title: Differential expression of genes associated with prenatal protein under-nutrition by albumen removal in the chicken

city: Heverlee

first: Els

last: Willems

state: Antwerp

address: Kasteelpark Arenberg 30 box 2456

department: Biosystems

country: Belgium

institute: KU Leuven

summary: Previously, long-term effects on body weight and reproductive performance have been demonstrated in the chicken model of prenatal protein undernutrition by albumen removal. Introduction of such persistent alterations in phenotype suggests stable changes in gene expression. A genome-wide screening for differences in hepatic transcriptome by RNA-Seq was performed in adult Isa Brown hens (55 weeks of age). Albumen-deprived hens were created by removal of 3 ml of the albumen from fertilized eggs  and replacement with saline early during embryonic development (embryonic day 1). Results were compared to mock-treated sham hens and non-treated control hens. Correlation between relative expression levels obtained from the RNA-Seq and qPCR results was very high (Pearson’s correlation coefficiënt = 0.85), confirming the validity of the RNA-Seq results. In addition, after expansion of the sample size, 7 out of 15 selected genes demonstrated the same significant gene expression differences in the qPCR as in the RNA-Seq dataset, and were thus biologically confirmed. Grouping of the differentially expressed (DE) genes according to biological functions revealed the involvement of processes such as ‘embryonic and organismal development’, ‘organ morphology’, ‘organ and tissue development’, ‘reproductive system development and function’. Molecular pathways that were altered were ‘amino acid metabolism’, ‘molecular transport’, ‘small molecule biochemistry’, ‘cell death and survival’, ‘cell-to-cell signaling and interaction’, ‘carbohydrate metabolism’ and ‘protein synthesis’. In conclusion, the present results demonstrated for the first time that prenatal protein undernutrition by albumen removal leads to long-term alterations of the hepatic transcriptome in the chicken.

overall_design: 3 biological replicates per group (control, sham, albumen-deprived) were analyzed

first: Eddy

last: Decuypere

first: Steven

last: Janssens

first: Johan

last: Buyse

first: Nadine

last: Buys

first: Nadia

last: Everaert


title: 7SK-BAF axis controls pervasive transcription at enhancers [ChIP-Seq]

status: Public on Feb 01 2016

city: Stanford

first: Ryan

middle: Alexander

last: Flynn

state: CA

address: 380 Roth Way, Room 265

country: USA

institute: Stanford University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Eukaryotic genomes are extensively transcribed, but unfettered transcription alters gene expression and leads to genome damage by several means. Divergent transcription occurs at active enhancers and promoters, distinct classes of cis-regulatory elements critical for precise control of gene expression. A key step in RNA Polymerase II (Pol II) transcription is promoter-proximal pausing, which occurs bidirectionally ~25-60 nucleotides downstream of transcription start sites (TSS). Promoter-proximal pause release is gated by the positive transcription elongation factor b (P-TEFb)-7SK snRNA pathway; release from 7SK allows P-TEFb phosphorylation of Pol II and subsequent elongation. The 7SK small nuclear ribonucleoprotein (snRNP) is thought to reside in the nucleoplasm, but it has been suggested that 7SK could operate physically on chromatin. Notably, while enhancer transcription is one of the earliest steps of gene activation12 and some enhancer RNAs (eRNAs) participate in gene regulation, far less is known about the control of eRNA transcription. Here we show that 7SK inhibits enhancer transcription by modulating nucleosome position. 7SK occupies enhancers and super enhancers genome-wide, and 7SK is required to limit eRNA initiation and synthesis in a manner distinct from promoter pausing. Clustered elements at super enhancers uniquely require 7SK to prevent convergent transcription of colliding polymerases. 7SK inhibits enhancer transcription by modulating chromatin structure, physically interacts with the BAF chromatin remodeling complex, and is required to recruit BAF to enhancers. Thus, 7SK employs distinct mechanisms to counteract diverse consequences of pervasive transcription that distinguish super enhancers, enhancers, and promoters

overall_design: Each experiment was performed in at least biological duplicate with input or other controls when appropriate.

middle: A

first: Brian

middle: T

last: Do

first: Adam

middle: J

last: Rubin

first: Eliezer

last: Calo

first: Byron

last: Lee

first: Michael

last: Rale

first: Ci

last: Chu

first: Joanna

last: Wysocka

first: Paul

last: Khavari

first: Howard

middle: Y

last: Chang


title: A ChIP-seq spike-in method enables detection of global histone modification changes across the genome

status: Public on Jan 31 2016

city: South San Francisco

first: Suchit

last: Jhunjhunwala

address: 1 DNA Way, MS-444A

institute: Genentech

summary: This study outlines a method that dramatically alters the interpretation of ChIP-seq data and will improve the quantitative comparison of histone modification maps across biological contexts or across various conditions within a given biological context.

overall_design: We introduced a small fraction of Drosophila chromatin into human ChIP samples and added a Drosophila-specific antibody as a means to consistently precipitate Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 levels is observed across the genome upon EZH2 inhibitor treatment.

last: Egan

first: Madeline

last: Craske

last: Labhart

first: Chih-Chi

last: Yuan

first: Gulfem

middle: D

last: Guler

first: David

last: Arnott

first: Tobias

last: Maille

first: Jennifer

last: Busby

first: Chisato

last: Henry

first: Theresa

middle: K

last: Kelly

first: Charles

last: Tindell

first: Feng

last: Zhao

first: Charlie

last: Hatton

first: Barbara

middle: M

last: Bryant

first: Marie

last: Classon

first: Patrick

last: Trojer


title: Transcriptional profiling of human and mouse nephron progenitor cells

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

type: Expression profiling by high throughput sequencing

summary: Nephron endowment is determined by the self-renewal and induction of a nephron progenitor pool established at the onset of kidney development. In the mouse, the related transcriptional regulators Six1 and Six2 play non-overlapping roles in nephron progenitors. Transient Six1 activity prefigures, and is essential for, active nephrogenesis. In contrast, Six2 maintains later progenitor self-renewal from the onset of nephrogenesis. We compared Six2’s regulatory actions in mouse and human nephron progenitors by chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq). Surprisingly, SIX1 was identified as a SIX2 target unique to the human nephron progenitors. Further, RNA-seq and immunostaining revealed overlapping SIX1 and SIX2 progenitor activity in the 16 week human fetal kidney. Human SIX1 ChIP-seq revealed a similar set of targets to SIX2, and predicted both factors bind DNA through an identical recognition site. In contrast to the mouse where Six2 binds its own enhancers but doesn’t interact with DNA around Six1, both human SIX1 and SIX2 bind homologous SIX2 enhancers and putative enhancers positioned around SIX1. Transgenic analysis of a putative human SIX1 enhancer in the mouse revealed a transient, mouse-like, pre-nephrogenic, Six1 regulatory pattern. Together, these data demonstrate a divergence in SIX-factor regulation between mouse and human nephron progenitors. In the human, an auto/cross-regulatory loop drives continued SIX1 and SIX2 expression during active nephrogenesis. In contrast, the mouse establishes only an auto-regulatory Six2 loop. It is tempting to speculate that differential SIX-factor regulation may contribute to species differences in the duration of progenitor programs and nephron output.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Profiling of human and mouse nephron progenitor cells with mRNA-Seq; cells were purified from human and mouse embryonic kidneys with ITGA+ Ab or transgenic Cited1TagRPF

first: Lori

last: O'Brien

first: Qiuyu

last: Guo

first: Anton

last: Valouev


title: Methylomes and Transcriptomes of Human Pluripotent-to-Cardiomyocyte Differentiation

status: Public on Jan 30 2016

city: Duarte

first: Joshua

last: Tompkins

address: 1500 E Duarte Road

department: DMRI

institute: City of Hope

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: 7SK-BAF axis controls pervasive transcription at enhancers [ATAC-Seq]

first: Ryan

last: Flynn

first: Brian

last: Do

first: Adam

last: Rubin

first: Eliezer

last: Calo

first: Byron

last: Lee

first: Michael

last: Rale

first: Ci

last: Chu

first: Joanna

last: Wysocka

first: Paul

last: Khavari

first: Howard

last: Chang


title: Methylomes and Transcriptomes of Human Pluripotent-to-Cardiomyocyte Differentiation [RNA-seq]

summary: In this report, Tompkins et al describe the derivation, differentiation stage-specific purification, and genome-wide analysis of cardiomyocytes derived from hESCs. Key features of the molecular programs that define human cardiac muscle cell differentiation were described and researchers observed that cells may harbor epigenetic DNA methylation “memories” that reflect the gene activation history of important developmental genes.

overall_design: For RNA-seq. Cardiomyocyte differentiation from human embryonic stem cells (H7). 11 time point pilot time series. D3 and D4 samples FACS sorted for primitive and cardiac mesoderm isolation, respectively. Data from negatives sorts (minus) included as well.


title: 7SK-BAF axis controls pervasive transcription at enhancers [ChIRP-Seq]


title: Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

city: University Park

first: Nabeel

last: Ahmed

state: PENNSYLVANIA

address: 407 Chemistry Building

department: The Huck Institutes of the Life Sciences

institute: Pennsylvania State University

summary: The rates at which domains fold and codons are translated are important factors in determining whether a nascent protein will co-translationally fold and function or misfold and malfunction. In this study, we develop a chemical kinetic model that calculates a protein domain’s co-translational folding curve using only the domain’s bulk folding and unfolding rates and codon translation rates. We show that this model accurately predicts the course of co-translational folding measured in vivo for four different protein molecules. As part of our chemical kinetic model, we assume that there is steady-state translation kinetics through the time-course of the experiment. To prove that this assumption is valid, we performed Ribo-Seq experiments on two biological replicates of yeast cells to compare their ribosome profiles. For genes with sufficient coverage across the open reading frames in both the replicates, we compare the ribosome profiles from both replicates and see a strong correlation. This implies there is a steady-state and our assumption is valid.

overall_design: Ribosome profiling of two biological replicates of S288C yeast cells

first: Ulrike

last: Friedrich

first: Daniel

last: Nissley

first: Ajeet

last: Sharma

first: Guenter

last: Kramer

first: Bernd

last: Bukau

first: Edward


title: Identification of microRNA targets in Arabidopsis by transcriptome profiling of wild-type and ago1-27 mutant plants

