title: Global Transcript Changes In Human Keratinocyte Cells Induced by Apratyramide, a Marine-Derived Peptidic Stimulator of VEGF-A and Other Growth Factors

status: Public on Dec 21 2017

city: Gainesville

first: Hendrik

last: Luesch

address: 1345 center drive

institute: University of Florida

summary: To elucidate the mode of action of apratyramide, we performed microarray profiling using the Affymetrix GeneChip® Human Transcriptome Array 2.0 to determine global changes in transcript levels in HaCaT cells treated with apratyramide. Comparativel analysis identified 371 differentially expressed genes after 12 h treatment with 30 μM apratyramide (p < 0.05, FDR corrected, fold change >1.5 or <0.67). Consistent with our previous data, VEGF-A appeared to be one of the most up-regulated genes.   To examine the molecular functions and genetic networks, the microarray data was analyzed using Ingenuity Pathways Aanalysis (IPA).The global changes of transcript levels are associated with increased downstream phenotypic effects including angiogenesis, mitogenesis, differentiation of epithelial tissue and formation of skin, and decreased effects such as apoptosis of liver cells and hypoplasia of organs.  IPA analysis of 371 microarray hits indicated the unfolded protein response (UPR) as the top canonical pathway with a p-value of 1.45 × 10-16.  The IPA also elucidated that the 371 hits were most related to a molecular network associated with the function of cellular compromise and cellular maintenance. The network contains molecular components from UPR pathway, NRF2-mediated oxidative stress response signaling as well as glucocorticoid receptor signaling.

overall_design: Four samples were analyzed in biological duplicates. Transcriptome profile of arpatyramide was compared to control.

first: Weijing

last: Cai


title: Expression data in Srf KO and Srf WT murine muscle cells

status: Public on Dec 20 2017

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary:
The objective of the study is to caracherize the genes that are regulated by Srf in myoblasts at day 0 (J0) and in differentiated cells at day 1 (J1)  and day 3 (J3).
We used microarrays to investigate gene expression in Srf KO and Srf WT muscle cells at day 0 (J0), day 1 (J1) and day 3 (J3) of differentiation

overall_design: Srf flox/flox muscle cells  were transduced twice with adenoviruses Ad-GFP (Srf WT)  and Ad-Cre-GFP (Srf KO. ). Two days after the first transduction, GFP-positive cells were sorted with BD FACSAriaIII and . Total mRNA were purified using Qiagen RNeasy minikit and DNAse treatment. The experiments were done in triplicate.

first: Voahangy

last: Randrianarison-Huetz

first: Athanassia

last: Sotiropoulos


title: c-MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification (ChIP-Seq)

status: Public on Dec 22 2017

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Childhood neuroblastoma is known for MYCN gene amplification, and here we show that in a separate subset of cases MYC-itself is activated due to enhancer hijacking from chromosomal translocations or duplications, thus defining a unique subset of high-risk disease.

overall_design: ChIP-Seq for H3K27ac and CTCF in high MYC expressing neuroblastoma cell types

first: Mark

middle: W

last: Zimmerman

first: Yu

last: Liu

first: Shuning

last: He

first: Adam

middle: D

last: Durbin

first: Brian

middle: J

last: Abraham

first: Nina

last: Weichert-Leahey

first: Shizhen

last: Zhu

first: Amish

last: Khan

first: Xiaoling

last: Zhang

first: Jinghui

first: A

middle: T

last: Look


title: Small RNA libraries from wildtype and Ago2 catalytic dead mouse fetal liver

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs were cloned from wildtype and Ago2 catalytic dead mouse fetal liver to uncover slicing dependent miRNAs in hematopoietic tissue

overall_design: Biological replicate libraries from wildtype control and Ago2 catalytic dead mutant fetal liver samples

first: David

last: Jee

first: Eric

last: C. Lai


title: Genome-wide methylation analysis of Silver-Russell patients

city: Helsinki

first: Juha

last: Kere

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

type: Methylation profiling by genome tiling array

summary: Illumina Infinium HumanMethylation450 assay was used to study genome-wide DNA methylation profiles of Silver-Russel sydrome (SRS) patients.

overall_design: 44 Silver-Russell syndrome patients, including 21 patients with 11p15 LOM, 10 patients with UPD(7)mat and 13 patients with clinical SRS were analyzed in comparison to 16 control samples. Also one individual with UPD(7)pat was included in the analysis.

first: Dario

last: Greco

first: Mari

last: Muurinen

first: Katariina

last: Hannula-Jouppi

first: Lovisa

middle: E

last: Reinius

first: Cilla

last: Söderhäll

first: Simon

middle: K

last: Merid

first: Anna

last: Bergström

first: Erik

last: Melén

first: Göran

last: Pershagen

first: Marita

last: Lipsanen-Nyman


title: RNAPII transit through nucleosomes in vivo produces hexasomal intermediates

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: All histone-DNA contacts in a nucleosome must be disrupted for RNA polymerase II (RNAPII) to transcribe through chromatin. However, the structural transitions of the nucleosome during transcription in vivo are unknown. To identify nucleosomal intermediates formed during transcription in vivo, we mapped subnucleosomal protections in Drosophila cells using Micrococcal Nuclease followed by deep sequencing. At the first nucleosome position downstream of the transcription start site, we identified hexasomes lacking an H2A/H2B dimer. Inhibiting topoisomerases or depleting histone chaperones increased dimer loss, whereas inhibiting release of paused RNAPII or reducing RNAPII elongation decreased dimer loss. Our results suggest that positive torsion generated by elongating RNAPII evicts the distal H2A/H2B dimer in vivo. We also identified diagnostic subnucleosomal particle remnants in cell-free human DNA data as a relic of transcribed genes from the tissue-of-origin. Thus the identification of subnucleosomal particle fragments from nuclease protection data represents a general strategy for structural epigenomics.

overall_design: Using MNase-seq, we mapped the subnucleosomal distribution of transcriptional intermediates at promoters.

first: Srinivas

last: Ramachandran

first: Steven


title: Mutational landscape of splicing genes and functional consequences across 33 cancer types

first: Silvia

last: Buonamici

address: 300 Technology Square #5

institute: H3 Biomedicine

type: Expression profiling by high throughput sequencing

summary: Hotspot mutations in the spliceosome component genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of this pathway in cancer. However, a comprehensive survey of splicing factor mutations across tumor types has not yet been performed. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA) in order to discover recurrent mutations in spliceosome components, identifying 119 genes with significant non-silent mutation patterns, including mutation overrepresentation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). We used RNA sequencing data to identify altered splicing events associated with these spliceosome mutations. In addition, we were able to discover common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of the splicing pathway is common in solid tumors and may represent an underappreciated hallmark of tumorigenesis.

overall_design: 6 U87MG cell line samples, including 3 treated with siRNA against FUBP1 and 3 with a non-specific siRNA

first: Michael

last: Seiler

first: Lihua

last: Yu


title: Comprehensive Expression Analysis of microRNAs and mRNAs in Osteoarthritic Synovial Tissue from a Mouse Model of Early Post-Traumatic OA [miRNA]

city: Melbourne

first: John

last: Bateman

address: Flemington Road

department: Skeletal Biology

institute: Murdoch Childrens Research Institute

summary: Our objective was to characterize disease-specific profiles of both microRNAs (miRNAs) and mRNA expression in synovial tissue from a mouse model of early post-traumatic OA to better understand the molecular processes involved in driving OA.

overall_design: OA was induced in 10-12 week old male C57BL6 mice by bilateral surgical destabilization of the medial meniscus (DMM). RNA was isolated from the anterior region of the synovium of DMM and sham-operated mice at 1 and 6 weeks post-surgery. Expression profiling was performed using Agilent miRNA and mRNA microarrays and validated by qPCR. OA severity was determined histologically in the contralateral joint.

