title: Transcriptional profile changes by Prox1 expression in thyroid cancer cells

city: Los Angeles

first: Young-Kwon

last: Hong

state: CA

address: 1450 Biggy St. NRT6501

institute: University of Southern California

summary: Human thyroid cancer cell line BCPAP was engineered for doxycyclin-mediated inducible expressoin of Prox1 and next generation sequcing was performed to study the transcriptional regulation by Prox1

overall_design: BCPAP cells were infected with rTTA2 lentivirus. The resulting cell populations were then stably transfected either with pIRES-hygromycin vector (Clontech) to generate BCPAP-Ctr cells, or with Flag-PROX1-IRES-hygromycin vector to generate BCPAP-Prx cells. PROX1 expression was induced or not in BCPAP-Ctr and BCPAP-Prx cells with 0.5 µg/ml doxycycline (Dox) for 48 hours and the total RNA samples were collected for sequencing.


title: Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer

status: Public on Mar 02 2016

city: Aurora

first: Joanna

last: Poczobutt

department: Medicine

country: USA

institute: University of Colorado Denver

type: Expression profiling by high throughput sequencing

summary: Macrophages represent an important component of the tumor microenvironment and play a complex role in cancer progression. These cells are characterized by a high degree of plasticity, and alter their phenotype in response to local environmental cues. While the M1/M2 classification of macrophages has been widely used, the complexity of macrophage phenotypes specifically in lung cancer has not been well studied. In this study we employed an orthotopic immunocompetent model of lung adenocarcinoma in which murine lung cancer cells are directly implanted into the left lobe of syngeneic mice. Using multi-marker flow cytometry we defined and recovered several distinct populations of monocytes/macrophages from tumors at different stages of progression. We used RNA-seq transcriptional profiling to define distinct features of each population and determine how they change during tumor progression. We defined an alveolar resident macrophage population that does not change in number and express multiple genes related to lipid metabolism and lipid signaling. We also defined a population of tumor-associated macrophages that increase dramatically with tumor, and selectively express a panel of chemokines genes. A third population, which resembles tumor-associated monocytes, expresses a large number of genes involved in matrix remodeling. By correlating transcriptional profiles with clinically prognostic genes, we show that specific monocyte/macrophage populations are enriched in genes that predict good or poor outcome in lung adenocarcinoma, implicating these subpopulations as critical determinants of patient survival. Our data underscore the complexity of monocytes/macrophages in the tumor microenvironment, and suggest that distinct populations play specific roles in tumor progression.

overall_design: mRNA profiles of macrophage/monocyte cells isolated from murine control or  tumor-bearing lung. From naive mice: MacA cells (MacA-N), MacB1 cells (MacB1-N), MacB2 cells (MacB2-N); from 2 week tumor bearing mice: MacA cells (MacA-2wk), MacB2 cells (MacB2-2wk), MacB3 cells (MacB3-3wk); from 3-week tumor bearing mice: MacB2 (MacB2-3wk), MacB3 cells (MacB3-3wk). Each population was analyzed in triplicate (cells were isolated in 3 independent experiments).

middle: M

first: Subhajyoti

last: De

first: Vinod

middle: K

last: Yadav

first: Teresa

middle: T

last: Nguyen

first: Howard

last: Li

first: Trisha

middle: R

last: Sippel

first: Mary

middle: C

last: Weiser-Evans

first: Raphael

middle: A

last: Nemenoff


title: Investigating GPR34 expression regulation using whole transcriptome sequencing of spleens and dendritic cells from wildtype and GPR34 knockout mice

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Institute of Biochemistry, Medical Faculty

country: Germany

institute: Leipzig University

summary: Naive spleens as well as naive and LPS-treated dendritic cells from wildtype and GPR34-/- mice were sequenced to integrate expression profiles with protein interaction networks and find functional modules that are affected by GPR34

overall_design: Expression profiles of dendritic cells and whole spleens were generated using Illumina HiSeq 2500/ Illumina HiScan

first: Angela

last: Schulz

first: Diana

last: LeDuc

first: Elisabeth

last: Jäger

first: Vera

last: Lede

first: Chen-Ching

last: Lin

first: Janet

last: Kelso


title: A systematic analysis of the time series gene expression in TGF-beta induced EMT by Next-generation sequencing

city: Shanghai

first: Mengzhu

last: Xue

address: No.100, Haike Road

country: China

institute: Shanghai Advanced Research Institute

summary: The goal of this study is to characterize time course gene expression profiles during TGF-beta induced EMT. In particular, we aim to identify and characterize master transcription factors regulate the transition into partial-EMT state.

overall_design: A time series mRNA profile in A549 cells is generated from TGF-beta induced EMT samples during 0h,6h,12h,24h,36h,48h,72h and 96h by deep sequencing, in duplicate, using Illumina HiSeq 2500

first: Hongyuan

last: Chang


title: The effect of knockdown Abl kinases on breast cancer cells' global transcriptome

city: Durham

first: Jun

last: Wang

state: North Carolina

address: 308 Research Drive LSRC C231

department: Pharmacology and Cancer Biology

institute: Duke University

summary: To gain insight into the signaling pathway(s) required for ABL1/ABL2-dependent bone metastasis, we evaluated the consequences of single or double inactivation of ABL1 and ABL2 on the transcriptome of breast cancer cells. Double ABL1/ABL2 knockdown was required to decrease the levels of p-CrKL by more than 90%, indicative of inactivation of the endogenous ABL kinases. To examine the consequences of depleting the ABL kinases on the transcriptome of metastatic breast cancer cells we employed next generation sequencing (RNAseq) analysis. We found that 180 genes were significantly down-regulated and 40 genes were significantly up-regulated in ABL1/ABL2 knockdown cells.

overall_design: Four samples were analyzed control, Abl single knockdown, Arg single knockdown, Abl/Arg double knockdown. Experiments were performed in triplicate.

first: Ann

last: Pendergast


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Striatum_miRNA]

status: Public on Mar 01 2016

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder that is characterized by motor, cognitive, and psychiatric alterations. The mutation responsible for this disease is an abnormally expanded and unstable CAG repeat within the coding region of the gene encoding huntingtin (Htt). Knock-in mouse models of HD with human exon 1 containing expanded CAG repeats inserted in the murine huntingtin gene (Hdh) provide a genetic reconstruction of the human causative mutation within the mouse model. The goal of this study is RNA expression profiling by RNA sequencing (RNA-seq) in 6  and 10 months old knock-in mice with CAG lengths of 20, 50, 92,  140 along with littermate control wild-type animals

overall_design: miRNA expression profiles were obtained via RNA-seq analysis performed on samples from the Striatum tissue of 6 and 10  months old knock-in mice with CAG lengths of 20, 50, 92, 140 along with littermate control wild-type animals.

first: Jim

last: Rosinski


title: Conservation-independent identification of novel miRNAs

city: Munich

first: Anne

last: Dueck

state: Bavaria

address: Biedersteiner Str.29

department: Institute of Pharmacology and Toxicology

institute: TUM

type: Non-coding RNA profiling by high throughput sequencing

summary: Motivation: MicroRNAs (miRNAs) are short regulatory RNAs derived from a longer precursor RNA. miRNA biogenesis has been studied in animals and plants, recently elucidating more diverse and complex aspects, such as non-conserved, speciesspecific, and heterogeneous miRNA precursor populations. Small RNA sequencing data can be used to computationally determine genomic loci of miRNA precursors. The challenge is to predict a valid miRNA precursor from inhomogeneous read coverage: while the mature miRNA typically produces hundreds of sequence reads, the remaining part of the precursor is covered very sparsely. Results: We introduce a new conservation-independent method for the identification of miRNA precursors, that allows for speciesspecific heterogeneous precursor populations. The algorithm requires small RNA sequencing data and evaluates precursor secondary structures, with key parameters that can be adjusted based on the specific organism under investigation (within animals, plants, algae). We illustrate the validity of results from our algorithm using sequencing data for the two Volvocine algae Chlamydomonas reinhardtii (Chlamydomonas) and Volvox carteri (Volvox). Both organisms show little cross-species miRNA sequence conservation, and a heterogeneous miRNA precursor population. We validate our list of Chlamydomonas miRNAs with annotated miRNAs, and demonstrate excellent agreement. Furthermore, we are able to identify additional novel miRNA precursors, with structures ranging from simple mammalian-like hairpins to precursor structures indicating the creation of multiple mature/star miRNA duplexes. Novel miRNAs identified in Volvox show no similarity to mature miRNAs in Chlamydomonas. These results confirm the need for conservationindependent miRNA identification methods.

overall_design: Examination of small RNAs of Volvox carteri during different stages of its life cycle

first: Maurits

last: Evers

first: Gunter

last: Meister

first: Julia

last: Engelmann


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Liver_miRNA]

overall_design: miRNA expression profiles were obtained via RNA-seq analysis performed on samples from the Liver tissue of 6 and 10  months old knock-in mice with CAG lengths of 20, 50, 92, 140 along with littermate control wild-type animals.


