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

first: Joan

last: Heath

summary: To determine the global impact of the clbn mutation on gene expression and efficiency of U2- and U12-type splicing, we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2-type and U12-type intron on a genome-wide scale to confirm that rnpc3 deficiency specifically impairs U12-type splicing. RNAseq and microarray data were combined to yield high-confidence lists of differentially expressed genes which show that impaired U12-type splicing has a wide-ranging effect on the developing transcriptome.

overall_design: RNAseq libraries prepared from 108 hours post-fertilization zebrafish larvae (approx. 60 embryos each, genotyped homozygous wildtype and homozygous clbns841 mutants, respectively)

first: Sebastian

last: Markmiller

first: Nicole

last: Cloonan

middle: J


title: AICAR can modulate the expression of microRNA in J1 mESC

status: Public on Feb 06 2014

city: Yangling

first: Xiaoyan

last: Shi

address: Taicheng Road

country: China

institute: Northwest A&F University

type: Non-coding RNA profiling by high throughput sequencing

summary: We have demonstrated AICAR can maintain J1 mouse ES cells pluripotency in our previous research, yet its effects on ES cells miRNAs expression remain a mystery. In this study, we performed small RNA (sRNA) High-throughput sequencing using Illumina HiSeq 2000 to investigate the influence of AICAR on J1 mouse ES cells miRNAs expression and further found the mechanism of how miRNAs affect ES cells pluripotency maintenance. Samples that treated by DMSO is used as a control.

overall_design: Compare microRNA expression of J1 mESC cultured with or without small molecule AICAR

first: Yongyan

last: Wu

first: Zhiying

last: Ai

first: Zekun

last: Guo


status: Public on Feb 05 2014

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

country: USA

institute: Emory University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The mammalian CCCTC-binding factor (CTCF) regulates gene expression through the formation of higher order chromatin structures.  Recent evidence has implicated a role for CTCF in regulating gene expression in the human MHCII locus.  To investigate the role of CTCF in murine MHCII gene expression we mapped CTCF binding sites in B cells (MHCII+ cells) and Plasmablasts which are differentiated B cells that have silenced MHCII gene expression.  These observations lead to the identification of differential CTCF binding during differentiation in these cell types and suggest mechanims of MHCII gene regulation.

overall_design: Comparison of CTCF binding in B cells and Plasmablasts in mice using ChIP-seq

first: C

first: J

last: Boss


title: Benchmark study of different chromatin isolation methods using the E2Fa transcription factor

status: Public on Feb 04 2014

city: Gent

first: Ken

last: Heyndrickx

address: Technologiepark 927

department: Department of Plant Biotechnology and Bioinformatics

country: Belgium

institute: Ghent University

summary: Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation (ChIP), this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis thaliana cells by tandem chromatin affinity purification (TChAP). Evaluation of TChAP using the E2Fa TF and comparison with traditional ChIP and single chromatin affinity purification illustrates the suitability of TChAP and provides a resource for exploring the E2Fa transcriptional network. Integration with transcriptome, cis-regulatory element, functional enrichment, and co-expression network analyses demonstrates the quality of the E2Fa TChAP-seq data and validates the identification of new direct E2Fa targets. TChAP enhances both TF target mapping throughput, by circumventing issues related to antibody availability, and output, by improving DNA enrichment efficiency.

overall_design: Illumina Seq analysis of E2Fa bound DNA elements isolated using different chromatin isolation methods. BioProject PRJNA172013; SRA study ID SRP014713

first: Aurine

last: Verkest

first: Thomas

last: Abeel

first: Klaas

last: Vandepoele

first: Geert

last: De Jaeger


title: Nucleosome positioning in Yeast

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: We report nucleosome poisitioning in Yeast

overall_design: Mono-nucleosome DNA was mapped

first: Vishwanath

middle: R


title: microRNA decay analysis in the first larval stage Caenorhabditis elegans

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: microRNAs (miRNAs) constitute a class of small non-coding RNAs (~22nt). They are thought to be generally stable with half-lives of many hours or even days. However, several miRNAs have been reported to decay rapidly in specific situations. In order to examine miRNA stability on a global scale, we quantify relative decay rates of miRNA in first larval stage C. elegans worms that are treated with a transcription inhibitor alpha-amanitin by deep sequencing. Several miRNAs including members of the miR-35 and miR-51 families exhibit accelerated decay. Moreover, biogenesis of miRNAs involves generation of a miRNA duplex intermediate consisting of the miRNA guide strand (miR) and the miRNA passenger strand (miR*). miR and miR* names were originally assigned based on the relative abundance of each strand, with the less abundant strand presumed to be inactive, and thus the miR*. However, subsequent research showed that at least individual miR*s can have biological activity. Our sequencing data reveal that miR*s, operationally defined on the basis of their relative abundance at time point t=1h, are substantially less stable than miRs. This would appear to support the notion that miR*s mainly constitute processing byproducts rather than a less abundant class of functional miRNAs.

overall_design: Examination of microRNA decay rates in the first larval stage C. elegans worms.

first: Takashi

middle: S

last: Miki

first: Helge

last: Großhans


title: RNA helicase A is necessary for KIF1Bβ tumor suppression in neuroblastoma

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: During development neuronal progenitors compete for growth factors such as nerve growth factor NGF and require the prolyl hydroxylase EglN3 and the kinesin KIF1Bβ for developmental apoptosis. Inherited KIF1Bβ loss-of-function mutations in neuroblastomas and pheochromocytomas implicate KIF1Bβ as a 1p36.2 tumor suppressor, however the mechanism of tumor suppression is unknown. We found that KIF1Bβ interacts with the RNA helicase A (DHX9) resulting in DHX9 nuclear accumulation to regulate apoptosis. KIF1Bβ-dependent DHX9 nuclear localization leads to transcription of the apoptotic target XIAP-associated factor 1. DHX9 is induced when NGF is limiting and required for apoptosis in cells deprived of NGF.

overall_design: NB1 cells were transduced to incorporate shRNA against DHX9 or a scrambled control, and transfected with a KIF1Bβ expression vector or control, then transfected cells were isolated and lysed after 48h.

first: Zhi

middle: X

last: Chen

last: Ramskold

first: Susanne

last: Schlisio


title: SMORE-seq maps both ends of transcripts and identifies widespread promoter-associated non-coding RNA governed by TATA elements.

summary: SMORE-seq (Simultaneous Mapping Of RNA Ends by sequencing) is developted to simultaneously identify the strongest TSS (Transcription Start Site) and PAS (Polyadenylation Site)

overall_design: SMORE-seq were performed in wild type Saccharomyces cerevisiae


title: Control of agricultural traits by hc-siRNA associated MITEs in rice

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: Transposable elements (TEs) and repetitive sequences comprise over 40% of rice genome. Different TEs are tightly regulated by distinct epigenetic mechanisms. For example, the activities of LTR retrotransposon Tos17 and non-LTR retrotransposon LINE element Karma are uniquely regulated by histone H3K9 methylation and histone H3K4 demethylation, respectively. Miniature inverted repeat transposable elements (MITEs) are one of the most high-copy-number DNA transposons, which are interspersed around rice genome and might influence nearby gene expression. In plants, 24-nucleotide (24-nt) heterochromatic small interfering RNAs (hc-siRNAs) derived from repeats and TEs. To what extent hc-siRNA associated TEs affect gene expression and therefore contribute to agricultural traits in rice remains elusive. Here, we show that OsDCL3a, one of Dicer-Like 3 (DCL3) homolog, is primarily responsible for 24-nt hc-siRNA processing in rice. Impaired OsDCL3a displayed altered important agricultural traits in rice. We found that genome-wide (281,563) 24-nt hc-siRNA clusters were OsDCL3a-dependent, among which MITEs were significantly enriched. Impaired OsDCL3a caused significant overlapping between reduced hc-siRNAs from MITEs and elevated nearby gene expression. Intriguingly, genes involved in Gibberellin and Brassinosteroid homeostasis were identified as direct targets of OsDCL3a, which may attribute to dwarfism and enlarged flag leaf angle upon OsDCL3a deficiency. Our work uncovers OsDCL3a-dependent hc-siRNAs derived from MITEs as broad spectrum of regulators for fine-tuning gene expression, and this observation may reflect a conserved mechanism in other higher plants with dispersed repeat- or TE-rich genomes.

overall_design: Examination of OsDCL3a-dependent hc-siRNAs derived from MITEs.

first: Liya

last: Wei

first: Xiaofeng

last: Cao


title: Mapping of somatic linker histone H1 variants in T47D-MTVL cells

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

summary: At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles, are distributed differentially along the genome, or regulate specific promoters. By taking advantage of specific antibodies to H1 variants and HA-tagged recombinant H1 variants expressed in a breast cancer-derived cell line, we have investigated the distribution of the different somatic H1 variants (H1.2 to H1.5, H1.0 and H1X) in particular promoters and genome-wide.

overall_design: Genome-wide analysis of H1.0, H1.2, H1.4, H1X and H3

first: Lluís

last: Millán-Ariño


title: Genomic distribution of human histone H1 subtypes

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Comparison of cardiomyocyte transcripts after knockdown of Gata4 in zebrafish embryos

city: New York

first: Gabriel

last: Rosenfeld

state: NY

address: 1300 York Ave. Rm. LC711

department: Cell and Developmental Biology

institute: Weill Cornell

summary: The Gata4 transcription factor is essential for normal heart development, but the molecular basis for its function remain poorly understood.  We profiled at the whole genome level transcript changes in cardiomyocytes when Gata4 is depleted from zebrafish embryos.  Our objective was to elucidate the cardiomyocyte-specific molecular program functioning downstream of Gata4 in order to better understand the role of Gata4 in cardiac morphogenesis.

overall_design: Six samples in total are deposited.  Three replicate control samples and three replicate Gata4 morphant samples were analyzed.

