title: Dual RNA-sequencing of nontypeable Haemophilus influenzae and host cell transcriptomes reveals new aspects of host-pathogen interface

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: Characterization of host-pathogen interactions is critical for the development of next-generation therapies and vaccines. Classical approaches involve the use of transformed cell lines and/or animal models which may not reflect the complexity and response of the human host. We reconstituted the ciliated human bronchial epithelium in vitro using primary bronchial epithelial cells to simultaneously monitor the infection-linked global changes in nontypeable Haemophilus influenzae (NTHi) and infected host epithelia gene expression by dual RNA-seq. Acquisition of a total of nearly 2,5 billion sequences allowed construction of high-resolution strand-specific transcriptome maps of NTHi during infection of host mucosal surface and monitoring of metabolic as well as stress-induced host-adaptation strategies of this pathogen. As a part of our screening, we identified a global profile of noncoding transcripts that are candidate small RNAs regulated during human host infection in Haemophilus species. Temporal analysis of host mRNA signatures revealed significant dysregulation of target cell cytoskeleton elicited by bacterial infection, with a profound effect on intermediate filament network of bronchial epithelium. Our data provide a robust and comprehensive catalogue of regulatory responses that drive NTHi pathogenesis and gives novel insights into complex crosstalk between the host and the invading pathogen.

sample_organism:
Haemophilus influenzae
Homo sapiens

platform_organism:
Haemophilus influenzae
Homo sapiens

overall_design: Primary human bronchial epithelium was infected with NTHi at a multiplicity of 100:1. Total RNA was isolated at 1, 6, 24 and 72 h post-infection in three biologically-independent experiments and cDNA libraries were prepared and sequenced with Illumina HiSeq 2500 sequencer. At each time point, between 60 and 180 million total reads per sample were obtained of which approximately one-third could be aligned to non-rRNA regions of the bacterial and human genomes

first: Buket

last: Baddal

first: Alessandro

last: Muzzi

first: Stefano

last: Censini

first: Giulia

last: Torricelli

first: Silvia

last: Guidotti

first: Anna

middle: R

last: Taddei

first: Antonello

last: Covacci

first: Mariagrazia

last: Pizza

first: Rino

last: Rappuoli

first: Marco

last: Soriani

first: Alfredo

last: Pezzicoli


title: Ikaros mediates gene silencing in T cells through Polycomb Repressive Complex 2

status: Public on Nov 03 2015

city: Illkirch

first: Attila

last: Oravecz

address: 1 rue Laurent Fries

country: France

institute: IGBMC

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide sequences bound by the transcription factors BLUEJAY and JACKDAW in Arabidopsis thaliana roots

status: Public on Nov 02 2015

city: Pozuelo de Alarcon

first: Miguel

middle: Angel

last: Moreno-Risueno

state: Madrid

department: Biotechnology

country: Spain

institute: Center for Plant Biotechnology and Genomics

summary: We report the genomic sequences bound by the C2H2 transcription factors BLUEJAY and JACKDAW as profiled by chromating immunoprecipitation experiments followed by Illumina high sequencing. Plants were carrying constructs of proteins (translational) fusions of these transcription factors to the yellow fluorescent protein.  Gene fusions were expressed under all their genomic regulatory regions using recombineering. The recombineering technique was used to recombine the fluorecent protein at the 3' end of their genomic regions in a JATY clone carrying these genes. Subsequently the JATY clones carrying these translational fusions were introgressed into plants. We performed ChIP on roots grown under standard conditions and fixed with formaldehyde in PBS-EDTA. Sequences bound by BLUEJAY and JACKDAW were immunoprecipitated with a-GFP AbCam290 at 4 °C overnight. Biological replicate samples were make into libraries of ~100 bp insert size and 50 bp of single ends sequenced through Illumina High Sequencing.

overall_design: Two biological replicates of samples of plants expressing the C2H2 transcription factors fused to the yellow fluorescent protein; and of control wild type plants processed through the same protocol.

first: Philip

last: Benfey


title: Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-RRBS

status: Public on Nov 01 2015

city: Moscow

first: Alexander

middle: S.

last: Tanas

address: Moskvorechie St., 1

country: Russia

institute: Research Centre for Medical Genetics

type: Methylation profiling by high throughput sequencing

summary: We describe XmaI-RRBS method for rapid and affordable genome-wide DNA methylation analysis, with library preparation taking only four days and sequencing possible within four hours. Small sizes of the XmaI-RRBS libraries allow their multiplexing and sequencing on the benchtop high-throughput machines. Described here is the first RRBS protocol validated for the Ion Torrent Personal Genome Machine.

overall_design: DNA from MCF7 cell line and 6 normal breast samples (total 7 samples) were subjected to reduced representation bisulfite sequencing analysis (XmaI-RRBS) by using Ion Torrent platform.

middle: S

first: Vladimir

middle: V

last: Strelnikov


title: JMJD1C is required for the survival of acute myeloid leukemia by functioning as a co-activator for key transcription factors

city: New York

first: Mo

last: Chen

state: NY

address: 1230 York Avenue

country: USA

institute: Rockefeller University

type: Expression profiling by high throughput sequencing


title: RNA expression analysis upon JMJD1C depletion

summary: The AML1-ETO fusion protein, a transcription factor generated by the t(8;21) translocation in acute myeloid leukaemia (AML), dictates a leukemic program by increasing self-renewal and inhibiting differentiation.  Here we demonstrate that the histone demethylase JMJD1C functions as a co-activator for AML1-ETO and is required for its transcriptional program. JMJD1C is directly recruited by AML1-ETO to its target genes and regulates their expression by maintaining low H3K9me2 levels. Analyses in JMJD1C knockout mice also establish a JMJD1C requirement for AML1-ETO’s ability to increase proliferation. We also show a critical role for JMJD1C in the survival of multiple human AML cell lines, suggesting that it is required for leukemic programs in different AML cell types through its association with key transcription factors.

overall_design:
Examination of RNA expression when Kasumi-1 cells are treated with control shRNA or two different JMJD1C shRNAs; in duplicate.
Please note that the 'shAML1_ETO_vs_shControl.all_gene_exp.tb.txtl' was generated comparing control and shRNA treated RNA abundance-using previously published data [GSE43834; GSM1071857 and GSM1071852].

first: Robert

middle: G

last: Roeder


title: The transcriptome of Serratia sp. ZM under different concentrations of (NH4)2SO4

city: shanghai

first: Pei

middle: Hai

last: yan

address: No. 130, meilong road, Shanghai

country: China

institute: East China University of Science and Technology

summary: The RNA-seq technique aims to identify genes that are differently expressed in low nitrogen (2mM (NH4)2SO4) and high nitrogen (10mM (NH4)2SO4) conditions.

overall_design: Two groups of Serratia sp. ZM were analysed by us, low nitrogen group and high nitrogen group.

first: HaiYan

last: Pei

first: LiMing

last: OuYang


title: The genomic foundation of heterotrophy to photoautotrophy transition in Oleaginous Chlorella

city: Shanghai

first: Jianhua

last: Fan

address: 130 Meilong Road

institute: East China University of Science & Technology

summary: The understanding of molecular events occurring in Chlorella during heterotrophy to photoautotrophy transition as well as sudden light stress and glucose starvation, are still largely unknown. To well grasp its cellular metabolism, particularly the regulation of biosynthesis and degradation pathways of lipid, protein and carbohydrates, as well as the diverse trophic adaptation affecting carbon partitioning during heterotrophy to photoautotrophy transition process, we sequenced the transcriptome (RNA-seq) in six time points to discover how transcriptional changes in C. pyrenoidosa modulate metabolic flux trends leading to intracellular components dynamic reassortment.

overall_design: Three independent biological experiments (biological replicates) were carried out in the same batch. In total, eighteen samples collected at six time points (0-, 24-, 72-h from heterotrophic cells and 2-, 8-, 24-h from phototrophic cells) were used for mRNA-Seq library preparation and then submitted to Solexa GA-IIx (Illumina, USA) for sequencing.

first: Kang

last: Ning

first: Jian

last: Xu

first: Yuanguang

last: Li


title: Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes [RNA-Seq P21]

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary:
Purpose: This study was carried out to determine the consequences of the Rfx2-/- genotype on spermatogenesis in the mouse
Methods: RNA was extracted from decapsulated testes of 21 day old mixed background mice of either genotype. Deep sequencing was used to determine quantitative expression of the genomes from independent replicates of each genotype
Results: RNA-Seq analysis identified some 105 genes that are down regulated at least 2-fold in Rfx2-/- testes, with ~50 being reduced at least 10-fold
Conclusion: Spermatogenesis undergoes complete arrest just prior to the end of the round spermatid period of sperm development in mutant mice. Sequencing results showed that approximately 105 genes were downregulated 2 fold or more in the testes of mutant mice. Comparison of similar studies of targeted mutations in genes for other transcription factor demonstrate that Rfx2 has a large and nearly unique set of genes that depend on it directly or indirectly. A large number of downregulated genes are identified with cilia function.

overall_design: Testicular mRNA profiles were determined by deep sequencing using testes from 5 independent wild type and 6 independent Rfx2-/- mice

first: W

last: S Kistler

first: Dominique

last: Baas

last: Lemeille

first: Marie

last: Paschaki

first: Emmanuèle

last: Barras

first: Wenli

last: Ma

first: Jean-Luc

last: Duteyrat

first: Laurette

last: Morlé

first: Bénédicte

last: Durand

first: Walter

last: Reith


title: Retroviral Replicating Vectors Deliver Cytosine Deaminase Leading to Targeted 5-FU-Mediated Cytotoxicity in Multiple Human Cancer Types

city: Foster City

first: Daniel

last: Hogan

state: California

address: private address

summary: Toca 511 is a modified Retroviral Replicating Vector based on Moloney g‑retrovirus with an amphotropic envelope. As an investigational cancer treatment, Toca 511 preferentially infects cancer cells without direct cell lysis and encodes an enhanced yeast cytosine deaminase that converts the antifungal drug 5‑fluorocytosine to the anticancer drug, 5-fluorouracil. A panel of established human cancers cell lines, derived from glioblastoma, colon, and breast cancer tissue was used to evaluate parameters critical for effective anticancer activity. As part of these analyses, we profiled relative mRNA levels across these cell lines via RNA sequencing.

overall_design: mRNA expression profiles across nine human cancer cell lines.