first: Louise

middle: H

last: Kung

first: Varshini

last: Ravi

first: Lynn

last: Rowley

first: Katrina

middle: M

last: Bell

first: Christopher

middle: B

last: Little

middle: F


title: c-MYC drives a subset of high-risk pediatric neuroblastomas and is activated through mechanisms including enhancer hijacking and focal enhancer amplification

first: Richard

last: Young

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

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Refer to individual Series


title: Comprehensive Expression Analysis of microRNAs and mRNAs in Osteoarthritic Synovial Tissue from a Mouse Model of Early Post-Traumatic OA

type:
Expression profiling by array
Non-coding RNA profiling by array


title: Expression data from Satellite cells and Endothelial cells isolated at different time points during skeletal muscle regeneration

city: Lyon

first: Benedicte

last: Chazaud

address: 8 Avenue Rockefeller

department: Institut NeuroMyoGène

institute: Université Claude Bernard Lyon 1

summary: Skeletal muscle regeneration is a highly dynamics process. The study aims at investigating gene expression by endothelial cells and satellite/myogenic cells during this process, in mouse, after a toxic injury

overall_design: Tibialis Anterior mouse muscle was injured with cardiotoxin and muscles were recovered before (day0) and days 2, 4, 8 post-injury. Muscles were minced, enzymatically digested. Endothelial cells (ECs)  and Satellite cells (SCs) were isolated by FACS as CD45-Sca1+CD34+CD31+ and as CD45-Sca1-CD34+/loCD31-alpha7integrin+, respectively.

first: Bénédicte

first: Claire

last: Latroche


title: Metabolic products of an obesity-associated microbiome impact host metabolism and disease risk by altering the epigenome

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Mammals have a complicated symbiotic relationship with their gut microbiome which is postulated to have broad impacts on host health and disease.
We used microarray to dectec the gene expressions in colon epithelium.

overall_design: Mice were on the HFD and LFD for 20 weeks and colon epithelium was collected to do the microarray.  Each group has three rpelicates.

first: Yufeng

last: Qin

last: Roberts

first: Sara

last: Grimm

first: Fred

last: Lih

first: Leesa

last: Deterding

first: Ruifang

last: Li

first: Kaliopi

last: Chrysovergis

first: Paul

last: Wade


title: Comprehensive Expression Analysis of microRNAs and mRNAs in Osteoarthritic Synovial Tissue from a Mouse Model of Early Post-Traumatic OA [mRNA]

first: John

last: Bateman

first: Louise

last: Kung


title: Functional dissection of hematopoietic stem cell population by a stemness-monitoring system with NS-GFP transgene

city: Kanazawa

first: Atsushi

last: Hirao

address: kakuma

department: Division of Molecular Genetics

country: Japan

institute: kanazawa university

summary: Hematopoietic stem cells (HSCs) in a steady state are efficiently purified by the combination of several cell surface markers, however, such markers do not consistently reflect HSC activity. In this study, we successfully isolated functional HSCs by a unique stemness monitoring system using a transgenic mouse, in which green florescence protein (GFP) is driven by promoter/enhancer region of nucleostemin (NS) gene. We found that phenotypically defined long-term (LT)-HSC population exhibited the highest level of the NS-GFP intensity, whereas it was remarkably down-regulated during differentiation in vitro and in vivo. Importantly, among the LT-HSC population, the NS-GFPhigh cells significantly exhibited higher repopulating capacity than NS-GFPlow cells. Gene expression analysis revealed that 9 genes, including Vwf and Cdkn1c (p57), are highly expressed in NS-GFPhigh cells, which may represent signature of functional HSCs, i.e., stemness signature.  When LT-HSCs suffered from remarkable stresses, such as transplantation or irradiation, NS-GFP intensity was downregulated, suggesting that NS-GFP accurately reflects HSC function. Finally, we found that functional HSCs were identified as NS-GFPhigh cells in CD34+ LSK cells, which has been recognized as progenitor cells without long-term reconstitution ability.  Thus, high NS-GFP intensity represents stem cell characteristics in hematopoiesis and this system is useful for identification of uncharacterized HSCs.

overall_design: The LSK cells from NS-GFP transgenic mice  were sorted, in which GFP is expressed under the control of particular region of NS promoter (NS-GFP).The murine LSK cells were fractionated into 4 subpopulations based on NS-GFP level , (a) NS-GFP1+, (b) -NS-GFP2+, (c) NS-GFP3+ and (d) NS-GFP4+


title: Microglia isolated from juvenile offspring of dams with allergic asthma exhibit methylation and transcriptional alterations to autism risk genes

city: Vancouver

first: Annie

middle: Vogel

last: Ciernia

state: British Columbia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

country: Canada

institute: University of British Columbia

type: Methylation profiling by high throughput sequencing


title: A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [Hi-C]

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

type:
Other
Third-party reanalysis

summary: The mammalian HoxD cluster is positioned at the boundary between two topologically associating domains (TADs), each of them matching a distinct, enhancer-rich regulatory landscape. During limb development, the telomeric TAD controls the early phase of Hoxd gene transcription in future forearm cells, whereas the centromeric TAD subsequently regulates transcription of more posterior Hoxd genes in presumptive digit cells. The TAD boundary is essential as it prevents the terminal Hoxd13 gene to respond to potent forearm enhancers, thereby allowing the formation of proper proximal limb structures. Here we apply chromosome conformation capture onto embryonic proximal and distal limb bud cells micro-dissected from a set of nested deletions involving part- or all- of this boundary region to try to understand the nature and function of this CTCF- and cohesin-rich DNA region. We document a progressive release of the boundary effect, allowing for inter-TAD contacts to be established, which were favoured by the functional status of the newly accessed enhancers. However, the boundary was highly resilient and only a 400kb large deletion including the whole gene cluster was eventually able to merge the two neighbouring TADs into a single structure. We propose that the whole HoxD cluster is a dynamic transcriptional boundary, showing slight variations depending on both the transcriptional status and the ontogenetic context

overall_design: Hi-C datasets of E12.5 limb tissues (distal or proximal forelimbs and hindlimbs) of Wt or serial HoxD-deleted alleles -delHoxd(1-13d9)lac and delHoxd(attP-Rel5)d9lac as well as the reanalysis of the CH12 dataset from Rao et al. 2014 (GSE63525, GSM15516333 to GSM15516347 = SRR1658716 to SRR1658730) and mESC dataset from Dixon et al. 2012 (GSE35156, GSM862720 = SRR443883 to SRR443885 and GSM862721 = SRR400251 to SRR400256) on mm10.

first: E

last: Rodriguez-Carballo

first: L

last: Lopez-Delisle

last: Beccari

first: D

last: Duboule


title: Microglia isolated from juvenile offspring of dams with allergic asthma exhibit methylation and transcriptional alterations to autism risk genes [RNA-Seq]

summary: Asthma is one of the most common chronic diseases among pregnant women, and symptoms often worsen during pregnancy. Dysregulation in immune responses during pregnancy, such as those that develop with chronic allergic asthma, increase the risk of a having a child with an Autism Spectrum Disorder (ASD).  We recently developed a mouse model of maternal allergic asthma (MAA) that induces alterations in behavioral outcomes of the offspring including changes in sociability, repetitive and perseverative behaviors. Pregnancy is also a time when epigenetic changes help a static genome adapt to the maternal environment, and consequently activation of the maternal immune system may alter the regulation of gene expression in the developing fetal brain.  Perinatal exposure to maternal asthma alters DNA methylation of immune-related genes in human infants, suggesting that maternal asthma has long-lasting effects on the offspring’s’ immune function.  Here we used the genome-wide approaches of whole genome bisulfite sequencing to examine DNA methylation combined with RNA sequencing to examine gene expression in acutely isolated microglia from juvenile MAA offspring.  Differential analysis revealed significant alterations in the epigenome of microglia from MAA compared to PBS treated control offspring and identified genes involved in controlling microglial sensitivity to the environment and shaping both synaptic and long-range neuronal connections in the developing brain.  Genes with altered methylation and expression in MAA juvenile microglia significantly overlapped with those identified in adult cortex from offspring of a different maternal immune activation (polyIC) autism model and with a curated list of autism risk genes in human, supporting a role for microglia in the pathogenesis of ASD.

