title: Transcriptome-wide analysis of dynamic variations in regulation modes of grapevine microRNAs on their target genes during grapevine development

status: Public on Oct 15 2015

city: Nanjing

first: Chen

last: Wang

state: Jiangshu

address: Weigang 1#

department: Horticulture College

institute: Nanjing Agriculture University

summary: microRNAs(miRNAs) play critical regulatory roles mainly through cleaving targeted mRNAs or repressing gene translation during plant developments. Grapevine is amongst the most economically important fruit crops with whole genome available, and the study on grapevine miRNAs (Vv-miRNAs) have also been emphasized. However, the regulation mode of Vv-miRNAs on their target mRNAs during grapevine development has not been studied well, especially on a transcriptome-wide level. Here, six small RNA (sRNA) and mRNA libraries from various grapevine tissues were constructed for Illumina and Degradome sequencing. Subsequently, the spatiotemporal variation in the Vv-miRNAs’ regulation on their target genes was systematically analyzed. Totally, 242 known and 132 novel Vv-miRNAs were identified, and 193 target mRNAs including 103 for known and 90 for novel miRNAs were validated in one or more of tissues examined. The interesting finding was that over 50% of novel miRNAs were expressed exclusively in flowers or berries where they had tissue-specific cleavage roles on their target genes, especially, the breadth of their cleavage sites in flower tissues. Moreover, six novel miRNAs in berries were found to response to exogenous gibberellin (GA) and/or ethylene by real time RT-PCR (qRT-PCR) analysis, confirming their regulatory functions during berry development. Other finding was that about 93.6% of the known miRNAs possessed the high conservation in various tissues where their expression levels exhibited some dynamic variations during grapevine development. Significantly, it was found the phenomena that some Vv-miRNA families exist one key member that act as the main regulator of their target genes during grapevine development.

overall_design: Six tissues  (young leaf, mature leaf, inflorescence, flower, young berry and mature berry) of grapevine were selected, and these samples can be extracted total RNA, and then were separated to small RNAs used for Solexa sequencing, respectively. Subsequenctly, we carried out the analysis of Solexa sequencing data, and performed the research on the dynamic variations of  regulatory modes of grapevine miRNAs on their target genes during grapevine development process at the whole transcriptome level.

first: Xiangpeng

last: Leng

first: Yanyi

last: Zhang

first: Emrul

last: Kayesh

first: Yanping

first: Jinggui

last: Fang


title: ChIP-Seq analysis of Helios and histone modifications in CD4+ and CD8+ Tregs

status: Public on Oct 16 2015

city: Boston

first: R. Anthony

last: Barnitz

state: MA

address: 450 Brookline Ave.

department: Department of Pediatric Oncology

country: USA

institute: Dana-Farbert Cancer Institute, Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The maintenance of immune homeostasis requires regulatory T cells (Tregs). Given their intrinsic self-reactivity, Tregs must stably maintain a suppressive phenotype to avoid autoimmunity. We report that impaired expression of the transcription factor (TF) Helios by FoxP3+ CD4 and Qa-1-restricted CD8 Tregs results in defective regulatory activity and autoimmunity in mice. Helios-deficient Treg develop an unstable phenotype during inflammatory responses characterized by reduced FoxP3 expression and increased effector cytokine expression secondary to diminished activation of the STAT5 pathway. CD8 Treg also require Helios-dependent STAT5 activation for survival and to prevent terminal T cell differentiation. Definition of Helios as a key transcription factor that stabilizes regulatory T-cells in the face of inflammatory responses provides a genetic explanation for a core property of regulatory T-cells.

overall_design: This is an examination of the transcription factor Helios with 2 different histone modifications in both CD4+ and CD8+ Tregs.  Appropriate control sequence files for ChIP input are also included.

first: R

middle: A

first: W

middle: N

last: Haining

first: Hye-Jung

last: Kim

first: Harvey

last: Cantor


title: Uridylation of RNA-hairpins by Tailor confines the emergence of novel miRNAs in Drosophila

status: Public on Oct 19 2015

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

type: Non-coding RNA profiling by high throughput sequencing

summary: Uridylation of diverse RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small RNA biogenesis and stability in plants, worms and mammals. Here, we report the first uridylyltransferase that acts on small RNAs in Drosophila, which we refer to as Tailor. Tailor is the source for the majority of 3´ terminal uridine-modifications in small RNAs and predominantly targets precursor-miRNAs. Uridylation modulates the characteristic two-nucleotide 3´ overhangs of miRNA hairpins, which regulates pre-miRNA processing by Dicer-1. Furthermore, Tailor preferentially uridylates mirtron hairpins, thereby impeding the production of non-canonical microRNAs. Mirtron-selectivity is explained by unique primary sequence specificity of Tailor, selecting RNA substrates ending with a 3´ guanosine, a feature not previously observed for terminal uridylyltransferases. In contrast to mirtrons, conserved Drosophila pre-miRNAs are significantly depleted in 3´ guanosine, thereby escaping regulatory uridylation.Our data support the hypothesis that evolutionary adaptation to pre-miRNA uridylation shapes the nucleotide composition of pre-miRNA 3´ ends and may serve as a barrier for the de novo creation of miRNAs in Drosophila.

sample_organism:
Drosophila melanogaster
synthetic construct

overall_design: 10 small RNA libraries (3 replicates untreated, 4 replicates control RNAi [GFP, GFP/Luc], and 3 replicates CG1091 RNAi [CG1091]) from Drosophila S2 cells; 3 RNA libraries from 40-100 nt RNA (untreated, control RNAi, and CG1091 RNAi) from Drosophila S2 cells; 5 small RNA libraries (w1118; CG1091[c4-1] heterozygous and homozygous; CG1091[c4-6] heterozygous and homozygous) from whole 2-5 day old male Drosophila melanogaster flies; 3 libraries (In vitro tailing randomized substrate, Input, 2 min CG1091 treamtent, 5 min CG1091 treatment) on in vitro tailing reaction using a 37mer RNA substrate with four randomized nucleotides at the 3´ end

first: Madalena

middle: M

last: Reimão-Pinto

first: Valentina

last: Ignatova

middle: R

first: Jui-Hung

last: Hung

first: Ivica

last: Sowemimo

first: Sara

last: Fariña-Lopez

first: Stefan

middle: L

last: Ameres


title: Combinatorial gene regulation by modulation of relative pulse timing

city: Pasadena

first: Yihan

last: Lin

state: CA

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology/HHMI

type: Expression profiling by high throughput sequencing

summary: We performed RNAseq with Saccharomyces cerevisiae cells under both transient and steady-state conditions to study the regulation of genes by two pulsatile transcription factors, Msn2 and Mig1. The transient data allowed us to identify combinatorial targets while the steady-state data was used to study target expression dependence on the relative pulse timing between the two TFs.

overall_design: For transition experiments, 18 samples (3 different strains x 3 dfferent conditions x 2 biological replicates) were analyzed. For steady-state experiments, one strain was analyzed at 9 different glucose concentrations and the other strain was analyzed at one glucose condition.

first: Chang

middle: H

last: Sohn

first: Chiraj

middle: K

last: Dalal

first: Long

last: Cai

first: Michael

middle: B

last: Elowitz


title: Uridylation of hairpin-RNAs by Tailor confines the emergence of miRNAs in Drosophila

summary: Uridylation of diverse RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small RNA biogenesis and stability in plants, worms and mammals.   Here, we report the first uridylyltransferase that acts on small RNAs in Drosophila, which we refer to as Tailor. Tailor is the source for the majority of 3´ end-modifications in microRNAs and predominantly targets precursor-hairpins. Uridylation modulates the characteristic two-nucleotide 3´ overhangs of microRNA hairpins, which regulates processing by Dicer-1 and destabilizes RNA hairpins. Furthermore, Tailor preferentially uridylates mirtron-hairpins, thereby impeding the production of non-canonical microRNAs. Mirtron-selectivity is explained by unique primary sequence specificity of Tailor, selecting RNA substrates ending with a 3´ guanosine, a feature not previously observed for TUTases. In contrast to mirtrons, conserved Drosophila pre-miRNAs are significantly depleted in 3´ guanosine, thereby escaping regulatory uridylation.  Our data support the hypothesis that evolutionary adaptation to pre-miRNA uridylation shapes the nucleotide composition of pre-miRNA 3´ ends. Hence, hairpin-uridylation may serve as a barrier for the de novo creation of miRNAs in Drosophila.

overall_design: mRNA sequencing of Drosophila S2 cells (3-times; control libraries) and three biological replicates of S2 cells stably depleted of CG1091/Tailor by CRISPR/Cas9

first: Raphael

last: Manzenreither

first: Veronika

last: Herzog

first: Brian

last: Reichholf


title: Panoramix enforces piRNA-dependent co-transcriptional silencing (small RNA-Seq)

city: Cold Spring Harbor

first: Yang

last: Yu

state: NY

address: One Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: The Piwi-interacting RNA (piRNA) pathway is a small RNA-based innate immune system that defends germ cell genomes against transposons. In Drosophila ovaries, the nuclear Piwi protein is required for transcriptional silencing of transposons, though the precise mechanisms by which this occurs are unknown. Here we show that CG9754 is a component of Piwi complexes that functions downstream of Piwi and its binding partner, Asterix, in transcriptional silencing. Enforced tethering of CG9754 protein to nascent mRNA transcripts causes co-transcriptional silencing of the source locus and the deposition of repressive chromatin marks. We have named CG9754 Panoramix, and propose that this protein could act as an adaptor, scaffolding interactions between the piRNA pathway and the general silencing machinery that it recruits to enforce transcriptional repression.

overall_design: Examination of small RNA levels from nos-GAL4 driven UAS-dsRNA knockdowns of the indicated genes in ovaries of Drosophila melanogaster by deep sequencing.

first: Jiaqi

last: Gu

first: Ying

last: Jin

first: Yicheng

last: Luo

first: Jonathan

last: Preall

first: Jinbiao

last: Ma

first: Benjamin

last: Czech

first: Gregory

middle: J

last: Hannon


title: Paf1 complex factors, Leo1 and Paf1, promote local histone turnover to modulate chromatin states in fission yeast

status: Public on Oct 18 2015

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

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

overall_design: Refer to individual Series


title: Massively parallel cis-regulatory analysis in the mammalian central nervous system

city: St. Louis

first: Joseph

middle: C

last: Corbo

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

summary: Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of candidate CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery of candidate CREs to target organs in vivo. As a proof-of-concept, we introduce a capture library of ~46,000 constructs, corresponding to ~3,500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as non-human primates and human stem cell-derived organoids.

