title: Identification of Rbfox1 binding in the cytoplasm of neurons by iCLIP

summary: Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes induced by knockdown, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that in nascent RNA Rbfox1 bound predominantly to introns, while cytoplasmic Rbox1 bound to 3' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and overlapped significantly with miRNA binding sites. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. In this data set, we included the data from iCLIP-seq experiments.

overall_design: We performed iCLIP procedures to identify Rbfox1 binding in the cytoplasm. Cultured mouse forebrain neurons were irradiated with UV and a cytoplasmic fraction was purified for immunoprecipitation. An anti-Rbfox1 antibody was used to immunoprecipitate Rbfox1 target RNAs and an anti-Flag antibody was used as control. Two samples were analyzed.

first: Andrey

last: Damianov

first: Douglas


title: Phosphorylation of an HP1-like protein regulates RNA-bridged heterochromatin body assembly for DNA elimination

status: Public on Dec 10 2015

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Casein kinase II promotes target silencing by miRISC through direct phosphorylation of the DEAD-box RNA helicase CGH-1

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

country: USA

institute: Johns Hopkins University

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study we show that global levels of mature miRNAs are unaffected in C. elegans after knockdown of either subunit of CK2 (encoded by kin-3 and kin-10) by RNAi.

overall_design: Small RNAs were quantified from wild-type animals at L4 stage fed either vector (L4440), kin-3, kin-10, or alg-1 RNAi. Mature miRNA counts were quantified by summing the total number of reads mapping to each miRNA and normalized to the total number of mapped reads per sequencing library.

middle: A

first: Amelia

middle: F

last: Alessi

first: Vishal

last: Khivansara

first: Ting

last: Han

first: James

middle: J

last: Moresco

first: Patricia

middle: G

last: Tu

first: Eric

last: Montoye

first: John

middle: R

last: Yates

first: Xantha

last: Karp

middle: K

last: Kim


title: RNA-Seq of DRG and dorsal cord after nerve injury

city: San Francisco

first: Zhonghui

last: Guan

state: CA

department: Anesthesia

institute: UCSF

type: Expression profiling by high throughput sequencing

summary: Genes are up and down regualted in DRG and spinal dorsal cord after peripheral nerve injury

overall_design: WT male adult with sciatic and femoral nerve transection 7 days, RNA was purified from ipilateral or contralateral L4-L6 DRGs or lumbar spinal dorsal cords


title: Comprehensive identification of sexual dimorphism-associated differentially expressed genes in two-factorial designed RNA-seq data on Japanese Quail (Coturnix coturnix japonica)

city: Seoul

first: Minseok

last: Seo

address: Kwan-ak ro 1

department: Interdisciplinary program of bioinformatics

country: South Korea

institute: Seoul National University

summary: Japanese quail (Coturnix coturnix japonica) reach sexual maturity early, breed rapidly and successfully, and cost less and require less space than other birds raised for their meat and eggs. Given the value of this species for commercial production and experimental use as well as recent increasing demand, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation in the species. Identification of sex-related genes can help target chromosomal regions for molecular sexing purposes. This study employed Trinity and edgeR for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeds of Japanese quail (wild, miniature, and jumbo). The initial goal was to identify genes related to sexual dimorphism, as well as potential novel candidate genes for molecular sexing. Analysis and interpretation of differentially expressed genes shared between female and male tissue contrast groups provided insight into sex-related differences. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (e.g. NIPBL, UBAP2), and other genes found differentially expressed in this study and not previously associated with sex-related differences may be considered potential candidates for molecular sexing (e.g. TERA, MYP0, PPR17, CASQ2). Additionally, other genes likely associated with neuronal and brain development (e.g. CHKA, NYAP), as well as body development and size differentiation (e.g. ANKRD26, GRP87) in quail were identified. Expression of homeobox protein regulating genes in the sex-related contrast group revealed two genes (HXC4, ISL1) that may regulate sex-specific anatomical development. Results of these analyses expand the currently limited pool of knowledge on the genetic features of the quail breed and could allow for more effective molecular sexing as well as selective breeding for traits important in commercial production.

first: Hak-Kyo

last: Lee

first: Ki-Duk

last: Song


title: The histone chaperone CAF-1 safeguards somatic cell identity during transcription factor-induced reprogramming

city: Boston

first: Peter

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

first: Konrad

last: Hochedlinger

first: Sihem

last: Cheloufi


title: Chromatin immunoprecipitation sequencing of heterochromatin-associated proteins in Tetrahymena

first: Kazufumi

last: Mochizuki

summary: In the ciliated protozoan Tetrahymena, de novo heterochromatin body formation is accompanied by programmed DNA elimination. Here, we show that the novel heterochromatin body component Jub1p promotes heterochromatin body formation and dephosphorylation of the Heterochromatin Protein 1 (HP1)-like protein Pdd1p. Through the identification and mutagenesis of the phosphorylated residues of Pdd1p, we demonstrate that Pdd1p dephosphorylation promotes the electrostatic interaction between Pdd1p and RNA in vitro and heterochromatin body formation in vivo. We therefore suggest that heterochromatin bodies are assembled by the Pdd1p-RNA interaction. Jub1p and Pdd1p dephosphorylation are required for heterochromatin body formation and DNA elimination but not for local heterochromatin assembly, indicating that heterochromatin body of itself plays an essential role in DNA elimination.

overall_design: New macronuclei (MACs) of exconjugants were isolated from wild-type different mutant cells at 12 hpm, shared chromatin was immunoprecipitated and precipitated DNA was analyzed by high-throughput sequencing.

first: Kensuke

last: Kataoka


title: Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus

city: Philadelphia

first: Daniel

middle: Francis

last: Simola

state: PA

address: 1041 BRB II/III

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: Comparison of transcriptome and histone acetylation in Camponotus floridanus minor scout brains following 45 day treatment with small molecule pharmacologicals. The goal of this study was to characterize the molecular changes in gene expression and histone modification caused by ad lib feeding small molecule HAT and HDAC inhibitors

overall_design: Treated ants: 21 individual single brain samples, generating by linear amplification of polyA+ cDNA prepared from 15% of single brains; ChIP-seq for H3K9ac and H3K27ac was also prepared from 9 of these brains; ChIP-seq for H2O and C646 treated larvae also included; RNA-seq for technical replicate subsamples of a single brain also included

first: Riley

last: Graham

first: Cristina

middle: M

last: Brady

first: Brittany

middle: L

last: Enzmann

first: Roberto

last: Bonasio

first: Claude

last: Desplan

first: Anandasankar

last: Ray

first: Juergen

last: Liebig

first: Danny

last: Reinberg

first: Shelley

last: Berger


title: The contribution of Alu exons to the human proteome

city: Los Angeles

first: Jinkai

last: Wang

address: 650 Charles E. Young Drive South, CHS 33-228

institute: University of California, Los Angeles

summary: Alu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of Alu exons to the human proteome remains unclear and controversial. The prevailing view is that exons derived from young repetitive elements, such as Alu elements, are restricted to regulatory functions and have not had adequate evolutionary time to be incorporated into stable, functional proteins. We adopt a proteotranscriptomics approach to systematically assess the contribution of Alu exons to the human proteome. Using RNA sequencing, ribosome profiling and proteomics data from human tissues and cell lines, we provide evidence for the translational activities of Alu exons and the presence of Alu exon derived peptides in human proteins. These Alu exon peptides represent species-specific protein differences between primates and other mammals, and in certain instances between humans and closely related primates. In the case of the RNA editing enzyme ADARB1, which contains an Alu exon peptide in its catalytic domain, RNA sequencing analyses of A-to-I editing demonstrate that both the Alu exon skipping and inclusion isoforms encode active enzymes. The Alu exon derived peptide may fine tune the overall editing activity and, in limited cases, the site selectivity of ADARB1 protein products. Our data indicate that Alu elements have contributed to the acquisition of novel protein sequences during primate and human evolution.

overall_design: Comparing the A-I RNA editing levels of HEK293 cells transfected with empty vector (CV) control, Alu exon inclusion (long) isoform of ADARB1, and Alu exon skipping (short) isoform of ADARB1. Each group has 3 replicates.

first: Lan

last: Lin

first: Peng

last: Jiang

first: Juw

middle: W

first: Zhi-xiang

last: Lu

first: Maggie

last: Lam

first: Peipei

last: Ping

first: Yi

last: Xing


title: The microRNA expression profiles changes associated with constant heat stress in porcine skeletal muscle as measured by deep sequencing

status: Public on Dec 09 2015

city: Beijing

first: Yue

last: Hao

address: No.2 Yuanmingyuan West Road

country: China

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

summary: To characterize the changes of miRNAs in skeletal muscle responding to heat stress, the miRNA expression profiles of longissimus dorsi muscles of pigs raised under constant heat stress (30°C, n=8) or control temperature (22 C, n=8) for 21 days were analyzed by Illumina deep sequencing. 58 differentially expressed miRNAs were identified with 30 down-regulated and 28 up-regulated and 63 differentially expressed target genes were predicted by miRNA-mRNA joint analysis. GO and KEGG analyses showed that the genes regulated by differentially expressed miRNAs were enriched in glucose metabolism, cytoskeletal structure and function, and stress response. Real-time PCR showed that the mRNA levels of PDK4, HSP90 and DES were significantly increased whereas those of SCD and LDH-A significantly decreased by heat exposure. The protein levels of CALM, DES and HIF1α were also significantly increased by constant heat. These results demonstrated that the change of miRNA expression in porcine longissimus dorsi muscle underlie the changes of muscle structure and metabolism in porcine skeletal muscle affected by constant heat stress.

overall_design: Characterize and compare expression profiling of the miRNA transcriptome in 2 groups of porcine skeletal muscle.

