title: ChIP-seq experiment analyzing binding of HDAC2 and HDAC3 to genomic loci in rat Neural Stem Cells

city: Stockholm

first: Ola

last: Hermanson

address: Retzius Väg 8

department: Neuroscience

institute: Karolinska Institutet

summary: Binding of HDAC2 and HDAC3 was assayed using antibodies SC-7899x and SC-11417x

overall_design: examination of HDAC2 and HDAC3 binding in rat neural stem cells

first: Tobias

last: Lilja


title: Pax5 restoration in a mouse model of B progenitor acute lymphoblastic leukemia

status: Public on Jun 18 2014

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

type: Expression profiling by high throughput sequencing

summary: Hypomorphic mutations of PAX5 occur in one third of B-progenitor acute lymphoblastic leukemias (B-ALLs), however their functional consequences remain undefined. Here we employ advanced transgenic RNAi in mice to suppress endogenous Pax5 expression in the hematopoietic compartment in vivo, which co-operates with activated STAT5 to induce B-ALL. In this model, restoring endogenous Pax5 expression in established B-ALL induces transcriptional and immunophenotypic changes reminiscent of normal B cell differentiation, disabling leukemia-initiating capacity and ultimately causing leukemia clearance.

overall_design: Comparison of leukemias harvested from triplicate untreated mice versus triplicate Dox-treated (3 days) mice

first: Grace

last: Liu

first: Yifang

last: Hu

first: Ross

last: Dickins


title: Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]

city: Madison

first: Rembrandt

last: Haft

state: WI

address: 1550 Linden Dr. Room 5445

department: Great Lakes Bioenergy Research Center

country: USA

institute: University of Wisconsin

summary: The molecular mechanisms of ethanol toxicity and tolerance in bacteria, while important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and revealed multiple mechanisms of tolerance, but it remains difficult to separate direct and indirect effects of ethanol. We used adaptive evolution to generate spontaneous ethanol-tolerant strains of Escherichia coli, then characterized the mechanisms of toxicity and resistance associated with select mutations. Evolved alleles of metJ, rho, and rpsQ were sufficient to recapitulate much of the observed ethanol tolerance, implicating translation and transcription as key processes affected by ethanol. We found that ethanol induces mistranslation errors during protein synthesis, and that the evolved rpsQ allele protects cells by rendering the ribosome hyper-accurate. Ribosome profiling and RNAseq analyses of the ethanol-tolerant strain versus the wild type established that ethanol negatively affects transcriptional and translational processivity. Ethanol-stressed cells exhibited ribosomal stalling at internal AUG codons, which may be ameliorated by the adaptive inactivation of the MetJ repressor of methionine biosynthesis genes. Ethanol also caused aberrant intragenic transcription termination for mRNAs with low ribosome density, which was reduced in a strain with the adaptive rho mutation. Furthermore, ethanol inhibited transcript elongation by RNA polymerase in vitro. We propose that ethanol-induced inhibition and uncoupling of mRNA and protein synthesis are major contributors to ethanol toxicity in E. coli, and that adaptive mutations in metJ, rho, and rpsQ protect central dogma processes in the presence of ethanol.

overall_design: Examination of wild-type and mutant strains at three different time points (one pre-ethanol-stress, two post-ethanol-stress)

middle: J

first: Robert

last: Landick


title: YHJ8 RNA-seq

status: Public on Jun 16 2014

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

summary: We report the application of next-generation sequencing technology for transcription profile analysis of S. cerevisiae strains with different genetic background. By combining the whole genome sequence of these strains, we sought to explore the effects of genome mutations on the transcription diversities.

overall_design: Comparsion of transcription profiles in S. cerevisiae Chinese rice wine strain with laboratory strain

first: Yudong

last: Li


title: Gene expression and genome-wide location analysis of breast cancer cell-lines

status: Public on Jun 17 2014

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Gene expression analysis of breast cancer cell-lines

summary: Recurrent mutations in histone modifying enzymes in multiple cancer types imply key roles in tumorigenesis. However, the functional relevance of these mutations remains unknown. Here we show that the JARID1B histone H3 lysine 4 demethylase is frequently amplified and overexpressed in luminal breast tumors and a somatic point mutation of JARID1B leads to the gain of luminal-specific gene expression programs. Downregulation of JARID1B in luminal breast cancer cells induces the expression of basal cell-specific genes and growth arrest, which is partially rescued by the inhibition of TGFBR thereby indicating a key role for TGFb signaling. Integrated genome-wide analysis of JARID1B chromatin binding, histone H3 lysine trimethyl (H3K4me3) and dimethyl (H3K4me2) patterns, and gene expression profiles in luminal and basal-like breast cancer cells suggest a key role for JARID1B in luminal cell-specific gene expression programs. A significant fraction of JARID1B binding-sites overlaps with CTCF in both luminal and basal-like breast cancer cells. CTCF also co-immunoprecipitates with JARID1B and it may influence its histone demethylase (HDM) activity as the H3K4me3/me2 ratio is lower at the CTCF-overlapping compared to JARID1B-unique sites. Additionally, a heterozygous JARID1B missense mutation (K1435R) in the HCC2157 basal-like breast cancer cell line is associated with unique JARID1B chromatin-binding and gene expression patterns implying gain of luminal features. In line with this, exogenous expression of this mutant in basal-like breast cancer cells leads to a gain of JARID1B binding at many luminal-specific genes. A PARADIGM score reflecting JARID1B activity in luminal breast cancer cells is associated with poor clinical outcome in patients with luminal breast tumors. Together, our data imply that JARID1B is a luminal lineage-driving oncogene and that its therapeutic targeting may represent a novel therapeutic strategy in treatment-resistant luminal breast tumors.

overall_design: RNA-Seq in breast cancer cell-lines transfected with JARID1B/CTCF/control siRNA. 50 cycles of sequencing on Illumina platform.

first: Shoji

last: Yamamoto

first: Zhenhua

last: Wu


title: Genome-wide location analysis in breast cancer cell-lines

overall_design: ChIP-Seq on JARID1B, H3K4me2, H3K4me3, CTFC, and input on breast cancer cell-lines. 50 cycles of sequencing on Illumina platform in 6 cell-lines.

first: Mohammed

middle: B

last: Ekram


title: Domain ChIRP reveals the modularity of long noncoding RNA architecture, function, and target genes

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

summary: Here we identify RNA-RNA, RNA-protein, and RNA-chromatin interactions of the roX1 lncRNA involved in dosage compensation in Drosophila.

overall_design: Identification of lncRNA-occupied genomic sites by Domain ChIRP in chromatin prepared from Clone 8 cells (D. melanogaster, male cell line).

first: Jeffrey

last: Quinn

first: Howard

middle: Y

last: Chang


title: Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with Eralpha

status: Public on Jun 15 2014

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: Background: The ZNF217 gene, encoding a C2H2 zinc finger protein, is located at 20q13 and found amplified and overexpressed in greater than 20% of breast tumors. Current studies indicate ZNF217 drives tumorigenesis, yet the regulatory mechanisms of ZNF217 are largely unknown. Because ZNF217 associates with chromatin modifying enzymes, we postulate that ZNF217 functions to regulate specific gene signaling networks. Here, we present a large-scale functional genomic analysis of ZNF217, which provides insights into the regulatory role of ZNF217 in MCF7 breast cancer cells. Results: ChIP-seq analysis reveals that the majority of ZNF217 binding sites are located at distal regulatory regions associated with the chromatin marks H3K27ac and H3K4me1. Analysis of ChIPseq transcription factor binding sites shows clustering of ZNF217 with FOXA1, GATA3 and ERalpha binding sites, supported by the enrichment of corresponding motifs for the ERalpha-associated cisregulatory sequences. ERalpha expression highly correlates with ZNF217 in lysates from breast tumors (n=15), and ERalpha co-precipitates ZNF217 and its binding partner CtBP2 from nuclear extracts. Transcriptome profiling following ZNF217 depletion identifies differentially expressed genes co-bound by ZNF217 and ERalpha; gene ontology suggests a role for ZNF217-ERalpha in expression programs associated with ER+ breast cancer studies found in the Molecular Signature Database. Data-mining of expression data from breast cancer patients correlates ZNF217 with reduced overall survival in multiple subtypes. Conclusions: Our genome-wide ZNF217 data suggests a functional role for ZNF217 at ERalpha target genes. Future studies will investigate whether ZNF217 expression contributes to aberrant ERalpha regulatory events in ER+ breast cancer and hormone resistance

overall_design: Differential RNA-seq profiling from triplicate biological replicates of MCF7 cells treated with scrambled siRNA or siZNF217.

first: Sheryl

middle: R

last: Krig

first: Henriette

last: O'Geen


title: Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria


title: Genome wide WT1 binding sites in developing mouse kidneys

city: Nice

first: Andreas

last: Schedl

address: Parc Valrose

department: iBV

country: France

institute: University of Nice

summary: We report the the identification of chrosomal regions bound by the Wilms' tumor suppressor gene WT1 during embryonic mouse kidney development.

overall_design: Two indepednent ChIP-Seq experiments on microdissected E18.5 developing mouse kidneys were carried out using either WT1-specific or IgG-antibodies as a negative control.

first: Michael

last: Clarkson

first: Kathrin

last: Saar

first: Norbert

last: Hübner

first: Stephen

last: Bradford

first: Fabian

last: Buske


title: Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program

city: Basel

first: Christoph

last: Handschin

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel


title: Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program [ChIP-Seq]

summary: Skeletal muscle tissue shows an extraordinary cellular plasticity, but the underlying molecular mechanisms are still poorly understood. Here we use a combination of experimental and computational approaches to unravel the complex transcriptional network of muscle cell plasticity centered on the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α), a regulatory nexus in endurance training adaptation. By integrating data on genome-wide binding of PGC-1α and gene expression upon PGC-1α over-expression with comprehensive computational prediction of transcription factor binding sites (TFBSs), we uncover a hitherto underestimated number of transcription factor partners involved in mediating PGC-1α action. In particular, principal component analysis of TFBSs at PGC-1α binding regions predicts that, besides the well-known role of the estrogen-related receptor α (ERRα), the activator protein-1 complex (AP-1) plays a major role in regulating the PGC-1α-controlled gene program of hypoxia response. Our findings thus reveal the complex transcriptional network of muscle cell plasticity controlled by PGC-1α.

overall_design: We performed ChIP-Seq experiments to identify all DNA recruitment sites for PGC-1alpha in C2C12 cells on genome-wide scale. The experiment was performed in duplicate and the Whole Cell Extract (WCE; =input DNA) was used as background condition.