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

country: China

institute: Tianjin Normal University

summary: The goal of this study is to establish the global gene expression profiles of Arabidopsis wild type and ago1-27 mutant plants, and identify novel potential miRNA targets.

overall_design: RNA-seq was performed using Arabidopsis wild type and ago1-27 mutant flower buds. Three biological replicates were conducted for each genotype.

first: Shengben

last: Li

first: Xuemei

last: Chen


title: Next generation sequencing analysis of transcriptomes of Plasmodium falciparum male and female gametocytes

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

summary:
Investigation of overall expression level in Plasmodium falciparum male and female mature gametocytes, and detection of any transcriptional differences between male and female gametocytes.
The Plasmodium falciparum parasite with green fluorescent protein (GFP) expression under the control of alpha tubulin II promoter facilitated the separation of male and female gametocyte. This engineered parasite strain in this study are further described in Miao J,  Fan Q,  Parker D,  Li X,  Li J,  et al.  (2013) Puf Mediates Translation Repression of Transmission-Blocking Vaccine Candidates in Malaria Parasites. PLoS Pathog 9(4): e1003268.  doi: 10.1371/journal.ppat.1003268

overall_design: A 12 RNA-seq study was performed. Based on GFP intensity, equal number (4-5.5 X 10 6 ) of mature male and female gametocytes were separated by cell-sorter. Total RNA with and without rRNA depletion were processed for generation libraries using the Illumina TruSeq Stranded mRNA Library Preparation kit (Illumina Inc., San Diego, CA).  Libraries were sequenced on an Illumina HiSeq 2500 in Rapid Run mode using 100 nucleotide single read sequencing. Altogether, this study investigated three experimental replicates of transcriptomes for mRNA and rRNA from male and female gametocytes (12 samples)

first: Miao

last: Jun

first: Cui

last: Liwang


title: Methylomes and Transcriptomes of Human Pluripotent-to-Cardiomyocyte Differentiation [MBD-seq]

first: Joshua

last: Tompkins

overall_design: For MBD-seq Cardiomyocyte differentiation from human embryonic stem cells (H7). 4 time point series. D3 and D4 samples FACS sorted for primitive and cardiac mesoderm isolation, respectively. Cardiomyocytes were percoll density purified (cTnT >90%)


title: Transcriptome profile analysis of overexpression of SlRBZ results in etiolation and dwarfism by impairing chlorophyll, carotenoid, and gibberellin biosynthesis in tomato

status: Public on Jan 29 2016

city: wuhan

first: Yanna

last: Gao

address: hongshan area, shizishan street

institute: Huazhong agricultural university

summary:
Purpose: Many studies have demonstrated that ZFPs have important functions in many biological processes, including plant growth and development, stress response, and phytohormone response. RanBP2-type zinc finger transcription factors have been characterized in animals and humans. However, their functions remain largely unknown in plants. Therefore, the functions of RanBP ZFPs in plants need further study to shed new insights into the importance of these transcription factors in developmental processes.
Methods: The transcriptomes of between overexpression of SlRBZ  transgenic and wild-type tomato by RNA-seq analysis were evaluated using the Illumina HiSeq™ 2000 sequencing platform. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by Tophat and DEGseq software.  qRT–PCR validation was performed using  SYBR Green assays.
Results: In this study, we identified a RanBP2-type zinc finger protein gene (SlRBZ) in tomato. SlRBZ was constitutively expressed in roots, stems, leaves, flowers and fruits. Overexpression of SlRBZ resulted in etiolated and dwarf phenotypes in tomato. Determination of physiological index showed that chlorophyll, carotenoid, and GAs contents were evidently decreased in transgenic plants. Furthermore, the qRT-PCR and RNA-Seq analyses demonstrated that the transcription of the genes involved in these biosynthesis pathways obviously decreased in SlRBZ-OE plants. In addition, ultrastructural observation by transmission electron microscopy indicated that plastids could not develop into mature chloroplasts with normal chloroplast membrane and thylakoid membrane system in SlRBZ-OE plants.
Conclusions: The results suggest that overexpression of SlRBZ may impair the biosynthesis of chlorophyll, carotenoid, and gibberellin through blocking chloroplast development, resulting in etiolation and dwarfism in tomato.

overall_design: The transcriptomes of between overexpression of SlRBZ transgenic and wild-type tomato by RNA-seq analysis were evaluated, in duplicate, using the Illumina sequencing platform.

first: Zhibiao

last: Ye

first: Changxian

last: Yang

first: Mingqin

last: Fan


title: Investigating the role of Lef1 in mouse embryonic stem cells.

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary:
Genome-wide analysis of gene expression in piggybac empty vector and  piggybac-lef1 transfected mouse embryonic stem cells (46C mouse ESCs)
Analysis of genes regulated by lef1, and we found that lef1 acts biphasically in mouse embryonic stem cells.

overall_design: Total RNA obtained from empty vector (PB)-transfected 46 ESCs or different states (passage 2 and passage 5)  of lef1-transfected (PB-Lef1 P2, PB-Lef1 P5) 46C mouse ESCs.

first: Ying

last: Qilong

first: Ye

last: Shoudong


title: Transcriptome profiling of HEK 293T cells and BJ foreskin fibroblasts depleted of endogenous miRNAs

city: New York

first: Benjamin

last: tenOever

state: NY

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai


title: Transcriptome profiling of BJ foreskin fibroblasts (ATCC: CRL-2522) depleted of endogenous miRNAs

summary: Purpose: To determine the impact endogenous miRNAs have on the overall transcriptome profile of fibroblasts and on the intrinsic response to virus

overall_design: mRNA profiles of BJ fibroblasts treated with type 5  Adeno vectors expressing either GFP or GFP-VP55 for indicated time points alone or prior to treatment with IFNB or dsRNA

middle: R


title: Transcriptome profiling of HEK 293T cells depleted of endogenous miRNAs

summary: To assess the impact of AdV-VP55 mediated degredation of host miRNAs on the cellular transcriptome.

overall_design: mRNA profiles of HEK 293T cells treated with type 5 Adeno vectors expressing either GFP or GFP-VP55 for 24 hours


title: Plasma extracellular RNA profiles in healthy and cancer patients

city: Milwaukee

first: Liang

last: Wang

state: Wisconsin

address: 8701 Watertown Plank Rd.

department: Pathology

institute: Medical College of Wisconsin

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular vesicles such as exosomes are selectively enriched in RNA that has potential for use as disease biomarkers. To systemically characterize circulating extracellular RNA profiles, we performed RNA sequencing analysis on plasma extracellular vesicles derived from 192 individuals including 100 colon cancer, 36 prostate cancer and 6 pancreatic cancer patients along with 50 healthy individuals. Of ~12.6 million raw reads for each of these subjects, the number of mappable reads aligned to RNA references was ~5.4 million including microRNAs(miRNAs) (~40.4%), piwi-interacting RNAs(piwiRNAs) (~40.0%), pseudo-genes (~3.7%), long noncoding RNAs (lncRNAs) (~2.4%), tRNAs (~2.1%), and mRNAs (~2.1%). To select the best candidates for potential extracellular RNA reference controls, we performed abundant level stability testing and identified a set of miRNAs showing relatively consistent expression. To estimate biological variations, we performed association analysis of expression levels with age and sex in healthy individuals. This analysis showed significant sex association with seven small noncoding RNAs (false discovery rate, or FDR<0.05), while no small noncoding RNAs were statistically associated with age. To identify disease-associated RNA transcripts, we performed analysis of covariance by including disease status, age, sex, RNA isolation and gel size selection dates. We observed a gradual increase of significantly associated RNAs (in particular, miRNAs) with disease advancement as denoted by cancer staging. We found significant association of miR-125a-5p and miR-1246-3p with all cancer types tested (FDR<0.05). Based on the disease associations, we developed cancer type-specific multivariate statistical models to predict disease status with an area under the ROC curve from 0.67 in stage I colon cancer to 0.92 in advanced prostate cancer. To date, this is the largest RNA-seq study to systematically profile extracellular RNA species, which has not only provided a baseline reference profile for circulating extracellular RNA, but also a set of RNA candidates for reference controls and disease biomarkers.

overall_design: RNAs fro plasma circulating microviscles in 192 individuals were sequenced and quantified. RNA expression stability testing was performed to identify stably expressed RNAs. Distribution of RNA species and individual RNA transcripts were compared in normal and cancer patients.

first: Tiezheng

last: Yuan

first: Xiaoyi

last: Huang


title: mRNA profiling  of Hepatocellular carcinoma (HCC)

city: Gaithersburg

first: Dong

last: Shen

state: MD

address: MedImmune Way

department: Translational Science

institute: Medimmune

summary: We did mRNA profiling and  showed that an interferon-inducible gene's deletion and under-expression is significantly associated with shorter time to tumor recurrence, shorter progression-free survival, and shorter overall survival in  HCC patients.

overall_design: We got the samples from HCC patients' matched primary and recurrent tumors (n=10) and primary tumors from non-recurrent patients (n=15), we conducted the RNAseq of those samples, and did the comparison.

first: Higgs

last: Brandon


title: Comparison of expression profiles of Ba/F3 cells transduced with human CALR or human CALR + Type 1 mutation (hCALR-del52) by RNA-seq

city: Vienna

first: Franz

last: Klein

address: Dr. Bohr-Gasse 9

department: Chromosome Biology

country: Austria

institute: Max Perutz Labs, University of Vienna

summary: Murine Ba/F3 cells were transduced with retroviral vectors (pMSCV-IRES-GFP) expressing hCALR or hCALR-del52 and treated with 1ng/ml interleukin-3 (IL-3). RNA-seq was performed in triplicates, with on average 109 M reads per group (36 M reads per replicate).

overall_design: Three replicates of Ba/F3 cells constitutively expressing hCALR or hCALR-del52 were treated with IL-3 and subjected to RNA-seq, followed by differential expression analysis.

first: Doris

last: Chen

first: Ciara

last: Cleary

first: Harini

last: Nivarthi

first: Robert

last: Kralovics


title: Comparison between lamina propria macrophages and muscularis macrophages

city: NEW YORK

first: Thiago

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Lamina propria and muscularis macrophages, were sorted at steady steate and 2h after oral exposure to an attenuated form of Salmonella, comparison among these populations showed that the muscularis macrophages quckly respond to the presence of intestinal bacteria, upregulating some important tissue protective genes.

