title: Whole transcriptome analysis of brain hippocampal tissue from young and old senescence-accelerated prone SAMP8 mice treated with control diet and J147-containing diet

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: AD drug discovery has rarely been addressed in the context of aging even though sporadic AD accounts for 99% of the cases. Phenotypic screens based upon old age-associated brain toxicities were used to develop the potent AD drug candidate J147. Here, we hypothesized that J147 would be effective against both brain aging and AD-associated pathology in rapidly aging SAMP8 mice, a model for early sporadic AD. An inclusive and integrative multi-omics approach was used to investigate protein expression, RNA expression, metabolite levels as well as cognition in old and young SAMP8 mice. J147 not only reduced the cognitive deficits and associated metabolic changes observed in old SAMP8 mice, it restored the levels of multiple markers of AD, vascular pathology, synaptic function, and inflammation to those approaching the young phenotype. Our data show that a drug candidate selected upon the basis of preventing old age-related brain toxicities also reduces AD-associated pathology.

overall_design: The aim of this project was to investigate whether the AD drug candidate J147 protects SAMP8 mice from aging and AD-associated pathology and to assay the associated metabolic changes. Three three-month old male SAMP8 mice were fed with vehicle diet and three three-month old male SAMP8 mice with J147 diet until they reached ten months old. Four three-month old male SAMP8 mice were used as young control group.

first: Antonio

last: Currais

first: Richard

last: Dargusch

first: David

last: Schubert


title: Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labelling

status: Public on Nov 19 2015

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

type: Expression profiling by high throughput sequencing

summary: RNA levels detected at steady state are the consequence of multiple dynamic processes within the cell. In addition to synthesis and decay, many transcripts undergo processing. For example, in the case of intron-containing transcripts, there is splicing to take into the equation.  Metabolic tagging with a nucleotide analogue is one way of determining the relative contributions of synthesis, decay and conversion processes globally.  By using a much refined method of 4-thiouracil labelling in Saccharomyces cerevisiae we can isolate RNA produced during as little as 1 min, allowing the detection of RNA species with high turn-over rates, including intron-containing pre-mRNAs and short-lived non-coding RNAs. Nascent RNA labelled for 1.5, 2.5 or 5 minutes was isolated and analysed by reverse transcriptase-quantitative PCR and RNA sequencing. From these data we measured the relative stability of pre-mRNA species with different high turn-over rates and investigated potential correlations with intron features. This extremely brief metabolic labeling method enables the isolation of short-lived RNA species and the production of transcriptome-wide high-resolution kinetic data with some unexpected results . Previous studies using reporter genes suggested that secondary structure in introns is favourable for efficient splicing and may affect splice site usage. In contrast, our data reveal that ribosomal protein transcripts with intron secondary structures that are predicted to be less stable, splice faster. These data, in combination with previous results, indicate that there is an optimal range of stability of intron secondary structures that allows for rapid splicing.

overall_design: Three 4-thio-Uracil labeling time points, one rRNA depleted ribosomal RNA sample per experiment. All experiments were performed in triplicate.

first: Jean

middle: D

last: Beggs


title: Reduced insulin production relieves endoplasmic reticulum stress and induces beta-cell proliferation

status: Public on Nov 16 2015

city: Vancouver

first: James

middle: Daniel

last: Johnson

state: British Columbia

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

summary: We define the effects of reduced insulin production in beta-cells from tamoxifen-treated Ins1-/-:Ins2f/f:Pdx1CreERT:mTmG mice studied at a time point when insulin production was reduced by ~50%.

overall_design: Examination of the transcriptome of adult pancreatic islets from mice with acute Ins2 gene knockout out on an Ins1 null background


title: Control of developmentally primed erythroid genes by combinatorial corepressor actions

city: Oxford

first: Supat

last: Thongjuea

address: Headington

department: MRC Molecular Haematology Unit

institute: The Weatherall Institute of Molecular Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: How transcription factors (TFs) cooperate within large protein complexes to allow rapid modulation of gene expression during development is still largely unknown. Here we show that the key haematopoietic LIM-domain-binding protein-1 (LDB1) TF complex contains several activator and repressor components that together maintain an erythroid-specific gene expression programme primed for rapid activation until differentiation is induced. A combination of proteomics, functional genomics and in vivo studies presented here identifies known and novel co-repressors, most notably the ETO2 and IRF2BP2 proteins, involved in maintaining this primed state. The ETO2–IRF2BP2 axis, interacting with the NCOR1/SMRT co-repressor complex, suppresses the expression of the vast majority of archetypical erythroid genes and pathways until its decommissioning at the onset of terminal erythroid differentiation. Our experiments demonstrate that multimeric regulatory complexes feature a dynamic interplay between activating and repressing components that determines lineage-specific gene expression and cellular differentiation.

overall_design: ChIP-Sequencing profiles of the IRF2BP2, GFI1B and LSD1 proteins were generated using mouse erythroleukemia (MEL) cells. RNA-seq experiments of Irf2bp2-WT, Irf2bp2-KD, Eto2-WT, Eto2-KD, Gfi1b-WT, Gfi1b-KD, Lsd1-WT, Lsd1-KD, MEL-non-induced, and MEL-induced stages were performed using standard RNA-seq protocol. Illumina HiSeq 2000 (standard TruSeq RNA sequencing protocol) was used for the sequencing.

first: Ralph

last: Stadhouders

first: Eric

last: Soler


title: Graded Foxo1 Activity in Tregs Differentiates Tumor Immunity from Spontaenous Autoimmunity

status: Public on Nov 15 2015

city: New York

first: Willey

last: Liao

state: NY

address: 101 Avenue of the Americas

department: Bioinformatics

country: USA

institute: New York Genome Center

summary: Regulatory T cells (Tregs) expressing the transcription factor Foxp3 have a pivotal role in maintaining immunological self-tolerance1-5; yet, excessive Treg activities suppress anti-tumor immune responses6-8.  Compared to resting phenotype Tregs (rTregs) in the secondary lymphoid organs, Tregs in non-lymphoid tissues including solid tumors exhibit an activated Treg (aTreg) phenotype9-11.  However, aTreg function and whether its generation can be manipulated to promote tumor immunity without evoking autoimmunity are largely unexplored.  Here we show that the transcription factor Foxo1, previously demonstrated to promote Treg suppression of lymphoproliferative diseases12,13, has an unexpected function in inhibiting aTreg-mediated immune tolerance.  We found that aTregs turned over at a slower rate than rTregs, but were not locally maintained in tissues.  Transcriptome analysis revealed that aTreg differentiation was associated with repression of Foxo1-dependent gene transcription, concomitant with reduced Foxo1 expression, cytoplasmic Foxo1 localization, and enhanced Foxo1 phosphorylation at sites of the Akt kinase.  Treg-specific expression of an Akt-insensitive Foxo1 mutant prevented downregulation of lymphoid organ homing molecules, and impeded Treg homing to non-lymphoid organs, causing CD8+ T cell-mediated autoimmune diseases.  Compared to Tregs from healthy tissues, tumor-infiltrating Tregs downregulated Foxo1 target genes more substantially.  Expression of the Foxo1 mutant at a lower dose was sufficient to deplete tumor-associated Tregs, activate effector CD8+ T cells, and inhibit tumor growth without inflicting autoimmunity.  Thus, Foxo1 inactivation is essential for the migration of aTregs that have a crucial function in suppressing CD8+ T cell responses; and the Foxo signaling pathway in Tregs can be titrated to preferentially break tumor immune tolerance.

overall_design: Transcriptome of splenic rTreg (CD4+Foxp3+CD62LhiCD44lo) and aTreg (CD4+Foxp3+CD62LhiCD44lo) were compared. Duplicates from biologically independent animials were used.

first: Chong

last: Luo

first: Will

first: Saida

last: Dadi

first: Ahmed

last: Toure

first: Ming

last: Li


title: MCTA-Seq for profiling hypermethylated CpG islands in plasma of hepatocellular carcinoma patients

city: Beijing

first: xiaomeng

last: liu

state: Beijing

address: Yiheyuan Road No.5

country: China

institute: Biodynamics Optical Imaging Center (BIOPIC), Peking University

type: Methylation profiling by high throughput sequencing

summary: Despite advances in DNA methylome analyses of cells and tissues, current techniques for genome-scale profiling of DNA methylation in circulating cell-free DNA (ccfDNA) remain limited. Here we describe a methylated CpG tandems amplification and sequencing (MCTA-Seq) method that can detect thousands of hypermethylated CpG islands simultaneously in ccfDNA. This highly sensitive technique can work with genomic DNA as little as 7.5 pg, which is equivalent to 2.5 copies of the haploid genome. We have analyzed a cohort of tissue and plasma samples (n=151) of hepatocellular carcinoma (HCC) patients and control subjects, identifying dozens of high-performance markers in blood for detecting small HCC (<=3 cm). Among these markers, 4 (RGS10, ST8SIA6, RUNX2 and VIM) are mostly specific for cancer detection, while the other 15, classified as a novel set, are already hypermethylated in the normal liver tissues. Two corresponding classifiers have been established, combination of which achieves a sensitivity of 94% with a specificity of 89% for the plasma samples from HCC patients (n=36) and control subjects including cirrhosis patients (n=17) and normal individuals (n=38). Notably, all 15 alpha-fetoprotein-negative HCC patients were successfully identified. Comparison between matched plasma and tissue samples indicates that both the cancer and noncancerous tissues contribute to elevation of the methylation markers in plasma. MCTA-Seq will facilitate the development of ccfDNA methylation biomarkers and contribute to the improvement of cancer detection in a clinical setting.

overall_design: First, for validation of the MCTA-Seq techique, we examined CpG hypermethylation in fully methylated genomic DNA, and the genomic DNAs of WBC and 2 cancer cell lines. Then, we performed the MCTA-Seq method to clinical samples, including 27 pairs of HCCs and matching adjacent noncancerous liver samples and 3 normal liver samples, as well as plasma cell-free DNAs obtained from 27 HCC patients, 16 cirrhosis patient and 29 healthy individuals as the training group, and plasma cell-free DNAs obtained from 9 HCC patients and 10 healthy individuals as the testing group.

first: Lu

last: Wen

first: Jingyi

first: Xiaomeng

last: Liu

first: Huahu

last: Guo

first: Fuchou

last: Tang

first: Yanyi

last: Huang

first: Jirun

last: Peng


title: Expression of human C9ORF72 hexanucleotide expansion reproduces RNA foci and dipeptide repeat proteins but not neurodegeneration in BAC transgenic mice

status: Public on Nov 14 2015

city: Worcester

first: Helene

last: Tran

address: 55 North Lake Avenue

department: Neurology

institute: UMASS

summary: Nuclear RNA foci are often associated with mis-regulation of RNA processing in repeat expansion diseases. Here we report transcriptomic analysis of mice expressing expanded G4C2 repeats, the most common genetic cause of FTD/ALS.  We show that the presence of numerous nuclear G4C2 repeat RNA foci does not cause extensive changes in RNA processing in this model organism.