first: Mario

last: Baresic

first: Silvia

last: Salatino

first: Erik

last: van Nimwegen

first: Barbara

last: Kupr


title: RNA-Seq Transcriptome Profiling Reveals Differentially Expressed Genes Involved in Sex Expression in Melon (Cucumis melo L.)

city: Harbin

first: Peng

last: Gao

state: Heilongjiang Province

address: No. 59, Mucai Street

department: College of Horticulture

institute: Northeast Agricultural University

summary: RNA-Seq was conducted among sergeant bulks of four sex types of melon flowers, namely monoecious (AAGG), gynoecious (AAgg), hermaphrodite (aaGG), and andromonoecious (aagg), a total of about 105 million reads were generated from the melon transcriptome using Solexa sequencing.Totally 79,698 unigenes were generated and 75,537 unigenes were mapped to 11,805 annotated  proteins in assembled melon genome (Garcia-Mas et al., 2012). Transcripts related to photomorphogenesis and flower development in plants were found, Most of the genes encoding plant hormone metabolism related protein, others related to flora development including Tasselseeds and male sterility genes which in phytohormones pathway were also detected. Comparison each two bulks (AAGG:AAgg, AAGG:aaGG, aagg:AAgg and aaGG:aagg ) exhibited different profiles of putative genes (include 745, 1342, 858 and 571 different expression genes, respectively).

overall_design: mRNA profiles of four sex types of melon flowers, namely monoecious (AAGG), gynoecious (AAgg), hermaphrodite (aaGG), and andromonoecious (aagg) were  were generated by deep sequencing using Illumina Hiseq 2000.

first: Yunyan

last: Sheng


title: Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs

first: Kun

last: Qu

type: Non-coding RNA profiling by high throughput sequencing

summary: Long noncoding RNAs (lncRNAs) are important regulators of cell fate, and their mis-expression has been implicated in many diseases. While distinct polymerases generate messenger vs. noncoding ribosomal or tRNAs3, little is known about distinct mechanisms controlling lncRNA expression. Here we show that transcription of lncRNAs is quantitatively different from that of messenger RNAs (mRNAs)--as revealed by deficiency of Dicer (Dcr), a key ribonuclease that generates microRNAs (miRNAs). Loss of Dcr in mouse embryonic stem cells (mESCs) led surprisingly to decreased level of the majority of lncRNAs. The canonical Dgcr8-Dcr-miRNA pathway is required for robust lncRNA expression, at the level of transcriptional initiation and elongation of lncRNA genes rather than at the level of their stability. cMyc, an oncogenic transcription factor, whose expression is indirectly regulated by Dcr-miRNA in mESCs, is partly responsible for lncRNA transcription. Loss of cMyc led to a more dramatic decrease of lncRNAs than mRNAs, and cMyc overexpression rescues lncRNA expression in Dcr KO cells. A quantitative metric of “mRNA-lncRNA decoupling” revealed that Dcr and cMyc differentially regulate lncRNAs vs. mRNAs in diverse cell types and in vivo, as evidenced by hundreds of microarray experiments. Thus, Dcr and cMyc may allow numerous lncRNAs to be activated or deactivated as a class, implicating lncRNAs to potential regulatory roles in development and disease states where Dcr and cMyc have been associated with.

overall_design: RNA was sequenced from WT and Dcr KO mESCs and the expression of lncRNAs and mRNAs are compared between WT and Dcr KO mESCs.

first: Grace

middle: X

last: Zheng

first: Brian

last: Do

first: Dan

last: Webster

first: Paul

last: Khavari

first: Howard

last: Chang


title: RNA-Seq analysis of Pseudomonas aeruginosa PAO1 cells infected with  PhiKZ phage

status: Public on Jun 14 2014

city: Leuven

first: Bob

middle: Gordon

last: Blasdel

state: Vlaams-Brabant

address: Kasteelpark Arenberg 21, bus 2462

department: Afdeling Gentechnologie

country: Belgium

institute: KU Leuven

summary: Pseudomonas aeruginosa bacteriophage PhiKZ is the type representative of the ‘giant’ phage genus with unusually large virions and genomes. By unraveling the transcriptional map of the 280 kb genome to single-nucleotide resolution, we show that it encodes 369 genes organized in 134 operons, 20% more than originally annotated. Early transcription is initiated from 28 highly conserved AT-rich promoters distributed over the PhiKZ genome, all located on the same strand. Transcription of middle and late genes is dependent on protein synthesis and mediated by very poorly conserved middle (6) and late (16) promoters. As a result of massive PhiKZ transcription, halfway through infection only 1.5% of all mRNAs in the infected cell remain bacterial. Unique to PhiKZ is its ability to complete its infection in complete absence of bacterial RNA polymerase (RNAP) enzyme activity. Its transcription is performed by the consecutive action of two PhiKZ-encoded, non-canonical RNAPs, one of which is packed within the virion. This unique, rifampicin-resistant transcriptional machinery is conserved among giant viruses, seems to function without auxiliary factors and might have its origin preceding the split between Gram-positive and Gram-negative bacteria.

sample_organism:
Pseudomonas aeruginosa
Phikzvirus phiKZ

platform_organism:
Pseudomonas aeruginosa
Phikzvirus phiKZ

overall_design: Construction of transcription maps for the PhiKZ phage and analysis of differential expression of host and phage genes using RNA-Seq data from samples taken in duplicate at 0, 5, 10, 15, and 35 minutes into infection.

first: Pieter-Jan

last: Ceyssens

middle: G


title: Early remodeling of the neocortex upon episodic memory encoding

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary: Understanding the mechanisms by which long-term memories are formed and stored in the brain represents a central aim of neuroscience. Prevailing theory suggests that long-term memory encoding involves early plasticity within hippocampal circuits, while reorganization of the neocortex is thought to occur weeks to months later to subserve remote memory storage. Here we report that long-term memory encoding can elicit early transcriptional, structural and functional remodeling of the neocortex. Parallel studies using genome-wide RNA-sequencing, ultrastructural imaging, and whole-cell recording in wild-type mice suggest that contextual fear conditioning initiates a transcriptional program in the medial prefrontal cortex (mPFC) that is accompanied by rapid expansion of the synaptic active zone and postsynaptic density, enhanced dendritic spine plasticity, and increased synaptic efficacy. To address the real-time contribution of the mPFC to long-term memory encoding, we performed temporally precise optogenetic inhibition of excitatory mPFC neurons during contextual fear conditioning. Using this approach, we found that real-time inhibition of the mPFC inhibited activation of the entorhinal-hippocampal circuit and impaired the formation of long-term associative memory. These findings suggest that encoding of long-term episodic memory is associated with early remodeling of neocortical circuits, identify the prefrontal cortex as a critical regulator of encoding-induced hippocampal activation and long-term memory formation, and have important implications for understanding memory processing in healthy and diseased brain states.

overall_design: 4 biological replicates per group were analyzed. The material analyzed was medial prefrontal cortex (mPFC; anterior cingulate cortex subregion) from both brain hemispheres, from which total RNA was extracted.

first: Adam

middle: W

last: Bero

first: Jia

last: Meng


title: An aging-like phenotype occurs in Tif1γ-/- hematopoietic stem cells

city: Dijon

first: ronan

last: quere

address: 7 bd Jeanne d'Arc

institute: Inserm U866

summary: To determine whether an accelerated aging-like phenotype occurs in hematopoiesis of young Tif1γ-/- mice (4 months old), we purified 200,000 hematopoietic stem cells (LSK: Lineage negative, Sca1+, c-Kit+) from Tif1γ-/- mice and performed high-throughput mRNA sequencing (RNA-seq). We compared this transcriptome to physiological aging by creating two other RNAseq libraries from young (4 months old) and old (20 months old) wild type mice.

overall_design: RNAseq study on young Tif1γ-/- mice (4 months old), young wild type mice (4 months old) and old wild type mice (20 months old).

first: Ronan

last: Quéré


title: Next Generation Deep Sequencing Facilitates Quantitative Analysis of microRNA affected by thapsigargin treatment

city: Edmonton

first: Marek

last: Michalak

state: Alberta

address: 87 Avenue

department: Biochemistry

country: Canada

institute: University of Alberta

summary:
Purpose: microRNA profiles were generated from NIH-3T3 cells control and thapsigargin treated, in duplicate.
The goal of this study was to compare microRNA profiles of untreated and thapsigargin treated NIH-3T3 fibroblast cells.
Methods: NIH-3T3 cells were grown to confluency and either untreated or treated with 500 nM thapsigargin in media for 24 hours. Cells were harvested with TriZol and RNA isolated according to manufacturers protocol
Analysis Outline: Short reads in fastq format were assembled using BclToFastq.pl script from Illumina CASAVA 1.8.1 software pipeline.Read quality was examined using FastQC program (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc). Adapters were trimmed at the 3'end using Btrim prgram (PMID:21651976), only sequences equal to and longer than 18nt were retained, leading N base was trimmed at the 5' end. Unique reads were collapsed using Raw_data_parse program from miRExpress suite (PMID:19821977) (the result of this process is a file that contains unique sequences in one column and number of times this sequence was found in the library in another). They can be found in *.merge files in trimmed_reads directory. Collapsed reads were reformatted and uploaded into miRanalyzer web-based pipeline (http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php; PMID:21515631) and matched to known mature miRNA (miRBase vesion 16), RFAM database (version 15) of known non-coding RNAs and known gene transcripts. The purpose of miRAnalyzer analysis was to only detect known miRNAs, prediction of novel miRNAs was not performed; search parameters were kept at default. MiRanalyzer output is saved in miRanalyzer folder with detailed information about mapping to known miRNA. Known miRNAs were divided into mature, maturestar (star sequences), maturestarunobs (star sequences not in miRBase) and hairpin. For each of the libraries there are files with unique and ambiguous mappings. Differentional expression analysis was based on unique alignments to known miRNAs (mature_unique.txt file in miRanalyzer folder). Mature_unique.txt has following columns: name: mature miRNA ID from miRBase; #unique reads: number of unique reads mapped; readCount: number of reads mapped; norm_expressed_all: normalized to all reads; norm_expressed_mapped: normalized to mapped reads. miRNA expression profiling was performed using edgeR bioconductor package (PMID:20478825). For differential expression analysis, used TMM normalization and analysis using common disperion (using tagwise dispersion yielded the same results). FDR was calculated according to Hochberg-Benjamini procedure (PMID:2218183). Results of differential expression analysis were saved in diff_exp folder as diff_exp.txt. diff_exp.txt contains miRNA concentrations in log scale, log2 ratio of WT to KO; p-values and FDR corrected p-values. miRNAs were sorted by p-value.

