promoters of repressed genes contain Rap1 binding motifs. Our data suggest that Gcn4 is a central regulator of protein synthesis under multiple perturbations - including ribosomal protein (RP) gene deletions, calorie restriction, rapamycin treatment - and provide an explanation for its role in longevity and stress response.

overall_design: Examination of Gcn4 binding sites via ChIP-seq.

first: Nitish

last: Mittal

first: Mihaela

last: Zavolan


title: Transciptome profiling of RNaseIII null cells reconstituted with Drosha

summary: To assess the impact of Drosha reconstitution on the overall transcriptome of RNaseIII null cells.

overall_design:
We utilized CRISPR techology to engineer an RNaseIII null cell line using the NoDice 293T (PMID: 24757167) as the parental cell line.
mRNA profiles of RNaseIII null cells were transfected with GFP plus empty plasmid or GFP-Drosha for 3 days.


title: The Gcn4 Transcription Factor Reduces Protein Synthesis Capacity and Extends Yeast Lifespan [RNA-Seq]

overall_design: Examination of transcriptome and ribosome occupancy in five different RPKO strains and wild type. Examination of transcriptome in two GCN4-overexpressing strains, one GCN4-mutant strain  and respective wild type.


title: Dynamic and stable enhancer-promoter contacts regulate terminal differentiation [RNA-Seq]

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Drive, CCSR 2150

institute: Stanford University

summary: Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.

overall_design: RNA-seq data from epidermal keratinocyte progenitor and differentiated cells.

first: Adam

last: Rubin

first: Brook

last: Barajas

middle: A


title: Dynamic and stable enhancer-promoter contacts regulate terminal differentiation [HiC_CHiC]

overall_design: Hi-C and CHi-C data from epidermal keratinocyte progenitor and differentiated cells.


title: Dynamic and stable enhancer-promoter contacts regulate terminal differentiation [ChIP-Seq]

overall_design: ChIP-seq data from epidermal keratinocyte progenitor and differentiated cells.


title: The FAM46C gene encodes a non-canonical poly(A) polymerase and acts as an onco-suppressor in multiple myeloma

status: Public on Jun 30 2017

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

summary: FAM46C is one of the most frequently mutated genes in multiple myeloma (MM) and encodes a protein of unknown function. Using a combination of in vitro and in vivo approaches, we demonstrate that FAM46C encodes an active cytoplasmic non-canonical poly(A) polymerase, which enhances mRNA stability and gene expression. Moreover, we also found that the reintroduction of active FAM46C into MM cell lines, but not its catalytically-inactive mutant, leads to broad polyadenylation and stabilization of mRNAs strongly enriched with those encoding endoplasmic reticulum-targeted proteins and induced cell death. This is, to our knowledge, the first report that directly associates cytoplasmic poly(A) polymerase with carcinogenesis. Furthermore, our data suggest that the human genome encodes at least eleven non-canonical poly(A) polymerases with four FAM46 family members. Since FAM46 proteins are differentially expressed during development, these proteins may positively regulate transcript stability and translational rate in a tissue-specific manner.

overall_design: The H929 and SKMM1 MM cells were transduced with lentiviruses carrying FAM46CWTGFP (WT) or FAM46CD90A,D92AGFP (catalitic mutant). 72h after transgene delivery total RNA was extracted and RNA-seq libraries were prepared.

first: Seweryn

last: Mroczek

middle: M

last: Kulinski

first: Justyna

last: Chlebowska

first: Dominika

last: Nowis

first: Andrzej

last: Dziembowski


title: mRNA profiling of liver-specific RORa KO mouse liver

city: Seoul

first: Young Suk

last: Yu

address: 1-Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: The retinoic acid receptor-related orphan receptor a (RORa) is a member of the NR1 subfamily of orphan nuclear hormone receptors. RORa is an important regulator of various biological processes, including cerebellum development, cancer and circadian rhythm. To determine molecular mechanism by which hepatic deletion of RORa induces obesity and insulin resistance, we performed global transcriptome analysis from high-fat diet (HFD)-fed RORa f/f and RORa LKO mouse liver tissues. This analysis provides insight into molecular mechanisms for RORa in high-fat-diet condition.

overall_design: mRNA expression profiles of RORa f/f and RORa LKO mice liver with control diet or high-fat-diet were examined by Illumina HiSeq 2500.

middle: H

last: Baek

first: Young

middle: S

first: Kyeongkyu

last: Kim

first: Daehee

last: Hwang

first: Jinhyuk

last: Bhin


title: Comparative transcriptomic analysis of Gardnerella vaginalis biofilms versus planktonic cultures using RNA-seq

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

summary: Bacteria assume distinct lifestyles during the planktonic and biofilm modes of growth. In biofilms, they are more tolerant to antibiotics and can evade the immune system response more effectively. However, little is known regarding the molecular determinants involved in biofilm formation by Gardnerella vaginali, the predominant species found in bacterial vaginosis (BV). Hence, to gain insight into the pathogenesis of G. vaginalis, we carried out a comparative transcriptomic analysis between planktonic and biofilm phenotypes, using RNA-sequencing. The major alterations observed were related with the transcription of genes involved in cell wall biogenesis and typical stress factors, in which was found significantly up-regulated in biofilms, resulting in a protected mode of bacterial growth. In addition, biofilm phenotype was characterized by low metabolic activity, which is appropriate to guarantee long term survival during BV recurrence.

overall_design: Transcriptomic profile of G. vaginalis cultivated under biofilm and planktonic conditions

first: Joana

last: Castro

first: Angela

last: Franca

first: Katie

last: Bradwell

first: Myrna

last: Serrano

first: Kimberly

middle: K

last: Jefferson

first: Nuno

last: Cerca


title: Transcriptome profiles of moderate dysplasia in oral mucosa associated with malignant conversion

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

summary: Oral malignancies are among the top most deadly cancers in the world. Early diagnosis of oral premalignant and malignant lesions is essential for treatment decision-making and prognosis improvement. In this study, we systematically evaluated the gene expression patterns during the pathogenesis of oral moderate dysplasia. RNA sequencing detected 21556 genes in moderate dysplasia and paired normal tissues from three patients. Hierarchical clustering analysis revealed distinct gene expression patterns between the moderate dysplasia samples. 346 differentially expressed genes that may contribute to the pathogenesis of moderate dysplasia were identified. Among these genes, ISG15 and MAGEA family showed different transcription profiles that close related with the alterations of gene expression patterns in moderate dysplasia samples and paired normal tissues. We speculated that, as the potential marker to signal the risk of malignant transformation, ISG15 and MAGEA together with their close related misexpressed genes may involve in two different pathways during the malignant conversion from oral dysplasia to oral squamous cell carcinoma.

overall_design: six samples, including oral moderate dysplasia samples and paired normal samples from three patients

first: Jiali

last: Zhang

first: Si

first: Xinming


title: Hypoxia is a Key Driver of Alternative Splicing in Human Breast Cancer Cells

status: Public on Jun 27 2017

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: Adaptation to hypoxia, a hallmark feature of many tumors, is an important driver of cancer cell survival, proliferation and the development of resistance to chemotherapy. Hypoxia-induced stabilization of hypoxia-inducible factors (HIFs) leads to transcriptional activation of a network of hypoxia target genes involved in angiogenesis, cell growth, glycolysis, DNA damage repair and apoptosis. Although the transcriptional targets of hypoxia have been characterized, the alternative splicing of transcripts that occurs during hypoxia and the roles they play in oncogenesis are much less understood. To identify and quantify hypoxia-induced alternative splicing events in human cancer cells, we performed whole transcriptome RNA-Seq in breast cancer cells that are known to provide robust transcriptional response to hypoxia. We found 2005 and 1684 alternative splicing events including intron retention, exon skipping and alternative first exon usage that were regulated by acute and chronic hypoxia where intron retention was the most dominant type of hypoxia-induced alternative splicing. Many of these genes are involved in cellular metabolism, transcriptional regulation, actin cytoskeleton organisation, cancer cell proliferation, migration and invasion, suggesting they may modulate or be involved in additional features of tumorigenic development that extend beyond the known functions of canonical full-length transcripts.

overall_design: Human breast cancer MCF7 cells were subjected to 4h and 24h hypoxia treatment with a 24h normoxia control. RNA extraction was carried out using the RNeasy Mini kit and subjected to 90bp paired-end sequencing (BGI). Read mapping was conducted using STAR 95 with the human genome issue 19 (hg19) as the annotation library.

first: Jian

last: Han

first: Jolene

last: Ho

first: Grace

last: Chia

first: Hiroyuki

last: Kato

first: Sudhakar

last: Jha

first: Henry

last: Yang

first: Lorenz

last: Poellinger

first: Kian

middle: L

last: Lee


title: Transciptome profiling of NoDice and RNaseIII null cells prior to and after virus infection

first: Benjamin

last: tenOever

summary:
To assess the impact of endogenous RNaseIII nucleases on the overall transcriptome and the response to virus infection.
We utilized CRISPR techology to engineer an RNaseIII null cell line using the NoDice 293T parental strain generated in the Cullen lab as the parental cell line.

overall_design: mRNA profiles of 293T, NoDice 293T, and RNaseIII null cells alone or treated with SINV for 8 hours


title: Transcriptome analysis of 5 white Italian grapevine varieties during berry development

city: Verona

first: Mélanie

last: Massonnet

state: Verona

address: Strada Le Grazie, 15

department: Biotechnology Department

country: Italy

institute: University of Verona

summary: We report the berry pericarp transcriptomic profiles of 5 white Vitis vinifera varieties: Vermentino, Garganega, Glera, Moscato bianco and Passerina at 4 growth stages: pea-sized berries (Bbch 75) at almost 20 days after flowering, berries beginning to touch (Bbch77) just prior véraison, the softening of the berries (Bbch 85) at the end of véraison and berries ripe for harvest (Bbch 89)

overall_design: mRNA profiles of 5 white grapevine varieties at 4 growth stages were generated by deep sequencing, in triplicate, using Illumina Hiseq 1000.