first: Todd

last: Evans


title: RNA polymerase

city: Ulsan

first: Donghyuk

last: Kim

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

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

type: Expression profiling by genome tiling array

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


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

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: 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

middle: L

last: Lung

first: Chi

middle: H

first: Siu

middle: C

last: Choi

first: Timothy

middle: T

last: Yip

first: Roger

middle: K

last: Ngan

first: George

last: Tsao


title: mRNA expression profiling in patients with Tetralogy of Fallot and healthy unaffected individuals

city: Berlin

first: Silke

last: Sperling

state: Berlin

address: Lindenberger Weg 80

department: Cardiovascular Genetics

country: Germany

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine

summary: Right ventricular mRNA profiles from 22 patients with Tetralogy of Fallot (TOF) and mRNA-seq profiles from the left and right ventricle (LV and RV, respectively) of 4 healthy unaffected individuals (NH) were generated. The total RNA was isolated from the 30 human heart samples using TRIzol. mRNAs were isolated from total RNA and prepared for sequencing using Illumina Kit RS-100-0801 according to the manufacturer's protocol (Preparing Samples for Sequencing of mRNA Sept 2008). The sequencing libraries were generated using a non-strand-specific library construction method. The purified DNA fragments were used directly for cluster generation, and 36 cycles of single-end read sequencing were performed using the Illumina Genome Analyzer. Sequencing reads were extracted from the image files using the open source Firecrest and Bustard applications (Illumina Genome Analyzer pipeline 1.3.2, 1.4.0 and 1.5.0).

overall_design:
Right ventricular mRNA-seq profiles from 22 patients with Tetralogy of Fallot and mRNA-seq profiles from the left and right ventricle of 4 healthy unaffected individuals.

Supplementary processed data files:
GSE36761_gene_expression_levels.txt: Gene expression profiling data for all samples.
GSE36761_gene_expression_levels_normalized.txt: Normalized gene expression profiling data for all samples.
GSE36761_transcript_expression_levels.txt: Transcript expression profiling data for all samples.
GSE36761_transcript_expression_levels_normalized.txt: Normalized transcript expression profiling data for all samples.
Genome build: hg18


title: RNA-seq analysis of the transcriptomes of Piwi-deficient iPSCs

status: Public on Feb 03 2014

city: New Haven

first: Haifan

state: CT

address: 10 Amistad Street

institute: Yale University

summary: genome wide RNA-seq analysis of the transcriptomes of iPSCs that are derived from Miwi(-/-), Mili(-/-), and Miwi2(-/-) triple-knockout (TKO) mouse embryonic fibroblast

overall_design: Four biological replicates were used for the Piw triple knockout and control, respectively


title: Pathways Disrupted in Human ALS Motor Neurons Identified Through Genetic Correction of Mutant SOD1

city: Cambridge

first: Kevin

last: Eggan

state: MA

address: 7 Divinity Avenue, Sherman Fairchild 258A

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Although many distinct mutations in a variety of genes are known to cause Amyotrophic Lateral Sclerosis (ALS), it remains poorly understood how they selectively impact motor neuron biology and whether they converge on common pathways to cause neural degeneration. Here, we have combined reprogramming and stem cell differentiation approaches with genome engineering and RNA sequencing to define the transcriptional changes that are induced in human motor neurons by mutant SOD1. Mutant SOD1 protein induced a transcriptional signature indicative of increased oxidative stress, reduced mitochondrial function, altered sub-cellular transport as well as activation of the ER stress and unfolded protein response pathways. Functional studies demonstrated that perturbations in these pathways were indeed the source of altered transcript levels.

overall_design: 5 samples, 2 patient-derived SOD1A4V and 3 isogenic control samples where the mutation has been corrected. All samples are motor neurons derived from induced pluripotent stem cells (iPSCs), and isolated after lentiviral infection with an Hb9:RFP construct and FACS purification. Each sample is a separate biological replicate.

first: Rob

last: Moccia

first: Evangelos

last: Kiskinis


title: Small RNA next generation sequencing of mice skin biopsies from acetone-treated healthy skins and DMBA/PMA-treated hyperplastic skins, papillomas and cutaneous Squamous Cell Carcinomas

city: Valbonne - Sophia-Antipolis

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: FVB/N mice were subjected to 7,12-Dimethylbenz[a]anthracene (DMBA) two-hit multistage skin carcinogenesis protocol. Mice were topically treated with 200 nmol of DMBA in 0.2 mL acetone then twice weekly for six weeks with 5 nmol PMA (Phorbol 12-myristate 13-acetate). A second hit of DMBA was performed on the eighth week followed by the resumption of PMA treatment for 14 more weeks. Control mice were only topically treated with 0.2 mL acetone vehicle. Healthy skins (acetone-treated), hyperplastic skins, papillomas and tumors were harvested throughout the protocol and biopsies were frozen for RNA extraction.

overall_design: Small RNA libraries were generated from total RNAs of control skins, hyperplastic skins, papillomas and cSCCs biopsies (n=5 in each group) corresponding to a total of 20 samples, and sequenced on the Applied Biosystems SOLiD System.

first: R

last: Rezzonico

first: C

last: Gastaldi

first: B

last: Mari

first: P

last: Barbry

first: K


title: Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development

city: Wageningen

first: Alice

last: Pajoro

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University


title: A GNAS mutation found in pancreatic intraductal papillary mucinous neoplasms induces drastic alterations of gene expression profiles with upregulation of mucin genes.

city: Sendai

first: Toru

last: Furukawa

address: 2-1 Seiryomachi, Aobaku

department: Department of Investigative Pathology

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: GNAS, a gene encoding G-protein stimulating alpha subunit, is frequently mutated in intraductal papillary mucinous neoplasms (IPMNs), which is an indolent and slow-growing pancreatic neoplasm that secretes abundant mucin. GNAS mutation is not observed in conventional ductal adenocarcinomas of the pancreas. To determine the functional significance of GNAS mutation in pancreatic ductal cells, we examined in vitro phenotypes and gene expression profiles of cells of pancreatic ductal lineage, HPDE, PK-8, PCI-35, and MIA PaCa-2, with exogenous expression of either wild-type or mutated (R201H) GNAS. We found that exogenous GNAS upregulated intracellular cyclic-adenine monophosphate, particularly in the mutated GNAS transfectants. Exogenous GNAS induced no obvious cell-growth promotion, but induced suppression in some cells. The exogenous GNAS upregulated MUC2 and MUC5AC in HPDE and PK-8, and the latter was most sensitive to exogenous GNAS, exhibiting drastic alteration of the global gene expression that is consistent with that of IPMN. Hence, PK-8 expressing exogenous mutated GNAS may be an ideal in vitro model of IPMN. On the other hand, exogenous GNAS downregulated expression of mucin genes and produced modest alteration of gene expression profiles in PCI-35 and MIA PaCa-2, indicating lower sensitivity to exogenous GNAS. Furthermore, we showed diverse and cell-type specific mucin expression pathways with complicated interactions between signaling pathways of the G-protein coupled receptor (GPCR), the mitogen-activated protein kinase (MAPK), and the phosphatidylinositol 3 kinase (PI3K), in which the GPCR pathway appeared to be dominant in some and the MAPK pathway in others. In conclusion, mutated GNAS found in IPMNs may extensively alter gene expression profiles, including expression of mucin genes, with the interaction with MAPK and PI3K pathways in pancreatic ductal-lineage cells, which may determine the characteristic phenotype of the neoplasm.

overall_design: Cells of pancreatic cancer cell lines, PK-8, PCI-35,and MIA PaCa-2, were seeded at 4 × 10^5 cells/well in 6-well plates and incubated for 24 hours at 37°C in 5% CO2 with humid atmosphere. Then the cells were transfected with either pcDNA 3.1/V5-His vector or pcDNA3.1-GNAS(R201H)-V5-His vector using Lipofectamine 2000 reagent (Life Technologies) according to the manufacturer’s recommendations. The cells were incubated for 24 hours and collected by dissociation using trypsin. Total RNAs were isolated using the RNeasy Mini kit (Qiagen, Hilden, Germany). Serial analysis of gene expression (SAGE) library was constructed using a SOLiD SAGE Kit (Life Technologies) according to the manufacture’s instruction. The constructed libraries were analysed by means of the massively parallel sequencing method using SOLiD 4 System (Life Technologies). The SAGE analysis was performed for samples obtained from single transfection experiment.

first: Hirotake

last: Komatsu


title: Developmental dynamics of floral gene regulation [ChIP-Seq]

summary: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programmes. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Here, we characterize the dynamic relationship of chromatin accessibility, gene expression and DNA-binding of two MADS-domain proteins during Arabidopsis flower development. The developmental dynamics of DNA-binding of APETALA1 and SEPALLATA3 is largely independent of chromatin accessibility, and our findings suggest that AP1 acts as 'pioneer factor' that modulates chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Our data provide a primer to the idea that cellular differentiation in plants can be associated to dynamic changes in chromatin accessibility, as consequence of the action of master transcription factors.

overall_design:
We used the AP1-GR system to conduct chromatin immunoprecipitation experiments with SEP3-specific antibodies and GR atibodies followed by deep-sequencing (ChIP-Seq) in order to determine SEP3 and AP1 binding sites on a genome-wide scale. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect 2, 4 and 8 days after treatment. As control, we performed ChIP experiments using pre-immune serum at the different time points. Experiments were done in two biological replicates for 4 days and 8 days time-points while one biological replicate was done for control samples and 2 days time-point.
The GSE47981 includes expression data that are complementary to the data in the GSE46986 and GSE46894.

first: Pedro

last: Madrigal

first: Kerstin

last: Kaufmann


title: Integrative Analyses of Gene Expression and DNA Methylation Profiles in a Breast Cancer Cell Line Model of Tamoxifen-Resistance Indicate a Crucial Role of Cells with Stem-like Properties

