title: Human Schlafen 5 (SLFN5) is a Regulator of Motility and   Invasiveness of Renal Cell Carcinoma (RCC) Cells

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: There is some emerging evidence that members of the Schlafen (SLFN) family of  proteins mediate antineoplastic responses, but the mechanisms accounting for these  effects are not known. We provide evidence that human SLFN5, an interferon (IFN)-  inducible member of the family, exhibits key roles in controlling motility and  invasiveness of renal cell carcinoma (RCC) cells. Our studies define the mechanism by  which this occurs, demonstrating that SLFN5 negatively controls expression of matrix  metalloproteinases (MMP)-1 and -13 and several other genes involved in the control of  malignant cell motility. Importantly, our data establish that SLFN5 expression correlates  with a better overall survival in a large cohort of patients with RCC. The inverse  relationship between SLFN5 expression and RCC aggressiveness raises the possibility of  developing unique therapeutic approaches in the treatment of RCC, by modulating  SLFN5 expression.

overall_design: Examination of 2 SLFN5 knockdown cells and 2 controls, in triplicate.

first: Antonella

last: Sassano

first: Leonidas

middle: C

last: Platanias


title: Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells (TAB-Seq)

status: Public on Jun 01 2015

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is an epigenetic mark thought to be robust to environmental perturbations on a short time scale. Here, we challenge that view by demonstrating that the infection of human dendritic cells with a live pathogenic bacteria is associated with rapid changes in methylation levels at thousands of loci. We performed an integrated analysis of data on genome-wide DNA methylation, histone mark patterns, chromatin accessibility, and gene expression, before and after infection. We found that infection-induced changes in methylation rarely occur at promoter regions and instead localize to distal enhancer elements. Active demethylation is associated with extensive epigenetic remodeling, including the gain of histone activation marks and the induction of enhancer RNAs, and is strongly predictive of changes in the expression levels of nearby genes. Collectively, our observations show that active, rapid changes in DNA methylation in enhancers play a previously unappreciated role in regulating the transcriptional response of immune cells to infection.

overall_design: DNA hydroxymethylation profiles of one non-infected and one MTB-infected dendritic cell sample.

first: Luis

middle: B

last: Barreiro


title: Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells (ChIP-Seq)

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examination of 6 different histone modifications in non-infected and MTB-infected dendritic cells, in duplicate.


title: The C-terminal region of the RNA helicase CshA is required for the interaction with the degradosome and turnover of bulk RNA in the opportunistic pathogen Staphylococcus aureus.

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

type: Expression profiling by high throughput sequencing

summary: Staphylococcus aureus is a versatile opportunistic pathogen that adapts readily to a variety of different growth conditions. This adaptation requires a rapid regulation of gene expression including the control of mRNA abundance. The CshA DEAD-box RNA helicase was previously shown to be required for efficient turnover of the agr quorum sensing mRNA. Here we show by transcriptome-wide RNA sequencing and microarray analyses that CshA is required for the degradation of bulk mRNA. Moreover a subset of mRNAs is significantly stabilised in absence of CshA. Deletion of the C-terminal extension affects RNA turnover similar to the full deletion of the cshA gene. In accordance with RNA decay data, the C-terminal region of CshA is required for an RNA-independent interaction with components of the RNA degradation machinery. The C-terminal truncation of CshA reduces its ATPase activity and this reduction cannot be compensated at high RNA concentrations. Finally, the deletion of the C-terminal extension does affect growth at low temperatures, but to a significantly lesser degree than the full deletion, indicating that the core of the helicase can assume a partial function and opening the possibility that CshA is involved in different cellular processes.

overall_design: 2 CshA mutants and a WT strain are prepared in duplicate for RNA decay assay. A time course after rifampicin treatment is performed on each preparation sampling at 4 time points: t=0s, t=150s, t=300s, t=600s. All samples are submitted for RNA-seq.

first: Caroline

last: Giraud

first: Stéphane

last: Hausmann

first: Sylvain

last: Lemeille

first: Peter

last: Redder

first: Patrick

last: Linder


title: CELF1, and RNA binding protein, regulates transcript networks in cultured embryonic cardiomyocytes.

city: Cleveland

first: Andrea

middle: N

last: Ladd

state: OH

address: 9500 Euclid Ave NC-10

department: Cellular and Molecular Medicine

country: USA

institute: Cleveland Clinic

summary: We report on the regulation of transcripts following siRNA-mediated depletion of an RNA binding protein, CELF1, in primary chicken embryonic cardiomyocytes in culture.

overall_design: Cultured chicken primary embryonic cardiomyocytes (isolated from embryonic day 8 hearts) were transfected with siRNA against CELF1 (n=3) or mock transfected (n=3) at 24 hours in culture.

first: Yotam

last: Blech-Hermoni


title: Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells (mRNA-Seq)

overall_design: Transcriptional profiles (polyA+) of 6 non-infected and 6 MTB-infected dendritic cell samples.


title: Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells

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

overall_design: Refer to individual Series


title: Identification and characterization of novel maize miRNAs involved in different genetic background

city: Hefei

first: Lei

last: Sheng

state: Anhui

address: Changjiang Road

department: School of Life Sciences

country: China

institute: Anhui Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition in plants and animals. At present there is relatively little information regarding the role of miRNAs in the response to drought stress in maize. In this study, two small RNA libraries were sequenced, and a total of 11,973,711 and 14,326,010 raw sequences were generated from growing leaves of drought-tolerant and drought-sensitive maize seedlings, respectively. Further analysis identified 192 mature miRNAs, which include 124 known maize (zma) miRNAs and 68 potential novel miRNA candidates. Additionally, 167 target genes (259 transcripts) of known and novel miRNAs were predicted to be differentially expressed between two maize inbred lines. Of these, three novel miRNAs were up-regulated and two were down-regulated under drought stress. The expression of these five miRNAs and nine target genes was confirmed using quantitative reverse transcription PCR. The expression of three of the miRNAs and their putative target genes exhibited an inverse correlation, and expression analysis suggested that all five may play important roles in maize leaves. Finally, GO annotations of the target genes indicated a potential role in photosynthesis, may therefore contribute to the drought stress response. This study describes the identification and characterization of novel miRNAs that are the differentially expressed in drought-tolerant and drought-sensitive inbred maize lines. This provides the foundation for further investigation into the mechanism of miRNA function in response to drought stress in maize.

first: Beijiu

last: Cheng


title: Role of Hopx in myogenesis and commitment

city: Philadelphia

first: Kyoung Jae

last: Won

address: 3400 Civic Center Blvd

department: Genetics

institute: University of Pennsylvania


title: RNA-Seq data for five HER2 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: Purpose: The goal was to capture the transcriptional activity due to over-expression of HER2 protein. We profiled this transcriptional activity using two different RNA-Seq alignment and quantification pipelines. We also used these samples to generate a gene expression signature of HER2 pathway activity. Over-expression was 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 FPKM and TPM .

overall_design: A profile of gene expression, downstream of ERBB2/HER2 over-expression, was generated in cells derived from breast and used to generate a gene-expression signature reflective of HER2 pathway activation status.

first: Laurie

middle: K

last: Jackson

middle: H

last: Bild

first: Stephen

middle: R

last: Piccolo


title: Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells (wtRNA-Seq)

last: Pacis

overall_design: Transcriptional profiles (ribo-minus) of non-infected and MTB-infected dendritic cell samples, in triplicate.


title: Genome-wide identification of MYB3R3-bound genes

city: Nagoya

first: Norihito

last: Nakamichi

state: Aichi

address: Furo-cho, Chikusa

department: Institute of Transformative Bio-Molecules

country: Japan

institute: Nagoya University

summary: Arabidopsis genome has 5 genes that encode for R1R2R3-type Myb transcription factors. We showed previously that two R1R2R3-Myb transcriptional factors, MYB3R1 and MYB3R4, bind to cis-acting motifs called MSA, which are commonly present in many G2/M-specific genes and act as transcriptional activator.  Here, we performed genome-wide approach to identify target genes of MYB3R3, which, together with MYB3R1 and MYB3R5, have potential functions in transcriptional repression of G2/M-specific genes. Our ChIP-seq analysis revealed that MYB3R3 preferentially binds to the G2/M-specific genes in vivo. In addition, our data also showed that MYB3R3 associates with the predicted target genes of E2F, well known transcription factors acting during G1/S. These results suggested that MYB3R3 may not only directly bind G2/M-specific genes though recognition of the MSA elements, but also indirectly associates with DNA replication genes through physical interaction with E2F.

overall_design: Chromatin immunoprecipitation was performed with MYB3R3-GFP-expressing Arabidopsis.  ChIPed and input DNA from MYB3R3-GFP plants were subjected to Next-generation sequencing.

first: Takamasa

last: Suzuki

first: Tetsuya

last: Higashiyama

first: Kosuke

last: Kobayashi

first: Toshiya

first: Masaki

last: Ito


title: Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells (ATAC-Seq)

first: Alain

overall_design: Chromatin accessibility profiles of one non-infected and one MTB-infected dendritic cell sample.

first: Luis

last: Barreiro


title: Identification of AP2-O targets [ChIP-seq II]

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

summary: Stage-specific transcription is a fundamental biological process in the lifecycle of the Plasmodium parasite. Proteins containing the AP2 DNA-binding domain are responsible for stage-specific transcriptional regulation, and belong to the only known family of transcription factors in Plasmodium parasites. A comprehensive identification of their target genes will advance our understanding of the molecular basis of stage-specific parasite development. In this study, we have used ChIP-seq technology to identify the target genes of the ookinete-specific AP2 transcription factor AP2-O.

overall_design: GFP-tagged AP2-O was IPed with anti-GFP antibody. Targets of this transcription factor were predicted.

first: Masao

last: Yuda

first: Izumi

last: Kaneko

first: Shiroh

last: Iwanaga

first: Tomomi

last: Kato


title: Identification of AP2-O targets [ChIP-seq I]

overall_design: GFP-tagged AP2-O was IPed with anti-GFP antibody. Targets of this transcription factor were predicted based on the AP2-O binding sites.