first: Marianna

last: Fasoli

first: Giovanni

last: Tornielli

first: Mario

last: Altieri

first: Marco

last: Sandri

first: Paola

last: Zuccolotto

last: Paci

first: Massimo

last: Gardiman

first: Sara

last: Zenoni

last: Pezzotti


title: Effect of O-GlcNAc transferase deficiency on intestinal epithelial cells in mice

city: Minneapolis

first: Hai-Bin

last: Ruan

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

summary: O-GlcNAcylation is the modification of serine and threonine residues with beta-N-acetylglucosamine (O-GlcNAc) on intracellular proteins. To investigate the role of protein O-GlcNAcylation on intestinal homeostasis, we generated intestinal epithelial cell (IEC)-specific O-GlcNAc transferase (OGT) knockout in mice. The KO mice developed spontanous intestinal inflammation. To determine the underlying molecular mechanisms, we performed RNA sequencing of ileum and colon epithelial cells of wildtype and IEC-OGT KO mice.

overall_design: mRNA profiling of intestinal epithelial cells (IECs) from the ileum and colon of 10-week-old wildtype and IEC-OGT KO male mice.


title: Transcriptome response of Chlamydomonas reinhardtii exposed to inorganic or methylmercury

city: Versoix

first: Rebecca

last: Beauvais-Flueck

address: 10 route de Suisse - CP 416

department: Institut F.-A. Forel

institute: University of Geneva

summary:
This study aims at investigating the link between internalized inorganic or methyl Hg and the global expression of genes, obtained by high-throughput sequencing (RNA-Seq), in the microalga Chlamydomonas reinhardtii.
Algal cells were exposed two hours in a simplified artificial medium spiked with series of inorganic Hg concentrations (0.1, 1, 100 nM Hg) or series of methyl Hg concentrations (0.05, 0.5, 5, 50 nM CH3Hg).

overall_design: Three biological replicates were assessed for each of the 8 tested conditions: Control, 3 Hg concentrations, 4 CH3Hg concentrations.

first: Claudia

last: Cosio

first: Vera

middle: I

last: Slaveykova


title: Effect of MDK expressing Melanoma cells conditioned media in Human LEC

city: Madrid

first: David

last: Olmeda

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

summary: Gene expression analysis in hLECs treated with gain of function or loss of function of MDK in human melanoma cells.

overall_design: Biological triplicates of hLEC treated for 3 days with EGM-2 MV conditioned media of melanoma cells. Cell line SK-Mel-147 KD for MDK (shMDK) and its corresponding control (shCtrl (LoF) and WM164 cell line overexpressing MDK (MDK)  or an empty vector (NEG) (GoF) were used to produce the conditioned media.

first: D

first: O

last: Graña

first: M

last: Soengas


title: Zoledronic acid inhibits NFAT and IL-2 signaling pathways in regulatory T cells and diminishes their suppressive function in patients with metastatic cancer

status: Public on Jun 26 2017

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: In order to identify the processes altered in T regulatory cells (Treg) by Zoledronic acid (ZA), we examined RNA expression by RNA-seq in Treg treated with and without ZA. We identified gene expression alterations in ZA-treated Treg that were essential to Treg function.

overall_design: Human T regulatory cells isolated from healthy donors (n=6) were cultured overnight with IL-2 and OKT3 (anti-CD3) in the presence or absence of ZA. RNA sequencing (Illumina HiSeq2500) was performed to identify differential gene expression induced by ZA treatment of Treg.

first: Shannon

last: Murray

first: Dhifaf

last: Sarhan

first: Andreas

last: Lundqvist


title: Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis.

city: San Antonio

first: Rong

last: Li

state: TX

address: 7703 Floyd Curl Drive

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary: Most BRCA1-associated breast tumors are basal-like yet originate from luminal progenitor cells. BRCA1 is best known for its functions in DNA repair and resolution of DNA replication stress. However, it is unclear whether loss of these ubiquitously important functions of BRCA1 fully explains the cell lineage-specific increase in breast tumor development. Cell culture-based studies implicate BRCA1 in elimination of R-loops, DNA-RNA hybrid structures involved in transcriptional regulation and genetic instability. We found that BRCA1 mutation-associated R-loop accumulates preferentially in luminal epithelial cells of cancer-free human breast tissue, and at the 5' end of those genes that experience promoter-proximal RNA polymerase II (Pol II) pausing. Genetic ablation of mouse NELF-B/COBRA1, a Pol II-pausing factor and BRCA1-binding protein, in Brca1 knockout mouse mammary epithelium ameliorates R-loop accumulation and reduces mammary tumorigenesis. Our studies show that Pol II pausing is a previously unappreciated contributor to BRCA1-associated R-loop accumulation and breast cancer development.

overall_design: Normal breast tissue samples from four BRCA1 mutation carriers (B1) and four non-carriers (NC) were procured, digested into single cells, and sorted by flow cytometry using established cell surface markers (EpCAM and CD49f). Four distinct cell populations were acquired: stromal cells, basal epithelial cells, luminal progenitor cells (LP), and mature luminal epithelial cells (ML). Global R-loops were examined in each population. Global Pol II and NELF were examined in non-carrier patient unsorted normal breast tissue.

first: Xiaowen

last: Zhang

first: Huai-Chin

last: Chiang

first: Yao

last: Wang


title: Widespread translational remodeling during human neuronal differentiation

city: San Francisco

first: Stephen

middle: N.

last: Floor

address: 513 Parnassus Ave, HSW 740

department: Cell and Tissue Biology

institute: University of California, San Francisco

summary: Faithful cellular differentiation requires precise coordination of changes in gene expression. However, the relative contributions of transcriptional and translational regulation during human cellular differentiation are unclear. Here, we induced forebrain neuronal differentiation of human embryonic stem cells (hESCs) and characterized genome-wide RNA and translation levels during neurogenesis. We find that thousands of genes change at the translation level across differentiation without a corresponding change in RNA level. Specifically, we identify mTOR complex 1 signaling as a key driver for elevated translation of translation-related genes in hESCs. In contrast, translational repression in active neurons is mediated by transcript 3′ UTRs, through regulatory sequences. Together, our findings identify a functional role for the dramatic 3′ UTR extensions that occur during brain development, and provide insights to interpret genetic variants in post-transcriptional control factors that influence neurodevelopmental disorders and diseases.

overall_design: Forebrain neural cultures differentiated from human embryonic stem cells were isolated and cellular RNA, polysomal RNA, and ribosome protected footprints were deep sequenced.

first: John

middle: D

last: Blair

first: Dirk

last: Hockemeyer

first: Jennifer

last: Doudna

first: Helen

last: Bateup

middle: N


title: Golgi Outpost Synthesis Impaired by Toxic Polyglutamine Proteins Contributes to Dendritic Pathology in Neurons

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

summary: Dendrite aberration is a common feature of neurodegenerative diseases caused by protein toxicity, but the underlying mechanisms remain largely elusive. Here, we show that nuclear polyglutamine (polyQ) toxicity resulted in defective terminal dendrite elongation accompanied with a loss of Golgi outposts (GOPs) and decreased supply of plasma membrane (PM) in Drosophila Class IV da (C4da) neurons. mRNA sequencing revealed that down-regulated genes by polyQ proteins included many secretory pathway-related genes, including COPII genes regulating GOP synthesis. Transcription factor enrichment analysis identified CREB3L1/CrebA, which regulates COPII gene expression. CrebA overexpression in C4da neurons restored the dysregulation of COPII genes, GOP synthesis, and PM supply. The ChIP-PCR assay revealed that CrebA expression was regulated by CBP, which was sequestered by polyQ proteins. Furthermore, co-overexpression of CrebA and Rac1 synergistically restored the polyQ-induced dendrite pathology. Collectively, our results suggest that GOPs impaired by polyQ proteins contribute to dendrite pathology through the CBP-CrebA-COPII pathway.

overall_design: mRNA expression profiles of the heads of Drosophila melanogaster with or without expressing MJDtr-78Q were examined by Illumina Hi-seq 2500.

first: Sung

last: Lee

first: Daehee

last: Hwang


title: High-resolution TADs reveal DNA sequences underlying genome organization in flies

city: Freiburg

first: Thomas

last: Manke

address: Stuebeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Eukaryotic chromatin is partitioned into domains called TADs that are broadly conserved between species and virtually identical among cell types within the same species. Previous studies in mammals have shown that the DNA binding protein CTCF and cohesin contribute to a fraction of TAD boundaries. However, the relative importance of the role of epigenetic activity (like histone marks and transcription) over the genetic information (DNA sequence) in TAD formation is still not understood. Using our new software, HiCExplorer,  we annotated high-resolution (570 bp) TAD boundaries in flies and identified eight DNA motifs enriched at boundaries. Known insulator proteins bind five of these motifs while the remaining three motifs are novel. We find that boundaries are either at core promoters of active genes or at non-promoter regions of inactive chromatin and that these two groups are characterized by different sets of DNA motifs. In contrast to mammals, the CTCF motif is not a major boundary motif in flies, while the motifs identified by M1BP and Beaf32 are highly enriched on boundaries. Using refined in-situ Hi-C experiments and analysis in cells depleted of M1BP, we show that M1BP is a new boundary protein that is important for fly genome organisation. We demonstrate that boundaries can be accurately predicted using only the motif sequences at open chromatin sites. We propose that DNA sequence itself encodes chromosome folding by allocation of boundary proteins in the genome.  Finally, we present an interactive online database to access and explore the spatial organization of fly, mouse and human genomes, available at http://chorogenome.ie-freiburg.mpg.de.

overall_design: Hi-C on wild type S2 cells, knockdown of  GST (control), Beaf-32,  M1BP and a double knockdown of Beaf-32 and M1BP on Drosophila melanogaster S2 cell line.

