title: Classification of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

summary: DNA methylation plays a significant role in assuring cell identity, thus potentiating its application in molecular classification of cancers in respect of tissue origins or clinically and aetiologically distinct subtypes. In this study, we adapted our liquid hybridization capture-based bisulfite sequencing approach on the targeted sequencing of promoter methylomes. We detected ten cell lines originated from different tissue origins and demonstrated a similar potentiality of promoter methylomes as classifiers for cancer cell lines from different tissue origins in comparison with gene expression profiles. Furthermore, promoter methylome can sensitively differentiate two different cell lines from the same tissue origin in respect of the CpG island methylator phenotype (CIMP), as in the case of AGS and BGC-823 gastric cancer cell lines. These results potentiate the targeted sequencing of promoter methylomes as a means for comprehensive screening and classifying cancer cells with respect to tissue-origins and CIMP subtypes in the future studies.

overall_design:
We proved the potentiality of promoter-targeted LHC-BS that requires reduced experimental cost and less amount of initial DNA samples in comparison with a previous design [23] using YH cell line. In addition, we generated single-base promoter methylomes for ten cell lines, including eight cancer cell lines generated from four types of tissues and one pair of model cell lines for ovarian cancer (T29 and T29H).
We proved the potentiality of promoter-targeted LHC-BS that requires reduced experimental cost and less amount of initial DNA samples in comparison with a previous design using YH cell line. In addition, we generated single-base promoter methylomes for ten cell lines, including eight cancer cell lines generated from four types of tissues and one pair of model cell lines for ovarian cancer (T29 and T29H).

first: Fei

last: Gao

first: Junwen

last: Wang

first: Guanyu

last: Ji

first: Siyang

last: Liu

first: Yu

last: Yao

first: Tong

first: Honglong

last: Wu

first: Yudong

last: Xia

first: Hui

last: Jiang

first: Huanming

last: Yang

first: Xiuqing


title: Transcriptome and Translatome Profiling of Caco-2 cells

status: Public on Feb 18 2014

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

country: China

institute: Jinan University

type: Expression profiling by high throughput sequencing

summary: This experiment performed RNA-seq of transcriptome and translatome (translating mRNA) of Caco-2 cells

overall_design: We extracted transcriptome and translatome from Caco-2 cells and deep sequenced them

first: Jiayong

last: Zhong

first: Yizhi

last: Cui

first: Jiahui

last: Guo

first: Guibin

first: Xingfeng

last: Yin

first: Qing-Yu

last: He


title: mRNA and RNC-mRNA deep sequencing of three hepatocellular carcinoma cell lines

summary: We sequenced the total mRNA and translating mRNA (RNC-mRNA) of three hepatocellular carcinoma cell lines Hep3B, HCCLM3 and MHCC97H

overall_design:
For each cell line, samples prepared from three independent and identical cell cultures were pooled with equal amounts.
C-HPP China Team

first: Zhi-Peng

last: Chen

first: Yi-Zhi

first: Wei

last: Gu


title: Genome binding profile of TFIIH helicases XPB and XPD in HT1080 cells

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

country: USA

institute: Allen Institute for Brain Science

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The conserved TFIIH helicases XPB and XPD play key roles in transcription initiation and DNA repair. To investigate the functions of these helicases on a genome-wide scale, we performed ChIP-seq of endogenous XPB and XPD in the HT1080 human fibrosarcoma cell line.

overall_design: 2 ChIP samples and 1 unenriched input control from the same crosslinked chromatin pool

first: Nancy

last: Maizels

first: Arnold

middle: D

last: Bailey

first: Jay

last: Shendure

first: Choli

last: Lee


title: Subtelomeric  CTCF and Cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline

city: Philadelphia

first: Nicholas

last: Stong

state: Pennsylvania

address: 3600 Spruce St

institute: Wistar Institute/UPenn

summary: We investigated the reported binding of telomere associated factor TERF1 and TERF2 to internal telomere sites using ChIP-Seq for these two factors in a lymphoblastoid cell line.  We mapped over 40 million reads for each sample to a custom reference genome that incorporates our subtelomere assembly, and generated signal tracks using only uniquely mapping reads, and also using a multimapping pipeline we developed.   We find that peaks are misshapen and made up of reads that cannot be distinguished from true telomere sequence.  Removing telomere identified reads removes all internal signal.

overall_design: Examination of TRF1 and TRF2

first: Paul

last: Lieberman


title: fourSig: A Method for Determining Chromosomal Interactions in 4C-Seq Data

status: Public on Feb 22 2014

city: Chapel Hill

first: Rex

middle: Lee

last: Williams

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina

summary: The ability to correlate chromosome conformation and gene expression gives a great deal of information regarding the strategies used by a cell to properly regulate gene activity. 4C-seq is a relatively new and increasingly popular technology where the set of genomic interactions generated by a single point in the genome can be determined.  4C-seq experiments generate large, complicated datasets and it is imperative that signal is properly distinguished from noise.  Currently there are a limited number of methods for analyzing 4C-seq data.  Here, we present a new method, fourSig, which, in addition to being simple to use and as precise as current methods, also includes a new feature to prioritize significantly enriched interactions and predict their reproducibility among experimental replicates.  Here, we demonstrate the efficacy of fourSig with previously published and novel 4C-seq datasets and show that our significance prioritization correlates with the ability to reproducibly detect interactions amongst replicates.  The datasets provided include those generated from allele-specific 4C-Seq with a viewpoint of the TSS for the gene Ibtk on mouse Chromosome 9.  FASTQ files, text files containing genomic coordiantes and read counts, and bedGraph formats for UCSC Genome Browser tracks are provided.  All sequences were mapped relative to mouse genome build mm9.

overall_design: Sequencing of circular chromosome conformation capture (4C-Seq) was performed at the transcription start site (TSS) for the gene Ibtk for three replicates in F1 hybrid mouse trophoblast stem (TS) cells.  Experiment was designed to detect allele specific patterns using SNP differences between the inbred lines mated to produce the TS cells (C57Bl/6 and CAST/EiJ)

middle: L

first: Joshua

last: Starmer

middle: W

last: Mugford

first: J

middle: M

last: Calabrese

first: Piotr

last: Mieczkowski

first: Della

last: Yee

first: Terry

last: Magnuson


title: Dendritic Cell Fate is Determined by BCL11A

status: Public on Feb 15 2014

city: Austin

first: Bum-Kyu

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

summary: Here we confirm an essential requirement for the BCL11A transcription factor in fetal pDC development, and for the first time demonstrate this lineage specific requirement in the adult organism. Genome-wide analyses of BCL11A DNA binding and expression revealed that BCL11A regulates transcription of E2-2 and other pDC differentiation modulators including ID2 and MTG16. Our results identify BCL11A as an essential, lineage-specific factor that regulates pDC development.

overall_design: ChIP sequenicng was performed for a transcription factor of BCL11A in Cal1 cell line. Input was sequenced and used as a control.

first: Haley

last: Tucker

first: Vishy

last: Iyer


title: Thermus thermophilus HB27 WT vs HB27Δago RNAseq

status: Public on Feb 17 2014

city: Wageningen

first: daan

middle: christianus

last: swarts

address: Dreijenplein 10

department: Agrotechnology and Food Sciences Group

country: Netherlands

institute: Wageningen UR

summary: raw RNAseq data from mid-log phase Thermus thermophilus HB27 WT and HB27Δago RNA

overall_design: Biological triplicates for each strain

first: D

middle: C

last: Swarts

first: E

middle: R

last: Westra

last: VanderOost


title: Primate iPS cells as tools for evolutionary analyses

status: Public on Feb 19 2014

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

country: Germany

institute: University of Luebeck

summary:
Induced pluripotent stem cells (iPSCs) are regarded as a central tool to understand human biology in health and disease. Similarly, iPSCs from closely related species should be a central tool to understand human evolution and to identify conserved and variable patterns of iPSC disease models. Here, we have generated human, gorilla, bonobo and cynomolgus monkey iPSCs. We show that these cells are well comparable in their differentiation potential and generally similar to human, cynomolgus and rhesus monkey embryonic stem cells (ESCs). RNA sequencing reveals that expression differences among clones, individuals and stem cell type are all of very similar magnitude within a species. In contrast, expression differences between closely related primate species are three times larger and most genes show significant expression differences among the analysed species. However, pseudogenes differ more than twice as much, suggesting that evolution of expression levels in primate stem cells is rapid, but constrained. These patterns in pluripotent stem cells are comparable to those found in other tissues except testis. Hence, primate iPSCs reveal insights into general primate gene expression evolution and should provide a rich source to identify conserved and species-specific gene expression patterns for cellular phenotypes.
Contributors:
Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany

sample_organism:
Macaca fascicularis
Macaca mulatta
Gorilla gorilla
Pan paniscus
Homo sapiens

overall_design: We used expression profiling to characterize five gorilla, two bonobo and three macaque iPS clones as well as three iPS clones from two human individuals, three human embryonic stem (ES) cell lines and three macaque ES cell lines. We generated tagged RNA-Seq libraries from these 19 samples including four technical replicates (23 samples). Over 100 million single end reads were generated on the Illumina platform.


title: The methylome of Drosophila melanogaster

city: Los Angeles

first: Dario

last: Boffelli

state: CA

address: 700 N San Vicente Blvd

department: Pediatrics

institute: Cedars Sinai

type: Methylation profiling by high throughput sequencing

summary: Cytosine methylation  in the genome of Drosophila melanogaster has been elusive and controversial: methylcytosine has been detected at very low levels in early embryos, but the genomic location and function of methylation has not been established. We have mapped cytosine methylation genomewide in Stage 5 Drosophila embryo DNA by combining immuno-enrichment for 5-methylcytosine, bisulfite conversion, and deep sequencing. Unlike methylation patterns observed in other eukaryotic species,  methylation in Drosophila is punctate and highly strand-asymmetrical; we confirmed this by direct PCR amplification and sequencing of bisulfite-converted DNA. Despite the locally asymmetric nature of methylation, large-scale patterns of methylation are symmetric. Methylated regions make up ~1% of the genome, and within these regions methylation of individual cytosines averages 2-10%.  Methylation is concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. It is depleted from promoters,  coding sequences, and most retrotransposons, and enriched in introns and in certain simple sequence repeats containing the commonly methylated motifs. Comparison with available gene expression data indicates that methylation in a gene is associated with lower expression; the X chromosome, which is subject to gene dosage compensation, is more densely methylated than the autosomes.  This study firmly establishes the presence of cytosine methylation in Drosophila; the temporal overlap of methylation with the maternal-zygotic transition raises the possibility that methylation participates in the transition to zygotic gene expression.

