title: Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals [RNA-seq]

summary: Background and Aims: Analysis of aging-induced impairments in satellite cells (SCs) – the stem cells of skeletal muscle that are required for its regeneration. Hox genes are known to control stem cell function and development of various tissues.

overall_design: Hindlimb muscles from young adult (3-4 months) and old (22-28 months) C57BL/6J mice were injured by BaCl2 injection in order to induce satellite cell activation. Satellite cells were isolated 3 days after injury and gene expression was analyzed.

first: Simon

last: Schwörer

first: Stefan

last: Tümpel

first: K

last: Rudolph


title: Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

status: Public on Nov 30 2016

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

country: USA

institute: University of Georgia

summary: Chromatin structure plays a pivotal role in facilitating proper control of gene expression. The ability of transcription factors (TF) to bind cis-elements is often associated with accessible chromatin regions. Therefore, identification of these accessible regions throughout plant genomes is important to understanding the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes. However, in plants, the existence of cell walls, subcellular organelles and the lack of stable cell lines have prevented routine application of this technique. Here, we describe an assay combining ATAC-seq with Fluorescence-Activated Nuclei Sorting (FANS) to identify and map open chromatin and TF-binding sites in plant genomes. FANS-ATAC-seq compares favorably with published DNaseI sequencing (DNase-seq) results and it only requires 500-50,000 nuclei for accurate identification of open chromatin states.

sample_organism:
Arabidopsis thaliana
Zea mays subsp. mays

overall_design:
Chromatin accessibility profiling (FANS-ATAC-seq) data collected from Arabidopsis 7-day old Col-0 whole seedlings, roots, 35S:H2AX-GFP/Col-0 whole seedlings, or 10-day old maize B73 overground parts. Replicates are included when available.
Please note that the *1million_reads raw data were used to generate the percentage of nuclear and organelle reads data, which is included in the associated manuscript as supplementary data table (therefore not included in the GEO records).

first: Zefu

last: Lu


title: The microRNA toolkit of insects

city: Barcelona

first: Guillem

last: Ylla

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37

country: Spain

institute: Institute of Evolutionary Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: Is there a correlation between miRNA diversity and levels of organismic complexity? Exhibiting extraordinary levels of morphological and developmental complexity, insects are the most diverse animal class on earth. Their evolutionary success was in particular shaped by the innovation of holometabolan metamorphosis in endopterygotes. Previously, miRNA evolution had been linked to morphological complexity, but astonishing variation in the currently available miRNA complements of insects made this link unclear. To address this issue, we sequenced the miRNA complement of the hemimetabolan Blattella germanica and reannotated that of two other hemimetabolan species, Locusta migratoria and Acyrthosiphon pisum, and of four holometabolan species, Apis mellifera, Tribolium castaneum, Bombyx mori and Drosophila melanogaster. Our analyses show that the variation of insect miRNAs is an artefact mainly resulting from poor sampling and inaccurate miRNA annotation, and that insects share a conserved microRNA toolkit of 65 families exhibiting very low variation. For example, the evolutionary shift toward a complete metamorphosis was accompanied only by the acquisition of three and the loss of one miRNA families.

overall_design: We sequenced the small RNA fraction for 2 control Blattella germanica specimens and 2 specimens treated with dsDicer-1.

first: Bastian

last: Fromm

first: Xavier

last: Belles

first: M

middle: D

last: Piulachs


title: Activin/Smad2-induced H3K27me3 reduction is crucial to initiate mesendoderm differentiation of ES Cells

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mesendoderm (ME) differentiation of human embryonic stem cells (hESCs) is directed by various extrinsic signals together with intrinsic epigenetic modifications.  However, the dynamics of epigenetic modifications and their regulation to initiate ME differentiation remain elusive.  In this study, we report that H3K27me3 is decreased during ME initiation, which is essential for the subsequent differentiation by collaborative effects of Activin and Wnt signaling.  Mechanistically, Activin decreases the H3K27me3 level via disruption of the SUZ12-EZH2 interaction and EZH2 degradation mediated by Smad2.  Our data suggest a two-step process of ME initiation: firstly H3K27me3-marked epigenetic priming and secondly transcription activation.  Our findings unravel a critical role of H3K27me3 priming and a direct interaction between extrinsic signals and epigenetic modifications during ME initiation.

overall_design: mRNA profile of H1-hESC and treated with Activin A, Wnt3a separately or together for 6h and 24h. Together with H3K27me3 and H3K4me3 profiles of H1-hESC and treated with Activin A, wnt3a seperately or together for 2h and 6h.

first: Lu

last: Wang

first: Jing-Dong

last: Han

first: Ye-Guang

last: Chen


title: Global analysis of truncated RNA ends reveals novel insights into ribosome stalling in plants

city: Nankang

first: Ho-Ming

state: Taipei

address: No. 128, Sec. 2, Academia Road

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

summary: High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied in the validation of cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome beyond miRNA targets is currently largely unclear which limits the application of RNA degradome. Here, we provide multiple lines of evidence to show that the plant RNA degradome contains in vivo ribosome-protected mRNA fragments. We observed a 3-nt periodicity and a bias toward the translational frame in the global analysis of 5' truncated mRNA ends mapped to the coding sequence (CDS) of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and soybean (Glycine max). In addition, predominant 5' termini of RNA degradation intermediates separated by a length equal to a ribosome-protected mRNA fragment were evident in some conserved peptide upstream open reading frames (uORFs) of Arabidopsis and rice. Through the analysis of RNA degradome data, we uncovered novel uORFs and CDS regions potentially associated with stacked ribosomes in Arabidopsis. Furthermore, the analysis of RNA degradome data suggested that the binding of Arabidopsis ARGONAUTE7 to a non-cleavable target site of miR390 might directly hinder ribosome movement. This work demonstrates an alternative use of RNA degradome data in the study of ribosome stalling.

overall_design: Profiling 5' ends of RNA degradation intermediate in Arabidopsis thaliana seedlings and inflorescences by parallel analysis  of RNA ends (PARE)

first: Cheng‐Yu

last: Hou

first: Wen‐Chi

last: Lee

first: Hsiao‐Chun

last: Chou

first: Ai‐Ping

first: Shu‐Jen

first: Ho‐Ming


title: The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions [RNA-seq]

first: Aikaterini

last: Nanou

state: Attiki

address: Soranou Efessiou 4

department: Hematology

country: Greece

institute: Biomedial Research Foundation Academy of Athens

summary: STAT5 interacts with other factors to control transcription, and the mechanism of regulation is of interest as constitutive active STAT5 has been reported in malignancies. Here LSD1 and HDAC3 were identified as novel STAT5a interacting partners in pro-B cells. Characterization of STAT5a, LSD1 and HDAC3 target genes by ChIP-seq and RNA-seq revealed gene subsets regulated by independent or combined action of the factors and LSD1/HDAC3 to play dual role in their activation or repression. Genes bound by STAT5a alone or in combination with weakly associated LSD1 or HDAC3 were enriched for the canonical STAT5a dimer motif, and such binding induced activation or repression. Strong STAT5 binding was seen more frequently in intergenic regions, which might function as distal enhancer elements. Genes bound weakly by STAT5a and strongly by LSD1/HDAC3 present a STAT5a monomer like motif, and are differentially regulated based on their biological role, genomic binding localization and affinity. STAT5a binding in monomer like motifs was found with increased frequency in promoters, indicating a requirement for stabilization by additional factors, which might recruit LSD1/HDAC3. Our study describes an interaction network of STAT5a/LSD1/HDAC3 and a dual function of LSD1/HDAC3 on STAT5-dependent transcription, defined by protein-protein interactions, genomic binding positions-affinities and motifs.

overall_design: Mouse pro-B Ba/F3 cells treated with lentiviral vectors expressing short-hairpins to knock-down various genes (STAT5a, STAT5b, LSD1 and HDAC3). All KDs were analysed versus cells treated with lentiviral construct expressing a No-Target short-hairpin at the same condition (either minus [IL3 deprivation for 6h] or plus [IL3 deprivation for 6h and IL3 stimulation for 30min]). Wild-type cells were also generated and compared between the two conditions. All samples contain biological replicates (3-5 depending on the sample).

first: Eleni

last: Katsantoni


title: Transcriptomic analysis of pancreas and kidney upon induction of reprogramming

city: Madrid

first: Lluc

last: Mosteiro

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: CNIO

summary: We profiled total mRNA of pancreas and kidney tissues of 3 different strains (p53-null; In4a/Arf-null and WT) of reprogrammable mouse lines (they all express OCT4, SOX2, KLF4, C-MYC under the control of a tetracycline promoter, activated by doxycycline)

overall_design: 5 mice of each genotype were treated with doxycycline to induce the expression of the reprogramming factors, they were sacrificed and total mRNA was extracted from pancreas and kidney tissues (we mapped >24M reads per sample)

first: Manue

last: Serrano


title: The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions [ChIP-seq]

overall_design: ChIP-seq data in mouse pro-B Ba/F3 cells of 3 different factors (STAT5a, LSD1 and HDAC3) in two different conditions (minus [IL3 deprivation for 6h] and plus [IL3 deprivation for 6h and 30min IL3 stimulation]). Two biological replicates are included per factor and condition, and one Input sample of Ba/F3 cells.


title: The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions.

