title: Identifying markers predicting successful graft outcome for clinical translation of hESC-based cell therapy for Parkinson’s disease

first: Malin

last: Parmar

address: BMC A11

institute: Wallenberg Neuroscience Center, and Lund Stem Cell Centre, Department of Experimental Medical Science, Lund University

summary: Stem cell treatments for neurodegenerative diseases are expected to reach clinical  trials soon. Most of the approaches currently under development involve  transplantation of immature progenitors that subsequently undergo phenotypic and  functional maturation in vivo, and predicting the long term graft outcome already at the  progenitor stage remains a challenge. Here, we took an unbiased approach to identify  predictive markers expressed in dopamine neuron progenitors that correlate with graft  outcome in an animal model of Parkinson's disease through gene expression analysis  of >30 batches of grafted hESC-derived progenitors. We found that many of the  commonly-used markers did not accurately predict in vivo subtype-specific maturation.  Instead, we identified a specific set of markers associated with the caudal midbrain that  correlate with high dopaminergic yield after transplantation in vivo. Using these  markers, we developed a GMP differentiation protocol for highly efficient and  reproducible production of transplantable dopamine progenitors from hESCs.

overall_design: H9 hESCs were differentiated in different batches towards ventral midbrain (VM) progenitors, and were grafted to the rat brain. Based on graft outcome, the batches were divided into two groups: DA-high and DA-low. The batch names listed here correspond to the batch names listed in Kirkeby et al (2016), Table S1. Sequencing libraries were prepared from isolated RNA from each of the batches of differentiated hESCs using the Smart-Seq2 protocol  (Picelli et al. Nature Methods 2013)

first: Agnete

last: Kirkeby

first: Katarina

last: Tiklova


title: CDK4 phosphorylation status and a linked gene expression profile predict sensitivity to Palbociclib [lines]

status: Public on Jan 01 2017

city: Brussels

first: Eric

middle: Stephane

last: Raspe

address: 808, route de Lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

summary:
Cyclin D-CDK4/6 are the first CDK complexes to be activated in G1 phase in response to oncogenic pathways. The specific CDK4/6 inhibitor PD0332991 (Palbociclib) was recently approved by the FDA to treat advanced ER+ breast tumors. Unfortunately, reliable predictive tools are lacking to identify potentially responsive or insensitive tumors. We have shown that the activating T172 phosphorylation of CDK4 is the central rate-limiting event that initiates the cell cycle decision and signals the presence of active CDK4. Here, we found that, in breast cancer cell lines, the CDK4 T172 phosphorylation best correlates with the sensitivity to PD0332991. Moreover, the modification profile of CDK4 differs among breast tumors and it associates with their subtypes and risk. A gene expression signature faithfully predicted CDK4 modification profiles in tumors and cell lines. This surrogate biomarker identifies tumors that are unlikely to respond to CDK4/6 inhibitors and could allow extending the indication of the drug to HER-2 positive and some basal-like tumors.
Predictive tools to identify breast cancer patients sensitive to Pfizer's new drug targeting CDK4/6 are lacking. We correlated the sensitivity of breast cancer cell lines to the drug to their post-translational modification profile of CDK4 revealed by 2D SDS/poly-acrylamide gel electrophoresis followed by CDK4 immuno-detection and their gene expression profiles. we revealed that breast tumors display similar CDK4 post-translational modification profiles as cell lines and that a gene expression profile can be used to predict the CDK4 post-translational modification profile of a tumor or cell line and thereby its sensitivity to CDK4 inhibitor

overall_design: 20 breast cell lines (10 basal, 7 HER2+, 3 Lum) were acquired at the ATCC. RNA was profiled using the Affymetrix HG-U133 Plus 2.0 chips while protein extracts were resolved by 2D SDS-PAGE and probed with anti CDK4 antibody. Gene expression profiles were compared to proteomic profiles to associate the CDK4 modification status to gene expression levels. The Affymetrix microarray data were normalized using fRMA. This submission represents the gene expression component of the study only. No replicate, no reference sample.

last: Raspé

first: Katia

last: Coulonval

first: Jaime

middle: M

last: Pita

first: Sabine

last: Paternot

first: Françoise

last: Rothé

first: Sylvain

last: Brohée

first: Ligia

last: Craciun

first: Denis

last: Larsimont

first: Martine

last: Piccart

first: Michail

last: Ignatiadis

first: Christos

last: Sotiriou

first: Pierre

middle: P

last: Roger


title: CDK4 phosphorylation status and a linked gene expression profile predict sensitivity to Palbociclib

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

overall_design: Refer to individual Series


title: CDK4 phosphorylation status and a linked gene expression profile predict sensitivity to Palbociclib [tumors]

overall_design: 31 tumors representing the different molecular subtypes [triple negative (ER-/PgR-/HER2-); HER2 positive (HER2+); luminal A (ER+/HER2-/histological grade 1), luminal B (ER+/HER2-/histological grade 3)] were obtained from patients recruited between 2007 and 2015 at the Institut Jules Bordet. RNA was profiled using the Affymetrix HG-U133 Plus 2.0 chips while protein extracts were resolved by 2D SDS-PAGE and probed with anti CDK4 antibody. Gene expression profiles were compared to proteomic profiles to associate the CDK4 modification status to gene expression levels. The Affymetrix microarray data were normalized using fRMA. This submission represents the gene expression component of the study only. No replicate, no reference sample.


title: Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

country: USA

institute: Rutgers University

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing


title: Comparison of Pax6 alpha enhancer Cre-Rblox/lox retinas to Pax6 alpha enhancer Cre-Rblox/lox TET-MYCN retinas at PND12

city: Seattle

first: David

last: MacPherson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: The most frequent focal alterations in human retinoblastoma are RB mutation and MYCN amplification. Whether MYCN overexpression drives retinoblastoma has not been assessed in model systems. Here, we show that Rb inactivation collaborates strongly with MYCN overexpression to lead to retinoblastoma in mice. MYCN overexpression in the context of Rb inactivation increased the expression of MYC, E2F and ribosome related gene sets, promoted excessive proliferation and led to retinoblastoma with anaplastic changes. Part of our study compares expression profiles in Rbnull vs Rbnull/MYCN overexpressing retinas collected at 12 days after birth.

overall_design: 4 samples of Rb null retina were compared to 4 samples of Rbnull MYCN overexpressing retina, dissected from PND12 peripheral retinas of Pax6alpha-enhancer-Cre;Rblox/lox or Pax6alpha-enhancer-Cre Rosa26LSL-RTTA;TRE-MYCN mice

last: Wu


title: Extracellular Matrix Proteolysis by MT1-MMP is Associated with Influenza-Related Mortality

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: The balance between protecting tissue integrity and efficient immune response is critical for host survival. Here we investigate the role of extracellular matrix (ECM) proteolysis in achieving this balance in the lung during influenza virus infection using a combined genomic and proteomic approach. We followed the transcriptional dynamics and ECM- related responses in a mouse model of influenza virus infection, integrated with whole tissue imaging and functional assays. Our study identifies MT1-MMP as a prominent host-ECM-remodeling collagenase in influenza virus infection. We show that selective inhibition of MT1-MMP-driven ECM proteolysis protects the tissue from infection-related structural and compositional damage. Inhibition of MT1-MMP did not significantly alter the immune response or cytokine expression, indicating its dominant role in ECM remodeling. We demonstrate that the available treatment for influenza virus (Tamiflu/ Oseltamivir) does not prevent lung ECM damage and is less effective than anti-MT1-MMP treatment in influenza virus and Streptococcus pneumoniae coinfection paradigms. Importantly, combination therapy of Tamiflu with anti-MT1-MMP shows a strong synergistic effect and results in complete recovery in mice. This study highlights the importance of tissue tolerance agents for surviving infectious diseases, and the potential of such host-pathogen therapy combination for respiratory infections.

overall_design: Overall 8 samples were included, in duplicates, both infected and non-infected control cells were includeda. Both MT1-MMP positive and MT1-MMP negative were tested were non-infectdd, MT1-MMP negative cells served as controls.

first: Dalit

middle: T

last: Frank

first: Zeev

last: Altboum

first: Inna

last: Solomonov

first: Yael

last: Udi

first: Diego

middle: A

last: Jaitin

first: Mordehay

last: Klepfish

first: Eyal

last: David

first: Alina

last: Zhuravlev

first: Hadas

middle: K

last: Shaul

first: Deborah

middle: R

last: Winter

first: Irit

middle: G

last: Viks

first: Michal

last: Mandelboim

first: Tamar

last: Ziv

last: Sagi


title: Derivation and functional annotation of hematopoietic subpopulations from single-cell DNA methylation data

city: Vancouver

first: Martin

last: Hirst

state: BC

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

type: Methylation profiling by high throughput sequencing

summary: We report the development of a bisulfite based whole genome protocol suitable for use on single index sorted primary mammalian cells. Application of this protocol to murine and human hematopoietic stem cells provided quantitative DNA methylation measurements of up to 5.7 million CpGs in a single cell. To analyze the resulting datasets we developed a novel analytical approach designed to detect differences at single CpG resolution and identified epigenetically distinct subpopulations within the highly purified and functionally defined stem and progenitor populations.  In silico merging of the methylation states from the single cells residing in each subpopulation allowed us to ascribe functional pathways to these epigenetically distinct subpopulations on the basis of their unique epigenetic states.

overall_design: Single-cell DNA methylation analysis of the heterogeneity within murine primary hematopoetic stem and progenitor cell popluations

first: Tony

last: Hui


title: Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans [pre-mRNA-seq]

first: Sam

last: Gu

summary: Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to the H3K9 trimethylation (H3K9me3) response and transcriptional repression of target genes. The H3K9me3 response induced either by exogenous dsRNA or endogenous siRNA (endo-siRNA) is highly specific to the target loci and transgenerationally heritable. Despite these features, the role of H3K9me3 in transcriptional repression and heritable gene silencing at native target genes has not been tested. To resolve this gap, we first determined that the combined activities of three H3K9 histone methyltransferases (HMTs), MET-2, SET-25, and SET-32, are responsible for virtually all of the detectable level of germline nuclear RNAi-dependent H3K9me3 at native genes, triggered either by exogenous dsRNA or endo-siRNAs. By performing RNA Polymerase II ChIP-seq and pre-mRNA-seq analyses, we found that the loss of the H3K9me3 response at germline nuclear RNAi targets in the met-2;set-25;set-32 mutant does not lead to any defect in transcriptional repression or heritable RNAi. Therefore, H3K9me3 is not required for exogenous dsRNA-induced heritable RNAi or the maintenance of endo siRNA-mediated transcriptional silencing in C. elegans germline.  This study provides a unique paradigm in which transcriptional silencing and heterochromatin, triggered by the same upstream pathway, can be decoupled.