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Cortex_miRNA]

overall_design: miRNA expression profiles were obtained via RNA-seq analysis performed on samples from the Cortex tissue of 6 and 10  months old knock-in mice with CAG lengths of 20, 50, 92, 140 along with littermate control wild-type animals.


title: Transcriptome profiling in knock-in mouse models of Huntington's disease [Cerebellum_miRNA]

overall_design: miRNA expression profiles were obtained via RNA-seq analysis performed on samples from the Cerebellum tissue of 6  and 10  months old knock-in mice with CAG lengths of 20, 50, 92, 140 along with littermate control wild-type animals.


title: Gene trapping in the Asian malaria vector, Anopheles stephensi

city: Columbia

first: William

last: Reid

state: Missouri

address: Connaway Hall, Bouchelle Ave

department: Veterinary Pathobiology

institute: University of Missouri

summary: A piggyBac transposon-based gene trap element was transformed into the Asian malaria vector, Anopheles stephensi, and remobilized using the jumpstarter approach using genetic crosses. Individuals that displayed a gene trap remobilization event were then photodocumented and their RNA and DNA complements were extracted. The DNA compelement was used to determine the genomic insertion site, while the RNA was used to determine the transcript coverage of the genes into which the transposons inserted. In nearly half of the cases, insertion was identified to fall within introns present in the 5'-UTR of transcripts- which are not indicated in the current ab initio models for Anopheles stephensi. The ability to utilize next generation RNA-Seq elucidated the functionality of the gene trap elements that inserted outside of the ab initio gene models, providing clear evidence that not only was the gene trap element working properly, but that it also had a bias towards 5'-end insertion, in particular, 5'-UTR intronic insertion.

overall_design: RNA from 200 pooled individually-extracted An. stephensi that demonstrated a gene trap remobilizable event.

first: D

last: O'Brochta

first: W


title: Club cells surviving influenza A virus infection induce temporary non-specific anti-viral immunity

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: Cells respond differently to influenza virus infection after already having been infected previously.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Anlysis of cellular RNA after influenza virus infection

middle: S


title: BET inhibition releases the Mediator complex from specific cis elements in acute myeloid leukemia cells (RNA-Seq II)

city: Cold Spring Harbor

first: Anand

last: Bhagwat

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Genome occupancy profiling by high throughput sequencing

overall_design: PolyA selected RNA-seq for shRNA-expressing MLL-AF9 transformed acute myeloid leukemia cells (RN2)

first: A

first: C

last: Vakoc


title: Polycomb dysregulation in gliomagenesis targets a Zfp423-dependent differentiation network [RNA-Seq]

city: Milano

first: Pasquale

last: Laise

address: Via Adamello,16

country: Italy

institute: IEO

summary: Malignant gliomas constitute one of the most significant areas of unmet medical need, due to the invariable failure of surgical eradication and their marked molecular heterogeneity. Accumulating evidence has revealed a critical contribution by the Polycomb axis of epigenetic repression. However, a coherent understanding of the regulatory networks affected by Polycomb during gliomagenesis is still lacking. Here we integrate transcriptomic and epigenomic analyses to define Polycomb-dependent networks that promote gliomagenesis, validating them both in two independent mouse models and in a large cohort of human samples. We found that Polycomb dysregulation in gliomagenesis affects transcriptional networks associated to invasiveness and de-differentiation. The dissection of these networks uncovers Zfp423 as a crtitical Polycomb-dependent transcription factor whose silencing negatively impacts survival. The anti-gliomagenic activity of Zfp423 requires interaction with the SMAD proteins within the BMP signaling pathway, pointing to a novel synergic circuit through which Polycomb inhibits BMP signaling.

overall_design: Transcriptomic  analysis of two different stages of gliomagenesis

first: Elena

last: Signaroldi

first: Silvia

last: Cristofanon

first: Arianna

last: Brancaccio

first: Elisa

last: Reisoli

first: Sina

last: Atashpaz

first: Maria

last: Terreni

first: Claudio

last: Doglioni

first: Giancarlo

last: Pruneri

first: Paolo

last: Malatesta

first: Giuseppe

last: Testa


title: Smad2 and Smad3 have differential sensitivity in relaying TGF b signaling and inversely regulate early lineage specification

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transforming growth factor beta (TGFβ) related signaling is one of the most important signaling pathways regulating early developmental events. Smad2 and Smad3 are structurally similar and it is mostly considered that they are equally important in mediating TGFβ signals. Here, we show that Smad3 is an insensitive TGFβ transducer as compared with Smad2. Smad3 preferentially localizes within the nucleus and is thus sequestered from membrane signaling. The ability of Smad3 in oligomerization with Smad4 upon agonist stimulation is also impaired given its unique linker region. Smad2 mediated TGFβ signaling plays a crucial role in epiblast development and patterning of three germ layers. However, signaling unrelated nuclear localized Smad3 is dispensable for TGFβ signaling-mediated epiblast specification, but important for early neural development, an event blocked by TGFβ/Smad2 signaling. Both Smad2 and Smad3 bind to the conserved Smads binding element (SBE), but they show nonoverlapped target gene binding specificity. We conclude that Smad2 and Smad3 possess differential sensitivities in relaying TGFβ signaling and have distinct roles in regulating early developmental events.

overall_design: GFP, GFP-Smad2 and GFP-Smad3 constitutively expressed Smad3-/- mouse ESCs were differentiated to day6 neuroepithelia and collected for Chip-Seq with an anti-GFP antibody.

first: Ling

last: Liu

first: Yanhua

last: Du


title: Physiological characterization and comparative transcriptome analysis of a developmentally retarded Chinese cabbage (Brassica campestris ssp. pekinensis) mutant

city: Shenyang

first: Shengnan

last: Huang

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

institute: Shenyang Agricultural University

summary: The leaf of Chinese cabbage is the major place of photosynthesis, the mutation of leaf may directly affect the rate of plant growth and development and the formation of leafy head, and ultimately influence the yield and quality of Chinese cabbage. We identified a developmentally retarded mutant (drm) exhibiting stable inheritance, which was derived from Chinese cabbage DH line ‘FT’ using a combination of isolated microspore culture and radiation treatment (60Co γ-rays). The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, as well as chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with wild-type line ‘FT’, the drm’s chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, the photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters may influence the growth and development of plant, ultimately resulting in the developmentally retarded phenotype of drm. To further understand the molecular regulatory mechanisms of phenotypic differences between ‘FT’ and drm, comparative transcriptome analysis were performed using RNA-Seq, a total of 338 differentially expressed genes (DEGs) were detected between ‘FT’ and drm. According to GO and KEGG pathway analysis, a number of DEGs which involved in the chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulatory mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics studies in Chinese cabbage.

overall_design: The RNA from  the third true leaves (day 15 to day 24 after the appearance of the third true leaves) of a developmentally retarded mutant (drm) and its wild type ‘FT’ in Chinese cabbage were sequenced by RNA-Seq, in triplicate.

first: Zhiyong

first: Danyang

last: Li

first: Runpeng

last: Yao

first: Li

last: Hou

first: Xiang

first: Hui

last: Feng


title: Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [HiC-Seq]

city: Utrecht

first: Elzo

last: de Wit

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale TAD repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic cell specific genome structures while establishing an embryonic stem cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable discerning their cell-of-origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin dependent gene expression patterns.

overall_design: Hi-C was performed in somatic cells (NSC, macrophages, MEFs and pre-B cells) and their corresponding early and late induced pluripotent stem cells. In addition Hi-C was performed in E14 embryonic stem cells

first: Wouter

last: de Laat


title: Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming

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

overall_design: Refer to individual Series


title: Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [ChIP-Seq]

overall_design: ChIPseq for CTCF and H3K27ac was performed on early and late iPS cells derived from different founders


title: Distinct activities of Myf5 and MyoD indicate sequential roles in skeletal muscle lineage specification and differentiation (ChIP-Seq)

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: In this work we compare the molecular functions of Myf5 and MyoD, two highly related bHLH transcription factors that regulate skeletal muscle specification and differentiation. We find MyoD and Myf5 bind the same sites genome-wide but have distinct functions: Myf5 induces histone acetylation without Pol II recruitment or robust gene activation, whereas MyoD induces histone acetylation, recruits PolII and robustly activates gene transcription.

overall_design: Chip-seq profiling of MyoD, Myf5, Histone H4 acetylation (H4Ac), and Pol II in MyoD-/-; Myf5-/- MEFs (M&M MEFs)

first: Melissa

middle: L

last: Conerly

first: Zizhen

first: Jun

middle: W

last: Zhong

first: Mark

last: Groudine

middle: J


title: Distinct activities of Myf5 and MyoD indicate sequential roles in skeletal muscle lineage specification and differentiation


title: Gene Networks and Blood Biomarkers of Methamphetamine-Associated Psychosis: A Preliminary Integrative RNA-Sequencing Report

city: CAPE TOWN

first: DAN

last: STEIN

address: Rondebosch

department: DEPARTMENT OF PSYCHIATRY

country: South Africa

institute: UNIVERSITY OF CAPE TOWN

summary:
The clinical presentation, course and treatment of methamphetamine-associated psychosis (MAP) are similar to that observed in schizophrenia (SCZ) and subsequently MAP has been hypothesized as a pharmacological and environmental model of SCZ. However, several challenges currently exist in accurately diagnosing MAP at the molecular and neurocognitive level before the MAP model can contribute to the discovery of SCZ biomarkers. We directly assessed subcortical brain structural volumes and clinical parameters of MAP within the framework of an integrative genome-wide RNA-Seq blood transcriptome analysis of subjects diagnosed with MAP (N=10), METH-dependency without psychosis (MA) (N=10) and healthy controls (N=10).
We used RNA-Sequencing gene expression to characterize molecular signatures associated to METH and MAP status compared to healthy control subjects.

overall_design: Peripheral blood luekocytes gene expression was subject to transcriptional analysis for 10 MAP subjects, 10 subjects with METH-dependency without psychotic symptomics and 10 healthy controls.

first: Michael

last: Breen

first: Dan

last: Stein


title: BET inhibition releases the Mediator complex from specific cis elements in acute myeloid leukemia cells (RNA-Seq I)

first: Anand

last: Bhagwat

first: A

first: C

last: Vakoc


title: BET inhibition releases the Mediator complex from specific cis elements in acute myeloid leukemia cells


title: Distinct activities of Myf5 and MyoD indicate sequential roles in skeletal muscle lineage specification and differentiation (RNA-Seq)

overall_design: RNA-Seq profiling of MyoD and Myf5


title: Targeted deletion of miR-132/212 impairs memory and alters the hippocampal transcriptome