middle: J

first: Derek

last: Ostertag


title: G9a is essential for epigenetic silencing of K+ channel genes in acute-to-chronic pain transition

city: Philadelphia

first: matteo

last: cesaroni

state: PA

address: 3307 N. Broad S, Rm 220, PAHB

institute: Temple University

summary:
AIM: We performed RNA-sequencing experiments seeking genes whose expression changed due to nerve injury. In addition, we wanted to test whether inhibition of the methyl transferase G9a/GLP, that methylates H3K9me2, could reverse those expression changes due to nerve ligation. G9a/GLP methylase was pharmacologically inhibited using UNC0638.
METHOD: We generated cDNA libraries from RNA purified from DRGs obtained from Sham operated (4), SNL (4), and SNL plus UNC0638 (3) rats. We sequenced the cDNA libraries generating single end 50 bp reads on the illumina HiSeq 2500 platform. Sequencing reads were aligned to the rat genome rn4 using TopHat
RESULTS: We were able to map 16876 genes, from which 2035 changed their expression values at least two fold when we compared SNL to Sham operated (p≤ 0.01). There were 1205 upregulated and 832 down-regulated genes. Next, we focused on genes whose expression was either up or down-regulated 2 fold due to nerve ligation, and the values would be normalized to control level after G9a/GLP inhibito (UNC0638)r treatment. We identified 639 genes in our data set that behave this way

first: Matteo

last: Cesaroni

first: Judit

last: Garriga

first: Geoffroy

last: Laumet


title: RNA-Sequencing shows novel transcriptomic signatures in failing and non-failing human heart

city: Naples

first: Valerio

last: Costa

state: Italy

address: Via P. Castellino, 111

department: Institute of Genetics and Biophysics

institute: National Research Council

summary: The knowledge of an expression network signature in end-stage heart failure (HF) diseased hearts may offer important insights into the complex pathogenesis of advanced cardiac failure, as well as it may provide potential targets for therapeutic intervention. In this study, the NGS sequencing of RNA (RNA-Seq) method was employed to obtain the whole transcriptome of cardiac tissues from transplant recipients with advanced stage of HF. The analysis of RNA-Seq data presents novel challenges and many methods have been developed for the purpose of mapping reads to genomic features and quantifying gene expression. The main goal of this work was to identify, characterize and catalogue all the transcripts expressed within cardiac tissue and to quantify the differential expression of transcripts in both physio- and pathological conditions through whole transcriptome analyses. Expression levels, differential splicing, allele-specific expression, RNA editing and fusion transcripts constitute important information when comparing samples for disease related studies. Analysis methods for RNA-Seq data are continuing to evolve. Thus, in order to find the best solution for filter generated list of differentially expressed genes, an informatic approach of NOISeq BIO method has been applied in this RNA-Seq analysis. Most of the genes obtained by filtering differentially expressed gene list, have been experimentally validated by Real time RT-PCR. Noteworthy, these findings provide valuable resources for further studies of the molecular mechanisms involved in heart ischemic response thus leading to potential novel biomarkers and targets for therapeutic intervention in the onset and progression of cardiomyopathies.

overall_design: Heart biopsies from candidates for solid organ transplantation were collected and their RNA samples were used for high-throughput sequencing purposes. Libraries were sequenced on the Illumina HiSeq2000 NGS platform.

first: Concetta

last: Schiano

first: Amelia

last: Casamassmi

first: Marianna

last: Aprile

first: Monica

last: Rienzo

first: Roberta

last: Esposito

first: Alfredo

last: Ciccodicola

first: Claudio

last: Napoli


title: The Candida albicans regulator ZCF21 controls the expression of cell wall components

city: Würzburg

first: Christian

last: Pérez

address: Joseph-Schneider-Straße 2

department: Institute for molecular Infection Biology

country: Germany

institute: Center for Infectious Biology

summary: We report that a transcriptional regulator that originated in the lineage that gave rise to multiple host-associated Candida species is a key component of the circuitry that governs the C. albicans cell surface composition. Specifically, we show that the transcription regulator ZCF21 controls the expression of genes encoding multiple cell surface proteins and cell wall modifying enzymes.

overall_design: Transcriptome (RNA-seq) analysis of 2 Candida albicans strains (reference strain and zcf21 deletion mutant) grown under 4 culture conditions (YPD broth at 30°C for 24h; YPD broth at 30°C in the presence of 15 mM caffeine for 24h; Todd-Hewitt agar at 37°C for 24h; Todd-Hewitt agar at 37°C for 24h in the presence of 5 mM caffeine).

first: Lena

last: Böhm

first: J

middle: C

last: Perez


title: Next Generation Sequencing Analysis of Wild Type and Rfx2-/- Testicular Transcriptomes

first: Sylvain

last: LEMEILLE

first: W

last: Kistler

first: Dominique

last: Baas

last: Lemeille

first: Marie

last: Paschaki

first: Emmanuèle

last: Barras

first: Wenli

last: Ma

first: Jean-Luc

last: Duteyrat

first: Laurette

last: Morlé

first: Bénédicte

last: Durand

first: Walter

last: Reith


title: Oncogenic deregulation of EZH2 as an opportunity for targeted therapy in lung cancer [RNA-Seq]

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: As a master regulator of chromatin structure and function, the EZH2 lysine methyltransferase orchestrates transcriptional silencing of developmental gene networks. Overexpression of EZH2 is commonly observed in human epithelial cancers, such as non- small cell lung carcinoma (NSCLC), yet definitive demonstration of malignant transformation by deregulated EZH2 has proven elusive. Here, we demonstrate the causal role of EZH2 overexpression in NSCLC with a new genetically-engineered mouse model of lung adenocarcinoma. Deregulated EZH2 silences normal developmental pathways leading to epigenetic transformation independent from canonical growth factor pathway activation. As such, tumors feature a transcriptional program distinct from KRAS- and EGFR-mutant mouse lung cancers, but shared with human lung adenocarcinomas exhibiting high EZH2 expression. To target EZH2-dependent cancers, we developed a novel and potent EZH2 inhibitor that arises from a facile synthesis and possesses improved pharmacologic properties. JQEZ5 promoted the regression of EZH2-driven tumors in vivo, confirming oncogenic addiction to EZH2 in established tumors and providing the rationale for epigenetic therapy in a defined subset of lung cancer.

overall_design: Gene expression analysis of 7 samples, 3 EZH2 OE tumors, 2 EZH2 OE normal lung samples, and 2 WT lung samples

first: Zhang

last: Haikuo

first: Qi

last: Jun


title: Oncogenic deregulation of EZH2 as an opportunity for targeted therapy in lung cancer [ChIP-Seq]

overall_design: ChIP-Seq for H3K27ac and H3K27me3 in murine normal and EZH2 overexpressed tumor lung tissue


title: Transcriptome sequencing to identify transcription factor regulatory network and alternative splicing in endothelial cells under VEGF stimulation

city: Shenyang

first: Fang

last: Liu

state: Liaoning

address: Nanqi west road no.5

department: Department of Neurology

institute: center hospital affiliated to Shenyang medical college

summary: Human umbilical vein vascular endothelial cells (HUVECs) are crucial for angiogenesis that benefits functional recovery after cerebral infarction. This study aims to investigate the mechanisms underlying the effects of vascular endothelial growth factor (VEGF) on HUVECs.

overall_design: HUVECs were treated with 16 ng/mL VEGF165 for 4 days

first: Xiandong

last: Zeng


title: Heterochromatin remodeling by CDK12 contributes to learning in Drosophila

city: Beijing

first: Li

middle: xia

last: Pan

state: Beijing

address: North Zhongguancun Street

department: School of medicine

institute: Tsinghua university

summary: We describe the epigenetic profiling of the H3K9me2 and HP1a in Drosophila third instar larvae before and after CDK12 depletion by RNA interference (RNAi). Here we show that CDK12 regulates heterochromatin dynamics in Drosophila chromosomes. Depletion of CDK12 induces the increased HP1a and H3K9me2 binding profile on the coding region of euchromatic genes, with the X chromosome being the most affected. These results are consistent with the polytene chromosome immunostaining pattern of HP1a and H3K9me2 after CDK12 knockdown in our initial cytological observations, which show that CDK12 depletion induce heterochromatin spreading on euchromatic arms, especially on the X chromosome. This study describes a novel role of the CDK12 complex in controlling the epigenetic transition between euchromatin and heterochromatin.

overall_design: Examination of the genome-wide H3K9me2 and HP1a binding profile in wildtype larvae (WT) and CDK12-depleted larvae (CDK12-KD). Examination of the genome-wide CDK12 binding profile in wildtype larvae (WT). Twelve independent immunoprecipitations were conducted for each antibody. Two biological replicates were performed.

middle: X

first: Wenbing

last: Xie

first: Kai

middle: L

last: Li

first: Zhihao

last: Yang

first: Jiang

last: Xu

first: Wenhao

last: Zhang

first: Lu

middle: P

first: Xingjie

last: Ren

first: Zhimin

last: He

first: Junyu

last: Wu

first: Jin

last: Sun

first: Hui

middle: M

last: Wei

first: Da

last: Wang

first: Wei

first: Jian

middle: Q

last: Ni


title: miRNA-99 family diverges physiological cardiac hypertrophy to pathological cardiac hypertrophy

city: Madurai

first: Subbiah

last: Ramasamy

state: Tamilnadu

address: Palkalainagar

department: Molecular Biology

country: India

institute: Madurai Kamaraj University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The physiological cardiac hypertrophy is an adaptive condition that does not associate with myocyte cell death while pathological hypertrophy is a maladaptive condition associated with myocyte cell death. Alpha-2 macroglobulin (α-2M) an acute phase protein induces cardiac hypertrophy via the ERK1,2 and PI3K/Akt signaling. This study is aimed at exploring the miRNome of α-2M induced hypertrophied cardiomyocytes and to understand the role of miRNAs in determination of pathological and physiological hypertrophy.
Methods: Hypertrophy was induced in H9c2 cardiomyoblasts using alpha-2 macroglobulin. The induction of hypertrophy is confirmed by microscopy and gene expression studies. Subsequently, the total RNA was isolated and small RNA sequencing was executed in Illumina HiSeq 2000.
Results: Analysis of small RNA reads revealed the differential expression of a large set of miRNAs during hypertrophy. Among the differentially expressed candidates, miR-99 family (miR-99a, miR-99b and miR-100) showed significant downregulation upon α-2M treatment while isoproterenol treatment (pathological hypertrophy) upregulated their expression. The binding site for Egr1 transcription factor was identified in the promoter region of miR-99 family, and interestingly all miRNAs with Egr1 binding site proven by ChIP-Seq were downregulated during physiological hypertrophy
Conclusions: The results proved Egr-1 mediated regulation of miR-99 family determines the uniqueness of pathological and physiological hypertrophy. Upregulated miR-99 expression during pathological hypertrophy suggests that it can be a valuable diagnostic marker and potential therapeutic target for cardiac hypertrophy and heart failure.