first: Fidel

last: Ramírez

first: Vivek

last: Bhardwaj

first: Laura

last: Arrigoni

first: Bjöern

last: Grünning

first: Kin

last: Chung Lam

first: Asifa

last: Akhtar


title: Effects of arsenic and Pseudomonas aeruginosa infection on gene expression in human airway epithelial cells

city: Lebanon

first: Britton

last: Goodale

state: NH

address: 1 Medical Center Drive

department: Dartmouth Cancer Center

institute: Geisel School of Medicine at Dartmouth

summary:
Purpose: To determine effects of arsenic on gene expression in polarized primary human bronchial epithelial (HBE) cells and impact on transcriptional response to Pseudomonas aeruginosa infection
Methods: mRNA profiles of HBE cells from 6 donors exposed to 0, 5, 10 or 50 ug/L total arsenic +/- Pseudomonas aeruginosa (48 samples) were generated using Illumina sequencing, aligned in CLC Genomics workbench and analyzed for DE in EdgeR
Findings: 20-30 million reads were mapped per sample and transcripts were identifed that were significantly differentially expressed in response to arsenic and Pseudomonas aeruginosa

overall_design: Gene expression profiles of HBE cells from 6 donors exposed to three concentrations of arsenic +/- Pseudomonas were generated using mRNA sequencing

first: Bruce

last: Stanton


title: ChIP-seq of H3K27me3 in Asxl1 or Asxl2 KO mice

city: New York

first: Omar

last: Abdel-Wahab

address: 1275 York Ave.

department: Medicine

institute: Memorial Sloan Kettering Cancer Center

summary: The goals of this study are to identify H3K27me3 changes in Asxl1 or Asxl2 KO mice

overall_design: Examination of H3K27me3 modification in Asxl1 or Asxl2 KO mice

first: Daichi

last: Inoue

first: Amit

middle: U

last: Sinha


title: ChIP-seq of H3K27Ac in SKNO1 cells after knockdown of ASXL2

summary: The goals of this study are to identify the changes of H3K27Ac in SKNO1 cells after knockdown of ASXL2

overall_design: Examination of the changes of H3K27Ac in SKNO1 cells after knockdown of ASXL2


title: RNA-seq transcriptonal profiling in whole hippocampus in WT and Arid1b+/- mice

city: Dallas

first: Hao

last: Zhu

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

summary: There is growing evidence for the involvement of ARID1B, a SWI/SNF ATP-dependent chromatin remodeling subunit, in a broad range of human disorders. Sequencing studies have recurrently implicated ARID1B haploinsufficiency in autism spectrum disorder (ASD), non-syndromic intellectual disability (ID), corpus callosum agenesis, and short stature. In addition, ARID1B is by far the most common cause of Coffin-Siris Syndrome (CSS), a monogenic developmental delay syndrome characterized by a combination of the neuropsychiatric and physical abnormalities mentioned above. To understand how ARID1B mutations lead to these phenotypes, we generated Arid1b mutant mice, which exhibited physical manifestations of developmental delay and behaviors reminiscent of ASD. In the brain, Arid1b haploinsufficiency resulted in changes in the expression of SWI/SNF- regulated genes implicated in ASD.

overall_design: WT and Arid1b+/- hippocampus at P80

first: Cemre

last: Celen

first: Jen-Chieh

last: Chuang

first: Xin

last: Luo


title: RUNX1-ETO and RUNX1-EVI-1 differentially program the chromatin landscape in t(3;21) and t(8;21) AML but share global C/EBP-alpha dysfunction (RNA-Seq)

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: RUNX1 is a frequent target of translocations in acute myeloid leukemia whereby its DNA binding domain fuses to different epigenetic regulators. To assess how different RUNX1 fusion proteins interact with the epigenome we compared the global binding patterns and the chromatin landscape of t(8;21) and t(3;21) AML which express RUNX1-ETO and RUNX1-EVI-1, respectively. We found that differential prognosis for these types of AML is reflected in fundamental differences in gene expression, chromatin landscape, binding patterns of the fusion proteins and other transcription factors as identified by genome-wide digital footprinting in patients. As previously shown for RUNX1-ETO, knockdown of RUNX1-EVI-1 expression initiates differentiation of t(3;21) cells which is associated with up-regulation of genes vital for myeloid differentiation, including C/EBPα. Furthermore, by expressing either dominant-negative C/EBP or an inducible C/EBPα construct in t(3;21) cells we show that C/EBPα is necessary and sufficient for the differentiation response of these cells to RUNX1-EVI-1 knockdown.

overall_design: RNA-seq expreiments have been used to study the chromatin landscape of t(8;21) and t(3;21) AML

first: Justin

last: Loke

first: Maria

last: Imperato

first: Anetta

last: Ptasinska

first: Pierre

last: Cauchy

first: Manoj

last: Raghavan

first: H

last: Delwel

first: Peter

last: Cockerill

first: Olaf

last: Heidenreich

first: Constanze

last: Bonifer


title: RUNX1-ETO and RUNX1-EVI-1 differentially program the chromatin landscape in t(3;21) and t(8;21) AML but share global C/EBP-alpha dysfunction (DNase-Seq)

overall_design: DNAse1-seq expreiments have been used to study the chromatin landscape of t(8;21) and t(3;21) AML

middle: R


title: Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding [rice]

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

country: France

institute: IRHS

summary: We report the application of a high-throughput sequencing approach that is specifically designed to analyze the active mobilome of eukaryotes after simultaneous inhibition of RNA polymerase II and/or DNA methylation in O. sativa japonica. We found that the simultaneous inhibition of Pol II and DNA-methylation activated the evolutionary young Houba-Retrotransposon in O. sativa suggesting a crucial role of Pol II in regulating retrotransposition in plants.

overall_design: Comparison of the mobilomes in 10-day-old rice seedlings after inhibition of Pol II and/or DNA-methylation compared to control conditions.

first: Michael

last: Thieme

first: Sophie

last: Lanciano

first: Marie

last: Mirouze

first: Nicolas

last: Daccord

first: Sandrine

last: Balzergue


title: RUNX1-ETO and RUNX1-EVI-1 differentially program the chromatin landscape in t(3;21) and t(8;21) AML but share global C/EBP-alpha dysfunction

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

overall_design: Refer to individual Series


title: Molecular characterization of human osteoblast-derived extracellular vesicle mRNA using next-generation sequencing

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we present the comparative transcriptome analysis of human osteoblasts and their corresponding EVs using next-generation sequencing. We demonstrate that osteoblast-EVs are specifically depleted of cellular mRNAs that encode proteins involved in basic cellular activities, such as cytoskeletal functions, cell survival and apoptosis. In contrast, EVs are significantly enriched with 254 mRNAs that are associated with protein translation and RNA processing. Moreover, mRNAs enriched in EVs encode proteins important for communication with the surrounding cells, in particular with osteoclasts, adipocytes and hematopoietic stem cells. Strikingly, EVs are particularly enriched with RAB13 mRNA, which is linked to vesicular trafficking. The latter suggests that EVs may affect vesicle production in target cells. These findings provide the foundation for understanding the molecular mechanism and function of EV-mediated interactions between osteoblasts and the surrounding bone microenvironment.

overall_design: Simian virus 40-immortalized human osteoblast cells (SV-HFO cells) were cultured for fourteen days and EV isolated. Total and EV RNA was isolated using TRIzol reagent, and mRNA/miRNA-Seq was performed as described.

first: Andre

last: van Wijnen

first: Amel

last: Dudakovic


title: RUNX1-ETO and RUNX1-EVI-1 differentially program the chromatin landscape in t(3;21) and t(8;21) AML but share global C/EBP-alpha dysfunction (ChIP-Seq)

first: Salam

last: Assi

overall_design: ChIP-seq expreiments have been used to study the chromatin landscape of t(8;21) and t(3;21) AML

first: Justin

middle: C

last: Loke

first: Maria

last: Imperato


title: Protein chaperones elicit a caloric restriction-like response to extend replicative lifespan

city: Split

first: Anita

last: Krisko

address: Mestrovicevo setaliste 45

country: Croatia

institute: Mediterranean Institute for Life Sciences

summary: The involvement of protein chaperones in aging is intriguing and their potential contribution has, so far, been attributed solely to their central role in proteostasis. Here we show that four protein chaperones from different cellular compartments extend replicative lifespan (RLS) in budding yeast by a common mechanism akin to caloric restriction. The RLS extension relies on the increased direct activation of Snf1 kinase by Hsp90, thereby bypassing the signal on the environmental glucose level. The chaperone-related RLS extension is accompanied by the uncoupling of the respiratory chain. A genomic approach confirmed the repression of glycolysis and cytoplasmic translation, and contrary, activation of gluconeogenesis and fatty acid oxidation. Our results set a novel paradigm for the role of protein chaperones: by modulation of the chaperone expression level one can affect metabolic features such as glucose sensing, fatty acid consumption, respiration rate, and, consequently, modify lifespan. We expect the described mechanism to open new avenues for research in aging and age-related diseases.

overall_design: mRNA sequencing in 4 different strains of budding yeast; overexpressing LHS1, SSC1, TCP1 and EGD2; 3 replicates for each, 2 replicates for EGD2

first: Kristian

last: Vlahovicek

first: Nuno

last: Raimundo


title: ATAC-seq of AML1-ETO9 leukemias

first: Omar

last: Abdel-Wahab

summary: The goals of this study are to identify ASXL2 binding sites in SKNO1 cells

overall_design: Examination of chromatin accessbility in AML1ETO9a leukemia with or without ASXL2

first: Amit

last: Sinha


title: ChIP-seq of ASXL2 in SKNO1 cells

overall_design: Examination of ASXL2 binding sites in SKNO1 cells


title: ChIP-seq of H3K27me3 in SKNO1 cells after knockdown of ASXL2

summary: The goals of this study are to identify the changes of H3K27me3 in SKNO1 cells after knockdown of ASXL2

overall_design: Examination of the changes of H3K27me3 in SKNO1 cells after knockdown of ASXL2


title: RNA-seq of ASXL2 shRNA KD in SKNO-1 cells

summary: The goals of this study are to compare transcriptome profiling (RNA-seq) of Asxl2 knockdowned SKNO-1 cells to control SKNO-1 cells. We found substantial number of genes are differentially expressed in Asxl2 knockdowned cells.

overall_design: SKNO-1 mRNA profiles of ASXL2 knockdowned and control cells were generated by deep sequencing, two differrent shRNA for ASXL2, in triplicate.


title: RNA-seq of primary patient AML samples

summary: The goals of this study are to compare transcriptome profiling (RNA-seq) of patients BM with or without ASXL2 mutations.