sample_organism:
Mus musculus
Synthetic plasmid

platform_organism:
Mus musculus
Synthetic plasmid

overall_design: MiSeq (2x250bp) paired-end sequencing was conducted to determine the barcode-CRE correspondence of the library. HiSeq (1x50bp) sequencing was conducted to quantify the RNA and DNA barcode abundance in retina and cortex.

first: Susan

middle: Q

last: Shen

first: Connie

last: Myers

first: Andrew

middle: E

last: Hughes

first: Leah

last: Byrne

first: John

middle: G

last: Flannery


title: Panoramix enforces piRNA-dependent co-transcriptional silencing (RNA-Seq)

overall_design: Examination of transcriptome from germline knockdown of either Piwi or CG9754 (comparing to a White control knockdown) or the loss-of-function mutations in CG9754 ORF from Drosophila ovaries

last: Cezch


title: Quadruplex ligand Tetra-Pt(bpy) Induces the Death of Human ALT Cancer Cells by Inhibiting Homologue Recombination-Mediated Telomere Elongation

city: Guangzhou

first: Yong

last: Zhao

state: Guangdong

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-Sen University

summary: The RNA-seq results reveal Tetra-Pt(bpy) has no effect on gene expression.

overall_design:
Examination of the gene expression of the following cells:
MRC5-untreated and Tetra-Pt(bpy)-treated
HeLa-untreated and Tetra-Pt(bpy)-treated
U2OS-untreated and Tetra-Pt(bpy)-treated

first: Xiao-Hui

last: Zheng

first: Yi-Min

last: Fang

first: Xin

last: Nie

first: Li-Xin

last: Xia

first: Zong-Wan

last: Mao

first: Hai-Ying

last: Liu

first: Jian

last: Ren

first: Feng

last: Wang


title: Panoramix enforces piRNA-dependent co-transcriptional silencing (GRO-Seq)

first: Yang

last: Yu

overall_design: Examination of nascent transcripts from germline knockdown of either Piwi or CG9754 from Drosophila ovaries

first: Jiaqi

last: Gu

first: Ying

last: Jin

first: Yicheng

last: Luo

first: Jonathan

last: Preall

first: Jinbiao

last: Ma

first: Benjamin

first: Gregory

last: Hannon


title: RNA sequencing of mice expressing NLS-hTDP-43

city: Philadelphia

first: Edward

last: Lee

state: PA

address: 605B Stellar Chance Laboratories, 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

summary: TAR DNA-binding protein 43 (TDP-43) is normally a nuclear RNA-binding protein that exhibits a range of functions including regulation of alternative splicing, RNA trafficking and RNA stability. However, in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), TDP-43 is abnormally phosphorylated, ubiquitinated, and cleaved, and is mislocalized to the cytoplasm where it forms distinctive aggregates. We previously developed a mouse model expressing human TDP-43 with a mutation in its nuclear localization signal (ΔNLS-hTDP-43) so that the protein preferentially localizes to the cytoplasm. These mice did not exhibit a significant number of cytoplasmic aggregates, but did display a loss of endogenous mouse nuclear TDP-43 as well as dramatic changes in gene expression as measured by microarray. Here, we analyze RNA-sequencing data from the ∆NLS-hTDP-43 mouse model, together with published RNA-sequencing data obtained previously from TDP-43 antisense oligonucleotide (ASO) knockdown mice and High Throughput Sequencing of RNA isolated by CrossLinking ImmunoPrecipitation (HITS-CLIP) data of TDP-43’s RNA binding targets to further investigate the dysregulation of gene expression in the ∆NLS model. This analysis reveals that the transcriptomic effects of the overexpression of the ΔNLS-hTDP-43 transgene are likely due to a gain of cytoplasmic function. Moreover, cytoplasmic TDP-43 expression alters transcripts that regulate chromatin assembly, the nucleolus, lysosomal function, and histone 3’ untranslated region (UTR) processing. These transcriptomic alterations correlate with observed histologic abnormalities in heterochromatin structure and nuclear size in transgenic mouse and human brains.

overall_design: RNAseq of bigenic (n=4) ∆NLS-hTDP-43 and control nontransgenic (n=4) mouse cortex

first: Alexandre

last: Amlie-Wolf


title: Yap dependent reprogramming of Lgr5+ stem cells drives intestinal regeneration and cancer

city: Worcester

first: Yu

address: AS5-1018, 368 Plantation Street

department: Program in Systems Biology

institute: University of Massachusetts Medical School

summary: Hippo signalling has been implicated as a key regulator of tissue regeneration. In the intestine, ex vivo organoid cultures model aspects of crypt epithelial regeneration. Therefore in order to uncover the Yap regulated transcriptional programs during crypt regeneration we performed RNA-sequencing of Yap wt and Yap deficient organoids, as well as organoids inducibly expressing Yap.

overall_design: Yap loss of function organoids were harvested from Yapfl/fl;VillinCre mice (Yap-/-). In addition, we developed Yap overexpressing organoids by generating a doxycycline-inducible wild-type Yap transgenic line under the control of a Cre driven reverse tetracycline transactivator (rtTA), referred to here as YapTg. Organoids were seeded on day 0 from whole crypts isolated from Yap+/D, YapD/D, YapTg mice and cultured for 24 hours at which time they were harvested for transcriptome analysis by RNAseq.

first: Alex

last: Gregorieff

first: Jeffrey

last: Wrana


title: Panoramix enforces piRNA-dependent co-transcriptional silencing


title: Panoramix enforces piRNA-dependent co-transcriptional silencing (ChIP-Seq)

overall_design: Examination of H3K9m3 marks from germline knockdown of either Piwi or CG9754 from Drosophila ovaries

last: Cezch


title: PRDM5 regulates collagen gene transcription by association with RNA polymerase II in developing bone

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary:
PRDM family members are transcriptional regulators involved in tissue specific differentiation. PRDM5 has been reported to predominantly repress transcription, but a characterization of its molecular functions
in a relevant biological context is lacking. We demonstrate here that Prdm5is highly expressed in developing bones; and, by genome-wide mapping of Prdm5 occupancy in pre-osteoblastic cells, we uncover a novel
and unique role for Prdm5 in targeting all mouse collagen genes as well as several SLRP proteoglycan genes. In particular, we show that Prdm5 controls both Collagen I transcription and fibrillogenesis by binding inside
the Col1a1 gene body and maintaining RNA polymerase II occupancy. In vivo, Prdm5 loss results in delayed ossification involving a pronounced impairment in the assembly of fibrillar collagens. Collectively, our results
define a novel role for Prdm5 in sustaining the transcriptional program necessary to the proper assembly of osteoblastic extracellular matrix.

overall_design: A total of six ChIP-Seq samples are available: two directed against Prdm5, using different antibodies (named ab1 and ab2), two directed against histone modifications (H3K4Me3 and H3K9Me3), one directed against the active transcribing RNA Polymerase II and a background model obtained using an unrelated IgG

first: Giorgio

last: Galli

first: Kristian

last: de Lichtenberg

first: Matteo

last: Carrara

first: Wolfgang

last: Hans

first: Manuela

last: Wuelling

first: Bettina

last: Mentz

first: Hinke

last: Multhaupt

first: Cathrine

last: Fog

first: Kalus

middle: T

last: Jensen

first: Juri

last: Rappsilber

first: Andrea

last: Vortkamp

first: Les

last: Coulton

first: Helmut

last: Fuchs

first: Valérie

last: Gailus-Durner

first: Martin

last: de Angelis

first: John

last: Couchman

first: Anders

last: Lund


title: Plasmodium parasites mount an arrest response against dihydroartemisinin [P. berghei RNA-Seq]

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

summary: Control of malaria is threatened by emerging parasite resistance to artemisinin drug (ART) therapies. The molecular details of how Plasmodium malaria parasites response to ART and how this relates to resistance is not clear. To determine how parasites respond to ART by altering gene expression, we performed a transcriptomic study of dihydroartemisinin (DHA) response in P. falciparum K1 strain and in P. berghei ANKA strain.  Microarray data from DHA-treated P. falciparum trophozoite stage parasites were compared with data from other ART treatments. Genes with consistent changes in expression were identified, which includes notably down-regulation of cytosolic ribosomal protein genes. RNA-seq data revealed a similar pattern of transcriptomic change, although the pattern was much clearer in that more than one-third of P. falciparum trophozoite genes are differentially expressed with greater statistical support for down-regulation of ribosomal protein genes. The poor overlap of differentially-expressed genes between microarray and RNA-seq and less-well defined patterns for the former suggests that the accuracy of microarray is limited by technological bias. The trophozoite response to DHA is overall “ring-like” and less “trophozoite-like”, which is consistent with previous findings that Plasmodium can enter a quiescent ring-like state to resist ART. RNA-seq data from DHA-treated P. falciparum rings reveal a more muted response, although there is considerable overlap of differentially expressed genes with DHA-treated trophozoites. In contrast, P. falciparum schizonts are unresponsive to DHA, suggesting that the protective response acts mainly to arrest parasite development through the G2/M checkpoint. The transcriptional response of P. berghei to DHA treatment in vivo in infected mice is strikingly similar to the P. falciparum in vitro ring and trophozoite responses, in which ribosomal protein genes are notably down-regulated. These results suggest Plasmodium species respond to DHA in the same way. This knowledge could be applied to outwit the parasite to deliver more effective artemisinin therapies, and maybe hinder the development of drug resistance.

overall_design: mRNA profiles of dihydroartemisinin (DHA)-treated parasites were compared with vehicle control treated parasites in duplicate; sequence data obtained from TruSeq stranded RNA-seq libraries sequenced on Illumina MiSeq  instrument

first: Sastra

last: Chaothieng

first: Pavita

last: Tipsombatboon

first: Jittima

last: Piriyapongsa

first: Chayaphat

last: Wongsombat

first: Nattida

last: Suwannakitti

first: Pongpisid

last: Koonyosying

first: Chairat

last: Uthaipibull

first: Sumalee

last: Kamchonwongpaisan

first: Yongyuth

last: Yuthavong


title: ChIP-seq of the androgen receptor (AR) in MDAMB453 cells after androgen stimulation

city: Cambridge

first: Kerstin

last: Meyer

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: Serum starved MDAMB453 cells were serum starved and treated for 4 hours with vehicle control (ethanol), 5α-dihydrotestosterone (DHT; 10nM) or medroxyprogesterone acetate (MPA; 10nM). AR binidng peaks were determined. Subsequent analysis showed that binding sites for androgen receptor are enriched at breast cancer risk loci.

overall_design: Each ChIP experiment was carried out in duplicate and consensus AR binding peaks were called. The conditions were vehcle (ethanol) treated, DHT and MPA stimulated cells.

first: Theresa

last: Hickey

first: Thomas

last: Campbell


title: Phloem-specific transcriptome profiling links gene expression, physiological characterization with phloem function in the pedicle and fruit of cucumber (Cucumis sativus L.)