sample_organism:
Drosophila melanogaster
Lambdavirus lambda

overall_design: To enrich for rare cytosine methylation in Drosophila at embryonic Stage 5 (2-3 hours post-fertilization),  we enriched sonicated Stage 5 genomic DNA for methylcytosine by immunoprecipitation with antibody to 5-methylcytosine. The immunoprecipitated DNA was then bisulfite converted and Illumina sequenced to obtain direct evidence for the presence of methylation. The presence and extent of DNA methylation was confirmed by Illumina sequencing of bisulfite-converted PCR amplicons.


title: Mouse spleen: Histone modification patterns in spleens from wild type and leukemic mice

city: Charlottesville

first: R. Ariel

last: Gomez

state: VA

institute: University of Virginia

summary: ChIP-Seq for H3K4me3 and H3K27me3 in wild type spleens and spleens from mice having deletion of RBP-J in cells of the renin lineage, which results in B-cell leukemia.

overall_design: Examination of 2 different histone modifications in wild type and mutant spleens.

first: R

middle: A

first: Ellen

middle: S

last: Pentz

first: Brian

last: Belyea

first: Maria

last: Sequeira-Lopez


title: Genome-wide maps of Lsd1 binding sites in escort cells/early follicle cells and cap cells/terminal filament cells

city: Dallas

first: Michael

last: Buszczak

state: Texas

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

summary: Loss of Lsd1 in Drosophila in specific cells of the Drosophila ovary results in increased BMP signaling outside the cap cell niche and an expanded germline stem cell (GSC) phenotype. To better characterize the function of Lsd1 in different cell populations within the ovary, we performed Chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq). This analysis shows that Lsd1 associates with a surprisingly limited number of sites in escort cells and fewer, and often, different sites in cap cells. These findings indicate that Lsd1 displays highly selective binding in specific cellular contexts.

overall_design: Examination of epitope tagged Lsd1 transgenes in specific cell populations within the Drosophila ovary

first: Susan

last: Eliazer


title: Imperfect centered miRNA binding sites are common and can mediate functional repression of target mRNAs [sequencing]

status: Public on Feb 14 2014

city: Herston

first: Nicole

last: Cloonan

state: Queensland

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Whole transcriptome identification of direct targets identify a new class of miRNA::mRNA interactions.

overall_design: This is a qualitative experiment to check transcript structure of mRNAs that bind to miR-17-5p. HEK293T cells were transfected with biotinylated miRNAs. The miRNAs and target mRNA were pulled down with streptavidin and profiled using stranded RNA-seq.


title: Imperfect centered miRNA binding sites are common and can mediate functional repression of target mRNAs

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

overall_design: Refer to individual Series


title: Sex-specific embryonic gene expression in species with newly evolved sex chromosomes

city: Davis

middle: E.

last: Lott

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

summary: Sex chromosome dosage differences between males and females are a significant form of natural genetic variation in many species. Like many species with chromosomal sex determination, Drosophila females have two X chromosomes, while males have one X and one Y. The model species D. melanogaster has five roughly equally sized chromosome arms, one of which is the X chromosome. However, fusions of sex chromosomes with autosomes have occurred along the lineage leading to D. pseudoobscura and D. miranda. The resulting neo-sex chromosomes are gradually evolving the properties of sex chromosomes, and neo-X chromosomes are becoming targets for the molecular mechanisms that compensate for differences in X chromosome dose between sexes. We have previously shown that D. melanogaster possess at least two dosage compensation mechanisms: the well- characterized MSL-mediated dosage compensation active in most somatic tissues, and another system active during early embryogenesis prior to the onset of MSL-mediated dosage compensation. To better understand the developmental constraints on sex chromosome gene expression and evolution, we sequenced mRNA from individual male and female embryos of D. pseudoobscura and D. miranda, from ~0.5 to 8 hours of development. Autosomal expression levels are highly conserved between these species. But, unlike D. melanogaster, we observe a general lack of dosage compensation in D. pseudoobscura and D. miranda prior to the onset of MSL-mediated dosage compensation. The extent of female bias on the X chromosomes decreases through developmental time with the establishment of MSL-mediated dosage compensation, but may do so more slowly in D. miranda than D. pseudoobscura. Thus either there has been a lineage-specific gain or loss in early dosage compensation mechanism(s), or increasing X chromosome dose may strain dosage compensation systems and make them less effective. These results also prompt a number of questions about whether species with more sex-linked genes have more sex-specific phenotypes, and how much transcript level variance is tolerable during critical stages of development.

sample_organism:
Drosophila miranda
Drosophila pseudoobscura

overall_design: We sequenced mRNA from D. pseudoobscura and D. miranda embryos, from eight timepoints, both female and male embryos, with three replicates (2 x 8 x 2 x 3). D. pseudoobscura embryos were F1s of a cross between Flagstaff-14 and PP1134 D. pseudoobscura lines, D. miranda embryos were F1s of a cross between the MSH22 and SP138 D. miranda lines.

middle: E

middle: B

last: Eisen


title: Massively parallel single-cell RNA-Seq for dissecting cell type and cell state compositions

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: In multi-cellular organisms, biological function emerges when cells of heterogeneous types and states are combined into complex tissues. Nevertheless unbiased dissection of tissues into coherent cell subpopulations is currently lacking. We introduce an automated, massively parallel single cell RNA sequencing method for intuitively analyzing in-vivo transcriptional states in thousands of single cells. Combined with unsupervised classification algorithms, it facilitates ab initio and marker-free characterization of classical hematopoietic cell types from splenic tissues. Importantly, modeling single cells transcriptional states in dendritic cells subpopulations, where a cell type hierarchy is difficult to define with marker-based approaches, uncovers complex combinatorial activity of multiple gene modules and capture cell-to-cell variability in steady state conditions and following pathogen activation. Massively parallel single cell RNA-seq thereby emerges as an effective tool for unbiased dissection of complex tissues.

overall_design:
CD11c+ enriched splenocyte mRNA profiles from single cells were generated by deep sequencing of thousands of single cells, sequenced in several batches in an Illumina Hiseq 2000

The 'umitab.txt' processed data file contains the mRNA counts (post-filtering RMT counts) of a gene per each well (columns)
The 'experimental_design.txt' contains a detailed information regarding each well.
The 'readme0421.txt' was provided with details about each supplementary file.

first: Amos

last: Tanay

first: Diego

last: Jaitin

first: Ephraim

last: Kenigsberg

first: Hadas

last: Keren-Shaul


title: Chronic cocaine-regulated epigenome in mouse [ChIP-Seq]

city: New York

first: Li

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Increasing evidence supports a role for altered gene expression in mediating the lasting effects of cocaine on the brain, and recent work has demonstrated the involvement of chromatin modifications in these alterations. However, all such studies to date have been restricted by their reliance on microarray technologies which have intrinsic limitations. Here, we used advanced sequencing methods, RNA-seq and ChIP-seq, to obtain an unprecedented view of cocaine-induced changes in gene expression and associated adaptations in numerous modes of chromatin regulation in the nucleus accumbens, a key brain reward region. We identify unique combinations of chromatin changes, or signatures, that accompany cocaine’s regulation of gene expression, including the dramatic involvement of pre-mRNA alternative splicing in cocaine action. Together, this delineation of the cocaine-induced epigenome in the nucleus accumbens reveals several novel modes of drug regulation, thereby providing new insight into the biological basis of cocaine addiction. More broadly, the combinatorial chromatin and transcriptional approaches that we describe serve as an important resource for the field, as they can be applied to other systems to reveal novel transcriptional and epigenetic mechanisms of neuronal regulation.

overall_design: ChIP-seq of 6 marks (H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me2, RNApolII) were done on mouse nucleus accumbens 24 hr after 7 day daily cocaine ip injection with saline as control. Three replicates for each condition.

first: Jian

last: Feng


title: Chronic cocaine-regulated epigenome in mouse


title: Genome-wide maps of H3K9me3 in control ESCs and Rif1 knockdown ESC.

status: Public on Feb 13 2014

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

institute: Yale Stem Cell Center

summary: We found that Rif1 depletion leads to reduced H3K9me3 levels at 1/3 of the H3K9me3-enriched genomic regions (H3K9me3 peaks), and that reduced H3K9me3 de-represses Zscan4 and other genes that are specific to the 2-Cell stage embryo.

overall_design: Examination of H3K9me3 histone modifications in 2 cell types.

first: Yifei

last: Liu

first: Tao

last: Wu


title: Chromatin In Situ Proximity (ChrISP): Single-cell analysis of chromatin proximities at a high resolution

status: Public on Feb 20 2014

city: Stockholm

first: Rolf

last: Ohlsson

address: Solnavägen 30, 171 64

department: Department of Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

summary: Current techniques analysing chromatin structures are hampered by either poor resolution of individual cells or high resolution in only large cell populations. Here we describe a new method, ChrISP,which reproducibly scores for chromatin fiber proximities in 3D in single cells with a resolution of < 170 A. Moreover, ChrISP visualizes higher order structures of individual chromosomes in relation to structural hallmarks of interphase nuclei beyond the resolution of the light microscope.

overall_design: Mapping of "unique" (chromosome territory) and "repeated" (COT1) dna used in ChrISP to asses its composition

first: Xingqi

last: Chen

first: Alejandro

last: Fernandez Woodbridge

first: Chengxi

last: Shi

first: Anita

last: Gondor

first: Samer

last: Yammine

first: Noriyuki

last: Sumida

first: Daniel

last: Ronnlund

first: Jerker

last: Widengren


title: Chronic cocaine-regulated epigenome in mouse [RNA-Seq]

overall_design: Total RNA was isolated from mouse nucleus accumbens 24 hr after 7 day daily cocaine or saline control ip injection for mRNA sequencing by following illumina RNA seq kit protocol. Another batch of acute cocaine RNA-seq was performed using the same parameters except the treatment group was given 6 days of saline injection followed by 1 day of cocaine injection. The acute cocaine batch serves as control experiments.