overall_design: In this study we tested if RNAi-mediated H3K9me3 is required for the heritable RNAi and transcriptional silencing at native endogenous and exogenous RNAi targets. Using genetic approach we generated nearly completely deficient H3K9me3 worm strain (met-2;set-25;set-32). Using Pol II ChIP-seq, pre-mRNA-seq and mRNA-seq we validated transcriptional changes at the endogenous targets in the H3K9me3 deficient condition (met-2;set-25;set-32). We performed oma-1 dsRNA feeding and heritable RNAi experiment and using H3K9me3 ChIP-seq measured level of RNAi-triggered H3K9me3 contribution by set-32 or met-2;set-25 or met-2;set-25;set-32 HMTs at the oma-1 gene. Using oma-1 mRNA and pre-mRNA qRT-PCR we tested heritable RNAi effect at oma-1 genomic locus in these HMT mutants.

first: Natallia

last: Kalinava

first: Julie

middle: Z

last: Ni

first: Kimberly

last: Peterman

first: Esteban

last: Chen


title: Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans [RNA-seq]


title: Nuclear RNA decay pathways aid rapid remodeling of gene expression in yeast

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: In budding yeast, the nuclear RNA surveillance system is active on all pre-mRNA transcripts and modulated by nutrient availability. To test the role of nuclear surveillance in reprograming gene expression, we identified transcriptome-wide binding sites for RNA polymerase II (Pol II) and the exosome cofactors Mtr4 (TRAMP complex) and Nab3 (NNS complex) by UV-crosslinking immediately following glucose withdrawal (0, 4, and 8 minutes).  In glucose, mRNA binding by Nab3 and Mtr4 was mainly restricted to promoter-proximal sites, reflecting early transcription termination. Following glucose withdrawal, many mRNAs showed reduced transcription but increased Nab3 binding, accompanied by downstream recruitment of Mtr4, and oligo(A) tailing. This indicates transcription termination followed by TRAMP-mediated RNA decay. Upregulated transcripts generally showed low or strongly reduced binding of Nab3 and Mtr4. We conclude that nuclear surveillance pathways regulate both positive and negative responses to glucose availability.

overall_design: CRAC datasets were collected for Rpo21, Nab3, and Mtr4 at 0, 4, and 8 minutes. Total RNA was measured by RNA-seq at 0, 8, and 16 minutes following glucose starvation.

first: Alex

last: Tuck

first: Desislava

last: Staneva

first: David

last: Tollervey


title: Tick-borne Pathogens Induce Differential Expression of Genes Promoting Cell Survival and Host Resistence in Ixodes ricinus Cells

city: Addlestone

first: Richard

last: Ellis

address: APHA Weybridge

institute: Animal and Plant Health Agency

summary: There has been an emergence and expansion of tick-borne diseases in Europe, Asia and North America in recent years, including Lyme disease, tick-borne encephalitis, and human anaplasmosis. The primary tick vectors implicated are hard ticks of the Ixodes genera.  Although much is known about the host response to these bacterial and viral pathogens, there is limited knowledge of the cellular responses to infection within the tick vector. The bacterium Anaplasma phagocytophilum (A. phagocytophilum), is able to bypass apoptotic processes in ticks, enabling infection to proceed.  However, the tick cellular responses to infection with the flaviviruses tick-borne encephalitis virus (TBEV) and louping ill virus (LIV), which cause tick-borne encephalitis and louping ill respectively, are less clear.  Infection of an Ixodes ricinus (I. ricinus) tick cell line with the viruses LIV and TBEV, and the bacterium A. phagocytophilum, identified activation of common and distinct cellular pathways.  In particular, commonly-upregulated genes included those that modulate apoptotic pathways (HSP70), putative anti-pathogen genes (FKBP and XBL1), and genes that influence the tick innate immune response, including selective activation of toll genes. These data provide an insight into potentially key genes involved in the tick cellular response to viral or bacterial infection.

overall_design: Comparison of differential gene expression in infected tick cell lines (Ixodes scapularis [ISE6] and Ixodes ricinus [IRE/CTVM20]) at 7 days post-infection, following infection with tick-borne flaviviruses, and Anaplasma phagocytophilum. Differential gene expression determined through comparison with mock-treated (uninfected) cells.

first: Karen

middle: L

last: Mansfield

middle: J


title: Maturation of conidia on conidiophores of Aspergillus niger

city: Utrecht

first: Wieke

last: Teertstra

address: Padualaan 8

department: Science, Biology

country: Netherlands

institute: Utrecht University

summary: An Aspergillus niger colony can produce a few billion conidia. Formation of conidia producing conidiophores starts in the centre of the colony and moves outwards ending a few millimetres from the edge of the radial extending mycelium. As a result, the conidia within the colony centre are older than those in the intermediate and sub-peripheral zones. Here, it was assessed whether this results in heterogeneity of conidia within the colony. Conidia were harvested from conidiophores of cultures resulting from a confluent inoculated plate. A total number of 645-2421 genes were differentially expressed (fold change ≥ 2) when expression profiles of 2-, 5-, and 8-day-old conidia freshly harvested from conidiophores were compared. Genes without a PFAM or KEGG annotation were enriched in the up-regulated genes.

overall_design: mRNA profiles of 2-day 5-day and 8-day old conidia of Aspergillus niger were generated by deep sequencing, in duplicate, using Illumina Hiseq.

first: Han

last: Wösten


title: Transcription profiling of PfSPZ Malaria Vaccine trial subjects in a malaria endemic region

first: Robert

middle: D

last: Morrison

address: 307 Westlake Ave N

institute: Center for Infectious Disease Research

summary: The Sanaria® PfSPZ Vaccine can confer sterilizing protection against liver stage infection by Plasmodium falciparum (Pf) in malaria naïve individuals. The vaccine consists of aseptically purified irradiated Pf sporozoites. The PfSPZ Vaccine trial in Mali was the first to evaluate the safety and efficacy of this vaccine in a malaria endemic region. Vaccinees received five doses of 2.7 X 105 irradiated sporozoites and the efficacy was measured against naturally occurring Pf Infections in Malian adults during the malaria transmission season.

overall_design: 44 samples from 2 time points, pre-vaccination (Day -7) and post-vaccination (Day 143), for 22 Malian adult participants ( 5 placebo controls and 17 vaccine recipients).  11 of the vaccinated participants remained infection free over the subsequent malaria transmission season.

first: Patrick

middle: E

last: Duffy


title: Osteoblast-specific deletion of Hrpt2/Cdc73 results in high bone mass and increased bone turnover

city: Grand Rapids

first: Casey

middle: James

last: Droscha

state: Michigan

address: 333 Bostwick Ave.

department: Program for Skeletal Disease and Tumor Microenviroment

institute: Van Andel Institute

summary: RNA-seq within OCN-Cre;Cdc73flox/flox osteoblasts showed that loss of Cdc73 led to a derepression of osteoblast-specific genes, specifically those for collagen and other bone matrix proteins.

overall_design: RNA-seq of Flow-sorted calvarial osteoblasts of C57Bl/6J mice

first: Bart

last: Williams


title: Genome-wide Transcriptome Analysis of CD36 Overexpression in HepG2.2.15 Cells to Explore Its Regulation Role of Metabolism and HBV Life Cycle

city: 遵义市

first: 健

last: 黄

state: 贵州省

address: 汇川区大连路149号遵义医学院附属医院

country: China

institute: 遵义医学院附属医院

summary: To understand the molecular basis underlying the response to increasing CD36 overexpression in HepG2.2.15 cell, we performed genome-wide sequencing of the mRNAs from HepG2.2.15-CD36OE cell and HepG2.2.15-vector cell using the RNA-seq technology to detect its differential transcriptomic profile.

overall_design: To better understand the molecular changes in the response of the CD36 overexpression in HepG2.2.15 cell, three cDNA libraries from HepG2.2.15-vector cell (Vector-1, Vector-2, Vector-3) and HepG2.2.15-CD36 overexpression cell (CD36OE-1, CD36OE-2, CD36OE-3) were constructed, respectively. After ensuring quality control, Ion ProtonTM Sequencer was used for sequencing the cDNA libraries.

first: Jian

last: Huang

first: Yaxi


title: TORC1 shapes the SUMO proteome to control RNA polymerase III activity

city: Oslo

first: Håvard

last: Aanes

address: Sognsvannsveien 20

department: Dept of microbiology

country: Norway

institute: Oslo University Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Loss of nutrient supply elicits alterations of the SUMO proteome and sumoylation is crucial to various cellular processes including transcription. However, the physiological significance of sumoylation of transcriptional regulators is unclear. To begin clarifying this, we mapped the SUMO proteome under nitrogen-limiting conditions in Saccharomyces cerevisiae. Interestingly, several RNA polymerase III (RNAPIII) components are major SUMO targets under normal growth conditions, including Rpc53, Rpc82, and Ret1, and nutrient starvation results in rapid desumoylation of these proteins. These findings are supported by ChIP-seq experiments that show that SUMO is highly enriched at tDNA genes. Furthermore, RNA-seq experiments revealed that preventing sumoylation results in significantly decreased tRNA transcription. TORC1 inhibition resulted in the same effect, and our data indicate that the SUMO and TORC1 pathways are both required for robust tDNA expression. Importantly, tRNA transcription was strongly reduced in cells expressing a non-sumoylatable Rpc82-4KR mutant, which correlated with a misassembled RNAPIII transcriptional complex. Our data suggest that in addition to TORC1 activity, sumoylation of RNAPIII is key to reaching full translational capacity under optimal growth conditions.

overall_design: microRNA profiling in wild-type and a SUMO ligase deficient yeast strain, with or without treatment with rapamycin

first: Pierre

last: Chymkowitch

first: Jorrit

last: Enserink


title: Decoupling the downstream effects of germline nuclear RNAi reveals that transcriptional repression and heritable RNAi are independent of the H3K9me3 response in C. elegans [ChIP-seq]

first: Sam

last: Gu

first: Natallia

last: Kalinava

first: Julie

last: Ni

first: Kimberly

last: Peterman

first: Esteban

last: Chen


title: RNA-sequencing data from Pseudomonas putida KT2440 wild-type and Hfq-tagged strain form co-immunoprecipitation experiment

city: Kgs. Lyngby

first: Klara

last: Bojanovic

address: Building 220, Kemitorvet

department: Novo Nordisk Foundation Center for Biosustainability

country: Denmark

institute: Technical University of Denmark

summary: The RNA-chaperone Hfq is a global post-transcriptional regulator in Bacteria, important especially for the fine-tuning of the gene expression when the environmental conditions change. We looked into sRNAome during the growth of Pseudomonas putida KT2440 and compared it to a strain without Hfq protein. Numerous sRNAs were upregulated at a specific point during the growth and many were affected in the Hfq absence. Further we identified Hfq-binding RNA transcripts with co-immunoprecipitation and experimentally validated 17 sRNAs. Many novel Hfq-binding sRNAs were identified and are directly or indirectly regulated by Hfq. In addition 1870 mRNAs were found to bind to Hfq during the growth. Together, 202 antisense and 355 intergenic sRNAs have been detected in this study, several of them being 3’UTR- or 5’UTR-derived, and IS-related.