overall_design: Small RNA profiles of control and hypertrophied cardiomyocyte H9c2 cells were generated by deep sequencing using Illumina HiSeq 2000

first: S

first: G

last: Velmurugan


title: Identification of differentially spliced genes by wild type or S34F mutation of U2AF1

city: Goyaongsi

first: Charny

last: Park

state: Gyeonggi-do

address: 323 Ilsan-ro,

country: South Korea

institute: National Cancer Center

overall_design: Examination of effects on splicing events by overexpressing wipdtype or S34F mutation of two U2AF1 isoforms in A549 cells. All experimental conditions are performed in duplicate.

first: Jaesang

last: Kim

first: Sanghyuk

last: Lee

first: Yeonjoo

last: Jung

first: Suyeon


title: Oncogenic deregulation of EZH2 as an opportunity for targeted therapy in lung cancer

first: James

last: Bradner


title: The Properties of Genome Conformation and Spatial Gene Interaction and Regulation Networks of Normal and Malignant Human Cell Types

city: columbia

first: Jianlin

middle: Jack

last: Cheng

state: MO

address: Engineering Building West 109

department: Computer Science Department

institute: University of Missouri,columbia

summary: In this work, we generated hundreds of millions of Hi-C paired end sequence reads for three different human cells (RL follicular lymphoma cell line, primary tumor B-cells from an acute lymphoblastic leukemia patient, and MHH-CALL-4 B-cell acute lymphoblastic leukemia cell line) using the Hi-C technique. An in-house Bioinformatics software pipeline was developed and applied to map sequence reads to the human reference genome, producing a large data set of high-quality and high-resolution chromosome contacts. Our computational analysis on these data reveal some interesting properties of human genome conformation, including conformational conservation and variation of the genomes of different cells, intra- and inter-chromosomal interactions, aberrant chromosomal translocation, spatial gene clusters, spatial gene-gene interactions, and spatial gene-regulatory-element interaction. Furthermore, we derived spatial interactions between functional elements (genes, transcription factor binding sites) from the chromosomal interaction data. The data were then used to generate chromosome-/genome-wide gene-gene interaction networks, transcription factor binding site (TFBS) – TFBS networks, and gene-TFBS networks. Remarkably, the connectivity in both networks shows the hallmark features of scale-free networks, suggesting that spatial interactions of gene-gene, gene-TFBS, and TFBS-TFBS in a genome are far from random.

overall_design: Three different human cells (RL follicular lymphoma cell line, primary tumor B-cells from an acute lymphoblastic leukemia patient, and MHH-CALL-4 B-cell acute lymphoblastic leukemia cell line) were analyzed

first: Zheng

first: Renzhi

last: Cao

first: Kristen

last: Taylor

first: Aaron

last: Briley

first: Charles

last: Caldwell


title: Genome-wide RNA Pol II-CTD occupancy in wild type and mutant worms

city: La Jolla

first: Xiang-Dong

last: Fu

state: CA

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

summary: We used RNA Pol II-CTD occupancy assay to identify mRNA isoform switch in mutant animals compared to wild type animals.

overall_design: Examination of RNA Pol II-CTD Ser5P recognized by 4H8 in wild type, sydn-1(0), ssup-72(0) and ssup-72(0);sydn-1(0)

first: Fei

last: Chen

first: Yu

last: Zhou

first: Hairi

last: Li

first: Yishi

last: Jin


title: The Prion Protein (PrP) is involved in translation via RNA granule-like mRNPs, a connection which is impaired during neurodegenerative diseases

city: Bonn

first: Clemens

last: Krost

address: Sigmund-Freud-Str. 25

institute: German Center for Neurodegenerative Diseases (DZNE)

type: Genome variation profiling by high throughput sequencing

summary:
Cytoplasmic RNA granules have emerged as important elements of posttranscriptional and translational regulation. Stress, germinal and neuronal granules contain RNA-binding proteins capable of self-assembly due to prion-like domains. Hyperassembly mediated by these prion-like domains causes several neurodegenerative diseases. Here, we report a subset of the mammalian prion protein (PrP), also prone to self-assembly, propagation and to cause devastating diseases, is a component of naturally occurring messenger ribonucleoproteins (mRNPs) in adult mouse brains. Biomolecules co-purified with PrP revealed a multitude of diverse RNA granule associated proteins and mRNAs encoding members of the translation machinery, indicating a role in a specialized translation process. Importantly, PrP mutations linked to Creutzfeldt-Jakob disease (CJD) or fatal familial insomnia (FFI) severely impaired recovery of mRNPs from preclinical mice, possibly representing a very early pathological process. Thus, mutant PrP may cause dysfunction in RNA regulation, thereby joining the constantly expanding ranks of disease associated RNP granule proteins.
The file Enrichment_analysis.xlsx contains mRNAs (FDR < 0.01) co-purified with PrP in both WT sample pools as identified by DESeq2 and the respective gene counts and log2 fold changes for CJD and FFI PrP:IP sample pools.

overall_design:
RIP-Seq analysis of mRNAs co-purified with PrP from murine brain cytoplasmic fractions in wild-type (WT), CJD and FFI mice. Each RIP-Seq and control (input) library represents a pool of 12 to 16 co-immunoprecipitation samples out of 3 to 4 mice.
To control for post-homogenization artifacts, we conducted an experiment in which we prepared homogenates from WT and PrP-KO (Prnp-/-) mice of different genetic backgrounds (C57BL/6 and 129S4) and identified SNPs in RIP-Seq and control libraries to finally identify specifically co-purified mRNAs.

first: Lech

last: Kaczmarczyk

first: Melvin

last: Schleif

first: Regina-Maria

last: Kolaitis

first: Vincenzo

last: Capece

first: J

first: Stefan

last: Bonn

first: Walker

last: Jackson


title: Efficient generation of stable chondrocytes from human iPSC through early induction of a pre-chondrogenic population

city: Stanford

first: Nidhi

last: Bhutani

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

institute: Stanford University

summary: Regeneration of human cartilage is inherently inefficient; an abundant autologous source like human induced pluripotent stem cells (hiPSC) is therefore attractive for engineering cartilage. Here, we report a defined growth factor based protocol for differentiating hiPSC into articular-like chondrocytes within two weeks with a high efficiency. The hiPSC-derived chondrocytes (hiChondrocytes) are stable and comparable to adult articular chondrocytes in global gene expression, extracellular matrix production and in their ability to generate cartilage tissue in vitro and in immune-deficient mice. Molecular characterization identified an early Sox9lowCD44lowCD140low pre-chondrogenic mesodermal population during hiPSC differentiation that eventually generates a homogenous population of Sox9highCD44highCD140high hiChondrocytes. Additionally, global gene expression analyses revealed two distinct Sox9-regulated gene networks in the Sox9low and Sox9high populations providing novel molecular insights into chondrogenic fate commitment and differentiation. Our findings present a favorable method for generation of hiPSC-derived articular chondrocytes in terms of safety and efficiency.

overall_design: 10 samples were analysed (duplicate sets of 5 time points) to assess changing gene expression over the course of differentiation from iPSC to hiChondrocyte. All samples were compared relative to the undifferentiated iPSC. Adult chondrocytes (2 samples) were also included for comparison. We analyzed the changes in gene expression with differentiation; genes with a fold-change ≥ or ≤1.5, with a difference in intensity of >100 and within the lower 90% confidence bound were selected.

first: Sarah

middle: E

first: Jieun

last: Lee


title: Whole blood derived cadmium responsive miRNome

first: Velmurugan

last: Ganesan

department: Department of Molecular Biology, School of Biological Sciences

summary:
Purpose: Cadmium is a nonessential heavy metal and a well known toxic agent. Cadmium is known to alter the gene expression and signaling but the role of miRNAs during Cadmium exposure is not understood.
Methods: Mice were treated with 100 mg/ ml cadmium chloride for 120 days and accumulation of cadmium in blood and organs are confirmed by GFAAS. Subsequently, the total RNA was isolated from the whole blood and small RNA sequencing was executed in Illumina HiSeq 1000.
Results: The reads were annotated to the mice genome and miRNAs in miRbase using miRDeep* and novel miRNAs were also predicted. The differential expression was studied by DeSeq
Conclusions: This is the first report to reveal the cadmium responsive miRNome. These candidate miRNAs can serve as biomarkers for cadmium

overall_design: Whole blood small RNA profiles of  control and cadmium exposed mice generated by deep sequencing using Illumina HiSeq 1000

first: G.

last: Velmurugan

first: S.

last: Ramasamy


title: Beauveria bassiana multiprotein bridging factor 1 (BbMBF1) regulating genes involved in fungal response to the prolonged thermal stress

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

summary: BbMBF1 played crucial roles in mediating response the prolonged thermal stress, a determinant to the environmental fitness of fungal entomopathogens. We characterized for the first time that disruption of BbMBF1 reduced  the mycelial tolerance to the 9-h thermal stress under 40°C. The global transcriptome  involved in the response to the thermal stress was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in fungal response to the themal stress.

overall_design: 1. Total RNA obtained from BbMBF1 disruption mutant were compared to that of wild type strain under control conditin (free of thermal stress); 2. Total RNA obtained from BbMBF1 disruption mutant were compared to that of WT strain under 9-h thermal stress at 40°C.

first: Sheng-Hua

first: Ming-Guang

last: Feng


title: The evolution of genic piRNA cluster loci expression patterns

city: BOSTON

first: NELSON

last: LAU

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

summary: This study examines the conservation of Piwi-interacting RNA (piRNA) clusters that come from protein coding gene transcripts.  By sequencing small RNA libraries from gonad tissues of Drosophilids and Glires we discover a diverse set of genic piRNA clusters conserved across animals. This dataset reveals new expression patterns for genic piRNA clusters and examines whether changing piRNA expression patterns correlates with sequence changes in piRNA cluster genomic sequence across a variety of animal species.

sample_organism:
Drosophila erecta
Drosophila melanogaster
Drosophila virilis
Drosophila yakuba
Oryctolagus cuniculus
Mus musculus
Rattus norvegicus

overall_design: We dissected gonad tissues consisting of ovaries from wildtype adult Drosophilids (D.melanogaster, D.erecta, D.yakuba, D.virilis) and testes from wildtype pre-pubsecent and adult mouse and rats.  Adult testes from rabbits were purchased from Pel-Freez Biologicals. Total or immunopreciptated RNAs were extracted from the pulvirized gonad tissues of Drosophilids and Glires.  Small RNAs were purified from these samples, converted into cDNA libraries, and sequenced on an Illumina HiSeq2000.

first: Nelson

last: Lau

first: Gung-wei

last: Chirn


title: Role of Tet1 and Tet3 genes and Chromatin Remodeling in Cerebellar Circuit Formation [hMe-Seal]

status: Public on Oct 31 2015

city: New York

first: Michelle E.