overall_design: Whole transcriptome RNA sequencing were performed on acutely isolated microglia from female C57BL6/J mice whose mother's had either received maternal immune activation (gestational day9,12, and 17) or PBS treatment. 3 MAA and 4 PBS biological replicates

first: Vogel

middle: C

last: Annie

first: LaSalle

last: Janine


title: Association with Aurora-A controls N-MYC-dependent promoter escape and pause release of RNA polymerase II during the cell cycle

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

summary: MYC proteins bind globally to active promoters and promote transcriptional elongation by RNA polymerase II (RNAPII). To identify effector proteins that mediate this function, we performed mass spectrometry on N-MYC complexes in neuroblastoma cells. The analysis shows that N-MYC forms complexes with TFIIIC, TOP2A and RAD21, a subunit of cohesin. N-MYC and TFIIIC bind to overlapping sites in thousands of RNAPII promoters and intergenic regions. TFIIIC promotes association of RAD21 with N-MYC target sites and is required for N-MYC-dependent promoter escape and pause release of RNAPII. Aurora-A competes with binding of TFIIIC and RAD21 to N-MYC in vitro and antagonizes association of TOP2A, TFIIIC and RAD21 with N-MYC during S-phase, blocking N-MYC-dependent release of RNAPII from the promoter. Inhibition of Aurora-A in S-phase restores RAD21 and TFIIIC binding to chromatin and partially restores N-MYC-dependent transcriptional elongation. We propose that complex formation with Aurora-A controls N-MYC function during the cell cycle.

overall_design: DNA-binding of N-MYC and TFIIIC upon inhibition of Aurora-A, RNAPII occupancy after shRNA-mediated depletion of TFIIIC5 or in S-phase arrested SH-EP-NMYCER cells and gene expression changes after depletion of RAD21, Aurora-A and TFIIIC5 or activation of NMYC.

first: Gabriele

last: Büchel

first: Anne

last: Carstensen

first: Ka-Yan

last: Mak

first: Isabelle

last: Roeschert

first: Eoin

last: Leen

first: Olga

last: Sumara

first: Julia

last: Hofstetter

first: Steffi

last: Herold

first: Jacqueline

last: Kalb

first: Apoorva

last: Baluapuri

first: Evon

last: Poon

first: Colin

last: Kwok

first: Louis

last: Chesler

first: Hans

last: Maric

first: David

middle: S

last: Rickman

first: Elmar

last: Wolf

first: Richard

last: Bayliss

first: Susanne

last: Walz


title: Smoking-associated AHRR hypomethylation enables monocyte-specific enhancer activation, and upregulation of noncoding and coding RNA

status: Public on Dec 19 2017

city: Research Triangle Park

first: Douglas

middle: A.

last: Bell

address: PO Box 12233

department: Immunity Inflammation and Disease Lab

institute: National Institute of Environmental Health Sciences

summary: While tobacco smoke exposure strongly influences DNA methylation and is causative in numerous human diseases, the underlying mechanistic links are obscure. Here we investigated genome-wide smoking-associated differentially methylated regions (SM-DMRs) using CD14 monocytes of smokers (n=47) and nonsmokers (n=46) from two independently recruited populations, the Multi-Ethnic Study of Atherosclerosis (MESA) and Clinical Research Unit (CRU) at NIEHS. We found that SM-DMRs preferentially occur at genomic regions with the characteristics of putative enhancer, open chromatin, and the enrichment of TF binding indicated by ENCODE/Roadmap Epigenome/BLUEPRINT datasets. Most of our selected candidate SM-DMRs identified in the two populations were also observed in other hematopoietic cell types (CD15 granulocytes, CD19 B cells, CD4 T cells, CD8 T cells, CD56 NK cells) and were successfully validated using a second method in an independently recruited group of subjects. Aryl-Hydrocarbon Receptor Repressor (AHRR) SM-DMR, located at an intragenic enhancer, was the most significantly affected DMR and we have previously reported that a methylation level of a CpG in this gene was associated with subclinical atherosclerosis. The AHRR DMR was also detected in saliva DNA and these results were highly correlated with effects in monocytes (r2 = 0.90), suggesting that saliva may provide a potential alternative, noninvasive source for biomarkers that use DNA. Mechanistically, our results suggested that AHRR SM-DMR upregulated AHRR mRNA through activating AHRR enhancer in monocytes of smokers but not in granulocytes, indicated by increased noncoding RNA. Taken together, our study suggests that cell type-specific activation of enhancers at SM-DMRs may represent a mechanism driving smoking-related disease.

overall_design:
RRBS using DNA samples of circulating CD14+ monocytes from MESA and CRU populations.

***This study complies with the NIH Genomic Data Sharing (GDS) Policy.  DNA samples were collected under NIH approved IRB protocols from volunteers who provided informed consent for analysis.  We provide here the DNA methylation values at individual nonpolymorphic CpGs for individual subjects (equivalent to 450K datasets) but not sequence read data which could be used to identify individuals.***

first: Ma

last: Wan

first: Brian

last: Bennett


title: RNA sequencing data of Candida albicans white, opaque, and white engineered cells under mating conditions

city: Providence

first: Christine

middle: Maria

last: Scaduto

state: RI

address: 171 Meeting Street

department: Molecular Microbiology and Immunology

institute: Brown University

summary: C. albicans white, opaque and white engineered cells were incubated on Spider medium for 8 hours. Crosses were between a and alpha cells of each phenotype, and a white cells alone or a opaque cells alone were also incubated as controls. White cells are no

overall_design: RNA sequencing libraries of white cells, opaque cells, and engineered white cells in mating conditions were generated in biological duplicate using the Illumina TrueSeq stranded mRNA library prep kit.


title: Role of Sox2 in preimplantation and postimplantation pluripotency

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: Sox2 is a key transcription factor directing embryonic stem cell (ESC) pluripotency. However, the role of SoxB1 proteins in epiblast stem cell (EpiSC) pluripotency is unknown. Here we compare the transcriptomes of pluripotent cells cultured in different conditions that express different levels of Sox2. While highest Sox2 level in ESCs are enriched for naive pluripotency markers, ESCs and EpiSCs expressing the same Sox2 level were transcriptionally distinct. Thus Sox2 levels do not dictate the distinction between ESC and EpiSC states.

overall_design: Microarray gene expression analysis of mouse embryonic stem cells in different culture conditions. 4 conditions: AFN=Activin/FGF/N2B27 (unsorted (All) or sorted by Sox2 expression into High or Low), PCLN=LIF/2i/N2B27, LBN=LIF/BMP/N2B27 (sorted by Sox2 expression into High and Low) and FCSL=LIF/FCS/GMEM (sorted by Sox2 expression into High and Low). 3 replicates per group. 24 samples total.

first: Andrea

last: Corsinotti

first: Frederick

last: Wong

first: Tülin

last: Tatar

first: Iwona

last: Szczerbinska

last: Colby

first: Sabine

last: Gogolok

first: Raphaël

last: Pantier

first: Kirsten

last: Liggat

first: Elham

last: Mirfazeli

first: Elisa

last: Hall-Ponsele

first: Nicholas

middle: P

last: Mullin

first: Valerie

last: Wilson

first: Ian

last: Chambers


first: Paul

middle: A

last: Wade

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

summary: We profiled the gut microbiome and chromatin features at DNA cis-regulatory elements in colon epithelium from mice fed either an obesogenic or control diet.