overall_design: Comparison of the transcriptomic profile of wild-type mice and mice expressing a human C9ORF72 BAC including 500 G4C2 repeats

first: Owen

last: Peters

first: Huaming

last: Sun

first: Fen-Biao

last: Gao

first: Chris

last: Mueller

first: Robert

last: Brown


title: H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-specific DNA Methylation Pauses Adipocyte Differentiation

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

country: Japan

institute: Akita University Graduate School of Medicine

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

overall_design: Refer to individual Series


title: miRNA-target chimeras identified with CLEAR-CLIP reveal miRNA 3' end pairing as a major determinant of Argonaute binding in vivo [human Huh7.5 AGO-CLIP & CLEAR-CLIP]

first: Michael

middle: John

last: Moore

address: 1230 York Ave Box 226

department: Molecular Neuro-Oncology

institute: The Rockefeller University

summary: microRNAs (miRNAs) act as sequence-specific guides for Argonaute (AGO) proteins, which mediate post-transcriptional silencing of target mRNAs. Despite their importance in many biological processes, rules governing AGO-miRNA targeting are only partially understood. We use a modified AGO HITS-CLIP strategy, termed CLEAR (Covalent Ligation of Endogenous Argonaute-bound RNAs) CLIP that enriches miRNAs ligated to their endogenous mRNA targets. CLEAR-CLIP mapped ~130,000 endogenous miRNA-target interactions in mouse brain and ~40,000 in human hepatoma cells. Motif and structural analysis define expanded pairing rules for over 200 mammalian miRNAs. Most interactions combine seed-based pairing with distinct, miRNA-specific patterns of auxiliary pairing. At some regulatory sites, this specificity confers distinct silencing functions to miRNA family members with shared seed sequences but divergent 3’ ends. This work provides a means for explicit biochemical identification of miRNA sites in vivo, leading to the discovery that miRNA 3’ end pairing is a general determinant of AGO binding specificity.

overall_design: In vivo microRNA-target interactions were identified with CLEAR-CLIP, a modified HITS-CLIP approach that allows direct ligation of microRNA and target within purified, endogenous AGO-RNA complexes. Native AGO-RNA complexes were purified under stringent conditions selectively preserve cross-linked AGO-target interactions, then microRNA and target mRNA were ligated within the AGO complex to form miRNA-target chimeras in addition to standard AGO CLIP reads. AGO-bound RNAs were cloned by addition of a pre-adenylated 3' linker, a 5' RNA linker containing a 4 nt degenerate barcode followed by a G (NNNNG), and RT-PCR amplification. A second round of PCR amplification added a 4 nt index (for multiplexing) followed by a 16 nt common priming sequence. Raw data files have been de-multiplexed, but are otherwise not modified.  Samples BR4 and BR5 are no-ligase controls in which chimera ligation was omitted.  Several 'mixing' controls experiments were also done to measure ligation of microRNAs to non-cross-linked targets due to post-lysis re-association by adding E. coli RNA (BR17-20) or Drosophila S2 cell lysates (BR21, BR22) into mouse brain lysates.

first: Troels

last: Scheel

first: Charles

last: Rice

last: Darnell


title: miRNA-target chimeras identified with CLEAR-CLIP reveal miRNA 3' end pairing as a major determinant of Argonaute binding in vivo

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: In Utero Cigarette Smoke Affects Allergic Airway Disease But Does Not Alter the Lung Methylome

city: Aurora

first: Kenneth

last: Eyring

state: CO

address: 12700 East 19th Avernue, 8611

department: Department of Medicine

institute: University of Colorado School of Medicine

summary:
Introduction: Prenatal and postnatal cigarette smoke exposure enhances the risk of developing asthma.  Despite this as well as other smoking related risks, 11% of women still smoke during pregnancy.  We hypothesized that cigarette smoke exposure during prenatal development generates long lasting differential methylation altering transcriptional activity that correlates with disease.
Methods: In a house dust mite (HDM) model of allergic airway disease, we measured airway hyperresponsiveness (AHR) and airway inflammation between mice exposed prenatally to cigarette smoke (CS) or filtered air (FA).  DNA methylation and gene expression were then measured in lung tissue.
Results: We demonstrate that HDM-treated CS mice develop a more severe allergic airway disease compared to HDM-treated FA mice including increased AHR and airway inflammation.  While DNA methylation changes between the two HDM-treated groups failed to reach genome-wide significance, 99 DMRs had an uncorrected p-value < 0.001.  6 of these 99 DMRs were selected for validation, based on the immune function of adjacent genes, and only 2 of the 6 DMRs confirmed the bisulfite sequencing data. Additionally, genes near these 6 DMRs (Lif, Il27ra, Tle4, Ptk7, Nfatc2, and Runx3) are differentially expressed between HDM-treated CS mice and HDM-treated FA mice.
Conclusions: Our findings confirm that prenatal exposure to cigarette smoke is sufficient to modify allergic airway disease, however, it is unlikely that specific methylation changes account for the exposure-response relationship.  These findings highlight the important role in utero cigarette smoke exposure plays in the development of allergic airway disease.

overall_design: Lung DNA methylation profiles of mice exposed in utero to cigarette smoke (CS) then treated with house dust mite (HDM, n = 8) or saline (n = 6), or exposed in utero to filtered air (FA) then treated with HDM (n = 9) or saline (n = 6)

middle: R

first: Brent

middle: S

last: Pedersen

first: Ivana

middle: V

last: Yang

first: David

middle: A

last: Schwartz


title: Multiplexed analysis of chromosome conformation at vastly improved sensitivity

first: James

middle: Oliver Joshua

last: Davies

state: Oxon

address: Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine, Oxford University

summary: Current methods for analysing chromosome conformation in mammalian cells are either insensitive and low resolution or low throughput.  Since the methods are expensive and relatively difficult to perform and analyse they are not widely used outside of specialised laboratories. Here we have re-designed the Capture-C method producing a new approach, called next generation (NG) Capture-C, which solves most of the current setbacks in analysing chromosome conformation. NG Capture-C produces unprecedented levels of sensitivity and reproducibility, which can be used to analyse any number of genetic loci and/or many samples in a single experiment.  NG Capture is straightforward to perform, requiring only standard reagents and access to basic next generation sequencing platforms.  The complete and detailed protocol presented here, with new publically available tools for library design and data analysis, will allow most laboratories to analyse chromatin conformation at levels of sensitivity and throughput that were previously impossible.

overall_design: NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments, in this case the promoters of genes were exclusively used.  The capture step has been optimised to markedly increase the sensitivity of the method (by introducing a double capture step), providing unprecedented levels of sensitivity and reliability for high resolution analysis of the chromatin landscape.

middle: O

first: Jim

last: Hughes


title: Genome-wide expression analysis of yeast with CRISPR-mediated inhibition of GAL10 ncRNA compared to wild-type.

city: Bethesda

first: Tineke

middle: Laura

last: Lenstra

state: MD

address: 41 Library Drive, Bldg 41, B302

department: Laboratory of Receptor Biology and Gene Expression

institute: National Cancer Institute, Center for Cancer Research

summary: We analyzed the genome-wide expression by RNA-seq of a yeast strain that expresses Cas9d and a guideRNA targeted to the GAL10 locus (called +116), which inhibits GAL10 ncRNA expression from the antisense strand. We compared this strain to a strain expressing a scrambled guideRNA. The goal was to examine the effects of ncRNA inhibition and to examine if CRISPR inhibition of gene expression has off-target effects.  We find that CRISPR-mediated inhibtion of GAL10 ncRNA only significantly changes expression of transcripts at the GAL1-10 locus, showing that CRISPR is highly specific, and that GAL10 ncRNA only control genes at the GAL locus.

overall_design: RNA-seq of 2 strains with CRISPR scrambled and 2 strains with CRISPR +116, the latter of which inhibits GAL10 ncRNA

middle: L

first: Daniel

last: Larson


title: Cycling transcriptional networks reduce the synthetic cost of genomes

status: Public on Nov 18 2015

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: The synthetic cost of cycling genes is higher than other genes, and the cyclic expression pattern of these genes is a strategy for reducing the overall energy usage of cells

overall_design: Samples for both conditions were taken over two metabolic cycles. For the fast cycling condition one sample was taken every 13 minutes for ~4.25 hours. For the slow cycling condition, samples were taken every 36 minutes for ~14.5 hours. Cycling genes were identified using JTK_Cycle (Hughes et al. (2010) Journal of Biological Rhythms).

first: Guang-Zhong

last: Wang

first: Stephanie

last: Lepp

first: Lei

last: Shi

first: Hung-Chung

last: Huang

first: Prachi

last: Nakashe

first: Nobuya

last: Koike

first: Benjamin

last: Tu

first: Joseph

last: Takahashi


title: Identifying synaptically enriched mRNA by using next generation sequencing

city: Zurich

first: Steven

middle: A.

last: Brown

address: Winterthurerstrasse 190

country: Switzerland

institute: University Zurich

summary: Preparation of Synaptosomes by density gradient and compare synaptically enriched mRNA to total homogenate transcriptome

overall_design: In brief, mouse brains were homogenized in 5 ml homogenization buffer (0.32 M sucrose, 1 mM EDTA pH 7.4, 1 mM dithiothreitol, phenylmethanesulfonyl fluoride solution (Sigma, 93482-50ML-F), complete mini-protease inhibitor (Roche Diagnostics) for 10 sec using a polytron. The homogenate was centrifuged at 1,000g for 10 min at 4 °C yielding the nuclear fraction (Nuc) and the supernatant (Sup). The supernatant was centrifuged at 31,000g for 5 min at 4°C using a discontinuous Percoll gradient. The layer between 3% and 10% of Percoll were collected, washed in 30 ml of homogenization buffer and further centrifuged at 22,000 × g for 15 min at 4°CT. The pellet was resuspended in in EBC buffer (50 mM Tris-HCl pH 8.0, 120 mM NaCl and 0.5% NP-40) containing complete mini-protease inhibitor (Roche Diagnostics) and phosphatase inhibitor cocktail 1 and 2 (Sigma–Aldrich)) for Western blot analysis or lysis buffer for RNA extraction (GenElute Mammalian Total RNA Miniprep Kit, Sigma).

first: Dennis

last: Mircsof


title: Comparative Analysis of the hippocampal transcriptome of WT and NONO KO mice

summary: Identifying causes of sporadic intellectual disability remains a considerable medical challenge.  Here, we demonstrate that null mutations in the NONO gene, a member of the Drosophila Behavior Human Splicing (DBHS) protein family, are a novel cause of X-linked syndromic intellectual disability. Comparing humans to Nono-deficient mice revealed related behavioral and craniofacial anomalies, as well as global transcriptional dysregulation. Nono-deficient mice also showed deregulation of a large number of synaptic transcripts, causing a disorganization of inhibitory synapses, with impaired postsynaptic scaffolding of gephyrin. Alteration of gephyrin clustering could be rescued by over-expression of Gabra2 in NONO-compromised neurons. These findings link NONO to intellectual disability and first highlight the key role of DBHS proteins in functional organization of GABAergic synapses.