overall_design: 12 samples were analyzed; two strains (wild type and Hfq-FLAG-tagged strain) were compared in 3 time points during the growth in LB medium in two replicates each

last: Bojanovič

first: K

middle: S

last: Long


title: RNA Sequencing Data in differentiating mouse embryonic stem cells [day2  and 2.5 in differentiation]

city: Ann Arbor

first: Vesa

middle: Matti

last: Kaartinen

state: MI

address: 1011 N. University

department: BMS

institute: University of Michigan

summary: ES cell lines were established from mouse embryos, which were homozygous for the Trim33-flox allele and carried the UbcCreERT2 transgene. Cells were cultured without feeder cells in the presence of LIF and 2i. Embryoid bodies (EBs) were generated using the ATCC protocol on low attachment dishes under differentiating conditions. EBs were induced with Tamoxifen at day 1 and harvested at days 2 and 2.5, respectively.

overall_design: Investigate differentially expressed genes in control and Trim33-deficient embryoid bodies derived from mouse embryonic stem cells

first: Sudha

last: Rajderkar


title: Global transcriptional responses to osmotic, oxidative, and imipenem stress conditions in Pseudomonas putida

summary: Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of Pseudomonas putida KT2440 to oxidative, osmotic, and membrane stress conditions at two time points was investigated via identification of differentially expressed mRNAs and sRNAs. A total of 440 small RNA transcripts were detected, where 10% correspond to previously annotated sRNAs, 40% are novel intergenic transcripts and 50% are novel transcripts antisense to annotated genes. Each stress elicits a unique response as far as the extent and dynamics of the transcriptional changes. Nearly 200 protein-encoding genes exhibited significant changes in all stress types, implicating their participation in a general stress response. Almost half of the sRNA transcripts were differentially expressed in at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a higher fraction of differentially expressed sRNAs with greater than 5-fold expression changes compared with mRNAs. The work provides detailed insights into the mechanisms through which P. putida responds to different stress conditions and increases understanding of bacterial adaptation in natural and industrial settings.

overall_design: 21 samples were analyzed. There were 6 tested conditions compared to the control. Each of them has 3 biological replicas. Osmotic stress (NaCl), oxidative stress (H2O2) and membrane (IP-imipenem)stress T1 (7 min) and T2 (60 min) after the compound addition = 3 conditions x 2 time points x 3 bio replicas + 3 bio replicas of the control (T0-before the addtion of the compound).

first: Bojanovič

last: Klara

first: Long

last: S. Katherine


title: RNA-sequencing data from Pseudomonas putida KT2440 wild-type and Δhfq mutant

overall_design: 18 samples were analyzed; two strains (wild type and hfq deletion mutant) were compared in 3 time points during the growth in LB medium

first: Katherine


title: Targeted genomic screen reveals focal long non-coding RNA copy number alterations in cancer

city: Gent

first: Pieter-Jan

last: Volders

address: De Pintelaan 185

institute: Ghent University

type: Genome variation profiling by genome tiling array

summary:
The landscape of somatic copy-number alterations (SCNAs) affecting long non-coding RNAs (lncRNAs) in human cancer remains largely unexplored. While the majority of lncRNAs remains to be functionally characterized, several have been implicated in cancer development and metastasis. Considering the plethora of lncRNAs genes that is currently reported, it is conceivable that several lncRNAs might function as oncogenes or tumor suppressor genes.
We devised a strategy to detect focal lncRNA SCNAs using a custom DNA microarray platform probing 20 418 lncRNA genes. By screening a panel of 80 cancer cell lines, we detected numerous focal aberrations targeting one or multiple lncRNAs without affecting neighboring protein-coding genes. These focal aberrations are highly suggestive for a tumor suppressive or oncogenic role of the targeted lncRNA gene. Although functional validation remains an essential step in the further characterization of the involved candidate cancer lncRNAs, our results provide a direct way of prioritizing candidate lncRNAs involved in cancer pathogenesis.

overall_design: 80 DNA samples from various cancer cell lines were analyzed on an in-house designed aCGH platform. For every sample, the gender-matched control was labeled in parallell and hybridized together.

first: Pieter

last: Mestdagh

first: Jo

last: Vandesompele


title: The effect of niclosamide on the growth and progression of endometriosis in an experimental mouse model

city: Pullman

first: Kanako

last: Hayashi

address: BLS345, 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

summary: Because niclosamide inhibits growth and progression of endometriotic lesions, we performed RNA-seq in order to identify genes whose expression is regulated by niclosamide in endometriotic lesions. Our results shown that niclosamide modulates several genes related to cell signaling, extracellular matrix, and inflammatory signaling.

overall_design: A direct comparison of endometriotic like lesions developed in mice (n=3 per group) treated orally with either vehicle control or 200 mg/kg bw day of niclosamide for 3 weeks.

first: Genna

last: Prather

first: James

last: MacLean


title: SNHG5 promotes colorectal cancer cell survival by counteracting STAU1-mediated mRNA destabilization

city: Copenhagen

first: Anders

middle: H

last: Lund

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Center

institute: University of Copenhagen

summary: We functionally characterize SNHG5 as an important lncRNA, which could constitute a  new therapeutic target in colorectal cancer, and provide a novel mechanism of action for a  cytoplasmic lncRNA

overall_design: RNA pull down of SNHG5 in HCT-116 cells and subsequent sequencing of the transcriptional interactome

first: Nkerorema

last: Damas

first: Roland

last: Baumgartner

first: Carsten

middle: F

last: Rundsten


city: Izmir

first: Yongsoo

last: Park

address: Balcova

country: Turkey

institute: Izmir International Biomedicine and Genome Institute (iBG-izmir)

summary:
Objectives: MicroRNA (miRNA) can be released to the extracellular medium and participates in neuronal communication. We investigate the mechanisms of miRNA exocytosis by vesicle fusion as a neuromodulator in a manner that are disparate from silencing gene expression.
Methods: Small RNA sequencing data of large dense-core vesicle were generated by next-generation sequencing (NGS) in triplicate using Illumina Hiseq 2500.
Results: Large dense-core vesicles contain a variety of known and novel miRNAs inside including miR-375.
Conclusion: miRNAs can be novel neuromodulators, which are stored in LDCVs and released by vesicle fusion by SNARE assembly and synaptotagmin-1

overall_design: Small RNA sequencing of large dense-core vesicle in bovine chromaffin cells from triplicate including technical replicate and biological replicate.

first: Gökhan

last: Karakülah


title: Rnf8 loss promotes breast carcinogenesis

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

country: Spain

institute: Institut Catala d'Oncologia IDIBELL

summary: Coordination of signaling pathways is essential for tissue homeostasis and for preventing cancer development. Here, we show that the E3 ligase Rnf8, an important component of the DNA double-strand break (DSB) signaling, is critical for cell-fate commitment of the mammary epithelial progenitors. Furthermore, we provide evidence that deficiency of Rnf8 predisposes mouse models for mammary tumorigenesis while low expression levels in breast cancer associates with poor patient prognosis. RNF8 mediates these novel functions through ubiquitylation and degradation of the activated form of NOTCH1, and thereby fine-tuning of NOTCH signaling. Accordingly, RNF8 level negatively correlates with the expression of NOTCH targets in mouse mammary and human breast tumors. Consistent with these findings, Rnf8-deficient mammary tumors are highly sensitive to pharmacological inhibition of NOTCH. Therefore, RNF8 inhibits breast cancer on two fronts, maintaining genomic stability through DSB signaling and regulating growth and differentiation through inhibition of the NOTCH pathway.

overall_design: RNA sequencing of Rnf8-/-;Trp53Δ/Δ mammary tumor cells and Rnf8-complemented Rnf8-/-;Trp53Δ/Δ mammary tumor cells

first: Razq

last: Hakem

first: Miguel


title: RNASequencing of nf-yc, hy5, and nf-yc hy5 mutants during photomorphogenic growth in Arabidopsis thaliana.

city: Norman

first: Ben

last: Holt

state: OK

address: 770 Van Vleet Oval

department: Microbiology and Plant Biology

institute: University of Oklahoma

summary:
Purpose: The purpose of this RNA Sequencing project was to investigate the transcriptional regulatory relationship between NF-YC3/4/9 and HY5
Methods: Total RNA was isolated, and then poly-A purified. 100ng of starting RNA was used to generate RNASeq libraries using the NEXTflex Illumina qRNA-Seq Library Prep Kit, and sequenced on an Illumina HiSeq2500 machine.
Results: NF-YC3/4/9 and HY5 have both shared and independent regulatory targets.

overall_design: mRNA profiles of 7-day old Wild Type (WT), nf-yc triple (Q3), hy5, and nf-yc triple hy5 (Q3hy5) seedlings grown in continuous white light were generated from two biological replicates through paired end deep sequencing on an Illumina HiSeq2500 platform.

first: Zachary

last: Myers

first: Roderick

middle: W

last: Kumimoto

first: Jan

last: Risinger


title: Genome-wide binding of Telomerase reverse transcriptase (TERT) in VA13 cells

city: Singapore

first: Vinay

last: Tergaonkar

address: 61, Biopolis Drive

department: IMCB

country: Singapore

institute: A*STAR

summary: VA13  cells show peaks only in repeat regions.

overall_design: Examination of TERT genome wide binding in VA13 cell line

first: Ekta

last: Khattar


title: OBP56h modulates social interactions in Drosophila

city: Raleigh

first: John

last: Shorter

state: NC

address: 112 Derieux Place 3510 Thomas Hall

department: Biological Sciences

institute: North Carolina State University

summary: Social interactions in insects are strongly driven by conspecific chemical signals that are detected via chemoreceptors of olfactory and gustatory neurons. Odorant binding proteins (Obps) transport volatile odorants to chemosensory receptors, but their pleiotropic effects on behaviors and other traits are not well characterized. Here, we knocked down expression of 14 Drosophila melanogaster Obp genes using RNAi and found that seven had reduced male aggressive behavior, particularly Obp56h. RNAi knockdown of Obp56h gene expression also reduced courtship latency; significantly impacted cuticular hydrocarbon production, with a major reduction in 5-Tricosene (5-T); and affected expression of many other genes, including Or19b, Gr97a and several genes associated with lipase activity. We propose that Obp56h plays a dual role in pheromone production and perception and that 5-T, an inhibitory sex pheromone produced by males that increases latency for early stages of courtship, is implicated as a possible ligand for Obp56h.