overall_design: Patient bone marrow mRNA profiles with or without ASXL1/2 mutations were generated by deep sequencing


title: Novel SF3B1 Deletion Mutations Result in Aberrant RNA Splicing in CLL Patients

city: Cambridge

first: Silvia

last: Buonamici

address: 300 Technology Square #5

institute: H3 Biomedicine

summary: Recurrent mutations in RNA splicing factors SF3B1, U2AF1, and SRSF2 have been reported in hematologic cancers including myelodysplastic syndromes (MDS) and chronic lymphocytic leukemia (CLL). However, SF3B1 is the only splicing associated gene to be found mutated in CLL and has been shown to induce aberrant splicing. To investigate if any other genomic aberration caused similar transcriptome changes, we clustered RNASeq samples based on an alternative 3’ splice site (ss) pattern previously identified in SF3B1-mutant CLL patients. Out of 215 samples, we identified 37 (17%) with alternative 3’ ss usage, the majority of which harbored known SF3B1 hotspot mutations. Interestingly, 3 patient samples carried previously unreported in-frame deletions in SF3B1 around K700, the most frequent mutation hotspot. To study the functional effects of these deletions, we used various minigenes demonstrating that recognition of canonical 3’ ss and alternative branchsite are required for aberrant splicing, as observed for SF3B1 p.K700E. The common mechanism of action of these deletions and substitutions result in similar sensitivity of primary cells towards splicing inhibitor E7107. Altogether, these data demonstrate that novel SF3B1 in-frame deletion events identified in CLL result in aberrant splicing, a common biomarker in spliceosome-mutant cancers.

overall_design: 13 CLL samples, 5 SF3B1 WT, 5 SF3B1 p.K700E, and 3 with in-frame deletions around the K700 position of SF3B1

last: Seiler


title: RNA-seq and ChIP-seq data of ASXL1/2 in Hematopoiesis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: P-bodies regulate transcriptional rewiring to promote DNA replication stress resistance

city: Toronto

first: Raphael

last: Loll-Krippleber

state: Ontario

address: 160 College street

department: Biochemistry

country: Canada

institute: University of Toronto

summary:
mRNA processing bodies (P-bodies) are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study, we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant down-regulation of a network of genes critical for DNA replication stress resistance. Among these genes we identify ALD6, whose de-repression is critical to prevent accumulation of acetaldehyde, a strongly toxic molecule during DNA replication stress.

This SuperSeries is composed of the SubSeries listed below.

overall_design: See GSE83455 and GSE83454 SubSeries for specific experimental design information.


title: Transcript profiling of Saccharomyces cerevisiae cells overexpressing YOX1 before and after 2 and 4 hours of hydroxyurea (HU) treatment (200 mM)

summary: mRNA processing bodies (P-bodies) are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study, we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant down-regulation of a network of genes critical for DNA replication stress resistance. Among these genes we identify ALD6, whose de-repression is critical to prevent accumulation of acetaldehyde, a strongly toxic molecule during DNA replication stress.

overall_design: WT containing pBY011 (control) or pBY011-YOX1 vectors were cultured in synthetic medium containing raffinose as unique carbon source. Cultures were then treated with hydroxyurea (HU) at a final concentration of 200 mM and galactose was added at the same time to induce YOX1 overexpression. Samples were collected before and after 2 and 4h of galactose induction and hydroxyurea treatment. Experiment was repeated twice.

first: Grant

middle: W

last: Brown


title: Transcript profiling of WT and lsm1∆ Saccharomyces cells before and after 1, 2 and 4 hours of hydroxyurea treatment (200 mM)

overall_design: WT and lsm1∆ cells were cultured in YPD. Sample were taken before and after 1, 2 and 4 hours of treatment with hydroxurea at a final concentration of 200 mM. Experiment was repeated twice.


title: Transcriptome analysis of mRNA and microRNA in the cestodes Echinococcus granulosus and Echinococcus multilocularis

city: Beijing

first: xiaosu

last: zhou

address: Dong Dan San Tiao 9

institute: Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: The cestodes Echinococcus granulosus and Echinococcus multilocularis, as the pathogens of cystic echinococcosis and alveolar echinococcosis respectively, can cause significant health problems to the host and considerable socio-economic losses as a consequence. Based on the genomic data regarding these two species available in public database recently, we carried out high-throughput mRNA and small RNA transcriptomic sequencing of them and generate enormous transcriptomic datasets. A total of 34,717,856 reads (79.79%) mapped to E. granulosus genome, and 38,882,179 reads (87.61%) mapped to E. multiloculari genome. A total of 24,550 (7,925 known and 16,625 novel transcripts) and 23,771 transcripts (8,432 known and 15,339 novel transcripts) were assembled for E. granulosus and E. multilocularis respectively, and the assembly yielded 11,330 genes (6,815 known and 4,515 novel genes) for E. granulosus and 10,101 genes (7,051 known and 3,050 novel genes) for E. multilocularis, compared with the reference genome data. Bioinformatic analysis identified 6,826 AS events from 3,774 E. granulosus genes (33.31%) and 6,644 AS events in 3,611 E. multilocularis genes (35.75%). A total of 76,674 distinct microRNAs of E. granulosus and 115,742 of E. multilocularis were also obtained from small RNA transcriptome sequencing reads. Of these, there were 20 microRNAs of E. granulosus and 22 microRNAs of E. multilocularis that belonged to 19 and 21 microRNA families common to other metazoan lineages separately. 76 and 90 novel microRNAs so far unique to E. granulosus and E. multilocularis were also identified respectively. This study represents an extensive mRNA and small RNA transcriptome dataset obtained from the deep sequencing of these two cestode species. The findings will facilitate a more fundamental understanding of cestode biology, evolution, the host-parasite interplay, and provide new insights into the pathophysiology of echinococcosis, contributing to the development of improved interventions for disease control.

sample_organism:
Echinococcus granulosus
Echinococcus multilocularis

overall_design:
small RNA trancriptmomes of the two species were generated by deep sequencing, in duplicate, using Illumina HiSeq™ 2000 instrument.
mRNA trancriptmomes of the two species were generated by deep sequencing, in duplicate, using Illumina HiSeq™ 2000 instrument.

first: Xiaosu

last: Zhou

first: Shuai

last: Liu

first: Qijun

last: Chen


title: CDYL ChIP-Seq in mouse hippocampus

status: Public on Jun 25 2017

first: yongqing

last: liu

address: 38 Xue Yuan Road

department: Department of Biochemistry and Molecular Biology

institute: Peking University Health Science Center

summary: Here we report that the epigenetic factor Chromodomain Y-like (CDYL) protein is a critical regulator for the initiation and maintenance of activity-dependent intrinsic neuroplasticity. Genome-wide ChIP-sequencing analysis revealed that CDYL regulates multiple neuronal functional pathways including voltage-gated ion channels in mouse brains. We showed that CDYL binds to a regulatory element in the intron region of SCN8A and mainly recruits H3K27me3 activity for transcriptional repression of the gene. Injection of lentivirally-delivered CDYL shRNA to rat hippocampal neurons resulted in augmented Nav1.6-mediated sodium currents, lower neuronal threshold and increased seizure susceptibility, whereas transgenic mice over-expressing CDYL had higher neuronal threshold and were less prone to epileptogenesis. Finally, examination of human brain tissues revealed decreased expression of CDYL and increased expression of SCN8A in the temporal lobe epilepsy group. Together, our findings indicate CDYL is a critical player for experience-dependent gene regulation in controlling intrinsic excitability, which potentially contributes to learning and memory and CNS disorders involving change in activity such as epilepsy.

overall_design: Examination of epigenetic factor CDYL in mouse hippocampus.

first: Yongqing

first: Jing

last: Liang


title: ChIP-seq of H3K4me1 and H3K4me3 in SKNO1 cells after knockdown of ASXL2

summary: The goals of this study are to identify the changes of H3K4me1 and H3K4me3 in SKNO1 cells after knockdown of ASXL2

overall_design: Examination of the changes of H3K4me1 and H3K4me3 in SKNO1 cells after knockdown of ASXL2


title: Sox11 expression in adult retina promotes regeneration of some ganglion cell types but kills others

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: At least 30 types of retinal ganglion cell (RGC) send distinct messages through the optic nerve to the brain. Strategies for promoting regeneration of RGC axons following injury act on only some of these types. Here we tested the hypothesis that over-expressing developmentally important transcription factors in adult RGCs could reprogram them to a “youthful” growth-competent state and promote regeneration of other types. From a screen of transcription factors expressed by developing RGCs, we found one, Sox11, that induced substantial axon regeneration. Transcriptome profiling confirmed that Sox11 activates genes involved in cytoskeletal remodeling and axon growth. Remarkably, alpha-RGCs, which preferentially regenerate following treatments such as PTEN deletion, were killed by Sox 11. Thus, Sox 11 promotes regeneration of non-alpha RGCs, which are refractory to PTEN. We conclude that Sox11 can reprogram adult RGCs to a growth-competent state and that different growth-promoting interventions act on distinct neuronal types.

overall_design: We compared transcriptomes of retinal ganglion cells between AAV-Control retinas, and retinas treated with AAV-Sox11 overexpression. We then performed optic nerve crush, and 3 days later purified RGCs using FACS. RGCs were marked with Thy1-PE-Cy7 antibody and with live/dead cell staining. We performed sample preparations in full triplicate, and in each replicate we always performed Control and Sox11 on the same day, in alternating order.

first: Michael

last: Norsworthy

first: Fengfeng

last: Bei

first: Chen

last: Wang

first: Qing

first: Benedikt

last: Brommer

first: Joshua

last: Sanes

first: Giovanni

last: Coppola

first: Zhigang

last: He


title: RNA-seq of Asxl2 KO LSK cells

first: Omar

last: Abdel-Wahab

summary: The goals of this study are to compare transcriptome profiling (RNA-seq) of Asxl2 KO LSK cells to that of Asxl2 wild-type cells. We found substantial number of genes are differentially expressed in Asxl2 KO cells.

