title: RNA-seq analysis determined the effect of pat or cobB mutation on transcriptional levels in Salmonella Typhimurium 14028s.

first: Yu

last: Sang

address: 280 S. Chongqing Rd

institute: Shanghai Jiao Tong University School of Medicine

summary:
Salmonella causes a range of diseases in different hosts, including enterocolitis and systemic infection. Lysine acetylation regulates many eukaryotic cellular processes, but its function in prokaryotes is largely unknown.
Reversible acetylation in Salmonella Typhimurium depends on acetyltransferase Pat and nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase CobB.
Here, we used cell and animal models to evaluate the virulence of pat and cobB deletion mutants in S. Typhimurium, and found that pat is essential for bacterial intestinal colonization, systemic infection and host inflammation response.
Next, to understand the underlying mechanism, genome-wide transcriptome was analyzed. RNA-seq data showed the expression of Salmonella pathogenicity islands 1 (SPI-1) is partially dependent on pat. In addition, we found that HilD is a substrate of Pat, which is essential for maintaining HilD protein level.
Taken together, these results suggested that protein acetylation system regulates SPI-1 expression by controlling HilD in a post-translational manner to mediate S. Typhimurium virulence.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

overall_design: To use RNA-seq to analyze the transcriptome patterns of pat or cobB mutation in Salmonella Typhimurium 14028s.

first: Jie

last: Ren

last: Lu

first: Yufeng

last: Yao


title: Tumor cell to fibroblast expression analysis

status: Public on Aug 06 2016

city: Lund

first: P. Olof

last: Olsson

state: Skåne

address: Medicion Village, hus 406, vånging 3

department: Labratory Medicin

country: Sweden

institute: Lund University

summary: High and moderate fibrosis inducing carcinoma cell lines gene expression and effect on human fibroblasts in 3 dimensional collagen gels.

overall_design: Cells grown in free floating 3 dimensional collagen gells contining cells for 48 hrs

first: Olof

first: Kristofer

last: Rubin


title: Genome-wide analysis of Dengue virus 2 infected cells

status: Public on Aug 09 2016

city: Ciudad Autonoma de Buenos Aires

first: Andrea

last: Gamarnik

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

type: Expression profiling by high throughput sequencing

summary: The goal of this study was to compare the transcriptional profile (RNA-seq) of Dengue virus 2 and mock infected cells at 24 and 36 hours post infection. Dengue virus NS5 protein plays multiple functions in the cytoplasm of infected cells, enabling viral RNA replication and counteracting host antiviral responses.  Here, we demonstrate a novel function of NS5 in the nucleus where it interferes with cellular splicing. Using global proteomic analysis of infected cells together with functional studies, we found that NS5 binds spliceosome complexes and modulates endogenous splicing. In particular, we show that NS5 alone, or in the context of viral infection, interacts with core components of the U5 snRNP particle, CD2BP2 and DDX23, alters the inclusion/exclusion ratio of alternative splicing events, and changes mRNA isoform abundance of known antiviral factors. Interestingly, a genome wide transcriptome analysis, using recently developed bioinformatics tools, revealed an increase of intron retention upon dengue virus infection, and viral replication was improved by silencing specific U5 components. Different mechanistic studies indicate that binding of NS5 to the spliceosome reduces the efficiency of pre-mRNA processing, independently of NS5 enzymatic activities. We propose that NS5 binding to U5 snRNP proteins hijacks the splicing machinery resulting in a less restrictive environment for viral replication.

overall_design: A549 cells where infected with Dengue virus 2 or mock and after 24 and 36 hours post infection mRNA was purified. Then the transcriptional profile of these cells was analyzed using RNA-seq.

first: Federico

last: De Maio

first: Guillermo

last: Risso

first: Gabriel

last: Iglesias

first: Priya

last: Shah

first: Berta

last: Pozzi

first: Leopoldo

last: Gebhard

first: Pablo

last: Mammi

first: Estefania

last: Mancini

first: Marcelo

last: Yanovsky

first: Raul

last: Andino

first: Nevan

last: Krogan

first: Anabella

last: Srebrow


title: Genome-wide binding of hSTN1 in response to hydroxyurea-induced replication stress

city: North Chicago

first: Weihang

last: Chai

state: Illinois

address: 3333 N Green Bay Rd, IRP 257

department: Center for Genetic Diseases

country: USA

institute: Rosalind Franklin University of Medicine and Sciences, Chicago Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We find that hSTN1 is preferentially enriched at GC-rich repetitive sequences genome-wide after hydroxyurea treatment.

overall_design: HeLa cells stably expressing myc-tagged hSTN1 were treated with 2 mM hydroxyurea, crosslinked, and ChIP-seq was performed.

first: M

last: Chastain

first: O

last: Shiva

first: L

last: Whitmore


title: Differentiation and specification of resident tissue macrophages [MARS-seq]

status: Public on Aug 08 2016

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Tissue resident macrophages are functionally diverse cells that share an embryonic mesodermal origin. However, the mechanism(s) that control their specification remain unclear. We performed transcriptional, molecular and in situ spatio-temporal analyses of macrophage development in mice. We report that Erythro-Myeloid Progenitors generate pre-macrophages (pMacs) that simultaneously colonize the head and caudal embryo from embryonic day (E)9.5 in a chemokine-receptor dependent manner, to further differentiate into tissue F4/80+ macrophages. The core macrophage transcriptional program initiated in pMacs, is rapidly diversified in early macrophages as expression of transcriptional regulators becomes tissue-specific. For example, the preferential expression of the transcriptional regulator Id3 initiated in early fetal liver macrophages appears critical for Kupffer cell differentiation, as inactivation of Id3 causes a selective Kupffer cell deficiency that persists in adults. We propose that colonization of developing tissues by differentiating macrophages is immediately followed by their specification as they establish residence, hereby generating the macrophage diversity observed in post-natal tissues.

overall_design: RNA-sequencing of sorted macrophage cell populations (Mac) and progenitors (EMP, pMac) from various tissues and collected at different time points, including technical and biological replicates

first: Elvira

last: Mass

first: Ivan

last: Ballesteros

first: Matthias

last: Farlik

first: Florian

last: Halbritter

first: Patrick

last: Günther

first: Lucile

last: Crozet

first: Christian

middle: E

last: Jacome-Galarza

first: Johanna

last: Klughammer

first: Yasuhiro

last: Kobayashi

first: Elisa

last: Gomez-Perdiguero

first: Joachim

middle: L

last: Schultze

first: Marc

last: Beyer

first: Frederic

last: Geissmann


title: Differentiation and specification of resident tissue macrophages

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

overall_design: Refer to individual Series


title: Epstein-Barr Viral miRNAs Broadly Inhibit Adaptive Immunity Early in Infection

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

summary: We revealed that, early in infection of human primary B cells, EBV's miRNAs regulate a wide array of immune functions encompassing antigen processing, HLAs and co-stimulatory molecules, and cytokine-cytokine receptor interactions.

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: Screening of mRNAs that are regulated by EBV's miRNAs examining transcriptomes and RISC-enriched RNAs from six human donors.

first: Takanobu

last: Tagawa

first: Jonathan

last: Hoser

first: Maximilian

last: Hastreiter


title: Negative reciprocal regulation between SIRT1 and Per2 in circadian clock during aging

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University


title: mRNA Poly(A)-tail Changes Specified by Deadenylation Broadly Reshape Translation in Drosophila Oocytes and Early Embryos

city: Cambridge

first: Stephen

last: Eichhorn

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute for Biomedical Research

summary: Because maturing oocytes and early embryos lack transcription, posttranscriptional regulatory processes must control their development.  To better understand this control, we profiled translational efficiencies and poly(A)-tail lengths throughout Drosophila oocyte maturation and early embryonic development.  The correspondence between translational-efficiency changes and tail-length changes indicated that tail-length changes broadly reshape translational activity until gastrulation, when this coupling disappears.  Relative changes were largely retained in the absence of poly(A)-tail lengthening, which indicated that selective poly(A)-tail shortening primarily specifies the changes.  Many translational changes depended on PAN GU and Smaug, and both acted primarily through tail-length changes.  Our results also revealed tail-length–independent mechanisms of translational control that repressed translation regardless of tail-length changes during oocyte maturation, maintained translation despite tail-length shortening during oocyte maturation, and prevented detectable translation of bicoid and several other mRNAs before egg activation.  In addition to these fundamental insights, our results provide valuable resources for future studies.

overall_design: 42 samples analyzed using RNA-seq, ribosome footprint profiling, and PAL-seq.

middle: W

first: Alexander

middle: O

last: Subtelny

first: Iva

last: Kronja

first: Terry

last: Orr-Weaver

first: David

middle: P

last: Bartel


title: Altered patterns of hydroxymethylation regulate oncogenic pathways in pancreatic cancer

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: Transcriptional deregulation of oncogenic pathways is a hallmark of cancer, and can be due to epigenetic alterations. 5-hydroxymethylcytosine is a recently discovered epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC enriched loci was conducted in low-passage pancreatic cancer cell lines and primary patient-derived xenografts and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected regulatory regions of the genome, specifically overlapping with H3K4me1 enhancers. Gain of 5-hmC was correlated with upregulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia. Specifically, BRD4 was overexpressed and acquired 5hmC at enhancer regions in majority of neoplastic samples. Functionally, acquisition of 5hmC at BRD4 promoter regulated increase in transcript expression. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human cancer.

first: Sanchari

last: Bhattacharyya

first: Amit

last: Verma


title: Acute effects of light on alternative splicing in light-grown plants

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

institute: Fundación Instituto Leloir. IIBBA- CONICET

summary: We report the results of a genome-wide analysis of AS in Arabidopsis thaliana plants exposed to a 2h light pulse given in the middle of the night, a treatment that simulates the effects of early dawn or late dusk signals. This  light affects the plant transcriptome at multiple regulatory layers, and that light regulation of mRNA levels of splicing regulatory factors is likely to mediate light effects on AS contributing to adjust plant physiological processes to the prevailing light environment.

overall_design: Arabidopsis seedlings of the Columbia ecotype were grown under 12 hr light/12 hr dark cycles for 9 days. On the 10th day, half of the plants were exposed to a two-hour pulse of white light given in the middle of the night (ZT18), while the other half were kept in darkness as controls. Both groups of plants were harvested at ZT 20 and light effects on mRNA levels and AS were analyzed through RNA-seq.