city: Columbus

first: Katelin

middle: Libby

last: Hansen

state: OH

address: 333 W. 10th Ave

department: Neuroscience

institute: The Ohio State University

summary: miR-132 and miR-212 are structurally-related microRNAs that have been found to exert powerful modulatory effects within the central nervous system (CNS). Notably, these microRNAs are tandomly processed from the same non-coding transcript, and share a common seed sequence: thus it has been difficult to assess the distinct contribution of each microRNA to gene expression within the CNS. Here, we employed a combination of conditional knockout and transgenic mouse models to examine the contribution of the miR-132/212 gene locus to learning and memory, and then to assess the distinct effects that each microRNA has on hippocampal gene expression. Using a conditional deletion approach, we show that miR-132/212 double knockout mice exhibit significant cognitive deficits in spatial memory, recognition memory, and in tests of novel object recognition. Next, we utilized transgenic miR-132 and miR-212 overexpression mouse lines and the miR-132/212 double knockout line explore the distinct effects of these two miRNAs on the transcriptional profile of the hippocampus. Illumina sequencing revealed that miR-132/212 deletion increased the expression of 1,138 genes; Venn analysis showed that 96 of these genes were also downregulated in mice overexpressing miR-132. Of the 58 genes that were decreased in animals overexpressing miR-212, only four of them were also increased in the knockout line. Functional gene ontology analysis of downregulated genes revealed significant enrichment of genes related to synaptic transmission, neuronal proliferation, and morphogenesis, processes known for their roles in learning, and memory formation. These data, coupled with previous studies, firmly establish a role for the miR-132/212 gene locus as a key regulator of cognitive capacity. Further, although miR-132 and miR-212 share a seed sequence, these data indicate that these miRNAs do not exhibit strongly overlapping mRNA targeting profiles, thus indicating that, these two genes may function in a complex, non-redundant manner to shape the transcriptional profile of the CNS. The dysregulation of miR-132/212 expression could contribute to signaling mechanisms that are involved in an array of cognitive disorders

overall_design: Hippocampal mRNA was isolated from CaMKII-Cre::miR-132/212f/f, tTA::miR132, and tTA::miR212 animals, as well as their respective nontransgenic controls. cDNA from six animals was pooled into three independent biological replicates for each. Libraries were prepared according to the Illumina TruSeqTM Sample Preparation Guide and sequenced using an Illumina Genome Analyzer II. Sequences were aligned to the UCSC mm9 reference genome using Bowtie v0.12.7 and custom R scripts. The sequence data have been submitted to the NCBI Short Read Archive with accession number in progress. Relative abundance was measured in Fragments Per Kilobase of exon per Million fragments mapped using Cufflinks v1.2.

first: Kensuke

last: Sakamoto

first: Andrea

last: Hesse

first: Chloe

middle: E

last: Page

first: Sydney

last: Aten

first: Simon

last: Arthur

first: Carl

last: Pelz

first: Soren

last: Impey

first: Karl

last: Obrietan


title: Histone Demethylase-Assisted Somatic Cell Nuclear Transfer  Facilitates Derivation of Human Pluripotent Stem Cells

city: Brookline

first: Yuting

last: Liu

state: MA

address: 82 Walnut St. Unit 3

department: Department of Genetics

institute: Harvard Medical School

summary: The extremely low efficiency of human embryonic stem cell (hESC) derivation using somatic cell nuclear transfer (SCNT) limits potential application. Blastocyst formation from human SCNT embryos occurs at a low rate and with only some oocyte donors. We previously showed in mice that reduction of histone H3 lysine 9 trimethylation (H3K9me3) through ectopic expression of the H3K9me3 demethylase Kdm4d greatly improves SCNT embryo development. Here we show that overexpression of a related H3K9me3 demethylase KDM4A improves human SCNT, and that, as in mice, H3K9me3 in the human somatic cell genome is an SCNT reprogramming barrier. Overexpression of KDM4A significantly improves the blastocyst formation rate in human SCNT embryos by facilitating transcriptional reprogramming, allowing derivation of NTESCs from all oocyte donors tested using adult AMD patient somatic nuclei donors. This conserved mechanistic insight has potential applications for improving SCNT in a variety of contexts, including regenerative medicine.

overall_design: Here we perform RNA-seq based transcriptome profiling in human Donor (fibroblast cells), in vitro fertilized embryos at 8-cell stages (IVF_8Cell), somatic cell nuclear transfer embryos at 8-cell stages (SCNT_8Cell), SCNT assisted by KDM4A 8-cell embryos (SCNT_KDM4A_8Cell). Besides, we also perform RNA-seq in Control human ES cells (CTR_hES) and SCNT assisted by KDM4A derived human ES cells (NTK) with duplicates.

first: Shogo

last: Matoba

first: Yi

last: Zhang


title: ChIP-seq validation of recombinant antibodies to histone post-translational modifications

city: Chicago

first: Takamitsu

last: Hattori

state: IL

address: 900 E. 57th Street

department: Department of Biochemistry and Molecular Biology

institute: The University of Chicago

summary: Recombinant antibodies to histone post-translational modifications (PTMs), with their essentially infinite renewability, could fundamentally eliminate a major source of low reproducibility in epigenetics research. Here, we report new recombinant antibodies to trimethylated Lys4 and Lys9, respectively, on histone H3. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications, including ChIP. These results demonstrate the feasibility of generating recombinant antibodies to a range of histone marks, which will accelerate epigenetics research.

overall_design: We characterized recombinant antibodies with native ChIP using HEK293 cells followed by deep sequencing.

first: Adrian

last: Grzybowski

first: Alexander

last: Ruthenburg

first: Shohei

last: Koide


title: Next Generation Sequencing of Wild Type and Glis3 Mutant Fetal Testis Transcriptomes

first: Humphrey

middle: Hung-Chang

last: Yao

address: 111 TW Alexander Drive

institute: NIEHS/NIH

summary:
The goals of this study are to utilize high-throughput transcriptome sequencing of mutant and control fetal testis samples to identify changes in both transcript and repeat element abundance in tissues harboring a homozygous mutation for Glis3.
672 unique genes were differentially expressed in mutant versus wild-type samples. Of the downregulated genes, there was a strong enrichment for piRNA pathway members, while upregulated genes were associated with leydig cell differentiation, meiosis, and histone cluster genes. Differential expression of several repeat elements was also detected in mutant samples.  Our findings provide valuable information on the potential mechanisms underlying the fetal germ cell loss observed in Glis3 mutant testes.

overall_design: Whole testis mRNA profiles of embryonic day 14.5 wild type (WT) and Glis3 mutant mice were generated by deep sequencing, using Illumina HiSeq2500


title: EWS-FLI1-induced osteosarcoma model unveiled a crucial role of impaired osteogenic differentiation on osteosarcoma development

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo


title: ChIP-seq for H3K27Ac and H3K4me3 in a pre-B-cell model of Acute Lymphoblastic Leukemia, no stimulation or treatment

city: Cambridge

first: Jennifer

middle: Lynn

last: Wilson

state: Massachusetts

address: 77 Massachusetts Ave, 16-244

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: We wanted to identify regions of active and open chromatin in a pre-B-cell model of Acute Lymphoblastic Leukemia (ALL). We did not stimulate or treat the cells, we merely maintained them in culture. We chose these conditions because we were building a computational model and needed a baseline read of histone activation.

overall_design: For each histone mark, we had one sample where we immunoprecipitated with an antibody for the histone mark of interest and we had one control where we immunoprecipitated with an IgG control.


title: EWS-FLI1-induced osteosarcoma model unveiled a crucial role of impaired osteogenic differentiation on osteosarcoma development [ChIP-seq]

summary: EWS-FLI1, a multi-functional fusion oncogene, is exclusively detectable in Ewing sarcomas. However, previous studies reported that a subset of osteosarcomas also harbor EWS-ETS family fusion, suggesting that the fusion gene may be involved in the development of a particular type of osteosarcomas. Here using the doxycycline inducible EWS-FLI1 system, we established an EWS-FLI1-dependent osteosarcoma model from murine bone marrow stromal cells. We revealed that the withdrawal of EWS-FLI1 expression enhances the osteogenic differentiation of sarcoma cells, leading to mature bone formation. Taking advantage of induced pluripotent stem cell (iPSC) technology, we also showed that the sarcoma-derived iPSCs with cancer-related genetic abnormalities exhibited the impaired differentiation program of osteogenic lineage irrespective of the EWS-FLI1 expression. Finally, we demonstrated that EWS-FLI1 contributed to in vitro sarcoma development from the sarcoma-iPSCs after osteogenic differentiation. These findings demonstrated that modulating cellular differentiation is fundamental principle of the EWS-FLI1-induced osteosarcoma development. Furthermore, the in vitro cancer model using sarcoma-iPSCs should provide a novel platform for dissecting relationship between cancer genome and cellular differentiation.

overall_design: Chip-seq in mouse EWS-FLI1-induced osteosarcoma cell lines (SCOS#2 )

first: Shingo

last: Komura

first: Fumiaki

last: Itakura


title: POU2AF1 Functions in the Human Airway Epithelium to Regulate Expression of Host Defense Genes [RNA-Seq]

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
In the process of seeking novel lung host defense regulators by analyzing genome-wide RNA sequence data from normal human airway epithelium, we detected expression of POU2AF1, a known transcription co-factor previously thought to be expressed only in lymphocytes. Lymphocyte contamination of human airway epithelial samples obtained by bronchoscopy and brushing was excluded by immunohistochemistry staining, the observation of up-regulation of POU2AF1 in purified airway basal stem/progenitor cells undergoing differentiation and analysis of differentiating single basal cell clones. Lentivirus-mediated up-regulation of POU2AF1 in airway basal cells induced up-regulation of host defense genes, including MX1, IFIT3, IFITM and known POU2AF1 downstream genes HLA-DRA, ID2, ID3, IL6, BCL6. Interestingly, expression of these genes paralleled changes of POU2AF1 expression during airway epithelium differentiation in vitro, suggesting POU2AF1 helps to maintain a "host defense tone" even in pathogen-free condition. Cigarette smoke, a known risk factor for airway infection, suppressed POU2AF1 expression both in vivo in humans and in vitro in human airway epithelial cultures, accompanied by deregulation of POU2AF1 downstream genes. Finally, enhancing POU2AF1 expression in human airway epithelium attenuated the suppression of host defense genes by smoking. Together, these findings suggest a novel function of POU2AF1 as a potential regulator of host defense genes in the human airway epithelium.
Methods: Massive parallel RNA sequencing was used to compare the transcriptome of lentivirus mediated POU2AF1 or RFP (control) gene expression in human primary airway epithelial cells (3 samples per group). Uninfected basal cell was used as a further control.
Conclusions: The genes up-regulated by POU2AF1 in human airway epithelial cells are mainly related to the intracellular or extracellular anti-pathogen response, suggesting POU2AF1 plays a role in airway epithelial host defense.

overall_design:
By genome-wide-based screening, POU2AF1, a known lymphocyte transcription co-factor, was found to be expressed in human airway epithelium and regulate host defense genes. It might be a drug target as smoking-compromised host defense is associated with down-regulation of POU2AF1.
In this Series, human airway epithelial cell transcriptomes (3 uninfected without treatment, 3 infected with lenti-RFP virus and 3 infected with lenti-POU2AF1 virus) were compared using massive parallel RNA sequencing (Illumina HiSeq 2000).

