title: Gene Networks Specific for Innate Immunity Define Post-traumatic Stress Disorder [RNA-Seq]

city: New York

summary:
The molecular factors involved in the development of Post-Traumatic Stress Disorder (PTSD) remain poorly understood. Previous transcriptomic studies investigating the mechanisms of PTSD apply targeted approaches to identify individual genes under a cross-sectional framework lack a holistic view of the behaviours and properties of these genes at the system-level. Here we sought to apply an unsupervised gene-network based approach to a prospective experimental design using whole-transcriptome RNA-Seq gene expression from peripheral blood leukocytes of U.S. Marines (N=188), obtained both pre- and post-deployment to conflict zones. We identified discrete groups of co-regulated genes (i.e., co-expression modules) and tested them for association to PTSD. We identified one module at both pre- and post-deployment containing putative causal signatures for PTSD development displaying an over-expression of genes enriched for functions of innate-immune response and interferon signalling (Type-I and Type-II). Importantly, these results were replicated in a second non-overlapping independent dataset of U.S. Marines (N=96), further outlining the role of innate immune and interferon signalling genes within co-expression modules to explain at least part of the causal pathophysiology for PTSD development. A second module, consequential of trauma exposure, contained PTSD resiliency signatures and an over-expression of genes involved in hemostasis and wound responsiveness suggesting that chronic levels of stress impair proper wound healing during/after exposure to the battlefield while highlighting the role of the hemostatic system as a clinical indicator of chronic-based stress. These findings provide novel insights for early preventative measures and advanced PTSD detection, which may lead to interventions that delay or perhaps abrogate the development of PTSD.
We used RNA-Sequencing gene expression to characterize both prognostic and diagnostic molecular signatures associated to PTSD risk and PTSD status compared to control subjects.

overall_design: Peripheral blood luekocytes gene expression was subject to transcriptional analysis for 94 service members both prior-to and following-deployment to conflict zones. Half of the subjects returned with Post-traumatic stress disorder (PTSD), while the other half did not.

first: Caroline

last: Nievergelt


title: NLRC5 specifically transactivates MHC class I and related genes through a distinctive SXY module

status: Public on Feb 27 2015

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: MHC class II (MHCII) genes are transactivated by the NOD-like receptor (NLR) factor CIITA, which is recruited to SXY regulatory modules of MHC promoters via a DNA-binding “enhanceosome” complex. NLRC5, another NLR protein, was recently found to control transcription of MHC class I (MHCI) genes. However, detailed understanding of its target-gene specificity and mechanism of action remained lacking. We therefore performed ChIP-sequencing experiments to gain comprehensive information on NLRC5-transactivated genes. In addition to classical MHCI genes, we identified novel NLRC5-targets exclusively in the H2-Q and H2-T regions of the MHCI locus, among which the best targets were found. Investigation of cells lacking the MHCII-enhanceosome factor RFX5 demonstrated its strict requirement for NLRC5 recruitment to the SXY module conserved in MHCI genes. Furthermore, patient-derived B cell lines deficient in RFX5, RFXAP, and RFXANK corroborated importance of the enhanceosome for MHCI transactivation. Although sharing similar SXY modules and common DNA-binding factors, CIITA and NLRC5 regulate distinct genes, as shown here using double-deficient Nlrc5-/-CIIta-/- mice. The identification of sequences occupied by NLRC5 in vivo allowed us to define a unique consensus motif for its recruitment, which diverges from that used by CIITA. Our results thus broaden our knowledge on transcriptional activity of NLRC5, highlighting its remarkable selectivity for genes encoding MHCI or related proteins and providing insights into the specificity of its recruitment.

overall_design: Analysis of Nlrc5 binding sites in T-cells

first: Kristina

last: Ludigs

first: Queralt

last: Seguín-Estévez

last: Lemeille

first: Isabel

last: Ferrero

first: Giorgia

last: Rota

first: Sonia

last: Chelbi

first: Chantal

last: Mattmann

first: H

middle: R

last: MacDonald

first: Walter

last: Reith

first: Greta

last: Guarda


title: Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.

status: Public on Feb 26 2015

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

country: United Kingdom

institute: Ucl

summary: Topological domains are key architectural building blocks of chromosomes in complex genomes. Their functional importance and evolutionary dynamics are however not well defined.  Here we performed comparative Hi-C in liver cells from four mammalian species, and characterized the conservation and divergence of chromosomal contact insulation and the resulting domain architectures within distantly related genomes. We show that the modular organization of chromosomes is robustly conserved in syntenic regions. This overall conservation is compatible with conservation of the binding landscape of the insulator protein CTCF.  Specifically, conserved CTCF sites are co-localized with cohesin, enriched at strong topological domain borders and bind to DNA motifs with orientations that define the directionality of CTCF’s long-range interactions. Interestingly, CTCF binding sites which are divergent between species are strongly correlated with divergence of internal domain structure. This divergence is likely driven by local CTCF binding sequence changes, demonstrating how genome evolution can be linked directly with a continuous flux of local chromosome conformation changes. Conversely, we provide evidence that large-scale domains are harder to break and that they are reorganized during genome evolution as intact modules.

sample_organism:
Macaca mulatta
Canis lupus familiaris
Oryctolagus cuniculus
Mus musculus

overall_design: Hi-C and 4C-seq experiments were conducted in primary liver cells obtained from mouse, rabbit, macaque and dog

first: Matteo

last: Vietri Rudan

first: Christopher

last: Barrington

first: Christina

last: Ernst

first: Duncan

middle: T

last: Odom

first: Amos

last: Tanay


title: Deep sequencing identify tissue-specific microRNAs and their target genes involved in tanshinones biosynthesis in Salvia miltiorrhiza

status: Public on Mar 01 2015

city: Hangzhou

first: Xiangbin

last: Xu

address: Xiasha xuelin street 16

country: China

institute: Hangzhou Normal University

type: Non-coding RNA profiling by high throughput sequencing

summary: Salvia miltiorrhiza is one of the most popular traditional medicinal herbs in Asian nations. Its dried root contains a number of tanshinones, protocatechuic aldehyde, salvianolic acid B and rosmarinic, and is used for the treatment of various diseases. To make clear the molecular mechanism of tanshinones biosynthesis in S. miltiorrhiza, the tissue-specific miRNAs and their target genes were identified by high-throughput sequencing and degradome analysis. A total of 452 known miRNAs corresponding to 589 pre-miRNAs, and 40 novel miRNAs corresponding to 24 pre-miRNAs were identified in different tissues of S. miltiorrhiza, respectively. Among them, 62 miRNAs express only in root, 95 miRNAs express only in stem, 19 miRNAs express only in leaf, and 71 miRNAs express only in flower, respectively. By the degradome analysis, 69 targets potentially cleaved by 25 miRNAs were identified. Among them, Acetyl-CoA C-acetyltransferase was identified in S. miltiorrhiza, which was cleaved by miR5072 and involved in the biosynthesis of tanshinones. This study provided valuable information for understanding the tissues expression patterns of miRNAs, and offered a foundation for future studies of the miRNA-mediated tanshinones biosynthesis in S. miltiorrhiza.

overall_design: The tissue-specific miRNAs and their target genes were identified by high-throughput sequencing and degradome analysis.

first: Hongmiao

last: Song


title: The Small Molecule ISRIB Reverses the Effects of eIF2α Phosphorylation on Translation and Stress Granule Assembly

city: Berkeley

first: Anna

middle: M

last: McGeachy

state: California

address: 416 Barker Hall

department: MCB

country: USA

institute: UC Berkeley

type: Expression profiling by high throughput sequencing

summary: We recently identified ISRIB as a potent inhibitor of the integrated stress response (ISR). ISRIB renders cells resistant to the effects of eIF2α phosphorylation and enhances long-term memory in rodents (10.7554/eLife.00498).  Here we show by genome-wide in vivo ribosome profiling that translation of a restricted subset of mRNAs is induced upon ISR activation. ISRIB substantially reversed the translational effects elicited by phosphorylation of eIF2α and induced no major changes in translation or mRNA levels in unstressed cells. eIF2α phosphorylation-induced stress granule (SG) formation was blocked by ISRIB. Strikingly, ISRIB addition to stressed cells with pre-formed SGs induced their rapid disassembly, liberating mRNAs into the actively translating pool. Restoration of mRNA translation and modulation of SG dynamics may be an effective treatment of neurodegenerative diseases characterized by eIF2α phosphorylation, SG formation and cognitive loss.

overall_design: Ribosome profiling with paired RNA-seq

first: Carmela

last: Sidrauski

first: Nicholas

last: Ingolia

first: Peter

last: Walter


title: Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining PAR-CLIP with Me-RIP, we identify 39,060 m6A-switches among hnRNP C binding sites transcriptome-wide. We show that m6A-methyltransferases METTL3 or METTL14 knockdown decreases hnRNP C binding at 16,582 m6A-switches. Taken together, 2,798 m6A-switches of high confidence are identified to mediate RNA-hnRNP C interactions and affect diverse biological processes including cell cycle regulation. These findings reveal the biological importance of m6A and provide insights into the sophisticated regulation of RNA-RBP interactions through m6A-induced RNA structural remodeling.

overall_design: Measure the m6A methylated hnRNP C binding sites transcriptome-wide by PARCLIP-MeRIP; measure the differential hnRNP C occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPC, METTL3 and METTL14 knockdown

first: N

last: Liu

first: Q

last: Dai

first: C

last: He

first: M

last: Parisien

first: T


title: RNA-seq data from six cell types for cell type phylogenetics

city: West Haven

first: Koryu

last: Kin

state: CT

address: 840 West Campus Drive

department: EEB

institute: Yale University

summary: We sequenced mRNA from a total of 12 samples (6 different cell types, each with two biological replicates) to infer the relationship among those cell types

overall_design: Examination of mRNA levels in six different human cell types grown in culture with two biological replicates for each cell type


title: CTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [ChIP-Seq]

city: New York City

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor Rm 211

institute: NYU School of Medicine / HHMI

summary: In this experiment, we sought to identify how the distribution of CTCF, H3K27me3, H3K4me3, Pol II, H2AK119Ub1, EZH2

first: Varun

last: Narendra

first: Disi

last: An

first: Esteban

last: Mazzoni


title: Targeting the MLL complex in castration-resistant prostate cancer

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan

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

overall_design: Refer to individual Series


title: CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation


title: CTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [4C-Seq]

summary: In this experiment, we sought to analyze how the spatial organization of WT, Δ5|6, and Δ5|6:7|9 cells vary during differentiation of ESCs into cervical motor neurons


title: TWIST1-induced microRNA-424 drives an intermediate epithelial-to-mesenchymal transition that opposes metastasis