overall_design: We used RNAseq to quantify differences in gene expression in heads and bodies of males and females of Dll-GAL4 x UAS-Obp56h and Dll-GAL4 x control F1 individuals. F1 individuals with CyO or TM3 balancer genotypes were discarded. Flies were aged for 5-6 days in a mixed sex environment at a density of approximately 20 in a vial. Flies were flash frozen over dry ice between 8:00 a.m. and 11:00 a.m. and 30 heads and bodies per sex and genotype were manually dissected and collected over three days in a randomized design, with four biological replicates per sex, genotype and tissue.   We extracted total RNA with Trizol with the RNAeasy Mini Kit (Qiagen Inc.). rRNA was depleted using the Ribo-Zero™ Gold Kit (Epicentre Inc.) with 5ug total RNA input. Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA. cDNA from each RNA sample was used to produce barcoded cDNA libraries using NEXTflex™ DNA Barcodes (Bioo Scientific Inc.) with an Illumina TrueSeq compatible protocol. Library size was selected using Agencourt Ampure XP Beads (Beckman Coulter Inc.) and centered on 250bp with average insert size around 130bp. Second strand DNA was digested with Uracil-DNA glycosylase before amplification to produce directional cDNA libraries. Libraries were quantified using Qubit dsDNA HS Kits (Life Technologies Inc.) and Bioanalyzer (Agilent Technologies Inc.) to calculate molarity. They were then diluted to equal molarity and re-quantified, and 32 libraries were pooled. Pooled library samples were quantified to calculate final molarity and finally denatured and diluted to 14pM. Pooled library samples were clustered on an Illumina cBot and sequenced on an Illumina Hiseq2500 using 125bp single-read v4 chemistry on each of two lanes.   The quality of the RNA-seq data was assessed using FASTQC (Andrews, 2010). Following quality assessment, adapter sequences were trimmed using Cutadapt (Martin, 2011). Ribosomal reads were filtered against a database of the most common ribosomal sequences using fast BWA alignment BWA-0.7.10 (Li & Durbin, 2009). The remaining reads were aligned to the Dmel_r5.57_FB2014_03 genome and transcriptome using STAR_2.4.1d (Dobin et al., 2013). Read count was performed using HTSeq-count HTSeq-0.6.1p1 (Anders et al., 2015). R software was used for further quality assessment and statistical analysis (R-Core-Team, 2012). The EDASeq package was used to plot principal components, and one replicate sample (HRNAiF1) was identified as a technical outlier, removed, and the remaining 31 samples were used for analysis. The edgeR package was used to calculate differential expression analysis for pairwise comparisons between the control and RNAi sample for sex and tissue as well as the interaction between genotype and tissue for each sex (Robinson et al., 2010). Biological pathway and gene ontology enrichment analyses were performed using DAVID (Huang et al., 2009).

first: Lauren

middle: M

last: Dembeck

first: Laura

last: Constance

first: Logan

last: Everett

first: Tatiana

middle: V

last: Morozova

first: Gunjan

last: Arya

first: Lavanya

last: Turlapati

first: Genevieve

last: Evans

first: Yasmeen

middle: N

last: Hussain

first: Charlene

last: Couch

first: Coby

last: Schal

first: Robert

last: Anholt

first: Trudy

middle: C

last: Mackay


title: Tissue-specific signatures in the transcriptional response to Anaplasma phagocytophilum infection of   Ixodes scapularis and Ixodes ricinus tick cell lines

first: Richard

last: Ellis

summary: We report differential gene expression with tissue-specific signatures in tick cell lines infected with Anaplasma phagocytophilum - transcriptional response to infection of I. scapularis ISE6 cells resembled that of tick hemocytes while the response in I. ricinus IRE/CTVM20 cells resembles that of tick midguts.

overall_design: Comparison of differential gene expression in infected tick cell lines (Ixodes scapularis [ISE6] and Ixodes ricinus [IRE/CTVM20]) at 7 days post-infection. Differential gene expression determined through comparison with mock-treated (uninfected) cells.  This series contains only Ixodes ricinus data.

first: Jose

last: de la Fuente


title: Genome-wide binding of telomerase reverse transcriptase (TERT) in cancer cells and human embryonic stem cells

first: Vinay

last: Tergaonkar

summary: We report the genome wide binding of endogeneous TERT in various cell types. The binding signature is highly overlapping with RNA polymerase III components.

overall_design: Examination of TERT genome wide binding in seven cell lines


title: The RNA-binding protein Hdlbp/Vigilin is increased in hepatic steatosis and regulates VLDL secretion through modulation of Apob mRNA translation

city: Zurich

first: Markus

last: Stoffel

address: Otto-Stern-Weg 7

department: Inst. f. Molecular Health Sciences

country: Switzerland

institute: ETH Zurich

summary: The liver exerts a wide range of essential functions including the synthesis of plasma proteins and the integration of glucose and lipid homeostasis. While the role of transcriptional networks in the tight regulation of these processes has been extensively studied in healthy and disease states, much less is known about post-transcriptional control of gene expression through RNA-binding proteins (RBP). Here, we report that the highly expressed and conserved RBP Hdlbp/Vigilin is upregulated in patients with non-alcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) and in livers of insulin resistant obese mice. Gain and loss of function studies revealed that Vigilin regulates VLDL secretion through the modulation of ApoB mRNA translation. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) analysis in primary hepatocytes demonstrated that Vigilin predominantly binds to CU-rich regions in coding sequences of transcripts of further metabolically relevant secretory proteins such as Apob/apoliproteinB, Ahsg/fetuin-A, Apoc3/apolipoproteinC-III, Fn1/fibronectin, Orm1/orosomucoid and Serpina1/alpha-1-antitrypsin. While mRNA levels of these targets did not change, protein levels were substantially decreased upon knockdown of Vigilin. Hepatic long-term knockdown via GalNAc-conjugated siRNAs ameliorated elevated VLDL/LDL levels and the formation of atherosclerotic plaques in Ldlr–/– mice. These studies uncover a role for Vigilin as a key regulator of hepatic Apob translation and secretion through binding to its mRNA and demonstrate the therapeutic potential of inhibiting Vigilin for cardiovascular diseases.

overall_design: PAR-CLIP of Hdlbp/Vigilin and poly(A) selected RNA-sequencing in mouse liver primary hepatocytes

first: Mehrpouya

middle: B

last: Mobin

first: Stefanie

last: Gerstberger

first: Daniel

last: Teupser

first: Benedetta

last: Campana

last: Heim

first: Muthiah

last: Manoharan

first: Thomas

last: Tuschl


title: Genome-wide expression change by SHARPIN knockdown in MCF-7 cells

city: Shenzhen

first: Qiangzu

last: Zhang

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

institute: Lemondata BioTechnology Limited

summary: We aim to investigate the role of SHARPIN in breast cancer progression. MCF-7 cells were used as the model and SHARPIN was silenced by siRNA.SHARPIN (SHANK-Associated RH Domain Interactor) is also named as SIPL1 and HSIPL1. The  gene is located in Chr 8. SHARPIN protein is shown to regulate cell adhesion and migration. Besides, SHARPIN is proved to the component of the LUBAC complex and is necessary for NKFB function, while SHARPIN KO mice will lead to chronic dermatitis and immune deficiency in B cells.

overall_design: The MCF-7 cells were treated with 50nM scramble siRNA and siSHARPIN. After 48 hours, cells were harvested and the total RNA was extracted by Qiagen kit. The RNA sample was sent to BGI for RNA expression analysis.

first: Jian

last: Zhu

first: Hui

last: Wang


title: Characterization of transcriptomic profile of ulcerated and intact stomach epithelium

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: To explore the processes and mechanisms that are up/downregulated following ulceration of the stomach, in order to identify key mechanisms underlying ulcer healing.
Methods: mRNA profiles of paired ulcerated and intact tissues were obtained from 4-month-old C57BL6 mice, in triplicate, 30 days after ulcer generation through 99% acetic acid.  With a workflow involving alignment, quantification, and statistical analysis in GeneSpring NGS, data were analyzed at the gene level using a paired t-test.
Results: Approximately 30million mRNA reads per sample aligned to over 34,000 known transcripts (UCSC mm10 genome).  Paired t-tests that compared within-mouse ulcerated to intact tissue, identified 1165 transcripts with a p-value < 0.05 and fold change > 1.5.
Conclusion:  Among significantly dysregulated transcripts in ulcerated tissues, we observe a significant enrichment of genes related to stem-ness, tissue repair, and cancer-related processes

overall_design: Ulcers were produced in the stomachs of C57BL6 mice using acetic acid.  Thirty days after ulceration, paired ulcerated and uninvolved tissues were obtained from the stomach corpus; their mRNA profiles were generated using RNA-sequencing.

first: Marshall

last: Montrose

first: Eitaro

last: Aihara


title: RNA-seq analysis of the degradation of chloroacetate by Burkholderia caribensis MBA4

city: Hong Kong

first: Jimmy

last: Tsang

address: Pokfulam Road

country: Hong Kong

institute: The University of Hong Kong

summary: Burkholderia caribensis MBA4 is able to metabolize monochloroacetate (MCA) as sole carbon and energy source for growth. A haloacid dehalogenase is mainly responsible for the cleavage of the carbon-halogen bond. The MCA will be hydrolyzed to glycolate which would be further transformed to glyoxylate by glycolate oxidase. In order to identify inducible genes involved in mineralization of MCA, transcriptomes of MBA4 cells grown on MCA, glycolate or pyruvate were determined using RNA-seq technology. After trimming and filtering, clean data of each transcriptome were mapped to an annotated genome of MBA4 and the expression values of various genes were calculated and compared. The results showed that there are specific sets of genes being induced by MCA and not by its dehalogenation product glycolate. Noticeably, among three glycolate oxidase operons identified in the genome their expressions were found to be  varied individually in response to MCA, glycolate and pyruvate. One of the operons was minimally expressed no matter what was the growth substrate. Another operon was inducible both by MCA and glycolate. This is expected and which suggested that this operon is most likely responds to the presence of glycolate. The third operon contains the structural genes, glcDEF, for glycolate oxidase, glcG, for an uncharacterized protein associated with glycolate metabolism, and glcB, for malate synthase G. This operon was inducible by MCA only and not by glycolate nor pyruvate.

overall_design: RNA-seq data obtained from pyruvate-, glycolate- or monochloroacetate-grown cells of a Burkholderia caribensis were analyzed and compared.

first: Yanling

last: Pan

first: Ka

last: Kong

last: Tsang.


