title: RNA Expression Profile of Calcified Bicuspid, Tricuspid and Normal Human Aortic Valves by RNA Sequencing [BAV]

city: Quebec

first: Sandra

last: Guauque-Olarte

address: 2725, chemin Sainte-Foy

institute: CRIUCPQ

summary:
Purpose: The molecular mechanisms leading to premature development of aortic valve stenosis (AS) in individuals with a bicuspid aortic valve (BAV) are unknown. The objective of this study was to identify genes differentially expressed between calcified BAV and tricuspid valves with (TAVc) and without (TAVn) calcification using RNA sequencing (RNA-Seq).
Methods: Ten human calcified BAV and nine TAVc were collected from men who underwent aortic valve replacement. Eight TAVn were obtained from men who underwent heart transplantation. mRNA levels were measured using the Illumina HiSeq 2000 system. Reads were aligned with TopHat. Cuffdiff, DESeq, edgeR, and SAMSeq were used to compare gene expression. Genes with adjusted P < 0.05 in the four methods were called differentially expressed. Pathway analysis was performed with IPA.
Results: Two genes were up-regulated and none were down-regulated in BAV compared to TAVc. There were 462 genes up-regulated and 282 down-regulated in BAV compared to TAVn. Compared to TAVn, 329 genes were up- and 170 were down-regulated in TAVc.
Conclusions: This is the first transcriptome study on calcified and normal aortic valves using RNA-Seq. BAV and TAVc have a highly similar expression profile. These results contribute to our molecular understanding of AS and the identification of new therapeutic targets that are urgently needed to prevent, slow the development or treat AS in patients with bicuspid and tricuspid valves.

overall_design: Samples of aortic valves were collected from 10 male patients undergoing aortic valve replacement surgery. RNA sequencing was performed using the Illumina Hiseq 2000.

first: Arnaud

last: Droit

first: Simon

last: Body

first: Jonathan

last: Seidman

first: Patrick

last: Mathieu

first: Philippe

last: Pibarot

first: Yohan

last: Bossé


title: Reduced CYFIP1 in human neural progenitors as 15q11.2 deletion model: donor specific dysregulation of schizophrenia/epilepsy genes

status: Public on Sep 22 2016

city: New Haven

first: Dejian

last: Zhao

state: CT

address: 333 Cedar St

department: Genetics

country: USA

institute: Yale School of Medicine

type: Expression profiling by high throughput sequencing

summary: Deletions at 15q11.2 have been established to increase risk for multiple neurodevelopmental disorders (NDDs) including schizophrenia and epilepsy, yet show variable expressivity between individuals. To investigate the potential role of CYFIP1, a gene within the locus, we carried out knockdown experiments in human neural progenitor cells derived from 15q11.2 neutral induced pluripotent stem cells. Transcriptional profiling and cellular assays support a prominent role for CYFIP1 in cytoskeletal remodeling across all lines examined. Validating the utility of this model for study of disease, genes implicated in schizophrenia and epilepsy but not other disorders or traits unrelated to the deletion, were enriched among mRNAs dysregulated following knockdown. Importantly, and consistent with the variable expressivity of 15q11.2 deletions, the magnitude of disease-related effects varied between donor lines. Towards mechanisms, FMRP targets and synaptic genes were overrepresented among dysregulated mRNAs and as such may contribute to the schizophrenia and epilepsy effects we observe. Further model validation, and new candidate epilepsy genes, comes from machine-learning analyses showing a striking similarity between a subset of dysregulated transcripts and well-established epilepsy genes. Results provide support for an important contribution of CYFIP1 in 15q11.2 mediated risk for NDDs and demonstrate that disease-related biological signatures are evident prior to neuronal differentiation. This new human model of disease will be useful in identifying compounds that could ameliorate outcomes in deletion carriers.

overall_design: Investigation of CYFIP1 shRNA knockdown in three neural progenitor cell lines derived from induced pluripotent stem cells  (3 control samples and 3 knockdown samples analyzed in each line)

first: Rebecca

middle: A

last: Nebel

first: Erika

last: Pedrosa

first: Herbert

middle: M

last: Lachman

first: Deyou

last: Zheng

first: Brett

middle: S

last: Abarahams


title: RNA Expression Profile of Calcified Bicuspid, Tricuspid and Normal Human Aortic Valves by RNA Sequencing

country: Canada

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

overall_design: Refer to individual Series


title: RNA Expression Profile of Calcified Bicuspid, Tricuspid and Normal Human Aortic Valves by RNA Sequencing [TAV]

overall_design: Samples of aortic valves were collected from 17 male patients undergoing aortic valve replacement surgery. RNA sequencing was performed using the Illumina Hiseq 2000.

middle: C

middle: G


title: miRNAs in RPE cells treated by clusterin

status: Public on Sep 21 2016

city: Beijing

first: zi

last: ye

address: FuXing Road 28

country: China

institute: PLA General Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Clusterin has been indicated to protect human retinal pigment epithelial (RPE) cells from oxidative stress-induced apoptosis. This study was conducted to identify aberrantly expressed microRNAs (miRNAs) downstream clusterin in RPE cells.

overall_design: RPE cell line D407 were treated with clusterin and cell viability was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium (MTT) assay. Genome-wide expression analysis of transcriptome and small RNA identified from D407 cells treated with clusterin or not was performed using next generation sequencing, followed by identification of differentially expressed genes and miRNAs as well as gene ontology and pathway enrichment analyses. The miRNA-regulated gene expression network was constructed to explore the regulatory role of miRNAs.

first: Zi

last: Ye

first: Zhaohui

last: Li

first: Shouzhi

last: He


title: Determination of the influence of caNrf2 expression and/or Dextran Sulfate Sodium treatment on genome wide mRNA expression in whole colon wall or colon epithelial cells

city: Zurich

first: Isabelle

last: Frey-Wagner

address: Raemistr. 100

department: Division of Gastroenterology

country: Switzerland

institute: University hospital Zurich

summary: The transcription factor NF-E2-related factor 2 (Nrf2) is a major modulator of the cellular antioxidant response. To study the role of Nrf2 on mucosal inflammation we used transgenic mice expressing a constitutively active Nrf2 in epithelial cells and induced mucosal inflammation by administration of dextran sulfate sodium. Genome wide expression was studied by mRNA sequencing.

overall_design: mRNA profiling of epithelial cell or colon wall samples from VilCre-caNrf2 or VilCre control mice treated with/without Dextran Sulfate Sodium, each condition was performed in triplicate

first: Alexandra

last: Gerstgrasser


title: Safety and Immunogenicity of the Recombinant BCG Vaccine AERAS-422 in Healthy BCG-naïve Adults: A Randomized, Active-controlled, First-in-human Phase 1 Trial

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

summary:
We report a first-in-human trial evaluating safety and immunogenicity of a recombinant BCG, AERAS-422, over-expressing TB antigens Ag85A, Ag85B, and Rv3407 and expressing mutant perfringolysin.
Interpretation: The unexpected development of VZV in two of eight healthy adult vaccine recipients resulted in discontinuation of AERAS-422 vaccine development. Immunological and transcriptomal data identified correlations with the development of TB immunity and VZV that require further investigation.

overall_design: This was a randomized, double-blind, dose-escalation trial in HIV-negative, healthy adult, BCG-naïve volunteers, negative for prior exposure to Mtb, at one US clinical site. Volunteers were randomized 2:1 at each dose level to receive a single intradermal dose of AERAS-422 (>105–< 10e6 CFU = low dose, ≥106– < 10e7 CFU = high dose) or non-recombinant Tice BCG (1–8 × 10e5 CFU). Randomization used an independently prepared randomly generated sequence of treatment assignments. The primary and secondary outcomes were safety and immunogenicity, respectively, assessed in all participants through 182 days post-vaccination. ClinicalTrials.gov registration number: NCT01340820

first: Azra

last: Blazevic

middle: F

last: Hoft

first: Smitha

last: Shankar

first: Alan

last: Aderem

middle: E


title: Transcriptomic analysis of Penicillium oxalicum wild type and the heterochromatin protein 1 genes deletion strains

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

institute: shandong university

summary: RNA-seq was used to compare differential gene expressions for Penicillium oxalicum wild type strain and heterochromatin protein 1 knock out strains.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and hepA knoutout strain )

first: Yuqi

last: Qin

first: Yinbo

last: Qu

first: Xiujun

last: Zhang


title: RNA-Seq analysis of MRL-871 and control-treated C57BL/6 thymocytes and Rorc over-expressing cell lines

city: Boston

first: Kenzie

last: MacIsaac

state: MA

address: 33 Avenue Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck Research Labs

summary: We report the genes that are differentially expressed in thymocytes upon treatment with MRL-871 in vitro and in vivo, and by Rorc over-expression in thymic lymphoma cell lines.

overall_design: For in vitro RNA-Seq experiment, whole thymocytes from 7-9 week old C57BL/6 mice were isolated and treated with DMSO control or MRL-871 for 2hr, and collected for RNA-Seq analysis. For in vivo analysis, C57BL/6 mice were treated with vehicle control or MRL-871 for 2hr and whole thymocytes were analyzed by RNA-Seq. Rorc-/- cell line was derived from a lymphoma that spontaneously developed in the thymus of a Rorc-/- mouse. The bicistronic MIGR1 retroviral vector expressing RORγT-GFP or GFP was used to transgect the Rorc-/- cell line.

first: Yanxia

last: Guo

first: Laura

last: Engstrom


title: Genome-wide expression profile in FH-deficient (UOK262) vs FH-competent (UOK262pFH) human cells derived from metastatsis to the mediastinum of a HLRCC patient

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

summary: Comparison of the transcriptome of human kideny cancer cells either wild-type for FH or FH-deficient. The UOK262 cells were isolated from mediastinum metastasis of a HLRCC patient (Yang et al. Cancer Genetics and Cytogenetics, Volume 196, Issue 1, 1 January 2010, Pages 45–55). FH function was restored in the UOK262 by re-expressing the FH transcript from an exogenous plasmid.

overall_design: Examination of gene transciption in 2 cell types.