title: Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells (Bisulfite-Seq)

summary:
Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats by Ficoll-Paque centrifugation. Blood monocytes were then purified from PBMCs by positive selection with magnetic CD14 MicroBeads (Miltenyi Biotech). Pure monocytes were cultured for 5 days in RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated FCS (Dutscher), L-glutamine (Invitrogen), GM-CSF (20 ng/mL; Immunotools), and IL-4 (20 ng/mL; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned. Before infection, we systematically checked the differentiation/activation status of the monocyte-derived DCs by flow cytometry, using antibodies against CD1a, CD14, CD83, and HLA-DR. Only samples presenting the expected phenotype for non-activated DCs – CD1a+, CD14-, CD83-, and HLA-DRlow – were used in downstream experiments.
Dendritic cells (DCs) were infected with a Mycobacterium tuberculosis (MTB) strain expressing green-fluorescent protein (H37Rv) for 18 h at a multiplicity of infection of 1-to-1. Full details can be found in Barreiro et al. (2012).

overall_design: DNA methylation profiles of 6 non-infected and 6 MTB-infected dendritic cell samples.


title: Identification of AP2-O targets [RNA-Seq]

overall_design: Plasmodium berghei transcriptomes were analyzed in ookinetes.


title: HSA21 Single-minded 2 (Sim2) binding sites co-localize with super-enhancers and pioneer transcription factors in pluripotent mouse ES cells [ChIP-Seq]

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

institute: University of Geneva Medical School

summary: Down syndrome (DS) results from trisomy of chromosome 21 (HSA21). Some DS phenotypes may be directly or indirectly related to the increased expression of specific HSA21 genes, in particular those encoding transcription factors. The HSA21 encoded Single-minded 2 (SIM2) transcription factor has key neurological functions and is a good candidate to be involved in the cognitive impairment of DS. ChIP-sequencing was used to map SIM2 binding in mouse embryonic stem cells and has revealed 1229 high-confidence SIM2-binding sites. Analysis of the SIM2 target genes confirmed the importance of SIM2 in developmental and neuronal processes and indicated that SIM2 may be a master transcription regulator. Indeed, SIM2 DNA binding sites share sequence specificity and overlapping domains of occupancy with master transcription factors such as SOX2, OCT4, NANOG or KLF4. The association between SIM2 and these pioneer factors is supported by the finding that SIM2 can be co-immunoprecipitated with SOX2, OCT4, NANOG or KLF4. Furthermore, the binding of SIM2 marks a particular sub-category of enhancers known as super-enhancers. These regions are characterized by typical DNA modifications and Mediator co-occupancy (MED1 and MED12). Altogether, we provide evidence that SIM2 binds a specific set of enhancer elements thus explaining how SIM2 can regulate its gene network in DS neuronal features.

overall_design: ChIP-Seq analysis of transcription factor binding sites in mES cells: Sim2 (in 3 replicates named A6, B8, C4 and in a control line named EB3), Oct4, Sox2, Nanog, Med1 and Med12 (in the A6 line).

first: Gilda

last: Cobellis

first: Alexandre

last: Fort

first: Federico

middle: A

last: Santoni

first: Marco

last: Garieri

first: Emilie

last: Falconnet

first: Pascale

last: Ribaux

first: Anne

last: Vannier

first: Michel

last: Guipponi

first: Piero

last: Carninci

first: Christelle

last: Borel

first: Stylianos

middle: E

last: Antonarakis


title: HSA21 Single-minded 2 (Sim2) binding sites co-localize with super-enhancers and pioneer transcription factors in pluripotent mouse ES cells [RNA-Seq]

overall_design: RNA-Seq analysis in Sim2 expressing cells (3 replicates A6, B8, C4) and EB3 control cells (3 replicates)


title: HSA21 Single-minded 2 (Sim2) binding sites co-localize with super-enhancers and pioneer transcription factors in pluripotent mouse ES cells.


title: Kinetics of transposon-derived transcripts and piRNAs in the absence of DNA methylation during mouse spermatogenesis

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie


title: Transposon-derived piRNA production in pre-natal and post-natal stages, in Dnmt3L and Miwi2 mutant tetses [small RNA-seq]

summary: We examined the kinetics of production of mRNAs and small RNAs derived from transposable elements during mouse spermatogenesis, in whole gonads of wildtype and DNA methylation-deficient males (Dnmt3L and Miwi2 mutants). We found that in absence of DNA methylation, transposon reactivation is not constitutive but rather occurs in a class- and development-specific manner : both the intensity of reactivation and the number of reactivated transposon classes increased as germ cells progress in meiosis. Moreover, we observed that transposon silencing before meiosis is not due to increased cleavage by the piRNA machinery. In contrast, the burst of transposon transcripts occurring at meiosis in the absence of DNA methylation serve as substrates for increased piRNA production

overall_design: Six whole testis samples were analyzed. Dnmt3L mutant animals were analyzed at 16.5dpc and 10dpp, and Miwi2 mutant animals at 10dpp, in parallel with control littermates.  For 16.5dpc, testes from 7/8 mice were pooled per genotype. For 10dpp, three mice were pooled per genotype.

first: Deborah

last: Bourc'his


title: Deep sequencing identify small molecule modulated microRNAs in the J1 mESCs

city: Yangling

first: Juan

last: Du

state: China/Shaanxi

address: 3 Taicheng Road

institute: College of Life Sciences

summary: Many small molecular compounds reported were involved in improving reprogramming efficiency during inducing pluripotent stem cells (iPSC) or maintain a blastocyst-like state in embryonic stem cells (ESC), including BIO, CHIR99021 (CHIR), and vitamin C et al. However, the knowledge about these small molecules regulating miRNAs in ESC was limited. To understand the role of miRNAs during small molecules induced ESC maintenance and gain an insight how these small molecules regulates miRNAs expression; we performed small RNA sequencing using Illumina HiSeq 2000 under the compounds treatment.The data show the miRNAs regulated by SB431542

overall_design: J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented with SB431542 for 24 hours, J1 treated with DMSO were set as the control treatment. Then total RNA was extracted for analysis.

first: Yongyan

last: Wu

first: Zhiying

last: Ai

first: Xiaoyan

last: Shi

first: Zekun

last: Guo


title: ALKBH5 is a New Mammalian Nuclear RNA Demethylase that Affects RNA Metabolism

city: Beijing

first: Shuhui

last: Song

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

summary: To identify ALKBH5-binding RNA, PAR-CLIP was performed to pull down ALKBH5-binding RNAs. After digestion with Rnase T1, small RNA-seq was performed. Through analysis of 50 million reads, we have found 933 ALKBH5-binding genes, among which mRNA accounts for 85%. further analysis revealed that ALKBH5 mainly binds to intron and exon region of mRNAs. among 933 genes,64 genes have been reported to be spermatogenesis related, and most of them are functionally related with p53 signaling. we have also found 9 consensus binding motifs based on the clusters significantly detected in RIP sample.

overall_design: There are two samples, RIP and CON. RIP sample is the RNA product specifically immunoprecipitated by ALKBH5 antibody, while CON means RNA product nonspecifically bound by IgG and protein A-sepharose 4B。

first: Yun-gui

last: Yang

first: Yamei

last: Niu


title: Dispersal, flight metabolism and gene expression in the Glanville fritillary butterfly

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

summary: We have measured flight effect in gene expression using individual-based RNA-seq data from two regional populations of the Glanville fritillary butterfly (Melitaea cinxia). Largest number of differentially expressed genes were between populations (3840 genes) and between males and females (1622 genes). 801 genes had significant flight effect. Enriched GO and KEGG categories among these genes included hypoxia, glycolysis, and TCA cycle.

overall_design: RNA-seq from thorax, 85 individuals from two populations in four groups (Flight and Control at two time points 1h and 20h). Populations 'AL' and 'PT' refer to two islands in Baltic Sea. 'AL' stands for Ã...land and 'PT' stands for Pikku TytÃ¤rsaari.

first: Jouni

last: Kvist

first: Anniina

last: Mattila

first: Virpi

last: Ahola

first: Petri

last: Auvinen

first: Lars

last: Paulin

first: Patrik

last: Koskinen

first: Liisa

last: Holm

first: Minna

last: Taipale

first: Jussi

first: Mikko

last: Frilander

first: Rainer

last: Lehtonen

first: Ilkka

last: Hanski


title: Role of Hopx in myogenesis and commitment [ChIP-Seq]

first: Kyoung Jae

last: Won

summary: Hopx is expressed in cardiomyoblasts, progenitors commited to the myocyte fate. ChIP-seq experiements were performed to understand Hopx occupancy in E9.5 hearts. An epitope tagged allele, in which a 3X-Flag sequence is appeneded to the endogenous Hopx transcript. Our results suggest that Hopx occupancy is enriched in regions close to Wnt family members, confirmed by gene ontology analysis and indepedent expression analysis.

overall_design: E9.5 hearts were microdissected and collected from Hopx3XFlag/+ embryos. Approximately 30-40 (5-6 litters) crosslinked hearts were pooled and sheered. ~10 ug of sheered chromatin was used in ChIP experiments. Each experiment contains a set of ChIP DNA product: input (background control) and IP as the Hopx binding product. Background noise was subtracted and signal was used in analyses. Since Hopx is a cofactor, and does not bind DNA directly, one sample included crosslinking in the presence of EGS (Ethylene glycol bis[succinimidylsuccinate]) in addition to formaldehdye, while the other replicate only included crosslinking in the presence of formaldehyde only.

first: Rajan

last: Jain

first: Lauren

last: Manderfield

first: Kyoung-Jae

first: Jonathan

last: Schug

last: Epstein


title: A Class of H3K4me1/H3K9me2 marked active GATA2 enhancers directs a GATA2-dependent transcription program underlying prostate cancer progression.

city: San Antonio

first: Zhenqing

last: Ye

state: Texas

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: The University of Texas Health Science Center at San Antonio

first: Dayong

last: Wu

first: Qianben

last: Wang


title: Identification of subset-specific dendritic cell progenitors reveals early commitment in the bone marrow

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network


title: RNA-seq analysis of S. pyogenes SP-PTP mutants

city: Columbus

first: Vijay

last: Pancholi

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

summary: We report the mRNA expression profile of Streptococcus pyogeens Type M1 strain M1T15448-derived mutant lacking phospotyrosine phosphatase.

overall_design: Measuring transcriptome profiling in M1T1DPTP mutants vs M1T1-WT5448 strain


title: Che-1 modulates the decision between cell cycle arrest and apoptosis by its binding to p53.