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

summary: Phloem is essential for higher plant development and survival by transporting photosynthetic products and systemic signals from source to sink organs. To date, most phloem studies were performed with the phloem exudate for physiological, transcriptomic or proteomic analyses. However, as yet, no transcriptomic profiling was performed to the phloem tissue itself, probably due to the technique difficulties to access the phloem tissue inside the plant body. In this study, laser microdissection combined with RNA-Seq technology was used to gain phloem-specific transcript profiling in three different organs (pedicle, stalk and fruit) of cucumber, a model plant species for phloem research. We found that transcription factors and biotic/abiotic stress related genes are highly enriched in the sink organs, while cell growth via calcium ion, hormone actions and cell cycle control was largely restricted in the pedicle and stalk, and genes implicated in transporting amino acids and sugars are mostly up-regulated in the pedicle. Further, we found excellent corroboration between phloem-specific gene expression, and physiological characterization with phloem function. In addition, we identified 432 cucumber-unique genes and several phloem-specific markers for future functional studies. This study provides new insights into the molecular genetics of the function of phloem tissue in cucumber, rather than the conventional phloem sap analyses.

overall_design: Transcriptome profiling by laser microdissection combined with  RNA sequencing analysis was employed to discover critical genes that are expressed and regulated in phloem tissue  in three different organs (pedicle, stalk and fruit) of cucumber. Two biological replicates were generated for each sample.

first: Zhao

last: Jianyu

first: Li

last: Yanqiang

first: Ding

last: Lian

first: Yan

last: Shuangshuang

first: Liu

last: Meiling

last: Xiaofeng

first: Jiang

last: Li

last: Wensheng

first: Ning

last: Kang

first: Che

last: Gen

first: Xia

last: Mengxue

first: Chen

last: Zijing

first: Wang

last: Qiang

last: Liying

last: Renyi

first: Zhang

last: Xiaolan


title: Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein beta binding sites

status: Public on Oct 14 2015

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Transcription factors (TFs) bind to thousands of DNA sequences in mammalian genomes, but most of these binding events appear to have no direct effect on gene expression.  It is unclear why only a subset of transcription factor bound sites are actively involved in transcriptional regulation, nor are the key genomic features known that discriminate between active and inactive TF binding events.  Recent studies have identified promoter-distal RNA polymerase II (RNAP2) binding at enhancer elements, suggesting that these interactions may serve as a potential marker for active regulatory sequences.  Despite these correlative analyses, a thorough functional validation of these genomic co-occupancies is still lacking.  To characterize systematically the gene regulatory activity of DNA sequences underlying promoter-distal TF binding events that co-occur with RNAP2 and TF sites devoid of RNAP2 occupancy using a functional assay, we performed cis-regulatory element sequencing (CRE-seq) reporter assays.  We tested more than 1,000 promoter-distal CCAAT/enhancer-binding protein beta (CEBPB) bound sites in two human cell types, HepG2 and K562.  We found that CEBPB bound sites that co-occur with RNAP2 were more likely to exhibit enhancer activity in our reporter assay and these active sequences display significantly stronger RNAP2 read enrichment and local enhancer RNA (eRNA) activity compared to inactive sites.  CEBPB-bound sites further maintained substantial cell type specificity, indicating that DNA sequence information at such sites can accurately convey cell type-specific regulatory information, supporting a strong role for local DNA sequence in distinguishing active from inactive TF-bound loci. By comparing our CRE-seq results to a comprehensive set of over 1,000 genome annotations, we identified a variety of genomic features that are strong predictors of regulatory element activity as well as cell type-specific activity.  Collectively, our functional assay results indicate that RNAP2 occupancy can be used as a key genomic marker that can discriminate active versus inactive transcription factor bound sites.

overall_design: CRE-seq reporter assay of replicate barcodes from plasmid DNA, transfected plasmid DNA, expressed RNA (cDNA).  CEBPB binding sites as well as scrambled control sequences were tested.

first: R

last: Myers

first: J

last: Gertz


title: Genome-wide RNA-Seq analysis of breast muscles of two broiler chicken groups differing in shear force

city: Balice

first: Katarzyna

last: Piorkowska

address: Krakowska 1

department: Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary:
Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with the level of meat tenderness in broiler chickens.

Methods: Chicken mRNA profiles of 6-weeks-old characterized by low (n=4) and high (n=4) shear force of pectoralis musle were generated by deep sequencing,  using Illumina HiScan SQ. The alignment and estimation of gene level expression was made using the RSEM package and TopHat splice junction mapper, each supported by a Bowtie2 aligner. Differentially expressed genes (DEG) and their corresponding p-values were determined using the Cufflinks package, edgeR and DESeq2. qRT–PCR validation was performed using TaqMan and SYBR Green assays

Results: A total of 11,560 transcripts and 9,824 genes per sample were identified. In the low shear force chicken group 19 genes were up-regulatated and 49 genes were down regutated. The up-regulated gene group included the ASB2 gene, which is probably involved in the meat conversion process, as its product results in the degradation of filamins, proteins which form muscle fibres. In the down-regulated gene group, genes which play a role in lipogenesis (THRSP, PLIN1) and in collagen synthesis (P4HA3, LEPREL4, PCOLCE2, COL16A1, COL20A1, VWA1) were detected.

Conclusions: Results obtained in our study sugest the involvement of the extracellular matrix in the determination of meat tenderness. In this study were identified a pool of genes that may participate in the tenderisation process in broiler chickens.

overall_design: Chicken mRNA profiles of 6-weeks-old characterized by low (n=4) and high (n=4) shear force of pectoralis musle were generated by deep sequencing,  using Illumina HiScan SQ in in two technical repetitions

last: Piórkowska

first: Kacper

last: Żukowski

first: Joanna

last: Nowak

last: Połtowicz

last: Ropka-Molik

first: Artur

last: Gurgul


title: piRNA expression in rat ovary

city: Madurai

first: Gopal

last: Pandi

state: Tamil Nadu

address: Department of Plant Biotechnology, School of Biotechnology

country: India

institute: Madurai Kamaraj University

summary:
Purpose: To study the expression profile of piRNAs in rat ovary
Methods: Ovary from eight-weeks old, adult wistar rats were harvested after sacrificing the animal. The total RNA is isolated using trizol reagent. Subsequently, small RNA library was contructed using illumina kit as per manufacturer's instructions.
Results: The reads were annotated to the rat genome (rn5) and piRNA database and their expression is studied
Conclusions: Large number of piRNAs are expressed in rat ovary

overall_design: Small RNA profile of rat ovary was generated by deep sequencing using Illumina HiSeq 1000

first: G

last: Velmurugan


title: Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

summary: To understand the evolution of genome regulation and cell differentiation, we investigated the transcriptional dynamics of the ichthyosporean Creolimax fragrantissima, a close relative of animals that undergoes coenocytic development. We report the transcriptional differences between the amoeboid stage and the multinucleate stage of this species, describing the various aspects of differential genome regualtion found in those samples.

overall_design: Examination of mRNA profiles from 2 stages of C. fragrantissima development.

first: Iñaki

last: Ruiz-Trillo


title: Chromatin environment shapes replication origin organization and defines origin classes

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

summary: To unveil the still-elusive nature of metazoan replication origins, we identified them genome-wide and at unprecedented high-resolution in mouse ES cells. This allowed initiation sites (IS) and initiation zones (IZ) to be differentiated. We then characterized their genetic signatures and organization and integrated these data with 43 chromatin marks and factors.  Our results reveal that replication origins can be grouped into three main classes with distinct organization, chromatin environment and sequence motifs. Class 1 contains relatively isolated, low-efficiency origins that are poor in epigenetic marks and are enriched in an asymmetric AC repeat at the initiation site.  Late origins are mainly found in this class. Class 2 origins are particularly rich in enhancer elements. Class 3 origins are the most efficient and are associated with open chromatin and polycomb protein-enriched regions. The presence of Origin G-rich Repeated elements (OGRE) potentially forming G-quadruplexes (G4) was confirmed at most origins. These coincide with nucleosome-depleted regions located upstream of the initiation sites, which are associated with a labile nucleosomes containing H3K64ac. These data demonstrate that specific chromatin landscapes and combinations of specific signatures regulate origin localization. They explain the frequently-observed links between DNA replication and transcription. They also emphasize the plasticity of metazoan replication origins, and suggest that in multicellular eukaryotes, the combination of distinct genetic features and chromatin configurations act in synergy to define and adapt the origin profile.

overall_design:
Examination of replication origins by high-throughput sequencing in mouse stem cells.