first: Vincent

last: Zecchini

first: Chistian

last: Frezza


title: Histone H3K36M mutation impairs mesenchymal differentiation and drives sarcoma development

status: Public on Sep 23 2016

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by high throughput sequencing


title: UtpA and UtpB chaperone nascent pre-ribosomal RNA and the U3 snoRNP to initiate eukaryotic ribosome assembly

city: Edinburgh

first: Hywel

last: Dunn-Davies

address: Max Born Crescent

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

summary: Early eukaryotic ribosome biogenesis involves large multi-protein complexes, which co-transcriptionally associate with pre-ribosomal RNA to form the small subunit processome. The precise mechanisms by which two of the largest multi-protein complexes – UtpA and UtpB – interact with nascent pre-ribosomal RNA have so far been poorly understood. We have combined biochemical and structural biology approaches with ensembles of RNA-protein cross-linking to elucidate the essential function of both complexes. Here we show that UtpA contains a large composite RNA binding site and captures the 5´ end of pre-ribosomal RNA. UtpB forms an extended structure that binds early pre-ribosomal intermediates in close proximity to key architectural sites such as an RNA duplex formed by the 5´ ETS and U3 snoRNA as well as the 3´ boundary of 18S rRNA. Both complexes therefore act as vital RNA chaperones to initiate eukaryotic ribosome assembly.

overall_design: 21 samples were analyzed in total from strains carrying HTP-tagged proteins from UTP-A and UTP-B complexes. Duplicate experiments were carried out.

first: Mirjam

last: Hunziker

first: Jonas

last: Barandun

first: Elisabeth

last: Petfalski

first: Dongyan

last: Tan

first: Hyojin

last: Kim

first: Kelly

last: Molloy

first: Clémentine

last: Delan-Forino

first: Yi

last: Shi

first: Malik

last: Chaker-Margot

first: Brian

middle: T

last: Chait

first: David

last: Tollervey

first: Thomas

last: Walz

first: Sebastian

last: Klinge


title: Response to programmed cell death-1 blockade in a murine melanoma syngeneic model requires costimulation, CD4 and CD8 T-cells

city: Los Angeles

first: Jennifer

last: Tsoi

state: CA

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

summary: The programmed cell death protein 1 (PD-1) limits effector T-cell functions in peripheral tissues and its inhibition leads to clinical benefit in different cancers. To better understand how PD-1 blockade therapy modulates the tumor-host interactions, we evaluated three syngeneic murine tumor models, the BRAFV600E-driven YUMM1.1 and YUMM2.1 melanomas, and the carcinogen-induced murine colon adenocarcinoma MC38. The YUMM cell lines were established from mice with melanocyte-specific BRAFV600E mutation and PTEN loss (BRAFV600E/PTEN-/-). Administration of anti-PD-1 or anti-PD-L1 antibody therapy had strong antitumor activity against MC38 and YUMM2.1, but not YUMM1.1. There was no difference in PD-L1 expression between the three models at baseline or upon interferon stimulation. While mutational load was high in MC38, it was lower in both YUMM models. In YUMM2.1, the antitumor activity of PD-1 blockade had a critical requirement for both CD4 and CD8 T-cells, as well as CD28 and CD80/86 co-stimulation, with an increase in CD11c+CD11b+MHC-IIhigh dendritic cells and tumor associated macrophages in the tumors after PD-1 blockade. Compared to YUMM1.1, YUMM2.1 exhibited a more inflammatory profile by RNA sequencing analysis, with an increase in chemokine-trafficking gene expression levels related to immune cell recruitment and T-cell priming. In conclusion, response to PD-1 blockade therapy in tumor models requires CD4 and CD8 T cells, and co-stimulation mediated by dendritic cells and macrophages.

overall_design: mRNA profiles of YUMM murine melanoma cell lines

first: Blanca

last: Homet Moreno

first: Jesse

last: Zaretsky

first: Angel

last: Garcia-Diaz

first: Giulia

last: Parisi

first: Lidia

last: Robert

first: Katrina

last: Meeth

first: Abibatou

last: Ndoye

first: Marcus

last: Bosenberg

first: Ashani

last: Weeraratna

last: Graeber

first: Begonya

last: Comin-Anduix

first: Siwen

last: Hu-Lieskovan

first: Antoni

last: Ribas


title: RNA-seq identified KLF16 as a negative regulator of adipogenesis

city: Daejeon

first: Lee

last: Sunwoo

address: #211, Next2Vill, 278-2, Jangdae-dong, Yuseong-gu

country: South Korea

institute: GenomicWorks

summary: We performed high throughput RNA sequencing at preadipocyte (D0) and differentiated adipocyte (D7) of primary brown preadipocyte and found that Kruppel-like factor 16 (KLF11) gene that was downregulated in D7 was a novel negative regulator of adipogenesis.

overall_design: To explore global view of gene expression during adipogenesis, RNA-seq was performed in the primary cultured brown preadipocyte (D0) and brown adipocyte after 7 day differentiation (D7).  Compared with D0, 6,668 genes were identified as 2 fold differentially expressed genes (DEGs) at D7 including 2,836-upregulated genes and 3,832 down-regulated genes.

first: Myeong

middle: H

last: Jung

first: Sunwoo

last: Lee


title: RRBS assessment of global methylation alterations alterations in Dnmt3aKO/FLT3-ITD leukemia

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

type: Methylation profiling by high throughput sequencing

summary: Using RRBS we assessed global DNA methylation changes in two mouse models of oncogenic FLT3-driven leukemia in the presence and absence of Dnmt3a.

overall_design: Mouse RRBS DNA methylation maps of Dnmt3aKO/FLT3-ITD leukemias, Dnmt3aKO/FLT3-ITD leukemias overexpressing Dnmt3a or GFP, FLT3-ITD leukemias, normal CD4+/CD8+ thymocytes, Dnmt3aKO thymocytes, heterozygous Dnmt3a/heterozygous Flt3-ITD knockin leukemias, and heterozygous Flt3-ITD knockin pre-leukemic bone marrow cells were obtained by sequencing on Illumina HiSeq 2000 or 2500.

first: Benjamin

last: Rodriguez

first: Wei

last: Li


title: Comparative analysis of Corynebacterium glutamicum transcriptome in response to expression of Egfp under the change of dissolved oxygen in bioreactor

status: Public on Sep 20 2016

city: wuxi

first: Sun

last: Yang

address: lihu avenue

department: School of Biotechnology

institute: JIANGNAN UNIVERSITY

summary: Purpose:dissolved oxygen (DO) level is an important factor that could significantly influence microorganisms’ growth, maintenance, metabolism and product yield.The goals of this study are to comparative analysis on Corynebacterium glutamicum transcriptome in response to expression of eGFP under the change of dissolved oxygen in bioreactor,find the critical pathways and genes.

overall_design: Method:three batches of fermentation were conducted with different DO level separately (50%, 30%, 0%),and sampled on 20h of fermentation,the transcriptome of Corynebacterium glutamicum generated using Illumina hiseq 2500.

first: Liu

last: Xiuxia

first: Bai

last: Zhonghu


title: Profiles of prostate cancer cell lines

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute


title: Transcriptome changes in mouse livers upon Bmal1 knock out

city: San Francisco

first: Zenghua

last: Fan

address: 1550 4th Street

institute: University of California, San Francisco

summary: To explore the circadian regulations of Bmal1, we examined the transcriptome changes in mouse livers upon Bmal1 knock out at two circadian time points, CT0 and CT12.

overall_design: RNA-seq of WT and KO at CT0 and CT12.

first: Jun

last: Yan


title: Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer (FFPE RNA-Seq II)

city: Spartanburg

first: Bernard

last: Omolo

state: SC

address: 800 University Way

department: Mathematics and Computer Science

institute: University of South Carolina - Upstate

summary:
Background: The KRAS gene is mutated in about 40% of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistatnce to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60% of patients with a wild type KRAS fail to respond to EGFRi treatment, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues.
Methods: In this study, we evaluated the translation of an 18-gene RAS pathway signature score from FF to FFPE in 54 CRC cases, using a head-to-head comparison of five technology platforms. FFPE-based technologies included the Affymetrix GeneChip (Affy), NanoString nCounter(NanoS), Illumina whole genome RNASeq (RNA-Acc), Illumina targeted RNASeq(t-RNA), and Illumina stranded Total RNA-rRNA-depletion (rRNA).
Results: Using Affy_FF as the "gold" standard, initial analysis of the 18-gene RAS scores on all 54 samples shows varying pairwise Spearman correlations, with (1) Affy_FFPE(r=0.233, p=0.090); (2) NanoS_FFPE(r=0.608, p<0.0001); (3) RNA-Acc_FFPE(r=0.175, p=0.21); (4) t-RNA_FFPE (r=-0.237, p=0.085); and (5) t-RNA (r=-0.012, p=0.93). These results suggest that only NanoString has successful FF to FFPE translation. The subsequent removal of identified "problematic" samples (n=15) and gene (n=2) further improves the correlations of Affy_FF with three of the five technologies: Affy_FFPE (r=0.672, p<0.0001); NanoS_FFPE (r=0.738, p<0.0001); and RNA-Acc_FFPE (r=0.483, p=0.002).
Conclusions: Of the five technology platforms tested, NanoString technology provides a more faithful translation of the RAS pathway gene expression signature from FF to FFPE than the Affymetrix GeneChip and multiple RNASeq technologies. Moreover, NanoString was the most forgiving technology in the analysis of samples with presumably poor RNA quality. Using this approach, the RAS signature score may now be reasonably applied to FFPE clinical samples.

overall_design: Fifty-four (54) FFPE evaluable tumor specimens were selected from a larger multi-center cohort of 468 well-characterized colorectal adenocarcinoma patients whose tissues were obtained between October 2006 and September 2010 at the University of South Florida. The sample cohort was composed of tumor samples that were available as matched fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pairs.

first: Mingli

first: Fang

middle: Y

last: Lo

first: Michael

middle: J

last: Schell

first: Sharon

last: Austin

first: Kellie

last: Howard

first: Anup

last: Madan

first: Timothy

last: Yeatman


title: Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer (FFPE RNA-Seq III)


title: Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer (FFPE RNA-Seq I)


title: Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of the double-homeodomain transcription factor DUX4 in skeletal muscle cells. Many different cell culture models have been developed to study the pathophysiology of FSHD, frequently based on endogenous expression of DUX4 in FSHD cells or by mis-expression of DUX4 in control human muscle cells. Although results generated using each model are generally consistent, differences have also been reported, making it unclear which model(s) faithfully recapitulate DUX4 and FSHD biology. In this study, we systematically compared RNA-seq data generated from three different models of FSHD—lentiviral-based DUX4 expression in myoblasts, doxycycline-inducible DUX4 in myoblasts, and differentiated human FSHD myocytes expressing endogenous DUX4—and show that the DUX4-associated gene expression signatures of each dataset are highly correlated (Pearson’s correlation coefficient, r ~ 0.75-0.85). The few robust differences were attributable to different states of cell differentiation and other differences in experimental design. Our study describes a model system for inducible DUX4 expression that enables reproducible and synchronized experiments and validates the fidelity and FSHD relevance of multiple distinct models of DUX4 expression.