overall_design: Examination of 2 different histone modifications and gene expression in mice colon epithelium, microbiome in male fecal samples

first: Yufeng

last: Qin

first: John

last: Roberts

first: Sara

last: Grimm

first: Fred

last: Lih

first: Leesa

last: Deterding

first: Ruifang

last: Li

first: Kaliopi

last: Chrysovergis


title: Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Novel Differences between Brown and White Adipocytes

status: Public on Dec 18 2017

city: Boston

first: Jonathan

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: This study predicted flux differences between brown and white adipocytes by integrating the results of extracellular flux analyzers, such as the Seahorse Analyzer, with metabolic modeling. The microarrays of the individuals' preadipocytes were used to support the predictions. These are the same individuals who were assayed by microarray in GSE68544.

overall_design: Paired microarrays of preadipocytes from white adipose tissue (WAT) and brown adipose tissue (BAT) from three individuals.

first: Alfred

last: Ramirez

first: Matthew

last: Lynes

first: Farnaz

last: Shamsi

first: Ruidan

last: Xue

first: Yu-Hua

last: Tseng

first: C

middle: R

last: Kahn

first: Simon

last: Kasif


title: FFK506-Binding Protein 12.6/1b, a negative regulator of [Ca2+], rescues memory and restores genomic regulation in the hippocampus of aging rats

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary: Hippocampal overexpression of FK506-binding protein 12.6/1b (FKBP1b), a negative regulator of ryanodine receptor Ca2+ release, reverses aging-induced memory impairment and neuronal Ca2+ dysregulation. Here, we test the hypothesis that FKBP1b also can protect downstream transcriptional networks from aging-induced dysregulation. We gave hippocampal microinjections of FKBP1b-expressing viral vector to male rats at either 13-months-of-age (long-term) or 19-months-of-age (short-term) and tested memory performance in the Morris water maze at 21-months-of-age. Aged rats treated short- or long-term with FKBP1b substantially outperformed age-matched vector controls and performed similarly to each other and young controls. Transcriptional profiling in the same animals identified 2342 genes whose hippocampal expression was up-/down-regulated in aged controls vs. young controls (the aging effect). Of these aging-dependent genes, 876 (37%) also showed altered expression in aged FKBP1b-treated rats compared to aged controls, with FKBP1b restoring expression of essentially all such genes (872/876, 99.5%) in the direction opposite the aging effect and closer to levels in young controls. This inverse relationship between the aging and FKBP1b effects suggests that the aging effects arise from FKBP1b deficiency. Functional category analysis revealed that genes downregulated with aging and restored by FKBP1b associated predominantly with diverse brain structure categories, including cytoskeleton, membrane channels and extracellular region. Conversely, genes upregulated with aging but not restored by FKBP1b associated primarily with glial-neuroinflammatory, ribosomal and lysosomal categories. Immunohistochemistry confirmed aging-induced rarefaction, and FKBP1b-mediated restoration, of neuronal microtubular structure. Thus, a previously-unrecognized genomic network modulating diverse brain structural processes is dysregulated by aging and restored by FKBP1b overexpression.

overall_design: All experiments and procedures were performed in accordance with the University of Kentucky guidelines and were approved by the Animal Care and Use Committee. Hippocampal overexpression of FKBP1b was induced using methods and doses similar to those we described and validated previously (Gant et al., 2015). Briefly, bilateral injection of adeno-associated virus (AAV) vector harboring the transgene for FKBP1b under control of the CAMKII promoter (AAV2/9.CAMKII 0.4.ratFkbp1b.RGB; or AAV-FKBP1b) into the CA1 region of the hippocampus. A control vector harboring the transgene for enhanced green fluorescent protein (AAV2/9.CAMKII 0.4.eGFP.RGB, or, AAV-eGFP) was administered with the same procedure to a vector control group of aged rats. The AAV vectors were constructed at the University of Pennsylvania vector core (Philadelphia, PA). A total of 23 male F344 rats that completed behavioral training were used for microarray measurement, divided into 4 treatment groups: 1) young controls receiving no injections (YC) (n = 6, 4-5 months of age at receipt) 2) Long-term aged vector control (AC) (n = 5, bilateral injections of AAV-eGFP 1.86e13 GC/mL, 2 µl per side; at 13 months-of-age; 3) Short-term FKBP1b (ST) (n = 6, bilateral injections of AAV.FKBP1b 1.99e12 GC/mL, 2 µl per side, at 19 months-of-age); and 4) Long-term FKBP1b (LT) (n = 6, bilateral injections of AAV-FKBP1b 1.99e12 GC/mL, 2 µl per side; at 13 months-of-age). All aged animals used in this study arrived together and were housed in our animal care facility for the same duration. All animals underwent Morris Water Maze (MWM) training similar to prior work (e.g., Rowe et al., 2007; Latimer et al., 2014) and brain dorsal hippocampi were harvested for gene chip as in prior work (Kadish et al., 2009; Searcy et al., 2012; Latimer et al., 2014; Gant et al., 2015). Tissue was placed in RNase-free sample tubes and stored at -80° C until further use. Dorsal hippocampal RNA was extracted according to standard protocols, and evaluated using Agilent Bioanalyzer. All samples were of sufficient quality and did not differ significantly among treatment groups (RNA Integrity Number [RIN]: 9.4 ± 0.1 for all groups; p = 0.16, ANOVA across YC, AC, ST and LT groups). Microarray procedures were similar to our prior microarray studies on hippocampal aging in rats (Blalock et al., 2003; Rowe et al., 2007; Kadish et al., 2009). Briefly, RNA extracted from dorsal hippocampus was labeled and hybridized to Affymetrix Rat Gene 1.0 ST arrays (one array per animal). Signal intensities were calculated using the Robust Multi-array Average (RMA) algorithm (Bolstad et al., 2003) at the transcript level and data were associated with vendor-provided annotation information. Total probe sets were filtered prior to statistical testing to retain only unique, annotated probe sets with adequate signal intensity (defined as unlogged signal intensity ≥ 40 on ≥ 4 arrays in the study), and outlier values (> 2 SD of the group mean) were treated as missing values. Filtered signal intensities were analyzed by one-way ANOVA to identify significant differences, and the False Discovery Rate (FDR) procedure (Hochberg and Benjamini, 1990) was used to estimate the error of multiple testing. Significant genes were assigned to one of four expression templates based on post hoc pairwise comparisons (Fisher’s protected Least Significant Difference- please see Results).

last: Gant

first: Kuey-Chu

last: Chen

first: Inga

last: Kadish

first: Olivier

last: Thibault

first: Nada

last: Porter

first: Philip

middle: W

last: Landfield


title: Gene expression changes due to frataxin deficiency and restoration in frataxin knockdown mouse model.

