title: Zinc finger transcription factors displaced SREBP proteins as the major sterol regulators during Saccharomycotina evolution

city: Dublin

first: Geraldine

last: Butler

address: Belfield

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: University Colege Dublin Conway Institute

summary: All but a few eukaryotes die without oxygen and respond dynamically to changes in the level of oxygen available to them. One ancient oxygen-requiring biochemical pathway in eukaryotes is the pathway for the biosynthesis of sterols, leading to cholesterol in animals and ergosterol in fungi. Mutations in this pathway are a frequent cause of azole drug resistance in pathogenic fungi. The regulatory mechanism for the sterol pathway is also widely conserved between animals and fungi and is centred on a transcription activator, SREBP, that forms part of a sterol-sensing complex. However, in one group of yeasts – the Saccharomycotina, which includes the major pathogen Candida albicans – control of the sterol pathway has been taken over by an unrelated regulatory protein, Upc2. We show here by analysis of the yeast Yarrowia lipolytica that the evolutionary switch from SREBP to Upc2 was a two-step process in which Upc2 appeared in an ancestor of Saccharomycotina, and SREBP subsequently degenerated and lost its sterol-regulatory function while retaining an ancient role in filamentation.

overall_design: RNA was isolated from Y. lipolytica wildtype (JMY2900) in normoxia (21% oxygen, 4 biological replicates),  wildtype (JMY2900) in hypoxia (1% oxygen, 5 biological replicates),  upc2 deletion (SMY2) in hypoxia (1% oxygen, 3 biological replicates), and from  sre1 (SMY5, SMY8) deletion in hypoxia (1% oxygen, 2 biological replicates). Gene expression was determined using strand-specific RNA-seq.

first: Sarah

last: Maguire

first: François

last: Brunnel

first: Cécile

last: Neuvéglise

first: Can

last: Wang

last: Wolfe

first: Jean-Marc

last: Nicaud


title: Transcriptome Sequencing During Mouse Brain Development  Identifies Long Non-Coding RNAs  Functionally Involved in Neurogenic Commitment

status: Public on Nov 18 2013

city: Dresden

first: Federico

last: Calegari

address: Fetscherstr. 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

country: Germany

institute: TU Dresden

type: Expression profiling by high throughput sequencing

summary:
Transcriptome analysis of somatic stem cells and their progeny is fundamental to identify new factors controlling proliferation versus differentiation during tissue formation. Here we generated a combinatorial, fluorescent reporter mouse line to isolate proliferating neural stem cells, differentiating progenitors and newborn neurons that coexist as intermingled cell populations during brain development. Transcriptome sequencing revealed numerous novel long non-coding (lnc)RNAs and uncharacterized protein-coding transcripts identifying the signature of neurogenic commitment. Importantly, most lncRNAs overlapped neurogenic genes and shared with them a nearly identical expression pattern suggesting that lncRNAs control corticogenesis by tuning the expression of nearby cell fate determinants. We assessed the power of our approach by manipulating lncRNAs and protein-coding transcripts with no function in corticogenesis reported to date. This led to several evident phenotypes in neurogenic commitment and neuronal survival indicating that our study provides a remarkably high number of uncharacterized transcripts with hitherto unsuspected roles in brain development. Finally, we focussed on one lncRNA, Miat, whose manipulation was found to trigger pleiotropic effects on brain development and aberrant splicing of Wnt7b. Hence, our study suggests that lncRNA-mediated alternative splicing of cell fate determinants controls stem cell commitment during neurogenesis.
“LncRNAs control neurogenesis”  Aprea, Prenninger, Dori, Monasor, Wessendof, Zocher, Massalini, Ghosh, Alexopoulou, Lesche, Dahl, Groszer, Hiller, Calegari, The EMBO Journal (In Press)

overall_design: mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.

first: Julieta

last: Aprea

first: Silvia

last: Prenninger

first: Martina

last: Dori

first: Laura

last: Sebastian Monasor

first: Elke

last: Wessendorf

first: Sara

last: Zocher

first: Simone

last: Massalini

first: Tanay

last: Ghosh

first: Dimitra

last: Alexopoulou

first: Mathias

last: Lesche

first: Andreas

last: Dahl

first: Matthias

last: Groszer

first: Michael

last: Hiller


title: Genome-wide maps of Runx3 bound regions in splenic CD8+ T cells.

city: Rehovot

first: Joseph

last: Lotem

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIP-seq was conducted using freshly isolated (resting) splenic  WT CD8+ T cells with anti-Runx3 antibody (Ab), anti-H3K4me1 Ab and non-immune serum (NIS) as control.

overall_design: Two biological Runx3 and two NIS IP repeats from splenic CD8+ T cells isolated by positive selection on anti-CD8 magnetic beads, collected from 18 WT mice.

first: Dena

last: Leshkowitz

first: Yoram

last: Groner


title: Genome-wide maps of Runx3 bound regions in IL-2-activated splenic NK cells

summary: ChIP-seq was conducted using splenic WT NK cells cultured for 7 days with IL-2 using anti-Runx3 antibodies (Ab), anti-H3K4me1 Ab and non-immune serum (NIS) as control.

overall_design: Two biological Runx3, one H3K4me1 and two NIS IP repeats from splenic NK cells isolated from individual mice by negative selection using NK cell isolation kit (R&D) cultured with IL-2.

first: Ditsa

last: Levanon


title: Structural variation-induced changes of chromatin architecture and gene expression

status: Public on Nov 20 2013

city: Lausanne

first: Marion

last: LELEU

address: Station 15

country: Switzerland

institute: EPFL

summary: Copy number variants (CNVs) influence the expression of genes that map not only within the rearrangement, but also to its flanks. To assess the possible mechanism(s) underlying this “neighboring effect”, we compared intrachromosomal interactions and histone modifications in cell lines of patients affected by genomic disorders and control individuals. Using chromosome conformation capture (4C-seq), we observed that a set of genes flanking the Williams-Beuren Syndrome critical region (WBSCR) were often looping together, possibly forming an interacting cluster with each other and the WBSCR. Deletion of the WBSCR disrupts the expression of this group of flanking genes, as well as long-range interactions between them and the rearranged interval. We also pinpointed concomitant changes in histone modifications between samples.We conclude that large genomic rearrangements can lead to chromatin conformation changes that extend far away from the structural variant, thereby possibly modulating expression globally and modifying the phenotype. For example, we determined that the chromatin conformation, histone marks and relative expression levels of the flanking AUTS2 gene, mutations of which are associated with autism and intellectual disabilities, are modified in cell lines from Williams-Beuren syndrome patients.

overall_design: Examination of 4C-seq interaction profile of seven different genes (of which three in duplicate) in 2 different cell lines.

first: Nele

last: Gheldof

last: Leleu

first: Eugenia

last: Migliavacca

first: Robert

middle: M

last: Witwicki

first: Alexandre

last: Reymond


title: Identification of transcripts altered upon LIN-41 knockdown in human embryonic stem cells

city: San Francisco

first: Kathleen

middle: A

last: Worringer

state: CA

address: 1650 Owens St.

country: USA

institute: Gladstone Institutes

summary: To identify transcripts altered upon LIN-41 knockdown, we transfected either a control siRNA or one of two different LIN-41 siRNAs into human embryonic stem cells and collected total RNA 72 hours after transfection.

overall_design: We compared transcript levels between control siRNA or LIN-41 siRNA treated cells.

first: K

first: Shinya

last: Yamanaka


title: Genome-wide maps of Runx3 bound regions in splenic NK cells

summary: ChIP-seq was conducted using freshly isolated (resting) splenic WT NK cells with anti-Runx3 antibody (Ab), anti-H3K4me1 Ab and non-immune serum (NIS) as control.

overall_design: Runx3 and H3K4me1 IP from splenic NK cells isolated by negative selection using NK cell isolation kit (R&D) followed by sorting of NKp46+ cells.


title: Characterization of the Imprinting Signature of Mouse Embryo Fibroblasts by RNA Deep Sequencing

city: Duarte

first: Xiwei

last: Wu

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: Beckman Research Institute

summary: Mouse embryo fibroblasts (MEFs) closely resemble mouse embryos and are convenient sources for biochemical studies when cell number may be limiting from mouse embryos. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we characterized them using strand- and allele-specific RNA deep sequencing. We used Sequenom allelotyping in embryo and adult organs to verify parental allele-specific expression patterns. We found correct parental allele-specific transcription of 32 known ubiquitously imprinted genes in MEFs. Our analysis did not reveal any novel imprinted genes in MEFs, but detected extended parental allele-specific transcription in several known imprinted domains: maternal allele-specific transcription downstream of Grb10 and downstream of Meg3, Rtl1as and Rian in the Dlk1-Dio3 cluster, an imprinted domain implicated in development. We detected paternal allele-specific transcription downstream of Nespas, Peg3, Peg12 and Snurf/Snrpn. These imprinted transcript extensions were not unique to MEFs, but were also present in other somatic cells. Their 5’ end points did not carry opposing chromatin marks or parental allele-specific DNA methylation, suggesting that their parental allele-specific transcription is under the control of the extended genes. Based on the imprinting signature of MEFs, they provide valid models for understanding the biochemical aspects of genomic imprinting.

overall_design: Strand-specific and parental allele-specific RNA-seq was done in female mouse embryo fibroblasts.

first: Diana

last: Tran

first: Piroska

middle: E

last: Szabo


title: C/EBPα poises B cells for rapid reprogramming into iPS cells [ChIP-Seq]

status: Public on Nov 17 2013

city: Houston

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary: C/EBPα induces transdifferentiation of B cells into macrophages at high efficiencies and enhances reprogramming into induced pluripotent stem cells (iPSCs) when co-expressed with Oct4, Sox2, Klf4 and Myc (OSKM). However, how C/EBPα accomplishes these effects is unclear. We now found that transient C/EBPα expression followed by OSKM activation induces a 100 fold increase in iPSC reprogramming efficiency, involving 95% of the cells. During this conversion pluripotency and epithelial-mesenchymal transition genes become dramatically up-regulated and 60% of the cells express Oct4 within 2 days. C/EBPα acts as a pathbreaker since it transiently makes the chromatin of pluripotency genes more accessible to DNase I. It also induces the expression of the dioxygenase Tet2 and promotes its translocation to the nucleus where it binds to regulatory regions of pluripotency genes that become demethylated following OSKM induction. In line with these findings, overexpression of Tet2 enhances OSKM‐induced B cell reprogramming. Since the enzyme is also required for efficient C/EBPα-induced immune cell conversion, our data suggest that Tet2 provides a mechanistic link between iPSC reprogramming and B cell transdifferentiation. The rapid iPS reprogramming approach described should help to fully elucidate the process and has potential clinical applications.