first: Xianhong

last: Gu


title: Dual RNA-seq of diverse human,  mouse and pig cell-types infected with various Salmonella strains

status: Public on Dec 11 2015

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

first: Alexander

last: Westermann

middle: U

first: Fabian

last: Amman

first: Lars

middle: E

last: Barquist

first: Leon

middle: N

last: Schulte

first: Yanjie

last: Chao

first: Lydia

last: Müller

first: Richard

last: Reinhardt

first: Peter

last: Stadler

first: Jörg

last: Vogel


title: Serum-based culture conditions provoke gene expression variability in mouse embryonic stem cells as revealed by single cell analysis

city: boston

first: Luca

last: Pinello

address: 450 brookline avenue

institute: Dana-Farber Cancer Institute

summary: Variation in gene expression is an important feature of mouse embryonic stem cells (ESCs). However, the mechanisms responsible for global gene expression variation in ESCs are not fully understood. We performed single cell mRNA-seq analysis of mouse ESCs and uncovered significant heterogeneity in ESCs cultured in serum. Using novel computational approaches we define highly variable gene clusters; and reveal their distinct epigenetic characteristics. We show that bivalent genes are prone to expression variation. At the same time, we identify an ESC priming pathway that initiates the exit from the naïve ESC state. Finally, we provide evidence that a large proportion of intracellular network variability is due to the extracellular culture environment. Serum free culture reduces cellular heterogeneity and transcriptome variation in ESCs.

overall_design: Single cell mRNA-seq analysis of ES cells cultured with serum

first: Guoji

last: Guo


title: Translational profiling identifies a cascade of damage initiated in motor neurons and spreading to glia in mutant SOD1-mediated ALS

city: La Jolla

first: Don

middle: W.

last: Cleveland

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

summary: Ubiquitous expression of ALS-causing mutations in superoxide dismutase 1 (SOD1) provoke non-cell autonomous paralytic disease. By combining ribosome affinity purification and high-throughput sequencing, a cascade of mutant SOD1-dependent, cell type-specific changes are now identified. Initial mutant-dependent damage is restricted to motor neurons and includes synapse and metabolic abnormalities, endoplasmic reticulum (ER) stress, and selective activation of the PERK arm of the unfolded protein response. PERK activation correlates with what we identify to be a naturally low level of ER chaperones in motor neurons. Early changes in astrocytes are to genes involved in inflammation and metabolism and that are targets of the PPAR and LXR transcription factors. Dysregulation of myelination and lipid signaling pathways and activation of ETS transcription factors occur in oligodendrocytes only after disease initiation. Thus, pathogenesis involves a temporal cascade of cell type selective damage initiating in motor neurons, with subsequent damage within glia driving disease propagation.

overall_design: Cell type-specific mRNA was purified by ribosome affinity purification from the spinal cord of bacTRAP reporter mice that label selective cell types by EGFP-tagged ribosome RPL10A. Sequencing libraries were prepared from 3-6 biological replicates for each genotype to determine the mutant induced gene expression changes in specific cell types.

first: Shuying

last: Sun

first: Ying


title: A XEN-like state bridges somatic cells to pluripotency during chemical reprogramming

first: Xu

last: Zhang

address: No.5 Yiheyuan Road

institute: Peking University

summary: Pluripotent stem cells can be generated from somatic cells by using pure chemicals.However, the cell fate dynamics and molecular events that occur during the chemical reprogramming process remain unclear. In this study, we found that the chemical reprogramming process requires the early formation of extra-embryonic endoderm (XEN)-like cells and a late transition from XEN-like cells to CiPSCs, a new route that differs from the pathway of transcription factor-induced reprogramming. Moreover, by more precisely manipulating the cell fate transition in a step-wise manner through the XEN-like state, we identified small-molecule boosters and established a robust chemical reprogramming system, with a yield up to 1,000-fold greater than that of the previously reported protocol. These findings demonstrate that chemical reprogramming is a unique and promising approach in the future manipulation of cell fates.

overall_design: We analyzed the gene expression profiles of intermediate cells obtained from diferent timepoints during chemical reprogramming process,using RNA-Sequencing. Embryo-derived XEN cells (eXENs), chemically-derived eXEN cell lines (CeXENs), embryonic stem cells (ESCs) and chemically-induced pluripotent stem cells (CiPSCs) are used as controls.

first: Yang

last: Zhao

first: Ting

first: Jingyang

last: Guan

first: Yao

last: Fu

first: Junqing

last: Ye

first: Hongkui

last: Deng


title: Somatosensory Neuron Types Identified by High-Coverage Single-Cell RNA-Sequencing and Functional Heterogeneity

city: Shanghai

address: 320 Yue Yang Road

department: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

institute: Institute of neuroscience

summary: Sensory neurons are distinguished by distinct signaling networks and receptive characteristics. Thus, sensory neuron types can be defined by linking transcriptome-based neuron typing with the sensory phenotypes. Here we classify somatosensory neurons of the mouse dorsal root ganglion (DRG) by high-coverage single-cell RNA-sequencing (10 950 ± 1 218 genes per neuron) and neuron size-based hierarchical clustering. Moreover, single DRG neurons responding to cutaneous stimuli are recorded using an in vivo whole-cell patch clamp technique and classified by neuron-type genetic markers. Small diameter DRG neurons are classified into one type of low-threshold mechanoreceptor and five types of mechanoheat nociceptors (MHNs). Each of the MHN types is further categorized into two subtypes. Large DRG neurons are categorized into four types, including neurexophilin 1-expressing MHNs and mechanical nociceptors (MNs) expressing BAI1-associated protein 2-like 1 (Baiap2l1). Mechanoreceptors expressing trafficking protein particle complex 3-like and Baiap2l1-marked MNs are subdivided into two subtypes each. These results provide a new system for cataloging somatosensory neurons and their transcriptome databases.

overall_design:
RNA-seq of mRNA levels in 197 individual DRG neurons
We performed RNA-seq on total 203  individual DRG neurons. Six of them were not qualified and thus, were excluded for further analysis.  To evaluate the quality of RNA-seq, we randomly devided No.72 neurons into two parts and performed RNA-seq seperately.  Thus, we had 204 individual samples from 203 individual DRG and 198 individual qualified samples from 197 individual DRG.  To evaluate the homogeneity of RNA-seq data from different mice at the same age just as used,  we performed RNA-seq on 5 single DRG from different mice. Here, these data from DRG were also considered as experimental control.
The 'DRG_neurons_RNA_Seq.txt' contains processed data for 204 samples and 'DRG_RNA_Seq.txt' for 5 samples.

first: Changlin

last: Li


title: AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [RNA-Seq]

first: Ben

middle: S

last: Wittner

address: 185 Cambridge Street

department: Cancer Center

institute: Massachusetts General Hospital

summary: Small-molecule inhibitors of AKT signaling are being in evaluated in patients with various cancer types, but have so far proven therapeutically disappointing for reasons that remain unclear. Here, we treat cancer cells with sub-therapeutic doses of Akti-1/2, an allosteric small molecule AKT inhibitor, in order to experimentally model pharmacologic inhibition of AKT signaling in vitro. We then apply a combined RNA, protein, and metabolite profiling approach to develop an integrated, multi-scale, molecular snapshot of this “AKTlow” cancer cell state. We find that AKT-inhibited cancer cells suppress thousands of mRNA transcripts, and proteins related to the cell cycle, ribosome, and protein translation. Surprisingly, however, these AKT-inhibited cells simultaneously up-regulate a host of other proteins and metabolites post-transcriptionally, reflecting activation of their endo-vesiculo-membrane system, secretion of inflammatory proteins, and elaboration of extracellular microvesicles. Importantly, these microvesicles enable rapidly proliferating cancer cells of various types to better withstand different stress conditions, including serum deprivation, hypoxia, or cytotoxic chemotherapy in vitro and xenografting in vivo. These findings suggest a model whereby cancer cells experiencing a partial inhibition of AKT signaling may actually promote the survival of neighbors through non-cell autonomous communication.

overall_design: Profiles of MCF7 and HCT116 Akti-1/2 treated cells and MCF7 and HCT116 vehicle (i.e. DMSO) treated cells were generated, each in duplicate, using RNA-Seq.

first: Xavier

last: Sole

last: Salony

first: Cleidson

middle: P

last: Alves

first: Ipsita

last: Dey-Guha

first: Laila

last: Ritsma

first: Myriam

last: Boukhali

first: Ju

middle: H

last: Lee

first: Joeeta

last: Chowdhury

first: Kenneth

last: Ross

first: Wilhelm

last: Haas

first: Shobha

last: Vasudevan

first: Sridhar

last: Ramaswamy


title: A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

city: Ghent

first: Sandra

last: Steyaert

address: Coupure Links 653

country: Belgium

institute: Ghent University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is tightly linked with gene expression regulation and has long been regarded a stable epigenetic mark in postmitotic cells. However, it recently became clear that postnatal brains appear to show stimulus-induced de novo CpG methylation or active demethylation related to neuronal plasticity. Due to striking homologies between the brains of birds and mammals, songbirds, especially the zebra finch, propose an attractive model for investigating the genome-wide DNA methylation profile and DNA methylation reconfiguration during brain development. In order to obtain a first genome-wide compendium of genes under putative DNA methylation control, we performed MethyCap-seq experiments on two recently cultured zebra finch cell lines, G266 and ZFTMA, also upon AZA-induced demethylation. First, the MethylCap-seq methodology in zebra finch was validated by comparison with RRBS generated data. Subsequently, quantitative analysis identified 30,700 significantly demethylated loci upon AZA-treatment. Further examination revealed enrichment of these regions in exons and promoters. To assess the influence of methylation on gene expression, RNA-seq experiments were performed. Comparison of the RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed obvious enrichment for neurological networks. A subset of genes was validated using qPCR and CpG pyrosequencing. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control.

overall_design: MethylCap-seq and RNA-seq experiments were performed on DMSO- and AZA-treated zebra finch cell lines, i.e. G266 and ZFTMA. As a quality control, also an untreated ZFTMA sample was analyzed with MethylCap-seq and RRBS.

first: Jolien

last: Diddens

first: Jeroen

last: Galle

first: Ellen

last: De Meester

first: Sarah

last: De Keulenaer

first: Antje

last: Bakker

first: Nina

last: Sohnius-Wilhelmi

first: Carolina

last: Frankl-Vilches

first: Annemie

last: Van der Linden

first: Wim

last: Van Criekinge

last: Vanden Berghe

first: Tim

last: De Meyer


title: DGCR8 acts as a novel adaptor for the exosome complex to degrade double-stranded structured RNAs