city: Gainesville

first: VIJAYENDRAN

last: CHANDRAN

state: FL

address: Assistant Professor, Department of Pediatrics,  University of Florida, School of Medicine, 1600 SW Archer Road, Box 100296

institute: University of Florida

summary: Friedreich's ataxia (FRDA), the most common inherited ataxia in humans, is caused by recessive mutations that lead to a substantial reduction in the levels of frataxin (FXN), a mitochondrial iron binding protein. FRDA is a multi-system disease, involving multiple neurological, cardiac, and metabolic manifestations whose study is hindered by a paucity of animal models that faithfully recapitulate human disease features. We developed an inducible (doxycycline) mouse model of Fxn deficiency (FRDAkd) that enabled us to control the onset, progression and potential rescue of disease phenotypes by the modulation of Fxn levels using RNA interference. We found that systemic knockdown of Fxn in adult mice led to multiple features paralleling those observed in human patients, including electrophysiological, cellular, biochemical and structural phenotypes associated with cardiomyopathy, as well as dorsal root ganglion and retinal neuronal degeneration and reduced axonal size and myelin sheath thickness in the spinal cord. Fxn knockdown mice also exhibited other abnormalities similar to patients, including weight loss, reduced locomotor activity, ataxia, reduced muscular strength, and reduced survival, as well as genome-wide transcriptome changes. We performed microarray analysis of heart, cerebellum and dorsal root ganglia in FRDAkd mouse model of frataxin deficiency, and found several molecular pathway dysfunction via genome-wide transcriptome analyses. We also found that, upon restoration of near wild-type FXN levels, we observed significant recovery of function, pathology and associated transcriptomic changes, even after significant motor dysfunction was observed. The rapidity of Fxn expression due to doxycycline removal and its robust correction of various parameters, even when restored after the onset of motor dysfunction, makes this FRDAkd mouse model an appealing potential preclinical tool for testing various therapeutics for FRDA.

overall_design: Heart, cerebellum and dorsal root ganglia samples from FRDAkd mouse model at week 0, 3, 12, 16, 20 and 4, 8 weeks post dox treatment (rescue) with four biological replicates were used for expression profiling.

first: Vijayendran

last: Chandran


title: EZH2-dependent chromatin accessibility changes during B cell differentiation

status: Public on Dec 16 2017

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To understand the role of EZH2 in B cell differentiation, EZH2 was inducibly deleted using tamoxifen and B cells stimulated to differentiate with LPS in vivo.  After 3 days, EZH2-sufficient and EZH2-deficient naive B cells and plasmablasts were FACS isolated from the spleens and ATAC-seq was performed to identify the chromatin accessibility changes that are programmed by EZH2.

overall_design: Bone marrow chimeric mice were established from CD45.1/2 CRE negative and CD45.2 CRE positive Ezh2-floxed mice to study the cell intrinsic role of Ezh2 during B cell differentiaiton.  Chimeric mice were treated with tamoxifen to induce deletion of Ezh2 in CD45.2 cells and subsequently inocculated with LPS to induce differentiation.  Three-days later naïve B cells (nB) and differentiated plasmablasts (Pb) were isolated from Ezh2-sufficient (CD45.1/2) and Ezh2-deficient (CD45.2) populations by FACS.

middle: D

first: J

last: Boss


title: KSHV vIRF3 promotes angiogenesis of lymphatic endothelial cells (LECs)

city: Los Angeles

first: Fan

last: Li

state: CA

address: 675 Charles E Young Drive South

department: Pediatrics

institute: University of California Los Angeles

summary: Herein, we report viral interferon regulatory factor 3 (vIRF3) as a pro-angiogenic factor together with HDAC5 that coordinates with LEC transcriptome, thus resulting in hyper-sprouting formation and ultimately leading to abnormal lymphangiogenesis. Overexpression of vIRF3 in LECs but not blood endothelial cells (BECs) exhibited a unique KSHV-associated angiogenic effect, evidenced by elongated spindle shape, sprouting, and tube formation. Furthermore, using vIRF3 knockout recombinant KSHV, we confirmed that vIRF3 is a critical factor of KSHV-mediated lymphangiogenesis in primary LECs.

overall_design: 3 control, 3 overexpressor each in LECs and BECs.

first: Hye

last: Lee

first: Jae

middle: U

last: Jung


title: The unfolded protein response impacts melanoma progression by enhancing FGF expression and can be antagonized by a chemical chaperone

first: Clemens

last: Röhrl

address: Währingerstraße 10

department: Department of Medical Chemistry

institute: Medical University of Vienna

summary: The mechanisms hallmarking melanoma progression are insufficiently understood. Here we studied the impact of the unfolded protein response (UPR) - a signalling cascade playing ambiguous roles in carcinogenesis - in melanoma malignancy. We identified isogenic patient-derived melanoma cell lines harboring BRAFV600E-mutations as a model system to study the role of intrinsic UPR in melanoma progression. We show that the activity of the three effector pathways of the UPR (ATF6, PERK and IRE1) was increased in metastatic compared to non-metastatic cells. Increased UPR-activity was associated with increased flexibility to cope with ER stress. The activity of the ATF6- and the PERK-, but not the IRE-pathway, correlated with poor survival in melanoma patients. Using whole-genome expression analysis, we show that the UPR is an inducer of FGF1 and FGF2 expression and cell migration. Antagonization of the UPR using the chemical chaperone 4-phenylbutyric acid (4-PBA) reduced FGF expression and inhibited cell migration and viability. Consistently, FGF expression positively correlated with the activity of ATF6 and PERK in human melanomas. We conclude that chronic UPR stimulates the FGF/FGF-receptor signalling axis and promotes melanoma progression. Hence, the development of potent chemical chaperones to antagonize the UPR might be a therapeutic approach to target melanoma.

overall_design: Non-metastatic melanoma cells (MCM1G) were compared to metastatic MCM1DLN cells and MCM1DLN cells treated with the chemical chaperon 4-PBA. Two independent experiments consisting of two biologic replicates each were analyzed.

first: Karin

last: Eigner

first: Yüksel

last: Filik

first: Florian

last: Mark

first: Birgit

last: Schütz

first: Günter

last: Klambauer

first: Richard

last: Moriggl

first: Markus

last: Hengstschläger

first: Herbert

last: Stangl

first: Mario

last: Mikula


title: EZH2 is required for gene repression in Plasmablasts

summary: To understand the role of EZH2 in Plasmablast function EZH2 was inducibly deleted using tamoxifen and B cells stimulated to differentiate with LPS in vivo.  After 3 days, CD138+ cells were enriched from the spleens and RNA-seq was performed to identify the genes targeted by EZH2 for repression.

overall_design: RNAseq on control or EZH2-deficient murine plasmablasts.

first: C


title: Hepatic Leukemia Factor maintains quiescence of hematopoietic stem cells and protects the stem cell pool during regeneration

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

summary: The transcription factor hepatic leukemia factor (HLF) is highly expressed in hematopoietic stem cells (HSCs) and has been proposed to influence both HSC self-renewal and leukemogenesis. However, the physiological role of HLF in hematopoiesis and HSC function has remained unknown. Here we report that mice lacking Hlf are viable with essentially normal hematopoietic parameters. By contrast, when challenged through transplantation, Hlf deficient HSCs demonstrate an impaired ability to reconstitute hematopoiesis and gradually exhaust upon serial transplantation. Transcriptional profiling displayed changes associated with cellular activation in Hlf deficient HSCs, and cell cycle analysis showed a significant reduction of dormant HSCs. Accordingly, Hlf deficient mice were hypersensitive to toxic insults targeting dividing cells that completely eradicated the HSC pool. In summary, our findings unravel a novel role for HLF as a critical regulator of HSC quiescence and as an essential factor to maintain the HSC pool during regeneration.

overall_design: Comparing HLF KO HSC with wildetype littermate HSC

first: Mattias

last: Magnusson

first: Karolina

last: Komrorowska


title: Defects in T cell independent B cell differentiation in the absence of EZH2

status: Public on Dec 15 2017

first: Chris

last: Scharer

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

overall_design: Refer to individual Series


title: CSL

city: Lausanne

first: Paolo

last: Angelino

address: Quartier Sorge, Bâtiment Génopode

department: BCF

institute: SIB Swiss Institute of Bioinformatics


title: Divergence in gene regulation in Shewanella baltica strains

city: Norman

first: Jie

last: Deng

state: OK

address: 101 David L Boren Blvd, SRTC 2022

institute: University of  Oklahoma

summary: Transcriptional profiling of Shewanella OS185 and OS195 strains grown under aerobic, anaerobic thiosulfate and nitrate respiratory conditions.