overall_design: Hippocampal mRNA profiles of adult wild type (WT) and NONO KO mice were generated by deep sequencing, in six replicates using Illumina


title: NONO mutations are a novel cause of syndromic intellectual disability and inhibitory synaptic defects


title: Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing

status: Public on Nov 17 2015

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: RBM15, an RNA binding protein, determines cell-fate specification of many tissues including blood. We demonstrate that RBM15 is methylated by protein arginine methyltransferase 1 (PRMT1) at residue R578 leading to its degradation via ubiquitylation by an E3 ligase (CNOT4). Overexpression of PRMT1 in acute megakaryocytic leukemia cell lines blocks megakaryocyte terminal differentiation by downregulation of RBM15 protein level. Restoring RBM15 protein level rescues megakaryocyte terminal differentiation blocked by PRMT1 overexpression. At the molecular level, RBM15 binds to pre-mRNA intronic regions of genes important for megakaryopoiesis such as GATA1, RUNX1, TAL1 and c-MPL. Furthermore, preferential binding of RBM15 to specific intronic regions recruits the splicing factor SF3B1 to the same sites for alternative splicing. Therefore, PRMT1 regulates alternative RNA splicing via reducing RBM15 protein concentration. Targeting PRMT1 may be a curative therapy to restore megakaryocyte differentiation for acute megakaryocytic leukemia.

overall_design: In order to understand how RBM15 regulates RNA metabolism, we used a leukemia cell line (MEG-01 cell) to establish stable cell lines with RBM15 knockdown. For RNA immunoprecipitation (RIP) assay, normal immunoglobulin was used as controls for sample 1,2; and anti-RBM15 antibody was used for samples 3,4.

first: Ngoc-Tung

last: Tran

first: Yuheng

last: Lu

first: Christina

last: Leslie

first: Xinyang

last: Zhao


title: Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

summary: Aberrant expression of cancer genes and non-canonical RNA species is a hallmark of cancer. However, the mechanisms driving such atypical gene expression programs are incompletely understood. Here, our transcriptional profiling of a cohort of 50 primary clear cell renal cell carcinoma (ccRCC) samples from The Cancer Genome Atlas (TCGA) reveals that transcription read-through beyond the termination site is a source of transcriptome diversity in cancer cells. Amongst the genes most frequently mutated in ccRCC, we identified SETD2 inactivation as a potent enhancer of transcription read-through. We further show that invasion of neighbouring genes and generation of RNA chimeras are functional outcomes of transcription read-through. We identified the BCL2 oncogene as one of such invaded genes and detected a novel chimera, the CTSC-RAB38, in 20% of ccRCC samples. Collectively, our data highlight a novel link between transcription read-through and aberrant expression of oncogenes and chimeric transcripts that is prevalent in cancer.

overall_design: RNA-seq of SETD2 mutant and wild-type ccRCC cell lines.

middle: P

last: Leite

first: Sílvia

last: Carvalho

first: Mafalda

last: Matos

first: Filipa

middle: B

last: Martins

first: Alexandra

middle: C

last: Vitor

first: Joana

last: Desterro

first: Maria

last: Carmo-Fonseca

first: Sérgio

middle: F

last: de Almeida


title: Nuclear retention of mRNA in mammalian tissues

status: Public on Nov 13 2015

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

summary: Messenger RNA is thought to predominantly reside in the cytoplasm, where it is translated and eventually degraded. Although nuclear retention of mRNA has a regulatory potential it is considered extremely rare in mammals. Here to explore the extent of mRNA retention in metabolic tissues we combine deep sequencing of nuclear and cytoplasmic RNA fractions with single molecule transcript imaging in mouse beta cells, liver and gut. We identify a wide range of protein coding genes for which the levels of spliced polyadenylated mRNA are higher in the nucleus than in the cytoplasm. These include genes such as the transcription factor ChREBP, Nlrp6, Glucokinase and Glucagon receptor. We demonstrate that nuclear retention of mRNA can efficiently buffer cytoplasmic transcript levels from noise that emanates from transcriptional bursts. Our study challenges the view that transcripts predominantly reside in the cytoplasm and reveals a role of the nucleus in dampening gene expression noise.

overall_design: we have total of 8 samples all are mice. liver nuclear RNA (2 replicates), liver cytoplasmic RNA (2 replicates), MIN6 (cell line) nuclear RNA (2 replicates), MIN6 (cell line) cytoplasmic RNA (2 replicates)

first: Kere

last: Halpern

first: Inbal

last: Caspi

first: Doron

last: Lemze

first: Maayan

last: Levy

first: Shanie

last: Landen

first: Eran

last: Elinav

first: Igor

last: Ulitsky

first: Shalev

last: Itzkovitz


title: Sphingomonas wittichii strain RW1 genome-wide gene expression shifts in response to dioxins and clay

city: East Lansing

first: Benli

last: Chai

state: Michigan

address: 567 Wilson Road Rm 2225 A

department: Center for Microbial Ecology

institute: Michigan State University

summary: Sphingomonas wittichii strain RW1 (RW1) is one of few strains that can grow on dibenzo-p-dioxin (DD). We conducted a transcriptomic study of RW1 using RNA-Seq to outline transcriptional responses to DD, dibenzofuran (DF), and the smectite clay mineral saponite (SAP), an important geosorbent of toxicants in soil, with succinate as carbon source. The ability to grow on DD is rare compared to growth on the chemically similar DF even though the same initial dioxygenase may be involved in oxidation of both substrates. Therefore we hypothesized the reason for this lies beyond catabolic pathways and may concern genes involved in processes for cell-substrate interactions such as substrate recognition and transport, and detoxification. Compared to succinate (SUC) as control carbon source, DF caused over 240 protein-coding genes to be differentially expressed, whereas more than 300 were differentially expressed with DD. Stress response genes were up-regulated by both DD and DF. This effect was stronger with DD than DF, suggesting a higher toxicity of DD compared to DF. Both DD and DF caused changes in expression of genes involved in active cross-membrane transport such as TonB dependent receptor proteins, but the patterns of changes differed between the two substrates. Multiple transcription factor genes also displayed expression patterns distinct to DD and DF growth. DD and DF induced the catechol ortho- and the  salicylate/gentisate pathways, respectively. Both DD and DF induced the shared down-stream aliphatic intermediate compound pathway.  Clay (SAP) caused category-wide down-regulation of genes for cell motility and chemotaxis, particularly those involved in the synthesis, assembly and functioning of flagella. This is environmentally important finding because clay is a major component of soil microbes’ microenvironment influencing local chemistry and may serve as geosorbent for toxic pollutants. Similar to clay, DD and DF also affect motility and chemotaxis.

overall_design: Differential expression analysis of transcriptomes sequnenced from two replicates from succinate (SUC, control), three from succinate in the presence of clay (SAP), three from DD, and three from DF.

first: Tamara

last: Tsoi

first: Shoko

last: Iwai

first: Cun

last: Liu

first: Jordan

last: Fish

first: Cheng

last: Gu

first: Timothy

last: Johnson

first: Gerben

last: Zylstra

first: Brian

middle: J

last: Teppen

first: Hu

last: Li

first: Syed

last: Hashsham

first: Stephen

last: Boyd

first: James

last: Cole

middle: M

last: Tiedje


title: Ribosome profiling and RNA sequencing of MCF10A-ER-Src and fibroblast cell transformation

city: Chicago

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

summary: We applied ribosome profiling and RNA sequencing to examine gene expression regulation during oncogenic cell transformation. One model involves normal mammary epithelial cells (MCF10A) containing ER-Src. Treatment of such cells with tamoxifen rapidly induces Src, thereby making it possible to kinetically follow the transition between normal and transformed cells. The other model consists of three isogenic cell lines derived from primary fibroblasts in a serial manner (Hahn et al., 1999). EH cell is immortalized by overexpression of telomerase (hTERT), and exhibits normal fibroblast morphology. EL cell expresses hTERT along with both large and small T antigens of Simian virus 40, and it displays an altered morphology but is not transformed. ELR cell expresses hTERT, T antigens, and an oncogenic derivative of Ras (H-RasV12).

overall_design: Ribosome profiling and RNA sequencing in two cancer cell models

first: Ruisheng

last: Song

first: Aviv

last: Regev

first: Kevin

last: Struhl


title: Sucrose- and fructose-specific effects on the transcriptome of Streptococcus mutans probed by RNA-Seq

status: Public on Nov 12 2015

city: Gainesville

first: Lin

last: Zeng

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: For Streptococcus mutans, the major etiologic agent of human dental caries, sucrose is the carbohydrate that contributes in the most significant manner to establishment, persistence and virulence of the organism. However, because this organism produces multiple extracellular sucrolytic enzymes that can release hexoses from sucrose, it has not been possible to study the specific effects of sucrose transport and metabolism on gene expression in the absence of carbohydrates that by themselves can elicit catabolite repression and induce expression of multiple genes. Employing RNA deep sequencing (RNA-Seq) technology and mutants that lacked particular sucrose-metabolizing enzymes, we compared the transcriptomes of S. mutans growing on glucose, fructose or sucrose as the sole carbohydrate. The results provide a variety of new insights into the impact of sucrose transport and metabolism by S. mutans, including the likely expulsion of fructose after sucrose internalization and hydrolysis, and identified a set of genes that are differentially regulated by sucrose versus fructose. The findings significantly enhance our understanding of the genetics and physiology of this cariogenic pathogen.

overall_design: mRNA profiling of a set of mutants lacking secreted sucrolytic enzymes, growing on media supported solely by glucose, fructose or sucrose.

first: Robert

last: Burne


title: miRNA-target chimeras identified with CLEAR-CLIP reveal miRNA 3' end pairing as a major determinant of Argonaute binding in vivo [mouse cortex CLEAR-CLIP]

first: Michael

middle: John

last: Moore

first: Troels

last: Scheel

first: Charles

last: Rice

last: Darnell


title: Study of the impact of G9a on DNA methylation in mouse embryonic cells [seq]

city: Illkirch

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

summary: We explored the role of the lysine-methyltrasferase G9a in the control of DNA methylation during mouse embryogenesis. We provide maps of cytosine methylation by MeDIP and RRBS in G9a-deficient mouse embryos and ES cells, as well as ChIP-Seq profiles for H3K9me2 in embryos and RNA-Seq expression profiles in G9a-deficient embryos.

overall_design:
We prepared RRBS libraries from single embryos and mapped DNA methylation by RRBS in four WT and three G9aKO E8.5 embryos.
We prepared RNA-Seq libraries from RNAs of single embryos and mapped the transcriptome of two WT and two G9aKO E8.5 embryos.
We prepared H3K9me2 ChIP-Seq libraries from three independant ChIP experiments on eight pooled E8.5 embryos.