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

overall_design: Refer to individual Series


title: m6A controls neurogenesis and sex determination in Drosophila via its nuclear reader protein YT521-B [RNA-Seq, S2R+ cells]

status: Public on Dec 07 2016

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

summary: N6-methyladenosine RNA (m6A) is the most abundant internal mRNA modification in mammals. While its role in the regulation of posttranscriptional gene expression is beginning to be unveiled, its function during development of complex organisms is poorly understood. Here, we identify Spenito as a novel member of the methyltransferase complex and show that m6A in Drosophila is necessary for proper synaptic growth, and in regulation of early steps of pre-mRNA splicing. Splicing of Sex-lethal and of its downstream targets are defective in animals lacking m6A, revealing also important roles in sex determination and dosage compensation. Finally, we implicate the nuclear m6A reader protein, YT521-B, as a crucial effector of m6A modifications in vivo. Altogether, our work provides important novel insights into m6A biology through identification and characterization of both m6A-writing and -reading proteins in Drosophila and their effects on splicing, neurogenesis and sex-determination within the context of the whole animal.

overall_design: RNA-Seq in S2R+ cells (7 conditions, triplicates)

first: Tina

last: Lence

first: Junaid

last: Akhtar

first: Marc

last: Bayer

first: Katharina

last: Schmid

first: Laura

last: Spindler

first: Cheuk

middle: H

last: Ho

first: Nastasja

last: Kreim

first: Miguel

middle: A

last: Andrade-Navarro

first: Burkhard

last: Poeck

first: Mark

last: Helm


title: Activation of Wnt/beta-catenin in Ewing sarcoma cells antagonizes EWS/ETS function and promotes phenotypic transition to more metastatic cell states

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

summary: Ewing sarcomas are characterized by the presence of EWS/ETS fusion genes in the absence of other recurrent genetic alterations and mechanisms of tumor heterogeneity that contribute to disease progression remain unclear. Mutations in the Wnt/beta-catenin pathway are rare in Ewing sarcoma but the Wnt pathway modulator LGR5 is often highly expressed, suggesting a potential role for the axis in tumor pathogenesis. We evaluated beta-catenin and LGR5 expression in Ewing sarcoma cell lines and tumors and noted marked intra- and inter-tumor heterogeneity. Tumors with evidence of active Wnt/beta-catenin signaling were associated with increased incidence of tumor relapse and worse overall survival. Paradoxically, RNA sequencing revealed a marked antagonism of EWS/ETS transcriptional activity in Wnt/beta-catenin activated tumor cells. Consistent with this, Wnt/beta-catenin activated cells displayed a phenotype that was reminiscent of Ewing sarcoma cells with partial EWS/ETS loss of function. Specifically, activation of Wnt/beta-catenin induced alterations to the actin cytoskeleton, acquisition of a migratory phenotype and up regulation of EWS/ETS-repressed genes. Notably, activation of Wnt/beta-catenin signaling led to marked induction of tenascin C (TNC), an established promoter of cancer metastasis, and an EWS/ETS-repressed target gene. Loss of TNC function in Ewing sarcoma cells profoundly inhibited their migratory and metastatic potential. Our studies reveal that heterogeneous activation of Wnt/beta-catenin signaling in subpopulations of tumor cells contributes to phenotypic heterogeneity and disease progression in Ewing sarcoma. Significantly, this is mediated, at least in part, by inhibition of EWS/ETS fusion protein function that results in de-repression of metastasis-associated gene programs.

overall_design: Differential gene expression in highly Wnt-responsive cells.

first: E

last: Lawlor

last: Pedersen


title: Transcriptomic analysis of the marine oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization.

city: Emeryville

first: Ankita

last: Kothari

state: CA

address: 5885 Hollis Str

institute: Lawrence Berkeley National Lab

summary: In this study we compare the transcriptome of the strain RAG-1 grown in dodecane, the corresponding alkanol, and sodium acetate for the characterization of genes involved in dodecane uptake and utilization.

sample_organism: Acinetobacter venetianus RAG-1 = CIP 110063

overall_design: RNA-seq was used to compare A. venetianus RAG-1 grown to mid log phase in the presence of either dodecane, dodecanol or sodium acetate (control condition) as the carbon source. The number of genes differentially expressed in the pairwise comparisons were studied to identify genes involved in dodecane uptake and metabolism.

first: Marimikel

last: Charrier

first: Yu-Wei

last: Wu

first: Stephanie

last: Malfatti

first: Steven

middle: W

last: Singer

first: Larry

last: Dugan

first: Aindrila

last: Mukhopadhyay


title: Dietary intake influences fertility and offspring development in zebrafish.

city: Dunedin

first: Julia

last: Horsfield

address: 58 Hanover Street

department: Department of Pathology

country: New Zealand

institute: University of Otago

summary: We report that increased nutrient availability increases breeding success and egg production. RNA-seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults.

overall_design: RNA from unfertilized eggs after two parental diets.

first: J

first: M

last: Meier

first: T

last: Newman


title: Allele-specific ATAC-seq across 16 neural progenitor cell clones

status: Public on Nov 29 2016

city: Stanford

first: Howard

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Dermatology

institute: Stanford University

summary: The two copies of a gene are canonically believed to be indistinguishable to the cell and are expressed in the same spatiotemporal manner in the absence of a loss-of-function mutation.  The mechanisms by which cells break this symmetry and express a gene from only one of the two alleles of the diploid genome are of great interest.  Monoallelic gene expression on the X-chromosome, at imprinted genes, and at olfactory receptor genes has been studied in detail and involves combinations of non-coding RNAs, DNA methylation, and histone modifications.  Recently, random monoallelic gene expression (RME), in which a gene can be expressed from either or both alleles in a clonal manner, has been described across many cell types and disease-relevant genes. However little is known about how RME is established and regulated.  Here we develop allele-specific ATAC-seq, a rapid and sensitive method for profiling active regulatory DNA allelically and genome-wide, and find that monoallelic chromatin accessibility is extensive, developmentally regulated, and epigenetically inherited. In clonal hybrid F1 murine neural progenitor cells, we find over 1800 monoallelically-accessible DNA elements across autosomes.  Randomly monoallelic regulatory elements tend to be promoter-proximal and located at RME genes identified by RNA-seq.  Following differentiation, they are highly stable across passages and bookmarked during mitosis.  Most RME genes have monoallelic promoters, but surprisingly, the nearby enhancer landscape around RME genes is biallelic.  This suggests that RME genes are regulated at the chromatin, not post-transcriptional level, and that highly localized promoter accessibility is the gatekeeper within a permissive regulatory landscape dictating monoallelic vs. biallelic expression.  These randomly monoallelic promoters are biallelically accessible in a previous developmental state, indicating that one allele is randomly shut down during NPC specification.  Furthermore, the distribution of active alleles for a subset of these randomly monoallelic regulatory elements across clones deviates from a binomial distribution, indicating a highly regulated, non-stochastic mechanism of establishment.

overall_design:
ATAC-seq was performed in mESCs and mNPCs. Libraries(2 replicates per line) were sequenced on an Illumina NextSeq (2x75bp) and data was analyzed allele-specifically.
Please note that [1] the .bed contains peaks for all NPCs. [2] Peaks for 'ESC_XX1 ATAC-seq' were previously published and also added to GEO (GSM1828645; duplicated sample record for the convenient retrieval of the complete raw data from SRA) [3] The ESC_XY2 raw sequencing reads was included in the analyses.  The peaks from this sample, however are not used and therefore not provided [4] Additional bigwigs will be provided separately as a hub with publication.

first: Ava

middle: C

last: Carter

first: Jin

last: Xu

middle: Y


title: Activation of the IGF1 pathway mediates changes in cellular contractility and motility in single-suture craniosynostosis

city: Seattle

first: Nathan

middle: J.

last: Sniadecki

state: Washington

address: Box 352600, Mechanical Engineeering

institute: University of Washington

summary: We examined the effect pg IGF1 actibation on cellular contractility and migration in SSC osteoblast cells. Based on microarray levels of IGF1 expression, we selected fifteen cases and nine controls spanning from the highest IGF1 expression to the lowest in cases and controls. Subsequently, the pattern of IGF1 expressions in these cells was assessed using high throughput RNA sequencing.

overall_design: RNA-seq based gene expression profiling of fifteen SSC osteoblasts and nine control osteoblasts.

first: Marsha

middle: M

last: Wheeler

first: Christopher

last: Frazar

first: Joshua

last: Smith


title: Gene expression analysis in a Brazilian wheat cultivar under drought

city: Passo Fundo

first: Jorge

middle: Fernando

last: Pereira

state: RS

address: Rodovia BR-285, Km 294

country: Brazil

institute: Embrapa Trigo

summary: The central part of Brazil, consisting mostly of the Cerrado Biome, is considered to be the new frontier for increasing Brazilian wheat production. However, rainfed wheat production in that area must cope with drought stress. In order to better understand the drought response, we analyzed the mRNA profiling under drought in roots and leaves of the cultivar MGS1 Aliança (a well-adapted cultivar to the Cerrado). We identified 4,422 candidate genes in roots and leaves.

overall_design: Seeds of wheat cultivar MGS1 Aliança were grown in pots in a glasshouse. Control plants were watered and grown for 5 weeks while, in the drought treatment, plants were watered for 2 weeks following 3 weeks of water deprivation. RNA extraction of pooled leaves or root tissues was carried out and four cDNA libraries (root control, root stressed, leaf control, and leaf stressed) were sequenced using Roche 454 FLX.

middle: F

first: Antonio

last: Nhani Jr

first: Gisele

last: Montan Torres

first: Luciano

last: Consoli

first: Liane

last: Balvedi Poersch-Bortolon

first: Maria

last: Bodanese-Zanettini

first: Márcia

last: Margis-Pinheiro


title: Comparative transcriptomic analyses of male and female adult Toxocara canis.

city: Rongchang

first: Guangxu

last: Ma

state: Chongqing

address: xueyuan road 160#

department: veterinary medicine

country: China

institute: Southwest university

summary: Toxocariasis is an important, neglected zoonosis caused mainly by Toxocara canis. Although our knowledge of helminth molecular biology is improving through completed draft genome projects, there is limited detailed information on the molecular biology of Toxocara species. Here, transcriptomic sequencing of male and female adult T. canis and comparative analyses were conducted. For each sex, two-thirds (66-67%) of quality-filtered reads mapped to the gene set of T. canis, and at least five reads mapped to each of 16,196 (87.1%) of all 18,596 genes, and 321 genes were specifically transcribed in female and 1467 in male T. canis. Genes differentially transcribed between the two sexes were identified, enriched biological processes and pathways linked to these genes established, and molecules associated with reproduction and development predicted. In addition, small RNA pathways involved in reproduction were characterized, but there was no evidence for piwi RNA pathways in adult T. canis. The results of this transcriptomic study should provide a useful basis to support investigations of the reproductive biology of T. canis and related nematodes.

overall_design: Using high-throughput RNA sequencing to produce the transcriptional profiles for individual male and female adult Toxocara canis; Conducting pairwise comparison on the two sexes of this parasite to indicate differentially transcribed genes and their involving biological processes and pathways.