first: Estefania

last: Mancini


title: Neuraminidase-exposed galactose promotes Streptococcus pneumoniae biofilm formation during colonization

status: Public on Aug 04 2016

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Galactose promotes pneumococcal biofilms in vivo

overall_design: 15 mRNA profiles of Streptococcus pneumoniae samples that were grown under different conditions were generated using deep sequencing.

first: Krystle

middle: A

last: Blanchette

first: Anukul

middle: T

last: Shenoy

first: Jeffrey

last: Milner II

first: Ryan

last: Gilley

first: Erin

last: McClure

first: Cecilia

last: Hinojosa

first: Nikhil

last: Kumar

middle: C

first: Luke

middle: J

last: Tallon

first: Sandra

last: Ott

first: Samantha

last: King

first: Daniela

middle: M

last: Ferreira

middle: B

last: Gordon

first: Hervé

last: Tettelin

first: Carlos

last: Orihuela


title: Pseudouridylation in Naf1+/- mice

status: Public on Aug 07 2016

first: Thomas

last: Carlile

state: Massachusetts

address: 77 Massachusetts Ave

institute: MIT

summary: Pseudo-seq was used to measure differences in the extent of pseudouridine (Ψ) modification in rRNA from mice haploinsufficient for the H/ACA biogenesis factor Naf1 compared to wild- type. We measured telomerase RNA levels as well as a sample of box H/ACA RNAs and found they were all decreased in Naf1+/- mice.  Nevertheless, Naf1+/- mice had minimally decreased levels of pseudouridylation at the rRNA sites queried.  This was not associated with any phenotypic abnormalities in vivo in these mice which we examined for hematopoeitic, liver, testes and brain defects.

overall_design: CMC treatment of RNA followed by next generation sequencing was used to measure the extent of pseudouridylation at mapped mouse rRNA Ψ sites.

first: Dustin

last: Gable

first: Mary

last: Armanios

first: Wendy

middle: V

last: Gilbert


title: Meiotic double-strand break end resection mapping by S1Seq

city: New York

first: Eleni

last: Mimitou

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: The DNA double-strand breaks that initiate homologous recombination during meiosis are subject to extensive 5ʹ→3′ exonucleolytic processing. This resection is a central and conserved feature of recombination, yet its mechanism is poorly understood. Using a purpose-made deep-sequencing method, namely S1Seq, we mapped meiotic resection endpoints genome-wide at high spatial resolution in Saccharomyces cerevisiae. Generating full-length resection tracts requires Exo1 exonuclease activity and the DNA-damage responsive kinase Tel1, but not the helicase Sgs1. Tel1 is also required for efficient and timely initiation of resection. We find that distributions of resection endpoints at individual genomic loci display pronounced heterogeneity that reflects a tendency for nucleosomes to block Exo1 in vivo, yet modeling experiments indicate that Exo1 digests chromatin with high apparent processivity and at rates approaching those for naked DNA in vitro. This paradox points to nucleosome destabilization or eviction as a determining feature of the meiotic resection landscape.

overall_design: 36 samples total: two biological replicate S1Seq maps of S.cerevisiae for each genetic background and time point in meiosis

first: Shintaro

last: Yamada

first: Scott

last: Keeney


title: Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus (ChIP-seq)

first: Michael

last: Laub

address: 31 Ames St

summary: An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism.

overall_design: An allele of phoB bearing a C-terminal 3x-flag tag was integrated at its native locus, and ChIP followed by deep sequencing on Illumina MiSeq was performed on samples grown in rich medium, phosphate-limited medium, and in a pstS::Tn5 mutant background in rich medium.

first: Emma

last: Lubin


title: Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus


title: Early developmental transcriptome of Musca domestica.

city: Santiago

first: Christian

last: Hodar

state: Santiago

address: Av. El Libano 5524

department: INTA

country: Chile

institute: Universidad de Chile

summary: Using mRNA next generation sequencing, we analyze the transcriptome of Musca domestica embryos through five stages of  early development: from syncytial blastoderm to dorsal closure stage.

overall_design: We select 100 embryos for five developmental stages: syncytial blastoderm, cellular blastoderm, gastrula, germ band extension and dorsal closure. A total of 10 samples of mRNA were obtained, represent two biological replicates for each stage.

first: Veronica

last: Cambiazo


title: Sex Differences in Nucleus Accumbens Transcriptome Profiles Associated with Susceptibility versus Resilience to Subchronic Variable Stress

first: Immanuel

last: Purushothaman

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Depression and anxiety disorders are more prevalent in females, but the majority of research in animal models, the first step in finding new treatments, has focused predominantly on males. Here we report that exposure to subchronic variable stress (SCVS) induces depression-associated behaviors in female mice, whereas males are resilient as they do not develop these behavioral abnormalities. In concert with these different behavioral responses, transcriptional analysis of nucleus accumbens (NAc), a major brain reward region, by use of RNA sequencing (RNA-seq) revealed markedly different patterns of stress regulation of gene expression between the sexes. Among the genes displaying sex differences was DNA methyltransferase 3a (Dnmt3a), which shows a greater induction in females after SCVS. Interestingly, Dnmt3a expression levels were increased in the NAc of depressed humans, an effect seen in both males and females. Local overexpression of Dnmt3a in NAc rendered male mice more susceptible to SCVS, whereas Dnmt3a knock-out in this region rendered females more resilient, directly implicating this gene in stress responses. Associated with this enhanced resilience of female mice upon NAc knock-out of Dnmt3a was a partial shift of the NAc female transcriptome toward the male pattern after SCVS. These data indicate that males and females undergo different patterns of transcriptional regulation in response to stress and that a DNA methyltransferase in NAc contributes to sex differences in stress vulnerability.

overall_design: mRNA profiles of sex-specific in stress response were generated in the Nucleus Accumbens for 3 female control mice, 3 male control mice, 3 stressed female mice, 3 stressed male mice. Cre-mediated Dnmt3a knock-out was performed on stressed mice, with 3 males and 3 females expressing control GFP and 3 males and 3 females expressing CRE/GFP.

first: Georgia

last: Hodes

last: Russo


title: Sox2 suppresses gastric tumorigenesis in mice

city: Boston

first: Abby

last: Sarkar

address: 185 Cambridge Street

department: Cancer Center

institute: Harvard University


title: Sox2 suppresses gastric tumorigenesis in mice [CHIP-seq]

summary:
Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach.
Methods: Sox2 ChIP-enriched DNA and input DNA was isolated from gastric glands of adult antrum from Sox2 KO and Sox2 WT mice. DNA was purified and genomic libraries were prepared as described (Sulahian et al., 2014), using four micrograms of goat anti-SOX2 (AF2018, R&D). Libraries were sequenced (50 bp, single-end reads) on an Illumina Hi-Seq 2000 instrument.
Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of wnt, intestinal and cancer related genes

overall_design: Examination of Sox2 targets in the stomachs of Sox2 WT and Sox2 KO mice.

first: Anthony

last: Anselmo

first: Konrad

last: Hochedlinger


title: Selective single cell isolation for genomics using microraft arrays

status: Public on Aug 05 2016

city: Ann Arbor

first: Joshua

middle: D.

last: Welch

state: MI

address: 100 Washtenaw Ave.

institute: The University of Michigan

summary: Genomic methods are used increasingly to interrogate the individual cells that compose specific tissues. However, current methods for single cell isolation struggle to phenotypically differentiate specific cells in a heterogeneous population and rely primarily on the use of fluorescent markers. Many cellular phenotypes of interest are too complex to be measured by this approach, making it difficult to connect genotype and phenotype at the level of individual cells. Here we demonstrate that microraft arrays, which are arrays containing thousands of individual cell culture sites, can be used to select single cells based on a variety of phenotypes, such as cell surface markers, cell proliferation and drug response. We then show that a common genomic procedure, RNA-seq, can be readily adapted to the single cells isolated from these rafts. We show that data generated using microrafts and our modified RNA-seq protocol compared favorably with the Fluidigm C1. We then used microraft arrays to select pancreatic cancer cells that proliferate in spite of cytotoxic drug treatment. Our single cell RNA-seq data identified several expected and novel gene expression changes associated with early drug resistance.

overall_design: 120 samples including cells isolated using microrafts and the Fluidigm C1

middle: D

first: Corbin

last: Jones


title: Sox2 suppresses gastric tumorigenesis in mice [RNA-seq]

summary:
Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach.
Methods: mRNA profiles of Sox2 WT and Sox2 KO gastric glands were generated by RNA-sequencing, in triplicate, using a Illumina HiSeq 2500 instrument, resulting in 36 million single-end 50bp reads per smaple. Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR (Dobin et al., 2013). Read counts over transcripts were calculated using HTSeq v.0.6.0 (Anders et al., 2015) based on a current Ensembl annotation file for mm10/GRCm38 (release 75).
Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of cancer and intestinal related genes.

overall_design: mRNA profiles of stomachs from 10 week old Sox2 WT and Sox2 KO mice were generated by  sequencing, in triplicate, using a Illumina HiSeq 2500.


title: Biased Expression of the FOXP3Δ3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy Resistance

first: Kelvin

last: Zhang

address: 35 CambridgePark Drive, Suite 500

institute: Codiak Biosciences

summary: This study shows for the first time that the FOXP3Δ3 isoform is preferentially expressed in bladder cancer and induces a more aggressive and luminal isoform is preferentially expressed in bladder cancer and induces a more aggressive and luminal regulation of cancer differentiation and the plasticity amongst cancer subtypes which can be leveraged to optimize therapeutic regimens. These findings also identify a novel molecular marker as a putative companion diagnostic to guide therapy and target to undermine chemotherapy resistance.

overall_design: examination of RNA-Seq in two bladder cancer cell lines

first: Arnold

last: Chin


title: GATA-2 occupancy in Kasumi-3 cell line

city: Madison

first: Kyle

last: Hewitt

state: Wisconsin

address: 1111 Highland Ave.

institute: University of Wisconsin

summary: GATA-2 is a master regulator of hematopoiesis which controls expression of multiple genes and is implicated in acute myeloid leukemia (AML). However, the molecular mechanism how GATA-2 deregulation causes leukemogenesis is still unclear. In this study, GATA-2 ChIP-squ analysis was conducted in Kasumi-3 AML cell line to identify GATA-2 target genes which play important roles in the pathogenesis of AML.

