title: De novo DNA methyltransferases DNMT3A and DNMT3B are essential of global DNA methylation maintenance [BS-Seq]

summary: DNA methylation is the net result of deposition by DNA methyltransferases (DNMT1, 3A and 3B) and removal by the Ten-Eleven Translocation 1-3 (TET1-3) family of proteins and/or passive loss by replication. The relative contribution of the individual enzymes and pathways is only partially understood. Here we comprehensively analyzed and mathematically simulated the dynamics of DNA de-methylation during the reprogramming of the hypermethylated serum-cultured mouse embryonic stem cells (ESCs) to the hypomethylated 2i-cultured ground state of mESC. We show that DNA demethylation readily occurs in TET[1-/-, 2-/-] ESCs with similar kinetics as their WT littermates. Vitamin C activation of TET causes accelerated and more profound DNA demethylation without markedly affecting reprogramming kinetics. We developed a mathematical model that highly accurately predicts the global level of 5methyl- and 5hydroxymethylcytosine during the transition. Modeling and experimental validation show that the concentration of DNMT3A and DNMT3B determines the steady state level of global DNA methylation and absence of DNMT3A/B even in continued presence of DNMT1 results in gradual loss of 5mC. Taken together, DNMT1 alone is insufficient to maintain DNA methylation but requires the action of DNMT3A/3B that act as a “dimmer switches”.

overall_design: whole genome 5mC profiling (BS-seq) time series was performed during the early time phase of serum to 2i transition in the presence and absence of vitamin C  (4h, 8h,32h), 1 replicate

first: Ehsan

last: Habibi

first: Ning

middle: Q

first: Ali

last: Salehzadeh-Yazdi

first: Miao

last: Yu

first: Zhenqing

last: Xie

first: Leonie

last: Kroeze

first: Joop

last: Jansen

first: Hehuang

first: Chuan

last: He


title: De novo DNA methyltransferases DNMT3A and DNMT3B are essential of global DNA methylation maintenance [RNA-Seq]

status: Public on Jun 03 2016

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

type: Expression profiling by high throughput sequencing

overall_design: RNA-seq time series was performed during the early time phase of serum to 2i transition in the presence and absence of vitamin C  (4h, 16h,24h, 32h), 1 replicate

last: Liu

middle: I

middle: H


title: De novo DNA methyltransferases DNMT3A and DNMT3B are essential of global DNA methylation maintenance [TAB-Seq]

type: Methylation profiling by high throughput sequencing

overall_design: whole genome 5hmC profiling (TAB-seq) time series was performed during the early time phase of serum to 2i transition in the presence and absence of vitamin C  (0h, 4h, 8h,32h), 1 replicate


title: Transcription rate and transcript length drive the formation of chromosomal interaction domain

status: Public on Jun 05 2016

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

summary: Chromosomes in all organisms are highly organized and divided into multiple chromosomal interaction domains, or topological domains. Regions of active, high transcription help establish and maintain domain boundaries, but precisely how this occurs remains unclear. Here, using fluorescence microscopy and chromosome conformation capture in conjunction with deep sequencing (Hi-C), we show that in Caulobacter crescentus both transcription rate and transcript length, independent of concurrent translation, drive the formation of domain boundaries. We find that long, highly expressed genes do not form topological boundaries simply through the inhibition of supercoil diffusion. Instead, our results support a model in which long, active regions of transcription drive local decompaction of the chromosome, with these more open regions of the chromosome forming spatial gaps in vivo that diminish contacts between DNA in neighboring domains. These insights into the molecular forces responsible for domain formation in Caulobacter likely generalize to other bacteria and possibly eukaryotes.

overall_design: Hi-C experiments were performed on (i) untreated wild type swarmer cells and drug-treated swarmer cells (Chloramphenicol) of Caulobacter crescentus CB15N; (ii) on swarmer cells that are starved in M2 salts for 90 minutes; (iii) on swarmer cells harboring van::PrsaA_rsaA as well as derivatives of rsaA with a cassette of 2xTAA 2x transcription terminator inserted at 60bp, 560bp, 1060 and 2060 bp from the transcription start site of the ectopic rsaA; (iv) on CB15N strain ML2000 (Plac::dnaA) at time points 90 min, 150 min, 210 min and 270 min after IPTG withdrawal; and (v) on CB15N strain overexpressing CtrAD51E_delta_omega at time point 0 min, 120 min and 180 min after addition of the inducer (xylose).      RNA-seq experiment were performed on RNA extracted from (i) wild-type CB15N cells growing at exponential phase in PYE; and (ii) wild-type CB15N cells starved in M2 salts for 90 min.

first: T

middle: B

first: M

middle: T

last: Laub


title: Study of RepID/PHIP in DNA Replication inhitiation in Mammalian Cells

status: Public on Jun 02 2016

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

country: USA

institute: NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mammalian chromosome replication starts from distinct sites, but the principles  governing initiation site selection are unclear because proteins essential for DNA  replication do not exhibit sequence-specific DNA binding. We identified a replication  initiation determinant (RepID) protein that binds a subset of replication initiation sites.  A large fraction of RepID binding sites share a common G-rich motif and exhibit elevated  replication initiation. RepID is required for initiation of DNA replication from Rep-ID  bound replication origins, including the origin at the human beta-globin (HBB) locus. At  HBB, RepID is involved in an interaction between the replication origin (Rep-P) and the  locus control region. RepID depleted murine embryonic fibroblasts exhibit abnormal  replication fork progression and fewer replication initiation events. These observations  are consistent with a model suggesting that RepID facilitates replication initiation at a  distinct group of human replication origins.

overall_design: Nascent strands were purified with the lambda exonuclease methods from HCT116 cells and sequenced. Chromatin from unsyncrhonized untreated cultures of U2OS cells was subjected to ChIP-Seq with antibody directed against RepID/PHIP

last: Aladjem


title: Transcriptome Engineering Promotes a Fermentative Transcriptional State

city: Saint Louis

first: Ezekiel

middle: John

last: Maier

state: MO

address: 4444 Forest Park Ave

department: Computer Science

institute: Washington University

summary:
Purpose: The ability to rationally manipulate the transcriptional states of cells would be of great use in medicine and bioengineering. We have developed a novel algorithm, NetSurgeon, which utilizes genome-wide gene regulatory networks to identify interventions that force a cell toward a desired expression state.
Results: We used NetSurgeon to select transcription factor deletions aimed at improving ethanol production in S. cerevisiae cultures that are catabolizing xylose. We reasoned that interventions that move the transcriptional states of cells utilizing xylose toward the fermentative state typical of cells that are producing ethanol rapidly (while utilizing glucose) might improve xylose fermentation. Some of the interventions selected by NetSurgeon successfully promoted a fermentative transcriptional state in the absence of glucose, resulting in strains with a 2.7-fold increase in xylose import rates, a 4-fold improvement in xylose integration into central carbon metabolism, or a 1.3-fold increase in ethanol production rate.
Conclusions: We conclude by presenting an integrated model of transcriptional regulation and metabolic flux that will enable future metabolic engineering efforts aimed at improving xylose fermentation to prioritize functional regulators of central carbon metabolism.

overall_design: Mutant and wildtype S. cerevisiae cells were put into 48 hour aerobic batch fermentations of synthetic complete medium supplmented with 2% glucose and 5% xylose and culture samples were taken at 4 hours and 24 hours for transcriptional profiling performed by RNA-Seq analysis. In addition, wildtype S. cerevisiae cells were grown in various single carbon sources for 12 hours and culture samples were taken for transcriptional profiling performed by RNA-Seq analysis.

first: Drew

last: Michael

middle: J

first: Holly

last: Brown

first: Stacey

middle: R

last: Gish

first: Christopher

last: Fiore

first: Randall

first: Michael

last: Brent


title: Dissection of a super-enhancer in vivo (ChIP-seq)

city: oxford

first: Jim

last: Hughes

address: Weatherall Institute Of Molecular Me

department: MHU

institute: University of Oxford

summary: Many genes determining cell identity are regulated by a set of enhancer elements collectively referred to as super-enhancers. It has been suggested that super-enhancers represent a new class of cis-element, in which the assembly of enhancers confers an emergent property from the extended regulatory domain. To investigate this, we used published criteria to define one of the strongest super-enhancers in mouse erythroid cells – a 24kb region regulating α-globin expression, which comprises five enhancer-like components. Using homologous recombination, we deleted each component of this super-enhancer, singly and in informative combinations, and examined hematologic phenotype, gene expression, chromatin structure and chromosome conformation. Each component behaves independently, in an additive rather than synergistic manner. We conclude that the sub-classification of enhancers is unjustified beyond a description of their strength, which is defined by the number of lineage-specific transcription factors they bind. These findings ask afresh why enhancer-like elements cluster at key genes.

overall_design: ChIP-seq for 2 samples

first: Mira

last: Kassouf

first: Maria

middle: C

last: Suciu


title: CELF RNA binding proteins promote axon regeneration in C. elegans and mouse through regulation of syntaxin

city: San Diego

first: Bing

last: Zhou

state: CALIFORNIA

address: 9500 Gilman Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: Axon injury triggers dramatic changes in gene expression. While transcriptional regulation of injury-induced gene expression is widely studied, less is known about the roles of RNA binding proteins (RBPs) in post-transcriptional regulation during axon regeneration. In C. elegans the CELF (CUGBP and Etr-3 Like Factor) family RBP UNC-75 is required for axon regeneration. Using crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq) we identify a set of genes involved in synaptic transmission as mRNA targets of UNC-75. In particular, we show that UNC-75 regulates alternative splicing of two mRNA isoforms of the SNARE syntaxin/unc-64. In C. elegans mutants lacking unc-75 or its targets, regenerating axons form growth cones, yet are deficient in extension. Extending these findings to mammalian axon regeneration, we show that mouse Celf2 expression is upregulated after peripheral nerve injury and that Celf2 mutant mice are defective in axon regeneration. CLIP-seq and expression analysis also reveal CELF2 dependent regulation of selective syntaxins. Our data delineate a post-transcriptional regulatory pathway with a conserved role in regenerative axon extension.

sample_organism:
Caenorhabditis elegans
Mus musculus

platform_organism:
Caenorhabditis elegans
Mus musculus

overall_design: CLIP-seq (crosslinking immunoprecipitation coupled with deep sequencing)

first: Lizhen

last: Chen

first: Zhijie

first: Yishi

last: Jin


title: Identification of Kdm4a and c target genes in MLL-AF9 transformed mouse GMPs (L-GMP) [ChIP-seq]

city: Copenhagen

first: Karl

last: Agger

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: In this study we identify genes, that are bound by Kdm4a and Kdm4c in L-GMP cells.