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

summary: The tumor suppressor p53 is mainly involved in the transcriptional regulation of a large number of growth-arrest- and apoptosis-related genes. However, a clear understanding of which factor/s influences the choice between these two opposing p53- dependent outcomes remains largely elusive. We have previously described that in response to DNA damage, the RNA polymerase II binding protein Che-1/AATF transcriptionally activates p53. Here, we show that Che-1 binds directly p53. This interaction essentially occurs in the first hours of DNA damage, whereas it is lost when cells undergo to apoptosis in response to post-transcriptional modifications. Moreover, Che-1 sits in a ternary complex with p53 and the oncosuppressor Brca1. Accordingly, our analysis of genome-wide chromatin occupancy by p53 revealed that p53/Che1 interaction results in preferential transactivation of growth-arrest p53 target genes over its pro-apoptotic target genes. Notably, exposure of Che-1+/- mice to ionizing radiations resulted in enhanced apoptosis of thymocytes, compared to wild-type mice. These results confirm Che-1 as an important regulator of p53 activity and suggest Che-1 to be a promising yet attractive drug target for cancer therapy.

overall_design: ChIP-Seq for p53 in control (DNA damage, IR) and Che-1 depleted Hct116 cells

first: Agata

last: Desantis

first: Tiziana

last: Bruno

first: Valeria

last: Catena

first: Francesca

last: De Nicola

first: Frauke

last: Goeman

first: Paolo

last: D' Onorio De Meo

first: Maurizio

last: Fanciulli


title: Identification of subset-specific dendritic cell progenitors reveals early commitment in the bone marrow [RNA-Seq]

summary: Dendritic cells (DCs) are antigen sensing and presenting cells that are essential for effective immunity. Existing as a multi-subset population, divided by distinct developmental and functional characteristics1,2, DC subsets play important and unique roles in responses to pathogens, vaccines and cancer therapies, as well as during immune-pathologies. Therefore therapeutic manipulation of the DC compartment is an attractive strategy. However, our incomplete knowledge of the inter-relationship between DC subsets and how they develop from progenitors in the bone marrow (BM) has so far limited the realization of their therapeutic potential. DCs arise from a cascade of progenitors that gradually differentiate in the BM; first, the macrophage DC progenitor (MDP), then common DC progenitor (CDP), and lastly the Pre-DC, which will leave the BM to seed peripheral tissues before differentiating into mature DCs3,4. While the basic outline of this process is known, how subset commitment and development is regulated at the molecular level remains poorly understood. Here we reveal that the Pre-DC population in mice is heterogeneous, containing uncommitted Ly6c+/-Siglec-H+ cells as well as Ly6c+Siglec-H- and Ly6c-Siglec-H- sub-populations that are developmentally fated to become Th2/17-inducing CD11b+ DCs and Th1-inducing CD8α+ DCs, respectively. Using single cell analysis by microfluidic RNA sequencing, we found that DC subset imprinting occurred at the mRNA level from the CDP stage, revealing that subset fate is defined in the BM and not in peripheral tissues. Single cell transcriptome analysis allowed identification of the molecular checkpoints between progenitor stages and revealed new regulators of DC-poiesis, shedding light on the role of cell cycle control and specific transcription factors in DC lineage development. These data advance our knowledge of the steady-state regulation of DC populations and open promising new avenues for investigation of the therapeutic potential of DC subset-specific targeting in vivo to improve vaccine-based and immunotherapeutic strategies.

overall_design: Single cell mRNA sequencing was used to investigate the transcriptomic relationships within the Dendritic cell precursor compartment within the BM as well as between single Dendritic cell precursors

first: Andreas

last: Schlitzer

first: Jinmiao

last: Chen

first: V

last: Sivakamasundari

first: Paul

last: Robson

first: Michael

last: Poidinger

first: Florent

last: Ginhoux


title: Next generation sequencing facilitates quantitative analysis of GATA2 binding profile in LNCaP cells.

first: Zhenqing

last: Ye

summary: We find  36,797 high-confidence (p<1E-8) GATA2 binding sites and  GATA2 bound primarily to distal elements in LNCaP cells.

overall_design: Examination of GATA2 binding sites in biological duplicate LNCaP samples.

first: Dayong

last: Wu

first: Qianben

last: Wang


title: Genome-wide maps of H3K9me3 and H3K4me3 state in failing heart with or without chaetocin in animal model

status: Public on May 31 2015

city: Shimotsuke

first: Ruri

last: KANEDA

state: Tochigi

address: 3311-1 Yakushiji

institute: Jichi Medical University

summary: Epigenetic status has been linked to cardiac hypertrophy and heart failure. Histone deacetylase inhibitors are promising drugs for preventing cardiac remodeling. We previously demonstrated very different patterns of histone H3 lysine 9 trimethylation (H3K9me3) and histone H3 lysine 4 trimethylation (H3K4me3) in failing hearts compared to control hearts in both animal models and clinical heart specimens. Here, we focused on a heart failure-specific histone modification, H3K9me3, and investigated the prognostic efficacy of administering a histone H3K9 methyltransferase inhibitor, chaetocin, to Dahl salt-sensitive rats, an animal model of heart failure. Chaetocin delayed the timing of transition from cardiac hypertrophy to heart failure, and prolonged survival in this animal model. Mitochondrial dysfunction was improved with inhibitor use in the failing heart. ChIP-seq analysis demonstrated that heart failure caused an increase in H3K9me3 alignments in thousands of repetitive elements, including regions neighboring mitochondrial genes, and a corresponding reduction of this effect with inhibitor use. However, at 35 loci, heart failure was conversely associated with a reduction in H3K9me3 alignments, and inhibitor use reversed this effect. These data suggest that excessive heterochromatinization of repetitive elements in the failing heart might impair pumping function with mitochondrial gene silencing. H3K9 methyltransferase inhibitors may be a promising novel therapy for chronic heart failure.

overall_design: Examination of 2 different histone modifications in 3 groups of rats.

first: Tomohiko

last: Ono

last: Kaneda


title: Genome-wide maps of chromatin state in pluripotent human embryonic stem cells.

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

institute: Stem Cell and Brain Research Institute

summary: We defined the genome-wideH3K4me3 and H3K27me3 chromatin profile of human ESCs in the primed state (F) and the naive state (TL2i).

overall_design: Examination of 2 different histone modifications marks in primed and naive human ESCs.

first: Pierre

last: Savatier


title: Expression profiling of small RNAs in wild type and Osaba1-1 rice seedlings

first: Qiu

last: Jin-Long

state: Beijing

address: 1 Beichen West Road,Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: We aimed to identify putative ABA-regulated miRNAs expressed in rice by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from Osaba1-1 and wild type rice leaves, and more than ten million small RNA sequence reads were generated for each library. We identified 13 ABA-regulated miRNAs via expression profiling of the miRNAs based on a comparative miRNAomic analysis in combination with experimental validation. To the best of our knowledge, this is the first report of a systematic investigation of ABA-regulated miRNAs and their targets in rice.

overall_design: Examination of 2 different small RNA expression profilings in the wild type and Osaba1-1 rice samples.

first: Z

last: Zuo

first: J

last: Qiu


title: Hi-seq 2000 sequencing facilitates quantitative analysis of transcriptomes in LNCaP cells with or without SiGATA2 treatment.

summary: We obtained 1,367 GATA2 up-regulated and 759 GATA2 down-regulated genes (p< 0.001).

overall_design: mRNA profiles of LNCaP cell treated with or without SiGATA2 were generated by deep sequencing  in duplicate using Hi-Seq 2000.


title: Gene expression by RNA_Seq

city: Xiamen

first: Dawang

last: Zhou

state: Fujian

address: Xiang'An south Rd

department: State Key Laboratory of Cellular Stress Biology

institute: School of Life Sciences,Xiamen Univeristy

summary: Analysis of gene expression modulated by TUDCA in primary mouse hepatocytes through RNA-Seq

overall_design: We sequenced mRNA from 2 independent experiments to generate gene expression modulated by TUDCA

first: Zhou

last: Dawang

first: Chen

last: Lanfen


title: Natural Variation and Timing of Stress Responses Promote and Predict Heterosis

city: Austin

first: Z Jeffrey

middle: Jeffrey

last: Chen

state: TX

address: 2506 Speedway NMS 3.122 Stop A500

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: Hybrid plants and animals grow larger and more vigorously than the parents, a common phenomenon known as hybrid vigor or heterosis. Heterosis often correlates with the genetic distance between hybridizing parents, but the mechanism for this is largely unknown. We found that genetic distance was correlated with natural variation of stress responses under the control of the circadian clock. CIRCADIAN-CLOCK-ASSOCIATED1 (CCA1) and LATE-ELONGATED-HYPOCOTYL (LHY) or CCA1 alone mediate expression amplitudes and periods of these stress-responsive genes in stress and non-stress conditions.  In Arabidopsis thaliana intraspecific hybrids, genome-wide expression of many biotic and abiotic stress-responsive genes was diurnally repressed to promote biomass heterosis, which is associated with several biomass quantitative trait loci (QTLs).  Expression differences in four selected stress-responsive genes among ten ecotypes could be used to predict heterosis in their hybrids.  Parent plants with larger expression differences between stress-responsive genes produced higher-vigor hybrids, while those with smaller differences produced lower-vigor hybrids.  Stress-responsive genes were epigenetically repressed in the hybrids under normal conditions but induced during times of stress at certain times of the day, balancing the tradeoff between stress responses and growth.  Consistently, repressing the stress genes in diploids increased growth vigor.  We demonstrate how hybrids manipulate diurnal stress-responsive gene expression to enhance growth vigor.  Both circadian and epigenetic regulation play key roles in the altered expression of stress-responsive genes in hybrids.  Our findings provide a conceptual advance and mechanistic understanding of heterosis, as well as selection criteria for parents to be effectively used for producing high-yield hybrids.

overall_design: Examination of gene expression in Arabidopsis thaliana F1 hybrids between Col and C24 and 3 time points using mRNA-seq

first: Miller

last: Marisa

first: Qingxin

last: Song

first: Xiaoli

last: Shi

first: Thomas

last: Juenger

first: Jeffrey

middle: Z


title: Transposon expression kinetics in Dnmt3L-/- developing testes [RNA-seq]

first: Nicolas

last: Servant

overall_design: Six whole testis samples were analyzed, corresponding to three time points (16.5dpc, 10dpp and 20dpp) each for Dnamt3L-/- animals and control littermates. For 16.5dpc, testes from 7/8 mice were pooled per genotype. For the other stages, three mice were pooled per genotype.