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

institute: MDC-Berlin

summary: The Microprocessor complex (DGCR8/Drosha) is required for microRNA (miRNA) biogenesis but also binds and regulates the stability of several types of cellular RNAs. Of particular interest, DGCR8 controls the stability of mature small nucleolar RNA (snoRNA) transcripts independently of Drosha, suggesting the existence of alternative DGCR8 complex/es with other nucleases to process a variety of cellular RNAs. Here, we found that DGCR8 co-purifies with subunits of the nuclear exosome, preferentially associating with its hRRP6-containing nucleolar form. Importantly, we demonstrate that DGCR8 is essential for the recruitment of the exosome to snoRNAs and to human telomerase RNA. In addition, we show that the DGCR8/exosome complex controls the stability of the human telomerase RNA component (hTR/TERC). Altogether, these data suggests that DGCR8 acts as a novel adaptor to recruit the exosome complex to structured RNAs and induce their degradation.

overall_design:
[i] Examination of the RNA binding profile of hRRP6 (also known as EXOSC10) via iCLIP.
[ii] HeLa cells were transiently depleted of hRRP6 or DGCR8 using siRNAs. For a control an non-targetting (siNon) siRNA was used. Three biological replicates of each samples were sent for RNA sequencing.

first: Sara

last: Macías

first: Ross

middle: A

last: Cordiner

first: Philippe

last: Gautier

first: Javier

middle: F

last: Cáceres


title: Epigenetic Program and Transcription Factor Circuitry of Dendritic Cell Development

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary: Dendritic cells (DC) are professional antigen presenting cells that develop from hematopoietic stem cells through successive steps of lineage commitment and differentiation. Multipotent progenitors (MPP) are committed to DC restricted common DC progenitors (CDP), which differentiate into specific DC subsets, classical DC (cDC) and plasmacytoid DC (pDC). To determine epigenetic states and regulatory circuitries during DC differentiation, we measured consecutive changes of genome-wide gene expression, histone modification and transcription factor occupancy during the sequel MPP-CDP-cDC/pDC. Specific histone marks in CDP reveal a DC-primed epigenetic signature, which is maintained and reinforced during DC differentiation. Epigenetic marks and transcription factor PU.1 occupancy increasingly coincide upon DC differentiation. By integrating PU.1 occupancy and gene expression we devised a transcription factor regulatory circuitry for DC commitment and subset specification. The circuitry provides the transcription factor hierarchy that drives the sequel MPP-CDP-cDC/pDC, including Irf4, Irf8, Tcf4, Spib and Stat factors. The circuitry also includes feedback loops inferred for individual or multiple factors, which stabilize distinct stages of DC development and DC subsets. In summary, here we describe the basic regulatory circuitry of transcription factors that drives DC development.

overall_design:
H3K4me3, H3K9me3 and H3K27me3 occupancy in MPP, CDP, cDC and pDC.
The ChIP-seq profiles are visualized by a customized UCSC genome browser track hub (http://www.molcell.rwth-aachen.de/dc/).

first: Qiong

last: Lin

first: Heike

last: Chauvistré

first: Ivan

middle: G

last: Costa

first: Eduardo

last: Gusmão

first: Saskia

last: Mitzka

first: Sonja

last: Haenzelmann

first: Bianka

last: Baying

first: Theresa

last: Klisch

first: Richard

last: Moriggl

first: Benoit

last: Hennuy

first: Hubert

last: Smeets

first: Kurt

last: Hoffmann

first: Vladimir

last: Benes

first: Kristin

last: Seré


title: TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer

city: Chicago

first: Christopher

last: Mariani

state: IL

institute: University of Chicago

summary: 5-hydroxymethylcytosine (5-mC) and gene expression profiling of T84 cell differentiation; 5-hmC profiling of colon cancer colonocyte fractions

overall_design: T84 cell differentiation was monitored as cells formed confluent monolayers in tissue culture

last: Chapman

middle: J

first: Feng

last: Wu

first: Alice

last: Chuang

first: Jozef

last: Madzo

first: Marc

middle: B

last: Bissonette

first: John

last: Kwon

first: Lucy

last: Godley


title: Genome wide mapping of H3K27me3 in differentiated mouse podocytes

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

department: Medicine

country: Canada

institute: St. Michael's Hospital

summary: We explored H3K27me3 binding sites in the genome of differentiated, conditionally immortalized mouse podocytes.  Cells were allowed to differentiate for 14 days, following thermoshifting, before treatment with either vehicle (DMSO) or the S-adenosylhomocysteine hydrolase inhibitor 3-deazaneplanocin A (DZNep, 5µM for 48 hours) which degrades the histone methyltransferase, EZH2 ordinarily responsible for H3K27 trimethylation (H3K27me3).  DNA was immunopreciptated with an H3K27me3-specific antibody.

overall_design: Studying H3K27me3 modification in Mouse Podocyte


title: AKT Inhibition Promotes Non-autonomous Cancer Cell Survival

first: Ben

last: Wittner

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

overall_design: Refer to individual Series


title: AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [GRO-Seq]

overall_design: Profiles of MCF7 and HCT116 Akti-1/2 treated cells and MCF7 and HCT116 vehicle (i.e. DMSO) treated cells were generated, each in duplicate, using GRO-Seq.

first: Xavier

last: Sole

last: Salony

first: Cleidson

last: Alves

first: Ipsita

last: Dey-Guha

first: Laila

last: Ritsma

first: Myriam

last: Boukhali

first: Ju

last: Lee

first: Joeeta

last: Chowdhury

first: Kenneth

last: Ross

first: Wilhelm

last: Haas

first: Shobha

last: Vasudevan

first: Sridhar

last: Ramaswamy


title: AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [Microvesicles small RNA-Seq]

overall_design: Microvesicle content profiles of MCF7 and HCT116 Akti-1/2 treated cells and MCF7 and HCT116 vehicle (i.e. DMSO) treated cells were generated, using technical replicates, using small RNA-Seq.


title: AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [Cellular small RNA-Seq]

overall_design: Profiles of MCF7 and HCT116 Akti-1/2 treated cells and MCF7 and HCT116 vehicle (i.e. DMSO) treated cells were generated, each in duplicate, using small RNA-Seq.


title: Transcriptomics and physiological analyses reveal coordinated alteration of metabolic pathways in Jatropha curcas drought tolerance

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

institute: Fraunhofer IGB

summary: Jatropha curcas, a multipurpose plant attracting much attention due to its high oil content and quality for biofuel, is recognized as a drought tolerant species. However, this drought tolerance is still poorly characterized. This study aims to contribute to uncover the molecular background of this tolerance, with the use of a combined approach of transcriptional profiling and morphophysiological characterization along a period of water withholding (49 days) followed by rewatering (7 days). Morphophysiological measurements evidenced that J. curcas plants presented different adaptations to withstand moderate and severe drought. Thus, RNA-Seq was performed for samples collected at moderate and severe stress followed by rewatering, for both roots and leaves. Transcriptomic analysis revealed organ-specific adaptations across all investigated conditions, except under severe stress, in which the drought response of J. curcas surpassed organ-specificity by dramatic transcriptomic reorganization. These changes in gene expression were clearly evidenced by the down-regulation of genes involved in growth and water uptake, and up-regulation of osmotic adjustments and cellular homeostasis related genes. However, organ-specific variations were also detected, such as strong up-regulation of chlorophyll and trehalose metabolism in leaves. Functional validation further corroborated the differentially expression of genes coding for enzymes involved in chlorophyll metabolism, which correlates with the metabolite content of this pathway.

overall_design: Two Jatropha curcas accessions were submitted to moderate and severe drought stress (water withholding) followed by recovery (3d re-watering), transcriptomic profiles were assessed by RNA-Seq.

first: Helena

last: Sapeta

first: Tiago

last: Lourenço

first: Stefan

last: Lorenz

first: Philipp

last: Kirstahler

first: Pedro

last: Barros

first: Joaquim

last: Costa

first: Kai

last: Sohn

first: M

last: Oliveira


title: Development and Plasticity of Alveolar Type 1 Cells

status: Public on Dec 08 2015

city: Houston

first: Edwin

middle: Justin

last: Ostrin

state: Texas

address: 1515 Holcombe Blvd, Unit 1462

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

summary: The alveolar type 1 (AT1) cell covers >95% of the gas exchange surface and is extremely thin to facilitate passive gas diffusion. The development of this highly specialized cell is poorly understood including fundamental questions regarding cell number and morphology. Using new molecular stereology and single cell imaging methods, we show that AT1 cells develop via a non-proliferative two-step process while maintaining proliferative potential. In the flattening step, AT1 cells remodel cell junctions and undergo molecular specification. In the folding step, AT1 cells are sculptured to match secondary septa formation, resulting in a single AT1 cell spanning multiple alveoli. AT1 cells grow in size by >10-fold, fueling most of the postnatal lung growth. Strikingly AT1 cells proliferate upon ectopic SOX2 expression and undergo stage-dependent cell fate reprogramming. These results contradict the traditional view of AT1 cells being terminally differentiated and provide insights to alveolar maturation. In this experiment, we conducted next-generation sequencing on flow-sorter AT1 cells isolated from mouse lungs ectopically expressing Sox2 under the control of the AT1-specific promoter Scnn1a versus control AT1 cells.

overall_design: Two samples of Sox2-expressing AT1 cells versus two control AT1 samples.

first: Jichao

last: Chen


title: Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation [RNA-seq]

city: Nagasaki

first: Daishi

last: Inoue

address: Sakamoto

department: medicine

country: Japan

institute: Nagasaki univiersity

summary: In mouse embryonic stem cells (mES cells), ubiquitylation of histone H2A lysine 119 represses a large number of developmental genes and maintains mES cell pluripotency. It has been suggested that a number of H2A ubiquitin ligases as well as deubiquitylases and related peptide fragments contribute to a delicate balance between self-renewal and multi-lineage differentiation in mES cells. Here, we tested whether known H2A ubiquitin ligases and deubiquitylases are involved in mES cell regulation and discovered that Dzip3, the E3 ligase of H2AK119, represses differentiation-inducible genes as well as Ring1B. The two sets of target genes partially overlapped but had different spectra. We found that Dzip3 represses gene expression by orchestrating changes in 3D organization in addition to regulating ubiquitylation of H2A. Our results shed light on the epigenetic mechanism of transcriptional regulation, which depends on 3D chromatin reorganization to regulate mES cell differentiation.