overall_design: MLL-AF9 transformed L-GMP cell lines conditional knockout for Kdm4a, b and c, were derived from leukemic mice.  The cells were treated with 4-hydroxytamoxifen and chromatin was prepared from untreated cells (Ctrl) and cells treated for 96hr.

first: Kristian

last: Helin


title: A Co-repressor CBFA2T2 regulates pluripotency and germline development [ChIP-seq]

city: New York City

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor Rm 211

institute: NYU School of Medicine / HHMI

summary: In this experiment, we sought to determine the relative distribution of CBFA2T2, PRDM14, RING1B POU5F1 and SUZ12

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq performed for factors in NCCIT Embryonal Carcinoma cells and KH2 mouse embryonic stem cells

first: Shengjiang

last: Tu

first: Varun

last: Narendra

first: Simon

middle: V

last: Villanueva

first: Luis

middle: A

last: Rojas

first: Xiaoshi

last: Wang

first: Sang

middle: Y

last: Kim

first: Benjamin

last: Garcia

first: Matthias

last: Stadtfeld


title: A Co-repressor CBFA2T2 regulates pluripotency and germline development [RNA-seq]

summary: In this experiment, we sought to determine how PRDM14 and CBFA2T2 regulate the transcriptome of mouse embryonic stem cells

overall_design: 3 KO mESC lines with 3 biological replicates for each (wild type (3), PRDM14-KO (3), CBFA2T2 (3))


title: Genetic dissection of the α-globin super-enhancer

first: Jim

last: Hughes

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

overall_design: Refer to individual Series


title: Identification of genes associated with pistil development by transcriptome analysis of a female sterility mutant (fsm) in Chinese cabbage (Brassica campestris ssp. pekinensis)

city: Shenyang

first: Shengnan

last: Huang

address: 120 Dongling Road Shenhe District Shenyang P.R. China

country: China

institute: Shenyang Agricultural University

summary: The female sterility mutants are ideal materials for studying the pistil development in plants. We identified a female sterility mutant (fsm) exhibiting stable inheritance, which was derived from a Chinese cabbage DH line ‘FT’ using the combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. Genetic analysis indicated that the phenotype of fsm was controlled by a single recessive nuclear gene. The morphological observations revealed that the differences in the floral organs were significant between fsm and its wild type ‘FT’, the pistil of fsm was smaller and shorter, especially the ovary; and the degenerated ovule in the ovary may directly result in the female sterility. Comparative transcriptome analysis of ‘FT’ and fsm were performed using RNA-Seq. A total of 1,872 differentially expressed genes were identified between ‘FT’ and fsm. Of these, a number of genes involved in the ovule development were found, such as PRETTY FEW SEEDS 2 (PFS2) and temperature-induced lipocalin (TIL), and these genes were all up-regulated in the fsm vs. ‘FT’ comparison. Furthermore, GO and KEGG pathway enrichment analyses of DEGs suggested a variety of biological processes and metabolic pathways were significantly enriched during the pistil development. In addition, the expression patterns of eighteen DEGs were analyzed using qRT-PCR to confirm the accuracy of the RNA-seq data. A total of 31,272 single nucleotide polymorphisms (SNPs) were specifically detected in fsm, which could be directly related to the female sterility phenotype. These results contribute to increase our understanding of the molecular mechanisms of pistil development in Chinese cabbage.

overall_design: The RNA from the developing flower buds of a female sterility mutant (fsm) and its wild type‘FT’at the full-bloom stage in Chinese cabbage were sequenced by RNA-Seq, in triplicate.

first: Zhiyong

last: Liu

first: Runpeng

last: Yao

first: Danyang

last: Li

first: Xiang

first: Li

last: Hou

first: Hui

last: Feng


title: Identification of Kdm4a, b and c target genes in MLL-AF9 transformed mouse GMPs (L-GMP)

first: Karl

last: Agger


title: Dissection of a super-enhancer in vivo (ATAC-seq)

overall_design: ATAC-seq on 18 Samples with different enhancer-like components

first: Maria

last: Suciu


title: Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

summary: Ribose methylation is one of the two most abundant modifications in human ribosomal RNA and is believed to be important for ribosome biogenesis, mRNA selectivity and translational fidelity. We have applied RiboMeth-seq to rRNA from HeLa cells for ribosome-wide, quantitative mapping of 2'-O-Me sites and obtained a comprehensive set of 106 sites, including two novel sites, and with plausible box C/D guide RNAs assigned to all but three sites. We find approximately two-thirds of the sites to be fully methylated and the remainder to be fractionally modified in support of ribosome heterogeneity at the level of RNA modifications. A comparison to HCT116 cells reveals similar 2'-O-Me profiles with distinct differences at several sites. This constitutes the first comprehensive mapping of 2'-O-Me sites in human rRNA using a high throughput sequencing approach and paves the way for experimental analyses of the role of variations in rRNA methylation under different physiological or pathological settings.

overall_design: HTC116 and HeLa cells were subjected to RiboMeth-seq analysis. 3 barcoded sequencing adapters were used to produce 3 individual libraries from HTC116 RNA sequenced on 1 individual Ion Proton sequencing chip, and 3 x 2 individual libraries from HeLa RNA sequenced on 2 individual Ion Proton sequencing chips. The 3 gzip compressed fastq files from the sequencings, and the 3 final spread-sheets with annotated data are available here.

first: Martin

middle: D

last: Jansson

first: Sophia

last: Häfner

first: Disa

last: Tehler

first: Ulf

last: Birkedal

first: Mikkel

last: Christensen-Dalsgaard

first: Anders

last: Lund

first: Henrik

last: Nielsen


title: A Co-repressor CBFA2T2 regulates pluripotency and germline development

first: Danny

last: Reinberg


title: SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

summary: The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization. SMARCA4 knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical forces and affect nuclear structure. ChIP-seq analysis of SMARCA4 localization and SMARCA4-bound super-enhancers demonstrated extensive binding at intergenic regions. Furthermore, Hi-C analysis showed extensive SMARCA4-mediated alterations in higher-order genome organization at multiple resolutions. First, SMARCA4 knockdown resulted in clustering of intra- and inter- sub-telomeric regions, demonstrating a novel role for SMARCA4 in telomere organization. SMARCA4 binding was enriched at TAD (Topologically Associating Domain) boundaries, and SMARCA4 knockdown resulted in weakening of TAD boundary strength. Taken together, these findings provide a dynamic view of SMARCA4-dependent changes in higher-order chromatin organization and gene expression, identifying SMARCA4 as a novel component of chromatin organization.

overall_design: Hi-C and RNA-seq  experiments were conducted in MCF-10A shSCRAM and shSMARCA4 cells.  SMARCA4 ChIP-seq was conducted in wildtype MCF-10A cells.  Hi-C was performed by using the HindIII restriction enzyme.

first: A

first: Bryan

last: Lajoie

first: Andrew

last: Fritz

first: Rachel

middle: P

last: McCord

first: Jeffrey

last: Nickerson

first: Andre

last: van Wijnen

first: Jane

last: Lian

first: Janet

middle: L

last: Stein

first: Job

last: Dekker

first: Gary

middle: S

first: Anthiny

middle: N

last: Imbalzano


title: A novel bivalent chromatin state exists at enhancers

city: Los Angeles

first: Jessica

last: Charlet

state: California

address: 1441 Eastlake Avenue

department: Norris Cancer Center

institute: USC Keck School of Medicine

summary: We assess global chromatin accessibility following 5-Aza-CdR treatment of HCT116 cells

overall_design: Simultaneous genome-wide mapping of DNA methylation and nucleosome occupancy of HCT116 cells

first: Christopher

last: Duymich

first: Fides

last: Lay

first: Gangning

last: Liang

first: Peter

last: Jones


title: MicroRNAs maintain bivalency in mouse embryonic stem cells

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences


title: MicroRNAs maintain bivalency in mouse embryonic stem cells [ChIP-seq]

summary: The protein Dicer is required for microRNA (miRNA) biogenesis, and therefore Dicer-deficient cells lack all mature, functional miRNAs. Here we investigated the binding of the PRC2 component Ezh2 in wildtype and Dicer-deficient mouse embryonic stem cells genomewide using ChIP-sequencing analysis.

overall_design: Examination of Ezh2 binding in mouse ES cells either proficient (wildtype) or deficient (KO) of the protein Dicer

first: Matthias

last: Merkenschlager

first: Bryony

last: Graham


title: A Basal Stem Cell Signature Identifies Aggressive Prostate Cancer Phenotypes

status: Public on Jun 01 2016

first: Bryan

last: Smith

state: CA

address: MRL 5-720, 675 Charles E. Young Drive South

department: Microbiology, Immunology, and Molecular Genetics

institute: UCLA

summary: Aggressive cancers and normal stem cells often share similar molecular and functional traits. It is unclear if aggressive phenotypes of prostate cancer molecularly resemble normal stem cells residing within the human prostate. We performed high-throughput RNA sequencing on uncultured, highly purified epithelial populations from human prostates obtained after radical prostatectomy. We found the basal population to be defined by genes associated with developmental programs, epigenetic remodeling, and invasiveness. We further generated a 91-gene basal signature and applied it to gene expression datasets from patients with organ-confined or castration-resistant, metastatic prostate cancer. Metastatic prostate cancer was more enriched for the basal stem cell signature than organ-confined prostate cancer. Moreover, histological subtypes within prostate cancer metastases varied in their enrichment of the stem cell signature with small cell neuroendocrine carcinoma being the most stem cell-like. Bioinformatic analysis of the basal cell and two human small cell gene signatures identified a set of E2F target genes common to all three signatures. These results suggest that the most aggressive variants of prostate cancer share a core transcriptional program with normal prostate basal stem cells.