title: Chromatin dynamics and the RNA exosome function in concert to regulate transcriptional homeostasis

first: Craig

last: Peterson

state: MASSACHUSETTS

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

type: Expression profiling by genome tiling array


title: Methylome analysis of deoxyadenosines in higher eukaryotes

city: Cambridge

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: Here, we report that we detected N-6-methyl-deoxyadenosine (dA6m) not only in frog DNA, but also in other species including mouse and humans. Our methylome analysis revealed that dA6m is widely distributed across the eukaryotic genome, and it is present in different cell types. dA6m is commonly depleted in gene exons, whilst it remains abundant in introns. Finally, we have identified the putative consensus sequence, where there is preferential methylation. Since dA6m is a direct modification of DNA, it has the potential to generate a significant impact on different biological areas. Ultimately, our work shows that deoxycytidine modifications might not be the only ones in higher eukaryotes, suggesting that DNA alterations might be more widespread than previously thought.

sample_organism:
Escherichia coli
Xenopus laevis
Mus musculus

overall_design: Determining regions of deoxyadenosine methylation in  M. musculus kidney and X. laevis fat, oviduct and testes

first: Magdalena

last: Koziol

middle: R

first: George

middle: E

last: Allen

first: Ana

last: Costa

first: Christian

last: Frezza

first: John

last: Gurdon


title: A spectral analysis approach to detects actively translated open reading frames in high resolution ribosome profiling data

first: Neelanjan

last: Mukherjee

department: BMG/RBI

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA sequencing protocols allow for quantifying gene expression regulation at each individual step, from transcription to protein synthesis. Ribosome Profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. Despite its great potential, a rigorous statistical approach to identify translated regions from Ribo-seq data is not yet available. To fill this gap, we developed RiboTaper, which quantifies the significance of the three-nucleotide periodicity of Ribo-seq reads via spectral analysis methods.

overall_design: Examination of RNA fragments protected by ribosome


title: Chromatin dynamics and the RNA exosome function in concert to regulate transcriptional homeostasis (ChIP-seq)

summary: The histone variant H2A.Z is a hallmark of nucleosomes flanking the promoters of protein coding genes, and is often found in nucleosomes that also carry lysine 56- acetylated histone H3 (H3-K56Ac), a mark which promotes rapid replication- independent turnover of nucleosomes. Although H2A.Z and H3-K56Ac have been generally implicated in transcriptional activation, their exact contributions have remained elusive. Here we find that H3-K56Ac promotes RNA polymerase II occupancy at a large number of protein coding and noncoding loci, yet neither H3- K56Ac nor H2A.Z has a significant impact on steady state mRNA levels in yeast. Instead, broad effects of H3-K56Ac or H2A.Z on levels of both coding and noncoding RNAs (ncRNAs) are only revealed in the absence of the nuclear RNA exosome. H2A.Z is also necessary for expression of divergent, promoter-proximal ncRNAs in mouse embryonic stem cells, suggesting a conserved role for H2A.Z across eukaryotes. Finally, we show that H2A.Z functions with H3-K56Ac in chromosome folding, facilitating formation of chromosome interaction domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA expression, perhaps in part by regulating higher order chromatin structures.

overall_design: 2 replicates of WT (CY1089), rtt109∆ (CY2210), rrp6∆ (CY2071) and one replicate of the W303 input (Sample 7). TableS5.xlsx contains the processed IP/input values for each ORF transcript.


title: Host-virus transcriptome dynamics determined from RNA-sequencing

first: Shany

last: Doron

department: Department of Molecular Genetics

institute: Weizmann Institute of Science,

summary: Cyanobacteria are highly abundant in the oceans and are constantly exposed to lytic viruses. The T4-like cyanomyoviruses are abundant in the marine environment and have broad host ranges relative to other cyanophages. It is currently unknown whether broad-host-range phages specifically tailor their infection program for each host, or employ the same program irrespective of the host infected. Also unknown is how different hosts respond to infection by the same phage. Here we used microarray and RNA-seq analyses to investigate the interaction between the Syn9 T4-like cyanophage and three phylogenetically, ecologically and genomically distinct marine Synechococcus strains: WH8102, WH7803 and WH8109. Strikingly, Syn9 led a nearly identical infection and transcriptional program in all three hosts. Different to previous assumptions for T4-like cyanophages, three temporally regulated gene expression classes were observed. Furthermore, a novel regulatory element controlled early gene transcription, and host-like promoters drove middle gene transcription, different to the regulatory paradigm for T4. Similar results were found for the P-TIM40 phage during infection of Prochlorococcus NATL2A. Moreover, genomic and metagenomic analyses indicate that these regulatory elements are abundant and conserved among T4-like cyanophages. In contrast to the near-identical transcriptional program employed by Syn9, host responses to infection involved host-specific genes primarily located in hypervariable genomic islands, substantiating islands as a major axis of phage-cyanobacteria interactions. Our findings suggest that the ability of broad host-range phages to infect multiple hosts is more likely dependent on the effectiveness of host defense strategies than on differential tailoring of the infection process by the phage.

sample_organism:
Synechococcus sp. WH 7803
Parasynechococcus marenigrum WH 8102
Synechococcus sp. WH 8109

overall_design: We investigated the transcriptional program of the Syn9 cyanophage during infection of three Synechococcus hosts (strains WH7803, WH8102 and WH8109) at different times after infection using whole transcriptome RNA sequence libraries. Four time points (5 min and 0.5, 1 and 2 h after infection) from two biological replicates of each of the three hosts were analyzed for a total of 24 samples. Pooled replicates of one of the infected Synechococcus hosts from 3 time points (0.5, 1 and 2 h after infection) were used for bisulfite strand-specific libraries (for a total of 3 samples). For 5?-end sequencing, Tobacco Acid Pyrophosphatase (TAP) treated libraries were prepared from two biological replicates for time points 0.5, 1 and 2 h after infection for a total of 18 samples. Untreated libraries were similarly prepared for one replicate of each infected host for a total of 9 libraries. All RNA-sequencing libraries were sequenced using the Illumina HiSeq platform at the Weizmann Institute.

first: Ayalla

last: Fedida

first: Iris

last: Karunker

first: Debbie

last: Lindell

first: Rotem

last: Sorek


title: Genome-wide analysis of HoxBlinc lncRNA downstream targets in mouse ESC-derived embryonic bodies

status: Public on Nov 11 2015

first: Lei

last: Zhou

department: Molecular Genetics and Microbiology

summary: We find a new non-coding transcript associated with active HoxB locus, which we named HoxBlinc lncRNA.  We report that HoxBlinc RNA  specifies Flk1+ mesoderm and then promotes the development of HS/PCs and cardiomyocytes. To understand the molecular pathways reguated by HoxBlinc, we generate two doxycycline inducible  KD ES R1E cell lines,  then differentiate these cell lines to day 6 via embryonic bodies stage. RNA-seq analysis were performed for day 6 EBs with or without doxycycline treatment starting at Flk1+ mesodermal stage.

overall_design: RNA from day 6 EBs targeting with 2 invidiual shRNAs with or without doxycycline treatment were combined together for RNA-seq analysis.

first: Changwang

last: Deng

first: Ying

last: Li

first: Joonseok

last: Cho

first: Bhavita

last: Patel

first: Nao

last: Terada

first: Yangqiu

first: Jörg

last: Bungert

first: Yi

last: Qiu

first: Suming

last: Huang


title: Revealing suspension adapation of CHO cell in serum free media

city: Daejeon

first: Namil

last: Lee

address: Daehakro

department: Biological science

country: South Korea

institute: KAIST

summary:
Purpose : We performed strand-specific RNA-seq analysis of CHO cells according to adaptation trajectory to identify the specific genes responded to the suspension adaptation.
Result : Cell growth, replication, and nucleotide metabolism categories were enriched in up regulated clusters whereas cellular community category which contains focal adhesion related genes were enriched in down regulated clusters

overall_design: CHO-K1 mRNA profiles during suspension adaptation generated by RNA sequencing, in duplicate, using Illumina MiSeq.

first: Jongoh

last: Shin

first: Suhyung

first: Byung-Kwan


title: Global Trabscriptome Analaysis Reveals that Poly(ADP-Ribose) Polymerase 1 Regulates Gene Expression through EZH2

city: Philadelphia

first: Italo

last: Tempera

state: PA

address: 3307 N. Broad Street, PAHB, Room 206

department: Fels Institute

institute: Temple University

summary: Post-translational modifications, such as poly(ADP-ribosyl)ation (PARylation), regulate chromatin-modifying enzymes, ultimately affecting gene expression. This study explores the role of poly(ADP-ribose) polymerase (PARP) on global gene expression in a lymphoblastoid B cell line. We found that inhibition of PARP catalytic activity with olaparib resulted in global gene deregulation, affecting approximately 11% of genes expressed. Gene ontology analysis revealed that PARP could exert these effects through transcription factors and chromatin-remodeling enzymes, including the Polycomb Repressive Complex 2 (PRC2) member EZH2. EZH2 mediates the trimethylation of histone H3 at lysine 27 (H3K27me3), a modification associated with chromatin compaction and gene silencing. Both pharmacological inhibition of PARP and knockdown of PARP1 induced the expression of EZH2 that resulted in increased global H3K27me3. Chromatin immunoprecipitation confirmed that PARP1 inhibition led to H3K27me3 deposition at EZH2-target genes, which resulted in gene silencing. Moreover, increased EZH2 expression is attributed to occupancy loss of the transcription repressor E2F4 at the EZH2 promoter following PARP inhibition. Together, these data show that PARP plays an important role in global gene regulation and identifies for the first time a direct role of PARP1 in regulating the expression and function of EZH2.

overall_design: Examination of the effect of PARP inhibition on global gene expression in LCLs cell lines. mRNA profiles of LCLs cells lines treated at different time points with olaparib were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Kayla

last: Martin


title: Host-virus transcriptome dynamics

first: Shany

last: Doron

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

sample_organism:
Synechococcus sp. WH 7803
Prochlorococcus marinus str. NATL2A
Parasynechococcus marenigrum WH 8102
Synechococcus sp. WH 8109

platform_organism:
Synechococcus sp. WH 7803
Parasynechococcus marenigrum WH 8102
Synechococcus sp. WH 8109
Synechococcus phage syn9
Cyanophage P-TIM40

overall_design: Refer to individual Series


title: Diverse and Targetable Kinase Alterations Drive Histiocytic Neoplasms

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Histiocytic neoplasms are clonal, hematopoietic disorders characterized by an accumulation of abnormal, monocyte-derived dendritic cells or macrophages in Langerhans Cell (LCH) and non-Langerhans (non-LCH) histiocytoses, respectively. The discovery of BRAFV600E mutations in ~50% of these patients provided the first molecular therapeutic target in histiocytosis. However, recurrent driving mutations in the majority of BRAFV600E-wildtype, non-LCH patients are unknown, and recurrent cooperating mutations in non-MAP kinase pathways are undefined for the histiocytic neoplasms. Through combined whole exome and transcriptome sequencing, we identified recurrent kinase fusions involving BRAF, ALK, and NTRK1, as well as recurrent, activating MAP2K1 and ARAF mutations in BRAFV600E-wildtype, non-LCH patients. In addition to MAP kinase pathway lesions, recurrently altered genes involving diverse cellular pathways were identified. Treatment of MAP2K1- and ARAF-mutated, non-LCH patients using MEK and RAF inhibitors, respectively, resulted in clinical efficacy demonstrating the importance of detecting and targeting diverse kinase alterations in these disorders.