overall_design: The Shewanella OS185 and OS195 strains were grown under aerobic, anaerobic thiosulfate and nitrate respiratory conditions. Three replicates were included. Therefore, there were a total of 18 samples analyzed. All sample cDNAs were labeled with Cy5. The same reference cDNA pool was labeled Cy3, and were used in all arrays.The reference cDNA pool was constructed using RNA from cells of all four strains OS155, OS185, OS195 and OS223 grown in HEPES medium containing either 10 mM sodium fumarate, 5 mM sodium nitrate or 10 mM sodium thiosulfate under anaerobic condition, or 10 mM sodium chloride under aerobic condition.

first: Jennifer

last: Auchtung


title: Determination of Lsd1 function in C2C12 myoblast cells by global transcriptome analysis

city: Freiburg

first: Roland

last: Schuele

state: Baden-Württemberg

address: Breisacherstr. 66

department: Urologie, Uniklinik Freiburg

institute: Zentrale Klinische Forschung

summary: First, we aimed to identify genes whose transcript levels change at the onset of myogenic versus adipogenic differentiation of muscle precursors. We therefore compared RNA-seq results obtained from C2C12 cells differentiated for 1 day in myogenic and adipogenic medium. Out of these genes, we wanted to determine those whose expression was affected by altered Lsd1 levels. To this end, we performed RNA-seq in C2C12 cells upon LSD1 overexpression and Lsd1 knock-down in adipogenic medium and compared them to corresponding control cells.

overall_design: Stable inducible LSD1 overexpressing C2C12 cell line was generated by infecting the cells with the lentivirus containing pSlik-Neo tetracycline-controlled transactivator (tTA) plasmid with Flag-tagged LSD1 construct downstream of the tetracycline-dependent promoter or empty vector and selecting with G418. To induce LSD1 overexpression, cells were treated with doxycycline (2 mg/ml) 48 h prior to differentiation and throughout the differentiation process. Lsd1 knock-down in C2C12 cells was induced by transfecting the cells with 20 nM siRNA against Lsd1 or unrelated control (Invitrogen) using DharmaFECT 3 reagent. Cells were differentiated for 1 day in adipogenic or myogenic medium and RNA was extracted with trizol. RNA integrity was confirmed by Bioanalyzer and cDNA library preparation and sequencing was performed (HiSeq 2000, paired-end, 100 bp). RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files). Reads were mapped to the mouse mm10 genome (NCBI Build 37) using TopHat version 2. The aligned reads were counted with the Homer software and differentially regulated genes were identified using EdgeR.

first: Milica

last: Tosic

first: Delphine

last: Duteil

first: Dominica

last: Willmann

last: Schüle


title: Temporal transcriptome analysis of the white-rot fungus Obba rivulosa shows expression of a constitutive set of plant cell wall degradation targeted genes during growth on solid spruce wood

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: The basidiomycete white-rot fungus Obba rivulosa, a close relative of Gelatoporia (Ceriporiopsis) subvermispora, is an efficient degrader of softwood. The dikaryotic O. rivulosa strain T241i (FBCC949) has been shown to selectively remove lignin from spruce wood prior to depolymerization of plant cell wall polysaccharides, thus possessing potential in biotechnological applications such as pretreatment of wood in pulp and paper industry. In this work, we studied the time-course of the conversion of spruce by the genome-sequenced monokaryotic O. rivulosa strain 3A-2, which is derived from the dikaryon T241i, to get insights to transcriptome level changes during prolonged solid state cultivation. During 8-week cultivation, O. rivulosa expressed a constitutive set of genes encoding putative plant cell wall degrading enzymes. High level of expression of the genes targeted towards all plant cell wall polymers was detected at 2-week time point, after which majority of the genes showed reduced expression. This implicated non-selective degradation of lignin by the O. rivulosa monokaryon. These results suggest high variation between mono- and dikaryotic strains of the white-rot fungi with respect to their abilities to convert plant cell wall polymers.

overall_design: The aim of the study is to study nutritional demands during a prolonged cultivation on wood by looking at the transcriptome at different time points, with special interes at CAZymes and central carbon metabolic genes. Obba rivulosa 3 A-2 growing on its natural substrate, spruce wood sticks was studied after 2, 4 and 8 weeks of solid state cultivation in order to follow wood depolymerization in more natural like conditions.

first: Mila

last: Marinović

first: Maria

middle: V

last: Aguilar-Pontes

first: Miaomiao

last: Zhou

first: Otto

last: Miettinen

first: Miia

last: Mäkelä

first: Kristiina

last: Hildén


title: CSL ChIP-Seq on human keratinocytes

summary: Down-modulation or loss-of-function mutations of the Notch 1 and 2 genes are associated with development of squamous cell carcinoma (SCC), a very frequent and therapy-resilient malignancy in skin, head/neck (H/N), lung and other surface epithelia. In this context, surprisingly little is known on the role of CSL (RBP-Jk), key effector of canonical Notch signaling endowed with intrinsic transcription repressive function. CSL expression is decreased in upper epidermal layers and differentiating primary human keratinocytes (HKCs), while it is up-regulated in premalignant and malignant SCC lesions and SCC cell lines from skin, Head/Neck and lung. Increased CSL levels enhance proliferation and self-renewal potential of HKCs and SCC cells, while its silencing induces growth arrest and apoptosis. In vivo, SCC cells with increased CSL levels give rise to rapidly expanding tumors, while upon CSL silencing they form smaller and more differentiated tumors with enhanced inflammatory infiltrate. Global transcriptomic analysis of HKC and SCC cells plus/minus CSL silencing reveals major modulation of apoptotic, cell cycle and pro-inflammatory genes, with no significant association with Notch or keratinocyte differentiation gene signatures. KDM6B, a histone demethylase gene with highly context dependent functions, is a direct CSL negative target, with an inverse role of CSL in HKC and SCC self-renewal and tumorigenesis, with IL6 as a target of likely significance. CSL / KDM6B protein expression could be used as biomarkers of SCC development and novel indicators of cancer treatment.

overall_design: CSL ChIP-Seq on HKCs (human keratinocytes)

first: Dania

last: Al Labban

first: Seung-Hee

last: Jo

first: Paola

last: Ostano

first: Massimo

last: Bongiovanni

first: G

last: Dotto


title: WT and IFN-I receptor deficient mouse macropahge expression profiling under virus infection or under IFNb stimulation

status: Public on Dec 14 2017

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

country: China

institute: SMMU

summary: To investigate the role of lncRNAs in viral infection and their relationship with the IFN-I system, we profiled lncRNA expression in wild type (WT) and IFN-I receptor deficient (Ifnar-/-) cells infected with or without vesicular stomatitis virus (VSV).

overall_design: Examination of RNA transcriptome of mouse macrophage in VSV infection or IFNb direct stimulation through high throughout microarray.

first: Pin

last: Wang


title: Identification of H3 Lysine 4 monomethylation Associated Proteins at Mammalian Enhancers

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

summary: Enhancers act to regulate cell type specific gene expression by facilitating the transcription of target genes. In mammalian cells active or primed enhancers are commonly marked by mono-methylation of Histone H3 at lysine 4 (H3K4me1) in a cell-type specific manner. While this histone modification regulates enhancer-dependent transcription programs in mammals, the exact mechanism has remained unclear. In the current study, we conducted SILAC Mass-spec experiments with mono-nucleosomes and identified multiple H3K4me1 associated proteins, including the mediator complex, Cohesin complex, as well as proteins involved in chromatin remodeling. We demonstrate that binding of these protein complexes to enhancers in vivo depends on H3K4me1. We have characterized the PHD domains of DPF1-3 and PHF10  and identified the amino acids involved in binding to H3K4me1. In addition, we discovered that H3K4me1 nucleosomes are more efficiently remodeled by BAF complex in vitro. Our results suggest that H3K4me1 plays an active role at enhancers through binding of a diverse set of chromatin regulators.