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

type: Methylation profiling by high throughput sequencing

summary:
Purpose: Development of resistance to tamoxifen is an important clinical issue in the treatment of patients with breast cancer. Tamoxifen resistance may be the result of the acquisition of epigenetic regulation such as DNA methylation within breast cancer cells resulting in changed mRNA expression of genes being pivotal for estrogen dependent growth. Alternatively, tamoxifen resistance may be due to selection of preexisting resistant cells, which may exhibit cancer stem-like characteristics or a combination of the two mechanisms.
Methods: To evaluate the contribution of these possible mechanisms to tamoxifen resistance, we applied modified DNA methylation-specific digital karyotyping (MMSDK) and digital gene expression (DGE) in combination with massively parallel sequencing to analyze a well-established tamoxifen resistant cell line model: MCF-7/S0.5 (tamoxifen sensitive parental cell line) and 4 high-dosage tamoxifen selected resistant offspring sublines (MCF-7/TAMR-1, MCF-7/TAMR-4, MCF-7/TAMR-7 and MCF-7/TAMR-8). MMSDK uses BssHII as mapping enzyme (DNA methylation sensitive enzyme). Both MMSDK and DGE use NlaIII and MmeI to produce 20-21 bp tag. The indexed single-end sequencing was performed by Illumina HiSeq 2000 in BGI-Shenzhen. A dynamic programming algorithm-FASTX-Toolkit implemented in Perl was used to trim the adaptor sequence. The trimmed tags were subjected to quality filtering, so that only tags with sequencing quality higher than 30 for more than 80% of the nucleotides were used for subsequent analysis. For MMSDK tag mapping, we generated a simulated reference library, i.e., BssHII reference library, by in silico enzyme digestion of the human genome (hg19, UCSC) regardless of the methylation state. This library was used as reference for subsequent mapping of the tags in the MMSDK analysis. In the DGE analysis, refMrna (hg19, UCSC) was used as reference for mapping cDNA tags. Subsequently, the Burrows–Wheeler Aligner (BWA) procedure for aligning the MMSDK and DGE tags to the simulated BssHII reference library and refMrna reference library, respectively, was applied.
Results: MMSDK libraries using BssHII/NlaIII were generated from the parental tamoxifen sensitive subline MCF-7/S0.5 and the 4 TAMR cell lines: TAMR-1, TAMR-4, TAMR-7 and TAMR-8. The 5 indexed MMSDK libraries were sequenced in one lane and 1.38 Gb clean tag data for all 5 cell lines were obtained, with an average sequencing amount of ~270 Mb per library. On average, 59.5 % of the tags with mapping quality ≥ 20 were mapped back to the simulated BssHII/NlaIII reference library. DGE libraries were also generated from MCF-7/S0.5 and the 4 TAMR cell lines. The 5 indexed DGE libraries were sequenced in one lane and obtained 1.71 Gb clean tag data for all 5 cell lines with an average sequencing amount of ~340 Mb per library. On average, 40.8 % with mapping quality ≥ 20 were mapped back to the simulated NlaIII human transcriptome (refMrna reference library). Our present study demonstrates large differences in global gene expression and DNA methylation profiles between parental tamoxifen-sensitive cell line and 4 high-dosage tamoxifen treatment selected resistant sublines. The tamoxifen resistant cell lines exhibited globally higher methylation level than the parental cell line and an inverse relationship between gene expression and DNA methylation in the promoter regions were noticed. High expression of SOX2 and alterations of other SOX gene family members, E2F gene family members and RB-related pocket protein genes as well as highlighted stem cell pathways imply that cancer initiating cells/stem cells are  involved in the resistance to tamoxifen.

overall_design: DNA methylation and mRNA expression profiles from tamoxifen sensitive parental cell line MCF-7/S0.5 and 4 high dosage of tamoxifen selected resistant offspring sublines (MCF-7/TAMR-1, MCF-7/TAMR-4, MCF-7/TAMR-7 and MCF-7/TAMR-8) were analyzed by MMSDK and DGE methods, respectively, in combination of massively parallel sequencing, using Illumina HiSeq 2000

first: Xue

last: Lin

first: Guangliang

last: Yin

first: Qian

last: Zhao

first: Daniel

last: Elias

first: Anne

middle: E

last: Lykkesfeldt

first: Jan

last: Stenvang

first: Nils

last: Brünner

first: Jun

last: Wang

first: Huanming

last: Yang

first: Lars

last: Bolund

first: Henrik

last: Ditzel


title: Inducible expression of macrolide efflux in Streptococcus pneumoniae is controlled by transcriptional attenuation of the mef(E)/mel operon

status: Public on Feb 01 2014

city: Baltimore

first: Hervé

last: Tettelin

state: MD

address: 801 W Baltimore St

department: Institute for Genome Sciences

institute: University of Maryland

summary:
Macrolide resistance, increasingly identified in Streptococcus pneumoniae and a wide range of other Gram-positive bacteria, is often due to efflux pumps encoded by the mef/mel(msr) operon found on discrete mobile genetic elements. The regulation of mef/mel(msr) in these elements is not well understood. We defined the promoter controlling the mef(E)/mel operon in S. pneumoniae, identified cis-acting 5′ regulatory elements and determined the mechanism of macrolide-inducible expression of the efflux pump.
The mef(E)/mel transcriptional start site was a guanine 327 bp upstream of the mef(E) start codon. Consensus pneumococcal promoter -10 (5′-TATACT-3′) and -35 (5′-TTGAAC-3′) boxes separated by a 17 bp spacer were identified 7 bp upstream of the start site. Analysis of the predicted secondary structure of the 327 bp 5’ region identified four pairs of inverted repeats R1-R8 predicted to fold into stem-loops, a small leader peptide (MTASMRLR) required for macrolide induction and a Rho-independent transcription terminator involving the R5/R6 stem loop. Mutational analyses of the regulatory region identified transcriptional attenuation as the model for the inducible expression of macrolide efflux, which was confirmed by RNA-Seq expression data. The 327 bp region 5’ of mef(E) was highly conserved in other mef/mel(msr)-containing genetic elements complexes including Tn1207.1 and the 5612IQ complex in pneumococci and Tn1207.3 in Group A streptococci. Induction of the mef(E)/mel operon and macrolide efflux occurs by anti-attenuation in the presence of inducing macrolides and appears to be a mechanism

overall_design: RNA-seq was performed on wild type and mutant cultures of four strains of Streptococcus pneumoniae untreated, or treated with spiramycin, LL-37 or erythromycin

first: Xianhe

last: Bai

first: Nikhil

last: Kumar

first: Elliott

middle: F

last: Drábek

first: Sean

last: Daugherty

first: Thomas

last: Colon

first: Sandra

last: Ott

first: Naomi

last: Sengamalay

first: Lisa

last: Sadzewicz

first: Luke

last: Tallon

first: David

last: Stephens

first: Scott

last: Chancey


title: Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [Beaf-32 ChIP-seq]

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

institute: CNRS

summary: Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions.

overall_design: Binding profiles of Beaf-32 in Drosophila S2 cells by ChIP-Seq (Illumina)

first: Suresh

last: Cuddapah

first: Adrien

last: Gamot

first: Gael

last: Micas

first: Keji

last: Zhao


title: Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins


title: RNA sequencing of bone marrow hematopoietic progenitor and Gr1+/Mac1+ cells derived from Diap1 wild type, heterozygous, and knockout mice.

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary: The goal of the experiment was to study the aberrant signalling pathways due to loss of or haploinsufficiency of Diap1 protein. We found that LPS receptor transcript is highly expressed in Diap1 deficient Gr1+/Mac1+ cells but not in Lin- cells, suggesting a role for Diap1 in determining the normal morphology of committed Gr1+/Mac1+ cells.

overall_design: Examination of gene expression profiles of bone marrow hematopoietic progenitor and Gr1+/Mac1+ myeloid cells from Diap1 wild type, heterozygous, and knockout mice.

first: Ji

last: Peng

first: Ganesan

last: Keerthivasan


title: Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL crosslinking and affinity purification

city: Boston

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

summary: Short-read sequencing of DNA fractions of the BioTAP-XL pull-downs on human EZH2 and interacting proteins.

overall_design: ChIP-seq-like pulldown/input samples

first: Mitzi

middle: I

last: Kuroda

first: Art

middle: A

last: Alekseyenko

middle: V


title: SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample

last: Harmin

address: 220 Longwood Avenue

department: Neurobiology

summary: mRNA synthesis, processing, and destruction involve a complex series of molecular steps that are incompletely understood.  Because the RNA intermediates in each of these steps have finite lifetimes, extensive mechanistic and dynamical information is encoded in total cellular RNA.  Here we report the development of SnapShot-Seq, a set of computational methods that allow the determination of in vivo rates of pre-mRNA synthesis, splicing, intron degradation, and mRNA decay from a single RNA-Seq snapshot of total cellular RNA.  SnapShot-Seq can detect in vivo changes in the rates of specific steps of splicing, and it provides genome-wide estimates of pre-mRNA synthesis rates comparable to those obtained via labeling of newly synthesized RNA.  We used SnapShot-Seq to investigate the origins of the intrinsic bimodality of metazoan gene expression levels, and our results suggest that this bimodality is partly due to spillover of transcriptional activation from highly expressed genes to their poorly expressed neighbors.  SnapShot-Seq dramatically expands the information obtainable from a standard RNA-Seq experiment.

overall_design: These data are total RNA-Seq data, from RNA sequencing of rRNA-depleted total cellular RNA -- except the LCL 4SU data, which derive from 4SU-labeled RNA.  Please see the associated paper for more details.

first: Jesse

middle: M

last: Gray

first: Michael

last: Springer


title: Pitx2 in the postnatal heart

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine


title: Function of Pitx2 in postnatal heart

summary: Pitx2 is the homeobox gene located in proximity to the human 4q25 familial atrial fibrillation locus. Pitx2 haploinsufficient mice are prone to pacing induced atrial fibrillation indicating that reduced Pitx2 promotes an arrhythmogenic substrate within the atrium. Here, we inactivated Pitx2 in postnatal heart and discovered that unstressed adult Pitx2 mutant mice had sinus node dysfunction with impaired atrial conduction, an arrhythmia closely associated with atrial fibrillation. A genome-wide search for Pitx2 transcriptional targets using ChIP-sequencing and RNA expression profiling shows that Pitx2 represses target genes encoding cell junction proteins, ion channels, and critical transcriptional regulators many of which have been implicated in human atrial fibrillation by genome wide association studies. Our findings unveil a Pitx2 postnatal arrhythmogenic function, novel Pitx2 target genes relevant to atrial fibrillation, and reveal that Pitx2 stabilizes the intercalated disc in postnatal atrium.