first: Robin

middle: B

last: Gasser

first: Rongqiong

last: Zhou


title: RNA-seq of YB5 cells treated with Proscillaridin A

status: Public on Nov 28 2016

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

summary: RNA-seq was performed after YB5 cells were treated with DAC, Proscillaridin A, or the combinatino of the two

overall_design: Biological triplicates were performed for a total of 12 samples. Fold change of each gene was calculated by comparing change in expression after inhibitor treatment to expression in the control samples

first: Noel

last: Raynal

first: Elodie

last: Da Costa

first: Justin

last: Lee

first: Vazganush

last: Gharibyan

first: Saira

last: Ahmed

first: Hanghang

last: Zhang

first: Takahiro

last: Sato

first: Gabriel

last: Malouf

first: Jean-Pierre

last: Issa


title: The SND proteins constitute an alternative targeting route to the endoplasmic reticulum

city: Cambridge

first: Jonathan

middle: S

last: Weissman

state: MA

address: 455 Main St

department: HHMI, Biology

institute: Whitehead Institute for Biomedical Research, MIT

summary: In eukaryotes, up to one-third of cellular proteins are targeted to the endoplasmic reticulum, where they undergo folding, processing, sorting and trafficking to subsequent endomembrane compartments. Targeting to the endoplasmic reticulum has been shown to occur co-translationally by the signal recognition particle (SRP) pathway or post-translationally by the mammalian transmembrane recognition complex of 40 kDa (TRC40) and homologous yeast guided entry of tail-anchored proteins (GET) pathways. Despite the range of proteins that can be catered for by these two pathways, many proteins are still known to be independent of both SRP and GET, so there seems to be a critical need for an additional dedicated pathway for endoplasmic reticulum relay. We set out to uncover additional targeting proteins using unbiased high-content screening approaches. To this end, we performed a systematic visual screen using the yeast Saccharomyces cerevisiae, and uncovered three uncharacterized proteins whose loss affected targeting. We suggest that these proteins work together and demonstrate that they function in parallel with SRP and GET to target a broad range of substrates to the endoplasmic reticulum. The three proteins, which we name Snd1, Snd2 and Snd3 (for SRP-independent targeting), can synthetically compensate for the loss of both the SRP and GET pathways, and act as a backup targeting system. This explains why it has previously been difficult to demonstrate complete loss of targeting for some substrates. Our discovery thus puts in place an essential piece of the endoplasmic reticulum targeting puzzle, highlighting how the targeting apparatus of the eukaryotic cell is robust, interlinked and flexible.

overall_design: Ribosome profiling of whole cell or streptavidin-purified ribosomes biotinylated by ER localized biotin ligase in yeast

first: Naama

last: Aviram

first: Tslil

last: Ast

first: Elizabeth

last: Costa

first: Eric

last: Arakel

first: Silvia

middle: G

last: Chuartzman

first: Calvin

last: Jan

first: Sarah

last: Haßdenteufel

first: Johanna

last: Dudek

first: Martin

last: Jung

first: Stefan

last: Schorr

first: Richard

last: Zimmermann

first: Blanche

last: Schwappach

first: Maya

last: Schuldiner


title: Expression data from triple negative breast cancer cells

city: Tianjin

first: Tieju

last: Liu

state: Tianjin

address: Qixiangtai Road No.22, Heping District

department: Pathology

institute: Tianjin Medical University

summary:
Treatment of triple-negative breast cancer has been challenging and paclitaxel resistance is one of the major obstacles to the better prognosis. Misregulation of alternative splicing (AS) may contribute to tumor progression and chemotherapy resistance. Human AS factor TRA2 has two separate gene paralogs encoding TRA2A and TRA2B proteins. TRA2B is associated with cancer cell survival and therapeutic sensitivity.
We used microarrays to detail the global programme of gene expression and alternative splicing events underlying paclitaxel treatment and TRA2A upregulation and identified distinct classes of up-regulated and down-regulate genes as well as alternative splicing genes during this process.

overall_design: Breast cancer cell MDA-MB-231 was given paclitaxel treatment and exogenous TRA2A expression before RNA extraction and hybridization on Affymetrix microarrays. Then we get three groups of samples: Control, PTX (MDA-MB-231 with paclitaxel treatment), 231T (MDA-MB-231 with exogenous TRA2A expression).

first: Baocun

last: Sun


title: Parental diet affects metabolism, obesity and hypothalamic DNA methylation in Psammomys obesus

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

type: Methylation profiling by high throughput sequencing

summary: Using methyl CpG binding domain capture and deep sequencing (MBD-seq) we examined the hypothalamus of offspring of dams and bucks either provided ad libitum a standard rodent diet or a low fat diet before fertilisation and during gestation. The offspring were provided a standard rodent diet.

overall_design: Examination of the differences in DNA methylation of offspring with different paternal diets.

first: Ishant

last: Khurana

first: Antony

last: Kaspi

first: Mark

last: Ziemann

first: Timothy

last: Connor

first: Briana

last: Spolding

first: Adrian

last: Cooper

first: Paul

last: Zimmet

first: Ken

last: Walder


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Uhrf1-/- fetal liver hematopoietic stem cell (FL-HSCs) Transcriptomes

city: new york

first: Xufeng

last: Chen

state: NY

address: 550 First Avenue, Smilow 1307

institute: NYU Langone Medical Center

summary: To investigate the molecular mechanism of Uhrf1 in controlling the self-renewal versus differentiation of FL-HSCs, high-throughput sequencing was performed to analyze the transcriptomes of WT and Uhrf1-deficient FL-HSCs.Consistent with the erythroid-biased differentiation of Uhrf1-deficient FL-HSCs, genes involved in erythrocyte differentiation were significantly enriched in Uhrf1-deficient FL-HSCs according to the Gene Ontology (GO) enrichment analysis. We generated gene signatures specific for stemness of HSCs (stem signature) or myeloerythroid progenitors (MEP signature) by subtracting the genes expressed in WT HPC(LK)s from those expressed in WT FL-HSCs or vice versa. Of the stem signature genes, 71.28% showed lower expression and 28.72% showed higher expression in Uhrf1-deficient FL-HSCs compared with WT FL-HSCs. Interestingly, among the MEP signature genes, genes enriched in erythroid differentiation (27.54%) were up-regulated in the absence of Uhrf1, whereas the remaining genes enriched in myeloid-specific genes (72.46%) were suppressed consistent with previous research. Particularly, in comparison to the WT control, Uhrf1-deficient FL-HSCs up-regulated certain erythrocyte differentiation-related genes (e.g., Gata1, Gata2, Gfi1b, Car1, Zfpm1 and Itga2b), most of which were physiologically up-regulated in HPC(LK)s, whereas some genes (Id2, Satb1, Hmga2) that play critical roles in HSC maintenance were down-regulated. These results suggested that Uhrf1 controls the self-renewal versus differentiation of FL-HSCs by suppressing the expression of the erythroid-specific genes and maintaining the expression of HSC stemness genes.

overall_design: FL-HSCs(LSKs) (approximately10,000 cells) were isolated from WT and Uhrf1-/- fetal livers by cell sorting (double sort, purity > 95%). RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Libraries were generated for sequencing using the TruSeq RNA sample preparation kit (Illumina). Libraries were sequenced using an Illumina HiSeq 2500 sequencer.Three independent experiments were performed.

first: Jingyao

last: Zhao

first: Xiaolong


title: Age-Related Gene Expression Changes in Prostate Cancer Patients [miRNA-Seq]

city: Duarte

first: Susan

last: Neuhausen

state: California

address: 1500 E duarte road

department: Population Sciences

institute: City of hope

summary: Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

overall_design: Gleason-score matched tumor and adjacent normal samples were collected to compare gene expression differences in early-onset versus late-onset prostate cancer patients

first: Yuan

last: Ding


title: Single-cell spatial reconstruction reveals global division of labor in the mammalian liver

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

summary: The mammalian liver consists of hexagonal-shaped lobules, radially polarized by blood flow and morphogens. Key liver genes have been shown to be differentially expressed along the lobule axis, a phenomenon termed zonation, but a detailed genome-wide reconstruction of this spatial division of labor has not been achieved. Here we measure the whole transcriptome of thousands of single mouse liver cells and infer their lobule coordinates using a panel of zonated landmark genes, characterized with single-molecule FISH. We obtain a genome-wide reconstruction of liver zonation profiles with unprecedented spatial resolution. We find that more than 50% of liver genes are significantly zonated and uncover abundant non-monotonic profiles that peak at the mid-lobule layers. Our approach can facilitate reconstruction of similar spatial genomic blueprints for other mammalian organs.

overall_design: mRNA profiles from single cells extracted from mouse liver were generated by deep sequencing of 1736 of single cells, sequenced in several batches in an Illumina NextSeq.

first: Shalev

last: Itzkovitz

first: Ido

last: Amit

last: Bahar Halpern

first: Orit

last: Matcovitch

first: Rom

last: Shenhav

first: Beata

last: Toth

first: Doron

last: Lemze

first: Shanie

last: Landen

first: Amir

last: Giladi

first: Matan

last: Golan

first: Shaked

last: Baydatch

first: Avigail

last: Stokar Avihail

first: Eyal

last: David

first: Alexander

last: Brandis

first: Efi

middle: E

last: Massasa

first: Andreas

last: Moor


title: RNA-seq analyses of ID4-EGFP+ undifferentiated spermatogonia and sorted subpopulations.