overall_design: We performed a systematic comparison of DUX4-regulated changes in the transcriptome in our inducible codon-altered DUX4 expression system (iDUX4), the endogenous DUX4 expression system (enDUX4), and cells transduced with lentivirus constitutively expressing DUX4 (vDUX4). The specific datasets used in this comparison are as follows: iDUX4 represents a new dataset generated from the MB135 immortalized human myoblasts with the doxycycline inducible codon-altered DUX4 (iDUX4), performed in biological triplicate fourteen hours after DUX4 induction in growth media, with uninduced cells as a control; enDUX4 represents the published dataset of differentiated FSHD myocytes that do or do not express endogenous DUX4, as determined using a DUX4-responsive fluorescent reporter and flow sorting (9); vDUX4 represents a published dataset wherein two different myoblast cell lines (MB135 and 54-1) were transduced with a lentiviral construct that drives constitutive DUX4 expression via the PGK promoter and maintained in growth media for 24 hours (MB135) or 36 hours (54-1) prior to harvesting RNA.

first: Robert

last: Bradley

first: Sujatha

last: Jagannathan


title: Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer


title: Context-dependent effects of HP1 assessed in high throughput

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporter genes (Akhtar, Cell, 2013; PMID: 23953119) with Gal4-mediated tethering of the protein of interest. We applied the assay to Drosophila Heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein working by a chromatin compaction mechanism but has also been linked to transcriptional activation. Probing the effects of HP1a in more than one thousand genomic locations revealed that HP1a is a potent repressor able to silence even highly expressing loci. However, the local chromatin context can modulate HP1a function. In pericentromeric regions, HP1a-induced repression was enhanced by two-fold. In regions marked by a H3K36me3-rich chromatin signature linked to transcriptional elongation, HP1a-dependent silencing was significantly decreased. We found no evidence for an activating function of HP1a in our experimental system. Furthermore, we did not observe stable transmission of repression over mitotic divisions after loss of targeted HP1a recruitment in any of the loci examined.  The multiplexed tethered reporter assay will be a useful tool to dissect combinatorial regulatory interactions in chromatin.

overall_design: TRIP assay in drosophila Kc167 cells combined with targeted recruitment of Gal4-HP1 to integrated 5xGa4UAS-pMT-GFP reporters. Two technical replicate experiments of TRIP pool transfected with Gal4-HP1, Gal4 or HP1 performed by day 2 and day 16 after transient transfection.

first: Laura

last: Brueckner

first: Joris

last: van Arensbergen

first: Waseem

last: Akhtar

first: Ludo

last: Pagie


title: HP1

overall_design: Refer to individual Series


title: Genome-wide HP1a occupancy measured by DamID-seq

summary: In order to map levels of genome-wide HP1a occupancy we applied DamID (van Steensel & Henikoff, Nat Biotech, 2000; PMID: 10748524) in combination with next-generation sequencing of methylated GATC fragments. Mapping by next-generation sequencing makes it possible to examine heterochromatic regions that were not covered by earlier datasets which were generated using microarrays.

overall_design: Wild-type Kc167 cells were transiently transfected in duplicates with Dam-HP1a or Dam only and collected by two days after transfection for quantification of genome-wide methylation levels via next-geneartion sequencing.


title: Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: In the yeast genome, a large proportion of nucleosomes occupy well-defined positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genomic context remains controversial. Through genome-wide, quantitative analysis of nucleosome positioning and high-resolution mutagenenesis of mononucleosomal DNA, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes. This effect is equally detected in transcribed and non-transcribed regions, suggesting the existence of sequence elements contributing to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is species-specific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open up the possibility of designing coding and non-coding DNA molecules capable of directing their own nucleosomal organization.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Samples from mononucleosomal DNA from S. pombe strains (h- 972) and S. cerevisiae (W303) harbouring different mutant sequences,  were sequenced (Illumina NextSeq 500 platform) using the pair-end read protocol

first: Sara

last: González-Moreno

first: Alicia

last: García

last: Vázquez

first: Rebeca

last: Serrano

first: Mar

last: Sánchez

first: Luis

last: Quintales

first: Francisco

last: Antequera


title: Circadian regulation of miR-378 mediates circadian controls of cell cycle and metabolism

city: ShangHai

first: Haifang

last: Wang

address: NO 320, Yueyang Road

department: functional genomics group

institute: PICB

summary: To explore the circadian functions of the miRNAs derived from these circadian primary miRNA transcripts, we focused on miR-378 and examined the transcriptome changes in mouse livers upon miR-378 over-expression at two circadian time points, CT10 and CT22. First, we observed a significant over-representation of the circadian oscillating genes affected by miR-378 over-expression. Cell cycle genes are further enriched in the affected circadian oscillating genes, which implied that miR-378 mediates the circadian control of cell cycle. Our examination of circadian regulatory network involving miR-378 suggests that miR-378 mediates the circadian control of cell cycle and metabolism by forming either coherent or incoherent feed-forward loops with circadian TFs.

overall_design: RNA-sequencing of liver tissue from ad-null or ad-378 (miR-378 overexpression) mice at CT10 and CT22 with two biological replicates.

first: Jun

last: Yan


title: IRF8 transcription factor controls survival and function of terminally differentiated conventional and plasmacytoid dendritic cells respectively

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: Interferon regulatory factor-8 (IRF8) has been proposed to be essential for development of monocytes, plasmacytoid dendritic cells (pDCs) and type 1 conventional dendritic cells (cDC1s) and remains highly expressed in differentiated DCs. Transcription factors that are required to maintain the identity of terminally differentiated cells are designated “terminal selectors”. Using BM chimeras, conditional Irf8fl/fl mice and various promotors to target Cre recombinase to different stages of monocyte and DC development, we have identified IRF8 as a terminal selector of the cDC1 lineage controlling survival. In monocytes, IRF8 was necessary during early but not late development. Complete or late deletion of IRF8 had no effect on pDC development or survival but altered their phenotype and gene expression profile leading to increased T cell stimulatory function but decreased type 1 interferon production. Thus, IRF8 differentially controls the survival and function of terminally differentiated monocytes, cDC1s and pDCs.

overall_design: pDCs from the spleen of Irf8fl/fl or Irf8fl/fl Itgax-cre mice were sorted by flow cytometry and RNA sequencing was performed. cDC1s and cDC2s from Irf8fl/fl mice were included as controls. For each sample, 4 replicates were analysed.

first: Dorine

last: Sichien

first: Charlotte

middle: L

last: Scott

first: Matthias

last: Vanderkerken

first: Sofie

last: Van Gassen

first: Maud

last: Plantinga

first: Thorsten

last: Joeris

last: De Prijck

first: Leen

last: Vanhoutte

first: Manon

last: Vanheerswynghels

first: Gert

last: Van Isterdael

first: Wendy

last: Toussaint

first: Filipe

last: Branco Madeira

first: Karl

last: Vergote

first: William

last: Agace

first: Björn

last: Clausen

first: Hamida

last: Hammad

first: Marc

last: Dalod

first: Yvan

last: Saeys

first: Bart

middle: N

last: Lambrecht

first: Martin

last: Guilliams


title: Sirtuin 1 Promotes Naïve Pluripotency by Deacetylation of Oct4 (RNA-seq)

first: Eric

last: Williams

state: Ma

department: Biology

institute: Massachusetts Institute of Technology

summary: The enhancer landscape is dramatically restructured as naïve preimplantation epiblasts transition to the post-implantation state of primed pluripotency. A key factor in this process is Otx2, which is upregulated during the early stages of this transition and ultimately recruits Oct4 to a different set of enhancers. In this study we discover that the acetylation status of Oct4 regulates the induction of the primed pluripotency gene network. Maintenance of the naïve state requires Oct4 deacetylation by the NAD-dependent deacetylase, SirT1. The activity of SirT1 is reduced during the naïve to primed transition, thereby increasing the acetylation of Oct4 and promoting its binding to an Otx2 enhancer to induce Otx2 expression. Induction of Otx2 causes the reorganization of acetylated Oct4 and results in the induction of the primed pluripotency gene network.  Regulation of Oct4 by SirT1 may link stem cell development to environmental conditions and provide strategies to manipulate epiblast cell state.

overall_design: Transcription profile to compare the expression changes during the naïve (ESCs) to primed (EpiLCs) transition to the expression changes caused by Sirt1 loss and Otx2 knockdown.

first: Leonard

last: Guarente


title: Expression Profiling of Livers From Female FC-ob Mice and MRKO-ob Mice

city: Shanghai

first: Yuyao

last: Zhang

address: 320 Yueyang Road

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
Objective: To investigate the effects of myeloid MR deletion on hepatic gene expression profiles in female mice
Methods: 12-week old female FC-ob and MRKO-ob mice were euthanized and livers were collected and snap-frozen with liquid nitrogen. Total RNA were extracted using Trizol. After assessing the RNA quality with an Agilent 2000 Bioanalyzer, cDNA library was constructed using TruSeq RNA-Seq Sample Prep Kits. Deep sequencing was carried out on Illumina HiSeq 2000. Different gene expressions were confirmed by QRT-PCR.
Results: With RNA-seq data, we identified 24 genes that differently expressed in MRKO-ob mice compared to FC-ob group. Confirmation with QRT-PCR revealed that the differently expressed genes were closely associated with hepatic steatosis, especially de novo lipogenesis.
Conclusions: Our study investigated for the first time the gene expression profiles of female ob/ob mice with or without myeloid MR ablation. These findings provided clues to explore the mechanisms underlied the crosstalk between macrophages and hepatocytes in females. These findings have provided new knowledge basis for potential new strategies to treat or prevent NAFLD and T2DM.