overall_design: Genomic occupancy profiling of transcriptional factor Pitx2 in postnatal heart.

first: Ye

last: Tao

first: James

last: Martin


title: Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [RNA-Seq]

last: Cuvier

overall_design: mRNA profiles of stably transfected Drosophila S2 cell lines expressing Wild-Type or Mutant Beaf by RNASeq (Illumina/TruSeq), in triplicates

first: Jun

last: Liang

last: Bouchez


title: Identification of biomarkers for Miltefosine resistance in Leishmania donovani

status: Public on Jan 31 2014

city: Varanasi

first: PUJA

last: TIWARY

state: India

address: C/O Prof. Shyam Sundar, Dept of Medicine

department: MEDICINE

country: India

institute: Banaras Hindu University

summary: To identify biomarkers specific for Miltefosin resistant parasites, we used DNA microarray to identify differentially expressed genes in resistant parasite in comparision to sensitive and further validated with real time PCR assay and immunoblotting assay

overall_design: Clinically proven miltefosine reistant as well as respondant parasite strains isolated from splenic aspirates and grown in M199 media. For microarray resistant and sensitive samples run in duplicate while  for real time PCR, 25 resistant and 33 sensitive strains used. For immunoblotting, confirmed genes were cloned and recombinant protein blotted against miltefosine failure and treated patients sera.

first: Puja

last: Tiwary

first: Dinesh

last: Kumar

first: Madhukar

last: Rai

first: Shyam

last: Sundar


title: Pol II docking and pausing at growth and stress genes in C. elegans

city: Durham

first: Colin

middle: Scott

last: Maxwell

state: NC

address: 4314 FFSC

department: Biology

institute: Duke University

summary: Fluctuations in nutrient availability profoundly impact gene expression. Previous work revealed post-recruitment regulation of RNA Polymerase II (Pol II) during starvation and recovery in Caenorhabitis elegans, suggesting promoter-proximal pausing promotes rapid response to feeding. To test this hypothesis, we measured Pol II elongation genome-wide by two complementary approaches and analyzed elongation in conjunction with Pol II binding and expression. We confirmed bona fide pausing during starvation and also discovered Pol II docking.  Pausing occurs at active stress-response genes that become down-regulated in response to feeding. In contrast  “docked” Pol II accumulates without initiating upstream of inactive growth genes that become rapidly up-regulated upon feeding. Beyond differences in function and expression, these two sets of genes have different core promoter motifs, suggesting alternative transcriptional machinery. Our work suggests that growth and stress genes are both regulated post-recruitment during starvation, but at initiation and elongation, respectively, coordinating gene expression with nutrient availability.

sample_organism:
Caenorhabditis elegans
Drosophila melanogaster

overall_design: We sequenced short, capped RNA (scRNA-seq) from N2 starved L1 C. elegans as well as a TFIIS mutant (RB2083). We also prepared scRNA-seq libraries from L1 larvae using one, two, or three of the enymes used to prepare the scRNA sequencing libraries as well as scRNA-seq libraries from Drosophila S2 cells using one or two of the enzymes. We further sequenced the 5' end of mRNA in starved C. elegans L1 larvae using the same enzymes as scRNA-seq.

first: L

last: Baugh


title: A genome-wide map of transcription start sites specific for acute promyelocytic leukemia reveals deregulation of full-length transcripts

city: Copenhagen

first: Johannes

middle: Eichler

last: Waage

address: Ole Maaløesvej 5

department: Biotech Research and Innovation Center

institute: University Of Copenhagen

summary: Transcription start sites are the focal points of transcriptional regulation, where information from regulatory elements is integrated to stabilize initiation of transcription. In humans, most genes have more than one transcription start site, and these often exhibit different tissue specificity, serving as distinct regulatory frameworks for the same gene.  Usage of such promoters can also result in differential gene function manifested on the protein level. Alternative promoter usage has been shown to be increased in several disease states, especially cancer.   In this study, we have applied the nanoCAGE method to create a genome-wide map of TSS usage in sorted leukemic blasts from acute myeloid leukemia patients, and corresponding normal controls.   We show that the nanoCAGE method can replace similar experiments made with microarrays in terms of expression, but also that it uniquely, allow for the identification of alternative promoter usage in cancer cells. We identify 2,162 putative promoters that are significantly differentially regulated between APL and controls. Interestingly, promoters whose usage is upregulated in APL have an increased propensity to be downstream alternative promoters, and conversely, the promoters producing the annotated longest gene variants are commonly downregulated in cancer. We show examples of genes with upregulated downstream promoters, and demonstrate protein domain loss that could contribute to leukemic induction and maintenance. In conclusion, we present the first genome wide promoterome study from rare purified human leukemic cells.

overall_design: nanoCAGE-seq of human acute myeloid leukemia samples vs. normal hematopoietic counterparts, both in replicates

first: Mette

last: Boyd

first: Kim

last: Theilgaard

first: Piero

last: Carninci

first: Nicolas

last: Rapin

first: Bo

last: Porse

first: Albin

middle: G

last: Sandelin


title: The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

institute: Chinese Academy of Sciences

summary: The neural fate commitment of pluripotent stem cells requires repression of extrinsic inhibitory signals and activation of intrinsic positive transcription factors. However, it remains elusive how these two events are integrated to ensure appropriate neural conversion. Here, we show that Oct6 functions as an essential positive factor for neural differentiation of mouse embryonic stem cells (ESCs), specifically during the transition from epiblast stem cells (EpiSCs) to neural progenitor cells (NPCs). Chimera analysis showed that Oct6 knockdown leads to markedly decreased incorporation of ESC in neuroectoderm. By contrast, Oct6-overexpressing ESC derivatives preferentially contribute to neuroectoderm. Genome-wide ChIP-seq and RNA-seq analyses indicate that Oct6 is an upstream activator of neural lineage genes, and also a repressor of BMP and Wnt signalings. Our results establish Oct6 as a critical regulator that promotes neural commitment of pluripotent stem cells through a dual role: activating internal neural induction programs and antagonizing extrinsic neural inhibitory signals.

overall_design: RNA-seq was performed to examine Oct6 function in ESC neural differentiation at Day2, Day4 and Day6 after dox induction. On Day4 EB, ChIP-seq assay was ultilized to characterize the targets of Oct6.

first: Qingqing

last: Zhu

first: Lu

last: Song

last: Sun


title: Developmental dynamics of DNA accessibility during flower development [DNaseI-Seq]

first: Alice

last: Pajoro

summary: Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programmes. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Here, we characterize the dynamic relationship of chromatin accessibility, gene expression and DNA-binding of two MADS-domain proteins during Arabidopsis flower development. The developmental dynamics of DNA-binding of APETALA1 and SEPALLATA3 is largely independent of chromatin accessibility, and our findings suggest that AP1 acts as ‘pioneer factor’ that modulates chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Our data provide a primer to the idea that cellular differentiation in plants can be associated to dynamic changes in chromatin accessibility, as consequence of the action of master transcription factors.

overall_design:
We used the AP1-GR system to conduct DNaseI hypersensitivity experiments at different stages of flower development. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect before treatment and 2, 4 and 8 days after treatment. As control, naked DNA from wild-type inflorescences was used. Experiments were done in two biological replicates.
The GSE47981 includes expression data that are complementary to the data in the GSE46986 and GSE46894.

first: Pedro

last: Madrigal

first: Kerstin

last: Kaufmann


title: Transcriptome analysis of 3 WT mouse lines and 3 NTD mutants with the BAF155^msp3 allele

city: Aurora

first: Lee

last: Niswander

state: Colorado

address: 12801 E. 17th Ave Bld RC1 South 12400

department: Pediatrics

institute: UC Denver Anschutz Medical Campus

summary: BAF155, as a component of a chromatin remodeling complex, is thought to be involved in the regulation of gene expression. Baf155 knockdown in ES cells results in misregulation of hundreds of genes (Ho et al., 2009). The Baf155msp3 allele presents a unique case for gene expression analysis wherein the BAF complex appears to be intact, in contrast to disruption of the BAF complex when BAF155 function is lost (Chen and Archer, 2005; Sohn et al., 2007). To examine gene expression in the Baf155msp3 mutant at the time of neural tube closure, we performed RNA-Seq and compared gene expression levels between homozygous wildtype and homozygous mutant embryos. After extensive analysis of the RNA-Seq data comparing all 3 mutants to all 3 WT replicates, 78 genes were identified as being upregulated on average in the mutant samples while 22 genes were downregulated. To facilitate an understanding of global gene expression differences, Ingenuity Pathway Analysis (IPA) was used to assign functional categories to the up- and down-regulated genes in the mutants. The most significant molecular and cellular functions of these genes were: 1. cellular movement (1.46E-04>p>4.12E-02), 2. cell death and survival (2.69E-04>p>4.12E-02), and 3. cell growth and proliferation (2.69E-04>p>3.41E-02). Many neuronal genes were significantly misregulated as well. Overall, the RNA-Seq analysis revealed that surprisingly few genes showed altered expression in Baf155 mutant neural tissue, given the broad epigenetic role of the BAF complex, but included genes involved in neural development and cell survival. Moreover, gene expression changes between individual mutants were variable even though the NTD was consistently observed. This suggests that inconsistent gene regulation contributes to failed neural tube closure.

overall_design: RNA was isolated from somite matched (21-23 somites) and phenotype matched cranial tissue of homozygous wildtype and homozygous mutant embryos (3 of each genotype) at E9.5 just after the time of neural tube closure. At E9.5, the vast majority of the embryonic neural tube is comprised of proliferating neural progenitor cells, constituting a relatively homogeneous cell population.