The Series supplementary files Combination_3replicates.wig, Initiation_Sites.bedGraph, and Initiation_Zones.bed contain combined data from the 3 replicates (GSM1668878, GSM1668879, GSM1668880).

first: Benoît

last: Ballester

first: Jacques

last: van Helden

first: Marcel

last: Mechali


title: Human ovarian granulosa cell methylome

city: Bronx

first: Bo

last: Yu

address: 1300 Morris Park Ave, Block 621

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: We used MethylCap-seq and RRBS to profile methylomes of purified human ovarian granulosa cells. Genomic DNA methylation patterns in ovarian granulosa cells were compared between two groups of women: i) oocyte donors (n=20) who were young (age 26 ± 2.2 years) and had robust response to ovarian stimulation during assisted reproductive technology (ART) (mean number of oocytes retrieved = 25); versus ii) poor responders (n=20) who were older (age 40 ± 2.3 years) and responded poorly to ovarian stimulation during ART (oocytes retrieved ≤4 and peak estradiol level ≤ 1000 pg/ml).  The first group served as healthy control.  The second group represented the majority of women in their early 40s who have the natural age-related decline of ovarian functions and therefore respond poorly to ovarian stimulation during ART.    We compared DNA methylomes in ovarian granulosa cells from oocyte donors versus poor responders using two approaches: MethylCap-seq for broader genomic coverage, and RRBS for absolute quantification.  Due to very limited amount of materials available from each poor responder, samples containing equal amounts of granulosa cell DNA were pooled from 10 individuals in each group.  A second set of experiments pooling granulosa cell DNA samples from independent donor and poor responder groups (ten individuals each) was then performed.

overall_design: mix 10 individuals into one sample; compare samples with age differences


title: Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using RNA-seq [ribo-depletion]

city: Ottawa

first: Anna

middle: Francina

last: Jackson

state: Ontario

address: 50 Colombine Drive, Tunney's Pasture

department: Environmental Health Center

country: Canada

institute: Health Canada

summary: Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using RNA-seq (ribo-depletion protocol).  All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one- and two-colour microarrays and RNA-seq (polyA-enrichment protocol) in order to determine the effect of the technology on gene expression profiles.

overall_design: In this study we examined the transcriptional response in liver tissue of female B6C3F1 mice exposed to furan for 3 weeks to 8 mg/kg bw furan (or vehicle control) and sacrificed four hours after the final exposure.  Each dose group had 4 biological replicates. There were a total of 24 samples included in the final analysis of the ribo-depletion RNA-seq.

first: A

middle: F

last: Webster

first: Paul

last: Zumbo

first: Jorge

last: Gandara

first: Leslie

last: Recio

first: Carole

last: Yauk

first: Christopher

last: Mason


title: Global gene expression analysis of fresh-frozen, furan-exposed mouse liver using RNA-seq [polyA enrichment]

summary: Furan is a mouse and rat hepatocarcinogen. We sought to determine if furan-induced gene expression changes could be detected in paired fresh-frozen and formalin-fixed paraffin embedded (FFPE) samples using RNA-seq (polyA-enrichment protocol).  All samples in this study (fresh-frozen, 18 hours in formalin, 3 weeks in formalin) were also examined using one- and two-colour microarrays and RNA-seq (ribo-depletion protocol) in order to determine the effect of the technology on gene expression profiles.

overall_design: In this study we examined the transcriptional response in liver tissue of female B6C3F1 mice exposed to furan for 3 weeks to 8 mg/kg bw furan (or vehicle control) and sacrificed four hours after the final exposure.  Each dose group had 4 biological replicates. There were a total of 24 samples included in the final analysis of the polyA enrichment RNA-seq experiment.


title: Evolutionary suppression of erythropoiesis via the modulation of TGF-β signaling in an Antarctic icefish

first: Peng

last: Hu

address: Huchenghuan Road 999

institute: Shanghai Ocean University

summary: The Antarctic icefish, a family (Channichthyidae) of teleosts within the perciform suborder Notothenioidei, are the only known vertebrates without oxygen-transporting hemoglobins and that are largely devoid of circulating erythrocytes. To elucidate the evo-devo mechanisms underpinning the suppressed erythropoiesis in the icefish, we conducted comparative studies on the transcriptomes and microRNAomes of the primary hematopoietic tissues between an icefish (Chionodraco hamatus) and two red-blooded notothenioids (Trematomus bernacchii and Gymnodraco acuticeps). We identified substantial remodeling of the hematopoietic programs in the icefish through which erythropoiesis is selectively suppressed. Experimental verification showed that erythropoietic suppression in the icefish may be attributable to the upregulation of TGF-β signaling, which coincides with reductions in multiple transcription factors essential for erythropoiesis and the upregulation of hundreds of microRNAs, the majority (> 80%) of which potentially target erythropoiesis regulating factors.

sample_organism:
Gymnodraco acuticeps
Chionodraco hamatus
Trematomus bernacchii

overall_design: Comparative transcriptome studies on 9 samples (hematopoietic tissues of three notothenioids fish)

first: Qianghua

last: Xu

first: Liangbiao

last: Chen


title: Human ovarian granulosa cell transcriptome

summary: We used mRNA-seq to profile transcriptomes of purified human ovarian granulosa cells

overall_design: 12 female individuals


title: Global gene expression analysis in paired fresh-frozen and FFPE furan-exposed mouse liver samples

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

overall_design:
Refer to individual Series

The '2014-10-28_Equivalent samples table_AFW.xlsx' describes the paired samples in each study.


title: Mitochondrial phosphoenolpyruvate carboxykinase (PCK2) regulates metabolic adaptation and glucose-independent tumor cell growth

first: Maxim

middle: N.

last: Artyomov

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Cancer cells must adapt metabolically to survive and proliferate when nutrients are limiting. Here we used combined transcriptional-metabolomic network analysis to identify metabolic pathways that support glucose-independent tumor cell growth. We found that glucose deprivation stimulated the re-wiring of the tricarboxylic acid (TCA) cycle and co-opting early steps of gluconeogenesis to promote cell proliferation under low glucose. Glucose limitation promoted the production of phosphoenolpyruvate (PEP) from glutamine, which was used to fuel biosynthetic pathways normally sustained by glucose, including serine and purine biosynthesis. Mitochondrial PEP-carboxykinase (PCK2) was required for this glutamine-dependent metabolic reprogramming. PCK2 expression was dependent on the hypoxia-inducible factors (HIFs), and required to maintain tumor cell proliferation under limiting glucose availability. Elevated PCK2 expression is observed in several human tumor types, and enriched in tumor tissue from non-small cell lung cancer (NSCLC) patients. Our results define a novel role for PCK2 in cancer cell metabolic reprogramming that promotes glucose-independent cell growth and metabolic stress resistance in human tumors.

overall_design: A549 cell line was obtained from ATCC (Manassas, VA, USA). A549 cells were cultured in the presence (25 mM) or absence of glucose for 48 hours prior to RNA extraction.

first: Alexey

middle: A

last: Sergushichev

middle: N


title: Several genes expression patterns in Desulfovibrio hydrothermalis sp. nov. AM13T in response to hydrostatic pressure

status: Public on Oct 13 2015

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

institute: TAGC INSERM U1090

summary: We have identified differentially expressed genes according to hydrostatic pressure growth conditions in Desulfovibrio hydrothermalis. The transcriptomic datasets report the molecular mechanisms which could be involved in such adaptation and give information for the piezophile sulfate-reducing bacteria research communities. The data obtained pointed out a gradual response of D. hydrothermalis to an increase of hydrostatic pressure, with a threshold above 10 MPa and the involvement of a quite limited number of genes and/or pathways involved in the adaptation to hydrostatic pressure.

sample_organism: Maridesulfovibrio hydrothermalis AM13 = DSM 14728

overall_design: Transcriptome data of Desulfovibrio hydrothermalis AM13T have been generated with culture at 0.1 MPa (atmospheric pressure, low hydrostatic pressure), 26 or 10 MPa (high hydrostatic pressures). All these cultures have been processed in duplicate.

first: Amira

last: Amrani

first: Aurélie

first: Hélène

last: Holota

first: Christian

last: Tamburini

first: Marc

last: Garel

first: Bernard

last: Ollivier

first: Jean

last: Imber

first: Alain

last: Dolla

first: Nathalie

last: Pradel


title: Plasmodium parasites mount an arrest response against dihydroartemisinin

first: Philip

last: Shaw

sample_organism:
Plasmodium berghei
Plasmodium falciparum

overall_design: Refer to individual Series


title: Genome-wide methylome study in cassava

status: Public on Oct 12 2015

city: Los Angeles

first: Steve

last: Jacobsen

address: 4045 Terasaki Life Sciences Building

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles


title: Genome-wide methylome study in cassava [RNA-seq]

summary: Bisulfite treatment, and mRNA libraries were made to characterize DNA methylation and expression of cassava.

overall_design: Genome-wide RNA profiling of cassava leaves was done by Illumina TruSeq preparation kits followed by high-throughput sequencing with Illumina HiSeq 2000.

first: Haifeng

last: Wang


title: Expression profiling of Murine and Zebrafish hair cells

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus


title: Androgen receptor programming in human tissue implicates HOXB13 in prostate pathogenesis [RNA-Seq]

city: Boston

first: Fugen

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: The androgen receptor (AR), a nuclear transcription factor (TF), is consistently reprogrammed during prostate tumorigenesis

overall_design: Gene expresion profiles when LHSAR with overexpressed FOXA1, HOXB13 or FOXA1 and HOXB13 together compared with LacZ control

first: Mark

middle: M

last: Pomerantz

first: David

last: Takeda

first: Apurva

last: Chonkar

first: Matthew

last: Chabot

first: Qiyuan

first: Paloma

last: Cejas

first: Francisca

last: Vazquez

first: Ramesh

last: Shivdasani

first: Ji-Heui

last: Seo

first: Michaela

last: Bowden

first: Rosina

last: Lis

first: William

last: Hahn

middle: W

last: Kantoff

first: Myles

last: Brown

first: Massimo

last: Loda

first: Henry

last: Long

last: Freedman


title: Genome-wide methylome study in cassava [methylation]

first: Steve

last: Jacobsen

overall_design: Genome-wide methylome profiling of cassava leaves was done by Illumina TruSeq preparation kits followed by high-throughput sequencing with Illumina HiSeq 2000.

first: Haifeng

last: Wang


title: RNA-seq of Drosophila 0-2 hr embryos

city: Singapore

first: Jun Wei

last: Pek

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: We report the identification of stable intronic sequence RNAs (sisRNAs) in Drosophila.

overall_design: RNA was obtained from 0-2 hr embryos and subjected to deep sequencing.

first: Jun


title: Developmental and metabolic plasticity of ripe Sémillon grape berries in response to Botrytis cinerea during noble rot

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

summary: Noble rot results from atypical infections of ripe grape berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and accumulation of secondary metabolites that enhance wine grape quality. Noble rot-infected berries of Sémillon, a white-skinned variety, were collected over three years from a commercial vineyard at the same time fruit were harvested for botrytized wine production. Transcriptomic and metabolomic data were integrated to identify pathways associated with distinct stages of noble rot. Botrytis induced the expression of known key regulators of pathways in secondary metabolism associated with berry ripening. The activation by Botrytis during noble rot of metabolic pathways associated with berry ripening was further supported by comparisons with transcriptomes of red-skinned varieties at véraison. A prominent and common outcome of noble rot and berry ripening was the enhancement of the phenylpropanoid metabolism. Induced synthesis of stilbenes, flavonoids, and anthocyanins was supported by both transcriptional and metabolite analyses. Enzyme assays and targeted gene expression analyses of samples from the three distinct years confirmed that the activation of central and peripheral phenylpropanoid pathways is a consistent hallmark of noble rot. Finally, we show that the impact of noble rot on grape metabolism is still detectable in botrytized wines. These results demonstrate that despite the late stage of terminal senescence of a plant organ, a biotic stress can cause a major reprogramming of plant metabolism leading, in case of noble rot, to the synthesis of important metabolites for grape berry flavor and aroma.