overall_design: Hepatic mRNA profiles of 12-week old female FC-ob and MRKO-ob mice

first: Shengzhong

last: Duan


title: Ribonuclease Selection for Ribosome Profiling

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

summary: Ribosome profiling has emerged as a powerful method to assess global gene translation, but methodological and analytical challenges often lead to inconsistencies across labs and model organisms. A critical issue in ribosome profiling is nuclease treatment of ribosome-mRNA complexes, as it is important to ensure both stability of ribosomal particles and complete conversion of polysomes to monosomes. We performed comparative ribosome profiling in yeast and mice with various ribonucleases including I, A, S7 and T1, characterized their cutting preferences, trinucleotide periodicity patterns, and coverage similarities across coding sequences, and showed that they yield comparable estimations of gene expression when ribosome integrity is not compromised. However, ribosome coverage patterns of individual transcripts had little in common between the ribonucleases. We further examined their potency at converting polysomes to monosomes across other commonly used model organisms, including bacteria, nematodes and fruit flies. In some cases, ribonuclease treatment completely degraded ribosome populations. Ribonuclease T1 was the only enzyme that preserved ribosomal integrity while thoroughly converting polysomes to monosomes in all examined species. This study provides a guide for ribonuclease selection in ribosome profiling experiments across most common model systems

sample_organism:
Mus musculus
Saccharomyces cerevisiae BY4741

overall_design: 8 Ribosome profiling samples (5 from yeast, 3 from mouse)

first: M

middle: V

first: V

last: Gladyshev


title: RNA in Fetal Bovine Serum Interferes with Cell Culture Studies

status: Public on Sep 19 2016

first: Zhiyun

last: Wei

address: 60 Fenwood Road

department: Neurology

summary: Fetal bovine serum (FBS) has been used in eukaryotic cell cultures for decades, and it represents one of the most commonly used reagents in life science research. However, little attention has been paid to the biological effects associated with RNA content of FBS on cell cultures. Here we report that FBS contains a diverse repertoire of protein-coding and regulatory RNA species, including mRNA, miRNA, rRNA, and snoRNA. The majority of them (>70%) are retained even after extended ultracentrifugation in the preparations of vesicle-depleted FBS (vdFBS) commonly utilized in the studies of extracellular vesicles (EV) and intercellular communication. FBS-associated RNA is co-isolated with cell-culture derived extracellular RNA (exRNA) and interferes with the downstream RNA analysis. Many evolutionally conserved FBS-derived RNA species can be falsely annotated as human or mouse transcripts. Notably, specific miRNAs abundant in FBS, such as miR-122, miR-451a and miR-1246, have been previously reported as enriched in cell-culture derived EVs, likely due to the confounding effect of the FBS. Furthermore, although the absolute amount of individual RNA species in FBS is low, they can be taken up by cultured cells and affect the results and interpretations of highly sensitive gene expression profiling technologies. Therefore, precautions for experimental design are warranted to minimize the interference and misinterpretations caused by FBS-derived RNA.

overall_design: 3 FBS samples were ultracentifuged, then RNA from the pellets and supernatants were sequenced to examine what human/mouse RNA species they could be mis-annotated to.

first: Z

first: A

last: Krichevsky


title: Transcriptome and gene/transcript expression profiling in melan-a cells

status: Public on Sep 18 2016

city: Bethesda

first: Derek

last: Gildea

state: MD

address: 12 South Drive Rm 4009-24

institute: NHGRI/NIH

summary: The melan-a cell line is derived from immortalized mouse melanocytes obtained from Ink4a-ARF-/- mice. RNA-seq was performed to assess the global nature of transcript and gene expression profiles in melan-a cells. These RNA-seq data, along with separate ChIP-seq performed in melan-a cells (GSE38498), were used to correlate gene expression patterns with the presence or absence of transcription factors of interest.

overall_design: Gene expression profiles were generated from three bioreplicate melan-a cell lines. These gene expression profiles were determined from RNA-seq performed on the Illumina HiSeq 2000 platform. Three lanes of sequencing were done for each bioreplicate.

first: Stacie

middle: K

last: Loftus

first: William

last: Pavan


title: Transcriptome responses to natural environments in Pseudotsuga menziesii (Douglas-fir)

city: Mississauga

first: Ingo

last: Ensminger

state: Ontario

address: 3359 Mississauga Road

department: Department of Biology

institute: University of Toronto, Mississauga

summary:
Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever-changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq).
Using linear mixed models, we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80% of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction.

overall_design: 25 trees were investigated on two field Sites. Sampling was conducted at noon (Sample_Time) in May, June, July and September (Month and Sample_date).


title: Differential transcription of small RNAs and mRNAs of Streptococcus pneumoniae TIGR4 when grown with the biofilm inhibitor Carolacton

city: Braunschweig

first: Jannik

last: Donner

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz-Center for Infection Research

summary: Carolacton is a novel biofilm inhibitor that kills biofilm cells of Streptococcus mutans in nanomolar concentrations. Interestingly, Carolacton also inhibits growth of the clinically relevant and human pathogenic bacterium Streptococcus pneumoniae TIGR4. The cellular target of Carolacton is still unknown. Here, we adressed the differential transcription of cellular RNAs when S. pneumoniae TIGR4 was grown in the presence of Carolacton. This was done to identify transcriptional regulatory networks that are directly affected by treatment of the pneumococcus with Carolacton. In order to gain insights into the primary transcriptional response, early time-points were chosen for sampling, which should not reflect secondary responses (e.g. due to differences in growth phase, drop in pH etc.). To achieve a thorough overview over all affected cellular RNA species, such as mRNAs, small regulatory RNAs and tRNAs, and not to lose small transcripts during library preparation, RNAs were separated according to size and used to construct two separate libraries for sequencing.

overall_design: For each of the six examined time-points (0, 5, 15, 60, 120, 180 min), two biological replicates of Carolacton-treated and untreated samples were collected.


title: Exploring the transcriptome of Staphylococcus aureus in its environmental niche

first: Diego

last: Chaves-Moreno

address: inhoffenstrasse 7

department: Department of Medical Microbiology (MMIK)

institute: Helmholtz Centrum for Infection Research

summary: In vivo comparison of the expression profiles in S. aureus colonizing the human nose

overall_design: General expression profile of S. aureus, colonizing the human nose of 4 volunteers

first: Melissa

last: Wos-Oxley

first: Ruy

last: Jáuregui

first: Eva

last: Medina

first: Andrew

middle: P

last: Oxley

first: Dietmar

last: Pieper


title: The microRNA cluster miR-183/96/182 contributes to long-term memory in a protein phosphatase 1 dependent manner

city: Zurich

first: Bisrat

middle: Tewhibe

last: Woldemichael

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

institute: Swiss Institute of Technology/University of Zurich

summary: Memory formation is a complex cognitive function regulated by coordinated synaptic and nuclear processes in neurons. In mammals, it is controlled by multiple molecular activators and suppressors, including the key signaling regulator protein phosphatase 1 (PP1). Here, we show that memory control by PP1 involves the miR-183/96/182 cluster, which is selectively regulated during memory formation. Inhibiting nuclear PP1 in mice brain or training in object recognition task similarly increases miR-183/96/182 expression in the hippocampus. Mimicking this increase by overexpressing miR-183/96/182 enhances object memory, while suppressing endogenous level of the cluster reduces it. This effect involves the modulation of many plasticity-related genes, and we identified HDAC9 as one of the functional targets. Further, PP1 controls miR-183/96/182 in a transcription-independent manner influencing processing of their precursors. These findings provide novel evidence for the role of miRNAs in memory formation and suggest the implication of PP1 in miRNAs processing in the adult brain.

overall_design: Analysis of small RNA (miRNA) expression profile in hippocampal samples from transgenic NIPP1* (loss of PP1 function through disinhibition of the PP1 protein) and wildtype mice after learning

first: Isabelle

last: Mansuy


title: RNA-Sequencing analysis of BET inhibitor resistant cell lines

city: South San Francisco

first: Simon

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

summary: Targeting BET bromodomain proteins utilizing small molecules in an emerging anti-cancer strategy with clinical evaluation of at least six inhibitors now underway. While MYC downregulation was initially proposed as a key mechanistic property of BET inhibitors, recent evidence suggests that additional anti-tumor activities are important. Using the Eμ-Myc model of B-cell lymphoma we demonstrate that BET inhibition with JQ1 is a potent inducer of p53-independent apoptosis that occurs in the absence of effects on Myc gene expression. JQ1 skews the expression of pro-apoptotic (Bim) and anti-apoptotic (BCL-2/BCL-xL) BCL-2 family members to directly engage the mitochondrial apoptotic pathway. Consistent with this, Bim knockout or Bcl-2 overexpression inhibited apoptosis induction by JQ1. We identified lymphomas that were either intrinsically resistant to JQ1-mediated death or acquired resistance following in vivo exposure. Strikingly, in both instances BCL-2 was strongly upregulated and was concomitant with activation of RAS pathways. Eμ-Myc lymphomas engineered to express activated Nras upregulated BCL-2 and acquired a JQ1-resistance phenotype. These studies provide important information on mechanisms apoptosis induction and resistance to BET-inhibition, while providing further rationale for the translation of BET inhibitors in aggressive B-cell lymphomas.

overall_design: RNA-Sequencing of JQ1 resistant and sensitive Eμ-Myc cell lines

first: Ricky

last: Johnstone

first: Stephin

last: Vervoort


title: Single-cell RNA-seq of murine epidermis

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: We used single-cell RNA sequencing to reveal how heterogeneity and plasticity of keratinocytes is tuned at the transcriptional level

overall_design: We isolated and analyzed totally 1422 epidermal cells from dorsal telogen skin of C57BL/6 mice aged 56 +/-4 days. Sca1-microbeads were used to increase HF cell numbers and Sca1- (HF) and Sca1+ (mainly IFE) cell fractions were captured in a ratio of  2:1 on a microfluidic Fluidigm C1 system.

last: Joost

first: Amit

last: Zeisel

first: Maria

last: Kasper


title: Progressive chromatin condensation and H3K9 methylation regulate the differentiation of embryonic and hematopoietic stem cells

city: Santa Cruz

first: Camilla

last: Forsberg

address: 1156 High st

department: Biomolecular engineering

institute: University of California Santa Cruz

summary: Epigenetic regulation serves as the basis for stem cell differentiation into distinct cell types, but it is unclear how global epigenetic changes are regulated during this process. Here, we tested the hypothesis that global chromatin organization affects the lineage potential of stem cells and that manipulation of chromatin dynamics influences stem cell function. Using nuclease sensitivity assays, we found a progressive decrease in chromatin digestion between pluripotent embryonic stem cells (ESCs), multipotent hematopoietic stem and progenitor cells (HSPCs), and mature hematopoietic cells. Quantification of chromatin composition by high-resolution microscopy revealed that ESCs contain significantly more euchromatin than HSPCs, with a further reduction in euchromatin as HSPCs transition into mature cells. Increased cellular maturation also led to heterochromatin localization to the nuclear periphery. Functionally, prevention of heterochromatin formation by inhibition of the histone methyltransferase G9a resulted in delayed hematopoietic stem cell (HSC) differentiation. Our results demonstrate significant global rearrangements of chromatin structure during embryonic and adult stem cell differentiation, and that heterochromatin formation by H3K9 methylation is an important regulator of HSC differentiation.