first: Laura

last: Harmacek


title: Genome wide maps of ZFX binding in human leukemia cell lines

status: Public on Jan 30 2014

city: New York

first: Stuart

last: Weisberg

address: 650 W 168th Street

department: Pathology and Cell Biology

institute: Columbia University

summary: Acute myeloid leukemia (AML) and acute T-lymphoblastic leukemia (T-ALL) maintain the undifferentiated phenotype and proliferative capacity of their respective cells of origin, hematopoietic stem/progenitor cells and immature thymocytes. The mechanisms that maintain these progenitor-like characteristics are poorly understood. We report that transcription factor Zfx is required for the development and propagation of experimental AML caused by MLL-AF9 fusion, and of T-ALL caused by Notch1 activation. In both leukemia types, Zfx activated progenitor-associated gene expression programs and prevented differentiation. Key Zfx target genes included mitochondrial enzymes Ptpmt1 and Idh2, whose overexpression partially rescued the propagation of Zfx-deficient AML. These studies identify a common mechanism that controls the cell-of-origin characteristics of acute leukemias derived from disparate lineages and transformation mechanisms.

overall_design: Analysis of genomic ZFX binding in the AML cell line NOMO-1 and the T-ALL cell line RPMI-8402

middle: P

first: Boris

last: Reizis


title: Next Generation Sequencing analysis of Functional Interactions among Insulator Proteins [CP190 ChIP-Seq]

first: Olivier

last: Cuvier

overall_design: Binding profiles of CP190 in stably transfected Drosophila S2 cell lines expressing in Wild-Type Beaf (Control) or Mutant Beaf by ChIP-Seq (Illumina)

first: Jun

last: Liang

last: Bouchez

first: Adrien

last: Gamot

first: Gael

last: Micas


title: ZFX controls the propagation and cell-of-origin characteristics of acute leukemia

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: SOX9: a Stem Cell Transcriptional Regulator of Secreted Niche Signaling Factors

status: Public on Jan 28 2014

city: ny

first: mingyan

last: lin

address: 1925 morris park ave

institute: aecom

summary: Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by hair follicle stem cells (HFSCs). We used RNA-seq to identify SOX9-dependent transcriptional changes and ChIP-seq to identify SOX9-bound genes in HF-SCs.

overall_design: Telogen quiescent hair follicle stem cells (HFSCs) and intefollicular epidermal cells (IFE) were FACS-purified for ChIP-sequcencing and HFSCs for RNA-Sequencing

first: Meelis

last: Kadaja

first: Elaine

last: Fuchs


title: Metabolic Reprogramming During Purine Stress in the Protozoan Pathogen Leishmania donovani

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

summary: The ability of Leishmania to survive in their insect or mammalian host is dependent upon an ability to sense and adapt to changes in the microenvironment. However, little is known about the molecular mechanisms underlying the parasite response to environmental changes, such as nutrient availability. To elucidate nutrient stress response pathways in Leishmania donovani, we have used purine starvation as the paradigm. The salvage of purines from the host milieu is obligatory for parasite replication; nevertheless, purine-starved parasites can persist in culture without supplementary purine for over 3 months, indicating that the response to purine starvation is robust and engenders parasite survival under conditions of extreme scarcity. To understand metabolic reprogramming during purine starvation we have employed global approaches. Whole proteome comparisons between purine-starved and purine-replete parasites over a 6-48 h span have revealed a temporal and coordinated response to purine starvation. Purine transporters and enzymes involved in acquisition at the cell surface are upregulated within a few hours of purine removal from the media, while other key purine salvage components are upregulated later in the time-course and more modestly.  After 48 h, the proteome of purine-starved parasites is extensively remodeled and adaptations to purine stress appear tailored to deal with both purine deprivation and general stress. To probe the molecular mechanisms affecting proteome remodeling in response to purine starvation, comparative RNA-seq analyses, qRT-PCR, and luciferase reporter assays were performed on purine-starved versus purine-replete parasites.  While the regulation of a minority of proteins tracked with changes at the mRNA level, for many regulated proteins it appears that proteome remodeling during purine stress occurs primarily via translational and post-translational mechanisms.

overall_design: One mRNA sample from each of Purine-Starved and Purine-Replete cells were analyzed using SL RNA-Seq methodology

first: Jessica

last: Martin

first: Phillip

last: Yates

first: Radika

last: Soysa

first: Joshua

last: Alfaro

first: Feng

last: Yang

first: Kristin

last: Burnum-Johnson

first: Vladislav

last: Petyuk

first: Karl

last: Weitz

first: David

last: Camp II

first: Richard

middle: D

last: Smith

last: Wilmarth

first: Larry

last: David

first: Peter

middle: J

last: Myler

first: Nicola

middle: S

last: Carter


title: Gene expression study of Drechslerella stenobrocha predating Caenorhabditis elegans.

city: Beijing

first: Keke

last: Liu

address: NO.1 Beichen West Road, Chaoyang District

institute: Institude of microbiology,Chinese academy of sciences

summary: we studied the gene expression conditions while Drechslerella stenobrocha predates Caenorhabditis elegans. The perpose of this study is to find genes in Drechslerella stenobrocha participateing in predation.

overall_design: Examination of 3 transcriptomes in different predation periods to find their different gene expression style.

first: Xingzhong


title: Whole transcriptome profiling of rat pineal glands and retinas collected throughout a 24-hour cycle

city: Bethesda

first: Steven

last: Coon

address: 49 Convent Drive Room 6A83

department: NICHD/PDEGEN

institute: NIH

summary: The rat pineal transcriptome is highly dynamic, with many hundreds of transcripts changing more than two-fold on a 24-hr basis, as revealed earlier using Affymetrix GeneChip analysis. The retina is evolutionally related to the pineal gland so these two tissues share many gene expression patterns. This study more completely characterizes the temporally dynamic transcriptomes of these tissues using RNA-Seq to capture information regarding alternative splicing, novel exons, unannotated mRNAs, non-coding RNAs, and coding transcripts not represented on the Affymetrix chips.  We also identified transcripts that were selectively expressed in the pineal gland relative to other tissues by comparing pineal samples to a sample of pooled non-pineal tissues.

overall_design:
The transcriptomes of the rat pineal gland and retina were sequenced using samples collected at 6 time points throughout a 24-hour cycle to identify rhythmically expressed transcripts. The transcriptomes of pools of mixed tissues collected at mid-day (ZT7) and mid-night (ZT19) were also sequenced for comparison to aid in determining pineal-enriched transcripts.
Contributor: NISC, Comparative Sequencing Program

middle: L

first: Cong

last: Fu

first: Samuel

last: Clokie

last: Munson

first: Praveen

last: Cherukuri

last: Sugden

first: James

last: Mullikin

last: Klein


title: ChIP analysis unravels an exceptionally wide distribution of binding sites for the NtcA transcription factor in a heterocyst-forming cyanobacterium.

city: Sevilla

first: Silvia

last: Picossi

address: Avda. Americo Vespucio 49

department: Instituto de Bioquímica Vegetal y Fotosíntesis

institute: CSIC

summary: The CRP-family transcription factor NtcA, universally found in cyanobacteria, was initially discovered as a regulator operating N control. It responds to the N regime signaled by the internal 2-oxoglutarate levels, an indicator of the C to N balance of the cells. NtcA-activated canonical promoters bear an NtcA-consensus binding site (GTAN8TAC) centered at about 41.5 nucleotides upstream from the transcription start point. In this study, we have used chromatin immunoprecipitation followed by high-throughput sequencing to identify the whole regulon of NtcA in cells of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 after the withdrawal of combined N. NtcA has been found to bind to 2,424 target regions in the genome of Anabaena, which have been ascribed to 2,153 genes. Interestingly, only a small proportion of those are involved in N assimilation and metabolism, and 65 % of the target regions were located intragenically. The NtcA regulon identified here constitutes the largest bacterial regulon described to date. Our results show that NtcA has a much wider role in the physiology of the cell than it has been previously thought, acting both as a global transcriptional regulator and possibly also as a factor influencing the superstructure of chromosome (and plasmids).

overall_design: Cells of Anabaena sp. PCC 7120 subjected to N-withdrawal for 3 h were used to perform chromatin immunoprecipitation with anti-NtcA antibody. The immunoprecipitated material was sequenced. Three ChIPs were performed from two independent sets of Anabaena cells. A sample of total DNA (not subjected to immunoprecipitation) was used as a control (Input sample).

first: Enrique

last: Flores

first: Antonia

last: Herrero


title: Compararitve Triprimate Peripheral Blood DNA Methylome

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

summary: DNA methylation is critical for development and is strongly associated with gene regulation. Variation in the DNA methylome between closely related species may reveal unique functional adaptation. We have implemented a novel inter-primate DNA methylation genome-wide analysis between human, chimpanzee and rhesus macaque to identify human species-specific Differentially Methylated Regions (human s-DMRs) in orthologous loci. We analysed the peripheral blood cell DNA methylomes of these primates and identified 22,758 hypomethylated and 15,858 hypermethylated human s-DMRs. These s-DMRs are globally enriched within weak promoter, enhancer and transcribed regions via comparison with ChromHMM segmentation. Human s-DMRs, (both hypo- and hypermethylated) are found to be more prevalent in CpG Island shores than within the islands themselves (?2 P = 1.80 x 10-32). Examining human-specific Transcription Factor Binding Site motif change within CpG islands, we show gain and loss, in hypomethylated and hypermethylated s-DMRs, respectively, of CTCF motifs. Epigenetically the most divergent human-specific locus was the immunological Leukotriene B4 receptor (LTB4R, aka BLT1 receptor), due to collocating hypomethylated s-DMRs within the promoter CpG island and shore, as well as inverse increased gene body methylation. This gene is vital in host immune responses and associated with the pathogenesis of a wide range of human inflammatory diseases. This finding was supported by additional neutrophil-only DNA methylome and lymphoblastoid H3K4me3 chromatin comparative data. Functional investigation of the consequences of these epigenetic differences identified this receptor to have increased expression, and have a higher response to the LTB4 ligand in human versus rhesus macaque peripheral blood mononuclear cells. This result further emphasises the exclusive nature of the human immunological system, its divergent adaptation even from closely related primates, and the power of comparative epigenomics to identify and understand human uniqueness.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: DNA methylome analysis of pooled Human, Chimpanzee and Macaque

first: G

last: Woszczek

first: L

last: Butcher

first: H

middle: R

last: Foster

first: A

last: Feber

first: C

last: Roos

last: Walter

first: S

last: Beck

last: Bell


title: Poly(A)-tail profiling reveals an embryonic switch in translational control

status: Public on Jan 29 2014

city: Cambridge

first: Stephen

last: Eichhorn

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other 'housekeeping' proteins tending to have shorter tails. As expected, tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos. However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA mediated deadenylation concurrently shifts from translational repression to mRNA destabilization.