first: Haixia

last: Zhou

first: Angelika

last: Brekman

first: Wu-Lin

last: Zuo

first: Xuemei

last: Ou

first: Renat

last: Shaykhiev

first: Francisco

last: Agosto-Perez

first: Rui

last: Wang

first: Matthew

last: Walters

first: Jacqueline

last: Salit

first: Michelle

last: Staudt

first: Robert

last: Kaner

first: Jason

middle: G

last: Mezey

first: Ronald

last: Crystal

first: Guoqing


title: Mammalian Heat Shock Response And Mechanisms Underlying Its Genome-wide Transcriptional Regulation

city: Ithaca

first: Dig

middle: Bijay

last: Mahat

address: 526 campus Rd

department: Molecular Biology & Genetics

institute: Cornell University

summary: Heat shock response (HSR) is critical for survival of organisms undergoing proteotoxic stress. Heat shock factor 1 (HSF1) is widely believed to be the master regulator of this response. Here, we examined the kinetics of the transcriptional response and HSF1 binding changes genome-wide after heat shock (HS) with high sensitivity and high spatial and temporal resolution using PRO-seq and ChIP-seq assays respectively in wild type and in hsf1-deletion mouse embryonic fibroblasts. The transcriptional response is rapid, dynamic, and extensive with activation of several hundred genes and repression of several thousands of genes. Although HSF1 is critically required for classical inducible Heat Shock Protein (HSP) genes, it is not required for the majority of gene activation. HSF1 acts mechanistically to promote RNA polymerase II (Pol II) release from the promoter-proximal pause, while recruitment and initiation of Pol II are predominantly HSF1-independent. Surprisingly, a major class of cytoskeleton genes is immediately (within 2.5 minutes) and transiently activated in an HSF1-independent manner. A second wave of regulation is characterized by robust activation or repression of new sets of genes. The broad repression of thousands of genes, a quarter of which are repressed immediately upon HS and the rest are repressed in the second wave of regulation, is mediated at the level of decreasing Pol II pause release and not at prior steps of Pol II recruitment or initiation. Notably, heat shock does not induce transcription of some previously defined HSP genes, and HSF2 – a homolog of HSF1 – does not compensate for the lack of HSF1. Together, these findings indicate that mammalian cells cope with stress by rapidly inducing pervasive and dramatic changes in transcription that are largely modulated at the step of pause release, and only a fraction of this regulation is HSF1-dependent.

overall_design: Examination of transcriptional regulation before and after heat shock in WT, HSF1-/-, and HSF1&2-/- MEFs

middle: B

first: Herbert

middle: H

last: Salamanca

first: Fabiana

last: Duarte

first: Charles

last: Danko

first: John

last: Lis


title: Yap and Taz in Neural Crest play a Crucial Role in Smooth Muscle Development

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

summary: We conditionally knocked out both Yap and Taz in cranial neural crest (CNC) using the Wnt1Cre driver and sequenced mRNA from embryonic day 10.5 mandibles.

overall_design: Examination of mRNA level in E10.5 mandibular tissues from control and Wnt1Cre Taz and Yap dKO mutant.

first: Jun

first: James

last: Martin


title: Distinct cognitive effects and underlying transcriptome changes upon inhibition of individual miRNAs in hippocampal neurons

city: Lund

first: Per

last: Brattas

address: Sölvegatan 17

country: Sweden

institute: Lund University

summary: MicroRNAs (miRNA) are small, non-coding RNAs mediating post-transcriptional regulation of gene expression. miRNAs have recently been implicated in hippocampus-dependent functions such as learning and memory, although the roles of individual miRNAs in these processes remain largely unknown. Here, we achieved stable inhibition using AAV-delivered miRNA sponges of individual, highly expressed and brain-enriched miRNAs; miR-124, miR-9 and miR-34, in hippocampal neurons. Molecular and cognitive studies revealed a role for miR-124 in learning and memory. Inhibition of miR-124 resulted in an enhanced spatial learning and working memory capacity, potentially through altered levels of genes linked to synaptic plasticity and neuronal transmission. In contrast, inhibition of miR-9 or miR-34 led to a decreased capacity of spatial learning and of reference memory, respectively. On a molecular level, miR-9 inhibition resulted in altered expression of genes related to cell adhesion, endocytosis and cell death, while miR-34 inhibition caused transcriptome changes linked to neuroactive ligand-receptor transduction and cell communication. In summary, this study establishes distinct roles for individual miRNAs in hippocampal function.

overall_design: Three RNA samples containing bilateral entire hippocampi from three different mice, per group. Group 1 were injected with vector containing GFP and a miR34sp/miR9sp and the other group were subjected to a vector expressing GFP only.

first: Josephine

last: Malmevik

first: Rebecca

last: Petri

first: Pina

last: Knauff

first: Malin

last: Akerblom

first: Johan

last: Jakobsson


title: Interactions of aCPs with Cytosine-rich Polypyrimidine Tracts Enhance Splicing of Cassette Exons

city: Los Angeles

first: Yu-Ting

last: Tseng

state: California

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

summary: Alternative splicing comprises a robust generator of mammalian transcriptome complexity. Splice site specification and activity are controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. A major subset of these interactions comprises interactions localized to the intronic U-rich polypyrimidine tract located immediately 5’ to the majority of splice acceptors.  alphaCPs (also referred to as polyC-binding proteins (PCBPs) and hnRNP Es) comprise a subset of KH-domain proteins with high specificity and affinity for C-rich polypyrimidine motifs. Prior studies have revealed that binding of alphaCPs to C-rich motifs can modulate splicing and 3’ processing of the human alpha-globin mRNA transcript in the nucleus as well as stabilization of the halpha-globin mRNA in the cytoplasm. In the current report, we demonstrate that alphaCPs have a positive impact on the activity of splice acceptor sites in a defined subset of mammalian transcripts via binding to polypyrimidine tracts that are predominantly C-rich. These findings lead us to conclude that the alphaCPs play a global role in determining the splicing activity and levels of cassette exon inclusion within the mammalian transcriptome.

overall_design: To test the impact of aCP proteins on alternative splicing, aCP proteins were knockdown from K562 cells by siRNA. Since aCP1 and aCP2 have redundent function, we therefore designed siRNAs capable of knockdown both isoform at the same time. 3 aCP1/2 combined knockdown and 3 control siRNA knockdown were performed in K562 cells. RNA-seq were then performed to identify alternative splicing pattern mediated by aCP proteins.

first: Yi

last: Xing

first: Stephen

last: Liebhaber


title: Genome-wide transcriptional response of the Arctic bacterium Pseudoalteromonas sp. A2 to oxidative stress

city: Qingdao

first: LI

last: Yang

state: Shandong

address: 6 Xian-Xia Ling Road

department: SOA

institute: The First Institute of Oceanography

summary:
Transcriptomic sequencing was performed to obtain the key functional genes involved in the adaptation of oxidative stress induced by hydrogen peroxide (H2O2) in the Arctic bacterium Pseudoalteromonas sp. A2. Exposure to 1 mmol/L H2O2 resulted in large alterations of the transcriptome profile, including significant upregulation of 109 genes and significant downregulation of 174 genes. Functional classification of differentially expressed genes revealed that most of genes affiliated with biological adhesion, negative regulation of biological process, enzyme regulator activity, protein binding transcription factor activity and structural molecular activity were upregulated, and most of genes affiliated with multicellular organismal process and extracellular region were downregulated. It was notably that fifteen genes affiliated with flagella and four genes affiliated with heat shock proteins were significantly upregulated. Meanwhile, nine genes affiliated with cytochrome and cytochrome oxidase, and five genes affiliated with TonB-dependent receptor, were significantly downregulated. However, eighteen genes with antioxidant activity categorized by GO analysis showed differential expressions. This overall survey of transcriptome and oxidative stress-relevant genes can contribute to understand the adaptive mechanism of Arctic bacteria.
five significant upregulated genes and five significant downregulated genes were selected using qRT-PCR to cinduct the  oxidative stress.

overall_design: overall survey of transcriptomic sequencing by RNA-Seq of the Pseudoalteromonas sp. A2, an isolate from seawater with high activity against H2O2

first: Linxue

last: zheng

first: Wangzhen

last: Liyang


title: Single Cell triple omics sequencing reveals genetic and epigenetic heterogeneity in hepatocellular carcinoma

city: Beijing

first: Yu

last: Hou

state: Beijing

address: No.5 Yiheyuan Street

department: School of life sciences

institute: Peking University

type: Methylation profiling by high throughput sequencing

summary: Single cell genome, DNA methylome, and transcriptome sequencing has been achieved separately. However, to analyze the regulation of RNA expression by genetic and epigenetic factors within an individual cell, it is necessary to analyze these omics simultaneously from the same single cell. Here we developed a single cell triple omics sequencing technique- scTrio-seq, to analyze the genome, DNA methylome, and transcriptome concurrently of a mammalian cell.

overall_design: 6 single human HepG2 cell line cells were sequenced using the newly developed scTrio-seq, other 2 HepG2 cells were sequenced using scRNA-seq and other 2 HepG2 cells were sequenced using scRRBS as technique control.  6 single mouse embryonic stem cells (mESCs) were sequenced using the newly developted scTrio-seq. Meanwhile, two scRNA-seq and two scRRBS were also completed using two mESCs separately. 26 single cells from hepatocellular carcinoma were sequenced using scTrio-seq to analyze the regulation relations between three omics of cancer cells.

first: Fuchou

last: Tang

first: Yanyi

last: Huang

first: Jirun

last: Peng


title: Reduced expression of RBM47 enhances Nrf2 activity to promote tumor growth in A549 lung adenocarcinoma cells