overall_design: Examination of gene expression profile of in vitro cultured mouse HSC with the G9a inhibitor UNC0638

first: Fernando

last: Ugarte

first: Jana

last: Krietsch

first: Rebekah

last: Sousae


title: Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity

city: Berkeley

first: Lior

last: Pachter

address: 378 Stanley Hall, University of California, Berkeley

department: Computer Science and Molecular and Cell Biology

institute: UC Berkeley

summary: Physical forces greatly influence the growth and function of an organism. Altered gravity can perturb normal development and induce corresponding changes in gene expression. Understanding this relationship between the physical and biological realms is important for NASA’s space travel goals. We use combined RNA-Seq and qRT-PCR to profile changes in early Drosophila melanogaster pupae exposed to chronic hypergravity (3 g, three times Earth’s gravity) to highlight gravity-dependent pathways and gene products. Robust transcriptional response was evident among the pupae developed in a hypergravity environment compared to control. 1,513 genes showed significantly (p < 0.05) altered gene expression in the 3 g samples. These findings were supported with qRT-PCR data. Major biological processes affected include ion transport, redox homeostasis, immune and humoral stress response, proteolysis, and cuticle development.

overall_design: 8 poly(A)+ RNA libraries from wildtype Canton-S Drosophila melanogaster at early pupal stage P6 multiplexed and sequenced on one lane of the Illumina HiSeq-2000. 4 replicates of 4 pooled control pupae and 4 replicates of 4 pooled treatment pupae exposed to 3g gravitational force throughout development.

first: Shannon

last: Hateley

first: Ravikumar

last: Hosamani

first: Shilpa

middle: R

last: Bhardwaj

first: Sharmila

last: Bhattacharya


title: Identification of differentially methylated regions between leaves and young fruits of the apple GDDH13

status: Public on Sep 17 2016

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

country: France

institute: INRA-IRHS

summary: The main objective of this analysis was to sequence the epigenome of the Apple (Malus domestica) doubled haploid 'Golden Delicious' tree. Our secondary objective was to identify differentially methylated regions between DNA purified from leaves and young fruits.

overall_design: Three samples have been analyzed. Two samples were collected from pools of young fruits, and one sample was collected from leaves. After DNA purification,  Bisulfite treatment was applied to determine the cytosine methylation status. Illumina reads of the three libraries were generated using an Illumina Hiseq instrument. Differencialy methylated regions were computed according to Hagmann et al. 2015.

first: Nicolas

last: Daccord

first: Etienne

last: Bucher


title: Gene expression across 3 days of lens-induced myopia and hyperopia induction in chick

city: Bundoora

first: Nina

last: Riddell

state: Victoria

address: La Trobe University, Plenty Rd.

department: Psychology and Public Health

country: Australia

institute: La Trobe University

summary: We sequenced mRNA from 34 retina/RPE/choroid samples taken from the right eyes of male chicks across a time-course of normal development or refractive error induction (defocus-induced myopia and hyperopia).

overall_design: Examination of mRNA levels in individual retina/RPE/choroid samples across three time-points (1, 2, and 3 days) and three lens conditions (no lens, +10 diopter lens, and -10 diopter lens)


title: The Calcium Channel Subunit Alpha2delta2 Suppresses Axon Regeneration in the Adult CNS

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

summary: Purpose: Injuries to the adult central nervous system (CNS) often result in permanent disabilities because neurons lose the ability to regenerate their axon during development. Although the developmental transition from a growing to a transmitting phase may represent one of the first steps in the gradual loss of axon growth and regeneration ability, the molecular mechanisms regulating this process has yet to be identified. The main goal of this study was to dissect the molecular mechanisms mediating the decline in axon growth ability and its relationship with regeneration failure in the adult CNS. To this end, we sequenced the whole transcriptome of dorsal root ganglia (DRG) neurons in both growth competent and incompetent states at different developmental stages, in diverse culture and in vivo experimental conditions.

overall_design: mRNA profiles of mouse embryonic E12.5 and E17.5 lumbar DRGs, conditioned and sham operated adult L4-5DRGs, and cultured adult lumbar DRG (6, 12, 24 and 36 hr after plating) neurons were generated by deep sequencing, in triplicate, using the Illumina TruSeq RNA Sample Prep Kits V2.

first: Andrea

last: Tedeschi

first: Sebastian

last: Dupraz

first: Claudia

middle: S

last: Laskowski

first: Jia

last: Xue

first: Thomas

last: Ulas

first: Marc

last: Beyer

first: Frank

last: Bradke


title: Transcriptome analysis of diverse cell types infected with human cytomegalovirus [RNA-Seq]

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Comprehensive RNA sequencing and splicing-sensitive microarray analysis of three diverse cell types infected with human cytomegalovirus (HCMV), including primary fibroblasts (HFFs), endothelial cells (ECs), and neural progenitors (NPCs) derived from embryonic stem cells. This global analysis includes both host and viral gene expression measurements, and an in-depth assessment of alternative RNA processing events. Extended comparisons were conducted through RNA sequencing analysis of human herpes simplex virus (HSV)-2 and human immunodeficiency virus type 1 (HIV-1) infections.

overall_design: Deep sequencing analysis component of the study. RNA-seq measurements of host and virus gene expression, and RNA processing events.

first: T

last: Stark

first: R

last: Batra

first: G


title: RNA binding protein CPEB1 remodels host and viral RNA landscapes [RNA-Seq]

summary: In this study, we report that HCMV infection results in widespread alternative splicing (AS), shorter 3′-untranslated regions (3′UTRs) and polyA tail lengthening in host genes and CPEB1 depletion reverses infection-related post-transcriptional changes.

overall_design: We performed RNA-seq for Mock (Non-targeting siRNA), human Cytomegalovirus (HCMV) with non-targeting siRNA, and CPEB1 siRNA treated human foreskin fibroblasts (HFFs). We also performed RNA-seq for lentivirus mediated GFP overexpression (OE) and CPEB1 overexpression human foreskin fibroblasts. Lastly, we performed TAIL-seq for Mock (Non-targeting siRNA), human Cytomegalovirus (HCMV) with non-targeting siRNA, and CPEB1 siRNA treated HFFs.

first: Ranjan

first: Brian

last: Yee


title: Transcriptome analysis of diverse cell types infected with human cytomegalovirus

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

overall_design: Refer to individual Series


title: Genome-wide epigenetic analyses and Transcriptional analysis  in NB4 cells expressing PML-RARalpha

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: Illumina High-Throughput ChIP Sequencing profiling was performed using the H3K9K14ac antibody in NB4 cells treated with the compounds ATRA, MS-275,MC2392 (a hybrid molecule of ATRA with a 2-aminoanilide tail of the HDAC inhibitor MS-275) or solvent, DMSO. We find that MC2392 induces changes in H3 acetylation at a small subset of PML-RARα binding sites but also in regions not regulated by ATRA. Moreover, MC2392 alters expression of a number of stress-responsive and apoptotic genes.

overall_design: Genome-wide ChIP-seq was performed in NB4 cells for histone3 acetylated in K9K14

first: Floriana

last: De Bellis

first: Vincenzo

last: Carafa

first: Angela

last: Nebbioso

first: Dante

last: Rotili

first: Francesca

last: Petraglia

first: Mariarosaria

last: Conte

first: Kees-Jan

last: Francoijs

first: Julien

last: Ablain

first: Sergio

last: Valente

first: Remy

last: Castellano

first: Armelle

last: Goubard

first: Yves

last: Collette

first: Filomena

last: Matarese

first: Joost

last: Martens

first: Hugues

last: de Thé

first: Antonello

last: Mai

first: Hendrik

first: Lucia

last: Altucci


title: Single-nucleotide-resolution mapping of HBV promoters using CAGE

status: Public on Sep 16 2016

city: Yokohama

first: Kosuke

last: Hashimoto

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

summary: We provide a comprehensive map of transcription start sites (TSSs) for HBV at single nucleotide resolution using CAGE.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Expression profiles using CAGE for HepG2.2.15 (3 replicates), primary human hepatocytes (3 replicates),  HepAD38 (2 replicates) and mouse liver tranduced with AAV-HBV (3 replicates)

first: Ishita

last: Gupta

first: Christine

last: Neuveut

first: Yu

last: Wei

first: Piero

last: Carninci

first: Marie

last: Annick


title: Position effects influence HIV provirus latency reversal

city: Barcelona

first: Guillaume

last: Filion

address: Dr. Aiguader 88

department: GRSCC

institute: CRG

summary: We propose a technology B-HIVE, which allows us to map HIV integrations in a cell population and measure their individual transcription. The principle of B-HIVE is to tag individual viral genomes with a unique barcode of 20 nucleotides that allows us to track the viral transcripts produced by each provirus in the cell population.

overall_design: We performed two independent infection on Jurkat T cells by barcoded HIV (2 biological replicates). Each sample preparation and data analysis was done in parallel in 2 replicates.

first: Heng-Chang

last: Chen

first: Eduard

last: Zorita


title: Distinct effects of p19 RNA silencing suppressor on small RNA mediated pathways in plants

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

summary:
RNA silencing is one of the main defense mechanisms employed by plants to fight viruses. In change, viruses have evolved silencing suppressor proteins to neutralize antiviral silencing. Since the endogenous and antiviral functions of RNA silencing pathway rely on common components, it was suggested that viral suppressors interfere with endogenous silencing pathway contributing to viral symptom development. In this work, we aimed to understand the effects of the tombusviral p19 suppressor on endogenous and antiviral silencing during genuine virus infection. We showed that ectopically expressed p19 sequesters endogenous small RNAs (sRNAs) in the absence, but not in the presence of virus infection. Our presented data question the generalized model in which the sequestration of endogenous sRNAs by the viral suppressor contributes to the viral symptom development. We further showed that p19 preferentially binds the perfectly-paired ds-viral small interfering RNAs (vsiRNAs) but does not select based on their sequence or the type of the 5’ nucleotide. Finally, co-immunoprecipitation of sRNAs with AGO1 or AGO2 from virus-infected plants revealed that p19 specifically impairs vsiRNA loading into AGO1 but not AGO2. Our findings, coupled with the fact that p19-expressing wild type Cymbidium ringspot virus (CymRSV) overcomes the Nicotiana benthamiana silencing based defense killing the host, suggest that AGO1 is the main effector of antiviral silencing in this host-virus combination.