first: Feng

last: Jian


title: Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to the control of osteoblastogenesis

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont


title: Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection [Dnase-seq]

city: Durham

first: Yoichiro

last: Shibata

address: 101 Science Dr

department: Inst. of Genome Sciences and Policy

institute: Duke University

summary: The human genome shares a remarkable amount of genomic sequence with our closest living primate relatives. Researchers have long sought to understand what regions of the genome are responsible for unique species-specific traits. Previous studies have shown that many genes are differentially expressed between species, but the regulatory elements contributing to these differences are largely unknown. Here we report a genome-wide comparison of active gene regulatory elements in human, chimpanzee, and macaque, and we identify hundreds of regulatory elements that have been gained or lost in the human or chimpanzee genomes since their evolutionary divergence. These elements contain evidence of natural selection and correlate with species-specific changes in gene expression. Polymorphic DNA bases in transcription factor motifs that we found in these regulatory elements may be responsible for the varied biological functions across species. This study directly links phenotypic and transcriptional differences between species with changes in chromatin structure.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: One biological replicate was analyzed for each of the 15 primate samples using DNase-seq.

first: Greg

last: Crawford


title: Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

platform_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens


title: miR-146a promotes the initiation and progression of melanoma  by activating Notch signaling

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

type: Non-coding RNA profiling by high throughput sequencing

summary: Oncogenic mutations in BRAF and NRAS occur in 70% of melanomas. Here we identify a microRNA, miR-146a, that is highly upregulated by oncogenic BRAF and NRAS. Expression of miR-146a increases the ability of human melanoma cells to proliferate in culture and form tumors in mice, whereas knockdown of miR-146a has the opposite effects. We show these oncogenic activities are due to miR-146a targeting the NUMB mRNA, a repressor of Notch signaling. Previous studies have shown that pre-miR-146a contains a single nucleotide polymorphism (C>G rs2910164). We find that the ability of pre-miR-146a/G to activate Notch signaling and promote oncogenesis is substantially higher than that of pre-miR-146a/C. Analysis of melanoma cell lines and matched patient samples indicates that during melanoma progression pre-miR-146a/G is enriched relative to pre-miR-146a/C, resulting from a C-to-G somatic mutation in pre-miR-146a/C. Collectively, our results reveal a central role for miR-146a in the initiation and progression of melanoma.

overall_design: WI-38 cells were either infected with BRAFV600E or Empty retroviral vectors and small RNA were prepared from these cells. As an additional control, WI-38 cells were serum starved and used to generate quiscent cells, which were also used to prepase small RNA.  The small RNA were then used to generate small RNA library and were used on Illumina genome analyzer.

first: Matteo

last: Forloni

first: Shaillay

last: Dogra

first: Yuying

last: Dong

first: Darryl

last: Conte

first: Julie

last: Zhu

first: Jianhong

last: Ou

first: April

last: Deng

first: Meera

last: Mahalingam

first: Michael

last: Green


title: Premature termination of in vivo reprogramming leads to cancer development through altered epigenetic regulation

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo


title: Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection [DGE-seq]

overall_design: DGE-seq


title: Premature termination of in vivo reprogramming leads to cancer development through altered epigenetic regulation [RRBS]

summary: We report a reprogrammable mouse system in which reprogramming factor expression in vivo can be controlled temporally by treatment with doxycycline (Dox).  Transient expression of reprogramming factors in vivo results in tumor development in various tissues, consisting of undifferentiated dysplastic cells.  We analyzed the kidney tumors developed in reprogrammable mice for global gene expressions and DNA methylations.

overall_design: Reprogrammable mice at 4 weeks of age were treated with Dox for 7 days followed by the withdrawal.  Seven days after the withdrawal, kidney tumors were analyzed for gene expressions and DNA methylations with microarray and RRBS method, respectively.  Normal kidney tissue at the same age and ES cells were analyzed as controls.  To examine the early changes of gene expressions, transgene-expressing kidney cells were FACS sorted and they are utilized for microarray analysis.  Primary liver tumors in reprogrammable mice and transplanted secondary kidney tumors in the subcutaneous tissues of immnodeficient mice were also analyzed for gene expressions.

first: Katsunori

last: Semi


title: Genome-wide mapping of Runx2 occupancy during the proliferation, matrix deposition, and mineralization stages of preosteoblast

summary: Osteogenesis is a highly regulated developmental process and continues during the turnover and repair of mature bone. Runx2, the master regulator of osteoblastogenesis, directs a transcription program essential for bone formation through both genetic and epigenetic mechanisms. While individual Runx2 gene targets have been identified, further insights into the broad spectrum of Runx2 functions required for osteogenesis are needed. By performing genome-wide characterization of Runx2 binding at the three major stages of osteoblast differentiation: proliferation, matrix deposition and mineralization, we identified Runx2-dependent regulatory networks driving bone formation. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) over the course of these stages, we discovered close to 80,000 significantly enriched regions of Runx2 binding throughout the mouse genome. These binding events exhibited distinct patterns during osteogenesis, and were associated with proximal promoters as well as a large percentage of Runx2 occupancy in non-promoter regions: upstream, introns, exons, transcription termination site (TTS) regions, and intergenic regions. These peaks were partitioned into clusters that are associated with genes in complex biological processes that support bone formation. Using Affymetrix expression profiling of differentiating osteoblasts depleted of Runx2, we identified novel Runx2 targets including Ezh2, a critical epigenetic regulator; Crabp2, a retinoic acid signaling component; Adamts4 and Tnfrsf19, two remodelers of extracellular matrix. We demonstrated by luciferase assays that these novel biological targets are regulated by Runx2 occupancy at non-promoter regions. Our data establish that Runx2 interactions with chromatin across the genome reveal novel genes, pathways and transcriptional mechanisms that contribute to the regulation of osteoblastogenesis.

overall_design: To identiy the genome-wide occupancy of Runx2, DNA bound by Runx2 at the prolieration, matrix deposition, and mineralization stages were recovered by Runx2 ChIP. Libraries of purified DNA were generated using Illumina SR adapters (Illumina) following manufacturer’s manual, and were selected for the inserted fragments of 200 ± 50 bp, and sequenced 36 bases on an Illumina Genome Analyzer II. Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6, Illumina). Two independent biological repeats of Runx2 ChIP-Seq libraries were prepared for each time point, and two input libraries were prepared with sonicated DNA from day 9 MC3T3-E1 cells. We pooled the reads from two biological replicates for peaking calling using MACS (version 1.4.1) with a stringent p value threshold (p < 1e-10) in contrast to input control, and used these peaks for further bioinformatic analyses. Each sample deposited here contains three files: the sequence file with short reads combined from two biological replicates, a Bed file with peaks called from the pooled short reads, and a Wig file with peak signals.

first: Hai

last: Wu

first: Troy

last: Whitfield

first: Jason

last: Dobson

first: Phillip

last: Tai

first: Andre

middle: J

last: van Wijnen

first: Janet

last: Stein

first: Gary

first: Jane

last: Lian


title: Transcriptome-based network analysis reveals a spectrum model of human macrophage activation [miRNA-seq]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Macrophage activation is associated with profound transcriptional reprogramming. Although much progress has been made in the understanding of macrophage activation, polarization and function, the transcriptional programs regulating these processes remain poorly characterized. We stimulated human macrophages with diverse activation signals, acquiring a dataset of 299 macrophage transcriptomes. Analysis of this dataset revealed a spectrum of macrophage activation states extending the current M1 versus M2-polarization model. Network analyses identified central transcriptional regulators associated with all macrophage activation complemented by regulators related to stimulus-specific programs. Applying these transcriptional programs to human alveolar macrophages from smokers and patients with chronic obstructive pulmonary disease (COPD) revealed an unexpected loss of inflammatory signatures in COPD patients. Finally, by integrating murine data from the ImmGen project we propose a refined, activation-independent core signature for human and murine macrophages. This resource serves as a framework for future research into regulation of macrophage activation in health and disease.

overall_design: Since transcriptional programs are further modulated on several levels including miRNAs we assessed the global spectrum of miRNA expression by miRNA-Seq in macrophages stimulated with IFNγ, IL4 or with the combination of TNFα, PGE2 and P3C

first: J

last: Xue

first: S

middle: V

last: Schmidt

last: Sander

first: A

last: Draffehn

first: W

last: Krebs

first: I

last: Quester

first: D

last: De Nardo

first: T

last: Gohel

first: M

last: Emde

first: L

last: Schmidleithner

first: H

last: Ganesan

last: Nino-Castro

last: Mallmann

last: Labzin

last: Theis

last: Kraut

last: Beyer

first: E

last: Latz

last: Freeman

last: Ulas


title: Integrated analysis of microRNA and mRNA expression and association with HIF binding in MCF-7 cells under hypoxia (miRNA-Seq)

city: Oxford

first: Carme

last: Camps

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics/ U. of Oxford

summary:
Purpose: We aimed to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression.
Methods: microRNA sequencing data and gene expression microarray data were generated from MCF-7 cells submitted to an hypoxia timecourse (16h, 32h and 48h at 1% Oxygen). Data was integrated to 500 published high-stringency HIF binding sites identified in MCF-7 cells.
Results: We identified 41 microRNAs significantly up- and 28 down- regulated, of which 38 mature and 20 star forms are reported in conjunction with hypoxia for the first time. HIF-1α and HIF-2α binding sites within 50kb distance of microRNA loci were found by integration of HIF ChIP-seq data, showing overall association between binding sites and up-regulation. Gene expression profiling analysis showed no full coordination between pri-miRNA and microRNA expression, pointing towards additional levels of regulation. Several transcripts playing a role in microRNA processing were found regulated by hypoxia, of which two were HIF dependent.
Conclusions: The data support the hypothesis that microRNA expression under hypoxia is regulated at transcriptional and post-transcriptional level. HIF is involved at both levels, regulating the transcription of certain microRNAs and also the expression of key elements of the microRNA processing pathway.

overall_design: microRNA-seq profiles of MCF-7 exposed to hypoxia (1% Oxygen) for 16h (2 replicates), 32h (2 replicates) and 48h (2 replicates) and to normoxia (2 replicates) were generated using Illumina sequencing platform.