overall_design: intestinal macrophages from 3 mice were pooled into one RNA sample, the experiment was done control X infected and was repeated twice

first: Ilana

last: Gabanyi

first: Paul

last: Muller

first: Daniel

last: Mucida


title: Cell and microvesicle urine microRNA deep sequencing profiles from healthy individuals

status: Public on Jan 28 2016

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

summary: Background: Urine is a potential source of biomarkers for diseases of the kidneys and urinary tract. RNA, including microRNA, is present in the urine enclosed in detached cells or in extracellular vesicles (EVs) or bound and protected by extracellular proteins. Detection of cell- and disease-specific microRNA in urine may aid early diagnosis of organ-specific pathology. In this study, we applied barcoded deep sequencing to profile microRNAs in urine of healthy volunteers, and characterized the effects of sex, urine fraction (cells vs. EVs) and repeated voids by the same individuals. Results: Compared to urine-cell-derived small RNA libraries, urine-EV-derived libraries were relatively enriched with miRNA, and accordingly had lesser content of other small RNA such as rRNA, tRNA and sn/snoRNA. Unsupervised clustering of specimens in relation to miRNA expression levels showed prominent bundling by specimen type (urine cells or EVs) and by sex, as well as a tendency of repeated (first and second void) samples to neighbor closely. Likewise, miRNA profile correlations between void repeats, as well as fraction counterparts (cells and EVs from the same specimen) were distinctly higher than correlations between miRNA profiles overall. Differential miRNA expression by sex was similar in cells and EVs. Conclusions: miRNA profiling of both urine EVs and sediment cells can convey biologically important differences between individuals. However, to be useful as urine biomarkers, careful consideration is needed for biofluid fractionation and sex-specific analysis, while the time of voiding appears to be less important.

overall_design: Two urine voids from 20 healthy volunteers (10 men, 10 women). From each void cells and extracellular vesicles were purified and total RNA extracted. Thus 80 samples overall (however only 79 processed because 1 women did not provide sufficient urine in second void for extracellular vesicle purification).

middle: Z


title: DNA methylation dynamics during development in the rice blast fungus [Bisulfite-Seq]

city: Gangneung

first: Jaeyoung

last: Choi

address: 679 Saimdang-ro

country: South Korea

institute: Korea Institute of Science and Technology

summary: Cytosine methylation is an important epigenetic modification of DNA that is involved in genome defense and transcriptional regulation in eukaryotes. Despite extensive efforts to understand genome-wide distribution and function of DNA methylation in mammals and plants, contribution of DNA methylation to biology of microbial eukaryotes is largely unknown to date. Here we used genetic manipulations and high-throughput bisulphite sequencing on the model plant pathogenic fungus, Magnaporthe oryzae to elucidate the dynamics and mechanics of DNA methylation during pathogenic development.

overall_design: Samples from three different developmental satges (mycelia, conidia and appressorium) and two DNA methyltransferase absent isolates (dmt1 and dmt2)

first: Junhyun

last: Jeon

first: Gir-Won

last: Lee

first: Sook-Young

last: Park

first: Aram

last: Huh

first: Ralph

last: Dean

first: Yong-Hwan


title: A NOVEL EPIGENETIC SILENCING PATHWAY INVOLVING the HIGHLY CONSERVED 5'-3' EXORIBONUCLEASE Dhp1/Rat1/Xrn2 in SCHIZOSACCHAROMYCES POMBE [CRAC-seq]

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

summary:
Epigenetic gene silencing plays a critical role in regulating gene expression and contributes to organismal development and cell fate acquisition in eukaryotes.
In fission yeast, Schizosaccharomyces pombe, heterochromatin-associated gene silencing is known to be mediated by RNA processing pathways including RNA interference (RNAi) and a 3’-5’ exoribonuclease complex exosome.
Here, we report a new RNA-processing pathway that contributes to epigenetic gene silencing and assembly of heterochromatin mediated by 5’-3’ exoribonuclease Dhp1/Xrn2.
Dhp1 mutation causes defective gene silencing both at peri-centromeric regions and at the silent mating type locus.
Intriguingly, mutation of either one of two well-characterized Dhp1-interacting proteins, the Din1 pyrophosphohydrolase or the Rhn1 transcription termination factor, does not show silencing defects at the main heterochromatic regions.
Dhp1 is essential in the sequential steps of establishing silencing in a manner independent of both RNAi and the exosome.
Genomic and genetic analysis suggest that Dhp1 is involved in post-transcriptional silencing of repetitive regions through its catalytic activity. Our study is the first investigation into an unexpected role of Dhp1/Rat1/Xrn2 in chromatin-based silencing. These results elucidate how various RNA-processing pathways, acting together or independently, contribute to epigenetic regulation of the eukaryotic genome.

overall_design: CRAC-seq

first: James

last: Tucker

first: Corina

last: Ohle

first: Géza

last: Schermann

first: Katja

last: Bendrin

first: Wei

last: Zhang

first: Tamás

first: Ke


title: DNA methylation dynamics during development in the rice blast fungus [RNA-Seq]

summary: Cytosine methylation is an important epigenetic modification of DNA that is involved in genome defense and transcriptional regulation in eukaryotes. Contribution of DNA methylation to biology of microbial eukaryotes is largely unknown to date. Here we used RNA-seq to examine the impact of DNA methylation on transcriptional output in the genome of a model pathogenic fungus, Magnaporthe oryzae by comparing expression profiles of wild-type and methylation-deficient mutant strains.

overall_design: Samples from wild type mycelia and two DNA methyltransferase absent isolates (dmt1 and dmt2)


title: KMT2D regulates specific programs in heart development via histone H3 lysine 4 dimethylation

city: San Francisco

first: Siang-Yun

last: Ang

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

summary: Histone modifying genes involved in histone H3 lysine 4 (H3K4) methylation are critical for heart development, but the roles of these genes are not well understood. Here, we demonstrate a requirement for the H3K4 methyltransferase KMT2D in cardiac precursors and cardiomyocytes during cardiogenesis. Gene expression analysis revealed upregulation of hypoxia response genes, as well as downregulation of ion transport and cell cycle genes, leading to altered calcium handling and cell cycle defects. We further determined that myocardial Kmt2d deletion led to decreased H3K4me2 at promoters and enhancers. Finally, we identified KMT2D binding regions in cardiomyocytes, of which a subset was associated with decreased gene expression and decreased H3K4me2 in mutant hearts. This subset included genes related to ion transport, hypoxia-reoxygenation and cell cycle regulation, suggesting that KMT2D is important for these processes. Our findings indicate that KMT2D is essential for regulating cardiac gene expression during heart development via H3K4 dimethylation.

overall_design: Examination of H3K4me1, H3K4me2 and H3K4me3 in E11.5 mouse embryonic hearts.

first: Alec

last: Uebersohn

first: Benoit

last: Bruneau


title: DNA methylation dynamics during development in the rice blast fungus

first: Jaeyoung

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

overall_design: Refer to individual Series


title: Genome-wide analysis of E. coli MukB distribution using ChIP-sequencing

city: Oxford

first: Sophie

last: Nolivos

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: Oxford University

summary: Paper abstract : The Escherichia coli SMC complex, MukBEF, interacts with the ParC subunit of topoisomerase IV (TopoIV), consistent with sequential roles in chromosome unlinking and segregation. Although clusters of MukBEF molecules are normally associated with the chromosome replication origin region (ori), we demonstrate their association with the replication termination region (ter), which is enhanced when ATP hydrolysis by MukB is impaired. We show that MukBEF interacts in vivo and in vitro with MatP, which binds matS sites in ter. The MatP-MukBEF interaction limits the stable association of MukBEF complexes with ter and the availability of functional TopoIV during decatenation of sister ters. The MukBEF-TopoIV interaction is influenced by the nucleotide state of MukBEF. The combined action of MukBEF and MatP helps position MukBEF clusters in relation to the chromosome, thereby, influencing chromosome organization and segregation. Finally, we demonstrate that the regulated sequential action of TopoIV and MukBEF promotes chromosome decatenation and segregation.

overall_design: ChIP-seq profiles of E. coli MukB and ATPase-deficient MukBEQ and MukBDA mutants in triplicates. ChIP-seq of MukB and MukBEQ have been done in wild-type and ∆matP strain. ChIP-seq profiles of MatP in triplicates

first: Julius

last: Müller

first: David

last: Sherratt


title: Deep sequencing, profiling and detailed annotation of miRNAs in Takifugu rubripes

city: Bunkyo-ku

first: chaninya

last: wongwarangkana

state: Tokyo

address: 1-1-1 Yayoi

department: aquatic bioscience

country: Japan

institute: the university of tokyo

summary: We performed extensive transcriptome analysis of the tiger pufferfish (Takifugu rubripes) using the next-generation sequencer SOLiD III, and profiled millions of small RNA sequences in somatic tissues and gonads, as well as identifying thousands of miRNAs. The number of miRNAs identified was the highest in fish species reported to date. We also report highly variable isomiR features.

overall_design: miRNA expression profiles of 9 tissues (7-somatic tissues and 2-gonads) of torafugu were generated by deep sequencing using SOLiD3.

first: Chaninya

last: Wongwarangkana

first: Kazuhiro

middle: E

last: Fujimori

first: Masaki

last: Akiba

first: Shigeharu

last: Kinoshita

first: Morimi

last: Teruya

first: Maiko

last: Nezuo

first: Tsukahara

last: Masatoshi

first: Shugo

last: Watabe

first: Shuichi

last: Asakawa


title: A NOVEL EPIGENETIC SILENCING PATHWAY INVOLVING the HIGHLY CONSERVED 5'-3' EXORIBONUCLEASE Dhp1/Rat1/Xrn2 in SCHIZOSACCHAROMYCES POMBE

first: Tamas

last: Fischer

type:
Expression profiling by array
Other


title: Aggression, cognitive and neurodevelopmental abnormalities associated with disruption of the intellectual disability and histone demethylase gene Kdm5c.

status: Public on Jan 27 2016

city: Ann Arbor

first: Saurabh

last: Agarwal

state: Michigan

address: 1241 E. Catherine St. 5815 Medical Science II

department: Human Genetics

institute: University of Michigan

summary: We conducted ChIP-Seq of KDM5c in neurons isolated from E16.5 mouse embryonic cortices from WT and SMCX KO mice and harvested after 10 days in vitro culture.