overall_design: Change in Cebpa genome binding/occupancy, comparing primary B-cells treated with estradiol for 18h to induce C/EBPa to untreated cells.

first: Thomas

last: Graf


title: Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a [Bisulfite-Seq]

first: Margaret

last: Goodell

address: One Baylor Plaza, N1030

type: Methylation profiling by high throughput sequencing

summary: Gains and losses in DNA methylation are prominent genomic features of all mammalian cell types.  To gain insight into mechanisms that could promote shifts in DNA methylation patterns and thus contribute to cell fate, including malignant transformation, we performed genome-wide mapping of 5-methylcytosine in purified wild type and Dnmt3a conditional knockout hematopoietic stem cells (HSCs). We generated 1,121 million (control HSCs), and 1,213 million (Dnmt3a knockout HSCs) raw reads; about 81.4% and 88.7%, respectively, were successfully aligned to either strand of the reference genome (mm9), obtainig an average CG coverage of 39.5-fold (wild type) and 47.0-fold (Dnmt3a kockout).

overall_design: Whole genome bisulfite sequencing of secondarily-transplanted wild-type and Dnmt3a conditional knockout hematopoietic stem cells using Illumina HiSeq 2000

first: Benjamin

last: Rodriguez

first: Wei

last: Li


title: Widespread Misinterpretable ChIP-seq Bias in Yeast

status: Public on Nov 15 2013

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: We report widespread ChIP-seq bias at highly expressed genes in yeast that could lead to misinterpretation

overall_design: ChIP-seq for multiple transcription or chromatin-associated factors and negative controls

first: Vishwanath

middle: R


title: Suppression of miRNA-708 by polycomb group promotes metastases by calcium-induced cell migration

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: The progression of cancer to metastatic disease is a major cause of death. We identified miR-708 being transcriptionally repressed by polycomb repressor complex (PRC2)-induced H3-K27 trimethylation in metastatic breast cancer.  miR-708 targets the endoplasmic reticulum protein neuronatin (Nnat) to decrease intracellular calcium (Ca2+) level, resulting in reduction of activation of ERK and FAK, decreased cell migration, and impaired metastases. Functional complementation experiments with Nnat-3’UTR mutant, which is refractory to suppression by miR-708, rescued cell migration and metastasis defects. In breast cancer patients, miR-708 expression was decreased in lymph node and distal metastases, suggesting a metastasis-suppressive role. Our findings uncover a mechanistic role for miR-708 in metastasis and provide a rationale for developing miR-708 as a therapeutic agent against metastatic breast cancer.

overall_design: Sequencing miRNAs from Human breast cancer cells: MCF10A, MCF7, MDA-MB-231, MDA-MB-LM2

first: Seongho

last: Ryu

first: Vivek

last: Mittal


title: Comparative transcriptome analysis of Ptf1aCre;Kras,Brg1-/- vs. Ptf1a;Kras;p53+/- subcutaneous pancreatic ductal adenocarcinoma

status: Public on Nov 14 2013

first: Nilotpal

last: Roy

address: 513 Parnassus Ave.

department: Diabetes Center

institute: UCSF

summary: In this experiment the RNA of s.c. grown tumors of cancer cell lines of murine Ptf1aCre;Kras,Brg1-/- vs. Ptf1a;Kras;p53+/- PDA was isolated and analyzed for gene expression. Ptf1aCre;Kras,Brg1-/- s.c. PDA grows more benign as compared to Ptf1a;Kras;p53+/- PDA; and the rationale of this study was to identify genes responsible for this different biological behavior.

overall_design: Total RNA of s.c. tumors of  Ptf1aCre;Kras,Brg1-/- vs. Ptf1a;Kras;p53+/- cancer cell lines was isolated, purified and analyzed on the deep sequencing platform.

first: Hebrok

last: Matthias

first: Hertel

last: Klemens


title: Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a [RNA-Seq]

status: Public on Nov 16 2013

summary: To investigate the global transcriptome expression in Wild Type mouse hematopoietic stem cells, we performed high-throughput sequencing of Poly A+ RNA (RNA-Seq) from purified HSCs (SP-KSL-CD150+). With biological duplicates, more than 200 million reads in total were obtained.

overall_design: Mouse hematopoietic stem cell mRNA profiles of wild type mice were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000.


title: Genome-wide analysis rice transcriptional change during the early stages of false smut formation caused by Ustilaginoidea virens

city: Wuhan

first: Chao

middle: Jin

last: Quan

state: Hubei

address: Bayi Road,Wuchang

department: College of Life Sciences

country: China

institute: Wuhan University

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

overall_design: Refer to individual Series


title: Large conserved domains of low DNA methylation maintained by 5-hydroxymethycytosine and Dnmt3a


title: Genome-wide maps of Runx3 bound regions in splenic IL-2-activated CD8+ T cells

first: Joseph

last: Lotem

summary: ChIP-seq was conducted on isolated splenic WT CD8+ T cells, TCR-activated and cultured with IL-2 using anti-Runx3 antibodies (Ab), anti-H3K4me1 Ab and non-immune serum (NIS) as control.

overall_design: Two biological Runx3 and two NIS IP repeats from TCR-activated and IL-2 cultured splenic CD8+ T cells isolated by positive selection on anti-CD8 magnetic beads.

first: Dena

last: Leshkowitz

first: Yoram

last: Groner


title: F11R is a novel monocyte prognostic biomarker for malignant glioma

status: Public on Nov 13 2013

city: St Louis

first: Winnie

middle: W

last: Pong

state: MO

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine


title: Perinatal bisphenol A exposure promotes dose-dependent alterations of the mouse methylome

city: Ann Arbor

first: Jung

last: Kim

state: MI

address: 1400 E. Medical Center Drive

institute: University of Michigan

summary: Environmental factors during perinatal development influence developmental plasticity and disease susceptibility via alterations to the epigenome.  Developmental exposure to the endocrine active compound, bisphenol A (BPA), has previously been associated with altered methylation at candidate gene loci. Here, we undertake the first genome-wide characterization of DNA methylation profiles in the liver of murine offspring perinatally exposed to multiple doses of BPA through the maternal diet. Using a tiered focusing approach, our strategy proceeds from unbiased broad DNA methylation analysis using methylation-based next generation sequencing technology to in-depth quantitative site-specific CpG methylation determination using the Sequenom EpiTYPER MassARRAY platform to profile liver DNA methylation patterns in offspring maternally exposed to BPA during gestation and lactation to doses ranging from 0 BPA/kg (Ctr), 50 µg BPA/kg (UG), or 50 mg BPA/kg (MG) diet (N=4 per group). Genome-wide analyses indicate non-monotonic effects of DNA methylation patterns following perinatal exposure to BPA, corroborating previous studies using multiple doses of BPA with non-monotonic outcomes. We observed enrichment of regions of altered methylation (RAMs) within CpG island (CGI) shores, but little evidence of RAM enrichment in CGIs. An analysis of promoter regions identified several hundred novel BPA-associated methylation events, and methylation alterations in the Myh7b and Slc22a12 gene promoters were validated. Using the Comparative Toxicogenomics Database, a number of candidate genes that have previously been associated with BPA-related gene expression changes were identified, and gene set enrichment testing identified epigenetically dysregulated pathways involved in metabolism and stimulus response. In this study, non-monotonic dose dependent alterations in DNA methylation among BPA-exposed mouse liver samples and their relevant pathways were identified and validated. The comprehensive methylome map presented here provides candidate loci underlying the role of early BPA exposure and later in life health and disease status.

overall_design: For this study, liver DNA from a subset of a/a wild-type animals was analyzed for full methylome characteristics: 1) standard diet (Ctr, n = 4 offspring; 2 male and 2 female); 2) 50 µg BPA/kg diet (UG, n = 4 offspring; 2 male and 2 female); 3) 50 mg BPA/kg diet (MG, n = 4 offspring; 1 male and 3 female).

middle: H

first: Maureen

last: Sartr

first: Laura

middle: S

last: Rozek

first: Christopher

last: Faulk

first: Olivia

last: Anderson

first: Tami

last: Jones

first: Muna

last: Nahar

first: Dana

middle: C

last: Dolinoy


title: Nfatc1 Orchestrates Aging in Hair Follicle Stem Cells

first: Brice

last: Keyes

address: 1230 York Ave, Box 300

institute: The Rockefeller University

summary: Mouse hair follicles undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by hair follicle stem cells (HFSCs). We used ChIP-seq to unfold genome-wide chromatin landscapes of Nfatc1 and dissect the biological relevence of its upstream BMP signaling in HFSC aging.

overall_design: Telogen quiescent hair follicle stem cells (HFSCs) were FACS-purified for ChIP-sequcencing.

first: Wen-Hui

last: Lien

first: Elaine

last: Fuchs


title: F11R is a novel monocyte prognostic biomarker for malignant glioma [Seq]

summary:
Objective:
Brain tumors (gliomas) contain large populations of infiltrating macrophages and recruited microglia, which in experimental murine glioma models promote tumor formation and progression. Among the barriers to understanding the contributions of these stromal elements to high-grade glioma (glioblastoma; GBM) biology is the relative paucity of tools to characterize infiltrating macrophages and resident microglia. In this study, we leveraged multiple RNA analysis platforms to identify new monocyte markers relevant to GBM patient outcome.

Methods:
High-confidence lists of mouse resident microglia- and bone marrow-derived macrophage-specific transcripts were generated using converging RNA-seq and microarray technologies and validated using qRT-PCR and flow cytometry. Expression of select cell surface markers was analyzed in brain-infiltrating macrophages and resident microglia in an induced GBM mouse model, while allogeneic bone marrow transplantation was performed to trace the origins of infiltrating and resident macrophages. Glioma tissue microarrays were examined by immunohistochemistry, and the Gene Expression Omnibus (GEO) database was queried to determine the prognostic value of identified microglia biomarkers in human GBM.

Results:
We generated a unique catalog of differentially-expressed bone marrow-derived monocyte and resident microglia transcripts, and demonstrated that brain-infiltrating macrophages acquire F11R expression in GBM and following bone-marrow transplantation.  Moreover, mononuclear cell F11R expression positively correlates with human high-grade glioma and additionally serves as a biomarker for GBM patient survival, regardless of GBM molecular subtype.