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

summary: P6 ID4-EGFP+ undifferentiated spermatogonia, including those stained robustly (high) or weakly (low) for TSPAN8 were isolated by FACS.

overall_design: Three replicate preparations of each population were used for independent RNA-seq using SMART-seq v4, Nextera XT libraries, Hiseq2500 sequencing, and TopHat/Bowtie/Cufflinks analyses.

first: Kazadi

last: Mutoji

first: Anukriti

last: Singh

first: Heidi

last: Gildersleeve

first: John

last: McCarrey


title: Gene expression profile of  Dnmt1 flox/flox, Dnmt3a flox/flox, Dnmt3b flox/flox, cre negative (Wild type) and Dnmt1 flox/flox, Dnmt3a flox/flox, Dnmt3b flox/flox, Rx-cre (Triple mutant) murine retina transcriptomes

city: Pittsburgh

first: Igor

last: Nasonkin

state: Pennsylvania

address: 200 Lothrop street

institute: University of Pittsburgh

summary:
Purpose: The goal of this study was to identify the gene expression profile of mouse retina which carries deletions in Dnmt1, Dnmt3a and Dnmt3b genes.
Method: Retinal mRNA profiles of Postnatal day 15 wild type mice and Dnmt1, Dnmt3a and Dnmt3b mutant mice were generated by deep-sequencing

overall_design: Retinal mRNA profiles of post natal day 15 wild type and mutant mice with Illumina HiSeq 2500

first: Ramya

last: Mallela


title: Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

city: Pretoria

first: Stanford

last: Kwenda

state: Gauteng

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

country: South Africa

institute: University of Pretoria

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

overall_design: Refer to individual Series


title: DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

summary: A subset of genomically silent childhood posterior fossa ependymomas show reduced H3K27me3, global DNA hypomethylation, are more invasive, exhibit poor prognosis and epigenetically deregulated genes converge on radial glial factors, suggesting developing cerebellar radial glia as candidate cells-of-origin.

overall_design: Quantification of CpG methylation in 3 ependymoma subtypes

first: Sriram

last: Venneti


title: Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes

city: St. Louis

first: Jeffrey

last: Gordon

state: MO

address: 4515 McKinley Research Building

department: Center for Genome Sciences & Systems Biology

institute: Washington University

summary: The gut microbiota impacts many aspects of host biology including immune function. One hypothesis is that microbial communities induce epigenetic changes with accompanying alterations in chromatin accessibility, providing a mechanism that allows a community to have sustained host effects even in the face of its structural or functional variation. We used ATAC-seq to define chromatin accessibility in predicted enhancer regions of intestinal αβ+ and γδ+ intraepithelial lymphocytes (IELs) purified from germ-free mice, their conventionally-raised (CONV-R) counterparts, and mice reared GF and then colonized with a CONV-R gut microbiota at the end of the suckling-weaning transition. Characterizing genes adjacent to traditional enhancers and super-enhancers revealed signaling networks, metabolic pathways, and enhancer-associated transcription factors affected by the microbiota. Our results support the notion that epigenetic modifications help define microbial community-affiliated functional features of host immune cell lineages.

overall_design: We interrogated chromatin accessibility using ATAC-seq in four cell types derived from mice (CD4+ T cells, CD8+ T cells, αβ+ intraepithelial lymphocytes, and γδ+ intraepithelial lymphocytes), across three gut microbial colonization states (germ-free, conventionally-raised, and conventionalized).

middle: I

first: Nicholas

middle: P

last: Semenkovich


title: Definition of the Ras/ERK signal induced chromatin modification at target gene promoters [RNA-seq & ChIP-seq]

city: London

first: Francesco

last: Gualdrini

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick Institute

summary: Ras plays roles across the spectrum of proliferation, invasion and metastasis. The activity of Ras genes, usually K-Ras, is altered by mutations in around 20% of human cancers, and activation of the Ras-ERK pathway is a critical event in melanomas, colorectal and renal cancers but the degree to which Ras- or Raf-driven transformation is dependent on the activity of the SRF network remains largely obscure.   Oncogenic active Ras is known to mediate the cellular response to multiple growth factors leading to the activation of immediate-early genes (IE). A key player in IE gene response is the SRF transcriptional network that we identified being crucial to mediate allegedly the entire transcriptional response downstream of Ras/ERK. The Serum response factor (SRF) is a transcription factor with low intrinsic transcriptional activity and requires the recruitment of one of two families of co-activators: the MRTFs (myocardin-related transcription factors) and the TCFs (ternary complex factors, Elk-1, SAP-1, Net). In particular the TCF, member of the wide family of ETS transcription factors, are specifically activated by MAPK signalling downstream of Ras.  We characterised the transcriptional program downstream of Ras/ERK signalling using short TPA stimulations (12-O-tetradecanoyl phorbol-13-acetate, compunt known to induced Ras/ERK activation) by RNA-seq.    The investigation of the transcriptional response was performed using Mouse Embryonic Fibroblasts (MEFs) derived from different animals: (i) wild type, (ii) TKO (MEFs derived from mice lacking all three TCFs), (iiI) TKO recon pMY Empty (TKO reconstituted with empty vectors by retrovirus infection), (iv) TKO recon Elk-1 wt (TKO reconstituted with retrovirus vectors expressing Elk-1 wild type by retrovirus infection), (v) TKO recon Elk-1 FW (TKO reconstituted with retrovirus vectors expressing Elk-1 mutant lacking the FW residues in its activation domain), (vi) TKO recon Elk-1 nonA (TKO reconstituted with retrovirus vectors expressing Elk-1 mutant where all phosphor-acceptor residues in its activation domain have been mutagenized to alanines).  In order to map SRF and Elk-1 binding sites we performed ChIP-seq of SRF in wild type MEFs and TKO and ChIP-seq of Elk-1 in TKO reconstituted cell lines.

overall_design: Chromatin immunoprecipitation (ChIP-seq) in Mouse Embryonic Fibroblasts (MEFs) derived from wild type mice (MEF WT) or animals lacking all three TCFs (TCF KO) after TPA (12-O-tetradecanoyl phorbol-13-acetate)  using antibodies against SRF (G-20 Lot: D3013 Santa Cruz). In addition the distribution of Elk-1 (in house antibody raised against Elk-1 activation domain able to recognise it regardless of the integrity of the phopsho-acceptor sites) have been assessed in TCF KO cells reconstituted with Elk-1 (one of the member of the TCF factos) variants: (i) TKO recon pMY Empty (TKO reconstituted with empty vectors by retrovirus infection), (ii) TKO recon Elk-1 wt (TKO reconstituted with retrovirus vectors expressing Elk-1 wild type by retrovirus infection), (iii) TKO recon Elk-1 FW (TKO reconstituted with retrovirus vectors expressing Elk-1 mutant lacking the FW residues in its activation domain), (iv) TKO recon Elk-1 nonA (TKO reconstituted with retrovirus vectors expressing Elk-1 mutant where all phosphor-acceptor residues in its activation domain have been mutagenized to alanines).   We performed strand specific total-RNA-seq following DSN normalisation and validation by qRT-PCR from the various cellular backgrounds: (i) wild type, (ii) TKO (MEFs derived from mice lacking all three TCFs), (iiI) TKO recon pMY Empty (TKO reconstituted with empty vectors by retrovirus infection), (iv) TKO recon Elk-1 wt (TKO reconstituted with retrovirus vectors expressing Elk-1 wild type by retrovirus infection), (v) TKO recon Elk-1 FW (TKO reconstituted with retrovirus vectors expressing Elk-1 mutant lacking the FW residues in its activation domain), (vi) TKO recon Elk-1 nonA (TKO reconstituted with retrovirus vectors expressing Elk-1 mutant where all phosphor-acceptor residues in its activation domain have been mutagenized to alanines). Each RNA-seq sample has been normalised/standardised to a set of  invariant genes across all the condition and background used. The selection of such set was performed using mixed-model distribution of the residuals between samples as genes not changing should present a distribution of the variation approximately normally distributed.

first: Gualdrini

last: Francesco

first: Cyril

last: Esnault

first: Stuart

last: Horswell

first: Phil

last: East

first: Gavin

last: Kelly

first: Aengus

last: Stewart

first: Nik

last: Matthews

first: Richard

last: Treisman


title: Conserved local hypomethylation control during the bacterial cell cycle and by superimposed environmental cues

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

institute: University of Geneva

summary: Heritable DNA methylation imprints occur in most genomes and underlie genetic variability in humans. The mechanism and consequences of establishing and propagating local hypomethylation through consecutive rounds of DNA replication and intermittent cell division cycles are poorly understood. Our genome-wide and site-specific methyl-N6-adenine (m6A-) analyses reveal a conserved local hypomethylation mechanism in two α-proteobacterial model systems. We show that MucR, a DNA-binding protein that uses an ancestral zinc-finger fold to control expression of virulence and cell cycle genes, competes with the cell cycle-regulated adenine-methyltransferase CcrM for target sites in S-phase, but not in G1-phase. Constitutive expression of CcrM or heterologous methylases during the cell cycle homogenizes m6A patterns even when MucR is present and controls transcription. We also find that environmental responses can impose methylation remodelling at certain sites, while the conserved cell cycle circuitry imposes systemic constraints on when local hypomethylation is instated.

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

overall_design: 4 ChIPseq samples in synchronized C. crescentus cells, SMRT methylation profiles of Wild type and ∆mucR1 ∆mucR2 cells, 6 RECseq samples in Wildtype C. crescentus, E. coli, S. meliloti, V. cholera El Tor and in mucR1 mutants of C. crescentus and S. meliloti.

first: Silvia

last: Ardissone

first: Peter

last: Redder

first: Giancarlo

last: Russo

first: Coaralie

last: Fumeaux

first: Andrea

last: Patrignani

first: Ralph

last: Schlapbach

first: Patrick

last: Viollier


title: Next Generation Sequencing Facilitates Quantitative Analysis of Sensory Neurons Transcriptomes in response to Trophic Withdrawal

status: Public on Nov 25 2016

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to uncover the changes in the transcriptome of sensory neurons in response to trophic withdrawal

overall_design: Methods:  mRNA profiles of sensory neurons in response to trophic withdrawal were generated by deep sequencing using Illumina GAIIx. Seven independent replicates of RNA purification from each condition were collected and pooled for each time point.

first: Maya

last: Maor-Nof

first: Avraham

last: Yaron


title: Molecular Mechanisms of Endothelial Hyperpermeability

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

summary: Vascular permeability reflects changes in the function of the endothelium,  its interendothelial junctions and transcellular delivery. Here, we show that common molecular mechanisms exist between VEGF and histamine in regulating  vascular hyperpermeability. Crosstalk between downstream signaling of VEGF and histamine receptors are involved in calcium signaling and cell proliferation. Understanding the molecular mechanisms of vascular permeability is crucial in order to reduce vascular hyperpermeability and oedema in various pathological conditions and in VEGF therapy.

overall_design: In despite of the substantial knowledge of VEGF and histamine signal transduction and their physiological responses, molecular mechanisms inducing endothelial cell permeability and proliferation have remained inconclusive. To monitor the transcriptional alteration of proteins known to regulate the endothelial permeability, next-generation RNA sequencing was used. Fold changes of several genes known to regulate calcium signaling, cell adhesion, cell proliferation, ion flux and immune response were compared between the permeabilizing agents.