overall_design: mouse ES cell mRNA profiles of control, Ring1B knock down, and Dzip3 knock down, in duplicate, using Illumina MiSeq.

first: Takashi

last: Ito


title: Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation


title: Type I and type II interferon coordinately regulate suppressive dendritic cell fate and function during viral persistence

first: Ameya

last: Champhekar

state: California

address: 700 Tiverton Ave, 11-272 Factor Bldg

department: Medicine, HemOnc Division

summary: We identified a population of immunosuppressive dendritic cells (iregDCs) that arises during LCMV-Cl13 infection. IregDCs have a distinct lineage, functional activity, and RNA expression profile compared to stimulatory dendritic cells (stimDCs) that are present within the same environment. While both are CD11b+ DCs, iregDCs develop from monocytes and stimDCs develop from conventional DC (cDC) precursors. IregDCs and stimDCs also respond differently to type I interferon (IFN-I) stimulation. IregDCs respond to IFN-I by upregulating the expression of immunosuppressive ligands while IFN-I blunts the expansion and proliferation of the stimDC population. The gene expression profiles of iregDCs and stimDCs overlap in many areas, however the production of many chemokines and cytokines as well as stimulatory and inhibitory cell surface ligands are quite distinct resulting in two dendritic cell populations with drastically different functions.

overall_design: The comparison of RNA expression profiles between immunosuppressive and stimulatory dendritic cells together with their naïve progenitors (monocytes and naïve dendritic cells, respectively)

first: C

middle: R

last: Cunningham

first: A

first: S

middle: T

last: Smale

first: D

last: Brooks


title: Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the discovery of a group of novel animally enriched RNAs, this study revealed a surprisingly low conservation of vegetal RNA localization between the two frog species.

sample_organism:
Xenopus laevis
Xenopus tropicalis

platform_organism:
Xenopus laevis
Xenopus tropicalis

overall_design: mRNA profiles of Xenopus laevis and Xenopus tropicalis animal and vegetal oocyte halves were generated by RNA-seq technology. For Xenopus laevis, animal and vegetal oocyte RNA preparations from two different females were generated in duplicates. For Xenopus tropicalis, animal and vegetal oocyte RNA preparations from two different females were analyzed.

first: Maike

last: Claußen

first: Tomas

last: Pieler


title: Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation [ChIP-seq]

summary: In mouse embryonic stem cells (mES cells), ubiquitylation of histone H2A lysine 119 represses a large number of developmental genes and maintains mES cell pluripotency. It has been suggested that a number of H2A ubiquitin ligases as well as deubiquitylases and related peptide fragments contribute to a delicate balance between self-renewal and multi-lineage differentiation in mES cells. Here, we tested whether known H2A ubiquitin ligases and deubiquitylases are involved in mES cell regulation and discovered that Dzip3, the E3 ligase of H2AK119, represses differentiation-inducible genes as well as Ring1B. The two sets of target genes partially overlapped but had　different spectra. We found that Dzip3 represses gene expression by orchestrating changes in 3D organization in addition to regulating ubiquitylation of H2A. Our results shed light on the epigenetic mechanism of transcriptional regulation, which depends on 3D chromatin reorganization to regulate mES cell differentiation.

overall_design: Examination of 3 different histone modifications in 1 cell type.


title: Expression data from dexamethasone treated mouse embryonic hypothalamic progenitor/stem cells isolated from wild type C57Bl/6 male or female mice

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: We used RNA-Seq to detail the global program of sexually dimorphic dexamethasone regulated gene expression in embryonic hypothalamic neural progenitor/stem cells.

overall_design: RNAseq on Primary E14.5 mouse hyothalamic neurosphere cultures. 4 conditions - Male Dex, Male EtOH, Female Dex and Female EtOH. There are 3 biological replicates for each condition and all the 12 samples are run on two lanes (techinical duplicates).

first: Donald

last: DeFranco


title: TDRD6 instructs correct assembly of mRNPs in the chromatoid body to potentiate UPF1 dependent mRNA decay.

city: Dresden

first: Rolf

last: Jessberger

state: Saxony

address: Fetscherstraße 74

department: Institut für Physiologische Chemie

institute: Technische Universität Dresden

summary: RNA sequencing of heterozygote or Tudor domain contian protein 6 (TDRD6) knockout round spermatid cells. Chromatoid bodies (CBs) are germ cell-specific organelles of largely unknown function. CBs harbor various RNA species, RNA-associated proteins and proteins of the tudor domain family such as TDRD6. Proteome analysis of purified CBs revealed components of the nonsense-mediated mRNA decay machinery such as UPF1. TDRD6 is essential for UPF1 localization to CBs, for UPF1-UPF2 interaction, and for assembly of UPFs and other RNA binding proteins into super-complexes. In absence of TDRD6, the association of some mRNAs with UPF1 is impaired, and the long 3’ UTR-stimulated but not the exon junction complex-stimulated pathway of NMD is distorted. Reduced association of mRNAs with UPF1 correlated with increased stability and presence in polysome fractions, i.e. enhanced translational activity. Thus, we define CBs as sites of UPF1-dependent mRNA degradation and provide evidence for the requirement for NMD in spermiogenesis. This function of CBs depends on TDRD6-promoted assembly of mRNA decay enzymes within mRNPs.

overall_design: RNA was extracted from quadruplicate samples and libraries generated for sequencing using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) at the Deep Sequencing Group SFB 655, Biotechnology Center of Technische Universität Dresden. After enrichment and XP bead (Agencourt AMPure Kit; Beckman Coulter, Inc.) purification, quality control was done using Fragment AnalyzerTM (Advanced Analytical). The bar-coded libraries were equimolarly pooled and subjected to 76 bp single-end sequencing on Illumina HiSeq 2000, resulting in an average of 33 million reads per sample.

first: Grigorios

last: Fanourgakis

first: Mathias

last: Lesche

first: Müge

last: Akpinar

first: Andreas

last: Dahl


title: Gene expression profile of calcified and normal tricuspid aortic valves by RNA sequencing.

city: Quebec

first: Sandra

last: Guauque-Olarte

address: 2725, chemin Sainte-Foy

institute: CRIUCPQ

summary:
Purpose: Calcific aortic valve stenosis (AS) is a fatal disease with currently no medical therapy. Some genes were associated with AS, but the genetic architecture of the disease has yet to be discovered. The objective of this study was to combine genome-wide association studies (GWAS) and gene expression in human valve tissues to identify new susceptibility genes of AS.
Methods: A meta-analysis was performed combining the results of two independent GWAS in 474 patients that underwent aortic valve replacement from Quebec city and 486 echocardiography cases from France. The controls consisted of 3,151 publically available individuals of European ancestry. Sixty-nine SNPs selected from the meta-analysis (p < 1 x 10-4) were followed-up for replication in a third cohort of 395 cases and 404 controls. Single marker and gene set association analyses were performed. The mRNA expression levels of susceptibility genes were evaluated in 19 human aortic valves with (n=9) and without (n=10) AS by RNA sequencing.
Results: Single marker analysis identified 15 SNPs with p values lower than 1 x 10-6 in the meta-analysis near the FAR2 gene on chromosome 12. At the replication stage, none of these SNPs were confirmed and three other SNPs on chromosomes 2 and 5 reached p < 0.05. Gene set analysis revealed more meaningful association with the calcium signaling pathway enriched for genes mapped to disease-associated SNPs. Genes in this pathway including F2R, GNA14, HTR4, P2RX6, and TNNC1 were found differentially expressed in valves with and without AS.
Conclusions: This integrative genomic study identified new AS susceptibility genes expressed in human valve tissue. Moderate but coordinated genetic association and expression patterns were observed for genes implicated in the calcium signaling pathway and may provide new therapeutic targets to treat this frequent and rising life-threatening disease.

overall_design: Samples of aortic valves were collected from 19 male patients undergoing aortic valve replacement surgery. RNA sequencing was performed using the Illumina Hiseq 2000. Three pairwise comparison among the two kind of valves were made.

first: Arnaud

last: Droit

first: Simon

middle: C

last: Body

first: Jonathan

last: Seidman

first: Patrick

last: Mathieu

first: Philippe

last: Pibarot

first: Yohan

last: Bossé


title: Epigenetic determinants of self-renewal in glioblastoma [ATAC-seq]

first: Alexander

middle: James

last: Murison

address: 101 College Street, TMDT room 11-706

institute: University Health Network

summary: We over-expressed an epigenetic regulator in a glioblastoma (GBM) primary culture from an adult patient. These GBM cells have cancer stem cell phenotypes, as they have self-renewal properties and tumor initiation potential when transplanted in immunocompromised mice. ATAC-seq was performed on cells over-expressing the epigenetic regulator and control cells expressing EGFP.

overall_design: ATAC-Seq on glioblastoma cells that over-express EGFP or an epigenetic regulator.

first: Marco

last: Gallo

first: Peter

last: Dirks

first: Alex

first: Mathieu

last: Lupien


title: Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation

city: San Francisco

first: Raga

last: Krishnakumar

address: 912E RMB, 35 Medical Center Way

institute: UCSF


title: Transcript expression in circulating whole blood after saline injections

city: Jefferson

first: John

middle: Francis

last: Bowyer

state: AR

address: 3900 NCTR Drive

department: Neurotoxicology

institute: National Center for Toxicological Research FDA

summary: These experiments were designed to produce the appropriate controls so that their cohort's transcript (mRNA) changes in whole circulating blood could be determined.  The cohorts were exposed to D-amphetamine under a neurotoxic and non-neurotoxic condition or subjected to elevated environmental temperatures that produced a hyperthermia very similar to heat stroke.  The cohort data is in a separate, but linked, GEO file.