Significance:
These studies establish F11R as a novel monocyte prognostic marker for GBM critical for defining a subpopulation of stromal cells for future potential therapeutic intervention.

overall_design:
Total RNA was isolated from three independently-generated sets of flow sorted bone marrow monocytes (CD11b+ CD45high CD115+ Ly6G- cells) and brainstem microglia (CD11b+ CD45low CD115low Ly6G- cells) for Illumina RNA-Seq, and two additional pools were subsequently generated and submitted for Affymetrix Mouse Exon 1.0ST microarray. Two of the RNA-Seq samples were additionally analyzed by the microarray, for a total of 6 samples (3 monocyte, 3 microglia) in each platform. Data outputs were analyzed by two analysis methods each (RNA-Seq data: ALEXA-Seq and Cufflinks; microarray data: Partek and Aroma). All four lists were merged into a new high-confidence gene list of transcripts that were significantly differentially expressed (DE) in three out of the four analyses.
In this dataset, we includeRNA-Seq data obtained from flow sorted mouse bone marrow monocytes and brainstem microglia.

first: Jason

last: Walker

first: Todd

last: Wylie

first: Vincent

last: Magrini

first: Jingqin

last: Luo

first: Ryan

middle: J

last: Emnett

first: Jaebok

last: Choi

first: Matthew

middle: L

last: Cooper

first: Malachi

last: Griffith

first: Obi

first: Joshua

middle: B

last: Rubin

first: Gregory

middle: N

last: Fuller

first: David

last: Piwnica-Worms

first: Xi

last: Feng

first: Dolores

last: Hambardzumyan

first: John

middle: F

last: DiPersio

last: Mardis

last: Gutmann


title: The transcription program of Runx3 in natural killer cells and CD8+ T cells

first: Joseph

last: Lotem


title: Genome-wide measurement of acetylated histone H3 in naïve cells under Treg-inducing conditon

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

summary: To investigate the molecular mechanism how butyrate promoter differentiation of naïve T cells into regulatory T cells

overall_design: Examination of acetylated histone H3 during the differentiation of regulatory T cells in the presence or absence of butyrate

first: Yukihiro

last: Furusawa

first: Koji

last: Hase


title: Genome-wide analysis rice transcriptional change during the early stages of false smut formation caused by Ustilaginoidea virens [set A]

first: Chao

last: Quan

summary: Rice false smut is a common fungal disease caused by Ustilaginoidea virens. As it only scatter occured in panicle at florescence, little information is known about this crop disease. Here, we injected suspension spores into a susceptible indica rice cultivar 9311 booting panicle (infected water as mock) and divided the early disease symptom into 3 uninterrupted stages(S) at 6 day post inoculation (dpi): the infected pistil became expand (S1), the hyphae began to infect the bottom of anthers (S2) and the hyphae growth went on and surrounded the floral organ forming a floral-hyphae complex (S3). To gain insight into rice putatively differential responses to U. virens, all 3 infected and mock spikes with same spike length were collected and analyzed by Solexa/Illuminaâs digital gene expression (DGE) system, BGI. Our results contribute to the knowledge of understanding rice molecular mechanism in response to U. virens infection.

overall_design: Four samples including one control (CK) and three infected (S1, S2, S3) were analyzed

first: Jinquan

last: Chao

first: Yingguo

last: Zhu


title: Chemical map of S. pombe reveals species-specific features in nucleosome positioning

status: Public on Nov 12 2013

city: Evanston

first: Ji-Ping

last: Wang

address: 2006 Sheridan Road

institute: Northwestern University

summary: Knowing the exact positions of nucleosomes not only advances our understanding of their role in gene regulation, but also the mechanisms that underlie between-species variation in chromatin structure. We have generated a chemical map of nucleosomes in vivo in Schizosaccharomyces pombe at base pair resolution. This new map reveals that S.pombe genome shares a similar periodic linker length distribution with Saccharomyces cerevisiae, but with major distinctions in nucleosomal/linker DNA sequence features. In S.pombe, A/T rich sequences are enriched in the nucleosome core region, particularly +/-20 bp of dyad, while they are disfavored in S.cerevisiae nucleosomes. The poly (dA-dT) tracts only slightly affect the nucleosome occupancy in S.pombe; and they possess preferential rotational positions within the nucleosome core with significant enrichment in the 10-30 bp region from the dyad for longer tracts. S.pombe does not have well-defined nucleosome free region immediately upstream of most transcription start sites (TSS), instead the -1 nucleosome is positioned with regular distance to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. The nucleosomes around TSS show more pronounced bidirectional phasing when the intergenic distance is relatively short, and the downstream nucleosome positioning is strongly correlated with DNA sequence features.  We discovered that heterochromatin regions tend to have sparse nucleosome positioning, mixed with both well-positioned and fuzzy nucleosomes. The S.pombe map suggests that some of nucleosome positioning codes, formerly thought to be intrinsic, may largely depend on species-specific extrinsic factors including linker histone, chromatin remodelers and other DNA-binding proteins.

overall_design: 2 samples were analyzed with high throughput paired-end parallel sequencing. Both samples were created using the same chemical mapping protocol

first: Georgette

last: Moyle-Heyrman

first: Tetiana

last: Zaichuk

first: Liqun

last: Xi

first: Quanwei

last: Zhang

first: Jonathan

last: Widom

first: Olke

last: Uhlenbeck

first: Robert

last: Holmgren


title: Transcriptomic analyses of TCDD treated zebrafish liver

city: Singapore

first: Zhiyuan

last: Gong

address: Kent Ridge

country: Singapore

institute: National University of Singapore

summary: To fully understand molecular toxicity of TCDD in an in vivo animal model, adult zebrafish were exposed to TCDD at 10 nM for 96 h and the livers were sampled for RNA-sequencing based transcriptomic profiling. A total of 1,058 differently expressed genes were identified based on fold-change>2 and TPM (transcripts per million) >10. Among the top 20 up-regulated genes, 10 novel responsive genes were identified and verified by qRT-PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle, endocrine disruptors, signal transduction and immune systems. Comparative analyses of TCDD-induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up-regulated while calcium signaling pathway and several immune-related pathways are generally down-regulated.

overall_design: Transcriptome profiling of treated sample (TCDD) and control sample (DMSO) were generated by deep sequencing using 3' RNA-SAGE with SOLiD system

first: Zhihua

last: Li

first: Hongyan

last: Xu

first: Weiling

last: Zheng

first: Siew

last: Lam


title: PARN mediates 3'-end trimming of Argonaute-cleaved precursor microRNAs

city: New Haven

first: Antonio

last: Giraldez

state: CT

address: 333 Cedar street

department: Genetics

institute: Yale

summary: microRNAs (miRNAs) are typically generated as ~22-nucleotide double-stranded RNAs via processing of precursor hairpins by the RNase III enzyme Dicer, after which they are loaded into Argonaute (Ago) proteins to form RNA-induced silencing complex (RISC). However, the biogenesis of miR-451, an erythropoietic miRNA conserved in vertebrates, does not require Dicer processing. Instead, the short pre-miR-451 precursor hairpin is directly loaded into Ago, followed by cleavage of the 3' arm and trimming of the 3' end to the mature length by PARN. Here we show the in vivo activity of miR-430 Ago2-hairpin, a canonical microRNA engineered to fit the structure of miR-451 and hence become Ago2-dependent. Moreover, we test a modified miR-430 Ago2-haipin with 3x phoshorothioate bonds that impairs trimmng. Surprisingly, our data show that trimming of Ago-cleaved pre-miRNAs is not essential for target silencing, indicating that RISC is functional with miRNAs longer than 22-nucleotides.

overall_design:
Rescue of MZdicer zebrafish mutant with the injection of trimmable and nontrimmable miR-430 Ago2 hairpins:
Transcriptome of wild type, MZdicer mutant, and MZdicer mutant micoinjected with miR-430 duplex, miR-430 (Ago2-haripin),  miR-430 (Ago2-haripin 3xPhosphorothioate)

first: Mayuko

last: Yoda

first: Daniel

last: Cifuentes

first: Natsuko

last: Izumi

first: Yuriko

last: Sakaguchi

first: Tsutomu

last: Suzuki

first: Hukihide

last: Tomari


title: Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for amyotrophic lateral sclerosis and frontotemporal dementia

city: La Jolla

first: John

last: Ravits

department: Neuroscience

institute: UCSD

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

city: Edinburgh

first: Musa

last: Hassan

state: Scotland

address: Easter Bush

department: Roslin

country: United Kingdom

institute: University of Edinburgh

summary: Alternative splicing and mRNA editing are known to contribute to transcriptome diversity. Although alternative splicing is pervasive and known to contribute to a variety of pathologies, including cancer, the genetic context for individual differences in isoform usage is still evolving. Similarly, although mRNA editing is ubiquitous and associated with important biological processes such as intracellular viral replication and cancer development, individual variations in and the genetic transmissibility of mRNA editing are equivocal. Here, we have used linkage analysis to show that both mRNA editing and alternative splicing are regulated by the macrophage genetic background and environmental cues. We show that distinct loci, potentially harboring variable splice factors, regulate the splicing of multiple transcripts. Additionally, we show that individual genetic variability at the Apobec1 locus results in differential rates of C-to-U(T) editing in murine macrophages; with mouse strains expressing mostly a truncated isoform of Apobec1 exhibiting lower rates of editing. As a proof of concept, we have used linkage analysis to identify 36 high confidence novel edited sites. These results provide a novel and complementary method that can be used to identify C-to-U editing sites in individuals segregating at specific loci and show that, beyond individual DNA sequence and structural changes, differential isoform usage and mRNA editing can contribute to intra-species genomic and phenotypic diversity.

overall_design: Bone marrow derived macrophages (BMDM) from female AxB/BxA mice were left unstimulated or stimulated with IFNG/TNF, or CpG for 18 hrs or infected with infected with type II (Pru A7) for 8 hrs. The transcriptional response was then measured using the illumina RNA-seq protocol on an illumuna HiSeq 2000.