overall_design: ChIP with GATA-2 antibody was conducted in Kasumi-3 AML cell line and ChIP-seq profile was generated by deep sequencing.

first: Koichi

last: Katsumura

first: Emery

middle: H

last: Bresnick

first: Peggy

last: Farnham


title: Transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure

city: Skudai

first: Chun Shiong

last: Chong

state: Johor

address: Building T02, Faculty of Biosciences and Medical Engineering Universiti Teknologi Malaysia

department: Department of Biotechnology and Medical Engineering

country: Malaysia

institute: Universiti Teknologi Malaysia

summary: By comparing the gene expression profiling in Anoxybacillus sp. SK 3-4 with and without aluminum exposure, the sets of gene up-regulated and down-regulated by aluminum were identified. The function of genes or proteins induced under these conditions can a reflection of the mechanism of resistance. Transcriptome profiling of Anoxybacillus sp. SK 3-4 treated by aluminum would allow a better understanding of the gene involving in tolerance and removal of aluminum.

overall_design: Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure

first: Jia

middle: c

last: Lim

first: Chun

middle: S

first: Kian

last: Goh


title: Memory of inflammation in regulatory T cells

first: Hyein

middle: Sophia

last: Cho

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptome and epigenome of Treg and effector T cells in various activation states.

overall_design: RNA-seq, ATAC-seq, and histone modification ChIP-seq of sorted cell populations

first: Joris

last: van der Veeken

first: Alvaro

last: Gonzalez

first: Hyunwoo

first: Aaron

last: Arvey

first: Christina

last: Leslie

first: Alexander

middle: Y

last: Rudensky


title: MYC activation and BCL2L11 silencing by a tumor virus through the large-scale reconfiguration of enhancer-promoter hubs

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

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

overall_design: Refer to individual Series


title: POLRMT regulates the switch between replication-primer formation and gene expression of mammalian mtDNA

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: Mitochondria are vital in providing cellular energy via their oxidative phosphorylation system, which requires the coordinated expression of genes encoded by both the nuclear and mitochondrial genomes (mtDNA). Transcription of the circular mammalian mtDNA depends on a single mitochondrial RNA polymerase (POLRMT). Although the transcription initiation process is well understood, it remains highly controversial if POLRMT also serves as the primase for initiation of mtDNA replication. In the nucleus, the RNA polymerases needed for gene expression have no such role. Conditional knockout of Polrmt in heart results in severe mitochondrial dysfunction causing dilated cardiomyopathy in young mice. We further studied the molecular consequences of different expression levels of POLRMT and found that POLRMT is essential for primer synthesis to initiate mtDNA replication in vivo. Furthermore, transcription initiation for primer formation has priority over gene expression. Surprisingly, mitochondrial transcription factor A (TFAM) exists in an mtDNA-free pool in the Polrmt knockout mice. TFAM levels remain unchanged despite strong mtDNA depletion and TFAM is thus protected from degradation of the AAA+ Lon protease in absence of POLRMT. Lastly, mitochondrial transcription elongation factor (TEFM) can compensate for a partial depletion of POLRMT in heterozygous Polrmt knockout mice, indicating a direct regulatory role for this factor in transcription. In conclusion, we present here the first in vivo evidence that POLRMT has a key regulatory role in replication of mammalian mtDNA and is part of a mechanism that provides a switch between RNA primer formation for mtDNA replication and mtDNA expression.

overall_design: Isolated heart mitochondria from three control mice (L/L) and three Polrmt knockout mice (L/L, cre), aged 3-4 weeks, were sequenced and analyzed for differential expression.

first: Aleksandra

last: Filipovska


title: A novel tumor-associated myeloid cell population inhibits antigen-specific immune responses in cancer patients

city: Nijmegen

first: Ghaith

last: Bakdash

address: Geert Grooteplein 26

country: Netherlands

institute: Radboudumc

summary: Tumor progression is associated with an immunosuppressive microenvironment that consists of several elements, such as regulatory T cells, type 2 macrophages and myeloid-derived suppressor cells. Here, we identify for the first time a BDCA1+CD14+ population of immunosuppressive cells that resides both in the blood and tumor of melanoma patients. We demonstrated that the presence of these cells in dendritic cell (DC)-based anti-tumor vaccines significantly suppresses CD4+ T cells in an antigen-specific manner. In an attempt to reveal the mechanism of this suppressive activity, we noticed that BDCA1+CD14+ cells express elevated levels of the check-point molecule PD-L1, which thereby hinders T cell proliferation. Importantly, although this suppressive BDCA1+CD14+ population expresses markers of both BDCA1+ DCs and monocytes, functional, transcriptome and proteome analyses clearly revealed that they comprise a unique population of cells that is exploited by tumors to evade immunity. Thus, targeting these cells may improve the efficacy of cancer immunotherapy.

overall_design: mRNA profiles of BDCA1+ DCs, BDCA1+CD14+ cells and monocytes, isolated from 3 healthy volunteers, were generated by deep RNA sequencing using HiSeq 2000 System (TruSeq SBS KIT-HS V3，Illumina)

first: Sonja

middle: I

last: Buschow

first: Mark

last: Gorris

first: Altuna

last: Halilovic

first: Stanleyson

last: Hato

first: Annette

middle: E

last: Sköld

first: Gerty

last: Schreibelt

first: Simone

last: Sittig

first: Ruurd

last: Torensma

first: Tjitske

last: Duiveman-de Boer

first: Christoph

last: Schröder

first: Evelien

middle: L

last: Smits

first: Carl

middle: G

last: Figdor

first: I

last: de Vries


title: Ccp1 homodimer mediates chromatin integrity  by antagonizing CENP-A loading

first: Fei

last: Li

address: 100 Washington Square East

institute: New York University

summary: CENP-A is a centromere-specific histone 3 variant essential for centromere specification. CENP-A partially replaces canonical histone H3 at the centromeres. How the particular CENP-A/H3 ratio at centromeres is precisely maintained is unknown. It also remains unclear how CENP-A is excluded from non-centromeric chromatin. Here we identify Ccp1, an uncharacterized NAP family protein in fission yeast that antagonizes CENP-A loading at both centromeric and non-centromeric regions. Like the CENP-A loading factor HJURP, Ccp1 interacts with CENP-A, and is recruited to centromeres at the end of mitosis in a Mis16-dependent manner. These data indicate that factors with opposing CENP-A loading activities are recruited to centromeres. Furthermore, Ccp1 also cooperates with H2A.Z to evict CENP-A assembled in euchromatin. Structural analyses indicate that Ccp1 forms a homodimer that is required for its anti-CENP-A loading activity. Our study establishes mechanisms for maintenance of CENP-A homeostasis at centromeres and the prevention of ectopic assembly of centromeres.

overall_design: Examination of cnp1 distribution in one wild type (wt) and two ccp1 mutants.


title: Epigenetic characteristics and gene-expression analysis of Derivative 3-3 de novo centromere in maize

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huazhong Agricultural University

summary: De novo centromeres originate occasionally from non-centromeric regions of chromosomes, providing an excellent model system to study centromeric chromatin. The maize mini-chromosome Derivative 3-3 contains a de novo centromere, which was derived from a euchromatic site on the short arm of chromosome 9 that lacks traditional centromeric repeat sequences. Our previous study found that the CENH3 binding domain of this de novo centromere is only 288 kb with a high-density gene distribution with low-density of transposons. Here we applied next generation sequencing technology to analyze gene transcription, DNA methylation for this region. Our RNA-seq data revealed that active chromatin is not a barrier for de novo centromere formation. Bisulfite-ChIP-seq results indicate a slightly increased DNA methylation level after de novo centromere formation, reaching the level of a native centromere. These results provide insight into the mechanism of de novo centromere formation and subsequent consequences.

overall_design: RNA-seq was carried out using material from seedling and young leaves between control and Derivative 3-3.  Bisulfite-ChIP-seq was carried out with anti-CENH3 antibodies using material from young leaves in Derivative 3-3.

first: Fangpu

last: Han

first: James

middle: A

last: Birchler


title: 17beta-HSD type 12-like is responsible for maturation-inducing hormone synthesis during oocyte maturation in masu salmon

city: Hakodate

first: Shigeho

last: Ijiri

state: Hokkaido

address: Minato-cho 3-1-1

department: Division of Marine Life Sciences

country: Japan

institute: Graduate School of Fisheries Sciences, Hokkaido University

summary: The maturation-inducing hormone 17alpha,20beta-dihydroxy-4-pregnen-3-one (DHP) was first identified in the amago salmon. However, although carbonyl reductase-like 20beta-hydroxysteroid dehydrogenase (CR/20beta-HSD) was reported to convert 17alpha-hydroxyprogesterone (17alpha-P) to DHP in rainbow trout, we previously found that CR/20beta-HSD mRNA was not up-regulated in stimulated granulosa cells from masu salmon, which suggests that DHP is synthesized by a different enzyme. Accordingly, the present study aimed to identify the specific 20beta-hydroxysteroid dehydrogenase (20beta-HSD) responsible for DHP production by granulosa cells during final oocyte maturation in masu salmon. Granulosa layers were isolated from ovarian follicles at one month before ovulation and incubated with or without forskolin, which was used to mimic luteinizing hormone. Subsequent RNA-sequencing yielded ~12 million reads, with an average length of 51 bp, and 71,062 contigs of >100 bp were constructed. Of the 953 contigs that were exclusively constructed from the reads of forskolin-induced granulosa layers, tBlastx analysis identified one contig (#f103496) that matched 17beta-hydroxysteroid dehydrogenase type 12. We found that mammalian cells transfected with full-length omhsd17beta12l exhibited considerable 20beta-HSD activity, as indicated by efficient conversion of exogenous 17alpha-P to DHP. In addition, we found that omhsd17beta12l mRNA levels were consistently low in follicles during vitellogenic growth; however, the levels increased significantly during final oocyte maturation. The levels of omhsd17beta12l mRNA were also considerably increased in granulosa layers in which 20beta-HSD activity was induced by salmon pituitary extract. Therefore, we suggest that omhsd17beta12l, not CR/20beta-HSD, is the 20beta-HSD responsible for DHP production by granulosa cells in masu salmon during final oocyte maturation.

overall_design: Comparison of mRNA levels between control and forskolin-incubated sample.