overall_design: Animals were given four doses of 1 ml/ kg of normal saline with two hours in between each dose.  The animals body temperature was determined every 1 h and the rats were sacrificed 3 h after the last saline injection.  Animals were not given access to food or water during this period so that they were more suitable controls for the amphetamine treatment groups

first: Nathaniel

middle: M

last: Crabtree

first: Nysia

middle: I

last: George


title: Changes in transcript expression in circulating whole blood resulting from exposure to neurotoxic doses of D-amphetamine or Heat Stroke/Hyperthermia

summary:
These experiments were designed to detect transcript (mRNA) changes in whole circulating blood in animals exposed to D-amphetamine under neurotoxic and non-neurotoxic conditions, or subjected to elevated environmental temperatures that produced a hyperthermia very similar to heat stroke.  The study objectives were: 1) to detect transcript changes in blood due to life-threatening hyperthermia produced by elevated environmental temperatures (39°C, produces no or minimal neurotoxicity); 2) detect transcripts that could serve as biomarkers specific for neurotoxic amphetamine exposures and not seen with environmentally-induced hyperthermia; and 3) determine the transcript changes related to the immune system in circulating blood produced by either non-neurotoxic or neurotoxic amphetamine exposures.
Amphetamine effects on gene expression are dependent on body temperature and indicate that many significant changes in genes related to the immune system occur, some likely in response to damage, even when animals remain normothermic during amphetamine exposure.  Also, hyperthermia alone produces many changes in immune related genes in blood

overall_design: Five groups of animals were necessary to meet the study objectives.  All groups were given 4 injections of either normal saline or amphetamine, and the injections were sequentially given with 2 h between each injection.  Dosing started at 7:30 to 8:30 a.m.  The groups are: 1) normothermic controls given normal saline in a 22.5°C environment; 2) controls given normal saline in a 16°C environment (also remained normothermic); 3) environmentally-induced hyperthermia given saline in a 39°C environment; 4) non-neurotoxic amphetamine given in a 16°C environment and 5) neurotoxic amphetamine group given amphetamine in a 22.5°C environment. Note the the saline controls (normothermic data) is contained in a separate but linked GEO file GSE62368


title: Human cerebral organoids recapitulate gene expression programs of fetal neocortex development.

status: Public on Dec 07 2015

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

summary: Cerebral organoids – three-dimensional cultures of human cerebral tissue derived from pluripotent stem cells – have emerged as models of human cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed in vivo remains unclear. Here we use single-cell RNA sequencing (scRNA-seq) to dissect and compare cell composition and progenitor-to-neuron lineage relationships in human cerebral organoids and fetal neocortex. Covariation network analysis using the fetal neocortex data reveals known and novel interactions among genes central to neural progenitor proliferation and neuronal differentiation. In the organoid, we detect diverse progenitors and differentiated cell types of neuronal and mesenchymal lineages, and identify cells that derived from regions resembling the fetal neocortex. We find that these organoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue in order to organize into cerebral cortex-like regions. Our comparison of in vivo and in vitro cortical single cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures.

overall_design: 734 single-cell transcriptomes from human fetal neocortex or human cerebral organoids from multiple time points were analyzed in this study. All single cell samples were processed on the microfluidic Fluidigm C1 platform and contain 92 external RNA spike-ins. Fetal neocortex data were generated at 12 weeks post conception (chip 1: 81 cells; chip 2: 83 cells) and 13 weeks post conception (62 cells). Cerebral organoid data were generated from dissociated whole organoids derived from induced pluripotent stem cell line 409B2 (iPSC 409B2) at 33 days (40 cells), 35 days (68 cells), 37 days (71 cells), 41 days (74 cells), and 65 days (80 cells) after the start of embryoid body culture. Cerebral organoid data were also generated from microdissected cortical-like regions from H9 embryonic stem cell derived organoids at 53 days (region 1, 48 cells; region 2, 48 cells) or from iPSC 409B2 organoids at 58 days (region 3, 43 cells; region 4, 36 cells).

first: Barbara

last: Treutlein


title: The Estrogen Receptor Co-Regulator Protein, Proline Glutamic Acid and Leucine Rich Protein 1 (PELP1) Mediates Estrogen Rapid Signaling and Neuroprotection in the Brain

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: We examined the role of PELP1 in E2-ER-mediated transcription in the hippocampus under conditions of GCI by perfroming global transcriptome analysis. E2-treated FLOX and PELP1 FBKO mice were subjected to GCI followed by 24 h reperfusion and the isolated RNA was utilized for RNA-seq analysis. Our results demonstrated that PELP1 is needed for optimal activation of E2-regulated genes following GCI.

overall_design: Total RNA was isolated from the hippocampus of ovariectomized FLOX and PELP1 FBKO mice (implanted with E2 mini pumps) that were subjected to GCI followed by 24 h reperfusion. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 2000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

last: Sareddy

first: Ratna

middle: K

last: Vadlamudi


title: Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation [ChIP-seq]

summary: Transcription factor/enhancer interactions determine cell specific gene expression.  Here, we followed enhancers during differentiations of embryonic stem (ESCs) to epiblast like cells (EpiLCs).  There were highly dynamic changes in histone lysine 27 acetylation at enhancer sites throughout the genome. These sites were enriched for a Foxd3 binding motif, a forkhead transcription factor essential in early embryonic development. Surprisingly, Foxd3 occupied largely mutually exclusive sites in the ESCs versus EpiLCs. Foxd3 bound to nucleosome occupied regions, simultaneously evicting the histones while inhibiting full gene expression through the recruitment of histone deacetylases. Knockout of Foxd3 resulted in hyperacetylation and transcriptional upregulation of neighboring genes, many of which were further upregulated at later stages of differentiation. These data show that Foxd3 primes enhancer sites during pregastrulation by removing nucleosomes, yet suppresses neighboring histone hyperacetylation. Such a mechanism may be common to many transcription factors that prepare enhancers for later gene activation during development.

overall_design:
ChIP-seq of H3K4me1, H3K27ac, H3K27me3, p300, H3K4me3, RNA Pol2 and Oct4 in four pluripotent states: embryonic stem cells (ESCs) day 1 ESC differentiation, Epi-like stem cells (EpiLCs), and epiblast stem cells (EpiSCs); ChIP-seq of 3XFlag tagged Foxd3 in ESCs and EpiLCs; ChIP-seq of H3K4me1, H3K27ac, H3K27me3, p300 and H3K4me3 in Foxd3 conditional knockout cells (tamoxifen-inducible) -/+ 36h Tamoxifen treatemnt.
ChIP seq of Flag-Foxd3 (third replicate), ChIP-seq of HDAC1 and Brg1 in WT and Foxd3 KO cells and MNase-ChIP-seq of H3K4me1

first: Robert

last: Blelloch


title: Roles of Cofactors and Chromatin Accessibility in Hox Protein Target Specificity

city: Cambridge

last: White

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

summary: Regulation of specific target genes by transcription factors is central to gene network control in development. How target specificity is achieved in eukaryotic genomes is poorly understood, as exemplified by the Hox family, which show limited in vitro DNA-binding specificity but clear functional specificity in vivo. We generated genome-wide binding profiles for three Hox proteins, Ubx, Abd-A and Abd-B, in Drosophila Kc167 cells, revealing clear target specificity and a striking influence of chromatin accessibility. Ubx and Abd-A bind to similar target sites in accessible chromatin whereas Abd-B binds additional specific targets. Provision of the TALE class cofactors, Exd and Hth, alters the Ubx binding profile, enabling binding to additional targets in the genome. Both the Abd-B specific targets and the cofactor-dependent Ubx targets are in relatively DNase1 inaccessible chromatin, suggesting that competition with nucleosomes is a key factor determining Hox protein target specificity.

overall_design: This ChIP-Seq study performed on Kc167 cells involves two experiments and 6 ChIP samples.  In Experiment 1, we generated genome-wide binding profiles for Ubx, Abd-A and Abd-B. An equal volume of input chromatin was retained from each of the Hox samples and combined to represent the input, which was purified alongside the ChIP samples. We performed two biological replicates for each sample. Sequencing was performed using the Illumina MiSeq platform.  In Experiment 2, we generated genome-wide binding profiles for Ubx, mutant Ubx and Ubx in the presence of Hth. We performed two biological replicates for each sample except Ubx where we performed just one. Sequencing was performed using the Illumina HiSeq 2000 platform.  For all samples, Experiment 1 input chromatin was used as the reference control to assay ChIP enrichment.

first: Ching Yew

last: Beh

first: Sherif

last: El-Sharnouby

first: Steven

last: Russell

first: Siew Woh

last: Choo


title: Lin28A binds active promoters and recruits Tet1 to regulate gene expression

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

summary: Lin28, a well-known RNA-binding protein, regulates diverse cellular properties. All physiological functions of Lin28A characterized so far have been attributed to its repression of let-7 miRNA biogenesis or modulation of the mRNA translational efficiency. Here we show that Lin28A directly binds to a consensus DNA sequence in vitro and in mouse embryonic stem cells in vivo. ChIP-seq and RNA-seq reveal the enrichment of Lin28A binding around transcription start sites, and a positive correlation between its genomic occupancy and expression of many associated genes. Mechanistically, Lin28A recruits 5-methylcytosine-dioxygenase Tet1 to genomic binding sites to orchestrate 5-methylcytosine and 5-hydroxymethylcytosine dynamics. Either Lin28A or Tet1 knockdown leads to dysregulated DNA methylation and expression of common target genes. These results reveal a surprising role for Lin28A in transcriptional regulation via epigenetic DNA modifications and provide a new framework for understanding mechanisms underlying versatile functions of Lin28A in mammalian systems.

overall_design: Examine the DNA binding ability of Lin28 and its roles in regulating gene expression by coordinating with Tet1


title: Dynamic reorganization of extremely long-range promoter-promoter interactions between two states of pluripotency

city: Nijmegen

first: Shuang-Yin

last: Wang

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: RIMLS

summary: Serum-to-2i interconversion of mouse Embryonic Stem Cells (mESCs) is a valuable in vitro model for early embryonic development. To assess whether 3D chromatin organization changes during this transition, we established Capture Hi-C with target-sequence enrichment of DNase I hypersensitive sites. We detected extremely long-range intra- and inter-chromosomal interactions between a small subset of H3K27me3 marked bivalent promoters involving the Hox clusters in serum grown cells. Notably, these promoter-mediated interactions are not present in 2i ground-state pluripotent mESCs but appear upon further development into primed-like serum mESCs. Reverting serum mESCs to ground-state 2i mESCs removes these promoter-promoter interactions in a spatiotemporal manner. H3K27me3, which is largely absent at bivalent promoters in ground-state 2i mESCs, is necessary but not sufficient to establish these interactions, as confirmed by Capture Hi-C on Eed-/- serum mESCs. Our results implicate H3K27me3 and PRC2 as critical players in chromatin alteration during priming of ESCs for differentiation.