overall_design: Examination of colocalization of multiple chromatin regulator complexes with H3K4me1 and dependency on H3K4me1 at mouse enahncers.

first: Andrea

last: Local

first: Inkyung

last: Jung


title: The transcriptome of livers in WT mice and lncRNA-ACOD1 knockout mice

summary: To gain an understanding of lncRNA-ACOD activity, we performed transcriptome analysis with microarray using liver tissues from mice with or without VSV for 12 hrs.

overall_design: We preformed our transcriptome microarray analysis (GENE 1.0, Affymetix) in lncRNA-ACOD1-/- and lncRNA-ACOD1+/+ liver tissues from mice infected with or without VSV for 12 hrs.


title: Mouse macropahge RNA-seq with or without virus infection

overall_design: Examination of RNA transcriptome of mouse macrophage in VSV infection through high throughout sequencing.

first: Xuetao

last: Cao


title: GOT2 binding RNA RIP-seq

summary: Flag-taged GOT2 binding RNAs were analyzed by imprinting RNA-sequencing of Flag antibody-retrieved complexes from MEF cells lysis.

overall_design: Examination of GOT2 binding site in RNA transcriptome of MEF


title: Ribosome binding RNA from mouse macrophage cells

summary: Ribosome binding RNAs were analyzed by imprinting RNA-sequencing of ribosome-retrieved complexes from mouse macrophage cells lysis.

overall_design: Examination of ribosome binding in RNA transcriptome of mouse macrophages


title: Gcn5 regulates FGF signaling outputs through c-Myc during early differentiation of embryoid bodies [ChIP-Seq]

city: Smithville

first: Li

state: TX

address: 1808 Park Rd 1C

department: Epigenetics and molecular carcinogenesis

institute: UT-MD Anderson Cancer Center

summary: Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers.  How particular chromatin modifying enzymes affect specific developmental processes is not well defined. Here we report that Gcn5, a HAT essential for embryonic development, is largely required for c-MYC target gene transcription downstream of FGF signaling in early embryoid bodies (EBs). Gcn5 null EBs display deficient activation of ERK and p38, disorganized cytoskeletal networks, and compromised capacity to differentiate toward mesodermal and endodermal lineages. These findings establish a regulatory role for Gcn5 in execution of a critical signaling pathway during early development.

overall_design: Day 5 embryoibodies (EBs) derived from Gcn5fx/fx (4_1, 6_1) and Gcn5-/- (4_C2, 6_C4) ES cells were subject to H3K9ac ChIP-seq experiments, in order to examine the changes in genomewide distribution of H3K9ac upon Gcn5 loss at early differentiation stage. ChIP DNA from 4 independent replicative experiments, including 2 replicates for each isolate pair (Gcn5fx/fx and Gcn5-/-), were used for deep sequencing.

first: Sharon

middle: Y

last: Dent

first: Yue

last: Lu


title: Gcn5 regulates FGF signaling outputs through c-Myc during early differentiation of embryoid bodies


title: Paternal easiRNAs establish the triploid block in Arabidopsis

city: Uppsala

first: Juan

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

institute: SLU

summary: Polyploidy, the presence of more than two sets of chromosomes within the nucleus, is a common phenomenon among plants that has shaped genome organization and is thought to be a major driver of speciation. The triploid block acts as a reproductive barrier that prevents successful backcrosses of newly formed polyploids with their progenitors. It is established in the endosperm, an ephemeral tissue that nurtures the developing embryo. Here we show that paternal 21/22 nucleotide epigenetically activated small interfering RNAs (easiRNAs) in Arabidopis thaliana are responsible for the establishment of the triploid block associated seed abortion. This dramatic phenotype is overcome when crosses are performed with a paternal mutant in the plant specific RNA polymerase IV (Pol IV). Loss of Pol IV reduces both easiRNAs and hetsiRNAs in the pollen grain. Seeds derived from crosses between wild type tetraploid fathers and diploid mothers have reduced levels of hetsiRNAs and cytosine methylation at transposable elements (TEs), indicating that they have suffered an excess of epigenetic reprogramming due to an excess of paternally derived easiRNAs. Paternal Pol IV mutants are able to buffer that easiRNA excess and rescue the abortion phenotype by rescuing both the cytosine methylation level at TEs and the 24 nt hetsiRNA accumulation levels. This mechanism highlights the elegant and important TE regulation mechanism controlled by the plant specific Pol IV that takes place pre-fertilization and regulates paternal easiRNAs and maternal hetsiRNAs, and determines the post-fertilization epigenetic stability and seed viability.

overall_design: 15 small RNA sequencing libraries, 8 genome-wide cytosine methylation libraries and 8 RNA-seq libraries. 7 small RNA libraries were generated from mature pollen grains of diploid and tetraploid Col-0 wt and nrpd1a mutants (1n and 2n pollen, respectively) and Col-0 wt and the mutant backgrounds dcl4 rdr6 and rdr6. 8 small RNA libraries were generated from seeds at 6 days after pollination from the cross of maternal Ler with paternal Col-0 wt and the mutant backgrounds osd1,nrpd1a, and nrpd1a osd1. 8 cytosine methylation libraries were generated from hand-dissected endosperm at 6-7 days after pollination from the cross of maternal Ler with paternal Col-0 wt and the mutant backgrounds osd1,nrpd1a, and nrpd1a osd1. 8 RNA-seq libraries were generated from hand-dissected endosperm at 6-7 days after pollination from the cross of maternal Ler with paternal Col-0 wt and the mutant backgrounds osd1,nrpd1a, and nrpd1a osd1.

first: German

last: Martinez

first: Philip

last: Wolff

first: Zhenxing

first: Jordi

last: Moreno-Romero

last: Santos-Gonzalez

first: Lei

last: Liu Conze

first: Christopher

last: DeFraia

first: Keith

last: Slotkin

first: Claudia

last: Köhler


title: Single Cell DNA Methylome Sequencing of Human Preimplantation Embryos

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

type: Genome variation profiling by high throughput sequencing

summary: Although the DNA methylome of human early embryos has been analyzed, some of the key features have not been addressed to date. Here, we performed single-cell DNA methylome sequencing for human preimplantation embryos and found that tens of thousands of genomic loci exhibited de novo DNA methylation. This finding indicates that genome-wide DNA methylation reprogramming during preimplantation development is a dynamic balance between strong global demethylation and significant focused re-methylation. Furthermore, the demethylation of the paternal genome is much faster and thorough than that of the maternal genome. From the 2-cell to post-implantation stage, methylation of the paternal genome is consistently lower than that on the maternal genome. We also showed that the genetic lineage of the early blastomeres could be traced by DNA methylation analysis. Our work paves the way for deciphering the secrets of DNA methylation reprogramming in human early embryos.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We did single cell PBAT DNA methylome sequencing analysis for cells from human mature oocytes and preimplantation embryos. For each individual cell, we sequenced 8.4 Gb of data on average.