first: Harpreet

middle: K

last: Saini

first: Anton

last: Enright

first: Jiannis

last: Ragoussis


title: Transcriptome-based network analysis reveals a spectrum model of human macrophage activation [ChIP-Seq]

last: Schultze

overall_design: To better understand active gene regulation in human macrophages during activation and differentiation in vitro with different stimuli ChIP-sequencing experiments were performed. Enrichment patterns of the permissive histone modification mark trimetylation of histone protein 3 (H3K4me3) and macrophage lineage-specific transcription factor PU.1 were analyzed.

last: Xue

last: Schmidt

last: Sander

last: Draffehn

last: Krebs

last: Quester

last: De Nardo

middle: D

last: Gohel


title: Integrated analysis of microRNA and mRNA expression and association with HIF binding in MCF-7 cells under hypoxia


title: Transcriptome-based network analysis reveals a spectrum model of human macrophage activation


title: Whole-genome analysis of 5-hydroxymethylcytosines and 5-methylcytosines at base resolution in human brain

city: Beijing

first: Yuexi

last: Tan

state: Beijing

address: 1 Qinghua Yuan, Haidian Dist.

institute: Tsinghua University

summary: 5-hydroxymethylcytosines (5hmC) is particularly abundant in mammalian brain with little-known functions. Here we present the first genome-wide and single-base-resolution maps of 5hmC and 5mC in human brain by combined application of TAB-Seq and MethylC-Seq. We report that the majority of modified cytosines are hydroxymethylated in adult human brain, a significant proportion of which are highly-hydroxymethylated with enrichment in active genic regions and distal-regulatory elements. 5hmC is more enriched in poised than active enhancers, and CpG island shores and enhancers show comparable 5hmC profiles. Notably, 5hmC spikes were identified at the 5’ splicing sites, suggesting a link between 5hmC and splicing. Additionally, we identified a transcription-correlated 5hmC bias towards to sense strand and a 5mC bias towards antisense strand of gene bodies, and a bias towards C-rich sequences surrounding the 5hmC sites. Our data imply multiple roles for 5hmC in alternative splicing and gene regulation in addition to be an intermediate of DNA demethylation in human brain.

overall_design:
Examination of hydroxymethylomes of 1 adult and 1 fetal brain tissue of frontal lobe, as well as 1 methylome of the same adult.

We performed both WGBS and TAB-seq for the adult brain, but only TAB-seq for the fetal brain. So the formats of the two .txt files are a little different. Both files have header lines, which may help you understand their formats.

Columns of "GSE46710_Ad_Front.hmC_sites_FDR_0.01.txt.gz":

1. Chromosome
2. Position: 0-based coordinate of the cytosine on the chromosome.
3. Strand: on which strand of the reference genome does the cytosine locates.
4. Context: CG/CHG/CHH
5. Depth(C+T)_from_MethylC-Seq: the sequencing depth (sum of cytosines and thymines) on this site of WGBS.
6. Non-converted_C_from_MethylC-Seq: the number of cytosines on this site of WGBS.
7. Modification_level_from_MethylC-Seq(%): the quotient in percentage of Non-converted_C_from_MethylC-Seq divided by Depth(C+T)_from_MethylC-Seq.
8. Depth(C+T)_from_TAB-Seq: the sequencing depth (sum of cytosines and thymines) on this site of TAB-seq.
9. Non-converted_C_from_TAB-Seq: the number of cytosines on this site of TAB-seq.
10. Modification_level_from_TAB-Seq(%): the quotient in percentage of Non-converted_C_from_TAB-Seq divided by Depth(C+T)_from_TAB-Seq, "NA" if it is not called as an hmC.
11. Calling_hmC_site(1-passed;0-failed): given that the FDR is smaller than 0.01, whether the cytosine should be called as an hmC.

first: Lu

last: Wen


title: The Transition from Primary siRNAs to Amplified Secondary siRNAs that Regulate Chalcone Synthase During Development of Glycine max Seed Coat

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: The I locus is a 27-kb inverted repeat cluster of chalcone synthase genes CHS1-3-4 that mediates siRNA down-regulation of CHS7 and CHS8 target mRNAs during seed development leading to yellow seed coats lacking anthocyanin pigments. Here, we report small RNA sequencing of ten stages of seed development from a few days post fertilization through maturity, revealing the amplification from primary to secondary short interfering RNAs (siRNAs) occurring during development. The young seed populations had a higher proportion of siRNAs representing the CHS1-3-4 gene family members, consistent with this region as the origin of the primary siRNAs. More intriguingly, the very young seed had a higher proportion of 22-nt CHS siRNAs than did the mid-maturation seed. We infer that the primary CHS siRNAs increase during development to levels sufficient to trigger amplification of secondary CHS siRNAs from the CHS7/8 target mRNAs, enabling the total levels of 21-nt CHS siRNAs to rise dramatically. Further, we demonstrate that the soybean system exhibits tissue-specific CHS siRNA production because primary CHS siRNA levels are not sufficient to trigger secondary amplification in tissues other than the seed coat.

overall_design: High-throughput sequencing using Genome Analyzer II and Illumina HiSeq 2000 was performed with two biological replicates (Some stages don't have replicate).

first: Young

last: Cho

first: Sarah

middle: I

last: Jones

middle: O


title: miR-125b: A Rheostat of Growth versus Stress-Induced MAPKs That Governs Stemness and OncomiR Addiction in Skin

status: Public on Feb 12 2014

first: liang

last: zhang

address: 1230 york Avenue

department: fuchs

institute: the Rockefeller University

summary: We analyze the globel gene expression changes in the tumor initiating cells of regressing miR-125b addicted tumors after oncomiR withdrawal

overall_design: For Histone-H2BGFP expression in DTG tumor cells, the U6 promoter was deleted in the PLKO-PGK-H2B-GFP vector throughNdeI-AgeI digestion, Quick Blunting Kit treatment (NEB), and self-ligation. The resulting PLNA-PGK-H2BGFP plasmid was packaged into lentivirus and used to infect ~1x106freshly sorted α6hiβ1hi DTG tumor cells. After 30 min, cells were then extensively washed and immediately engrafted onto backskins of Nude mice by intradermal transplantation. GFP+α6hiβ1hicells were FACS-isolated from resulting tumors and then serially transplanted as above. For RNA seq analysis of the miR-125b addicted tumor regression process, H2BGFP labeled DTG tumor cells were intradermally engrafted onto backskins of Nude mice (1x104cells/site). Tumors were allowed to grow to ~1cm diameter. Mice were then taken Off Dox by transferring them to regular food for 0, 4, 7 days. GFP+α6hiβ1hiwere then FACS-isolated from the tumors. Two or three independent replicates were collected for each time point. Total RNAswere extracted from the FACS-sorted cells using the miRNeasy Mini Kit (Qiagen) according to the vender’s protocol. Expression of miR-125b in each sample was quantified by RT-PCR using TaqMan MicroRNA Assays (Applied Biosystems). For RNA seq, RNA samples were submitted to the Genomics Resources Core Facility of the Weill Cornell Medical College for library construction using IlluminaTruSeq Stranded mRNA Sample Prep Kit and then sequencing using Illumina HiSeq2000. Resultswere analyzed via the Galaxy web platform using TopHat for initiate mapping and Cufflinks for transcripts assembling and expression level estimation (Computing FPKM: fragments per kilobase of exon per million fragments mapped). The MM9 genome assembly (UCSC Genome Browser) was used as reference genome for all analyses. Low expression genes

first: Liang

last: Zhang

first: Elaine

last: Fuchs


title: hnRNP L-RNA in HeLa

city: Giessen

first: Lee-Hsueh

last: Hung

state: Hessen

address: Heinrich-Buff-Ring 58

institute: University of Giessen

overall_design: Refer to individual Series


title: Individual-nucleotide resolution CLIP and high-throughput sequencing to map hnRNP L-RNA interactions in HeLa cells

summary:
Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was used to generate a transcriptome-wide binding map of hnRNP L.

Supplementary file GSE37560_hnRNPL_crosslink_site.bed includes filtered crosslink sites of hnRNPL: combining data from all 3 experiments.

overall_design: 3 biological replicates of hnRNP L-specific and control (Flag) co-immunoprecipitated RNA after  UV-crosslinking in HeLa cells

first: Oliver

last: Rossbach

first: Albrecht

last: Bindereif


title: Loss of imprinting at the CTCF binding sites in the DLK1-DIO3 domain reactivates microRNA expression in acute promyelocytic leukaemia

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

summary: We report the DNA-methylation profiling of 10 regions selected from the DLK1-DIO3 domain on chromosome 14q32 in BM/PB samples from patients with acute promyelocytic leukaemia (APL), other subclasses of acute myeloid leukaemia and healthy donors, using high-throughput amplicon bisulfite sequencing with Roche 454 technology. We identify monoallelic-hypermethylation in APL only at the differentially methylated region (DMR) located upstream from the MEG3 gene (MEG3-DMR), whereas no changes in the DNA methylation profile were detected at the imprinting control region of the domain (IG-DMR) among the samples analysed. We show that the expression profile of 6 miRNAs clustered downstream from the MEG3-DMR correlates with the methylation profile at both DMRs. We demonstrate that miRNAs expression negatively correlates with DNA-methylation at the IG-DMR and MEG3 gene-body, whereas the correlation was positive for the CpGs located in the promoter of MEG3, including the binding sites for the insulator CTCF. We propose a loss of imprinting at the CTCF binding sites in patients with APL. These results are consistent with the previously reported DLK1-DIO3 miRNAs overexpression in APL, indicating a possible involvement of these ncRNAs in the pathogenesis of the disease.

overall_design: Investigation of the epigenetic regulation of the miRNAs clustered in 14q32 by next-generation sequencing

first: Floriana

last: Manodoro

first: Tracy

last: Chaplin

first: Jun

last: Wang

first: Sameena

last: Iqbal

first: John

middle: G

last: Gribben

first: Bryan

last: Young

first: Silvana

last: Debernardi


title: Global DNA methylation study of trisomy 8 AML

summary: We report the application of methylated DNA immunoprecipitation followed by next-generation sequencing to trisomy 8 AML. Through a global study and quantifying the methylation signals, we demonstrated a characteristic DNA methylation distribution for trisomy 8 indicating the impact of the hypermethylation of the extrachromosome 8 on suppressing the signals on the rest of the chromosomes.