overall_design: We sequenced KDM5c ChIP and Input samples from mouse embryonic cortical neurons cultured in vitro for 10 days using Active Motif's Spike-In ChIP-protocol. Experiments were performed in biological and technical duplicates.

first: Shigeki

last: Iwase

first: Emily

last: Brookes

first: Christina

middle: N

last: Vallianatos

first: Aimee

middle: I

last: Badeaux

first: Yang

last: Shi


title: Comprehensive identification of sexually dimorphic genes using RNA-seq with several tissues of cattle

city: Seoul

first: Minseok

last: Seo

address: Kwan-ak ro 1

department: Interdisciplinary program of bioinformatics

institute: Seoul National University

summary: Sexual dimorphism is one of the important topic in mammal species because appearance of males and females is obvious different in all mammal species. In addition to this, molecular mechanisms also very different each other. Furthermore, it is important to employ a variety of tissues in RNA-seq experiment because recent studies imply gene expression pattern are highly tissue specific. Although previous related studies discovered numerous sexually dimorphic mechanism in mammal species, but still, many mechanisms are undiscovered in case of non-model organisms. One of the representative mammal organism is a cattle which is less researched about sexual dimorphism. For investigate bovine sexual dimorphism, we generated two-way factorial designed 40 samples RNA-seq data composed with two factors such as gender and tissues. Two statistical approaches are employed for identifying bovine sexually dimorphic genes using such two-way factorial designed RNA-seq data. As a result, we observed that detected sexually dimorphic genes exhibited strong tissue specific pattern, but fat tissue showed relatively small tissue specificity than the others. In addition, we observed that sex-related genes are shared in two mammal species such as cattle and rat through qRT-PCR experiments. Finally, we investigated pros and cons of two statistical approaches for complex structured RNA-seq analysis.

overall_design: In this study, we aimed to identify genetic factors that contribute to sexual dimorphism in bovine metabolism. To achieve this goal, we have employed RNA-seq for elaborated estimation of gene expression in liver, muscle, visceral adipose tissue and pituitary gland.

first: Jin-Young

last: Jeong

first: Hyun-Jeong

last: Lee


title: Active DNA demethylation at enhancers during the vertebrate phylotypic period

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

summary: The vertebrate body plan and organs are shaped during a conserved embryonic phase called the phylotypic stage, however the mechanisms that guide the epigenome through this transition and their evolutionary conservation remain elusive. Here we report widespread DNA demethylation of enhancers during the phylotypic period in zebrafish, Xenopus and mouse. These enhancers are linked to developmental genes that display coordinated transcriptional and epigenomic changes in the diverse vertebrates during embryogenesis. Binding of Tet proteins to (hydroxy)methylated DNA, and enrichment of hydroxymethylcytosine on these regions, implicated active DNA demethylation in this process. Furthermore, loss of function of Tet1/2/3 in zebrafish caused reduced chromatin accessibility and increased methylation levels specifically on these enhancers, indicative of DNA methylation being an upstream regulator of phylotypic enhancer function. Overall, our study reveals a novel regulatory module associated with the most conserved phase of vertebrate embryogenesis and uncovers an ancient developmental role for the Tet dioxygenases.

sample_organism:
Danio rerio
Xenopus tropicalis
Mus musculus

overall_design: MethylC-Seq in zebrafish embryos, MethylC-seq in Xenopus tropicalis embryos, MethylC-seq in mouse embryos, MethylC-seq in zebrafish tissues, MethylC-seq in Xenopus tropicalis tissues, TAB-seq in zebrafish embryos, TAB-seq in Xenopus tropicalis embryos, TAB-seq in mouse embryos, RNA-seq in zebrafish embryos, RNA-seq in mouse embryos

first: Ryan

last: Lister


title: Effect of high-sugar feeding on wandering third instar larval fat body gene expression in Drosophila melanogaster

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

address: 4400 Vestal Parkway East

department: Biological Sciences

institute: Binghamton University

summary: We compared gene expression in the Drosophila fat body on control and high-sugar diets in order to gain insight into the role of this organ during caloric overload. Differential expression analysis revealed changes in gene expression suggestive of a role for CoA metabolism in the ability to tolerate high-sugar feeding. This led us to perform biochemical and mutant studies supporting a model where CoA is limiting in the face of caloric overload.

overall_design: Wild-type Drosophila were reared on control (0.15M sucrose) and high-sugar (0.7M sucrose) diets until the wandering stage. Fat bodies were isolated and RNA extracted to determine the effects of diet on gene expression using Illumina RNA-seq.

first: Thomas

last: Baranski


title: Suboptimal culture conditions induce more deviations in gene expression in male than in female bovine blastocysts

city: Gent

first: Dieter

last: De Coninck

address: J. Plateaustraat 22

department: Applied Ecology and Environmental Biology

institute: Ghent University

summary:
Background: Since the development of in vitro embryo production in cattle, different supplements have been added to embryo culture media to support development, with serum being the most popular. However, the addition of serum during embryo culture can induce high birth weights and low viability in calves (Large Offspring Syndrome). Global gene expression analysis of bovine embryos through RNA sequencing produced in different conditions (in vivo, in vitro with serum added and in vitro without addition of serum) can provide valuable information to optimize culture media for in vitro embryo production, which is necessary to obtain healthy offspring.
Results: Here, we used RNA sequencing to examine the effect of in vitro embryo production, either in serum or in serum-free conditions, on the global gene expression pattern of individual bovine blastocysts. For this purpose, we compared in vitro produced with in vivo derived embryos. The embryos produced in serum had ten times more genes differentially expressed than the embryos produced in serum-free conditions (1,106 vs. 110). Importantly, in vitro production appeared to have a different impact on the embryos according to their sex, with male embryos showing more deviations in their gene expression pattern than their female counterparts. In particular, embryos produced in the presence of serum showed the largest difference, with male embryos having eight times more genes differentially expressed than the females (1,561 vs. 200). This difference was reduced when the embryos were produced in serum-free conditions, where the male embryos had only about double the number of genes differentially expressed than their female counterparts (64 vs. 35). The pathways affected by in vitro production differed depending on the supplementation. While embryos produced in serum conditions had altered genes involved in RNA processing and mitosis, embryos produced in serum-free conditions showed aberrations in genes involved in lipid metabolism.
Conclusions: Serum supplementation had a major impact on the gene expression pattern of the embryos. On the contrary, the transcriptome of embryos produced in serum-free conditions resembled more in vivo derived embryos, although genes involved in lipid metabolism were altered. Male embryos appeared to be most affected by in vitro production, especially after serum supplementation.

overall_design: mRNA profiles of early blastocysts from both sexes grown in three different conditions (in vivo, in vitro with serum, in vitro without serum) were generated by deep sequencing using Illumina HiSeq 2000. Three to five replicates were used for each combination condition/sex.

first: Sonia

last: Heras

first: Mario

last: Van Poucke

first: Karen

middle: B

last: Goossens

first: Osvaldo

last: Pascottini

first: Filip

last: Van Nieuwerburgh

last: Deforce

first: Petra

middle: L

last: De Sutter

first: Jo

last: Leroy

first: Alfonso

last: Gutierrez-Adan

first: Luc

last: Peelman

first: Ann

last: Van Soom


title: The effects of 24-hour withdrawal from cocaine on nucleus accumbens transcript expression.

first: Immanuel

last: Purushothaman

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: The goal of the study was to determine how 24-hour  withdrawal from cocaine affects the expression profile of transcripts in the nucleus accumbens using genome-wide RNA-sequencing.  11-week old male C57/BL6 mice were injected mice intraperitoneally (IP) with saline (0.9%) or cocaine (20 mg/kg dissolved in 0.9% saline) for 7-days consecutive days, and 24-hours after the last injection, NAc tissue was dissected.  Mice were housed in group of 5 mice per cage, and all mice in a cage were injected with either saline or cocaine and thus there was no counter-balancing between groups.

overall_design: The nucleus accumbens from 5 mice (2 hemispheres per mouse) were combined per replicate, with 3 replicates for saline and cocaine in total.

first: Michael

last: Cahill


title: RNA-Seq in neurons from E16.5 mouse embryonic cortices from WT and SMCX KO mice

first: Saurabh

last: Agarwal

summary: We conducted RNA-Seq (using Direct Ligation of Adapters to first strand cDNA) in neurons from E16.5 mouse embryonic cortices from WT and SMCX KO mice and harvested after 10 days in vitro culture.

overall_design: We sequenced RNA samples after 10 days in vitro cultures in biological and technical duplicates. 4 RNA samples from WT and SMCX KO neurons. We also sequenced RNA samples from same neurons after stimulation with KCl for 60 mins. So a total of 8 RNA-Seq samples.

first: Shigeki

last: Iwase

first: Emily

last: Brookes

first: Aimee

last: Badeaux

first: Christina

last: Vallianatos

first: Yang

last: Shi


title: An epigenetic switch ensures transposon repression upon acute loss of DNA methylation in ES cells (ChIP-Seq)

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: DNA methylation profoundly impacts genome regulation, notably through the control of transposons. DNA methylation is extensively remodeled during two developmental periods in mammals, gametogenesis and early embryogenesis. Most of transposons families become then hypomethylated, raising the question of their regulation in absence of DNA methylation. To induce genome-wide demethylation, we relied on hypomethylation-inducing culture conditions of murine embryonic stem cells. Surprisingly, we observed two phases of transposon regulation. After a burst of derepression, which correlates with DNA methylation disappearance, both LTR and non-LTR retrotransposons were efficiently re-silenced. While histone H3 lysine 9 trimethylation (H3K9me3) remained stable, H3 lysine 27 trimethylation (H3K27me3) was reorganized upon loss of DNA methylation and contributed to transposon re-silencing. Interestingly, we observed that H3K9me3 and H3K27me3 co-occurred but in distinct regions of unmethylated transposon sequences. This unusual pattern may provide a mechanistic relay ensuring genome stability during developmental periods of programmed loss of DNA methylation.