To further support our hypothesis we investigate whether the ability of p19 to bind endogenous sRNA without virus infection has biological important impact on endogenous pathways and is this reduced if the virus is present. To asses this we made mRNA sequencing from mock inoculated and Cym19stop infected p19syn plants. Cym19stop infected wild type plant was sequenced as a control.
The sequencing data results supports our claims. An increase in transcriptional levels were found in case of genes known to be under small RNA regulation in uninfected p19syn plants and expressional levels return to normal Cym19stop p19syn plants.

overall_design:
In this study we analyzed how p19 of CymRSV interacts with small RNAs and how this effects AGO1 and AGO2 in Nicotiana benthamiana. To have a better understanding on how p19 works with or without viral background we used wild type and synthetic p19 expressing plants (p19syn) combined with wild type and p19 deficient CymRSV (cym19stop). We made small RNA seq from RNAs co-immunoprecipitating with p19 from samples where p19 was expressed trans (p19syn x cym19s ), expressed cis (wt Nb x CymRSV) and p19 without viral background (p19syn x mock inoculation). Input samples for each were also sequenced for comparing. mRNA seq were made from direct RNA extraction from a parallel experiments.
AGO1 and AGO2 immunoprecipitation were made from mock, cym19s and CymRSV infected plants. Small RNAs from the input and pulldown samples were sequenced. A biological replicate was made to enhance reliability. Small RNA seq was made from RNA directly extracted from Cym19s
A biological repeat was made to increase credibility of the small RNA sequencing of small RNAs co-immunoprecipitating with AGO1 and AGO2. This experiment was conducted exactly as the previous one.

first: Levente

last: Kontra

first: Tibor

last: Csorba

first: Mario

last: Tavazza

first: Alessandra

last: Lucioli

first: Raffaela

first: Simon

last: Moxon

first: Viktoria

last: Tisza

first: Anna

last: Medzihradszky

first: Massimo

last: Turina

first: Jozsef

last: Burgyan


title: Polarized regulatory landscape and Wnt responsiveness underlie Hox activation in embryos

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Sequential 3’ to 5’ activation of the Hox gene clusters in early embryos is a most fascinating issue in developmental biology. Neither the trigger nor the regulatory elements involved in the transcriptional initiation of the 3’-most Hox genes have been unraveled in any organism. We demonstrate that a series of enhancers, some of which Wnt-dependent, is located within a HoxA 3’ subTAD. This subTAD forms the structural basis for multiple layers of 3’-polarized features, including DNA accessibility and enhancer activation. Deletion of the cassette of Wnt-dependent enhancers proves its crucial role in initial transcription of HoxA at the 3’ side of the cluster.

overall_design: ChIP-sequencing for several antibodies, ATAC-seq and 4C on epiblast stem cells (EpiSCs). Additionally, we performed ATAC-seq on different early stage mouse embryos.

first: R

last: Neijts

first: S

last: Amin

first: C

last: van Rooijen

last: Tan

first: M

last: Creyghton

first: W

last: de Laat

first: J


title: Myeloid Leukemia Factor acts in a chaperone complex to regulate transcription factor stability and gene expression

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: Regulation by MLF and DnaJ1.

overall_design:
ChIP-seq for dMLF and dDnaJ1 in Drosophila melanogaster S2 cells.
RNA-seq in Drosophila melanogaster S2 cells when dMLF and dDnaJ1 are knocked down.

first: Arnob

last: Dutta

first: Jerry

last: Workman


title: The control of rRNA synthesis during the directed differentiation of human embryonic stem cells precedes heterochromatin formation.

city: Boston

first: Jessica

last: Woolnough

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

summary: It has become increasingly clear that proper cellular control of pluripotency and differentiation is related to the regulation of rRNA synthesis.  To further our understanding of the role that the regulation of rRNA synthesis has on pluripotency we monitored the reduction of rRNA synthesis after the induction of endoderm-specific gene expression in human embryonic stem cells (hESCs) using a brief Activin A treatment.  We discovered that the reduction in rRNA synthesis during directed differentiation is rapid (within 6 hours of Activin A treatment), correlates with a reduction in the binding of UBTF, and precedes heterochromatin formation throughout the rRNA gene.  The loss of pluripotency and the induction of lineage specific gene expression markers can be induced by reducing rRNA synthesis directly with the Pol I inhibitor, CX-5461.  Activin A and CX-5461 both appear to reduce pluripotency and alter lineage-specific transcription, but likely do so via distinct mechanisms.

overall_design: UBF Binding by ChIP-seq in untreated and Activin A treated H9 hESCS.  mRNA expression level by mRNA-seq in untreated, Activin A treated, and CX-5461 treated H9 hESCs

first: K

last: Giles


title: Roadmap to implantation- RNA seq of ovine LE, GE and conceptus during early pregnancy

city: Columbia

first: Thomas

last: Spencer

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: RNA seq analysis of laser capture microdissected luminal and glandular epithelium from ewes on day of pregnancy 10, 12, 14, 16 and 20. As well as RNA seq of whole conceptuses, and trophectoderm tissue from day 12, 14, 16 and 20 of pregnancy. Determination of gene expression changes in the uterine epithelium and conceptus during early pregnancy helps to improve our understanding of early pregnancy events and provides a basis of new strategies to improve fertility and reproductive efficiency in ruminants.

overall_design: RNA seq analysis of 4 samples of each tissue type (luminal epithelium (LE), glandular epithelium (GE) and conceptus) for 4 animals. Pre-sequencing amplification of LE, GE and day 12 conceptus samples.

first: Kelsey

last: Brooks

first: Gregory

last: Burns


title: Exploring miRNAs involved in citrus nucellar embryo initiation by high-throughput small RNA sequencing

city: Wuhan

first: Jianmei

last: Long

state: Hubei

address: shizishan street NO.1

institute: Huazhong Agricultural University

summary: To identify miRNAs related nucellar embryo intiation (NEI) in citrus, we performed small RNA sequencing in ovules of two pairs of poly- and mono-embryonic cultivars  right prior to and at NEI stages. Nearly 150 miRNAs including ~90 conserved and ~60 novel miRNAs were identified in ovules of each cultivar pair.

sample_organism:
Citrus maxima
Citrus x paradisi
Citrus reticulata
Citrus x clementina

overall_design: Two pairs of poly- and mono-embryonic citrus cultivars were used. One pair are mandarins, the polyembryonic Ponkan ‘Huagan No.2’ (PK, Citrus reticulata Blanco) and the monembryonic Nour clementina (CM, C. Clementine). The other pair are pummelo/grapefruit, the polyembryonic Cocktail grapefruit (GF, C. paradisi Osbeck) and the monoembryonic Huanong red pummelo (PU, C. grandis (L.) Osbeck). Histological analysis indicated that the NEI cells began to emerge at 3 DAF in ovules of grapefruit but at 7 DAF in ovules of Ponkan mandarin, so we took  0 DAF for grapefruit and 3 DAF for Ponkan as the stage just before NEI cells formed, i.e. the ‘pre-NEI’ stage; whereas 3 DAF for grapefruit and 7 DAF for Ponkan were taken as the stage when NEI cells emerged, i.e. the ‘NEI’ stage. Ovules were collected in two continuous years as biological replicates for high throughput sequencing. The overlapped differentially expressed miRNAs between two pairs were considered as the key miRNAs involved in nucellar embryo initiation.

first: Wenwu

last: Guo


title: Translatome profiling of Drosophila intestinal enterocytes upon Dietary Restriction

city: Novato

first: Nuno

middle: Miguel

last: Luis

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

summary: We determined the actively translated mRNA induced/repressed by a Dietary Restriction intervention specifically in the differentiated enterocytes of the intestine. For this, we did a "genetic dissection" by expressing a tagged ribosomal subunit (RpL13A-His6FLAG) under the control of the tissue specific Myo1A-GAL4 driver, targetting its expression exclusively to the intestinal enterocytes. By performing a anti-flag pulldown we are then able to enrich our mRNA pool for transcripts that are directly bound to ribosomes and being actively translated. In this manner, we become one step closer to protein synthesis while profiling gene expression.

overall_design: 2-3 day old Myo1A-GS X Ribotag Drosophila adult flies were placed on Ad Libitum (AL) or Dietary Restriction (DR) diets and maintained for 10 days prior to polysomal pulldown.

first: Patrick

last: Li

first: Pankaj

last: Kapahi


title: Cisplatin DNA Damage and Repair Maps of the Human Genome at Single-nucleotide Resolution

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

summary: Platinum chemotherapies induce damages in DNA that distort the helical structure. In human cells, these adducts are removed primarily by the Nucleotide Excision Repair pathway. In this study, we mapped both cisplatin and oxaliplatin induced damages and their repair at single nucleotide resolution across the human genome.

overall_design: We performed Damage-seq to map 2 types of damages in two different human cell lines. The damages were cisplatin and oxaliplatin induced DNA adducts. The two cell lines were normal human skin fibroblasts NHF1 and the GM12878 human lymphoblastoid cells. As control, cisplatin damages were induced in genomic DNA from GM12878. For comparison to repair, XR-seq was performed for cisplatin and oxaliplatin treated GM12878 cells.

first: S

last: Hu

middle: D

last: Lieb

first: A

last: Sancar


title: Impaired removal of H3K4 methylation affects cell fate determination and gene transcription

status: Public on Sep 15 2016

city: Copenhagen

first: Anna Elisabetta

last: Salcini

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: Methylation of Histone 3 Lysine 4 (H3K4) is largely associated with promoters and enhancers of actively transcribed genes and it is finely regulated during development by the action of histone methyltransferases and demethylases. H3K4me3 demethylases of the KDM5 family have been previously implicated in development, but how the regulation of H3K4me3 level controls developmental processes is not fully established. Here, we show that the H3K4 demethylase RBR-2, the unique member of the KDM5 family in C. elegans, acts cell-autonomously and in a catalytic- dependent manner to control vulva precursor cells fate acquisition, by promoting the LIN-12/Notch pathway. Using genome-wide approaches, we show that RBR-2 reduces the H3K4me3 level at transcription start sites (TSSs) and in regions upstream the TSSs, and acts both as a transcription repressor and activator. The analysis of the lin-11 genetic locus, a direct RBR-2 target gene required for vulva precursor cell fate acquisition, shows that RBR-2 controls the epigenetic signature of the lin-11 vulva- specific enhancer and lin-11 expression, providing in vivo evidences that RBR-2 can positively regulate transcription and cell fate acquisition by controlling enhancer activity.

overall_design: Genome-wide H3K4me3 distribution in wild type and rbr-2(tm3141).