overall_design: Examination of  3 relapse trisomy 8 AML patients

first: Marwa

middle: H

last: Saied

first: Sabah

last: Khalid

first: Paul

last: Smith

first: Gael

last: Molloy


title: Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: Here we delineate the roles of RNA binding for WDR5 function on chromatin state and murine embryonic stem cell (ESC) maintenance.

overall_design: Examination of global transcriptional changes and mapping genome-wide transcription factors occupancy at distinct time points during the transdifferentiation process

first: Yul

last: Yang

first: Ryan

middle: A

last: Flynn

first: Howard

middle: Y

last: Chang


title: Tissue specific expression of chalcone synthase siRNAs

first: Lila

last: Vodkin

summary: In a previous study, seed coat and cotyledon tissues of Williams, Richland and T157 soybean lines were investigated to show tissue specificity of CHS siRNA expression (Tuteja et al., 2009). Here, we investigated more tissues such as leaf, root and germinating cotyledon to ascertain the tissue specificity of CHS siRNAs in Williams. Data from multiple small RNA libraries were sequenced deeply by the Illumina high-throughput sequencing technology. The total numbers of small RNA reads were from three million to thirty million, providing sufficient data to show the tissue specificity of CHS siRNA.

overall_design: High-throughput sequencing using Genome Analyzer II and Illumina HiSeq 2000 was performed.

first: Young

last: Cho


title: Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice [RNA-Seq]

first: Gerold

last: Bongers

address: 1425 Madison Ave, 12-26A

department: Immunology Institute

summary:
The preferential localization of some neoplasms, such as serrated polyps, in specific areas of the intestine suggests that non-genetic factors may be important for their development. To test this hypothesis, we took advantage of transgenic mice that expressed HB-EGF throughout the intestine, but develop serrated polyps only in the cecum.
Here we show that a host-specific microbiome was associated with serrated polyps, and that alterations of the microbiota induced by antibiotic treatment or by embryo-transfer rederivation markedly inhibited the formation of serrated polyps in the cecum. Mechanistically, development of serrated polyps was associated with a local decrease in epithelial barrier-function, bacterial invasion, production of antimicrobials, and increased expression of several inflammatory factors such as IL-17, Cxcl2, Tnf-α, and IL-1. Increased number of neutrophils were found within the serrated polyps, and their depletion significantly reduced polyp growth.
Together these results indicate that non-genetic factors contribute to the development of serrated polyps and suggest that the development of these intestinal neoplasms in the cecum is driven by the interplay between genetic changes in the host, an inflammatory response, and a host-specific microbiota.

overall_design: We obtained serrated polyp (SP) and surrounding normal (NM) tissue from the ceca of three affected mice (paired design) and assessed expression differences by RNA-Seq.

first: Michelle

last: Pacer

first: Thais

last: Geraldino

first: Lili

last: Chen

first: Zhengxiang

last: He

first: Daigo

last: Hashimoto

first: Glaucia

middle: C

last: Furtado

first: Jordi

last: Ochando

first: Kevin

last: Kelley

first: Jose

last: Clemente

first: Miriam

last: Merad

first: Harm

last: van Bakel

first: Sergio

last: Lira


title: Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 kinase mediated histone H3S10 phosphorylation in drosophila

city: Ames

first: Jorgen

last: Johansen

state: Iowa

address: MBB3142, Iowa State Univeristy

department: BBMB

institute: Iowa State Universtiy

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

first: Weili

last: Cai

first: Chao

last: Wang

first: Yeran

last: Li

first: Lu

last: Shen

first: Sanzhen

last: Liu

first: Changfu

last: Yao

first: Xiaomin

last: Bao

first: Patrick

middle: S

last: Schnable

first: Jack

last: Girton

first: Jørgen

first: Kristen

middle: M


title: Transcriptome analysis of cells of different cycling speed during Yamanaka reprogramming

first: Vince

last: Schulz

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary: Reprogramming somatic cells to induced pluripotency by Yamanaka factors is usually slow and inefficient, and is thought to be a stochastic process. We identified a privileged somatic cell state, from which acquisition of pluripotency could occur in a non-stochastic manner. Subsets of murine hematopoietic progenitors are privileged, whose progeny cells predominantly adopt the pluripotent fate with activation of endogenous Oct4 locus after 4-5 divisions in reprogramming conditions. Privileged cells display an ultrafast cell cycle of ~8 hours. In fibroblasts, a subpopulation cycling at a similar ultrafast speed is observed after 6 days of factor expression, and is increased by p53-knockdown. This ultrafast-cycling population accounts for >99% of the bulk reprogramming activity in wildtype or p53-knockdown fibroblasts. We compared the transcriptomes of the fast cycling cells with those of slower hematopoietic progenitors, bulk fibroblasts and established iPS cells.

overall_design: 3-5 replicates for each of the six cell types were included: 4 replicates for established iPS cells, 4 replicates for bulk mouse embryonic fibroblasts (MEF), 4 replicates for fast cycling MEF, 4 replicates for slow cycling MEF, 5 replicates for fast cycling granulocyte monocyte progenitors (GMP) and 3 replicates for slow cycling GMP.

first: Shangqin

last: Guo

first: Vincent

middle: P


title: Genome wide analysis of transcriptome wild type and JIL-1 mutant [RNA-seq: 4 samples]

summary: Comparison of global transcription profiles in salivary glands from wild-type and JIL-1 null mutant larvae revealed that the expression levels of 1539 genes changed at least two-fold in the mutant and that a substantial number (49%) of these genes were upregulated whereas 51% were downregulated.

overall_design: Examination of 2 different transcriptome  in 2 genotypes with two replicates.


title: Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice

first: Gerold

last: Bongers

institute: Icahn School of Medicine at Mount Sinai

first: Michelle

middle: E

last: Pacer

first: Thais

last: Geraldino

first: Lili

last: Chen

first: Zhengxiang

last: He

first: Daigo

last: Hashimoto

first: Glaucia

last: Furtado

first: Jordi

last: Ochando

first: Kevin

last: Kelley

first: Jose

first: Miriam

first: Harm


title: Arabidopsis Root Methylation and Root Nucleosome Positioning

status: Public on Feb 11 2014

city: los angeles

first: matteo

last: pellegrini

address: 610 charles young drive east

institute: UCLA

summary: DNA methylation and nucleosome densities play a critical role in the regulation of gene expression. While much is known about the mechanisms of transcriptional control that are mediated by these, less is known about the degree to which they are tissue-specific. By comparing DNA methylation, nucleosome densities and transcriptional levels in different tissue types we can gain a clearer understanding of the extent to which these mechanisms influence gene expression in a tissue-specific manner. We compared DNA methylation in Arabidopsis shoots and roots and found extensive differences across the genome. We computed DNA methylation differences between roots and shoots at single cytosines and found that one in every 173 cytosines was differentially methylated. In addition, we compared DNA methylation with tissue-specific gene expression and nucleosome density measurements to identify associations between these. We also identified a group of genes that are strongly correlated with these epigenetic marks and are significantly differentially methylated between roots and shoots. These root-specific genes are part of the extensin family, and are preferentially methylated and have at least 10-fold higher expression and lower nucleosome density in roots relative to shoots.

overall_design: No replicates, two libraries for root methylation.

first: Nicolas

last: Widman


title: Deep RNA Sequencing Reveals Dynamic Regulation of Myocardial Noncoding RNA in Failing Human Heart and Remodeling with Mechanical Circulatory Support

status: Public on Feb 10 2014

city: Taipei

first: Kai-Chien

last: Yang

address: No.1, Sec. 1, Jen-Ai Rd, 1150R

department: Graduate Institute and Department of Pharmacology

country: Taiwan

institute: National Taiwan University

summary: Complete transcriptome profiling in human failing and non-failing control hearts using next-gen sequencing

overall_design: Poly-A selected RNA and small RNA sequencing carried out in 5 groups of samples: NF, ICM, NICM, ICM+LVAD, NICM+LVAD

first: Jeanne

last: Nerbonne


title: Genomic analyses reveal miR-137 broad impact on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells

city: Los Angeles

first: Philip

middle: James

last: Uren

address: 1050 Childs Way, RRI201

institute: University of Southern California

summary: miR-137 plays critical roles in the nervous system and tumor development. An increase in its expression is required for neuronal differentiation while its reduction is implicated in gliomagenesis. To evaluate the potential of miR-137 in glioblastoma therapy, we conducted genome-wide target mapping in glioblastoma cells by measuring levels of associations between PABP and mRNAs in cells transfected with miR-137 mimics vs. controls via RIPSeq. Impact on mRNA levels was also measured by RNASeq. By combining the results of both experimental approaches, 1468 genes were determined to be negatively impacted by miR-137; among them, 595 (40%) contain miR-137 predicted sites.  The most relevant targets include oncogenic proteins and players in neurogenesis like c-KIT, YBX1, AKT2, CDC42, CDK6 and TGFβ2. Interestingly, we observed that several identified miR-137 targets are also predicted to be regulated by miR-124, miR-128 and miR-7, which are equally implicated in neuronal differentiation and gliomagenesis. We suggest that the concomitant increase of these four miRNAs in neuronal stem cells or their repression in tumor cells could produce a robust regulatory effect with major consequences to neuronal differentiation and tumorigenesis.

overall_design: Identification of genes affected by miR137 transfection via RIP-Seq and RNA-Seq in U251 and U343 cells

middle: J

first: Dat

middle: T

last: Vo

first: Luiz

last: Penalva


title: Epigenetic regulation of gene expression is instructed by promoter sequence and refined by developmental progression

city: RTP

first: ruifang

last: li

address: 111 T.W. Alexander Drive

institute: NIEHS

summary: A large body of literature suggests that local features of chromatin are crucial in determining functional properties of underlying DNA.  The extent to which DNA sequence plays an active role in the establishment and maintenance of patterns of histone and DNA modification at promoters in cells and tissues in an adult animal remains poorly understood.  Likewise, whether passage through development is required for refinement of transcriptional states and chromatin marks characteristic of fully differentiated adult cells remains unclear.  Here we undertook analysis of gene expression along with the genomic distribution of DNA methylation and a set of histone marks in primary tissues derived from different primordial germ layers in adult mice.  We find that promoter CpG content correlated strongly with specific repressive mechanisms.  Likewise, RNA polymerase II occupancy and active histone marks were omnipresent on CpG rich promoters regardless of transcriptional output and of cell type.  However, these same chromatin features cleanly demarcate transcriptional activity on promoters with low CpG content.  While these observations imply an instructive role for DNA sequence in establishment and maintenance of epigenetic states, experimental evidence presented here also suggests an additional role for development in refining these features at individual promoters.