overall_design: WGBS, RNA-seq, ChIP-seq of J1 ES cell during conversion from serum to 2i+vitC medium

first: Marius

last: Walter

first: Aurelie

last: Teissandier

first: Raquel

last: Pérez-Palacios

first: Deborah

last: Bourc'his


title: Deep sequencing of C. elegans microRNAs under starvation conditions

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

summary: In nature, animals often face feast or famine conditions. We aimed to identify the miRNAs of Caenorhabditis elegans that changed their expression under starvation conditions in stage L4 larvae. Our results highlight 14 miRNAs that show differential expression in starved versus well-fed larvae. In particular, miRNAs of the miR-35-3p/miR-41-3p family were upregulated 6-20 fold upon starvation. We verified the upregulation of miR-35-3p with qPCR. Additionally, we showed that the expression of gld-1, important in ovogenesis, and a validated target of miR-35-3p, was downregulated when the expression of miR-35-3p was higher. This study represents a starting point for a more comprehensive understanding of the role of miRNAs during starvation in C. elegans.

overall_design: Illumina small RNA sequencing of starved and well-fed L4 worms.

first: Laura

last: García-Segura

first: Martha

last: Pérez-Andrade

first: Armando

last: Hernández-Mendoza

first: Tzvetanka

last: Dinkova

first: Luis

last: Padilla-Noriega

first: Juan

last: Miranda-Rios


title: An epigenetic switch ensures transposon repression upon acute loss of DNA methylation in ES cells (RNA-Seq)


title: An epigenetic switch ensures transposon repression upon acute loss of DNA methylation in ES cells


title: Chromosome Conformation of Human Fibroblasts Grown in 3-Dimensional Spheroids

status: Public on Jan 26 2016

first: Indika

last: Rajapakse

state: MI

address: 1600 Huron Parkway, NCRC Building 520, Rm. 3392

department: Department of Computational Medicine & Bioinformatics

summary: In the study of interphase chromosome organization, genome-wide chromosome conformation capture (Hi-C) maps are often generated using 2-dimensional (2D) monolayer cultures. These 2D cells have morphological deviations from cells that exist in 3-dimensional (3D) tissues in vivo, and may not maintain the same chromosome conformation. We used Hi-C maps to test the extent of differences in chromosome conformation between human fibroblasts grown in 2D cultures and those grown in 3D spheroids. Significant differences in chromosome conformation were found between 2D cells and those grown in spheroids. Intra-chromosomal interactions were generally increased in spheroid cells, with a few exceptions, while inter-chromosomal interactions were generally decreased. Overall, chromosomes located closer to the nuclear periphery had increased intra-chromosomal contacts in spheroid cells, while those located more centrally had decreased interactions. This study highlights the necessity to conduct studies on the topography of the interphase nucleus under conditions that mimic an in vivo environment.

overall_design: Genome wide chromosome conformation capture (Hi-C) data from primary human fibroblasts grown in 2D and 3D plates, 2 replicates

last: Seaman

first: Haiming

last: Chen


title: Mapping of internal monophosphate 5’ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains

city: New York

first: David

middle: H

last: Bechhofer

address: One Gustave L. Levy Place, Box 1603

department: Department of Pharmacology and Systems Therapeutics

summary: The narrow-specificity endoribonuclease RNase III and the 5’ exonuclease RNase J1 have been recently found to be not essential in the Gram-positive model organism, Bacillus subtilis. In this study, we performed a global analysis of internal 5’ ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5’ monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions were direct targets of RNase III. A set of regular RNA-seq experiments were performed to investigate RNA profiles in these strains and used to account for the changes in RNA abundance indirectly caused by the loss of RNase III in PARE. The PARE analysis also revealed an accumulation of 3’-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. In addition, an endonuclease cleavage just two nucleotides downstream of the 16S rRNA 3’ end was discovered with PARE analysis. This latter observation begins to answer, at least for B. subtilis, a long-standing question on the exonucleolytic vs. endonucleolytic nature of 16S rRNA maturation

overall_design: Examination of 5' monophosphate ends of Bacillus sutbtilis RNAs in wild-type and ribonucleases-mutant strains by PARE (Parallel Analysis of RNA Ends)

first: Bo

last: Liu

first: Jeanne

last: DiChiara


title: Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-dose Ultraviolet Radiation in High-altitude Environments

city: Beijing

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

summary: Tibetan chickens exhibit specific adaptations to high-altitude conditions compared with their lowland counterparts. To illustrate the genetic mechanisms of such adaptations in highland chickens, the genomes of four highland and four lowland chicken populations were resequenced. Our results showed that genes under positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune response, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of non-synonymous single nucleotide polymorphisms between highland and lowland populations was also analyzed by chi-square test. The results showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development, which were related to adaptations to hypoxia and intense radiation. RNA sequencing also revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Additionally, an evident admixture found in Tibetan chickens suggested a history of introgression from lowland gene pools. Overall, our data provided new insights into the unique adaptation of highland animals to extreme environments.

overall_design: The genomes from eight chicken populations were resequenced by Illumina Hiseq 2000 to identify positively selected genes in highland populations and RNA-Seq of four chicken populations was also performed for differential expressed genes analysis. This series contains only the RNA-seq data.

first: Qian

first: Hao


title: Analysis of transcriptional targets of KLF6 in HCC through gene expression profiling and ChIP-sequencing

city: Worcester

first: Brian

middle: C

last: Lewis

state: Massachusetts

address: 364 Plantation Street; LRB 521

department: PGFE

institute: University of Massachusetts Medical School


title: Aggression, cognitive and neurodevelopmental abnormalities associated with disruption of the intellectual disability and histone demethylase gene Kdm5c

first: Saurabh

last: Agarwal


summary: We conducted ChIP-Seq of H3K4 methylation in neurons isolated from E16.5 mouse embryonic cortices from WT and SMCX KO mice and harvested after 10 days in vitro culture.

overall_design: We sequenced H3K4me1, H3K4me3 ChIP and Input samples from mouse embryonic cortical neurons cultured in vitro for 10 days. Experiments were performed in biological and technical duplicates.

first: Shigeki

last: Iwase

first: Emily

last: Brookes

first: Aimee

last: Badeaux

first: Christina

last: Vallianatos

first: Yang

last: Shi


title: RNA-Seq of Pre-frontal cortex (PFC) and Amygdala from 3-6 month old adult mice

summary: We sequenced RNA from Pre-frontal cortex (PFC) and Amygdala from 3-6 month old adult mice.

overall_design: The amygdala and the frontal cortex were dissected from three adult mice for each genotype (WT and SMCX KO) and homogenized in trizol. RNA was purified using Qiagen RNEasy kit and ribosomal RNA was depleted using Ribominus Eukaryote v2 kit from Life Technologies. RNA-Seq libraries were prepared using Direct Ligation of Adapters to first strand cDNA (DLAF) and subjected to 50 base sequencing on Illumina HiSeq2000.


title: LPS and brain inflammation

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
Normal mice were injected i.p. with LPS or saline. 24h later, perfused brains were dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields ~100ng for neurons, ~20ng for microglia, and ~10ng for astrocytes.
cDNA was generated from up to 25 ng of total RNA using Nugen's RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 μg of sheared cDNA was taken into further processing, starting at end repair step, using Illumina's TruSeq RNA Sample Preparation Kit v2 (Illumina).
The "SAMID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0005404

overall_design: Astrocytes, microglia and neurons were sorted from LPS or saline treated mice. n=4 or 5 per group.

first: Karpagam

last: Srinivasan

last: Hansen


title: Embryonic stem cells exhibit mRNA isoform-specific translational regulation

city: Singapore

first: Vivek

last: Tanavde

state: Singapore

address: 30 Biopolis Street, #07-01, Matrix

department: Genome and Gene Expression Data Analysis Division

country: Singapore

institute: Bioinformatics Institute, A*STAR, Singapore

summary: Investigation of the differential translation rates of individual mRNA variants in embryonic stem cells (ESCs) and in ESC-derived neural precursor cells (NPCs) using polysome profiling coupled to RNA sequencing.

overall_design: Mouse ESCs were differentiated into Sox1-positive neural precursor cells (NPCs). One replicate of ESCs and NPCs were harvested and subjected to polysome fractionation. Fractions containing polysomes were purified and analysed by SOLiD sequencing. Expression levels in NPCs were compared to ESCs.

first: Queenie

middle: W

last: Wong

first: Candida

last: Vaz

middle: Y

last: Lee

first: Tian

last: Zhao

first: Raymond

last: Luo

first: Stuart

last: Archer

first: Thomas

last: Preiss

first: Leah

last: Vardy


title: Gene expression analysis following JQ1 treatments in colon cancer lines

first: Florian

last: Gnad

institute: Genentech

summary: RNAseq is performed (50bp single end reads) on SW480, HT-29, HCT-15, HCT-116, COLO 205, and COLO 320 cell lines after DMSO or JQ1 treatment

overall_design: Examination of transcriptomic changes after JQ1 treatment

first: Ron

last: Firestein

first: Mark

last: McCleland


title: CCAT1 is a cMYC super-enhancer templated RNA that predicts BET sensitivity in cancer

summary: ChIP-seq for Brd4 and H3K27ac in a panel of CIMP(+) and CIMP(-) colon cancer cell lines

overall_design: Examination of Brd4 binding patterns and H3K27ac patterns to identify super-enhancers

first: Kathryn

last: Blaschke


title: Gene expression analysis of BRD4 knockdown in HT-29 and HCT116 cells

summary: RNAseq is performed (50bp single end reads) on HT-29 and HCT-116 cell lines utilizing two independent shRNAs against BRD4 and a non-targeting control shRNA (NTC)

overall_design: Examination of transcriptomic changes after knockdown of BRD4


title: Ambient O2 pressure induces NF-kB1/RelA related inflammatory response in human lung epithelial cells in vitro

city: Tuxedo

first: Suresh

last: Cuddapah

address: 57 Old Forge Road

department: Environmental Sciecne

institute: New York University Langone Medical center

summary:
Purpose: Oxygen (O2) levels in cell culture conditions is typically 2-5 fold higher than the physiological O2 levels that most tissues experience in vivo. The ambient atmospheric O2 (21%) is known to induce cell proliferation defects and cellular senescence in stem cell and primary cell cultures. Therefore, culturing these cells under lower O2 levels (2-9%) is currently a standard practice. However, the non-cancerous immortalized cells and cancer cells, which evade cellular senescence are normally cultured under 21% O2 levels and the effects of higher O2 levels on these cells are not fully understood.
Methods: Gene expression (RNA seq transcriptomics) analysis of immortalized human bronchial epithelial (BEAS-2B) cells cultured at ambient 21% O2 and lower 10% O2 levels for 3 days and 3 weeks. Further the beneficial effects of cuturing cells under lower oxygen tension is evalulated
Results: Our results show NF-κB/RelA mediated activation of pro-inflammatory cytokines as a major outcome of cells being cultured 21% O2. Moreover, we demonstrate increased RelA binding at the NF-κB1/RelA target gene promoters at 21% O2. Interestingly, contrary to cells cultutred at 21% O2, external stress induced by H2O2 exposure did not induce inflammatory response in cells grown at 10% O2, suggesting increased ability to handle external stress in cells cultured at lower O2 levels.