sample_organism:
Arabidopsis thaliana
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Drosophila melanogaster
Danio rerio
Xenopus laevis
Homo sapiens
Mus musculus

overall_design: 64 samples from a variety of species

first: Alexander

middle: O

last: Subtelny

middle: W

first: Grace

last: Chen

first: Hazel

last: Sive

first: David

last: Bartel


title: Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci

city: Los Angeles

first: Peggy

last: Farnham

state: CA

address: 1450 Biggy Street 6514 NRT

department: Molecular Biology and Biochemistry

institute: University of Southern California

summary: Genome-wide association studies (GWAS) have revolutionized the field of cancer genetics, but the causal links between increased genetic risk and onset/progression of disease processes remain to be identified. Here we report the first step in such an endeavor for prostate cancer. We provide a comprehensive annotation of the 77 known risk loci, based upon highly correlated variants in biologically relevant chromatin annotations- we identified 727 such potentially functional SNPs.  We also provide a detailed account of possible protein disruption, microRNA target sequence disruption and regulatory response element disruption of all correlated SNPs at r^2≥0.5.  Greater than 88% of the 727 SNPs fall within putative enhancers, many of which alter critical residues in the response elements of transcription factors known to be involved in prostate biology. We define as risk enhancers those regions with enhancer chromatin biofeatures in prostate-derived cell lines with prostate-cancer correlated SNPs. To aid in the identification of these enhancers, we performed genomewide ChIP-seq for H3K27-acetylation, a mark of actively engaged enhancer regions, as well as the transcription factor TCF7L2. We analyzed in depth three variants in risk enhancers, two of which show significantly altered androgen sensitivity in LNCaP cells. This includes rs4907792, that is in linkage disequilibrium (r^2=0.91) with an eQTL for NUDT11 (on the X chromosome) in prostate tissue, and rs10486567, the index SNP in intron 3 of the JAZF1 gene on chromosome 7. Rs4907792 is within a critical residue of a strong consensus androgen response element that is interrupted in the protective allele, resulting in a 56% decrease in its androgen sensitivity, whereas rs10486567 affects both NKX3-1 and FOXA-AR motifs where the risk allele results in a 39% increase in basal activity and a 28% fold-increase in androgen stimulated enhancer activity. Identification of such enhancer variants and their potential target genes represents a preliminary step in connecting risk to disease process.

overall_design: ChIP-seq analysis of H3K27Ac in LNCaP charcoal-stripped serum, H3K27Ac in LNCaP charcoal-stripped serum +DHT, TCF7L2 in LNCaP

first: Malaina

last: Gaddis


title: A single exposure to a sublethal pediocin concentration initiates a resistance-associated temporal cell envelope and general stress response in L. monocytogenes

city: Kgs. Lyngby

first: Gitte

middle: M.

last: Knudsen

state: Not applicable

address: Matematiktorvet, Bldg 301

department: Department of Systems Biology

institute: Technical University of Denmark

summary: We report the effect of the pediocin-containing supernatant of L. plantarum WHE 92 on the temporal transcriptomic profile of L. monocytogenes EGD

overall_design: Examination of mRNA and sRNA profiles from L. monocytogenes EGD cells exposed to sublethal levels of the pediocin-containing supernatant of L. plantarum WHE 92 at 10, 60 and 180 min of exposure.

first: Martin

last: Laursen

first: Lone

last: Gram


title: KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation [RNA-Seq]

status: Public on Jan 27 2014

city: Detroit

first: Benjamin

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

summary: Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. Here, we show that KDM5B, which demethylates lysine 4 of histone H3, co-localizes with H3K4me3 near promoters and enhancers of active genes in ES cells; its depletion leads to spreading of H3K4 methylation into gene bodies and enhancer shores, indicating that KDM5B functions to focus H3K4 methylation at promoters and enhancers. Spreading of H3K4 methylation to gene bodies and enhancer shores is linked to defects in gene expression programs and enhancer activity, respectively, during self-renewal and differentiation of KDM5B-depleted ES cells. KDM5B critically regulates H3K4 methylation at bivalent genes during differentiation in the absence of LIF or Oct4. We also show that KDM5B and LSD1, another H3K4 demethylase, co-regulate H3K4 methylation at active promoters but they retain distinct roles in demethylating gene body regions and bivalent genes. Our results provide global and functional insight into the role of KDM5B in regulating H3K4 methylation marks near promoters, gene bodies, and enhancers in ES cells and during differentiation.

overall_design: RNA-Seq of murine shLuc and shKdm5b ES cells differentiated for 72h in the absence of LIF.

first: Gangqing

last: Hu

first: Keji

last: Zhao


title: RNA-seq Analysis of RFX1-dependent Genes in Fusarium graminearum Z-3639

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

institute: Seoul National University

summary: Fusarium graminearum is a major pathogen of Fusarium head blight in wheat, barley, and rice, as well as ear rot and stalk rot in maize. Regulatory Factor X (RFX) transcription factors are well-conserved in animals and fungi, but their functions are diverse, ranging from DNA-damage response to ciliary gene regulation. We investigated the role of the sole RFX transcription factor, RFX1, in F. graminearum. Deletion of rfx1 resulted in multiple defects in hyphal growth, conidiation, virulence, and sexual development. Deletion mutants of rfx1 were more sensitive to various types of DNA damage than the wild-type strain. Septum formation was inhibited and micronuclei were produced in the rfx1 deletion mutants. The results of the neutral comet assay demonstrated that disruption of rfx1 function caused spontaneous DNA double-strand breaks. To understand regulatory mechanisms of rfx1 in F. graminearum, we obtained and analyzed genome-wide transcription profiles generated from the RNA-sequencing data of the wild-type and Δrfx1 strains. RNA-sequencing-based transcriptomic analysis revealed that RFX1 suppressed the expression of many genes, including genes for the repair of DNA damage.

overall_design: 2 samples examined: mycelia harvested 24 h after inoculation of wild-type conidia in complete medium; mycelia harvested 32 h after inoculation of Δrfx1 conidia in complete medium

first: Jae-Yun

last: Lim

first: Kyunghun

last: Min

first: Yin-Won

last: Lee


title: Antioxidants Accelerate Lung Cancer Progression in Mice

city: Gothenburg

first: Erik

last: Larsson

address: Medicinaregatan 9A

department: Medical Biochemistry

institute: University of Gothenburg

summary: Antioxidants are widely used to protect cells from damage induced by reactive oxygen species (ROS). The concept that antioxidants can help fight cancer is deeply rooted in the general population, promoted by the food supplement industry, and supported by some scientific studies. However, clinical trials have reported inconsistent results. Here, we show that supplementing the diet with the antioxidants N-acetylcysteine (NAC) and vitamin E markedly increases tumor progression and reduces survival in mouse models of B-RAF- and K-RAS-induced lung cancer. RNA sequencing revealed that NAC and vitamin E, which are structurally unrelated, produce highly coordinated changes in tumor transcriptome profiles, dominated by reduced expression of endogenous antioxidant genes. NAC and vitamin E increase tumor cell proliferation by reducing ROS, DNA damage, and p53 expression in mouse and human lung tumor cells. Inactivation of p53 increases tumor growth to a similar degree as antioxidants and abolishes the antioxidant effect. Thus, antioxidants accelerate tumor growth by inactivating the ROS-p53 axis. Because p53 inactivation occurs late in tumor progression, antioxidants may accelerate the growth of early tumors or precancerous lesions in high-risk populations such as smokers and patients with chronic obstructive pulmonary disease who receive NAC to relieve mucus production.

overall_design: There were 3 experimental groups (untreated, NAC-treated and Vitamin E-treated. Each group consisted of 5 animals, and from each animal we harvested 2 tumor samples. Hence, in total 3x10=30 samples were profiled.

first: Volkan

last: Sayin

first: Mohammed

middle: X

last: Ibrahim

first: Jonas

last: Nilsson

first: Per

last: Lindahl

last: Bergo


title: KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation [ChIP-Seq]

overall_design: ChIP-Seq for KDM5B, H3K4 methylation and H3K27ac in murine shLuc, shKdm5b, shLuc-LSD1i, shKdm5b-LSD1i ES cells, and during differentiation of shLuc and shKdm5b ES cells for 2 days, 3 days, and 4 days without LIF.


title: Comparative genomic and transcriptomic analysis of Wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen

first: Christina

last: Cuomo

address: 7 Cambridge Center

institute: Broad Institute

summary: We sequenced mRNA from Wangiella dermatitidis at two pH conditions (2.5 and 6), including three biological replicates of each sample.

overall_design: Examination of transcript level changes in reponse to low pH stress.

first: Zehua

last: Chen

first: Zheng

last: Wang


title: KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation


title: DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy [Bisulfite-Seq2]

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

institute: CIC bioGUNE

summary: DNA methylation is a key epigenetic regulator of mammalian embryogenesis and somatic cell differentiation. Using high-resolution genome-scale maps of methylation patterns, we show that the formation of myelin in the peripheral nervous system, proceeds with progressive DNA demethylation, which coincides with an upregulation of critical genes of the myelination process. More importantly, we found that, in addition to expression of DNA methyltransferases and demethylases, the levels of S-adenosylmethionine (SAMe), the principal biological methyl donor, could also play a critical role in regulating DNA methylation during myelination and in the pathogenesis of diabetic neuropathy. In summary, this study provides compelling evidence that SAMe levels need to be tightly controlled to prevent aberrant DNA methylation patterns, and together with recently published studies on the influence of SAMe on histone methylation in cancer and embryonic stem cell differentiation show that in diverse biological processes, the methylome, and consequently gene expression patterns, are critically dependent on levels of SAMe.