first: Deborah

last: Bourc'his


title: Condensin mediates the chromosomal clustering of highly transcribed genes  in bacteria

status: Public on May 29 2015

city: Pasadena

first: Long

last: Cai

state: California

address: 1200 E.california blvd

department: Chemistry and chemical engineering

institute: Caltech

summary:
Purpose: Study  MukB, RNAP, TopA, and ParC binding profiles on E.coli chromosome.
Methods: We constructed affinity tagged MukB, ParC, and TopA strains, and immunoprecipitated using anti-FLAG antibodies as well as an RNAP primary antibody.
Results: MukB, RNAP, TopA, and ParC were all bound to rDNAs on the coding sequences, as well as the coding regions of 244 highly transcribed genes, including tRNAs, genes coding for ribosomal proteins, housekeeping genes (for example, atpA and rpoB), as well as OriC.
Conclusions:  We found that the bacterial condensin, MukB, is recruited to actively transcribed genes such as rDNA through transcription induced supercoiling.

overall_design: E.coli CHIPseq on Illumina HiSeq machine.

first: Timur

last: Zhiyentayev

first: Wen

first: William

last: Letsou


title: RING1B O-GlcNAcylation regulates gene targeting of Polycomb Repressive Complex 1 in human embryonic stem cells

first: Chadi

last: El Farran

address: 61 Biopolis Drive

institute: Institute of Molecular and Cell Biology

summary: We report the DNA binding profile of RING1B (ChIP_HA) and O-GlcNAcylated RING1B (re-ChIP_WGA) in human embryonic stem cells (hESC).

overall_design: HA-RING1B was recombinantly expressed in hESC. DNA bound by HA-RING1B was enriched through HA-ChIP. DNA bound by O-GlcNAcylated HA-RING1B was enriched thourgh WGA-ChIP.

first: Julien

middle: J

last: Maury

last: EL Farran

first: Yuin-Han

last: Loh

first: Andre

last: Choo


title: RNA-seq analysis of MEF cell transcriptome after Salmonella Typhimurium infection

city: Amsterdam

first: Jeroen

last: Bakker

address: Plesmanlaan 121

department: Cell Biology II

country: Netherlands

institute: NKI

summary: We infected Mouse Embryonic Fibroblast and cultured them in anchorage independent conditions to study tranformation induced by the bacterium. We cultured these transformed cells multiple rounds in the presence of Ciprofloxacin to remove intracellular Salmonella after transformation occured. By doing RNA sequencing we indentified genes of which expression was altered upon infection. This helps us to understand how Salmonella alters the host cell, resulting in transformation

overall_design: We Cultered two biological duplicates of infected MEF cells, which we compared to a non transformed MEF control sample

first: Tiziana

last: Scanu

first: Robbert

last: Spaapen

first: Jacques

last: Neefjes


title: A resource of ribosomal RNA-depleted RNA-seq from different normal adult and fetal human tissues

first: Melissa

middle: Jane

last: Fullwood

address: 14 Medical Drive, #12-01

department: Centre for Translational Medicine

institute: Cancer Science Institute of Singapore

summary: Gene expression is the most fundamental level at which the genotype leads to the phenotype of the organism. Enabled by ultra-high-throughput next-generation DNA sequencing, RNA-Seq involves shotgun sequencing of fragmented RNA transcripts by next-generation sequencing followed by in silico assembly, and is rapidly becoming the most popular method for gene expression analysis. Poly[A]+ RNA-Seq analyses of normal human adult tissue samples such as Illumina’s Human BodyMap 2.0 Project and the RNA-Seq atlas have provided a useful global resource and framework for comparisons with diseased tissues such as cancer. However, these analyses have failed to provide information on poly[A]- RNA, which is abundant in our cells. The most recent advances in RNA-Seq analyses use ribosomal RNA-depletion to provide information on both poly[A]+ and poly[A]- RNA. In this paper, we describe the use of Illumina’s HiSeq 2000 to generate high quality rRNA-depleted RNA- Seq datasets from human fetal and adult tissues. The datasets reported here will be useful in understanding the different expression profiles in different tissues.

overall_design:
mRNA profiles were generated from 2 different fetal normal tissues and 6 different adult normal tissues by high throughput sequencing using Illumina HiSeq.
Bioproject: PRJNA283012, SRA study: SRP058036

first: J

middle: Y

last: Choy

first: P

middle: L

last: Boon

first: N

last: Bertin

first: M


title: Dnmt1 is essential to maintain progenitors in the perinatal intestinal epithelium.

city: Philadelphia

first: Ellen

last: Elliott

state: PA

address: 12-164 Smilow TRC, 3400 Civic Center Blvd

institute: University of Pennsylvania Perelman School of Medicine

summary: We report that Dnmt1 is crucial during perinatal intestinal development. Loss of Dnmt1 in intervillus progenitor cells causes global hypomethylation, DNA damage, premature differentiation, and apoptosis, and consequently, loss of nascent villi. We further confirm the critical role for Dnmt1 during crypt development using the in vitro organoid culture system, and illustrate a clear differential requirement for Dnmt1 in immature versus mature organoids. These results demonstrate an essential role for Dnmt1 in maintaining genomic stability during intestinal development and the establishment of intestinal crypts.

overall_design: We performed RNA-Seq of control and Dnmt1-ablated intestinal progenitor cells isolated from parrafin embedded tissues by laser capture microdissection (LCM).

first: Klaus

last: Kaestner


title: Congenital scolisis may be associated with both of rare mutation and allele-specific methylation

city: ShenZhen

first: Zhixiang

last: Yan

address: Beishan Industrial Zone, Yantian District

institute: BGI

summary: Congenital scoliosis (CS) is a congenital disease that results in anomalous vertebral development. Research indicates that both genetic and environmental factors during pregnancy contribute to the risk of CS development, however, the exact mechanisms underlying CS pathogenesis remain unclear.  To address this issue, we have generated both genetic (by exon capture sequencing) and epigenetic (by MeDIP) maps from a CS disease-discordant monozygotic twin pair. We compared the differences in the presence of common and rare SNPs between the twins as well as investigated differences in methylation patterns. Our data indicated that rare mutations are more likely to underlie CS development than common mutations, and that these are also more likely to play a role than do genomic methylation patterns. We did, however, identify a difference in the allele-specific-methylation between the twins in the SVIL gene which has functions in categories relevant to this disease, which raises the possibility of a novel mechanism promoting CS pathogenesis.

overall_design: DNA was extracted from peripheral blood of a monozygotic twin pair that was discordant for CS, with T-P affected with CS and T-H non-affected. Followed by MeDIP-seq and exome-seq.

first: Xuesong

last: Zhang

first: Qian

last: Zhao


title: Global analysis of mouse polyomavirus infection reveals dynamic regulation of viral and host gene expression

city: Boston

first: Seth

last: Garren

state: MA

address: 185 Cambridge St

department: Systems Biology

institute: Massachusetts General Hospital

summary: We have used deep sequencing to follow polyomavirus infection of mouse NIH3T6 cells.  We carried out RNA-seq at various times after infection and analyzed the host transcriptomes.  Alignment of sequencing reads to the host genome showed that by late times in infection, 359 host transcripts were seen to be upregulated and 857 were downregulated more than 1.5 fold.

overall_design: Infect NIH 3T6 cells with the Py59RA strain of polyomavirus at an MOI of 50 and harvest RNA from 12, 18, 24, 36 hours from infected and mock samples to compare host transcription.

first: Michael

middle: O

last: Duff

first: Gordon

middle: G

last: Carmichael


title: Chromatin context and ncRNA highlight physiological targets of MECP2 in brain.

status: Public on May 30 2015

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

summary: Analysis of chromatin and sequence context and RNA highlighting MeCP2 function in the genome

overall_design: ChIP-seq data uses 2 libraries for each sample comprising a bound and input reference, RNA-seq data uses MeCP2 null sample compared with 2 wild type replicate samples, Methylminer-seq data uses 1 high methylation sample and 1 low methylation sample, RNA-immunoprecipitated data uses 3 replicate samples.

first: Scott

last: Maxwell

first: Gregory

last: Pelka

first: Patrick

last: Tam


title: Activation of proto-oncogenes by disruption of chromosome neighborhoods [chIA-PET]

status: Public on May 28 2015

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: Mutations such as gene fusion, translocation and focal amplification are a frequent cause of proto-oncogene activation during tumorigenesis, but such mutations do not explain all cases of proto-oncogene activation. Here we show that disruption of local chromosome conformation can also activate proto-oncogenes in human cells. We mapped chromosome structures in T-cell acute lymphoblastic leukemia (T-ALL), and found that active oncogenes and silent proto-oncogenes generally occur within insulated neighborhoods formed by the looping of two interacting CTCF sites co-occupied by cohesin. Recurrent microdeletions frequently overlap neighborhood boundary sites in T-ALL genomes, and we demonstrate that site-specific perturbation of loop boundaries is sufficient to activate the respective proto-oncogenes in non-malignant cells. We found somatic genomic rearrangements affecting loop boundaries in many cancers. These results suggest that chromosome structural organization is fundamental to identify functional somatic alterations in cancer genomes.

overall_design: Two replicates of SMC1 ChIA-PET in T-ALL Jurkat Cells

first: Denes

last: Hnisz

first: Abraham

middle: S

last: Weintraub

first: Zi

middle: P

last: Fan

first: Brian

last: Abraham

first: Alla

last: Sigova

first: Jessica

last: Reddy

first: Tong

middle: I

last: Lee


title: Interaction and Signaling Between a Cosmopolitan Phytoplankton and Associated Bacteria

city: Seattle

first: E.

middle: Virginia

last: Armbrust

state: WA

address: Ben Hall IRB, 616 NE Northlake Pl, Room 306

department: Oceanography

institute: University of Washington

summary: We isolate the cultivable microbiome of a diatom and show that different bacteria have commensal, antagonistic, or synergistic effects on the diatom. One synergistic bacterium enhances growth of the diatom by production of auxin, a phytohormone. The diatom and its synergistic bacterium appear to use auxin and tryptophan as signaling molecules that drive nutrient exchange. Detection of auxin molecules and biosynthesis gene transcripts in the Pacific Ocean suggests that these interactions are widespread in marine ecosystems.