overall_design: RNA Seq gene expression comparision done in replicates

first: Max

last: Coasta

first: Lakshmanan

last: Jagannathan


title: Genome-wide distribution and function of ATP-dependent chromatin remodelers in embryonic stem cells

city: Gif-sur-Yvette

first: Matthieu

last: GERARD

address: SBIGeM bldg 142

institute: CEA

summary: This study describes the distribution and functional analysis of ATP-dependent chromatin remodelers in mouse 46C ES cells. The remodelers for which ChIP-Seq profiles were generated are Brg1, Chd1, Chd2, Chd4, Chd6, Chd8, Chd9 and Ep400. We first generated ES cell lines expressing individual remodelers fused to an affinity tag at the C-terminus, from their endogenous loci. Remodelers were then formaldehyde-crosslinked to chromatin in vivo, MNase digested to release individual nucleosomes, then immunoprecipitated sequentially with two distinct antibodies against the tag. DNA fragments immunoprecipitated with each factor  were then identified by high throughput sequencing. Control experiments were realized by applying the same protocol to untagged ES cells. Pol II distribution was examined by ChIP-exo in ES cells depleted of either Ep400, Brg1 and Chd4. Chromatin access was studied by ATAC-seq in remodeler-depleted cells. Finally, nucleosomal occupancy was  explored by MNase-seq.

overall_design: ChIP-Seq profiling, FAIRE-seq profiling, RNA-Seq profiling, ATAC-seq profiling, MNase-seq profiling, ChIP-exo profiling on mouse ES cells

first: Isabelle

last: Hmitou

first: Maud

last: de Dieuleveult

first: Arnaud

last: Depaux

first: Sophie

last: Chantalat

first: Kuangyu

last: Yen

first: B

middle: F

last: Pugh

last: Gérard


title: RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations

status: Public on Jan 25 2016

city: Tjelle

first: Tina

middle: Sorensen

last: Dalgaard

address: Blichers Allé 20

department: Department of Animal Science

country: Denmark

institute: Aarhus University

summary:
Background: Avian infectious bronchitis (IB) is an acute and highly contagious disease of the upper-respiratory tract caused by infectious bronchitis virus (IBV). Understanding the molecular mechanisms involved in the interaction between innate and adaptive immune responses to IBV infection is a crucial element for further improvements in strategies to control IB. To this end, two chicken lines, selected for high and low serum concentration of mannose-binding lectin (MBL), a soluble pattern recognition receptor, were studied. In total, 32 birds from each line (designated L10H for high and L10L for low MBL serum concentration, respectively) were used. Sixteen birds from each line were infected with IBV at 3 weeks of age and sixteen birds were left uninfected. Eight uninfected and eight infected birds from each line were euthanized at 1 and 3 weeks post infection. RNA sequencing was performed on spleen samples from all 64 birds used in the experiment. Differential gene expression analysis was performed for four comparisons: L10L line versus L10H line for uninfected birds at weeks 1 and 3, respectively, and L10L line versus L10H line for infected birds at weeks 1 and 3, respectively.  Functional analysis based on the differentially expressed genes was performed using Gene Ontology (GO) Immune System Process terms specific for Gallus gallus.
Results: Comparing uninfected L10H and L10L birds, we identified 1698 and 1424 differentially expressed (DE) genes at weeks 1 and 3, respectively. For the IBV-infected birds, 1934 and 866 DE genes were identified between the two lines at weeks 1 and 3, respectively. In both cases DE genes had FDR-adjusted p-value <0.05. The two most enriched GO terms emerging from the comparison of  uninfected birds between the two lines were “Lymphocyte activation involved in immune response” (GO:0002285) and “Somatic recombination of immunoglobulin genes involved in immune response” (GO:0002204) at weeks 1 and 3, respectively. When comparing IBV-infected birds between the two lines, the most enriched GO terms were “Alpha-beta T cell activation” (GO:0046631) and “Positive regulation of leukocyte activation” (GO:0002696) at weeks 1 and 3, respectively.
Conclusion: Healthy birds from the two lines showed significant differences in expression profiles for subsets of both adaptive and innate immunity-related genes, whereas comparison of the IBV-infected birds from the two lines showed differences in expression of immunity-related genes involved in T cell activation and proliferation. The observed transcriptome differences between the two lines indicate that selection for MBL had a much wider effect than solely on serum MBL concentration, and in addition influenced the innate and adaptive immune responses. Future research will focus on identifying signatures of selection in order to further understand molecular pathways be responsible for differences between the two lines as well as for efficient IBV immune protection.

overall_design: For this study 64 spleen samples were harvested and used for RNA sequencing from birds originating from the two Aarhus University inbred lines, L10H and L10L. The birds were infected at age of 3 weeks and they were sacrificed 1 and 3 weeks post infection by cervical dislocation and spleen samples were collected. At both time points, eight samples from the two lines, L10H and line L10L, from each group (uninfected and infected) were collected.

middle: S

first: Edin

last: Hamzic


title: Next generation sequencing based transcriptomic analysis of oxidative stress response in Bifidobacterium longum BBMN68

first: Fanglei

last: Zuo

address: No. 17 Qinghua East Road, Haidian District

summary: Bifidobacterium longum strain BBMN68 is resistant to low concentrations of oxygen. In this study, a transcriptomic study was performed to detail the cellular response of B. longum strain BBMN68 to oxidative stress. Oxygen and its intermediate metabolites, reactive oxygen species (ROS), induced abundant changes in gene expression at the mRNA level. Increased expression was found for genes involved in ROS detoxification and the redox homeostasis system, protein and DNA synthesis and repair, the Fe–S cluster assembly system, and biosynthesis of branched-chain amino acids and tetrahydrofolate. Among them, two classes of ribonucleotide reductase (RNR), which are important for deoxyribonucleotide biosynthesis, were rapidly and persistently induced: first, the class Ib RNR NrdHIEF and then the class III RNR NrdDG. The increased resistance to oxygen and hydrogen peroxide conferred by NADH oxidase was confirmed by its heterogeneous overexpression in B. longum strain NCC2705. In addition, cell-membrane and cell-wall compositions were modified, probably by an increase in cyclopropane fatty acids and a decrease in polysaccharides, respectively, resulting in improved cell hydrophobicity and autoaggregation; this subsequently reduced the permeation of dissolved oxygen into the cell. Taken together, the proposed cell model of B. longum responses to oxygen stress suggests that this bacterium employs a complex molecular defense mechanism against oxygen-induced stresses.

overall_design: Whole mRNA profiles of B. longum BBMN68 grown in the absence or presence of 3% oxygen were generated using AB SOLiD technology and differentially expressed genes were analyzed.

first: Shangwu

last: Chen


title: Genome-wide sequencing of hippocampal 5-hydroxymethylcytosine  links plasticity genes to acute stress

city: Madison

first: Reid

last: Alisch

address: 6001 Research Park Blvd

institute: University of Wisconsin-Madison

summary: We used an established chemical labeling and affinity purification method coupled with high-throughput sequencing technology to generate the first genome-wide profile of hippocampal 5hmC following exposure to acute restraint stress and a one-hour recovery. This approach found a genome-wide disruption in 5hmC associated with acute stress response, primarily in genic regions, and identified known and potentially novel stress-related targets that have a significant enrichment for neuronal ontological functions. Integration of these data with hippocampal gene expression data from these same mice found stress-related hydroxymethylation correlated to altered transcript levels and sequence motif predictions indicated that 5hmC may function by mediating transcription factor binding to these transcripts. Together, these data reveal an environmental impact on this newly discovered epigenetic mark in the brain and represent a critical step toward understanding stress-related epigenetic mechanisms that alter gene expression and can lead to the development of psychiatric disorders.

overall_design: Examined the effect of a 30 minutes acute stress on hippocampal 5hmC profile of adult C57BL/6J background male mice.

first: Sisi

last: Li

first: Ligia

last: Papale

first: Qi

last: Zhang

first: Andy

last: Madrid

first: Li

first: Pankaj

last: Chopra

first: Sündüz

last: Keleş

first: Peng

last: Jin


title: Sorted cells_PS2APP brains_7/13mo

first: Brad

last: Friedman

summary:
Mice of indicated ages and genotypes were perfused and their brains dissected and dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields ~100ng for neurons, ~20ng for microglia, and ~10ng for astrocytes.
cDNA was generated from up to 25 ng of total RNA using Nugen’s RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 μg of sheared cDNA was taken into further processing, starting at end repair step, using Illumina’s TruSeq RNA Sample Preparation Kit v2 (Illumina).
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0006149

overall_design: Astrocytes, microglia and neurons were sorted from 7- or 13-month old PS2APP or non-transgenic mice, 4 ≤ n ≤ 7 per group.

first: Karpagam

last: Srinivasan

first: David

last: Hansen


title: DNA binding sites of KLF6 in murine HCC

first: Brian

last: Lewis

summary: We sequenced DNA isolated from performing ChIP of full-length KLF6 and an Input sample in an HCC cell line. The goal is to determine KLF6 binding sites in a mouse-derived HCC cell line.

overall_design: Determination of KLF6 binding sites in an HCC cell line using 2 control input libraries and 2 KLF6-ChIP libraries

first: Leanne

middle: G

last: Ahronian


title: Distinct expression profiles of soft tissue sarcomas

city: Stanford

first: Xiangqian

last: Guo

address: 300 Pasteur Dr.