title: Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [reChIP-seq]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Cancer metabolism has been actively studied to gain insights into tumorigenic survival mechanisms and susceptibilities. In melanoma, we identify HEXIM1, a transcription elongation regulator, as a novel melanoma suppressor that participates in nucleotide stress regulation. HEXIM1 expression is low in melanoma. Its overexpression suppresses melanoma while its inactivation accelerates tumor onset in vivo. HEXIM1 responds to nucleotide stress. Knockdown of HEXIM1 rescues neural crest and melanoma nucleotide stress phenotypes in vivo. Mechanistically, under nucleotide stress, HEXIM1 is induced to form an inhibitory complex with P-TEFb, the kinase that initiates transcription elongation, to pause transcription at tumorigenic genes. The resulting alteration in gene expression also causes anti-tumorigenic transcripts to bind to and be stabilized by HEXIM1. HEXIM1 therefore plays an important role in inhibiting cancer cell-specific gene transcription while also facilitating anti-cancer gene expression. Our study reveals a novel role for HEXIM1 in coupling nucleotide metabolism with transcriptional regulation in melanoma.

overall_design: reChIP-seq analysis of HEXIM1 and CDK9 chromatin cobinding in human A375 melanoma cells.

first: Justin

last: Tan

first: Song

last: Yang

first: Yi

last: Zhou

middle: I


title: Effector regulatory T cell differentiation and immune homeostasis depend on the transcription factor Myb

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary: FoxP3-expressing regulatory T (Treg) cells are essential to maintain immune homeostasis. Activated Treg cells undergo further differentiation into an effector state that highly express genes critical for Treg cell function. Here we demonstrate that mice lacking the transcription factor Myb in Treg cells succumb to a multi-organ inflammatory disease. Myb was specifically expressed in, and required for the differentiation of, thymus-derived effector Treg cells. The combination of transcriptome and DNA binding analyses revealed that Myb directly regulates a large proportion of the effector Treg cell specific gene expression in mouse and human cells. This study identifies a critical role for Myb in the gene regulatory network controlling effector Treg cell differentiation and function.

overall_design: Transcriptional profiling of naïve, activated and effector Treg cell populations using RNA sequencing

first: Sheila

last: Dias

first: Gordon

middle: K

last: Smyth

first: Stephen

last: Nutt


title: Genome-wide analysis of FOXO1 binding features in early stage of chicken myoblast differentiation

city: Guangzhou

first: Xinzheng

last: Jia

state: Guangdong

address: Wushan Road

department: Animal Science

institute: South China Agricultural University

summary: Chromatin immunoprecipitation and high-throughput sequencing (ChIP-Seq) were performed for FOXO1 in early differentiated myoblasts. Based on FOXO1-occupied features, 234 coding genes were annotated including 39 targets overlapped with mouse ChIP-seq data. Function analysis demonstrated that these targets were enriched in myogenic proliferation, death and hypotrophy. Moreover, FOXO1 manipulated myoblast proliferation through promoting TGFBR2 and MYCN and repressing G0S2 at transcriptional level. On the other side, FOXO1 negatively regulated Bcl6 expression in myoblast, indicating that in the early stage of differentiation, myoblast apoptosis induced by miR-16 might be coordinated by impacts of FOXO1 on Bcl6.

overall_design: More than 10^8 differentiated myoblast cells  were used for constructed two DNA sequencing libraries (ChIP and input) performed by HiSeq2000 system (Illumina).

first: Qinghua

last: Nie


title: Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [FAST-iCLIP]

overall_design: FAST-iCLIP analysis of HEXIM1 in human A375 melanoma cells treated with either DMSO or 25 μM A771726 for 48 hrs.

middle: L

first: Ryan

middle: A

last: Flynn

first: Howard

middle: Y

last: Chang


title: Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [RNA-Seq1]

overall_design: RNA-seq analysis of human A375 melanoma cells treated with either DMSO or 25 μM A771726 for 0-72 hrs.


title: Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [ChIP-Seq2]

overall_design: ChIP-seq analysis of SP1 chromatin binding in human A375 melanoma cells treated with either DMSO or 25 μM A771726 for 48 hrs.


title: Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [RNA-Seq2]

overall_design: RNA-seq analysis of human Tet-On HEXIM1-inducible A375 melanoma cells treated with either DMSO or 1 μg/mL doxycycline in triplicate for 48 hrs.

first: Anne

last: Bothmer

first: Pier

last: Pandolfi


title: RNA-seq analysis of rice leaves, nodes and stems

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: To explore the molecular mechanism of callus formation in nodes, we performed an RNA-seq experiment, using a mixture of nodes I and II compared to stems and mature leaves. We identified 1,741 candidate genes that were preferentially expressed in the node.

overall_design: Total RNA obtained from the mature leaf, node and stem tissues from rice.


title: Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription

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

overall_design: Refer to individual Series


title: Ingested double-stranded RNA engages multiple silencing mechanisms in C. elegans

city: College Park

first: Antony

middle: Merlin

last: Jose

state: MD

address: Rm 2136, Bioscience Research Building

department: Cell Biology and Molecular Genetics

institute: University of Maryland College Park

summary: Double-stranded RNA (dsRNA) can cause specific gene silencing upon ingestion in many animals and is being developed as a pesticide to target essential genes in animal pests. However, the organismal response to ingested dsRNA that leads to eventual gene silencing within animals is unknown. In the worm C. elegans, ingested dsRNA is recruited into the RNA interference pathway by the dsRNA-binding protein RDE-4 for eventual gene silencing by Argonaute proteins. We found that when RDE-4 was expressed at high levels within a tissue, silencing by ingested dsRNA could occur in rde-4(-) somatic tissues but not in the rde-4(-) germline. Such silencing by dsRNA-derived mobile RNA had different Argonaute requirements and could escape inhibition by expressed repetitive DNA. Thus, our results suggest that, when animals ingest dsRNA, the ingested dsRNA and dsRNA-derived mobile RNAs use distinct mechanisms to silence genes.

overall_design: The wild-type N2 strain was subjected to L4440 feeding RNAi (control) or bli-1 feeding RNAi in liquid culture. Total RNA was isolated from both worm cultures and subjected to poly-A-selected RNA-Seq using the Illumina HiSeq1500 platform. The coverage for each gene of interest was determined after mapping to ce6 using TopHat2.


title: LARP4B is an mRNA stability factor that acts via AU-rich sequence elements

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

summary: mRNAs are key molecules in gene expression and subject to diverse regulatory events. Regulation is accomplished by distinct sets of trans-acting factors that interact with mRNAs and form defined mRNA-protein complexes (mRNPs). The resulting “mRNP code” determines the fate of any given mRNA and thus determines the gene regulation at the post-transcriptional level. The La-related protein 4B (LARP4B) belongs to an evolutionarily conserved family of RNA binding factors characterized by the presence of a La-module implicated in direct RNA binding. Biochemical experiments have shown direct interactions of LARP4B with factors of the translation machinery. This finding along with the observation of an association with actively translating ribosomes suggested that LARP4B is a factor contributing to the mRNP code. To gain insight into the function of LARP4B in vivo we tested its mRNA association at the transcriptome level and its impact on the proteome. PAR-CLIP analyses allowed us to identify the in vivo RNA targets of LARP4B. We show that LARP4B binds to a distinct set of cellular mRNAs by contacting their 3´UTRs. Biocomputational analysis combined with in vitro binding assays identified the LARP4B binding motif on mRNA targets. The reduction of cellular LARP4B levels leads to a marked destabilization of its mRNA targets and consequently to their reduced translation. Our data identify LARP4B as a component of the mRNP code that influences the expression of its mRNA targets by affecting their stability.

overall_design: RNAseq experiments of HEK293 cells which were transfected with siRNAs targeting LARP4B and firefly luciferase as controls. The experiment was performed in triplicates.

first: Maritta

last: Küspert

first: Yasuhiro

last: Murakawa

first: Katrin

last: Schäffler

first: Jens

last: Vanselow

first: Elmar

last: Wolf

first: Stefan

last: Juranek

first: Andreas

last: Schlosser

first: Markus

last: Landthaler

first: Utz

last: Fischer


title: MLL3/MLL4 are required for CBP/p300 binding on enhancers and super-enhancer formation in brown adipogenesis

city: Bethesda

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

summary: Histone H3K4me1/2 methyltransferases MLL3/MLL4 and H3K27 acetyltransferases CBP/p300 are major enhancer epigenomic writers. To understand how these epigenomic writers orchestrate enhancer landscapes during cell differentiation, we have profiled genomic binding of MLL4, CBP, lineage-determining transcription factors, as well as transcriptome and epigenome during adipogenesis of immortalized preadipocytes derived from mouse brown adipose tissue (BAT). We show that MLL4 and CBP drive the dynamic enhancer epigenome, which correlates with the dynamic transcriptome. MLL3/MLL4 are required for CBP/p300 binding on enhancers activated during adipogenesis. Further, we show that MLL4 and CBP identify super-enhancers of adipogenesis and that MLL3/MLL4 are required for the formation of super-enhancers. Finally, in brown adipocytes differentiated in culture, MLL4 identifies primed super-enhancers of genes fully activated in BAT such as the thermogenic Ucp1. Comparison of MLL4-defined super-enhancers in brown and white adipogenesis predicted a list of brown-specific super-enhancers SEs associated genes that are likely to be important to BAT functions. These results establish MLL3/MLL4 and CBP/p300 as master enhancer epigenomic writers and suggest that enhancer-priming by MLL3/MLL4 followed by enhancer-activation by CBP/p300 sequentially shape dynamic enhancer landscapes during cell differentiation. Our data also provide a rich resource for understanding epigenomic regulation of brown adipogenesis.

overall_design: Expression profiling by RNA-seq, profiling of transcription factors (EBF2, C/EBPβ, C/EBPα, PPARγ, and CTCF) binding, co-factors (MLL4, CBP, and Med1) and Pol II localization, and histone modifications (H3K4me1/2/3, H3K27ac, H3K36me3, H3K9me2, and H3K27me3) by ChIP-seq, and chromatin accessibility profiling by FAIRE-seq at four time points (D-3, D0, D2, D7) during adipogenesis of Ppargf/f brown preadipocytes in culture. ChIP-seq of CBP/p300 are performed at day2 of adipogenesis of Mll3-/-;Mll4f/f and Mll3-/-;Mll4-/- mouse brown preadipocytes in culture. In addition, ChIP-Seq of MLL4 are performed at day7 of aidpogenesis of 3T3L1 preadipocytes in culture.

first: Lai

last: Binbin

first: Lee

last: Ji-Eun

first: Wang

last: Lifeng

first: Jang

last: Younghoon

first: Peng

last: Weiqun

first: Ge

last: Kai


title: RNA-Seq data for AKT, BAD, ERBB2, IGF1R, RAF1 and ERK1 over-expressed samples with twelve green fluorescent protein control samples using human mammary epithelial cells