overall_design: 13 patient samples were analyzed by RNA-seq and had 2 replicates.

first: Omar

last: Abdel-Wahab


title: A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University


title: Expression profile of mouse carotid body and adrenal medulla

city: Stanford

first: Mark

last: Krasnow

state: CA

address: 279 Campus Dr

institute: Stanford School of Medicine


title: Whole-body transcriptomics of Nasonia vitripennis females as they respond to sex allocation cues

city: St. Andrews

first: David

last: Shuker

address: Greenside Place

department: School of Biology

institute: University of St Andrews

summary: Linking the evolution of the phenotype to the underlying genotype is a key aim of evolutionary genetics and is crucial to our understanding of how natural selection shapes a trait. Here we consider the genetic basis of sex allocation behaviour in the parasitoid wasp Nasonia vitripennis using a transcriptomics approach. Females allocate offspring sex in line with Local Mate Competition (LMC) theory. Female-biased sex ratios are produced when one or few females lay eggs on a patch. As the number of females contributing offspring to a patch increases, less female-biased sex ratios are favoured. We contrasted the transcriptomic responses of females as they oviposit under conditions known to influence sex allocation: foundress number (a social cue) and the state of the host (parasitised or not). We found, that when females encounter other females on a patch, or assess host quality with their ovipositors, the resulting changes in sex allocation is not associated with significant changes in whole-body gene expression. We also found that the gene expression changes produced by females, as they facultatively allocate sex in response to a host cue and a social cue, are very closely correlated. We expanded the list of candidate genes associated with oviposition behaviour in Nasonia, some of which may be involved in fundamental processes underlying the ability to facultatively allocate sex, including sperm storage and utilisation.

overall_design: 2 x 3 factorial design. Females were placed into 1 of 2 "foundress number" groups: 1) alone or 2) in the presence of 9 other females (co-foundresses). Females were further subdivided into host treatment groups: i) given no host, ii) given a fresh host and iii) given a pre-parasitised host. This gives a total of 6 possible treatment combinations. For each of these 6 groups, 7 pools of 10 females were sequenced giving 42 libraries altogether.

first: Nicola

last: Cook

first: Eran

last: Tauber

first: Michael

middle: G

last: Ritchie

first: Bart

last: Pannebakker


title: The glucose-sensing transcription factor MLX promotes myogenesis via myokine signaling

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Metabolic stress and changes in nutrient levels modulate many aspects of skeletal muscle function during aging and disease. Growth factors and cytokines secreted by skeletal muscle, known as myokines, are important signaling factors but it is largely unknown whether they modulate muscle growth and differentiation in response to nutrients. Here, we find that changes in glucose levels increase the activity of the glucose-responsive transcription factor MLX, which promotes and is necessary for myoblast fusion. MLX promotes myogenesis not via an adjustment of glucose metabolism but rather by inducing the expression of several myokines, including insulin like-growth factor-2 (IGF2), whereas RNAi and dominant-negative MLX reduce IGF2 expression and block myogenesis. This phenotype is rescued by conditioned media from control muscle cells and by recombinant IGF2, which activates the myogenic kinase Akt. Importantly, MLX null mice display decreased IGF2 induction and diminished muscle regeneration in response to injury, indicating that the myogenic function of MLX is conserved in vivo. Thus, glucose is a signaling molecule that regulates myogenesis and muscle regeneration via MLX/IGF2/Akt signaling. The data pproided are histome H4 acetlation data for MLX DN and MLX wt samples;

overall_design: 3 MLX DN H4 Ac Chip seq samples , 3 Inputs, 3 MLX WT H4 Ac samples and 3 WT inputs

first: Liam

last: Hunt

first: Beisi

last: Xu

first: Yiping

last: Fan

first: Patrick

middle: A

last: Caroll

first: Pei-Fang

last: Cheng

first: Robert

middle: N

last: Eisenman

first: Fabio

last: Demontis


title: Expression profile of mouse carotid body and adrenal medulla [RNA-Seq]

summary: The carotid body is a chemoreceptor that senses decreases in blood oxygen to increase breathing in hypoxia. To look for candidate oxygen sensors in the carotid body, we compared the gene expression of the carotid body to the adrenal medulla, a similar tissue that does not have oxygen sensitivity in adults.

overall_design: For each sample, we pooled 18 carotid bodies and 10 adrenal medullas from 10 adult mice.

first: Andy

last: Chang

first: Fabian

last: Ortega


title: Divergent residues within histone H3 define a unique chromatin structure in S. cerevisiae

status: Public on Nov 10 2015

city: Vancouver

first: Benjamin

last: Martin

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

institute: UBC

summary: Histones are among the most conserved proteins known, but organismal differences do exist. In this study we examined the contribution that divergent amino acids within histone H3 make to cell growth and chromatin structure in S. cerevisiae. We show that, while amino acids that define histone H3.3 are dispensable for yeast growth, substitution of residues within the histone H3 alpha 3 helix with the human counterparts results in a severe growth defect. Mutations within this domain also result in altered nucleosome positioning, both in vivo and in vitro, which is accompanied by increased preference for nucleosome favoring sequences. These results suggest that divergent amino acids within the histone H3 alpha 3 helix play organismal roles in defining chromatin structure.

overall_design: Mnase-seq for two replicates each of wildtype and H3 c-terminal mutants.

first: LeAnn

last: Howe

first: Kristina

last: McBurney


title: UV-B-induced gene expression changes in Chlamydomonas reinhardtii

city: Geneva 14

first: PIerre

last: Burkhard

address: 4 rue Gabrielle-Perret-Gentil

department: Department of Clinical Neurosciences

institute: HUG

summary: We analysed global gene expression changes in Chlamydomonas reinhardtii in response to 1h UV-B, applied at the same low level that was seen to promote subsequent UV-B stress tolerance, in order to elucidate the transcriptional reprogramming that leads to UV-B acclimation.

overall_design: mRNA profiles generated by deep sequencing from triplicate replicate Chlamydomonas reinhardtii samples sourced from independent cultures either protected from UV-B or exposed to 1h acclimation-level UV-B.

first: Kimberley

last: Tilbrook

first: Roman

last: Ulm


title: Combined loss of Tet1 and Tet2 promotes B-cell, but not myeloid malignancies in mice

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

summary: TET1/2/3 are methylcytosine dioxygenases regulating cytosine hydroxymethylation in the genome. Tet1 and Tet2 are abundantly expressed in HSC/HPCs and implicated in the pathogenesis of hematological malignancies. Tet2-deletion in mice causes myeloid malignancies, while Tet1-null mice develop B-cell lymphoma after an extended period of latency. Interestingly, TET1 and TET2 were often concomitantly down-regulated in acute B-lymphocytic leukemia. Here, we investigated the overlapping and non-redundant functions of Tet1/Tet2 in HSC maintenance and development of hematological malignancies using Tet1/2 double knockout (DKO) mice. DKO and Tet2-/- HSC/HPCs had overlapping and unique 5hmC and 5mC profiles and behaved differently. DKO mice exhibited strikingly decreased incidence and delayed onset of myeloid malignancies compared to Tet2-/- mice and in contrast developed lethal B-cell malignancies. Transcriptome analysis of DKO tumors revealed expression changes in many genes dysregulated in human B-cell malignancies, such as LMO2, BCL6 and MYC. These results highlight the critical roles of TET1 or TET2 individually and their cross-talks in the pathogenesis of hematological malignancies.

overall_design: Given the role of Tet proteins in 5mC oxidation, we employed a previously established chemical labeling and affinity purification method coupled with high-throughput sequencing (hMe-Seal) to profile the genome-wide distribution of 5hmC, as well as methylated DNA immunoprecipitation (MeDIP) coupled with high-throughput sequencing (MeDIP-seq) to profile 5mC using BM LK cells purified from young WT, Tet2-/- and DKO mice (6-10 wks old).

first: Mingjiang


title: The direction of cross affects obesity after puberty in male but not female offspring

city: Berlin

first: Gudrun

last: Brockmann

address: Invalidenstraße 42

department: Züchtungsbiologie und molekulare Tierzüchtung

country: Germany

institute: Humboldt-Universität zu Berlin

summary: We investigated parent-of-origin and allele-specific expression effects on obesity and hepatic gene expression in reciprocal crosses between the Berlin Fat Mouse Inbred line (BFMI) and C57Bl/6NCrl (B6N). We sequenced mRNA extracted from liver tissue of 10 M. Musculus individuals. 4 liver samples were collected from 10 week old inbred strains (1 male and 1 female Berlin Fat Mouse Inbred line (BFMI), 1 male and 1 female C57Bl/6NCrl (B6N)) and 6 liver samples collected from 10 week old F1 males using a reciprocal cross design (3 paternal BFMI (patBFMI) vs 3 maternal BFMI (matBFMI)).

overall_design: Reciprocal crosses were generated from the Berlin Fat Mouse Inbred line BFMI860-12/Hber (BFMI) and C57BL/6NCrl (B6N). Seven BFMI males were mated with seven B6N females and six B6N males with six BFMI860 females to generate 48 F1 animals (deemed patBFMI and matBFMI, respectively). Each reciprocal F1 offspring groups consisted of 12 males and 12 females. From these animals three F1 males from three BFMI females and three F1 males from three B6N females were used for RNA-seq measurements. One high fat diet raised male and female from each inbred parental strain (BFMI and B6N) were used as parental strain control animals and measured via RNA-seq as well.

first: Stefan

last: Kärst

first: Danny

last: Arends

first: Sebastiaan

last: Heise

first: Jan

last: Trost

first: Marie-Laure

last: Yaspo

first: Vyacheslav

last: Amstislavskiy

first: Thomas

last: Risch

first: Hans

last: Lehrach


title: HCT116 cells treated with the p97 inhibitior CB-5083

status: Public on Nov 09 2015

city: Burlingame

first: Stevan

middle: Nicholas

last: Djakovic

state: California

address: 866 Malcolm Rd #100

department: Biology

institute: Cleave Biosciences

summary: The goal of this study was to analyze differential gene expression 8 hr after treatment of CB-5083, a small molecule inhibitor of p97 (VCP), in HCT116 cells grown in culture.