first: Seishi

last: Hagihara


title: INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer

status: Public on Aug 03 2016

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH


title: G-quadruplex structures mark human regulatory chromatin

first: Dario

last: Beraldi

address: Robinson Way

institute: Cambridge Research Institute

summary: G-quadruplex (G4) structural motifs have been linked to transcription, replication and genome instability and are implicated in cancer and other diseases. However, it is crucial to demonstrate the bona fide formation of G4 structures within an endogenous chromatin context. Herein we address this through the development of G4 ChIP-seq, an antibody-based G4 chromatin immunoprecipitation and high-throughput sequencing approach. We find ∼10,000 G4 structures in human chromatin, predominantly in regulatory, nucleosome-depleted regions. G4 structures are enriched in the promoters and 5' UTRs of highly transcribed genes, particularly in genes related to cancer and in somatic copy number amplifications, such as MYC. Strikingly, de novo and enhanced G4 formation are associated with increased transcriptional activity, as shown by HDAC inhibitor-induced chromatin relaxation and observed in immortalized as compared to normal cellular states. Our findings show that regulatory, nucleosome-depleted chromatin and elevated transcription shape the endogenous human G4 DNA landscape.

overall_design: Two cell lines, treated with entinostat or untreated, analyzed to detect gene expression differences, presence of G-Qudruplexes and chromatin state. Each combination of conditions replicated in duplicates or triplicates.

first: Robert

last: Hänsel-Hertsch

first: Stefanie

last: Lensing

first: Giovanni

last: Marsico

first: Marco

last: Di Antonio

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: Modeling human brain evolution using induced pluripotent stem cells: comparative analysis of neuronal development in humans and chimpanzees

city: La Jolla

first: Inigo

last: Narvaiza

state: CA

address: 10010 N Torrey Pines Rd

department: Laboratory of Genetics

institute: Salk Institute

summary: Understanding evolutionary mechanisms underlying expansion and reorganization of the human brain represents an important aspect in analyzing the emergence of cognitive abilities typical of our species. Comparative analyses of neuronal phenotypes in closest living relatives (Pan troglodytes; the common chimpanzee) can shed the light into changes in neuronal morphology compared to the last common ancestor (LCA), opening possibilities for analyses of the timing of their appearance, and the role of evolutionary mechanisms favoring a particular type of information processing in humans. Here, we use induced pluripotent stem cell (iPSC) technology to model neural progenitor cell migration and early development of cortical pyramidal neurons in humans and chimpanzees. In addition, we provide morphological characterization of the early stages of neuronal development in human and chimpanzee transplanted cells, and examine the role of developmental mechanisms previously proposed for the evolutionary expansions of the human brain on the early development of pyramidal neurons in the two species. The strategy proposed here lay down the basis for further comparative analysis between human and non-human primates and opens new avenues for understanding cognitive capability and neurological disease susceptibility differences between species.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: PolyA RNA-Seq profiling of neural progenitor cells (NPCs) and neurons differentiated from human and chimpanzee iPSCs.

first: Maria

middle: C

last: Marchetto

first: Christopher

last: Benner

first: Fred

last: Gage


title: MYC activation and BCL2L11 silencing by a tumor virus through the large-scale reconfiguration of enhancer-promoter hubs [EREB]

first: Simon

last: Andrews

summary: Lymphomagenesis in the presence of deregulated MYC expression requires suppression of MYC-driven apoptosis, often through downregulation of the pro-apoptotic BCL2L11 gene (Bim). Transcription factors (EBNAs) encoded by the lymphoma-associated Epstein-Barr virus (EBV) activate MYC and silence BCL2L11. We show that EBNA2 upregulates MYC by reconfiguring the 3 Mb MYC locus to increase upstream and decrease downstream enhancer-promoter interactions. EBNA2 recruits the SWI/SNF ATPase BRG1 to drive MYC enhancer-promoter interactions. MYC-Immunoglobulin translocation breakpoints in EBV-positive endemic Burkitt lymphoma localise to EBNA2-activated upstream MYC regions. This implicates EBV in the genesis and localisation of breakpoints, since active enhancers are targeted by activation-induced cytidine deaminase. We identify a novel haematopoietic BCL2L11 enhancer hub that is inactivated by EBNA3A and EBNA3C through recruitment of the H3K27 methyltransferase EZH2. Reversal of enhancer inactivation using an EZH2 inhibitor upregulates BCL2L11 and induces apoptosis. EBV therefore drives lymphomagenesis by hijacking long-range enhancer hubs and specific cellular co-factors.

overall_design: A study of MYC enhancer-promoter interactions using 4C on induction of MYC by the Epstein-Barr virus transcription factor EBNA2 in a lymphoblastoid cell line.

first: Michelle

last: West

last: Wood


title: MYC activation and BCL2L11 silencing by a tumor virus through the large-scale reconfiguration of enhancer-promoter hubs [Bcell]

overall_design: A study of MYC enhancer-promoter interactions using 4C on induction of MYC by Epstein-Barr virus infection of CD19+ primary B cells. B cells physiologically activated by treatment with CD40 ligand and IL-4 were studied as a control.

first: Hildegonda

last: Veenstra


title: Hierarchical RNA processing is rate limiting for mitochondrial ribosome assembly

first: Stefan

middle: J

last: Siira

summary: In animals the organization of the compact mitochondrial genome and lack of introns have necessitated a unique mechanism for RNA processing. To date the regulation of mitochondrial RNA processing and its importance for ribosome biogenesis and energy metabolism are not clear. To understand the in vivo role of the endoribonuclease component of the RNase P complex, MRPP3, we created conditional knockout mice. Here we show that MRPP3 is essential for life, and heart and skeletal muscle-specific knockout leads to a cardiomyopathy early in life, indicating that it is the only RNase P enzyme in mitochondria. We show that RNA processing is required for the biogenesis of the respiratory chain and mitochondrial function. Transcriptome-wide parallel analyses of RNA ends (PARE) and RNA-Seq enabled us to identify the in vivo cleavage sites of RNase P. Cleavage of the 5′ tRNA ends precedes 3′ end processing in vivo and is required for the correct biogenesis of the mitochondrial ribosomal subunits and mitoribosomal proteins that are differentially stabilized or degraded in the absence of mature rRNAs. Finally we identify that large mitoribosomal proteins can form a subcomplex on a precursor mt-RNA containing the 16S rRNA indicating that mitoribosomal biogenesis proceeds co-transcriptionally. Taken together our data show that RNA processing links transcription to translation via assembly of the mitoribosome.

overall_design: Total RNA was isolated from heart tissue from 11 week old control (Mrpp3loxP/loxP) and Mrpp3 knockout mice (Mrpp3loxP/loxP, +/Ckmm), TruSeq libraries produced in triplicate, sequenced and analysed for differential expression. Mitochondrial RNA was isolated from heart tissue from 11 week old control (Mrpp3loxP/loxP) and Mrpp3 knockout mice (Mrpp3loxP/loxP, +/Ckmm), PARE libraries produced  in triplicate and sequenced for analysis of mitochondrial RNA processing.

first: Irina

last: Kuznetsova

first: Aleksandra

last: Filipovska


title: A long noncoding RNA regulates sister chromatid cohesion [RNA-seq]

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

summary: Long noncoding RNAs (lncRNAs) have appeared to be involved in the most diverse cellular processes through multiple mechanisms. Here we describe a previously uncharacterized human lncRNA, CONCR (cohesion regulator noncoding RNA), transcriptionally activated by MYC, which is upregulated in multiple cancer types. The expression of CONCR is cell cycle-regulated, and it is required for cell cycle progression and DNA replication. Moreover, cells depleted of CONCR show severe defects in sister chromatid cohesion, suggesting an essential role for CONCR in cohesion establishment during cell division. CONCR interacts with and regulates the activity of DDX11, a DNA-dependent ATPase and helicase involved in DNA replication. These findings suggest a novel mechanism of action for CONCR in the modulation of DDX11 enzymatic activity, unveiling the direct involvement of a lncRNA in the establishment of sister chromatid cohesion.

overall_design: Characterization of the function of the long noncoding RNA CONCR. HCT116 p53-/- cells were left untreated (0h) or treated with the DNA damaging drug 5-FU for 4h and 12h.

first: Francesco

middle: P

last: Marchese

first: Elena

last: Grossi

first: Oskar

last: Marín-Béjar

first: Sanjay

middle: K

last: Bharti

first: Ivan

last: Raimondi

first: Jovanna

last: González

first: Dannys

last: Martínez-Herrera

first: Alejandro

last: Athie

first: Alicia

last: Amadoz

middle: M

last: Brosh


title: STAT5 is a key transcription factor IL-3-mediated inhibition of RANKL-induced osteoclastogenesis

city: Gwangju

first: Nacksung

last: Kim

address: B218, 160, Baekseo-ro, Dong-gu

department: Pharmacology

country: South Korea

institute: Chonnam National University Medical School

summary:
Purpose: Among the diverse cytokines involved in osteoclast differentiation, IL-3 has been shown to inhibit RANKL-induced osteoclastogenesis. However, the mechanism underlying IL-3-mediated inhibition of osteoclast differentiation is not fully understood. In the present study, we demonstrate that IL-3 activation of STAT5 inhibits RANKL-induced osteoclastogenesis through the induction of Id genes.
Methods: To investigate the effect of STAT5 on osteoclast differentiation and IL-3-mediated inhibition of osteoclast differentiation, bone marrow derived macrophages isolated from STAT5 wild-type (Stat5fl/fl) or STAT5 cKO (STAT5;MX1-Cre) were differentiated to osteoclast in the presence of M-CSF and RANKL with or without IL-3; and bone marrow derived macrophges from STAT5 wild-type and STAT5 cKO were overexpressed with PMX-FIG (control) or STAT5A1*6 (constitutively active form of STAT5A) and differentiated to osteoclast. To analyze bone phenotype, femurs and tibiae of 16 week-old STAT5 wild-type and STAT5 cKO were subjected to micro CT analysis and histomorphometry, respectively.
Results: Overexpression of STAT5 inhibited RANKL-induced osteoclastogenesis. However, RANKL did not regulate either expression or activation of STAT5 during osteoclast differentiation. STAT5 deficiency prevented IL-3-mediated inhibition of osteoclastogenesis, suggesting that STAT5 plays an important role in IL-3-mediated inhibition of osteoclast differentiation. In addition, IL-3-induced STAT5 activation upregulated expression of the Id1 and Id2 genes, which are negative regulators of osteoclastogenesis. Overexpression of ID1 or ID2 in STAT5-deficient cells reversed osteoclast development recovered from IL-3-mediated inhibition. Moreover, micro-computed tomography and histomorphometric analysis revealed that STAT5 conditional knockout mice showed reduced bone mass, with an increased number of osteoclasts. Furthermore, IL-3 inhibited RANKL-induced osteoclast differentiation less effectively in STAT5 conditional knockout mice than in wild-type mice in a RANKL injection model.
Conclusion: Taken together, our results suggest that STAT5 is a key transcription factor for IL-3-mediated inhibition of RANKL-induced osteoclastogenesis through Id gene expression.