sample_organism:
Pseudo-nitzschia multiseries
Sulfitobacter sp. SA11

overall_design: Transcriptomes were collected for triplicate diatom cultures harvested at the mid-exponential growth phase in the defined seawater medium Aquil either without any bacteria, i.e. axenic (control), or with a Sulfitobacter sp. SA11 that was previously isolated from the diatom (Pseudo-nitzschia multiseries). In addition, transcriptomes were collected for triplicate bacterial cultures (Sulfitobacter sp. SA11) harvested at the mid-exponential phase in the defined seawater medium Aquil either without the diatom (supplemented with 1 uM glucose to allow for bacterial growth) or with the diatom (P. multiseries strain PC9). The SOLiD sequencer (version 4) was used to generate the transcriptomes and the SEAStAR software package was used to process the SOLiD reads and to calculate gene counts. For the diatom transcriptome, pooled counts for the +bacterium treatment were normalized to pooled counts for the axenic “control” treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor. For the bacterial transcriptome, pooled counts for the +diatom treatment were normalized to pooled counts for the +glucose “control” treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor.

first: Shady

last: Amin

first: Laura

last: Hmelo

first: Bryndan

last: Durham

first: Chris

middle: T

last: Berthiaume

first: Matthew

middle: M

last: Parsek

first: Rhonda

last: Morales

first: Mary

last: Moran

first: E

middle: V


title: Activation of proto-oncogenes by disruption of chromosome neighborhoods

first: Richard

middle: A

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of cellulolytic fungus Penicillium oxalicum and transcription factor mutant strains in response to different carbon sources

city: Qingdao

first: Guodong

last: Liu

state: Shandong

address: Binhai Road 72

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: RNA-seq was used to compare the responses of Penicillium oxalicum strains to different carbon sources including carbon-starvation, glucose and cellulose. The wild-type strain and transcription facor (ClrB, CreA and AmyR) mutants were studied.

overall_design: A total of 24 samples were analzyed, which include biological triplicates. The wild-type strain cultured without carbon source was considered as a reference.

first: Zhonghai

last: Li

first: Guangshan

last: Yao

first: Ruimei

last: Wu

first: Liwei

last: Gao

first: Qinbiao

last: Kan

first: Yuqi

last: Qin

first: Xin

last: Song

first: Yaohua

last: Zhong

first: Xu

last: Fang

first: Yinbo

last: Qu


title: Activation of proto-oncogenes by disruption of chromosome neighborhoods [ChIP-Seq]

last: Young

overall_design:
CTCF ChIP-seq and input control in Jurkat T-ALL cells

H3K27Ac, RUNX1, and GATA3 ChIP-seq and input control in Jurkat T-ALL cells

CTCF ChIP-seq and input control in wildtype and mutant HEK293T cells

first: Denes

last: Hnisz

first: Abraham

last: Weintraub

first: Zi

last: Fan

first: Brian

last: Abraham

first: Alla

last: Sigova

first: Jessica

last: Reddy

first: Tong

last: Lee


title: RNA sequencing of cells treated with DMSO or Retinoic acid during cardiac differentiation

city: Leiden

first: Nannan

last: He

address: Einthovenweg 20

institute: Leiden University Medical Center

summary: Analysis of transcriptional differences between control and RA-treated cells during cardiac differentiation. The hypothesis tested in these samples is that addition of RA during differentiation towards atrial-like cardiomyocytes while control cells treated with DMSO result in ventricular-like cardiomyocytes.

overall_design: NKX2.5 (eGFP/w)-hESCs were differentiated to cardiomyocytes with spin EB protocol, with the addition of RA or DMSO. Cells were sorted at day-31 based on GFP resulting in CTplus, CTminus, RAplus or RAminus goups. RNA was isolated from each of these fractions for sequencing.

first: Matthias

last: Roost

first: Liesbeth

last: van Iperen

first: Yavuz

last: Ariyurek

first: Henk

last: Buermans

first: Wibowo

last: Arindrarto

first: Harsha

middle: D

last: Devalla

first: Robert

last: Passier

first: Christine

last: Mummery

first: Françoise

last: Carlotti

first: Eelco

last: de Koning

first: Erik

middle: W

last: van Zwet

first: Jelle

last: Goeman

first: Susana

last: de Sousa Lopes


title: Genome-Wide Specificity of DNA-Binding, Gene Regulation, and Chromatin Remodeling by TALE- and CRISPR/Cas9-Based Transcription Factors

city: Durham

first: Gregory

last: Crawford

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

summary: Use DNase-seq to assess genome-wide chromation remodeling which occurred in CRISPR/Cas9 and TALE genome engineering systems

overall_design: Determining  chromatin structural changes in transfected cells vs. the parent HEK293T cells

first: Lingyun

last: Song


title: Identification of AP2-O targets

city: tsu

first: masao

last: yuda

address: edobashi 2-174

institute: mie university

platform_organism:
Plasmodium berghei
Plasmodium berghei ANKA


title: A human fetal transcriptional atlas

first: Nannan

last: He

summary: Gene expression is highly dynamic during fetal development and determines tissue specification and function. In humans, the transcriptional profile of different organs during development has not been systematically studied. However, understanding how a particular tissue acquires its tissue identity will give insight into the development and maturation of tissues from a developmental biology perspective.

overall_design: Next-generation sequencing (DeepSAGE) dataset of 111 RNA samples representing 21 different human fetal organs and the maternal endometrium at three timepoints (gestational ages) during first and second trimester development (W9, W16-18, W22)

last: Chuva de Sousa Lopes


title: H3K9me3 ChIP-seq in HeLa cells lacking TASOR, MPP8, periphilin and SETDB1

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: We performed ChIP-seq to measure H3K9me3 levels in wild-type HeLa cells and HeLa cells lacking TASOR, MPP8, periphilin and SETDB1 generated through CRISPR/Cas9-mediated gene disruption.

overall_design: H3K9me3 ChIP-seq using the Abcam antibody ab8898

first: Richard

last: Timms

first: Paul

last: Lehner


title: H3K9me3 ChIP-seq in KBM7 cells

summary: We performed ChIP-seq to measure H3K9me3 levels in KBM7 cells


title: Transfer RNAs mediate rapid adaptation of Escherichia coli under oxidative stress

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

institute: Jinan University

summary: We performed tRNAome sequencing to assess the tRNA changes of E.coli under oxidative stress. We found that the global translation inhibition is caused by global down-regulation of almost all tRNA species under oxidative stress. The translation elongation speed is resumed after the cells are fully adapted to the oxidative environment.

sample_organism:
Escherichia coli BL21(DE3)
Escherichia coli BW25113

overall_design: E. coli BL21(DE3) cells were grown in M9 minimal medium under normal condition and oxidative stress (0.5mM H2O2). After application of H2O2, samples were taken at 15min, 30min and 90min. The tRNAs were sequenced. We also performed three independent biological replicates, growing cells in 15N labeled M9 minimal medium under normal conditions, to assess the reproducibility of the tRNAome sequencing.  E. coli BW25113 cells were grown in M9 minimal medium under normal condition and oxidative stress (0.5mM H2O2). After application of H2O2, samples were taken at 15min and 90min. The tRNAs were sequenced.

first: Jiayong

last: Zhong

first: Wei

last: Gu


title: The Landscape of Antisense Gene Expression in Human Cancer

city: Ann Arbor

first: Oscar

middle: Alejandro

last: Balbin

state: Michigan

address: Comprenhensive Cancer Center

institute: University of Michigan


title: Whole Genome Bisulfite Sequencing (WGBS) of cKIT+ sorted cells from 57-137 day old fetal testes and ovaries.

city: Los Angeles

first: Sofia

last: Gkountela

address: 621 Charles E Young Dr S

department: MCDB

institute: UCLA

summary: We performed WGBS analyses on 6 human fetal samples at 53-137 days of development, 4 female and 2 male. We show that methylation reprogramming in the human germline is global yet incomplete with exons, 3’UTRs and human-specific transposons remaining methylated.

overall_design: Whole Genome Bisulfite-Seq of cKIT+ cells analyzed from 4 biological samples for fetal ovaries from 57-113 days of development and 2 samples for fetal testes at 59 and 137 days of development.

first: Kelvin

middle: X

first: Tiasha

last: Shafiq

first: Wen-Wei

last: Liao

first: Joseph

last: Hargan-Calvopiña

first: Pao-Yang

last: Chen

first: Amander

last: Clark


title: Allelic imbalance is a prevalent and tissue-specific feature of the mouse transcriptome

city: Farmington

first: Stefan

middle: F

last: Pinter

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health

summary: We perform a systematic classification of allelic imbalance in mouse hybrids derived from reciprocal crosses of divergent strains. We observe that deviation from balanced biallelic expression is common, occurring in ~20% of the mouse transcriptome. Allelic imbalance attributed to genotype is by far the most prevalent class and typically is tissue-specific. However, some genotype-based imbalance is maintained across tissues and is associated with greater genetic variation, especially in 5’ and 3’ termini of transcripts. We further identify novel random monoallelic and imprinted genes, and find that genotype can compete with parental origin even in the setting of large imprinted regions.

overall_design: PolyA-selected RNA-sequencing in F1 hybrid and parental cells of Mm. musculus and Mm. castaneus origin

first: David

last: Colognori

first: Ruslan

last: Sadreyev

first: Bernhard

last: Payer

first: Eda

last: Yildirim

first: Jeannie

last: Lee


title: RNA-Seq of cKIT+ sorted cells from 53-137 day old fetal testes and ovaries and RNA-Seq of TRA-1-81+ H1 and UCLA1 hESCs.

summary: We performed RNA-Seq analyses on 15 human fetal samples at 53-137 days of development, 9 female and 5 male, and identified the transcriptional changes during the transition of human cKIT+ primordial germ cells (PGCs), the precursors of gametes, to the generation of Advanced Germline Cells. Comparing the transcriptional profile of PGCs to that of H1 and UCLA1 hESCs identifies differences between the two cell types and pinpoints molecules that can be used in the development of in vitro germ cell differentiation protocols starting from human pluripotent stem cells.

overall_design: RNA-Seq of cKIT+ cells analyzed from 6 biological samples for testes and 9 samples for ovaries from 53-137 days. 2 biological replicates of TRA-1-81+ cells sorted from H1 and UCLA1 hESCs. WGBS of cKIT+ cells analyzed from 4 biological samples of ovaries and 1 biological sample of testes at 57-137 days of development.


title: The Landscape of Antisense Gene Expression in Human Cancers [I]

summary: High throughput RNA sequencing has revealed pervasive transcription of human genome than previously anticipated. However, the extent of natural antisense transcripts (NATs) expression, their regulation of cognate sense genes, and the role of NATs in cancer remain poorly understood. Here, we use strand-specific paired-end RNA sequencing (ssRNASeq) data from 376 cancer patients covering 9 tissue types to comprehensively characterize the landscape of antisense expression. We found consistent antisense expression in at least 38% of annotated transcripts, which in general is positively correlated with sense gene expression. Investigations of sense/antisense pair expression across tissue types revealed lineage-specific, ubiquitous and cancer-specific antisense loci transcription. Comparisons between tumor and normal samples identified both concordant (same direction) and discordant (opposite direction) sense/antisense expression patterns. Finally, we provide oncoNAT, a catalog of cancer related genes with significant antisense transcription, which will enable future investigations of sense/antisense regulation in cancer.  Using oncoNAT we identified several functional NATs, including NKX2-1-AS that regulates the NKX2-1 oncogene and cell proliferation in lung cancer cells. Overall, this study provides a comprehensive account of NATs and supports a role for NATs regulation of tumor suppressors and oncogenes in cancer biology.

overall_design:
Strand-specific RNA sequencing data (ssRNASeq) of cancer and benign samples. SRP048484 (PRJNA262128).