overall_design: LSK mRNA profiles of Asxl2-/- mice and Asxl2wt/wt (WT)  were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Amit

last: Sinha


title: Genome-wide comparative transcriptome profiling of two contrasting chilling tolerant rice genotypes in response to early chilling stress

city: Nanning

first: Jijing

last: Luo

state: Guangxi

address: 100 Daxue Rd.(East)

institute: Guangxi University

summary: To understand the molecular mechanisms underlying chilling tolerance in rice, transcriptomic deep sequencing was performed to reveal the differentially expressed genes between chilling tolerance chromosome substitution line (CSL), DC90 and its chilling-sensitive recurrent parent 9311 under early chilling stress events. Our results revealed a set of DEGs with higher basal expression in DC90 by comparison with 9311. They were functionally enriched in GO terms, such as, response to stress, response to stimulus, and response to abiotic stimulus, suggesting their positive role in intrinsic chilling tolerance. Common up-regulated and down-regulated DEGs were enriched in 26 and 34 GO terms, including response to stimulus, response to stress, and response to abiotic stimulus, respectively. Furthermore, comparative transcriptomic analysis between DC90 and 9311 in response to early chilling stress revealed 502 DEGs specifically identified in DC90. Most of gene loci were located beyond introgressed regions, implying that the introgression led to reprogramming of transcriptome in response to early chilling stress. CARMO platform analysis of these DEGs presented a complex regulatory network, including phytohormone signaling, photosynthesis pathway, that coordinately involved in chilling tolerance response of DC90. Here, the unveiled molecular regulatory network shed light on deep understanding the mechanisms of rice chilling tolerance. As well, chilling tolerant-QTLs and co-localized DEGs in introgressed fragments, will be focused for further functional investigation of the molecular mechanisms of early chilling stress response in rice.

overall_design: Transcriptomic profiling of DC90 and 9311 (YD6) were performed by RNA sequencing using Illumina Hiseq platform

first: Yongliang


title: To identify redox-dependent global regulator WhiB4 binding sites on Mycobacterium tuberculosis genome

status: Public on Jun 24 2017

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

institute: Institut Pasteur

summary: We have performed ChIP-Seq experiment for the redox-dependent global regulator WhiB4 in Mtb.

overall_design: To understand the influence of WhiB4, we over-expressed FLAG-tagged WhiB4 in Mtb.

first: Manbeena

last: Chawla

first: Saurabh

last: Mishra

first: Aswin

last: Seshasayee


title: PRC2 specifies ectoderm lineages and maintains pluripotency in primed but not naïve ESCs

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: Polycomb repressive complex 2 and the epigenetic mark that it deposits, H3K27me3, are evolutionarily conserved and play critical roles in development and cancer. However, their roles in cell fate decisions in early embryonic development remain poorly understood. Here we report that knockout of polycomb repressive complex 2 genes in human embryonic stem cells causes pluripotency loss and spontaneous differentiation toward a meso-endoderm fate, owing to de-repression of BMP signalling. Moreover, human embryonic stem cells with deletion of EZH1 or EZH2 fail to differentiate into ectoderm lineages. We further show that polycomb repressive complex 2-deficient mouse embryonic stem cells also release Bmp4 but retain their pluripotency. However, when converted into a primed state, they undergo spontaneous differentiation similar to that of hESCs. In contrast, polycomb repressive complex 2 is dispensable for pluripotency when human embryonic stem cells are converted into the naive state. Our studies reveal both lineage- and pluripotent state-specific roles of polycomb repressive complex 2 in cell fate decisions.

overall_design: We compared the transcriptome of deletion of core components of PRC2 in human embryonic stem cells and their wildtype counterparts by RNA-Seq.

first: Yongli

last: Shan

first: Qianyu

last: Chen

first: Guangjin

last: Pan

first: Juan

last: Du

first: Zhongzhou

last: Yang

first: Andrew

last: Hutchins


title: Global transcriptome analysis of WT versus HEB-/- hESCs

first: Yang

last: Li

address: Xueyuan Road 38,Haidian District

institute: Peking University

summary: To examine genome-wide changes in mRNA expression, we performed RNA-Seq on HEB-/- and WT hESCs. There were 274 significant changes in mRNA expression (p<0.05) between HEB-/- and WT hESCs; 126 transcripts were lower and 148 transcripts were higher

overall_design: mRNA profiles of  wild type (WT) and HEB-/- hESCs were generated by RNA sequencing, in triplicate, using Illumina GAIIx.

first: Michele

last: Anderson

last: Zúñiga-Pflücker


title: Altered gene expression by C1orf106 in papillary thyroid cancer cells

status: Public on Jun 23 2017

first: Weiwei

last: Liang

address: 58 Zhongshan Road II

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: Chromosome 1 open reading frame 106 (C1orf106) has been shown to be elevated in lung adenocarcinoma. However, its expression and function in papillary thyroid cancer (PTC) are totally unknown. To explore the role of C1orf106 in PTC, we analyzed the gene expression in TPC1 cells with or without C1orf106 overexpression.

overall_design: The mRNA profiles of TPC1-Vector and TPC1-C1orf106 cells were generated by sequencing, in duplicate, using an Illumina HiSeq 4000.

first: Hongyu

last: Guan

first: Yan

last: Guo

first: Yanbing


title: Dynamic and stable enhancer-promoter contacts regulate terminal differentiation

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Drive, CCSR 2150

institute: Stanford University

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

overall_design: Refer to individual Series


title: Gene expression profiles of Hes1 positive retinal subsets

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

summary: To analyze Mueller glia specific gene expression, Hes1-promoter-dEGFP mice was used. dEGFP positive and negative retinal fractions were purified by a cell sorter and subjected to RNA-seq

overall_design: Examination of mRNA expression patterns in Hes1-positive (Hes1P) retinal cells and Hes1-negative (Hes1N) retinal cells at 2 developmental timepoints.

first: Kazuko

last: Ueno


title: Ontogeny of alveolar macrophages is a critical determinant of function during lung fibrosis [RNA-seq]

city: Chicago

first: Alexander

last: Misharin

state: IL

address: 240 E Huron M-300

department: Medicine - Pulmonary

institute: Northwestern University Feinberg School of Medicine

summary: Little is known about the relative importance of monocyte and tissue-resident macrophages in the development of lung fibrosis. We show that specific genetic deletion of monocyte-derived alveolar macrophages after their recruitment to the lung ameliorated lung fibrosis, whereas tissue-resident alveolar macrophages did not contribute to fibrosis. Using transcriptomic profiling of flow-sorted cells, we found that monocyte to alveolar macrophage differentiation unfolds continuously over the course of fibrosis and its resolution. During the fibrotic phase, monocyte-derived alveolar macrophages differ significantly from tissue-resident alveolar macrophages in their expression of profibrotic genes. A population of monocyte-derived alveolar macrophages persisted in the lung for one year after the resolution of fibrosis, where they became increasingly similar to tissue-resident alveolar macrophages. Human homologues of profibrotic genes expressed by mouse monocyte-derived alveolar macrophages during fibrosis were up-regulated in human alveolar macrophages from fibrotic compared with normal lungs. Our findings suggest that selectively targeting alveolar macrophage differentiation within the lung may ameliorate fibrosis without the adverse consequences associated with global monocyte or tissue-resident alveolar macrophage depletion.

overall_design: Monocytes, interstitial macrophages, and alveolar macrophages separated by high or low expression of Siglec F were isolated from Casp8flox/flox at 14 and 19-21 days following bleomycin-induced fibrosis and Siglec F high alveolar macrophages were isolated from naïve mice. The same experiment was repeated for CD11cCreCasp8flox/flox and LysMCreCasp8flox/flox mice and was repeated without naïve mice for CD11cCreCasp8flox/floxRIPK3-/- and LysMCreCasp8flox/floxRIPK3-/- mice.  Donor and recipient alveolar macrophages were isolated 10 months following bleomycin injury from bone marrow chimeras. Transcriptome analysis was performed. Experiments were performed with 2-5 replicates.

middle: V

first: GR

last: Budinger

first: Harris

last: Perlman

last: Reyfman

first: Kishore

last: Anekalla

first: Stacy

last: Marshall

first: Vince

last: Morgan


title: Type I IFNs and TNF Cooperatively Reprogram Epigenomic Landscape of Human Macrophages to Promote Inflammatory Activation [RNA-seq]

first: Lionel

last: Ivashkiv

address: 535 E 70th St

institute: Hospital For Special Surgery

summary: Crossregulation of TLR responses by cytokines is essential for effective host defense, avoidance of toxicity, and homeostasis, but underlying mechanisms are not well understood. A comprehensive approach integrating RNA-seq, ChIP-seq and ATAC-seq digital footprinting showed that TNF and type I IFNs extensively remodel chromatin states in human macrophages to differentially regulate transcriptional induction of NF-κB, STAT, antiviral, and metabolic genes by LPS. IFN-α potentiated TNF inflammatory function by abrogating feedback silencing of inflammatory genes via priming of chromatin to enable robust transcriptional responses to weak upstream signals. Similar chromatin regulation occurred in human diseases. Our findings provide insights into epigenomic mechanisms by which cytokines reprogram inflammatory responses, and identify new functions and mechanisms of action of TNF and IFNs.

overall_design: Analysis of transcriptional changes in human macrophages stimulated with or without TNF and LPS

first: Sungho

last: Park


title: HPIP controls osteoarthritis cartilage degeneration  [RNA-seq]

first: Quanbo

last: Ji

address: #28, Fuxing Road.

institute: The 301 hospital

summary: To underly the potential downstream transcriptional regulation of HPIP that could account for cartilage and skeletal development. RNA-seq analysis were performed in HPIP knockout and control primary chondrocytes.Among the 1271 significantly differentially expressed genes, transcripts for 486 (7%) of them were upregulated while transcripts for 785 (11%) were downregulated in HPIP knockout  chondrocytes compared to the controls. We found HPIP was closely correlated with the cartilage development.

overall_design: Total RNA was isolated with TRIzol from the HPIP knockout and the control primary chondrocytes. Complementary DNA library were prepared and then sequenced by Novel Bioinformatics Co, Ltd (https://en.novogene.com/). Clean reads was obtained from the raw reads by removing the adaptor sequence before read mapping. Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl). HTSeq V0.6.1 was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the genes reads count mapped to this gene. Differential expression analysis was performed using the DESeq R package (1.10.1).