overall_design: To study dynamics in chromatin architecture and to characterize long-range interaction, we performed Hi-C using DpnII as the restriction enzyme, potentially reaching a genome-wide coverage at a less than 1Kb resolution. We subsequently performed enrichment of interaction by a target capture similar to the exome sequencing approach. We enriched for DNaseI hyper-sensitive sites (DHS’s) in chromatin from mESCs. Probes were designed against the union of all DHS’s of Serum and 2i mESCs. Capture Hi-C reveals Extremely Long-Range Interactions (ELRI) in Serum but not in 2i ESCs. We observed H3K27me3 as a prominent characteristic, but not exclusive feature of ELRI loci in Serum mESCs. To further elucidate the involvement of constituents of PRC1 and PRC2 in ELRI, we performed ChIP-seq experiment on Suz12 and Ring1B during serum-to-2i transition. In addition, RNA-seq was performed to compare the expression levels of genes.

first: Onkar

last: Joshi

first: Shuang

middle: Y

first: Yaser

last: Atlasi

first: Tianran

last: Peng

first: Sadia

last: Saeed

first: Lusy

last: Handoko

first: Tatyana

last: Kuznetsova


title: Detection of chromatin accessibility in WT and SRC-2-/- mice in liver

first: Bokai

last: Zhu

address: One Baylor Plaza, M813

department: MCB

institute: Baylor College of Medicine

summary: We futher characterized genome-wide chromatin accessibility of WT and SRC-2-/- mouse liver at CT10 through DNase-Seq.  In addition,chromatin accessibility was significantly reduced in SRC-2-/- mouse liver compared to WT mice at CT10.

overall_design: DNase-Seq was carried out in WT and SRC-2-/- mice in liver at CT10 using two doses of DNaseI.

first: Brian

last: York

first: Bert

middle: W

last: O'Malley


title: Genome-wide maps of BAF180 and REV-ERBα binding

summary: We generated genome-wide cistromes of BAF180 subunit of the SWI-SNF chromatin remodeling complex in mouse liver at CT10 and CT22. In addition, we performed ChIP-Seq analysis on REV-ERBα in WT and  SRC-2-/- mouse liver at CT10. We found circadian oscilation of BAF180 chromatin recruitment in mouse liver with peak recruitment at CT22 and nadir at CT10. Further,REV-ERBα chromatin recruitment was significantly reduced in SRC-2-/- mouse liver compared to WT mice at CT10.

overall_design: ChIP-Seq for BAF180 was performed in WT mice liver at CT10 and CT22 using two different antibodies. ChIP-Seq for REV-ERBα was performed in WT and SRC-2-/- mice in liver at CT10 with biological replicates.


title: Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin

city: Philadelphia

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

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

overall_design: Refer to individual Series


title: Coactivator-Dependent Oscillation of Chromatin Accessibility Dictates Circadian Gene Amplitude through REV-ERB Loading


title: Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin [Mnase-seq]

summary: Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure directly regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification, occurring on the nucleosomal lateral surface. We show that H4K44ac is specific to yeast sporulation, rising during yeast meiosis and displaying genome-wide enrichment at recombination hotspots in meiosis. The H4K44 residue is required for normal meiotic recombination, for normal levels of double strand breaks during meiosis, and for optimal sporulation. Non-modifiable substitution H4K44R results in reduced MNase digestion and decreased binding of recombination-associated proteins at hotspots. Our results show that H4K44ac creates an accessible chromatin environment for key proteins to facilitate meiotic recombination.

overall_design:
Two samples, one WT MNase-seq and one MNase-seq from yeast with a lysine->arginine mutation at H4K44, no replicates

Two replicates each of MNase-seq in WT and H4K44->R mutant yeast grown in YPD or YPA.

first: Jialei

last: Hu

first: Greg

first: Jean

last: Dorsey

first: Jérôme

last: Govin

first: Parisha

middle: P

last: Shah

first: Zuofei

last: Yuan

first: Benjamin

last: Garcia

first: Shelley

middle: L

last: Berger


title: Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation [ChIP-Seq]

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

institute: Uniklinik-Freiburg

summary: The aim of the study is to identify AR target gens in LNCaP cells

overall_design:
5 samples corresponding to LSD1 K114me2 or CHD1 genome-binding in DHT-treated and control LNCaP cells.
6 samples corresponding to LSD1 K114me2 or CHD1 genome-binding in LNCaP cells knocked-down for LSD1 or CHD1 and treated with DHT.

first: Dominica

last: Willmann

first: Roland

last: Schüle


title: Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin [ChIP-seq]

overall_design:
One sample, H4K44ac chIP from 4hrs sporulation yeast and one background H4 chIP from the same, two replicates each

Two replicates each of H3K4me3 and H3K56ac chIP-seq in WT and H4K44->R mutant yeast, with two replicates of H3 chIP-seq in each genetic background

Two replicates each of Rad51 chIP-seq in WT and H4K44->R mutant yeast with a single replicate of accompanying input DNA in each genetic background

middle: A


title: Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation


title: Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation [RNA-Seq]

overall_design: 6 samples correponding to 2 times 3 replicates were used for the study


title: Tet1 and Tet2 mediate epigenetic regulation of developmental genes by protecting DNA methylation canyons against hypermethylation [Bisulfite-Seq]

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

summary: This study uses whole methylome sequencing to characterize the methylomes of mouse embryonic fibroblasts (MEF's). Two conditions were analyzed, MEF cells with intact TET1/TET2 enzymes (WT) and MEF cells with TET1/TET2 knocked out (DKO). Our results identify sets of differentially methylated genes which are correlated with TET1/TET2 induced expression changes of the corresponding genes.

overall_design: Whole methylome analysis of M. musculus MEF cells. Two conditions were sequenced and analyzed, the first is wild type (WT), the second (DKO) corresponds to knock-out of TET1 and TET2 enzymes.

first: F

last: Lyko

first: R

last: Jaenisch


title: Tet1 and Tet2 mediate epigenetic regulation of developmental genes by protecting DNA methylation canyons against hypermethylation


title: Global transcript analysis of quantitative trait loci (QTL) associated with meat tenderness in pigs

status: Public on Dec 06 2015

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

summary: We sequenced mRNA from 32 muscles (n=16 semimembranosus,n=16 longisimus dorsi) of two pig breeds (Puławska and Polish Landrace), which are differing in firmness. The differences between pig groups with respect to shear force of coocked meat were significant and amounted to 64.88 N (P<0.01) in longisimus dorsi and 14.8 N (P<0.05) for semimembranosus.

overall_design: Examination of mRNA levels between pig breeds differing in shear force. Project ID: 217776 founded National Science Centre (NCN), title: Application of targeted next generation sequencing (NGS) in the identification of genetic markers associated with the pork quality

first: K

last: Piórkowska

last: Żukowski

last: Ropka-Molik

first: A

last: Gurgul


title: Natural diversity in pentose fermentation is explained by variations in histone deacetylases

status: Public on Dec 04 2015

city: Los Angeles

first: Zvi

last: Tamari

address: 5531 Boelter Hall

institute: UCLA

summary: The extent to which carbon flux is directed towards fermentation vs. respiration differs between cell types and environmental conditions. Understanding the basic cellular processes governing carbon flux is challenged by the complexity of the metabolic and regulatory networks. To reveal the genetic basis for natural diversity in channeling carbon flux, we applied Quantitative Trait Loci analysis by phenotyping and genotyping hundreds of individual F2 segregants of budding yeast that differ in their capacity to ferment the pentose sugar xylulose. Causal alleles were mapped to the RXT3 and PHO23 genes, two components of the large Rpd3 histone deacetylation complex. We show that these allelic variants modulate the expression of SNF1/AMPK-dependent respiratory genes. Our results suggest that over close evolutionary distances, diversification of carbon flow is driven by changes in global regulators, rather than adaptation of specific metabolic nodes. Such regulators may improve the ability to direct metabolic fluxes for biotechnological applications.

overall_design: mRNA profiles of S. cerevisiae strain BY4741 with either the RXT3 or PHO23 genes either deleted, replaced by S. cerevisiae T73 allele or replaced by S. cerevisiae PHO23 allele

first: Naama

last: Barkai


title: Transcriptomic gene profiling of porcine muscle tissue depending on histological properties

summary:
Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with fiber-type distribution and cell size in porcine muscle tissue.
Methods: The histological profile of the longissimus lumborum muscle was establish by method involving detection of NADPH dehydrogenase (diaphorase) and immunohistochemically detection of myosin chains. The muscle transcriptome sequencing was performed for 11 pigs using Illumina HiScan SQ in 50 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Sus scrofa reference genome (assembly Sscrofa10.2). Differentially expressed genes were detected by edgeR, baySeq and DESeq2. The RNA-seq results were validated using by qPCR.
Results: The RNA-seq approach allows to identify 397 differentially expressed genes (DEGs) indicated as significant (FDR<0.05) using three software: DESeq2, edgeR and baySeq. Detected genes and pathways deregulated in muscle depend on tissue microstructure were associated with metabolic processes – 158 genes; cellular processes – 122; biological regulation – 62; localization – 51 and 35 genes with developmental processes. The detected DEGs were included in such pathways as: PI3K-Akt; FoxO and MAPK signaling pathways, regulation of actin cytoskeleton, lysine degradation and insulin signaling pathway as well as in mTOR and Hippo signaling.
Conclusions: This results highlight the mainly metabolic pathways related with glucose metabolism and contraction processes of muscle cells. The comparison of whole gene expression profiles between muscles characterized by different fiber-type distribution showed that processes of growth and proliferation of different fiber types are determined by diverse molecular mechanism, which conditioned the unique histological structure of muscle tissue.

overall_design: The muscle (longissimus lumborum) transcriptome sequencing was performed for 11 pigs using Illumina HiScan SQ in 50 single-end cycles and in five technical repetitions.

last: Bereta

first: G

last: Żak


title: Addressing bias in small RNA library preparation for sequencing: a new protocol recovers microRNAs that evade capture by current methods

city: Chapel Hill

first: Jeanette

last: Baran-Gale

state: NC

address: 120 Mason Farm Rd.