Five samples in this series are missing raw data: GSM1630768, GSM1630773, GSM1630781, GSM1630784 and GSM1630790

first: Arul

last: Chinnaiyan


title: Combined heterozygous loss of Ebf1 and Pax5 allows for T-lineage conversion of B-cell progenitors

status: Public on May 27 2015

city: Linkoping

first: Rajesh

last: Somasundaram

address: Dept of Clinical and Experimental Medicine (IKE)

department: Microbiology and Molecular Medicine

country: Sweden

institute: Linkoping University

summary: In order to investigate how transcription factor dose impacts B-lymphocyte development, we generated mice carrying transheterozygous mutations in the Pax5 and Ebf1 genes. While combined reduction of Pax5 and Ebf1 dose had minimal impact on the development of the earliest CD19+ progenitors, these cells displayed an increased T-cell potential in vivo and in vitro. Alteration in lineage fate depended on a Notch1 mediated conversion process while no signs of de-differentiation could be detected. The differences in functional response to Notch signaling in Wt and Pax5+/-Ebf1+/- pro-B cells was reflected in the transcriptional response because even though cells of both genotypes responded by the generation of intracellular Notch1 and activation of a set of target genes, only the Pax5+/-Ebf1+/- pro-B cells down-regulated genes central for the preservation of stable B-cell identity. This report stresses the importance of transcription factor dose in lymphocyte development and suggests that Pax5 and Ebf1 collaborate to modulate the transcriptional response to Notch signaling after the generation of activated intracellular Notch1. This provides an insight to how transcription factors like Ebf1 and Pax5 preserve cellular identity during differentiation.

overall_design:
EBF-1 ChIP-seq: Cultivated CD43+IgM- cells (ProB) cells from Wt, EBF-1 +/-, PAX-5 +/- and EBF-1 +/- PAX-5 +/- (TH) were assessed for EBF-1 binding by ChIP-seq. Replicate Ebf1 ChIP-seq runs on each genotype (Wt, TH, Ebf1+/- and Pax5+/-) and corresponding inputs were pooled into one dataset and analyzed as one combined sample per genotype.
RNA-seq no treatment: Briefly, ProB-cells from C57BL/6J Ebf1+/-Pax5+/- (n=4), WT (n=4), Ebf1+/- (n=2) and Pax5+/- (n=2) were sorted and RNA extracted with Qiagen RNeasy Micro Kit. RNA was sent to UCLA Microarray Core for library preparation and were subsequently for 50 cycles of HiSeq 2000 SBS sequencing generating 20-30 million reads/sample. Data analysis was performed with Arraystar® (DNASTAR)).
RNA-seq 1 day on OP9DL1 and OP9: In short, in vitro expanded ProB-cells from C57BL/6J Ebf1+/-Pax5+/- (n=4) and WT (n=4) were exposed either on OP9 or OP9-DL1 stromal cells for 24 hours and RNA extracted with Qiagen RNeasy Micro Kit. Due to low reads, two Wt and Ebf1+/-Pax5+/- were sequenced twice. Libraries were constructed using Nugen's Ovation Ultralow Library systems and were subsequently for 50 cycles of NextSeq500 sequencing generating 20-30 million reads/sample. Data analysis was performed with Arraystar® (DNASTAR)).

first: Jonas

last: Ungerbäck

first: Josefine

last: Åhsberg

first: Tobias

last: Strid

first: Mikael

last: Sigvardsson


title: Large scale sequencing of viroid derived small RNA in Potato spindle tuber viroid infected tomato plants

city: Sherbrooke

first: Charith Raj

last: Adkar-Purushothama

state: Quebec

address: 3201 rue Jean-Mignault

department: Biochemistry

institute: Université de Sherbrooke

summary: In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. The primers were trimmed and only 21- to 24-nt long small RNAs were filtered after quality check of the raw data. The filtered 21- to 24-nt was mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm. The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism.

overall_design: Evaluation of the vd-sRNA production in PSTVd infected tomato plants by high-throughput sequencing of small RNAs.

first: Charith

middle: R

first: Jean-Pierre

last: Perreault

first: Teruo

last: Sano


title: Transcription factor trapping by RNA in gene regulatory elements (ChIP-Seq)

first: Richard

last: Young

summary: Transcription factors (TFs) bind specific sequences in promoter-proximal and distal DNA elements in order to regulate gene transcription.  RNA is transcribed from both promoter-proximal and distal DNA elements, and some DNA-binding TFs have also been shown to bind RNA.  These obsevations led us to postulate that RNA transcribed from regulatory elements contributes to stable TF occupancy at these regulatory elements.  We show here that the ubiquitously expressed TF YY1 binds to both proximal and distal regulatory elements and to the RNA species associated with these elements near active genes in embryonic stem cells.  Inhibition of transcription from these elements reduces YY1 occupancy.  In contrast, tethering of RNA species near YY1 DNA binding sites enhances YY1 occupancy.  We propose that RNA acts as trap to maintain certain TFs at active enhancer and promoter-proximal regulatory elements.  Thus, transcriptional control generally involves a positive feedback loop, where YY1 and other TFs stimulate local transcription, and newly transcribed nascent RNA reinforces local TF occupancy.   This model helps explain why TFs occupy only the small fraction of their consensus motifs in the mammalian genome where transcription is detected.

overall_design: Affinity purification (ChIP-Seq) for YY1 in mouse embryonic stem cells treated with transcription-affecting compounds

first: Alla

last: Sigova

first: Brian

middle: J

last: Abraham

first: Xiong

last: Ji

first: Benoit

last: Molinie

first: Mohini

last: Jangi

first: Yang

middle: E

last: Guo

first: Nancy

last: Hannett

first: Cosmas

middle: C

last: Giallourakis

first: Phillip

last: Sharp


first: Christopher

last: Vockley

address: 101 science drive rm 2193

summary: Synthetic DNA-binding proteins have found broad application in gene therapies and as tools for interrogating biology. Engineered proteins based on the CRISPR/Cas9 and TALE systems have been used to alter genomic DNA sequences, control transcription of endogenous genes, and modify epigenetic states. Although the activity of these proteins at their intended genomic target sites have been assessed, the genome-wide effects of their action have not been extensively characterized.  Additionally, the role of chromatin structure in determining the binding of CRISPR/Cas9 and TALE proteins to their target sites and the regulation of nearby genes is poorly understood.  Characterization of the activity these proteins using modern high-throughput genomic methods would provide valuable insight into the specificity and off-target effects of CRISPR- and TALE-based genome engineering tools. We have analyzed the genome-wide effects of TALE- and CRISPR-based transcriptional activators targeted to the promoters of two different endogenous human genes in HEK293T cells using a variety of high-throughput DNA sequencing methods. In particular, we assayed the DNA-binding specificity of these proteins and their effects on the epigenome. DNA-binding specificity was evaluated by ChIP-seq and RNA-seq was used to measure the specificity of these activators in perturbing the transcriptome. Additionally, DNase-seq was used to identify the chromatin state at target sites of the synthetic transcriptional activators and the genome-wide chromatin remodeling that occurs as a result of their action. Our results show that these genome engineering technologies are highly specific in both binding to their promoter target sites and inducing expression of downstream genes when multiple activators bind to a single promoter. Moreover, we show that these synthetic activators are able to induce the expression of silent genes in heterochromatic regions of the genome by opening regions of closed chromatin and decreasing DNA methylation. Interestingly, the transcriptional activation domain was not necessary for DNA-binding or chromatin remodeling in these regions, but was critical to inducing gene expression. This study shows that these CRISPR- and TALE-based transcriptional activators are exceptionally specific. Although we detected limited binding of off-target sites in the genome and changes to genome structure, these off-target event did not lead to any detectable changes in gene regulation.  Collectively, these results underscore the potential for these technologies to make precise changes to gene expression for gene and cell therapies or fundamental studies of gene function.

overall_design: HEK293T cells were transfected in triplicate with plasmids expressing synthetic transcription factors. The synthetic TFs were either (a) dCas9-VP64 fusion protein and a targeting guide RNA (gRNA), or (b) a TALE-VP64 fusion protein engineered to bind to a specific target site in the genome. As a control, cells were transfected with plasmids expressing GFP. After transfection, RNA-seq was used to identify both on-target and off-target binding sites for the synthetic TFs. The data in this submission were generated using the TALE transfection experiments.