first: Vincent

last: Butty

first: Kirk

middle: D

last: Jensen

first: Jeroen

middle: P

last: Saeij


title: Gene expression profile analysis of normal and type 2 diabetic mouse liver

city: Shanghai

first: Qiwei

last: Zhai

address: 294 Taiyuan Road

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Gene expression profiles in the liver of 9-week-old wild type and diabetic db/db mice were measured by high-throughput sequencing to detect the differentially expressed genes

overall_design: Gene expression profiles of 9-week-old wild type and diabetic db/db mice were generated by high-throughput sequencing using Illumina Genome Analyzer

first: Fang

last: Zhang

first: Xiang


title: Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for amyotrophic lateral sclerosis and frontotemporal dementia (strand specific RNA-seq)

summary:
Purpose: The purpose of this experiment is to identify expression changes after ASO-dependent depletion of mouse C9orf72 in the spinal cord of wild-type C57Bl/6 female mice.
Methods: Strand specific RNA-seq was performed using RNAs extracted from spinal cord of C57Bl/6 mice two weeks after intracerebroventricular stereotactic injection of saline (n=3), a control ASO (n=3) or an ASO targeting mouse C9orf72 (n=3). C9orf72 RNA levels were reduced to approximately 30% of control levels in spinal cords from mice treated with the C9orf72 ASO.
Results: Statistical comparison of RPKM values between RNAs from C9orf72 and control ASO treated animals or C9orf72 and saline treated samples revealed that only 12 genes were consistently upregulated (defined by P<0.05 adjusted for multiple testing) and 12 genes including C9orf72 were downregulated (defined by P<0.05 adjusted for multiple testing).
Conclusions: Only few RNA expression changes were identified in the spinal cord following reduction of C9orf72.

overall_design: Use of strand specific RNA-seq to test the consequences of C9orf72 loss of function in mouse spinal cord.

first: Clotilde

last: Lagier-Tourenne

first: Michael

last: Baughn

first: Frank

last: Rigo

first: Patrick

last: Liu

first: Kasey

last: Hutt

first: Gene

last: Yeo

first: Don

last: Cleveland


title: Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation

status: Public on Nov 11 2013

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: Genome-wide transcriptome analyses have allowed for systems-  level insights into gene regulatory networks. Due to the limited depth of   quantitative proteomics, however, our understanding of post-transcriptional   gene regulation and its effects on protein complex stoichiometry are lagging   behind.   Here, we employ deep sequencing and iTRAQ technology to determine transcript   and protein expression changes of a Drosophila brain tumour model at near   genome-wide resolution. In total, we quantify more than 6,200 tissue-specific   proteins, corresponding to about 70% of all transcribed protein-coding genes.   Using our integrated data set, we demonstrate that post-transcriptional gene   regulation varies considerably with biological function and is surprisingly   high for genes regulating transcription. We combine our quantitative data with   protein-protein interaction data and show that post-transcriptional mechanisms   significantly enhance co-regulation of protein complex subunits beyond   transcriptional co-regulation. Interestingly, our results suggest that only   about 11% of the annotated Drosophila protein complexes are co-regulated in   the brain. Finally, we refine the composition of some of these core protein   complexes by analysing the co-regulation of potential subunits.  Our comprehensive transcriptome and proteome data provide a rich resource for   quantitative biology and offer novel insights into understanding post-  transcriptional gene regulation in a tumour model.

overall_design: Transcriptomes of 1-3 day old adult female Drosophila melanogaster heads of control and brat mutant were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Christoph

last: Jüschke

first: Heike

last: Harzer

first: Juergen

last: Knoblich


title: Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for amyotrophic lateral sclerosis and frontotemporal dementia (Multiplex Analysis of PolyA-linked Sequences)

first: John

last: Ravits

summary:
Purpose: The purpose of this experiment is to identify a C9-ALS/FTD specific genomic profile in fibroblast lines that is distinct from sporadic ALS without C9orf72 expansion and non-neurologic control cells. The study will then evaluate the effect on this identified profile of ASO treatment targeting the sense strand RNA transcript of the C9orf72 gene.
Methods: Expression profiling was performed on RNAs from fibroblasts of four C9orf72 patients, four control individuals and four sporadic ALS patients using Multiplex Analysis of PolyA-linked Sequences method.
Results: Hierarchical clustering of expression values for all genes showed that the four C9orf72 patient lines had an expression profile distinct from control and sporadic ALS lines. Statistical comparison of expression values between the four C9orf72 lines and the four control lines revealed that 122 genes were upregulated (defined by a False Discovery Rate FDR<0.05) and 34 genes were downregulated (defined by a False Discovery Rate FDR <0.05) in C9orf72 patient fibroblasts.
Conclusions: A genome wide RNA signature can be defined in fibroblasts with C9orf72 expansion. ASO-mediated reduction of C9orf72 RNA levels in fibroblasts with the hexanucleotide expansion efficiently reduced accumulation of GGGGCC RNA foci. This did not, however, generate a reversal of the C9orf72 RNA profile.

overall_design: Use of Multiplex Analysis of PolyA-linked Sequences to identify expression changes in fibroblasts from amyotrophic lateral sclerosis and frontotemporal dementia patients harboring an hexanucleotide expansion in the C9orf72 gene.

first: Hai-Ri

last: Li

first: Jinsong

last: Qiu

first: Xiang-Dong

last: Fu


title: Genome-wide analysis rice transcriptional change during the early stages of false smut formation caused by Ustilaginoidea virens [2011].

first: Chao

last: Quan

summary: Rice false smut is a common fungal disease caused by Ustilaginoidea virens. As it only scatter occured in panicle at florescence, little information is known about this crop disease. In the previous study, 3 uninterrupted infecting stages were divided and each stage was monitored by Solexa/Illumina’s digital gene expression (DGE) system, and all data were submitted to NCBI (GSE32010). As the disease was greatly affected by environment and to eliminate environment factor, an experimental replication was done in 2011. Samples collection and analysis were described in GSE32010. Our results contribute to the knowledge of understanding rice molecular mechanism in response to U. virens infection.

overall_design: Four samples including one control (CK) and three infected (S1, S2, S3) were analyzed.

first: Jinquan

last: Chao

first: Yingguo

last: Zhu


title: Genome-wide maps of chromatin state in Williams-Beuren (WBS), Williams-Beuren Region duplication (WBRdupS), Smith-Magenis (DGS), DiGeorge (DGS) lymphoblastoid cell lines

city: Lausanne

first: Alexandre

last: Reymond

address: Dorigny

department: CIG

institute: UNIL

summary: Copy number variants (CNV) influence the expression of genes that map not only within, but also on their flanks. To assess the possible mechanism(s) underlying this “neighboring effect”, we compared intrachromosomal interactions and histone modifications in cell lines of patients affected by genomic disorders and control individuals. We detected alteration of intrachromosomal interactions (chromosomal looping) between the loci of affected genes and the rearranged interval using chromosome conformation capture (4C-seq). These results are consistent with the observed gene expression alterations. We also pinpointed concomitant changes in histone modifications between samples. Modified genes were often looping together, possibly forming an interacting cluster. We conclude that large genomic rearrangements can lead to chromatin conformation changes that extend far away from the structural variant, thus possibly modulating expression globally and modifying the phenotype. For example, we observe that the chromatin conformation, histone marks and relative expression levels of the AUTS2 gene, mutations of which are associated with autism and intellectual disabilities, are modified in Williams-Beuren syndrome patients cell lines.

overall_design: Examination of 2 different histone modifications in genomic disorders patients' cell lines.

first: Robert

middle: M

last: Witwicki

first: Eugenia

last: Migliavacca

first: Nele

last: Gheldof


title: Transcription Start Site analysis of Mouse Ter119+ erythroid cells

city: oxford

first: Jim

last: Hughes

address: Weatherall Institute Of Molecular Me

department: MHU

institute: University of Oxford

summary: Transcription Start Site analysis in Mouse Ter119+ erythroid cells

overall_design: Strand Specific Paired end NanoCage analysis of Total RNA from Mouse Ter119+ erythroid  cells

first: Monika

last: Kowalczyk

first: Doug

last: Higgs


title: Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

summary: We analyzed a deletion mutant of the ECF σ factor SigX and applied mRNA profiling to define the SigX dependent regulon in P. aeruginosa in response to low osmolarity medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and c-di-GMP signaling. In accordance, a sigX deletion mutant exhibited an altered fatty acid composition of the cell membrane, reduced cytotoxicity, impaired swarming activity, elevated c-di-GMP levels and increased biofilm formation. In conclusion, a combination of ChIP-seq with transcriptional profiling and bioinformatic approaches to define consensus DNA binding sequences proved to be effective for the elucidation of the regulon of the alternative σ factor SigX revealing its role in complex virulence-associated phenotypes in P. aeruginosa.

overall_design: Transcriptome profiling of the SigX deletion mutant and overexpressing wildtype complemented by ChIP-seq

first: Andrea

last: Blanka

first: Sebastian

last: Schulz

first: Raimo

last: Franke

first: Agata

last: Bielecka

first: Tanja

last: Nicolai

first: Fiordiligi

last: Casilag

first: Juliane

last: Düvel

first: Wolf-Rainer

last: Abraham

first: Volkhard

last: Kaever

first: Susanne

last: Häussler


title: Transcriptome analysis of Mouse Ter119+ erythroid  cells [PolyA-]

summary: Analysis of Non-Polyadenylated gene expression in  Mouse Ter119+ erythroid  cells

overall_design: Paired end RNA-seq analysis of PolyA Minus RNA from Mouse Ter119+ erythroid  cells


title: Transcriptome analysis of Mouse Ter119+ erythroid  cells [PolyA+]

summary: Analysis of gene expression in  Mouse Ter119+ erythroid  cells

overall_design: Paired end RNA-seq analysis of PolyA selected RNA from Mouse Ter119+ erythroid  cells


title: Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

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

overall_design: Refer to individual Series


title: The Cryptococcus transcriptome at the site of human meningitis

status: Public on Nov 10 2013

city: Durham

first: John

last: Perfect

state: NC

address: 0557 Duke South, blue zone

department: Division of Infectious Disease

institute: Duke University Medical Center

summary: Cryptococcus neoformans is a major cause of fungal meningitis in immunocompromised individuals worldwide. Studies have categorized the transcriptome of Cryptococcus under various stresses, such as temperature, nitric oxide, iron, antifungal drugs and macrophages. However, an accurate and comprehensive transcriptome profiling of C. neoformans in the human host may allow an even better understanding of its survival and disease production. In this study, we isolated RNA from yeast cells taken directly from CSF of two individuals with cryptococcal meningitis. RNA-Seq was used to generate and compare transcriptional profiles from those yeast cells exposed to three environmental conditions. Under same conditions, similar expression patterns were found between the two strains with different genotypes. Yeast cells from in vivo CSF appear to be more metabolically active compared to those exposed to ex vivo CSF. Moreover, genes that were identified as significantly up-regulated in both ex vivo CSF and in vivo CSF conditions compared with growth in YPD appear to be important for the virulence of Cryptococcus. In the central nervous system, differentially expressed genes, single nucleotide variants and novel genes between strains were identified to emphasize that strains have consensus expression patterns but they do have their unique features. Genes with transporter functions were found to be enriched in the regulated transcripts demonstrating this important function of yeasts under host stress. These findings provide the platform for further interrogation into how this yeast survives in humans to provide identification of possible antifungal target(s) and/or genetic signatures to predict outcome.