first: J

last: Chris


title: Molecular link between leaf coloration and gene expression of flavonoid and carotenoid biosynthesis in Camellia sinensis cultivar ‘Huangjinya’

city: Nanjing

first: Qingping

last: Ma

state: Jiangsu

address: Weigang No. 1

institute: Nanjing Agricultural University

summary: The transcriptome of a light sensitive tea cultivar ‘Huangjinya’ plants exposed to sunlight and shade were analyzed by high-throughput sequencing followed by de novo assembly.

overall_design: Comparison of the ‘Huangjinya’ under sunlight and shading.

first: Lubin

last: Song

first: Xinghui

last: Li


title: An erythroid-specific enhancer of ATP2B4 mediates red blood cell hydration and malaria susceptibility [RNA-seq]

city: Montreal

first: Guillaume

last: Lettre

state: Québec

address: 5000 rue Bélanger

institute: Montreal Heart Institute

summary: Few genotype-phenotype associations identified by genome-wide association studies (GWAS) have been defined mechanistically, precluding thorough assessment of their impact on human health. We conducted an expression quantitative trait loci (eQTL) mapping analysis in human erythroblasts and found erythroid-specific eQTLs for ATP2B4, the main calcium ATPase of red blood cells (RBC). The same SNPs were previously associated with mean corpuscular hemoglobin concentration (MCHC) and susceptibility to severe malaria infection. We showed that Atp2b4-/- mice demonstrate increased MCHC, confirming ATP2B4 as the causal gene at this GWAS locus. Using CRISPR-Cas9, we fine-mapped the genetic signal to an erythroid-specific enhancer bound by GATA1 and TAL1. These results illustrate the importance to combine transcriptome, epigenome, and genome editing approaches in phenotype-relevant cells to characterize non-coding regulatory elements associated with human complex diseases and traits. Our studies suggest ATP2B4 as a potential target to modulate RBC hydration in erythroid disorders and malaria infection.

overall_design: mRNA profiles of fetal (N=12) and adult (N=12) erythroblasts were generated by RNA-sequencing with an Illumina HiSeq2000 sequencer using stranded cDNA library and a paired-ends 100 bp protocol.

first: Samuel

last: Lessard

first: Emily

last: Stern

first: Mélissa

last: Beaudoin

first: Patrick

middle: G

last: Schupp

first: Falak

last: Sher

first: Syed

middle: A

last: Ali

first: Sukhpal

last: Prehar

first: Ryo

last: Kurita

first: Yukio

last: Nakamura

first: Esther

last: Baena

first: Jonathan

last: Ledoux

first: Delvac

last: Oceandy

first: Daniel

middle: E

last: Bauer


title: Type I IFNs and TNF Cooperatively Reprogram Epigenomic Landscape of Human Macrophages to Promote Inflammatory Activation [ChIP-seq]

city: New York

first: Lionel

last: Ivashkiv

first: Sungho

last: Park


title: Mechanistic roles of microRNAs in hepatocarcinogenesis: A study of thioacetamide with multiple doses and time-points of rats

city: Jefferson

first: Yuping

last: Wang

state: AR

address: 3900 NCTR RD

department: National Center for Toxicological Research

institute: Food and Drug Administration

summary:
Environmental chemicals exposure are one of the primary factors for liver toxicity and hepatocarcinoma. Thioacetamide (TAA) is a well-known hepatotoxicant and could be a liver carcinogen in humans.The discovery of early and sensitive biomarkers in liver injury and tumor progression could improve cancer diagnosis, prognosis, and management.

In the present study, we studied the dynamic changes in microRNAs (miRNAs) expression and explored the potential mechanistic role of miRNAs in rat liver treated with TAA at multiple doses and time points. Sprague-Dawley rats were administrated with TAA at three doses [low (4.5 mg/kg), middle (15mg/kg) and high (45mg/kg)] and four repeated treatment durations (3-, 7-, 14- and 28-days). Expressions of miRNAs in livers were profiled using next generation sequencing and analyzed.

Overall, 330 unique differentially expressed miRNAs (DEMs) were identified in the entire TAA-treatment course. Of these, 129 DEMs were found significantly enriched for the “liver cancer” annotation. These results were further complemented by pathway analysis in which “Molecular Mechanisms of Cancer”, “p53-”, “TGF-β-”, “MAPK-” and “Wnt-signaling” were significantly enriched in most TAA-treatment conditions. Two miRNAs (rno-miR-34a-5p and rno-miR-455-3p) out of 48 DEMs (common across all the treatment conditions) were identified to be early and sensitive biomarkers for TAA-induced hepatocarcinogenicity. Upregulation of rno-miR-34a-5p was further confirmed by qPCR.

These findings reveal the critical role of miRNAs in the mechanisms underlying hepatocarcinogenesis and potential application for human risk assessment. Most importantly, rno-miR-34a-5p is the most suitable early and sensitive biomarker for TAA-induced hepatocarcinogenesis due to its consistent elevation during the entire treatment course.

overall_design: The animal study was conducted as described previously (Uehara 2011). Briefly, male Sprague-Dawley (SD) rats were consecutively administered with TAA once daily at doses of 4.5 (low dose), 15 (middle dose), or 45 (high dose) mg/kg for 3, 7, 14, and 28 days (referred as 3-d, 7-d, 14-d and 28-d hereafter) with the time-matched control group receiving vehicle alone.

first: Weida

last: Tong

first: Binsheng

last: Gong


title: m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

city: Bar Harbor

first: Shengdong

last: Ke

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: HeLa cell chromatin associated nascent pre-mRNA (CA-RNA) contains many unspliced introns and m6A in exons, but very rarely in introns. m6A methylation of exons in CA-RNA frequently occur before splicing of exons and is essentially completed upon the release of mRNA into the nucleoplasm. m6A modifications are virtually the same in the newly synthesized CA-RNA, nucleoplasmic mRNA in transit and in the steady state cytoplasmic mRNA. This result suggests quantitatively little cytoplasmic methylation or demethylation. Only ~10% of m6As in CA-RNA are within 50 nucleotides of 5' or 3' splice sites arguing against a common splicing function of methylation. Both HeLa and mouse embryonic stem cell mRNAs showed a distinct increase of m6As, some in clusters, in short-lived mRNAs. Thus there is an unanticipated observation that m6A is added to exons presumably coincident with or soon after exon definition in nascent pre-mRNA, linking nuclear methylation to cytoplasmic mRNA stability.

overall_design: Precise mapping m6A sites in human HeLa cells (CA-RNA, nucleoplasmic RNA and cytoplasmic RNAs) and mouse embryonic stem (ES) cells by m6A-CLIP/IP (briefly m6A-CLIP); mRNA half-life quantification by Actinomycin-D treatment and followed with RNA-Seq at different time points with biological replicates in mouse ES cells; RNAseq of HeLa CA-RNA (Ribo 0), nucleoplasmic RNA (Ribo 0), cytoplasmic RNA (Ribo 0) and cytoplasmic RNA (polyA+)

first: James

last: Darnell Jr

first: Robert

middle: B

last: Darnell


title: hnRNP C is a key regulator of protein synthesis in mitosis

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary:
Purpose: The goal of this study is to characterize the role of hnRNP C in translation regulation of a specific set of mRNAs during mitosis.
Methods: mitotic HeLa S3 cells expressing a Dox-inducible shRNA against hnRNP C were used and profiles of total mRNAs and ribosome footprints (RFs) of either untreated (wild type) cells or hnRNP C-knockdown cells were generated by deep sequencing, using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to a reference set of human curated protein‐coding transcripts (plus the five human rRNA transcripts) using bowtie2. Expression estimates were further normalized using quantile normalization. qRT–PCR validation was performed using SYBR Green assays.
Results: RNA‐seq and Ribo/RF‐seq datasets were combined according to gene ID. Only genes with expression level of at least 1.0 RPKM in both datasets were included in subsequent analyses. The combined dataset includes 10,996 genes. Transcripts encoding components of the translation machinery (Gene Ontology Biological Process [GOBP] “Translation” annotation) show reduced ribosome occupancy during mitosis under hnRNP C knockdown (p-value = 1.07 x 10-13) although their total mRNA levels are increased (p-value = 1.78 x 10-5). Translation efficiency (TE) calculations of ribosome occupancy per mRNA level showed a statistically-significant reduction for mRNAs encoding ribosomal proteins (Gene Ontology Cellular Compartment [GOCC] “Ribosome” annotation; p-value = 9.92 x 10-12). In particular, the TE of 5’ TOP-containing mRNAs was found to be significantly reduced under hnRNP C knockdown (p-value = 5.16 x 10-4).
Conclusions: Our study represents the first detailed analysis of the translation effeciency of mRNAs in wild type and hnRNP C knockdown HeLa S3 cells during mitosis using RNA-Seq and Ribo-Seq. Our results show that the translation of a specific subset of mRNAs (5' TOP mRNAs) is regulated by hnRNP C in mitosis.

overall_design: Profiles of total mRNAs and RFs of either wild type or hnRNP C knockdown cells in mitosis were generated by deep sequencing Illumina HighSeq 2500.

first: Ranen

last: Aviner


title: Genome-wide maps of chromatin state during the differentiation of hESC into hNECs

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine


title: A highly clonogenic subset of adult mouse biliary duct cells

city: Portland

first: Bin

last: Li

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Oregon Stem Cell Center

institute: Oregon Health and Science University

summary: Our goal is to find the heterogeneity of mouse liver ductal cells in the wild type mouse liver. We separated the MIC1-1C3+ mouse liver ductal cells into two populations with the cell surface marker: ST14. We found that ST14hi1C3+ cells have higher colonal geneity comparing to the ST14lo1C3+ population.

overall_design: Mouse liver NPCs were sorted by flowcytometry. The MIC1-1C3+CD26- non blood cells are seperated into two parts: ST14high and ST14low. Fresh sorted cells are put into TRIzol for RNA. RNA seq libraries were made with illumina TruSeq kit under the manufacture's protocol.