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

summary: We identified RNA binding motif protein 47 (RBM47) as a target gene of transforming growth factor (TGF)-beta in mammary gland epithelial cells (NMuMG cells) that have undergone the epithelial-to-mesenchymal transition (EMT). TGF-beta repressed RBM47 expression in NMuMG cells and lung cancer cell lines. Expression of RBM47 correlated with good prognosis in patients with lung, breast, and gastric cancer. RBM47 suppressed the expression of cell metabolism-related genes, which were the direct targets of nuclear factor erythroid 2-related factor 2 (Nrf2; also known as NFE2L2). RBM47 bound to KEAP1 and Cullin3 mRNAs, and knockdown of RBM47 inhibited their protein expression, which led to enhanced binding of Nrf2 to target genomic regions. Knockdown of RBM47 also enhanced the expression of some Nrf2 activators, p21/CDKN1A and MafK induced by TGF-beta. Both mitochondrial respiration rates and the side population cells in lung cancer cells increased in the absence of RBM47. Our findings, together with the enhanced tumor formation and metastasis of xenografted mice by knockdown of the RBM47 expression, suggested tumor suppressive roles for RBM47 through the inhibition of Nrf2 activity.

overall_design: Effect of shRNA for RBM47 and TGF-beta on gene expression was evaluated by RNA-seq and RBM47-bound RNAs were identified by RIP-seq in A549 cells.

first: Tsubasa

last: Sakurai

first: Kazunobu

last: Isogaya

first: Satoshi

last: Sakai

first: Masato

last: Morikawa

first: Yasuyuki

last: Morishita

first: Shogo

last: Ehata

first: Kohei

last: Miyazono


title: BET inhibition releases the Mediator complex from specific cis elements in acute myeloid leukemia cells (ChIP-Seq I)

city: Cold Spring Harbor

first: Anand

last: Bhagwat

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Genome occupancy profiling by high throughput sequencing

overall_design: ChIP-seq of Brd4 and Mediator with or without JQ1 treatment in MLL-AF9 transformed acute myeloid leukemia cells (RN2)

first: A

first: C

last: Vakoc


title: Endogenous DAF-16 genome-wide recruitment under low Insulin signaling condition in Caenorhabditis elegans

city: Delhi

first: Arnab

last: Mukhopadhyay

state: Delhi

address: Aruna asaf ali marg

country: India

institute: National Institute of Immunology

summary: In order to understand the complexity of gene regulation downstream of IIS, we used anti-DAF-16 antibody, we report the first genome-wide ChIP-sequencing study of endogenous DAF-16 recruitment  in daf-2(e1370). We also report the average bin-wise normalized read count of ZFP-1 and DAF-16 on DAF-16 summits

overall_design: ChIP-Seq profile of DAF-16 in mix stage

first: N

last: Kumar


title: Bovine mammary gene expression profiling during the onset of lactation

city: Tai'an

first: yuanyuan

last: gao

address: Daizong Street 61#

institute: Shandong Agricultural University

summary: Lactogenesis includes two stages. Stage Ⅰ begins a few weeks before parturition, and stage Ⅱ begins a few weeks before parturition. In order to better understand the molecular events driving lactogenesis in dairy cows, genome-wide gene expression profiling was conducted using digital gene expression profiling (DGE) on bovine mammary tissue at three time points (on approximately day 35 before parturition (-35d), day 7 before parturition (-7d) and day 3 after parturition (+3d)). Approximately 6.2 million, 5.8 million and 6.1 million 21-nt cDNA tags were sequenced in the three cDNA libraries (-35d, -7d and +3d), respectively. After aligning to the reference sequences, the three cDNA libraries included 8,662, 8,363 and 8,359 genes, respectively. With a fold change cutoff criteria of ≥2 or ≤-2 and a false discovery rate (FDR) of ≤0.001, a total of 812 genes were significantly differentially expressed at -7d compared with -35d (stage Ⅰ). There were 234 genes upregulated and 578 genes downregulated, accounting for 28.8％ and 71.2％ of differentially expressed genes respectively. A total of 1,189 genes were significantly differentially expressed at +3d compared with -7d (stag Ⅱ). Of these genes with significant expression changes, 274 (23.0％) genes were upregulated. 915 (77.0％) genes were downregulated. The results suggest that the mammary gland begins to lactate not only by a gain of function but also by a broad suppression of function to effectively push most of the cell＇s resources towards lactation.

overall_design: Examination of genome-wide gene expression profiling using digital gene expression profiling (DGE) on bovine mammary tissue at three time points of approximately day 35 before parturition, day 7 before parturition and day 3 after parturition. There were 6 cows in each group. The mammary tissue from cows in the same group were pooled together for RNA isolation. The total RNA was used to sequence.

first: Yuanyuan

last: Gao

first: Zhonghua

last: Wang


title: Genome-wide screening for ELF4-binding sites.

city: Bunkyo-ku

first: Mizuo

last: Ando

state: Tokyo

address: 7-3-1 Hongo

department: Otolaryngology-Head and Neck Surgery

institute: The University of Tokyo

summary: ELF4 (also known as MEF) is a member of the ETS family of transcriptional factors. While an oncogenic role has been demonstrated for ELF4 mainly in hematopoietic malignancies, its definitive function in human carcinogenesis is not clear yet. Here we demonstrate that a wide array of human tumors carry somatic, loss-of-function mutations in ELF4 for its transcriptional activity, and restoring its function exerts anti-proliferative effects. To further explore the tumor suppressive function of ELF4, its binding sites were searched among the human genome with the use of chromatin immunoprecipitation coupled with sequencing (ChIP-seq).

overall_design: Examination of binding site for FLAG-immunoprecipitated mock, ELF4 (WT) and ELF4 (L211M) with each input sample as a control.

first: Toshihide

last: Ueno

first: Hiroyuki

last: Mano


title: Temporal and spatial domain-specific transcriptomic analysis of a vital reproductive meristem in Arabidopsis thaliana

status: Public on Feb 29 2016

city: Raleigh, NC

first: Robert

last: Franks

address: Campus Box 7614

department: Plant & Microbial Biology Department

institute: NC State University

summary:
Background: The carpel margin meristem is a vital multi-potent structure located in the medial domain of the Arabidopsis thaliana gynoecium, the female floral reproductive organ. The carpel margin meristem generates ovules that upon fertilization become seeds. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present an analysis of the transcriptional profile of the medial domain of the Arabidopsis gynoecium highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development.
Results: Using a floral synchronization system and a SHATTERPROOF2 domain-specific reporter construct, paired with fluorescence-activated cell sorting, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. Our analysis reveals a set of genes that are differentially-expressed within the SHATTERPROOF2 expression domain that marks portions of the developing medial domain. Many members of this gene set have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Other uncharacterized members of this gene set, including a set of differentially-expressed cis-natural antisense transcripts, are potential novel regulators of medial domain development and candidates for future functional studies. Several members of the REM family of transcriptional regulators were enriched in the SHP2-expressing cell population including a previously unrecognized REM family member (At5g60142). Analysis of the abundance of specific transcriptional isoforms identified genes that may exhibit “isoform switching” behavior during gynoecial development.
Conclusions: This data set provides genome-wide transcriptional insight into the development of the gynoecial medial domain that contains the carpel margin meristem, an important reproductive structure that gives rise to the ovules in Arabidopsis thaliana.

overall_design: Four samples (YFP-positive, YFP-negative, all-sorted, and non-sorted). Four biological replicates of each sample (except YFP-positive, collected in triplicated). Strand-specific libraries were sequenced (single-end) in two lanes of a HiSeq 2500 Illumina flow cell (each lane was later analyzed as a technical replicate).

first: Gonzalo

last: Villarino


title: Sir2 mutants versus Controls at 2 weeks of age

city: SALT LAKE CITY

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah School of Medicine

summary: Although SIRT1 plays a central role in maintaining metabolic homeostasis, the molecular mechanisms remain unclear. Here we show that loss of the Drosophila SIRT1 homolog sir2 leads to the progressive onset of diabetic phenotypes, similar to studies of SIRT1 in mice. Sir2 function is both necessary and sufficient in the fat body to maintain peripheral insulin sensitivity. This activity is mediated by the Drosophila HNF4 nuclear receptor, which is deacetylated and stabilized through protein interactions with Sir2. This study demonstrates that the key metabolic activities of SIRT1 have been conserved through evolution and establishes HNF4 as a critical downstream target.

overall_design: 4 sir2 mutant, 4 control samples, independent biological replicates

first: Rebecca

last: Palu


title: AP-1 family members act at DNA targets in conjunction with Sox9 to promote chondrocyte hypertrophy

first: Xinjun

last: He

state: CA

address: 1425 San Pablo St

department: BROAD CIRM Center

institute: University of Southern California

summary: A comprehensive analysis of Sox9 binding profiles in developing chondrocytes identified marked enrichment of an AP-1-like motif (Ohba et al. 2015). Here, we have explored the functional interplay between Sox9 and AP-1 in mammalian chondrocyte development. Among AP-1 family members, Jun and Fosl2 were highly expressed within prehypertrophic and early hypertrophic chondrocytes. Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) showed a striking overlap in Jun- and Sox9-bound regions throughout the chondrocyte genome, a reflection of direct binding of each factor to target motifs in shared enhancers, and physical interactions of AP-1 with Sox9. In vitro expression analysis indicates that direct co-binding of Sox9 and AP-1 at target motifs enhanced target gene expression, while protein-protein interactions suppressed AP-1- and Sox9-driven transcription. Analysis of prehypertrophic chondrocyte removal of Sox9 demonstrated Sox9 was essential for hypertrophic chondrocyte development, while in vitro and ex vivo analyses showed AP-1 promotes chondrocyte hypertrophy. Sox9 and Jun co-bound and co-activated a Col10a1 enhancer in Sox9 and AP-1 motif-dependent manners consistent with their combined action promoting hypertrophic gene expression. Together, the data support a model where AP-1-family members promote Sox9-action in the transition of chondrocytes to a terminal hypertrophic program.

overall_design: Intersection of ChIP-seq data from Sox9 and AP-1 factor Jun, RNA-seq data from developing rib chondrocytes and Col10a1mCherry positive hypertrophic chondrocytes in neonatal mice to uncover regulation of Sox9 by AP-1 factors during chondrocyte hypertrophy.

first: Shinsuke

last: Ohba

first: Hironori

last: Hojo

first: Andrew

middle: P

last: McMahon


title: Chromatin Remodeler CHD7 mutated in CHARGE Syndrome Interacts with Sox10 to Regulate Timing of CNS Myelination and Remyelination.

city: Cincinnati

first: Richard

last: Lu

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: RNA-seq study of major P.aeruginosa PA14 transcription factors