first: Lauren

last: Polstein

first: Pablo

last: Perez-Pinera

first: Dewran

last: Kocak

first: Peggy

last: Bledsoe

first: Alexias

last: Safi

first: Lingyun

last: Song

first: Gregory

last: Crawford

first: Timothy

last: Reddy

first: Charles

last: Gersbach


title: Asymmetry of STAT action in driving IL-27 and IL-6 transcriptional outputs and cytokine specificity

city: Bethesda

first: Yuka

last: Kanno

state: MD

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

summary: IL-6 and IL-27 have antagonistic and overlapping functions, signal through a shared receptor subunit and employ the same downstream STAT proteins. To evaluate the degree of specificity and redundancy for these cytokines, we quantified global transcriptomic changes induced by the two cytokines and determined the relative contributions of STAT1 and STAT3 using genetic models and ChIP-seq. We found a high degree of overlap of the transcriptomes induced by IL-6 and IL-27 and extremely few examples in which the cytokines acted in opposition. Using STAT deficient cells and T cells from patients with gain-of-function STAT1 mutations, we show that STAT3 was responsible for the overall transcriptional output driven by both cytokines, whereas STAT1 was the driver of cytokine specificity. STAT1 did not compensate for the lack STAT3; on the contrary, much of STAT1 binding to chromatin was STAT3 dependent. Thus, STAT1 shapes the specific cytokine signature superimposed upon STAT3’s action.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Integrated analysis of transcriptome and transcription factor binding data from cytokine treated CD4+T cells

first: K

last: Hirahara

first: H-W

last: Sun

first: S

last: Brooks

first: G

last: Gutierrez-Cruz

last: Iwata

first: Y

first: J

last: O'Shea


title: Determinants of nucleosome positioning and their influence on plant gene expression

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Academia sinica

summary: We report the global nuclesome posiitons to study the relationship between nucleosome occupancy and gene expression in response to Coronatine in Arabidopsis

overall_design: We examined nucleosome occupancy and mRNA abundance in response to Coronatine in Arabidopsis rosette leaves

first: Shin-Han

last: Shiu


title: Activation of proto-oncogenes by disruption of chromosome neighborhoods [RNA-Seq]

first: Richard

last: Young

summary: Mutations such as gene fusion, translocation and focal amplification are a frequent cause of proto-oncogene activation during tumorigenesis, but such mutations do not explain all cases of proto-oncogene activation. Here we show that disruption of local chromosome conformation can also activate proto-oncogenes in human cells. We mapped chromosome structures in T-cell acute lymphoblastic leukemia (T-ALL), and found that active oncogenes and silent proto-oncogenes generally occur within insulated neighborhoods formed by the looping of two interacting CTCF sites co-occupied by cohesin. Recurrent microdeletions frequently overlap neighborhood boundary sites in T-ALL genomes, and we demonstrate that site-specific perturbation of loop boundaries is sufficient to activate the respective proto-oncogenes in non-malignant cells. We found somatic genomic rearrangements affecting loop boundaries in many cancers. These results suggest that chromosome structural organization is fundamental to identify functional somatic alterations in cancer genomes.

overall_design: Paired-end 80x80 Poly-A RNA-seq in Jurkat T-ALL

first: Denes

last: Hnisz

first: Abraham

middle: S

last: Weintraub

first: Zi

last: Fan

first: Brian

last: Abraham

first: Alla

last: Sigova

first: Jessica

first: Tong

last: Lee


title: Drosophila Imp iCLIP identifies an RNA assemblage co-ordinating F-actin formation

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

country: Germany

institute: MDC-Berlin

summary: In this study, we employed a combination of RIP-seq and short- and long-wave iCLIP technologies to identify transcripts associated with cytoplasmic RNPs containing the RNA-binding protein Drosophila Imp. We also made a Imp knockdown vs luciferase control experiment.

overall_design: Two biological iCLIP-seq, as well as two mRNAseq made on cells harvested on the same day. Two biological PAR-iCLIP-seq. Two biological RIP-seq, as well as two mRNAseq made on cells harvested on the same day.  Three biological mRNAseq of imp dsRNA treated cells as well as three control mRNAseq of cells treated with Luciferase dsRNA.

first: Heidi

last: Hansen

first: Simon

middle: H

last: Rasmussen

first: Sidsel

last: Adolph

first: Anders

last: Krogh

first: Jeremy

last: Sanford

first: Finn

last: Nielsen

first: Jan

last: Christiansen


title: Slit2 modifies VEGF-induced angiogenic responses in rabbit skeletal muscle by inducing capillary sprouting and decreasing vascular permeability via reduced eNOS activity

status: Public on May 26 2015

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

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

institute: University of Eastern Finland

summary:
Rationale: Slit2 is a possible modulator of vascular endothelial growth factor (VEGF) - induced angiogenesis, but its effects have not been tested in large animal models.
Objective: We studied the effect of Slit2 on therapeutic angiogenesis induced by VEGF receptor 2 (VEGFR2) ligands Vammin and VEGF-DΔNΔC in vivo in rabbit skeletal muscles. The Slit2 target genes were also studied by RNA sequencing (RNA-Seq) in endothelial cells.
Methods and Results: Adenoviral intramuscular gene transfers were performed into rabbit hindlimbs. Confocal and multiphoton microscopy were used for blood vessel imaging. Signaling experiments and gene expression analyses were performed to study mechanisms of Slit2 action. Slit2 decreased VEGFR2-mediated vascular permeability. It also reduced VEGFR2-mediated increase in blood perfusion and capillary enlargement, whereas sprouting of the capillaries was increased. Slit2 gene transfer alone did not have any effects on vascular functions or morphology. VEGFR2 activation was not affected by Slit2, but eNOS phosphorylation was diminished. The transcriptome profiling showed Slit2 downregulating angiogenesis-related genes such as nuclear receptor subfamily 4 group A member 1 (NR4A1) and Stanniocalcin-1 (STC-1) as well as genes related to endothelial cell migration and vascular permeability.
Conclusions: Combining Slit2 with VEGFs adjusts VEGFR2-mediated angiogenic effects into a more physiological direction. This possibly allows the use of higher VEGF vector doses to achieve a more widespread vector and VEGF distribution in the target tissues leading to a better therapeutic outcome while reducing excess vascular permeability.

overall_design: HUVEC mRNA profiles after adenoviral vector gene transfers in duplicate.

first: Tiina

last: Nieminen

first: Pyry

middle: I

last: Toivanen

first: Johanna

middle: P

last: Laakkonen

first: Tommi

last: Heikura

first: Kari

last: Airenne

first: Seppo

last: Ylä-Herttuala


title: Chip-seq analysis of CHD8 distribution in T47D cells

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

summary: CHD8 is an ATPase of the SNF2 family involved in ATP-dependent nucleosome remodeling. Here we report data of the occupancy of CHD8 by ChIP-seq in human breast carcinoma T47D cells under different growing conditions. We show that under normal proliferation conditions CHD8 is mostly associated with promoters. Then, cells were subjected to 48 h or serum starvation followed by stimulation with the progesterone receptor (PR) agonist R5020 or with vehicle (ethanol), for 5 and 45 minutes. R5020 induced the fast association of CHD8 with a number of intergenic or intronic regions. We found that these regions were enriched in PR binding sites. Furthermore, they were enriched in H3K4me1 and P300, typical markers of enhancers. Therefore, our data indicate that in the presence of the PR agonist CHD8 is recruited to a number of PR enhancers. In additional experiments we demonstrated that CHD8 is required for activation of PR enhancers and for transcriptional regulation of progesterone-dependent genes.

overall_design: Examination of CHD8 distribution in five different growing conditions and one IgG control sample.

first: Alicia

last: Subtil-Rodriguez


title: cKIT+ sorted cells from 57-137 day old fetal testes and ovaries

first: Sofia

last: Gkountela

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

overall_design: Refer to individual Series


title: Transcriptome-wide identification of LARP4B binding sites in HEK293 cells

city: Berlin

first: Markus

last: Landthaler

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrück-Center for Molecular Medicine

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 controlling gene expression at the post-transcriptional level. The La-related protein 4B (LARP4B) belongs to an evolutionarily conserved family of RNA binding proteins characterized by the presence of a La-module implicated in direct RNA binding. Biochemical experiments have shown previously 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 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: PAR-CLIP experiments for LARP4B in HEK293cells in two biological replicates

first: Emanuel

last: Wyler

first: Yasuhiro

last: Murakawa


title: Distinct roles of DNMT1-dependent and –independent methylation patterns in the genome of mouse ES cells

city: Dalian

first: Zhiguang

last: Li

state: Liaoning

address: 9 Lvshun Road South

department: Institute of Cancer Stem Cell, Cancer Center

institute: Dalian Medical University

summary: We generated base-resolution DNA methylomes of a series of DNMT knockout (KO) ES cells with improved coverage at highly repetitive elements. We find that DNMT1- and DNMT3a/3b-dependent activities actually work complementarily and simultaneously to establish symmetric CG methylation and CHH (H=A, T or C) methylation, and unexpectedly have “division of labor” to suppress retrotransposon long terminal repeats (LTRs) and long interspersed elements (LINEs), respectively. Our data also reveal CG density number of 30 seems like a 'threshold' to predetermine the level of methylation in wild type cells and the magnitude of methylation reduction in KO cells. Only genes with low CG number are either induced or surprisingly suppressed in hypomethylated genome. Our data unveil the concerted action of DNMT enzymes in the establishment/maintenance of methylation patterns.

overall_design: Genomic DNA from four different cell lines were treated with bisulfite and sequenced with the Illumina HiSeq platform using paired end reads.

first: Hongzheng

last: Dai

first: Beisi

last: Xu

first: Guangjing

last: Zhu

first: Teng

first: Dustin

last: Schones

first: Zhibin

last: Wang


title: hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function

city: New York

first: Sean

last: O'Keeffe

address: 701 West 168th Street

institute: Columbia University

summary: We profiled the gene expression/splicing program of normal and hnRNP U-deficient mouse hearts by RNA-seq.

overall_design: RNA-seq profiles of control and Hnrnpu mutant hearts at postnatal day 14. Hnrnpu mutant hearts were generated by breeding the Hnrnpu conditional knockout mice with Ckmm-Cre transgenic mice.