institute: University of North Carolina at Chapel Hill

summary: We performed deep sequencing of small RNA from mouse insulinoma (MIN6) cells or mouse liver using different library prepartion methods.

overall_design: Libraries were preapred using MIN6 or Mouse Liver total RNA using (1) Illumina v1.5 small RNA library prep kit, (2) Illumina TruSeq kit, or (3) Bioo Scientific NEXTFlexV2

first: C

last: Kurtz

first: Michael

last: Erdos

first: Christina

last: Sison

first: Alice

last: Young

first: Emily

middle: E

last: Fannin

first: Peter

middle: S

last: Chines

first: Praveen

last: Sethupathy


title: Human Embryoid Body Transcriptomes Reveal Maturation Differences Influenced by Size and Formation in Custom Microarrays

status: Public on Dec 05 2015

city: Buffalo

last: Buck

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: SUNY at Buffalo

summary: Stem cell differentiation strategies and optimization for generating lineage-specific cells and tissues most frequently rely on a three-dimensional embryoid body (EB) intermediate. We previously applied nanotechnology tools of photolithography to generate custom microarrays that allow high throughput uniform formation of EBs of custom size for precise downstream analysis. Formation of EBs of 200 or 500 micron size revealed distinct morphological differences that are single or multicystic cores, respectively, independent of method of formation from single cells or two-dimensional (2D) clusters. Here we utilize photolithographic array generated EBs to obtain 3D cultures under a standardized platform for transcriptome analysis to compare EB size and the method of EB formation from single cells or mechanically passaged 2D clusters. Our analysis evaluates RNA expression in EBs formed from the human embryonic stem cell (hESC) line WA09 and from ethnically diverse human induced pluripotent stem cell lines (ED-iPSC) of African American and Hispanic Latino ethnicity recently derived in our laboratory. This is the first comprehensive study on EB transcriptomes including multiple size parameters, EB formation methodologies, and ethnicities. Our analysis indicates upregulation of genes involved in wound healing for mechanically passaged cells and of genes for embryonic tube formation in 500 micron multicystic EBs. We propose that EB maturation may be a longer process then previously realized. In addition, the type or extent of maturation possible may be influenced by EB size, with larger EBs capable of more extensive remodeling as revealed by multicystic morphology and initiation of early tube formation pathways while retaining pluripotency status. We anticipate that this information will be broadly useful to the stem cell and bioengineering communities in optimization of tissue engineering with pluripotent stem cells and understanding sources of variation.

overall_design: mRNA profiles by RNA-seq from embryoid bodies generated by different methods

first: M

last: Tomov

middle: J

last: sompana

first: Z

last: Olmsted

first: J

last: Paluh


title: PIWI slicing and EXD1 drive biogenesis of nuclear piRNAs from cytosolic targets of the mouse piRNA pathway

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

summary: PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposable elements in animal gonads. Here we demonstrate that in the mouse embryonic male germline, endonucleolytic cleavage (slicing) of a transcript by cytosolic MILI acts as a trigger to initiate its further 5??3? processing into non-overlapping fragments. These fragments accumulate as new piRNAs within the nuclear PIWI protein MIWI2. We identify Exonuclease domain-containing 1 (EXD1) as a partner of the established MIWI2 piRNA biogenesis factor TDRD12. Although EXD1 homodimers are inactive as a nuclease, it functions as an RNA adapter within a PET (PIWI-EXD1-Tdrd12) complex. Loss of Exd1 impacts biogenesis of MIWI2 piRNAs and displays a reduction in sequences generated by MILI slicing. This results in selective depletion of repeat piRNAs that target active retrotransposons like LINE1, which are de-repressed in the mutant. We propose that PIWI slicing and EXD1 promote coordination of nucleo-cytoplasmic silencing via piRNA biogenesis.

overall_design: Immunoprecipitated or total small RNAs were purified and sequenced from P0 mouse testis of Exd1+/- and Exd1 -/- mice. Testes of three males were pooled together and MILI and MIWI2 immunoprecipitation was performed or  total small RNAs were purified. Two replicas from different pools were prepared. For Rosa26-pi reporter mouse P0 testes of three males were pooled together and MILI and MIWI2 immunoprecipitation was performed.

first: Zhaolin

last: Yang

first: Kuan-Ming

last: Chen

first: Radha

last: Pandey

first: David

last: Homolka

last: Reuter

first: Bruno

last: Janeiro

first: Ravi

last: Sachidanandam

first: Marie-Odile

last: Fauvarque

first: Andrew

last: McCarthy


title: The ancestral gene repertoire of animal stem cells

city: Kyoto

first: Noriko

last: Funayama

state: Kyoto

address: Kitashirakawa-Oiwake, Sakyo-ku

department: Biophysics

institute: Kyoto University

summary: This work reveals the deeply conserved gene repertoire of animal stem cells, from sponges to mammals.

overall_design: mRNA profiles totipotent stem cells (archeocytes), choanocytes, other differentiated cell types in a freshwater sponge and were mapped on the reference transcriptome generated in the same study

first: Alexandre

last: Alié


title: BMP signaling in mouse embryonic stem cells (ESCs) in the naïve and primed pluripotent states [ChIP-Seq]

city: Tokyo

first: Masato

last: Morikawa

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

institute: Teikyo University

summary: Carrying out both RNA-seq and Smad1/5 genome-wide chromatin immunoprecipitation and sequencing (ChIP-seq) analyses of mESCs in the naïve or primed states, we revisit the roles of BMP signaling in mESCs.

overall_design: Smad1/5 binding sites in 2 cell types; mESCs and ES-derived EpiSC (ESD-EpiSCs).

first: Daizo

last: Koinuma

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: Parkin-mediated mitophagy evokes perinatal cardiac mitochondria maturation

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: Exclusion of Parkin from mitochondria of perinatal cardiomyocytes interrupts structural and molecular transformations essential to normal perinatal-adult mitochondrial replacement. mRNA-sequencing from cardiac total RNA was performed at P1, P21 and 5-week stages of nontransgenic (ntg) and human-Mfn2-overexpressing (Mfn2wt) hearts, and also of tet-off control (tetoff) and human-Mfn2 T111A/S442A-overexpressing (Mfn2AA) hearts.

overall_design: Libraries from all P1 samples were prepared and analyzed together, and similarly all P21 libraries, and all 5-week libraries together.  To facilitate comparison across time points by accounting for batch effect, new libraries were prepared starting from total RNA from selected P21 ntg and 5-week ntg hearts subjected to prior analysis, during the same batch preparation as all P1 samples, and analyzed together.  Correction for differences observed between libraries prepared from the same total RNA, but at different times, allows comparison across timepoints.

first: Gerald

last: Dorn


title: BMP signaling in mouse embryonic stem cells (ESCs) in the naïve and primed pluripotent states


title: ChIPseq analyses in germinal center B cells

city: New York

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: Germinal center B cells were isolated from human tonsil tissue and crosslinked. ChIP was performed on two distinct pools of germinal center cells, each obtained from 3-5 donors.

overall_design: The experiment includes two biological replicates (germinal center cell pools from different donors). ChIP was performed on both pools and subject to library preparation and sequencing. Input DNA was sequenced for both pools.

first: Katia

last: Basso

first: Antony

middle: B

last: Holmes


title: CRISPR-Cas9 based screen for p53-bound enhancers that function in oncogene-induced senescence

status: Public on Dec 03 2015

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: We exained using RNA-seq the effect of targeting selected p53-bound enhancers on the p53-induced response to oncogenic stress

overall_design: RNA-seq was applied to examine transcriptional response to oncogenic stress (induced by RASG12V activation) in control and genetically manipulated hTERT-immortalized BJ cells

first: Gozde

last: Korkmaz

first: Rui

last: Lopes

first: Rani

first: Reuven

last: Agami


title: Identification of RNAs bound to endogenous PUM2 in HCT116 cells

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center Dallas

summary:
Purpose: PUMILIO proteins are known to repress target genes by binding to PUMILIO response elements (PREs) in target mRNAs. The goal of this study was to demonstrate binding of endogenous PUM2 to the noncoding RNA NORAD and to identify PUM2 target genes in NORAD wild-type and knockout HCT116 cells.
Methods: PAR-CLIP was performed with endogenous PUM2 in HCT116 cells and isogenic NORAD knockout cells.
Results: Endogenous PUM2 binds to NORAD in HCT116 cells. In addition, PUM2 target genes were identified in HCT116 cells.
Conclusions: PUM2 binds to NORAD through multiple PREs on NORAD. Compared to all other PUM2 target genes in HCT116, NORAD is the preferred binding partner of endogenous PUM2.

overall_design: RNAs bound to endogenous PUM2 were identified in HCT116 NORAD wild-type and knockout cells using PAR-CLIP and deep sequencing using Illumina NextSeq 500.

first: Sungyul

last: Lee

first: Florian

last: Kopp

first: Tsung-Cheng

last: Chang

first: Beibei

last: Chen

first: Yang

last: Xie


title: Coordination of RNA Polymerase II Pausing and 3’ end processing factor recruitment with alternative polyadenylation

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

summary: Sites of RNA polymerase II (pol II) pausing and processing factor recruitment change depending on which alternative poly(A) site is utilized at the IgM locus. In contrast, the extent of pol II CTD Ser2 phosphorylation did not closely correlate with poly(A) site selection. We conclude that changes in properties of the transcription elongation complex closely correlate with utilization of different poly(A) sites.

overall_design: The function of co-transcriptional events in the selection of alternative poly(A) sites was investigated. RNA polymerase II pausing, Ser2 CTD phosphorylation and processing factor CstF recruitment at WT and mutant mouse IgM transgenes that use alternative poly(A) sites to produce mRNAs encoding the secreted and membrane-bound forms of the Ig heavy chain. The mutants used were pA21 a 21 bp deletion of the uS polyA site consensus and 5'SP which mutates 3 bases in the 5' splice site of the Cu4-M1 intron to strengthen it.

first: Hyunmin

last: Kim


title: RNA-seq of the killifish Nothobranchius furzeri strain MZM-0410

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

summary:
The study consists of 12 samples of 39-week-old N. furzeri (skin and brain).