overall_design: Examination of mRNA expression levels under three different conditions of two different strains with different genotypes

first: Yuan

last: Chen


title: RNA-seq Analysis of FlbD-, AbaA-, and WetA-dependent Genes in Fusarium graminearum Z-3639

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

country: South Korea

institute: Seoul National University

summary: Fusarium graminearum (teleomorph Gibberella zeae) is a prominent pathogen that infects major cereal crops, such as wheat, barley, and maize. Conidiogenesis had been intensively studied in Aspergillus nidulans and regulatory pathway genes have been known to regulate conidiogenesis in stage specific manner. We reported the functional analyses of flbD, abaA, and wetA orthologs in F. graminearum. To understand genome-wide transcriptional profiling of conidiation, we employed RNA-seq of the wild-type Fusarium graminearum Z-3639 and each gene deletion mutants with three time courses (0 h, 6 h and 12 h after induction of conidiogenesis).

overall_design:
AbaA experiment: 6 samples examined: 0 h, 6 h and 12 h after induction of conidiogenesis of Fusarium graminearum Z-3639 wild type and ΔabaA(ΔabaA::gen) mutant strains
WetA experiment: 3 samples examined: 0 h, 6 h and 12 h after induction of conidiogenesis of Fusarium graminearum ΔwetA(ΔwetA::gen) mutant strains
flbD experiment: 3 samples examined: 0 h, 6 h and 12 h after induction of conidiogenesis of Fusarium graminearum ΔflbD(ΔflbD::gen) mutant strains

first: Jae-Yun

last: Lim

first: Yin-Won

last: Lee


title: Genome-wide maps of chromatin accessibility in C57bl\6 mouse erythroid cells.

first: Jim

last: Hughes

summary: Genome-wide identification of active regions in the mouse erythroid genome using DNase-seq.

overall_design: DNAse-seq was performed in C57bl\6 mouse erythroid Ter119+ cells.

first: Mona

last: Hosseini

first: Jonathan

last: Flint

first: Doug

last: Higgs


title: Cooperative transcriptional repression by BCL6 and BACH2 in germinal center B-cell differentiation

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: The transcriptional repressors BCL6 and BACH2 are crucial regulators of germinal center (GC) B-cell fate, and are known to interact and repress transcription of PRDM1, a key driver of plasma cell differentiation. How these factors cooperate is not fully understood. Herein we show that while GC formation is only minimally impaired in Bcl6+/- or Bach2+/- mice, double heterozygous Bcl6+/-Bach2+/- mice exhibit profound reduction in GC formation. Splenic B-cells from Bcl6+/- Bach2+/- mice display accelerated plasmacytic differentiation and high expression of key plasma cell genes such as Prdm1, Xbp1 and CD138. ChIP-seq revealed that in B-cells BACH2 is mostly bound to genes together with its heterodimer partner MAFK. The BACH2-MAFK complex binds to sets of genes known to be involved in the GC response, 60% of which are also targets of BCL6. Approximately 30% of BACH2 peaks overlap with BCL6 including cis-regulatory sequences of the PRDM1 gene. BCL6 also modulates BACH2 protein stability and their protein levels are positively correlated in GC B-cells. Therefore, BCL6 and BACH2 cooperate to orchestrate gene expression patterning in GC B cells through both transcriptional and biochemical mechanisms, which collectively determine the proper initiation and timing of terminal differentiation.

overall_design: ChIP-seq using P18 antibodies in OCI-Ly7 cells

first: Chuanxin

last: Huang

first: Ari

last: Melnick


title: Genome-wide maps of chromatin modifications in C57bl\6  mouse erythroid cells.

summary: Regions of chromatin modified by H3K4me1 and H3K4me3 were identified in mouse erythroid cells using ChIP-seq.

overall_design: Chip-seq experiements were performed in C57bl\6  mouse erythroid Ter119+ cells.

first: Monika

last: Kowalcyzk


title: Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast

city: Taichung

first: Li-Ching

last: Hsieh

address: 145 Xingda Rd.

department: Graduate Institute of Genomics and Bioinformatics

country: Taiwan

institute: National Chung Hsing University

summary: Gene expression evolution can be caused by changes in cis- or trans-regulatory elements or both. As cis and trans regulation operate through different molecular mechanisms, cis and trans mutations may show different inheritance patterns and may be subjected to different selective constraints. To investigate these issues, we obtained and analyzed gene expression data from two Saccharomyces cerevisiae strains and their hybrid, using high-throughput sequencing. Our data indicate that compared to other types of genes, those with antagonistic cis-trans interactions are more likely to exhibit over- or under-dominant inheritance of expression level. Moreover, in accordance with previous studies, genes with trans variants tend to have a dominant inheritance pattern while cis variants are enriched for additive inheritance. In addition, cis regulatory differences contribute more to expression differences between species than within species, whereas trans regulatory differences show a stronger association between divergence and polymorphism. Our data indicate that in the trans component of gene expression differences genes subjected to weaker selective constraints tend to have an excess of polymorphism over divergence compared to those subjected to stronger selective constraints. In contrast, in the cis component, this difference between genes under stronger and weaker selective constraint is mostly absent. To explain these observations, we propose that purifying selection more strongly shapes trans polymorphism than cis polymorphism.

overall_design: Study the gene expression patterns in two strains of yeast (BY and RM)

first: Wen-Hsiung

last: Li

first: Bernhard

last: Schaefke

first: James

last: Emerson

first: Tzi-Yuan

last: Wang

first: Mei-Yeh

last: Lu


title: A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development

city: Nijmegen

first: Gert Jan

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

summary: To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between an early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts, the majority of which show hallmarks of being long non-coding RNAs both in terms of their coding potential and gene structure.

overall_design: Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development

first: Sarita

last: Paranjpe

first: Ulrike

middle: G

last: Jacobi

first: Simon

last: van Heeringen

first: Gert


title: Consequences of beta-PDGFR deletion on hepatic stellate cells during hepatic regeneration

status: Public on Nov 08 2013

city: New York

first: Peri

last: Kocabayoglu

address: 1425 Madison Avenue

department: Liver Diseases

institute: Icahn School of Medicine at Mount Sinai

summary:
Purpose: The goal of this study was to determine biological consequences during liver regeneration following partial hepatectomy in mice by next-generation sequencing. A particular interest was to compare mice with either a floxed b-PDGFR allele to mice that harbored a deletion of b-PDGFR in hepatic stellate cells (HSCs), by crossing b-PDGFR fl/fl mice with transgenic GFAP-Cre mice.
Methods: b-PDGFR fl/fl mice or mice with a HSC-specific deletion of b-PDGFR underwent either sham operation or 70% partial hepatectomy. Following 72 hours, livers were collected and total RNA was extracted using tizol, followed by a purification using Quiagen spin columns including an on-column DNAse digestion step.
Conclusion: Our study represents a detailed analysis of hepatic transcriptome, with biologic replicates, generated by RNA-seq technology of livers following sham operation or partial hepatectomy in b-PDGFR fl/fl mice or b-PDGFRfl/fl/GRAP-Cre mice.

overall_design: Whole liver mRNA profiles of sham operated livers or livers collected 72hours after partial hepatectomy of beta-PDGFR fl/fl and beta-PDGFR fl/fl/GFAP-Cre (creating a hepatic stellate cell-specific deletion of b-PDGFR) mice were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.

first: Scott

last: Friedman


title: A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function

city: Chicago

first: Ann

last: Harris

state: IL

address: 2430 N Halsted Street Box 211

institute: Lurie Children's Hospital of Chicago Research Center


title: Translational landscape of photomorphogenic Arabidopsis

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

institute: Academia sinica

summary: We report the application of ribosome profiling method to map ribosome locations on transcripts in de-etiolating Arabidopsis seedlings

overall_design: Examine steady-state mRNA and ribosome-protected mRNA abundance in 4-day-old etiolated seedlings with/without 4-h light treatment

first: Shu-Hsing

last: Wu


title: iPSC derived motor neuron cultures from C9ORF72 carriers

status: Public on Nov 07 2013

city: Los Angeles

first: Robert

last: Baloh

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative condition characterized by loss of motor neurons in the brain and spinal cord. Expansions of a hexanucleotide repeat (GGGGCC) in the noncoding region of the C9ORF72 gene are the most common cause of the familial form of ALS (C9-ALS), as well as frontotemporal lobar degeneration and other neurological diseases. How the repeat expansion causes disease remains unclear, with both loss of function (haploinsufficiency) and gain of function (either toxic RNA or protein products) proposed. We report a cellular model of C9-ALS with motor neurons differentiated from induced pluripotent stem cells (iPSCs) derived from ALS patients carrying the C9ORF72 repeat expansion. No significant loss of C9ORF72 expression was observed, and knockdown of the transcript was not toxic to cultured human motor neurons. Transcription of the repeat was increased, leading to accumulation of GGGGCC repeat–containing RNA foci selectively in C9-ALS iPSC-derived motor neurons. Repeat-containing RNA foci colocalized with hnRNPA1 and Pur-α, suggesting that they may be able to alter RNA metabolism. C9-ALS motor neurons showed altered expression of genes involved in membrane excitability including DPP6, and demonstrated a diminished capacity to fire continuous spikes upon depolarization compared to control motor neurons. Antisense oligonucleotides targeting the C9ORF72 transcript suppressed RNA foci formation and reversed gene expression alterations in C9-ALS motor neurons. These data show that patient-derived motor neurons can be used to delineate pathogenic events in ALS.

overall_design: Transcriptome profiling from iPSC derived motor neurons compared to controls


title: Transcriptional profiling of embryonic skeletal muscle stem/progenitor cells

city: Paris

first: Shahragim

last: Tajbakhsh

address: 25 rue du Dr Roux

department: Dept. of Developmental & Stem Cell Biology

country: France

institute: Pasteur Institute

summary: Muscle stem cells (MuSC) change molecular and functional properties during development. Using a transgenic Tg:Pax7-nGFP mice, we FACS-isolated MuSC from embryonic (E12.5) and foetal (E17.5) stages to understand the differences and similarities amongst the myogenic stem/progenitor populations.

overall_design: Pax7-nGFP+ cells were isolated by FACS from limb buds of E12.5 and E17.5 Tg:Pax7-nGFP embryos following enzymatic digestion.  Affymetrix microarrays were performed on biological triplicates.