overall_design: Examination of 4 different combination of osteoclast differentiation condition of bone marrow derived macrophages.

first: Semun

last: Seong

first: Jongwon

last: Lee


title: Transcriptomic profile of lignocellulose degradation from Trametes versicolor on poplar wood

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

summary: The Trametes versicolor genome is predicted to encode many enzymes that can effectively degrade lignin, making it a has potentially useful application intool for biopulping and biobleaching. Poplar is an important and widely cultivated species of tree species, which isand extensively applied used in the pulping industry. However, the wood degradation mechanism of T. versicolor from transcriptomic level is not clear. To reveal identify the enzymes that contributeing to lignocellulose degraredauction and its degradation mechanisms, we evaluated transcriptomic how study theof T. versicolor transcriptome was changes during evaluated growthing on the poplar wood relative to growth on glucose medium. 853 genes were differentially expressed;, 360 genes were up-regulated on poplar wood, and 493 genes were down-regulated on poplar wood. Notably, most genes relative involved into lignin degradation were up-regulated, including eight lignin peroxidase (LiP) genes, and two manganese peroxidase (MnP) genes etc. Genes encoding cellulose and hemicelluloses degrading-enzymesation were mostly down-regulated, including six endo-β-1, 4-glucanase genes, three cellobiohydrolase I genes, and one cellobiohydrolase II gene, etc. MeanwhileAdditionally, expression of more significant expansion of P450s in T. versicolor genome, along with differences in carbohydrate- and lignin-degrading enzymes, could bewere correlated withto poplar wood degradation. Our results revealed transcriptomic characterizeation  transcriptomic changes related toof lignocellulose degradation. Therefore, our results cwould be benuseful for the development ofefit T. versicolor as a tool to improve the efficiency of lignin degradation, and provide a theoretical foundation for a new paper pulp manufacturing processe

overall_design: 1,T.versicolor groewn on PDA medium. 2, T. versicolor growing on the a glucose carbon medium of glucose. 3, T. versicolor growing on poplar medium

first: Li-Ping

last: Zhang

first: Bo

last: Huang


title: VirR and RevR regulate many Clostridium perfringens genes in a reciprocal manner

city: Clayton

first: Julian

last: Rood

state: VIC

address: Wellington Rd

department: Microbiology

institute: Monash University

summary: We further characterize the VirSR and RevR regulatory networks by profiling the C. perfringens strain JIR325 and its isogenic virR and revR regulatory mutants using strand-specific RNA-seq. Two independent biological replicates were sequenced for each strain, generating more than 90 million sequence reads for each RNA-seq library (wild type, 97,289,148 reads; virR mutant, 116,505,992 reads and revR mutant, 131,811,486 reads). Using the edgeR analysis package, 223 genes in the virR mutant and 88 genes in the revR mutant were found to be differentially expressed. Comparative transcriptomic analysis revealed that VirR acts as a global negative regulator, whilst RevR acts as a global positive regulator. Therefore, about 88% of the differentially expressed genes were up-regulated in the virR mutant, whereas 75% of the differentially expressed genes were down-regulated in the revR mutant. Importantly, we identified 22 genes that were regulated by both VirR and RevR.  Of these genes, 18 or 82%, which included the sporulation-specific spoIVA, sigG and sigF genes, were regulated positively and negatively by RevR and VirR, respectively.  Furthermore, mapped RNA-seq reads visualized as a user plot showed that there were 97 previously unannotated transcripts in the intergenic regions. These transcripts may potentially encode novel genes or small RNA molecules. This study has identified genes, antisense transcripts, and transcripts within intergenic regions and on the native plasmid, which are controlled by the VirSR or RevR regulatory system.  The knowledge obtained will enable a more thorough annotation of the C. perfringens genome.

overall_design: Comparative transcriptomic analysis on the virR and revR regulatory mutants, and the wild-type strain JIR325

first: Lee-Yean

last: Low

first: Paul

middle: F

last: Harrison

first: Ya-Hsun

last: Lin

first: John

last: Boyce

first: Jackie

last: Cheung


title: Orientation-specific RAG activity in chromosomal loop domain contribute to Tcrd V(D)J recombination during T cell development

first: Lijuan

last: Zhao

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: T cell antigen receptor δ (Tcrd) variable region exons are assembled by RAG-initiated V(D)J recombination. Here, we employ a high throughput method to map hundreds of thousands of RAG-initiated Tcrd D segment (Trdd1 and Trdd2) rearrangements in developing thymocytes. We find that Trdd2 joins directly to Trdv, Trdd1, and Trdj segments, but Trdd1 joining is ordered with joining to Trdd2 a prerequisite for further rearrangement. We also find frequent, previously unappreciated Trdd1 and Trdd2 rearrangements that inactivate Tcrd. Moreover, we find numerous RAG off-targets that are generated via unidirectional RAG tracking across the loop-domain containing Trdd1, Trdd2 and Trdj. Correspondingly, disruption of the upstream domain boundary causes spreading of on- and off-target RAG activity to the proximal Trdv domain.

overall_design: RAG-initiatd Tcrd D segment rearrangements in developing thymocytes were generated by deep sequencing using illumine Miseq

first: Frederick

middle: W

last: Alt


title: Early pregnancy biomarkers

city: Easter Bush

first: Jason

last: Ioannidis

state: Midlothian

address: Easter Bush Veterinary Campus

institute: The Roslin Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Low fertility remains a leading cause of poor productivity in dairy cattle. In this context, there is significant interest in developing novel tools for accurate early diagnosis of pregnancy. MicroRNAs (miRNAs) are short RNA molecules which are critically involved in regulating gene expression during both health and disease. MiRNAs have been shown to regulate ovarian function, uterine receptivity, embryonic development and placental function. Circulating miRNAs can provide useful biomarkers of tissue function and disease; importantly, differential miRNA profiles have been linked to pregnancy and preeclampsia in humans. This study sought to establish the potential of circulating miRNAs as biomarkers of early pregnancy in cattle. We applied Illumina small-RNA sequencing to profile miRNAs in plasma samples collected from eight non-pregnant heifers on Days 0, 8 and 16 of the oestrous cycle and 11 heifers on Days 16 and 24 of pregnancy. We sequenced a total of 46 samples and generated 9.2 million miRNA reads per sample. There were no differences in miRNA read abundance between any of the pregnant and non-pregnant time-points (FDR > 0.1). As a complementary approach, we analysed sample pools (3-4 samples/pool) corresponding to Days 0, 8 and 16 of the oestrous cycle and Day 24 of pregnancy (n = 3 pools/group) using Qiagen PCR arrays. A total of 16 miRNAs were differentially expressed (FDR < 0.1) in plasma between pregnant and non-pregnant animals. RT-qPCR validation using the same plasma samples confirmed that miR-26a was differentially upregulated on Day 16 pregnant relative to non-pregnant heifers (1.7-fold; P = 0.043), whereas miR-1249 tended to be upregulated in Day 16 pregnant heifers (1.6-fold; P = 0.081). Further validation in an independent group of heifers confirmed an increase in plasma miR-26a levels during early pregnancy, which was significant only on Day 24 (2.0-fold; P = 0.027). Through genome-wide analyses we have successfully profiled plasma miRNA populations associated with early pregnancy in cattle. We have identified miR-26a as a potential circulating biomarker of early pregnancy.

overall_design: Sequencing of three sequencial samples from each of eight cycling animals (Days 0, 8 and 16, total 24 samples) and two samples from each of 11 pregnant animals (Days 16 and 24, total 22 samples). Main comparisons were between non-pregnant and pregnant groups

first: F

middle: X

last: Donadeu


title: Genome-wide expression screening discloses long noncoding RNAs involved in thyroid carcinogenesis

city: Columbus

first: Albert

last: de la Chapelle

state: OH

address: 460 W 12th Ave

institute: The Ohio State University

summary: Context: Long non-coding RNAs (lncRNAs) regulate pathological processes, yet their potential roles in papillary thyroid carcinoma (PTC) are poorly understood. Objective: To profile transcriptionally dysregulated lncRNAs in PTC and identify lncRNAs associated with clinicopathological characteristics.

overall_design: We performed RNA sequencing of 12 paired PTC tumors and matched noncancerous tissues and correlated the expression of lncRNAs with clinical parameters.

first: Sandya

last: Liyanarachchi

first: Wei

last: Li

first: Pearlly

last: Yan

first: Ralf

last: Bundschuh

first: Pamela

last: Brock

first: Leigha

last: Senter

first: Matthew

middle: D

last: Ringel

first: Huiling

last: He


title: RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

institute: UNSW

summary: Using a targeted Gtf2ird1 knockout mouse, we employed massively-parallel sequencing of mRNA (RNA-Seq) to understand changes in the transcriptional landscape associated with inactivation of Gtf2ird1 in lip tissue. We found widespread dysregulation of genes including differential expression of 78 transcription factors or coactivators, several involved in organ development including Hey1, Myf6, Myog, Dlx2, Gli1, Gli2, Lhx2, Pou3f3, Sox2, and Foxp3. We also found that the absence of GTF2IRD1 is associated with increased expression of genes involved in cellular proliferation, including growth factors consistent with the observed phenotype of extreme thickening of the epidermis. At the same time, there was a decrease in the expression of genes involved in other signalling mechanisms, including the Wnt pathway, indicating dysregulation in the complex networks necessary for epidermal differentiation and facial skin patterning. Several of the differentially expressed genes have known roles in both tissue development and neurological function, such as the transcription factor Lhx2 which regulates several genes involved in both skin and brain development.

overall_design: mRNA sequencing of lip tissue from 3 wild type mice (WT) and 3 Gtf2ird1 knockout mice generated by deep sequencing using Illumina HiSeq 2000 platform at the Ramaciotti Centre for Genomics UNSW.