overall_design: NIH-3T3 cells grown to confluency and treated with 500 nM thapsigargin in media for 24 hours

first: Jody

last: Groenendyk


title: The ribonuclease activity of SAMHD1 is required for HIV-1 restriction

status: Public on Jun 13 2014

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

institute: Psomagen Inc

summary: SAMHD1  restricts  HIV-1  replication  in  dendritic  and  other  myeloid  cells. SAMHD1 has been shown to possess a dGTP-dependent dNTP triphosphatase (dNTPase) activity and is proposed to inhibit HIV-1 replication by depleting the intracellular dNTP pool. Arguing against a role for SAMHD1 dNTPase in HIV-1 restriction, the phosphorylation of SAMHD1 regulates the restriction activity toward HIV-1 without affecting its ability to decrease cellular dNTP levels. Here, we show that SAMHD1 is a phospho-regulated RNase and that the RNase function is required for HIV-1 restriction. Mutation of the SAMHD1 D137 residue in the allosteric site (SAMHD1D137N) abolishes dNTPase activity but has no effect on RNase activity. This dNTPase-defective SAMHD1D137N mutant is able to restrict HIV-1 infection to nearly the same extent as wild-type SAMHD1. SAMHD1 associates with and degrades the HIV-1 genomic RNA during the early phases of infection. SAMHD1 silencing in macrophages and CD4+ T cells from healthy donors increases HIV-1 RNA stability, thus rendering the cells permissive for HIV-1 infection. Furthermore, the phosphorylation of SAMHD1 at position T592 abolishes the RNase activity toward HIV-1 RNA, and consequently the ability of SAMHD1 to restrict HIV-1 infection, uncovering the phosphorylation of SAMHD1 T592 as a negative regulatory mechanism of RNase activity. Together, our results demonstrate that SAMHD1 is an essential RNase that prevents HIV-1 infection by directly degrading HIV-1 genomic RNA in a phosphorylation-regulated manner. The unique property of SAMHD1 that cleaves HIV-1 genomic RNA with no sequence preferences could be exploited to develop a new class of intervention for error-prone retroviruses.

overall_design: Ribosomal RNA-depleted total RNA profiles of mock, SAMHD1 wild type and mutants infected with HIV-1 were examined at the time of 0, 1, 3 h by Illumina Hiseq2500.

first: Jeongmin

last: Ryoo

first: Sungchul

last: Kim

first: Kwangseog

last: Ahn


title: Transcription Factor Network Specifying Inhibitory versus Excitatory Neurons in the Dorsal Spinal Cord [RNA-Seq]

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: The proper balance of excitatory and inhibitory neurons is crucial to normal processing of somatosensory information in the dorsal spinal cord. Two neural basic helix-loop-helix transcription factors, Ascl1 and Ptf1a, are essential for generating the correct number and sub-type of neurons in multiple regions of the nervous system.   In the dorsal spinal cord, Ascl1 and Ptf1a have contrasting functions in specifying inhibitory versus excitatory neurons. To understand how Ascl1 and Ptf1a function in these processes, we identified their direct transcriptional targets genome-wide in the embryonic mouse neural tube using ChIP-Seq and RNA-Seq. We show that Ascl1 and Ptf1a regulate the specification of excitatory and inhibitory neurons in the dorsal spinal cord through direct regulation of distinct homeodomain transcription factors known for their function in neuronal sub-type specification. Besides their roles in regulating these homeodomain factors, Ascl1 and Ptf1a each function differently during neuronal development with Ascl1 directly regulating genes with roles in several steps of the neurogenic program including, Notch signaling, neuronal differentiation, axon guidance, and synapse formation. In contrast, Ptf1a directly regulates genes encoding components of the neurotransmitter machinery in inhibitory neurons, and other later aspects of neural development distinct from those regulated by Ascl1. Moreover, Ptf1a represses the excitatory neuronal fate by directly repressing several targets of Ascl1. Examination of the Ascl1 and Ptf1a bound sequences shows they are enriched for a common E-Box with a GC core and with additional motifs used by Sox, Rfx, Pou, and Homeodomain factors. Ptf1a bound sequences are uniquely enriched in an E-Box with a GA/TC core and in the binding motif for its co-factor Rbpj, providing two keys to specificity of Ptf1a binding. The direct transcriptional targets identified for Ascl1 and Ptf1a provide a molecular understanding for how they function in neuronal development, particularly as key regulators of homeodomain transcription factors required for neuronal sub-type specification.

overall_design: Examination of gene expression in Ascl1 and Ptf1a lineage cells in the developing neural tube.

first: Mark

middle: D

last: Borromeo

first: David

middle: M

last: Meredith

first: Diogo

middle: S

last: Castro

first: Joshua

middle: C

first: Kuang-Chi

last: Tung

first: Francois

last: Guillemot


title: Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state

first: Yarden

last: Katz

address: 9 Cambridge Center

department: Dept. of Biology and Whitehead Institute

summary: mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-binding proteins

overall_design: Study of the global effects of Musashi (Msi) proteins on the transcriptome of embryonic neural stem cells. Neural stem cells were derived from brains of E12.5 or E13.5 embryos engineered to have inducible Msi1 or Msi2 genes, or from embryos with double floxed alleles of Msi1 and Msi2 carrying a Tamoxifen-induclble Cre (CreER). The overexpression mice were made using the Flp-in system (OpenBioSystems), where a cDNA of interest (in this case Msi1 or Msi2) is knocked into the Collagen (Col1A1) locus. The expression of the cDNA of interest is driven by m2rTTA that is knocked into the Rosa26 locus (R26). KH2 describes a strain containing the R26-m2rTTA but lacking Msi1 or Msi2 cDNA. MSI1 describes a strain containing R26-m2rTTA and Msi1 cDNA in Col1A1. MSI2 describes a strain containing R26-m2rTTA and Msi2 cDNA in Col1A1. C1 describes a strain lacking the CreER allele but containing double floxed alleles of Msi1/Msi2 (used as Tamoxifen control). C4 describes a strain carrying the CreER allele and double floxed alleles of Msi1/Msi2.

first: Christopher

last: Burge


title: piRNA pathway targets active LINE1 elements to establish repressive H3K9me3 mark in germ cells

city: Pasadena

first: Sergei

middle: A

last: Manakov

address: 1200 E California blvd, MC 147-75

department: Biology and Biological Engeneering

institute: California Institute of Technology

summary: Transposable elements (TEs) occupy large fraction of metazoan genomes and pose constant threat to genomic integrity. This threat is particularly critical in germ cells, as changes in the genome that are induced by TEs will be transmitted to the next generation. Small non-coding piwi interacting (pi)RNAs recognize and silence a diverse set of TEs in germ cells. In mice, piRNA-guided transposon repression correlates with establishment of CpG DNA methylation on their sequences, yet the mechanism and the spectrum of genomic targets of piRNA silencing are unknown. Here we show that in addition to DNA methylation, the piRNA pathway is required to maintain a high level of the repressive H3K9me3 histone modification on long interspersed nuclear elements (LINEs) in germ cells. piRNA-dependent chromatin repression targets exclusively full-length elements of actively transposing LINE families, demonstrating the remarkable ability of the piRNA pathway to recognize active elements among the large number of genomic transposon fragments.

overall_design: Total of 34 libraries were analyzed. In case of ChIP libraries, every 'input' sample was used for normalization of the respective ChIP (H3K9me3 or H3) sample; the input libraries preceed ChIP libraries in the list below. There are four replicates (input-ChIP pairs) for H3K9me3 ChIP on liver cells, two for ChIP on testicular somatic cells for each genotype (Miwi2 Het and KO); and four for ChIP on male germ cells for each genotype (one from FACS-sorted germ cells, and three from MACS-sorted germ cells). Each replicate has a Het/KO pair, and the respective libraries were cloned from the material isolated from littermates. One H3 ChIP for each genotype is included, with respective inputs.

first: Dubravka

last: Pezic

first: Alexei

last: Aravin


title: Transcription Factor Network Specifying Inhibitory versus Excitatory Neurons in the Dorsal Spinal Cord

overall_design: Refer to individual Series


title: The glycogen scaffolding protein PTG coordinately regulates glycogen and lipid storage

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: Glycogen and lipid are major storage forms of energy that are tightly regulated by hormones and metabolic signals. Here, we evaluate the role of the glycogenic scaffolding protein PTG/R5 in energy homeostasis. We demonstrate that feeding mice a high-fat diet (HFD) increases hepatic glycogen, corresponding to increased PTG levels, increased activity of the mechanistic target of rapamycin complex 1 (mTORC1) and induced expression of sterol regulatory element binding protein 1c (SREBP1c). PTG promoter activity was increased by activation of mTORC1 and SREBP1, and PTG and glycogen levels were augmented in mice and cells in which mTORC1 is constitutively active. HFD-dependent increases in hepatic glycogen were prevented by deletion of the PTG gene in mice. Interestingly, PTG knockout mice fed HFD exhibited improved liver steatosis and decreased lipid levels in muscle, in coordination with decreased glycogen, suggesting possible crosstalk between glycogen and lipid stores in the overall control of energy metabolism. Together, these data suggest that transcriptional regulation of PTG by dietary and nutritional cues has profound effects on energy storage and metabolism.fi

overall_design: RNA-Seq analysis was used to characterize hepatic diet-associated gene expression changes between wild-type and PTG KO mice. Mice were maintained on a normal chow diet or a high-fat diet as indicated. 2-3 biological replicates per genotype/diet.

first: Binbin

last: Lu

first: Alan

last: Saltiel


title: Polyadenylated RNA Sequencing of C57BL/6J Embryonic, Adult and Pressure-Overloaded Hearts

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: A few reports have implicated specific lncRNAs in cardiac development or failure, but precise details of lncRNAs expressed in hearts and how their expression may be altered during embryonic heart development or by adult heart disease is unknown. By comparing lncRNA profiles of normal embryonic (~E14), normal adult, and hypertrophied adult hearts we defined a distinct fetal lncRNA abundance signature that includes 157 lncRNAs differentially expressed compared to adults (fold-change ≥ 50%, FDR=0.02), and which was only poorly recapitulated in hypertrophied hearts (17 differentially expressed lncRNAs; 13 of these observed in embryonic hearts).  Analysis of protein-coding mRNAs from the same samples identified 22 concordantly and 11 reciprocally regulated mRNAs within 10 kb of dynamically expressed lncRNAs, reciprocal relationships of lncRNA and mRNA levels was validated for the Mccc1 and Relb genes using in vitro lncRNA knockdown in C2C12 cells. Network analysis suggested a central role for lncRNAs in modulating NFkappaB- and CREB1-regulated genes during embryonic heart growth and identified multiple mRNAs within these pathways that are also regulated, but independently of lncRNAs.