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

institute: University of Utah

summary: The goal was to capture the transcriptional activity due to over-expression of AKT, BAD, ERBB2, IGF1R, RAF1 and ERK1 genes.Over-expressions were validated using Western Blots. Illumina RNA-Seq technology was used to capture the downstream transcriptional activity. Reads were 101 base pairs long and single ended. An R open source package “Rsubread” was used to align and quantify the read using UCSC hg19 annotation. The integer-based gene counts were later normalized in TPM .

overall_design: Profiles of gene expression, downstream of  AKT, BAD, ERBB2, IGF1R, RAF1 and ERK over-expression, were generated in cells derived from breast and used to generate a gene-expression signatures.

first: L

last: Jackson

first: M

first: S

last: MacNeil

middle: R

last: Piccolo

first: A

last: Bild


title: Transcriptomic analysis of  rapeseed (Brassica napus) flower buds exposure to male gametocide amidosulfuron

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

summary: To reveal the possible molecular mechanism underpinning the male sterility induced by a sulfonyflurea herbicide amidosulfuron, a comparative transcriptome analysis between rapeseed under amidosulfuron folia spray and the contrast was conducted  by using Illumina digital gene expression tag profiling technology (DGE). A total of 54 up-regulated and 119 down-regulated DETs (differentially expressed transcripts) were annotated by 357 GOs and 32 KEGG pathways, indicating that the reaction to amidosulfuron exposure is complicated in rapeseed. Some interesting GOs included (1) amino acid metabolite, (2) energy metabolite, (3) carbohydrate, lipid, protein metabolite, (4) cell division, growth and death, (5) stimulus and defense response, (6) chlorophyll and mitochondria, (7) hormone, (8) oxidoreductase, and (9) flavonoid biosynthesis. Expression of most genes in cell division, growth and death category, and flavonoid biosynthesis were down-regulated. Ethylene mediated signaling pathway was up-regulated, while auxin mediated signaling pathway was down-regulated. Stimulus and defense response were induced.

overall_design: Two groups of DGE libraries including the amidosulfuron treatment (DAT group) and the control (F group), each in three biological replications, were constructed using total RNA of young floral buds of amidosulfuron-treated cultivar Qinyou3 and the control with Illumina’s Digital Gene Expression Tag Profiling Kit according to the manufacturer’s protocol. We performed a single end sequencing on an Illumina GAIIX platform following the vendor's recommended protocol. The raw data containing adaptor sequences, tags with low quality sequences and unknown nucleotides N were filtered to obtain clean reads with 36 nt in length. Clean reads were then conducted for quality assessment. All clean tags were aligned to the unigenes of a previous assembled transcripts dataset (Trinity_rapeseed.fa.gz attachment of gene expression Omnibus GSE69638) by Bowtie2 ver 2.1.0 (http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.1.0/), only 1 bp mismatch is allowed. The assembled unigenes were matched to Brassica rapa genome FPsc v1.3 in JGI (http://genome.jgi.doe.gov/). The number of perfect clean reads corresponding to each gene was calculated and normalized to the number of Reads Per Kilobase of exon model per Million mapped reads (RPKM). The transcripts of low-frequency with the 3rd quartile of counts in all samples <10 were removed. Based on the expression levels, the significant DETs among two groups of samples were identified with a criteria of p value ≤0.05 and log2 fold-change≥1. The analysis of gene ontology (http://www.geneontology.org/) was conducted for functional classification of DETs and the pathway analysis was carried out by using KEGG (Kyoto Encyclopedia of Genes and Genomes) database retrieved from http://www.genome.jp/kegg/.

first: Jungang

last: Dong


title: Modulation effects of nitric oxide on thalidomide treated chicken embryo transcriptome

city: Cochin

first: Ravi

last: Gupta

state: Kerala

address: Plot no: 43A,SDF, 3rd floor, A Block,CSEZ, Kakkanad

department: Bioinformatics

country: India

institute: SciGenom Labs Pvt. Ltd.

summary:
Purpose: The aim of this study is to analyse and compare the differentially expressed genes between nitric oxide treated and thalidomide treated chick embryos
Methods: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 75 database. Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 75 gene model of chicken with default parameter settings. After alignment, Cuffdiff (v2.2.0) program was used for performing differential expression analysis. Pathway analysis of differentially expressed genes was performed using DAVID program. Heat maps were constructed using R package software 3.1.0.

overall_design: The mRNA profiles of thalidomide and spermine NONOate pretreated 6th day of chick embryo were generated by deep sequencing, using Illumina HiSeq 2500 platform.

first: Vimal

last: Veeraiah

first: Suvro

last: Chatterjee


title: Defining the regulon of a CzcRS-like two-component system in Burkholderia cenocepacia K56-2 (ChIP-Seq)

city: Exeter

first: Alan

middle: Reid

last: Brown

state: Devon

address: Geoffrey Pope Building, Stocker Road

department: Biosciences

institute: University of Exeter

summary: BACKGROUND: We identified that a putative CzcRS-like two-component system (TCS) in Burkholderia cenocepacia K56-2 is required for heavy metal resistance and virulence. In an attempt to identify genes directly regulated by the CzcR response regulator, we performed ChIP-seq analysis to identify genomic regions bound by CzcR. METHODS. Sequence encoding a FLAG octapeptide (Sigma-Aldrich) was introduced to the 3’ end of the czcR gene at its native chromosomal position in wild-type B. cenocepacia K56-2. Wildtype K56-2 and the CzcR-FLAG strain were grown in 50 ml tryptone soya broth (TSB) in the presence or absence of 1.5 mM zinc chloride. After overnight incubation, anti-FLAG immunoprecipitation of CzcR-bound genomic DNA was performed. Wildtype K56-2 was processed in parallel, to serve as a control against which to assess for enrichment of genomic regions. Illumina sequencing libraries were prepared from the resulting DNA using the Nextflex ChIPseq protocol (Bioo Scientific) with indexed adapters. Libraries were amplified by 18 cycles PCR, purified using 0.8 volumes Ampure XP beads (Beckman Coulter) and quantified with a Bioanalyzer 7500 assay (Agilent). Libraries ranged in size from 150 bp to 800 bp with a average insert size of 310 bp. Libraries were pooled in equimolar concentrations, denatured and diluted to 6.5 pM, clustered  on a flowcell using a cBOT (Illumina) and sequenced on a HiSeq2000 (Illumina). Paired-end reads were filtered using the fastq-mcf package from the ea-utils suite to remove reads with less than 90% Q20 scores or above and to trim off adaptor sequence. The reads were then aligned against the B. cenocepacia J2315 genome (NC_011001-NC_011003) using BWA (0.5.9) and converted to BAM format using Samtools. Potential PCR duplicates were removed using the samtools rmdup command.  The MACS package (v1.4) was used to compare and contrast the control and sample data using the –call-subpeaks and –w options. RESULTS: Relative to wildtype B. cenocepacia K56-2, the only genomic region that was found to be enriched by the ChIP-seq analysis of the CzcR-FLAG strain mapped to nucleotide coordinates 787809-798988 on chromosome 2. This region includes the czcRS genes and those encoding the associated efflux pump (CzcCBA).

overall_design: Genomic regions bound by the CzcR response regulator were identified by ChIP-seq analysis of a strain expressing a FLAG-tagged CzcR protein. Enriched genomic regions were determined by comparison to the wildtype (parental) strain which did not possess a FLAG tag. Sequencing was performed on an Illumina HiSeq2000.

first: Konrad

last: Paszkiewicz


title: Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [ChIP-Seq]

first: Leonard

last: Zon

overall_design: ChIP-seq analysis of HEXIM1, CDK9 and RNA Pol II chromatin binding in human A375 melanoma cells treated with either DMSO or 25 μM A771726 for 48 hrs.

first: Justin

last: Tan

first: Song

last: Yang

first: Zi

middle: P

last: Fan

first: Yi

last: Zhou

first: Richard

last: Young


title: Single-cell mRNA isoform diversity in the mouse brain

city: Stockholm

first: Kasper

last: Karlsson

address: Scheeles väg 2

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Single-cell isoform regulation is increasingly being studied. To get a full view of alternative isoform usage, from transcription start site and alternative splicing to transcription termination site, full-length sequences have to be studied. Here we use PacBio long read sequencing technology combined with unique molecular identities to get a full and accurate picture of alternative isoform usage of different stages in maturing oligodendrocyte single cells. We see that the majority of molecules in single-cells are separate isoforms, even after applying a conservative definition of what constitutes an isoform. Few isoforms are common between cells of the same cell-type but the common isoforms are higher expressed. We also see that exon junctions in coding regions are better regulated than exon junctions in non-coding regions and that genes often express more than one coding isoform.

overall_design: Six samples analysed, no replicated

first: Sten

last: Linnarsson


title: Genes expression patterns in Desulfovibrio piezophilus sp. nov. C1TLV30T in response to hydrostatic pressure

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

summary: We have identified differentially expressed genes according to hydrostatic pressure growth conditions in Desulfovibrio piezophilus. The transcriptomic datasets report the molecular mechanisms which could be involved in such adaptation and give information for the piezophile sulfate-reducing bacteria research communities. The data obtained pointed out different responses of D. piezophilus to an increase of hydrostatic pressure.

overall_design: Transcriptome data of Desulfovibrio piezophilus have been generated with culture at 0.1 MPa (atmospheric pressure, low hydrostatic pressure), 26 or 10 MPa (high hydrostatic pressures). All these cultures have been processed in duplicate.

first: Amira

last: Amrani

first: Aurélie

first: Hélène

last: Holota

first: Bernard

last: Ollivier

first: Jean

last: Imbert

first: Nathalie

last: Pradel

first: Alain

last: Dolla


title: Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.)

first: Han

last: Ran

address: No.3 Taicheng Road

department: College of Life Sciences

summary:
Background: MicroRNAs regulate various biological processes in plants. Considerable data are available on miRNAs involved in the development of rice, maize and barley. In contrast, little is known about miRNAs and their functions in the development of wheat. In this study, five small RNA (sRNA) libraries from wheat seedlings, flag leaves, and developing seeds were developed and sequenced to identify miRNAs and understand their functions in wheat development.

Results: Twenty-four known miRNAs belonging to 15 miRNA families were identified from 18 MIRNA loci in wheat in the present study, including 15 (9 MIRNA loci) first identified in wheat, 13 miRNA families (16 MIRNA loci) being highly conserved and 2 (2 MIRNAs loci) moderately conserved. In addition, fifty-five novel miRNAs were also identified. The potential target genes for 15 known miRNAs and 37 novel miRNAs were predicted using strict criteria, and these target genes are involved in a wide range of biological functions. Four of the 15 known miRNA families and 22 of the 55 novel miRNAs were preferentially expressed in the developing seeds with  logarithm of the fold change of 1.0～7.6, and half of them were seed-specific, suggesting that they participate in regulating wheat seed development and metabolism. From 5 days post-anthesis to 20 days post-anthesis, miR164 and miR160 increased in abundance in developing seeds, whereas miR169 decreased, suggesting their coordinating functions in the different developmental stages of wheat seed. Moreover, eight known miRNA families and 28 novel miRNAs exhibited tissue-biased expression in wheat flag leaves, with the logarithm of the fold changes of 0.5～5.2. The putative targets of these tissue-preferential miRNAs were involved in various metabolism and biological processes, suggesting complexity of the regulatory networks in different tissues. Our data also suggested that wheat flag leaves have more complicated regulatory networks of miRNAs than developing seeds.