sample_organism:
Vitis vinifera
Botrytis cinerea

platform_organism:
Vitis vinifera
Botrytis cinerea

overall_design: The experimental design consists of 4 treatments, berries at 3 distinct stages of noble rot and berries without apparent symptoms of infection. From each treatment a total of 4 biological replicates were sequenced with RNAseq, each replicate corresponded to independent pools of 10-15 berries harvested from adjacent grapevines.

first: Barbara

last: Blanco-Ulate

first: Katherine

last: Amrine

first: Thomas

middle: S

last: Collins

first: Rosa

last: Rivero

first: Ariel

middle: R

last: Vicente

first: Carolyn

middle: L

last: Doyle

first: Zirou

last: Ye

first: Greg

last: Allen

first: Hildegarde

last: Heymann

first: Susan

last: Ebeler

first: Dario

last: Cantu


title: Unbiased evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary:
Objective: Amniotic fluid (AF) is a proximal fluid to the fetus containing higher amounts of cell-free fetal RNA/DNA than maternal serum, thereby making it a promising source for novel biomarker discovery of fetal development and maturation. Our aim was to compare AF transcriptomic profiles at different time points in pregnancy to demonstrate unique genetic signatures that would serve as potential biomarkers indicative of fetal maturation.
Methods: We isolated AF RNA from 16 women at different time points in pregnancy: 4 from 18-24 weeks, 6 from 34-36 weeks, and 6 from at 39-40 weeks. RNA-sequencing was performed on cell-free RNA. Gene expression and splicing analyses were performed in conjunction with cell-type and pathway inference.
Results: Sample-level analysis at different time points in pregnancy yielded a strong correlation with cell types found in the intrauterine environment and fetal respiratory, digestive and external barrier tissues of the fetus, using high-confidence cellular molecular markers. While some genes and splice variants were present throughout pregnancy, an abundant number of transcripts were uniquely expressed at different time points in pregnancy and associated with distinct fetal co-morbidities (respiratory distress and gavage feeding), indicating fetal immaturity.
Conclusions: The AF transcriptome exhibits unique cell- and organ-selective expression patterns at different time points in pregnancy that can potentially identify fetal organ maturity and predict neonatal morbidity. Developing novel biomarkers indicative of the maturation of multiple organ systems can improve upon our current methods of fetal maturity testing which focus solely on the lung, and better inform obstetrical decisions regarding delivery timing.

overall_design: RNA-Seq from cell-free was used to idenitfy mRNA transcripts indicative of overall fetal maturity.

first: Beena

middle: D

last: Kamath-Rayne

first: Yina

last: Du

first: Maria

last: Hughes

first: Erin

last: Wagner

first: Emily

last: DeFranco

first: Jeffery

last: Whitsett

first: Louis

middle: J

last: Muglia

first: Yan

last: Zu


title: Gene expression in the developing murine utricle

first: Ksenia

last: Gnedeva

address: 1501 San Pablo St

department: USC Caruso Department of Otolaryngology – Head and Neck Surgery

institute: USC

summary: We report a gene expression changes during development and maturation of the murine utricle

overall_design: Using RNA-sequencing, we examined the gene expression in the murine utricle at E17.5, p0, and p9

first: A

last: Hudspeth


title: Plasmodium parasites mount an arrest response against dihydroartemisinin [P. falciparum RNA-Seq]

first: Philip

last: Shaw

address: 113 Phahonyothin Road

institute: National Science and Technology Development Agency

summary: Control of malaria is threatened by emerging parasite resistance to artemisinin drug (ART) therapies. The molecular details of how Plasmodium malaria parasites response to ART and how this relates to resistance is not clear. To determine how parasites respond to ART by altering gene expression, we performed a transcriptomic study of dihydroartemisinin (DHA) response in P. falciparum K1 strain and in P. berghei ANKA strain.  Microarray data from DHA-treated P. falciparum trophozoite stage parasites were compared with data from other ART treatments. Genes with consistent changes in expression were identified, which includes notably down-regulation of cytosolic ribosomal protein genes. RNA-seq data revealed a similar pattern of transcriptomic change, although the pattern was much clearer in that more than one-third of P. falciparum trophozoite genes are differentially expressed with greater statistical support for down-regulation of ribosomal protein genes. The poor overlap of differentially-expressed genes between microarray and RNA-seq and less-well defined patterns for the former suggests that the accuracy of microarray is limited by technological bias. The trophozoite response to DHA is overall “ring-like” and less “trophozoite-like”, which is consistent with previous findings that Plasmodium can enter a quiescent ring-like state to resist ART. RNA-seq data from DHA-treated P. falciparum rings reveal a more muted response, although there is considerable overlap of differentially expressed genes with DHA-treated trophozoites. In contrast, P. falciparum schizonts are unresponsive to DHA, suggesting that the protective response acts mainly to arrest parasite development through the G2/M checkpoint. The transcriptional response of P. berghei to DHA treatment in vivo in infected mice is strikingly similar to the P. falciparum in vitro ring and trophozoite responses, in which ribosomal protein genes are notably down-regulated. These results suggest Plasmodium species respond to DHA in the same way. This knowledge could be applied to outwit the parasite to deliver more effective artemisinin therapies, and maybe hinder the development of drug resistance.

overall_design: mRNA profiles of dihydroartemisinin (DHA)-treated parasites were compared with vehicle control treated parasites in duplicate; sequence data obtained from TruSeq stranded RNA-seq libraries sequenced on Illumina MiSeq  instrument

first: Sastra

last: Chaothieng

first: Pavita

last: Tipsombatboon

first: Jittima

last: Piriyapongsa

first: Chayaphat

last: Wongsombat

first: Nattida

last: Suwannakitti

first: Pongpisid

last: Koonyosying

first: Chairat

last: Uthaipibull

first: Sumalee

last: Kamchonwongpaisan

first: Yongyuth

last: Yuthavong


title: Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq]

status: Public on Oct 11 2015

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

summary: Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. However, until now, the evolutionary turnover and dynamics of TF binding sites among plant species has not yet experimentally determined. Here, we performed comparative ChIP-seq studies of the MADS-box TF SEPALLATA3 (SEP3) in inflorescences of two Arabidopsis species: A. thaliana and A. lyrata. Comparative RNA-seq analysis shows that the loss/gain of BSs is often followed by a change in gene expression.

sample_organism:
Arabidopsis thaliana
Arabidopsis lyrata

platform_organism:
Arabidopsis thaliana
Arabidopsis lyrata

overall_design: RNA-seq libraries were generated from 3 tissues: A. lyrata leaves, A. lyrata inflorescences, and A.thaliana inflorescences. 3 biological replicates were sequenced.

first: Suzanne

last: de Bruijn

first: Martin

last: Vingron

first: Gerco

middle: C

last: Angenent

first: Kerstin

last: Kaufmann


title: RNA-seq of chemostat grown yeast (Y11335 BY4742 )

status: Public on Oct 10 2015

city: Manchester

first: Craig

last: Lawless

address: Dover Street

department: Faculty of Life Sciences

institute: University of Manchester

summary: We profiled total-mRNA from yeast cells grown in identical conditions to match samples submitted for proteome-wide absolute quantification. Matching mRNA profiles to absolute protein copies numbers enables a more accurate comparison of transcript to final protein levels. Here we were able to show direct comparison results in a correlation of Rsquared of 0.58, show suggesting as much as ~40% of final protein levels in yeast cannot be determined from mRNA levels alone. Reads were mapped to a reference genome of S. cerevisiae, downloaded from the Saccharomyces Genome Database (SGD), using Bowtie version 1 (74). Mapped sequences were then assembled into transcripts and quantified using Cufflinks version 2.0 (75) (using the SGD reference genome GTF file).

overall_design: mRNA profile of 4 biological replicates of S.cerevisiae to match quantitative analysis of the proteome

first: Simon

last: Hubbard


title: Androgen receptor programming in human tissue implicates HOXB13 in prostate pathogenesis [ChIP-Seq]

first: Fugen

last: Li

overall_design: Mapping AR binding sites in patient prostate tumor and normal tissues

first: Mark

last: Pomerantz

first: David

last: Takeda

first: Apurva

last: Chonkar

first: Matthew

last: Chabot

first: Qiyuan

first: Paloma

last: Cejas

first: Francisca

last: Vazquez

first: Ramesh

last: Shivdasani

first: Ji-Heui

last: Seo

first: Michaela

last: Bowden

first: Rosina

last: Lis

first: William

last: Hahn

first: Philip

last: Kantoff

first: Myles

last: Brown

first: Massimo

last: Loda

first: Henry

last: Long

last: Freedman


title: Spatial interplay between Polycomb and Trithorax complexes controls transcriptional activity in T lymphocytes [ChIP-Seq]

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

summary: Trithorax group (TrxG) and Polycomb group (PcG) proteins are two mutually antagonistic chromatin modifying complexes, however, how they together mediate transcriptional counterregulation remains unknown.  Genome-wide analysis revealed that binding of Ezh2 and Menin, central members of the PcG and TrxG complexes, respectively, were reciprocally correlated.  Moreover, we identified a developmental change in the positioning of Ezh2 and Menin in differentiated T lymphocytes compared to embryonic stem cells.  Ezh2-binding upstream and Menin-binding downstream of the transcription start site (TSS) was frequently found at genes with higher transcriptional levels, and Ezh2-binding downstream and Menin-binding upstream was found at genes with lower expression in T lymphocytes.  Interestingly, of the Ezh2 and Menin co-occupied genes, those exhibiting occupancy at the same position displayed greatly enhanced sensitivity to loss of Ezh2.  Finally, we also found that different combinations of Ezh2 and Menin occupancy were associated with expression of specific functional gene groups important for T cell development.  Therefore, spatial cooperative gene regulation by the PcG and TrxG complexes may represent a novel mechanism regulating the transcriptional identity of differentiated cells.

overall_design: Binding profiles of Trithorax group (TrxG) and Polycomb group (PcG) proteins in ES cells, B cells and T cells are assessed by ChIP-seq.