overall_design: Cardiac polyadenylated RNA (mRNA and lncRNA) profiles were generated from C57BL/6J mouse hearts were generated on Illumina HiSeq 2000 instruments.  7 independent E13.5 hearts, 12 adult hearts (6 at 6 weeks of age, 6 at 16 weeks of age), 4 sham-operated hearts at 12 weeks of age, and 4 hearts after 4 weeks of pressure overload (TAC) at 12 weeks of age.

first: Gerald

last: Dorn


title: Mtg16 regulates E protein activity and lineage specification in dendritic cell development (ChIP-seq)

city: New York

first: Hiyaa

middle: Singhee

last: Ghosh

state: NY

address: 701 W 168th Street

institute: Columbia University Medical Center

summary: E protein transcription factors specify major immune cell lineages including lymphocytes and interferon-producing plasmacytoid dendritic cells (pDCs). Corepressors of the ETO family can bind to and block transactivation by E proteins, but the physiological role of these interactions remained unclear. We report that ETO protein Mtg16 binds chromatin primarily through the pDC-specific E protein E2-2 in human pDCs. Mtg16-deficient mice showed impaired pDC development and functionality, whereas the specification of the classical dendritic cells (cDCs) was enhanced. The deletion of Mtg16 caused aberrant expression of E protein antagonist Id2 in pDCs. Thus, Mtg16 acts as a cofactor of E2-2 to promote pDC differentiation and restrict cDC development, revealing an unexpected positive role of ETO proteins in E protein activity.

overall_design: Analysis of E2-2 and Mtg16 immunoprecipitated chromatin from CAL-1 cell line.

first: Boris

last: Reizis


title: Mtg16 regulates E protein activity and lineage specification in dendritic cell development

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves

city: Warsaw

first: Anna

last: Lukasik

state: mazowieckie

address: Pawinskiego 5a

department: Department of Bioinformatics

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: Plant microRNAs are short (~21 nt), non-coding molecules that regulate gene expression by targeting mRNA cleavage or protein translation inhibition. In this manner, they play many important roles in the cells of living organisms. One of the plant species in which the entire set of miRNAs has not been yet completely identified is Brassica oleracea var. capitata (cabbage). For this reason and for the economic and nutritional importance of this food crop, Illumina high-throughput small RNAs sequencing has been performed to discover novel and conserved miRNAs in the mature cabbage leaves. In this study, raw reads generated from three small RNA libraries were bioinformatically processed and further analyzed to select sequences homologous to known B. oleracea and other plant miRNAs. As a result of this step, 267 conserved miRNAs (belonging to 62 families) have been discovered. The remaining unannotated tags were used in the prediction and evaluation of novel miRNAs, which resulted in the 26 potential miRNAs proposal. The expression of 13 selected miRNAs was analyzed by northern blot hybridization. To determine the functions and processes that these molecules may potentially regulate in cabbage leaves, GO annotation, GO enrichment analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway mapping of the predicted targets were performed. Taken together, for the first time, the large set of miRNAs was identified in the mature cabbage leaves. Potential target designation for these miRNAs may suggest their important role in the plant growth, development and other primary biological processes. The presented study not only supplements the knowledge about B. oleracea miRNAs, but also may be used in other researches concerning the improvement of the cabbage cultivation.

overall_design: High-throughput sequencing of three small RNA libraries was performed to identified conserved and novel miRNAs in mature cabbage leaves, while the potential targets designation was carried out to suggest the functions and roles that identified miRNAs might play in this food crop.

first: Halina

last: Pietrykowska

first: Zofia

last: Szweykowska-Kulinska

first: Piotr

last: Zielenkiewicz


title: Next Generation Sequencing of Wild-Type FVB/NJ Mouse Primary Cardiomyocyte and Cardiac Nonmyocyte Polyadenylated RNA and small RNA

summary: Cells from three adult, wild-type, FVB hearts were separated into cardiomyocyte and nonmyocyte fractions using Langendorff perfusion, collagenase digestion and gravity filtration. Total RNA was prepared immediately from myocytes, while nonmyocytes were passaged twice to yield a culture from which total RNA was prepared.

overall_design: 6 cardiac polyadenylated RNA (mRNA and lncRNA) and small RNA (microRNA) profiles of isolated cardiomyocytes (CM) and nonmyocytes (fibro) from 12-wk FVB/NJ mouse hearts were generated on Illumina HiSeq 2000 instruments.


title: dRNA-seq of Shewanella oneidensis MR-1

status: Public on Jun 12 2014

city: Berkeley

first: Wenjun

last: Shao

address: 2151 Berkeley Way

department: Molecular and Cell Biology

institute: University of California

summary: We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. Overall, the dRNA-seq results support the validity of our predictions for TSS.

overall_design: S. oneidensis MR-1 was grown to mid-log phase in Luria-Bertani broth (LB) or defined lactate minimal medium, and total RNA was isolated and used for differential RNA-sequencing (dRNA-seq) by next-generation sequencing, which is used to verify genome-wide transcription start sites. For dRNA-seq, total RNA was partially treated with Terminator Exonuclease (TEX) to digest processed RNA and thereby enrich for primary transcript ends.

first: Morgan

middle: N

last: Price

first: Adam

last: Deutschbauer

middle: P

last: Arkin


title: The histone lysine demethylase Kdm6b is required for activity-dependent preconditioning of hippocampal neuronal survival

city: Durham

first: Christopher

middle: L

last: Frank

state: NC

address: 101 Science Dr.

institute: Duke University

summary: We profiled basal and bicuculline+4-AP inducible mRNA expression in cultured mouse hippocampal neurons with or without viral shRNA mediated knockdown of Kdm6b

overall_design: We harvested mRNA from neurons under four conditions (pLKO vector/treatment control, pLKO vector/3hr bicuculline+4AP, Kdm6b knockdown/treatment control,Kdm6b knockdown/3hr bicuculline+4AP). Libraries were generated and used for RNA sequencing.

first: Ranjula

last: Wijayatunge

first: Liang-Fu

last: Chen

first: Young

last: Cha

first: Anthony

last: Zanna

first: Anne

last: West


title: A zebrafish model for hyperinsulinemia shows that induction of insulin resistance and immune suppression is mediated by ptpn6/shp.1

city: Bad Nauheim

first: Rubén

last: Marín-Juez

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute

summary: Type 2 Diabetes, obesity and metabolic syndrome are pathologies impacting a large population worldwide where insulin resistance plays a central role. These pathologies are usually associated to a dysregulation of insulin secretion leading to a chronic exposure of the tissues to high insulin levels (i.e. hyperinsulinemia) what diminishes the concentration of key downstream elements causing insulin resistance. The complexity of the study of insulin resistance relies on the heterogeneity of the metabolic states where it’s observed. In consequence, animal models for the study of insulin resistance, can not completely recapitulate the metabolic status of insulin resistant humans, what is translated in contradictory observations.   To contribute to the understanding of the mechanisms triggering insulin resistance we have developed a zebrafish model to study insulin metabolism and its associated disorders. Zebrafish embryos appeared to be sensitive to human recombinant insulin, becoming insulin resistant when exposed to a high dose of the hormone, as confirmed by glucose measurements. Moreover RNAseq-based transcriptomic profiling of these embryos revealed a strong down regulation of a number of immune relevant genes as a consequences of the exposure to hyperinsulinemia. Interestingly, as an exception, the negative immune modulator ptpn6 appeared to be up regulated in insulin resistant embryos. Knockdown of ptpn6 showed to counteract the observed down regulation of the immune system and insulin signalling pathways effects at the transcriptional level caused by hyperinsulinemia.  These results show that ptpn6 is a mediator of the metabolic switch between insulin sensitive and insulin resistant states. Our zebrafish model for hyperinsulinemia has therefore demonstrated it suitability to discover novel regulators of insulin resistance. In addition, our data will be very useful to further study the function of immunological determinants in a non-obese model system.

overall_design: 16 samples in total were analyzed. 4 replicates from control samples (injected with PBS) and 4 replicates of insulin injected samples at 0.5 hpi and 4 hpi. In each sample 10 embryos were pooled.

first: Herman

last: Spaink


title: Pseudomonas aeruginosa Ceftolozane-Tazobactam Resistance Development Requires Multiple Mutations Leading to Overexpression and Structural Modification of AmpC.

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

institute: Technische Universität Braunschweig

summary: We compared the dynamics and mechanisms of resistance development to ceftazidime, meropenem, ciprofloxacin, and ceftolozane-tazobactam in wild-type (PAO1) and mutator (PAOMS, ∆mutS) P. aeruginosa. The strains were incubated for 24 h with 0.5 to 64× MICs of each antibiotic in triplicate experiments. The tubes from the highest antibiotic concentration showing growth were reinoculated in fresh medium containing concentrations up to 64× MIC for 7 consecutive days. The susceptibility profiles and resistance mechanisms were assessed in two isolated colonies from each step, antibiotic, and strain. Ceftolozane-tazobactam-resistant mutants were further characterized by whole-genome analysis through RNA sequencing (RNA-seq). The development of high-level resistance was fastest for ceftazidime, followed by meropenem and ciprofloxacin. None of the mutants selected with these antibiotics showed cross-resistance to ceftolozane-tazobactam. On the other hand, ceftolozane-tazobactam resistance development was much slower, and high-level resistance was observed for the mutator strain only. PAO1 derivatives that were moderately resistant (MICs, 4 to 8 ug/ml) to ceftolozane-tazobactam showed only 2 to 4 mutations, which determined global pleiotropic effects associated with a severe fitness cost. High-level-resistant (MICs, 32 to 128 ug/ml) PAOMS derivatives showed 45 to 53 mutations. Major changes in the global gene expression profiles were detected in all mutants, but only PAOMS mutants showed ampC overexpression, which was caused by dacB or ampR mutations. Moreover, all PAOMS mutants contained 1 to 4 mutations in the conserved residues of AmpC (F147L, Q157R, G183D, E247K, or V356I). Complementation studies revealed that these mutations greatly increased ceftolozane-tazobactam and ceftazidime MICs but reduced those of piperacillin-tazobactam and imipenem, compared to those in wild-type ampC. Therefore, the development of high-level resistance to ceftolozane-tazobactam appears to occur efficiently only in a P. aeruginosa mutator background, in which multiple mutations lead to overexpression and structural modifications of AmpC.