last: Ehrlich

address: 1 Gustave L. Levy Pl, New York, NY 10029

department: Department of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary: Although mechanisms underlying early steps in cerebellar development are known, evidence is lacking on genetic and epigenetic changes during the establishment of the synaptic circuitry. Using metagene analysis, we report pivotal changes in multiple reactomes of epigenetic pathway genes in cerebellar granule cells (GCs) during circuit formation.  During this stage, Tet genes are up-regulated and vitamin C activation of Tet enzymes increases the levels of 5-hydroxymethylcytosine (5hmC) at exon start sites of up-regulated genes, notably axon guidance genes and ion channel genes.  Knockdown of Tet1 and Tet3 by RNA interference in ex vivo cerebellar slice cultures inhibits dendritic arborization of developing GCs, a critical step in circuit formation.  These findings demonstrate a role for Tet genes and chromatin remodeling genes in the formation of cerebellar circuitry.

overall_design: 5hmC-enriched genomic DNA fragments were purified with a selective labeling strategy known as hMe-Seal and carried out DNA deep sequencing using Illumina HiSeq 2500.

first: Xiaodong

last: Zhu

first: David

last: Girardo

first: Eve-Ellen

last: Govek

first: Keisha

last: John

first: Marian

last: Mellén

first: Pablo

last: Tamayo

first: Jill

last: Mesirov

first: Mary

last: Hatten


title: Understanding the Regulatory Networks of Three LacI Transcriptional Repressors in Clostridium thermocellum DSM1313

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

summary: Clostridium thermocellum is a candidate for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol.  Understanding how this organism regulates gene expression is of importance for developing a better fundamental understanding of this industrial relevant bacterium.  We are primarily interested in gene regulation by three predicted LacI regulators.  A previous report of one LacI regulator in C. thermocellum ATCC27405 (Cthe_2808) indicated this was a transcriptional repressor of neighboring genes with repressor activity relieved in the presence of laminaribiose (a β-1,3 disaccharide).   The current work is aimed at understanding if a homolog of this LacI transcriptional regulator in C. thermocellum DSM1313 and two others putatively characterized as LacI regulators are in fact global regulatory proteins with extensive regulons or, if like the majority of LacI transcription factors, the regulation is limited to local genomic regions.  Each of the three LacI regulators was deleted in C. thermocellum DSM1313.  Genome re-sequencing was used to confirm the deletion and ensure nonspecific recombination events were avoided during the gene deletion strategy.  Growth of each strain on cellobiose was unaffected by any of the gene deletions under pH controlled fermentations. Global gene expression patterns taken at mid-log phase for each strain identified glycoside hydrolase genes encoding hemicellulases, including cellulosomal enzymes, that were highly up-regulated (up to 9 fold) in the absence of each LacI regulator.  Thus suggesting these were repressed under wild type conditions.  Electrophoretic mobility shift assays have confirmed LacI transcription factor binding to specific regions of gene promoters with putative motifs ranging from 16-18 bp. Work is ongoing to confirm the specific binding motif recognized by the two previously un-characterized transcription factors and assess the occurrence of this motif in the C. thermocellum DSM1313 genome. The identification of LacI repressor activity on hemicellulose gene expression is a key result of this work and will add to the small body of existing literature on the area of gene regulation in C. thermocellum.

overall_design: Four strains of C. thermocellum DSM1313 including a parental strain (Δhpt) and three others with deletion in lacI transcription factors were characterised by RNA-seq. The strains were grown in 1L bioreactors, cells (from 50 ml samples) were harvested at mid exponential, late exponential and 30 min after acid production halted during the transition to stationary phase.  The growth studies were performed in triplicate and thirty six samples were analyzed by RNA-sequencing.

first: Dawn

last: Klingeman

first: Steven

middle: D

last: Brown


title: Expression profiling of small, noncoding RNAs in physiologically hypertrophied rat hearts

first: Subbiah

last: Ramasamy

summary:
Purpose: Different studies revealed the importance of microRNAs (miRNAs) in pathological hypertrophy but their role during physiological hypertrophy is largely unexplored. Hence, this study is aimed at revealing the global expression profile of miRNAs during physiological cardiac hypertrophy.
Methods: Chronic swimming protocol continuously for eight weeks resulted in induction of physiological hypertrophy in rats and histopathology revealed the absence of tissue damage, apoptosis or fibrosis. Subsequently, the total RNA was isolated and small RNA sequencing was executed in Illumina HiSeq 2000.
Results: Analysis of small RNA reads revealed the differential expression of a large set of miRNAs during physiological hypertrophy. The expression profile of the significantly differentially expressed miRNAs were validated by qPCR.
Conclusions: This is the first report to reveal the involvement of a large number of apoptotic miRNAs during physiological cardiac hypertrophy including the previously unknown cardiac players like miR-99, miR-100, miR-191, miR-181 and miR-19. Our data indicates that regulation of these apoptotic miRNAs can be one of the major key factor in determining pathological or physiological hypertrophy by controlling apoptosis, fibrosis and cell death mechanisms.

overall_design: Heart small RNA profiles of 16-week old control and physiologically hypertrophied wistar rat were generated by deep sequencing using Illumina HiSeq 2000

first: S

first: G

last: Velmurugan


title: Chemical modifications mark alternatively spliced and actively degrading messenger RNAs in Arabidopsis and humans

first: Lee

middle: Elliott

last: Vandivier

address: 433 S. University Ave Rm 104

institute: University of Pennsylvania

summary: Post-transcriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as transfer RNAs (tRNAs), growing evidence indicates that messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) are likewise modified. Here, we apply our High-throughput Annotation of Modified Ribonucleotides (HAMR) pipeline to identify and classify modifications that affect Watson-Crick base-pairing at three different levels of the human and Arabidopsis thaliana transcriptomes (polyadenylated, small, and degrading RNAs). We find modifications primarily within actively degrading mRNAs and lncRNAs, suggesting they can act as a potent signal for RNA turnover. Additionally, modifications within stable mRNAs mark alternatively spliced introns, suggesting they regulate splicing. Furthermore, these modifications target mRNAs with coherent functions, including stress responses. Thus, our comprehensive analysis of RNA modification across multiple RNA classes yields new functional insights into these covalent RNA additions.

sample_organism:
Arabidopsis thaliana
Homo sapiens

platform_organism:
Arabidopsis thaliana
Homo sapiens

overall_design: polyA-selected RNA-seq, smRNA-seq, and polyA-selected global mapping of uncapped transcripts (GMUCT) in Arabidopsis thaliana; smRNA-seq in HEK293T and HeLa human cell lines.

first: Rafael

last: Campos

first: Pavel

last: Kuksa

first: Ian

last: Silverman

first: Li-San

last: Wang

first: Brian

last: Gregory


title: Trans-effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models

status: Public on Oct 30 2015

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptome sequencing of Nile tilapia hepatopancreas in different salinity

city: Shanghai

first: Xu

last: Zhixin

address: 500 Dongchuan Rd.,Shanghai 200241

institute: East China Normal University

summary: In this study, RNA-Seq was used to reveal the differences of molecular pathways in hepatopancreas of O. niloticus adapated to water with salinity of 8 or 16 practical salinity (psu), respectively, with fish at  freshwater as the control,. Significantly changed pathways were mainly related to lipid metabolism, glucose utilization, protein consumption, osmotic regulation, signal transduction and immunology. Based on the tendencies from freshwater to 8 or 16 psu, the differentially expressed gene unions were categorized into eight unique models, which were further classified into three categories which were constant-change (either keep increasing or decreasing), change-then-stable and stable-then-change. In constant-change category, steroid biosynthesis, steroid hormone biosynthesis, fat digestion and absorption, complement and coagulation cascades were extremely significantly affected by ambient salinity (P < 0.01), indicating that these pathways play pivotal roles in molecular response to salinity acclimation from freshwater to saline water in O. niloticus, and should be the main research focus in the future. In change-then-stable category, ribosome, oxidative phosphorylation, peroxisome proliferator-activated receptors (PPAR) signaling pathway, fat digestion and absorption changed significantly with ambient increasing salinity (P < 0.01), showing these pathways were sensitive to environmental salinity variation, but had a response threshold, and would stop changing once salinity exceeds the threshold. In stable-then-change category, protein export, protein processing in endoplasmic reticulum, tight junction, thyroid hormone synthesis, antigen processing and presentation, glycolysis/gluconeogenesis and glycosaminoglycan biosynthesis - keratan sulfate were the top changed pathways (P < 0.01), suggesting that these pathways were not sensitive to salinity variation, but these pathways will respond significantly under salinity exceeding a certain level. The pathways and genes reported in this study laid on a solid foundation for future studies in understanding the underlying mechanism for salinity adaptation of freshwater fish.

overall_design: Examination of 3 different salinities treated hepatopancreas in Nile tilapia

first: Zhixin

last: Xu


title: Trans-effects of sub-chromosomal duplications on DNA methylation patterns in mouse models of Down syndrome: whole genome bisulfite sequencing of cerebral samples from Dp(10)1Yey  and Dp(16)1Yey mouse models.

summary: Background: Trisomy 21 causes Down syndrome (DS), but the mechanisms by which the extra chromosome leads to deficient intellectual and immune function are not well understood.  Results: Here, we profile CpG methylation in DS and control cerebral and cerebellar cortex of adults and cerebrum of fetuses. We purify neuronal and non-neuronal nuclei and T-lymphocytes and find biologically relevant genes with DS-specific methylation (DS-DM) in brain cells. Some genes show brain-specific DS-DM, while others show stronger DS-DM in T cells. Both 5-methyl-cytosine and 5-hydroxy-methyl-cytosine contribute to the DS-DM. Thirty percent of genes with DS-DM in adult brain cells also show DS-DM in fetal brains, indicating early onset of these epigenetic changes, and we find early maturation of methylation patterns in DS brain and lymphocytes. Some, but not all, of the DS-DM genes show differential expression. DS-DM preferentially affected CpGs in or near specific transcription factor binding sites, implicating a mechanism involving altered transcription factor binding. Methyl-seq of brain DNA from mouse models with sub-chromosomal duplications mimicking DS reveals partial but significant overlaps with human DS-DM and shows that multiple chromosome 21 genes contribute to the downstream epigenetic effects.  Conclusions: These data point to novel biological mechanisms in DS and have general implications for trans effects of chromosomal duplications and aneuploidies on epigenetic patterning.

overall_design: Examination of methylation changes in two mouse models of Down syndrome with sub-chromosomal duplications, Dp(10)1Yey  and Dp(16)1Yey, compared to one littermate wild type mouse using whole genome bisulfite sequencing.

first: Maite

last: Mendioroz

first: Catherine

last: Do

first: Xiaoling

last: Jiang

first: Chunhong

last: Liu

first: Huferesh

middle: K

last: Darbary

first: Charles

middle: F

last: Lang

first: John

last: Lin

first: Anna

last: Thomas

first: Sayeda

last: Abu-Amero

first: Philip

last: Stanier

first: Alexis

last: Temkin

first: Alexander

last: Yale

first: Meng-Min

first: Yang

last: Li

first: Martha

last: Salas

first: Kristi

last: Kerkel

first: George

last: Capone

first: Wayne

first: Eugene

last: Yu

first: Gudrun

last: Moore

first: Jerzy

last: Wegiel


title: Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation

first: Michelle E.