first: Markus

last: Grompe

first: Carl

last: Pelz


title: Genome-wide maps of chromatin state during the differentiation of hESC into hNECs (MNase-Seq)

summary: To study the epigenetic regulation during neuroectoderm specification process, we generated in-depth maps of nucleosome and histone modifications.We found that the depletion of nucleosome marked with H2A.Z in promoter regions contributes to the activation of key neuroectoderm related genes as providing open chromatin state for Pol II binding. Meanwhile, HMs undergo active remodeling with recruiting key transcription factors.So our study provided a full view on the transcriptional regulation of epigenome during neuroectoderm specification.

overall_design: Examination of nucleosome positioning, four classical histone marks(H3K4me3,H3K9ac,H3K27me3,H3K36me3), binding profiles of transcription factor Sox2 for hESC and hNEC.

first: Cizhong

last: Jiang

first: Yanhua

last: Du


title: Alloantigen-Induced Regulatory T Cells Generated in Presence of Vitamin C Display Enhanced Stability of Foxp3 Expression and Promote Skin Allograft Acceptance

status: Public on Jun 22 2017

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

summary: Regulatory T cells (Tregs) are critical for the maintenance of immune homeostasis and self‑tolerance, and can be therapeutically used for prevention of unwanted immune responses such as allotransplant rejection. Tregs are characterized by the expression of the transcription factor Foxp3, and recent work suggested that epigenetic imprinting of Foxp3 and other Treg‑specific epigenetic signatures genes is crucial for the stabilization of both Foxp3 expression and immunosuppressive properties within Tregs. Lately, Vitamin C was reported to enhance the activity of enzymes of the ten‑eleven‑translocation family, thereby fostering the demethylation of Foxp3 and other Treg‑specific epigenetic signatures genes in developing Tregs. Here, we in vitro generated alloantigen‑specific Foxp3+ Tregs (allo‑iTregs) in presence of vitamin C, and those Tregs showed a pronounced demethylation of Foxp3 and other Treg‑specific epigenetic signatures genes, accompanied with an enhanced stability of Foxp3 expression. However, RNA‑seq analysis revealed an only minor impact of Vitamin C on the transcriptome of allo‑iTregs. Importantly, when being tested in vivo in a highly immunogenic skin transplantation model vitamin C‑treated allo‑iTregs showed a superior suppressive capacity as compared to allo‑iTregs generated in absence of vitamin C. Together, our results might pave the way for the establishment of novel protocols for the in vitro generation of allo‑antigen specific Foxp3+ Tregs for therapeutic usage in transplantation medicine.

overall_design: FACS sorted allo-iTregs (CD4+CD90.2+Foxp3RFP+) from cultures in presence or absence of vitamin C

first: Eirini

last: Nikolouli

first: Jochen

last: Huehn


title: Sin3a regulates epithelial progenitor cell fate during lung development

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

summary: Comparison of global transcription profiles in mouse E12.5 embryonic lung from Shh-Cre;Sin3a flox/+ control with Shh-Cre;Sin3a flox/flox revealed a large change genes due to loss of Sin3a in early lung development.

overall_design: Examination of 2 different transcriptomes in 2 genotypes with three replicates.

first: Gianni

last: Carraro

first: Bindu

last: Konda

first: Xiangrong

last: Guan

first: Takako

last: Mizuno

first: Norika

last: Chiba

first: Mathew

last: Kostelny

first: Adrianne

last: Kurkciyan

first: Gregory

last: David

first: Jonathan

last: McQualter

first: Barry

last: Stripp


title: Genome-wide maps of chromatin state during the differentiation of hESC into hNECs (ChIP-Seq)

first: yanhua

last: du


title: Analysis of gene expression changes in early mouse embryos lacking Tgif1 and Tgif2

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: We report the differences in gene expression between wild type and Tgif1;Tgif2 double null mouse embryos at approximately 9.0 days after fertilization.

overall_design: Stage matched individual mouse embryos at approximately 9.0 days after fertilization (~9-10 somites) were analyzed by RNA-seq. We analyzed four wild type embryos and eight conditional double mutant embryos, lacking both alleles of Tgif1 and both Tgif2 alleles.

first: Anoush

last: Anderson


title: Expression profiling of lncRNAs, miRNAs and mRNAs and their differential expression in leiomyoma using next generation RNA sequencing

city: Torrance

first: Tsai-Der

last: Chuang

state: California

address: 1124 WEST CARSON STREET

department: OB-GYN

institute: LA Biomed at UCLA medical center

summary: Total RNA was isolated from leiomyoma and paired myometrium (N=8) and samples from three pairs were subjected to RNA sequencing. After analysis, 5941 lncRNAs (2813 up- and 3128 down-regulated at ≥1.5 fold), 148 miRNAs (56 up- and 96 down-regulated at ≥1.5 fold) and 3855 mRNAs (2030 up- and 1855 down-regulated at ≥1.5 fold) were differentially expressed in leiomyomas. Using QRT-PCR we further confirmed the expression of HULC, lnc-MEG3, LINC00890, TSIX, LINC00473, lnc-KLF9-1 and lnc-POTEM-3 (lncRNA-ATB) in leiomyoma and matched myometrium (N=8). Our results presented here provide a comprehensive expression profile of lncRNAs in leiomyomas with concurrent integrated expression of miRNAs and mRNAs in leiomyomas.

overall_design: Identify the expression profile of lncRNAs with concurrent assessment of miRNAs and mRNAs profiles in leiomyomas and paired myometrium using next generation RNA sequencing

first: Omid

last: Khorram


title: The histone acetyltransferase Mst2 prevents epigenetic silencing via specific acetylation of the ubiquitin ligase Brl1 [NGS data]

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: Faithful propagation of distinct chromatin states is crucial to maintain cellular identity. Whereas mechanisms that sustain repressed states have been intensely studied, regulatory circuits that protect active chromatin from inactivating signals are not well understood. Here we report the discovery of a self-reinforcing feedback loop that preserves the transcription-competent state of RNA polymerase II transcribed genes. We found that the chromatin reader Pdp3 recruits the histone acetyltransferase Mst2 to H3K36me3 marked chromatin. Thereby, Mst2 binds to all transcriptionally active regions genome-wide. Besides histone H3K14, Mst2 specifically acetylates Brl1, a component of the histone H2B ubiquitin ligase complex (HULC). Brl1 acetylation results in increased histone H2B ubiquitination, which together with H3K14ac positively feeds back on transcription and prevents assembly of ectopic heterochromatin. Our work uncovers a molecular pathway that secures epigenome integrity and highlights the importance of opposing feedback loops for the partitioning of chromatin into transcriptionally active and inactive states.

overall_design: The study comprises of 5 small RNAs and 3 RNA sequencing data sets from cells expressing a ade6-cox4 hairpin construct that gives rise to siRNAs against endogenous mutant ade6 and a second functional ade6 reporter gene. Experiments were performed in wt and paf1-Q264Stop and paf1Q264Stop,mst2D mutant, brl1-K242R, and brl1-K242R,mst2D cells. Furthermore, we conducted RNA-Seq from cells with the same ade6-cox4 hairpin construc in WT, pdp3D and mst2D cells.

first: Valentin

last: Flury

first: Paula

last: Georgescu

first: Vytautas

last: Iesmantavicius

first: Yukiko

last: Shimada

first: Tahsin

last: Kuzdere

first: Sigurd

last: Braun

first: Marc

last: Bühler


title: The histone acetyltransferase Mst2 prevents epigenetic silencing via specific acetylation of the ubiquitin ligase Brl1

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Human oocyte DNA methylome

city: Bronx

first: Bo

last: Yu

state: NY

address: 1300 Morris Park Ave, Block 621

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: We used single-cell WGBS to profile DNA methylomes of human oocytes at different maturation stages

overall_design: Single oocytes in GV, MI, MII stages from different individuals


title: EPCR Expression Defines the Most Primitive Subset of Human HSPC and Is Required for Their In Vivo Activity

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: Cell purification technology combined with whole transcriptome sequencing and small molecule agonist of hematopoietic stem cell self-renewal has allowed us to identify the endothelial protein c receptor protein (EPCR) as a surface maker that defines a rare subpopulation of human cells which is highly enriched for stem cell activity in vivo. EPCR-positive cells exhibit a robust multi-lineage differentiation potential and serial reconstitution in immunocompromised mice. In culture, most if not all of the HSC activity is detected in the EPCR+ subset, arguing for the stability of this marker on the surface of cultured cells, a feature not found with more recently described markers such as CD49f. Functionally EPCR is essential for human HSC activity in vivo. Cells engineered to express low EPCR expression proliferate normally in culture but lack the ability to confer long-term reconstitution. EPCR is thus a stable marker for human HSC. Its exploitation should open new possibilities in our effort to understand the molecular bases behind HSC self-renewal.

overall_design: Examining 3 cellular subsets: EPCR+, EPCRlow, EPCR- derived form CD34+CD45RA- cord blood cells after 7 day expansion in UM171

first: Iman

last: Fares


title: Transient Hes5 activity instructs mesodermal cells toward a cardiac fate

city: Boston

first: avinash

last: waghray

state: MA

address: 185 Cambridge Street, CPZN Room 4254A

department: Center for Regenerative Medicine

institute: Massachussets General Hospital

summary: Notch signaling plays a role in specifying a cardiac fate but the downstream effectors remain unknown. In this study we implicate the Notch downstream effector HES5 in cardiogenesis. We show transient Hes5 expression in early mesoderm of gastrulating embryos and demonstrate, by loss and gain-of-function experiments in mouse embryonic stem cells, that HES5 favors cardiac over primitive erythroid fate. Hes5 overexpression promotes upregulation of the cardiac gene Isl1, while the hematopoietic regulator Scl is downregulated. Moreover, whereas a pulse of Hes5 instructs cardiac commitment, sustained expression after lineage specification impairs progression of differentiation to contracting cardiomyocytes. These findings establish a role for HES5 in cardiogenesis and provide insights into the early cardiac molecular network.

overall_design: ChIP-Seq was performed on the indicated cell lines.