overall_design: Mutants of Pseudomonas aeroginosa PAO1 and PAO1 ∆mutS against Ceftolozane-tazobactam were generated and analysed using RNA-Seq

first: Gabriel

last: Cabot

first: Sebastian

last: Bruchmann

first: Xavier

last: Mulet

first: Laura

last: Zamorano

first: Bartolomé

last: Moyà

first: Carlos

last: Juan

first: Susanne

last: Haussler

first: Antonio

last: Oliver


title: Genome-wide ChIP sequencing of NUCKS

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: NUCKS has a DNA binding domain at C-terminal region. We found that NUCKS has important roles in regulating glucose homeostasis. To get an unbiased handle on the plausible mechanism(s) of NUCKS action, we performed a genome-wide Chromatin Immunoprecipitation (ChIP)-sequencing for NUCKS in primary hepatocytes. We successfully mapped 25mln reads to the mm9 genome and detected NUCKS binding at 10203 sites, 60% of which were located in the proximity of a Transcription Start Sites (TSS). The peaks of NUCKS occupancy were often broad with some around 1Kb, suggesting that multiple NUCKS molecules could bind cooperatively to the same genomic loci. This study provides information of NUCKS binding sites in Mus musculus genome.

overall_design: Examination of NUCKS binding in mouse primary hepatocytes by Chromatin immunoprecipitation followed by deep sequencing.

middle: H

first: Beiying

last: Qiu


title: A crucial role of the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham


title: Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

city: Lausanne

first: Kyle

middle: Bergin

last: Gustafson

state: Suisse

address: EPFL-UPNAE

department: IBI

institute: EPFL

summary: Here, we present PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first.

overall_design: High-resolution characterization of PolII at promoters in mouse liver

middle: B

first: Mathieu

last: Quinodoz


title: A crucial role of the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification [ChIP-Seq]

summary: Mammalian development is regulated by the interplay of tissue-specific and ubiquitously expressed transcription factors, such as Sp1. Sp1 knock-out mice die in utero with multiple phenotypic aberrations, but the underlying molecular mechanism of this differentiation failure has been elusive. Here we used conditional knock-out mice as well as the differentiation of mouse ES cells as a model to address this issue. To this end we examined differentiation potential, global gene expression patterns and Sp1 target regions in Sp1 wild-type and deficient cells representing different stages of hematopoiesis. Sp1-/- cells progress through most embryonic stages of blood cell development but cannot complete terminal differentiation. For most Sp1 target and non-target genes, gene expression is unaffected by Sp1 inactivation. However, Cdx and multiple Hox genes are stage-specific targets of Sp1 and are down-regulated at an early stage. As a consequence, expression of genes involved in hematopoietic specification are progressively deregulated, highlighting the regulatory hierarchy of hematopoietic specification. Our work demonstrates that the early absence of active Sp1 sets a cascade in motion that culminates in a failure of terminal hematopoietic differentiation and emphasizes the role of ubiquitously expressed transcription factors for tissue-specific gene regulation.

overall_design: Two ChIP-Seq data from Sp1 transcription factor obtained from FLK+ and progenitor cells

first: Jane

last: Gilmour

first: Ulrike

last: Jaegle

first: Divine

last: Kulu

first: Harmen

last: van de Werken

first: Deborah

last: Clarke

first: David

middle: R

last: Westhead

first: Sjaak

last: Philipsen

first: Constanze

last: Bonifer


title: Polysome profiling and ribosome footprinting of Drosophila mature oocyte and activated egg

city: Cambridge

first: Iva

last: Kronja

institute: Whitehead Institute for Biomedical Research

summary: We use mRNA-seq in combination with polysome profiling to determine translational status for all mRNAs in Drosophila mature oocytes and activated eggs. Puromycin-treated lysates are used as a negative control in polysome profiling experiments. Additionally, we use ribosome footprinting to globally measure translational efficiency of mRNAs in wild type mature oocytes as well as wild type and png mutant activated eggs.

overall_design: Lysates of hand-dissected Drosophila mature oocytes  (containing ~540 μg of total RNA) were subjected to separation by velocity sedimentation through sucrose gradients. In this way, free mRNAs (present in RNPs fraction) or those comigrating with ribosomal subunits (40S or 60S+80S fractions) or with varying numbers of bound ribosomes (low polysomes (2-4 ribosomes), medium polysomes (5-9 ribosomes), and heavy polysomes (more than 10 ribosomes) can be separated based on their size and collected as sucrose gradient fractions. To compare quantitatively the levels of every mRNA across the polysome gradient fractions, we added 5ng of S. cerevisiae mRNA as an exogenous spike-in to each of the six fractions of interest: RNPs, 40S, 60S+80S, low polysomes, medium polysomes and heavy polysomes. RNA was extraced from these fractions, follwing proteinase K treatment, by hot acid phenol method.  In case of unfractionated lysates, RNA was extracted using TRIzol (Invitrogen) according to manufacturer’s instructions. mRNA-seq samples were prepared from 1 μg of total RNA (in case of sucrose gradient fractions and unfractionated lysates) and subject to Illumina based sequencing. Puromycin-treated lysates of mature oocytes or 0-2h Drosophila activated  eggs (containing ~540 μg of total RNA) were also subjected to separation by velocity sedimentation through sucrose gradients. Puromycin causes premature termination of elongating ribosomes and thus it can be used to determine whether the mRNAs co-sedimenting with the polysomal peaks (defined here as ≥5 ribosomes) were actively engaged in translation. As an independent approach to assess translation and obtain information on the position of ribosomes on mRNAs, we employed ribosome footprinting. In addition to analyzing the same samples, as by polysome profiling, we also analyzed png mutant activated eggs by ribosome footprinting. Ribosome footprint profiling measures the number of ribosome-protected fragments (RPFs) derived from the mRNAs of each gene, resulting in a singular value of translational efficiency (TE) for each gene (TE=RPF/RNA).

first: Stephen

last: Eichhorn

first: Bingbing

last: Yuan

last: Bartel

first: Terry

last: Orr-Weaver


title: KDM6 demethylase independent loss of histone H3 lysine 27 trimethylation during early embryonic development

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: H3K27me3 represses developmental genes at initial embryonic stages. The KDM6 family, comprised of UTX and JMJD3, are the only known proteins that demethylate H3K27me3 and they are hypothesized to catalyze the rapid removal of repressive chromatin in early mammalian development. However, we report that male embryos carrying mutations in both Utx and Jmjd3 survive to term and appear phenotypically normal at mid-gestation. We utilize several cell culture models to demonstrate that H3K27me3 is lost from repressed promoters in the absence of active KDM6 demethylation. Our data indicate that KDM6 H3K27me3 demethylation is not essential in the early embryo and that H3K27me3 loss from developmental genes occurs via novel mechanisms.

overall_design: Examination of 2 different histone modifications (H3K27me3 and H3K4me3) in 2 cell types (ES and retinoic acid treated ES cells) comparing WT to UTX and JMJD3 KOs.  In ES cells, there are two WT replicates and two KO replicates, both measuring H3K27me3, and one replicate measuring input.  In retinoic acid treatment, there are two replicates each for measuring H3K27me3 and H3K4me3 in WT and KO cell lines, and one replicate measuring input.

first: Karl

last: Shpargel

first: Della

last: Yee

first: Michael

last: Pohlers

last: Magnuson


title: Rapid isolation of extracellular vesicles from cell culture and biological fluids using a synthetic peptide with specific affinity for heat shock proteins

city: Moncton

first: Nicolas

last: Crapoulet

state: NB

address: 35 Providence street

institute: Atlantic cancer research institute

summary: Background: Exosomes and extracellular vesicles (EVs) are increasingly recognized as important sources of biomarkers for disease study and diagnosis. Results: A synthetic peptide, Vn96, allows for capture of EVs from biological fluids using basic laboratory equipment. Conclusion: The Vn96-captured EVs are qualitatively equivalent or superior to exosomes isolated by ultracentrifugation. Significance: The Vn96 peptide provides an effective affinity-capture method for the isolation of EVs from biological fluids.

overall_design: In order to compare different methods of exosome purification, we compared RNA content of exosomes purified with each method. We used two different breast cancer cell lines MCF7 and MDA-MB-231. We processed data in order to identify large RNAs as well as small RNA by using different methods for the alignment

first: Anirban

last: Ghosh

first: Michelle

last: Davey

first: Ian

last: Chute

first: Steven

middle: G

last: Griffiths

first: Scott

last: Lewis

first: Simi

last: Chacko

last: Barnett

first: Sébastien

last: Fournier

first: Andrew

last: Joy

last: Caissie

first: Amanda

last: Ferguson

first: Melissa

last: Daigle

first: Vicki

last: Meli

first: Rodney

middle: J

last: Ouellette


title: Transcription Factor Network Specifying Inhibitory versus Excitatory Neurons in the Dorsal Spinal Cord [ChIP-Seq]

first: Jane

middle: E

last: Johnson

department: Neuroscience

summary: The proper balance of excitatory and inhibitory neurons is crucial to normal processing of somatosensory information in the dorsal spinal cord. Two neural basic helix-loop-helix transcription factors, Ascl1 and Ptf1a, are essential for generating the correct number and sub-type of neurons in multiple regions of the nervous system.   In the dorsal spinal cord, Ascl1 and Ptf1a have contrasting functions in specifying inhibitory versus excitatory neurons. To understand how Ascl1 and Ptf1a function in these processes, we identified their direct transcriptional targets genome-wide in the embryonic mouse neural tube using ChIP-Seq and RNA-Seq. We show that Ascl1 and Ptf1a regulate the specification of excitatory and inhibitory neurons in the dorsal spinal cord through direct regulation of distinct homeodomain transcription factors known for their function in neuronal sub-type specification. Besides their roles in regulating these homeodomain factors, Ascl1 and Ptf1a each function differently during neuronal development with Ascl1 directly regulating genes with roles in several steps of the neurogenic program including, Notch signaling, neuronal differentiation, axon guidance, and synapse formation. In contrast, Ptf1a directly regulates genes encoding components of the neurotransmitter machinery in inhibitory neurons, and other later aspects of neural development distinct from those regulated by Ascl1. Moreover, Ptf1a represses the excitatory neuronal fate by directly repressing several targets of Ascl1. Examination of the Ascl1 and Ptf1a bound sequences shows they are enriched for a common E-Box with a GC core and with additional motifs used by Sox, Rfx, Pou, and Homeodomain factors. Ptf1a bound sequences are uniquely enriched in an E-Box with a GA/TC core and in the binding motif for its co-factor Rbpj, providing two keys to specificity of Ptf1a binding. The direct transcriptional targets identified for Ascl1 and Ptf1a provide a molecular understanding for how they function in neuronal development, particularly as key regulators of homeodomain transcription factors required for neuronal sub-type specification.