first: Johanna

last: Laakkonen


title: Deletion of Histone Deacetylase 3 in Adult Beta Cells Improves Glucose Tolerance via Increased Insulin Secretion

status: Public on Nov 26 2016

city: Boston

first: Manashree

last: Damle

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

summary: Objective: Histone deacetylases are epigenetic regulators known to control gene transcription in various tissues. A member of this family, histone deacetylase 3 (HDAC3), has been shown to regulate metabolic genes. Cell culture studies with HDAC-specific inhibitors and siRNA suggest that HDAC3 plays a role in pancreatic β-cell function, but a recent genetic study in mice has been contradictory. Here we address the functional role of HDAC3 in β-cells of adult mice.    Methods: An HDAC3 β-cell specific knockout was generated in adult MIP-CreERT transgenic mice using the Cre-loxP system. Induction of HDAC3 deletion was initiated at 8 weeks of age with administration of tamoxifen in corn oil (2 mg/day for 5 days). Mice were assayed for glucose tolerance, glucose-stimulated insulin secretion, and islet function 2 weeks after induction of the knockout. Transcriptional functions of HDAC3 were assessed by ChIP-seq as well as RNA-seq comparing control and -cell knockout islets.   Results: HDAC3 β-cell specific knockout (HDAC3βKO) did not increase total pancreatic insulin content or β-cell mass. However, HDAC3βKO mice demonstrated markedly improved glucose tolerance. This improved glucose metabolism coincided with increased basal and glucose-stimulated insulin secretion in vivo as well as in isolated islets. Cistromic and transcriptomic analyses of pancreatic islets revealed that HDAC3 regulates multiple genes that contribute to glucose-stimulated insulin secretion.   Conclusions: HDAC3 plays an important role in regulating insulin secretion in vivo and therapeutic intervention may improve glucose homeostasis.

overall_design: Genomic occupancy profiled by high throughput sequencing (ChIP-seq) from mouse islets for HDAC3 (3 control and 3 KO, and corresponding inputs); and transcriptome profiling through RNA-seq of control mouse islets and those lacking histone deacetylase 3 (two separate experiments, n=3 an n=5)

first: Jarrett

middle: R

last: Remsberg

first: Mitch

last: Lazar


title: RNA sequencing of  C57BL/6NJ (B6NJ) x C57BL/6J (B6J) - F2 mice

city: Medford

first: Eric

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

summary: RNA-seq analysis of 16 B6J x B6NJ-F2 mice which are homozygous for either the wild-type B6J allele (binge-resistant; J/J) or mutant B6NJ allele (binge-prone; N/N), at rs240617401, a marker denoting a missense SNP in Cyfip2.  Genotype identity is denoted as either J for binge-resistant; J/J, or N for binge-prone; N/N.

overall_design: A sample size of N=8 per genotype was employed (4 females, 4 males; 69-100 days old at the time of sacrifice). Striatum punches were harvested on Day 24 immediately following the 5-min behavioral test on the EPM, stored in RNAlater for 48 h, blotted dry with a kimwipe, and transferred to -80ºC. Total RNA was isolated and shipped to the University of Chicago Genomics Core Facility for cDNA library preparation using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (50 bp single-end reads). Samples were sequenced using the Illumina HiSeq 4000 with 16 samples per lane over four lanes (technical quadruplicates). FASTQ files were quality checked via FASTQC and all samples exhibited Phred quality scores greater than 30 (i.e. less than 0.1% sequencing error). FASTQ files were used to align reads to the reference genome using TopHat (mm10; UCSC Genome Browser). Read counts per gene were quantified using the HTSeq Python package.

first: Stacey

last: Kirkpatrick

first: Camron

last: Bryant


title: H3K4me3 involvement in long-term effects of sulfomethoxazole on Caenorhabditis elegans over 11 consecutive generations and their first non-exposed progeny

status: Public on Nov 24 2016

city: Shanghai

first: Zhenyang

last: Yu

state: Shanghai

address: Siping Rd 1239

department: College of Environmental Science and Engeering

institute: Tongji University

summary: Caenorhabditis elegans, a free-living nematode, were exposed to sulfomethaxozale (SMX) for 11 consecutive generations. The F11 nematodes and their first non-exposed progeny (F14’) went through chromatin immune-precipitation at H3K4me3 site and a subsequent DNA-sequencing. Results showed that F11 and F14’ nematodes had 3-fold more H3K4me3 biding genes than the control. These genes showed the highest enrichment in the promoter region with 42.11% and 73.72% in F11 and F14’ nematodes, respectively, indicating increased activity of their regulated genes. In F11 nematodes, the genes regulating metabolic and biosynthetic processes of phospholipid, glycerolipid and glycerophospholipid were significantly activated with a mean enrichment fold change of 50.57. The genes regulating nervous system and development were also activated with a mean enrichment fold change of 65.03 and 58.14, respectively. In F14’ nematodes, 96 and 67 genes showed up- and down-regulations compared with those in F11 nematodes. In the up-regulation, genes regulating development, reproduction and transmembrane transport showed mean enrichment fold changes of 2.52, 22.41 and 34.47, respectively. The down-regulated genes were also related with development, reproduction and transmembrane activities with mean enrichment fold changes ranging from 1.51 to 8.32. Our findings demonstrated the epigenetic involvement in the SMX trans-generational effects.

first: Jing

last: Zhang


title: Transcriptome profiling of HEK 293T Dicer -/- cells with or without VP55

city: New York

first: Benjamin

last: tenOever

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

summary: To assess the impact of VP55 expression on cells already lacking endogenous miRNAs

overall_design: HEK 293T Dicer -/- (NoDice) cells transfected with either pEGFP or pEGFP-VP55 for 24 hrs


title: Massive dysregulation of genes involved in cell signaling and placental development in cloned cattle conceptus and maternal endometrium

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: A major unresolved issue in the cloning of mammals by somatic cell nuclear transfer (SCNT) is the mechanism by which the process fails after embryos are transferred to the uterus of recipients, prior to or during the implantation window. We investigated this problem by using RNA-seq to compare the transcriptomes in cattle conceptuses produced by SCNT and artificial insemination (AI) at d18 (pre-implantation) and d34 (post-implantation) of gestation. In addition, endometrium was profiled in order to identify the communication pathways that might be affected by the presence of a cloned conceptus, ultimately leading to mortality prior to or during the implantation window. At d18, the effects on the transcriptome associated with SCNT were massive, involving more than 5,000 differentially expressed genes (DEGs). Among them are 121 genes that have embryonic lethal phenotypes in mice, cause defects in trophoblast and placental development, and/or affect conceptus survival in mice. In endometria at d18, <0.4% of expressed genes were affected by the presence of a cloned conceptus, whereas at d34, ~36% and <0.7% of genes were differentially expressed in intercaruncular and caruncular tissues, respectively. Functional analysis of DEGs in placental and endometrial tissues suggests a major disruption of signaling between the cloned conceptus and the endometrium, particularly the intercaruncular tissue. Our results support a bottleneck model for cloned conceptus survival during the peri-implantation period determined by gene expression levels in extra-embryonic tissues and the endometrial response to altered signaling from clones.

overall_design: polyA+ mRNA profiles of 14 samples of day 18 extra-embryonic tissue, 12 samples of day 34 CHO, 9 samples of day 34 ALL, 14 samples of day 18 endometrial CAR, 14 samples of day 18 endometrial ICAR, 12 samples of day 34 endometrial CAR, and 12 samples of day 34 endometrial ICAR

first: Harris

middle: A

last: Lewin


title: Aberrant transcriptional networks in neurogenesis of Paroxysmal Kinesigenic Dyskinesia-induced pluripotent stem cell lines though neural induction method of dual inhibition of SMAD signaling

first: Kunshan

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

summary: Paroxysmal kinesigenic dyskinesia (PKD) is an episodic movement disorder with autosomal-dominant inheritance and marked variability in clinical manifestations.Proline-rich transmembrane protein 2 (PRRT2) has been identified as a causative gene of PKD, but the molecular mechanism underlying the pathogenesis of PKD still remains a mystery. The phenotypes and transcriptional patterns of the PKD disease need further clarification. Here, we report the generation and neural differentiation of iPSC lines from two familial PKD patients with c.487C>T (p. Gln163X) and c.573dupT (p. Gly192Trpfs*8) PRRT2 mutations, respectively. Notably, an extremely lower efficiency in neural conversion from PKD-iPSCs than control-iPSCs is observed by using the iPSC-neural differentiation protocol that relies on the dual inhibition of SMAD signaling. Moreover, we show the high expression level of PRRT2 throughout the human brain and the expression pattern of PRRT2 in other human tissues for the first time. To gain molecular insight into the development of the disease, we conduct global gene expression profiling of PKD cells at four different stages of neural induction and identify altered gene expression patterns, which peculiarly reflect dysregulated neural transcriptome signatures and a differentiation tendency to mesodermal development, in comparison to control-iPSCs. Additionally, functional and signaling pathway analyses indicate significantly different cell fate determination between PKD-iPSCs and controls-iPSCs. Together, the establishment of PKD-specific in vitro models and the illustration of transcriptome features in PKD cells would certainly help us with better understanding of the defects in neural conversion as well as further investigations in the pathogenesis of the PKD disease.

overall_design: RNA-Seq of 16 cell samples derived from different neural differentiation stages of PKD-iPSCs and 7 cell samples from that of normal iPSCs

first: Chun

last: Li

first: Yu

last: Ma

first: Junjie

last: Gu

first: Fan

last: Tang

first: Shengdi

last: Chen

first: Li

last: Cao

first: Siguang

first: Ying

last: Jin


title: Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis

city: Stockholm

first: Klementy

last: Shchetynsky

state: Stockholm

address: CMM L8:04 Karolinska University Hospital Solna

department: Medicine, Solna

country: Sweden

institute: Karolinska Institutet

summary:
Purpose: The goal of the study was to integrate verified signals from previous genetic association studies with gene expression and pathway analysis for discovery of new candidate genes and signalling networks, relevant for rheumatoid arthritis (RA).
Method:RNA-seq based expression analysis of 377 genes from previously verified RA-associated loci was performed in blood cells from 5 newly diagnosed, non-treated RA patients, 7 patients with treated RA and 12 healthy controls. Differentially expressed genes sharing a similar expression pattern in treated and untreated RA sub-groups were selected for pathway analysis. A set of “connector” genes derived from pathway analysis was then tested for differential expression in the initial discovery cohort.
Results: 11 qualifying genes were selected for pathway analysis and grouped into 2 evidence-based functional networks, containing 29 and 27 additional “connector” molecules.  The expression of genes, corresponding to connector molecules was then tested in the initial RNA-seq data. 3 genes showed similar expression difference in both treated and non-treated RA patients and additional nine genes were differentially expressed in at least one patients’ group compared to healthy controls.
Conclusion: Integration of RNA-seq data with findings from association studies, and consequent pathway analysis implicate new candidate genes in the pathogenesis of RA.