Conclusions: Our work identified and characterised wheat miRNAs, their targets and expression patterns. This study is the first to elucidate the regulatory networks of miRNAs involved in wheat flag leaves and developing seeds, and provided a foundation for future studies on specific functions of these miRNAs.

overall_design: To identify more miRNAs and understand the regulatory roles of miRNAs in wheat flag leaf and developing seed, five sRNA libraries from seedling, flag leaf, 5-d seed, 10-d seed and 20-d seed were sequenced

first: Ran

last: Han

first: Hui-xian

last: Zhao

first: Yan

last: Yan


title: Characterization of the TCT motif reveals a crucial role of the core promoter micro-environment in gene regulation

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

country: USA

institute: University of California, San Diego (UCSD)

summary: The signals initiating gene expression are eventually integrated at the core promoter where diverse core promoter motifs interact with the basal transcription machinery to recruit the RNA polymerase. The diversityThe signals initiating gene expression are eventually integrated at the core promoter where diverse core promoter motifs interact with the basal transcription machinery to recruit the RNA polymerase. The diversity in core promoter motif poises their composition as a means to regulate gene expression. We utilized genome-wide (5’GRO-seq) and biochemical methods to characterize the TCT motif in humans and Drosophila and show that it is a functionally conserved RNA polymerase II core promoter element. Human TCT-containing promoters are ~3-fold enriched for the TATA box motif while Drosophila promoters are depleted. The downstream core promoter element (DPE) is underrepresented. Combinatorial analysis revealed the TCT motif to cooperatively facilitate transcription with the TATA box in some instances, but not others implying a role for the core promoter micro-environment in gene regulation. The interaction among core promoter elements is therefore not as straightforward as previously thought. TCT-containing promoters predominantly regulate the expression of genes involved in translation, thereby providing an example how core promoter motifs facilitate regulatory specialization. This may explain why diverse translation-related genes are observed as commonly altered in some cancers.

overall_design: Nascent transcript initiation profiles in S2 cells using 5'GRO-Seq

first: Sascha

middle: H

last: Duttke

first: James

middle: T

last: Kadonaga


title: Digital gene expression profiling of mouse skin gene expression after cyclophosphamide (CYP) treatment

city: Fuzhou

first: Yue

last: Zhicao

state: Fujian

address: Institute of Life Sciences, Fuzhou University

department: Institute of Life Sciences

institute: Fuzhou University

summary: Chemotherapy often causes adverse effects including hair loss, however, the molecular basis remains unclear. A common assumption is that by targeting actively dividing cancer cells, chemo-drugs would inevitably damage normal proliferating cells as a “side effect”. Using both mouse hair and avian feather as models, here we show that down-regulation of sonic hedgehog (Shh) signaling is a critical event mediating chemo-drug induced tissue damage. Reduced expression of Shh is also apparent in human patients who experience hair loss after receiving chemotherapy, and in animal models treated with several frontline chemo-drugs. Supplementation of Shh protein or steroid hormones that activate Shh signaling prevented hair loss, but interestingly, not the damage to the pigment system. Together, our results have elucidated a molecular mechanism underlying chemotherapy-induced tissue damage, and suggested novel concepts and methodologies for future clinical interventions and drug development.

overall_design: Cyclophosphamide (CYP) was i.p. administered to 2-month-old male C57B/6 mice at 150mg/kg, which were depilated 9 days earlier to induce active hair growth. Total RNAs were extracted from whole skin at designated times, quality monitored by Agilent 2100 analysis, and proceeded for sequencing by Illumina Genome Analyzer in Beijing Genome Institute (BGI), Shenzhen, China. The sequencing results were annotated according to a reference mouse gene database provided by BGI.

last: Hao


title: Znf143 binding sites in U937 cells by ChIPexo

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

institute: Ecole Normale Superieure

summary: We performed ChIPexo sequencing to identify the binding sites of Znf143 in the U937 cell line.

overall_design: ChIPexo in u937 cells

first: Annouck

last: Luyten

first: Samuel

first: Daniel

middle: G

last: Tenen


title: Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue [miRNA]

status: Public on Dec 31 2016

city: Beijing

first: Zhixiu

last: Wang

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

summary: miRNA sequences (from miRNA-seq) from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small Ear pig [DSP] and Tibetan pig [TP]) and two introduced pig breeds (Landrace [LL] and Yorkshire [YY]) were examined using HiSeq 2000 to identify and compare the differential expression of functional genes related to muscle growth and lipid deposition. With miRNA-seq, we obtained 23.78 M reads and 320 positively expressed miRNAs from muscle tissues, including 271 known pig miRNAs and 49 novel miRNAs. In those 271 known miRNAs, 20 were higher and 10 lower expressed in DSP-TP than in LL-YY. The target genes of the 30 miRNAs were mainly participated in MAPK, GnRH, insulin and Calcium signaling pathway and others involved in cell development, growth and proliferation, etc. Combining the DEGs and the differentially expressed (DE) miRNAs, we drafted a network of 46 genes and 18 miRNAs for regulating muscle growth and a network of 15 genes and 16 miRNAs for regulating lipid deposition. We identified that CAV2, MYOZ2, FRZB, miR-29b, miR-122, miR-145-5p and miR-let-7c, etc, were key genes or miRNAs regulating muscle growth, and FASN, SCD, ADORA1, miR-4332, miR-182, miR-92b-3p, miR-let-7a and miR-let-7e, etc. were key genes or miRNAs regulating lipid deposition.

overall_design: microRNA sequences from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small Ear pig [DSP] and Tibetan pig [TP]) and two introduced pig breeds (Landrace [LL] and Yorkshire [YY]) were examined using HiSeq 2000.

first: Qinggang

last: Li

first: Hao

last: Zhang


title: The Drosophila transcriptional network is structured by microbiota

city: London

first: Adam

last: Dobson

address: Gower Street

department: GEE

institute: University College London

summary: Resident microorganisms (microbiota) have far-reaching effects on the biology of their animal hosts, with major consequences for the host’s health and fitness.  Some of these effects can be explained by microbial impacts on the expression of individual genes but a full understanding of microbiota-dependent gene regulation requires analysis of the overall architecture of the host transcriptome. In this study, we investigated the impact of the microbiota on the global structure of the transcriptome of Drosophila. Our transcriptomic analysis of 17 Drosophila lines representative of the global genetic diversity of this species yielded a total of 11 transcriptional modules of co-expressed genes.  For 7 of these modules, the strength of the transcriptional network (defined as gene-gene coexpression) differed significantly between flies bearing a defined gut microbiota (gnotobiotic flies) and flies reared under microbiologically-sterile conditions (axenic flies). Furthermore, the network structure was uniformly stronger in these microbiota-dependent modules than in both the microbiota-independent modules in gnotobiotic flies and all modules in axenic flies, indicating that the presence of the microbiota tightens gene regulation in a subset of the transcriptome.  The genes constituting the microbiota-dependent transcriptional modules include regulators of growth, metabolism and neurophysiology, previously implicated in mediating phenotypic effects of microbiota on Drosophila phenotype. Together these results provide the key first evidence that the microbiota strengthens the co-expression of genesin specific networks of functionally-related transcripts relative to the animal’s intrinsic baseline level of co-expression. Our system-wide analysis demonstrates that the presence of microbiota enhances the structure of the transcriptional network in the animal host. This finding has potentially major implications for understanding of the mechanisms by which microbiota affect host health and fitness, and the ways in which hosts and their resident microbiota coevolve.

overall_design: 36 samples total. 16 D. melanogaster genotypes ± microbiota

middle: J

first: John

middle: M

last: Chaston

first: Angela

middle: E

last: Douglas


title: Characterization of CAMTA mutant plants

city: Beltsville

first: Sunchung

last: Park

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

summary:
Arabidopsis thaliana Col-0 as a wild type and camta1/2/3/sid2-1 as a mutant were compared in their gene expression at the end of day.
By comparing the transcriptomes, we showed the presence of SA-independent and CAMTA-dependent pathway at ambient temperature.

overall_design: Examination of mRNA levels in the Arabidopsis grown in soil at warm conditions.

first: YongSig

last: Kim

first: SunChung

first: Michael

last: Thomashow


title: DUX4-induced dsRNA and MYC mRNA Stabilization Activate Apoptotic Pathways in Human Cell Models of Facioscapulohumeral Dystrophy

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: Facioscapulohumeral muscular dystophy (FSHD) is caused by the mis-expression of DUX4 in skeletal muscle cells. DUX4 is a transcription factor that activates genes normally associated with stem cell biology and its mis-expression in FSHD cells results in apoptosis. To identify genes and pathways necessary for DUX4-mediated apoptosis, we performed an siRNA screen in an RD rhabdomyosarcoma cell line with an inducible DUX4 transgene. Our screen identified components of the MYC-mediated apoptotic pathway and the double-stranded RNA (dsRNA) innate immune response pathway as mediators of DUX4-induced apoptosis. Further investigation revealed that DUX4 expression led to increased MYC mRNA, accumulation of nuclear dsRNA foci, and activation of the dsRNA response pathway in both RD cells and human myoblasts. Nuclear dsRNA foci were associated with aggregation of the exon junction complex component EIF4A3. The elevation of MYC mRNA, dsRNA accumulation, and EIF4A3 nuclear aggregates in FSHD muscle cells suggest that these processes might contribute to FSHD pathophysiology.

overall_design: RNA-seq of human rhabdomyosarcoma cells with an inducible DUX4 transgene (RD-DUX4i) cells was performed on RNA samples collected from 3 separate experimental replicates induced from 16-18 hours with doxycycline, as indicated and compared to the respective uninduced condition.

first: Sean

middle: C

last: Shadle

first: Jun

middle: W

last: Zhong

first: Amy

last: Campbell

first: Melissa

last: Conerly

first: Sujatha

last: Jagannathan

first: Chao-Jen

last: Wong

first: Timothy

middle: D

last: Morello


title: Conversion of Human Fibroblasts to Stably Self-Renewing Neural Stem Cells with a Single Zinc-Finger Transcription Factor