first: Ramkumar

last: Sambasivan

first: Philippos

last: Mourikis

first: Swetha

last: Gopalakrishnan

first: Ugo

last: Borello


title: Advancing Functional Utility of PAR-CLIP by Quantifying Background Binding to mRNAs and lncRNAs

first: Matthew

middle: Burk

last: Friedersdorf

address: 207 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

summary: We developed a method for measuring non-specific background in PAR-CLIP data demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal.  Furthermore, we show that quantitative determination of background is essential for identifying targets of weakly binding RNA-binding proteins and can substantially improve motif analysis.

overall_design: To define background binding events in PAR-CLIP data we performed the standard PAR-CLIP protocol (Hafner et al., Cell 2010.) on lysates expressing a commonly used non-RBP control, FLAG-GFP.  After FLAG-tag immunopurification of UV 365nm irradiated lysates prepared from cells supplemented with 4-thiouridine (4SU), RNA was partially digested with RNase T1, radiolabeled and separated by SDS-PAGE.  Reads were sequenced by Illumina HiSeq.  PAR-CLIP was also performed for HuR.  Included as well is a total from lysates treated like PAR-CLIP, but without immunoprecipitation (see sample description for more detail).

first: M

first: J

last: Keene


title: Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

city: Bethesda

first: Francis

last: Collins

state: MD

address: 1 Center Drive, Rm 126

department: Genome Technology Branch

institute: NHGRI


title: Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (RNA-seq)

summary: Chromatin-based functional genomic analyses and genomewide association studies (GWASs) together implicate enhancers as critical elements influencing gene expression and risk for common diseases. Here, we performed systematic chromatin and transcriptome profiling in human pancreatic islets. Integrated analysis of islet data with those generated by the ENCODE project in nine cell types identified specific and significant enrichment of type 2 diabetes and related quantitative trait GWAS variants in islet enhancers. Our integrated chromatin maps reveal that most enhancers are short (median = 0.8 kb). Each cell type also contains a substantial number of more extended (≥3 kb) enhancers. Interestingly, these stretch enhancers are often tissue-specific and overlap locus control regions, suggesting that they are important chromatin regulatory beacons. Indeed, we show that (i) tissue specificity of enhancers and nearby gene expression increase with enhancer length; (ii) neighborhoods containing stretch enhancers are enriched for important cell type-specific genes; and (iii) GWAS variants associated with traits relevant to a particular cell type are more enriched in stretch enhancers compared with short enhancers. Reporter constructs containing stretch enhancer sequences exhibited tissue-specific activity in cell culture experiments and in transgenic mice. These results suggest that stretch enhancers are critical chromatin elements for coordinating cell type-specific regulatory programs and that sequence variation in stretch enhancers affects risk of major common human diseases.

overall_design:
Integrated analysis of islet chromatin modification and transcriptome data with those generated by the ENCODE project.

NISC Comparative Sequencing Program

first: Steve

last: Parker

first: Michael

last: Stitzel

first: D

last: Taylor

first: Jose

last: Orozco

middle: R

last: Erdos

first: Jennifer

middle: A

last: Akiyama

first: Kelly

last: van Bueren

first: Peter

last: Chines

first: Narisu

last: Narisu

first: Brian

last: Black

first: Axel

last: Visel

first: Len

last: Pennacchio


title: ChIP-seq analysis of GATA4 in whole liver of adult mice

city: Philadelphia

first: Rena

last: Zheng

state: PA

address: 3615 Civic Center Blvd. Abramson Research Center 315A

institute: Children's Hospital of Philadelphia

summary: GATA4 regulates the liver development, but it's function and the gene transcriptional programs it regulates in the adult liver is unknown.  In this study, we determined the genome-wide occupancy sites of GATA4 by performing ChIP-seq of whole livers.  We have identified 4409 GATA4 enrichment peaks using two peak calling methods and irreproducible discovery rate (IDR) analysis. This corresponds to 3075 genes with GATA4 peaks within -5 kb of transcription start site (TSS) and +5 kb of transcription termination site (TTS).  MEME analysis shows that approximately 90% of the peaks have the WGATAR motif, suggesting direct binding by GATA4.  The peaks containing the WGATAR motif have a ChIP-seq higher tag enrichment score than peaks lacking the motif.  Genome Regions Enrichment of Annotations Tool (GREAT) analysis of genes bound by GATA4 identified ontologies with liver specific functions.  In summary, our study shows for the first time genome-wide occupancy profile of GATA4in the adult mouse liver.

overall_design: ChIP-sequencing of whole mouse livers from 2-3 month old mice

first: Boris

last: Rebolledo-Jaramillo


title: GATA4


title: A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function (DNase-hypersensitivity)

first: Ann

last: Harris

summary: Distal cell-type-specific regulatory elements may be located at very large distances from the genes that they control and are often hidden within intergenic regions or in introns of other genes. The development of methods that enable mapping of regions of open chromatin genome wide has greatly advanced the identification and characterisation of these elements. Here we use DNase I hypersensitivity mapping followed by deep sequencing (DNase-seq) to generate a map of open chromatin in primary human tracheal epithelial (HTE) cells and use bioinformatic approaches to characterise the distribution of these sites within the genome and with respect to gene promoters, intronic and intergenic regions. Genes with THE-selective open chromatin at their promoters were associated with multiple pathways of epithelial function and differentiation. The data predict novel cell-type-specific regulatory elements for genes involved in HTE cell function, such as structural proteins and ion channels, and the transcription factors that may interact with them to control gene expression. Moreover, the map of open chromatin can identify the location of potentially critical regulatory elements in genome-wide association studies (GWAS) in which the strongest association is with single nucleotide polymorphisms in non-coding regions of the genome. We demonstrate its relevance to a recent GWAS that identifies modifiers of cystic fibrosis lung disease severity. Since HTE cells have many functional similarities with bronchial epithelial cells and other differentiated cells in the respiratory epithelium, these data are of direct relevance to elucidating the molecular basis of normal lung function and lung disease.

overall_design: To identify cis-regulatory elements for genes expressed in human tracheal epithelial cells we generated genome-wide maps of open chromatin by DNase-seq. HTE cells were isolated from these trachea and grown as described previously (Davis P.B. et al.1990).

last: Bischof

first: C

last: Ott

first: S

middle: H

last: Leir

first: N

last: Gosalia

first: L

last: Song

last: London

first: T

last: Furey

middle: U

last: Cotton

first: G

middle: E

last: Crawford

first: A


title: RNA methylation-dependent RNA processing controls the speed of the circadian clock

city: Manchester

first: Jean-Michel

last: Fustin

state: England

address: Faculty of Biology, Medicine and Health, , Oxford road

department: Centre for Biological Timing

institute: University of Manchester

summary: To investigate the major components of the response to the methylation inhibitor 3-deazadenosine

overall_design: U2OS cells were plated in 20 cm dishes and grown until confluence. Cells were then treated with 100 microM deazaadenosine or vehicle (PBS) for 24 hours. Three replicate dishes for each treatment were analysed.

first: Masao

last: Doi

first: Yoshiaki

last: Yamaguchi

first: Shininchi

last: Nishimura

first: Minoru

last: Yoshida

first: Takayuki

last: Isagawa

first: Masaki

last: Suimye Morioka

first: Hideaki

last: Kakeya

first: Ichiro

last: Manabe

first: Hitoshi

last: Okamura


title: RNA-seq reveals differential gene expression in Staphylococcus aureus at single-nucleotide resolution

first: Joseph

last: Osmundson

address: 1230 York Ave

department: Molecular Biophysics

institute: The Rockefeller University

summary: Staphylococcus aureus is a gram-positive cocci and an important human commensal bacteria and pathogen.  S. aureus infections are increasingly difficult to treat because of the emergence of highly resistant MRSA (Methicillin-resistant S. aureus) strains. Here we present a method to study differential gene expression in S. aureus using high-throughput RNA-sequencing (RNA-seq).  We use RNA-seq to examine the differential gene expression in S. aureus RN4220 cells containing an exogenously expressed transcription factor and between two S. aureus strains (RN4220 and NCTC8325-4).  The information provided by RNA-seq was a significant advance over previously described microarray based techniques. We investigated the sequence and gene expression differences between RN4220 and NCTC8325-4 and used the RNA-seq data to identify S. aureus promoters suitable for in vitro analysis.  We used RNA-seq to describe, on a genome wide scale, genes positively and negatively regulated by a phage encoded transcription factor, gp67.  RNA-seq offers the ability to study differential gene expression with single-nucleotide resolution, and is a considerable improvement over the predominant genome-wide transcriptome technologies used in S. aureus.

overall_design: RNA-seq analysis of Staphylococcus aureus RN4220 (electrocompetent strain) carrying either empty pRMC2 (inducible expression vector) or pRMC2 carrying the ORF67 gene (encodes gp67).  Both strains were grown to OD 0.2 and transgene expression was induced with 100ng/ml anhydrotetracycline.   As a control, Staphylococcus aureus strain NCTC8325-4 (non-electrocompetent strain) was grown under identical conditions except without the addition of anhydrotetracycline.

first: Scott

last: Dewell


title: mRNA-sequencing of breast cancer subtypes and normal tissue

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 Eye Street NW

department: Biochemistry and Molecular Medicine

institute: GWU

summary:
Goal: To define the digital transcriptome of three breast cancer subtypes (TNBC, Non-TNBC, and HER2-positive) using RNA-sequencing technology. To elucidate differentially expressed known and novel transcripts, alternatively spliced genes and differential isoforms and lastly expressed variants in our dataset.
Method: Dr. Suzanne Fuqua (Baylor College of Medicine) provided the human breast cancer tissue RNA samples. All of the human samples were used in accordance with the IRB procedures of Baylor College of Medicine. The breast tumour types, TNBC, Non-TNBC and HER2-positive, were classified on the basis of immunohistochemical and RT-qPCR classification.
Results: Comparative transcriptomic analyses elucidated differentially expressed transcripts between the three breast cancer groups, identifying several new modulators of breast cancer. We discovered subtype specific differentially spliced genes and splice isoforms not previously recognized in human transcriptome. Further, we showed that exon skip and intron retention are predominant splice events in breast cancer. In addition, we found that differential expression of primary transcripts and promoter switching are significantly deregulated in breast cancer compared to normal breast.  We also report novel expressed variants, allelic prevalence and abundance, and coexpression with other variation, and splicing signatures. Additionally we describe novel SNPs and INDELs in cancer relevant genes with no prior reported association of point mutations with cancer

overall_design: mRNA profiles of 17 breast tumor samples of three different subtypes (TNBC, non-TNBC and HER2-positive) and normal human breast organoids (epithelium) samples (NBS) were sequenced using Illumina HiSeq.