first: Ana

last: Freire

first: Avinash

last: Waghray

first: Perpétua

last: Pinto-do-Ó

first: Ihor

last: Lemischka


title: RNA-sequencing of human post-mortem brain tissues

city: Huntsville

first: Kevin

last: Bowling

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute

summary: RNA-seq profiling was conducted on clinically-annotated human post-mortem brain tissues

overall_design: We measured the transcriptome in 281 clinically-annotated human post-mortem brain tissues

middle: M

first: Ryne

last: Ramaker

first: Brittany

last: Lasseigne

first: Sara

middle: J

last: Cooper

first: Richard

last: Myers


title: Transcriptomes of enriched mouse islet alpha cells

status: Public on Jun 21 2017

city: DALLAS

first: WEN-HONG

last: LI

state: Texas

address: 6000 Harry Hines Blvd.

department: Department of Cell Biology

institute: UT Southwestern Medical Center

summary:
Glucagon supports glucose homeostasis by stimulating
hepatic gluconeogenesis, in part by promoting the uptake and conversion of amino acids into gluconeogenic precursors. Genetic disruption or pharmacologic inhibition of glucagon signaling results in elevated plasma amino acids and compensatory glucagon hypersecretion involving expansion of pancreatic a cell mass. Recent findings indicate that hyperaminoacidemia triggers pancreatic a cell
proliferation via an mTOR-dependent pathway. We confirm and extend these findings by demonstrating that glucagon pathway blockade selectively increases expression of the sodium-coupled neutral
amino acid transporter Slc38a5 in a subset of highly proliferative a cells and that Slc38a5 controls the pancreatic response to glucagon pathway blockade; most notably, mice deficient in Slc38a5 exhibit markedly decreased a cell hyperplasia to glucagon pathway blockade-induced hyperaminoacidemia. These results show that Slc38a5 is a key component of the feedback circuit between glucagon receptor
signaling in the liver and amino-acid-dependent regulation of pancreatic a cell mass in mice.

overall_design: Examination of the transcriptomes of islet non-beta-cells of GcgR knock out mice.

first: Yan

last: Xu

first: Zhi-Jiang

last: Huang

first: Qing

last: Liu

first: Wen-Hong

last: Li


title: Gene expression and 4sUDRB-seq for NF90/NF110 of human scramble and KD HeLa cells.

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: We have optimized the metabolic tagging of newly transcribed RNAs by 4-thiouridine (4sU) to identify newly-transcribed (nascent) circRNAs from human HeLa cells.

overall_design: Poly(A)+ RNA-seq for gene expression, ribo–/poly(A)– for steady-state circRNA, Ribo– 4sUDRB-seq for characterizing nacent circRNA biogenesis and iCLIP-seq of NF90 for RNA binding analysis.

first: Wei

last: Xue

first: Xiang

first: Chu-Xiao

first: Jia

last: Wei

first: Ling-Ling

last: Chen


title: A structural “toggle” in the RNaseH domain of Prp8 helps balance splicing fidelity and catalytic efficiency

city: Ithaca

first: Jeffrey

last: Pleiss

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

summary:
Purpose: To assess the global impacts of RNaseH domain alleles of Prp8 on the in vivo splice site selection for native introns.
Conclusions: Our study reveals functional links between distinct spliceosomal conformations and splicing fidelity.

overall_design: Lariat sequencing of PRP8 WT and four mutants in the RNaseH domain of Prp8 in the background of Δdbr1 to profile global locations of splice site activation and compare aberrant activation rate across the five strains. Two additional lariat sequencing libraries were prepared as technical replicates for a second biological sample of strain prp8-N1869D to assess the technical reproducibility of the method.

first: Madhura

last: Raghavan

first: Nicholas

last: Stepankiw


title: RNA-Seq analysis of Caulobacter crescentus wild-type and delta_hfq (CJW5477) strains

city: West Haven

first: Irnov

last: Irnov

state: Connecticut

address: 840 West Campus Drive

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

summary: We report the global changes in the gene expression profile of Caulobacter crescentus in the absence of Hfq.

overall_design: Transcriptomic profiles were generated from cultures grown in PYE until exponential phase at 30C

first: Christine

last: Jacobs-Wagner


title: Deep evolutionary conservation of autism-related genes

first: Michael

middle: C.

last: Saul

address: 600 Main St

institute: The Jackson Laboratory

summary: E.O. Wilson proposed in Sociobiology that similarities between human and animal societies reflect common mechanistic and evolutionary roots. When introduced in 1975 this controversial hypothesis was beyond science’s ability to test and remains unproven. We used genomic analyses to determine whether superficial behavioral similarities in humans and the highly social honey bee reflect common molecular mechanisms. Here we report that gene expression signatures for individual bees unresponsive to various salient social stimuli are significantly enriched for autism spectrum disorder-related genes. These signatures occur in the mushroom bodies, a high-level integration center of the insect brain. Further, our finding of enrichment was unique to autism spectrum disorders; brain gene expression signatures from other honey bee behaviors do not show this enrichment, nor do data sets from other human behavioral and health conditions. These results demonstrate deep conservation for genes associated with a human social pathology and individual differences in insect social behavior, thus providing an example of how comparative genomics can be used to test sociobiological theory.

overall_design: In this experiment, we sequenced a total of 36 mushroom body samples. Seven-day-old worker bees from two single-drone-inseminated (SDI) colonies were chosen for sequencing From each colony, we sequenced the whole transcriptome from the mushroom body of six worker bees from each of three different behavioural types: nurses, guards, and unresponsive bees. Thus, a total of 12 mushroom body samples for each behavioural type and a total of 18 samples from each colony were sequenced.

first: Hagai

middle: Y

last: Shpigler

first: Frida

last: Corona

first: Lindsey

last: Block

first: Amy

last: Cash-Ahmed

first: Gene

last: Robinson


title: Deletions in the ATAD3 gene cluster cause cerebellar developmental defects with mitochondrial DNA abnormalities owing to local cholesterol insufficiency

city: London

first: ian

middle: james

last: holt

address: 1 Midland Road

institute: Crick Institute

summary: The DNA in mitochondria is associated with the inner of two membranes and it co-fractionates with the limited amount of cholesterol in the organelles. However, the effects of mitochondrial cholesterol deficiency are largely unknown, and mitochondrial disorders relating to this area of cell metabolism have not been reported hitherto. Using detailed SNP array analysis we have identified patients with impaired cerebellar development and neurological dysfunction who have large deletions in the locus encoding the ATAD3A, ATAD3B and ATAD3C genes. Patient cells with inherited ATAD3 defects display aberrant mitochondrial DNA organization and synthesis associated with disrupted cholesterol metabolism. Moreover drug-induced perturbations of cholesterol metabolism cause mitochondrial DNA disorganization in control cells. The interdependence of mitochondria and cholesterol homeostasis is further corroborated by the presence of mitochondrial DNA aggregation in the genetic cholesterol trafficking disorder Niemann Pick type C disease. Thus, we conclude, mitochondria are fully integrated in the circuitry of cellular cholesterol homeostasis, in which ATAD3 plays a critical role, and the dual problem of perturbed cholesterol homeostasis and mitochndrila dysfunction may be widespread in neurological and neurodegenerative diseases.

overall_design: We designed the experiment to compare the expression profiles of cells carrying deletions in the ATAD3 gene cluster (ATAD3CAS & ATAD3F) with that of a normal control cell line. Because we suspected that cholesterol metabolism would be altered by ATAD3 deficiency we also prepared RNA from the same three cell lines treated with a drug, pravastatin, that inhibits the rate limiting step of cholesterol synthesis, to determine if the drug produced similar effects on gene expression to ATAD3 deficiency. In practice, pravastatin had almost no signficant effects (FDR 0.05) on any of the cells and none related to cholesterol homeostasis, indicating the drug does not act at the level of gene expression. This proved convenient as two RNA samples from ATAD3CAS failed QC, but the ATAD3CAS + pravastatin versus control (with or without pravastatin) provided additional replicates and displayed almost identical differences to ATAD3CAS (no drug) vs Control.

first: Radha

last: Desai

first: Ann

last: Frazier

first: Romina

last: Durigon

first: Harshil

last: Patel

first: Ilaria

last: Rosa

first: Nicole

last: Lake

first: Alice

last: Mitchell

first: Deb

last: Jackson

first: Abdul

middle: K

last: Sesay

first: Miriam

last: Re

first: Johannes

last: Spelbrink

first: Derek

last: Burke

first: George

last: McGillivray

first: Simone

last: Mandelstam

first: Alison

last: Compton

first: Hayley

last: Mountford

first: David

last: Francis

first: Fanny

last: Mochel

first: Boris

last: Keren

first: Claude

last: Jardel

first: Anne

last: Turner

first: Lambert

middle: P

last: van den Heuvel

first: Jan

last: Smeitink

first: Simon

last: Heales

last: Lombès

first: Ian

last: Holt

last: Thorburn

first: Antonella

last: Spinazzola


title: Differentially expressed genes during pancreatic bud differentiation in cellular aggregates

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: Analysis of pathways altered by aggregation culture during differentiation from pancreatic progenitor cells into pancreatic bud cells. The hypothesis tested in the present study was that the high-cell density culture induces specific signals to facilitate the differentiation into pancreatic bud cells. Results provide the differentially regulated pathways between the low-cell density cultures and the high-cell density cultures.

overall_design: Total RNA obtained from human ES cell-derived pancreatic progenitor cells subjected to differentiate into pancreatic bud cells. The pancreatic progenitor cells were cultured at the low-cell density or in the cellular aggregates. Samples were obtained 0, 1, 2, 3 and 4 days after culturing.

first: Taro

last: Toyota

first: Masahiro

last: Nakamura

first: Chihiro

last: Okada

first: Kenji

last: Osafune


title: Genome-Wide Direct Target Identification Reveals the transcriptional regulatory Framework of WOX11 in Root Development in Rice

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: WUSCHEL-related homeobox domain trancription factor WOX11 is a key regulator of crown root growth and development in rice (Oryza sativa. L). However, the gene regulatory network downstream of WOX11 remains largely unknown. To dissect WOX11 transcriptional regulatory framework, we determined the transcriptome of wox11 mutants and corresponding wild type (Hwayoung) by using RNA-seq technology.

overall_design: Genome-wide analysis of root tip transcriptome of wox11 mutant and corresponding wild type.

first: S

last: Zhou

first: J

last: Wei

first: Y

last: Zhao