overall_design: Illumina RNA-seq was performed on RNA from pereferial blood mononuclear cells taken from 12 healthy individuals, 5 untreated RA patients, and 7 treated RA patients

first: Lina

middle: D

last: Gallo

first: Leonid

last: Padyukov


title: Expression profile of TRAMP-C1 cell line with PAX8-NFE2L2 overexpression

city: Göteborg

first: Erik

last: Larsson Lekholm

address: Box 440

department: Institute of biomedicine

institute: University of Gothenburg

summary: We synthesized the PAX8-NFE2L2 fusion transcript and cloned it into a lentiviral vector, and used this to overexpress it in the murine prostate adenocarcinoma cell line TRAMP-C1.

overall_design: We used high coverage RNA sequencing (>30 million reads per sample) to compare the expression profiles of cells expressing the PAX8-NFE2L2 fusion transcript to cells transduced with an empty vector.

last: Larsson

first: Babak

last: Alaei-mahabadi

first: Joydeep

last: Bhadury

first: Jonas

last: Nilsson

first: Joakim

middle: W

last: Karlsson


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ppr10 deletion  Schizosaccharomyces pombe cell Transcriptomes

status: Public on Nov 23 2016

city: Nanjing

last: Huang

address: 1 wenyuan rd

institute: Nanjing Normal University

summary: The goals of this study are to compare Wild Type and ppr10 deletion Schizosaccharomyces pombe cell Transcriptomes and to find the cause of cell apoptosis.

overall_design: Cell mRNA profiles of logarithmic phase wild-type (WT) and ppr10 deletion Schizosaccharomyces pombe cells were generated by deep sequencing, using Illumina His4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.The goals of this study is to  find the cause of cell apoptosis.


title: Aggf1 regulates the activation of hepatic stellate cells

first: Bisheng

last: Zhou

state: Jiangsu

address: 140 Hanzhong Rd

department: Department of Pathophysiology

institute: Nanjing Medical University

summary: Digital gene expression profiling was used to invesigate the differetiated genes between primary mouse hepatic stellate cells infected with AGGF1 adenovirus particles or negative control adenovirus pairticles.

overall_design: Primary hepatic stellate cells isolated from mice were cultured in vitro, infected with AGGF1 adenovirus particles or negative control adenovirus particles, at day 8, total RNA were prepared and used for digital gene expression tag profiling.


title: Comparative transcriptome analysis reveals genes regulating myogenesis and adipogenesis in Laiwu pigs over four developmental stages

city: Taian

first: Yuding

last: Wang

address: No. 61, Daizong Street

institute: Shandong Agricultural University

summary: We performed transcriptome analysis of the longissimus dorsi (LD) muscle during four development stages (60, 120, 240 and 400 days after birth) in Laiwu pigs, an indigenous fatty pig breed in North China. This study provides a reference for exploring transcriptome regulation mechanisms affecting muscle growth and development in obese pigs.

overall_design: Examination of  transcriptional variation over four different development stages in Laiwu pig.

first: Cai

last: Ma

first: Yi

last: Sun

last: Kang

first: Yunliang

last: Jiang


title: Identification and profiling of microRNAs in two developmental stages of the model cestode parasite Mesocestoides corti

city: Porto Alegre

first: Tatiana

middle: N

last: Basika

state: Rio Grande do Sul

address: Av. Bento Gonçalves 9500, Prédios 43421/43431 - Setor IV

department: Centro de Biotecnologia

institute: Universidade Federal do Rio Grande do Sul

summary: MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in fundamental biological processes such as metabolism and development. The particular developmental characteristics of cestode parasites highlight the importance of studying miRNA gene regulation in these organisms. Here, we performed a comprehensive analysis of miRNAs in two developmental stages of the model cestode Mesocestoides corti. Using a high-throughput sequencing approach, we found transcriptional evidence of 42 miRNA loci in tetrathyridia larvae and strobilated worms. Tetrathyridium and strobilated worm-specific miRNAs were found, as well as differentialy expressed miRNAs between these developmental stages, suggesting miRNA regulation of stage-specific features. Moreover, it was shown that uridylation is a differential mechanism of post-transcriptional modification of M. corti miRNAs. The whole set of M. corti miRNAs represent 33 unique miRNA families, and confirm the remarkable loss of conserved miRNA families within platyhelminth parasites, reflecting their relatively low morphological complexity and high adaptation to parasitism. Overall, the presented results provide a valuable platform to studies aiming to identify and characterize novel miRNA-based molecular mechanisms of post-transcriptional gene regulation in cestodes, necessary for the elucidation of developmental aspects of the complex biology of these parasites.

overall_design: Small RNA libraries from tetrathyridia (TT) and strobilated worm (ST) of M. corti were sequenced using Illumina technology. For each sample type, three libraries were constructed from three independent samples in order to have biological replicates.

first: Natalia

last: Macchiaroli

first: Marcela

last: Cucher

first: Sergio

last: Espínola

first: Laura

last: Kamenetzky

first: Arnaldo

last: Zaha

first: Mara

last: Rosenzvit

first: Ferreira

last: Henrique


title: Canalization of gene expression is a major signature of regulatory cold adaptation in temperate "Drosophila melanogaster"

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

country: Germany

institute: University of Munich

summary: Transcriptome analysis may provide means to investigate the underlying genetic causes of shared and divergent phenotypes in different populations and help to identify potential targets of adaptive evolution. Applying RNA sequencing to whole male Drosophila melanogaster from the ancestral tropical African environment and a very recently colonized cold-temperate European environment at both standard laboratory conditions and following a cold shock, we seek to uncover the transcriptional basis of cold adaptation.  In both the ancestral and the derived populations, the predominant characteristic of the cold shock response is the swift and massive upregulation of heat shock proteins and other chaperones. Although we find ~30% of the genome to be differentially expressed following a cold shock, only relatively few genes (n=26) are up- or down-regulated in a population-specific way. Intriguingly, 24 of these 26 genes show a greater degree of differential expression in the African population. Likewise, there is an excess of genes with particularly strong cold-induced changes in expression in Africa on a genome-wide scale.   The analysis of the transcriptional cold shock response most prominently reveals an upregulation of components of a general stress response, which is conserved over many taxa and triggered by a plethora of stressors. Despite the overall response being fairly similar in both populations, there is a definite excess of genes with a strong cold-induced fold-change in Africa. This is consistent with a detrimental deregulation or an overshooting stress response. Thus, the canalization of European gene expression might be responsible for the increased cold tolerance of European flies.

overall_design: mRNA profiles of whole Drosophila melanogaster adult males from a Africa (4 lines) and Europe (4 lines) during a 7h cold shock experiment. Samples include room temperature controls, 3.5h into the cold shock, 15 minutes after recovery and 90 minutes after recovery. 2 biological replicates each.

first: Korbinian

last: von Heckel

first: Wolfgang

last: Stephan


title: RNA-sequencing analysis in human glioma stem cell

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

summary: Glioblastomas show heterogeneous histological features. These distinct phenotypic states are thought to be associated with the presence of glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells that have different functional characteristics. To investigate Glioblastomas (GBMs) show heterogeneous histological features. These distinct phenotypic states are thought to be originated by the glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells. Notch signaling has been shown to be important for maintenance of GSC population both in vitro and in vivo. A recent study showed that NOTCH -triggered oncogenic activity can be due to not only its ability to regulate coding genes but also long non-coding RNAs (lncRNAs). Here, we investigated the molecular effects of lncRNA in GSC, whose expression is induced by Notch signaling. We searched for downregulated lncRNAs in GSCs by treatment of small interfering RNA (siRNA) targeting Notch1 and JAG1 (si-Notch1 and si-JAG1).

overall_design: Profiles of gene expression including lncRNA in GSC were generated by RNA-seq.

first: Atsushi

last: Natsume

first: Fumiharu

last: Ohka

first: Keiko

last: Shinjo

first: Akira

last: Hatanaka

first: Norihisa

last: Ichimura

first: Yutaka

last: Kondo


title: Engineered human pluripotent stem cell-derived intestinal tissues with a functional enteric nervous system

city: Cincinnati

first: Michael

last: Helmrath

state: OH

address: 3333 Burnet Avenue

department: CuSTOM

institute: Cincinnati Children's Hospital Medical Center

summary: The enteric nervous system (ENS) of the gastrointestinal (GI) tract controls many diverse functions including motility and epithelial permeability. Perturbations in ENS development or function are common, yet a human model to study ENS-intestinal biology is lacking. We have used a tissue engineering approach with pluripotent stem cells (PSCs) to generate human intestinal tissue containing a functional ENS. We recapitulated normal intestinal ENS development by combining PSC-derived neural crest cells (NCCs) with developing human intestinal organoids (HIOs). When cultured alone, NCCs had full differentiation potential in vitro, however when recombined with HIOs they differentiated into neurons and glial cells. NCC-derived ENS neurons self-assembled within the developing intestinal mesenchyme and exhibited neuronal activity as measured by rhythmic waves of calcium transients. ENS-containing HIOs grown in vivo formed neuroglial structures similar to a myenteric and submucosal plexus, formed interstitial cells of Cajal, and had an electro-mechanical coupling that regulated waves of propagating contraction. This is the first demonstration of a human PSC-derived intestinal tissue with a functional ENS.

overall_design: We examined 4 conditions (3 replicates per condition) of HIO in vitro that include mRNA profiles of HIO (Control); HIO with NCCs (HIOs+ENS); HIO with PHOX2B-/+ NCCs (HIO+ENS_Phox2b_Het); HIO with PHOX2B-/- NCCs (HIO+ENS_Phox2b_Homo). Samples were sequenced using Illumina TruSeq RNA sample prep kit.

first: Stephen

last: Trisno

middle: M

last: Workman

first: Maxime

last: Mahe

first: James

last: Wells


title: MLL-AF4 binds directly to a BCL-2 specific enhancer and impacts H3K27 acetylation