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary: Epithelial-to-mesenchymal transition (EMT) is a dynamic process that relies on cellular plasticity; an EMT/MET axis is critical for metastatic colonization of carcinomas. Unlike epithelial programming, regulation of mesenchymal programming is not well understood in EMT. Here we describe the first microRNA that enhances exclusively mesenchymal programming. We demonstrate that microRNA-424 is up-regulated early during a TWIST1/SNAI1-induced EMT, and that it causes cells to express mesenchymal genes without affecting epithelial genes, resulting in a mixed/intermediate EMT. Further, microRNA-424 increases motility, decreases adhesion and induces a growth arrest, changes associated with a complete EMT. Patient microRNA-424 levels positively associate with TWIST1/2 and EMT-like gene signatures and is increased in primary tumors versus matched normal breast. However, microRNA-424 is down-regulated in metastases versus matched primary tumors. Correspondingly, microRNA-424 decreases tumor initiation and is post-transcriptionally down-regulated in macrometastases in mice. RNA-seq identified microRNA-424 regulates numerous genes associated with EMT and breast cancer stemness including the novel miR-424 target, TGFBR3, which regulates mesenchymal phenotypes without influencing miR-424 effects on tumor-initiating phenotypes; instead, we show that ERK signaling is critical for such tumor-initiating effects of miR-424. These findings suggest microRNA-424 plays distinct roles downstream of EMT-inducing factors, facilitating earlier stages, but repressing later stages, of metastasis.

overall_design: Examination of mRNA levels in MCF12A human breast cell lines that stably over-expressed miR-424 or an empty vector (EV) control. Each group has three replicates.

first: David

middle: J

last: Drasin

middle: L

last: Guarnieri

first: Deepika

last: Neelakantan

first: Joshua

middle: H

last: Cabrera

first: Chu

middle: A

last: Wang

first: Vadym

last: Zaberezhnyy

first: Pierluigi

last: Gasparini

first: Luciano

last: Cascione

first: Kay

last: Heubner

first: Aik

middle: C

last: Tan

first: Heide

last: Ford


title: CTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [RNA-Seq]

last: Reinberg

summary: In this experiment, we sought to analyze how the transcriptome of WT, Δ5|6, and Δ5|6:7|9 cells vary during differentiation of ESCs into cervical motor neurons


title: Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum

city: Durham

first: Christopher

last: Frank

state: NC

address: 101 Science Dr.

institute: Duke University

summary: To identify chromatin mechanisms of neuronal differentiation, we characterized the relationship between chromatin accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing mouse. We used DNase-seq to globally map accessibility of cis-regulatory elements and RNA-seq to profile transcript abundance at key points in postnatal neuronal differentiation in vivo and in culture. We observed thousands of chromatin accessibility changes as CGNs differentiated and determined that many of these regions function as stage-specific neuronal enhancers. Motif discovery within differentially accessible chromatin regions suggested a novel role for the Zic family of transcription factors in CGN maturation, and we confirmed the association of Zic with these elements by ChIP-seq. Knockdown of Zic1 and Zic2 indicated Zic transcription factors are required to coordinate mature neuronal gene expression patterns. These data reveal chromatin dynamics at thousands of gene regulatory elements that facilitate gene expression patterns necessary for neuronal differentiation and function.

overall_design: Biological triplicate DNase-seq and RNA-seq samples from 3 in vivo cerebellum developmental stages (P7, P14, P60) and 3 cultured CGN stages (isolated granule neuron precursors, +3DIV, and +7DIV) obtained.  Zic1 and Zic2 were separately knocked down by lentiviral shRNA in cultured CGNs followed by RNA-seq (2 biological replicates per KD and 2 controls). Zic1/2 and H3K27ac ChIP-seq was performed with in vivo cerebellum at two developmental stages (P7 and P60) in duplicate with matching input and IgG controls.

first: Fang

last: Liu

first: Ranjula

last: Wijayatunge

first: Lingyun

last: Song

first: Matthew

last: Biegler

first: Marty

middle: G

last: Yang

last: Vockley

first: Alexias

last: Safi

first: Charles

last: Gersbach

first: Gregory

middle: E

last: Crawford

first: Anne

last: West


title: Transcript profiles in longissimus dorsi muscle and subcutaneous adipose tissue: A comparison of pigs with different post-weaning growth rates.

status: Public on Feb 25 2015

city: Ames

first: Andrew

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

summary: The objective of this experiment was to use transcriptional profiling of skeletal muscle and adipose tissue to develop a better understanding of the metabolic basis for poor weaned-pig transition. A total of 1,054 pigs were reared in commercial conditions and weighed at birth, weaning, and 3 weeks post- weaning. Transition average daily gain (tADG) was calculated as the average daily gain for the 3-week period post-weaning. Nine pigs from each of the lowest 10th percentile (low tADG) and the 60th-70th percentile (high tADG) were harvested at 3 weeks post-weaning. Differential expression analysis was conduced in both tissues using RNA-Seq methodology

overall_design: mRNA profiling in two different tissues (skeletal muscle and adipose tissue) harvested at 3 weeks post-weaning

first: Chad

last: Pilcher

first: Cassandra

middle: K

last: Jones

first: Martine

last: Schroyen

first: John

middle: F

last: Patience

first: Chris

last: Tuggle

first: James

last: Koltes


title: An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development

city: San Francisco

first: Hunter

last: Richards

state: CA

address: 513 Parnassus Ave., HSW 863

department: Orofacial Sciences

institute: UCSF

summary: Rag1 and Rag2 gene expression in CD4+CD8+ double positive (DP) thymocytes depends on the activity of a distant anti-silencer element (ASE) that counteracts the activity of an intergenic silencer. However, the mechanistic basis for ASE activity is unknown. Here we show that the ASE physically interacts with the distant Rag1 and Rag2 gene promoters in DP thymocytes, bringing the two promoters together to form an active chromatin hub. Moreover, we show that the ASE functions as a classical enhancer that can potently activate these promoters in the absence of the silencer or other locus elements. In thymocytes lacking the chromatin organizer SATB1, we identified a partial defect in Tcra gene rearrangement that was associated with reduced expression of Rag1 and Rag2 at the DP stage. SATB1 binds to the ASE and Rag promoters, facilitating inclusion of Rag2 in the chromatin hub and the loading of RNA polymerase II to both the Rag1 and Rag2 promoters. Our results provide a novel framework for understanding ASE function and demonstrate a novel role for SATB1 as a regulator of Rag locus organization and gene expression in DP thymocytes.

overall_design: Sequencing of Satb1-ChIP and input control from 6 wk old thymus

middle: W

first: Ichiro

last: Taniuchi

first: Y

last: Kohwi

first: T

last: Kohwi-Shigematsu

first: Michael

middle: S

last: Krangel


title: Exposure to 60 minutes of hyperoxia upregulates myocardial humanins in patients with coronary artery disease

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

summary: Background. In experimental setting the concept of myocardial preconditioning-by hyperoxia has been introduced and different intracellular protective mechanisms and their effects have been described. To study whether similar protective phenotype can be induced by hyperoxia also in humans, gene expression profile after hyperoxic exposure was analyzed.   Methods and Findings. Adult patients were randomized to be ventilated with either FiO2 0.4 (n=14) or 1.0 (n=10) for 60 minutes before coronary artery bypass grafting. A tissue sample from the right atrial appendage was taken for gene analysis and expression profile analysis on genome wide level by gene chip analysis was applied.  Exposure to > 96% oxygen for 60 minutes significantly changed the expression of 20 different genes, including upregulation of two different humanins - MTRNR2L2 and MTRNR2L8, and activated a “cell survival” network as detected by Ingenuity Pathway Analyses.  Conclusions. Administration of > 96% oxygen for 1 hour changes gene expression in the myocardium of the patients with coronary artery disease and may enhance cell survival capability.   Background. In experimental setting the concept of myocardial preconditioning-by hyperoxia has been introduced and different intracellular protective mechanisms and their effects have been described. To study whether similar protective phenotype can be induced by hyperoxia also in humans, gene expression profile after hyperoxic exposure was analyzed.   Methods and Findings. Adult patients were randomized to be ventilated with either FiO2 0.4 (n=14) or 1.0 (n=10) for 60 minutes before coronary artery bypass grafting. A tissue sample from the right atrial appendage was taken for gene analysis and expression profile analysis on genome wide level by gene chip analysis was applied.  Exposure to > 96% oxygen for 60 minutes significantly changed the expression of 20 different genes, including upregulation of two different humanins - MTRNR2L2 and MTRNR2L8, and activated a “cell survival” network as detected by Ingenuity Pathway Analyses.  Conclusions. Administration of > 96% oxygen for 1 hour changes gene expression in the myocardium of the patients with coronary artery disease and may enhance cell survival capability.

overall_design: 24 samples, 14 controls and 10 with intervention

first: Inga

last: Karu

first: Peeter

last: Tähepõld

first: Arno

last: Ruusalepp

first: Ene

last: Reimann

last: Kõks

first: Joel

last: Starkopf


title: Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing [Hi-C]

status: Public on Feb 24 2015

city: Atlanta

first: Victor

last: Corces

state: GA

address: 1510 Clifton Rd

department: Biology

institute: Emory University

summary: Chromosomes of metazoan organisms are partitioned in the interphase nucleus into discrete topologically associating domains (TADs). Borders between TADs are preferentially formed in regions containing high density of active genes and clusters of architectural protein binding sites. Transcription of most genes is turned off during the heat shock response in Drosophila. Here we show that temperature stress induces relocalization of architectural proteins from TAD borders to inside TADs, and this is accompanied by a dramatic rearrangement in the 3D organization of the nucleus. TAD border strength declines, allowing for an increase in long-distance inter-TAD interactions. Similar but quantitatively weaker effects are observed upon inhibition of transcription or depletion of individual architectural proteins. New heat shock-induced inter-TAD interactions result in increased contacts among enhancers and promoters of silenced genes, which recruit Pc and form Pc bodies at the nucleolus. These results suggest that the TAD organization of metazoan genomes is plastic and can be quickly reconfigured to allow new interactions between distant sequences.