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

summary: Gene regulation via transcription factors influences the metabolic, adaptive and pathogenic capabilities of the organism. We report the transcriptomes of the mutants of six major P. aeruginosa PA14 trancription factors - RhlR, LasR, Anr, GacA, FleQ and CbrB.

overall_design: The P. aeruginosa PA14 transposon mutants were analyzed by RNA-seq. All samples were cultivated in LB medium until reaching an OD600 of 2.0. For each biological replicate, three cultures were pooled for RNA extraction, library preparation and sequencing.

first: Tanja

last: Nicolai

first: Susanne

last: Häussler


title: Chromatin Remodeler CHD7 mutated in CHARGE Syndrome Interacts with Sox10 to Regulate Timing of CNS Myelination and Remyelination [RNA-seq]

summary: Mutations in CHD7, encoding ATP-dependent chromodomain-helicase-DNA-binding protein 7, in CHARGE syndrome leads to multiple congenital anomalies including growth retardation, craniofacial malformations and neurological dysfunction. Currently, mechanisms underlying the CNS phenotypes remain poorly understood. Here, we show that Chd7 is a direct transcriptional target of oligodendrogenesis-promoting factors Olig2 and Brg1 and required for proper timing of CNS myelination and remyelination. Genome-occupancy analyses coupled with transcriptome profiling reveal that Chd7 cooperates with Sox10 to target the enhancers of key myelinogenic genes, and identify novel Chd7 target.

overall_design: 4 RNA-Seq samples from P8 spinal cords of Ctrl and Chd7 cKO mice (duplicatess, Ctrl and cKO)

first: Danyang

first: Chuntao

last: Zhao


title: Chromatin Remodeler CHD7 mutated in CHARGE Syndrome Interacts with Sox10 to Regulate Timing of CNS Myelination and Remyelination [ChIP-seq]

overall_design: Examination of Chd7 and Sox10 genomewide occupancy in differentiating oligodendrocytes


title: Differentially Expressed Pseudogenes in HIV-1 Infection

city: Newark

first: Aditi

last: Gupta

state: NEW JERSEY

address: 185 South Orange Ave, MSB-A920G

department: Medicine

institute: Rutgers University

summary: We analyzed transcriptomic data from infected and uninfected T-cells to identify pseudogenes and their parent genes showing differential expression in HIV-1 infection

overall_design: H9 T-cell line was infected with NL4-3 strain of HIV-1 obtained by transfection of 293T cells. RNA from infected and uninfected cells was extracted 7 days post infection.

first: Chris

last: Adami


title: Oocyte-expressed Yes-associated Protein (YAP) is a Key Activator of the Early Zygotic Genome in Mouse

status: Public on Feb 28 2016

city: beijing

first: yujiao

last: dang

address: Yihe road

institute: BIOPIC

summary: We generated maternal and paternal mouse models with Yap1-deletion, and elucidated the function of maternal YAP in zygotic genome activation.

overall_design: RNA sequencing with 2 WT oocyte samples at GV stage, 2 YAP-/- oocyte samples at GV stage, 1 WT embryo samples at 4cell stage, 1 YAP-/- embryo samples at at 4-cell stage.

first: Chao

last: Yu

first: Yujiao

last: Dang


title: Epigenomic landscapes of human inflammation associated macrophages [ChIP-seq]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary:
We previously demonstrated by genomic and bioinformatical approaches that human macrophage (MΦ) activation is best described by a spectrum model (Xue et al, Immunity, 2014). MΦ integrate exogenous input signals on transcriptional level in a unique fashion to generate specific functional programs, enabling the plasticity in disease-related pathophysiologies. Such versatile responsiveness requires fast changes of transcription mediated by transcriptional regulators (TRs) or epigenomic changes.
To better understand the principles of this regulation during human MΦ activation, we assessed histone modifications including H3K4me1, H3K4me3, H3K27me3, and H3K27Ac by ChIP-sequencing allowing us to characterize the functional state of promoters (active, poised, repressed) and enhancers (active, inactive, intermediate).
Using transcriptome data from our MΦ spectrum model, we generated a co-regulation network of all TRs. Next, we overlaid epigenomic information and transcriptional changes of major TRs over time onto the TR network. We observed that input signals like IFNγ or TNFα induce a specific network of TRs that are transcriptionally regulated themselves, the combination of regulated TRs changes over time with a boost of transcriptional regulation of dozens of TRs 4 to 12 hrs post input signal exposure, almost all TRs within the network show active promoters, even if the TR itself is not expressed, and similar results are obtained for enhancers with open or at least intermediated states.
These findings strongly suggest that in MΦ, the TR-defined cellular ‘switch panel’ is always accessible thereby allowing MΦ to quickly respond to the diverse input signal repertoire from the environment.

overall_design: Epigenetic analysis of promoter and enhancer sites in primary human macrophage subtypes and correlation to RNA-seq expression data

middle: V

last: Schmidt

first: Wolfgang

last: Krebs

first: Thomas

last: Ulas

first: Jia

last: Xue

first: Jil

last: Sander

first: Katrin

last: Klee

first: Heidi

last: Theis

first: Michael

last: Kraut

first: Marc

last: Beyer

first: Patrick

last: Günther

first: Kevin

last: Baßler


title: RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM® genes for hereditary disorders of hearing and balance

city: Las Cruces

first: Daniel

last: Ramire-Gordillo

state: New Mexico

address: PO Box 30001, MSC 3AF

department: Biology

institute: New Mexico State University

summary:
Purpose: To identify orthologous genes in Xenopus that are implicated in deafness and vestibular disorders in humans and to compare RNA-Seq and microarray to determine the advantages of each technology for Xenopus transcriptomic analysis.
Methods: Inner ear RNA from X. laevis stages 56-58 was isolated with the Qiagen® RNeasy® Mini Kit. RNA quality was assessed using the Agilent 2100 Bioanalyzer. The RNA was sent to the National Center for Genome Resources, for Illumina-Solexa sequencing using the genome analyzer II and to MIT for microarray processing usign the Affymetrix GeneChip® X. laevis Genome 2.0 Array.  The OMIM database was mined for identification of genes causing deafness and vestibular disorder in humans. Human sequences for each of the deafness and vestibular disorders genes were downloaded from Ensembl. Blast-2.2.27+ was used to mapped the human sequences against X. tropicalis predicted proteins from JGI or to Xenopus consensus sequences downloaded from Affymetrix.  The alignment of the human sequences to the predicted proteins resulted in the identification of the protein designation number.  The protein designation number was used to obtain the sacaffold number and coordinates from JGI genome browser.  The scaffold number and coordinates were input into Alpheus sequence variant detection pipeline to obtain the number of reads associated with each gene.  The reads were log2 transformed for comparison to the microarray. In the case of the alignment of the human sequences to the Xenopus consensus sequences resulted in the PSID.  The PSID was used to obtain the GCRMA intensity value.  The GCRMA value and the number of reads were compared to determine which technology detected more genes.
Results: Using Affymetrix GeneChip® X. laevis Genome 2.0 Arrays and Illumina-Solexa sequencing methods, we determined that the transcriptional profile of the Xenopus inner ear comprises hundreds of genes that are orthologous to OMIM® genes implicated in deafness and vestibular disorders in humans. Analysis of genes that mapped to both technologies showed that RNA-Seq detected more of both deafness and vestibular disorder than the Microarray.  RNA-Seq and microarray detected 108 genes but RNA-Seq detected 48 genes that were below threshold criteria for microarray.  While the microarray detected 11 genes that were below the expression criteria for RNA-Seq and 23 genes were below the threshold criteria for both technologies. Further analysis of the 108 genes detected by both technologies showed a minor correlation between the two technologies.
Conclusions: As part of this study we identified candidate scaffold regions of the Xenopus tropicalis genome that can be used for gene mutagenesis. Furthermore, results from this study showed that the two technologies can complement each other and that a combination of both approaches can provide a more complete analysis of gene expression than either method alone.

overall_design: Inner ear RNA from X. laevis larval stages 56-58 was isolated and shipped to the National Center for Genome Resources, for Illumina-Solexa sequencing or to the Massachusetts Institute of Technology BioMicro Center for microarray analysis with the Affymetrix GeneChip® X. laevis Genome 2.0 Array. RNA-Sequencing was completed using the Illumina-Solexa platform for sequencing by synthesis.  Short-insert paired end (SIPE) libraries were prepared from total RNA according to Illumina’s mRNA-Seq Sample Prep Protocol v2.0 (Illumina, San Diego, CA, USA).  The resultant double-stranded cDNA concentration was measured on a NanoDrop spectrophotometer, and size and purity were determined on the 2100 Bioanalyzer using a DNA 1000 Nano kit. The cDNA libraries were cluster amplified on Illumina flowcells, sequenced on the GAII Sequencer as 36-cycle single-end reads, and processed using Illumina software v1.0.  Illumina reads were aligned to the X. tropicalis genome using the algorithm for genomic mapping and alignment program (GMAP) and Alpheus® Sequence Variant Detection System v3.1.

last: Ramirez-Gordillo

first: TuShun

middle: R

last: Powers

first: Casilda

last: Trujillo-Provencio

first: Jennifer

last: van Velkinburgh

first: Faye

last: Schilkey

first: Elba

last: Serrano


title: Epigenomic landscapes of human inflammation associated macrophages

first: Joachim

last: Schultze


title: Global Analysis of the developmental dynamics of Gossypium hirsutum based on strand-specific transcriptome

city: Anyang

first: Lei

last: Ma

state: Henan

address: NO.38 Yellow River Road

institute: Institute of Cotton Research, Chinese Academy of Agricultural Sciences

summary: Cotton is the most important economic crop that provides natural fibre and by-products such as oil and protein. The global gene expression could provide insight into the biological processes underlying growth and development, which involving suites of genes expressed with temporal and spatial controls by regulatory networks. Improvement of cotton fiber in yield and quality is the main goal for molecular breeding, but many previous research have been largely focused on identifying genes only in fibres, so that we ignore seed which may play an important role in the development of fibers. In this study, we constructed and systematically analyzed twenty-one strand-specific RNA-Seq libraries on Gossypium hirsutum L. covering different tissues, organs and development stages, of which approximately 970 million reads were generated. In total, 5,6754 transcripts derived from 2,9541 unigenes were obtained to provide a global view of gene expression for cotton development. Hierarchical clustering of transcriptional profiles suggests that transcriptomes among tissues or organs corresponded well to their developmental relatedness. The organ (tissue)-specific gene expressions were investigated efficiently and provided further insight into the dynamic programming of the transcriptome, in particularly for coordinating development between fiber cell and seed (ovule). We identified series of transcription factors and seed-specific genes, which as the candidate genes should help elucidate key mechanisms and regulatory networks that underlie fiber and seed development. This report identified comprehensive transcriptome changes in different stage of cotton development and will serves as a valuable genome-wide transcriptome resource for cotton breeding.