first: Cesar

last: Canales

first: Marc

middle: R

last: Wilkins

first: Stephen

last: Palmer


title: INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer [RNA-seq]

first: Li

last: Wang

summary: Epigenetic regulators are attractive targets for the development of new cancer therapies. Among them, the ATP-dependent chromatin remodeling complexes control the chromatin architecture and play important roles in gene regulation. They are often found to be mutated and de-regulated in cancers, but how they influence the cancer gene expression program during cancer initiation and progression is not fully understood. Here we show that the INO80 chromatin remodeling complex is required for oncogenic transcription and tumor growth in non-small cell lung cancer (NSCLC). Ino80, the SWI/SNF ATPase in the complex, is highly expressed in NSCLC cells compared to normal lung epithelia cells. Further, its expression, as well as that of another subunit Ino80b, negatively correlates with disease prognosis in lung cancer patients. Functionally, Ino80 silencing inhibits NSCLC cell proliferation and anchorage-independent growth in vitro and tumor formation in mouse xenografts. It occupies enhancer regions near lung cancer-associated genes, and its occupancy correlates with increased genome accessibility and enhanced expression of downstream genes. Together, our study defines a critical role of INO80 in promoting oncogenic transcription and NSCLC tumorigenesis, and reveals a potential treatment strategy for inhibiting the cancer transcription network by targeting the INO80 chromatin remodeling complex.

overall_design: Human lung cancer cell line A549 cells were infected with shNT or shIno80, and total RNA was extracted 4 days after infection. The RNA was submitted to RNA-Seq subsequently. For ChIP-Seq, A549 infected with shNT or shIno80, was used for ChIP-Seq for corresponding factors.

first: Shu

last: Zhang

first: Bingying

last: Zhou

first: Brian

last: Bennett

first: Liangan

last: Chen

first: Guang

last: Hu


title: Transcriptome profiling of murine lungs after treatment with vector to deplete endogenous miRNAs

city: New York

first: Benjamin

last: tenOever

state: NY

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: To assess the impact of AdV-VP55 mediated degredation of host miRNAs on the murine whole lung transcriptome profile

overall_design: Non-replicateive Adeno vectors were delivered intranasally to 6-8 week old C57BL/6 mice for 48hrs. Whole lung tissue was isolated and used for transcriptome profiling.


title: T cell oxygen-sensing proteins establish an immunologically tolerant metastatic niche

city: Cambridge

first: Rahul

last: Roychoudhuri

address: Tennis Court Road

department: Department of Pathology

institute: University of Cambridge

summary: Cancer cells must evade immune responses at distant sites to establish metastases. The lung is a frequent site for metastasis. We hypothesized that lung-specific immunoregulatory mechanisms create an immunologically permissive environment for tumor colonization. We found that T cell-intrinsic expression of the oxygen-sensing prolyl-hydroxylase (PHD) proteins is required to maintain local tolerance against innocuous antigens in the lung, but powerfully licenses colonization by circulating tumor cells. PHD proteins limit pulmonary type helper (Th)-1 responses, promote CD4+-regulatory T (Treg) cell induction, and restrain CD8+ T cell effector function. Tumor colonization is accompanied by PHD protein-dependent induction of pulmonary Treg cells and suppression of IFN-g-dependent tumor clearance. T cell-intrinsic deletion or pharmacological inhibition of PHD proteins limits tumor colonization of the lung and improves the efficacy of adoptive cell transfer immunotherapy. Collectively, PHD proteins function in T cells to coordinate distinct immunoregulatory programs within the lung that are permissive to cancer metastasis.

overall_design: RNA expression was measured by RNA-Seq at day 4 following stimulation of naïve FACS-sorted CD4+ T cells with anti-CD3 and anti-CD28 antibodies in the presence of indicated doses of TGF-b. Gene expression was analysed separately in control Cd4Cre (WT) and Egln1fl/fl Egln2fl/fl Egln3fl/fl Cd4Cre (tKO) cells, or in cells treated with the pharmacological PHD inhibitor dimethyloxaloylglycine (DMOG) and control vehicle-treated cells.

first: David

last: Clever

first: Michael

last: Constantinides

middle: H

last: Askenase

first: Madhusudhanan

last: Sukumar

first: Christopher

last: Klebanoff

first: Robert

last: Eil

first: Heather

last: Hickman

first: Zhiya

last: Yu

first: Jenny

last: Pan

first: Douglas

first: Anthony

middle: T

last: Phan

first: John

last: Goulding

first: Luca

last: Gattinoni

first: Ananda

last: Goldrath

first: Yasmine

last: Belkaid

first: Nicholas

last: Restifo


title: Cotranslational signal independent SRP preloading during membrane targeting

city: Stanford

first: Justin

middle: William

last: Chartron

state: California

address: Clark Center E200, 318 Campus Drive

institute: Stanford University

summary: Cotranslational targeting into the endoplasmic reticulum (ER) by the Signal Recognition Particle (SRP) is a key event determining polypeptide fate in eukaryotic cells. Here, we globally define the principles and mechanisms of SRP binding and ER targeting in vivo. Cotranslational targeting through SRP is the dominant route into the ER for all secretory proteins, regardless of targeting signal characteristics. Cytosolic SRP functions in a pioneer translation round that builds a membrane-resident mRNAs pool, explaining how low SRP levels suffice for the secretory load. SRP does not induce an elongation arrest; consequently, kinetic competition between targeting and translation elongation dictates which substrates are translocated post-translationally. Unexpectedly, SRP binds most secretory ribosomal complexes before targeting signals are synthesized. We show non-coding mRNA elements can promote signal-independent SRP pre-recruitment. Our study defines the complex kinetic interplay between elongation and determinants in the polypeptide and mRNA modulating SRP-substrate selection and membrane targeting in vivo.

overall_design: Ribosome profiling (RiboSeq) and RNA-seq of subcellular fractions of ribosomes. Soluble and membrane bound ribosomes are separated by centrifugation, and SRP-bound ribosomes are immunoprecipitated from the soluble fraction. Polysomes and monosomes are separated by sucrose gradient ultracentrifugation.

first: Katherine

last: Hunt

first: Judith

last: Frydman


title: Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Embryonic Stem Cells (RRBS)

status: Public on Aug 02 2016

city: Los Angeles

first: Andrew

last: King

address: Gonda Bldg Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

summary: In this study, we mapped modification of lysine 4 and lysine 27 of histone H3 genome-wide in a series of mouse embryonic stem cells (mESCs) varying in DNA methylation levels based on knock-out and reconstitution of DNA methyltransferases (DNMTs). We extend previous studies showing cross-talk between DNA methylation and histone modifications by examining a breadth of histone modifications, causal relationships, and direct effects. Our data shows a causal regulation of H3K27me3 at gene promoters as well as H3K27ac and H3K27me3 at tissue-specific enhancers. We also identify isoform differences between DNMT family members. This study provides a comprehensive resource for the study of the complex interplay between DNA methylation and histone modification landscape.

overall_design: Reduced representation bisulfite sequencing (RRBS) performed on wild-type, Dnmt triple knock-out (Dnmt1/3a/3b; TKO), Dnmt double knock-out (Dnmt3a/3b; DKO), and respective reconstitution mouse embryonic stem cell lines.

first: Matteo

last: Pellegrini

first: Guoping

last: Fan


title: INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer [ChIP-seq]

first: Li

last: Wang

first: Shu

last: Zhang

first: Bingying

last: Zhou

first: Brian

last: Bennett

first: Liangan

last: Chen

first: Guang

last: Hu


title: IMP2 axonal localization, RNA interactome, and function in development of axon trajectories

city: Boston

first: John

last: Flanagan

state: MA

address: 240 Longwood Avenue

department: Cell Biology

institute: Harvard Medical School

summary: RNA-based regulatory mechanisms play important roles in the development and plasticity of neural circuits and neurologic disease. Developing axons provide a well suited model to study RNA-based regulation, and contain specific subsets of mRNAs that are locally translated and have roles in axon pathfinding. However, the RNA-binding proteins involved in axon pathfinding, and their corresponding mRNA targets, are still largely unknown.  Here we find that the RNA-binding protein IMP2 (Igf2bp2) is strikingly enriched in developing axon tracts, including in spinal commissural axons. We used the HITS-CLIP approach to perform a genome-wide identification of RNAs that interact directly with IMP2 in the native context of developing brain. This IMP2 interactome was highly enriched for mRNA targets related to axon guidance. Accordingly, IMP2 knockdown in the developing spinal cord led to strong defects in commissural axon trajectories at the midline intermediate target.  These results reveal a highly distinctive axonal enrichment of IMP2, show that it interacts with a network of axon guidance-related mRNAs, and reveal its requirement for normal axon pathfinding during vertebrate development.

overall_design: CLIP-seq


title: Elucidating Combinatorial Chromatin States  at Single-Nucleosome Resolution

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

department: School of Engineering

country: Israel

institute: The Hebrew University of Jerusalem

summary: Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) has been instrumental to our current view of chromatin structure and function. It allows genome-wide mapping of histone marks, which demarcate biologically relevant domains. However, ChIP-seq is an ensemble measurement reporting the average occupancy of individual marks in a cell population. Consequently, our understanding of the combinatorial nature of chromatin states relies almost exclusively on correlation between the genomic distributions of individual marks. Here, we report the development of Combinatorial-iChIP to determine the genome-wide co-occurrence of histone marks at single nucleosome resolution.  By comparing to null model, we show that certain combinations of overlapping marks (H3K36me3 and H3K79me3) co-occur more frequently than expected by chance, while others (H3K4me3 and H3K36me3) do not, reflecting differences in the underlying chromatin pathways. We further use combinatorial-iChIP to illuminate aspects of the Set2-RPD3S pathway. This approach promises to improve our understanding of the combinatorial complexity of chromatin.

overall_design: Combinatorial iChIP in yeast.

first: Sadeh

last: Ronen

first: Launer-Wach

last: Roee

first: Wandel

last: Hava

first: Rahat

last: Ayelet

first: Friedman

last: Nir


title: Post-transcriptional manipulation of TERC reverses molecular hallmarks of telomere disease