first: Rakesh

last: Kumar


title: Transcriptome Analysis of Sexual Dimorphism in the Chinese White Wax Scale Ericerus pela Using RNA-seq

status: Public on Nov 09 2013

city: Kunming

first: Pu

last: Yang

address: Bailongsi

institute: Insect

summary: We constructed eight libraries of female and male E. pela at different developmental stages using RNA-seq technology. Many genes and pathways related to sexual dimorphism were identified.The female and male E. pela take different developmental patterns. The sexual dimorphism in E. pela may involve many different regulatory components.

overall_design: Female and male E. pela at different developmental stages using RNA-seq technology

first: Xiao-Ming

last: Chen

first: Wei-Wei

last: Liu

first: Ying

last: Feng


title: High-resolution genome replication profiles, modeling and single-cell imaging define the stochastic nature of replication initiation and termination

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

summary: Eukaryotic genome replication is stochastic with each cell using a different cohort of replication origins. Interpreting high-resolution genome replication profiles with a mathematical model allowed us to quantify the stochastic nature of genome replication. This approach included estimation of the activity of every replication origin and the genome-wide location of replication termination events. Single-cell measurements verified the inferred values for stochastic origin replication time. Strains in which multiple origins had been inactivated, confirmed that the location of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci.

overall_design: Measurement of genome replication time for two S. cerevisiae strains. For each strain six S phase samples werecompared with a non-replicating sample.

first: Carolin

last: Müller

first: Michelle

last: Hawkins

first: Renata

last: Retkute


title: Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors

status: Public on Nov 06 2013

city: Hanover

first: Gavin

last: Grant

state: NH

address: 7400 Remsen

department: Genetics

institute: Geisel School of Medicine

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

overall_design: Refer to individual Series

first: Michael

last: Whitfield


title: Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors [ChIP-seq]

summary: We report the genome wide DNA binding patterns of wild type FOXM1 in asynchronous HeLa cells using chromatin precipitation followed by high-throughput sequencing (ChIP-seq).  We find that FOXM1 is bound to the promoter of a number of cell cycle genes including PLK, AURKB, and CCNB1.

overall_design: FOXM1 ChIP-seq in asynchronous HeLa cells


title: A retrotransposon-driven Dicer variant enhances endogenous RNAi in mouse oocytes

city: Prague 4

first: Radek

last: Malik

address: Videnska 1083

department: Dep. of Epigenetics Regulations

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

summary: Mammals have one Dicer gene required for biogenesis of small RNAs in microRNA (miRNA) and RNA interference (RNAi) pathways. Yet, endogenous RNAi is highly active in oocytes but not in somatic cells. Here, we provide a mechanistical explanation for high RNAi activity in mouse oocytes. The main Dicer isoform in oocytes is transcribed from an intronic MT-C retrotransposon, which functions as a promoter of an oocyte-specific Dicer isoform (denoted DicerO). DicerO lacks an N-terminal helicase domain and has a higher cleavage activity than the full-length Dicer from somatic cells.  DicerO can rescue the miRNA pathway and, in addition, it efficiently produces small RNAs from long dsRNA substrates. Thus, control of endogenous RNAi activity in mice occurs via alternative Dicer isoform and the phylogenetic origin of DicerO demonstrates evolutionary plasticity of RNA silencing pathways.

overall_design: NIH3T3 cells or mouse embryonic stem cells expressing oocyte-specific or somatic form of Dicer were transiently transfected with a plasmid expressing long double-stranded RNA (within the 3'-UTR of EGFP reporter) or left without transfection for controls.

first: Matyas

last: Flemr

first: Vedran

last: Franke

first: Jana

last: Nejepinska

first: Kristian

last: Vlahovicek

first: Petr

last: Svoboda


title: FOXA2-regulated genes in the adult mouse uterus

city: Columbia

first: Thomas

last: Spencer

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri


title: Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (ChIP-seq)

first: Francis

middle: S

last: Collins

summary: Chromatin-based functional genomic analyses and genomewide association studies (GWASs) together implicate enhancers as critical elements influencing gene expression and risk for common diseases. Here, we performed systematic chromatin and transcriptome pro- filing in human pancreatic islets. Integrated analysis of islet data with those generated by the ENCODE project in nine cell types identified specific and significant enrichment of type 2 diabetes and related quantitative trait GWAS variants in islet enhancers. Our integrated chromatin maps reveal that most enhancers are short (median = 0.8 kb). Each cell type also contains a substantial number of more extended (≥3 kb) enhancers. Interestingly, these stretch enhancers are often tissue-specific and overlap locus control regions, suggesting that they are important chromatin regulatory beacons. Indeed, we show that (i) tissue specificity of enhancers and nearby gene expression increase with enhancer length; (ii) neighborhoods containing stretch enhancers are enriched for important cell type– specific genes; and (iii) GWAS variants associated with traits rele- vant to a particular cell type are more enriched in stretch enhancers compared with short enhancers. Reporter constructs containing stretch enhancer sequences exhibited tissue-specific activity in cell culture experiments and in transgenic mice. These results suggest that stretch enhancers are critical chromatin elements for coordinating cell type–specific regulatory programs and that sequence variation in stretch enhancers affects risk of major common human diseases.

first: Steve

middle: C

last: Parker

last: Stitzel

first: D

last: Taylor

first: Jose

last: Orozco

last: Erdos

first: Jennifer

last: Akiyama

first: Kelly

last: van Bueren

first: Peter

last: Chines

first: Narisu

last: Narisu

first: Brian

last: Black

first: Axel

last: Visel

first: Len

last: Pennacchio


title: Fine Tuning of Craniofacial Morphology by Distant-Acting in vivo Enhancers

city: Berkeley

first: Alex

last: Nord

state: CA

address: 1 Cyclotron Road, Mail Stop 84-171

department: Genomics Divsion

institute: Lawrence Berkeley National Laboratory

summary: The shape of the human face is largely genetically determined, but the genetic drivers of craniofacial morphology remain poorly understood.  In particular, little is known about the contributions of gene regulatory sequences active in the developing face to craniofacial morphology.  Here we used a combination of epigenomic profiling, in vivo characterization of more than 200 craniofacial candidate enhancer sequences in transgenic mice, and targeted deletion experiments to examine the role of distant-acting enhancers in craniofacial development.  We identified complex regulatory landscapes with thousands of enhancers genome-wide that drive a remarkable spatial complexity of in vivo expression patterns. The ChIP-seq experiments in this entry was the basis for the genome-wide analysis of craniofacial enhancers and served as the source for substantialin vivo characterization via transgenic reporter mice and for enhancer knockout experiments.

overall_design: p300 ChIP-seq experiment on mouse embryonic tissue (e11.5)

first: C

last: Attanasio

first: Z

last: Li

first: A


title: Leucegene: ALL sequencing

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: RNA sequencing of human leukemia

overall_design: The goals of this project are to obtain a comprehensive study of mutations and gene expression in human T ALL (acute lymphoblastic leukemia). Methods: T ALL cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an Illumina HiSeq 2000 sequencer.

first: Camille

last: Simon

first: Jalila

last: Chagraoui

first: Jana

last: Krosl

first: Patrick

last: Gendron

last: Wilhelm

first: Sébastien

last: Lemieux

first: Geneviève

last: Boucher

first: Pierre

last: Chagnon

first: Simon

last: Drouin

first: Raphaëlle

last: Lambert

first: Claude

last: Rondeau

first: Annie

last: Bilodeau

first: Sylvie

last: Lavallée

first: Martin

first: Josée

last: Hébert


title: The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres

city: Madison

first: Tao

last: Zhang

state: WI

address: 1575 Linden Dr.

department: Horticulture

institute: University of Wisconsin Madison

summary: Plant and animal centromeres comprise megabases of highly repeated satellite sequences, yet centromere function can be specified epigenetically on single-copy DNA by the presence of nucleosomes containing a centromere-specific variant of histone H3 (cenH3). We determined the positions of cenH3 nucleosomes in rice (Oryza sativa), which has centromeres composed of both the 155-bp CentO repeat and single-copy non-CentO sequences. We find that cenH3 nucleosomes protect 90-100 bp of DNA from micrococcal nuclease digestion, sufficient for only a single wrap of DNA around the cenH3 nucleosome core. cenH3 nucleosomes are translationally phased with 155-bp periodicity on CentO repeats, but not on non-CentO sequences. CentO repeats have a ~10-bp periodicity in WW dinucleotides and in micrococcal nuclease cleavage, providing evidence for rotational phasing of cenH3 nucleosomes on CentO, and suggesting that satellites evolve for translational and rotational stabilization of centromeric nucleosomes.

overall_design: Examination of measured size of rice centromere nucleosome

first: Paul

middle: B

last: Talbert

first: Wenli

first: Yufeng

last: Wu

first: Zujun

last: Yang

first: Jorja

last: Henikoff

first: Jiming

last: Jiang

first: Steve


title: Transcriptome of Primitive Human Hematopoietic Cells: A New Resource to Find hHSC-Specific Genes

first: Guy

last: Sauvageau

summary: We analysed the transcriptome of different HSC-enriched subpopulations of cells sorted from human umbilical cord blood and isolated from several individuals with different genetic backgrounds. We aim at identifying new cell surface markers associated with human HSC and downstream mature hematopoietic cell activity.

overall_design: RNA-seq of CD34+CD45RA- cord blood cells from 17 non-pooled individuals.

first: Eric

last: Deneault


title: RNA-seq transcriptome profiling of motor neurons (MNs) and surrounding white matter glia (WM) microdissected from pre-symptomatic mouse model of spinal muscular atrophy (SMA)

status: Public on Nov 05 2013

first: Zhenxi

address: 415 Curie Blvd., 330 CRB

department: Biochemistry and Biophysics

institute: University of Pennsylvania School of Medicine

summary: We report tramscriptome perturbations in MNs and WM of SMA mouse, prior to first morphological and biochemical synaptic defects

overall_design: Examination of ventral horn MNs and WM isolated from lumbar segment spinal cords from wild type (WT) and SMA mice

first: Wei

last: Wang

first: Gideon

last: Dreyfuss


title: 5'RNA-seq analysis of hypertrophic cardiomyopathy (HCM) in mice that carry a human missence mutation in the myosin heavy chain

city: Boston

first: Jonathan

last: Seidman

state: MA

address: 77 Avenue Louis Pasteur, NRB256

institute: Harvard Medical School

summary: We developed a 5'RNA-seq methodology to concurrently assess gene expression and start-site usage changes. We applied this methodology to study hypertrophic cardiomyopathy in mice harboring a human deleterious mutation.