first: Yvonne

middle: C

last: Lussi

first: Luca

last: Mariani

first: Carsten

last: Friis

first: Juhani

last: Peltonen

first: Toshia

last: Myers

first: Claudia

last: Krag

first: Garry

last: Wong

first: Anna


title: Effects of long-term endocrine disrupting compound exposure on Macaca mulatta embryonic stem cells

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

country: USA

institute: Michigan State University

summary: Endocrine disrupting chemicals (EDCs) exert significant effects on health and physiology, many of which are traceable to effects on stem cell programming underlying organismal development.  Understanding risk of low-level, chronic EDC exposure will be enhanced by knowledge of effects on stem cells.  We exposed rhesus monkey embryonic stem cells to low levels of five different EDCs for 28 days, and evaluated effects on gene expression by RNAseq transcriptome profiling.  EDCs tested included bisphenol A (BPA), atrazine (ATR), tributyltin (TBT), perfluorooctanoic acid (PFOA), and di-(2-ethylhexyl) phthalate (DEHP).  We observed little effect of BPA, and small numbers of affected genes (119 or fewer) with the other EDCs.  There was substantial overlap in effects across two, three, or four treatments. Ingenuity Pathway analysis indicated suppression of cell survival genes, activation of cell death genes, suppression of genes downstream of several stress response mediators, and modulations in several genes that regulate pluripotency, differentiation, and germ layer development. Potential adverse effects of these changes on development are discussed.

overall_design: Effects of chronic exposure to low concentrations of 5 EDCs were tested in rhesus monkey embryonic stem cells

first: Kailey

middle: A

last: Vincent

first: Catherine

last: VandeVoort

first: Keith

middle: E

last: Latham


title: Correlative gene expression to protective seroconversion in Rift Valley Fever vaccinates

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

summary: Rift Valley Fever Virus (RVFV), a negative-stranded RNA virus, is the etiological agent of the vector-borne zoonotic disease, Rift Valley Fever (RVF). In both humans and livestock, protective immunity can be achieved through vaccination. Earlier and more recent vaccine trials in cattle and sheep demonstrated a strong neutralizing antibody and total IgG response induced by the RVFV vaccine, MP-12. From previous work, protective immunity in sheep and cattle vaccinates normally occurs from 7 to 21 days after inoculation with MP-12. While the serology and protective response induced by MP-12 has been studied, little attention has been paid to the underlying molecular and genetic events occurring prior to the serologic immune response. To address this, we isolated RNA from whole blood from vaccinates over a time course of 21 days before and after inoculation during a recent vaccine trial with MP-12. This RNA time course was deeply sequenced by RNASeq and bioinformatically analyzed. Our results revealed time-dependent activation or repression of numerous gene ontologies and pathways related to immune response and regulation. Additional analyses identified a correlative relationship between specific genes related to immune activity and protective immunity prior to serologic detection of antibody response. These data provide an important proof of concept for identifying molecular and genetic components underlying the immune response to vaccination and protection prior to serologic detection.

overall_design:
Experimental Animals: Healthy, 4 – 6 month old Bos taurus heifer and steer calves were used in the present study.  The calves were seronegative to both bovine viral diarrhea and bovine leukemia virus by antigen capture enzyme-linked immunosorbent assay (ELISA) analyses done at the Texas Veterinary Medical Diagnostic Laboratory, College Station, Texas and had no detectable neutralizing antibodies to RVFV by PRNT80 at the time of vaccination.  The animal experiments were performed under an Institutional Animal Care and Use Committee approved protocol #2010-192.  Vaccines: The authentic recombinant MP-12 (MP12) is an attenuated RVFV vaccine prepared for use in humans by the U. S. Army Medical Research Institute of Infectious Diseases. Vaccines were propagated and prepared at University of Texas Medical Branch in Galveston, TX. Experimental Design: The calves were housed in an ABSL2 Ag biocontainment facility where they were randomized into test groups and acclimated to the facility for 14 days.  Animals were inoculated either subcutaneously (s.c.) or intramuscularly (i.m.) with 1x105 PFU of MP-12 (3 animals in each group). Whole blood was collected prior to inoculation on Days 0 through 7, 10, 14, 21 and preserved for serum neutralization studies (PRNT) or total RNA purification for RNASeq analysis. Experimentally determined PRNT values were used to determine the “serologic response status” for animals “unvaccinated”, “vaccinated, not protected”, or “vaccinated, protected” with animals having a serum dilution ration of >1:80 being considered protected. Only RNA samples that met the minimum quality and quantity thresholds were used for the sequencing analysis. Rectal temperatures were recorded each time blood was collected and their health status was documented daily.  At the end of the respective studies, the calves were euthanized with pentobarbital sodium (120 mg/kg i.v.).  All calves were healthy and clinically normal at the termination of the respective studies.
Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Jing Wu, Roberta Pugh, Pooja Kanani, L. Garry Adams, Shinji Makino, C. J. Peters. Immunogenicity of a Recombinant Rift Valley Fever MP-12 Vaccine Candidate in Calves.  Vaccine. 2013. doi:10.1016/j.vaccine.2013.08.003.  238. Morrill, John C., Richard C. Laughlin, Nandadeva Lokugamage, Roberta Pugh, Elena Sbrana, William J. Weise, L. Garry Adams, Shinji Makino and C. J. Peters..  Safety and Immunogenicity of Recombinant Rift Valley Fever MP-12 Vaccine Candidates in Sheep. Vaccine 10.1016/j.vaccine.2012.10.118, 2012.

first: L

middle: G

first: Richard

last: Laughlin

first: Kenneth

last: Drake


title: Acetylation-Dependent Control of Global Poly(A) RNA Degradation by CBP/p300 and HDAC1/2

city: Heidelberg

first: Georg

last: Stoecklin

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: Acetyltransferases and histone deacetylases regulate gene expression at the level of chromatin, mainly by affecting transcription. In this study, we report that hyperacetylation induced by inhibition of histone deacetylases (HDACs) causes massive degradation of mRNA. The effect is promoter-independent and affects poly-A mRNA globally. HDAC inhibition leads to the removal of poly-A tails from mRNAs through activation of the deadenylase CAF1a, which we find to be acetylated together with its activator BTG2 by the histone acetyl transferases (HATs) p300 and CBP. By mutation of critical lysine residues, we provide evidence that acetylation of CAF1a and BTG2 induces enhanced poly-A mRNA degradation. Our study reveals a fundamental mechanism by which cells coordinate epigenetic and transcriptional control of gene expression with posttranscriptional control of poly-A mRNA stability. In this experiment, HeLa cells were exposed to the HDAC inhibitor trichostatin A (TSA) for 16 hours, followed by treatment with actinomycin D. Total RNA was isolated after 0, 2, 4 and 6 hours, and analysed by RNA sequencing. The half-lives of 7431 RNAs were calculated after normalization to rRNA (18S + 28S) levels. The experiment shows that TSA treatment causes a general reduction of poly-A RNA stability, while replication-dependent histone mRNA stability is not affected.

overall_design: RNA half-lives were measured in TSA-treated or untreated HeLa cells by RNA-Seq using Illumina HiSeq 2000.

first: Sahil

last: Sharma

first: Fabian

last: Poetz

first: Marius

last: Bruer

first: Thi Bach Nga

last: Ly-Hartig

first: Johanna

last: Schott

first: Bertrand

last: Séraphin


title: Multiple hierarchies of Polycomb targeting to Drosophila genome (Part 3)

city: Umeå

first: Yuri

middle: B

last: Schwartz

address: Byggnad 6L, NUS

institute: Umeå University

summary: Polycomb group (PcG) proteins are critical epigenetic regulators of development. Here we compared genomic distribution of Polycomb (Pc) protein in cultured Drosophila cells lacking Su(z)12 protein to that of the wild type.

overall_design: ChIP of Pc protein coupled to next-generation sequencing from wild-type and Su(z)12 - null cultured cells. Done in two replicates, with DNA from corresponding chromatin inputs sequenced as a control.

first: Y

first: T

last: Kahn


title: YTHDF3 facilitates translation and decay of the N6-methyladenosine-modified RNA

city: Chicago

first: Chuan

last: He

state: ILLINOIS

address: 929 E 57th St., GCIS E319

department: Department of Chemistry

institute: The University of Chicago

summary: N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNAs (mRNAs), and plays important roles in cell differentiation and organism development. It regulates multiple steps throughout the RNA life cycle including RNA processing, translation, and metabolism, via the recognition by selective binding proteins. In cytoplasm, m6A binding protein YTHDF1 facilitates translation of m6A-modified mRNAs, and YTHDF2 accelerates the decay of m6A-modified transcripts. The biological function of YTHDF3, another cytoplasmic m6A binder of the YTH domain family, remains unknown. Here, we report that YTHDF3 promotes protein synthesis in synergy with YTHDF1, and affects methylated mRNA decay mediated by YTHDF2. Cells deficient in all of YTHDF proteins experience the most dramatic accumulation of the m6A-methylated transcripts. These results indicate that in cytoplasm, YTHDF proteins act in an integrated and cooperative network to accelerate metabolism of m6A-modified mRNAs. The combinative and dynamic nature of YTHDF proteins may collectively impact fundamental biological processes and diseases related to m6A RNA methylation.

overall_design: We utilized PAR-CLIP triplicates and RIP replicates to identify binding sites and target transcripts of YTHDF3, and performed ribosome profling replicates to assess the consequences of YTHDF3 siRNA knock-down in HeLa cells.

first: Hailing

last: Shi

first: Xiao

last: Wang

first: Zhike

last: Lu

first: Boxuan

last: Zhao

first: Honghui

last: Ma

first: Phillip

middle: J

last: Hsu


title: Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California


title: Germline NLRP1 mutations cause skin inflammatory and cancer susceptibility syndromes via inflammasome activation

city: Singapore

first: Franklin

last: ZHONG

state: Singapore

address: 11 Mandalay Road

country: Singapore

institute: NTU LKC School of Medicine

summary: We profiled the transcriptional changes in N/TERT-1 immortalized keratinocytes after doxycylin induction of gain-of-function mutants of the inflammasome sensor protein  NLRP1.

overall_design: Stable N-TERT/1 cell lines were generated using lentiviral transduction. Experimental group includes doxycline-treated N/TERT cells expressing NLRP1 mutants A54T, M77T and A66V. Control group includes doxyclin-treated vector-transduced N/TERT cells and two NLRP1 mutant-transduced cell lines that were not treated with doxycycline. All cells were harvested three days after induction. Total RNA was isolated using Trizol reagent.