overall_design: Examination of transcriptome of  cotton

first: Ma

last: Lei


title: Loss of CSL unlocks a hypoxic response and enhanced tumor growth potential in breast cancer cells

city: Stockholm

first: Urban

last: Lendahl

state: State...

address: SE-171 77 Stockholm

department: CMB

institute: Karolinska Insitute

summary: Notch signaling is an important regulator of stem cell differentiation. All canonical Notch signaling is transmitted through the DNA-binding protein CSL and hyperactivated Notch signaling is associated with tumor development; thus it may be anticipated that CSL deficiency should reduce tumor growth. In contrast, we report that genetic removal of CSL in breast tumor cells caused accelerated growth of xenografted tumors. Loss of CSL unleashed a hypoxic response during normoxic conditions, manifested by stabilization of the HIF1± protein and acquisition of a polyploid giant-cell, cancer stem cell-like, phenotype. At the transcriptome level, loss of CSL upregulated more than 1750 genes and less than 3% of those genes were part of the Notch transcriptional signature. Collectively, this suggests that CSL exerts functions beyond serving as the central node in the Notch signaling cascade and reveals a novel role for CSL in tumorigenesis and regulation of the cellular hypoxic response.

overall_design: CSL +/+ and CSL -/- MDA-MB-231 were subjected to Notch activation/inhibition and xenograft experiment. Total RNA were extracted from the samples and sent to NGS. Single Cell RNA-sequencing was also performed from cells isolated from xenograft tumors.

first: Yat

last: Tsoi

first: Eike

last: Benjamin

last: Ramsköld


title: Genome-wide distribution of Pbx1/2/3 in mouse cortex at embryonic day 12.5 [ChIP-seq]

status: Public on Feb 27 2016

city: san francisco

first: olga

last: golonzhka

address: 1550 4th street

department: psychiatry

institute: UCSF

summary: We demonstrate using conditional mutagenesis that Pbx1, with and without Pbx2+/ sensitization, regulates regional identity and laminar patterning of the developing mouse neocortex in cortical progenitors (Emx1-Cre) and in newly generated neurons (Nex1-Cre). Pbx1/2 mutants have three salient molecular phenotypes of cortical regional and laminar organization: hypoplasia of the frontal cortex, ventral expansion of the dorsomedial cortex, and ventral expansion of Reelin expression in the cortical plate of the frontal cortex, concomitant with an inversion of cortical layering in the rostral cortex. Molecular analyses, including PBX ChIP-seq, provide evidence that PBX promotes frontal cortex identity by repressing genes that promote dorsocaudal fate.

overall_design: Chromatin immunoprecipitation was performed using antibody against Pbx1/2/3 (sc-888, Santa Cruz). Wild type E12.5 mouse whole cortex was used for the analysis.

first: John

last: Rubenstein

first: Olga

last: Golonzhka


title: Epigenomic landscapes of human inflammation associated macrophages [RNA-seq]

first: Susanne

last: Schmidt

first: Wolfgang

last: Krebs

first: Thomas

last: Ulas

first: Jia

last: Xue

first: Jil

last: Sander

first: Katrin

last: Klee

first: Heidi

last: Theis

first: Michael

last: Kraut

first: Marc

last: Beyer


title: Endogenous DAF-16 genome-wide recruitment under low Insulin signalling condition in Caenorhabditis elegans

first: Arnab

last: Mukhopadhyay

summary: In order to understand the complexity of gene regulation downstream of IIS, we did RNA-seq in mixed culture in wild-type, daf-2(e1370), daf-16(mgDf50);daf-2(e1370) and daf-2(e1370);daf-12(m20 and correlated it with ChIP-seq data

overall_design: RNA-seq profile of different mutants in mix stage

first: Neeraj

last: Kumar


title: Estrogen and mTORC1 dependent genes in the uterus of uterine-specific Tsc2-null mice

status: Public on Feb 26 2016

city: Rochester

first: Stephen

last: Hammes

state: NY

address: 601 Elmwood Ave, Box 693

institute: University of Rochester

summary: To uncover genes regulated by mTORC1 and estradiol in uterine Tsc2-null LAM like cells, we performed RNAseq on uteri from 12-week old wild-type (WT) and uterine-specific Tsc2-null (KO) mice that were either untreated (intact), oopherectomized (ovx) or oopherectomized + treated with 17β-estradiol pellets (E2) for 8 weeks. We identified genes that were both estradiol- and TSC2-mediated.

overall_design: Uterine mRNA profiles of 12 week old wild type (WT) and uterine-specific Tsc2-null (KO) mice in the presence or absence of estradiol were generated using Illumina HiSeq2500

first: Hen

last: Prizant

first: Myers

last: Jason

first: Ashton

last: John


title: Signaling Role of Acetoacetate in Accelerating Muscle Regeneration and Ameliorating Muscular Dystrophy

city: Beijing

first: Jun

last: Cai

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics

summary: Acetoacetate (AA) is a ketone body and acts as a fuel to supply energy for cellular activity of various tissues. Here, we performed differential RNA-Seq analyses of proliferating and differentiating C2C12 myoblasts in the present or absent of AA. Differentially regulated genes and gene set enrichment analysis revealed that altered expression of the AA-mediated genes in both GM (growth medium) and DM (differentiation medium) were highly enriched in the signaling pathways associated with cell proliferation and differentiation, however, the genes encoding enzymes in biochemical pathways of ketolysis for energy production were not transcriptionally changed in the cells cultured in either GM or DM in response to AA. Notably the genes differentially expressed between GM and DM were also significantly regulated by AA. This indicates that AA-mediated myogenic cell function by transcriptional regulation of the genes required for cell proliferation and differentiation. Taken together, the data from our multi-parameter analyses consistently support the notion that AA plays a non-metabolic role in regulating muscle cell function.

overall_design:
We sequenced mRNA from C2C12 cells in GM or DM treated with AA for 12 h or not to generate genes response to AA during C2C12 proliferation and differentiation. Three of duplication was performed.
Examination of mRNA levels in proliferating or differentiating C2C12 cells between AA-treated groups and control groups.

first: Xiaoting

last: Zou

first: Dahai

last: Zhu


title: 4C-ker: A method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments

city: New York

first: Jane

last: Skok

address: 550 First Ave, Smillow 307

institute: NYU

summary: 4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or "bait") that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cis and trans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cis and trans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition, we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cis and trans chromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.

overall_design: 4C-Seq experiments from Igh and Cd83 bait in activated B cells and Tcrb (Eb) bait in double negative T cells and immature B cells. RNA-Seq and ATAC-Seq experiments in DN and Immature B cells.

first: Richard

last: Bonneau


title: RNA sequencing of primary thymic, bone and skin mesenchymal cells

city: Montreal

first: Julien

last: Patenaude

state: Quebec

address: 2950 chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and cancer (IRIC)

summary:
Purpose : Elucidate post-natal role of SCA1+ thymic mesenchymal cells (tMCs) and evaluate the functional overlap between thymic, bone and skin MCs.
Method : By high speed cell sorting, we isolated primary MCs (Lin- SCA1+ cells) from mouse thymus, bone and skin. We extracted their respective total RNA and compared their transcriptome by high-throughput RNA-sequencing.
Results : We found a total of 2036 differentially expressed genes (FC>5, p-adj<0.1 and RPKM>1) between the 3 MC populations. IPA analyses revealed that each MC population was enriched for genes associated to phagocyte chemotaxis. We also denoted 2850 genes with shared expression across MC populations. IPA analysis of those shared genes also revealed an enrichment for genes influencing phagocyte migration, chemotaxis and function. Finally, MC transcriptomes showed that all 3 MC populations were expressing genes associated with hematopoietic stem and progenitor cell (HSPC) support, strongly suggesting that MCs from thymic, bone and skin all possess the ability to support HSPCs.
Conclusion : Overall, our study highlighted 3 potential novel roles for tMCs : 1) Promoting macrophage/monocyte chemotaxis, 2) Enhacing the apoptotic cell clearance process and 3) setting an inviting niche for hematopoietic progenitors. These novel biological roles for tMCs could have substantial effets on thymic biology. Finally, our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions related mesenchymal cell biology.

overall_design: Transcriptome comparison between MC populations

first: Claude

last: Perreault


title: 24hr CA treatment vs. DMSO in HCT116 cells (from 'Identification of CDK8 and CDK19 substrates in human cells using cortistatin A and quantitative phosphoproteomics')

city: Boulder

first: Dylan

last: Taatjes

state: Colorado

address: 3415 Colorado Ave.

department: Molecular and Cell Biology

institute: University of Colorado, Boulder

summary: Cortistatin A (CA) is a highly selective inhibitor of the Mediator kinases CDK8 and CDK19. Using CA, we report here the first large-scale identification of Mediator kinase substrates in human cells (HCT116).  Among over 16,000 quantified phosphosites, we identified 78 high-confidence Mediator kinase targets within 64 proteins, including DNA-binding transcription factors and proteins associated with chromatin, DNA repair, and RNA polymerase II.  Although RNA-Seq data correlated with Mediator kinase targets, CA effects on gene expression were limited and distinct from CDK8 or CDK19 knockdown.  Quantitative proteome analyses, which tracked about 7,000 proteins across six time points (0 – 24h), revealed that CA selectively affected pathways implicated in inflammation, growth, and metabolic regulation; contrary to expectations, increased turnover of Mediator kinase targets was not generally observed.  Collectively, these data support Mediator kinases as regulators of chromatin and RNA polymerase II activity and suggest cellular roles beyond transcription, including metabolism and DNA repair.

overall_design: HCT116 cells were treated with either 100nM CA or DMSO in biological triplicate for each population (6 samples total). Treatment was for 24h for compound and vehicle.