last: Ehrlich


title: Loss of function of myosin chaperones triggers Hsf1-mediated transcriptional response in skeletal muscle cells

city: Eggenstein-Leopoldshafen

first: olivier

last: ARMANT

address: Hermann-von-Helmholtz-Platz 1

department: ITG

institute: Karlsruhe Institute of Technology

summary: Transcriptional analysis of zebrafish embryos and larvae from wild type and muscles mutants

overall_design: Biological samples sequenced in duplicates

first: Olivier

first: Christelle

last: ETARD


title: Mapping of 5-hydroxymethylcytosine by selective chemical labeling (SCL-seq) in human naive B cells and in vitro differentiated plasmablasts (P1 cells) [HTS]

city: Rennes

first: Gilles

last: Salbert

address: Avenue du Général Leclerc

department: Biology

institute: University of Rennes 1

summary: We report the genome-wide mapping of 5hmC in naive B cells and in vitro differentiated plasmablasts (P1 cells). In addition, H3K4me1 and H3K27ac histne marks were mapped in in vitro differentiated plasmablasts from two healthy donors (BN358 and BN369) by ChIP-seq.

overall_design: Genomic DNA from human primary cells was extracted and submitted to the SCL protocol using the Hydroxymethyl Collector kit from Active Motif. After sequencing on an Illumina HiSeq 2000, reads were mapped to the human hg19 genome. H3K4me1 and H3K27ac were mapped in in vitro differentiated plasmablasts (P1 cells) by ChIP-seq.

first: Stéphane

last: Avner


title: RNA sequencing analysis in WT and Pc4-OE mESC lines.

city: Seoul

first: Boyoun

last: Park

address: 50 Yonsei-ro, Seodaemun-gu

department: Systems biology

institute: Yonsei University

summary: Spermatogonial stem cells (SSCs) can spontaneously dedifferentiate into embryonic stem cell (ESC)-like cells, which are designated as multipotent SSCs (mSSCs), without ectopic expression of reprogramming factors. SSCs express key OSKM reprogramming factors at some levels, and do not require ectopic expression of any gene for the acquisition of pluripotency during reprogramming to mSSCs. Therefore, we reasoned that additional factors are required to regulate SSC reprogramming. In this study, we first compared the expression of reprogramming signature genes among somatic cells, iPSC, SSCs, mSSCs, and partially reprogramed cells, and found that they appear to have similar pluripotency states, whereas their transcriptional program differs. We developed a systems biology approach to prioritise genes for pluripotency regulatory factors by integrating transcriptome and interactome data on the genome-wide functional network. Then, we performed a series of systematic gene prioritisation steps and identified 53 candidates, which included some known reprogramming factors. We experimentally validated one particular candidate, Positive cofactor 4 (Pc4), which was expressed in PSCs and yielded a positive RNA interference (RNAi) response in an Oct4 reporter assay. We demonstrated that Pc4 enhanced the efficiency of OSKM-mediated reprogramming by promoting the transcriptional activity of key pluripotency factors, and by regulating the expression of many protein- and miRNA-encoding genes involved in reprogramming and somatic cell-specific genes.

overall_design: Pc4-overexpressing mESC lines were established by Venus (YFP)-expressing lentiviral transfection. The mESCs were split at a density of 2 ´ 104 cells onto fresh MEF feeder cells seeded into a 6 well dish (containing mESC growth medium) with virus particles, and 25 μg/ml polybrene (Sigma Aldrich) was added. After 24 h, the medium was replaced with fresh growth medium. After 4 days later, mESC colonies expressing YFP were picked and replated. Three different Pc4-overexpressing mESC lines were established.

first: Dong

middle: R

last: Lee

first: Insuk


title: Cell cycle-dependent reconfiguration of the DNA (hydroxy) methylome during terminal differentiation of human B cells into plasma cells

type: Methylation profiling by genome tiling array


title: Comprehensive role of Zfp217 in m6A methylation [RIP-seq]

first: Martin

middle: J.

last: Walsh

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

summary: Many transcriptional and epigenetic networks must be integrated to maintain self-renewal and pluripotency in embryonic stem cells (ESCs) and to enable induced pluripotent stem cell (iPSC) reprogramming.  Here, we explore the role of Zfp217and Mettl3 as RNA-binding proteins.

overall_design: Identification and characterization of RNAs associated with Zfp217 and Mettl3 in mouse embryoinc stem cells

first: Francesca

last: Aguilo

first: Fan

last: Zhang

first: Weijia


title: Comprehensive role of Zfp217 in m6A methylation [RNA-seq RA]

summary: Mouse stem cells were differenciated with retinoic acid and cells were harvested at the indicated time points.

overall_design: RNA-seq was used to measure gene expression levels in retinoic acid-differentiated mouse stem cells


title: Comprehensive role of Zfp217 in m6A methylation


title: modENCODE_White Lab: genome-wide ChIP data of Yki from Kc167 on Illumina Genome Analyzer.

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Yki from Kc167 generated by ChIP and analyzed on Illumina Genome Analyzer.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022  and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

overall_design:
A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Most factors binding profiles are generated by using specific antibodies for the protein of interest. However, some factors have been tagged by GFP in a transgenic line. In that case, ChIP is generated using an anti-GFP antibody.

This submission represents the ChIP-seq component of the study.

first: Nicolas

last: Negre

first: Nicholas

middle: A

last: Bild


title: RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass and molecular pathway cancer diagnostics

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

summary: We report RNA-sequencing data of 283 blood platelet samples, including 228 tumor-educated platelet (TEP) samples collected from patients with six different malignant tumors (non-small cell lung cancer, colorectal cancer, pancreatic cancer, glioblastoma, breast cancer and hepatobiliary carcinomas). In addition, we report RNA-sequencing data of blood platelets isolated from 55 healthy individuals. This dataset highlights the ability of TEP RNA-based 'liquid biopsies' in patients with several types with cancer, including the ability for pan-cancer, multiclass cancer and companion diagnostics.

overall_design: Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the human reference genome using STAR, and intron-spanning reads were summarized using HTseq. The processed data includes 285 samples (columns) and 57736 ensemble gene ids (rows). The supplementary data file (TEP_data_matrix.txt) contains the intron-spanning read counts, after data summarization by HTseq.

middle: G

first: Thomas

last: Wurdinger


title: An integrated systems biology approach identifies positive cofactor 4 as a pluripotency regulatory factor


title: Abo1, a conserved bromodomain AAA-ATPase maintains global nucleosome occupancy and organization

city: Cardiff

last: Kent

address: Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

summary: Maintenance of the correct level and organization of nucleosomes is crucial for genome function. Here we uncover a role for a conserved bromodomain AAA-ATPase, Abo1, in maintenance of nucleosome architecture in fission yeast. Cells lacking abo1+ experience both a reduction and mis-positioning of nucleosomes at transcribed sequences in addition to increased intragenic transcription, phenotypes that are hallmarks of defective chromatin re-establishment behind RNA polymerase II.  Abo1 is recruited to gene sequences and associates with histone H3 and the histone chaperone FACT. Furthermore, the distribution of Abo1 on chromatin is disturbed by impaired FACT function. The role of Abo1 extends to some promoters and also to silent heterochromatin.  Abo1 is recruited to pericentromeric heterochromatin independently of the HP1 ortholog, Swi6, where it enforces proper nucleosome occupancy. Consequently, loss of Abo1 alleviates silencing and causes elevated chromosome mis-segregation. We suggest that Abo1 provides a histone chaperone function that maintains nucleosome architecture genome-wide.

overall_design: A chromatin-seq/MNase-seq approach called Chromatin Particle Spectrum Analysis (Kent et al., (2011) Nucleic Acids Res. 39:e26) was used to map and compare nucleosome position in wild-type (strain 972) and isogenic abo1 knock-out (strain HM463) fission yeast cells. For each strain, three independent in vivo MNase digest bio-reps were performed and the purified DNA pooled. CPSA was performed using paired-end mode Illumina technology with pooled samples multiplexed over two HiSeq2000 lanes. Each CPSA paired read describes a microcococcal nuclease (MNase) resistant DNA species from chromatin, with the insert-size equivalent to the size of DNA protection. For each strain type, two analysed data sets are provided here: one listing the genomic distribution of MNase-protected DNAs of 150bp (“150bp CPSA size class”) and corresponding to mono-nucleosomes; the other listing the genomic distribution of MNase-protected DNAs of 300bp (“300bp CPSA size class”) and corresponding to di-nucleosomes.

first: Simon

last: Whitehall


title: Broiler responses to virulent and avirulent Clostridium perfringens

city: Guelph

first: Valeria

middle: Regina

last: Parreira

state: ON

address: 50 Stone Rd E

department: Pathobiology

country: Canada

institute: University of Guelph

summary:
Purpose: Analyze gene expression during C. perfringens colonization in the chicken
Transcriptomic profile of mRNA  from C. perfrinegns from in vivo and in vitro conditions were determined in biological duplicates by RNA-Seq using Illumina HiSeq 2500

overall_design: Comparison of gene expression through RNA sequencing of necrotic enteritis C. perfrinegns  type A of in vivo (chicken loops) and in vitro (lab culture)

first: John

last: Prescott


title: RNA-Seq analysis of mouse group 2 innate lymphoid cells (ILC2s) cultured with IL-33, IFN-g, and IL-27

city: Yokohama, Tsurumi-ku

first: Hiroki

last: Kabata

state: Kanagawa

address: Suehirocho 1-7-22

country: Japan

institute: RIKEN-IMS

summary:
Purpose: We found that IFN-g and IL-27 had suppressive effects on ILC2s cultured with IL-33. The goal of this study is to clarify the expressions of RNA induced by IFN-g and IL-27 in ILC2s.
Methods: ILC2s were isolated from fat-asociated lymphid clusters (FALC) of wild-type mice. They were cultured with IL-33 (10ng/ml), IL-33 + IFN-g (10ng/ml), or IL-33 + IL-27 (10ng/ml) for 48hrs. RNA was isolated by Allprep DNA/RNA Micro Kit (QIAGEN), and cDNA libraries were prepared by TruSeq RNA Sample Preparation kits v2 (Illumina) according to the manufacturer’s low sample protocol. A HiSeq 1500 system (Illumina) was used for 50 single-end bases (50SE)　sequencing.
Results: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the reference genome (mm9) using Bowtie2 v2.1.0 and TopHat2 v2.0.8. The transcript abundances were estimated as FPKM (fragments per kilobase of exon million fragments mapped) value using Cufflinks v2.1.1. We found that both IL-27 and IFN-g upregulated the expression of STAT1 and IRF1 which are regulated downstream of IFN-g receptor signaling, but there was no difference in the expression of GATA3, a critical transcription factor for ILC2 functions.
Conclusions: Our study represents the detailed differences of RNA expressions by RNA-seq technology.