overall_design: Analysis of 3D chromatin organization using Hi-C in Drosophila Kc167 cells. Cells were grown at 25 C and heat shocked for 20 min at 36.5 C. Cells were also treated with flavopiridol or triptolide to inhibit transcription elongation or initiation, respectively. Cells were depeleted of Cap-H2 or Rad21 using RNAi. Finally, cells depleted of RAd21 were subjected to heat shock at 36.5 C for 20 min.

first: Li

last: Li

first: Xiaowen

last: Lyu


title: Transcriptome response to heat stress in the chicken hepatocellular carcinoma cell line

city: Newark

first: Carl

last: Schmidt

state: DE

address: 531 South College Ave

department: Dept. of Animal and Food Sciences

institute: University of Delaware

summary:
Background: Heat stress triggers an evolutionarily conserved set of responses in cells. The transcriptome responds to hyperthermia by altering expression of genes to adapt the cell or organism to survive the heat challenge. RNA-seq technology allows rapid identification of environmentally responsive genes on a large scale. In this study, we have used RNA -seq to identify heat stress responsive genes in the chicken male white-leghorn hepat ocellular (LMH) cell line.
Result: The transcripts of 812 genes were responsive to heat stress (p <0.01) with 235 genes up- regulated and 577 down-regulated following 2.5 hours of heat stress. Among the up- regulated were genes whose products function as chaperones, along with genes aff ecting collagen synthesis and deposition, transcription factors, chromatin remodelers and genes modulating the WNT and TGF-beta pathways. Predominant among the down-regulated genes were ones that affect DNA replication and repair along with chromosom al segregation. Many of the genes identified in this study have not been previously implicated in the heat stress response.
Conclusion: These data extend our understanding of the transcriptome response to heat stress. Many of the identified biological processes and pathways likely function in adapting cells and organisms to hyperthermic stress. This study may provide important guides to future efforts attempting to improve species abilities to withstand heat stress through genome wide association studies and breeding. In addition, the genes down regulated by heat stress may provide important targets for improving hyperthemic treatment in cancer patients.

overall_design: Cells were grown at either control ( 37oC) or heat stress (43oC) temperatures for 2.5 hours.

first: Liang

last: Sun


title: Role of Tet1 and 5-hydroxymethylcytosine in cocaine action

status: Public on Feb 23 2015

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

type: Methylation profiling by high throughput sequencing


title: Single-cell DNA methylome sequencing and bioinformatic inference of epigenetic cell state dynamics

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: Here we describe a method for whole genome bisulfite sequencing in very small cell populations (µWGBS) and in single cells (scWGBS). Our method is optimized for profiling DNA methylation in many samples at low coverage, and we developed a bioinformatic method that uses collections of single-cell methylomes to infer cell state dynamics. Using these technological advances, we studied epigenetic cell state dynamics in three in vitro models of cellular differentiation and pluripotency and identified patterns of epigenetic remodeling and cell-to-cell heterogeneity.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 1-cell or 4-cell samples were collected from a variety of human and mouse cell lines (KBM7, CCE, K562, 32D, HL60). We also included negative controls (no cells), and cross controls (cells of one species aligned to the other). K562 cells were treated with 5-azacytidine in a final concentration of 1µM to induce demethylation. HL60 cells were treated with 1α,25-dihydroxyvitamin D3 in a final concentration of 10nM to induce differentiation. Naïve pluripotency of CCE ES cells was induced by culturing the cells in ESGRO-2i medium with the addition of 1% FCS. Differentiation of CCE ES cells was induced by treating the cells with all-trans retinoic acid (ATRA) in a final concentration of 0,3µM every third day along with complete LIF-free medium exchange. Embryoid body formation from CCE ES cells was induced by hanging-drop culture for 5 days, followed by 9 days on gelatinized dishes (see treatment annotation). Each experiment, with treated and untreated cells, was performed in multiple biological replicates.  We then measured DNA methylation in the individual 1-cell or 4-cell experiments with bisulfite treatment and high-throughput sequencing. For sequencing, most experiments pooled a 4-cell experiment from one species with a 1-cell experiment from the other, but some replicates were sequenced as a single cell (indicated with SC in the replicate annotation). Two samples (marked as “deep”) were sequenced much deeper than the others. See Farlik et al. (2015) Cell Reports for complete study details.

first: Matthias

last: Farlik

first: Nathan

last: Sheffield

first: Angelo

last: Nuzzo

first: Paul

last: Datlinger

first: Andreas

last: Schoenegger

first: Johanna

last: Klughammer


title: A survey of imprinted gene expression in mouse trophoblast stem cells

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC-Chapel Hill

summary: Several hundred mammalian genes are expressed preferentially from one parental allele due to a process called genomic imprinting. Genomic imprinting is particularly prevalent in extra-embryonic tissue, where it plays an essential role during development. Here, we profiled imprinted gene expression via RNA-Seq in a panel of six mouse trophoblast stem (TSC) lines, which are ex vivo derivatives of a progenitor population that gives rise to the placental tissue of the mouse. We found evidence of imprinted expression for 48 genes, 31 of which had previously been described as imprinted and 17 of which we suggest as candidate imprinted genes. An equal number of maternally and paternally biased genes were detected. Several genes showed variability in imprinted expression between the six TSC lines. Sixteen of the 48 known and candidate imprinted genes were previously or newly annotated noncoding RNAs, and six encoded for a total of 60 annotated microRNAs. Pyrosequencing across a panel of six TSC lines returned levels of imprinted expression that were concordant with RNA-Seq measurements for eight genes examined in all six independently derived TSC lines. Our results solidify TSCs as a cell culture-based experimental model to study genomic imprinting, and provide a quantitative foundation upon which to delineate mechanisms by which the process is maintained in the mouse.

overall_design: RNA-Seq from F1 hybrid TSC lines generated from crosses between Cast and B6 mice.


title: Role of Tet1 and 5-hydroxymethylcytosine in cocaine action (5hmC-Seq and ChIP-Seq)

city: New York

summary: Here we show that Tet1 is down-regulated in mouse nucleus accumbens (NAc), a key brain reward structure, by repeated cocaine administration which enhances behavioral responses to cocaine. Through genome-wide 5hmC profiling, we identified 5hmC changes selectively clustered in both enhancer and coding regions of genes with several annotated neural functions. By coupling with mRNA sequencing, we found cocaine-induced alterations in 5hmC correlate positively with alternative splicing. We also demonstrated that 5hmC alteration at certain genes lasts up to a month after cocaine exposure.

overall_design: DNA Nac samples were collected at various time points after 7 daily cocaoine ip administration for 5hmC and transcriptome analysis

first: Jian

last: Feng


title: Role of Tet1 and 5-hydroxymethylcytosine in cocaine action (RNA-Seq)

overall_design: RNA Nac samples were collected at various time points after 7 daily cocaoine ip administration for 5hmC and transcriptome analysis


title: Functions of BET proteins in GATA1-mediated transcription [ChIP-seq]

city: Philadelphia

first: Aaron

middle: James

last: Stonestrom

state: PA

address: 315 ARC 3615 Civic Center Blvd

department: Hematology

institute: Children's Hospital of Philadelphia

summary:
Transcription factor GATA1 binding in erythroblasts in the presence and absence of BET inhibitor JQ1, and BET protein BRD3 and BRD4 binding in erythroblasts in the presence and absence of GATA1.

Inhibitors of Bromodomain and Extra-Terminal motif proteins (BETs) are being evaluated for the treatment of cancer and other diseases yet their physiologic mechanisms remain largely unknown. We used genomic and genetic approaches to examine BET function in a hematopoietic maturation system driven by GATA1, an acetylated transcription factor previously shown to interact with BETs. We found that while BRD3 occupied the majority of GATA1 binding sites, BRD2 and BRD4 were also recruited to a subset of GATA1-occupied sites. Functionally, BET inhibition impaired GATA1-mediated transcriptional activation, but not repression, genome-wide. Co-activation by BETs was accomplished both by facilitating genomic occupancy of GATA1 and subsequently supporting transcription activation. Using a combination of CRISPR/CAS9-mediated genomic engineering and shRNA approaches we observed that depletion of either BRD2 or BRD4 alone blunted erythroid gene activation, while depletion of BRD3 only affected erythroid transcription in the setting of BRD2 deficiency. These results suggest that pharmacologic BET inhibition should be interpreted in the context of distinct steps in transcriptional activation and partially overlapping functions among BET family members.

overall_design: GATA1 null erythroblasts (G1E) conditionally expressing GATA1 as a GATA1-ER fusion protein were induced to express GATA1 by addition of 100nM estradiol for 24 hours. For GATA1 binding experiments this occurred in the absence or presence of 250nM JQ1. For BRD3 and BRD4 occupancy experiments G1E cells were compared to G1E cells with activated GATA1-ER fusion protein.

first: Belinda

last: Giardine


title: Feedback Inhibition of CREB Signaling Promotes Beta Cell Dysfunction in Insulin Resistance.

city: La Jolla

first: Sam

last: Van de Velde

address: 10010 North Torrey Pines Road

department: Peptide Biology Laboratories

institute: Salk Institute

summary: Although persistent elevations in circulating glucose concentrations promote compensatory increases in pancreatic islet mass, unremitting insulin resistance causes a deterioration in beta cell function that disrupts glucose balance and signals the progression to diabetes 1. Glucagon like Peptide 1 (GLP1) agonists improve glucose tolerance in insulin resistance, although some individuals are unresponsive to treatment.  Here we show that increases in GLP1 during feeding promote beta cell function in part through the PKA-mediated activation of CREB and its coactivator CRTC2 2. Mice with a knockout of CRTC2 in beta cells have impaired oral glucose tolerance due to decreases in circulating insulin concentrations. CRTC2 was found to promote beta cell function in part by stimulating the expression of the transcription factor MafA. Chronic hyperglycemia associated with high fat or high carbohydrate diet feeding disrupted cAMP signaling in pancreatic islets. Indeed, prolonged elevations in circulating glucose concentrations interfered with CREB signaling by activating the mTOR pathway and triggering the hypoxia inducible factor (HIF1)-dependent induction of  the Protein Kinase A Inhibitor beta (PKIB), a potent inhibitor of PKA catalytic activity 3. As disruption of the PKIB gene restored glucose tolerance and insulin secretion in obesity, our results demonstrate how cross-talk between nutrient and hormonal  pathways contributes to loss of pancreatic islet function in insulin resistance.