overall_design: Transcriptional analysis of 10 uncultured prostatic basal and luminal populations from either the benign or malignant prostate tissue of 8 human prostate cancer patients by high-throughput RNA-seq


title: Transcriptional responses of Fusarium graminearum when exposed to bacterial MAMPs

city: Frederiksberg C

first: Stefan

last: Olsson

address: 40 thorvaldsensvej

department: Plant and Environmental Sciences

summary: The plant fungal pathogen Fusarium graminearum which has part of its life cycle in the soil generally comes in contact with bacteria. Therefore the fungus was used as fungal model to test fungal responses to bacterial presence and ascertain the presence of an innate immune system in fungi through a transcriptomics study. Bacterial presence was established by exposing young fungal cultures to the well characterised MAMPs (Microbe Associated Molecular Pattern) such as Flagellin (FLG), Lipooligosacharides (LOS) and Peptidoglycans (PGN) and water was used as the control. The results showed that the fungus reacts to the presence of MAMPs within hours and that the 3 MAMPs up-regulated a set of common genes. These significantly up-regulated common genes can be classified into categories such as energy generation, amino acid metabolism, iron uptake, secondary metabolism and transporters related to secondary metabolism. Analysis of the transcriptional reponse from FLG showed that the MAMP which was obtained comercially was blended with sucrose and this was later confirmed by the commercial provider.

overall_design: Fungal cultures in biological triplicates were treated for 1,2 and 4 hours with MAMPs (LOS, PGN or FLG) and MQ water as control. Treatment with FLG and MQ water was repeated in a different laboratory to assess reproducibility.

first: Simon

last: Ipcho

first: Mari-Anne

last: Newman

first: Corby

last: Kistler


title: Prep1 and Meis1 competition for Pbx1 binding regulates protein stability and tumorigenesis

city: Milan

first: Francesco

last: Blasi

address: Via Adamello 16

country: Italy

institute: IFOM


title: Human Cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion.

city: Lausanne

first: Mauro

last: Delorenzi

address: Génopode Building, Quartier Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: We analysed whole PolyA+ RNA from human osteosarcoma U2OS cells depleted for human Cactin or transfected with a control shRNA.

overall_design: Two independent shRNAs targeting human Cactin (shCac_C and shCac_D), a control shRNA (shCtrl), a single cell line (U2OS)

first: Isabella

last: Zanini

first: Claus

middle: M

last: Azzalin


title: 5-hydroxymethylcytosine poises expression of genes involved in hematopoietic differentiation

city: Oslo

first: Xavier

last: Tekpli

address: Montebello

department: Department of Genetics

country: Norway

institute: Institute for Cancer Research

summary: Epigenetic processes regulate hematopoietic stem cell homeostasis. The recent discovery of 5-hydroxymethylcytosine (5hmC) provides new insights into the epigenetic regulation of gene expression during development. We used reduced representation of 5-hydroxymethylcytosine profiling (RRHP) to characterize the genome-wide distribution of 5hmC in human CD34+ hematopoietic stem/progenitor cells, lymphocytes, monocytes and granulocytes. We show that 5hmC levels decrease during cell differentiation and that 5hmC is associated with H3K4me1 and H3K27ac histone modifications, indicative of active enhancers. In CD34+ cells, the presence of 5hmC at presumed active enhancers correlates with increased binding of RUNX1 and FLI1, two transcription factors essential for hematopoiesis. Moreover, in progenitor cells, 5hmC poises the expression of transcription factors regulating hematopoietic lineage commitment, such as RUNX1, FOXO1 and C/EBP-alpha. Our study provides the first comprehensive genome-wide overview of 5hmC distribution in human hematopoietic cells and of its potential role in transcriptional network regulation during hematopoiesis.

overall_design: RRHP: profiling of 5-hydroxymethylcytosine and RNA-seq in human blood cells

first: Judith

last: Staerk


title: New insights into antifungal resistance mechanisms in Fusarium species revealed by high throughput sequencing

city: Bogota

first: Silvia

last: Restrepo

state: Bogota

address: Carrera Primera #18A-12,

department: Biology

country: Colombia

institute: Universidad de los Andes

summary:
Fusarium spp. are fungal pathogens of humans and plants. Fusarium oxysporum and Fusarium solani are important species isolated from infections such as onychomycosis, fungal keratitis, invasive infections, and disseminated diseases. These pathologies have a very difficult therapeutic management and poor therapeutic responses, especially in patients with disseminated infection. Little information is available regarding the molecular mechanisms responsible for antifungal resistance in these fungi.
methods: In this study, we performed a quantitative analysis of the transcriptional profile of F. oxysporum and F. solani, challenged with amphotericin B (AMB) and posaconazole (PSC) using RNA-seq. Quantitative real-time reverse transcription PCR (qRT-PCR) was used to validate the results
results: Several genes related to mechanisms of antifungal resistance such as efflux pumps, ergosterol pathway synthesis, and responses to oxidative stress were found. Genes such as ERG11, ERG5, the Major Facilitator Superfamily (MFS), thioredoxin, and different dehydrogenase genes may explain the reduced susceptibility of Fusarium spp. against azoles and the possible mechanisms that may play an important role in induced resistance against polyenes.
conclusions: Important differences in the levels of transcriptional expression were found between F. oxysporum and F. solani exposed to the two different antifungal treatments. Knowledge on the gene expression profiles and gene regulatory networks in Fusarium spp. during exposure to antifungal compounds, may help to identify possible molecular targets for the development of novel, better, and more specific therapeutic compounds.

sample_organism:
Fusarium oxysporum
Fusarium solani

platform_organism:
Fusarium oxysporum
Fusarium solani

overall_design: profile transcriptional of Fusarium spp changed to antifungal treatments in vitro

first: Adriana

last: Castillo

first: Juan

last: Castro

first: Giovana

last: Dannies

first: Joseph

last: Guarro

last: Celis


title: Dissection of a super-enhancer in vivo (Capture-C)

first: Jim

last: Hughes

overall_design: NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments, in this case the promoters of genes were exclusively used.  The method was applied to Wlidtype erythroid cells and to in vivo models where the globin R1 and R2 regulatory elements and the R2 and R3 regulatory elements were deleted in combination.

first: James

middle: O

last: Davies

first: Deborah

last: Hay

first: Doug

last: Higgs

first: A

last: Oudelaar


title: Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [cell models RNA-seq]

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

summary:
Transcriptomic changes and estrogen and progesterone receptor binding in multiple ER+/PR+ models (eight ER+/PR+ patient tumors, various T47Ds, ZR75) and multiple ER+/PR-negative models (four ER+/PR- patient tuumors, PR-deficient T47D and MCF7 cells) treated with various hormone combinations.
Results: In isolation, estrogen and progestin act as genomic agonists by regulating the expression of common target genes in similar directions, but at different levels. Similarly, in isolation, progestin is also a weak phenotypic agonist of estrogen action. However, in the presence of both hormones, progestin behaves as a phenotypic estrogen antagonist. PR remodels nucleosomes to noncompetitively redirect ER genomic binding to distal enhancers enriched for BRCA1 binding motifs and sites that link PR and ER/PR complexes. Importantly, when both hormones are present, progestin modulates estrogen action such that responsive transcriptomes, cellular processes and ER/PR recruitment to genomic sites correlate with those observed with PR alone, but not ER alone.
Conclusions: Genomic Agonism and Phenotypic Antagonism between Estrogen and Progesterone Receptors in Breast Cancer. Individual and concerted actions of ER and PR highlight the prognostic and therapeutic value of PR in ER+/PR+ breast cancers.

overall_design: ER+/PR+ and ER+/PR-deficient model systems were deprived of steroids by culturing them in phenol red free RPMI 1640 media that is supplemented with 10% charcoal-stripped fetal bovine serum and 1% penicillin/streptomycin. Subsequently, these steroid-deprived models were treated with either vehicle, 10 nM estradiol, 10 nM progestin R5020 or 10 nM of both the hormones and genomics (ChIP-seq and RNA-seq) was performed. ChIP-seq was done after 45 minutes of hormone treatments. For cell models, RNA-seq was done after 12 hours of hormone treatments. Tumor explants were treated with either 24 or 48 hours.

first: Geoffrey

last: Greene


title: Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [ChIP-seq]


title: Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [tumor samples RNA-seq]


title: Transcriptome response of Methanobrevibacter ruminantium to lauric acid in cell culture.

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

institute: University of Zurich

summary: Medium chain fatty acids (MCFA) have been shown to inhibit methanogenesis, disrupt the cell envelope, and decrease survival of Methanobrevibacter ruminantium M1 in a dose-, time-, and protonation level dependent way.  However, the exact mechanisms behind these observations are still unknown. Although the biochemistry of the metabolic processes of M. ruminantium has been well studied and its genome sequence is now available, little is known about the overall transcriptome regulation of M. ruminantium in response to inhibitors like MCFA. In the present study, we used RNA Sequencing to evaluate the effects of lauric acid (C12) on M. ruminantium. Pure M. ruminantium cell cultures in the mid-exponential growth phase were exposed to C12 in concentrations of 0.4 mg/mL, dissolved in DMSO  for 1 h, and the transcriptomic changes compared to DMSO-only treated control samples (final DMSO concentration 0.2 %), were investigated. Gene expression changes upon exposure to C12 were not dramatic in magnitude (log2 fold change mostly below +/- 3) and in gene number (214 genes). However, the observed expression changes affected mostly genes which encoded cell-surface associated proteins (adhesion-like proteins, membrane-associated transporters and hydrogenases), or proteins, which were involved in detoxification or DNA repair processes. The transcriptional response of M. ruminantium M1 to C12 did not specifically inhibit methanogenesis. Instead, the data indicated a non-specific antimicrobial action by lauric acid, which involves destruction of the cell membrane and interferences with cellular energetics in M. ruminantium. To date, there has been no systematic characterization of a ruminal methanogen transcriptome by deep sequencing. Our results give first hints on the molecular inhibitory mechanism of C12 on M. ruminantium.

overall_design: RNA profiles of M. ruminantium treated in vitro (lauric acid disolved in DMSO), non-treated=controls (DMSO supplementation) and non-treated=blanks (no supplementation) were generated by deep sequencing, in triplicates, by using Illumina HiSeq2500

first: Xuan

last: Zhou

first: Johanna

last: Zeitz

first: Stefan

last: Neuenschwander

first: Angela

last: Schwarm

first: Michael

last: Kreuzer

first: Anna

last: Bratus-Neuenschwander


title: Cortisol-treated zebrafish embryos develop into pro-inflammatory adults with aberrant immune gene regulation

city: Orono

first: Benjamin

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine


title: Response to low-dose cortisol treatment in zebrafish embryos [larvae]

summary: Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid-induced developmental programming. To gain insight into such programming we treated zebrafish embryos with 1 micromolar cortisol and examined the effects on larvae. Treated larvae had elevated whole-body cortisol and glucocorticoid signaling, and up-regulated genes associated with defense response and immune system processes.