overall_design: RNA-Seq analysis of ILC2s cultured with IL-33 (10ng/ml), IL-33 + IFN-g (10ng/ml), or IL-33 + IL-27 (10ng/ml) for 48hrs.

first: Ohara

last: Osamu

first: Moro

last: Kazuyo


title: Comprehensive role of Zfp217 in m6A methylation [RNA-seq]

state: NY

summary: Comprehensive RNA-seq experiments in control and zfp217 shRNA infected cells delineate a Zfp217-driven network required for ES cell self-renewal.

overall_design: RNA-seq was used to measure gene expression levels in luciferase control and Zfp217 short hairpin RNA (shRNA) infected mouse stem cells

middle: J


title: Hyper-excitability of Neurons generated from Patients with Bipolar Disorder

city: San Diego

first: Son

last: Pham

state: California

address: 10010 N Torrey Pines Rd

department: LOG

institute: Salk Institute

summary: Bipolar Disorder (BD) is a complex neuropsychiatric disorder that is characterized by intermittent episodes of mania and depression and, without treatment, 15% of patients commit suicide1. Hence, among all diseases, BD has been ranked by the WHO as a top disorder of morbidity and lost productivity2. Previous neuropathological studies have revealed a series of alterations in the brains of BD patients or animal models3, such as reduced glial cell number in the patient prefrontal cortex4, up-regulated activities of the PKA/PKC pathways5-7, and changes in dopamine/5-HT/glutamate neurotransmission systems8-11. However, the roles and causation of these changes in BD are too complex to exactly determine the pathology of the disease; none of the current BD animal models can recapitulate both the manic and depressive phenotypes or spontaneous cycling of BD simultaneously12,13. Furthermore, while some patients show remarkable improvement with lithium treatment, for yet unknown reasons, other patients are refractory to lithium treatment. Therefore, developing an accurate and powerful biological model has been a challenge for research into BD. The development of induced pluripotent stem cell (iPSC) technology has provided such a new approach. Here, we developed a human BD iPSC model and investigated the cellular phenotypes of hippocampal dentate gyrus neurons derived from the patient iPSCs. Using patch clamp recording, somatic Ca2+ imaging and RNA-seq techniques, we found that the neurons derived from BD patients exhibited hyperactive action potential (AP) firing, up-regulated expression of PKA/PKC/AP and mitochondria-related genes. Moreover, lithium selectively reversed these alterations in the neurons of patients who responded to lithium treatment. Therefore, hyper-excitability is one endophenotype of BD that is probably achieved through enhancement in the PKA/PKC and Na+ channel signaling systems, and our BD iPSC model can be used to develop new therapies and drugs aimed at clinical treatment of this disease.

overall_design: total RNAseq from neurons generated from BD patient-specific iPS cells

first: Jun

last: Yao

first: Fred

middle: H

last: Gage


title: MeDIP analysis of 5mC and 5hmC marks in human ataxia-telangiectasia cerebellum

city: Piscataway

first: Ronald

last: Hart

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary:
Genomic DNA was prepared, fragmented, and immunoprecipitated with antibodies specific for 5mC or 5hmC prior to standard sequencing.

The neurodegenerative disease known as ataxia-telangiectasia (A-T) is caused by the absence of the ATM (A-T mutated) protein. A long-standing mystery surrounding A-T is why cerebellar Purkinje cells (PCs) appear uniquely vulnerable to ATM-deficiency. Here, we present that 5-hydroxymethylcytosine (5hmC), a newly recognized epigenetic marker found at high levels in neurons, is substantially reduced in human A-T and Atm-/- mouse cerebellar PCs. TET1, an enzyme that converts 5mC to 5hmC, responds to DNA damage. Manipulation of TET1 activity directly affects neuronal cell cycle reentry and cell death after the induction of DNA damage. Quantitative, genome-wide analysis of 5hmC of samples from human cerebellum showed that in ATM-deficiency there is a remarkable genome-wide reduction of 5hmC enrichment at both proximal and distal regulatory elements. These results reveal a role of TET1-mediated 5hmC in DNA damage response, and provide insights into the basis of a PC-specific DNA demethylation alteration in ATM-deficiency.

overall_design: There are two groups, A-T and Control. For each group, cerebellar DNA samples were immunoprecipitated with anti-5mC (n=1) or anti-5hmC (n=3). There were also two replicates of input control for each group.

middle: P

first: Jiali

last: Li

first: Karl

last: Herrup


title: modENCODE_White Lab: genome-wide ChIP data of Tango from Kc167 on Illumina Genome Analyzer.

first: Kevin

last: White

summary:
This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor Tango from Kc167 generated by ChIP and analyzed on Illumina Genome Analyzer.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022  and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

last: Negre


title: Genome-wide map of JMJD1C binding in Kasumi-1 cells [ChIP-seq]

first: Mo

last: Chen

address: 1230 York Avenue

institute: Rockefeller University

summary: The AML1-ETO fusion protein, a transcription factor generated by the t(8;21) translocation in acute myeloid leukaemia (AML), dictates a leukemic program by increasing self-renewal and inhibiting differentiation.  Here we demonstrate that the histone demethylase JMJD1C functions as a co-activator for AML1-ETO and is required for its transcriptional program. JMJD1C is directly recruited by AML1-ETO to its target genes and regulates their expression by maintaining low H3K9me2 levels. Analyses in JMJD1C knockout mice also establish a JMJD1C requirement for AML1-ETO’s ability to increase proliferation. We also show a critical role for JMJD1C in the survival of multiple human AML cell lines, suggesting that it is required for leukemic programs in different AML cell types through its association with key transcription factors.

overall_design: Examination of JMJD1C and LYL1 chromatin binding in Kasumi-1 cells, HL-60 cells, NB-4 cells and THP-1 cells,  including ChIP-seqs of JMJD1C  and LYL1, and input DNAs for Kasumi-1, HL-60, NB4.

first: Robert

last: Roeder


title: Comprehensive role of Zfp217 in m6A methylation [MeRIP-seq]

first: Martin

last: Walsh

summary: Many transcriptional and epigenetic networks must be integrated to maintain self-renewal and pluripotency in embryonic stem cells (ESCs) and to enable induced pluripotent stem cell (iPSC) reprogramming.  Here, we explore the role of Zfp217 as a key transcriptional factor in maintaining ES cell self-renewal by performing meRIP analysis in control and Zfp217-depleted mouse stem cells.

overall_design: Examination of m6A levels from total RNA in control and Zfp217 shRNA infected mouse stem cells

first: Francesca

last: Aguilo

first: Fan

last: Zhang

first: Weijia


title: Role of polycomb repressive complex 1 in the intestinal homeostasis [RNA-seq 2]

status: Public on Oct 29 2015

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

institute: IFOM-IEO

summary: These data include RNA Seq data generated from wild type and Ring1a Ring1b dKO Villi from Rosa26-CreERT2 Cdkn2a-/- and Rosa26-CreERT2 Cdkn2a-/- Ring1a-/- Ring1bf/f mice.

overall_design: Total RNA extracted from wild type and Ring1a Ring1b dKO Villi.

first: Alessandra

last: Rossi

first: Fulvio

last: Chiacchiera

first: Sri

first: Diego

last: Pasini


title: Transcriptomic analysis of Grapevine (cv. Summer Black) leaf at four developmental stages, using the Illumina Platform

city: Nanjing

first: Tariq

last: Pervaiz

state: Jaingsu

address: wei Gang

department: Horticulture

institute: Nanjing Agricultural University

summary: conducted to find out the transcriptional system that is connected with the development of leaves and production of metabolites during photosynthesis.  We examine the cellular expression by use the up-to-date RNA sequencing expertise to carry out a complete analysis of the transcriptional profile of V. vinifera leaves at four different developmental stages.

overall_design: Total RNA extracted from 4 samples with three replication for each and compared within all samples.

first: T

first: J

last: Fang


title: Effects of Pseudorabies Virus Infection on the Tracheobronchial Lymph Node Transcriptome

city: Ames

first: Laura

last: Miller

state: Iowa

address: 1920 Dayton Ave

department: Virus and Prion Research Unit

institute: USDA-ARS-National Animal Disease Center

summary: RNA isolated from draining tracheobronchial lymph nodes (TBLN) from 5-week old pigs, either clinically infected with a feral isolate of Pseudorabies virus or uninfected were interrogated using Illumina Digital Gene Expression Tag Profiling. Over 100 million tag sequences were observed, representing 4,064,189 unique 21-base sequences collected from TBLN at time points 1, 3, 6 and 14 days post-infection (dpi)

overall_design: RNA isolated from draining tracheobronchial lymph nodes (TBLN) from 5-week old pigs (% per group pooled), either clinically infected with feral isolate FS268 of Pseudorabies virus or uninfected at 1, 3, 6, and 14 days post inoculation. Over 100 million tag sequences were observed, representing 4,064,189 unique 21-base sequences.

middle: C

first: Darrell

middle: O

last: Bayles

first: Eraldo

middle: L

last: Zanella

first: Kelly

middle: M

last: Lager


title: Comprehensive role of Zfp217 in m6A methylation [ChIP-seq]

city: New York

summary: Many transcriptional and epigenetic networks must be integrated to maintain self-renewal and pluripotency in embryonic stem cells (ESCs) and to enable induced pluripotent stem cell (iPSC) reprogramming.  Here, we explore the role of Zfp217 as a key transcriptional factor in maintaining ES cell self-renewal by permorming genome-wide ChIP-Seq analyses.

overall_design: Examination of Zfp217 binding profiling by high throughput sequencing in mouse stem cells


title: HiCUP: pipeline for mapping and processing Hi-C data

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: HiCUP is a pipeline for processing sequence data generated by Hi-C, a technique used to investigate the three-dimensional organisation of a genome. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also provides an easy-to-interpret yet detailed quality control report that may be used by researchers to refine their experimental protocol for future studies. The software is freely available and has already been used for processing Hi-C data in several recently published peer-reviewed research articles.    This experiment investigates the impact of using HiCUP to remove putative PCR amplification products in heavily duplicated Capture Hi-C libraries.

overall_design: Examination of three Capture Hi-C libraries

middle: W

first: Phillip

last: Ewels

first: Mayra

last: Furlan-Magaril

first: Takashi

last: Nagano

first: Stefan

last: Schoenfelder

first: Peter

last: Fraser

first: Simon

last: Andrews


title: Transcription factor trapping by RNA in gene regulatory elements (CLIP-Seq)