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

summary: Direct conversion of somatic cells into neural stem cells (NSCs) by defined factors holds great promise for mechanistic studies, drug screening, and potential cell therapies for different neurodegenerative diseases. Here, we report that a single zinc-finger transcription factor, Zfp521, is sufficient for direct conversion of human fibroblasts into long-term self-renewable and multipotent NSCs. In vitro, Zfp521-induced NSCs maintained their characteristics in the absence of exogenous factor expression and exhibited morphological, molecular, developmental, and functional properties that were similar to control NSCs. Additionally, the single seeded induced NSCs were able to form NSC colonies with efficiency comparable to control NSCs and expressed NSC markers. The converted cells were capable of surviving, migrating and attaining neural phenotypes after transplantation into neonatal mouse- and adult rat brains, without forming tumors. Moreover, the Zfp521-induced NSCs predominantly expressed rostral genes. Our results suggest a facilitated approach for establishing human NSCs through Zfp521-driven conversion of fibroblasts.

overall_design: RNA-Seq of 3 replicates each of iNSC, WT-NSC, and HNF

first: Ebrahim

last: Shahbazi

first: Sharif

last: Moradi

first: Shiva

last: Nemati

first: Leila

last: Satarian

first: Mohsen

last: Basiri

first: Hamid

last: Gourabi

first: Narges

last: Zare Mehrjardi

first: Patrick

last: Günther

first: Angelika

last: Lampert

first: Kristian

last: Händler

first: Firuze

middle: F

last: Hatay

first: Diana

last: Schmidt

first: Marek

last: Molcanyi

first: Jürgen

last: Hescheler

first: Tomo

last: Šarić

first: Hossein

last: Baharvand


title: Dicer maintains the identity and function of proprioceptive sensory neurons

city: Basel

first: Sean

last: O'Toole

state: Basel-Stadt

address: Maulbeerstrasse 66

department: Neuroscience

institute: FMI

summary: During development neurons achieve a high degree of specialization (Fishell and Heintz, 2013). Over time, while continuously recycling their components and despite transcriptional noise, their own respective properties remain intact. The transcription factors that play a large role in initially establishing neuronal identity can be required for maintaining it (Deneris and Hobert, 2014). Post-transcriptional regulation is also important to differentiation (Bian and Sun, 2011) but its role in maintaining cell identity is less established. To better understand how post-transcriptional regulation might contribute to cell identity, we examined the proprioceptive neurons in the dorsal root ganglion (DRG), a highly specialized sensory class, whose properties are well established and display clear differences when compared to other neurons in the ganglion. By conditionally ablating Dicer in mice, using a parvalbumin (Pvalb) driven cre, we impaired post-transcriptional regulation in the proprioceptive sensory neuron population. KO animals display a progressive form of ataxia at the beginning of the fourth postnatal week that is mirrored by a cell-death within the DRG. Before cell-loss, expression profiling shows a reduction of proprioceptor specific genes and an increased expression of non-proprioceptive genes normally enriched in other ganglion neurons. Furthermore, although central connections of these neurons are intact, the peripheral connections to the muscle are functionally impaired. Post-transcriptional regulation is therefore necessary to retain the transcriptional identity and support functional specialization of the proprioceptive sensory neurons.

overall_design: mRNA levels were examined in the lumbar 4 dorsal root ganglion parvalbumin positive neurons with and without conditional ablation of dicer driven by parvalbumin-cre.

first: S

middle: B

last: Nelson


title: Transcriptional and genome organization changes in HT1080 cells after overexpression of tissue-specific nuclear transmembrane proteins (NETs)

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

institute: University of Edinburgh

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

overall_design: Refer to individual Series


title: Defining the role of a CzcRS-like two-component system in Burkholderia cenocepacia K56-2 (RNA-Seq)

first: Alan

last: Brown

summary: BACKGROUND: We identified that a putative CzcRS-like two-component system (TCS) in Burkholderia cenocepacia K56-2 is required for heavy metal resistance and virulence. To investigate this TCS further, we applied RNA-seq to determine the transcriptional response of wildtype and CzcRS-deficient B. cenocepacia to subinhibitory concetrations of zinc. METHODS. Wildtype B. cenocepacia K56-2 was cultured in LB broth with and without 1.5 mM zinc chloride. In parallel, a ΔczcRS mutant strain was also cultured in 1.5 mM zinc chloride. Total RNA was extracted from triplicate mid log-phase cultures for each strain/culture condition.  Illumina Sequencing libraries were prepared from 50 ng ribosomal-depleted RNA using ScriptSeq v2 with indexing and 15 cycles of PCR amplification using Kapa HiFi DNA polymerase. The amplified libraries were purified using a 1:1 ratio of Ampure XP beads resulting in 45-75nM concentrations and average insert size of 350 bp. Libraries were pooled in equimolar concentrations, denatured and diluted to 6.5 pM before clustering on a cBOT (Illumina). Libraries were subjected to 100-bp paired-end sequencing on a HiSeq 2000 using TruSeq SBS v 3 reagents (Illumina). Paired-end reads were filtered using the fastq-mcf package from the ea-utils suite to remove reads with less than 90% Q20 scores or above and to trim off adaptor sequence. The reads were then aligned against the B. cenocepacia J2315 genome (NC_011001-NC_011003) using Bowtie 1 to remove reads mapping to ERCC spike-in. Abundance of ERCC spike-ins was then checked against predicted values to confirm successful library preparation. Tophat v2.0.4 was used to align reads against the reference genome. The Bedtools multicov command was used to extract per-gene counts for each gene. The DESeq suite was used to determine statistical significance of differential expression between conditions. RESULTS: Wildtype B. cenocepacia K56-2 showed a restricted transcriptional response to 1.5 mM zinc chloride, with only 54 genes exhibiting significant differential expression (≥ 1.5-fold; P < 0.05) compared to unsupplemented LB. This transcriptional response included genes encoding the CzcRS-like TCS itself and the associated efflux pump  (CzcCBA). In contrast, the ΔczcRS mutant strain when cultured in 1.5 mM zinc chloride exhbited a profound transcriptional response with 767 genes differentially expressed. Many genes showing differential expression in the ΔczcRS strain are indicative of a stress response, indicating the pivotal role of the CzcRS-like TCS in maintaining cellular homeostasis in response to zinc.

overall_design: The transcriptional profile of wildtype Burkholderia cenocepacia K56-2 and the corresponding  ΔczcRS mutant to 1.5 mM zinc chloride was assessed in triplicate by Illumina HiSeq2000 sequencing.

first: Konrad

last: Paszkiewicz


title: Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue

first: Zhixiu

last: Wang


title: Genomic CpG methylation profiles of peripheral blood mononuclear cells in KD patients and non-KD normal subjects

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

type: Methylation profiling by genome tiling array

summary:
Peripheral blood samples were taken from a total of 48 individuals (24 KD patients and 24 normal controls) and subjected to access DNA CpG methylation state using Infinium HumanMethylation450 BeadChips. This array consists of probes to determine the site-specific methylation status of more than 450K CpG loci across the human genome.
Approximately 500 ng of bisulfate-converted DNA (BCD) was used per BeadChip for hybridization in accordance with the protocol and instructions of Infinium HD methylation. After completing the whole-genome amplification step and then controlled enzymatic end-point fragmentation, BCD samples were precipitated and re-suspended for hybridization for 16 h at 48°C. During this process, the DNA molecules are annealed to two bead types with methylated loci (C)-specific and unmethylated loci (T)-specific oligomers. Afterward, the non-hybridized or mis-hybridized DNA was washed away, followed by single-base extension using 2,4-dinitrophrnol- and biotin-labeled ddNTPs and the annealed BCD as templates.

overall_design: Bisulfite converted DNA from 48 PBMC samples (with 24 normal subjects and 24 KD patients) was hybridized to the Illumina Infinium HumanMethylation450 BeadChip array.

first: Ho-Chang

last: Kuo

first: Kai-Sheng

last: Hsieh

first: Wei-Teng

last: Weng


title: Transcriptome comparison of LUBEL catalytic dead mutant to its parental line

city: Wien

first: Fumiyo

last: Ikeda

address: Dr. Bohr-Gasse 3

country: Austria

institute: Institute of Molecular Biotechnology

summary: Effect of LUBEL catalytic dead mutation upon Heastshock

overall_design: Mutation was introduced in CG11321 catalytic region by CRISPR/Cas9 techonology in Drosophila melanogaster and  transcriptome was compared in untreated and heatshocked samples

first: Sini

last: Junttila


title: Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue [mRNA]

summary: RNA sequences (from RNA-seq) from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small Ear pig [DSP] and Tibetan pig [TP]) and two introduced pig breeds (Landrace [LL] and Yorkshire [YY]) were examined using HiSeq 2000 to identify and compare the differential expression of functional genes related to muscle growth and lipid deposition. We obtained 27.18 G clean data through the RNA-seq and detected that 18,208 genes were positively expressed and 14,633 of them were co-expressed in the muscle tissues of the four samples. In all, 315 DEGs were found between the Chinese pig group and the introduced pig group, 240 of which were enriched with functional annotations from the David database and significantly enriched in 27 Gene Ontology (GO) terms that were mainly associated with muscle fiber contraction, cadmium ion binding, response to organic substance and contractile fiber part. Based on functional annotation, we identified 85 DEGs related to growth traits that were mainly involved in muscle tissue development, muscle system process, regulation of cell development, and growth factor binding, and 27 DEGs related to lipid deposition that were mainly involved in lipid metabolic process and fatty acid biosynthetic process.

overall_design: RNA sequences from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small Ear pig [DSP] and Tibetan pig [TP]) and two introduced pig breeds (Landrace [LL] and Yorkshire [YY]) were examined using HiSeq 2000.

first: Qinggang

last: Li

first: Hao

last: Zhang


title: Transcriptional changes during Mycobacterium tuberculosis reactivation from persistence

city: Newark

first: Lanbo

last: Shi

state: NJ

address: 185 South Orange

institute: Rutgers University

summary: We observe that M. tuberculosis reactivation is associated with a global gene expression program that defines the initiation of an ordered programmed reactivation process in the lag phase.

overall_design: We characterized the global transcriptomic profiles of M. tuberculosis during reactivation from hypoxia-induced persistence, at day 0, 1, 2, 3, and 4, in triplicates, and performed network analysis.

first: Peicheng

last: Du


title: Transcriptional profiling of parental mouse erythroleukemia (MEL) and HMBA-resistant (MEL-R) cells

city: Madrid

first: Dora

last: Krimer

address: Ramiro de Maeztu 9

department: Cell and Molecular Biology

institute: National Spanish Research Council (CSIC)

summary: We have previously isolated a murine erythroleukemia cell line refractive to re-enter a cell differentiation program as opposite to the progenitor cell line. We use RNA-seq to identify differentially expressed genes in both cell lines

overall_design: Gene expression levels from MEL DS19 and MEL-R cell cultures were compared by next generation sequencing using standard RNA-seq protocols

first: Vanessa

last: Fernandez-Calleja

first: Maria-Jose

last: Fernandez-Nestosa