overall_design: DMSO treated cells were compared to cells treated with 1uM CB-5083 after 8 hr.

first: Daniel

last: Anderson


title: Pancreatic Beta Cell Enhancers Regulate Rhythmic Transcription of Exocyst Triggering and Diabetes

first: Mark

last: Perelis

state: IL

address: 303 E Superior Street Lurie Research Center Rm 7-220

institute: Northwestern University


title: Genome-wide Circadian Control of Transcription at Active Enhancers Regulates Insulin Secretion and Diabetes Risk

summary: The molecular clock is a transcriptional oscillator present in brain and peripheral cells that coordinates behavior and physiology with the solar cycle. Here we reveal that the clock gates insulin secretion through genome-wide transcriptional control of the pancreatic exocyst across species. Clock transcription factors bind to unique enhancer sites in cycling genes in beta cells that diverge from those in liver, revealing the dynamics of inter-tissue clock control of genomic and physiologic processes important in glucose homeostasis.

overall_design: Transcriptome profiling in mouse and human islets at serial 4-hour time intervals by polyA RNA-Seq

first: Biliana

last: Marcheva

first: Grant

middle: D

last: Barish

first: Joseph

last: Bass


title: Pancreatic Beta-Cell Enhancers Regulate Rhythmic Transcription of Exocyst Triggering and Diabetes [ChIP-seq]

overall_design: ChIP-Seq in Beta-TC6 mouse beta cells


title: Loss of histone demethylase JARID1C triggers genomic instability in cancer.

city: Milano

first: Davide

last: Cittaro

address: via Olgettina 58

department: Center for Traslational Genomics and Bioinformatics

country: Italy

institute: Ospedale San Raffaele

summary: Chromatin remodelers are recurrently mutated in cancer. Among these, JARID1C, (KDM5C) a histone demethylase, is frequently inactivated in clear cell renal cell carcinoma (ccRCC) patients. How the genetic inactivation of JARID1C leads to cancer remains largely unknown. Here we report that JARID1C binds to broad chromatin domains characterized by the trimethylation of lysine 9 (H3K9me3), an histone mark enriched in heterochromatin. We also found that JARID1C localizes on heterochromatin, is required for heterochromatin replication, and forms a complex with established and novel players of heterochromatin assembly, such as SUV39H1 and HP1 and the CUL4 complex adaptor protein DDB1, respectively. To safeguard the genome, transcription on heterochromatin is tightly suppressed. JARID1C inactivation leads to the unrestrained expression of heterochromatic ncRNAs, that in turn trigger genomic instability. Remarkably, ccRCC patients harbouring JARID1C mutations show aberrant ncRNA expression and increased genomic rearrangements when compared with tumors endowed with other genetic lesions. Together, these data suggest that the inactivation of JARID1C in renal cancer leads to heterochromatin disruption and to aggressive, genomically rearranged ccRCCs, shedding light on a novel mechanism underlying genomic instability in sporadic cancers.

overall_design: We performed ChIP-sequencing for KDM5C, H3K9me3, H3K4me1 and H3K4me3 in Caki-1 untreated cells. Platform  HiSeq2500.

first: Beatrice

last: Rondinelli

first: Dalia

last: Rosano

first: Elena

last: Antonini

first: Michela

last: Frenquelli

first: Laura

last: Montanini

first: DaChuan

last: Huang

first: Simona

last: Segalla

first: Kosuke

last: Yoshihara

first: Samir

last: Amin

first: Dejan

last: Lazarevic

first: Bin

middle: T

last: The

first: Roel

middle: W

last: Verhaak

first: PAndrew

last: Futreal

first: Luciano

last: Di Croce

first: Lynda

last: Chin

first: Giovanni

last: Tonon


title: Study of the impact of G9a on DNA methylation in mouse embryonic cells

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

institute: CNRS

type: Methylation profiling by genome tiling array


title: Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation

city: Bethesda

first: Alan

middle: G.

last: Hinnubusch

address: 6 Center Dr. Bldg 6, Rm 230

institute: NICHD

summary: Chaperones, nucleosome remodeling complexes and histone acetyltransferases have been implicated in nucleosome disassembly at promoters of particular yeast genes, but whether these co-factors function ubiquitously, and the impact of nucleosome eviction on transcription genome-wide, are poorly understood. We used chromatin immunoprecipitation of histone H3 and RNA polymerase II (Pol II) in mutants lacking single or multiple co-factors to address these issues for ~200 genes belonging to the Gcn4 transcriptome, of which ~70 exhibit marked reductions in H3 promoter occupancy on induction by amino acid starvation.  Examining four target genes in a panel of mutants indicated that SWI/SNF, Gcn5, the Hsp70 co-chaperone Ydj1, and chromatin-associated factor Yta7 are required downstream of Gcn4 binding for robust H3 eviction in otherwise wild-type cells. Using ChIP-seq to interrogate all 70 exemplar genes in single, double and triple mutants implicated Gcn5, Snf2 and Ydj1 in H3 eviction at most, but not all Gcn4 target promoters, with Gcn5 generally playing the greatest role and Ydj1 the least. Remarkably, these 3 co-factors cooperate similarly in H3 eviction at virtually all yeast promoters. Defective H3 eviction in co-factor mutants was coupled with reduced Pol II occupancies for the Gcn4 transcriptome and the most highly expressed uninduced genes, but the relative Pol II levels at most genes were unaffected or even elevated. These findings indicate that nucleosome eviction is crucial for robust transcription of highly expressed genes, but that other steps in gene activation are more rate-limiting for most other yeast genes.

overall_design: Chromatin immunoprecipitated DNA from WT (induced(+SM) and uninduced(no SM)) and mutants (induced(+SM)) followed by paired-end sequencing. Nucleosomal DNA obtained by MNase digestion were also subjected to paired-end sequencing.

first: Hongfang

last: Qiu

first: R

last: Chereji

first: Cuihua

last: Hu

first: H

last: Cole

first: Y

last: Rawal

first: D

last: Clark

first: A

last: Hinnebusch


title: A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases (ChIP-Seq)

first: Danuta

last: Gawel

summary: For the purpose of the Gene Regulatory Network validation we have performed chromatin-immunoprecipitation sequencing (ChIP-Seq) experiment for three transcription factors; namely GATA3, MAF and MYB.

overall_design: ChIP-Seq of GATA3, MAF and MYB in human naïve CD4+ T-cells differentiated toward Th1 and Th2 until day 6. Matched INPUT samples were also sequenced for each condition.

first: Mika

last: Gustafsson

first: Lars

last: Alfredsson

first: Sergio

last: Baranzini

first: Janne

last: Björkander

first: Robert

last: Blomgran

first: Sandra

last: Hellberg

first: Daniel

last: Eklund

first: Jan

last: Ernerudh

first: Ingrid

last: Kockum

first: Aelita

last: Konstantinell

first: Riita

last: Lahesmaa

first: Antonio

last: Lentini

last: Liljenström

first: Lina

last: Mattson

first: Andreas

last: Matussek

first: Johan

last: Mellergård

first: Melissa

last: Mendez

first: Tomas

last: Olsson

first: Miguel

last: Pujana

first: Omid

last: Rasool

first: Jordi

last: Serra-Musach

first: Margaretha

last: Stenmarker

first: Subhash

last: Tripathi

first: Miro

last: Viitala

first: Hui

last: Wang

first: Huan

last: Zhang

first: Colm

last: Nestor

first: Mikael

last: Benson


title: Genome-wide DNA methylation change due to lncRNA H19 knockdown in myotubes

city: Farmington

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

summary: We used Methyl-MiniSeq platform from Zymo Research company to identify genome-wide methylation changes affected by lncRNA H19 knockdown in myotubes. Following H19 knockdown, we observed extensive genome-wide mthylation pattern changes relative to siCon cells, with some genes showing incresed methylation, others showing decreased methylation, and a third group with no significant change.

overall_design: Myotubes differentiated from mouse C3H myoblasts were transfected with either control siRNA or siH19, 48h later, cellular genomic DNA was extracted and subjected to genome-scale DNA methylation mapping using the platform of an improved version of Reduced Representation Bisulfite Sequencing (RRBS).

first: Karolyn

last: Giang

first: Hunter

last: Chung

first: Xueguang

last: Sun


title: Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [additional 4C]

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: Upon recruitment to active enhancers and promoters, RNA polymerase II (Pol_II) generates short non-coding transcripts of unclear function. The mechanisms that control the length and the amount of ncRNAs generated by cis-regulatory elements are largely unknown. Here, we show that the adapter protein WDR82 and its associated complexes actively limit such non-coding transcription. WDR82 targets the SET1/COMPASS H3K4 methyltransferase and the nuclear Protein Phosphatase 1 (PP1) complexes to the initiating Pol_II. WDR82 and PP1 also interact with components of the transcriptional termination and RNA processing machineries. Depletion of WDR82, SET1 or the PP1 subunit required for its nuclear import caused distinct but overlapping transcription termination defects at highly expressed genes, active enhancers and promoters, thus enabling the increased synthesis of unusually long ncRNAs. These data indicate that transcription initiated from cis-regulatory elements is tightly coordinated with termination mechanisms that impose the synthesis of short RNAs.

overall_design: 4C-seq was performed on four different viewpoints (either at the 5' or the 3' of the Mpeg1 and Lgals3 genes, indicated as sx or dx, respectively) in BMDMs. Experiments were carried out in cells containing either a short hairpin targeting Wdr82 or a scrambled as a control.

first: Liv

last: Austenaa

first: Marta

last: Simonatto

first: Silvia

last: Masella

first: Giulia

last: Della Chiara

first: Serena

last: Ghisletti

first: Alessia

last: Curina

first: Elzo

last: de Wit

first: Britta

last: Bouwman

first: Stefano

last: de Pretis

first: Viviana

last: Piccolo

first: Alberto

last: Termanini

first: Elena

last: Prosperini

first: Mattia

last: Pelizzola

first: Wouter

last: de Laat

first: Gioacchino

last: Natoli


title: Genome-wide DNA-methylation and transcriptome change due to lncRNA H19 knockdown in myotubes

last: Zhang

overall_design: Refer to individual Series


title: Enhancers reside in a unique epigenetic environment during early development

city: Los Angeles

first: Andrew

last: Smith

address: 1050 Childs Way

department: Molecular and Computational Biology

institute: University of Southern California

summary: During development and differentiation, enhancers, and not promoters are most dynamic in their DNA methylation status. However, the causal relationship between enhancer activity and methylation is not clear. Here, we describe that during early zebrafish development, enhancer activity has little influence on DNA methylation, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the maternal-zygotic transition (MZT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity. In conclusion, we demonstrate that early development in zebrafish represents a time-window characterized by non-canonical DNA methylation-enhancer relationships, including global DNA hypo-methylation of inactive enhancers and DNA hyper-methylation of active enhancers.