overall_design: 6 samples total were analyzed. 3 DMSO controls, and 3 cortisol treated (1 micromolar).

first: Ellen

middle: I

last: Hartig

first: Shusen

last: Zhu

last: Coffman


title: Alternative splicing regulation by homologous Muscleblind proteins

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: We provide data showing alternative splicing regulation by Muscleblind proteins in MEFs. MEFs lacking functional Muscleblind (DKO MEFs) were stably reconstituted with Muscleblind proteins from Homo sapiens, Ciona intestinalis, Drosophila melanogaster, Caenorhabditis elegans or Trichoplax adhaerens and splicing regulation was explored using RNA-seq analysis followed by MISO (Mixture of Isoforms).

overall_design: Alternative splicing was accessed using RNA-sequencing data from five DKO MEF lines reconstituted with different GFP-tagged Muscleblind homologs or GFP alone and compared to RNA-seq data from three WT MEF lines and three control DKO MEFs (no Muscleblind reconstitution). A total of 12 samples were used for high-throughput sequencing.

first: Julia

last: Oddo

first: Tanvi

last: Saxena


title: MicroRNA-SEQ analysis of kidney and liver damage in rat

city: Cambridge

first: Pooja

last: Shah

state: MA

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose : Identification of novel microRNA biomarkers in urine and plasma from rats with kidney or liver damage

overall_design: micoRNA-SEQ was used to analyze changes in miRNA profiles of tissue, plasma and urine samples of rats treated with either a nephrotoxicant (cisplatin) or one of two hepatotoxicants (Acetaminophen [APAP] or Carbon Tetrachloride [CCL4]).

first: Francis

last: Wolenski


title: Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer.

first: Hari

last: Singhal

overall_design: Refer to individual Series

last: Greene


title: Transforming growth factor-β and Notch ligands act as opposing environmental cues in the plasticity of type 3 innate lymphoid cells

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary: Group 3 innate lymphoid cells (ILC3) are composed of NCR- and NCR+ subsets located at mucosal sites exposed to billions of commensal microbes and potentially harmful pathogens. Together with T cells, the various ILC3 subsets maintain the balance between homeostasis and immune activation. Using genetic mapping, we reveal here the existence of a new subset of NCR- ILC3 transiently expressing Ncr1 but strongly related to unlabeled NCR- ILC3, demonstrating previously unsuspected heterogeneity within the NCR- ILC3 population. Notch signaling is required for the differentiation of NCR- ILC3 into NCR+ ILC3. However, we show here that Notch signaling must be sustained for the maintenance of the NCR+ phenotype and that TGF-β impairs the development of NCR+ ILC3. Thus, ILC3 diversity and the plasticity of the NCR- and NCR+ subsets is regulated by the balance between the opposing effects of Notch and TGF-β signaling, maintaining homeostasis in the face of continual challenges.

overall_design: Transcriptional profiling of three ILC subsets (NCR-FM-, NCR-FM- and NCR+FM+) using RNA sequencing

first: Charlotte

last: Viant

first: Lucille

last: Rankin

last: Vivier

first: Gabrielle

last: Belz


title: Essential role of the transcription factors E2A and E2-2 in germinal center B cell and plasma cell development

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

summary: E2A is an essential regulator of early B-cell development. Here we demonstrated that E2A together with E2-2 controlled germinal-center B-cell and plasma cell development. As shown by identification of regulated E2A,E2-2 targets in activated B-cells, these E-proteins directly activated genes with important functions in germinal-center B-cells and plasma cells by inducing or maintaining DNase I hypersensitive sites. Through controlling multiple enhancers in the Igh 3’ regulatory region and Aicda locus, E-proteins regulated class switching by inducing both Igh germline transcription and AID expression. By regulating 3’ Igk enhancers and a distal element at the Prdm1 (Blimp1) locus, E-proteins contributed to Igk, Igh and Prdm1 activation in plasmablasts. These data identified E2A and E2-2 as central regulators of B-cell immunity.

overall_design: 56 samples in total: A) 38 RNA-Seq samples in 5 cell types: Follicular B cells (FO B cell, 2 genotypes, 2 replicates each) Activated B cells (Act B cell, 2 genoytpes, 6 stimulations, 2 replicates each) Pre-Plasmablasts (Pre-PB, 1 genotype, 2 stimulations, 2 replicates each) Plasmablasts (PB, 1 genotype, 2 stimulations, 2 replicates each) Germline Center B cells (GC B cell, 1 genotype, 2 replicates); B) 13 ChIP-Seq samples in 5 cell types: FO B cell (E2A, 2 crosslinking types, 1 replicate each) Act B cell (E2A, 2 crosslinking types, 2 stimulations, 1 replicate each; H3K27ac, 1 crosslinking type, 1 stimulation, 2 genotypes, 1 replicate each) Pre-PB (E2A, 2 crosslinking types, 1 stimulation, 1 replicate each) PB (E2A, 2 crosslinking types, 1 stimulation, 1 replicate each) Mature B cell (input); C) 5 ATAC Seq samples in 2 cell types: Act B cell (2 stimulations, 2 genotypes, 1 replicate each), Pre-PB (1 stimulation, 1 genotype, 1 replicate).

first: Miriam

last: Wöhner

first: Hiromi

last: Tagoh

first: Ivan

last: Bilic

first: Markus

last: Jaritz

first: Daniela

last: Kostanova Poliakova

first: Maria

last: Fischer

first: Meinrad

last: Busslinger


title: Unlinking a lncRNA from its associated cis element [Capture-C]

city: Philadelphia

first: Vikram

last: Paralkar

state: PA

address: 3400 Civic Center Boulevard, Perelman Center, 7th Floor, South Pavilion Extension

institute: University of Pennsylvania

summary: Capture-C using probes at the Cdkn1b promoter and the Lockd promoter

overall_design: Many long non-coding (lnc) RNAs are reported to regulate gene expression and protein functions. However, the proportion of lncRNAs with biological activities among the thousands expressed in mammalian cells is controversial. We studied Lockd (LncRNA downstream of Cdkn1b), a 434 bp polyadenylated lncRNA originating 4 kb 3’ to the Cdkn1b gene. Heterozygous and homozygous deletion of the 25 kb Lockd locus reduced Cdkn1b transcription by approximately 35 and 70% respectively in a mouse erythroid cell line. In contrast, homozygous insertion of a polyadenylation cassette 80 bp downstream of the Lockd transcription start site reduced the entire lncRNA transcript level by > 90%, but had no effect on Cdkn1b transcription. The promoter of the Lockd gene contains a DNase hypersensitive site, binds numerous transcription factors (TFs), and physically associates with the Cdkn1b promoter in chromosomal conformation capture (NG Capture-C) studies. Thus, the Lockd gene positively regulates Cdkn1b transcription through an enhancer-like cis element, while the lncRNA itself is dispensable. These findings demonstrate that the biological activities of a lncRNA cannot be inferred from phenotypes that arise after deleting the corresponding gene. Rather, the model of an inert transcript arising from a functional genomic cis element should be considered while investigating the biology of any lncRNA.

first: Mitch

last: Weiss


title: Genome-wide analysis of gene expression of IWR1/Y27632-maintained epiblast stem cells (EpiSCs)

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary: Analysis of specific genes regulated by IWR1 and Y27632 (Y27), respectivly.

overall_design: Total RNA obtained from No Treatment (NT) control EpiSCs and EpiSCs treated by 2 µM IWR1 or 0.5 µM Y27.

first: Ying

last: Qilong

first: Ye

last: Shoudong


title: Activin A regulates human T follicular helper (Tfh) cell differentiation

city: La Jolla

first: Shane

last: Crotty

address: 9420 Athena Circle

institute: La Jolla Institute of Allergy and Immunology

summary: To determine the role of the cytokine activin A in the regulation of human T follicular helper (Tfh) cell gene program, we performed a transcriptomic analysis (RNA-seq) of human naïve CD4 T cells differentiated in vitro with activin A. The analysis of the gene expression profile driven by activin A, alone or in combination with IL-12 (a know regulator of human Tfh differentiation/function), revealed that activin A can regulate the expression of multiple molecules involved in the differentiation and/or function of human Tfh cells.

overall_design: Human naïve CD4 T cells were isolated from fresh PBMCs of healthy control subjects by magnetic bead isolation. Purity was measured by FACS as percentage of CD4+CD45RA+ cells and was 95% or higher.  Upon isolation, naïve CD4 T cells were stimulated with anti-CD3/CD28 coated beads in the presence of the following cytokine combinations: no exogenous cytokines (beads only), activin A, IL-12, activin A+IL-12, TGFb, TGFb +IL12. Following 5 days of in vitro culture, live CD4 T cells were FACS sorted and gene expression was analyzed by RNA-seq. Data are from independent donors.

first: Michela

last: Locci

first: Jennifer

last: Wu


title: Transcriptomic approaches in the zebrafish model for tuberculosis – insights into host- and pathogen-specific determinants of the innate immune response

city: Leiden

first: Annemarie

middle: H.

last: Meijer

address: Einsteinweg 55

department: Animal Sciences and Health

institute: Institute of Biology, Leiden University

summary: Both embryonic and adult zebrafish Mycobacterium marinum infection studies have contributed to our knowledge of the development and function of tuberculous granulomas, which are typical for mycobacterial pathogenesis. In this review we discuss how transcriptome profiling studies have helped to characterize this infection process and we include new RNA sequencing (RNA-Seq) data that reveals three main phases in the host response to M. marinum during the early stages of granuloma development in zebrafish embryos and larvae. The late-phase response shares common components with the strong and acute host transcriptome response that has previously been reported for S. typhimurium infection in zebrafish embryos. In contrast, the early/mid-phase response to M. marinum infection, characterized by suppressed pro-inflammatory signaling, is strikingly different from the acute response to S. typhimurium infection. Furthermore, M. marinum infection shows a collective and strongly fluctuating regulation of lipoproteins, while S. typhimurium infection has pronounced effects on amino acid metabolism and glycolysis.

overall_design: Embryos were infected at 28 hpf by injecting 250 colony forming units of M. marinum Mma20 in 2%PVP into the caudal vein, or mock-injected with PBS/2%PVP. After injections, embryos were transferred into fresh egg water containing 0.003% 1-phenyl-2-thiourea (Sigma-Aldrich) to prevent melanization and incubated at 28°C. After the incubation period, infected and uninfected groups of 30 embryos were snap-frozen in liquid nitrogen and RNA was isolated for Illumina RNAseq analysis. Samples were taken at the following timepoints: 2, 4, 6, 8 hpi and 1, 2, 3, 4, 5 dpi.