overall_design: Examination of H3K36me3, S5ph pol2, and S2ph pol2 in liver using ChIP-seq.

first: Ruifang

last: Li

first: Paul

last: Wade

first: Sara

last: Grimm


title: Developmentally Abnormal Human Embryos Trigger a Maternal ER Stress Response

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study were to compare signals from competent and abnormal human embryos impacted differently on the expression of endometrial receptivity genes in mouse uteri using transcriptome profiling (RNA-seq).
Methods: Immature female (25 d C57BL/6) mice were given a hormone treatment of a single dose 1 mg progesterone and 10 mg/kg/day β-estradiol for a total of 3d to prime the uterus for embryo transfer. The uterine horns of control and study mice were injected with an equal volume (50 μl) of either unconditioned embryo culture medium (ECM), serving as controls, or pooled conditioned media from competent (n = 9) or arresting embryos (n = 18). Uterine mRNA profiles of 25-day-old wild-type (WT)  were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 platform. The sequence reads that passed quality filters were analyzed with the following methods: Bowtie Alignment followed by TopHat (splice juntions mapper) and Cufflinks (transcript abundance). qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the uteri WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of maternal uterine reponse to signals from competent and abnormal human embryos, with biological replicates, generated by RNA-seq technology.

overall_design: Supernatant from competent and abnormal human embryos were flushed into the uterine horns of 25d old C57BL/6 female mice. Uterine mRNA profiles of 21-day old mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 platform (HiSeq).

first: Madhuri

last: Salker


title: Small RNAs from Nicotiana benthamiana leaves

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

summary: Small RNA expression from Nicotiana benthamiana leaves was profiled with the primary goal of ascertaining microRNA isoform diversity for known, conserved families. A secondary goal was to provide a baseline small RNA expression atlas for this species and tissue.

overall_design: Two biological replicates of leaves from growth-room grown plants. The two libraries were each run twice on different runs, so there are a total of four datasets. For most analyses, it will be appropriate to combine the run1 and run2 versions for the libraries.

first: Qikun

last: Liu


title: lncRNA-Activated by TBGF-β-induced transcriptional changes and binding targets in hepatocellular carcinoma cells

status: Public on Feb 08 2014

city: shanghai

first: shu-han

last: sun

address: 800 Xiang-Yin Road

institute: Second Military Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array
Other


title: High-resolution mapping defines the cooperative architecture of Polycomb Response Elements

city: Boston

first: Guillermo

last: Orsi

state: Massachusetts

address: 240 Longwood Ave.

department: BCMP

institute: Harvard Medical School

summary: Polycomb-mediated chromatin repression modulates gene expression during development in metazoans. Binding of multiple sequence-specific factors at discrete Polycomb Response Elements (PREs) is thought to recruit repressive complexes that spread across an extended chromatin domain. To dissect the structure of PREs, we applied high-resolution mapping of non-histone chromatin proteins in native chromatin of Drosophila cells. Analysis of occupied sites reveal cooperative interactions between transcription factors that stabilize Polycomb anchoring to DNA, and implicate the general transcription factor Adf1 as a novel PRE component. By comparing two Drosophila cell lines with differential chromatin states, we provide evidence that repression is accomplished at multiple steps in transcription, including inactivation of distant enhancers, enhanced Polycomb recruitment to PREs and target promoters, and elevated stalling of RNAPII in repressed genes. These results suggest that the stability of complexes bridging promoters, enhancers, and PREs is a crucial aspect of developmentally regulated gene expression.

overall_design: Native chromatin immunoprecipitation of histones, transcription factors and Polycomb protein in Drosophila cell lines.

first: Sivanathan

last: Kasinathan

first: Sarah

last: Saminadin-Peter

first: Kelly

last: Hughes

first: Steven

last: Henikoff

first: Kami

last: Ahmad


title: Stage-specific control of early B cell development by the transcription factor Ikaros

status: Public on Feb 09 2014

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: Ikaros is an essential regulator of lymphopoiesis. Here, we studied the B-cell-specific function of Ikaros by conditional Ikzf1 inactivation in pro-B cells. B-cell development was arrested at an aberrant ‘pro-B’ cell stage characterized by increased cell adhesion and loss of pre-B cell receptor signaling. Ikaros was found to activate genes coding for pre-BCR signal transducers and to repress genes involved in the downregulation of pre-BCR signaling and upregulation of the integrin signaling pathway. Unexpectedly, derepression of Aiolos expression could not compensate for the loss of Ikaros in pro-B cells. Ikaros differentially controlled active chromatin at promoters and enhancers of repressed and activated target genes. Notably, Ikaros binding and target gene expression was dynamically regulated at distinct stages of early B-lymphopoiesis.

overall_design: 16 RNA-Seq samples in pre-proB cells (4 replicates, for each 2 controls and 2 experimental samples);  4 RNA-Seq samples in pro-B cells in Rag2-/- backgrounds (Ikzf1 deleted versus non deleted, 2 replicates each);  4 RNA-Seq samples in c-Kit high pro-B cells (Ikzf1 deleted versus non deleted, 2 replicates each); 4 RNA-Seq samples in pro-B cells (Ikzf1 deleted versus non deleted, 2 replicates each);  2 RNA-Seq samples pre-B cells wild type;  8 chromatin ChIP-Seq samples (4x H3K9ac, 4x H3K4me3, Ikzf1 deleted/non deleted, two replicates each).; 4 Transcription factor ChIP-Seq samples in pro-B cells; 1 Transcription factor ChIP-Seq samples in DP-T cells; 1 Transcription factor ChIP-Seq samples in pre-pro-B cells; 2 Mi-2b Chip-Seq samples (Ikzf1 deleted versus non deleted); 1 ChIP-Seq input track for pro-B cells;  1 ChIP-Seq input track for DP-T cells

first: Tanja

last: Schwickert

first: Hiromi

last: Tagoh

first: Sinan

last: Gültekin

first: Aleksander

last: Dakic

first: Elin

last: Axelsson

first: Martina

last: Minnich

first: Anja

last: Ebert

first: Barbara

last: Werner

first: Mareike

last: Roth

first: Luisa

last: Cimmino

first: Ross

last: Dickins

first: Johannes

last: Zuber

first: Markus

last: Jaritz

first: Meinrad

last: Busllinger


title: Ikaros mutation confers integrin-dependent pre-B cell survival and progression to acute lymphoblastic leukemia

city: Charlestown

first: Katia

last: Georgopoulos

state: MA

address: 1st and 13th St

department: CBRC

summary: Deletion of the Ikaros DNA-binding domain generates dominant-negative isoforms that interfere with Ikaros family activity and correlate with poor prognosis in human precursor B cell acute lymphoblastic leukemias (B-ALL).  Here, we show that conditional inactivation of the Ikaros DNA binding domain in early pre-B cells arrests their differentiation at a stage where integrin-dependent niche adhesion augments mitogen-activated protein kinase signaling, proliferation, and self-renewal, and attenuates pre-B cell receptor signaling and differentiation. Transplantation of polyclonal Ikzf1 mutant pre-B cells results in long-latency oligoclonal pre-B-ALL, demonstrating that loss of Ikaros contributes to multistep B-leukemogenesis. These results explain how normal pre-B cells transit from a highly proliferative and stromal-dependent to a stromal-independent phase where differentiation is enabled, providing potential therapeutic strategies for IKZF1 mutant B-ALL.

overall_design: One of the analyses described in this manuscript is the differential gene expression of large preB cells sorted from the bone marrow of WT and IKDN mice. The RNASeq method and Deseq analysis algorithm were employed

first: Ila

last: Joshi

first: Toshimi

last: Yoshida

first: Nilamani

last: Jena

first: Xiaoqing

last: Qi

first: Jiangwen

last: Zhang

first: Richard

last: Van Etten


title: Characterization of the connection between protein synthesis and amino acid biosynthesis gene expression to growth rate in budding yeast

status: Public on Feb 07 2014

city: Rehovot

first: Noam

last: Ohana

address: 234 Herzl St.

department: Molecular Genetics

institute: Weizmann Institute of Science

summary: In unicellular organisms, growth rate is the major phenotype that is being selected through evolution. In order to grow efficiently, living cells should synchronize the quantity of their ribosome and RNA polymerase levels according to  the respective  rates by which amino acids and nucleotides pool are replenished. Gene expression patterns and their relationship with growth rate have been widely investigated in various conditions, and a large set of transcripts which included genes associated with ribosome biogenesis (Ribi) and with the stress response, was shown to be expressed in coordination with cell growth rate. Interestingly, decoupling of this correlation was found for certain mutants and conditions, including in my lab when mutant growth rate was examined and when yeast were grown on xylulose, a carbon source not available in the wild. Under those conditions, amino-acid biosynthesis genes regulated by the GCN4 transcription factor were found to have a strong inverse correlation with growth rate, while Ribi and stress genes showed no such correlation. I hypothesized that this decoupling of the general coupling between growth rate and gene expression is a result of a lack of evolutionary optimization to this carbon source or to genetic mutations. The goal of my study was to examine this hypothesis at a greater depth. To this end, I defined the growth rate and genome-wide expression profile of 328 strains deleted of individual genes that show different levels of growth defect. As predicted, growth rate of those strains was correlated with the expression level of GCN4-dependent genes, but not with the Ribi or stress genes, similar to the correlation observed in our xylulose experiment.