overall_design: DNA methylome maps of mouse Schwann cells in which GNMT was silenced by lentiviral vectors, cultured in normal medium or low methionine medium.

first: Ashwin

last: Woodhoo


title: Oct4 affects E-cadherin expression via regulating Rnd1 associated cytoskeleton rearrangement in breast cancer cells

status: Public on Jan 25 2014

city: Tianjin

first: Long

last: Shen

address: 22 Qixiangtai Road

institute: School of Basic Medical Sciences, Tianjin Medical University

summary: Oct4, a key transcription factor for maintaining the pluripotency and self-renewal of stem cells has been reported previously. It also plays an important role in tumor proliferation and apoptosis, but the role of Oct4 been in tumor metastasis is still not very clear. Here, we found that ectopic expression of Oct4 in breast cancer cells can inhibit their migration and invasion. Detailed examinations revealed that Oct4 up-regulates expression of E-cadherin, indicative of its inhibitory role in epithelial-mesenchymal transition (EMT). RNA-sequence assay showed that Oct4 down-regulates expression of Rnd1. As an atypical Rho protein, Rnd1 can affect cytoskeleton rearrangement and regulate cadherin-based cell-cell adhesion by antagonizing the typical Rho protein, RhoA. Ectopic expression of Rnd1 in MDA-MB-231 cells changes cell morphology which influences cell adhesion and increases migration. It is reported that EMT is accompanied by cytoskeleton remodeling, we hypothesized that Rnd1 may play a role in regulating EMT. Over-expression of Rnd1 can partly rescue the inhibitory effects induced by Oct4, not only migration and invasion, but also in E-cadherin level and cellular morphology. Furthermore, silencing of Rnd1 can up-regulate the expression of E-cadherin in MDA-MB-231 cells. These results present evidence that ectopic expression of Oct4 increases E-cadherin and inhibits metastasis, effects which may be related to Rnd1 associated cell-cell adhesion in breast cancer cells.

overall_design: Examination of mRNA profiles in MDA-MB-231 cells with OCT4 overexpressing

first: L

first: X

last: Tan


title: DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy [Bisulfite-Seq]

overall_design: DNA methylome maps of developmental Schwann cell myelination, GNMT-KO and diabetic mice were generated by Reduced-Representation Bisulfite Sequencing, with 2-3 replicates per sample group.


title: DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy

overall_design: Refer to individual Series


title: The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts [Whole genome bisulfite sequencing]

city: Montreal

first: Tomi

middle: Markku

last: Pastinen

state: Quebec

address: 740, Dr. Penfield Avenue

country: Canada

institute: McGill University and Génome Québec Innovation Centre

summary: Background DNA methylation has long been known to play an essential role in the epigenetic regulation of gene expression and other cellular functions, and has been in some cases linked to genetic variation. While its presence near the transcription start site of a gene has been associated with reduced expression, the variation in methylation levels across individuals, its environmental or genetic causes, and its association with gene expression remain poorly understood.  Results We report the joint analysis of sequence variants, gene expression and DNA methylation in primary fibroblast samples derived from a set of 62 unrelated individuals. Approximately 2% of the most variable CpG sites are mappable in cis to sequence variation, usually within 5kb. However, only 5% of those mappable CpG sites also have methylation levels that correlate in cis with a gene's expression level. Methylation and gene expression are often correlated but not always in the expected direction (negative for promoter CpGs, positive for gene body CpGs). Population-level correlation between methylation and expression is strongest in a subset of developmentally significant genes, including all four HOX clusters. The presence and sign of this correlation are best predicted using specific histone marks or DNase hypersensitivity rather than position of the CpG site with respect to the gene, showing that other epigenetic markers are necessary to interpret downstream effects of individual methylation variants.  Conclusion Our results indicate strong relationships between gene expression and DNA methylation in untransformed adult human fibroblasts, with considerable involvement of chromatin features and relatively modest involvement of sequence variation.

overall_design: Four human skin fibroblast samples obtained from Coriell. Bisulfite converted DNA was sequenced using the Illumina HiSeq 2000 system.

first: Stephan

last: Busche

first: Tony

last: Kwan

first: Bing

last: Ge

first: James

last: Wagner

first: Mathieu

last: Blanchette


title: Next generation sequencing reveals differentially expressed genes associated with development of PSE turkey meat.

city: East Lansing

first: Yuwares

last: Malila

state: Michigan

address: 3340 Anthony Hall

department: Food Science and Human Nutrition

institute: Michigan State University

summary: The success of turkey breeding for rapid growth rate and larger breast size has coincided with an increasing incidence of a meat quality defect described as pale, soft and exudative (PSE). We hypothesized that this defect, which is associated with an abnormally rapid rate of postmortem metabolism, derives from altered expression of genes involved in metabolic regulation. Our objective was to use deep transcriptome RNA sequence analysis (RNAseq) to identify differentially expressed genes between normal and PSE turkey breasts. Following harvest of turkey breasts (n = 43), the pH at 15 min post-slaughter and percent marinade uptake at 24h post-slaughter were determined. Breast samples were classified as normal or PSE based on marinade uptake (high = normal; low = PSE). Total RNA from samples with the highest (n=4) and lowest (n=4) marinade uptake were isolated and sequenced using the Illumina GAIIX platform. Of 21,340 gene loci discovered by RNAseq, 8480 loci completely matched the turkey reference genome, and 480 genes were differentially expressed (false discovery rate, FDR<0.05) between normal and PSE samples. Two highlights were the genes nephroblastoma overexpressed (NOV), upregulated about 38-fold and pyruvate dehydrogenase kinase isoform 4 (PDK4), downregulated 14-fold in PSE samples. Pathway analysis suggested that several biological functions, including carbohydrate metabolism and energy production, were affected by meat quality. Because PDK4 regulates conversion of pyruvate to acetyl CoA, differences in regulation of oxidative metabolism may exist among turkeys. Accelerated early postmortem metabolism would result in faster pH decline in PSE meat. This hypothesis was supported by the fact that decreased expression of PDK4 was associated with lower pH in PSE samples (pH[PSE] = 5.59±0.09, pH[normal] = 5.77±0.17). The RNAseq results provided a greater molecular mechanistic understanding of development of PSE turkey, which will be a foundation for new intervention strategies to prevent development of this defect.

overall_design: The mRNA profiles of normal and PSE turkey breast muscle were generated by deep sequencing using Illumina GAIIx platform. Multiplexing was performed (2 samples/lane). Afterwards, difference in gene expression between normal and PSE samples were tested.

first: Kelly

last: Sporer

first: Kevin

last: Carr

first: Gale

last: Strasburg


title: Hypermethylation in the ZBTB20 gene is associated with major depressive disorder

city: Herston

first: Lutz

last: Krause

state: QLD

address: 300 Herston Rd

department: Genetics and Computational Biology

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: Genome-wide MeDIP-Sequencing of 23 monozygotic twin pairs (n=46) from Australia discordant for major depressive disorder (MDD).

overall_design: MeDIP-seq of 23 monozygotic twin pairs discordant for major depressive disorder. MZ twin pairs were compared to identify significantly differently methylated sites associated with MDD.

first: Matthew

middle: N

last: Davies

first: Jordana

middle: T

last: Bell

first: Fei

last: Gao

first: Kirsten

last: Ward

first: Honglong

last: Wu

first: Hanlin

last: Lu

first: Yuan

last: Liu

first: Pei-Chein

last: Tsai

first: David

middle: A

last: Collier

first: Jonathan

last: Mill

first: Anjali

last: Henders

first: Enda

last: Byrne

first: Naomi

last: Wray

first: Nicholas

last: Martin

first: Tim

last: Spector

first: Jun


title: High-throughput SOLEXA sequencing of endogenous small RNAs from Arabidopsis thaliana wild-type

city: Poznan

first: Wojciech

last: Karlowski

address: Umultowska 89

country: Poland

institute: Adam Mickiewicz University

summary: The length of Arabidopsis microRNA genes and their precursors (pri-miRNAs) can very between several hundreds bp to several thousands bp. They may contain introns, precursors may undergo alternative splicing, and often there are more than one polyadenylation site.  An intriguing question arise: why to transcribe thousands of  base pairs to produce a small RNA molecule of about 21 nt in length? We decided to sequence small RNAs from 35-day-old rosette leaves and to map the obtained reads of 18-26 nt in length to Arabidopsis pri-miRNAs. Our analyses revealed the presence of sRNAs that can derive only from miRNA precursors. An example is the identification of a substantial number of miR319b.2 reads. This sRNA is a product of pri-miR319b processing. Our further experimental analyses show that it carries multiple signatures of  a functional microRNA

overall_design: 2 samples examined: wild type

first: Lukasz

last: Sobkowiak

first: Zofia

last: Szweykowska-Kulinska


title: Novel microRNA-like viral small regulatory RNAs arising during human hepatitis A virus infection

status: Public on Jan 24 2014

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

country: China

institute: Institute of Medical Biology

summary: MicroRNAs (miRNAs), including host miRNAs and viral miRNAs, play vital roles in regulating host-virus interactions. DNA viruses encode miRNAs that regulate the viral life cycle. However, it is generally believed that cytoplasmic RNA viruses do not encode miRNAs, owing to inaccessible cellular miRNA processing machinery. Here, we provide a comprehensive genome-wide analysis and identification of miRNAs that were derived from hepatitis A virus (HAV; Hu/China/H2/1982), which is a typical cytoplasmic RNA virus. Using deep-sequencing and in silico approaches, we identified 2 novel virally encoded miRNAs, named hav-miR-1-5p and hav-miR-2-5p. Both of the novel virally encoded miRNAs were clearly detected in infected cells. Analysis of Dicer enzyme silencing demonstrated that HAV-derived miRNA biogenesis is Dicer dependent. Furthermore, we confirmed that HAV mature miRNAs were generated from viral miRNA precursors (pre-miRNAs) in host cells. Notably, naturally derived HAV miRNAs were biologically and functionally active and induced post-transcriptional gene silencing (PTGS). Genomic location analysis revealed novel miRNAs located in the coding region of the viral genome. Overall, our results show that HAV naturally generates functional miRNA-like small regulatory RNAs during infection. This is the first report of miRNAs derived from the coding region of genomic RNA of a cytoplasmic RNA virus. These observations demonstrate that a cytoplasmic RNA virus can naturally generate functional miRNAs, as DNA viruses do. These findings also contribute to improved understanding of host-RNA virus interactions mediated by RNA virus-derived miRNAs.