first: Erica

last: Benard

first: Julien

last: Rougeot

first: Peter

last: Racz

first: Herman

last: Spaink

middle: H


title: Targeted deletion of circadian clock gene Arntl in the nephron results in dysregulation of diverse metabolic pathways

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

summary: The circadian clock controls a wide variety of metabolic and homeostatic processes in a number of tissues, including the kidney. However, the role of the renal circadian clocks remains largely unknown. To address this question we performed transcriptomic analysis in mice with inducible and conditional ablation of the circadian clock system in the renal tubular cells (Bmal1lox/lox/Pax8-rtTA/LC1 mice). Deep sequencing of the renal transcriptome revealed significant changes in the expression of genes related to metabolic pathways and organic anion transport. In parallel, kidneys from Bmal1lox/lox/Pax8-rtTA/LC1 mice exhibited a significant decrease in the NAD+/NADH ratio suggesting an increased anaerobic glycolysis and/or decreased mitochondrial function. In-depth analysis of two selected pathways revealed (i) a significant increase in plasma urea levels correlating with increased renal arginase 2 (Arg2) activity, hyperargininemia and increase of the kidney arginine content; (ii) a significantly increased plasma creatinine concentration and reduced capacity of the kidney to secrete anionic drugs (furosemide), paralleled by a ~80% decrease in the expression levels of organic anion transporter OAT3 (SLC22a8). Collectively, these results indicate that the renal circadian clocks control a variety of metabolic/homeostatic processes at both the intra-renal and systemic levels and are involved in drug disposition.

overall_design: Mice with a specific ablation of the Arntl gene encoding BMAL1 in the renal tubular cells were compared to wild-type littermate at ZT4 and ZT16 (ZT – Zeitgeber time units; ZT0 is the time of light on and ZT12 is the time of light off).

first: Svetlana

last: Nikolaeva

first: Camille

last: Ansermet

first: Gabriel

last: Centeno

first: Natsuko

last: Tokonami

first: Dmitri

last: Firsov


title: Transcriptome sequencing of porcine liver samples

city: Madrid

first: Angel Mario

middle: Martinez

last: Montes

address: Crta. de la Coruña, km 7,5

department: Mejora Genetica Animal

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA

summary: Identification of genes and causal mutations regulating growth and fatness traits in pig.

overall_design: Transcriptome sequencing of 10 liver samples of two groups of divergent pigs for growth and fatness.

first: Ana

last: Fernandez Avila

first: Angel

last: Martinez Montes

first: Dafne

last: Perez Montarelo


title: Cortisol-treated zebrafish embryos develop into pro-inflammatory adults with aberrant immune gene regulation [adults]

first: Benjamin

last: King

summary: Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid-induced developmental programming. To gain insight into such programming, we treated zebrafish embryos with cortisol and examined the effects on adults. In adulthood, the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol, and constitutively mis-expressed genes involved in defense response and its regulation. Adults derived from cortisol-treated embryos displayed defective tailfin regeneration, heightened basal expression of pro-inflammatory genes, and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro-inflammatory adult phenotype, at the expense of immunoregulation and somatic regenerative capacity.

overall_design: 30 samples total were analyzed. 9 caudal fins samples (0, 2 and 4dpa), 3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples (0, 2 and 4dpa), 3 blood samples and 3 muscle samples from adults exposed to cortisol (1 micromolar) as embryos.

first: Ellen

last: Hartig

first: Shusen

last: Zhu

first: James

last: Coffman


title: Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay

city: Bar Harbor

first: Ryan

last: Tewhey

address: 600 Main Street

institute: Jackson Laboratory

summary: Although genetic studies have identified many hundreds of loci associated with human traits and diseases, pinpointing the causal alleles remains difficult, particularly for non-coding variants. To address this challenge, we have enhanced the sensitivity and reproducibility of the massively parallel reporter assay (MPRA), adapting it to identify variants that directly modulate gene expression. We then applied it to over 29,000 single nucleotide and insertion/deletion polymorphisms from 3,965 cis-expression quantitative trait loci (eQTL). We demonstrate strong correlation between our MPRA approach and existing measures of regulatory function, and determine an approximate sensitivity of ~20% with a positive predictive value of 60-65% to detect an eQTL causal allele. We identify 842 variants showing differential expression between alleles, including 53 well-annotated variants associated with diseases and traits. Thus, we have created a resource of concrete leads for understanding the genetic basis of specific phenotypes and illustrate the promise of this kind of approach for comprehensively interrogating how non-coding polymorphism shapes human biology.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: The study consists of two separate MPRA experiments, a 78,958 oligo (79k study) and a 7,500 oligo library (7.5k). For each library we processed independent transfections into two lymphoblastoid cell lines; in total we completed 5 replicates of NA12878 and 3 replicates of NA19239. For the 79k library we also performed 5 replicate transfections into the hepatocarcinoma cell line HepG2. Raw data is provided as Illumina reads of the 20 bp barcode from the RNA extracted 24 hours post transfection as well as from the plasmid library used for transfection. We also provide oligo/barcode combinations from the ∆gfp vector in the form of a tab delimited file containing the raw sequence reads of the barcode (column 1) and genomic sequence (column 2). Processed count files are unnormalized counts for each oligo acquired by summing all barcode matches together for each replicate.


title: Next generation sequencing of Coccinella septempunctata L. with non-diapause, diapause, and diapause-terminated states

city: Beijing

first: Xiaoyang

last: Qi

address: haidian area,zhongguancun south street

institute: Chinese Academy of Agricultural Sciences

summary: The most common ladybird beetle, Coccinella septempunctata L., is an excellent predator of crop pests such as aphids and white flies, and it shows a wide range of adaptability, a large appetite and a high reproductive ability. In this study, we collected female adults in three different states, i.e., non-diapause, diapause and diapause termination, for transcriptome sequencing.

overall_design: The experimental insects consisted of three different states as follows: Non-diapause female insects were reared at 24±1°C, with a RH of 70±10% and a 16:8 h light: dark (L: D) photoperiod and collected after their first oviposition. Female adults in diapause were reared at 18±1°C at an RH of 70±10% and a 10:14-h (L:D) photoperiod. The experimental diapause insects were collected after 30 days. Diapause-terminated adults were transferred to another climatic cabinet with the 30-day diapause insects and reared under the same conditions as the non-diapause insects. After their first oviposition, the female insects were collected and stored at -80°C. Three biological replicates per treatment (non-diapause, diapause, diapause-terminated) were sequenced using Illumina HiSeq 2500.

first: Lisheng

last: Zhang


title: The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus

city: Cologne

first: Fei

last: He

address: Zuelpicher Str. 47 B

department: Botanical Institute

country: Germany

institute: University of Cologne

summary: We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. Because the sister species were both crossed to an outgroup species, it was possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed in only one of the two hybrids were likely to be derived, whereas those observed in both hybrids either predate predated the split between the two species or arose along the A. thaliana lineage. By contrasting the distribution of cis-regulatory mutations derived in the A. halleri to those derived on the A. lyrata lineage, we could establish relative rates of cis-acting evolution across polygenic molecular functions and detect lineage-specific polygenic adaptation to environmental challenges.

sample_organism: Arabidopsis thaliana x Arabidopsis lyrata

sample_organism: Arabidopsis thaliana x Arabidopsis halleri

overall_design: A.thalianaxA.lyrata under cold, dehydration and standard conditions, 3 biological replicates; A.thalianaxA.halleri under cold, dehydration and standard conditions, 3 biological replicates; toal 18 RNA-seq samples

first: Agustin

last: Arce

first: Gregor

last: Schmitz

first: Andreas

last: Beyer

first: Maarten

last: Koornneef

first: Polina

last: Novikova

first: Juliette

last: de Meaux


title: DNA methylation changes induced by overexpression of IDH1mut or treatment with 2HG in the sorted mouse bone marrow cells

city: Hannover

first: Anuhar

last: Chaturvedi

address: Cral Neuberg Strasse-1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

summary: Mutations in the enzymes IDH1 and IDH2 have been identified in a wide variety of tumors like glioma, chondrosarcoma, thyroid cancer, lymphoma, melanoma, and in acute myeloid leukemia. Mutated IDH1/2 produces the metabolite 2-hydroxyglutarate (2HG), which interferes with epigenetic regulation of gene expression, and thus may promote tumorigenesis.

overall_design: HoxA9 immortalised bone marrow cells from C57BJ/6 mice were tranduced with either empty vector or pSF91-IDH1wt-IRES-EGFP, or pSF91-IDH1mut-IRES-GFP and transplanted in irradiated recipient mice. Alternatively, HoxA9 immortalised cells transduced with empty vector transplanted mice were treated with R-2HG at dose of 1mg/day for four weeks. Four weeks after transplantation/treatment GFP+ cells were sorted from mouse bone marrow, from which total DNA was extracted and subjected to Reduced Representation Bisulfite Sequencing (RRBS) to determine the genome-wide methylation signature.

first: Michael

last: Heuser


title: MicroRNA-offset RNA regulates gene expression and cell proliferation (Small RNA-Seq)

city: Boston

first: Gavin

middle: R.

last: Schnitzler

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

summary: MicroRNA-offset RNAs (moRs) were first identified in simple chordates and subsequently in mouse and human cells by deep sequencing of short RNAs. MoRs are derived from sequences located immediately adjacent to microRNAs (miRs) in the primary miR (pri-miR). Currently moRs are considered to be simply a by-product of miR biosynthesis that lack biological activity. Here we show for the first time that a moR is biologically active. We now demonstrate that endogenous and over-expressed moR-21 significantly alters gene expression and inhibits the proliferation of vascular smooth muscle cells (VSMC). We report that the "seed region" of moR-21 as well as the "seed match region" in the target gene 3'UTR are indispensable for moR-21-mediated gene down-regulation. We further demonstrated that moR-21-mediated gene repression is Argonaute 2 (Ago2) dependent. In addition, we find that miR-21 and moR-21 may regulate different genes in a given pathway and can oppose each other in regulating certain genes. Taken together, these findings provide the first evidence that microRNA offset RNA regulates gene expression and is biologically active.