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital

department: Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine

summary: Survival rates for children diagnosed with acute lymphoblastic leukemia (ALL) have drastically improved, but those carrying mutations in the Mixed Lineage Leukemia (MLL) gene continue to have a very poor prognosis. The most common MLL mutation in ALL is the t(4;11)(q21;q23) chromosome translocation that fuses MLL in frame with the AF4 gene producing MLL-AF4 and AF4-MLL fusion proteins. Previously, we showed that MLL-AF4 binds to the BCL-2 gene and directly activates it through DOT1L recruitment and increased H3K79me2/3 levels. We went on to show that MLL leukemias are particularly sensitive to treatment with the BCL-2 inhibitor venetoclax which synergizes with both standard chemotherapeutic agents as well as DOT1L inhibitors. Altered expression of other BCL-2 family members is a major cause of resistance to ventoclax, so here we perform a detalied analysis of MLL-AF4 regulation of the entire BCL-2 family. By measuring nascent RNA production, we find that of all the BCL-2 family genes, MLL-AF4 directly controls the transcription of both BCL-2 and MCL-1, but only BCL-2 shows a significant loss of steady state RNA levels. Interestingly however, both MCL-1 and BCL-XL protein levels are dependent on MLL-AF4 activity through an unknown and likely indirect mechanism. Finally, we analyze MLL-AF4 regulation of the BCL-2 gene in greater detail and using Capture C we identify a major BCL-2 specific enhancer consisting of two clusters of H3K27Ac. Loss of MLL-AF4 activity results in a reduction of H2K27Ac levels at the major BCL-2 enhancer, revealing a novel regulatory dependence on MLL-AF4 function at BCL-2.

overall_design: Examination of MLL-AF4-mediated regulation at BCL2-family genes using nascent RNA-seq to observe gene expression changes following siRNA-mediated knockdown and treatment with the DOT1L inhibitor EPZ-5676. We also investigated changes in histone mark occupancy at the BCL2 promoter and enhancer following siRNA-mediated knockdown of MLL-AF4

first: Jon

last: Kerry


title: Transcriptome analysis of Drosophila melanogaster third instar larval ring glands points to novel functions and uncovers a cytochrome p450 required for development

status: Public on Nov 27 2016

city: Parkville

first: Trent

last: Perry

state: Victoria

address: 30 Flemington Road

department: Biosciences

institute: The University of Melbourne

summary: In Drosophila melanogaster larvae the ring gland is a control center that orchestrates major developmental transitions. It is a composite organ, consisting of the prothoracic gland, the corpus allatum and the corpora cardiaca, each of which synthesizes and secretes a different hormone. Until now, the ring gland’s broader developmental roles beyond endocrine secretion have not been explored. RNA sequencing and analysis of a new transcriptome resource from D. melanogaster wandering third instar larval ring glands has provided a fascinating insight into the diversity of developmental signalling in this organ. We have found strong enrichment of expression of two gene pathways not previously associated with the ring gland: immune response and fatty acid metabolism. We have also uncovered strong expression for many uncharacterized genes. Additionally, RNA interference against ring gland-enriched cytochrome p450s Cyp6u1 and Cyp6g2 produced a lethal ecdysone deficiency and a juvenile hormone deficiency respectively, flagging a critical role for these genes in hormone synthesis. This transcriptome provides a valuable new resource for investigation of roles played by the ring gland in governing insect development.

overall_design: Investigation of genome-wide expression in the third instar larval ring gland of two strains: Celera and Armenia-14. Three biological replicates were examined. For differential expression analysis, duplicate RNA-seq reads for the third instar larval central nervous system were obtained from the modMINE database (accession: SRX029398) [i.e., third-party re-analysis].

first: Danielle

last: Christesen

first: Ying Ting

last: Yang

first: Jason

last: Somers

first: Charles

last: Robin

first: Tamar

last: Sztal

first: Philip

last: Batterham


title: Transcriptomic response to different biomass in Myceliophthora thermophila (Sporotrichum thermophile)

city: Montreal

first: Ian

last: Reid

state: QC

address: 7141 Sherbrooke West

department: Biology

country: Canada

institute: Concordia University

summary: The thermophilic filamentous fungi Myceliophthora thermophila (Sporotrichum thermophile) has an ability to decompose cellulolytic biomass. To identify the genes and proteins involved in this process, we explored the transcriptomes of M. thermophila grown at 45 °C on different agricultural straws (oat, triticale, canola, flax straws).

overall_design: RNA was extracted from M. thermophila cultures in early growth stage growing with oat, triticale, canola and flax straws as carbon source at 45C

first: Adrian

last: Tsang

first: Magdalena

last: Kolbusz

first: Marcos

last: di Falco

first: Nadeeza

last: Ishmael

first: Sandrine

last: Marqueteau

first: Marie-Claude

last: Moisan

first: Cassio

last: da Silva Baptista

first: Justin

last: Powlowski


title: Instructive role of MLL fusion proteins revealed by a faithful model of t(4;11) proB acute lymphoblastic leukemia

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: The t(4;11)(q21;q23) fuses MLL to AF4, the most common MLL fusion partner. Here we show that MLL fused to murine Af4, highly conserved with human AF4, produces high-titer retrovirus permitting efficient transduction of human CD34+ cells to generate a faithful model of t(4;11) proB ALL that fully recapitulates the immunophenotypic and molecular aspects of the disease. MLL-Af4 induces a distinct B-ALL from MLL-AF9 through differential DNA binding of the fusion proteins leading to specific gene expression patterns. MLL-Af4 cells can assume a myeloid state under environmental pressure but retain lymphoid-lineage potential. We observed this incongruity in t(4;11) patients who evaded CD19-directed therapy by undergoing myeloid-lineage switch. Our model provides a valuable tool to unravel the pathogenesis of MLL-AF4 leukemogenesis.

overall_design: MLL-AF4 ChIP-seq expreiment has been used in this study

first: Shan

last: Lin

first: Roger

middle: T

last: Luo

first: Anetta

last: Ptasinska

first: Jon

last: Kerry

first: Mark

last: Wunderlich

first: Toshihiko

last: Imamura

first: Joseph

middle: J

last: Kaberlein

first: Ahmad

last: Rayes

last: Althoff

first: John

last: Anastasi

first: Maureen

last: O’Brien

first: Ruhi

last: Meetei

first: Thomas

last: Milne

first: Constanze

last: Bonifer

first: James

middle: C

last: Mulloy

first: Michael

last: Thirman


title: Forward genetic screens in zebrafish identify novel molecular pathways regulating early T cell development

city: Freiburg im Breisgau

last: Boehm

address: Stübeweg 51

department: Immunology

institute: MPI-IE Freiburg

summary: Lymphocytes represent basic components of vertebrate adaptive immune systems, suggesting the utility of non-mammalian models to define the molecular basis of their development and differentiation. Our forward genetic screens in zebrafish for recessive mutations affecting early T cell development revealed several major genetic pathways. The identification of lineage-specific transcription factors and specific components of cytokine signaling and DNA replication/repair pathways known from studies of immuno-compromised mammals provided an evolutionary cross-validation of the screen design. Unexpectedly, however, certain pre-mRNA processing factor genes, including tnpo3, encoding a regulator of alternative splicing, were also found to play a specific role in early T cell development. In both zebrafish and mouse, TNPO3 deficiency impairs intrathymic T cell differentiation, illustrating evolutionarily conserved and cell type-specific functions of certain pre-mRNA processing factor.

overall_design: Taking advantage of the apparent evolutionary conservation of lymphocyte-based immunity, we conducted genetic screens in zebrafish aimed at identifying novel regulators of T lymphocyte development. Apart from mutations in genes encoding lymphoid lineage-specific transcription factors, and components of cytokine signaling and DNA replication/repair pathways, mutations in genes encoding pre-mRNA processing factors were also found. To examine the molecular consequences, transcriptome analyses were conducted for three mutants, snapc3, lsm8, tnpo3.

first: Norimasa

last: Iwanami

first: Katarzyna

middle: O

last: Sikora


title: The long non-coding RNA GAS5 differentially regulates cell cycle arrest and apoptosis in human neuroblastoma

city: Orlando

last: Mazar

state: FL

address: 13535 Nemours Parkway

department: Research

country: USA

institute: Nemours Children's Hospital

summary: Comparison of the global transcriptional profiles of the neurblastoma cell line IMR-32 48 hours after transfection with a Negative Control siRNA compared to an siRNA for the lncRNA GAS5.

overall_design: MYCN-amplified Neuroblastoma cells were being examined for the global transcriptional effect of the loss of the lncRNA GAS5 in connection to recognized phenotypes associated with cell cycle control, proliferation, and apoptosis.


title: Repo-Man/PP1 regulates heterochromatin formation in interphase

first: Silvia

last: Salatino

address: Roosevelt Drive

institute: Wellcome Centre for Human Genetics

summary: Repo-Man chromatin binding sites were obtained by expression of GST:Repo-Man and incubation with nucleosomes extracted from HeLa cells (GST alone signal was used as a negative control and subtracted from the GST:Repo-Man chromatin bound fraction)

overall_design: Two replicates were produced for GST:Repo-Man and GST alone bound nucleosomes

first: Ines

last: de Castro

last: Budzak

first: Maria

middle: L

last: Di Giacinto

first: Lorena

last: Ligammari

first: Ezgi

last: Gokhan

first: Christos

last: Spanos

first: Daniela

last: Moralli

first: Christine

last: Richardson

first: Jose

last: de las Heras

first: Eric

last: Shirmer

first: Katharine

last: Ullman

first: Wendy

last: Bickmore

first: Catherine

last: Green

first: Juri

last: Rappsilber

first: Sarah

last: Lamble

first: Martin

last: Goldberg

first: Veronica

last: Vinciotti

first: Paola

last: Vagnarelli


title: Chemical Mapping Reveals Novel Features of The Nucleosome Landscape in Mouse Embryonic Stem Cells

city: Evanston

first: Liqun

last: Xi

state: IL

address: 2006 Sheridan Road

department: Statistics

institute: Northwestern University

summary: Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. Using this strategy, we uncover surprising new features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites. We show that a subset of DNA-binding proteins including insulator CTCF and pluripotency factors co-occupy DNA targets with nucleosomes. Furthermore, we provide in vivo evidence that promoter-proximal nucleosomes, with the +1 nucleosome in particular, contribute to the pausing of RNA Polymerase II. Lastly, we find a characteristic preference for nucleosomes at exon-intron junctions. Altogether, we establish an accurate method for defining the nucleosome landscape, and provide a valuable resource for studying nucleosome-mediated gene regulation in mammalian cells.

overall_design: 5 samples total. Chemical sample was analyzed with high throughput paired-end parallel sequencing.  MNase samples were analyzed with high throughput paired-end parallel sequencing. 4 RNA samples from mouse ES cells (H4S47C Chemical vs WT) treated with 2i or Lif culture conditions.