first: Damon

last: Tumes

first: Yukiko

last: Watanabe

first: Kiyoshi

last: Hirahara

last: Kaneda

first: Fumihiro

last: Sugiyama

first: Yutaka

last: Suzuki

first: Toshinori

last: Nakayama


title: HDAC inhibition impedes epithelial–mesenchymal plasticity and suppresses metastatic, castration-resistant prostate cancer

first: Yu-Ting

last: Tseng

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics


title: Spatial interplay between Polycomb and Trithorax complexes controls transcriptional activity in T lymphocytes


title: Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [ChIP-Seq]

first: Jose

last: Muino

overall_design: Chromatin was crosslinked and isolated from wildtype A. lyrata inflorescences up to floral stage 10/11. The immunoprecipitation of protein-DNA complexes was performed using a peptide SEP3  antibody that was raised against A. thaliana SEP3, and is also able to recognize the homolog from A. lyrata due to protein similarity. As a control, de-crosslinked 'input-DNA' was used. SEP3 ChIP-seq on Arabidopsis thaliana can be found in the accessions GSM364939 and GSM364941. Re-analyzed peak positions for these samples are included as a  supplementary file on the series level (SEP3Ratiobg5@TAIR10-win.csv).

first: Suzanne

last: de Bruijn

first: Martin

last: Vingron

first: Gerco

last: Angenent

first: Kerstin

last: Kaufmann


title: Spatial interplay between Polycomb and Trithorax complexes controls transcriptional activity in T lymphocytes [RNA-Seq]

overall_design: Gene expression profiles of ES cells, B cells and T cells are assessed by RNA-seq.


title: Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor


title: Deregulation of HIF-Responsive Demethylases Causes Synthetic Lethality Between the VHL Tumor Suppressor Gene and the EZH1 Histone Methyltransferase

first: William

middle: G

last: Kaelin

state: Massachusetts

address: 450 Brookline Ave, M457

department: Medical Oncology

summary: Comparison of ccRCC cells with high HIF or low HIF activity

overall_design:
Cells expressing control (VEC) were compared to cells with ARNT1 loss using sh/sgRNA targeting ARNT1
The samples labeled 'con' are parental Vhl-null cells and represent the 'high HIF' state. The other 2 cell lines represent the 'low HIF' state. The cell line labeled shArnt have loss of a protein named ARNT by virtue of RNAi-mediated knockdown using a shRNA targeting ARNT. The sample labeled lcARNT has loss of ARNT protein using a lenti-crispr mediated sgRNA.

first: Abhishek

last: Chakraborty

last: Kaelin Jr


title: KAP1 Recruitment of the 7SK snRNP to Promoters Enables Transcription Elongation by RNA Polymerase II

status: Public on Oct 09 2015

city: Dallas

first: Ivan

last: D'Orso

state: TX

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

summary: The transition from transcription initiation into elongation at promoters of primary response genes (PRG) in metazoan cells is controlled by inducible transcription factors, which utilize P-TEFb to phosphorylate RNA Polymerase II (Pol II) in response to stimuli.  Prior to stimulation, a fraction of P-TEFb is recruited to promoters in a catalytically inactive state bound to the 7SK small nuclear ribonucleoprotein (snRNP).  However, it remains unclear how and why the 7SK snRNP is assembled at promoters.  Here we report that the transcriptional regulator KAP1 directly recruits the 7SK snRNP  to facilitate localized release of P-TEFb, promoting rapid Pol II elongation and PRG synthesis in response to stimuli.  Collectively, we have discovered and characterized a novel complex, which we term the KEC, which dictates rapid and robust PRG induction upon stimuli.

overall_design: KAP1, 7SK snRNP and Pol II at human genes

first: Ryan

middle: P

last: McNamara

first: Iván


title: mRNA-Seq reads aligned to HTT in hg38/GENCODEv21

first: Adam

last: Labadorf

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

summary: Despite 20 years since its discovery, the gene responsible for Huntington’s Disease, HTT, has still not had its function or transcriptional profile completely characterized. In response to a recent report by Ruzo et al. of several novel splice forms of HTT in human embryonic stem cell lines, we have analyzed a set of mRNA sequencing datasets from post mortem human brain from Huntington’s disease, Parkinson’s disease, and neurologically normal control subjects to evaluate support for previously observed and to identify novel splice patterns. A custom analysis pipeline produced supporting evidence for some of the results reported by two previous studies of alternative isoforms as well as identifying previously unreported splice patterns. All of the alternative splice patterns were of relatively low abundance compared to the canonical splice form.

overall_design: 29 Huntington's Disease, 29 Parkinson's Disease, and 50 Neurologically normal control samples from human post-mortem prefrontal cortex

middle: T


title: Androgen receptor programming in human tissue implicates HOXB13 in prostate pathogenesis

first: Fugen

last: Li

overall_design: Refer to individual Series


title: Loss of BAF (mSWI/SNF) complexes causes global transcriptional and chromatin state changes in forebrain development

city: Goettingen

first: Cemil

last: Kerimoglu

address: Grisebachstr. 5

institute: UMG Göttingen

summary: We report the genome-wide increase in H3K27 trimethylation (H3K27me3) in murine embryonic cortices as a result of conditional double knock-out (dcKO) of BAF155/BAF170 complex.

overall_design: 1) Comparison of H3K27me3 levels in murine cortical tissues from embryonic day 13.5 (E13.5) in Emx1-Cre BAF155/BAF170 dcKO and controls. 2) Comparison of H3K27me3 levels in murine cortical tissues from postnatal day 1 (P1) in Nex-Cre BAF155/BAF170 dcKO and controls.

first: Andre

last: Fischer


title: Mini-kidneys from human pluripotent cells model normal human fetal kidney development and response to nephrotoxicity

city: Parkville

first: Melissa

middle: H

last: Little

state: Victoria

address: Flemington Road

department: Cell Biology

country: Australia

institute: Murdoch Childrens Research Institute

summary: RNA-seq of mini-kidneys derived from human pluripotent stem cells, derived from WT2-iPS (Clone 32) (Briggs et al, Stem Cells, 2013).

overall_design: Sequencing of mini-kidneys at 4 time points: 0 days, 3 days, 11 days, 18 days

first: Gregory

last: Baillie

first: Minoru

last: Takasato


title: An IL-23R/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses [RIP-Seq]

city: New York

first: Wendy

last: Huang

address: 540 First Ave Skirball 2-14

institute: NYU School of Medicine

summary:
Purpose: The goals of this study are to compare RNAs bound by translating ribosomes in the presence or absence of Segmented Filamentous Bacteria (SFB) colonization of the small intestine
Methods: EDTA fractions containing small intestine epithelial cells from SFB negative and SFB positive mice were harvested. TRAP assay enriching for ribosome bound fraction were enriched using anti-GFP antibodies against GFP-ribosomeL10 fusion protein. mRNA profiles were generated by deep sequencing, using Illumina HighSeq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) and TopHat followed by CuffDiff. qRT–PCR validation was performed using SYBR Green assays.
Results: SFB colonization upregulate a subset of mRNAs being translated by ribosomes.
Conclusions: SFB changes small intestine epithelial cell translation profile.

first: Dan

last: Littman


title: An IL-23R/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses

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


title: Hira is essential for normal transcriptional regulation and efficient de novo DNA methylation during mouse oogenesis

city: Cambridge

first: Gavin

last: Kelsey

address: Babraham Research Campus

institute: The Babraham Institute

summary: The integrity of chromatin, which provides a dynamic template for all DNA related processes in eukaryotes, is maintained through replication dependent and independent assembly pathways. To address the role of replication independent histone deposition, we deleted the histone H3.3 chaperone Hira in developing mouse oocytes. We show that chromatin of non-replicative developing oocytes is highly dynamic, and that lack of continuous H3.3/H4 deposition alters chromatin structure, resulting in increased DNase I sensitivity, the accumulation of DNA damage, and, ultimately, a severe fertility phenotype. On the molecular level, abnormal chromatin structure leads to a dramatic decrease in the dynamic range of gene expression, the appearance of spurious transcripts, and inefficient de novo DNA methylation. In contrast to the only minor transcriptional phenotype observed in mouse pluripotent cells, we unequivocally show the importance of histone replacement and chromatin homeostasis for transcriptional regulation and normal developmental progression in an in vivo context.

overall_design: DNA methylome using BS-Seq of Hira wild-type and Hira deleted MII oocytes

first: B

last: Nashun

first: P

last: Hill

first: S

last: Smallwood

first: G

last: Dharmalingam

first: R

last: Amouroux

last: Clark

first: V

last: Sharma

first: E

last: Ndjetehe

last: Pelczar

last: Festenstein

last: Hajkova


title: An IL-23R/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses II [RNA-Seq]

summary:
Purpose: The goals of this study are to compare in vitro polarized T helper 17 cell transcriptome profiling (RNA-seq) in the presence or absence of recombinant murine SAA1
Methods: Th17 mRNA profiles of 96hrs in vitro cultured T helper 17 cells treated with vehicle or recombinant murine SAA1 were generated by deep sequencing, using Illumina RapidRun. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) and TopHat followed by CuffDiff. qRT–PCR validation was performed using SYBR Green assays.
Results: 177 genes were changed more than 2 folds in the presence of recombinant murine SAA1.
Conclusions: Our study suggest that SAA1 could augment subset of Th17 transcription program in vitro.

overall_design: mRNA profiles of 48hr in vitro cultured Th17 from wild type (WT) mice were generated by deep sequencing using Illumina RapidRun.


title: Genome distribution of binding sites of ScbR and ScbR2 in Streptomyces coelicolor

city: Beijing

first: Xiao

last: Li

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: By ChIP-seq of ScbR and ScbR2 binding sites across M145 chromosome, 143 and  492 peaks of ScbR and ScbR2 were identified, respectively. And they shared numurous same sites.