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription.  RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA.  These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements.  We show here that the ubiquitously expressed TF YY1 binds to both proximal and distal regulatory elements and to the RNA species associated with these elements near active genes in embryonic stem cells.  Inhibition of transcription from these elements reduces YY1 occupancy.  In contrast, tethering of RNA species near YY1 DNA binding sites enhances YY1 occupancy.  We propose that RNA acts as trap to maintain certain TFs at active enhancer and promoter-proximal regulatory elements.  Thus, transcriptional control generally involves a positive feedback loop, where YY1 and other TFs stimulate local transcription, and newly transcribed nascent RNA reinforces local TF occupancy.   This model helps explain why TFs occupy only the small fraction of their consensus motifs in the mammalian genome where transcription is detected.

overall_design: CLIP-Seq for YY1 in mouse embryonic stem cells

first: Alla

last: Sigova

first: Brian

last: Abraham

first: Xiong

last: Ji

first: Benoit

last: Molinie

first: Mohini

last: Jangi

first: Yang

middle: E

last: Guo

first: Nancy

last: Hannett

first: Cosmas

last: Giallourakis

last: Sharp


title: Transcription factor trapping by RNA in gene regulatory elements (RNA-Seq)

overall_design: RNA-Seq in mouse embryonic stem cells before and after knockdown of exosome protein


title: Role of polycomb repressive complex 1 in the intestinal homeostasis [ChIP-seq 2]

first: Sri Ganesh

last: Jammula

summary: These data include the genome wide occupancy of histone modifications and transcription factors by ChIP sequencing in mouse villi cells and in mouse ISCs.

overall_design: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from wild type Villi cells and wild type and Ring1a Ring1b dKO ISCs using specific antibody against different target protein/modification.

first: Alessandra

last: Rossi

first: Fulvio

last: Chiacchiera

first: Sri

first: Diego

last: Pasini


title: Transcriptome-wide high-throughput deep m6A-seq reveals unique m6A methylation differential patterns among three organs in Arabidopsis

status: Public on Oct 28 2015

city: Yangling

first: Yizhen

last: Wan

address: Taicheng Road

institute: Northwest Agriculture and Forestry University

summary: m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, m6A differential patterns among organs have not been well characterized.  The goal of the study is to comprehensively analyze m6A patterns of numerous types of RNAs, the relationship between transcript level and m6A methylation extent, and m6A differential patterns among organs in Arabidopsis.

overall_design: In total, 18 libraries were sequneced. For the 3 organs: leaf, flower and root, each organ has mRNA-Seq, m6A-Seq and Input sequenced. And each sequence has 2 replicats.

first: Kai

last: Tang

first: Shaojun

last: Xie


title: Transcriptome Profiling of Developing Murine Lens through RNA Sequencing

city: Baltimore

first: S. Amer

last: Riazuddin

state: Maryland

address: 600 N. Wolfe St

institute: Johns Hopkins University School of Medicine

summary:
Purpose: Transcriptome is the entire repertoire of all transcripts present in a cell at any particular time. We undertook next-generation whole transcriptome sequencing approach to gain insight of the transcriptional landscape of the developing mouse lens.
Methods: We ascertained mice lenses at six developmental time points including two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). The ocular tissue at each time point was maintained as two distinct pools serving as biological replicates for each developmental stage. The mRNA and small RNA libraries were paired-end sequenced on Illumina HiSeq 2000 and subsequently analyzed using bioinformatics tools.
Results: Mapping of mRNA and small RNA libraries generated 187.56 and 154.22 million paired-end reads, respectively. We detected a total of 14,465 genes in the mouse ocular lens. Of these, 46 genes exhibited 40-fold differential expression compared to transcriptional levels at E15. Likewise, small RNA profiling identified 379 microRNAs (miRNAs) expressed in mouse lens. Of these, 49 miRNAs manifested an 8-fold or higher differential expression when compared, as above to the microRNA expression at E15.
Conclusion: We report the first comprehensive profile of developing murine lens transcriptome including both mRNA and miRNA through next-generation RNA sequencing. A complete repository of the lens transcriptome of six developmental time points will be monumental in elucidating processes essential for development of the ocular lens and maintenance its transparency.

overall_design: Whole transcrtiome and microRNA profilling of mouse lens using 2 embryonic (E15 and E18) and 4 postnatal stages (P0, P3, P6 and P9) in duplicates through high-throughput sequening using Illumina HiSeq2000.

first: Shahid

middle: Y

last: Khan

first: Sean

middle: F

last: Hackett

first: Mei-Chong

last: Lee

first: Nader

last: Pourmand

first: C

last: Talbot Jr

first: S


title: CTCF binding polarity determines chromatin looping [ChIP-seq]

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

institute: Hubrecht Institute

overall_design: CTCF ChIPseq was performed in E14 embryonic stem cells and neural precursor cells

first: Wouter

last: de Laat


title: Role of polycomb repressive complex 1 in the intestinal homeostasis [RNA-Seq]

first: Sri Ganesh

summary: These data include RNA Seq data generated from wild type and Ring1a Ring1b dKO ISCs from Lgr5Gfp-CreERT2, Lgr5Gfp-CreERT2 Ring1a-/- Ring1bf/f, Lgr5Gfp-CreERT2-Ctnnb1-ex3 and Lgr5Gfp-CreERT2 Ring1a-/- Ring1bf/f-Ctnnb1-ex3 mice.

overall_design: Total RNA extracted from sorted wild type and Ring1a Ring1b dKO ISCs.


title: CTCF binding polarity determines chromatin looping [4C]

summary: CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentally stable and dynamic chromatin loops. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR-Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher order chromatin structure.

overall_design: 4C-seq was performed on a large number of viewpoints in E14 embryonic stem cells, neural precursor cells and primary fetal liver cells


title: Differential RNA-seq of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42 Reveals sRNA Bas01 involved in Sporulation and Biofilm Formation

city: Irvine

first: Lei

last: Li

address: University of California, Irvine

institute: University of California, Irvine

summary: Bacillus amyloliquefaciens FZB42 is a representative organism for Gram positive soil bacteria associated with plant roots and beneficial to plant growth. It is of immense importance to understand mechanisms of this class of bacteria adapting to rhizosphere. In this work employing differential RNA sequencing (RNA-seq) and Northern blot, we systematically identified transcription start sites of mRNAs as well as non-coding regulatory RNAs in FZB42. The genes regulated at different growth phases and located in polycistronic operons were also identified. A set of genes were re-annotated. In addition, a sRNA named Bas01 was identified to be involved in Bacillus sporulation and biofilm formation. The result we obtained provides valuable data for investigation of Bacillus gene expression and molecular details of rhizobacterial interaction with host plants.

overall_design: Examination of transcriptome profile of rhizobacterium B. amyloliquefaciens FZB42 grown under six conditions.

first: Ben

last: Fan

first: Yanjie

last: Chao

first: Konrad

last: Förstner

first: Jörg

last: Vogel

first: Rainer

last: Borriss

first: Xiao

middle: Q

last: Wu


title: Transcription factor trapping by RNA in gene regulatory elements

first: Richard

last: Young

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

overall_design: Refer to individual Series


title: Role of polycomb repressive complex 1 in the intestinal homeostasis

last: Jammula


title: RNA profiling for mouse B10+ cells and B10- B cells

first: Jianbo

last: Sun

department: Microbiology and Immunology

institute: Columbia University

summary: we used genome-wide transcriptome analysis to profile the mRNA, long noncoding RNA (lncRNA), and microRNA (miRNA) expression of B10 cells, an antigen-specific Cd1dhiCd5+Cd19hiIl10 competent regulatory B cell. Potential key upstream regulators (including transcription factors, cytokines, trans-membrane receptors, and kinases) for Breg biogenesis and function were identified.

overall_design: B10+ B cells (Cd1dhiCd5+Cd19hiIl10+) and B10- cells (Cd1d-Cd5-Cd19hiIl10-) from mouse splenic B cell were sorted for RNA preparation. Two independent repeats were prepared for RNA-seq

first: Uttiya

last: Basu


title: A MYC-driven change in mitochondrial dynamics limits stem cell properties of mammary epithelial cells (ChIP-seq)

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: In several developmental lineages, an increase in expression of the MYC proto-oncogene drives the transition from quiescent stem cells to transit amplifying cells. The mechanism by which MYC restricts self-renewal of adult stem cells is unknown. Here, we show that MYC activates a stereotypic transcriptional program of genes involved in protein translation and mitochondrial biogenesis in mammary epithelial cells and indirectly inhibits the YAP/TAZ co-activators that are essential for mammary stem cell self-renewal. We identify a phospholipase of the mitochondrial outer membrane, PLD6, as the mediator of MYC activity. PLD6 mediates a change in the mitochondrial fusion/fission balance that promotes nuclear export of YAP/TAZ in a LATS- and RHO-independent manner. Mouse models and human pathological data confirm that MYC suppresses YAP/TAZ activity in mammary tumors. PLD6 is also required for glutaminolysis, arguing that MYC-dependent changes in mitochondrial dynamics balance cellular energy metabolism with the self-renewal potential of adult stem cells.

overall_design: ChIP-Seq experiments for MYC-HA (HA-IP) performed in IMEC primary breast epithelial cells. Input-samples were sequenced as controlls.

first: Björn

last: von Eyss

first: Laura

last: Jaenicke

first: Roderik

last: Kortlever

first: Nadine

last: Royla

first: Katrin

last: Wiese

first: Sebastian

last: Letschert

first: Markus

last: Sauer

first: Andreas

last: Rosenwald

first: Gerard

middle: I

last: Evan

first: Stefan

last: Kempa


title: Role of polycomb repressive complex 1 in the intestinal homeostasis [ChIP-Seq]

first: Sri Ganesh

summary: These data include the genome wide occupancy of histone modifications and transcription factors by ChIP sequencing in mouse crypt cells and in mouse ISCs.

overall_design: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from wild type and Ring1a Ring1b dKO crypt cells and from WT ISCs using specific antibody against different target protein/modification.

first: Alessandra

last: Rossi

first: Fulvio

last: Chiacchiera

first: Sri

first: Diego

last: Pasini


title: Transcription factor trapping by RNA in gene regulatory elements (GRO-Seq)

first: Richard

middle: A

last: Young

overall_design: GRO-Seq in mouse embryonic stem cells treated with transcription-altering drugs

first: Alla

last: Sigova

first: Brian

last: Abraham

first: Xiong

last: Ji

first: Benoit

last: Molinie

first: Mohini

last: Jangi

first: Yang

last: Guo

first: Nancy

last: Hannett

first: Cosmas

last: Giallourakis

first: Phillip

last: Sharp


title: CTCF binding polarity determines chromatin looping

first: Elzo

last: de Wit


title: An PWI- and RRM Motif-Containing Protein Is Critical for Pre-mRNA Splicing and ABA Responses in Arabidopsis

city: MD

first: Jianhua

last: Zhu

address: 2102 Plant Sciences Building  College Park

institute: University of Maryland

summary: We used RNA-seq platform to determine role of a splicing factor RBM25 in regulation of gene expression and pre-mRNA splicing.  We found that a loss-of-function allele of RBM25, rbm25-1, causes up- and down-regulation of a large number of genes. We further found that the rbm25-1 mutation results in defects in altenative splicing of transcripts of many genes including signal transduction components in stress responses.