sample_organism:
Homo sapiens
Hepatovirus A

platform_organism:
Homo sapiens
Hepatovirus A

overall_design: Examination of small RNA populations in KMB17 cells infected by human hepatitis A virus genotype IA (isolate H2) (21 days post-infected cells) and mock-infected KMB17 cells (21 days mock-infected control cells).

first: Yunzhang

last: Hu


title: Non-growing Rhodopseudomonas palustris increases the hydrogen gas yield from acetate by shifting from the glyoxylate shunt to the tricarboxylic acid cycle

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

country: USA

institute: University of Washington

summary: Transcriptome analysis was performed in order to better understand the metabolic activity of non-growing cells of Rhodopseudomonas palustris for improve biofuel production.

overall_design: Gene expression profilings of cells from various time points during non-growing phase were compared using RNA-seq.

first: James

middle: B

last: McKinlay

first: Martin

last: Rühl

first: Amanda

last: Posto

first: Uwe

last: Sauer

first: Caroline

last: Harwood


title: The Atlas of Chromatoid Body Components

city: Cold Spring Harbor

first: Semir

last: Beyaz

state: NY

address: 1 Bungtown road

institute: Cold Spring Harbor Laboratory

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

first: Oliver

last: Meikar

first: Vasily

middle: V

last: Vagin

first: Karin

last: Sõsta

first: Aurélie

last: Lardenois

first: Molly

last: Hammell

first: Ying

last: Jin

first: Matteo

last: Da Ros

first: Kaja

last: Wasik

first: Jorma

last: Toppari

first: Gregory

last: Hannon

first: Noora

last: Kotaja


title: RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe

status: Public on Jan 23 2014

city: Huddinge

first: Agata

last: Smialowska

address: Halsovagen 7

department: Biosciences and Nutrition

institute: Karolinska Institute

platform_organism:
Schizosaccharomyces pombe
Schizosaccharomyces pombe 972h-


title: MUT-14 and SMUT-1 DEAD box RNA helicases have overlapping roles in germline RNAi and endogenous siRNA formation in C. elegans

city: Fort Collins

first: Taiowa

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

summary: This data series contains small RNA high-throughput sequencing data for each of the mutator class genes. Samples are from stage-matched adult C. elegans grown at 20˚C.

overall_design: Small RNAs were isolated from synchronized wild type and mutant C. elegans and subjected to Illumina HiSeq sequencing. The series contains fastq and tab-separated files for 19 libraries.


title: RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe [Illumina Genome Analyzer]

summary: RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe.

overall_design: Small RNA library from wild type S. pombe.

first: Ingela

last: Djupedal

first: Jingwen

last: Wang

first: Per

last: Kylsten

first: Peter

last: Swoboda

first: Karl

last: Ekwall


title: The Atlas of Chromatoid Body Components [small RNA-seq]

first: Semir

last: Beyaz

summary: The genome of male germ cells is actively transcribed during spermatogenesis to produce phase-specific protein coding mRNAs and a considerable amount of different non-coding RNAs. Ribonucleoprotein (RNP) granule-mediated RNA regulation provides a powerful means to secure the quality and correct expression of the requisite transcripts. Haploid spermatids are characterized by a unique, unusually large cytoplasmic granule, the chromatoid body (CB), that emerges during the switch between the meiotic and post-meiotic phases of spermatogenesis. To better understand the role of the CB in male germ cell differentiation, we isolated CBs from mouse testes and revealed its full RNA and protein composition. We showed that the CB is mainly composed of RNA-binding proteins and other proteins involved RNA regulation. The CB was loaded with RNA, including pachytene piRNAs, a diverse set of mRNAs and a number of uncharacterized long non-coding transcripts. The CB was demonstrated to accumulate nascent RNA during all the steps of round spermatid differentiation. Our results revealed the CB as a large germ cell -specific RNP platform that is involved in the control of the highly complex transcriptome of haploid male germ cells.

overall_design: Small RNA profiling of purified chromatoid body, each steps of chromatoid body purification, and sortred round spermatid cells

first: Oliver

last: Meikar

first: Vasily

last: Vagin


title: The Atlas of Chromatoid Body Components [RNA-seq]

summary: The genome of male germ cells is actively transcribed during spermatogenesis to produce phase-specific protein coding mRNAs and a considerable amount of different non-coding RNAs. Ribonucleoprotein (RNP) granule-mediated RNA regulation provides a powerful means to secure the quality and correct expression of the requisite transcripts. Haploid spermatids are characterized by a unique, unusually large cytoplasmic granule, the chromatoid body (CB), that emerges during the switch between the meiotic and post-meiotic phases of spermatogenesis. To better understand the role of the CB in male germ cell differentiation, we isolated CBs from mouse testes and revealed its full RNA and protein composition. We showed that the CB is mainly composed of RNA-binding proteins and other proteins involved RNA regulation. The CB was loaded with RNA, including pachytene piRNAs, a diverse set of mRNAs and a number of uncharacterized long non-coding transcripts. The CB was demonstrated to accumulate nascent RNA during all the steps of round spermatid differentiation. Our results revealed the CB as a large germ cell-specific RNP platform that is involved in the control of the highly complex transcriptome of haploid male germ cells.

overall_design: Transcriptome profling of purified chromatoid body, each steps of chromatoid body purification, and sortred round spermatid cells

first: Karin

last: Sõsta

first: Aurélie

last: Lardenois

first: Molly

last: Hammell


title: Conservation of mRNA and protein expression during development of C. elegans

city: Freiburg

first: Dominic

last: Grün

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Spatiotemporal control of gene expression is crucial for development and subject to evolutionary changes. Although proteins are the final product of most genes, the developmental proteome of an animal has not yet been comprehensively defined, and the correlation between RNA and protein abundance during development is largely unknown. Here, we globally measured and compared protein and mRNA expression changes during the life cycle of the nematodes C. elegans and C. briggsae, separated by ~30 million years of evolution. We observed that developmental mRNA and protein changes were highly conserved, to a surprisingly similar degree, but poorly correlated within a species, suggesting important and widespread post-transcriptional regulation. Post-transcriptional control was particularly well conserved if mRNA fold changes were buffered on the protein level, indicating a predominant repressive function. Finally, among divergently expressed genes, we identified insulin signaling, a pathway involved in life span determination, as a putative target of adaptive evolution.

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans

overall_design: Samples of C. elegans and C. briggsae were collected at major developmental stages throughout the nematode life cycle. These stages comprise a population of mixed embryonic stages (E), populations of all four larval stages (L1, L2, L3, L4), late L4 larvae (LL4), young adults (YA), and a reference sample consisting of a mixture of all stages. To obtain synchronized worm populations, embryos were extracted by bleaching gravid adults and synchronized by starvation. Later stages were picked at fixed timepoints after determining the developmental stages by microscopic observation. For all stages, at least a single poly(A)-extracted mRNA library was sequenced on a single lane of an Illumina Genome Analyzer IIx.

first: Marieluise

last: Kirchner

first: Nadine

last: Thierfelder

first: Marlon

last: Stoeckius

first: Matthias

last: Selbach

first: Nikolaus

last: Rajewsky


title: Human iPSC-based Modeling of Late-Onset Disease using Progerin-induced Aging

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) sets their identity back to an embryonic age. This presents a fundamental hurdle for modeling late-onset disorders using iPSC-derived cells. We therefore developed a strategy to induce age-like features in multiple iPSC-derived lineages and tested its impact on modeling Parkinson’s disease (PD). We first describe markers that predict fibroblast donor age and observed the loss of these age-related markers following iPSC induction and re-differentiation into fibroblasts. Remarkably, age-related markers were readily induced in iPSC-derived fibroblasts or neurons following exposure to progerin including dopamine neuron-specific phenotypes such as neuromelanin accumulation. Induced aging in PD-iPSC-derived dopamine neurons revealed disease phenotypes requiring both aging and genetic susceptibility such as frank dendrite degeneration, progressive loss of tyrosine-hydroxylase expression and enlarged mitochondria or Lewy body-precursor inclusions. Our study presents a strategy for inducing age-related cellular properties and enables the modeling of late-onset disease features.

overall_design: Induced pluripotent stem cell-derived midbrain dopamine neurons from a young and old donor overexpressing either GFP or Progerin.

first: Justine

last: Miller

first: Robert

last: Bowman

first: Lorenz

last: Studer


title: Genome-wide profiling  of H3K4me3 and H3K27me3 enrichment and mRNA levels in young leaves of Arabidopsis thaliana

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

institute: Ecole Normale Supérieure de Lyon

summary: Chromatin and RNA were extracted from young A. thaliana Col-0 rosette leaves. Chromatin immunoprecipitation experiments were performed using commercially available antibodies and analyzed by Illumina sequencing (ChIP-seq). Transcriptome data were generated by RNA-seq.

overall_design: ChIP-seq analysis of H3K4me3 and H3K27me3 enrichment profiles in 2 biological replicates. RNA-seq analysis of mRNA levels in 1 biological replicate.

first: Claudia

last: Chica

first: Bogna

last: Szarzynska

last: Roudier

first: Vincent

last: Colot