overall_design: 328 S. Cerevisiae deletion strains relatively to the wild type strain


title: Analysis of Allelic bias in gDNA, cDNA and ChIP with H3K27me3 and H3K36me3 antibody with multiplexed padlock probe approach

city: La Jolla

first: Kun

address: 9450 Gilman Drive

department: Bioengineering

institute: UCSD

summary:
In this experiment, we asked how the allelic distribution of the active and repressive chromatin marks in clonal cell lines relates to the transcriptional allelic bias.  A multiplexed padlock probe approach (Zhang et al., 2009) enabled us to assess allelic bias in heterozygous exonic SNPs in two clones with GM12878 genotype, and four clones from GM13130 cells. We used this approach to assess allelic bias in H3K27me3 and H3K36me3 ChIP samples simultaneously with cDNA from the same cells, as well as ChIP input and genomic DNA controls.
In order to pool data from two individuals, one of which (GM13130) lacked complete genotypes for parents, we assessed SNP bias as reference and alternative alleles (rather than maternal or paternal bias).  SNPs in cDNA were assigned to one of three bins: reference allele bias; no bias; and alternative allele bias. For these groups, allelic bias in H3K27me3 (Fig.4B) and H3K36me3 (Fig.4C) was determined. In unbiased loci, both H3K27me3 and H3K36me3 were equally represented. In contrast, preferential expression of an allele was associated with elevated levels of H3K36me3 and decreased levels of H3K27me3 on that allele.  Both effects were highly significant (p<2x10e-9).
Genes predicted to have MAE were about four-fold over-represented among genes where SNPs showed significant bias (Fig.4D). SNPs with skewed H3K27me3 and H3K36me3 distribution were highly enriched in the genes predicted as MAE (p<10e-6 and p=0.01, respectively; two-tailed Fisher's exact test). This suggests that the asymmetric distribution of the histone modifications is to a large extent due to the genes that have the chromatin signature of monoallelic expression.

overall_design: Samples analyzed were A. polyclonal cell line GM12878 , and clones derived from it: DF1 and DF2, B. Polyclonal GM13130 (H0) and clones derived from it: H7, H14 and H16. gDNA, cDNA, ChIP material and input were used.

first: Anwesha

last: Nag

first: Virginia

last: Savova

first: Alexander

last: Gimelbrant

first: Ho-Lim

last: Fung


title: Ribonuclease L and Metal-Ion-Independent Endoribonuclease Cleavage Sites in Host and Viral RNAs

city: Aurora

first: Daphne

middle: A.

last: Cooper

state: CO

department: Department of Microbiology

institute: University of Colorado

summary: We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs.

sample_organism:
Homo sapiens
Poliovirus 1
hepatitis C virus genotype 1a

overall_design: To make cDNA libraries, we exploited the 2’, 3’-cyclic phosphate at the end of RNA fragments produced by RNase L and other metal-ion-independent endoribonucleases. Using Arabidopsis thaliana tRNA ligase, RNA fragments with 2’, 3’-cyclic phosphates were covalently attached to defined RNA linkers containing an 8-base long unique molecular identifier (UMI) sequence. Libraries prepared in this manner contain cDNA derived exclusively from RNA fragments with 2', 3'-cyclic phosphates. The UMI sequence allows for detailed quantitation. We optimized and validated 2’, 3’-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A, and RNA from uninfected and poliovirus-infected HeLa cells.

first: Babal

middle: K

last: Jha

first: Robert

last: Silverman

first: Jay

middle: R

last: Hesselberth

first: David

last: Barton


title: RNase J is required for processing of a small number of RNAs in Rhodobacter sphaeroides

status: Public on Feb 06 2014

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: A comparative RNA-seq approach between R. sphaeroides 2.4.1 wild type and an RNase J deletion strain 2.4.1∆rnj revealed the accumulation of different mRNA fragments in the mutant. The structural characteristics of these RNA fragments suggest that RNase J is responsible for the decay of degradation intermediates that cannot serve as substrates for the 3´-to-5´ exoribonucleases.

overall_design: Total RNA from exponentially grown cultures (OD660 0,4) of 2.4.1 wild type and 2.4.1∆rnj has been isolated in triplicates using the hot phenol method and prepared for sequencing on a Illumina Genome Analyzer IIx machine.

first: Tom

last: Rische-Grahl

first: Lennart

last: Weber

first: Bernhard

last: Remes

middle: U

first: Gabriele

last: Klug


title: MicroRNAs in a multicellular green alga Volvox carteri

city: Beijing

first: Yijun

last: Qi

state: Bejing

address: Biotech. Building

department: School of Life Sciences

institute: Tsinghua University

summary: We identified 174 miRNAs expressed in Volvox carteri. Some of Volvox miRNAs are highly enriched in gonidia or somatic cells. Subsequently, we predicted the targets of Volvox miRNAs and found many of target genes were regulated through mRNA degradation. Conservation analysis suggests the common origin of miRNA between Volvox and Chlamydomonas and high frequency of birth and death of Volvox miRNAs.

overall_design: Identification of miRNAs in multicellular green Volvox

first: Jingrui

last: Li

first: Yang

last: Wu


title: Euchromatic transposon insertions trigger production of novel pi- and endo-siRNAs at the target sites in the Drosophila germline

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

summary: The control of transposable element (TE) activity in germ cells provides genome integrity over generations. A distinct small RNA-mediated pathway utilizing Piwi-interacting RNAs (piRNAs) suppresses TE expression in gonads of metazoans. In the fly, primary piRNAs derive from so-called piRNA clusters, which are enriched in damaged repeated sequences. These piRNAs launch a cycle of TE and piRNA cluster transcript cleavages resulting in the amplification of piRNA and TE silencing. Using genome-wide comparison of TE insertions and ovarian small RNA libraries from two Drosophila strains, we found that individual TEs inserted into euchromatic loci form novel dual-stranded piRNA clusters. Formation of the piRNA-generating loci by active individual TEs provides a more potent silencing response to the TE expansion. Like all piRNA clusters, individual TEs are also capable of triggering the production of endogenous small interfering (endo-si) RNAs. Small RNA production by individual TEs spreads into the flanking genomic regions including coding cellular genes. We show that formation of TE-associated small RNA clusters can down-regulate expression of nearby genes in ovaries. Integration of TEs into the 3' untranslated region of actively transcribed genes induces piRNA production towards the 3'-end of transcripts, causing the appearance of genic piRNA clusters, a phenomenon that has been reported in different organisms. These data suggest a significant role of TE-associated small RNAs in the evolution of regulatory networks in the germline.

overall_design: The fractions of small RNAs (19-29 nt) from ovaries of y[1]; cn[1] bw[1] sp[1] line of Drosophila melanogaster were sequenced using Illumina HiSeq 2000.

first: Sergey

last: Shpiz

first: Ivan

last: Olovnikov

first: Alla

last: Kalmykova


title: Transcription Factor Regulation and Chromosome Dynamics in Pseudohyphal Growth

city: Collegeville

last: Mayhew

address: 1250 South Collegeville Road

department: Target Sciences, Computation Biology, R&D

institute: GlaxoSmithKline

summary: Pseudohyphal growth is a developmental pathway seen in some strains of yeast, in which cells elongate and form multicellular filaments in response to environmental stresses.  Regulation of this process is complex and involves multiple signaling pathways and a large number of transcription factors (TFs).  We used multiplexed transposon “Calling Cards” to simultaneously record the genome-wide binding patterns of 28 TFs in nitrogen-starved yeast. We were able to identify TF targets relevant for pseudohyphal growth, producing a detailed map of the regulatory network that governs this process.  Using tools from graph theory, we identified 8 transcription factors that lie at the center of this network, including Flo8, Mss11, and Mfg1, which bind as a complex.  Surprisingly, the DNA binding preferences for these key transcription factors were not known.  Using Calling Card data, we predicted the in vivo DNA binding motif for the Flo8-Mss11-Mfg1 complex and validated it using a reporter assay.  We found that this complex binds several important targets, including FLO11, at both their promoter and termination sequences.  We demonstrated that this binding pattern is the result of DNA-looping, which regulates the transcription of these targets and is stabilized by an interaction with the nuclear pore complex.  This looping provides yeast cells with a transcriptional memory, enabling them to more rapidly execute the filamentous growth program when nitrogen-starved if they have been previously exposed to this condition.

overall_design: These data contain mapped insertion sites from Ty5 transposon "Calling Cards" in Σ1278b yeast sequenced using an Illumina Hiseq.  Other sequencing data present are RNA-seq reads.

first: Robi

last: Mitra


title: Functional signature for the recognition of specific target mRNAs by human staufen1 protein

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

summary: Cellular mRNAs are permanently associated to proteins in the form of ribonucleoprotein particles. In addition to the hnRNP and SR protein families, the double-stranded RNA-binding (DRB) proteins play important roles in mRNA synthesis, modification, activity and decay (Dreyfuss et al, 2002; Stutz & Izaurralde, 2003). Staufen is a DRB protein first described as a maternal factor involved in the localised translation of specific mRNAs during early development in the fly (Riechmann & Ephrussi, 2001). One of the human homologues, human Staufen1 (hStau1) forms ribonucleoprotein complexes known as RNA granules that contain proteins involved in translation regulation as well as cytoskeleton and motor proteins to allow the movement of the granule on the microtubules. Although many cellular mRNAs have been found associated to these RNA granules, the specificity of such binding and the mechanims of hStau1-RNA interaction are still unclear. Here we identified a protected sequence signature with high homology to human Alu family of short interspersed elements at the 3’-untranslated region of mRNAs specifically associated to hStau1 protein. Using a combination of affinity chromatography, RNAse-protection, deep-sequencing and bioinformatic analyses to compare the mRNAs differentially associated to hStau1 or a mutant protein unable to bind RNA we defined a collection of mRNAs specifically associated to wt hStau1. A common sequence signature consisting of two opposite-polarity Alu motifs was present in the hStau1-associated mRNAs and was shown to be sufficient for binding to hStau1 and hStau1-dependent stimulation of protein expression. Our results unravel how hStau1 identifies a wide spectrum of cellular target mRNAs to control their localisation, expression and fate. We suggest that mammalian Staufen1 protein has adapted to use the evolutionary recent Alu elements as recognition signals thereby increasing its possibilities for rapid identification to new mRNA targets.

overall_design: Staufen (wild type or mutant) associated RNAs were extracted from HEK293T cells and sequenced according the illumina mRNA-seq potocol (HiSeq2000 sequencer). A third sample, of RNA, associated to a wild type Staufen, was treated with RNase T1 so only RNA fragments directly attached to Staufen were purified and sequenced.