overall_design: Rat insulinoma cells were used to interrogate the impact of glucose exposure and CREB activity on cAMP dependent gene regulation in the pancreatic beta cells

first: Emilie

last: Blanchet

first: Ezra

last: Wiater

first: Marc

last: Montminy


title: Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing

first: Victor

last: Corces


title: WGBS data of pediatric B-cell acute leukemias

first: Seung-Tae

last: Lee

address: 1450 3rd Street

summary:
We investigated DNA methylomes of 227 pediatric B-cell acute lymphoblastic leukemias (B-ALLs) using whole-genome bisulfite sequencing and high-definition microarrays, along with RNA expression profiles.
The current study identified a link between DNA methylome of B-cell acute lymphoblastic leukemias (B-ALLs) and embryonic stem cell (ESC) bivalency, through which tumor cells can mimic the pluripotency of ESCs.

overall_design: A total of 231 pediatric patients with B-ALL were utilized from the California Childhood Cancer Study. After informed consent, bone marrow specimens packed with leukemic blasts were obtained in each patient. Expression and methylation data of purified Pre-B cells in four developmental stages were retrieved from our previous study (Lee et al., Nucleic Acids Res 2012).

first: Joseph

last: Wiemels


title: NR2C/F orphan receptors induce telomere-genome rearrangements in ALT

city: MONTPELLIER CEDEX 5

first: Jérôme

last: Déjardin

address: 141, rue de la Cardonille

country: France

institute: Institute of Human Genetics

summary: Most sarcomas have complex karyotype and are characterized by multiple chromosomal rearrangements. Moreover, sarcomas very frequently maintain their telomeres by recombination in the process called Alternative Lengthening of Telomeres (ALT) which enables their continuous growth and immortalization. Previously our group showed that orphan receptors bind specifically to the ALT telomeres and that their presence is important for the ALT mechanism. In these studies we focus on the function of orphan receptors at the telomeres and their contribution to telomeric recombination. We demonstrate that orphan receptors induce proximity of their binding sites in telomeric and genomic context and reveal novel aspects of ALT which are telomere-genome rearrangements which can underlie complexity of sarcomas. Our data perturb the dogma of telomere function in protecting the genome integrity. Here we show that in some cases telomeres may in fact drive genomic instability and chromosomal rearrangements by recombination with genomic sites.

overall_design: Characterization of TRF2 and orphan receptor NR2F/C2 binding sites in ALT (-) and ALT (+) cells.

first: Paulina

last: Marzec

first: Claudia

last: Armenise

first: Gaelle

last: Perrot

first: Frederic

last: Chibon


title: Two-Track Epigenetic Remodeling and Backtracking to Embryonic Stem Cell Bivalency in B-cell Acute Lymphoblastic Leukemias

type: Methylation profiling by genome tiling array

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


title: Zic2, an enhancer-binding factor required for embryonic stem cell specification

city: Kansas City

first: Joan

last: Conaway

state: MO

institute: Stowers Institute

summary: The Zinc finger protein of the cerebellum 2 (Zic2) is one of the vertebrate homologs of the  Drosophila pair-rule gene odd-paired (opa). Our molecular and biochemical studies have  demonstrated that Zic2 to preferentially bind to transcriptional enhancers and functions as  a cofactor that interacts with the NuRD complex in ES cells. Detailed genome-wide studies  demonstrate that Zic2 function with Mbd3/NuRD in regulating the chromatin state and  transcriptional output of genes linked to differentiation. Zic2 is dispensable for the selfrenewal  of ES cells but is required for proper differentiation, similar to what has been  previously reported for Mbd3/NuRD. Our study identifies Zic2 as a key factor in the  execution of the pluripotency program with Mbd3/NuRD in ES cells.

overall_design: ChIP-seq of Zic2, Chd4, Mbd3 and Zic3 in mES cells. ChIP-seq of H3K27me3, H3K27ac, H3K4me3, H3K4me1 and PolII in mES cells after Zic2 shRNA and non-targeting shRNA. RNA-seq of mES cells after Zic2, Zic3, Mbd3 and Mta2 shRNA and non-targeting shRNA.

first: Zhuojuan

last: Luo

first: Xin

last: Gao

first: Ali

last: Shilatifard


title: The Effects of Nanog HD Mutants on Mouse Embryonic Stem Cells

status: Public on Feb 21 2015

first: Gladstone

last: Bioinformatics

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

summary: We examined global gene expression patterns of mouse embryonic stem cells overexpressing EGFP, Nanog wild-type, or Nanog L122A mutants in normal, "-LIF" or "+RA" culture conditions by RNA-seq experiments. In “+RA” culture conditions, the expression patterns of the RA-responsive genes were slightly different in WT transfectants and more different in L122A transfectants compared with EGFP transfectants. These results suggested that L122A transfectants showed partial resistant activity against RA-induced differentiation, which was not found in WT mNANOG transfectants.

overall_design: Examination of 3 different transfectants from mouse embryonic stem cell, RF8 line, in 3 different culture conditions.

first: Yohei

last: Hayashi

first: Shinya

last: Yamanaka


title: Functions of BET proteins in GATA1-mediated transcription

first: Aaron

last: Stonestrom

overall_design: Refer to individual Series


title: Genome-wide DNA methylation maps in chronic lymphocytic leukemia cells determined by next-generation sequencing (RRBS)

city: Augusta

first: Huidong

last: Shi

department: Georgia Cancer Center

institute: Augusta University

summary: Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). We conducted a genome-wide DNA methylation analysis in CD19+ B-cells from a group of 43 CLL patients using reduced representation bisulfite sequencing (RRBS). Using base-pair resolution methylation sequencing, 2323 differentially methylated regions between CLL and normal B-cells (CLL-specific DMRs) and 569 between M-CLL and U-CLL samples (IGHV-specific DMRs) were identified in the CLL genomes. The IGHV-specific DMRs are mostly unique when compared to the CLL-specific DMRs. Less than 10% of the IGHV-specific DMRs are located in promoter regions; however, more than half of these overlap with known DNase I hypersensitive sites, enhancer regions marked by histone modification (H3K4Me1 and H3K27Ac), and transcription factor binding sites in the ENCODE datasets, which indicates that these DMRs contain regulatory sequences. Distinctive DNA methylation patterns were observed in M-CLL and U-CLL samples. Overall, U-CLL was found to contain 50% more hypermethylated regions than M-CLL samples. The hypermethylated loci observed in the U-CLL samples also appear to be hypermethylated in normal naïve B-cells as compared memory B-cells, suggesting that M-CLL and U-CLL differ in differentiation status corresponding to normal B-cell differentiation stages. RNA-seq analysis performed using matched samples (n=34), in which both DNA methylation and gene expression data were available, demonstrated excellent correlation between DNA methylation and gene expression. Several genes whose expression status was previously shown to be associated with CLL prognosis such as ZAP70, CRY1, LDOC1, SEPT10, LAG3, and LPL were differentially methylated in the promoter regions between M-CLL and U-CLL samples indicating that DNA methylation plays an important role in defining the gene expression patterns of these prognostic genes. We further validated 9 genes with IGHV-specific DMRs in the promoter regions using bisulfite pyrosequencing, and the results demonstrated excellent correlation between differential methylation and IGHV mutation status. These novel differentially methylated genes could be developed into biomarkers for CLL prognosis. In addition, DNA hypomethylation was observed in a significant number of genes involved in lymphocyte activation such as PDCD1, NFAT1, and CD5. DNA hypomethylation was observed in the proximal promoter and far up-stream enhancer regions of CD5, an important cell surface marker that uniquely identifies CLL. Overall, the DNA methylation landscape in CLL patients indicates that CLL B cells possess an active B-cell phenotype; at the same time, U-CLL and M-CLL are faithfully committed to their lineage resembling either naïve or memory B-cells.  In summary, this comprehensive DNA methylation analysis has identified a large number of novel epigenetic changes in CLL patients. The results from this study will further advance our understanding of the epigenetic contribution to molecular subtypes in CLL.

overall_design: To perform a genome-wide analysis of DNA methylation in CLL, we applied the Reduced Representation Bisulfite Sequencing (RRBS) to CD19+ B-cells isolated from normal control and CLL peripheral blood samples.  The genomic DNA from each sample was digested with the methylation-insensitive restriction enzyme MspI (restriction site, CCGG) and ligated to Illumina sequencing adaptors containing methylated cytosine residues. The ligated MspI fragments were size-selected, treated with sodium bisulfite, and amplified by PCR. The PCR products were purified and sequenced using Illumina Hiseq2000 sequencer with a read length of 100bp.  32 CLL B-cell samples, 10 normal control samples including one each of normal CD19+, CD19+/ IgD+ naïve, and CD19+/CD27+ memory B-cell sample. We generated 20-30 million Illumina sequencing reads for each sample.


title: Effect of Dnmt3a deletion on the global DNA methylation status of osteoclasts

city: Kyotanabe

first: Keizo

last: Nishikawa

state: Kyoto

address: 1-3, Tatara Miyakodani

department: Medical Life Systems

country: Japan

institute: Graduate School of Life and Medical Sciences

summary: Epigenetic regulation is a fundamental mechanism mediating various cellular processes. However, epigenetic mechanisms in osteoclastogenesis remain to be elucidated. We performed MBD-seq analysis to investigate DNA methylation in osteoclasts derived from wild-type and osteoclast-specific Dnmt3a knockout  mice.

overall_design: Examination of DNA methylation in 2 cell types.


title: Next Generation Sequencing Identifies Hoxa1 and Hoxc13 as Downstream Targets of Yap in Mouse Epithelial Tissues

city: Boston

first: Ming

last: Liu

state: MA

address: 188 Longwood Ave

department: Developmental Biology

institute: Harvard School of Dental Medicine

summary: The goals of this study are to identify in vivo downstream targets of Yap through NGS-derived tooth germ transcriptome profiling. The mRNA profiles of wild-type, Yap conditional knockout (CKO) and YAP transgenic (Tg) mouse tooth germs at embryonic day 14.5 were generated by deep sequencing using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level via DNAnexus. The validation was performed through qRT–PCR and in situ hybrydization. A set of Hox genes were differentially expression in Yap CKO and YAP Tg mouse tooth germs, demonstating concurrent expression changes with Yap transcripts. This study provides a platform to systematically identify in vivo downstream targets of genes of interest.

overall_design: The mRNA profiles of wild type, Yap CKO and YAP Tg mouse tooth germs at embryonic day 14.5 were generated by deep sequencing using Illumina Hiseq.