overall_design: Oversee binding sites distribution of ScbR at 30h and of ScbR2 at 42h across the genome

first: Weishan

last: Wang


title: Chromatin Response to UV Damage

city: Mainz

first: Vijay

middle: K

last: Tiwari

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: These findings reveal the global chromatin response to UV damage and its relation to impaired gene regulation

overall_design: Comparison of FAIRE-seq, H3K27ac ChIP-seq and RNA-seq data for untreated and UV-exposed mouse fibroblasts

first: Sandra

last: Schick

first: David

last: Fournier

first: Sudhir

last: Thakurela

first: Sanjeeb

last: Sahu

first: Garding

last: Angela


title: Transcriptome profiling of the ovine pars tuberalis in long and short photoperiod conditions [4-22 weeks]

first: Shona

middle: Hiedi

last: Wood

address: Oxford road

summary: Persistent free-running circannual (circa 1-year) rhythms have  evolved in animals to regulate hormone cycles and time annual reproduction.  In mammals, these are synchronized by environmental photoperiod and the  melatonin signal. Long summer-like photoperiods (LP) activates thyrotrophs  and thyroid-stimulating hormone (TSH) expression in the melatonin target  tissue, the pars tuberalis (PT) region of the pituitary gland, driven by the  transcriptional co-activator EYA3. TSH in turn stimulates thyroid hormone  (TH) conversion in hypothalamic ependymal tanycytes, thus timing breeding  seasons. In contrast to our new knowledge defining photoperiodic input, it is  still not known which cells, tissues and pathways generate the underlying  circannual cycle. We used seasonal sheep to characterise the circannual cycle, transferring animals from short winter-like photoperiods (SP)  to prolonged LP conditions, and assaying prolactin to track circannual phase  in individual animals. Using RNA-seq, we profiled PT cells at different phases of  the circannual cycle, and defined extensive changes of cellular-remodeling  pathways and genes encoding synaptic guidance proteins in the PT.

overall_design: Short photoperiod 4 weeks (SP4) - 4 samples, Long photoperiod 4 weeks (LP4) - 4 samples, LP 22 weeks (LP22) - 4 samples, SP 16 weeks (SP16) - 4 samples

first: Helen

last: Christian

first: Katarzyna

last: Miedzinska

first: Ben

last: Saer

first: Mark

last: Johnson

first: Bob

last: Paton

first: Le

last: Yu

first: Judith

last: McNeilly

first: Julian

last: Davis

first: Alan

last: Burt

first: Andrew

last: Loudon


title: Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila

status: Public on Oct 08 2015

city: Durham

first: Jason

middle: Alan

last: Belsky

state: NC

address: LSRC Room C333

department: Pharmacology and Cancer Biology

institute: Duke University

summary: The methylation state of lysine 20 on histone H4 (H4K20) has been linked to cell cycle progression, Origin Recognition Complex (ORC) binding, and replication origin regulation. Monomethylation of H4K20 (H4K20me1) is mediated by the cell cycle-regulated histone methyltransferase PR-Set7, which is essential for genome integrity and cell cycle progression. PR-Set7 depletion in mammalian cells results in defective S-phase progression and the accumulation of DNA damage, which could be partially attributed to a defect in pre-Replication Complex (pre-RC) formation and origin activity. However, these studies were limited to a handful of mammalian origins, and it remains unclear how PR-Set7 and H4K20 methylation impact the replication program on a genomic scale. Using Drosophila Kc167 cells, we employed genetic, cytological, and genomic approaches to better understand the role of PR-Set7 and H4K20 methylation in regulating DNA replication and governing genome stability. We find that depletion of Drosophila PR-Set7 and loss of H4K20me1 result in the accumulation of DNA damage and an ATR-dependent cell cycle arrest. The cell cycle arrest occurs during the second S-phase following loss of PR-Set7 activity, suggesting that accumulation of nascent H4K20 is recalcitrant to the DNA replication program. Deregulation of H4K20 methylation had no impact on origin activation throughout the genome; instead, we found that the DNA damage marker, phosphorylated H2A.v (γ-H2A.v), accumulated specifically in late replicating domains in the absence of PR-Set7. This suggests that the molecular basis for the cell cycle arrest and accumulation of DNA damage resulting from loss of PR-Set7 is stochastic fork collapse within late replicating domains.

overall_design: Examination of BrdU enrichment in the presence of hydroxyurea to map activation of early replication origin under control, PR-Set7, ATR, and ATR/PR-Set7 RNAi treatment conditions in duplicates using Illumina HiSeq and Miseq respectively; map early origin in 6 other conditions using Illumina HiSeq; examination of H4K20me1 in early or late S-phase with two different experimental methods, using Hiseq; examination of a histone variant with control or PR-Set7 RNAi treatment, in duplicates, using Hiseq.

first: Yulong

last: Li

middle: A

last: MacAlpine


title: Adaptive aneuploidy protects against thiol peroxidase deficiency by increasing respiration via key mitochondrial proteins

city: Woolloongabba

first: Inge

last: Seim

state: Queensland

address: 37 Kent St

institute: Queensland University of Technology

summary: We characterized the mechanisms that allow yeast cells to survive under conditions of thiol peroxidase deficiency. Two thiol peroxidase null yeast (delta8) strains independently acquired a second copy of chromosome XI and increased expression of genes encoded by it. Delta-8 strains were compared to the Wt-M11 strain, which is characterized by duplication of chr-XI.

overall_design: Examination of thiol peroxidase-deficient yeast strains.

first: Alaattin

last: Kaya


title: Mapping of histone modifications in episomal HBV cccDNA uncovers an unusual chromatin conformation amenable to epigenetic manipulation

city: Emeryville

first: Philipp

last: Tropberger

address: 4560 Horton Street

institute: Novartis Institutes for BioMedical Research

summary: Chronic hepatitis B virus (HBV) infection affects 240 million people worldwide and is a major risk factor for liver failure and hepatocellular carcinoma. Current antiviral therapy inhibits cytoplasmic HBV genomic replication, but is not curative since it does not eliminate nuclear HBV cccDNA, the genomic form that templates viral transcription and sustains viral persistence. Novel approaches that directly target the transcriptional regulation of cccDNA would therefore be highly desirable. cccDNA is assembled with cellular histone proteins into chromatin, but little is known about the regulation of HBV chromatin by histone posttranslational modifications (PTMs). Here, using a new cccDNA ChIP-Seq approach, we report the first genome-wide maps of PTMs in cccDNA-containing chromatin from de novo infected HepG2 cells, primary human hepatocytes and from HBV infected liver tissue. We find high levels of PTMs associated with active transcription enriched at specific sites within the HBV genome, and surprisingly very low levels of PTMs linked to transcriptional repression even at silent HBV promoters. We show that transcription and active PTMs in HBV chromatin are reduced by the activation of an innate immunity pathway, and that this can be recapitulated with a small molecule epigenetic modifying agent, opening the possibility that chromatin-based regulation of cccDNA transcription could be a new therapeutic approach to chronic HBV infection.

overall_design: Mapping of mutiple histone modifications in HBV cccDNA from infected HepG2 cells, primary hepatocytes and HBV infected liver tissue

first: Alexandre

last: Mercier

first: Margaret

last: Robinson

first: Weidong

last: Zhong

first: Don

last: Ganem

first: Meghan

middle: M

last: Holdorf


title: Autophagy mediates degradation of nuclear lamina

city: Philadelphia

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Autophagy is a catabolic membrane trafficking process involved in degradation of cellular constituents through lysosomes, which maintains cell and tissue homeostasis.  While much attention has been focused on autophagic turnover of cytoplasmic materials, little is known regarding the role of autophagy in degrading nuclear components.  Here we report that autophagy machinery mediates degradation of nuclear lamina in mammalian cells, a process we term laminophagy.  The autophagy protein LC3 is present in the nucleus and directly interacts with the nuclear lamina protein Lamin B1, and associates with lamin-associated domains (LADs) on chromatin.  This interaction does not downregulate Lamin B1 during starvation, but mediates nuclear lamina degradation upon tumorigenic insults, such as by oncogenic Ras. Laminophagy is achieved by nucleus-to-cytosol transport that delivers Lamin B1 to lysosome for degradation.  Inhibiting autophagy or LC3-Lamin B1 interaction prevents oncogenic Ras-induced Lamin B1 loss and delays oncogene-induced cell cycle arrest.  Our study unveils a role of autophagy in degrading nuclear materials, and suggests laminophagy as a guarding mechanism protecting cells from tumorigenesis.

overall_design: Study includes two replicates each of lamin B1, LC3, and input to control for sonication efficiency. Only one condition is included.

first: Zhixun

last: Dou

first: Caiyue

last: Xu

first: Greg

first: Takeshi

last: Shimi

first: Ji-An

last: Pan

first: Jiajun

last: Zhu

first: Andre

last: Ivanov

first: Brian

last: Capell

first: Adam

last: Drake

first: Parisha

last: Shah

first: Joseph

last: Catanzaro

first: M

last: Ricketts

first: Trond

last: Lamark

first: Stephen

last: Adam

first: Ronen

last: Marmorstein

first: Wei-Xing

last: Zong

first: Terje

last: Johansen

first: Robert

last: Goldman

first: Peter

last: Adams

first: Shelley

last: Berger


title: Liver and muscle gene expression and cow fertility at late pregnancy, early lactation and mid lactation

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

summary: The transition between pregnancy and lactation is a major physiological change that dairy cows must contend with. Complex systemic and local processes involving gluconeogenesis, energy balance, utilisation of body reserves, insulin resistance and involution of the uterus can have an effect on animal health and farm profitability. Here we used an established Holstein cow model of fertility that displayed genetic and phenotypic divergence in calving interval, a trait used to define reproductive performance using a national breeding index in Ireland. Cows had similar genetic merit for milk production traits, but either very good genetic merit for fertility (‘Fert+’; n = 8) or very poor genetic merit for fertility (‘Fert-‘; n = 8). We investigated three distinct time-points, late pregnancy, early lactation and mid lactation (-18, 1 and 147 days on average with day 0 being birth), using RNA sequencing from both liver and muscle tissue biopsies and conducting a differential expression (DE) analysis. We found 807 and 815 unique genes to be DE in at least one time-point in liver and muscle respectively, of which 79% and 83% were only found in a single time-point; 40 and 41 genes were found DE at every time-point indicating possibly systemic or chronic dysregulation. Functional annotation resulted in evidence for two major physiological processes: immune and inflammation, and metabolic, lipid and carbohydrate-binding. These processes indicate areas of previous interest as well as specific systems that appear differentially regulated, and point towards interesting avenues of further research in a broad and complex field.