first: Susana

last: de Lucas

first: Mónica

last: Chagoyen

last: Ortín


title: Genome-wide maps of WT and over-expressing CenH3/CENP-A in Human HeLa S3 cells

city: Paris

first: Genevieve

last: Almouzni

state: Ille De France

address: 26 Rue D'Ulm

department: Nuclear Dynamics and Genome Plasticity

country: France

institute: Institut Curie

summary: Centromeres are essential to ensure proper chromosome segregation in eukaryotes. Their definition relies on the presence of a centromere-specific H3 histone variant CenH3, known as CENP-A in mammals. Its overexpression in aggressive cancers raises questions concerning its effect on chromatin dynamics and contribution to tumorigenesis. We find that CenH3 overexpression in human cells leads to ectopic enrichment at sites of active histone turnover. Furthermore, in over-expressing conditions, we see the formation of a novel heterotypic particle (CenH3-H4/H3.3-H4) that occludes CTCF binding, but this occlusion has only a minor effect on gene expression. Ectopic localization and CTCF occlusion depends on the H3.3 chaperone DAXX, rather than its dedicated chaperone HJURP. This DAXX-dependent occlusion also occurs in naturally overexpressing cancer cells. Furthermore, our cellular model reveals a DAXX-dependent survival advantage when challenged by DNA damage. Our findings illustrate how changes in histone variant levels can disrupt chromatin dynamics in disease and provides a possible mechanism for cell resistance to anti-cancer treatments.

overall_design: Examination of CenH3 ChIP-seq and RNA-seq transcriptional programs in two conditions - WT and CenH3 over-expressing.

first: Adam

last: Woolfe

first: Nicolas

last: Lacoste


title: Wnt/β-catenin signaling integrates patterning and metabolism of the insect growth zone.

city: Göttingen

first: Georg

last: Oberhofer

state: Lower Saxony

address: Justus von Liebig Weg 11

department: Developmental Biology

institute: University Göttingen

summary:
Purpose: Combination of systemic RNAi with RNAseq to identify target genes of important pathways in early development

Wnt/β-catenin and hedgehog (Hh) signaling are essential for transmitting signals across cell membranes in animal embryos. Early patterning of the principal insect model, Drosophila melanogaster, occurs in the syncytial blastoderm, where diffusion of transcription factors obviates the need for signaling pathways. However, in the cellularized growth zone of typical short germ insect embryos, signaling pathways are predicted to play a more fundamental role. Indeed, the Wnt/β-catenin pathway is required for posterior elongation in most arthropods, although which target genes are activated in this context remains elusive. Here, we use the short germ beetle Tribolium castaneum to investigate two Wnt and Hh signaling centers located in the head anlagen and in the growth zone of early embryos. We find that Wnt/β-catenin signaling acts upstream of Hh in the growth zone, whereas the opposite interaction occurs in the head. We determine the target gene sets of the Wnt/β-catenin and Hh pathways and find that the growth zone signaling center activates a much greater number of genes and that the Wnt and Hh target gene sets are essentially non-overlapping. The Wnt pathway activates key genes of all three germ layers, including pair-rule genes, and Tc-caudal and Tc-twist. Furthermore, the Wnt pathway is required for hindgut development and we identify Tc-senseless as a novel hindgut patterning gene required in the early growth zone. At the same time, Wnt acts on growth zone metabolism and cell division, thereby integrating growth with patterning. Posterior Hh signaling activates several genes potentially involved in a proteinase cascade of unknown function.

overall_design:
10-11 h old whole embyro mRNA profiles of the following treatments:
reference: wild type 100bp single read triplicates
reference: wild type 50bp single read triplicates
treatment: Tc-arrow RNAi knockdown 50 bp single read triplicates
treatment: Tc-frizzled1/2 RNAi double knockdown 50 bp single read triplicates
treatment: Tc-hedgehog RNAi knockdown 100bp single reads quadruplicates
treatment: Tc-orthodenticle RNAi knockdown 100bp single reads triplicates
treatment: Tc-torso RNAi knockdown 100bp single reads triplicates
treatment: Tc-wntless RNAi knockdown 50bp single reads triplicates
Total: 2 references, 6 treatments, 25 sequencing runs

first: Daniela

last: Grossmann

first: Janna

middle: L

last: Siemanowski

first: Tim

last: Beissbarth

first: Gregor

last: Bucher


title: Transcriptome sequencing of nasopharyngeal carcinoma model system

status: Public on Feb 05 2014

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

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

overall_design: Refer to individual Series


title: Identification of transcription factor binding sites from ChIP-seq data at high-resolution

city: Kansas City

first: Samuel

middle: Richard

last: Meier

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

summary: Genome-wide mapping of protein–DNA interactions is essential for a full understanding of transcriptional regulation. A precise map of binding sites for transcription factors, core transcriptional machinery is vital for deciphering the gene regulatory networks that underlie various biological processes. Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for genome-wide profiling of DNA-binding proteins. However, our conventional ChIP–seq occasionally gives wider peaks which might be due to overlapping binding sites of two or more transcription factors. Therefore, to improve the resolution of our conventional ChIP–seq which have DNA-protein footprint of ~100 bp, we decreased the size of DNA-protein footprint to ~ 50 bp by DNaseI digestion of whole cell extract (WCE).

overall_design: ChIP-seq for Twist transcription factor in Drosophila embryos

first: Sangeeta

last: Bafna

first: Anais

middle: F

last: Bardet

first: Jonas

last: Steinmann

first: Alexander

last: Stark

first: Julia

last: Zeitlinger


title: Transcriptome sequencing of nasopharyngeal carcinoma model system (mRNA)

summary: Nasopharyngeal carcinoma (NPC) is a prevalent malignancyt disease in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq) of NPC model systems.

overall_design: Matched total mRNA and small RNA of undifferentiated Epstein-Barr virus (EBV)-positive NPC xenograft X666 and its derived cell line C666, well-differentiated NPC cell line HK1, and the immortalized nasopharyngeal epithelial cell line NP460 have been sequenced by Solexa technology.

first: Carol

middle: Y

last: Szeto

first: Maria

last: Lung

first: Chi

middle: H

first: Siu

middle: C

last: Choi

first: Timothy

last: Yip

first: Roger

last: Ngan

first: George

last: Tsao


title: Next generation sequencing in ZS rats

city: Indianapolis

first: Hai

address: 410 W 10th St

institute: IUPUI

summary: Next generation sequencing in a rat model of diabetic nephropathy was employed to study in depth the pathogenic alterations involved in progressive diabetic kidney damage. We employed the obese, diabetic ZS rat, a model that develops renal failure and fibrosis, the hallmarks of human disease. We then used RNA-seq to examine in a comprehensive manner the combined effects of renal cells and infiltrating inflammatory cells acting as a pathophysiological unit.

overall_design: 12 samples (4 independent samples for each of 3 groups, 1 control group)

first: Jesus

last: Dominguez

first: Katherine

last: Kelly

first: Chirayu

last: Goswami

first: Yunlong

last: Liu

first: Jizhong

last: Zhang


title: Genome-wide identification of transcripts associated with lncRNA-ATB by RIP-seq

city: shanghai

first: shu-han

last: sun

summary: The role of TGF-β-induced epithelial-mesenchymal transition (EMT) in cancer cell dissemination is well established, but the involvement of lncRNAs in TGF-β signaling is still unknown. In this study, we observed that the lncRNA-Activated by TGF-β (lncRNA-ATB) was upregulated in hepatocellular carcinoma (HCC) metastases and associated with poor prognosis. lncRNA-ATB upregulated ZEB1 and ZEB2 by competitively binding the miR-200 family and then induced EMT and invasion. In addition, lncRNA-ATB promoted organ colonization of disseminated tumor cells by binding IL11 mRNA, inducing autocrine of IL11 and triggering STAT3 signaling. Globally, lncRNA-ATB promotes the invasion-metastasis cascade. Thus, these findings suggest that lncRNA-ATB, a mediator of TGF-β signaling, could predispose HCC patients to metastases and may serve as a potential target for anti-metastatic therapies.

overall_design: To identify mRNA species bound by lncRNA-ATB, we performed an RIP to pull down endogenous mRNAs associated with the lncRNA-ATB and sequenced the retrieved RNA.

first: Ji-hang

last: Yuan

first: Shu-han

last: Sun


title: Genome-wide analysis of H3K9me2 and JIL-1 kinase mediated histone H3S10 phosphorylation in drosophila [ChIP-seq: 13 samples]

city: Ames

first: Jorgen

last: Johansen

address: MBB3142, Iowa State Univeristy

department: BBMB

institute: Iowa State Universtiy

summary: In this study we have determined the genome-wide relationship of JIL-1 kinase mediated H3S10 phosphorylation with gene expression and the distribution of the epigenetic H3K9me2 mark.  We show in wild-type salivary gland cells that the H3S10ph mark is predominantly enriched at active genes whereas the H3K9me2 mark largely is associated with inactive genes.

overall_design: Examination of 2 different histone modifications  in 2 genotype types.

first: Weili

last: Cai

first: Chao

last: Wang

first: Yeran

last: Li

first: Lu

last: Shen

first: Sanzhen

first: Changfu

last: Yao

first: Xiaomin

last: Bao

first: Patrick

middle: S

last: Schnable

first: Jack

last: Girton

first: Jørgen

first: Kristen

middle: M


title: Genome-wide analysis of gene expression and intron retention during development in a U12-type splicing-deficient zebrafish mutant

city: Parkville

first: Joan

middle: Kathleen

last: Heath

state: Victoria

address: 1G Royal Parade

department: Development and Cancer

institute: Walter and Eliza Hall Institute of Medical Research

first: Sebastian

last: Markmiller

first: Nicole

last: Cloonan

first: Rea

last: Lardelli

first: Karen

last: Doggett

first: Maria-Cristina

last: Keightley

first: Yeliz

last: Boglev

first: Andrew

last: Trotter

first: Annie

last: Ng

first: Simon

last: Wilkins

first: Heather

last: Verkade

first: Elke

middle: A

last: Ober

first: Holly

last: Field

first: Sean

last: Grimmond

first: Graham

last: Lieschke

first: Didier

last: Stainier


title: Genome-scale reconstruction of the sigma factor network in E. coli

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for Escherichia coli under different conditions. By obtaining sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-wide TSS (transcription start site) maps for E. coli.  This TSS-map was integrated with ChIP-chip data generated for 6 sigma factors in E. coli, resulting in reconstruction of sigma factor network in E. coli.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Examination of transcription start sites by biological duplicates from E. coli for 3 different conditions

first: Byung-Kwan

last: Cho

first: Bernhard

middle: O

last: Palsson