department: Department of Pathology

institute: Stanford University

summary: Soft tissue sarcomas (STTs) are neoplasms of mesenchymal cells, and are composed of more than 60 subtypes. Although many of these STTs could be distinguished from each other by morphology and limited IHC biomarkers, the precise diagnosis of STTs with similar morphology is still difficult to achieve. Therefore developing novel diagnosis biomarker and molecular signatures will be very helpful to pathologist in clinic.

overall_design: Within this study, 3’ end RNA Sequencing (3SEQ) was used to expression profile different subtypes of soft tissue sarcomas.

first: Shirley

middle: X

last: Zhu

first: Sushama

last: Varma

first: Robert

last: West

first: Matt

last: van de Rijn


title: RNA-Seq analysis of INO80 complex deletion mutants

first: Devin

middle: Aalpoel

last: King

address: 371 Serra Mall

department: Biology

summary: ATP-dependent chromatin remodeling complexes are essential for transcription regulation, and yet it is unclear how these multisubunit complexes coordinate their activities to facilitate diverse transcriptional responses. In this study, we found that the conserved Arp5 and Ies6 subunits of the Saccharomyces cerevisiae INO80 chromatin-remodeler form an abundant and distinct subcomplex in vivo and stimulate INO80-mediated activity in vitro. Moreover, our genomic studies reveal that the relative occupancy of Arp5-Ies6 correlates with nucleosome positioning at transcriptional start sites and expression levels of >1,000 INO80- regulated genes. Notably, these genes are significantly enriched in energy metabolism pathways. Specifically, arp5d, ies6d, and ino80d mutants demonstrate decreased expression of genes involved in glycolysis and increased expression of genes in the oxidative phosphorylation pathway. Deregulation of these metabolic pathways results in constitutively elevated mitochondrial potential and oxygen consumption. Our results illustrate the dynamic nature of the INO80 complex assembly and demonstrate for the first time that a chromatin remodeler regulates glycolytic and respiratory capacity, thereby maintaining metabolic stability.

overall_design: RNA-Seq was performed on two biological replicates of each of the following yeast strains: WT (BY4741), ino80del, arp8del, arp5del, and ies6del.

first: Wei

last: Yao


title: Histone variant 3 regulates RNA polymerase II transcription termination and dual strand transcription of siRNA loci in Trypanosoma brucei

city: Athens

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: Histone variant 3 (H3V) is a kinetoplastid specific histone variant that is enriched at RNA polymerase II termination sites and telomeres. We previously found that the DNA modification base J, which co-localizes with H3V, functions to prevent readthrough transcription within gene clusters in T. brucei. We now demonstrate a similar role for H3V, where the loss of this histone variant results in increased expression of downstream genes. The effect is larger when both H3V and J are lost. Additionally, removal of H3V results in increased siRNAs from dual strand transcribed loci as well as increased expression of silent VSGs, indicating a role of H3V in the regulation of antigenic variation

overall_design: The role of H3V in regulating transcription termination was investigated using WT and H3V KO T. brucei cell lines. The role of J was also studied by treating each of these cell lines with DMOG, an inhibitor of J synthesis. We used 4 RNA seq libraries to determine gene expression changes following the loss of H3V and J

last: Sabatini

last: Reynolds

first: Laura

last: Cliffe

first: Nicolai

last: Siegel

first: Magdy

last: Alabady

first: Brigitte

last: Hofmeister


title: Identification of factors involved in target RNA-directed microRNA degradation

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: The mechanism by which micro (mi)RNAs control their target gene expression is now well understood. It is however less clear how the level of miRNAs themselves is regulated. Under specific conditions, abundant and highly complementary target RNA can trigger miRNA degradation by a mechanism involving nucleotide addition and exonucleolytic degradation. One such mechanism has been previously observed to occur naturally during viral infection. To date, the molecular details of this phenomenon are not known. We report here that both the degree of complementarity and the ratio of miRNA/target abundance are crucial for the efficient decay of the small RNA. Using a proteomic approach based on the transfection of biotinylated antimiRNA oligonucleotides, we set to identify the factors involved in target-mediated miRNA degradation. Among the retrieved proteins, we identified members of the RNA-induced silencing complex, but also RNA modifying and degradation enzymes. We further validate and characterize the importance of one of these, the Perlman Syndrome 3’-5’ exonuclease DIS3L2. We show that this protein interacts with Argonaute 2 and functionally validate its role in target-directed miRNA degradation both by artificial targets and in the context of mouse cytomegalovirus infection.

overall_design: To show the importance of TUT1 and DIS3L2 in target-induced miRNA decay we knocked-down by RNAi these two genes, either individually or in combination, and measured the effect of antimiRNA oligonucleotides by cloning and sequencing small RNAs. As a negative control, we used an siRNA directed against the RLUC gene. We generated one library per condition.

first: Gabrielle

last: Haas

first: Semih

last: Cetin

first: Mélanie

last: Messmer

first: Béatrice

last: Chane-Woon-Ming

first: Olivier

last: Terenzi

first: Johana

last: Chicher

first: Lauriane

last: Kuhn

first: Philippe

last: Hammann


title: PS2APP whole tissue RNAseq

first: Brad

last: Friedman

state: CA

summary:
RNA was purified from intact cerebrocortical tissue of female PS2APP or non-transgenic mice, perfused at 7 or 13 months of age.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0007648

overall_design: RNA from whole cortex of female PS2APP or non-transgenic mice at 7 or 13 months.

first: Karpagam

last: Srinivasan

first: David

last: Hansen


title: Identification of sex-biased miRNA involved in sex differentiation and spermatogenesis in yellow catfish by comparative transcriptome analysis

status: Public on Jan 24 2016

city: Wuhan

first: Jie

last: Mei

state: Hubei

address: No.7, Donghu South Road, Wuchang District

department: Institute of Hydrobiology

institute: Chinese Academy of Sciences

summary: In this study, three small RNA libraries constructed from gonad tissues of XX female, XY male and YY super-male yellow catfish were sequenced by Solexa high-throughput sequencing technology to investigate the expression pattern of sex-biased microRNA. The sequencing data generated a total of 384 conserved miRNAs and 113 potential novel miRNAs, among which 23, 30 and 14 miRNAs were specifically detected in XX ovary, XY testis, and YY testis, respectively. Interestingly, more abundant piRNAs were found in ovary compared to testis in yellow catfish, which phenomenon is also observed in other fish species but opposite in mammalians. We detected a number of microRNAs differentially expressed between ovary and testis, such as miR-21, miR-462, miR-430 and -200 family. When compared the transcriptome between XY and YY testis, we observed relative lower expression of miR-141 and miR-429 in YY testis. Histological analysis indicated that YY super-males have more spermatids and less spermatocytes in spermatogenic cyst than XY males under the same age and culturing conditions. The expression level of miR-141 and 429 coincides with the progression of spermatogenesis both in yellow catfish and human. At last, The expression pattern of nine arbitrarily selected miRNAs detected by quantitative RT-PCR was consistent with the Solexa sequencing results. Our study provides a comprehensive miRNA transcriptome analysis for gonad of yellow catfish with different sex genotypes, and identifies a number of  sex-biased miRNAs that are potentially involved in sex differentiation and spermatogenesis.

overall_design: Examination of small RNA expression profilings in yellow catfish gonads of three sex genotypes

first: Jing

last: Jing


title: An epigenetic switch ensures transposon repression upon acute loss of DNA methylation in ES cells (WGBS)

first: Nicolas

last: Servant

address: 26 rue d'ulm

summary: DNA methylation profoundly impacts genome regulation, notably through the control of transposons. DNA methylation is extensively remodeled during two developmental periods in mammals, gametogenesis and early embryogenesis. Most of transposons families become then hypomethylated, raising the question of their regulation in absence of DNA methylation. To induce genome-wide demethylation, we relied on hypomethylation-inducing culture conditions of murine embryonic stem cells. Surprisingly, we observed two phases of transposon regulation. After a burst of derepression, which correlates with DNA methylation disappearance, both LTR and non-LTR retrotransposons were efficiently re-silenced. While histone H3 lysine 9 trimethylation (H3K9me3) remained stable, H3 lysine 27 trimethylation (H3K27me3) was reorganized upon loss of DNA methylation and contributed to transposon re-silencing. Interestingly, we observed that H3K9me3 and H3K27me3 co-occurred but in distinct regions of unmethylated transposon sequences. This unusual pattern may provide a mechanistic relay ensuring genome stability during developmental periods of programmed loss of DNA methylation.

overall_design: WGBS, RNA-seq, ChIP-seq of J1 ES cell during conversion from serum to 2i+vitC medium

first: Marius

last: Walter

first: Aurelie

last: Teissandier

first: Raquel

last: Pérez-Palacios

first: Deborah

last: Bourc'his


title: Distinct routes of lineage development reshape the human blood hierarchy across ontogeny

status: Public on Jan 23 2016

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

country: Canada

institute: UHN

summary: In a classical view of hematopoiesis, the various blood cell lineages arise via a hierarchical scheme starting with multipotent stem cells that become increasingly restricted in their differentiation potential through oligopotent and then unipotent progenitors. We developed a cell-sorting scheme to resolve myeloid (My), erythroid (Er), and megakaryocytic (Mk) fates from single CD34+ cells and then mapped the progenitor hierarchy across human development. Fetal liver contained large numbers of distinct oligopotent progenitors with intermingled My, Er and Mk fates. However, few oligopotent progenitor intermediates were present in the adult bone marrow. Instead only two progenitor classes predominate, multipotent and unipotent, with Er-Mk lineages emerging from multipotent cells. The developmental shift to an adult 'two-tier' hierarchy challenges current dogma and provides a revised framework to understand normal and disease states of human hematopoiesis.

overall_design: Using SMARTseq, the expression profile of the new subsets identified in the linked study (12 samples in duplicates) were analyzed using RNA sequencing. The indicated subsets are all derived from neonatal cord blood.

first: Faiyaz

last: Notta

first: Gavin

last: Wilson

first: John

middle: E

last: Dick


title: Identification and comparative profiling of microRNAs in an early flowering mutant of trifoliate orange (Poncirus trifoliata (L.) Raf.) and its wild type by genome-wide high throughput sequencing