first: Xiu-Ping

last: Wang


title: Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity

city: Berlin

first: Xintian

middle: Arthur

last: YOU

address: Robert-Roessle-str. 10

country: Germany

institute: Max-Delbrueck-Center for Molecular Medicine

summary:
Circular RNAs (circRNAs), formed by the atypical head-to-tail splicing of exons, have re-emerged as a potentially interesting RNA species given recent reports of a surprising diversity and abundance of circRNA in organisms ranging from worm to human. Here, using deep RNA sequencing, we profiled different RNA species in mouse and observed that circRNAs are significantly enriched in neural tissue, relative to other tissues.
Using PacBio sequencing, we determined, for the first time, the circular structure of this population of circRNAs as well as their full-length sequences. We discovered that a disproportionate fraction of the brain circRNA population is derived from host genes that code for synaptic proteins.
Moreover, based on the separate profiling of the RNAs localized in neuronal cell bodies and neuropil (enriched in axons and dendrites), we found that, on average, circular RNAs are more enriched in the neuropil than their host gene mRNA isoforms. Using high resolution in situ hybridization we, for the first time, directly visualized circRNA punctae in the dendrites of neurons.
The host gene origin and location of the circRNA in neurons suggest the possibility that circRNAs might participate in the regulation of synaptic function and plasticity. Consistent with this idea, we observed via profiling at different developmental stages, that the abundance of many circular RNAs changes abruptly at a time corresponding to synaptogenesis.
In addition, following a homeostatic downscaling of neuronal activity many circRNAs exhibit significant up or down-regulation. These data indicate that brain circRNAs are positioned to respond to and regulate synaptic function.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Circular RNA profiling in 13 different samples in mice and four samples in rat, using Illumina sequencing

last: You

first: Irena

last: Vlatkovic

first: Ana

last: Babic

first: Tristan

last: Will

first: Irina

last: Epstein

first: Sun

last: Wei


title: Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing [ChIP]

first: Victor

last: Corces

overall_design: Analysis of the distribution of architectural proteins, chromatin proteins and histone modifications in Drosophila Kc167 cells. Cells were grown at 25 C (NT) or heat shocked for 20 min at 36.5 C (HS). Both control and reference samples are included. For some of the samples, replicates are also included.

first: Li

last: Li

first: Xiaowen

last: Lyu


title: The Transcriptome of Basilar Papilla Hair Cell Regeneration in the Avian Inner Ear

city: London

first: Michael

last: Lovett

state: London

address: Dovehouse St

department: NHLI

institute: Imperial College

summary: A comprehensive transcriptome profile of chicken basilar papilla hair cell across a 7 days regenerative time course.

overall_design: Compare gene expression changes in chicken basilar papilla treated with streptomycin to the control. A total of 60 samples were collected from 8 different time points. Each time point contains 2 biological samples.

first: Anastasia

last: Filia


title: Single Cell Analysis Reveals Unexpected Transcriptional Heterogeneity of Neural Progenitors in the Developing Human Cortex

first: Matthew

middle: Bonser

last: Johnson

state: Massachusetts

address: 300 Longwood Ave.

department: Genetics and Genomics

institute: Boston Children's Hospital

summary: The human cerebral cortex depends for its normal development and size on a precisely controlled balance between self-renewal and differentiation of diverse neural progenitor cells. Specialized progenitors that are common in humans, but virtually absent in rodents, called ‘outer radial glia’ (ORG), have been suggested to be crucial to the evolutionary expansion of the human cortex. We combined cell type-specific sorting with transcriptome-wide RNA-sequencing to identify genes enriched in human ORG, including targets of the transcription factor Neurogenin, and previously uncharacterized, evolutionarily dynamic, long noncoding RNAs. Single-cell transcriptional profiling of human, ferret, and mouse progenitors showed that more human RGC co-express proneural Neurogenin targets than in ferret or mouse, suggesting greater self-renewal of neuronal lineage-committed progenitors in humans. Finally, we show that activating the Neurogenin pathway in ferret RGC promotes delamination and outward migration. Thus, we find that the abundance of human ORG is paralleled by increased transcriptional heterogeneity of cortical progenitors.

overall_design: Three biological replicates of human late mid-fetal cortex (18 to 19 weeks  of gestation) were dissociated and immunolabeled. Apical and outer radial glial cells were purified by FACS and compared to an immunonegative population, predominantly neurons.

first: Christopher

last: Walsh

middle: B

first: Peter

middle: P


title: Transcriptome analysis and Genome-wide DNA methylation maps in chronic lymphocytic leukemia cells determined by next-generation sequencing

status: Public on Feb 20 2015

first: Huidong

last: Shi


title: Questioned validity of GEDDs in DS

first: Long

last: Do

address: 9500 Gilman Drive

institute: University of California, San Diego, School of Medicine

summary: Recently, in studies examining fibroblasts obtained from the tissues of one set of monozygotic twins (i.e. fetuses derived from the same egg) discordant for trisomy 21 (Down syndrome; DS), Letourneau et al. reported the presence of a defined pattern of dysregulation within specific genomic domains they referred to as Gene Expression Dysregulated Domains (GEDDs). GEDDs were described as alternating segments of increased or decreased gene expression affecting all chromosomes. Strikingly, GEDDs in fibroblasts were largely conserved in induced pluripotent cells (iPSCs) generated from the twin’s fibroblasts as well as in fibroblasts from the Ts65Dn mouse model of DS.  Our recent analysis failed to find GEDDs.  We reexamined human iPSCs RNAseq data from Letourneau et al., and data from this same research group published earlier examining iPSCs from the same monozygotic twins. In addition, an independent analysis of RNAseq data from Ts65Dn fibroblasts also failed to confirm presence of GEDDs.  Our analysis questions the validity of GEDDs in DS.

overall_design: Ts65Dn mouse model of DS

first: Nishant

last: Singhal

first: William

last: Mobley


title: Nitrobacter winogradskyi transcriptomic response to ammonia

city: Corvallis

first: Luis

last: Sayavedra-Soto

state: OR

address: Cordley Hall 2082

department: Botany and Plant Pathology

institute: Oregon State University

summary: The comparison was done in chemostats. Cultures maintained nitrite. The transcritome responses were compared at three ammonium concentrations.

overall_design: The comparison was done in chemostats. Single cultures maintained with 60 mM nitrite, and the ammonium supllemented as appropiate.

first: Jose

last: Perez

first: Alex

last: Buchanan

first: Brett

last: Mellbye

first: Rebecca

last: Ferrrel

first: Jeff

last: Chang

first: Frank

last: Chaplen

last: Bottomley


title: Genome-wide characterization of HSF1 binding in human 451Lu melanoma cancer cells under basal conditions

first: Nikos

last: Kourtis

address: 550 First Avenue

institute: NYU School of Medicine

summary: HSF1 orchestrates a transcriptional program vital for cancer cells. In this study we assayed for genome-wide localization of HSF1 enrichment in the 451Lu melanoma in untreated cells. These results revealed a transcriptional program enriched for metastasis-related genes.

overall_design: Twenty million cells were used for the ChIP and precipitated using 5 micrograms of antibody (cell signaling, 4356) against human HSF1


title: Accumulation of inorganic polyphosphate mediates metabolic downshift and antibiotic tolerance in Mycobacterium tuberculosis

city: New Haven

first: Yu-Min

last: Chuang

state: CT

address: 1 Gilbert St TAC S410

department: Infectious disease

institute: Yale University

summary: The stringent response, involving the regulatory molecules inorganic polyphosphate (poly P) and (p)ppGpp, is believed to mediate Mycobacterium tuberculosis persistence. In this study, we identified a novel exopolyphosphatase responsible for poly P hydrolysis. Using two different poly P-accumulating M. tuberculosis recombinant strains, we found that increased poly P content drives the organisms into early growth arrest, and contributes to tolerance to the cell wall-active agent isoniazid, increased resistance to stress conditions, and improved survival in macrophages. Transcriptomic and metabolomics analysis revealed metabolic downshift manifested by reduced expression of the transcriptional and translational machinery, and shift from utilization of glucose as a carbon source. In summary, regulation of the poly P balance is critical for persister formation in M. tuberculosis.

overall_design: The transcriptome of  poly P accumulation strains, Rv1026 knock-down and ppk1 knock-in were compared to empty vector strains by RNA-seq.

first: Nirmalya

last: Bandyopadhyay

first: Dalin

last: Rifat

first: Harvey

last: Rubin

first: Joel

last: Bader

first: Petros

last: Karakousis


title: Genome-wide characterization of HSF1 binding in human WT and FBXW7 KO colon cancer cells under basal conditions and upon heat shock

summary:
FBXW7 modulates stress response by post-translational modification of HSF1
HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. In this study we assayed for genome-wide localization of HSF1 enrichment in the HCT116 FBXW7 KO colon cells and their wild type counterpart in untreated cells and upon heat shock. These results revealed that accumulation of nuclear HSF1 in FBXW7 KO cells results in rewiring of the HSF1 transcriptional program.

overall_design: Five million cells were used for the ChIP and precipitated using 5 micrograms of antibody (cell signaling, 4356) against human HSF1


title: mRNA sequencing of two brain regions (prefrontal cortex and hippocampus) and left myocardial tissue in mice with chronic heart failure vs. sham-operated control mice

city: Würzburg

first: Anna

last: Frey

address: Straubmühlweg 2a

department: Comprehensive Heart Failure Center (CHFC)

institute: University Hospital of Würzburg

summary: After induction of ischemic chronic heart failure (CHF), mice exhibited depression-like behavior, in terms of increased anhedonia, and decreased both exploratory activity and interest in novelty. On histology, ischemic CHF mice showed no alterations in overall cerebral morphology. To further evaluate relevant behavioral changes found in CHF mice, RNA-sequencing analysis of prefrontal cortex and hippocampus - the brain regions, whose structural and functional alterations are associated with an increased risk for developing major depressive disorder - and of left myocardial tissue was performed in CHF vs. sham-operated animals. RNA-sequencing revealed relevant changes in hippocampal or prefrontal cortical expression of genes responsible for axonal vesicle transport (Kif5b), signal transduction (Arc, Gabrb2), limitation of inflammation (RORA; Nr4a1) and of hypoxic brain damage (Hif3a). Besides, the actual literature describes some of the genes (RORA, Gabrb2, Npas4, and Junb) being associated with depression-like behavior. Nr4a1 significantly regulated in both brain and heart tissue after induction of ischemic CHF could be a potential link and reveals the central role of inflammation in the interrelation of the brain and the failing heart.

overall_design: Heart failure vs. sham-operation were performed in C57BL/6 male mice. After development of chronic heart  failure (CHF) 8 weeks after the operation RNA was extracted out of prefrontal cortex, hippocampus and left ventricular myocardium in both groups. RNA of 3 ischemic CHF mice versus 6 sham operated mice was pooled and further subjected to RNA sequencing. To fabricate singular pools each probe of the group equally contributed with the final amount of 2 µg RNA per pool with the result that we had 6 different pools to be further evaluated. The mRNA profile was generated by IGA Technology, Italy (http://www.igatechnology.com/) by deep sequencing, using Illumina HiSeq 2000 platform (HiSeq). CLC-Bio Genomics Workbench software (CLC Bio, Denmark) was used to calculate gene expression levels based on Mortazavi et al. (Nat Methods. 2008;5:621-628) approach.

first: Sandy

last: Popp

first: Antonia

last: Post

first: Simon

last: Langer

first: Marc

last: Lehmann

first: Ulrich

last: Hofmann

first: Anna-Leena

last: Sirén

first: Leif

last: Hommers

first: Angelika

last: Schmitt

first: Tatyana

last: Strekalova

first: Georg

last: Ertl

first: Klaus-Peter

last: Lesch

first: Stefan

last: Frantz


title: Pi3kcb links Hippo-YAP and PI3K-AKT signaling pathways to promote cardiomyocyte proliferation and survival

first: Fei

last: Gu

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School


title: Transriptional profiling upon heat shock and recovery in cells deficient for FBXW7 and their wild type counterpart.

first: Nikos

last: Kourtis

summary:
FBXW7 modulates stress response by post-translational modification of HSF1
HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. Genes positively regulated by HSF1 show increeased expression during heat shock while their expression is reduced during recovery. Genes negatively regulated by HSF1 show the opposite pattern. In this study we utilized the HCT116 FBXW7 KO colon cell line and its wild type counterpart to monitor gene expression changes during heat shock (42oC, 1 hour) and recovery (37oC for 2 hours post heat shock) using RNA sequencing. These results revealed that the heat-shock response pathway is prolonged in cells deficient for FBXW7.

overall_design: Whole RNA was extracted from 1 million HCT116 WT or FBXW7KO  cells using the RNAeasy kit (Qiagen) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Differential gene expression analysis was performed for each matched recovery versus heat-shock pairs, separately in each biological replicate and cell line (WT or KO). Two types of comparisons were tested: (a) WT recovery vs WT heat shock, (b) FBXW7 KO recovery vs heat shock.


title: Methylation dynamics of mouse neuron by MeDIP-seq and MRE-seq

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: Study DNA methylation of mouse neuron using MeDIP-seq and MRE-seq

first: Ting

last: Wang

first: Xiaoyun

last: Xing

first: GiNell

last: Elliott


title: Activin A and BMP4 Modulation of Wnt/β-catenin Signaling Directs Fate Specification of Mesoderm Derivatives from Human Embryonic Stem Cells

city: Seattle

first: Chuck

last: Murry

state: WA

address: 850 Republican St., Box 358050

department: Institute for Stem Cell and Regenerative Medicine, Center for Cardiovascular Biology

institute: University of Washington

summary: We report the derivation of 2 different methods of generating cardiac myocytes from human ESCs. The traditional route is via cardiac progenitor cells and the second, new approach is through re-directing hemogenic endothelium into the cardiac lineage using inhibition of Wnt/b-catenin signaling

overall_design: Examination of 2 different cardiac populations using RNA-seq

first: Nathan

middle: J

last: Palpant

first: Charles


title: Identification of Cbt target genes in Drosophila wing imaginal discs

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

summary: We performed a genome-wide ChIP analysis to find the set of target genes regulated by Cbt in Drosophila wing imaginal discs. We reported multiple transcriptional regulators and genes involved in the developlment, growth and patterning of the fruit fly.

overall_design: Identification of Cabut binding sites in Wing imaginal discs cells

first: Marina

last: Ruiz-Romero

first: Nuria

last: Paricio

first: Florenci

last: Serras

first: Montserrat

last: Corominas


title: Characterizing gene expression in lung tissue of COPD subjects using RNA-seq

city: Seoul

first: JaeHyun

last: Lim

address: Department of Biomedical Sciences, Seoul National University Graduate School, Biomedical Science Building 117, 103 Daehakro, Jongro-gu

country: South Korea

institute: Seoul National University

summary: We analyzed gene expression profiling of lung tissue to define molecular pathway of COPD using recent RNA sequencing technology.Lung tissue was obtained from 98 COPD subjects and 91 subjects with normal spirometry. RNA isolated from these samples was processed with RNA-seq using HiSeq 2000. Gene expression measurements were calculated using Cufflinks software. Differentially expressed genes and isoforms were chosen using t-test. Some of differentially expressed genes were validated by quantitative real-time PCR.

overall_design: Examination of lung tissue in COPD patients versus normal control

first: Woo

last: Kim

first: Jae

first: Juhan

last: Lee

first: Yeon-Mok

last: Oh

first: Sang

middle: D


title: Genome-wide maps of chromatin state in E12.5 mouse forelimbs

first: Chrissa

last: Kioussi

address: 1601 SW Jefferson Ave

summary: The chromatin state in developing body parts provides a zip code to cellular populations that direct their cell fates. We used antibodies for H3K4me3, H3K27me3 and Pol2, to identify the chromatin state signature of the mouse forelimb during mid-gestation, at embryonic day 12. The families of genes marked included those related to transcription, transcriptional regulation, and embryonic organ development. Transcription factors specific for muscle development were characterized by bivalent chromatin, as E12 is a transition time point from embryonic to fetal myogenesis. The identified chromatin state of muscle specific genes was in strong correlation with their observed expression profile.

overall_design: Examination of the histone marks H3K4me3, H3k27me3, and Pol2 in whole E12.5 forelimnb tissues using the Illumina HiSeq 2000.

first: Diana

last: Eng

first: Walter

last: Vogel


title: Expression and epigenetic profiling during mouse ESC neural differentiation

status: Public on Feb 19 2015

city: shanghai

first: Naihe

last: Jing

address: 320 Yue Yang Road

institute: institute of biochemistry and cell biology

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

overall_design: Refer to individual Series


title: Transcriptome analysis in chronic lymphocytic leukemia cells using RNA sequencing (RNA-seq)

first: Huidong

last: Shi

institute: Augusta University

summary: Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). We conducted a genome-wide DNA methylation analysis in CD19+ B-cells from a group of 43 CLL patients using reduced representation bisulfite sequencing (RRBS). Using base-pair resolution methylation sequencing, 2323 differentially methylated regions between CLL and normal B-cells (CLL-specific DMRs) and 569 between M-CLL and U-CLL samples (IGHV-specific DMRs) were identified in the CLL genomes. The IGHV-specific DMRs are mostly unique when compared to the CLL-specific DMRs. Less than 10% of the IGHV-specific DMRs are located in promoter regions; however, more than half of these overlap with known DNase I hypersensitive sites, enhancer regions marked by histone modification (H3K4Me1 and H3K27Ac), and transcription factor binding sites in the ENCODE datasets, which indicates that these DMRs contain regulatory sequences. Distinctive DNA methylation patterns were observed in M-CLL and U-CLL samples. Overall, U-CLL was found to contain 50% more hypermethylated regions than M-CLL samples. The hypermethylated loci observed in the U-CLL samples also appear to be hypermethylated in normal naïve B-cells as compared memory B-cells, suggesting that M-CLL and U-CLL differ in differentiation status corresponding to normal B-cell differentiation stages. RNA-seq analysis performed using matched samples (n=34), in which both DNA methylation and gene expression data were available, demonstrated excellent correlation between DNA methylation and gene expression. Several genes whose expression status was previously shown to be associated with CLL prognosis such as ZAP70, CRY1, LDOC1, SEPT10, LAG3, and LPL were differentially methylated in the promoter regions between M-CLL and U-CLL samples indicating that DNA methylation plays an important role in defining the gene expression patterns of these prognostic genes. We further validated 9 genes with IGHV-specific DMRs in the promoter regions using bisulfite pyrosequencing, and the results demonstrated excellent correlation between differential methylation and IGHV mutation status. These novel differentially methylated genes could be developed into biomarkers for CLL prognosis. In addition, DNA hypomethylation was observed in a significant number of genes involved in lymphocyte activation such as PDCD1, NFAT1, and CD5. DNA hypomethylation was observed in the proximal promoter and far up-stream enhancer regions of CD5, an important cell surface marker that uniquely identifies CLL. Overall, the DNA methylation landscape in CLL patients indicates that CLL B cells possess an active B-cell phenotype; at the same time, U-CLL and M-CLL are faithfully committed to their lineage resembling either naïve or memory B-cells.  In summary, this comprehensive DNA methylation analysis has identified a large number of novel epigenetic changes in CLL patients. The results from this study will further advance our understanding of the epigenetic contribution to molecular subtypes in CLL.

overall_design: To perform a transcriptome analysis in CLL, we generated sequencing libraries from total RNA isolated from purified B-cells of CLL patients and healthy donnors. The RNA-seq libraries were sequenced using Illumina HiSeq2000 sequencer with a read length of 100bp.  11 CLL B-cell samples, 3 normal control samples including one each of normal CD19+ B cells were studied. We generated 20-30 million Illumina sequencing reads for each sample.


title: The dicerlike1 homologue, fuzzy tassel, is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize

city: St. Louis

first: Blake

middle: C.

last: Meyers

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: We have characterized a maize mutant, fuzzy tassel (fzt) with striking inflorescence and pleiotropic defects.  fzt contains a mutation in the maize dicer-like1 homolog, a key enzyme required for microRNA (miRNA) biogenesis. By profiling the small RNA population in fzt mutants, we investigated the impact of fzt mutation on miRNA abundance in seedling and tassel primordia. We also investigated the transcript abundance of potential target genes of miRNA that were impacted in fzt mutant by transcriptome profiling. The result provides an avenue for future research to link specific miRNAs and their targets to discrete phenotypes and developmental roles.

overall_design: Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with Illumina HiSeq 2000 platform.

first: Beth

last: Thompson

first: Tzuu-fen


title: BolA is a transcriptional switch that turns off motility and turns on biofilm development (ChIP-seq)

city: Oeiras

first: Cecilia

middle: M.

last: Arraiano

address: Av. Republica, Apt 127

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa

summary: Bacteria are extremely versatile organisms which rapidly adapt to changing environments. When Escherichia coli cells switch from planktonic growth to biofilm, flagellum formation is turned off, and the production of fimbriae and extracellular polysaccharides is switched on. Here we show that BolA protein is a new bacterial transcription factor which modulates the switch from planktonic to sessile lifestyle. BolA negatively modulates flagella biosynthesis and thus swimming capacity. Furthermore, BolA overexpression favors biofilm formation and involvesinvolving fimbriae-like adhesins and curli production. Our results unraveled for the first time that BolA is a protein with high affinity to DNA, involved in the regulation of several genes of E. coli at a genome-wide scale level. Moreover, this observation further demonstrated that the most significant targets of this protein involved a complex network of genes encoding proteins extremely necessary in biofilm development processes. Herein we propose that BolA is a motile/adhesive transcriptional switch, specifically involved in the transition between the planktonic and the attachment stage of biofilm formation process.

overall_design: In the study presented here DNA enrichment was analyzed in 2 different strains, a strain containing bolA-3xflag-tag and a deletion mutant for this gene, which was used as the control sample.

first: Clémentine

last: Dressaire

first: Ricardo

middle: N

last: Moreira

first: Susana

last: Barahona

first: António

last: de Matos

first: Cecília

middle: M


title: Integrin αvβ3 acting as membrane receptor for thyroid hormones mediates angiogenesis in malignant T cells

status: Public on Feb 18 2015

city: New York

first: Tharu

last: Fernando

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

summary: We have found that thyroid hormones (THs), acting as soluble integrin αvβ3 ligands, activate growth-related signaling pathways in T-cell lymphomas (TCL). Specifically, TH-activated αvβ3 integrin signaling promotes TCL proliferation and angiogenesis, in part, via the up-regulation of VEGF.

overall_design: CUTLL1 cells were treated with T3- and T4-bound agarose or agarose alone for 24hrs. Total RNA was harvested from cells and used for expression profiling via RNA-seq.

first: Leandro

last: Cerchietti

first: Florencia

last: Cayrol


title: Conserved epigenomic signatures between mouse and human elucidate immune basis of Alzheimer's disease

city: Cambridge

first: Andreas

middle: R

last: Pfenning

address: Computer Science and Artificial Intelligence Laboratory

department: CSAIL

institute: Massachusetts Institute of Technology

summary: Alzheimer’s disease (AD) is a severe1 age-related neurodegenerative disorder characterized by accumulation of beta-amyloid (Aβ) plaques and neurofibrillary tangles, synaptic and neuronal loss, and cognitive decline.  Several genes have been implicated in AD, but chromatin state alterations during neurodegeneration remain uncharacterized.  Here, we profile transcriptional and chromatin state dynamics across early and late pathology in the hippocampus of an inducible mouse model of AD-like neurodegeneration.  We find a coordinated downregulation of synaptic plasticity genes and regulatory regions, and upregulation of immune response genes and regulatory regions, which are targeted by factors that belong to the ETS family of transcriptional regulators, including PU.1.  Human regions orthologous to increasing-level enhancers show immune cell-specific enhancer signatures as well as immune cell expression quantitative trait loci (eQTL), while decreasing-level enhancer orthologs show fetal brain specific enhancer activity.  Surprisingly, AD-associated genetic variants are specifically enriched in increasing-level enhancer orthologs implicating immune processes in AD predisposition.  Indeed, increasing enhancers overlap known AD loci lacking protein-altering variants and implicate additional loci that do not reach genome-wide significance.  Our results reveal new insights into the mechanisms of neurodegeneration and establish the mouse as a useful model for functional studies of AD regulatory regions.

overall_design: We profiled gene expression levels through RNA-Seq and histone mark levels through ChIP-Seq to compare control mice to the CK-p25 Alzheimer's disease model at 2 weeks and 6 weeks after induction of neurodegeneration.

first: Elizabeta

last: Gjoneska

first: Anshul

last: Kundaje

first: Li-Huei

last: Tsai

first: Manolis

last: Kellis


title: Genome-wide anaylsis of histone acetylation during mouse ESC differentiation [ChIP-seq]

first: Naihe

last: Jing

summary: Using acetylated histone H3 ChIP-seq, we reveal that the histone H3 acetylation level is gradually increased on the neural gene loci while decreased on the neural-inhibitory gene loci during mouse ESC neural differentiation. By overlapping with the targets of HDAC1 ChIP-seq, we identify Nodal as a target gene repressed by histone deacetylation. Thus, our study reveals an intrinsic mechanism that epigenetic histone deacetylation ensures neural fate commitment by restricting Nodal signaling.

overall_design: Examination of HDAC1 in differentiated day 2 cells and acetylated histone H3 in day 2, day 4 and day 6 cells.

first: Pingyu

last: Liu


title: Pi3kcb links Hippo-YAP and PI3K-AKT signaling pathways to promote cardiomyocyte proliferation and survival [ChIPseq]

first: Fei

last: Gu

summary: Background—YAP, the nuclear effector of Hippo signaling, regulates cellular growth and survival in multiple organs, including the heart, by interacting with TEAD sequence specific DNA-binding proteins. Recent studies showed that YAP stimulates cardiomyocyte proliferation and survival. However, the direct transcriptional targets through which YAP exerts its effects are poorly defined.   Methods and Results—To identify genes directly regulated by YAP in cardiomyocytes, we combined differential gene expression analysis in YAP gain- and loss-of-function with genome-wide identification of YAP bound loci using chromatin immunoprecipitation and high throughput sequencing. This screen identified Pik3cb, encoding p110β, a catalytic subunit of phosphoinositol-3-kinase (PI3K), as a candidate YAP effector that promotes cardiomyocyte proliferation and survival. We validated YAP and TEAD occupancy of a conserved enhancer within the first intron of Pik3cb, and show that this enhancer drives YAP-dependent reporter gene expression. Yap gain- and loss-of-function studies indicated that YAP is necessary and sufficient to activate the PI3K-Akt pathway. Like Yap, Pik3cb gain-of-function stimulated cardiomyocyte proliferation, and Pik3cb knockdown dampened the YAP mitogenic activity. Reciprocally, Yap loss-of-function impaired heart function and reduced cardiomyocyte proliferation and survival, all of which were significantly rescued by AAV-mediated Pik3cb expression.   Conclusion—Pik3cb is a crucial direct target of YAP, through which the YAP activates PI3K-AKT pathway and regulates cardiomyocyte proliferation and survival.

overall_design: Yap wild type ChIPseq and input

first: Zhiqiang

last: Lin

first: Alexander

last: von Gise

first: Pingzhu

last: Zhou

first: Qing

last: Ma

first: Jiangming

last: Jiang

first: Allan

middle: L

last: Yau

first: Jessica

last: Buck

first: Katryna

middle: A

last: Gouin

first: Pim

last: van Gorp

first: Bin

first: Jinghai

last: Chen

first: Jonathan

middle: G

last: Seidman

first: Da-zhi

last: Wang

first: William

middle: T

last: Pu


title: Transcription factor binding dynamics during human ES cell differentiation

last: Tsankov

address: 7 Divinity Drive

institute: Harvard University

summary: Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage specific behavior of selected factors. In addition to the orchestrated remodeling of the chromatin landscape, we find that the binding of several transcription factors is strongly associated with specific loss of DNA methylation in one germ layer and in many cases a reciprocal gain in the other layers. Taken together, our work shows context-dependent rewiring of transcription factor binding, downstream signaling effectors, and the epigenome during human embryonic stem cell differentiation.

overall_design: 200 ChIP-seq experiments profiling 38 transcription factors (TFs) and several chromatin marks in 5 cell types--male human ES cell line HUES64 and directed differentiation of HUES64 towards mesendoderm (dMS, 12 hours), endoderm (dEN, 120 hours), mesoderm (dME, 120 hours), and ectoderm (dEC, 120 hours). In addition, three ES cell lines were derived with shRNA mediated knockdown of GATA4 and differention toward endoderm (dEN_shGATA4) and mesoderm (dME_shGATA4). These cell lines were used for MNChIP-seq of GATA4, SMAD1, and H3K27Ac and for 4 RRBS experiments in GATA4 knockdown and control cell lines.

first: Alex

last: Meissner


title: Genome-wide profiling of miRNA expression dynamics in monocyte-derived dendritic cells following infection with a panel of intra-cellular bacteria

city: Paris

first: Katherine

last: Siddle

address: 28 rue du Dr Roux

institute: Institut Pasteur

summary: We report the application of RNA sequencing to assess the expression dynamics of miRNAs and their isoforms over time upon infection with a panel of six intracellular bacteria (Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis Beijing strain GC1237, Mycobacterium bovis BCG, Salmonella typhimurium strain Keller, Staphloccocus epidermidis and Yersinia pseudotuberculosis)

overall_design: Study of miRNA expression dynamics of monocyte-derived dendritic cells upon bacterial infection using RNA sequencing

first: Lluis

last: Quintana-Murci


title: A multi-scale approach reveals that NFkB cRel enforces a B-cell decision to divide.

city: Los Angeles

last: Hoffmann

address: 570 Boyer Hall

department: MIMG

institute: UCLA

summary: The transcriptomes of individual small and large B cells after 24 h of stimulation were sequenced and genes upregulated in small or large cells were found and analyzed to provide a global charactarization of transcription patterns in growing B cells.

overall_design: We identified 5 large and 5 small viable B cells from images of the C1 IFC containing captured cells. We prepared libraries for the 10 individual cells, a positive bulk control (containing diluted bulk cDNA), a negative control containing only the ERCC spikeins, and a 0h bulk control.

first: Maxim

last: Shokhirev

first: Theresa

last: Russell

first: Jeremy

last: Davis-Turak

first: Harry

last: Birnbaum


title: MicroRNA expression profiles from eggs of different qualities associated with post-ovulatory ageing in rainbow trout

city: Morgantown

first: Hao

last: Ma

state: WV

address: Agriculture Science Building, Evansdale Drive

department: Animal & Nutritional Sciences

institute: West Virginia University

summary: Egg quality is an important aspect in rainbow trout farming. Post-ovulatory aging is one of the most important factors affecting egg quality. MicroRNAs (miRNAs) are the major regulators in various biological processes and their expression profiles could serve as reliable biomarkers for various pathological and physiological conditions. Egg samples from 32 females on day 1, day 7, and day 14 post-ovulation (D1PO, D7PO and D14PO), which had the fertilization rates of 91.8%, 73.4% and less than 50%, respectively, were collected and small RNAs isolated from these samples were subjected to deep sequencing using the Illumina platform. Six miRNAs were found to be differentially expressed between D1PO and D14PO eggs. GO analysis of the target genes of the 6 miRNAs that were down-regulated in D14PO eggs revealed significantly enriched GO terms that are related to stress response, cell death, DNA damage, ATP generation, signal transduction and transcription regulation.