overall_design: DNA methylation profiles of 4 time points during zebrafish early development.

first: Lucas

last: Kaaij

first: Michal

last: Mokry

first: Meng

last: Zhou

first: Michael

last: Musheev

first: Geert

last: Geeven

first: Adrien

last: Melquiond

first: Christof

last: Niehrs

first: René

last: Ketting


title: RNA sequencing of Control, ΔCop1β, ΔCop1β and ΔCop1β ΔETV1/4/5β islets

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

address: 1 DNA Way

institute: Genentech

summary: Identify genes which are differentially expressed in ΔCop1β compared to control islets and are also  signficantly rescued in ΔCop1Β ΔETV1/4/5β

overall_design: Islets were harvested from 5 biological replicates of the followig genotypes: Control, ΔCop1β and ΔCop1Β ΔETV1/4/5β. Islets were individually handpicked and total RNA was isolated and purified for library preperation and Next Generation Sequencing.

first: Rowena

last: Suriben


title: Transcriptome analysis of sexual dimorphism in the somatic gonadal precursor cells of Caenorhabditis elegans

city: Minneapolis

first: Mary

middle: B

last: Kroetz

state: MN

address: 515 Delaware St SE, 5-143 Moos Tower

department: Genetics, Cell Biology & Development

institute: University of Minnesota

summary: The Caenorhabditis elegans somatic gonad was the first organ to have its cell lineage determined, and the gonadal lineages of the two sexes differ greatly in their pattern of cell divisions, cell migration and cell types. Despite much study, the genetic pathways that direct early gonadal development and establish its sexual dimorphism remain largely unknown, with just a handful of regulatory genes identified from genetic screens. To help define the genetic networks that regulate gonadal development, we employed cell-specific RNA-seq. We identified transcripts present in Z1/Z4 or Z1/Z4 daughter cells in each sex at the onset of somatic gonadal sexual differentiation. For comparison, transcripts were identified in whole animals at both time points. Pairwise comparisons of samples identified several hundred gonad-enriched transcripts, including most known Z1/Z4-enriched mRNAs, and reporter analysis confirmed the effectiveness of this approach. Prior to the Z1/Z4 division few sex-biased Z1/Z4 transcripts were detectable, but less than six hours later, we identified more than 250 sex-biased transcripts in the Z1/Z4 daughters, of which about a third were enriched in the somatic gonad cells compared to cells from whole animals. This indicates that a robust sex-biased developmental program, some of it gonad-specific, initiates in these cells around the time of the first Z1/Z4 division. Cell-specific analysis also identified approximately 70 previously unannotated mRNA isoforms that are enriched in Z1/Z4 or their daughters. Our data suggest that early sex differentiation in the gonad is controlled by a relatively small suite of differentially expressed genes, even after dimorphism has become apparent.

overall_design: 20 total sample: two time points, two sexes, and gonadal cells or whole animals. The earlier time point was collected in triplicate and was harvested 9.5 hours after starved, hatched L1s were fed. The later time point was collected in duplicate and was harvested 15 hour after starved, hatched L1 were fed. Replicates of either dissociated whole animals or gonadal cells (Z1/Z4 or Z1/Z4 daughter) from both male and hermaphrodites were harvested for each time point.

first: David

last: Zarkower


title: Insight into the role of thyroid hormone on neocortex development through global transcriptome analysis of primary cerebrocortical cells: Identification of genes regulated directly and indirectly by triiodothyronine in specific cell types

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

summary: Thyroid hormones, thyroxine and triiodothyronine (T3) are crucial for cerebral cortex development acting through regulation of gene expression. To define the transcriptional program under T3 regulation we have performed RNA-Seq of T3-treated and untreated primary mouse cerebrocortical cells. The expression of 1,145 genes or 7.7% of expressed genes was changed upon T3 addition, of which 371 responded to T3 in the presence of cycloheximide indicating direct transcriptional regulation. The results were compared with available transcriptomic datasets of defined cellular types. In this way we could identify genomic targets of T3 in astrocytes and neurons, and in neuron subtypes, such as layer-specific neurons, and neurons expressing specific markers such as prepronociceptin, cholecystokinin, or cortistatin. T3 up-regulates mostly genes related to cell membrane events, such as G-protein signaling, neurotransmission, and ion transport, and down-regulates genes involved in nuclear events, such as cell division, M phase of cell cycle, and chromosome organization and segregation. Remarkably the transcriptomic changes induced by T3 sustain the transition from embryonic to adult patterns of gene expression. The results allowed us to define in molecular terms the elusive role of thyroid hormones on neocortical development.

overall_design: Pregnant dams were euthanized on gestational day 17.5, and the fetuses were extracted and euthanized by decapitation. The cerebral cortices were dissected, disaggregated and finally the cells were suspended in culture medium. After 9 days incubation cells were incubated for 24 hours before adding T3 at a final concentration of 10 nM. The cells were harvested 24 hours later. Cells without T3 were incubated in parallel. Cerebral cortices from individual fetuses originated two replicas for the cell culture, one with T3 and another without T3. Number of samples: 6.

first: Pilar

last: Gil-Ibañez

last: Garcia-Garcia

first: Joaquín

last: Dopazo

first: Juan

last: Bernal

first: Beatriz

last: Morte


title: Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: Early mouse development is accompanied by dynamic changes in chromatin modifications, including G9a-mediated histone H3 lysine 9 dimethylation (H3K9me2), which is essential for embryogenesis. Here we show that H3K9me2 directs repression of 2-cell stage specific genes in nascent embryos to facilitate preimplantation development. Thereafter, genome-wide accumulation of H3K9me2 is crucial for postimplantation development, and coincides with redistribution of EZH2-dependent histone H3 lysine 27 trimethylation (H3K27me3). Loss of G9a or EZH2 results in upregulation of distinct gene sets involved in processes such as cell cycle regulation as well as germline and embryonic development. Accumulation of H3K9me2 not only occurs at promoters and gene bodies, but also extends to active enhancer elements to promote their developmentally-linked silencing. This epigenetic mechanism is important for priming gene regulatory networks in epiblast cells undergoing rapid cell proliferation in preparation for critical cell fate decisions.

overall_design: Examination of 2 histone modification in 3 cell types and transcriptional analysis of G9a and Ezh2 KO epiblasts and Whole genome bisulfite sequencing in two cell types

first: Jan

last: Zylicz

first: Sabine

last: Dietmann

first: Ufuk

last: Günesdogan

first: Jamie

last: Hackett

first: Delphine

last: Cougot

first: Dang

middle: V

last: Do

first: Carolin

last: Lee

first: M

last: Surani


title: Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [Hi-C]

first: Iros

last: Barozzi

overall_design: Hi-C experiments on biological replicates of BMDMs

first: Liv

last: Austenaa

first: Marta

last: Simonatto

first: Silvia

last: Masella

first: Giulia

last: Della Chiara

first: Serena

last: Ghisletti

first: Alessia

last: Curina

first: Elzo

last: de Wit

first: Britta

last: Bouwman

first: Stefano

last: de Pretis

first: Viviana

last: Piccolo

first: Alberto

last: Termanini

first: Elena

last: Prosperini

first: Mattia

last: Pelizzola

first: Wouter

last: de Laat

first: Gioacchino

last: Natoli


title: Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [4C]

overall_design: 4C-seq was performed on two different viewpoints (TSSs of the genes Ccl2 and Jun) in BMDMs.


title: gene expression analysis in Pbx1; Emx1-cre mutant cortex at embryonic day

city: san francisco

first: olga

last: golonzhka

address: 1550 4th street

department: psychiatry

institute: UCSF

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


title: Developmental dynamics of C. elegans dosage compensation

city: New York

first: Sevinc

last: Ercan

state: NY

address: 12 Waverly Place

institute: New York University

summary: In Caenorhabditis elegans, the dosage compensation complex (DCC) specifically binds to and represses transcription from both X chromosomes in hermaphrodites. The DCC is composed of an X-specific condensin complex that interacts with several proteins. During embryogenesis, DCC starts localizing to the X chromosomes around the 40-cell stage, and is followed by X-enrichment of H4K20me1 between 100-cell to comma stage. Here, we analyzed dosage compensation of the X chromosome between sexes, and the roles of dpy-27 (condensin subunit), dpy-21 (non-condensin DCC member), set-1 (H4K20 monomethylase) and set-4 (H4K20 di-/tri-methylase) in X chromosome repression using mRNA-seq and ChIP-seq analyses across several developmental time points. We found that the DCC starts repressing the X chromosomes by the 40-cell stage, but X-linked transcript levels remain significantly higher in hermaphrodites compared to males through the comma stage of embryogenesis. Dpy-27 and dpy-21 are required for X chromosome repression throughout development, but particularly in early embryos dpy-27 and dpy-21 mutations produced distinct expression changes, suggesting a DCC independent role for dpy-21. We previously hypothesized that the DCC increases H4K20me1 by reducing set-4 activity on the X chromosomes. Accordingly, in the set-4 mutant, H4K20me1 increased more from the autosomes compared to the X, equalizing H4K20me1 level between X and autosomes. H4K20me1 increase on the autosomes led to a slight repression, resulting in a relative effect of X derepression. H4K20me1 depletion in the set-1 mutant showed greater X derepression compared to equalization of H4K20me1 levels between X and autosomes in the set-4 mutant, indicating that H4K20me1 level is important, but X to autosomal balance of H4K20me1 contributes only slightly to X-repression. Thus H4K20me1 by itself is not a downstream effector of the DCC. In summary, X chromosome dosage compensation starts in early embryos as the DCC localizes to the X, and is strengthened in later embryogenesis by H4K20me1.

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans

overall_design:
RNA-Seq profiles of C. elegans wild type hermaphrodite, mixed sex, at 5 time points and dpy-27, set-4, dpy-21, set-1 and RNAi at 2-3 time points with 3-4 replicates each.

RNA-Seq profiles of C. elegans. Strains are N2 (wild type), BS553 fog-2(oz40) V, CB428 dpy-21(e428) V, MK4 dpy-27(y56) III, MT14911 set-4 (n4600) II, SS1075 set-1(tm1821)/hT2g[bli-4(e937) let-?(q782) qIs48] (I;III). Set-1 collections made as heterozygotes and dpy-27(y56) homozygotes. Spike in RNA-seq libraries have AF16 wild type C. briggsae L1s added at a 1:10 ratio. Timepoints are early embryos (synchronized collection, <40 cells), comma embryos (synchronized early embryos aged for 4 hours), mixed embryos (mixed stage embryos from unsynchronized population), L1 (synchronized L1 larvae), L3 (synchronized L3 larvae), and YA (synchronized young adults, collected before embryos present in hermaphrodite gonad). Biological replicates for each strain/stage listed separately.