first: Lilien

last: Voong

first: Amy

last: Sebeson

first: Bin

last: Xiong

first: Jiping

last: Wang

first: Xiaozhong


title: Single cell RNAseq of meningeal cortical cells

city: Heidelberg

first: Ana

last: Martin-Villalba

state: Deutschland

address: Im Neuenheimer Feld 280

department: Molekulare Neurobiologie (A290)

institute: German Cancer Research Center (DKFZ)

summary: Heterogeneity of meningeal cortical cells was deciphered on the molecular level using single cell RNA seq

overall_design: RNA sequencing of 179 meningeal cortical cells isolated from naive wild-type mice

first: Enric

last: Llorens-Bobadilla

first: Sheng

last: Zhao

first: Mieke

last: Dewerchin

first: Peter

last: Carmeliet


title: Multivalent histone and DNA engagement by a PHD/BRD/PWWP triple reader cassette recruits ZMYND8 to K14ac-rich chromatin

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

summary:
Elucidation of interactions involving DNA and histone
post-translational-modifications (PTMs) is essential for providing
insight into complex biological functions. Reader assemblies connected
via flexible linkages facilitate avidity and increase affinity,
however little is known of the contribution to the recognition process
of multiple PTMs due to rigidity in the absence of conformational
flexibility. We report here the high resolution crystal structure of
the triple-reader module (PHD-Bromo-PWWP) of ZMYND8 which forms a
stable unit capable of simultaneously recognizing multiple histone
PTMs, while presenting a charged platform for association with DNA.
Single domain disruptions destroy the functional network of
interactions initiated by ZMYND8, impairing recruitment to sites of
DNA damage. Our data establish proof-of-principle that rigidity can be
compensated by concomitant DNA and histone PTM interactions,
maintaining multivalent engagement of transient chromatin states, thus
identifying an important underappreciated role for rigid multivalent
reader modules in nucleosome binding and chromatin function.

overall_design: Investigation of the genome-wide occupancy of ZMYND8 using H3K27ac as a landmark of enhancer regions, as well as the putative histone mark H3K14ac recognized by ZMYND8

first: Chen-Yi

first: Anastasia

last: Samsonova

first: Panagis

last: Filippakopoulos


title: Hepatic gene expression co-regulated by diet-microbiota interactions (19 wk)

city: Madison

first: John

middle: M.

last: Denu

state: Wisconsin

address: 330 N. Orchard Street

department: Biomolecular Chemistry

institute: University of Wisconsin-Madison

summary: Abstract: Histones are small proteins that form the core of nucleosomes, around which eukaryotic DNA wraps to ultimately form the highly organized and compressed structure known as chromatin. The N-terminal tails of histones are highly modified, and the modification state of these proteins dictates whether chromatin is permissive or repressive to processes that require physical access to DNA, including transcription and DNA replication and repair. The enzymes that add and remove histone modifications are known to be exquisitely sensitive to endogenous small molecule metabolite availability. In this manner, chromatin can adapt to changes in environment, particularly diet-induced metabolic state. Importantly, gut microbiota contribute to robust host metabolic phenotypes, and produce a myriad of metabolites that are detectable in host circulation. Further, gut microbial community composition and metabolite production are regulated by host diet, as a major source of carbon and energy for the microbiota. While prior studies have reported robust host metabolic associations with gut microbiota, the mechanisms therein remain largely unknown. Here we demonstrate that microbial colonization regulates global histone acetylation and methylation in multiple host tissues including colon, adipose tissue, and liver. This regulatory relationship is altered by diet: a “Western-type” diet leads to a general suppression of the microbiota-dependent chromatin changes observed in a polysaccharide rich diet. Finally, we demonstrate that supplementation of germ-free mice with major products of gut bacterial fermentation (i.e., short-chain fatty acids acetate, propionate, and butyrate) is sufficient to recapitulate many of the effects of colonization on host epigenetic states. These findings have profound implications for understanding the complex functional interactions between diet, gut microbiota, and host health.

overall_design: 15 samples in total (biological n=3 per for each of 5 conditions; 19kw old male C57BL/6J mouse liver): (1) GF mouse liver on chow diet, (2) ConvR mouse liver on chow diet, (3) ConvD mouse liver on chow diet, (4) GF mouse liver on HF/HS diet, (5) ConvR mouse liver on HF/HS diet

first: Federico

middle: E

last: Rey


title: Hepatic gene expression co-regulated by diet-microbiota interactions (14 wk)

overall_design: 9 samples in total (biological n=3 per for each of 3 conditions; 14kw old male C57BL/6J mouse liver): (1) GF mouse liver on chow diet, (2) ConvD mouse liver on chow diet, (3) GF mouse liver on chow diet + supplemented drinking water with short chain fatty acids


title: Knockdown of ADNP in HCT116 colon cancer cells

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

summary: RNASeq data from replicates after siRNA mediated knockdown of human ADNP in HCT116 colon cancer cells

overall_design: 3 biological replicates of cells treated with siADNP or siControl

first: Cristina

last: Blaj

first: Helmut

last: Blum

first: David

last: Horst


title: Identification and characterization of potato long noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection [Strand-specific RNA-seq]

city: Pretoria

first: Stanford

last: Kwenda

address: Lunnon Road, Hilcrest

department: Microbiology and Plant Pathology Forestry and Agricultural Biotechnology Institute (FABI)

institute: University of Pretoria

summary: Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation of gene expression, both in mammals and plants. While much progress has been made in determining the biological functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the roles of lncRNAs in plant defense responses are yet to be fully explored. Here, we used strand-specific RNA sequencing to identify 1649 lncRNAs in potato (Solanum tuberosum) from stem tissues. The lncRNAs are expressed from all 12 potato chromosomes and generally smaller in size compared to protein-coding genes. Like in other plants, most potato lncRNAs (86%) are transcribed from intergenic regions and possess single exons. A time-course RNA-seq analysis between a tolerant and susceptible potato cultivar challenged with Pectobacterium carotovorum subsp. brasilience revealed that 227 of these lncRNAs could be associated with response to this pathogen. These results suggest that lncRNAs have potential functional roles in potato defense responses. This work provides the foundation for further functional studies in understanding potato defense mechanisms.

overall_design: Strand-specific RNA-seq analysis of two potato cultivars, Solanum tuberosum cv. Valor (susceptible) and S. tuberosum cv BP1 (tolerant)

first: Paul

last: Birch

first: Lucy

last: Moleleki


title: RNA-seq of zebrafish melanoma cells after metastatic dissemination

city: New York

first: Richard

middle: Mark

last: White

state: NY

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: We report how the zebrafish melanoma cell line ZMEL1 changes after intravascular injection into 2dpf zebrafish embryos, as compared to the cells growing in vitro.

overall_design: Examination of ZMEL1 cells in vitro versus ~21 days in vivo in the zebrafish

first: Isabella

last: Kim


title: MicroRNA sequencing of umbilical cord mesenchymal stem cells (uMSCs) and HEK293T cells derived exosomes

city: Shanghai

first: Chen

last: Xu

address: No, 800, Rd. Xiangyin

institute: The Second Military Medical University

summary: Exosomes are cell-derived vesicles that were found in many biological fluids such as blood, urine, and cultured medium. Exosomes are small vesicles (approximately 100nm in diameter) that contain many functional molecules like cytokines, receptors and regulating RNAs. In this study, we found that uMSC-derived exosomes accelerates wound healing and reduce myoblast formation in vivo. In vitro study showed uMSC-exosomes specific microRNAs take major roles in inhibiting myoblast differentiation of fibroblast. MicroRNA sequencing of both uMSC- and HEK293T-derived exosomes revealed significant differences between these exosomes. Further infomatic and functional analysis showed that uMSC-exosomes specific microRNA-21, -23,-145, and -125b can target different components of TGF-β signaling which attenuates the expression of α-SMA in fibroblasts, thus inhibiting myoblast differentiation

overall_design: Exosomes were collected form cell culture medium by serial centrifugation and ultracentrifugation.

first: Shuo

last: Fang


title: CHO-S transcriptome in batch culture

city: La Jolla

first: Nathan

last: Lewis

state: CA

address: 9500 Gilman Dr. MC 0760

institute: UCSD

summary: Transcriptomic data from CHO-S cells were gathered from multiple time points during batch culture to provide information about gene presence/absence for generation of a CHO-S cell line specific model using the GIMME algorithm.

overall_design: CHO-S cells were grown in batch culture (n=4), samples were taken every 12 hours between t=72 and t=180h for sequencing.

first: Hooman

last: Hefzi

first: Shangzhong

last: Li

first: Johnny

last: Arnsdorf

first: Karen

middle: K

last: Brøndum

first: Zulfiya

last: Sukhova

first: Bjørn

middle: G

last: Voldborg


title: High-throughput RNA-sequencing analysis in human glioma stem cell

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

institute: Nagoya City University Graduate School of Medical Sciences

summary: Glioblastomas show heterogeneous histological features. These distinct phenotypic states are thought to be associated with the presence of glioma stem cells (GSCs), which are highly tumorigenic and self-renewing sub-population of tumor cells that have different functional characteristics. To investigate gene expression including lncRNA (long non-coding RNA) in GSC, we have performed high-throughput RNA-sequencing (RNA-seq) experiment using Illumina GAIIx.

overall_design: Profiles of gene expression including lncRNA in GSC were generated by RNA-seq using Illumina GAIIx.

first: Atsushi

last: Natsume

first: Fumiharu

last: Ohka

first: Keiko

last: Shinjo

first: Akira

last: Hatanaka

first: Norihisa

last: Ichimura

first: Yasushi

last: Totoki

first: Tatsuhiro

last: Shibata

first: Shinya

last: Sato

first: Satoru

last: Takahashi

first: Yutaka

last: Kondo


title: RNA-seq profiling of Hoxa2/Hoxb2 mutants versus wild type in Math1 positive cells from the Cochlear Nucleus

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

summary: Differential gene expression was analyzed for FACS sorted Math1::Cre; ROSA-tdTomato from hand dissected cochlear nuclei of wild type and Hoxa2/Hoxb2 mutant mice

overall_design: In order to investigate the role of Hoxa2 and Hoxb2 transcription factors in a subset of cells of the cochlear nucleus, we generated double conditional knock-out by crossing the deleter line Math1::Cre crossed with Rosa tdTomato; Hoxa2fl/fl; Hoxb2fl/fl and Rosa tdTomato wild type background. FACS sorted cells from hand dissected cochlear nuclei were than processed and RNA-seq performed (see extract protocol and library construction protocol).

first: Alberto

last: Loche

first: Kajari

last: Karmakar

first: Filippo

last: Rijli

first: Stephane

last: Thiry