overall_design: Small RNAs were harvested from mouse aortic smooth muscle cells (AoSMCs), with three biological replicates, using miReasy kits (Qiagen) according to the manufacturer’s instructions. RNA was quantified using a Nanodrop spectrophotometer. Small RNA library construction and illumina HiSeq 75bp single read sequencing were performed at the Yale Center for Genome Analysis. Reads were trimmed to remove adaptor sequences, and inserts longer than 13 bases were mapped to the mouse mm10 genome using Bowtie (with settings –n 0 -m 5 --best  --strata, allowing 0 mismatches and up to 5 genomic loci with a perfect match, {Genome Biol. 2009;10(3):R25, Langmead B, Trapnell C, Pop M, Salzberg SL}). Reads that mapped to within 50 bp of more than one annotated mouse pri-miR (as defined by miRBase {Kozomara A, Griffiths-Jones S. Nucelic Acids Res 2014 42:D68-D73}), were allotted evenly between these locations. Reads that fell entirely within established miRbase 3p or 5p miR coordinates, plus or minus 3 bp, were counted as 3p or 5p miRs, respectively. Reads that fell entirely within the range of 35 bp 3’ to 3 bp 5’ of the last base of a 3p miR were counted as 3p moR reads. Those that fell entirely between 3bp 3’ and 35 bp 5’ of the first base of a 5p miR were counted as 5p moR reads. On average each library contained 17.4 million qualifying inserts, of which 13.8 million (79.3%) mapped to one of these four regions, indicating that the large majority of inserts represented miR or moR sequences. Reads were divided by the number of million reads mapping to these regions in each library to give normalized reads per million reads (RPMR) values.

first: J

last: Zhao

first: G

middle: R

first: L

middle: K

last: Iyer

first: W

middle: E

last: Baur

first: R

last: Karas


title: Small RNA and mRNA expression profiling during zebrafish caudal fin regeneration

first: Benjamin

last: King

summary: Previous studies of zebrafish caudal fin regeneration have shown that multiple genetic programs are moduled through regulatory factors.  MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs.  Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration.  We characterized microRNA expression during zebrafish caudal fin regeneration using small RNA sequencing.  The stages of caudal fin regeneration were assayed for mRNA expression using mRNA sequencing.

overall_design: Small RNA and mRNA gene expression profiling during 0 and 4 days post amputation.

first: Viravuth

last: Yin


title: Small RNA and mRNA expression profiling during axolotl forelimb regeneration

summary: Previous studies of appendage regeneration in the axolotl have shown that multiple genetic programs are modulated through regulatory factors.  MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs.  Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration.  We characterized microRNA expression during Axolotl forelimb regeneration using small RNA sequencing.  The same samples were assayed for mRNA expression using mRNA sequencing.

overall_design: Small RNA and mRNA gene expression profiling during 0, 3, 6 and 14 days post amputation.


title: Small RNA and mRNA expression profiling during Polypterus senegalus (bichir) pectoral fin regeneration

summary: Previous studies of vertebrate appendage regeneration have shown that multiple genetic programs are moduled through regulatory factors.  MicroRNAs are short highly conserved non-coding genes that suppress expression of target genes and thereby control multiple genetic programs.  Given their important regulatory roles and evolutionary conservation, we hypothesize that microRNAs define a conserved genetic regulatory circuit important for appendage regeneration.  We characterized microRNA expression during Polypterus senegalus (bichir) pectoral fin regeneration using small RNA sequencing.  The same samples were assayed for mRNA expression using mRNA sequencing.

overall_design: Small RNA and mRNA gene expression profiling during 0, 3, 7 and 14 days post amputation.


title: Transcriptional profiling of TH2 cells identifies pathogenic features associated with asthma

first: Pandurangan

last: Vijayanand

address: 9420 Athena Cir

institute: La Jolla Institute for Allergy and Immunology

summary: Allergic asthma and rhinitis are two common chronic allergic diseases that affect the lungs and nose, respectively. Both diseases share clinical and pathological features characteristic of excessive allergen-induced type 2 inflammation, orchestrated by memory CD4+ T cells that produce type 2 cytokines (TH2 cells). However, a large majority of subjects with allergic rhinitis do not develop asthma, suggesting divergence in disease mechanisms. Since TH2 cells play a pathogenic role in both these diseases and are also present in healthy non-allergic subjects, we performed global transcriptional profiling to determine whether there are qualitative differences in TH2 cells from subjects with allergic asthma, rhinitis and healthy controls. TH2 cells from asthmatic subjects expressed higher levels of several genes that promote their survival as well as alter their metabolic pathways to favor persistence at sites of allergic inflammation. In addition, genes that enhanced TH2 polarization and TH2 cytokine production were also upregulated in asthma. Several genes that oppose T cell activation were downregulated in asthma, suggesting enhanced activation potential of TH2 cells from asthmatic subjects. Many novel genes with poorly defined functions were also differentially expressed in asthma. Thus, our transcriptomic analysis of circulating TH2 cells has identified several molecules that are likely to confer pathogenic features to TH2 cells that are either unique or common to both asthma and rhinitis.

overall_design: RNA-sequencing of circulating TH2 cells isolated from a cohort of patients with allergic rhinitis (25), asthma (40) patients and healthy non allergic subjects (15). Cells were directly isolated from blood by flow cytometry. Total RNA was extracted, messenger RNA was selected and cDNA was amplified linearly with a PCR based method (Picelli et al. 2014). Libraries were prepared using the NexteraXT Illumina sequencing platform.

first: Grégory

last: Seumois

first: Jose

last: Zapardiel-Gonzalo

first: Brandie

last: White

first: Divya

last: Singh

first: Veronique

last: Schulten

first: Myles

last: Dillon

first: Denize

last: Hinz

first: Alessandro

last: Sette

first: Bjoern

last: Peters


title: Unstranded RNA sequencing data

first: Jason

middle: Daniel

last: Buenrostro

address: 415 Main Street

institute: Broad Institute

summary: A single hematopoietic stem cell can give rise to all blood cells with remarkable fidelity. Here, we define the chromatin accessibility and transcriptional landscape controlling this process in thirteen primary cell types that traverse the hematopoietic hierarchy. Exploiting the finding that enhancer landscapes better reflect cell identity than mRNA levels, we enable "enhancer cytometry" for accurate enumeration of pure cell types from complex populations. We further reveal the lineage ontogeny of genetic elements linked to diverse human diseases. In acute myeloid leukemia, chromatin accessibility reveals distinctive regulatory evolution in pre-leukemic HSCs (pHSCs), leukemia stem cells, and leukemic blasts. These leukemic cells demonstrate unique lineage infidelity, confirmed by single cell regulomes. We further show that pHSCs have a competitive advantage that is conferred by reduced chromatin accessibility at HOXA9 targets and is associated with adverse patient outcomes. Thus, regulome dynamics can provide diverse insights into human hematopoietic development and disease.

overall_design: Transcription profiles of hematopoietic and leukemic cell types, assayed using unstranded RNA-seq, across 13 normal hematopoietic cell types and 3 acute myeloid leukemia cell types. The complete data set contains a total of 81 samples.


title: Osmosensory neurons modulate hypertonic stress resistance in C. elegans by controlling protein damage in non-neuronal cells

address: 5735 Hitchner Hall

institute: University of Maine

summary: Protein function is controlled by the cellular proteostasis network.  Proteostasis is energetically costly and those costs must be balanced with the energy needs of other physiological functions.  Hypertonic stress causes widespread protein damage in C. elegans.  Suppression and management of protein damage is essential for optimal survival under hypertonic conditions.  ASH chemosensory neurons allow C. elegans to detect and avoid strongly hypertonic environments.  We demonstrate that gene mutations that disrupt ASH mediated hypertonic avoidance behavior or genetic ablation of ASH neurons enhance survival during hypertonic stress.  Enhanced survival is not due to altered systemic volume homeostasis or organic osmolyte accumulation.  Instead, loss of ASH neuron function reduces protein damage in non-neuronal cells.  Improved proteostasis capacity is due in part to upregulation of genes that play important roles in managing protein damage.  We propose that inhibitory signaling from ASH neurons normally suppresses expression of genes required for non-neuronal cell proteostasis.  Because all cells have the capacity to sense and respond to stressors, inhibitory neuronal signaling may be important for minimizing activation of cellular stress resistance and proteostasis pathways during short duration and less extreme stressors or stressors that can be avoided by behavioral changes.  Neuronal regulation of systemic proteostasis allows the nervous system to monitor environmental variables and more effectively partition finite energy resources between different organismal processes.  Our studies add to a growing body of work demonstrating that intercellular communication between neuronal and non-neuronal cells plays a critical role in integrating cellular stress resistance with other organismal physiological demands and associated energy costs.

overall_design: mRNA expression profiling of synchronized L4 stage wild-type N2 Bristol and VC1262 osm-9(ok1677) C. elegans strains under control (51mM NaCl) and hypertonic stress (200mM NaCl).

first: Kevin

last: Strange


title: Modulation of Indoleamine 2, 3-dioxygenase 1 Expression by Activated Human T cells in Breast Cancer Cells is Controlled by DNA Promoter Methylation

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: Tumor infiltrating lymphocytes (TILs) play a critical role in modulating the immunoediting features in certain malignancies like triple negative breast cancer (TNBC). Nevertheless, much is still unknown concerning the specific responses of tumors when challenged by lymphocyte infiltration.  Based on this void, we conducted a immuno-phenotype comparison using mRNA sequencing between the TNBC cell line MDA-MB-231 and the luminal breast cancer cell line MCF7 after both were co-cultured with activated human T-cells. We found that, though the cytokine-induced immune signature of the two cell lines was similar, MDA-MD-231 cells were able to transcribe IDO1 at a significantly higher level than MCF7 cells. Though no differences occurred in upstream JAK/STAT1 signaling or IDO1 mRNA stability between the two cell lines, stimulation with IFNγ was able to differentially induce IDO protein expression and enzymatic activity in ER- cell lines compared to ER+ cell lines. Further experiments show that 5-aza-deoxycytidine treatment was able to reverse suppression of IDO1 expression in MCF7 cells, suggesting DNA methylation as a potential determinant in IDO1 induction. By analyzing TCGA breast cancer datasets, we discovered subtype-specific mRNA and promoter methylation differences in IDO1, with TNBC/basal subtypes exhibiting lower methylation/higher expression and ER+/luminal subtypes exhibiting higher methylation/lower expression. We confirmed this trend of IDO1 methylation by bisulfite pyrosequencing breast cancer cell lines and an independent cohort of primary breast tumors. Taken together, these findings suggest that IDO1 methylation regulates anti-immune responses in breast cancer subtypes and could be used as a predictive biomarker for IDO inhibitor-based immunotherapy.