first: Zachary

middle: C

last: Poss


title: Genome-wide identification of microRNAs in pomegranate (Punica granatum L.) by high throughput sequencing

status: Public on Feb 25 2016

city: Institute

first: Umesh

middle: K

last: Reddy

state: West Virginia

address: 141, Hamblin Hall, WVSU

department: Department of Biology

institute: West Virginia State University

summary:
Background: MicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression posttranscriptionally, play multiple key roles in plant growth and development and the stress response. Knowledge of and the roles of miRNAs in pomegranate fruit development have not been explored.
Results: Pomegranate, which accumulates a large amount of anthocyanins in skin and arils, is valuable to human health, mainly because of antioxidant properties. In this study, we developed a small RNA library from pooled RNA samples from young seedling to matured fruits and identified both conserved and pomegranate-specific miRNA from 29,948,480 high-quality reads. For the pool of 15- to 30-nt small RNAs, ~50% were 24 nt. The miR157 family was the most abundant, followed by miR156, miR160, and miR159, with many variants within each family. The base bias at the first position from the 5’ end has a strong preference for U for most 18- to 26-nt miRNAs but a preference for A for 18-nt miRNAs. In addition, for all 24-nt miRNAs, the nucleotide U is preferred (97%) in the first position. RT-qPCR was used to validate the expression of the predominant miRNA families in leaves, male and female flowers, and multiple fruit developmental stages; miR156, miR156-v1, miR159, miR159-v1, and miR319 were upregulated during the later stages of fruit development. Gene ontology and KEGG pathway analyses revealed predominant metabolic processes and catalytic activities, important for fruit development. In addition, KEGG pathway analyses revealed the involvement of miRNAs in ascorbate and linolenic acid, starch and sucrose metabolism; RNA transport; plant hormone signaling pathways; and circadian clock.
Conclusion: Pomegranate largely contains anthocyanin, flavonoids, and antioxidants, which play critical roles in treating cancer, Alzheimer disease, and preventing heart attacks. Our first and preliminary report of novel miRNAs provides information on the biochemical compounds of pomegranate for future research. The functions of the targets of these novel miRNAs need further investigation.

overall_design: Profiling of miRNAs in pomegranate using Illumina HiSeq 2000 platform

first: Thangasamy

last: Saminathan


title: Characterization of a novel mutation in O-GlcNAc transferase that segregates with disease in a family with X-linked intellectual disability

city: Athens

first: Lance

last: Wells

state: Georgia

address: 315 Riverbend Road

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: An X-chromosome exome sequencing analysis identified a mutation in O-GlcNAc transferase (OGT) (pL254F) in a family with X-linked intellectual disability (XLID). Affected patient lymohoblastoids exhibit decreased steady state OGT levels owing to an unstable protein compared to the unaffected, related male controls. Suprisingly, global O-GlcNAc levels remained remained unaltered. This prompted us to check the both protein and mRNA levels of the other cycling enzyme, O-GlcNAcase (OGA) which was also lowered. This implies that a compensation mechanism exists, however imperfect, owing to the disease state of the individuals. We performed glabal transcriptome analysis to assess any other changes in message between patients and controls.

overall_design: Our study highlights small differences in the global transcriptome of patient lymhoblastoids that have the L254F mutation in O-GlcNAc transferase when compared to familial controls using Illumina sequencing of total RNA

first: Krithika

last: Vaidyanathan


title: Oxidative stress related long non-coding RNAs (lncRNAs) in human umbilical vein endothelial cells

city: Shijiazhuang

first: Rui

last: Zhang

address: No.89, Donggang Road

institute: The First Hospital of Hebei Medical University

summary: Long non-coding RNAs (lncRNAs) exhibit a poor interspecies conservation and often show spatial- and temporal-specific expression patterns. What, if any, role they have in oxidative stress remains unknown. To identify potential roles for lncRNAs, we examined their expression in normal and H2O2-treated human umbilical vein endothelial cells. Oxidative stress related lncRNAs were generated by deep sequencing, using Illumina HiSeq 2000 or 2500 platform. Sequencing of the cDNA libraries from H2O2-treated HUVECs generated 12.5 million uniquely valid reads, meanwhile, 10.2 million valid fragments were obtained from control group in our experiment. A total of 10, 765 known and 30, 629 novel putative lncRNAs were identified according to RNA-Seq. Among them, 2, 091 of known and 25, 800 of novel lncRNAs were differentially expressed in H2O2-treated HUVECs compared with control HUVECs, and 12 of these were validated with qRT–PCR. Taken together, our findings provide evidence differentially expressed lncRNAs were mediated by oxidative stress in HUVECs, it is, therefore, likely that aberrant expression of lncRNAs, at least in part, participate in the process of endothelial injury caused by oxidative stress.

overall_design: Examination of lncRNAs in the oxidative-stressed human umbilical vein endothelial cells

last: zhang


title: Histone acetylation H2BK20ac marks cell-state specific active regulatory elements

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Characterisation of different histone modifications is crucial to understand gene regulation. In order to study the most predictive histone modification for active enhancers we created unbiased set of enhancers and used machine learning approach. Our approach revealed an unconventional histone modification H2BK20ac as most efficient marker of active enhancers. H2BK20ac also showed superior coverage of tissue specific active enhancers in complex invivo samples. Adding H2BK20ac to set of conventional histone modifications lead to identification of new chromatin state which could be active enhancers. H2BK20ac tends to occur only at cell-type specific active promoters and showed higher specificity for related disease mutations than H3K27ac and other histone modifications. Using transient state of BV2 microglia cells after lipopolysaccharide based activation, we found that H2BK20ac also marks cell-state specific cis-regulatory elements. Further analysis using inhibition of TGF-beta pathway in BV2 cells and LPS stimulation, revealed differential patterns of H2BK20ac and H3K27ac at genome locations associated with opposite roles response to stmulation. Our study about H2BK20ac hints about a new mechanism of regulation of cell-type specificity and a distinct mode of action of pathways to maintain balance between cell-responses.

overall_design: Chip-seq of H2BK20ac and other histone modifcation was performed in 3 cell types and embryonic mouse forebrain. The sensitivity for active enhancers was compared for different histone modification ChIP-seq.The level of H2BK20ac at promoters and enhancers was assesed for relationship to cell-type specific expression. H2BK20ac signals were also analysed during cell-state transition when microgila are stimulated by LPS

first: Muratani

last: Masafumi

first: Shyam

last: Prabhakar


title: Grainyhead-like 2 (GRHL2) maintains the epithelial status of ovarian cancer through miR-200-ZEB1 regulatory networks (ChIP-Seq)

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

institute: National University of Singapore

summary: Epithelial ovarian cancer (EOC) is clinically heterogeneous, comprising different histological and biological subtypes. Multiple studies have implicated epithelial-mesenchymal transition (EMT), a biological process by which polarized epithelial cells convert into a mesenchymal phenotype, to contribute significantly to this molecular heterogeneity of EOC. From gene expression analyses of a collection of EMT-characterized EOC cell lines, we found that the expression of the transcription factor Grainyhead-like 2 (GRHL2) correlates with E-cadherin expression and the epithelial phenotype. EOC tumors with lower levels of GRHL2 are associated with the Mes (mesenchymal) molecular subtype and show poorer overall survival in patients. Here, we demonstrate that shRNA-mediated knockdown of GRHL2 in EOC cells with an epithelial phenotype resulted in EMT changes, with increased cell migration, invasion and motility. By ChIP-sequencing and gene expression microarray, we identified a variety of target genes regulated by GRHL2, including protein-coding and non-coding genes. Our data suggest that GRHL2 maintains the epithelial phenotype of EOC cells through the regulatory networks of miR-200b/a, ZEB1 and E-cadherin. These findings support GRHL2 as a crucial player in the molecular heterogeneity of EOC.

overall_design: 3 samples were analyzed (GRHL2 ChIP sample for 3 cell lines)

first: Vin-Yee

last: Chung

first: Tuan-Zea

first: Ming

first: Meng-Kang

last: Wong

first: Kuee-Theng

last: Kuay

first: Zhe

last: Yang

first: Jieru

last: Ye

first: Julius

last: Muller

first: Cheryl-Mei-Yi

last: Koh

first: Ernesto

last: Guccione

first: Jean-Paul

last: Thiery

first: Ruby-Yun-Ju

last: Huang


title: Swi1/Timeless prevents repeat instability at fission yeast telomeres

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

summary: Genomic instability associated with DNA replication stress is linked to cancer and genetic pathologies in humans. If not properly regulated, replication stress, such as fork stalling and collapse, can be induced at natural replication impediments present throughout the genome. The fork protection complex (FPC) is thought to play a critical role in stabilizing stalled replication forks at several known replication barriers including eukaryotic rDNA genes and the fission yeast mating-type locus. However, little is known about the role of the FPC at other natural impediments including telomeres. Telomeres are considered to be difficult to replicate due to the presence of repetitive GT-rich sequences and telomere-binding proteins. However, the regulatory mechanism that ensures telomere replication is not fully understood. Here, we report the role of the fission yeast Swi1/Timeless, a subunit of the FPC, in telomere replication. Loss of Swi1 causes telomere shortening in a telomerase-independent manner. Our epistasis analyses suggest that heterochromatin and telomere-binding proteins are not major impediments for telomere replication in the absence of Swi1. Instead, repetitive DNA sequences impair telomere integrity in swi1Δ mutant cells, leading to the loss of repeat DNA. In the absence of Swi1, telomere shortening is accompanied with an increased recruitment of Rad52 recombinase and more frequent amplification of telomere/subtelomeres, reminiscent of tumor cells that utilize the alternative lengthening of telomeres pathway (ALT) to maintain telomeres. These results suggest that Swi1 ensures telomere replication by suppressing recombination and repeat instability at telomeres. Our studies may also be relevant in understanding the potential role of the FPC in regulation of telomere stability in cancer cells.

overall_design:
Genome-wide distributions of Rad52 in wild type and in swi1 deletion in fission yeast
The'SP1173_WT ChIP-seq' is an input sample (non-tagged data).

first: Mariana

last: Gadaleta

first: Mukund

middle: M

last: Das

first: Ya-Ting

last: Chang

first: Ken-ichi

last: Noma

first: Toru

last: Nakamura

first: Eishi

last: Noguchi