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

institute: Huazhong Agricultural University

summary: Solexa sequencing was performed at different developmental stages both an early flowering mutant of trifoliate orange (precocious trifoliate orange, Poncirus trifoliata L. Raf.) and its wild-type in this study, resulting in the obtainment of a total of 143 known miRNAs belonging to 99 families and 75 novel miRNAs in four libraries. A total of 317 potential target genes were predicted based on the 50 novel miRNAs families, GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in diverse cellular processes in plants, including development, transcription, protein degradation and cross adaptation. To characterize those miRNAs expressed at the juvenile and adult development stages of the mutant and its wild-type, further analysis on the expression profiles of several miRNAs through real-time PCR was performed. The results revealed that most miRNAs were down-regulated at adult stage compared with juvenile stage both the mutant and its wild-type. These results indicate that both conserved and novel miRNAs may play important roles in citrus growth and development, stress responses and other physiological processes.

overall_design: To understand whether miRNA was involved in the lowering process, the miRNA levels was investigated in juvenile and adult precocious trifoliate orange and its wild-type by Solexa sequencing.

first: Jin-zhi

last: Zhang

first: Chun

last: Hu


title: Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age (RNA-Seq)

city: Baltimore

first: Andrew

last: Jaffe

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

institute: Lieber Institute for Brain Development

summary: Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine. We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue. We hypothesized that these differences in culture success were related to epigenetic differences between the cultured fibroblasts by sampling location, and therefore generated genome-wide DNA methylation and transcriptome data on 11 intrinsically matched pairs of dural and scalp fibroblasts from donors across the lifespan (infant to 85 years). While these cultured fibroblasts were several generations removed from the primary tissue and morphologically indistinguishable, we found widespread epigenetic differences by sampling location at the single CpG (N=101,989), region (N=697), “block” (N=243), and global spatial scales suggesting a strong epigenetic memory of original fibroblast location. Furthermore, many of these epigenetic differences manifested in the transcriptome, particularly at the region-level. We further identified 7,265 CpGs and 11 regions showing significant epigenetic memory related to the age of the donor, as well as an overall increased epigenetic variability, preferentially in scalp-derived fibroblasts -83% of loci were more variable in scalp, hypothesized to result from cumulative exposure to environmental stimuli in the primary tissue. By integrating publicly available DNA methylation datasets on individual cell populations in blood and brain, we identified significantly increased inter-individual variability in our scalp- and other skin-derived fibroblasts on a similar scale as epigenetic differences between different lineages of blood cells. Lastly, these epigenetic differences did not appear to be driven by somatic mutation - while we identified 64 probable de-novo variants across the 11 subjects, there was no association between mutation burden and age of the donor (p=0.71). These results depict a strong component of epigenetic memory in cell culture from primary tissue, even after several generations of daughter cells, related to cell state and donor age.

overall_design: We performed RNA sequencing (RNA-seq) on scalp- and dura-derived cultured fibroblasts derived from 11 postmortem donors (22 samples) from across the lifespan, ranging from early infancy to 85 years. We removed one dura sample (2533.Dura) prior to aligning the reads to the genome, because it did not pass quality control in the first stage of our experiment (the DNA methylation data from that sample was lower in quality compared to the other samples). Data from this sample (2533.Dura) is not included in the processed data files deposited to GEO, but fastq files from that sample are available on SRA. The tissue donor demographics are tabulated in S1 Table in the publication. Briefly, 1 donor was female, the rest were male. 1 donor was African American, 1 was Hispanic, and the others were all Caucasian. 2 donors were diagnosed with Bipolar disorder, the diagnosis was unknown for 5 of the donors, and the remaining 4 donors were Controls.

first: Nikolay

last: Ivanov

first: Thomas

middle: M

last: Hyde


title: RNA-seq. and DNA-seq. of Pseudomonas aeruginosa PAO1 derived membrane vesicles

city: Tsukuba

first: Masanori

last: Toyofuku

address: Tennoudai 1-1-1

institute: University of Tsukuba

summary: The purpose of this study is to identify RNA and DNA associated with outer membrane vesicle and compare it with the cells

overall_design: Rna-Seq and DNA-Seq of purified OMV and cells

first: Gabriella

last: Pessi

first: Ulrich

last: Omasits

first: Christian

last: Ahrens

first: Leo

last: Eberl


title: Midgut-specific gene expression by MacoNPV baculovirus during infection of the bertha armyworm, Mamestra configurata

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

summary: Infection of lepidopterans by baculoviruses has been traditionally studied using in vitro systems which enable efficient and highly synchronous infection. Many studies using varied virus-host combinations have yielded great insight into the molecular processes by which these large double-stranded DNA viruses achieve infection of host cells. However, a key difference in the virus strategy for infection between individual hosts, and within an individual host, lies with the production of two different forms of the virus; occlusion derived virus, which enables primary infection of insect gut tissues and budded virus, which efficiently infects a variety of different insect tissues throughout the host. To examine the primary infection of midgut cells specifically, we used MacoNPV infection of Mamestra configurata fourth instar larvae as our model and measured the expression of viral genes over a time course of infection. Both digital PCR and RNA sequencing methods showed the profile of transcription to be different from those typically seen with in vitro methods, having unique collections of genes expressed early, as well as much greater expression of p6.9 and much reduced expression of polh and p10 late, in comparison with in vitro studies. These differences likely reflect unique characteristics of midgut cell infection, and provide clues as to the processes these viruses use to regulate expression of different viral forms used to access different host tissues.    Baculoviruses are versatile DNA viruses with great potential both as gene therapy vehicles and as biological control tools. Extensive study of their transcriptome in vitro has yielded valuable tools for use in protein expression systems, however it is critical that we obtain a fuller understanding of their in vivo activities before their full medical and agricultural potential can be realized. In these studies we have assessed the gene expression program from a group II alphabaculovirus in the midgut of its complementary larval host and confirmed that the in vivo activities of baculoviruses are unique from what is known of their in vitro transcriptome. These studies provide a first foray with next-generation molecular tools into the characterization of baculovirus biology in vivo.

sample_organism: Mamestra configurata nucleopolyhedrovirus A

overall_design: We sequenced RNA from the excised midguts of 4th instar Mamestra configurata larvae at 6 timepoints after infection with MacoNPV baculovirus.  2 biological replicates were performed, along with uninfected controls

first: Cam

last: Donly

first: Emine

last: Kaplanoglu

first: David

last: Theilmann

first: Doug

last: Baldwin

first: Edyta

last: Sieminska

middle: D

first: Martin

last: Erlandson


title: LSD1 Corepressor Rcor2 Orchestrates Neurogenesis in the Developing Mouse Brain

status: Public on Jan 22 2016

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

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

overall_design: Refer to individual Series


title: Activation of proto-oncogenes by disruption of chromosome neighborhoods [5C-Seq]

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Mutations such as gene fusion, translocation and focal amplification are a frequent cause of proto-oncogene activation during tumorigenesis, but such mutations do not explain all cases of proto-oncogene activation. Here we show that disruption of local chromosome conformation can also activate proto-oncogenes in human cells. We mapped chromosome structures in T-cell acute lymphoblastic leukemia (T-ALL), and found that active oncogenes and silent proto-oncogenes generally occur within insulated neighborhoods formed by the looping of two interacting CTCF sites co-occupied by cohesin. Recurrent microdeletions frequently overlap neighborhood boundary sites in T-ALL genomes, and we demonstrate that site-specific perturbation of loop boundaries is sufficient to activate the respective proto-oncogenes in non-malignant cells. We found somatic genomic rearrangements affecting loop boundaries in many cancers. These results suggest that chromosome structural organization is fundamental to identify functional somatic alterations in cancer genomes.

overall_design: 5C analysis of Tal1 and LMO2 in wildtype and mutant HEK293T cells

first: Denes

last: Hnisz

first: Abraham

last: Weintraub

first: Daniel

last: Day

first: Anne-Laure

last: Valton

first: Rasmus

middle: O

last: Bak

first: Charles

last: Li

first: Johanna

last: Goldmann

first: Bryan

middle: R

last: Lajoie

first: Zi

middle: P

last: Fan

first: Alla

last: Sigova

first: Jessica

last: Reddy

first: Diego

last: Borges-Rivera

first: Tong

middle: I

last: Lee

first: Rudolf

last: Jaenisch

first: Matthew

last: Porteus

first: Job

last: Dekker


title: Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age

first: Andrew

last: Jaffe

state: MD

relation:
SuperSeries of: GSE77131
SuperSeries of: GSE77135


title: Genome-wide analysis of DNA methylation in grapevine fruits

city: Nanjing

first: Lingfei

last: Shangguan

state: Jiangsu

address: 1 Weigang Rd

department: Horticultural Department

institute: Nanjing Agri. University

summary: To examine the grapevine genomic methylation landscape and assess its functional significance, we generated whole genome DNA methylome maps for grapevine fruits of developmental stages. The results showed that DNA methylation happened in the grapevine fruit ripening process, and mostly happened in the biological process from the first growth stage fruit transfer to the véraison stage fruit. It further demonstrated that DNA methylation repress the gene expression. The whole-genome methylomes of grapevine fruits obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of grapevine epigenetics and the epigenetic differentiation among different fruit developmental stages.

overall_design: DNA methylation analysis of grapevine fruits during different developmental stages

first: Jinggui

last: Fang


title: LSD1 Corepressor Rcor2 Orchestrates Neurogenesis in the Developing Mouse Brain [RNA-Seq]

first: Shaorong

last: Gao

summary: RNA-seq analysis of Rcor2fl/fl and Rcor2cko embryonic cortex.

overall_design: we dissected VZ-SVZ regions of Rcor2fl/fl and Rcor2cko cortex at E13.5 and E15.5 for RNA-seq respectively.

first: Yixuan

last: Wang

first: Qian

last: Wu

first: Peng

last: Yang

first: Chenfei

first: Jing

last: Liu

first: Wenyu

last: Ding

first: Wensu

first: Yei

last: Bai

first: Yuanyuan


title: LSD1 Corepressor Rcor2 Orchestrates Neurogenesis in the Developing Mouse Brain [ChIP-Seq]

summary: ChIP-seq analysis using Flag M2, LSD1 and H3K4me2 antibodies respectively in Rcor2Flag embryonic brain.

overall_design: we constructed Rcor2Flag mice by knockin 3X Flag sequences using CRISPR/Cas9 system, and performed ChIP-seq using Flag M2 antibody, LSD1 antibody and H3K4me1 antibody respectively.