overall_design: Examination of Ascl1 and Ptf1a genome-wide binding in developing neural tube.

first: Mark

middle: D

last: Borromeo

first: David

middle: M

last: Meredith

first: Diogo

last: Castro

first: Joshua

last: Chang

first: Kuang-Chi

last: Tung

first: Francois

last: Guillemot


title: Flag-RBM47 HITS-CLIP in brain metastatic derivatives of MDA-MB-231

status: Public on Jun 11 2014

first: Christina

middle: Beate

last: Marney

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary:
Brain metastatic breast cancer cells were subjected to HITS-CLIP to identify the targets of the RNA binding protein RBM47
MDA231-BrM2a is characterized in PMID: 19421193;  Related data published together with these data are found in GSE53779

overall_design: Non-clonal brain metastatic breast cancer cells stably expressing Flag-tagged, wild-type RBM47 under a doxycline-inducible promoter were treated for three days with doxycycline then  UV-irradiated and subjected to Flag HITS-CLIP

first: Aldo

last: Mele

first: Robert

last: Darnell


title: Gene expression changes after loss of C/EBPα in transformed HSCs [CEBPA RNA-seq]

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 medimmune way

department: Respiratory, Inflammation and Autoimmunity

institute: Medimmune

summary: RNAseq characterization of gene expression changes 72 hours after genomic excision of Cebpa in murine hematopoietic progenitors from Cebpaf/f;CreER mice transformed by Hoxa9/Meis1. In the presence of tamoxifen (4OHT), Cre-ER localizes to the nucleus of cells allowing for excision of Cebpa and loss of C/EBPα protein levels. Loss of C/EBPα leads to a decrease in cellular proliferation.

overall_design: Examination of gene expression by RNAseq in two conditions in biological replicates.

first: Jay

last: Hess


title: Regulation of gene expression through genome-wide co-binding of Hoxa9 and C/EBPα in transformed HSCs

overall_design: Refer to individual Series


title: Gene expression changes after loss of Hoxa9 in transformed HSCs [HOXA9 RNA-seq]

summary: Characterization of gene expression changes 72 hours after withdrawal of tamoxifen in murine hematopoietic progenitors transformed by Hoxa9-ER/Meis1 using RNAseq. In the presence of tamoxifen (4OHT), Hoxa9-ER localizes to the nucleus of cells allowing for transformation, while withdrawal of 4OHT (culture in EtOH) leads to loss of nuclear Hoxa9-ER. Loss of Hoxa9-ER leads to a decrease in cellular proliferation and differentiation along the myeloid lineage.


title: Identification of alternatively spliced transcripts in brain metastatic derivatives of MDA-MB-231 breast cancer cells in response to RBM47 expression

summary:
Changes in alternative splicing in breast cancer cells expressing control, empty vector or Flag-tagged wild type RBM47 were analyzed using paired-end, 100bp RNAseq.
Related data published together with these data are found in GSE53779

overall_design: Triplicate RNAseq libraries were prepared from non-clonal brain metastatic breast cancer cells stably expressing empty-vector, and a clonal cell line (wt#10) expressing Flag-tagged, wild-type RBM47 under a doxycline-inducible promoter, both treated for three days with doxycycline to induce transgene expression


title: Genome-wide co-occupancy of Hoxa9 and C/EBPα in Hoxa9/Meis1 transformed HSCs [ChIP-seq]

summary: Identification of the genome-wide binding sites of Hoxa9 and C/EBPα in a murine myeloblastic cell line transformed by Hoxa9/Meis1. Over 50% of Hoxa9 binding sites are co-bound by C/EBPα, providing mechanistic insight into the requirement of C/EBPα for Hoxa9-mediated leukemogenesis. Additionally, genome-wide occupancy of H3K4 monomethylation and H3K27 trimethylation provide additional information on the functionality of Hoxa9/C/EBPα cobound loci.

overall_design: Examination of two transcription factor binding sites and two histone modifications in a transformed cell line.


title: MicroRNA editing in Xenopus tropicalis

city: Heidelberg

first: Maria

last: Warnefors

address: Center for Molecular Biology of Heidelberg University (ZMBH)

institute: University of Heidelberg

summary: We collected small RNA sequencing data from brain and heart of an adult Xenopus tropicalis individual to investigate the conservation of site-specific miRNA editing events identified in mammals.

overall_design: Sequencing of 2 small RNA sequencing libraries

first: Angélica

last: Liechti

first: Jean

last: Halbert

first: Delphine

last: Valloton

first: Henrik

last: Kaessmann


title: Breast Cancer RNA-seq

city: Salt Lake City

first: Katherine

last: Varley

state: UT

address: 2000 Circle of Hope, Room 3719

department: Department of Oncological Sciences

institute: Huntsman Cancer Institute University of Utah

summary: RNA-seq was performed on breast cancer cell lines and primary tumors

overall_design: RNA-seq was performed on 28 breast cancer cell lines, 42 Triple Negative Breast Cancer (TNBC) primary tumors, and 42 Estrogen Receptor Positive (ER+) and HER2 Negative Breast Cancer primary tumors, 30 uninovlved breast tissue samples that were adjacent to ER+ primary tumors, 5 breast tissue samples from reduction mammoplasty procedures performed on patients with no known cancer, and 21 uninvolved breast tissue samples that were adjacent to TNBC primary tumors.

first: Richard

last: Myers


title: The histone lysine demethylase JMJD3/KDM6B is recruited to p53 bound promoters and enhancer elements in a p53 dependent manner

city: Copenhagen

first: Kristine

last: Williams

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: The JmjC domain containing protein JMJD3/KDM6B catalyses H3K27me3 and H3K27me2 demethylation. JMJD3 appears to be highly regulated at the transcriptional level and is upregulated in response to diverse stimuli such as differentiation inducers and stress signals. Accordingly, JMJD3 has been linked to the regulation of different biological processes such as differentiation of embryonic stem cells, inflammatory responses in macrophages, and induction of cellular senescence via regulation of the INK4A-ARF locus. Here we show here that JMJD3 interacts with the tumour suppressor protein p53. We find that the interaction is dependent on the p53 tetramerization domain. Following DNA damage, JMJD3 is transcriptionally upregulated and by performing genome-wide mapping of JMJD3, we demonstrate that it binds genes involved in basic cellular processes, as well as genes regulating cell cycle, response to stress and apoptosis. Moreover, we find that JMJD3 binding sites show significant overlap with p53 bound promoters and enhancer elements. The binding of JMJD3 to p53 target sites is increased in response to DNA damage, and we demonstrate that the recruitment of JMJD3 to these sites is dependent on p53 expression. Therefore, we propose a model in which JMJD3 is recruited to p53 responsive elements via its interaction with p53 and speculate that JMJD3 could act as a fail-safe mechanism to remove low levels of H3K27me3 and H3K27me2 to allow for efficient acetylation of H3K27.

overall_design: Examination of JMJD3 and p53 genome-wide binding in untreated BJ cells or cells exposed to DNA damage (IR, 10 Gy)


title: Genome-wide nucleosome maps for wild type and Rsc8-depleted Saccharomyces cerevisiae

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

institute: NICHD, NIH

summary: Paired-end sequencing study of nucleosomes from MNase-digested nuclei.

overall_design: Nucleosomal DNA from wild type and Rsc8-depleted cells was subjected to paired-end sequencing.

first: Dwaipayan

last: Ganguli

first: Hope

middle: A

last: Cole


title: The RNA-binding protein RBM47 suppresses metastatic breast cancer progression

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

summary: Through integrative analysis of clinical breast cancer gene expression datasets, cell line models of breast cancer progression, and mutation data from cancer genome resequencing studies, we have identified RNA binding motif protein 47 (RBM47) as a candidate suppressor of breast cancer metastasis. RBM47 inhibited breast cancer progression in experimental models. Transcriptome-wide analysis of RBM47 localization by HITS-CLIP revealed widespread binding to mRNAs, preferentially at the 3' UTRs. RBM47 altered the abundance of a subset of its target mRNAs. Some of the mRNAs stabilized by RBM47, as exemplified by dickkopf WNT signaling pathway inhibitor 1 (DKK1), mediate tumor suppressive effects downstream of RBM47. This work identifies RBM47 as a suppressor of breast cancer progression and highlights the potential of global RNA modulatory events as a source of metastasis-promoting phenotypic traits.

overall_design: Cancer cells transduced with doxycycline-inducible wildtype RBM47 or the RBM47-I281fs mutant, treated with increasing concentrations of doxycycline.

first: Yilong

last: Zou

first: Joan

last: Massagué


title: Characterizing the profiles of Ebf1 in mouse fat cells (ChIP-seq)

status: Public on Jun 10 2014

city: Boston

first: Evan

last: Rosen

state: MA

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

summary: ChIP-seq data from mouse adipocyte.

overall_design: Mature 3T3-L1 adipocytes were cross-linked with 1% formaldehyde 10 days after induction with MDI. Frozen cell pellets were submitted to the Broad Institute for subsequent analysis of Ebf1-bound regions using anti-Ebf1 antibody (Abnova H00001879-M01).

first: Michael

last: Griffin

first: Yiming

last: Zhou

first: Sona

last: Kang

first: Xiaolan

last: Zhang

first: Tarjei

middle: S

last: Mikkelsen


title: Environmental factors transmitted by aryl hydrocarbon receptor influence severity of psoriatic skin inflammation

city: London

first: Gitta

last: Stockinger

address: The Ridgeway

department: Division of Molecular Immunology

institute: National Institute for Medical Research

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


title: Single cell RNA-seq of primary human glioblastomas

city: BOSTON

first: Anoop

last: Patel

address: 185 Cambridge St

department: Pathology

institute: Massachusetts General Hospital

summary: We report transcriptomes from 430 single glioblastoma cells isolated from 5 individual tumors and 102 single cells from gliomasphere cells lines generated using SMART-seq. In addition, we report population RNA-seq from the five tumors as well as RNA-seq from cell lines derived from 3 tumors (MGH26, MGH28, MGH31) cultured under serum free (GSC) and differentiated (DGC) conditions. This dataset highlights intratumoral heterogeneity with regards to the expression of de novo derived transcriptional modules and established subtype classifiers.

overall_design:
Operative specimens from five glioblastoma patients (MGH26, MGH28, MGH29, MGH30, MGH31) were acutely dissociated, depleted for CD45+ inflammatory cells and then sorted as single cells (576 samples). Population controls for each tumor were isolated by sorting 2000-10000 cells and processed in parallel (5 population control samples). Single cells from two established cell lines, GBM6 and GBM8, were also sorted as single cells (192 samples).