overall_design: Examination of mRNA levels in bulked individual wild type and rbm25-1 mutant seedlings before and after ABA treatment.

first: Xiangqiang

last: Zhan

first: Bilian

last: Qian

first: Wenwu

last: Wu


title: A MYC-driven change in mitochondrial dynamics limits stem cell properties of mammary epithelial cells

first: Martin

last: Eilers


title: Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation

city: Durham

first: Jeff

last: Blackinton

state: NC

address: 207 Research Dr Rm 412

department: Molecular Genetics and Microbiology

institute: Duke University

summary: We evaluated changes in mRNA stability and transcription using 4sU metabolic pulse labeling across a four hour time course following activation of Jurkat T cells with PMA and PHA

overall_design: Measurement of total mRNA (T) and 4sU labeled mRNA (IP) in three biological replicates at five time points: prior to activation (U) and the first four hours after activation (1-4)

middle: G

first: Jack

middle: D

last: Keene


title: A Dach2-Hdac9-Myog-Gdf5 signaling system regulates regeneration of neuromuscular synapses

city: Ann Arbor

first: Ana

middle: Rodrigues

last: Grant

state: MI

address: 100 Washtenaw Avenue

department: Computational Medicine & Bioinformatics

institute: University of Michigan

summary: Muscle denervation due to injury, disease or aging results in impaired motor function.  Restoring neuromuscular communication requires axonal regrowth and regeneration of neuromuscular synapses.  Muscle activity inhibits neuromuscular synapse regeneration. The mechanism by which muscle activity regulates regeneration of synapses is poorly understood.  Dach2 and Hdac9 are activity-regulated transcriptional co-repressors that are highly expressed in innervated muscle and suppressed following muscle denervation.  Here, we report that Dach2 and Hdac9 inhibit regeneration of neuromuscular synapses. Importantly, we identified Myog and Gdf5 as muscle-specific Dach2/Hdac9-regulated genes that stimulate neuromuscular regeneration in denervated muscle.  Interestingly, Gdf5 also stimulates presynaptic differentiation and inhibits branching of regenerating neurons.  Finally, we found that Dach2 and Hdac9 suppress miR206 expression, a microRNA involved in enhancing neuromuscular regeneration.

overall_design: RNAseq on innervated and 3 day denervated adult soleus muscle from wildtype mice is compared with that from 3 day denervated soleus muscle from Dach2/Hdac9 deleted mice to identify Dach2/Hdac9-regulated genes.

middle: R

first: Daniel

last: Goldman


title: The PIAS-like coactivator Zmiz1 directly and selectively coregulates Notch1 in T-cell development and leukemia [RNA-Seq]

first: Mark

middle: Yat-fung

last: Chiang

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

summary: The most recurrently mutated oncogene in T-cell acute lymphoblastic leukemia (T-ALL) is NOTCH1. The core Notch complex consists of an ICN protein, a Maml cofactor, and the DNA binding factor Rbpj. The known direct cofactors of Notch appear to act nonselectively, homogeneously driving Notch gene expression functions. It is unclear whether there are direct cofactors of Notch that act selectively and heterogeneously regulate ICN. We discovered that Zmiz1, a Protein Inhibitor of Activated STAT (PIAS)-like coactivator, directly bound ICN1.  ChIP-Seq showed that Zmiz1 selectively co-bound only a subset of Notch-regulated enhancers. This led to hypothesize that Zmiz1 regulates only a subset of Notch1 target genes. To investigate this, we performed RNA-Seq on four 8946 cell linesin which L1601P (activated Notch1) or Zmiz1 were expressed alone or in combination. Zmiz1 induced  ~10% of Notch target genes. The Notch target gene that was most strongly induced by Zmiz1 was Myc. Our data suggest that Zmiz1 selectively amplifies a subset of Notch target genes with strong amplification of Myc.

overall_design: RNA-Seq in a murine T-ALL cell line

last: Pinnell


title: RNA sequencing of Bifidobacterium longum subsp. infantis in response to various substrates

city: Davis

first: Danielle

last: Lemay

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

summary: The purpose of this project was to determine the whole transcriptome response of Bifidobacterium longum subsp. Infantis to pooled and individual human milk oligosaccharides (HMO) relative to lactose

sample_organism: Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

overall_design: Bacterial isolates grown on lactose, pooled human milk oligosaccharides (HMO), lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), 2’fucosyllactose (2’FL), 3-fucosyllactose (3FL), and 6’sialyllactose (6’SL). RNA was extracted and sequenced, in duplicate, on an Illumina HiSeq. Early, mid, and late timepoints in response to pooled HMO were additionally sequenced in duplicate.

first: David

last: Mills

last: Garrido


title: The PIAS-like coactivator Zmiz1 directly and selectively coregulates Notch1 in T-cell development and leukemia


title: Transcriptomic profiling of sequential tumours from breast cancer patients provides a global view of metastatic expression changes following endocrine therapy

city: Dublin

first: Leonie

last: Young

address: York Street

department: Surgery

country: Ireland

institute: Royal College of Surgeons, Ireland

summary: We profiled primary breast cancer, nodal and liver metastatic tumours from three patients. At the time of initial diagnosis, all three patients presented with luminal breast cancer with adjacent nodal metastasis. They all received 5 years of enodrine therapy and all subsequently developed liver metastasis.

overall_design: Examination of mRNA differences between primary, nodal and metastatic tumour samples.

middle: S

first: Ailis

last: Fagan


title: A multiplexed system for quantitative comparisons of chromatin landscapes

status: Public on Oct 27 2015

city: Boston

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

summary: Genome-wide profiling of histone modifications can provide systematic insight into the regulatory elements and programs engaged in a given cell type. However, conventional chromatin immunoprecipitation and sequencing (ChIP-seq) does not capture quantitative information on histone modification levels, requires large amounts of starting material, and involves tedious processing of each individual sample. Here we address these limitations with a technology that leverages DNA barcoding to profile chromatin quantitatively and in multiplexed format. We concurrently map relative levels of multiple histone modifications across multiple samples, each comprising as few as a thousand cells. We demonstrate the technology by monitoring dynamic changes following inhibition of P300, EZH2 or KDM5, by linking altered epigenetic landscapes to chromatin regulator mutations, and by mapping active and repressive marks in purified human hematopoietic stem cells. Hence, this technology enables quantitative studies of chromatin state dynamics across rare cell types, genotypes, environmental conditions and drug treatments.

overall_design:
Five datasets are included:
(1) K562 cells were treated with with DMSO, C646 or GSK126 (Fig 3C in manuscript). Three separate experiments were performed: Exp004-5 had 1 replicate, and also included libraries with mouse YAC-1 cells to check for contamination (Fig. 1D in manuscript), whereas Exp004-8 and Exp004-9 were performed in triplicate. Immunoprecipiation was performed for H3K27ac, H3K27me3 and total H3 for normalization.
(2) K562 cells were treated with DMSO or KDM5-C70 (Fig 3E-J in manuscript). This experiment (Exp015-5) was performed in triplicate at 2 MNase concentrations and 2 barcodes per condition. Immunoprecipitation was performed for H3K4me3 and total H3 for normalization. All DMSO or KDM5-C70 conditions were merged for visualization (tdf).
(3) K562 cells were analyzed at low input and different MNase concentrations (Fig. 1B, Fig. 2A-C in manuscript). Two separate experiments were performed: Exp004-2 had 5 MNase concentrations, 4 cell numbers, and 4 marks (H3, H3K4me3, H3K27ac and H3K27me3). Exp015-2 had 5 MNase concentrations, 4 cell numbers, and 2 marks (H3K4me3 and H3K27me3).
(4) Pfeiffer, SKM-1 or Toledo cells were treated with DMSO or GSK126 (Fig. 4 in manuscript). This experiment (Exp016-3) was performed in duplicate at 2 MNase concentrations. Immunoprecipitation was performed for H3K27ac, H3K27me3 and total H3 for normalization.
(5) Human HSCs were analyzed (Fig. 2D-F in manuscript). Cells were digested at 2 MNase concentrations with 2 barcodes each. Immunoprecipitation was performed for H3K27ac, H3K27me3 and H3K36me3. A total of 6,000 cells was used per mark and data was merged for visualization (tdf).

first: Aaron

last: Viny

first: Oren

last: Ram

first: Russell

middle: J

last: Ryan

first: Matthew

last: Cotton

first: Laura

last: Donohue

first: Cem

last: Sievers

first: Yotam

last: Drier

first: Brian

middle: B

last: Liau

first: Shawn

last: Gillespie

first: Kaitlin

last: Carroll

first: Michael

last: Cross

first: Ross

last: Levine

first: Bradley

last: Bernstein


title: The PIAS-like coactivator Zmiz1 directly and selectively coregulates Notch1 in T-cell development and leukemia [ChIP-Seq]

first: Mark

last: Chiang

summary: The most recurrently mutated oncogene in T-cell acute lymphoblastic leukemia (T-ALL) is NOTCH1. The core Notch complex consists of an ICN protein, a Maml cofactor, and the DNA binding factor Rbpj. The known direct cofactors of Notch appear to act nonselectively, homogeneously driving Notch gene expression functions. It is unclear whether there are direct cofactors of Notch that act selectively and heterogeneously regulate ICN. We discovered that Zmiz1, a Protein Inhibitor of Activated STAT (PIAS)-like coactivator, directly bound ICN1. In order to determine whether this interaction occured at chromatin, we performed ChIP-Seq. We identified significant overlap between ICN1, Rbpj, and Zmiz1 peaks.  75% of overlapping ICN1/Rbpj peaks overlapped with Zmiz1 (HA) peaks (273 peaks).  The size of Zmiz1 (HA) peaks had moderate correlation with the size of Rbpj and ICN1 peaks. Like Rbpj and ICN1 peaks, Zmiz1 (HA) peaks were associated with activating H3K27ac, H3K4me1, and H3K4me3 chromatin marks and were devoid of repressive H3K27me3 marks. These data suggest that Zmiz1 is a selective Notch regulator. It co-binds only a subset of ICN1 and Rbpj-regulated sites.

overall_design: Zmiz1, ICN1, Rbpj, histone mehylation ChIP-Seq in murine T-ALL cell line

first: Nancy

last: Pinnell