overall_design: 96 samples total; 8 Fert+ ('high fertility'), 8 Fert- ('low fertility'); no controls; Fert+, Fert- differential gene expression at three timepoints in two tissues

last: Butler

first: Christopher

last: Creevey


title: Exome of Holstein Friesian Cows

type: Genome variation profiling by high throughput sequencing

summary: Despite the large amounts of transcriptome data generated for many non-model organisms, there has been a much lesser uptake of individual genomic sequencing for detecting SNPs and determining haplotypes in these species. Transcriptome data represents a source of variant information, specifically for coding DNA, however there is little information on the accuracy, coverage and limitations of using transcriptomic data for the identification of single nucleotide polymorphisms (SNPs) in non-model organisms. To investigate this, we generated the first whole exome design for bovine using the Roche Nimblegen Developer system (Roche, USA) and used it to sequence and call SNPs from a lactating dairy cow model with genetically divergent fertility phenotypes (Fert+, n=8; Fert-, n=8). We compared these results to SNPs called from liver and muscle transcriptomes from the same animals. Our exome demonstrated 99.1% coverage of the target design of 56.7MB, whereas the transcriptomes only covered 60 and 54.5% of 44.2 and 42.8MB in liver and muscle respectively. We found that specificity of SNP detection in the transcriptome data is ~75% following basic hard-filtering, but could be increased marginally to ~80% by increasing the minimum threshold of reads covering a SNP, and number of samples in which it was found. Functional annotation of non-synonymous SNPs specific to both the high and low fertility phenotype identified immune response-related genes, supporting previous work that identified this process as key to the phenotype.

overall_design: 16 samples total; 8 Fert+ ('high fertility'), 8 Fert- ('low fertility')


title: In vivo oncomiR screen identifies miR-21* independent of miR-21 as a driver in skin cancer

first: Yejing

last: Ge

state: NY

address: 1230 York Ave

country: USA

institute: The Rockefeller University

summary: MicroRNAs are conserved small non-coding RNAs that act post-transcriptionally to orchestrate a wide spectrum of physiological and pathological processes in stem cells and in human cancers. We use miRNAseq to profile miRNA expression and DNA sequencing to quantify inserted miR expression vectors within genomic DNA during an in vivo tumorigenic screen

overall_design: MicroRNA expression patterns from fluorescence-activated cell sorted (FACS) progenitors from embryonic and adult skin epithelia, tumor-initiating stem cells (SCs) from oncogenic HRas-induced benign papillomas and SCCs are analyzed with miRNAseq (12 samples); SA-miR counts (enginnered library inserted into the host cell genome by in utero lentiviral transduction) from in vivo tumorigenic screen are analyzed with DNA seq (5 samples)

first: Elaine

last: Fuchs


title: Disruption of Ah Receptor Signaling during Mouse Development Leads to Abnormal Cardiac Structure and Function in the Adult

status: Public on Oct 07 2015

first: Mario

last: Medvedovic

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: The Developmental Origins of Health and Disease (DOHaD) Theory proposes that the environment encountered during fetal life and infancy permanently shapes tissue physiology and homeostasis such that damage resulting from maternal stress, poor nutrition or exposure to environmental agents may be at the heart of adult onset disease. Interference with endogenous developmental functions of the aryl hydrocarbon receptor (AHR), either by gene ablation or by exposure in utero to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a potent AHR ligand, causes structural, molecular and functional cardiac abnormalities and altered heart physiology in mouse embryos. To test if embryonic effects progress into an adult phenotype, we investigated whether Ahr ablation or TCDD exposure in utero resulted in cardiac abnormalities in adult mice long after removal of the agent. Ten-months old adult Ahr-/- and in utero TCDD-exposed Ahr+/+ mice showed sexually dimorphic abnormal cardiovascular phenotypes characterized by echocardiographic findings of hypertrophy, ventricular dilation and increased heart weight, resting heart rate and systolic and mean blood pressure, and decreased exercise tolerance. Underlying these effects, genes in signaling networks related to cardiac hypertrophy and mitochondrial function were differentially expressed. Cardiac dysfunction in mouse embryos resulting from AHR signaling disruption seems to progresses into abnormal cardiac structure and function that predispose adults to cardiac disease, but while embryonic dysfunction is equally robust in males and females, the adult abnormalities are more prevalent in females, with the highest severity in Ahr-/- females. The findings reported here underscore the conclusion that AHR signaling in the developing heart is one potential target of environmental factors associated with cardiovascular disease.

overall_design: TCDD treatment and control samples during mouse embryoning development mesuared in triplicate by RNA-seq at nine months of age.

first: Vinicius

last: Carreira

first: Yunxia

last: Fan

first: Hisaka

last: Kurita

first: Qing

last: Wang

first: Chia-I

last: Ko

first: Mindi

last: Naticchioni

first: Min

last: Jiang

first: Sheryl

last: Koch

first: Xiang

last: Zhang

first: Jacek

last: Biesiada

first: Ying

last: Xia

first: Jack

last: Rubinstein

first: Alvaro

last: Puga


title: An IL-23R/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses [RNA-Seq]

first: Wendy

last: Huang

summary:
Purpose: The goals of this study are to compare mRNAs expressed by Th17 cells and ILC3s in small intestine of lamina propria of mice.
Methods: Small intestine were digested with collagenase, dispase, and DNase. Percoll enriched lamina propria Th17 and ILCs sorted by BD ARIA II. Total RNA were harvested and sequencing were performe. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) and TopHat followed by CuffDiff. qRT–PCR validation was performed using SYBR Green assays.
Results: Small intestine Th17 cells and ILCs exhibit differential gene expression profiles.

first: Dan

last: Littman


title: Epigenetic regulation of monocyte heterogeneity

city: Frankfurt am Main

first: GenXPro

last: GenXPro

address: Altenhöferallee 3

institute: GenXPro GmbH

summary: Human monocytes are a heterogeneous cell population consisting of three subsets: classical CD14++CD16-, intermediate CD14++CD16+ and nonclassical CD14+CD16++ monocytes. Intermediate monocytes contribute to inflammation, and their circulating cell counts are increased in many chronic inflammatory diseases, even though the underlying pathways are poorly characterized. We tested in how far epigenetic mechanisms regulate human monocytes heterogeneity in chronic kidney disease, which is a proinflammatory condition of substantial epidemiological importance.  By applying next-generation Methyl-Sequencing (Methyl-Seq) we characterized genome-wide DNA methylation within the three monocyte subsets and analyzed the impact of uremia on DNA methylation in differentiating monocytes.  We found that each monocyte subset displays a unique phenotype with regards to DNA methylation. Genes with differentially methylated promoter regions in intermediate monocytes were linked to distinct immunological processes, which is in line with results from recent gene expression analyses. In vitro, uremia induced a dysregulation of DNA methylation in differentiating monocytes which affected several transcription factors important for monocyte differentiation (e.g. FLT3, HDAC1, MNT) and led to enhanced generation of intermediate monocytes. As a potential mediator, the uremic toxin and DNA methylation inhibitor S-Adenosylhomocysteine induced shifts in monocyte subsets in vitro, and associated with monocyte subset counts in vivo.  In summary, our data support the concept of monocyte trichotomy and the distinct role of intermediate monocytes in human immunity. The shift in monocyte subsets which occurs in chronic kidney disease, a proinflammatory condition of substantial epidemiological impact, may be induced by the accumulation of specific uremic toxins that mediate epigenetic dysregulation.

overall_design: Seven healthy donors were recruited for DNA methylation analysis of the three monocyte subsets; DNA methylation analysis of differentiating monocytes was performed in 5 independent experiments

first: Adam

last: Zawada

first: Jenny

last: Schneider

first: Anne

middle: I

last: Michel

first: Kyrill

last: Rogacev

first: Björn

last: Hummel

first: Nicolas

last: Krezdorn

first: Soeren

last: Müller

last: Rotter

first: Peter

last: Winter

first: Rima

last: Obeid

first: Jürgen

last: Geisel

first: Danilo

last: Fliser

first: Gunnar

last: Heine


title: Chromatin-remodelling complex NURF is essential for differentiation of adult melanocyte stem cells

city: Illkirch

first: Patrick

last: Laurette

address: 1 Rue Laurent Fries

institute: IGBMC

summary: MIcrophthalmia-associated Transcription Factor (MITF) regulates melanocyte and melanoma physiology. ShRNA-mediated silencing of the NURF subunit BPTF revealed its essential role in several melanoma cell lines and in untransformed melanocytes in vitro. Comparative RNA-seq shows that MITF and BPTF co-regulate overlapping gene expression programs in cell lines in vitro. Somatic and specific inactivation of Bptf in developing murine melanoblasts in vivo shows that Bptf regulates their proliferation, migration and morphology. Once born, Bptf-mutant mice display premature greying where the second post-natal coat is white. This second coat is normally pigmented by differentiated melanocytes derived from the adult melanocyte stem cell (MSC) population that is stimulated to proliferate and differentiate at anagen. An MSC population is established and maintained throughout the life of the Bptf- mutant mice, but these MSCs are abnormal and at anagen, give rise to reduced numbers of transient amplifying cells (TACs) that do not express melanocyte markers and fail to differentiate into mature melanin producing melanocytes. MSCs display a transcriptionally repressed chromatin state and Bptf is essential for reactivation of the melanocyte gene expression program at anagen, the subsequent normal proliferation of TACs and their differentiation into mature melanocytes.

overall_design: 5 samples corresponding to mRNA profiles of 501Mel and Hermes3A after BPTF shRNA-mediated knockdown were generated by deep sequencing in triplicate (Hermes 3A) or duplicate (501Mel), using HiSeq2500.

first: Dana

last: Koludrovic

first: Irwin

last: Davidson


title: H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

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

overall_design: Refer to individual Series


title: Small RNA profiles in wt and swi6 deletion strains

summary: Proteins of the conserved HP1 family are elementary components of heterochromatin and are generally assumed to play a central role in creating a rigid heterochromatic network that is densely packed and inaccessible to the transcription machinery. In this study we demonstrate that the fission yeast HP1 protein Swi6 exists as a single highly dynamic population and rapidly exchanges in cis and in trans between different heterochromatic regions. Binding to methylated H3K9 or to heterochromatic RNA decelerates Swi6 mobility. We further show that Swi6 is largely dispensable to maintain heterochromatin domains. In contrast, our results disclose an unexpected role of Swi6 in demarcating constitutive heterochromatin from neighboring euchromatin. Our results are consistent with a stochastic model of heterochromatin and imply that heterochromatin is permissive for transcription throughout the cell cycle. Rather than promoting maintenance and spreading of heterochromatin, Swi6 appears to limit these processes to ensure that heterochromatin is appropriately confined.

overall_design: Examination of small RNA populations in wt and swi6∆ cells

first: Claudia

last: Keller

first: Rieka

last: Stunnenberg

first: Marc

last: Buehler