overall_design: To determine the immunomodulatory effects of cytokines secreted by activated human T-cells on breast cancer cells, we performed RNAseq analysis in MCF7 and MDA-MB-231 cells, after co-culturing them with normal PBMCs activated with anti-CD3/CD28 antibodies in a contact-independent manner. MDA-MB-231 or MCF7 cells were co-cultured with PBMCs alone or the conditioned-media or a combination of both for 24 hrs, and then total RNA was harvest for RNA-seq analysis.


title: Small RNA sequencing of human K562 cells transduced with lentiviral vectors overexpressing RUNX1

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: miRNA-Sequencing of RUNX1 overexpressing K562 cells were compared to K562 cells transduced with an empty vector control to analyse the differential expression of miRNAs in hematopoiesis.

overall_design: K562 cells were transduced either with an empty lentiviral vector as control or a lentiviral vector overexpressing human RUNX1. The samples were biological triplicates and the results were validated by qRT-PCR using SYBR green.

first: Nicole

last: Kohrs

first: Jörn

last: Lausen


title: Unlinking a lncRNA from its associated cis element

first: Vikram

last: Paralkar

type:
Expression profiling by array
Other

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

overall_design: Refer to individual Series


title: Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach

city: Wuxi

first: sun

last: shengming

state: Jiangsu

address: No.9, Shanshui Rd East

institute: Freshwater Fisheries Research Center (FFRC) of Chinese Academy of Fishery Sciences (CAFS),


title: Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach [miRNA-Seq]

summary: MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs.

overall_design: In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from four M. nipponense tissues (gill, hepatopancreas, muscle and hemocytes). In total, 9,227,356 reads were obtained, 4,293,155 of which were related to 267 unique miRNAs, including 203 conserved and 64 prawn-specific miRNAs. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by M. nipponense miRNAs. In addition, 880 co-expressed and 39 specific (25 normoxia-specific and 14 hypoxia-specific) miRNAs of four combined tissues of prawns that may be involved in the response to hypoxia were confirmed using miRNA microarray analysis. Real-time quantitative PCR (qPCR) analysis of eight miRNAs in the normoxia and hypoxia groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of M. nipponense miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of hypoxia processes.

first: Shengming

last: Sun


title: microRNA sequencing in kidney glomeruli from diabetic and control mice

city: Duarte

first: Nancy

last: Chen

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

summary: identified cluster of microRNAs significantly increased in kidney glomeruli from diabetic mice compared to nondiabetic control mice

overall_design: RNAs from kidney glomeruli from control mice and STZ-injected diabetic mice were extracted.

first: Mitsuo

last: Kato

first: Zhuo

first: Rama

last: Natarajan


title: Selectivity of ORC binding sites in the human genome and the relation to replication timing, fragile sites, and recurrent deletions in cancers

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

summary: The origin recognition complex (ORC) binds specific sites in mammalian genomes, from which DNA replication is initiated.   Here, we address ORC binding selectivity in vivo by mapping ~52,000 ORC2 binding sites throughout the human genome.  The ORC binding profile is broader than that of sequence-specific transcription factors, suggesting that it does not bind to specific DNA sequences.  Instead, ORC binds to open (DNase I hypersensitive) regions in which histone H3 tails are hyperacetylated and also di-methylated at lysine 4. Our results suggest that ORC binding selectivity in vivo is determined by a novel mechanism involving non-specific interaction with accessible DNA and recognition of modified histones.  ORC sites are far more prevalent in early replicating regions, suggesting that replication timing is primarily due to ORC density and stochastic firing of origins. Large genomic regions lacking ORC2 binding sites are strongly associated with common fragile sites and recurrent deletions in cancers.

overall_design:
ChIP-seq for ORC2 in K562 cells
Please note that the raw data for the 'ORC2 ChIP-seq N-terminus antibody' sample is lost and thus, only its processed data is provided.

first: Benoit

last: Miotto

last: Struhl


title: The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect genomic features

summary: We report the generation and characterization of four novel marmoset monkey ES cell lines, derived from natural preimplantation embryos. Two cell lines were obtained from non-compacted morulae (DPZcjESC1 and 2), while the other two cell lines were derived from a compacted morula (DPZcjESC3) and an expanded blastocyst (DPZcjESC4), respectively. DPZcjESC1 and 2 showed trisomies for one and two chromosomes respectively, while DPZcjESC3 and 4 are euploid. We detected no obvious differences between morula- and blastocyst-derived cell lines. However, quantitative chromosome-wise transcriptome analyses precisely reflected the trisomies. We also show that the female ES cell lines exhibit different states of X-inactivation which is also impressively reflected by the abundance of the lncRNA X inactive-specific transcript (XIST).

overall_design: mRNA profiles of four different ES cell lines were generated by deep sequencing, in duplicate, using an Illumina HiSeq2000.

first: Katharina

last: Debowski

first: Charis

last: Drummer

first: Jana

last: Lentes

first: Ralf

last: Dressel

first: Thomas

last: Lingner

last: Salinas-Riester

first: Sigrid

last: Fuchs

first: Erika

last: Sasaki

first: Rüdiger

last: Behr


title: Tissue-Specific Transcriptomics and Proteomics of a Filarial Nematode and its Wolbachia Endosymbiont

city: Ipswich

first: Barton

last: Slatko

state: Massachusetts

address: 240 County Road

institute: New England Biolabs

summary: We sequenced total RNA from Dirofilaria immitis in order to generate the first tissue-specific gene expression profile of a filarial nematode and its Wolbachia endosymbiont.

overall_design: Examination of transcript levels in 7 different Dirofilaria immitis tissues, in duplicate, using Illumina GAIIx.

first: Ashley

last: Luck


title: MicroRNA-offset RNA regulates gene expression and cell proliferation

first: Gavin

last: Schnitzler


title: Spontaneous transformation of murine oviductal epithelial cells: A model system to investigate the onset of fallopian-derived tumors

first: Joanna

last: Burdette

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

summary: High grade serous ovarian cancer (HGSOC) can originate from fallopian tube epithelium (FTE) and ovarian surface epithelium (OSE). We report the application of unique spontaneous model that mimics cellular aging for understanding the origin and progression of HGSOC from oviductal epithelium. Oviductal epithelium is equivalent to human FTE. Serial passaging of the outbred mouse CD1 oviductal cells (MOE low) to MOE high produced transformed cells that lead to benign tumors. To understand the altered molecular signaling pathways in MOEhigh cells versus MOElow cells, we performed RNA sequencing. Total RNA was extracted from MOELOW (passages 8, 9, & 10) and MOEHIGH (passages 90, 103, & 113) cells. Each total RNA sample had ribosomal RNA removed using TruSeq Stranded Total RNA with Ribo-Zero (Illumina, San Diego, CA). Strand-specific libraries were constructed and quantitated using Qubit, and cDNAs verified by qPCR. qRT–PCR validation was performed using SYBR Green assays. Samples were barcoded and sequenced using Illumina HiSeq2500 sequencing. The reads were aligned to the Mus musculus genome (mm10) using TopHat, version and were used to determine the expression of known mmu10 gene annotations from the University of California-Santa Cruz website using Cuffdiff version. By merging the individual transcript from Cuffdiff into a single gene annotation file, we determined the differential expression analysis. By applying a false discovery rate (FDR)-adjusted p-value, where significance was set to p ≤ 0.05, statistically significant differential expression was determined. Furthermore, pathway analysis was performed on transcript lists from both cell lines using GeneCoDis to identify the KEGG and Panther pathways that are significantly different between MOELOW and MOEHIGH cell lines. We find that the splicesome, RNA transport, the cell cycle, and DNA replication were the most highly upregulated pathway whereas the repressed pathways included processing in the endoplasmic reticulum, focal adhesion, and the lysosome. RNA sequencing revealed that p53 in MOELOW and MOEHIGH cells was not mutated; however, MOEHIGH cells had a significant upregulation of a splice variant of p53. The splice variant behaved like wild-type on few targets and missense on some transcriptional targets by qRT-PCR. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. This model provides a framework to uncover a step-wise progression of tumor formation from an oviductal origin to be compared to human disease.

overall_design: Examination of altered molecular signaling pathways in 2 cell types.

first: Michael

last: Endsley


title: RNA-directed DNA Methylation is associated with gene expression via chromosomal Interactions

city: Omaha

first: M

middle: Jordan

last: Rowley

state: NE

address: 601 S Saddle Creek Rd

department: GCBA

institute: Univ of Nebraska Medical Center

summary: RNA-directed DNA methylation (RdDM) is a process, where small interfering RNA (siRNA) and long non-coding RNA (lncRNA) work together to repress transposons. In addition to controlling repetitive sequences, it contributes to the regulation of gene expression. Molecular mechanisms of transcription regulation by RdDM remain mostly unknown. We show that RdDM is involved in repression of long range chromosomal interactions. We propose a model where RdDM contributes to the regulation of gene expression by controlling looping between genes and their distant enhancers.

overall_design: Differential expression in ago4 compared to Col-0. Examination of Long Distance Chromosomal Interactions by Hi-C.

middle: J

first: Gudrun

last: Böhmdorfer

first: Jan

last: Kuciński

first: Andrzej

last: Wierzbicki


title: RNA-seq analysis of single cells of the oligodendrocyte lineage from nine distinct regions of the anterior-posterior and dorsal-ventral axis of the mouse juvenile central nervous system

status: Public on Jun 10 2016

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: 5069 transcriptomes of single oligodendrocyte cells from spinal cord, substantia nigra-ventral tegmental area, striatum, amygdala, hypothalamic nuclei, zona incerta, hippocampus, and somatosensory cortex of male and female mice between post-natal day 21 and 90. The study aimed at identifying diverse populations of oligodendrocytes, and revealing dynamics of oligodendrocyte maturation.

overall_design: 5069 individual cells were sampled from CNS regions of mice of various strains as detailed in the protocols section

first: Sueli

last: Marques

first: Amit

last: Zeisel

first: Gonçalo

last: Castelo-Branco


title: Sublethal concentrations of antibiotics cause shift to anaerobic metabolism in Listeria monocytogenes and induce phenotypes linked to antibiotic tolerance

city: Kgs. Lyngby

first: Gitte

middle: M.