overall_design: 5'RNA-seq analysis of transcriptomes from mouse hearts with or without hypertrophic cardiomyopathy. Biological replicates were pooled into a single sequencing run. 5'RNA-seq methodology consists of enhanced sequencing of 5' ends and computational assessment of changes at start-sites of genes.

first: Jon


title: RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

first: Ian

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

department: Biology

institute: University of Pennsylvania

summary: RNAs are continuously associated with RNA-binding proteins (RBPs), and these interactions are necessary for many key cellular processes ranging from splicing to chromatin regulation. Although numerous approaches have been developed to map RNA-binding sites of individual RBPs, few methods exist that allow assessment of global RBP-RNA interactions. Here, we describe a universal, high-throughput, ribonuclease-mediated protein footprint sequencing approach that reveals RNA-protein interaction sites throughout a transcriptome of interest. We apply this method to the HeLa transcriptome and compare RBP binding sites found using different cross-linkers and ribonucleases. From this analysis, we identify numerous putative RBP binding motifs, reveal novel insights into co-binding by RBPs, and uncover a significant enrichment for disease-associated polymorphisms within RBP interaction sites.

overall_design: Protein interaction profile sequencing (PIP-seq) in HeLa cells. Two crosslinkers (formaldehyde and UV) with two RNases (dsRNase and ssRNase) each, as well as a no-crosslink sample. Performed with and without proteins. Three replicates for formaldehyde, two replicates for UV, single replicate for no crosslinker.

first: Fan

last: Li

first: Brian

last: Gregory


title: The acute transcriptional response of the coral Acropora millepora to immune challenge: expression of GiMAP/IAN genes links the innate immune response of corals with those of mammals and plants

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

country: Australia

institute: The Australian National University

summary: This studies investigates the acute response of the coral Acropora millepora to two immunogenes: MDP (bacterial mimic) and pIC (viral mimic). Three members of the GiMAP familly were found to respond strongly to MDP treatment, showing analalogy to the immune response in vertebrates and plants.

overall_design: Differential gene expression following treatment with two immunogenes

last: FORET

first: Yvonne

last: Weiss

first: David

last: HAYWARD

first: Eldon

last: BALL

last: MILLER


title: Tudor domain containing 12 (TDRD12) is essential for secondary piRNA biogenesis in mice

status: Public on Nov 04 2013

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: Piwi-interacting RNAs (piRNAs) are gonad-specific small RNAs that provide defence against transposable genetic elements called transposons. Our knowledge of piRNA biogenesis is sketchy, partly due to an incomplete inventory of the factors involved. Here, we identify Tudor domain-containing 12 (TDRD12; also known as ECAT8) as a novel piRNA biogenesis factor in mice. TDRD12 is detected in complexes containing MILI (PIWIL2), its associated primary piRNAs, and TDRD1, all of which are already implicated in secondary piRNA biogenesis. Male mice carrying either a nonsense point mutation (repro23 mice) or a targeted deletion in the Tdrd12 locus are infertile, and de-repress retrotransposons. We find that TDRD12 is dispensable for primary piRNA biogenesis but essential for production of secondary piRNAs that enter MIWI2 (PIWIL4). Cell culture studies with the insect orthologue of TDRD12 suggest a role for the multi-domain protein in mediating complex formation with other participants during secondary piRNA biogenesis.

sample_organism:
Bombyx mori
Mus musculus

platform_organism:
Bombyx mori
Mus musculus

overall_design: Total small RNA and immunoprecipitated small RNA were purified from mouse testis extract and Bmn4 cells for preparation of high-throughput sequencing libraries.

first: Radha

last: Pandey

first: Yoshimi

last: Tokuzawa

first: Zhaolin

last: Yang

first: Eri

last: Hayashi

first: Tomoko

last: Ichisaka

first: Shimpei

last: Kajita

first: Yuka

last: Asano

first: Tetsuo

last: Kunieda

first: Ravi

last: Sachidanandam

first: Shinichiro

last: Chuma

first: Shinya

last: Yamanaka


title: Global discovery of erythroid long non-coding RNAs reveals novel regulators of red cell maturation

city: Cambridge

first: Harvey

middle: F.

last: Lodish

address: 9 Cambridge Center

institute: Whitehead Institute

summary: Erythropoiesis is regulated at multiple levels to ensure the proper generation of mature red cells under multiple physiological conditions. To probe the contribution of long non-coding RNAs (lncRNAs) to this process, we examined >1 billion RNA-Seq reads of polyadenylated and nonpolyadenylated RNA from differentiating mouse fetal liver red blood cells, and identified 655 lncRNA genes including not only intergenic, antisense and intronic but also pseudogene and enhancer loci. Over 100 of these genes are previously unrecognized and highly erythroidspecific. By integrating genome-wide surveys of chromatin states, transcription factor occupancy, and tissue expression patterns, we identify multiple lncRNAs that are dynamically expressed during erythropoiesis, show epigenetic regulation and are targeted by key erythroid transcription factors GATA1, TAL1 or KLF1. We focus on 12 such candidates and find that they are nuclear-localized and exhibit complex developmental expression patterns. Depleting them severely impaired erythrocyte maturation, inhibiting cell size reduction and subsequent enucleation. One of them, alncRNA-EC7, is transcribed from an enhancer and is specifically needed for activation of the neighboring gene encoding BAND3. Our study provides an annotated catalog of erythroid lncRNAs, readily available through an online resource, and shows that diverse types of lncRNAs participate in the regulatory circuitry underlying erythropoiesis.

overall_design: one Ter119- total RNA, one Ter119+ total RNA, one Ter119+ poly(A)+ RNA,  one Ter119+ poly(A)- RNA, all are Hi-seq Ilumina data

first: Juan

last: Alvarez-Dominguez

first: Wenqian

last: Hu

first: Bingbing

last: Yuan


title: RNAseq comparison of gene expression profiles in Osr1 mutant and control mouse embryonic tongue

city: cincinnati

first: HAN

last: LIU

state: oh

address: 3333 burnet avenue

department: DEVELOPMENTAL BIOLOGY

institute: CINCINNATI CHILDREN'S HOSPITAL

summary:
The tongue is a muscular organ in the vertebrate oral cavity that performs complex functions in daily life, including feeding and phonetic articulation. The tongue consists of mesenchyme cells of two distinct origins: the muscle cells are derived from occipital somites whereas the tendons and other connective tissues derived from the cranial neural crest. Cranial neural crest cells are important for the initiation of tongue swelling and proper patterning of intrinsic and extrinsic tongue muscle groups. However, little is known regarding the molecular and cellular mechanisms of tongue morphogenesis. We show that the odd-skipped related 1 (Osr1) transcription factor exhibits dynamic expression in the tongue mesenchyme during early tongue development. Tissue-specific inactivation of Osr1 in the early neural crest cells resulted in ectopic cartilage formation in the mouse tongue. We show that Sox9, the master regulator of chondrocyte differentiation, is initially widely expressed in the neural crest derived mesenchyme in the tongue and subsequently down-regulated concomitant by up-regulation of Osr1 expression. Osr1 mutant embryos exhibit persistent expression of Sox9 and chondrocyte differentiation from the neural crest derived tongue mesenchyme. Further biochemical analyses indicate that Osr1 may directly suppresses Sox9 gene expression in the tongue mesenchyme. These data reveal a novel mechanism in suppression of chondrogenic fate during tongue development. Remarkably, the ectopic cartilage in the Osr1 mutant mice resembles the entoglossal cartilage naturally develops in the avian tongue. These results suggest that modulation of expression of Osr1 may underline the evolutionary divergence in tongue cartilage formation.
RNAs were isolated from microdissected E12 embryonic mouse tongue of Osr1f/-;Wnt1cre and control littermates and characterized by RNAseq

overall_design: E12 mouse embryonic tongues were micro-dissceted, 3 pairs of control and mutant samples were pooled for the RNA extraction

first: Jiang

last: Rulang

first: Liu

last: Han


title: Chromatin Immunoprecipitation of TRA-1 in C. elegans and C. briggsae

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

summary: The goal of this study is to identify and characterize sites in the C. elegans genome bound by the transcription factor TRA-1.

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans

overall_design: TRA-1 ChIP-seq was performed in the following stages of animals in duplicate: 1) L2 stage of C. elegans wild-type N2 strain; 2) L3 stage of C. elegans wild-type N2 strain; 3) young adult stage of C. elegans glp-4(bn2) mutant; 4) young adult stage of C. elegans spe-11(hc77) mutant; 5) L3 stage of C. briggsae wild-type AF16 strain. As a negative control, TRA-1 ChIP-seq was also performed in C. elegans L3 stage with tra-1(e1834) homozygous and heterozygous mutation. Input DNA was also sequenced in each condition.

first: Matthew

last: Berkseth

first: Jason

last: Lieb

first: David

last: Zarkower


title: A unique epigenetic signature is associated with active DNA replication loci in human embryonic stem cells

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

summary: The cellular epigenetic landscape changes as pluripotent stem cells differentiate to somatic cells or when differentiated cells transform to a cancerous state. These epigenetic changes are commonly correlated with differences in gene expression. Whether active DNA replication is also associated with distinct chromatin environments in these developmentally and phenotypically diverse cell types has not been known. Here, we used BrdU-seq to map active DNA replication loci in human embryonic stem cells (hESCs), normal primary fibroblasts and a cancer cell line, and correlated these maps to the epigenome. In all cell lines, the majority of BrdU peaks were enriched in euchromatin and at DNA repetitive elements, especially at microsatellite repeats, and coincided with previously determined replication origins. The most prominent BrdU peaks were shared between all cells but a sizable fraction of the peaks were specific to each cell type and associated with cell type-specific genes. Surprisingly, the BrdU peaks that were common to all cell lines were associated with H3K18ac, H3K56ac, and H4K20me1 histone marks only in hESCs but not in normal fibroblasts or cancer cells. Depletion of the histone acetyltransferases for H3K18 and H3K56 dramatically decreased the number and intensity of BrdU peaks in hESCs. Our data reveal a unique epigenetic signature that distinguishes active replication loci in hESCs from normal somatic or malignant cells.

overall_design: To investigate relationship between DNA replication and epigenetic modifications

first: Bing

last: Li

first: Trent

last: Su

first: Roberto

last: Ferrari

first: Jing-Yu