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

summary: The telomerase RNA component (TERC) is a critical determinant of cellular self renewal. Poly(A)-specific ribonuclease (PARN) is required for post-transcriptional maturation of TERC. PARN mutations lead to incomplete 3′ end processing and increased destruction of nascent TERC RNA transcripts, resulting in telomerase deficiency and telomere diseases. Here, we determined that overexpression of TERC increased telomere length in PARN-deficient cells and hypothesized that decreasing post-transcriptional 3′ oligo-adenylation of TERC would counteract the deleterious effects of PARN mutations. Inhibition of the noncanonical poly(A) polymerase PAP-associated domain–containing 5 (PAPD5) increased TERC levels in PARN-mutant patient cells. PAPD5 inhibition was also associated with increases in TERC stability, telomerase activity, and telomere elongation. Our results demonstrate that manipulating post-transcriptional regulatory pathways may be a potential strategy to reverse the molecular hallmarks of telomere disease.

overall_design: mRNA sequencing of induced pluripotent stem cells and 293 cell line.

first: Boris

last: Boyraz

first: Suneet

last: Agarwal


title: Functional analysis of AEBP2, a PRC2 Polycomb protein, reveals a Trithorax phenotype in embryonic development and in ES cells

city: Oxford

first: Michal

middle: R.

last: Gdula

address: South Parks Road

institute: Oxford University

summary: The Polycomb repressive complexes PRC1 and PRC2 are key mediators of heritable gene silencing in multicellular organisms.  Here we characterize AEBP2, a known PRC2 cofactor which, in vitro, has been shown to stimulate PRC2 activity. We show that AEBP2 localises specifically to PRC2 target loci, including the inactive X   chromosome. Proteomic analysis confirms that AEBP2 associates exclusively with PRC2 complexes.  However, analysis of embryos homozygous for a targeted mutation of Aebp2 unexpectedly revealed a Trithorax phenotype, normally linked to antagonism of Polycomb function. Consistent with this we observe elevated levels   of PRC2 mediated histone H3K27 methylation at target loci in Aebp2 mutant embryonic stem cells.  We further demonstrate that mutant ES cells assemble atypical hybrid PRC2 sub-complexes, potentially accounting for enhancement of Polycomb activity, and suggesting that AEBP2 normally plays a role in defining the mutually exclusive composition of PRC2 sub-complexes.

overall_design: H3K27me3, SUZ12, and AEBP2 ChIP-Seq in wild-type and AEBP2 KO mouse ESCs, biological replicates, pre-cleared chromatin as input, additionally FS2 ChIP-Seq in cells with FS2 tagged AEBP2, HiSeq2000

first: Anne

last: Grijzenhout

first: Jonathan

last: Godwin

first: Haruhiko

last: Koseki

first: Dorota

last: Szumska

first: Joanna

last: McGouran

first: Shoumo

last: Bhattacharya

first: Benedikt

last: Kessler

first: Neil

last: Brockdorff

first: Sarah

last: Cooper


title: A long noncoding RNA regulates sister chromatid cohesion [ChIP-seq]

first: Maite

last: Huarte

summary: Long noncoding RNAs (lncRNAs) have appeared to be involved in the most diverse cellular processes through multiple mechanisms. Here we describe a previously uncharacterized human lncRNA, CONCR (cohesion regulator noncoding RNA), transcriptionally activated by MYC, which is upregulated in multiple cancer types. The expression of CONCR is cell cycle-regulated, and it is required for cell cycle progression and DNA replication. Moreover, cells depleted of CONCR show severe defects in sister chromatid cohesion, suggesting an essential role for CONCR in cohesion establishment during cell division. CONCR interacts with and regulates the activity of DDX11, a DNA-dependent ATPase and helicase involved in DNA replication. These findings suggest a novel mechanism of action for CONCR in the modulation of DDX11 enzymatic activity, unveiling the direct involvement of a lncRNA in the establishment of sister chromatid cohesion.

overall_design: Characterization of the function of the long noncoding RNA CONCR. Analysis of DDX11 chromatin binding by ChIP-seq in the presence or absence of CONCR.

first: Francesco

last: Marchese

first: Elena

last: Grossi

first: Oskar

last: Marín-Béjar

first: Sanjay

last: Bharti

first: Ivan

last: Raimondi

first: Jovanna

last: González

first: Dannys

last: Martínez-Herrera

first: Alejandro

last: Athie

first: Alicia

last: Amadoz

first: Robert

last: Brosh


title: Yap reprograms glutamine metabolism to increase nucleotide biosynthesis and enable liver growth

first: Andrew

last: Cox

address: 77 Avenue Louis Pasteur

department: Brigham and Women's Hospital

summary: The Hippo pathway is an important regulator of organ size and tumorigenesis. It is unclear, however, how Hippo signaling provides the cellular building blocks required for rapid growth. Here, we report that transgenic zebrafish expressing an activated form of the Hippo pathway effector Yap1 develop enlarged livers and are prone to liver tumor formation. Transcriptomic profiling reveals that Yap1 reprograms genes involved in glutamine metabolism.

overall_design: Analysis of gene expression in WT and lf:Yap transgenic zebrafish livers.

first: Wolfram

last: Goessling


title: Myocardin-related Transcription Factors Are Required for Skeletal Muscle Development

city: Chicago

first: Bercin

last: Cenik

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Myocardin-related transcription factors (MRTFs) play a central role in the regulation of actin expression and cytoskeletal dynamics. Stimuli that promote actin polymerization allow for shuttling of MRTFs to the nucleus where they activate serum response factor (SRF), a regulator of actin and other cytoskeletal protein genes.  SRF is an essential regulator of skeletal muscle differentiation and numerous components of the muscle sarcomere, but the potential involvement of MRTFs in skeletal muscle development has not been examined. We explored the role of MRTFs in muscle development in vivo by generating mutant mice harboring a skeletal muscle-specific deletion of MRTF-B and a global deletion of MRTF-A. These double knockout (dKO) mice were able to form sarcomeres during embryogenesis. However, the sarcomeres were abnormally small and disorganized, causing skeletal muscle hypoplasia and perinatal lethality. Transcriptome analysis demonstrated dramatic dysregulation of actin genes in MRTF dKO mice, highlighting the importance of MRTFs in actin cycling and myofibrillogenesis. MRTFs were also necessary for the survival of skeletal myoblasts and for the efficient formation of intact myotubes. Our findings reveal a central role for MRTFs in sarcomere formation during skeletal muscle development and point to the potential involvement of these transcriptional coactivators in skeletal myopathies.

overall_design: Gene expression profile was generated comparing wild type (WT) and HSA-Cre, MRTF-A/B double knockout mice, by deep seqencing, with three biological replicates, using Illumina HiSeq 2500.

first: Eric

middle: N

last: Olson


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (Col), hda6, hda5, hda9, fld and fve mutants

city: Taipei

first: Keqiang

last: Wu

address: No.1, Sec.4, Roosevelt Rd.

department: Institute of Plant Biology

country: Taiwan

institute: National Taiwan University

summary: The goals of this study are to compare the RNA profiling by NGS in different mutants and Genome-wide analysis of gene regulatory networks

overall_design: 14-day old plant of Col and each mutants were generated by deep sequencing, using Illumina HiSeq™ 2500

first: Chun-Wei

last: Yu


title: TDP-43 regulates cancer-associated microRNAs

city: Beijing

first: Xiaowei

last: Chen

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, CAS

summary: MicroRNAs (miRNAs) play important roles in a wide range of cellular processes. Aberrant regulation of miRNA genes contributes to human diseases, including cancer. The TAR DNA binding protein 43 (TDP-43), a DNA/RNA binding protein associated with neurodegeneration, is involved in miRNA biogenesis. Here, we systematically examined miRNAs whose expression levels are regulated by TDP-43 using RNA-Seq coupled with siRNA-mediated knockdown approach. TDP-43 knocking down affected the expression of a number of miRNAs. Alterations in isomiR patterns and miRNA arm selection after TDP-43 knockdown suggest a role of TDP-43 in miRNA editing. We examined correlation of selected TDP-43 associated miRNAs and their candidate target genes in human cancers. Our data reveal highly complex roles of TDP-43 in regulating different miRNAs and their target genes. Our results suggest that TDP-43 may promote migration of lung cancer cells by regulating miR-423-3p expression. On the other hand, TDP-43 increases miR-500a-3p expression and binds to the mature miR-500a-3p sequence. Low expression of miR-500a-3p was associated with poor survival of lung cancer patients, suggesting that TDP-43 may have a suppressive role in cancer by regulating miR-500a-3p. Our experiments reveal that cancer-associated genes LIF and PAPPA may be targets of miR-500a-3p. Together with other studies, our work suggests that TDP-43-regulated miRNAs may play multi-facet roles in the pathogenesis of cancer.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
small RNA seq in SH-SY-5Y, SNB-19 and HT22 (TDP-43 siRNA VS Control siRNA).
3’ adapter RA3: 5’-TGGAATTCTCGGGTGCCAAGG-3’


title: Small RNA deep sequencing of HEK 293T cells treated with an Adeno vector encoding the  Vaccinia virus VP55 protein

first: Benjamin

last: tenOever

summary: To assess the efficacy of AdV-VP55 mediated degredation of host miRNAs.

overall_design: Small RNA profiles of HEK 293T cells treated with type 5  Adeno vectors expressing either GFP or GFP-VP55 for 24 hours


title: Differential gene expression profiling of MIHA cells transfected with C-terminal truncated HBx mutants