first: Junqiang

last: Ye

first: Tom

last: Maniatis


title: Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development (ChIP-seq)

city: London

first: Robert

last: Lowe

address: 4 Newark Street

department: Blizard Institute

institute: QMUL

summary: As sex determines mammalian development, understanding the nature and developmental dynamics of the sexually dimorphic transcriptome is important. To explore this, we generated 72 genome-wide RNA-seq profiles from mouse eight-cell embryos, late gestation and adult livers, together with 4 ground-state pluripotent embryonic (ES) cell lines from which we generated both RNA-seq and multiple ChIP-seq profiles. We complemented this with previously published data to yield 5 snap-shots of pre-implantation development, late-gestation placenta and somatic tissue and multiple adult tissues for integrative analysis. We define a high-confidence sex-dimorphic signature of 56 genes in eight-cell embryos. Sex-chromosome-linked components of this signature are largely conserved throughout pre-implantation development and ES cells, whilst the autosomal component is more dynamic. Sex-biased gene expression is reflected by enrichment for activating and repressive histone modifications. The eight-cell signature is largely non-overlapping with that defined from fetal liver, neither was it correlated with liver or other adult tissues analysed. Fetal and adult liver gene expression signatures are also substantially different, yet a core set of common genes showing modest dimorphic expression was identified. Dramatic sex-specific expression of olfactory receptors was found in fetal liver. Sex-biased expression differences unique to adult liver were enriched for growth hormone-responsiveness. The majority of sex-chromosome based differences identified from eight-cell embryos are also present in placenta but not somatic tissue at the same gestational age. This systematic study identifies three distinct phases of sex dimorphism throughout mouse development, and has significant implications for understanding the developmental origins of sex-specific phenotypes and disease in mammals.

overall_design: ChIP seq of Es Cell


title: Wide-spread disruption of transcription termination in HSV-1 infection: Next-generation sequencing of translational activityd by ribosome profiling

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at various times during infection with minor modification to the protocol described in Stern-Ginossar N et al., Science 2012

overall_design: Ribosome profiling was performed a 0, 1, 2, 4, 6 and 8 h post infection. Two biological replicates were analysed.

first: Andrzej

last: Rutkowski

first: Florian

last: Erhard

first: Anne

last: L'Hernault

first: Thomas

last: Bonfert

last: Schilhabel

first: Colin

last: Crump

first: Philip

last: Rosenstiel

first: Stacey

last: Efstathiou

first: Ralf

last: Zimmer

first: Lars

last: Dölken


title: Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs (RNA-Seq)

city: Singapore

first: Jingxian

last: Zhang

state: Singpaore

address: 61 Biopolis Drive Proteos

department: IMCB

institute: Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore

summary: Oxidative stress (OS) is caused by an imbalance between pro-oxidant and antioxidant reactions which leads to accumulation of reactive oxygen species (ROS) within cells. ROS can be harmful, due to their damaging effects on several cellular components, but are at the same time essential components of signaling cues. We investigate the effect of OS on the immediate early transcriptional response at a genomic level, by deep sequencing of nuclear and cytosolic RNA fractions, in in human fibroblasts treated for 30 or 120 minutes with sub-lethal doses of H2O2.  In contrast to most of the protein-coding transcriptome, OS induces de novo transient transcription of thousands of previously uncharacterized genomic loci.  We classify these stress induced long non coding RNAs (lncRNA) based on their genomic annotation and strand orientation relative to their nearest gene: distal, overlapping, terminal-associated or promoter-associated. The latter class of stress-induced promoter associated antisense lncRNAs (si-paancRNAs), is preferentially transcribed by PolII, which elongates from bidirectional promoters, enriched for specific transcription factor-binding sites (ZFP161, ZFX, MEF2A and divergent-FOS motives). Interestingly the associated sense-coding genes belong to specific functional categories (cellular response to stress and others). We finally demonstrate that a subset of si-paancRNAs associate better with the translation machinery, which is stalled, upon OS.   Most studies to date have focused on the repertoire of lncRNAs present in physiological conditions. We here report the surprising result that thousands of lncRNAs are transcriptionally upregulated upon OS from specific loci possibly playing a role in physiological or pathological response to stress.

overall_design: RNA-Sequencing profiles of nuclear and cytosolic fractions of fibroblast cell lines after 0, 30 and 120 minutes of treatment with H2O2.

first: Antonis

last: Giannakakis

first: Piroon

last: Jenjaroenpun

first: Diana

last: Low


title: Molecular signatures of heterogeneous stem cell populations are resolved by linking single cell functional assays to single cell gene expression

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

summary: The discovery of significant heterogeneity in the self-renewal durability of adult haematopoietic stem cells (HSCs) has challenged our understanding of the molecules involved in population maintenance throughout life.  Gene expression studies in bulk populations are difficult to interpret since multiple HSC subtypes are present and HSC purity is typically less than 50% of the input cell population.  Numerous groups have therefore turned to studying gene expression profiles of single HSCs, but again these studies are limited by the purity of the input fraction and an inability to directly ascribe a molecular program to a durable self-renewing HSC.  Here we combine single cell functional assays with flow cytometric index sorting and single cell gene expression assays to gain the first insight into the gene expression program of HSCs that possess durable self-renewal.  This approach can be used in other stem cell systems and sets the stage for linking key molecules with defined cellular functions.

overall_design: single-cell RNA-Seq of haematopoietic stem cells

first: Nicola

last: Wilson


title: Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development (RNA-seq)

first: Robert

last: Lowe

overall_design: Examination of the sexual dimorphisim during developmental stages of 8 Cell, Es Cell, Fetal Liver and Adult Liver


title: Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs (ChIP-Seq)

overall_design: Chromatin immunoprecipitation coupled sequencing of 2 histone modifications in BJ (hTert/sT) and total levels of RNA polymerase II after 0, 30 and 120 minutes of treatment with H2O2 in MRC5 cells.


title: Sexually dimorphic gene expression emerges with embryonic genome activation and is dynamic throughout development


title: POS-1 protects posterior gut specification by blocking GLD-3/2 polyadenylation of anterior factor neg-1

status: Public on May 25 2015

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

institute: Monash University

summary: The Poly(A)-Tail focused RNA-seq, or PAT-seq approach was utilised to determine the gene expression, poly(A)-site and polyadenylation state of the transcriptome of early C. elegans embryos having been depleated for a series of RNA binding proteins. Namely;  pos-1 and mex-5 were independently knocked down using dsRNA expressing E. coli HT115(DE3) fed to ~100,000 starved/synchronized L1 larvae. When half of the population reached adulthood and half were still in the L4 stage, worms were bleached and embryos harvested and stored in Trizol. This ensured an enrichment of early embryos between 1 and 24 cell stage. mex-6(pk440) were synchronized and grown on OP50 until the same time point and embryos harvested in the same manner. Since prolonged gld-3 and gld-2 RNAi result in sterility, starved/synchronized L1 larvae were fed diluted OP50 (200uL of concentrated OP50 diluted in 2mL of M9 and starved L1s) for 16 hours. At that point the OP50 had been mostly consumed by the larvae and concentrated gld-3 or gld-2 dsRNA expressing E. coli were added to the plates. When half of the population reached adulthood and half were still in the L4 stage, worms were bleached and embryos harvested and stored in Trizol. Total RNA was isolated using standard procedures.

overall_design: Analysis of poly(A) dynamics in early C. elegans embryos reponding to depletion of specific RNA binding proteins and adneylation state regulators

first: Ahmed

last: Elewa

first: Paul

last: Harrrison


title: Commensal microbiota constantly control maturation and function of microglia in the central nervous system

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: As tissue macrophages of the central nervous system (CNS), microglia are critically involved in diseases of the CNS. However, it remains unknown what controls their maturation and activation under homeostatic conditions. Here we reveal significant contributions of the host microbiota to microglia homeostasis as germ-free (GF) mice displayed global defects in microglia with altered cell proportions and an immature phenotype leading to impaired innate immune responses. Temporal eradication of host microbiota severely changed microglia properties. Limited microbiota complexity also resulted in defective microglia. In contrast, recolonization with a complex microbiota partially restored microglia features. We determined that short-chain fatty acids (SCFA), microbiota-derived bacterial fermentation products, regulate microglia homeostasis. Accordingly, mice deficient for the SCFA receptor FFAR2 mirrored microglia defects found under GF conditions. These findings reveal that host bacteria vitally regulate microglia maturation and function, whereas microglia impairment can be restored to some extent by complex microbiota.

overall_design: Examination of 1000 microglia cells per brain (SPF conditions: 7 samples and germ-free conditions: 7 samples)

first: Daniel

last: Erny

first: Anna

middle: L

last: Hrabě de Angelis

first: Diego

last: Jaitin

first: Peter

last: Wieghofer

first: Ori

last: Staszewski

first: Eyal

last: David

first: Hadas

last: Keren-Shaul

first: Tanel

last: Mahlakoiv

first: Kristin

last: Jacobshagen

first: Thorsten

last: Buch

first: Vera

last: Schwierzeck

first: Olaf

last: Utermöhlen

first: Eunyoung

last: Chun

first: Wendy

last: Garrett

first: Kathy

last: McCoy

first: Andreas

last: Diefenbach

last: Staeheli

first: Bärbel

last: Stecher

first: Marco

last: Prinz


title: Piwi is a key regulator of both somatic and germline stem cells in the Drosophila testis

status: Public on May 23 2015

city: New Haven

last: Liu

address: 10 Amistad st

institute: Yale University

summary: The Piwi-piRNA pathway is well known for its germline function, yet its somatic role remains elusive. We show here that Piwi is required autonomously not only for germline stem cell (GSC) but also for somatic cyst stem cell (CySC) maintenance in the Drosophila testis. Reducing Piwi activity in the testis caused defects in CySC differentiation. Accompanying this, GSC daughters expanded beyond the vicinity of the hub but failed to differentiate further. Moreover, Piwi deficient in nuclear localization caused similar defects in somatic and germ cell differentiation, which was rescued by somatic Piwi expression. To explore the underlying molecular mechanism, we identified Piwi-bound piRNAs that uniquely map to a gene key for gonadal development, Fasciclin 3, and demonstrate that Piwi regulates its expression in somatic cyst cells. Our work reveals the cell-autonomous function of Piwi in both somatic and germline stem cell types, with somatic function possibly via its epigenetic mechanism.

overall_design: Examination of Piwi-piRNAs in fly testis

first: Hongying

last: Qi


title: Pervasive genomic transcription during oxidative stress generates thousands of previously uncharacterized lncRNAs

first: Jingxian

last: Zhang


title: RNA-seq in two ER+ breast cancer cell lines with and without progestins

status: Public on May 22 2015

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary: Exploring effect of progesterone/progestin treatment on gene expression

overall_design: Two cell lines, three conditions (Full Media with E2, E2+ Progesterone, Full Media + R5020 Progestin)

first: Hisham

last: Mohammed

first: Rory

last: Stark

first: Suraj

last: Menon