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 12 samples of N. furzeri, MZM-0401, 39w: 6x brain, 6x skin.

first: Marco

last: Groth

first: Mario

last: Baumgart

first: Steffen

last: Priebe

first: Matthias

last: Platzer

first: Alessandro

last: Cellerino


title: BMP signaling in mouse embryonic stem cells (ESCs) in the naïve and primed pluripotent states [RNA-Seq]

first: Masato

last: Morikawa

overall_design: RNA-seq analysis in 2 cell types; mESCs and ES-derived EpiSC (ESD-EpiSCs).

first: Daizo

last: Koinuma

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: Elimination of chromosomal island SpyCIM1 from Streptococcus pyogenes strain SF370 reverses the mutator phenotype and alters global transcription

city: Oklahoma City

first: William

middle: Michael

last: McShan

state: OK

address: 1110 N. Stonewall Ave.

department: Pharmaceutical Sciences

institute: University of Oklahoma Health Sciences Center

summary: Streptococcus pyogenes chromosomal island M1 (SpyCIM1) integrates by site-specific recombination into the 5’ end of DNA mismatch repair (MMR) gene mutL in strain SF370SmR, blocking transcription of it and the downstream operon genes.  During exponential growth, SpyCIM1 excises from the chromosome and replicates as an episome, restoring mutL transcription.  This process is reversed in stationary phase with SpyCIM1 re-integrating into mutL, returning the cells to a mutator phenotype.  Here we show that elimination of SpyCIM1 relieves this mutator phenotype.  The downstream MMR operon genes, multidrug efflux pump lmrP, Holliday junction resolution helicase ruvA, and DNA base excision repair glycosylase tag, are also restored to constitutive expression by elimination of SpyCIM1.  The presence of SpyCIM1 alters global transcription patterns in SF370SmR.  RNA sequencing (RNA-Seq) demonstrated that loss of SpyCIM1 in the SpyCIM1 deletion mutant, CEM1∆4, impacted the expression of many genes both in early exponential phase, when the SpyCIM1 is episomal, as well as at the onset of stationary phase, when SpyCIM1 has reintegrated into mutL.  Among these changes, the up regulation of the genes for the antiphagocytic M protein (emm1), streptolysin O (slo), capsule operon (hasABC), and streptococcal pyrogenic exotoxin (speB), are particularly notable.  The expression pattern of the DNA mismatch repair (MMR) operon confirmed our earlier observations that these genes are transcribed in early exponential phase but silenced as stationary phase is approached. The direct role of SpyCIM1 in causing the mutator phenotype is confirmed by these studies, and its influence upon the biology of S. pyogenes was found to impact multiple genes in addition to the MMR operon.  We suggest that such chromosomal islands are a remarkable evolutionary adaptation to promote the survival of its S. pyogenes host cell in changing environments.

overall_design: Comparison of two strains differing by the presence of a phage-like chromosomal island at early log and late log growth at either 37°C or 39°C


title: Tet1 and Tet2 mediate epigenetic regulation of developmental genes by protecting DNA methylation canyons against hypermethylation [RNA-Seq]

first: Guenter

last: Raddatz

summary: This study uses whole-transcriptome sequencing to characterize the transcriptomes of mouse embryonic fibroblasts (MEF's). Two conditions were analyzed, MEF cells with intact TET1/TET2 enzymes (WT) and MEF cells with TET1/TET2 knocked out (DKO). Our results identify sets of differentially expressed genes which are correlated with TET1/TET2 induced methylation changes of the corresponding genes.

overall_design: Whole transcriptome analysis of M. musculus MEF cells. Two conditions were sequenced and analyzed, the first is wild type (WT), the second corresponds to knock-out of TET1 and TET2 enzymes.

first: F

last: Lyko

first: R

last: Jaenisch


title: Perturbed gastrulation in embryos from diabetic pregnancies.

city: Baton Rouge

first: J. Michael

last: Salbaum

state: LA

address: 6400 Perkins Road

department: Regulation of Gene Expression

institute: Pennington Biomedical Research Center

summary: Maternal diabetes is a teratogen that can lead to neural tube closure defects in the offspring. In neurulation-stage embryos from diabetic dams, we detected abnormal tissue protruding from the open neural tube. To determine the origin of such protrusions, we compared gene expression profiles between open neural plate with normal morphology, and protrusion tissue. Neurulation-stage mouse embryos at 8.5 days of gestation were used to prepare open neural tube at the anterior aspect of neural tube closure site 1 by laser capture microdissection. For each sample, 10 sections were pooled, total RNA was extracted, and 7 ng of total RNA were used for expression profiling by Tag sequencing using an Applied Biosystems SolidSAGE kit for library construction, and an AB SOLiD 5500 XL instrument for sequencing. Protrusion tissue was prepared from whole embryos by microdissection, and 12ng of total RNA per sample was used for Tag sequencing. Sequence reads were mapped to RefSeq RNA, and count data per gene were obtained using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software.

overall_design: Neural plate protrusion compared to open neural plate anterior of closure site 1 with normal morphology

first: J


title: Differential DNA Methylation Analysis without a Reference Genome

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

summary: Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for studying DNA methylation in non-model organisms, we developed an integrated approach for studying DNA methylation differences without a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, zebrafish, carp, and sea bass). Bioinformatically, we developed the RefFreeDMA software (http://RefFreeDMA.computational-epigenetics.org) to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions. These regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.

sample_organism:
Cyprinus carpio
Homo sapiens
Bos taurus

platform_organism:
Cyprinus carpio
Homo sapiens
Bos taurus

overall_design:
FACS (FSC/SSC)-sorted blood cell types (granulocytes, lymphocytes, monocyes, granMonocyte , erythrocytes) isolated from peripheral blood of 4 individuals (2M, 2F biological replicates) of 3 different species (human, cow and carp).

Submitter states that human raw sequence data are being deposited at EBI-EGA.

first: Johanna

last: Klughammer

first: Paul

last: Datlinger

first: Dieter

last: Printz

first: Nathan

middle: C

last: Sheffield

last: Farlik

last: Hadler

first: Gerhard

last: Fritsch


title: DNA repair in species with extreme lifespan differences

city: Bronx

first: Sheila

last: MacRae

address: 1301 Morris Park Ave, Rm 468

department: Genetics

institute: Albert Einstein College of Medicine

summary: We compared RNA-seq expression patterns in liver, an organ with high oxidative metabolism and abundant spontaneous DNA damage, from humans, naked mole rats, and mice, differing in maximum lifespan over a range of ~100, 30, and 3 years, respectively, for 130 genes involved in DNA repair. The results show that the longer-lived species, human and naked mole rat, share higher expression of these DNA repair genes, including core genes in several DNA repair pathways. A more systematic approach of signaling pathway analysis (SPA) indicates statistically significant upregulation of several DNA repair signaling pathways in human and naked mole rat compared with mouse.

sample_organism:
Homo sapiens
Mus musculus
Heterocephalus glaber

overall_design: Compare steady-state RNA levels from 3 samples each of adult liver tissue of human, naked mole rat, and mouse. Mouse samples available in the Short Reads Archive: SRX871336, SRX871370, SRX871395 (SRP053350) and BioProject PRJNA274780.

last: Macrae

first: Matthew

last: Croken

first: Robert

last: Calder

first: Alexander

last: Aliper

last: Zhavoronkov

first: Zhengdong

middle: D

last: Zhang

first: Andrei

last: Seluanov

first: Vera

last: Gorbunova

first: Jan

last: Vijg


title: A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation

city: San Francisco

last: Fields

state: CA

address: 1700 4th Street

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

summary: A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribosome profiling and linear regression, for systematic identification and quantification of translation. Application of this approach to lipopolysaccharide-stimulated mouse dendritic cells and HCMV-infected human fibroblasts identifies thousands of novel CDSs, including micropeptides and variants of known proteins, that bear the hallmarks of canonical translation and exhibit comparable translation levels and dynamics to annotated CDSs. Remarkably, many translation events are identified in both mouse and human cells even when the peptide sequence is not conserved. Our work thus reveals an unexpected complexity to mammalian translation suited to provide both conserved regulatory or protein-based functions.

overall_design: 37 ribosome footprint samples from mouse BMDCs across a time course of LPS stimulation and in the presence or absence of translation inhibitors cycloheximide, harringtonine, or lactimidomycin. A mock (non-LPS stimulated) time course is also included, collected in the presence of cycloheximide. Two replicates are available for the LPS timecourse under CHX treatment. Reads include the 3' linker sequence CTGTAGGCACCATCAAT.

first: Edwin

middle: H

last: Rodriguez

first: Marko

last: Jovanovic

first: Noam

last: Stern-Ginossar

first: Brian

last: Haas

first: Philipp

last: Mertins

first: Raktima

last: Raychowdhury

first: Nir

last: Hacohen

first: Steven

last: Carr

first: Nicholas

middle: T

last: Ingolia

first: Aviv

last: Regev

first: Jonathan

last: Weissman


title: Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Obesity is a heritable disorder, with children of obese fathers at higher risk of developing obesity.  Environmental factors epigenetically influence somatic tissues, but the contribution of these factors to the establishment of epigenetic patterns in human gametes is unknown. Here, we hypothesized that weight loss remodels the epigenetic signature of spermatozoa in human obesity. Comprehensive profiling of the epigenome of sperm from lean and obese men showed similar histone positioning, but small non-coding RNA expression and DNA methylation patterns were markedly different. In a separate cohort of morbidly obese men, surgery-induced weight loss was associated with a dramatic remodeling of sperm DNA methylation, notably at genetic locations implicated in the central control of appetite. Our data provide evidence that the epigenome of human spermatozoa dynamically changes under environmental pressure, and offers  insight into how obesity may propagate metabolic dysfunction to the next generation.

overall_design: Examination of the DNA methylation status, histone retention and sncRNA expression of the semen of 13 lean and 10 obese individuals; as well as the DNA methylation status of the semen of 6 obese men undergoing Roux-en-Y GBP surgery, at three time points: approximately 1 week before, 1 week after and 1 year after the surgery.

first: Ida

last: Donkin

first: Soetkin

last: Versteyhe

middle: R

first: Kui

last: Qian

first: Mie

last: Mechta

first: Loa

last: Nordkap

first: Brynjulf

last: Mortensen

first: Niels

last: Jørgensen

first: Viggo

last: Kristiansen

first: Christopher

last: Workman

first: Juleen

last: Zierath

first: Romain

last: Barrès