last: Zhong

first: Bruno

last: Reversade


title: Lower Expression of SLC27A1 Enhances Intramuscular Fat Deposition in Chicken Via Down-Regulated Fatty Acid Oxidation Mediated by CPT1A

city: Nanchang

first: Fengfang

last: Qiu

state: Jiangxi

address: Guanglan Road No.418

department: School of Chemistry, Biology and Material Science

country: China

institute: East China University of Technology

summary:
Purpose: The goals of this study are to investigate the differentially expressed genes between High IMF chickens (WC) and Low IMF chickens (WRR) breast muscles by Illumina deep sequencing, to reveal the mechanism underlying chicken IMF deposition.
Methods: Both WC chickens and WRR chickens were raised up to 120 d of age (D120) or 180 d of age (D180), two female birds of similar weight from each breed per age were subjected to RNA-sequencing by Illumina Hiseq 2000. So eight muscle samples in total were subjected to RNA-seq analysis, four WC chicken samples including WC.D120.B-1, WC.D120.B-3, WC.D180.B-2 and WC.D180.B-3, and four WRR chicken samples including WRR.D120.B-4, WRR.D120.B-6, WRR.D180.B-2 and WRR.D180.B-5.
Results: The clean reads of each sample were over 20 million, the expressed genes ranged from 16202 to 17838, and a little higher in WRR samples than in WC samples. Differentially expresse analysis showed that there were 525, 161, 23, 87 DEGs detected in the comparisons of WRR.D120.B-VS-WC.D120.B, WRR.D180.B-VS-WC.D180.B, WC.D120.B-VS-WC.D180.B and WRR.D120.B-VS-WRR.D180.B, respectively. Many genes related to lipid catabolism were down-regulated in WC chickens.
Conclusions: Our present study suggest that lower lipid catabolism exists in WC chickens but not in WRR chickens, and lower expression of SLC27A1 is through down-regulating fatty acid oxidation mediated by CPT1A to facilitate IMF deposition. Moreover, these findings indicate that reduced lipid catabolism, rather than increased lipid anabolism, contributes to chicken IMF deposition.

overall_design: Two female birds from WC and WRR chickens at 120 d of age (D120) and 180 d of age (D180) respectively were subjected to RNA-sequencing by Illumina Hiseq 2000.

first: Liang

last: Xie

first: Xiquan

last: Zhang


title: Activity of uncleaved caspase-8 controls anti-bacterial immune defense and TLR-induced cytokine production independent of cell death

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: Caspases regulate cell death programs in response to environmental stresses, including infection and inflammation, and are therefore critical for the proper operation of the mammalian immune system.  Caspase-8 is necessary for optimal production of inflammatory cytokines and host defense against infection by multiple pathogens including Yersinia, but whether this is due to death of infected cells or an intrinsic role of caspase-8 in TLR-induced gene expression is unknown. Caspase-8 activation at death signaling complexes results in its autoprocessing and subsequent cleavage and activation of its downstream apoptotic targets. Whether caspase-8 activity is also important for inflammatory gene expression during bacterial infection has not been investigated. Here, we report that caspase-8 plays an essential cell-intrinsic role in innate inflammatory cytokine production in vivo during Yersinia infection. Unexpectedly, we found that caspase-8 enzymatic activity regulates gene expression in response to bacterial infection as well as TLR signaling independently of apoptosis. Using newly-generated mice in which caspase-8 autoprocessing is ablated (Casp8DA/DA), we now demonstrate that caspase-8 enzymatic activity, but not autoprocessing, mediates induction of inflammatory cytokines by bacterial infection and a wide variety of TLR stimuli. Because unprocessed caspase-8 functions in an enzymatic complex with its homolog cFLIP, our findings implicate the caspase-8/cFLIP heterodimer in control of inflammatory cytokines during microbial infection, and provide new insight into regulation of antibacterial immune defense.

overall_design: Two biological replicates were analyzed for each of 6 conditions (three genotypes; two treatments per genotype)

first: Daniel

last: Beiting

first: Naomi

last: Philip

first: Igor

last: Brodsky


title: Multiple hierarchies of Polycomb targeting to Drosophila genome (Part2)

first: Yuri

last: Schwartz

summary: PcG proteins are critical epigenetic regulators of development. Here we compared genomic distribution of Psc protein in cultured Drosophila cells lacking Su(z)12 protein to that of the wild type.

overall_design: ChIP of Psc protein coupled to next-generation sequencing from wild-type and Su(z)12 - null cultured cells. Done in two replicates, with DNA from corresponding chromatin inputs sequenced as a control.

first: Y

first: T

last: Kahn


title: DMS-MaPseq: A genome-wide or targeted approach for RNA structure probing in vivo

city: Cambridge

first: Silvi

last: Rouskin

address: 455 Main Street

institute: Whitehead Institute

summary: Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features for each molecule, and allows genome-wide studies as well as focused investigations of low abundance RNAs. We apply DMS-MaPseq to Drosophila melanogaster ovaries—the first experimental analysis of RNA structure in an animal tissue—and demonstrate its utility in the discovery of a functional RNA structure involved in the non-canonical GUG translation initiation of the human FXR2 mRNA. Additionally, we use DMS-MaPseq to compare the in vivo structure of messages in their pre-mRNA and mature forms. These applications illustrate DMS-MaPseq’s capacity to dramatically expand our ability to monitor RNA structure in vivo.

sample_organism:
Saccharomyces cerevisiae
Drosophila melanogaster
Homo sapiens

overall_design: Development and application of novel RNA structure probing method in mammalian cells and Drosophila ovaries. Cells were treated with DMS in vivo and RNA was isolated. TGIRT was used to reverse transcribe either randomly fragmented mRNA or gene specific products. TGIRT inserts mismatches at the DMS modified RNA, which are read our mutations when sequencing dsDNA. Samples were prepared using standard library generation approaches (attaching a 3'linker, followed by RT,  circlularization and PCR for attaching sequencing adapters) or Nextera XT kit/ LM-PCR for gene specific samples.

first: Meghan

last: Zubradt

first: Paromita

last: Gupta

first: Sitara

last: Persad

first: Alan

last: Lambowitz

first: Jonathan

last: Weissman


title: Multiple hierarchies of Polycomb targeting to Drosophila genome (Part 1)

summary: PcG proteins are critical epigenetic regulators of development. Here we compared genomic distribution of E(z) protein in cultured Drosophila cells lacking Psc/Su(z)2 proteins to that of the wild type.

overall_design: ChIP of E(z) protein coupled to next-generation sequencing from wild-type and Psc/Su(z)2 - null cultured cells. Done in two replicates, with DNA from corresponding chromatin inputs sequenced as a control.


title: Elevation of GPRC5A expression in colorectal cancer promotes tumor progression through VNN-1 induced oxidative stress

status: Public on Sep 14 2016

city: shanghai

first: zheng

middle: yan

last: sen

state: shanghai

address: NO.500 dong chuan road

institute: ECNU

summary: The clearance of oxidative stress compounds is critical for the protection of the organism from malignancy, but how this key physiological process is regulated is not fully understood. Here we found that the expression of GPRC5A, a well-characterized tumor suppressor in lung cancer, was elevated in colorectal cancer tissues in patients. In both cancer cell lines and a colitis-associated cancer model in mice, we found that GPRC5A deficiency reduced cell proliferation and increased cell apoptosis as well as inhibited tumorigenesis in vivo. Through RNA-Seq transcriptome analysis, we identified oxidative stress associated pathways were dysregulated. Moreover, in GPRC5A deficient cells and mouse tissues, the oxidative agents were reduced partially due to increased glutathione (GSH) level. Mechanistically, GPRC5A regulates NF-κB mediated Vanin-1 expression which is the predominant enzyme for cysteamine synthesis. Administration of cystamine (the disulfide form of cysteamine) in GPRC5A deficient cell lines inhibited γ-GCS activity leading to restoration of GSH level and increase of cell growth. Taken together, our studies suggest that GPRC5a is a potential biomarker for colon cancer and promotes tumorigenesis through stimulation of Vanin-1 expression and oxidative stress in colitis associated cancer. This study revealed an unexpected oncogenic role of GPRC5A in colorectal cancer suggesting there are complicated functional and molecular mechanism differences of this gene in distinct tissues.

overall_design: RNA-Seq was employed to profile the differentially expressed genes in colorectal tumor tissues from WT and Gprc5a KO mice

first: Long

first: Sen

middle: Y

last: Zheng


title: Bi-allelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney

city: Ann Arbor

first: Chinnaiyan

middle: M

last: Arul

state: Michigan

address: 5309 Comprehensive Cancer Center, 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

institute: University of Michigan

summary: Mucinous tubular and spindle cell carcinoma (MTSCC) is a relatively rare subtype of renal cell carcinoma with distinctive morphologic and cytogenetic features. Here we carry out whole exome and transcriptome sequencing of a multi-institutional cohort of MTSCC (n=22). We demonstrate the presence of either biallelic loss of Hippo pathway tumor suppressor genes (TSGs) and/or evidence of alteration of Hippo pathway genes in 85% of samples.  PTPN14 (31%) and NF2 (22%) were the most commonly implicated Hippo pathway genes while other genes such as SAV1 and HIPK2 were also involved in a mutually exclusive fashion.  Mutations in the context of recurrent chromosomal losses amounted to bi-allelic alterations in these TSGs. As a read-out of Hippo pathway inactivation, a majority of cases (90%) exhibited increased nuclear YAP1 protein expression. To identify transcriptional targets of the Hippo pathway in kidney we performed PTPN14 knockdown followed by RNA-seq in 2 kidney cancer cell lines (CAKI-1 and A-704) and a normal kidney epithelial cell line (HK-2).  PTPN14 siRNAs were first functionally validated in a MCF-7 TEAD reporter luciferase stable cell line. Both siRNAs showed comparable knockdown efficiency and significantly increased luciferase reporter activity. In 2 of the kidney cell lines PTPN14 knockdown increased cell proliferation compared to non-target controls. While we observed excellent correlation between genes dysregulated by either PTPN14 or LATS1 knockdown within each cell line (HK2, CAKI-1 and A704), the overlap across the 3 cell lines was only 23 genes. Further, these 23 genes did not show concordant differential expression in MTSCC tumors. Overall, these results illustrate the marked tissue specificity of Hippo pathway targets.Finally, taken together, nearly all cases of MTSCC exhibit some evidence of Hippo pathway dysregulation.

overall_design: Cell lines (CAKI-1, HK2 or A704) were either transfected with 2 independent siRNAs or non-target controls.  Forty eight hours post transcription total RNA was isolated and subjected to RNA-seq analysis

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