last: Knudsen

state: Not applicable

address: Matematiktorvet, Bldg 301

department: Department of Systems Biology

institute: Technical University of Denmark

summary: The human pathogenic bacterium Listeria monocytogenes was exposed to antibiotics both during clinical treatment and as a saprophyte. As one of the keys to successful treatment is continued antibiotic sensitivity, the purpose of this study was to determine if exposure to sublethal antibiotic concentrations would affect the bacterial physiology and potentially induce tolerance to antibiotics. Transcriptomic analyses demonstrated that each of four antibiotics caused a compound-specific gene expression pattern related to (the) mode-of-action of the particular antibiotic. All four antibiotics caused the same changes in expression of several metabolic genes indicating a shift from aerobic to anaerobic metabolism driven by the induction of lmo1634 and the repression of alsA and lmo1992. This shift in metabolism could be a survival strategy in response to antibiotics and is further supported by the observation that a Δlmo1634 mutant was more sensitive to bactericidal antibiotics. The monocin locus encoding a cryptic prophage was induced by co-trimoxazole and repressed by ampicillin and gentamicin. This expression pattern correlated with the observed antibiotic-dependent biofilm formation, indicating a role of monocin in antibiotic-induced biofilm formation and a ΔlmaDCBA mutant confirmed this correlation. Thus, sublethal concentrations of antibiotics caused metabolic and physiological changes indicating that the organism is preparing to withstand lethal concentrations of antibiotics.

overall_design: Investigation of mRNA and sRNA expression profiles of L. monocytogenes EGD cells exposed to sublethal concentrations of four different antibiotics i.e. ampicillin, tetracycline, gentamicin and co-trimoxazole for 3h.

first: Lone

last: Gram


title: Protein SUMOylation is required for regulatory T cell expansion and function

status: Public on May 31 2016

first: Xiaopeng

last: Ma

state: Outside US and Canada

address: HaiDian district

department: Biology

institute: Tsinghua Univeristy

summary: Foxp3-expressing regulatory T (Treg) cells are essential regulators in the immune system; molecular mechanisms underlying Treg cell expansion and function are still not well understood. SUMOylation is an important post-translational modification characterized by covalent attachment of SUMO moieties to lysine within proteins. UBC9 is the only E2 conjugation enzyme involved in this process and loss of UBC9 completely impairs the SUMOylation pathway. Here we report that selective deletion of Ubc9 within the Treg cell lineage resulted in fatal early-onset autoimmunity as the Foxp3 mutant mice. Ubc9-deficient Treg cells exhibited severe defects in TCR-driven homeostatic proliferation, accompanied by impaired activation and compromised suppressor function. Importantly, TCR-enhanced SUMOylation of IRF4, a critical regulator of Treg cell function downstream of TCR signals, regulates its stability in Treg cells. Our data thus have demonstrated an essential role of SUMOylation in the expansion and function of Treg cells.

overall_design: RNA-seq library was generated using mRNA of CD4+ YFP+ Treg cells sorted from lymph nodes and spleen of Foxp3cre/wtUbc9fl/wt or Foxp3cre/wtUbc9fl/fl mice, each sample contained pooled Treg cells from 5~10 mice.

first: Xiao

last: Ding


title: Ten day time course of effect of influenza vaccination on gene expression profiles of lymph node cells (unselected cells and B cells) in mice

city: Rochester

first: Martin

last: Zand

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary: Study was to explore the immune and transcriptomic response to seasonal influenza vaccination (TIV) in mice. For more information see Immport study SDY583.

overall_design: 22 total samples, 6 mice per sample: 11 unselected cell samples (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days post-vaccine boost) and 11 B cell samples  (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days post-vaccine boost)


title: Ten day time course of effect of influenza vaccination on gene expression profiles of spleen cells (unselected cells and B cells) in mice


title: Immune and transcriptomic response to seasonal influenza vaccination (TIV) in mice


title: Genome-wide maps of m6dA bases in drosophila ovary genomic DNA

city: beijing

first: liu

last: di

address: No.18, Shuangqing road, Haidian district

institute: rcees, cas

summary: We report the m6dA modification on the Drosophila genome. We collected ovary genomic DNA from 2-day wild-type and DMAD mutant files and performed DNA-immunoprecipitation(DNA-IP)experiments using anti-m6dA antibody. The generated DNA library was subjected to a high-throughput deep sequencing analysis. In this assay, the IgG-immunoprecipited DNA from the same amount of wild-type ovaries was used as the control, and the high-throughput sequencing resulted in a range of approximately 3 to 4.6 million reads. In sum, we identified 50 and 195 peaks from wild-type and DMAD mutant samples. Importantly, m6dA is mainly utilized to modify the transposon sequence on the chromosomes.

overall_design: Examination of m6dA modifications in Genomic DNA of WT and DMAD mutant ovary.

first: Hailin

last: Wang

first: Dahua

last: Chen

first: Di

last: Liu

first: Xiaoling

first: Ying

last: Cheng

first: Guoqiang

last: Zhang

first: Hua

last: Huang


title: Ten day time course of effect of influenza vaccination on gene expression profiles of PBMC and circulating B cells in mice

overall_design: 22 total samples, 6 mice per sample: 11 PBMC samples (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days post-vaccine boost) and 11 B cell samples  (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days post-vaccine boost)


title: Prep1 and Meis1 competition for Pbx1 binding regulates protein stability and tumorigenesis [hP]

city: Milan

first: Francesco

last: Blasi

address: Via Adamello 16

institute: IFOM

summary: Prep1 is a tumor-suppressor, whereas Meis1 is an oncogene. We show that to perform these activities in MEFs both proteins competitively hetero-dimerize with Pbx1. Meis1 alone transforms Prep1-deficient fibroblasts while Prep1 overexpression inhibits Meis1 tumorigenicity. Pbx1 can therefore alternatively act as oncogene or tumor-suppressor. Prep1 post-translationally controls the level of Meis1 decreasing its stability by sequestering Pbx1. The different levels of Meis1 and the presence of Prep1 are followed at the transcriptional level by the induction of specific transcriptional signatures. The decrease of Meis1 prevents Meis1 interaction with Ddx3x and Ddx5, which are essential for Meis1 tumorigenesis, and modifies the growth promoting DNA binding landscape of Meis1 to the growth controlling landscape of Prep1. Hence the key feature of Prep1 tumor inhibiting activity is the control of Meis1 stability.

overall_design: Examination of Prep1 and Meis1 in two cell types

first: Leila

last: Dardaei


title: Transcriptional impact of removing H2A.Z

city: San Francisco

first: Yulia

last: Mostovoy

state: CA

address: 555 Mission Bay Blvd South

institute: University of California, San Francisco

summary: We profiled the strand-specific transcriptome of Saccharomyces cerevisiae lacking SWR1 and HTZ1 and compared it to the wild-type transcriptome

overall_design: 3'-end RNA-seq was performed on RNA from Saccharomyces cerevisiae wild-type and swr1 htz1 strains (two biological replicates each)

first: Tiffany

middle: Y

last: Hsu

first: Rachel

middle: B

last: Brem


title: Characterising the transcriptional profile of murine 3T3-L1 adipocytes with altered expression of IRF3.

first: Evan

last: Rosen

address: 3 Blackfan Cir

department: Endocrinology

institute: Beth Israel Deconess Medical Center

summary: The chronic inflammatory state that accompanies obesity is a major contributor to insulin resistance and other metabolic dysfunction features. Despite recent advances in our understanding of the cellular and secreted factors that promote the inflammatory milieu of obesity, we have much less insight into the transcriptional pathways that drive these processes. While most attention has focused on the canonical inflammatory transcription factor NF-KB, other potentially important factors exist, including members of the interferon regultory factor (IRF) family. Here we show that IRF3 expression is upregulated in the adipocytes of obese mice and humans. TLR3/TLR4 activation induces insulin resistance in adipocytes, which can be prevented by IRF3 knockdown. Furthermore, Irf3KO mice display improved insulin sensitivity, associated with reduced intra-adipose and systemic inflammation in the high-fat fed state, enhanced browning of subcutaneous fat, and increased adipose expression of Glut4. Taken together, our data indicates that IRF3 is a major transcriptional regulator of adipose inflammation to maintain systemic glucose and energy homeostasis.

overall_design: Transcriptional profiling of murine 3T3-L1 adipocytes with altered expression of IRF3. Overexpression or knockdown of IRF3 was achieved by lentivirus transduction for 6 days. 3T3-L1 adipocytes with IRF3 knockdown were further treated in the absence or presence of LPS for 6 days. Samples consist of triplicate replica with appropriate control.

first: Manju

last: Kumari

first: Anna

last: Lyubetskaya

first: Danielle

last: Tenen

middle: D


title: Comparative transcriptomics of Clostridium thermocellum wild type (Δhpt) and Type I glutamine synthetase (Clo1313_2031) deletion strains using RNA-seq

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

summary: RNA-seq analysis revealed that genes involved in urea uptake and metabolism were significantly upregulated in the Clo1313_2031 deletion strain, suggesting that deletion of Clo1313_2031 mimics nitrogen starvation in C. thermocellum.  Additionally, genes encoding the RNF-complex were also more highly expressed and in turn may have a potential role in increasing ethanol production.

overall_design: Samples for RNA-seq were taken from mid-exponential phase (OD ~ 0.33) batch cultures grown in MTC on 4.5 g/l cellobiose

first: Thomas

last: Rydzak

first: Adam

last: Guss

middle: M

first: Steven

last: Brown

first: David

last: Garcia


title: Genome-wide distribution of UHRF2 and ZNF618 in 293T cells.

city: Hangzhou

first: Lin-Yu

last: Lu

state: Zhejiang

address: 268 Kaixuan Road, North Central Building, Room 536

institute: Zhejiang University

summary: We have identified ZNF618 as a novel binding partner of UHRF2. We have found that UHRF2 and ZNF618 co-localize at many genomic loci.

overall_design: Examination of genome-wide distribution of SFB-tagged UHRF2 and ZNF618 in 293T cells using ChIP-seq.

first: Xiaochun

last: Yu


title: Arabidopsis AGO3 predominantly recruits 24-nucleotide small RNAs to regulate epigenetic silencing

city: Beijing

first: Xiuying

last: Liu

address: Yard 28, Science Park Road, Changping District

institute: Changping Laboratory

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

overall_design: Refer to individual Series