SMART-seq protocol was implemented to generate single cell full length transcriptomes (modified from Shalek, et al Nature 2013) and sequenced using 25 bp paired end reads. Single cell cDNA libraries for MGH30 were resequenced using 100 bp paired end reads to allow for isoform and splice junction reconstruction (96 samples, annotated MGH30L). Cells were also cultured in serum free conditions to generate gliomasphere cell lines for MGH26, MGH28, and MGH31 (GSC) which were then differentiated using 10% serum (DGC). Population RNA-seq was performed on these samples (3 GSC, 3 DGC, 6 total). The initial dataset included 875 RNA-seq libraries (576 single glioblastoma cells, 96 resequenced MGH30L, 192 single gliomasphere cells, 5 tumor population controls, 6 population libraries from GSC and DGC samples). Data was processed as described below using RSEM for quantification of gene expression. 5,948 genes with the highest composite expression either across all single cells combined (average log2(TPM)>4.5) or within a single tumor (average log2(TPM)>6 in at least one tumor) were included. Cells expressing less than 2,000 of these 5,948 genes were excluded.

The final processed dataset then included 430 primary single cell glioblastoma transcriptomes, 102 single cell transcriptomes from cell lines(GBM6,GBM8), 5 population controls (1 for each tumor), and 6 population libraries from cell lines derived from the tumors (GSC and DGC for MGH26, MGH28 and MGH31). The final matrix (GBM_data_matrix.txt) therefore contains 5948 rows (genes) quantified in 543 samples (columns).

Please note that the samples which are not included in the data processing are indicated in the sample description field.

first: Patel

last: Anoop

first: Tirosh

last: Itay


title: Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

city: Berkeley

first: Liana

middle: F

last: Lareau

state: CA

address: Barker Hall 424

department: California Institute for Quantitative Biosciences

institute: University of California, Berkeley

summary: During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA fragments reveals not only the position of each ribosome but also, unexpectedly, its particular stage of the elongation cycle. Sequencing reveals two distinct populations of ribosome footprints, 28-30 nucleotides and 20-22 nucleotides long, representing translating ribosomes in distinct states, differentially stabilized by specific elongation inhibitors. We find that the balance of small and large footprints varies by codon and is correlated with translation speed. The ability to visualize conformational changes in the ribosome during elongation, at single-codon resolution, provides a new way to study the detailed kinetics of translation and a new probe with which to identify the factors that affect each step in the elongation cycle.

overall_design: Ribosome profiling, or sequencing of ribosome-protected mRNA fragments, in yeast. We assay ribosome footprint sizes and positions in three conditions: untreated yeast (3 replicates) and yeast treated with translation inhibitors cycloheximide (2 replicates) and anisomycin (2 biological replicates, one technical replicate). We also treat yeast with 3-aminotriazole to measure the effect of limited histidine tRNAs on ribosome footprint size and distribution (two treatment durations).

first: Dustin

last: Hite

first: Gregory

last: Hogan

first: Patrick

middle: O

last: Brown


title: Discovering differentially expressed genes in early floral buds of SlREVRis overexpression line and wild type in tomato

city: Chongqing

first: Guojian

last: HU

address: No. 174 Shazhengjie, Shapingba

department: School of Life Sciences

institute: Chongqing University

summary: Versatile roles of REVOLUTA (REV), a Class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, have been mainly depicted in Arabidopsis and Populus. In this study, we investigated the functions of its tomato homolog, namely SlREV. Over-expression of a microRNA166-resistant version of SlREV (35S::REVRis) not only resulted in vegetative abnormities such as curly leaves and fasciated stems, but also caused dramatic reproductive alterations including continuous production of flowers at pedicel abscission zone (AZ) and ectopic fruit formation on receptacles. Microscopic analysis showed that meristem-like structures continuously emerged out from the exodermises of pedicel AZs and ectopic carpels formed between the first and the second whorl of floral buds in 35S::REVRis plants. Therefore, we performed Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing methodTranscriptional data to dicover differential expressed genes in early buds (1-2 mm floral buds at stage 6-8) of overexpression line SlREVRis-1. The result suggests that SlREV may regulate genes related to meristem maintenance and cell differentiation in the development of flower pedicel abscission zone, and modulate genes in homodomain and MADS-box families and hormone pathways during fruit formation. These results reveal important roles of SlREV in tomato.

overall_design: 1-2 mm floral buds at stage 6-8 were sampled from three individual plants of 35S::REVRis-1 and corresponding WT control. Three aliquots of RNA from transgenic or WT plants were pooled. Then, the digital expression profile were generated by Illumina Cluster Station and Illumina HiSeq™ 2000 System (BGI Inc.).

last: Hu

first: Jing

last: Fan

first: Zhiqiang

last: Xian

first: Wei

last: Huang

first: Dongbo

last: Lin

first: Zhengguo

last: Li


title: Environmental factors transmitted by aryl hydrocarbon receptor influence severity of psoriatic skin inflammation [RNA-Seq]

summary: Environmental stimuli are known to contribute to psoriasis pathogenesis and that of other autoimmune diseases, but the mechanism is unknown. Here we show that the aryl hydrocarbon receptor (AhR), a transcription factor that senses environmental stimuli, modulates pathology in psoriasis. AhR-activating ligands reduced inflammation in the lesional skin of psoriasis patients, whereas AhR antagonists upregulated inflammation. Similarly, AhR signaling via the endogenous FICZ ligand reduced the inflammatory response in the imiquimod-induced model of psoriasis and AhR deficient mice exhibited a substantial exacerbation of the disease, compared to AhR sufficient controls. Non-haematopoietic cells, in particular keratinocytes, were responsible for this hyper-inflammatory response, which involved increased reactivity to IL-1beta and upregulation of AP-1 family members of transcription factors. Thus, our data suggest a critical role for AhR in the regulation of inflammatory responses and open the possibility for novel therapeutic strategies in chronic inflammatory disorders.

overall_design: Total RNA obtained from skin explants taken from psoriatic patients or healthy donors cultured in the presence of AhR agonist or antagonist

first: Brigitta

first: Paola

last: Di Meglio

first: Joao

last: Duarte


title: Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli

city: Leeds

first: Kenneth

last: McDowall

address: Clarendon way

department: Faculty of biological sciences

institute: University of Leeds

summary: Here we show using RNA-seq that cleavage by RNase E direct entry pervades in both the degradation and processing of RNA. We also give further evidence that direct entry is facilitated by cooperative interaction with segments in addition to the ones in which cleavage occurs.

overall_design: RNA-seq profiles were compared between a temperature-sensitive mutant of rne and its congenic wild-type incubated at a non-permissive temperature. RNA seq profiles were also compared between samples before and after incubation with a 5'-sensing mutant of RNase E in vitro.

first: Justin

last: Clarke

first: Louise

last: Kime

first: David

last: Romero A


title: The identification of RBM47 binding sites and RBM47-dependent alternative splicing events in brain metastatic breast cancer cells

city: New York

first: Christina

last: Marney


title: GPBAR1 agonism has a broad impact on blocking macrophage activation

city: Ridgefield

first: Jonathan

middle: Daryl

last: Hill

state: CT

address: 900 Ridgebury Road

department: Computational Biology

institute: Boehringer Ingelheim Pharmaceuticals Inc

summary: Human D14+ / CD16+  monocytes were treated with GPBAR1 agonists or controls, and were stimulated with interferon gamma and LPS.  At 6 and 24 hours, the cells were profiled by RNAseq

overall_design: 40 total samples, 5 per group with eight groups.  Individual donors used for multiple comparisons, so paired analysis is possible.  Control samples include unstimulated cells, and stimulated cells treated with vehicle control (DMSO).

first: Nuruddeen

last: Lewis

first: Lori

last: Patnaude

first: Susan

last: Lukas

first: F

last: King

middle: K

last: Modis


title: Integrative DNA, RNA and protein evidence connects TREML4 to coronary artery calcification

first: Shurjo

middle: Kumar

last: Sen

address: 10 Center Drive, Room 7N317

institute: NHGRI

summary: Peripheral blood RNA-Seq from human coronary artery calcification cases and controls; Coronary artery calcification (CAC) is a heritable and definitive morphologic marker of atherosclerosis that strongly predicts risk for future cardiovascular events. To search for genes involved in CAC, we used an integrative transcriptomic, genomic, and protein expression strategy using next-generation DNA sequencing in the discovery phase with follow-up studies using traditional molecular biology and histopathology techniques.

overall_design: Eight cases and eight controls (matched for gender, age and ancestry); RNA sequencing of peripheral blood from a discovery set of eight CAC cases and eight matched controls was used to identify dysregulated genes, which were validated using the NanoString® and Affymetrix GeneChip® Human Exon ST Array platforms.  The median CAC scores for cases in the screening and validation sets were 1531.5 and 668.5, respectively, while all controls had a score of zero.


title: Comparative total RNA and mRNA sequencing and systems analysis reveals nascent transcriptional response to early HIV-1 infection in a CD4+ T cell line

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: To systematically investigate early host transcriptional response to HIV-1 infection, including polyadenylated and non-polyadenylated transcripts, we separately sequenced Total RNAs (Total RNA-seq) from HIV-1-infected SupT1 cells, a human CD4+ T cell line. We show many non-polyadenylated RNAs were also differentially expressed upon HIV-1 infection, as expected only detected by Total RNA-seq. Interestingly, we identified 8 times more differentially expressed genes at 12 hour post-infection by Total RNA-seq than by mRNA-seq, mostly protein-coding genes.

sample_organism:
Homo sapiens
Human immunodeficiency virus 1

overall_design:
6 Total RNA sample sets were sequenced. Samples were either Mock infected, HIV-1 infected, or UV-inactivated viron infected for either 12 hours or 24 hours. Each sample set contains replicates.
mRNA-seq data was processed previously and is part of a different study. It was referenced in this study. The mRNA-seq data can be found in GSE38006. This data set refers to the Whole Transcriptome data from similar samples.