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: To compare the differentially expressed transcriptomes between MIHA cells transfected with empty vector control or different C-terminal truncated HBx mutants (14 or 35 amino acid carboxyl-terminal truncation - i.e. d14 and d35)

overall_design: mRNA profiles of MIHA cells stably overexpressing empty vector control or different C-terminal truncated HBx mutants (delta 14 and delta 35) were generated by PolyA mRNA sequencing using Illumina HiSeq 1500 platform

first: Stephanie

last: Ma


title: Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Embryonic Stem Cells (RNA-seq)

last: King

overall_design: RNA-seq performed on wild-type, Dnmt triple knock-out (Dnmt1/3a/3b; TKO), Dnmt double knock-out (Dnmt3a/3b; DKO), and respective reconstitution mouse embryonic stem cell lines

first: Guoping

last: Fan


title: Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Embryonic Stem Cells

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

overall_design: Refer to individual Series


title: CXCR5+ follicular cytotoxic T cells control viral infection in B cell follicles

status: Public on Aug 01 2016

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

institute: IMP

summary: In response to infection, antigen-specific CD8+ T cells are primed in the T cell zone of secondary lymphoid organs and differentiate into cytotoxic effector T (TC) cells. Concurrently, CD4+ T cells differentiate into follicular helper T (TFH) cells that localize to B cell follicles and promote protective antibody responses. During unresolved infections, however, some viruses including human immunodeficiency virus (HIV) or Epstein–Barr virus (EBV) escape immune control and persist in TFH cells and B cells, respectively. Exclusion of Tc cells from B cell follicles is thought to be a major mechanism of immune evasion. New strategies are therefore needed to eradicate infected cells in follicles for a permanent cure. Using mouse infection models and human samples, we here identify a specialized group of TC cells expressing the chemokine receptor CXCR5 that can selectively enter B cell follicles and eradicate infected TFH and B cells. We demonstrate that differentiation of these cells, which we term follicular cytotoxic T (TFC) cells, requires the transcription factors Bcl6, E2A and Tcf1, whereas the transcriptional regulators Blimp1, Id3 and Id2 inhibit their development. We demonstrate that Blimp1 and E2A directly regulate Cxcr5 expression, and together with Bcl6 and Tcf1 form a transcriptional circuit that guides the TFC differentiation. The identification of a follicular subset of TC cells has far reaching implications for developing better strategies for the control of infections that target B cells and TFH cells and for the eradication of B cell derived malignancies. There is no associated input.

overall_design: The E2A Bio-ChIP-seq was performed with total thymocytes from Tcf3Bio/Bio Rosa26BirA/BirA mice

first: Ivan

last: Bilic

first: Martina

last: Minnich

first: Markus

last: Jaritz


title: dCAP-D3 ChIP-seq in Drosophila S2 cells

city: Cleveland

first: Michelle

middle: Suzanne

last: Longworth

address: 9500 Euclid Ave NE20

department: Molecular Genetics

institute: Cleveland Clinic Foundation

summary: The goal of this experiment was to identify genomic dCAP-D3 binding sites in Drosophila S2R+ cells

overall_design: dCAP-D3 was immunoprecipitated in two separate experiments with antibody YZ834 which was developed in the Longworth lab.  IgG immunoprecipiation was performed alongside the dCAP-D3 immunoprecipitation to serve as controls for each experiment.  Input chromatin was also harvested from each of the two experiments.

middle: S


title: Differential Peak Calling of ChIP-Seq Signals with Replicates with THOR

city: Aachen

first: Manuel

last: Allhoff

address: Schinkelstr. 2

institute: AICES

summary: Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells in bone marrow by successive steps of lineage commitment and differentiation. Different DC subsets were identified based on phenotype, localisation and function: (i) classical DC (cDC) and plasmacytoid DC (pDC) are found in lymphoid organs and (ii) migratory tissue DC are spread throughout peripheral organs, including Langerhans cells, the cutaneous contingent of DC. We have developed a two-step culture system that recapitulates DC development in vitro (Felker et al., J. Immunol. 185, 5326-5335, 2010). In this system multipotent hematopoietic progenitors (MPP) progress into DC-restricted common DC progenitors (CDP) and further into the two major DC subsets cDC and pDC. We employed chromatin immunoprecipitation (ChIP) with deep sequencing (ChIP-seq) to determine the dynamics of H3K27ac occupancy in MPP, CDP, cDC and pDC. Additionally, we monitored changes in gene expression in MPP, CDP, cDC and pDC by RNA-seq.

overall_design: Histone modification H3K27ac and RNA-Seq in MPP, CDP, cDC and pDC

first: Kristin

last: Seré

first: Juliana

last: Freitas

first: Martin

last: Zenke

middle: G

last: Costa


title: Dual randomization of oligonucleotides to reduce the bias in ribosome-profiling libraries

city: Muenster

first: Benedikt

middle: Sebastian

last: Nilges

address: Von-Esmarch-Straße 54

department: RNA Biology Group

institute: Max Planck Institute for Molecular Biomedicine

summary: Protein translation is at the heart of cellular metabolism and its in-depth characterization is key for many lines of research. Recently, ribosome profiling became the state-of-the-art method to quantitatively characterize translation dynamics at a transcriptome-wide level. However, the strategy of library generation affects its outcomes. Here, we present a modified ribosomeprofiling protocol starting from yeast, human cells and vertebrate brain tissue. We use a DNA linker carrying four randomized positions at its 5’  and a reverse-transcription (RT) primer with three randomized positions to reduce artifacts during library preparation. The use of seven randomized nucleotides allows to efficiently detect library-generation artifacts. We find that the effect of polymerase chain reaction (PCR) artifacts is relatively small for global analyses when sufficient input material is used. However, when input material is limiting, our strategy improves the sensitivity of gene-specific analyses. Furthermore, randomized nucleotides alleviate the skewed frequency of specific sequences at the 3’  end of ribosome-protected fragments (RPFs) likely resulting from ligase specificity. Finally, strategies that rely on dual ligation show a high degree of gene-coverage variation. Taken together, our approach helps to remedy two of the main problems associated with ribosome-profiling data. This will facilitate the analysis of translational dynamics and increase our understanding of the influence of RNA modifications on translation.

overall_design: Ribosome profiling and mRNA-seq libraries from wt yeast comparing different library preparation approaches using different combinations of randomized and non-randomized linkers and RT primers.

first: Aaron

last: Lecanda

first: Puneet

last: Sharma

first: Danny

last: Nedialkova

first: Juliane

last: Schwarz

first: Juan

last: Vaquerizas

first: Sebastian

middle: A

last: Leidel


title: Characterization of active piRNAs and piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12

city: Cold Spring Harbor

first: Delphine

last: Fagegaltier

address: One Bungtown Rd

department: Genomics Division

institute: Cold Spring Harbor Lab


title: mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development [RNA-seq Drosophila oocyte stages]

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

institute: Seoul National University

summary: Eukaryotic mRNAs are subject to multiple types of tailing which critically influence mRNA stability and translatability. To investigate RNA tails at the genomic scale, we previously developed TAIL-seq, but its low sensitivity precluded its application to biological materials of minute quantity. In this study, we report a new version of TAILseq (mRNA TAIL-seq or mTAIL-seq) with enhanced sequencing depth for mRNAs (by ~1000 fold compared to the previous version). The improved method allows us to investigate the regulation of poly(A) tail in Drosophila oocytes and embryos. We find that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and that further modulation occurs upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates the vast majority of maternal mRNAs with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAILseq data with ribosome profiling data, we find a strong coupling between poly(A) tail length and translational efficiency during egg activation. Our data suggest that regulation of poly(A) tail in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing in diverse biological systems.

overall_design: Two sets of RNA-seq on 3 developmental stages (immature oocyte, mature oocyte, and activated egg) of wild type and wispy mutant of Drosophila melanogaster.

first: Mihye

last: Lee

first: Ahyeon

last: Son

first: Hyeshik

last: Chang

first: V

last: Kim


title: CBP regulates promoter-proximal RNA polymerase II

city: Ithaca

first: Dig

middle: Bijay

last: Mahat

address: 526 campus Rd

department: Molecular Biology & Genetics

institute: Cornell University

summary: Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is not fully understood. Here we identify a novel activity of the co-regulator and histone acetyltransferase p300/CBP in positioning promoter-proximal paused Pol II. We find that CBP inhibition impedes transcription through the +1 nucleosome, causing “dribbling” of Pol II from the canonical pause site genome-wide. We further discovered that promoters strongly occupied by Drosophila CBP and GAGA-factor have high levels of paused Pol II, a unique chromatin signature and strong expression regardless of cell type. Interestingly, CBP activity is rate-limiting for Pol II recruitment to these highly-paused promoters but for transit into elongation at other genes. Thus, we uncover a key role for CBP during transcription in directly controlling different rate-limiting steps depending on promoter features.

overall_design: Examination of transcriptional regulation with and without CBP inhibition for 10 minutes in Drosophila S2 cells. Two biological replicates for each condition.

first: Ann

last: Boija

middle: B

first: Aman

last: Zare

first: Per-Henrik

last: Holmqvist

first: Philge

last: Philip

first: David

middle: J

last: Meyers

first: Philip

last: Cole

first: John

last: Lis

first: Per

last: Stenberg

first: Mattias

last: Mannervik


title: Characterization of active piRNAs and an piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12 (small RNA)

summary: We have found that oncogenic Ras combined with loss of the Hippo tumour-suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells, coincident with oncogenic transformation. In these cells, Piwi becomes loaded with piRNAs derived from generative loci, which are normally restricted to either the germline or the somatic follicle cells. Negating the pathway leads to increases in the expression of a wide variety of transposons and also to altered expression of some protein coding genes.  This correlates with a reduction in the proliferation of the transformed cells in culture, suggesting that at least in this context, the piRNA pathway may play a functional role in cancer.

overall_design: Small RNAs cloned from whole cells, piwi-bound small RNAs and long RNA-Seq were performed in wts-RNAi;RasV12 cells to identify piRNAs and gene expression and compared to RasV12 cells, somatic OSS cells, and germline UAS-wts-RNAi;UAS-RasV12 control ovaries. After knock-down of several components of the piRNA machinery in WRR-1 cells (piwi, zuchini, armitage, aubergine, argonaute3) and GFP and/or dsRED control knock-downs, small RNAs were cloned and gene expression profiles (RNA-Seq) were established.

first: Gregory

last: Hannon


title: mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens


title: Characterization of active piRNAs and piRNA machinery in WRR-1 cells deficient for the Hippo pathway (deficient for the warts tumor suppressor) and expressing activated RasV12 (RNA-seq)

first: Delphine

last: Fagegaltier

overall_design: Small RNAs cloned from whole cells, Piwi-bound small RNAs and long RNA-Seq were performed in wts-RNAi;RasV12 cells to identify piRNAs and gene expression changes compared to RasV12 cells, somatic OSS cells, and germline UAS-wts-RNAi;UAS-RasV12 control ovaries. After knock-down of components of the piRNA machinery in WRR-1 cells ([piwi, zuchini, armitage, aubergine, argonaute3) and GFP and/or dsRED control knock-downs, small RNAs were cloned and gene expression  (RNA-Seq) profiles were established.


title: A long noncoding RNA regulates sister chromatid cohesion

city: Pamplona

first: Maite

last: Huarte

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada