title: Candida albicans induces monocyte training via epigenetic programming through a dectin 1-dependent pathway

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

summary: Non-specific protective effects against reinfection have been described following infection with Candida albicans. Here we show that mice defective in functional T and B lymphocytes were protected against reinfection with C. albicans in a monocyte-dependent manner. C. albicans and beta glucans induced functional programming of monocytes, leading to enhanced cytokine production in vivo and in vitro. The training required the beta glucan receptor dectin 1 and the non-canonical Raf 1 pathway. Monocyte training by beta-glucans was mediated by epigenetic mechanisms through genome-wide changes in histone trimethylation at H3K4. Pathway analysis showed specific induction of epigenetic changes in genes of innate immunity. The functional programming of monocytes, reminiscent of similar properties of NK cells, has been termed “trained immunity” and may be employed for the design of improved vaccination strategies.

overall_design: Chromatin-IP at day7 followed by highthroughput sequencing to look at the differences in  H3K4me3 and H3K27me3  binding in Monocytes either cultured in RPMI only versus those trained for 24hrs with beta glucan. Additionally expression analysis was performed by doing strandspecific RNAseq also for both unstimulated and beta glucan trained monocytes for correlating the histone modification changes with the expression changes. Biological replicates were generated from independent samples for H3K4me3 and RNAseq. Additional H3K4me3 ChIP-seq assays were performed for day0 untreated, 24hrs control and beta glucan trained monocytes. H3K4me3 ChIP-seq was also performed for Mouse macrophages both saline(control) and low dose Candida treated.

first: Jessica

last: Quintin

first: Sadia

last: Saeed

first: Joost

last: Martens

first: Evangelos

last: Giamarellos-Bourboulis

first: Daniela

last: Ifrim

first: Colin

last: Logie

first: Liesbeth

last: Jacobs

first: Trees

last: Jansen

first: Bart-Jan

last: Kullberg

first: Cisca

last: Wijmenga

first: Leo

last: Joosten

first: Ramnik

last: Xavier

first: Jos

last: vander Meer

first: Henk

first: Mihai

last: Netea


title: Transcriptomic analysis of XIST+ and XIST- hES cells

status: Public on Dec 21 2012

city: Paris

first: Céline

last: Vallot

address: 35 rue Hélène Brion

country: France

type: Expression profiling by high throughput sequencing

summary:
Purpose: Compare the transcriptome of homogeneous XIST+ and XIST- hES cell populations.
Methods: We isolated homogeneous XIST+ and XIST- cell populations. The XIST+ cells correspond to cells with a XIST cloud and one ATRX pinpoint. The XIST- cells correspond to cells with no XIST cloud and one ATRX pinpoint.
Results: We took advantage of the clonal pattern of X-chromosome inactivation in H9 cells and analyzed the data in an allelic manner.  By comparing the RNA-Seq data with known H9 SNPs, we identified genomic positions which were relaxed from XCI in XIST- cells compared to XIST+ cells.
Conclusions: Genic as well as unannotated transcripts are massively relaxed from XCI in H9 cells when XIST expression is lost, however, this reactivation is only partial and a large region around the centromere is protected from relaxation of silencing.

overall_design: Total RNA (rRNA depleted) profiles of XIST+ and XIST- human embryonic stem cells

first: Celine

first: Claire

last: Rougeulle


title: Polycomb Cbx orthologs mediate the balance between Hematopoietic Stem Cell self-renewal and differentiation

city: Groningen

first: Leonid

last: Bystrykh

state: Groningen

address: A. Deusinglaan 1

department: European Research Institute for the Biology of Ageing - ERIBA

country: Netherlands

institute: University Medical Center Groningen

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
By genome-wide ChIP-seq analyses we show that Cbx7 and Cbx8 share ~95% of their targets in bone marrow cells.
Cbx7 and Cbx8 have only ~200 targets that are not overlapping between the two proteins.
These distinct Cbx7 and Cbx8 targets show reciprocal expression patterns along hematopoietic differentiation.

overall_design: Overexpression of empty vector (negative control), flag-Cbx7 and flag-Cbx8 in 5-FU treated bone marrow cells (progenitor and stem cells), followed by 1 week culture and subsequent ChIP using flag-M2 agarose beads.

first: K

last: Klauke

first: V

last: Radulovic

first: M

middle: J

last: Broekhuis

first: E

last: Weersing

last: Zwart

first: S

middle: G

last: Olthof

last: Ritsema

first: X

last: Wu

last: Helin

first: L

middle: V

first: G

last: de Haan


title: The Intracellular Life of Mycobacterium avium subsp. paratuberculosis During Macrophage Stress: A Key Role for the Alternative Sigma Factor, SigH

status: Public on Dec 29 2012

city: Madison

first: Pallab

last: Ghosh

address: 1656 Linden Dr

country: USA

institute: UW-Madison

summary: Mycobacterium avium subspecies paratuberculosis (a.k.a. M. paratuberculosis) causes Johne’s disease, an enteric infection in cattle and other ruminants, greatly afflicting the dairy industry worldwide.  Once inside the cell, M. paratuberculosis is known to survive harsh microenvironments, especially those inside activated macrophages.  To improve our understanding of M. paratuberculosis pathogenesis, we examined the phagosome maturation associated with transcriptional responses of M. paratuberculosis during macrophage infection.  Monitoring cellular markers, only live M. paratuberculosis bacilli were able to prevent phagosome maturation and reduce its acidification.  On the transcriptional level, over 300 of M. paratuberculosis genes were significantly, differentially regulated in both naïve and IFN-γ-activated macrophages.  These genes include the sigma factor H (sigH) that was shown to be important during persistent infection in M. tuberculosis.  Interestingly, a sigH-knockout mutant showed increased sensitivity to a sustained level of thiol-specific oxidative stress.  Large-scale RNA sequence analysis revealed that a large number of genes belong to the sigH regulon, especially following diamide stress.  Genes involved in oxidative stress and virulence were among the induced genes in the sigH regulon with a putative consensus sequence for SigH binding was recognized in a subset of these genes (N=30), suggesting direct regulation with SigH.  Finally, mice infections showed a significant attenuation of the ∆sigH mutant compared to its parental strain suggesting a role for sigH in M. paratuberculosis virulence.  Such analysis could identify potential targets for further testing as vaccine candidates against Johne’s disease.

sample_organism: Mycobacterium avium subsp. paratuberculosis K-10

overall_design: Examination of  role played by alternative sigma factor, SigH during M. paratuberculosis infection.

first: Adel

middle: M

last: Talaat


title: Small RNA analysis of Tu And SJD zebrafish strain and their progeny

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA libraries from total RNA isolated from adult ovaries

overall_design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .

first: Rene

middle: F

last: Ketting

first: Lucas

middle: L

last: Kaaij


title: The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer. [human ChIP-Seq]

status: Public on Dec 27 2012

city: Darlinghurst

first: Mark

last: Cowley

state: NSW

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

country: Australia

institute: Garvan Institute of Medical Research

summary: The ets transcription factor ELF5 specifies the differentiation of mammary progenitor cells to establish the milk-secreting lineage. ER- and poor prognosis basal breast cancers arise from this progenitor cell and these cancers express high levels of Elf5. Knockdown of ELF5 expression in basal breast cancer cell lines, or forced expression in luminal breast cancer cell lines, resulted in reduced cell proliferation. Transcript profiling and chromatin immunoprecipitation revealed that the transcriptional activity of ELF5 specified the gene expression patterns that distinguish basal from luminal breast cancer, including suppression of FOXA1, GATA3 and ER, key estrogen-action genes. Tamoxifen treatment of luminal MCF7 cells upregulated Elf5 expression and cells that acquired resistance to Tamoxifen became dependent on ELF5 for proliferation. ELF5 is a regulator of breast cancer cell proliferation, transcriptionally specifies the basal molecular subtype and is utilised by ER+ breast cancer cells to escape proliferative arrest caused by Tamoxifen.

overall_design: ChIP-Seq using an antibody to ELF5, in T47D breast carcinoma cell lines

first: Maria

last: Kalyuga

first: David

last: Gallego-Ortega

first: Heather

last: Lee

first: Liz

last: Caldon

first: Andrew

last: Stone

first: Stephanie

last: Allerdice

first: Fatima

last: Valdes-Mora

first: Rosalind

last: Launchbury

first: Aaron

last: Statham

first: Nicola

last: Armstrong

first: Chehani

last: Alles

first: Adelaide

last: Young

first: Andrea

last: Egger

first: Wendy

last: Au

first: Catherine

last: Piggin

first: Cara

last: Evans

first: Tilman

last: Brummer

first: Warren

last: Kaplan

first: Julia

last: Gee

first: Robert

middle: I

last: Nicholson

last: Sutherland

first: Alex

last: Swarbrick

first: Matthew

last: Naylor

first: Susan

last: Clark

first: Jason

last: Carroll

first: Christopher

last: Ormandy


title: The evolutionary landscape of alternative splicing in vertebrate species

status: Public on Dec 22 2012

city: Toronto

first: Nuno

last: Barbosa-Morais

state: ON

address: 160 College Street, Room 908

department: The Donnelly Centre

country: Canada

institute: University of Toronto

summary: How species with similar repertoires of protein coding genes differ so dramatically at the phenotypic level is poorly understood. From comparing the transcriptomes of multiple organs from vertebrate species spanning ~350 million years of evolution, we observe significant differences in alternative splicing complexity between the main vertebrate lineages, with the highest complexity in the primate lineage. Moreover, within as little as six million years, the splicing profiles of physiologically-equivalent organs have diverged to the extent that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are governed by the highly variable use of a largely conserved cis-regulatory code. However, a smaller number of pronounced species-dependent splicing changes are predicted to remodel interactions involving factors acting at multiple steps in gene regulation. These events are expected to further contribute to the dramatic diversification of alternative splicing as well as to other gene regulatory changes that contribute to phenotypic differences among vertebrate species.

sample_organism:
Xenopus tropicalis
Gallus gallus
Mus musculus
Anolis carolinensis
Tetraodon nigroviridis

overall_design: mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) generated by deep sequencing using Illumina HiSeq

first: Claudia

last: Kutter

first: Stephen

last: Watt

first: Duncan

middle: T

last: Odom

first: Benjamin

last: Blencowe


title: Defining a molecular roadmap of cellular reprogramming into iPS cells [ChIP-Seq]

status: Public on Dec 20 2012

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Factor induced reprogramming is a slow and inefficient process with only rare cells progressing towards induced pluripotent stem cells (iPSCs). Owing to these restraints, mechanistic studies have been limited to analyses of heterogeneous bulk populations undergoing reprogramming and partially reprogrammed cell lines. Here, by combining surface markers (Thy1, SSEA1) and an Oct4-GFP fluorescent reporter allele, we analyzed defined intermediate cell populations poised to becoming iPSCs at the transcriptional and epigenetic levels using genome-wide and single cell technologies. We found that factor-induced reprogramming elicits two discernible transcriptional waves that are characterized by the initial extinction of the somatic gene expression program and the concomitant acquisition of an ESC-like proliferative and metabolic state, followed by the activation of an embryonic pluripotent state primed for differentiation. The first wave is mostly driven by gene activation through c-Myc and gene repression by Klf4, whereas the second wave is a result of gradually activated Oct4/Sox2 targets in cooperation with Klf4 targets and other downstream regulators. While microRNA expression and enrichment for individual histone modifications (H3K4me3 or H3K27me3 enriched promoters) mirrored the observed biphasic transcriptional pattern, the establishment of bivalent domains (H3K4me3/H3K27me3 enriched promoters) occurred more gradually. In contrast, changes in DNA methylation took place predominantly at the end of reprogramming when cells assumed a stable pluripotent state. Cells that became refractory to reprogramming activated the first but failed to initiate the second transcriptional wave. However, introduction of additional copies of the reprogramming transgenes into these cells rescued their ability to form iPSCs, indicating that suboptimal transcription factor levels are a limiting factor for efficient iPSC formation. This integrative analysis allowed us to identify novel genes and microRNAs that enhance reprogramming and surface markers that further subdivide intermediate cell populations. Collectively, our data offer new mechanistic insights into the nature and sequence of molecular events inherent to cellular reprogramming and provide a valuable resource of molecules that may act as roadblocks during iPSC formation.

overall_design: Time series design with samples sorted into subpopulations according to surface markers.

first: Jose

last: Polo

first: Endre

last: Anderssen

first: Ryan

last: Walsh

middle: A

last: Schwarz

first: Christian

last: Nefzger

first: Sue

last: Lim

first: Marti

last: Borkent

first: Effie

last: Apostolou

first: Sara

last: Alaei

first: Jeniffer

last: Cloutier

first: Ori

last: Bar-Nur

first: Sihem

last: Cheloufi

first: Matthias

last: Stadtfeld

first: Maria

middle: E

last: Figueroa

first: Daisy

last: Robinton

first: Sridaran

last: Natesan

first: Ari

last: Melnick

first: Jinfang

last: Zhu

first: Sridhar

last: Ramaswamy

first: Konrad

last: Hochedlinger


title: Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation [DGE]

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

country: China

institute: Agricultural Genomes Institute at Shenzhen

summary: 5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC). Genome-wide profiling of 5-hmC thus far indicated 5-hmC may not only be an intermediate form of DNA demethylation but could also constitute an epigenetic mark per se. We describe a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. This method involves the selective glucosylation of 5-hmC residues, short-sequence tag generation and high-throughput sequencing. We tested this method by screening H9 human embryonic stem cells and their differentiated embroid body cells, and found that differential hydroxymethylation preferentially occur in bivalent genes during cellular differentiation. Especially, our results support hydroxymethylation can regulate key transcription regulators with bivalent marks through demethylation and affect cellular decision on choosing active or inactive state of these genes upon cellular differentiation.

overall_design: In order to explore the role of methylation and hyroxymethylation in regulating gene expression upon cellular differentiation to EBs, we examined  the gene expression level in  H9 human embryonic stem cells and their differentiated embroid body cells by Digital gene expression (DGE), respectively.

first: Fei

last: Gao

first: Yudong

last: Xia

first: Junwen

last: Wang


title: The Mediator MED23 plays opposing roles in directing smooth muscle cell and adipocyte differentiation

city: Shanghai

first: Jingwen

last: Yin

address: yueyang road

institute: SIBCB, CAS

summary: The Mediator complex functions as a control center orchestrating diverse signalings, gene activities, and biological processes. However, how Mediator subunits determine distinct cell fates remains to be fully elucidated. Here, we show that Mediator MED23 controls the cell fate preference that directs differentiation into smooth muscle cells (SMCs) or adipocytes. Med23-deficiency facilitates SMC differentiation but represses adipocyte differentiation from the multipotent mesenchymal stem cells. Gene profiling revealed that the presence or absence of Med23 oppositely regulates two sets of genes: the RhoA/MAL-targeted cytoskeleton/SMC genes and the Ras/ELK1 targeted growth/adipocyte genes. Mechanistically, MED23 favors ELK1-SRF binding to SMC gene promoters for repression, whereas the lack of MED23 favors MAL-SRF binding to SMC gene promoters for activation. Remarkably, the effect of MED23 on SMC differentiation can be recapitulated in zebrafish embryogenesis. Collectively, our data demonstrate the dual, opposing roles for MED23 in regulating the cytoskeleton/SMC and growth/adipocyte gene programs, suggesting its “Ying-Yang” function in directing adipogenesis vs. SMC differentiation.

overall_design: Examination of SRF enrichment in sictrl and si23 10T1/2 cells

first: Xiao

last: Yao

first: Gang


title: H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-renewal and Differentiation

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Chromatin modifications have been implicated in the self-renewal and differentiation of embryonic stem cells (ESCs). However, the function of histone variant H2A.Z in ESCs remains unclear. We show that H2A.Z is highly enriched at promoters and enhancers and is required for both efficient self-renewal and differentiation of murine ESCs. H2A.Z deposition leads to an abnormal nucleosome structure, decreased nucleosome occupancy and increased chromatin accessibility. In self-renewing ESCs, knockdown of H2A.Z compromises OCT4 binding to its target genes and leads to decreased binding of MLL complexes to active genes and of PRC2 complex to repressed genes in self-renewal of ESCs. During differentiation of ESCs, inhibition of H2A.Z also compromises RA-induced RARα binding, activation of differentiation markers and the repression of pluripotency genes. We propose that H2A.Z mediates such contrasting activities by acting as a 'general facilitator' that generates access for a variety of complexes both activating and repressive.

overall_design: ChIP-Seq in murine embryonic stem (mES) cells for H2A.Z and acetylated H2A.Z. ChIP-Seq of H3K4me3, H3K27me3, RbBP5, SUZ12 and OCT4 for mES cells of both H2A.Z RNAi knockdown and shLuc control. ChIP-Seq of RARalpha in H2A.Z knockdown (withdraw of LIF and exposure to RA for 3h) and control cells. MNase-Seq and chromatin accessibility assay using Benzonase digestion followed by next-generation sequencing for mES cells of both H2A.Z RNAi knockdown and shLuc control. ChIP-Seq of H2A.Z and H3K4me3 for mES cells of both MLL4 RNAi knockdown and shLuc control. RNA-Seq for mES cells of H2A.Z knockdown and shluc control. RNA-Seq for embryonic bodies derived from mES cells (H2A.Z knockdown and shLuc control) at day 3 and day 7.

first: Kairong

last: Cui

first: Daniel

last: Northrup

first: Chengyu

last: Liu

first: Chaochen

first: Qingsong

last: Tang

first: Kai

last: Ge

first: David

last: Levens

first: Colyn

last: Crane-Robinson

first: Keji

last: Zhao


title: RNA-Seq of head tissue from Drosophila melanogaster Wild Type and Adar5G1dAdar-/-  mutant

city: Stanford

first: Rui

last: Zhang

state: California

address: 300 Pasteur Drive

institute: Stanford

summary:
Purpose: Validation of Drosophila A-to-I editing sites
Methods: We collected heads of 5 day old male dAdar-/- mutant (y, Adar5G1, w)26 and wild type (w1118) flies. Poly(A)+ RNA was used to prepare RNA-seq libraries which were subsequently sequenced single-end by an Illumina GAII
Results:We builded a framework to identify RNA editing events using RNA-seq data alone in Drosophila. To validate whether the identified A-to-G sites were bona fide A-to-I editing events, we performed RNA-seq for the D.melanogaster wild-type strain (w1118) and for the Adar5G1 null mutant that eliminates RNA editing. We found that our method achieved high accuracy; 98.2% of all A-to-G sites showed only adenosine in the Adar5G1 sample
Conclusions: We anticipate that our method will be very effective in the future to identify RNA editing events in different species.

overall_design: mRNA profiles of heads of 5 day old male dAdar-/- mutant (y, Adar5G1, w)26 and wild type (w1118) flies

first: Liam

middle: P

last: Keegan

first: Mary

last: O'Connell


title: Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation [HMST-Seq]

first: Desheng

last: Gong

type: Methylation profiling by high throughput sequencing

overall_design: We developed a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. In this method, we took advantage of the differential enzymatic sensitivities of the isoschizomers MspI and HpaII. HpaII cleaves only a completely unmodified site, any modification at either cytosine blocks the cleavage, while MspI recognizes and cleaves both 5-mC and 5-hmC, but not the newly discovered 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Furthermore, beta-glucosyltransferase (beta-GT) can transfer a glucose to the hydroxyl group of 5-hmC and generate beta-glucosyl-5-hydroxymethylcytosine (5-ghmC) that blocks MspI digestion. Thus, either by combining beta-GT treatment with MspI digestion or simply applying MspI/HpaII digestion, short sequence tags generated can be used for inferring hydroxymethylation or methylation status in around 1.8 million cytosine sites in the human genome. We tested this method by screening H9 human embryonic stem cells and their differentiated embroid body cells.

first: Fei

last: Gao

first: Yudong

first: Junwen


title: Gene expression analysis of Photobacterium profundum DB110 and TW30 toxR mutant strain at 0.1 MPa and 28 MPa

city: Padova

first: Stefano

last: Campanaro

address: Via Ugo Bassi 58/b

department: Biology

country: Italy

institute: University of Padua

summary: Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of wild type (DB110) and toxR (TW30) mutant strains of the deep-sea bacterium Photobacterium profundum. ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae and able to regulate numerous genes involved in virulence. In P. profundum the abundance and activity of the same protein is influenced by hydrostatic pressure and is able to regulate genes in a pressure-dependent manner. To better characterize the ToxR regulon, we have compared the genes differentially expressed in response to pressure changes with those whose expression is altered between wild type and toxR mutant strains.

overall_design: Four samples were analyzed: DB110 strain grown at 0.1 MPa, DB110 strain grown at 28 MPa, TW30 strain grown at 0.1 MPa, TW30 strain grown at 28 MPa. Two independent coltures (replicates) were grown for each sample, RNA was extracted from each replicate and RNAs from the two replicates were pooled together to reduce biological variability. No replicates were included in experimental design.

first: Douglas

last: Bartlett

first: Giorgio

last: Valle


title: Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation [MeDIP_hMeDIP]

overall_design: We developed a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. In order to validate the results generated by this method, we applied MeDIP-seq and hMeDIP-seq to screen H9 human embryonic stem cells in comparison with the newly developed method.

last: Xia

last: Wang


title: Poised RNA Polymerase II changes over developmental time and prepares genes for future expression (MNase-seq data)

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

institute: Stowers Institute for Medical Research

summary: Poised RNA polymerase II is predominantly found at developmental control genes and is thought to allow their rapid and synchronous induction in response to extracellular signals. How the recruitment of poised RNA Pol II is regulated during development is not known. By isolating muscle tissue from Drosophila embryos at five stages of differentiation, we show that the recruitment of poised Pol II occurs at many genes de novo and this makes them permissive for future gene expression. When compared to other tissues, these changes are stage-specific and not tissue-specific. In contrast, Polycomb group repression is tissue-specific and in combination with Pol II (the balanced state) marks genes with highly dynamic expression. This suggests that poised Pol II is temporally regulated and is held in check in a tissue-specific fashion. We compare our data to mammalian embryonic stem cells and discuss a framework for predicting developmental programs based on chromatin state.

overall_design: MNase-seq data for examining nucleosome occupancy in specific Drosophila tissues during development

first: Bjoern

last: Gaertner

first: Jeff

last: Johnston

last: Chen


title: Poised RNA Polymerase II changes over developmental time and prepares genes for future expression (ChIP-seq data)

overall_design: ChIP-seq for Pol II, H3K4me3 and H3K27me3 in various Drosophila embryos and tissues

first: Kai


title: Evolutionary dynamics of gene and isoform regulation in mammalian tissues

city: Cambridge

first: Jason

last: Merkin

email: jmerkin@mit.edu, jjmerkin@gmail.com

address: 31 Ames St

institute: MIT

summary: Most mammalian genes produce multiple distinct mRNAs through alternative splicing, but the extent of splicing conservation is not clear.  To assess tissue-specific transcriptome variation across mammals, we sequenced cDNA from 9 tissues from 4 mammals and one bird in biological triplicate, at unprecedented depth.  We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific.  Thousands of novel, lineage-specific and conserved alternative exons were identified; widely conserved alternative exons had signatures of binding by MBNL, PTB, RBFOX, STAR and TIA family splicing factors, implicating them as ancestral mammalian splicing regulators.  Our data also indicates that alternative splicing is often used to alter protein phosphorylatability, delimiting the scope of kinase signaling.

sample_organism:
Gallus gallus
Macaca mulatta
Bos taurus
Mus musculus
Rattus norvegicus

overall_design: Tissue transcriptomes from 9 tissues from 5 species, 3 individuals per species, were sequenced and compared (two samples for mouse_heart)

first: Christopher

middle: B

last: Burge


title: Poised RNA Polymerase II changes over developmental time and prepares genes for future expression (RNA-seq data)

overall_design: mRNA-seq of Drosophila tissues during development

first: Karin

last: Zueckert-Gaudenz

first: Ariel

last: Paulson


title: Digital Gene Expression (DGE) of thyroid hormone (T3)-responsive genes in C17.2 cells stably transfected with thyroid hormone receptors alpha and beta

status: Public on Dec 31 2012

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

institute: INSERM

summary: Tagged versions of thyroid hormone receptors alpha (TRa) and beta (TRb) were stably transfected in two C17.2 cell lines, C17.2a and C17.2b, respectively. Cells were treated with 10-7 M T3 for 6, 12 or 24h or left untreated. We performed DGE by sequencing all polyA RNA according to a SAGE-derived method. Differential gene expression after T3 treatment was computed and the T3 responses induced by the two receptors were compared. We could conclude that, in a similar environment, target genes are only partially shared and that a significant proportion show receptor preference and even selectivity.

overall_design: Examination of thyroid hormone target genes over time in two cell lines (C17.2a, C17.2b), each expressing one of the thyroid hormone receptors (alpha, beta).

first: Romain

last: Guyot

first: Frédéric

last: Flamant


title: Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation

first: Desheng

last: Gong

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

overall_design: Refer to individual Series


title: Effect of glucose availability on microRNA expression and Ago2 occupancy.

status: Public on Dec 17 2012

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: For cells to grow and proliferate both a growth signal and available nutrients are required.  Several lines of evidence suggest that there is recriprocal regulation of nutrients by growth signals and growth signals by nutrients.  Since microRNAs are regulated by growth signals, we sought to determine if microRNAs could also be regulated by nutrient availability.  We found that several microRNAs change expression following glucose starvation and that their Ago2 occupancy remains constant.

overall_design: Immortalized Bax/Bak double-knockout mouse embryonic fibroblasts were deprived of glucose for 5 days and then re-fed glucose for 2 days.  Cells were collected at the beginning of the starvation period (d0), following five days of glucose deprivation (d5), and following two days of glucose re-feed (d7).  Total RNA was isolated from half of the collected cells using Trizol and the remaining cells were used to perform Ago2 immunoprecipitation followed by isolation of bound RNA.

first: Scott

middle: H

last: Olejniczak

first: Craig

last: Thompson


title: Poised RNA Polymerase II changes over developmental time and prepares genes for future expression

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus


title: Genome-wide identification of alternate bearing-associated miRNA in the olive tree (Olea europaea)

status: Public on Dec 18 2012

city: cankiri

first: mine

last: turktas

address: ballica campus

country: Turkey

institute: cankiri karatekin university

summary: We aimed to identify miRNA regulated by alternate bearing in O. europaea. For this purpose, six olive (Olea europaea L. )(Ayvalık variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on-year" and "off-year" mature -leaven in November and juvenile - leaven in July plants) and sequenced by high-throughput Illumina sequencing. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in olive tree. In addition, 38 novel miRNA were discovered in the datasets. Expression of olive tree miRNA varied greatly among the six libraries, indicating contribution of diverse miRNA in balancing between reproductive and vegetative phases. The differential expression of miRNA was evaluated on the basis of the developmental phase of the samples.

overall_design: Sequences of six olive miRNAs (Olea europaea L. )(Ayvalık variety) plants (ripe and unripe fruits, leaves of mature and juvenile plants of both "on-year" and "off-year") were generated by Illumina sequencing

first: Huriye

last: Yanik

first: Mine

last: Turktas

first: Ekrem

last: Dundar

first: Pilar

last: Hernandez

first: Gabriel

last: Dorado

first: Turgay

last: Unver


title: Estrogen-responsive Estrogen Receptor alpha binding sites in MCF-7 by ChIP-seq

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary:
Identification of Estrogen Receptor alpha (ERa) binding sites by ChIP-seq in MCF-7 breast cancer cells following an estrogen treatment.
This study describes molecular effects of estradiol treatment and subsequent regulation by ER for a single gene/locus. A public ER chipseq (available in SRA as ERR011973), in addition to our own data, guided us to regulatory regions were ER was binding that were then analyzed in detail using "manual" ChIP.

overall_design: MCF-7 cells were treated for 1 h either 10 nm estradiol (E2) or vehicle (ethanol) and subjected to ChIP using antibodies against ERa or IgG.

first: Jorma

last: Palvimo

last: Väisänen

first: Marjo

last: Malinen


title: Defining a molecular roadmap of cellular reprogramming into iPS cells

first: Ben

last: Wittner

type: Methylation profiling by genome tiling array

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae


title: Transcriptome sequencing of Pteropus alecto and  Myotis davidii

city: shenzhen

first: zhiyong

last: huang

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

institute: BGI-Shenzhen, Shenzhen 518083, China

summary: Deep sequencing of mRNA from  Pteropus alecto and  Myotis davidii

sample_organism:
Pteropus alecto
Myotis davidii

platform_organism:
Pteropus alecto
Myotis davidii

overall_design: Analysis of ploy(A)+ RNA of Pteropus alecto and  Myotis davidii

first: Guojie

last: Zhang

first: Chris

last: Cowled

first: Zhiyong

last: Huang

first: Linfa

last: Wang


title: cis-Regulation of Shh-directed neural pattering

status: Public on Dec 15 2012

city: Los Angeles

first: Kevin

last: Peterson

state: CA

address: 1425 San Pablo St.

department: Department of Stem Cell Biology and Regenerative Medicine

institute: Eli and Edythe Broad-CIRM Center for Regenerative Medicine, University of Southern California Keck School of Medicine


title: Iron uptake controls the generation of Leishmania infective forms through regulation of ROS levels .

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

summary: During its life cycle Leishmania undergoes extreme environmental changes, alternating between insect vectors and vertebrate hosts. In mammals the parasites replicate within parasitophorous vacuoles of macrophages, compartments that contain low concentrations of iron. Here we show that stimulation of iron transport, which is induced in Leishmania amazonensis by an iron-poor environment, triggers the differentiation of avirulent promastigotes into virulent amastigotes. Iron depletion from the culture medium triggered expression of the LIT1 ferrous iron transporter, growth arrest, and differentiation of wild type promastigotes into infective amastigotes. In contrast, LIT1 null promastigotes showed continued exponential growth in iron-poor media, followed by massive cell death. Iron depletion from the medium and LIT1 upregulation increased iron superoxide dismutase activity (FeSOD) in wild type, but not in LIT1 null parasites. Notably, the superoxide-generating drug menadione or H2O2 were sufficient to trigger differentiation of wild type promastigotes into fully infective amastigotes. On the other hand, LIT1 null promastigotes accumulated superoxide radical and initiated amastigote differentiation after exposure to H2O2, but not to menadione. Our results reveal a novel role for FeSOD activity and reactive oxygen species (ROS) in orchestrating the differentiation of Leishmania infective stages, in a process regulated by iron availability.

overall_design: Four samples were obtained in total from wild-type L. amazonensis promastigotes grown for 24 hours in culture. Two of these  samples derived from medium with iron and two from mediam without iron.These two samples derived from each culture served as biological replicates.

first: Bidyottam

last: Mittra

first: Mauro

last: Cortez

first: Andrew

last: Haydock

first: Peter

last: Myler

first: Norma

middle: W

last: Andrews


title: Comparative Genomic and Transcriptomic Analysis of NaCl-Tolerant Staphylococcus sp. OJ82 from Fermented Seafood

status: Public on Dec 19 2012

city: Seoul

first: Sungjong

last: Choi

address: Anam-dong Seongbuk-Gu

country: South Korea

institute: Korea university

summary: Analysis of gene expression of Staphylococcus sp.OJ82 from fermented seafood  in salted environment

overall_design: Total RNA obtained from Staphylococcus sp.OJ82 in 1% and 11% NaCl condition


title: Genome-wide identification of enhancers in skeletal muscle

first: Brian

last: Dynlacht

address: 550 1st avenue

institute: NYU Langone Medical Center

summary: In an effort to identify the compendium of regulatory elements that govern myogenic differentiation, we generated chromatin state maps based on the recruitment of factors (p300 and PolII) and histone modifications (H3K4me1, H3K27ac) that typify enhancers in myoblasts and myotubes. We found a remarkable concordance between the location of these newly defined, active enhancers and MyoD1 binding events. In addition, we found a striking association between the position of enhancers and RNA polymerase II recruitment, which resulted in the expression of previously disclosed non-coding RNAs, as well as potentially new transcripts identified ab initio, throughout the enhancer region.

overall_design: Mapping of H3K27ac and p300 in growing myoblasts (MB) and fully differentiated myotubes (MT). Mapping of c-Jun in growing myoblasts (MB).

first: Roy

last: Blum

first: Vasupradha

last: Vethantham

first: Christopher

last: Bowman

first: Michael

last: Rudnicki

middle: D


title: Knockdown of CDKN1C (p57kip2) and PHLDA2 results in developmental changes in bovine pre-implantation embryos

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Transcriptome of CDKN1C-siRNA-injected embryos were compared to sham-injected embryos using RNA-sequencing to determine the genes and pathways downstream of the silenced gene that may have been altered.

overall_design: Transcriptome comparison between two pools of embryos (i.e. CDKN1C-siRNA-injected vs sham-injected embryos)

first: Ashley

last: Driver

first: Wen

first: Jenna

last: Kropp

first: Hasan

last: Khatib


title: Differentially regulated genes in TOR knockdown Arabidopsis lines

city: Saskatoon

first: Raju

last: Datla

state: SK

address: 110 Gymnasium Place

department: Plant Biotechnology Institute

institute: National Research Council

summary: Rapamycin-sensitive transgenic Arabidopsis lines (BP12) expressing yeast FK506 Binding Protein12 (FKBP12) were developed. Inhibition of TOR in BP12 plants by rapamycin resulted in slower overall root, leaf and shoot growth and development leading to poor nutrient uptake and light energy utilization. Genetic and physiological studies together with RNA-Seq and metabolite analysis of TOR-suppressed lines revealed that TOR regulates development and lifespan in Arabidopsis by restructuring cell growth, carbon and nitrogen metabolism, gene expression, ribosomal RNA and protein synthesis.

overall_design: Arabidopsis WT (Col)and BP12-2 (TOR knockdown line) seedlings at 15 DAG were treated with rapamycin for 3 days by transferring from 0.5 MS medium to 0.5 MS+10 µg/ml rapamycin. Triplicate samples of rapamycin treated WT and BP12-2 seedlings were used for RNA-Seq analysis (Illumina Hiseq 2000). Paired-end alignments were obtained through aligning short reads onto the reference Arabidopsis Genome (TAIR9) using Bowtie. More than 80% of the reads mapped onto the genome. Htseq-count was used to count the reads from the Bowtie derived output files. Differential expressed genes were identified using edgeR. The FDR-corrected P value for differential expression was set to be ≤0.05.

first: Maozhi

last: Ren

first: Prakash

last: Venglat


title: ChIP-seq analysis of Gli1 and Sox2 input to neural progenitor program and integration with actve histone marks

first: Kevin

last: Peterson

summary: In the vertebrate neural tube, regional Sonic hedgehog (Shh) signaling invokes a time- and concentration-dependent induction of six different cell populations mediated through Gli transcriptional regulators. Elsewhere in the embryo, Shh/Gli responses invoke different tissue appropriate regulatory programs. To elucidate Shh/Gli regulation of neural fate sepcification, we performed Gli1  ChIP-Seq analysis. We further analyzed two transcription factors whose motifs were enriched in Gli1 ChIP data (Sox2 and Foxa2).  Two active histone marks (H3K4me2 and H3K27ac) were additionally analyzed to study activity status of Shh-responsive cis-elements.

overall_design: Active enhancer histone marks and transcription factor binding patterns were obtained from neuralized emrbyoid bodies. Biological replicates were performed for Gli1 and mock FLAG chips. Histone profiling for enhancer marks were taken from  time course experiment performed in parallel.

first: Yuichi

last: Nishi

first: Andrew

last: McMahon


title: ChIP-seq analysis of KAP1 binding and H3K9me3 modifications in mouse T cell progenitors

status: Public on Dec 16 2012

city: Milan

first: Francesca

middle: R.

last: Santoni de Sio

address: via Olgettina 58

department: SR-TIGET

institute: San Raffaele Scientific Institute

summary: Chromatin remodelling at specific genomic loci controls lymphoid differentiation. Here, we investigated the role played in this process by Kruppel-Associated Box (KRAB)- Associated Protein 1 (KAP1), the universal cofactor of KRAB-zinc finger proteins (-ZFPs), a tetrapod-restricted family of transcriptional repressors. T cell-specific Kap1-deleted mice displayed a significant expansion of immature thymocytes, imbalances in CD4+/CD8+ cell ratios and impaired responses to TCR stimulation when compared to littermate KAP1 control mice. Transcriptome and chromatin studies revealed that KAP1 binds T cell-specific cis-acting regulatory elements marked by the H3K9me3 repressive mark and enriched in Ikaros/NuRD complexes. Also, KAP1 directly controls the expression of several genes involved in TCR and cytokine signalling. Among these, regulation of FoxO1 seems to play a major role in this system. Likely responsible for tethering KAP1 to at least part of its genomic targets, a small number of KRAB-ZFPs are selectively expressed in T lymphoid cells. These results reveal the so-far unsuspected yet important role of KAP1-mediated epigenetic regulation in T lymphocyte differentiation and activation.

overall_design: Examination of KAP1 binding sites and H3K9me3-enriched regions in wild type and KAP1 KO mouse thymocytes.

middle: R

first: Adamandia

last: Kapopoulou

first: Didier

last: Trono


title: Magnesium Availability Regulates Development of Root Hairs in Arabidopsis thaliana

status: Public on Dec 14 2012

city: Hangzhou

first: Gulei

last: Jin

state: Zhejiang

address: Yuhangtang Road 388#

institute: Zhejiang University

summary: Root hairs are frequently reported to be plastic in response to nutrient supply, but relatively little is known about their development in response to magnesium (Mg) availability, and evidence is scarce about the signals involved in this process. Here, we showed that both density and length of root hairs of Arabidopsis decreased logarithmically with increasing Mg supply in the media , which correlated with the initiation of new trichoblast files and likelihood of trichoblasts to form hairs. Low Mg resulted in greater concentrations of reactive oxygen species (ROS) and Ca2+ in the roots and displayed a stronger tip-focused gradient of ROS and cytosolic Ca2+ concentration ([Ca2+]c) during initiation and elongation of root hairs. This gradient could be eliminated by DPI or BAPTA. Application of either DPI or BAPTA to low Mg treatment blocked the enhanced development of root hairs. The opposite was true when the plants under high Mg were supplied with Ca2+ or PMS. Whole-genome transcriptome data revealed that the maximum differential expressed genes involved in ‘stress’, ‘oxidation reduction’, ‘ion transport and homeostasis’ and ‘cell wall organization’. A greater fraction of morphogenetic H-genes and root hair -specific genes as well as genes involved in ‘cell wall structure’ were up-regulated by 7-d treatment of 0.5 μM Mg but down-regulated by 7-d treatment of 10,000 μM Mg. It is concluded that a distinct and previously poorly characterized response of root hair development to Mg availability is presented in Arabidopsis where ROS and Ca2+ are the signaling molecules that control this response.

overall_design: Roots were sampled from five-week-cultivated Arabidopsis after 4d and 7 d treatments of low Mg (supplied with 0.5 μM Mg2+) and high Mg (supplied with 10 mM Mg2+).

first: Yaofang

last: Niu

first: Rushan

last: Cai

first: Lijuan

last: Liu

first: Miao

first: Caixian

last: Tang

first: Yongsong

last: Zhang


title: Pregnancy-induced gene expression and differentiation of mouse mammary epithelium are co-governed by Nuclear Factor IB (NFIB) and STAT5

status: Public on Dec 13 2012

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

institute: Dankook University

summary: Cytokines control the expression of common and cell-specific genes through the transcription factor STAT5. In mammary tissue specifically, expression of approximately 570 genes is induced during pregnancy by prolactin through STAT5, which binds to putative regulatory sequences. We have now asked whether mammary-specific induction of these genes can be linked to the presence of additional transcription factors, which would act in concert with STAT5. RNA-seq analysis at parturition identified 370 genes that were under NFIB control. Notably, 75% of these genes, encoding proteins linked to the differentiation of mammary epithelium, were also regulated by STAT5. This study demonstrates that the STAT5-NFIB module is an essential part of genes that define differentiation and function of the mammary gland.

overall_design: Expression profiling by high throughput sequencing in wild-type (WT) and Nfib-null (KO) mammary gland tissues

first: Yong

first: Kyung

last: Yoo

first: Bingmei

last: Zhu

first: Daisuke

last: Yamaji

first: Richard

last: Gronostajski

first: Gertraud

last: Robinson

first: Lothar

last: Hennighausen


title: DICER- and AGO3-dependent generation of retinoic acid-induced DR2 Alu RNAs regulates human stem cell proliferation

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

address: 9500 Gilman Drive

institute: HHMI/UCSD


title: Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays [RNA-Seq]

city: Miami

first: Camilo

last: Valdes

state: FL

address: Locator C-213.  1120 NW 14 Street

department: Center for Computational Science

institute: University of Miami

summary: In order to study molecular changes in the stroma from tissue samples it is recommended to separate tumor tissue from stromal tissue. This is particularly relevant to mouse tumor xenograft models where tumor, particularly metastatic tumors, can be small and difficult to separate from the host tissue. In our research we compared qualitatively the ability of high-throughput mRNA sequencing, RNA-Seq, and microarrays to detect tumor (human) and stromal (mouse) expression from mixed tumor-stromal samples in terms of the genes and pathways that are involved in cross-alignment (RNA-Seq) and cross-hybridization (microarrays).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human samples consisted of total RNA obtained from MDA-MB-231 human breast carcinoma cell line and isolated from three independent cultures of sub-confluent MDA-MB-231 cell lines in exponential phase of growth.  Mouse samples were obtained from NOD scid gamma mice, and normal lung tissue was harvested from three independent age-matched mice.

first: Jennifer

last: Clarke


title: FMR1 targets distinct mRNA sequence elements to regulate protein expression [PAR-CLIP]

first: Manuel

last: Ascano

address: 1230 York Avenue Box 186

department: HHMI/Laboratory of RNA Molecular Biology

institute: The Rockefeller University

summary: Fragile-X Syndrome (FXS) is a multi-organ disease leading to mental retardation, macro-orchidism in males, and premature ovarian insufficiency in female carriers. FXS is also a prominent monogenic disease associated with autism spectrum disorders (ASD). FXS is typically caused by the loss of FRAGILE X-MENTAL RETARDATION 1 (FMR1) expression, which encodes for the RNA-binding protein (RBP), FMR1 (or FMRP). We report the discovery of the RNA recognition elements (RREs), binding sites, and mRNA targets for wild-type and I304N mutant FMRP isoforms as well as its paralogs, FXR1 and FXR2. RRE frequency, ratio, and distribution determine target mRNA association with FMRP. Among highly-enriched targets, we identified many genes involved in ASD and demonstrate that FMRP can affect their protein levels in cell culture, mice, and human brain. Unexpectedly, we discovered that these targets are also dysregulated in Fmr1-/- mouse ovaries, showing signs of premature follicular overdevelopment. These results indicate that FMRP targets shared signaling pathways across different cellular contexts. As it is become increasingly appreciated that signaling pathways are important to FXS and ASD, our results here provide an invaluable molecular guide towards the pursuit of novel therapeutic targets for these devastating neurological disorders.

overall_design: PAR-CLIP profiling for wild-type and I304N mutant FMRP isoforms as well as paralogs, FXR1 and FXR2.

first: Neelanjan

last: Mukherjee

first: Pradeep

last: Bandaru

first: Jason

last: Miller

first: Jeff

last: Nusbam

first: David

last: Corcoran

first: Christine

last: Langlois

first: Mathias

last: Munschauer

first: Markus

last: Hafner

first: Zev

last: Williams

first: Uwe

last: Ohler

first: Thomas

last: Tuschl


title: Characteristics of Cross-Hybridization and Cross-Alignment in Pseudo-Xenograft samples by RNA-Seq and Microarrays


title: SKIP Is a Component of the Spliceosome Linking Alternative Splicing and the Circadian Clock in Arabidopsis

city: Shenyang

first: Xiaoxue

last: Wang

state: Liaoning

address: 120 Dongling Road, Shenhe District

department: Rice Research Institute

institute: Shenyang Agricultural University

summary: Circadian clocks generate endogenous rhythms in most organisms from cyanobacteria to humans and facilitate entrainment to environmental diurnal cycles, thus conferring a fitness advantage. Both transcriptional and posttranslational mechanisms are prominent in the basic network architecture of circadian systems. Posttranscriptional regulation, including mRNA processing, is emerging as a critical step for the clock function. However, little is known about the molecular mechanisms linking RNA metabolism to the circadian clock network. Here we report that a conserved SNW/SKIP domain protein, SKIP, a splicing factor and component of the spliceosome, is involved in the posttranscriptional regulation of circadian clock genes in Arabidopsis. Mutation in SKIP lengthens the circadian period in a temperature sensitive manner, affects light input and the sensitivity of light resetting to the clock. SKIP physically interacts with the spliceosomal splicing factor SR45 and associates with the pre-mRNA of clock genes, such as PRR7 and PRR9, and is necessary for the regulation of their alternative splicing and mRNA maturation. Genome-wide investigations reveal that SKIP functions in regulating alternative splicing of many genes, presumably through modulating recognition or cleavage of 5' and 3' splicing site. Our study addresses a fundamental question on how the mRNA splicing machinery contributes to circadian clock functions at a posttranscriptional level.

overall_design: Our findings revealed that AtSKIP is a splicing factor and a component of spliceosome. To further investigate effects of mutation in SKIP on the genome-wide changes of alternative splicing, we performed ultra-highthroughput RNA sequencing, using 10-day old seedlings. Two biological replicates for both wild type (Col-0) and skip-2 were designed.

first: Ying

first: Shuangshuang

last: Ma

first: Yuling

last: Jiao

first: Ligeng


title: Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

summary: Alternative cleavage and polyadenylation (APA) generates diverse mRNA isoforms. We developed 3' region extraction and deep sequencing (3'READS) to address mispriming issues that commonly plague poly(A) site (pA) identification, and we used the method to comprehensively map pAs in the mouse genome. Thorough annotation of gene 3' ends revealed over 5,000 previously overlooked pAs (~8% of total) flanked by A-rich sequences, underscoring the necessity of using an accurate tool for pA mapping. About 79% of mRNA genes and 66% of long noncoding RNA genes undergo APA, but these two gene types have distinct usage patterns for pAs in introns and upstream exons. Quantitative analysis of APA isoforms by 3'READS indicated that promoter-distal pAs, regardless of intron or exon locations, become more abundant during embryonic development and cell differentiation and that upregulated isoforms have stronger pAs, suggesting global modulation of the 3' end–processing activity in development and differentiation.

overall_design: 3'READS to map pAs in mouse genome

first: Mainul

last: Hoque

last: JI

first: Dinghai

last: Zheng

first: Wenting

last: Luo

first: Wencheng

last: Li

first: Bei

last: You

first: Ji

middle: Y

last: Park

first: Ghassan

last: Yehia

first: Bin

last: Tian


title: Gene specific signatures by H3K4me2 and H3K27me3 modifications during retina maturation

city: Hershey

first: Samuel

middle: Shao-Min

last: Zhang

state: PA

address: 500 University Drive

department: Neural and Behavioral Sciences

institute: Penn State University College of Medicine

summary: Control of neural organogenesis is a complex process and the epigenetic contribution is largely unknown. Here we have followed the genome-wide distribution of two important histone H3 modifications, H3K4me2 and H3K27me3 during late mouse retina development. We found that genes expressed only in mature rod photoreceptors, have a unique signature consisting of de-novo accumulation of H3K4me2 both at the transcription start site (TSS) and over the whole gene that correlates with the increase in transcription, but no accumulation of H3K27me3 at any stage. We also found that distribution of H3K4me2 and H3K27me3 on the genes widely expressed is not always associated with their transcriptional levels. Genes without H3K4me2 and H3K27me3 accumulation at any stage represent a group of transcripts never expressed in retina. The epigenetic signatures defined by H3K4me2 and H3K27me3 can distinguish cell-type specific genes from widespread transcripts and may be reflective of cell specificity during retina maturation.

overall_design: Examination of 2 different histone modifications during late mouse retina development.

middle: S


title: Deposition of histone variant H2A.Z within gene bodies regulates responsive genes

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

summary: The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes.  Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that a loss of H2A.Z in Arabidopsis does not affect the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is caused by the exclusion of H2A.Z from methylated DNA.  RNA-seq and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness.  We find that a loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to both endogenous and exogenous stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes.

overall_design: Examination of DNA methylation and transcription in an h2a.z mutant

first: Daniel

last: Zilberman


title: FMR1 targets distinct mRNA sequence elements to regulate protein expression

city: New York

first: Manuel

last: Ascano

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

overall_design: Refer to individual Series


title: Transcriptome response to salinity stress in the Pacific oyster Crassostrea gigas

city: Qingdao

first: Xuelin

last: Zhao

address: Yushan Road 5

department: Fisheries College

institute: Ocean University of China

summary: Low salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas can be tolerant to relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 1665 up-regulation genes and 1815 down-regulation genes that may regulate osmotic stress in C. gigas. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlight genes related to osmoregulation and signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytosqueleton and cell cycle. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates.

overall_design: Twelve Pacific oysters were exposed in low salinity (8‰) seawater and in optimal salinity (25‰) seawater, respectively. Gills from six oysters in each condition were balanced mixed respectively. The transcriptomes of two samples were generated by deep sequencing, using Illumina HiSeq2000.

first: Hong

last: Yu

first: Lingfeng

last: Kong

first: Qi


title: TET2 KD and ChIP-Seq

status: Public on Dec 11 2012

city: Ann arbor

first: qiang

last: chen

state: Michigan

address: 1150 W. medical school road

institute: umich


title: Differential Chromatin Binding of the Drosophila Dosage Compensation Complex

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

type: Genome binding/occupancy profiling by genome tiling array


title: OGT, H2B S112GlcNAc, TET2 ChIP-seq results

summary: TET2 directly interacts with OGT, which is important for the chromatin association of OGT in vivo. Although this specific interaction does not regulate the enzymatic activity of TET2, it facilitates OGT-dependent histone O-GlcNAcylation. Moreover, OGT associates with TET2 at transcription starting sites (TSS). Down-regulation of TET2 reduces the amount of H2B S112 GlcNAc marks in vivo, which are associated with gene transcription regulation.

overall_design: We found that OGT interacts with TET2 tightly. Using ChIP-seq with specific antibodies, we tested the co-localization of TET2 and OGT in genome level.

first: Qiang

last: Chen

first: Xiaochun

first: Yibin

first: Chunjing

last: Bian


title: Human Linker Histone H1.5

status: Public on Dec 12 2012

city: Los Angeles

first: Jing-Yu

address: 615 Charles E. Young Dr. South BSRB 357

institute: University of California, Los Angeles


title: Differential analysis of gene regulation at transcript resolution by RNA-Seq

city: Cambridge

first: Cole

last: Trapnell

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University


title: Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation

last: Li

summary: Linker histones are essential components of chromatin but the distributions and functions of many during cellular differentiation is not well understood. Here, we show that H1.5 binds to genic and intergenic regions, forming blocks of enrichment, in differentiated human cells from all three embryonic germ layers but not in embryonic stem cells. In differentiated cells, H1.5, but not H1.3, binds preferentially to genes that encode membrane and membrane-related proteins. Strikingly, 37% of H1.5 target genes belong to gene family clusters, groups of homologous genes that are located in proximity to each other on chromosomes. H1.5 binding is associated with gene repression and is required for SIRT1 binding, H3K9me2 enrichment and chromatin compaction. Depletion of H1.5 results in loss of SIRT1 and H3K9me2, increased chromatin accessibility, deregulation of gene expression and decreased cell growth. Our data reveal for the first time a specific and novel function for linker histone subtype H1.5 in maintenance of condensed chromatin at defined gene families in differentiated human cells.

overall_design: Examine human linker histone H1.5 (HIST1H1B) binding pattern in H1 hESCs and IMR90 fibroblasts

first: Michaela

last: Patterson

first: Hanna

middle: K

last: Mikkola

first: William

last: Lowry

first: Siavash

last: Kurdistani


title: ChIP-Seq profiles of MSL1, MSL2, MSl3, MOF, MLE, H4K16ac and RNA Polymerase II phosphorlyated on Serine 5 in Drosophila S2 cells

overall_design: MSL1, MSL2, MSL3, MOF, MLE, H4K16ac and RNA Polymerase II phosphorlyated on Serine 5 ChIP in Drosophila S2 cells. 1-3 biological replicates per experiment. Performed in single-read and paired-end read mode.

first: T

first: A

last: Mitterweger

first: G

last: Gilfillan

first: C

last: Feller

first: P

last: Becker


title: Genome-wide mapping of the TET3 CXXC domain binding sites

status: Public on Dec 10 2012

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

summary: The TET3 CXXC domain has unique DNA binding properties. It binds to DNA in a cytosine-dependent manner that prefers binding to CpG dinucleotides but is not restricted by the CpG-content, distinct from other well-characterized CXXC domains. To map the TET3 CXXC domain binding sites across the human genome, we purified the GST-tagged TET3 CXXC domain protein and performed the GST pull-down assay using the genomic DNA purified from HEK293T cells. The enriched DNA fragments were then sequenced and aligned to human genome(hg19).

overall_design: We used the GST pull-down assay followed by DNA deep sequencing to map the DNA bound by the TET3 CXXC domain in vitro.

first: Yufei

last: Xu

first: Yujiang

last: Shi


title: RECURRENT SETBP1 MUTATIONS IN ATYPICAL CHRONIC MYELOID LEUKEMIA

status: Public on Dec 07 2012

city: Monza

first: Roberta

last: Spinelli

state: MB

address: Via Cadore 48

department: Department of Health Science

institute: University of Milano Bicocca

summary: RNA-Seq analysis of atypical chronic myeloid leukemia samples

overall_design: We sequenced leukemic mRNA from 13 Atypical Cronic Mieloid Leukemia (aCML) samples  by Illumina GAIIx. Transcriptomic profiles, differentially expressed genes and pathway enrichment analysis were obtained comparing 7 SETBP1-mutated samples and 6 non-mutated (WT) samples by using TopHat aligner and SAMMate gene expression quantifier. We focused on the gene expression profile of known coding transcripts. A dataset of 20,907 protein-coding Ensembl Genes was obtained from the RNA-Seq by using the Human Ensembl GTF annotation file vs54 dowloaded from ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/.

first: Rocco

last: Piazza

first: Alessandra

last: Pirola

first: Carlo

last: Gambacorti-Passerini


title: Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals

city: Worcester

first: Ryuya

last: Fukunaga

state: Ma

address: 364 Plantation st.

department: BMP

institute: Umass Medical School

summary: Drosophila Dicer-1 produces microRNAs (miRNAs) from pre-miRNA, whereas Dicer-2 generates small interfering RNAs (siRNAs) from long dsRNA. loquacious (loqs) encodes three Dicer partner proteins, Loqs-PA, Loqs-PB, and, Loqs-PD, generated by alternative splicing. To understand the function of each Loqs isoform, we constructed loqs isoform-specific rescue flies. Loqs-PD promotes siRNA production in vivo by Dicer-2. Loqs-PA or Loqs-PB is required for viability, but the proteins are not fully redundant: Loqs-PB is required to produce a specific subset of miRNAs. Surprisingly, Loqs-PB tunes the product size cleaved by Dicer-1 from pre-miR-307a, generating a longer miRNA isoform with a distinct seed sequence and target specificity. The mouse and human Dicer-binding partner TRBP, a homolog of Loqs-PB, similarly tunes the site of pre-miR-132 cleavage by mammalian Dicer. Thus, Dicer-binding partner proteins can change the choice of cleavage site by Dicer, producing miRNAs with different target specificities than those that would be made by Dicer alone.

overall_design: Examination of Dicer-binding proteins on small RNA profiles of female fly heads, fly ovaries, mouse embryonic fibroblasts, and mouse tail fibroblasts.

first: Bo

last: Han

first: Jui

last: Hung

first: Jia

first: Zhiping

last: Weng

first: Phillip

last: Zamore


title: Cross-species transcriptional network analysis defines shared inflammatory responses in murine and human lupus nephritis[Tubulointerstitial]

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

type:
Expression profiling by array
Third-party reanalysis

summary:
Expression data from human with hypertensive nephropathy (HT)
We used microarrays to analyze the transcriptome of microdissected renal biopsies from patients with HT

overall_design: RNA from glomeruli and tubulointerstitial compartments was extracted and processed for hybridization on Affymetrix microarrays.

first: Celine

middle: C

last: Berthier

first: Tania

last: Gonzalez-Rivera

first: Ramalingam

last: Bethunaickan

first: Meera

last: Ramanujam

first: Weija

last: Zhang

first: Erwin

last: Bottinger

first: Stephan

last: Segerer

first: Anne

last: Davidson

first: Matthias

last: Kretzler


title: Differential analysis of HOXA1 in adult cells at isoform resolution by RNA-Seq [Illumina]

first: Cole

last: Trapnell

summary: High-throughput RNA sequencing (RNA-Seq) has enabled accurate gene discovery and expression estimation, but robust differential analysis of gene and transcript abundances has proven difficult. We present a new algorithm, implemented in the freely available tool Cuffdiff, which integrates transcript-level expression estimation with a method to control for variability across replicate samples. Cuffdiff robustly identifies differentially regulated isoforms and genes and reveals differential splicing or promoter-preference changes. We demonstrate the accuracy of our approach through differential analysis of lung fibroblasts in response to loss of the developmental transcription factor HOXA1 and uncover a critical role for this gene in the maintenance of adult cells. We show that HOXA1 is required for lung fibroblast and HeLa cell cycle progression, and loss of HOXA1 results in significant expression level changes in thousands of individual transcripts, along with isoform switching events in key regulators of the cell cycle.

overall_design: Lung Fibroblasts were transfected with either a HOXA1 directed siRNA pool or a scramble non-targeting siRNA control. RNA was collected 48 hours after transfection and changes in gene expression were assayed for using Agilent microarrays.

first: David

last: Hendrickson

first: Martin

last: Sauvageau

first: John

last: Rinn

first: Lior

last: Pachter


title: Next Generation Sequencing Facilitates Quantitative Analysis of Cyp26b1-/-skin and En1cre;Cyp26b1f/- epidermal and dermal Transcriptomes

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived skin transcriptome profiling (RNA-seq) to determine pathways and networks dependent on retinoic acid during skin development.
Methods: Skin mRNA profiles of embryonic day E16.5 wild-type (WT) and Cyp26b1 knockout (Cyp26b1−/−), and of control and of dermal and epidermal skin fractions of Engrailed1cre;Cyp26b1f/- (En1cre;Cyp26b1f/-) conditional knockout mice were generated by deep sequencing, in duplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level  by ANOVA (ANOVA) and TopHat. qRT–PCR validation was performed using TaqMan and SYBR Green assay.
Results: RNA-Seq data were generated with Illumina’s HiSeq 2000 system. Raw sequencing data were processed with CASAVA 1.8.2 to generate fastq files. Reads of 50 bases were mapped to the mouse transcriptome and genome mm9 using TopHat 1.3.2. Gene expression values (RPKM) were calculated with Partek Genomics Suite 6.6, which was also used for the ANOVA analysis to determine significantly differentially expressed genes.
Conclusions: Our study represents the first detailed analysis of Cyp26b1-/- skin and En1cre;Cyp26b1f/- dermis/epidermic transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.  We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Skin mRNA profiles of embryonic-day 16.5 wild type (WT) and Cyp26b1-/- mice and of dermis and epidermis of embryonic day 18.5 control and En1cre;Cyp26b1f/- were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.

first: Maria

middle: I

last: Morasso

first: Junko

last: Okano

first: Clara

last: Levy

first: Ulrike

last: Lichti

first: Stuart

last: Yuspa

first: Hong-Wei

first: Yasuo

last: Sakai


title: Sip1 in cortical interneuron migration

city: Leuven

first: Bram

last: Van de Sande

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KU Leuven

summary: We sequenced mRNA from 6 samples of FACsorted telencephalons from E14.5 Sip1|Nkx2-1 knockout and WT|Nkx2-1 control mouse embryos to find differentially expressed genes in the absence of the transcription factor Sip1.

overall_design: Examination of mRNA levels in 3 control and 3 Sip1|Nkx2-1 knockout samples

first: Eve

last: Seuntjens

first: Stein

last: Aerts


title: Comparison of the genome-wide DNA methylation profiles between fast-growing and slow-growing broilers

status: Public on Dec 06 2012

city: Guangzhou

first: Xinzheng

last: Jia

state: Guangdong

address: Wushan Road

department: Animal Science

institute: South China Agricultural University

summary: Chicken growth traits are important in poultry production, however, little is known for its regulatory mechanism at epigenetic level. Therefore, this study aims to compare DNA methylation profiles between fast- and slow-growing broilers in order to identify candidate genes underlying chicken growth. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) was used to investigate the genome-wide DNA methylation pattern in high and low tails of Recessive White Rock (WRRh, WRRl) and that of Xinhua Chickens (XHh, XHl). The results showed that the average of methylation density was the lowest in CGIs followed by promoters. Within the gene body, the methylation density of introns was higher than UTRs and exons. Moreover, different methylation levels were observed in different repeat types with the highest in LINE/CR1. Methylated CGIs were prominently distributed in the intergenic regions and were enriched in the size range of 200-300 bp. In total 13,294 methylated genes were found in four samples, including 4,085 differentially methylated genes between WRRh and WRRl, 5,599 between XHh and XHl, 4,204 between WRRh and XHh, as well as 7,301 between WRRl and XHl. Moreover, 132 differentially methylated genes related to growth and metabolism were observed in both inner contrasts (WRRh Vs. WRRl and XHh Vs. XHl), whereas 129 differentially methylated genes related to growth and metabolism were found in both across-breed contrasts (WRRh Vs. XHh and WRRl Vs. XHl). Further analysis showed that overall 75 genes exhibited altered DNA methylation in all four contrasts, which included some well-known growth factors of IGF1R, FGF12, FGF14, FGF18, FGFR2, and FGFR3. In addition, we further validate the MeDIP-seq results by bisulfite sequencing in some regions.

overall_design: 12 Breast muscle samples were collected from two breeds of different growth rate, Recessive White Rock (WRR) and Xinhua Chickens (XH). Each breed included low and high-weight groups and 3 samples from each group were pooled equally for methylated DNA immunoprecipitation-sequencing (MeDIP-seq).

first: Yongsheng

last: Hu

first: Haiping

last: Xu

first: Zhenhui

last: Li

first: Xuejuan

last: Zheng

first: Qinghua

last: Nie

first: Xiquan

last: Zhang


title: Cross-species transcriptional network analysis defines shared inflammatory responses in murine and human lupus nephritis

first: Viji

last: Nair

first: Celine

last: Berthier

first: Tania

last: Gonzalez-Rivera

first: Ramalingam

last: Bethunaickan

first: Meera

last: Ramanujam

first: Weija

first: Erwin

last: Bottinger

first: Stephan

last: Segerer

first: Anne

last: Davidson

first: Matthias

last: Kretzler


title: Rapid and synchronous clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation

city: University Park

first: Shaun

last: Mahony

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University


title: Geminin knockdown in embryonic stem cell-derived neural precursors

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

summary: Regulating the transition from lineage-restricted progenitors to terminally differentiated cells is a central aspect of nervous system development. Here, we investigated the role of the nucleoprotein Geminin in regulating neurogenesis at a mechanistic level during both Xenopus primary neurogenesis and mammalian neuronal differentiation in vitro. The latter work utilized both neural cells derived from embryonic stem and embryonal carcinoma cells in vitro and neural stem cells from mouse forebrain. In all of these contexts, Geminin antagonized the ability of neural bHLH transcription factors to activate transcriptional programs promoting neurogenesis. Furthermore, Geminin promoted a bivalent chromatin state, characterized by the presence of both activating and repressive histone modifications, at genes encoding transcription factors that promote neurogenesis. This epigenetic state restrains the expression of genes that regulate commitment of undifferentiated stem and neuronal precursor cells to neuronal lineages. Geminin is highly expressed in undifferentiated neuronal precursor cells but is downregulated prior to differentiation. Therefore, these data support a model whereby Geminin promotes the neuronal precursor cell state by modulating both the epigenetic status and expression of genes encoding neurogenesis-promoting factors. Additional developmental signals acting in these cells can then control their transition toward terminal neuronal or glial differentiation during mammalian neurogenesis.

overall_design: A mouse embryonic stem (ES) cell line for inducible knockdown of the small nucleoprotein Geminin was utilized. ES cells were used to generate neural precursor cells by monolayer culture in N2B27 media for 5 days, and doxycycline-inducible knockdown of Geminin was performed from day 3. Changes in gene expression resulting from Geminin knockdown were assessed by RNA sequencing. Three experimental replicates were generated for Geminin knockdown (plus Dox) with a corresponding no-Dox control. These were subjected to sequencing, and data were analyzed using TopHat and Cufflinks/Cuffdiff. Transcripts were considered as differentially expressed upon Gem knockdown if data met statistical significance cutoffs in Cuffdiff (sufficient sequence alignments were obtained for analysis and transcript had significant change in FPKM value (normalized transcript abundance; fragments per kb of exon per million fragments mapped) between the no Dox and plus Dox sample pairs) in at least two of the three replicates.

first: Dhananjay

last: Yellajoshyula

first: Jong

last: Lim

first: Dominic

middle: M

last: Thompson

first: Jacob

last: Witt

first: Ethan

last: Patterson


title: Cross-species transcriptional network analysis defines shared inflammatory responses in murine and human lupus nephritis [Glomeruli]

first: Viji

summary:
Expression data from human with IgA nephropathy (IgAN) and hypertensive nephropathy (HT)
We used microarrays to analyze the transcriptome of microdissected renal biopsies from patients with IgAN and HT

last: Zhang


title: Genome-wide profiles of RNA polymerase II (Pol 2) DNA occupancy and the histone modifications H3K4me3 and H3K36me3 around the circadian cycle

city: Lausanne

first: Nouria

last: Hernandez

state: Vaud

address: Dorigny

department: CIG

country: Switzerland

institute: UNIL

summary:
To understand the transcriptional basis of circadian rhythms in mouse liver, we generated genome-wide profiles of RNA polymerase II (Pol 2) DNA occupancy and the histone modifications H3K4me3 and H3K36me3 around the circadian cycle. We found that Pol 2 occupancy at promoters and in gene bodies cycle in synchrony, suggesting that Pol 2 recruitment at promoters underlies circadian gene transcription. On average, Pol 2 occupancy precedes mRNA accumulation by about three hours. Promoters of transcribed genes have tri-methylated H3K4 residues even at their trough activity times, and the tri-methylation levels increase in phase with Pol 2 loading. In contrast, the tri-methylation of H3K36 residues lags transcription by three hours with amplitudes that are markedly shallower, indicating that this mark is less dynamic on the circadian time scale. The comparison of Pol 2 occupancy and mRNA accumulation revealed that both transcriptional and post-transcriptional regulatory mechanisms can account for diurnal mRNA profiles. Additional processed data and visualization tools are available at http://cyclix.vital-it.ch/

Contributed by members of CycliX consortium (http://cyclix.vital-it.ch/)

overall_design: 28 samples examinded, 7 Polr2b, 7 H3K4me3, 7 H3k36me3, 7 input samples.

first: Gwendal

last: Le Martelot

first: Donatella

last: Canella

first: Laura

last: Symul

first: Eugenia

last: Migliavacca

first: Federica

last: Gilardi

first: Robin

last: Liechti

first: Olivier

last: Martin

first: Bart

last: Deplancke

first: Mauro

last: Delorenzi

first: Béatrice

last: Desvergne

first: Winship

last: Herr

first: Jacques

last: Rougemont

first: Ueli

last: Schibler

first: Nicolas

last: Guex

first: Felix

last: Naef


title: Genome-wide DNA methylation events in TMPRSS2:ERG fusion negative prostate cancers implicate an EZH2 dependent mechanism with miRNA-26a hypermethylation.

city: Berlin

first: Michal-Ruth

last: Schweiger

address: Ihnestr. 63-73

department: Vertebrate Genomics

institute: Max-Planck-Institut for Molecular Genetics

summary: Prostate cancer is the second most common cancer among men worldwide. Alterations in the DNA methylation pattern can be one of the leading causes for prostate cancer formation. This study is the first high throughput sequencing study investigating genome-wide DNA methylation patterns in a large cohort of 51 tumor and 53 benign prostate samples using MeDIP-Seq. Comparative analyses identified more than 147,000 cancer-associated epigenetic alterations. Additionally, global methylation patterns demonstrate significant differences based on the TMPRSS2:ERG rearrangement status. We propose the hypermethylation of miRNA-26a as an alternative pathway of ERG rearrangement independent EZH2 activation. The observed increase in differential methylation events in fusion negative tumors can explain the tumorigenic process in the absence of genomic rearrangements.

overall_design: Genomewide examination of methylation profiles in 51 prostate cancer samples

first: Stefan

middle: T

last: Boerno

first: Axel

last: Fischer

first: Martin

last: Kerick

first: Maria

last: Faelth

first: Mark

last: Laible

first: Jan

last: Brase

first: Ruprecht

last: Kuner

first: Andreas

last: Dahl

first: Christina

last: Grimm

first: Behnam

last: Sayanjali

first: Melanie

last: Isau

last: Roehr

first: Andrea

last: Wunderlich

first: Bern

last: Timmermann

first: Rainer

last: Claus

first: Christoph

last: Plass

first: Markus

last: Graefen

first: Ronald

last: Simon

first: Francesca

last: Demichelis

middle: A

last: Rubin

first: Guido

last: Sauter

first: Thorsten

last: Schlomm

first: Holger

last: Sueltmann

first: Hans

last: Lehrach

first: Michal


title: Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.

first: Scot

last: Wolfe

address: 364 Plantation Street, LRB 619

department: MCCB

institute: UMass Medical School

summary: Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have characterized the DNA-binding specificities of 130 Zinc finger sets from Drosophila melanogaster using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 71 unique genes and 22 alternate splice isoforms. This represents the largest block of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites and potential regulatory targets for these factors within the fruit fly genome.  We have characterized subsets of fingers from these ZFPs to define the correct orientation and register of the zinc fingers on their defined binding sites.  By correlating individual fingers with motif subsites, we can assign finger specificity throughout each ZFP. This reveals the diversity of recognition potential within the naturally-occurring zinc fingers of a single organism, where the characterized fingers can specify 47 of the 64 possible DNA triplets.  To confirm the utility of our finger recognition models, we have employed subsets of Drosophila fingers in combination with an existing archive of zinc finger modules to create ZFPs with novel DNA-binding specificity. These finger combinations can be used to create novel functional Zinc Finger Nucleases for editing vertebrate genomes.

overall_design: Illumina sequencing of Barcoded Binding sites obtained after B1H selection of Cys2-His2 zinc finger proteins cloned as a C-terminal fusions to the omega subunit of E. coli RNA polymerase in the B1H system.

first: Metewo

last: Enuameh

first: Yuna

last: Asriyan

first: Adam

last: Richards

first: Ryan

last: Christensen

first: Victoria

last: Hall

first: Majid

last: Kazemian

first: Cong

last: Zhu

first: Hannah

last: Pham

first: Qiong

last: Cheng

first: Charles

last: Blatti

first: Jessie

last: Brasefield

first: Matthew

last: Basciotta

first: Jianhong

last: Ou

first: Joseph

last: McNulty

first: Lihua

middle: J

first: Susan

middle: E

last: Celniker

first: Saurabh

last: Sinha

first: Gary

last: Stormo

first: Michael

last: Brodsky


title: Genome wide maps of p53 binding in IMR90 cells

status: Public on Dec 05 2012

city: New York

first: Ozlem

last: Aksoy

state: NY

address: 415 East 68th Street

department: Watson School of Biological Sciences

institute: CSHL

summary: Oncogene-induced senescence is an anti-proliferative stress response program that acts as a fail-safe mechanism to  limit oncogenic transformation and is regulated by the retinoblastoma protein (RB) and p53 tumor suppressor  pathways. We identify the atypical E2F family member E2F7 as the only E2F transcription factor potently upregulated  during oncogene-induced senescence, a setting where it acts in response to p53 as a direct transcriptional  target. Once induced, E2F7 binds and represses a series of E2F target genes and cooperates with RB to efficiently  promote cell cycle arrest and limit oncogenic transformation. Disruption of RB triggers a further increase in E2F7,  which induces a second cell cycle checkpoint that prevents unconstrained cell division despite aberrant DNA  replication. Mechanistically, E2F7 compensates for the loss of RB in repressing mitotic E2F target genes.

overall_design: Examination of p53 binding in either growing or senescent IMR90 cells with different hairpins.

first: Xiaowo

last: Wang

first: Agustin

last: Chicas

first: Scott

middle: W

last: Lowe

first: Tianying

last: Zeng


title: Identification of a Novel Angiogenesis and Tumor Suppressor Gene   Rab25 in Esophageal Squamous Cell Carcinoma

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

institute: University of Notre Dame

summary: Twelve clinical samples from human esophageal squamous cell carcinoma (ESCC) (seven tumors and five non-tumors) were sequenced using Illumina high-throughput sequencing and the RNA-Seq profiling was investigated with 1730 genes significantly differentially expressed. The gene Rab25 was found to be down-regulated in tumors (p-value < 1E-20) and identified as a novel candidate tumor suppressor gene. The down-regulation of Rab25 was examined in a large cohort of ESCC and non-tumor cases by qPCR and immunohistochemistry analyses. Aberrant methylation in the promoter region of Rab25 was studied by demethylation treatment with 5-aza-dC and bisulfite genomic sequencing (BGS). In order to assess the effect of Rab25 on tumor growth and angiogenesis, in vitro and in vivo functional studies in ESCC cell lines using lentiviral-based overexpression or knockdown models were also performed.

overall_design: 7 tumor and 5 normal samples

first: Si

last: Lok

first: Xin-Yuan

last: Guan

first: Stephanie

last: Ma

first: Carol

last: Tong


title: Geminin regulates the transcriptional and epigenetic status of neuronal fate promoting genes during mammalian neurogenesis

first: Kristen

last: Kroll

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

sample_organism:
Xenopus laevis
Mus musculus

platform_organism:
Xenopus laevis
Mus musculus

overall_design: Refer to individual Series


title: Kinetic RNA polymerase II occupancy, associated histone marks, and mRNA accumulation reveal transcriptional and post-transcriptional mechanisms underlying circadian gene expression

first: Nouria

last: Hernandez


title: Genome Sequencing of Gastric Cancer Reveals Diverse Mutational and Pathogen Signatures

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

institute: University of Cologne

type: Genome variation profiling by high throughput sequencing

summary: We leveraged massively parallel sequencing approach to comprehensively characterize the spectrum of somatic mutations and genomic rearrangements in two intestinal-type gastric adenocarcinomas from patients with and without active Helicobacter pylori infections. The tumours exhibited distinct patterns of genomic changes with more than 16,000 somatic substitutions on average, focal amplifications and rearrangements in the non-active infected tumour and a 7-fold enrichment of micro-deletions in the infected tumour. Paired-end sequences from large insert libraries revealed the structure and origins of large amplicons, including one involving the oncogene KRAS. The mutational frequencies of the tumours revealed patterns of H. pylori infection and mutagenesis and a unique exome signature, providing insights into mechanisms that define the mutational landscape of gastric cancer. For the tumour with active infection, we also reconstructed the genome of the pathogenic H. pylori strain from the raw sequence reads, demonstrating the power of whole-genome shotgun sequencing for simultaneously characterizing the tumour and its associated carcinogen genome.

overall_design: Single nucleotide variations and indels were identified by whole genome short insert sequencing and structural variations were identified by long insert DNA paired-end tag (DNA-PET) sequencing.

first: Niranjan

last: Nagarajan

first: Yijun

last: Ruan

last: Hillmer


title: Inactivation of BCL11A reactivates silenced human HbF in adult mice

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital


title: TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells

status: Public on Dec 04 2012

first: Adamandia

last: Kapopoulou

address: Station 15

department: Sciences de la Vie

institute: EPFL

summary: TRIM28 (KAP1 - KRAB-associated protein 1) is critical for the silencing of endogenous retroviruses (ERVs) in embryonic stem (ES) cells. Here, we reveal that an essential impact of this process is the protection of cellular gene expression in early embryos from perturbation by cis-acting activators contained within these genetic invaders. In TRIM28-depleted ES cells, repressive chromatin marks at ERVs are replaced by histone modifications typical of active enhancers, stimulating transcription of nearby cellular genes, notably those harboring bivalent promoters. Correspondingly, ERV-derived sequences can repress or enhance expression from an adjacent promoter in transgenic embryos depending on their TRIM28-sensitivity in ES cells. TRIM28-mediated control of ERVs is therefore crucial not just to prevent retrotransposition, but more broadly to safeguard the transcriptional dynamics of early embryos.

overall_design: Analyses of transcriptional profiles and chromatin state in TRIM28 WT and KO cells

first: Helen

last: Rowe

first: Andrea

last: Corsinotti

first: Liana

last: Fasching

first: Todd

last: Macfarlan

first: Yara

last: Tarabay

first: Stéphane

last: Viville

first: Johan

last: Jakobsson

first: Samuel

last: Pfaff

first: Didier

last: Trono


title: Transcriptome profiling of SOD1 mutant  ALS model motor neurons.

city: Philadelphia

first: Justin

last: Cotney

address: 3501 Civic Center Blvd

department: Surgery

institute: Children's Hospital of Philadelphia

summary: Recent genetic studies of ALS patients have identified several forms of ALS that are associated with mutations in RNA binding proteins.  In animals or cultured cells, such defects broadly affect RNA metabolism.  This raises the question of whether all forms of ALS have general effects on RNA metabolism.  We tested this hypothesis in a mouse model of ALS that is transgenic for a human disease-causing mutation in the enzyme superoxide dismutase 1 (SOD1).  We analyzed RNA from laser-captured spinal cord motor neuron cell bodies of the mutant SOD1 strain, comparing the RNA profile with that from a corresponding wild-type SOD1 transgenic strain.  We prepared the samples from animals that were presymptomatic, but which manifested abnormalities at the cellular level that are seen in ALS, including aggregation of the mutant protein in motor neuron cell bodies and defective morphology of neuromuscular junctions, the connections between neuron and muscle.  We observed only minor changes in the level and splicing of RNA in the SOD1 mutant animals as compared with wild-type, suggesting that mutant SOD1 produces the toxic effects of ALS by a mechanism that does not involve global RNA disturbance.

overall_design: RNA-Seq of laser microdissection of motor neuron bodies from two biological replicates each of SOD1 YFP (wildtype 592) and SOD1 G85R YFP (737) transgenic mice.

first: Wayne

last: Fenton

first: Arthur

last: Horwich


title: Rodent trophoblast epigenome

city: Boulder

first: Edward

last: Chuong

address: 596 UCB

department: BioFrontiers

institute: University of Colorado Boulder

summary: We characterized the trophoblast stem cell epigenome and gene expression profiles in rat and mouse.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: We profiled 5 histone modifications (+ chromatin input) using ChIP-Seq, and digital expression profiles (3' RNA-Seq) for trophoblast stem cells derived from rat and mouse. Furthermore, for mouse, we profiled key trophoblast stem cell factors Elf5, Cdx2, and Eomes. We found that enhancer regions (defined as distal regions of H3K27ac/H3K4me1 enrichment) were enriched for species-specific endogenous retroviral elements.

middle: B

first: Julie

last: Baker


title: Creation of an anti-inflammatory GR cistrome by TLR4 signaling

city: La Jolla

first: Ruth

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: An unresolved molecular paradox is how the glucocorticoid receptor (GR) activates some genes while potently repressing others. We carried out genome-wide localization and expression profiling experiments in primary bone marrow-derived mouse macrophages treated with Dexamethasone in the presence or absence of LPS. Unexpectedly, we find that the anti-inflammatory GR cistrome, which is principally composed of 'canonical' GREs colocalizing with NFkB and AP-1 co-enriched with the myeloid lineage factors C/EBP and Pu.1, is shaped by TLR4-directed chromatin dynamics, suggesting that context rather than sequence may be a critical determinant of function.

overall_design: Identification of GR, cJun, NFkB(p65) binding sites in primary bone-marrow derived macrophages unstimulated and LPS-stimulated (3hrs) that were untreated or pre-treated with Dexamethasone for 16 hrs

first: N

middle: H

last: Uhlenhaut

first: Ronald

last: Evans


title: Limitations and possibilities of low cell number ChIP-seq

status: Public on Dec 03 2012

city: Oslo

first: Gregor

middle: Duncan

last: Gilfillan

address: Medisinsk Genetikk

department: Medical Genetics

country: Norway

institute: Oslo Universitetssykehus

summary: ChIP-seq experiments using low numbers of input cells, scaled down to the point where data quality is unnacceptably compromised, reveals limits of the technique.

overall_design: Two-part ChIPseq study using native chromatin (non-crosslinked) generated with MNase from human CD4+ cells. Part 1: Previously published protocol (Barski et al, 2007, Cell 129:823, hereafter called "Benchmark") used with 2x10e7 cells / ChIP with H3K4me3 antibody, compared to modified method ("new") with decreasing input cell numbers spanning 1000-fold range from 2x10e7 cells / IP to 2x10e4 cells/ IP. Part 2: reproducibility of new method studied using triplicate samples at lowest two cell numbers tested: 1x10e5 and 2x10e4 / ChIP, using H3K4me3 and H3K27me3 antisera.

middle: D

first: Robert

last: Lyle