first: Xinxia

last: Peng

first: Pavel

last: Sova

first: Jeffrey

last: Weiss

first: G

middle: L

last: Law

first: Robert

last: Palermo


title: Thermal plasticity of the miRNA transcriptome during Senegalese sole development

status: Public on Jun 09 2014

city: Bodø

first: Jorge

middle: M. O.

last: Fernandes

address: Stoverveien 65E

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: University of Nordland

summary:
We report the effect of incubation temperature on embryos and larvae of Solea senegalensis subjected to two different incubation temperatures (15 °C or 21 °C).
We found that at some stages, a higher incubation temperature was associated with the expression of miRNAs positively related with growth

overall_design: Examination of miRNA expression in Senegalese sole whole embryos and larvae subjected to two different incubation temperatures, using the SOLiD platform and validation by qPCR

first: Catarina

last: Campos

first: Arvind

middle: Y

last: Sundaram

first: Luísa

last: Valente

first: Luís

last: Conceição

first: Sofia

last: Engrola


title: Transcriptomic analysis of the Novel Middle East Respiratory Syndrome Coronavirus (Human, MRC5 cells)

city: Baltimore

first: David

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

summary: We will use the EMC/2012 strain of the novel beta Coronavirus called Middle East Respiratory Syndrome Coronavirus (MERS-CoV). It was initially passaged on Vero E6 cells in Saudi Arabia before being sequenced at the Erasmus Medical College in Rotterdam, Netherlands by Dr Ron Fouchier. We propose to perform a time course of infection of hCoV-EMC on MRC5 cells (Human Lung origin) and Vero cells (African Green Monkey Kidney cells). Both cell lines readily grow and replicate the virus. Importantly these cell lines show signs of Cytopathic effect (CPE), such as cell rounding and release from the petri dish that coincide with time points high virus replication demonstrating the effects of virus replication on the cells. Transcriptomic analysis will be performed after infection with MERS-CoV and SARS-CoV (Urbani strain) to compare the host gene induction that occurs during infection.

overall_design: MRC5 and Vero E6 cells will be infected at an MOI of 0.1 and 3 and RNA harvested from cells at 24 and 48 post infection. RNA will be processed for library creation and sequenced on an Illumina Hiseq. Sequencing reads will be analyzed and compared across the time course and between each virus to identify common response pathways induced during infection as well as unique pathways specific to each virus.

first: Matthew

last: Frieman

first: Chris

last: Coleman

first: Sean

middle: C

last: Daugherty

first: Kent

last: Shefchek

first: Naomi

last: Sengamalay

first: Luke

last: Tallon

first: Lisa

last: Sadzewicz

first: Claire

last: Fraser


title: Strand-specific transcriptomes of Saccharomyces cerevisiae and Saccharomyces paradoxus

city: Taipei

first: Daryi

last: Wang

address: 128 Academia Road Sec. 2, Nankang Taipei 115 Taiwan

department: Biodiversity Research Center

country: Taiwan

institute: Academia Sinica

summary:
Background: Recent studies have demonstrated that antisense transcription is pervasive in budding yeasts and is conserved between Saccharomyces cerevisiae and S. paradoxus. While studies have examined antisense transcripts of S. cerevisiae for inverse transcription in stationary phase and stress conditions, there is a lack of comprehensive analysis of the conditional specific evolutionary characteristics of antisense transcription between yeasts. Here we attempt to decipher the evolutionary relationship of antisense transcription of S. cerevisiae and S. paradoxus cultured in mid log, early stationary phase, and heat shock conditions.
Results: Massively parallel sequencing of sequence strand-specific cDNA library was performed from RNA isolated from S. cerevisiae and S. paradoxus cells at mid log, stationary phase and heat shock conditions. We performed this analysis using a stringent set of sense ORF transcripts and non-coding antisense transcripts that were expressed in all the three conditions, as well as in both species. We found the divergence of the condition specific anti-sense transcription levels is higher than that in condition specific sense transcription levels, suggesting that antisense transcription played a potential role in adapting to different conditions. Furthermore, 43% of sense-antisense pairs demonstrated inverse transcription in either stationary phase or heat shock conditions relative to the mid log conditions. In addition, a large part of sense-antisense pairs (67%), which demonstrated inverse transcription, were highly conserved between the two species. Our results were also concordant with known functional analyses from previous studies and with the evidence from mechanistic experiments of role of individual genes.
Conclusions: This study provides a comprehensive picture of the role of antisense transcription mediating sense transcription in different conditions across yeast species. We can conclude from our findings that antisense regulation could act like an on-off switch on sense regulation in different conditions.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces paradoxus

overall_design: Transcriptomes of two yeast species under mid-log phase, early stationary phase, and after heat shock treatment were generated by Illumina HiSeq 2000 paired-end sequencing

first: Krishna

middle: B

last: Swamy

first: Chih-Hsu

last: Lin

first: Ming-Ren

last: Yen

first: Chuen-Yi


title: Transcriptomic Analysis Of The Novel Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

relation:
SuperSeries of: GSE56192
SuperSeries of: GSE56193

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

overall_design: Refer to individual Series


title: The expression of mRNAs and small RNAs after prg-1 mutation

city: Beijing

first: Jiajia

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences


title: RNA expression of both host, virus and virus deletion mutants at different MOI concentrations

summary: human lung epithelial cell line infected with hRSV to measure gene expression

overall_design: 10 samples, duplicates of each condition

first: Tom

last: McCarty

first: Peter

last: Collins


title: The expression mRNAs after prg-1 mutation

summary: Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that the prg-1 mutation causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.To systematically demonstrate the function of PRG-1 on regulating small RNAs and their targets. We use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs in six stages(embryo,L1,L2,L3,L4,young audlt) and mRNAs in four stages (L1,L2,L3,L4) after prg-1 mutation. prg-1 mutation can not only lead to a decrease in the expression of 21U-RNAs, but also cause 35~40% of miRNAs to be significantly down-regulated; approximately 3% (6.00% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60~70% of these substantially changed protein-coding genes are up-regulated.

overall_design: Examination of small RNA expression in six different developmental stages (embryo, L1, L2, L3, L4, young adult) and mRNA expression in four stages (L1,L2,L3,L4) of C. elegans prg-1 mutant (wm161) .

first: Jia-Jia

first: Dong-Ya

last: Cui

first: Tengfei

last: Xiao

first: Peng

last: Zhang

first: Shunmin

last: He


title: Conservation of transcription start sites within genes across a bacterial genus

first: Wenjun

last: Shao

address: 2151 Berkeley Way

department: Molecular and Cell Biology

institute: University of California

type: Expression profiling by genome tiling array

sample_organism:
Shewanella sp. MR-4
Shewanella sp. MR-7
Shewanella sp. ANA-3
Shewanella oneidensis MR-1
Shewanella putrefaciens CN-32
Shewanella loihica PV-4
Shewanella amazonensis SB2B
Shewanella sp. W3-18-1


title: Mapping of nascent RNA upon release of DRB in WT and KD of RECQL5

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary: Global Run-On has been performed on WT or KD for RECQL5 cells after release from DRB.  When RECQL5 is knocked-down the transcriptional wave front is more advanced, suggesting that transcription is faster.

overall_design: Constitutive knock-down cell lines expressing or not endogenous levels of shRNA resistant RECQL5 under a Doxycycline inducible promoter were treated with high doses of DRB to block transcription. Upon release into fresh medium we were able to follow how much and how fast the RNA Pol II progresses through genes by mapping nascent RNA by Run-On.  The experiment was performed in two cell line clones.

first: Marco

last: Saponaro

first: Jesper

middle: Q

last: Svejstrup


title: RECQL5 Controls Transcript Elongation and Suppresses Transcription-Associated Genome Instability


title: The expression of small RNAs after prg-1 mutation


title: Genome wide profiling of RNA Polymerase II upon knock-down or overexpression of RECQL5

summary: RECQL5 globally effects the distribution of RNA Polymerase II on genes in a dose dependent manner.  Knock-down of RECQL5 reduces RNA Polymerase II density in the gene body, while increasing density on TSS and TTS.  Overexpression shows exactly the opposite effect.  We postulate that RECQL5 acts as a regulator of the elongation rate, more specifically, that the knock-down increases elongation rate while the overexpression decreases it.

overall_design: RNA Polymerase II ChIP-Seq upon knock-down of RECQL5 with either of two specific shRNAs or a CTRL shRNA, and upon Doxycycline induced overexpression of RECQL5 .


title: A Gpr120 Selective Agonist Improves Insulin Resistance and Chronic Inflammation

status: Public on Jun 07 2014

city: La Jolla

first: Roman

last: Sasik

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

summary: We report that a high affinity, selective, small molecule Gpr120 agonist (cpdA), exerts potent anti-inflammatory effects on macrophages in vitro, and in obese mice in vivo. Gpr120 agonist treatment of high fat diet (HFD)/obese mice causes improved glucose tolerance, decreased hyperinsulinemia, increased insulin sensitivity and decreased hepatic steatosis. This suggests that Gpr120 agonists could become new insulin sensitizing drugs for the treatment of Type 2 diabetes and other human insulin resistant states in the future.

overall_design: Examination of effects of DHA and compound A on primary macrophages stimulated by LPS, 3 replicates for each condition


title: Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

city: Durham

first: Christopher

last: Frank

address: 101 Science Dr.

institute: Duke University

summary: We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota. We show that regional differences in gene transcription along the intestinal tract were accompanied by major alterations in chromatin organization. Surprisingly, we discovered that microbiota modify host gene transcription in IECs without significantly impacting the accessible chromatin landscape. Instead, microbiota regulation of host gene transcription might be achieved by differential expression of specific TFs and enrichment of their binding sites in nucleosome depleted CRRs near target genes. Our results suggest that the chromatin landscape in IECs is pre-programmed by the host in a region-specific manner to permit responses to microbiota through binding of open CRRs by specific TFs.

overall_design: mRNA and accessible chromatin (DNase-seq) profiles from colonic and ileal IECs were compared between conventionally-raised (CR), germ-free (GF), and conventionalized (CV) C57BL/6 mice.

first: J

middle: G

last: Camp

first: Colin

middle: R

last: Lickwar

first: Harendra

last: Guturu

first: Tomas

last: Rube

first: Aaron

middle: M

last: Wenger

first: Jenny

last: Chen

first: Gill

last: Bejerano

first: Gregory

middle: E

last: Crawford

first: John

last: Rawls