overall_design: Examination of small RNA populations in eggs of different qualities caused by post-ovulatory aging.

first: Gregory

last: Weber

first: Jianbo

last: Yao


title: c-Myc Transcriptionally Amplifies Sox2 Target Genes to Regulate Self-Renewal in Multipotent Otic Progenitor Cells

city: Boston

first: David

last: Corey

address: 220 Longwood Ave.

department: Neurobiology

institute: Harvard Medical School


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and snf[148] ovary Transcriptomes

status: Public on Feb 17 2015

city: Cleveland

first: Helen

middle: Karen

last: Salz

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

institute: Case Western Reserve University School of Medicine

summary: Comparison of wild type and tumorous ovaries reveals that tumors inappropriately express a large number of testis genes

overall_design: mRNA profiles of ovaries from 0-24 hour virgin wild type (WT) and 3 day old snf[148] females were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.


title: c-Myc Transcriptionally Amplifies Sox2 Target Genes to Regulate Self-Renewal in Multipotent Otic Progenitor Cells [ChIP-Seq]

summary: An immortalized multipotent otic progenitor (iMOP) cell was generated by transient expression of c-Myc in Sox2-expressing otic progenitor cells. The procedure activated endogenous c-Myc expression in the cells and amplified existing Sox2-dependent transcripts to promote self-renewal. Downregulation of c-Myc expression following growth factor withdrawal resulted in a molecular switch from self-renewal to otic differentiation.

overall_design: ChIP-Seq was accomplished by immunoprecipitating endogenous RNA PolII, c-Myc and Sox2

first: Kelvin

last: Kwan

first: Jun

last: Shen


title: Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway

status: Public on Feb 16 2015

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

summary:
Purpose: The oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress, limiting neurodegeneration and maintaining normal lifespan in eukaryotes. However, the molecular function of OXR1 is still unknown. Previously we showed that human OXR1 regulates expression of antioxidant genes GPX2 and HO-1 via the p21 signaling pathway.  To examine the role of hOXR1 in global transcription regulation during cellular stress, we employed RNA sequencing to investigate the transcription profile in hOXR1 depleted HeLa cells.
Methods: Control siRNA (siCon) and human OXR1 siRNA (siOXR1) transfected HeLa cells were either harvested directly (siCon_NT, siOXR1_NT) or exposed to 0.5 mM H2O2 for 1 h and then harvested immediately without recovery (siCon_R0h, siOXR1_R0h). Total RNA pooled from duplicate samples was used for RNA sequencing on an Illumina HiSeq2000 platform. The sequence reads that passed quality filters were analyzed at gene level. The Blast2GO program was used to generate gene ontology (GO) annotation of differentially expressed genes (DEGs).The WEGO software was used to further perform GO functional classification and to predict pathways affected. qRT–PCR validation was performed using SYBR Green assays.
Results: In total, in non-treated and hydrogen peroxide exposed cells, hOXR1 depletion results in the down-regulation of 554 genes and the up-regulation of 253 genes. These differentially expressed genes include transcription factors (i.e. HIF1A, SP6, E2F8 and TCF3) and numerous genes of the p53 signaling pathway involved in cell-cycle arrest (i.e. cyclin D, CDK6 and p21) and apoptosis (i.e. CytC and CASP9). Western blot analysis reveals that hOXR1 suppresses CASP9 protein expression and reduces post-translational cleavage into its active form. After exposure to hydrogen peroxide (1 h), 56 early response genes were up-regulated in hOXR1 depleted cells, in which 38 of these genes were not induced in control cells. In addition, a subset of the commonly up-regulated early response genes showed a stronger induction in hOXR1 depleted cells (i.e.  FOS, JUN and DUSP1). Out of a total of 52 differentially expressed transcription factors in hOXR1 depleted cells under normal physiology and oxidative stress condition, 14 genes (including HIF1A, STAT5A, E2F8 and TCF3) are differentially regulated under H2O2 treatment in hOXR1 silenced cells as compared to control cells.  Finally, we demonstrate that hOXR1 depleted cells undergo cell cycle arrest in G2/M phase during oxidative stress.
Conclusions: Human OXR1 is important for regulation of the early stress response to oxidative stress in HeLa cells. HOXR1 modulates the p53 signaling pathway via regulation of genes involved in cell cycle arrest, apoptosis and anti-oxidation. Further, hOXR1 regulates numerous transcription factors of importance for cellular stress responses. In summary, hOXR1 may act as a sensor of cellular oxidative stress to regulate the transcriptional networks required to detoxify reactive oxygen species (ROS) and modulate cell cycle arrest and cell death (apoptosis).

overall_design: The mRNA profiles of hOXR1 depleted and control Hela cells with or without H2O2 treatment 1 h were generated by RNA sequencing using Illumina Hiseq 2000.

first: Xiaolin

last: Lin

first: Alexander

last: Rowe

first: Torbjorn

last: Rognes

first: Lars

last: Eide

first: Magnar

last: Bjoras


title: Functional characterization of human T cell hyporesponsiveness induced by CTLA4-Ig

city: Cincinnati

first: Artem

last: Barski

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

summary: During activation, T cells integrate multiple signals from APCs and cytokine milieu. The blockade of these signals can have clinical benefits as exemplified by CTLA4-Ig, which blocks interaction of B7 co-stimulatory molecules on APCs with CD28 on T cells. Variants of CTLA4-Ig, abatacept and belatacept are FDA approved as immunosuppressive agents in arthritis and transplantation whereas murine studies suggested that CTLA4-Ig can be beneficial in a number of other diseases.  However, detailed analysis of human CD4 cell hyporesponsivness induced by CTLA4-Ig has not been performed. Herein, we established a model to study effect of CTLA4-Ig on the activation of human naïve T cells in a human mixed lymphocytes system. Comparison of human CD4 cells activated in the presence or absence of CTLA4-Ig, showed that co-stimulation blockade during TCR activation does not affect NFAT signaling but results in decreased activation of NF-kB and AP-1 transcription factors followed by profound decrease in proliferation and cytokine production. The resulting T cells become hyporesponsive to secondary activation and, although capable of receiving TCR signals, fail to proliferate or produce cytokines, demonstrating properties of anergic cells. However, unlike some models of T cell anergy, these cells did not possess increased levels of TCR signaling inhibitor CBLB. Rather, the CTLA4-Ig induced hyporesponsiveness was associated with an elevated level of p27kip1 cyclin-dependent kinase inhibitor.

overall_design: Time series. Human resting and activated T cell dUTP mRNA-Seq profiles were generated on Illumina HiSeq2500


title: Gene Expression Defines Natural Changes in Mammalian Lifespan

first: Alexey

last: Fushan

state: Seodaemun-gu

address: 52, Ewhayeodae-gil

institute: EWHA

summary: Mammals differ more than hundred fold in maximum lifespan, which can be altered in either direction during evolution, but the molecular basis for natural changes in longevity is not understood. Divergent evolution of mammals also led to extensive changes in gene expression within and between lineages. To understand the relationship between lifespan and variation in gene expression, we carried out RNA-seq-based gene expression analyses of liver, kidney and brain of 33 diverse species of mammals. Our analysis uncovered parallel evolution of gene expression and lifespan, as well as the associated life history traits, and identified the processes and pathways involved. These findings provide direct insights into how Nature reversibly adjusts lifespan and other traits during adaptive radiation of lineages.

sample_organism:
Erinaceus europaeus
Suncus murinus
Tadarida brasiliensis
Chlorocebus aethiops
Canis lupus familiaris
Ursus americanus
Meles meles
Felis catus
Equus caballus
Sus scrofa
Bos taurus
Capra hircus
Oryctolagus cuniculus
Mesocricetus auratus
Peromyscus leucopus
Meriones unguiculatus
Acomys cahirinus
Mus musculus
Rattus norvegicus
Cavia porcellus
Petaurus breviceps
Tamias sibiricus
Murina leucogaster

overall_design: RNA-seq gene expression profiling in normal liver, kidney and brain of 33 mammalian species.

first: Anton

last: Turanov

first: Sang

last: Lee

first: Eun

last: Kim

middle: V

last: Lobanov

first: Sun

middle: H

last: Yim

first: Vadim

last: Gladyshev


title: Transcriptome changes in Fusarium verticillioides caused by mutation in the transporter-like gene FST1

city: West Lafayette

first: Charles

middle: Peter

last: Woloshuk

state: IN

address: 915 West State St

institute: Purdue University

summary: An gene-expression comparison of the wild type and strain delta-fst1 of Fusarium verticillioides grown on autoclaved maize kernels for six days was conducted.

overall_design: Comparison of gene-expression between the wild type and strain delta-fst1 of Fusarium verticillioides grown on autoclaved maize kernels for six days.  For each strain, RNA was isolated from four biological replicates.  Sequences was obtain by HiSeq Illumina sequencer.

first: Chenxing

last: Niu

first: Gary

last: Payne


title: Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals [ncRNA-Seq]

city: Sherbrooke

first: Sherif

middle: Abou

last: Elela

state: Québec

address: 3201 Jean Mignault

department: Microbiologie and Infectiologie

country: Canada

institute: Université de Sherbrooke Centre of Excellence in RNA Biology

summary: Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that stability of the yeast transcriptome is regulated by malleable RNA degradation signals that permit dynamic response to changes in growth conditions.

overall_design: Total RNA from rnt1d strain was divided in two samples. One sample was treated with purified Rnt1p. The other was only incubated with buffer. The two samples were then enriched for small RNA.

first: Jules

last: Gagnon

first: Mathieu

last: Lavoie

last: Catala

first: Francis

last: Malenfant


title: RNA-Seq of Aged Polg Mutator Mouse Brains

city: Bethesda

first: Mark

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

summary: We have performed both proteomic and transcriptomic analyses of the brains of one-year old Polg mutator mice. As part of this analysis, we generated RNA-Seq data from RNA isolated from one cerebral hemisphere of these mice. mRNA levels and protein  abundance levels were compared in this study.

overall_design: 11 samples of RNA isolated from mouse cerebral hemisphere. 7 Polg D257A/D257A, 1 Polg D257A/WT, and 3 Polg WT/WT. The samples were collected from one-year old male mice.

first: David

last: Hauser

first: Allissa

last: Dillman

first: Jinhui

last: Ding

first: Yan

last: Li