ChIP-seq profiles of C. elegans DCC subunit dpy-27, H4K20me1 histone modification and RNA pol II large subunit ama-1 in 3-6 replicates from mixed stage (unsynchronized) embryos and synchronized L3 larvae. Corresponding inputs are labelled with "Input_" plus ChIP name.

first: Max

middle: L

last: Kramer

first: Anna-Lena

last: Kranz


title: SOX15 governs a transcriptional program in human esophageal stratified epithelium and in a subset of esophageal adenocarcinomas

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary:
We identified spatially restricted transcription factors and found SOX15 expression confined to stratified esophageal epithelium, with attenuation in Barrett's esophagus.
SOX15 binds esophagus-specific loci and its loss in human esophageal cells affected esophagus-specific transcripts

overall_design:
[RNA-Seq] Total RNA isolated from CPA control cells and CPA cells following SOX15 depletion, samples were prepared for sequencing using the TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer's instructions. 75 base pair single-end reads were sequenced on an Illumina NextSeq 500 instrument. The data include 2 independent biological replicates per genotype.
[ChIP-Seq] Examine SOX15-chromatin binding in CPA cells.

first: Rita

last: Sulahian

first: Justina

last: Chen

first: Zoltan

last: Arany

first: Unmesh

last: Jadhav

first: Shouyong

last: Peng

first: Anil

last: Rustgi

first: Adam

middle: J

last: Bass

first: Amitabh

last: Srivastava

first: Jason

last: Hornick


title: Integrative Functional Characterization of Cancer-Testis Antigens Defines Obligate Participation in Multiple Hallmarks of Cancer

city: Dallas

first: Angelique

last: Whitehurst

state: TX

address: 5323 Harry Hines Blvd.

department: Simmons Cancer Center

institute: UT Southwestern


title: Genomic localization of Cockayne syndrom B protein upon genotoxic stresses

city: Philadelphia

first: Jieun

last: Jeong

address: 3400 Civic Center Blvd

institute: The University of Pennsylvania

summary: Cockayne syndrome is an inherited premature aging syndrome associated with developmental and neurological disorders.  Mutations in the genomic locus encoding CSB are associated with 80% Cockayne syndrome cases.  CSB is invovled in relieving UV-induced and oxidative stree. To gain more insights into the fucntion of CSB under these stress, we  use ChIP-seq to determine the genomic localization of CSB 1 hour after UV irradiation and menadione treatment.

overall_design: Genomic localization of CSB and remodeling deficient CSB∆N1

first: K-J

last: Won

first: Robert

last: Lake

first: Erica

last: Boetefuter

first: Pei-Fang

last: Tsai

first: Hua-Ying

last: Fan


title: Transcription and Imprinting Dynamics in Developing Postnatal Male Germline Stem Cells

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: Paternal imprinting initiates in primordial germ cells (PGCs), and is considered largely completed at birth.  The resulting postnatal spermatogonial stem cells (SSCs) thenself-renew and proliferate to populate the testicular niche, with sexual maturation enabling productive gametogenesis.

overall_design:
mRNA profiles of neonatal wild type (WT) mice testis were generated by deep sequencing using Illumina HiSeq 2000
Examination of 2 different histone modifications in mouse spermatogonia
Please note that ChIPSeq_Kitplus samples are samples isolated with MACS CD117 microbeads from Miltenyi and ChIPSeq_Kitminus are samples that were not positively selected for Kit.

middle: H

first: Sue

middle: S

last: Hammoud


title: Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination [additional RNA]

first: Iros

last: Barozzi

overall_design: total-mRNAs or 4sU-labeled RNAs from BMDMs, either untreated or treated for with lipopolysaccharide (LPS) for the indicated time. Experiments were carried out in cells containing either a short hairpin targeting either of these: 1) Wdr82; 2) Menin; or a scrambled as a control.

first: Liv

middle: M

last: Austenaa

first: Marta

last: Simonatto

first: Silvia

last: Masella

first: Giulia

last: Della Chiara

first: Serena

last: Ghisletti

first: Alessia

last: Curina

first: Elzo

last: de Wit

first: Britta

last: Bouwman

first: Stefano

last: de Pretis

first: Viviana

last: Piccolo

first: Alberto

last: Termanini

first: Elena

last: Prosperini

first: Mattia

last: Pelizzola

first: Wouter

last: de Laat

first: Gioacchino

last: Natoli


title: BCL9/9L-β-catenin Signaling is Associated With Poor Outcome in Colorectal Cancer

status: Public on Nov 08 2015

city: Basel

first: Andreas

last: Moor

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

institute: ETH Zurich

summary:
Canonical Wnt signaling output is mediated by β-catenin, which interacts with LEF/TCF transcription factors and recruits a general transcriptional activation complex to its C-terminus. Its N-terminus binds BCL9/9L proteins, which bind co-activators that in mammals contribute to fine-tuning the transcriptional output. We found that a BCL9/9L-dependent gene expression signature was strongly associated with patient outcome in colorectal cancer and that stem cell and mesenchymal genes determine its prognostic value. Abrogating BCL9/9L-β-catenin signaling in independent mouse colorectal cancer models resulted in virtual loss of these traits, and oncogenic intestinal organoids lacking BCL9/9L proteins proved no longer tumorigenic. Our findings suggest that the BCL9/9L arm of Wnt-β-catenin signaling sustains a stemness-to-differentiation equilibrium in colorectal cancer, which critically affects disease outcome.
Mutational activation of the Wnt pathway is a key oncogenic event in colorectal cancer. Targeting the pathway downstream of activating mutations is challenging, and the therapeutic window is limited by intestinal toxicity. Contrasting with phenotypes caused by inactivating key Wnt pathway components, ablation of BCL9/9L proteins in adult mice indicated that they were dispensable for intestinal homeostasis, consistent with their role in tuning transcription. Cancer stem cells are increasingly recognized as responsible for tumor recurrence. The correlation between stemness traits in colorectal cancer models and BCL9/9L-β-catenin signaling suggests that high Wnt signaling output is required for their maintenance. Our findings suggest that pruning Wnt-β-catenin signaling might be well tolerated and prove sufficient for trimming stemness traits and improving disease outcome.

overall_design: Examination of Bcl9/9l-knockout versus wild-type transcriptome in murine AOM-DSS tumors, APC-Kras tumors and healthy colocyte extracts.

middle: E

first: Pascale

last: Anderle

first: Claudio

last: Cantù

first: Tomas

last: Valenta

first: Norbert

last: Wiedemann

first: Frédérique

last: Baruthio

first: Patrick

last: Rodriguez

first: Jürgen

last: Deka

first: Sylvie

last: André

first: Balázs

last: Györffy

first: Mauro

last: Delorenzi

first: Konrad

last: Basler

first: Michel

last: Aguet


title: ZFP57 recognizes multiple and closely spaced sequence motif variants to maintain repressive epigenetic marks in mouse embryonic stem cells

status: Public on Nov 06 2015

city: Naples

first: Marco

last: Cammisa

state: Naples

address: Via Castellino Pietro, 111

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

summary: In mouse embryonic stem cells SNPs disrupting closely-spaced hexanucleotide motifs are associated with lack of ZFP57 binding and H3K9me3 enrichment.

overall_design: Examination of ZFP57-KAP1 allele-specific binding in two lines of mouse embryonic stem cells JB1 and BJ1 generated from F1 hybrids derived from JF1 x B6 and B6 x JF1 crosses respectively.

first: Zahra

last: Anvar

first: Vincenzo

last: Riso

first: Ilaria

last: Baglivo

first: Harpreet

last: Kukreja

first: Angela

last: Sparago

first: Michael

last: Girardot

first: Shraddha

last: Lad

first: Italia

last: De Feis

first: Flavia

last: Cerrato

first: Claudia

last: Angelini

first: Robert

last: Feil

first: Paolo

last: Pedone

first: Giovanna

last: Grimaldi

first: Andrea

last: Riccio


title: Transcriptome-wide mapping of cut sites of the viral endoribonuclease SOX from Kaposi's sarcoma-associated herpesvirus (KSHV)

status: Public on Nov 07 2015

city: Madison

first: Marta

middle: Maria

last: Gaglia

state: WI

address: 1525 Linden Dr

institute: University of Wisconsin Madison

summary: Purpose: identify sites in endogenous mRNAs that are cut by KSHV SOX; Method: parallel analysis of RNA ends (PARE, following Zhai et al., 2014); Results: SOX cuts at discrete locations in mRNAs

overall_design: human Xrn1 was knocked down in HEK293T cells by shRNAs or siRNAs to stabilize degradation fragments with free 5' ends; GFP-SOX or GFP were transfected for ~24 hrs; total RNA samples were collected and subjected to PARE protocol (Zhai et al., 2014)

first: Britt

middle: A

last: Glaunsinger


title: Enhancers reside in a unique epigenetic environment during early zebrafish development

city: mainz

first: lucas

last: kaaij

address: ackermannweg 4

department: RNA silencing

institute: IMB


title: Enhancers reside in a unique epigenetic environment during early zebrafish development [4C-seq]

summary: We describe that during early zebrafish development, DNA methylation has little influence on enhancer activity, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are generally hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the mid blastula transition (MBT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active later in development and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity.

overall_design: We performed 6 different 4C-Seq experiment at two different timepoints and in adult brain.

first: Lucas

last: Kaaij


title: On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero]

city: Woods Hole

first: Esther

middle: Jane

last: Pearl

address: 7 MBL Street

department: National Xenopus Resource

institute: Marine Biological Laboratory

summary: A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs expressed over time during embryogenesis. Here we present a comprehensive characterization of protein and mRNA dynamics across early development in Xenopus. Surprisingly, we find that most proteins change very little and duplicated genes are expressed similarly. While the correlation between mRNA levels and protein expression is poor, a mass action kinetics model parametrized by the protein synthesis and degradation rates regresses protein dynamics to RNA dynamics, corrected for initial protein concentration. This study provides a rich resource for developmental biologists, unveiling detailed data for absolute levels of ~10K proteins and ~28K transcripts via convenient web portal. It underscores the lasting impact of maternal dowry, finds surprisingly few cases where degradation alone drives a change in protein level, and highlights the importance of transcription in shaping the proteome.

overall_design: mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification.

first: Leonid

last: Peshkin

first: Martin

last: Wuhr

first: Wilhelm

last: Haas

last: Freeman

first: John

middle: C

last: Gerhart

first: Allon

middle: m

last: Klein

first: Marko

last: Horb

first: Steven

middle: P

last: Gygi

first: Marc

last: Kirscher


title: Enhancers reside in a unique epigenetic environment during early zebrafish development [ChIP-seq & ATAC-seq]

overall_design: we analyzed 5 novel ChIP-Seq libraries where we used the following AB (H3K27ac,H3K4me1,H3K4me2 and H3K27ac) and an Atac-Seq library.


title: On the relationship of protein and mRNA dynamics in vertebrate embryonic development

overall_design: Refer to individual Series