first: Ping

last: Zhu

first: Yixin

first: Yu

last: Hou

first: Liying

last: Yan

first: Jie

last: Qiao

first: Fuchou

last: Tang


title: Transcriptomic analysis of CD11b+ DsRed+ CD45hi cells harvested from the ischemic brain of Selplg-KODsRed → WT chimeras and Selplg-WTDsRed→ WT chimeras at 7 days after 30 min MCAo/reperfusion

status: Public on Dec 13 2017

city: Berlin

first: Ria

last: Göttert

address: Charitéplatz 1

department: experimental Neurology

institute: Charité

summary: In order to assess whether PSGL-1 (SELPLG) deficiency impacts key characteristics of invading cells in our stroke model, we performed a detailed transcriptomic analysis of retrovirally transduced CD11b+ CD45hi cells harvested from the ischemic brain at 7 days after MCAo

overall_design: Comparison of FACS sorted Psgl1+/+ (PI- DsRed+ CD11b+ Ly6G- CD3- CD45hi) and Psgl1-/- (PI- DsRed+ CD11b+ Ly6G- CD3- CD45hi) cells from ischemic brain tissue at 7 days after 30 min MCAo/ reperfusion.

first: Karen

last: Gertz

last: Uhlemann


title: Pan-genome and methylome analysis reveals the diversity of restriction/modification systems in the gut commensal Bifidobacterium breve.

city: Cork

first: Francesca

last: Bottacini

address: Western Road

department: APC Microbiome Institute & School of Microbiology

country: Ireland

institute: University College Cork

summary: Bifidobacterium breve represents one of the most abundant (bifido)bacterial species in the gastro-intestinal tract of (breast-fed) infants, where their presence is believed to be beneficial. In the present study whole genome sequencing, employing PacBio’s Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variome. Availing of the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BiSeq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, cloning of a selected methyltransferase-encoding gene validated the activity of the corresponding R/M system, and was shown to overcome the barrier they impose to genetic accessibility, thus allowing future genetic manipulation of members of this species.

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Following growth, total bifidobacterial DNA was isolated as described by O’Riordan et al. (1998) and then labelled using the Kreatech ULS labelling kit according to the manufacturer’s instructions (Kreatech, Amsterdam, The Netherlands). Labelled total gDNA was hybridised as described in the Agilent manual Two-Color Microarray-Based Gene Expression Analysis (v4.0) (publication no. G4140-90050) to the B. breve UCC2003 microarray slides (feature format: 4 x 44K and 2 x 11 K) overnight at 65 °C (NB. B. breve UCC2003 was used as the reference strain and as a positive control). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data sets were processed as previously described (Garcia De La Nava et al., 2003). Differential signal intensity tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). Data were analysed and visualized using the Multi-experiment Viewer Tmev v.4.9 with hierarchical clustering analysis based on covariance method and complete linkage.

first: Ruth

last: Morrissey

first: Douwe

last: van Sinderen


title: Genome-wide Lsd1 chromatin occupancy in myoblast C2C12 cells by chromatin immunoprecipitation using an Lsd1 antibody followed by massive parallel sequencing

first: Roland

last: Schuele

summary:
Purpose: The aim of this study is to identify the Lsd1 genome binding profile in myoblast C2C12 cells during myogenic and adipogenic differentiation.
ChIP-seq libraries were prepared, sequenced using the standard Illumina protocol (HiSeq2000, single read, 50 bp v3), and mapped to the mouse mm10 reference genome by Bowtie. Data were further analyzed using the peak finding algorithm MACS 1.4.2. Homer software was used to annotate peaks, and all peaks with false discovery rate less than 1 % were included.

overall_design: For ChIP-seq experiment, C2C12 cells were fixed for 6 minutes with 1 % PFA at 4 °C followed by 5 minutes blocking in 125 mM glycine. Nuclei preparation was performed using previously described NEXON protocol (Arrigoni et al., 2015), by sonicating the cells with Covaris E220 focused ultrasonicator for 2 minutes at peak power 75 W, duty factor 2 % and 200 Cycles/burst at 4 °C. Chromatin was sheared using Covaris E220 focused ultrasonicator to obtain a fragment size distribution of 100–800 bp (peak power: 140 W; Duty factor: 5 %; Cycles/burst: 200, water temperature 4 °C). Chromatin was immunopercipitated using homemade antibody directed against C-terminus of Lsd1 protein (Biogenes, 20752).

first: Milica

last: Tosic

first: Delphine

last: Duteil

first: Dominica

last: Willmann

first: Laura

last: Arrigoni

last: Schüle


title: Replication stress shapes a protective chromatin environment across fragile genomic regions

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

summary: Recent integrative epigenome analyses highlight the importance of functionally distinct chromatin states for gene regulation, cellular differentiation and accurate cell function. How these states are established and maintained is a matter of intense investigation. Here, we present evidence for DNA damage as an unexpected means to shape a protective chromatin environment at genomic regions of recurrent replication stress. Upon aberrant fork stalling within these fragile regions, DNA damage signaling and concomitant H2AX phosphorylation coordinate the FACT histone chaperone -dependent deposition of macroH2A1.2, a histone H2A variant that promotes DNA repair by homologous recombination (HR). MacroH2A1.2, in turn, facilitates the accumulation of the tumor suppressor and HR effector BRCA1 at replication forks to protect from replication stress-induced DNA damage. Consequently, replicating primary cells steadily accrue macroH2A1.2 at fragile regions, whereas macroH2A1.2 loss in these cells triggers DNA damage signaling-dependent senescence, a hallmark of replication stress. Altogether, our findings demonstrate that recurrent DNA damage critically contributes to the chromatin landscape to ensure both the epigenetic and functional integrity of dividing cells.

overall_design: Detection of the histone protein macroH2A1.2 via ChIP-Seq, along with the DNA damage marker gH2Ax, in wild-type K562 and in conditions of macroH2A deficiency or ablation, before and after induction of replication stress

first: Jeongkyu

last: Kim

first: Robin

last: Sebastian

first: Andy

last: Tran

first: Garrett

last: Edwards

first: Simran

last: Khurana

first: Alex

last: Kruswick

first: Sandra

last: Burkett

first: Eri

last: Hosogane

first: Urbain

last: Weyemi

first: William

last: Bonner

first: Karolin

last: Luger

first: Philipp

last: Oberdoerffer


title: The Adenovirus E1A C Terminus Suppresses a Delayed Antiviral Response and Modulates RAS Signaling [IRF3_ChIP]

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: UCSD

summary: The N-terminal half of adenovirus e1a assembles multimeric complexes with host proteins that repress innate immune responses and force host cells into S-phase. In contrast, the functions of e1a's C-terminal interactions with FOXK, DCAF7, and CtBP are unknown. We found that these interactions modulate RAS signaling, and that a single e1a molecule must bind all three of these host proteins to suppress activation of a subset of IFN-stimulated genes (ISGs). These ISGs were otherwise induced in primary respiratory epithelial cells at 12 hr p.i. This delayed activation of ISGs required IRF3 and coincided with an ∼10-fold increase in IRF3 from protein stabilization. The induced IRF3 bound to chromatin and localized to the promoters of activated ISGs. While IRF3, STAT1/2, and IRF9 all greatly increased in concentration, there were no corresponding mRNA increases, suggesting that e1a regulates the stabilities of these key activators of innate immune responses, as shown directly for IRF3.

overall_design: Examination of IRF3 binding profile by ChIP-seq

first: Nathan

last: Zemke

first: Arnold

middle: J

last: Berk


title: Purification of replicating pancreatic β-cells for gene expression studies

city: Vic

first: NOELIA

last: TELLEZ

state: Barcelona

address: Can Baumann. Carretera de Roda, 70

department: Department of Medicine

country: Spain

institute: UVIC-UCC

summary:
β-cell proliferation is a rare event in adult pancreatic islets. To study the replication-related β-cell biology we designed a replicating β-cells sorting system based on EdU incorporation for gene expression experiments.
The global transcriptome of replicating and quiescent pancreatic β-cells was analysed using gene expression arrays.

overall_design: 6 samples were included in the experimental design, from 3 different batches of islets. Each batch of islets was obtained from 4 rats and contained a biological replicate of replicating beta cells, and a biological replicate of quiescent beta cells.

first: Reyes

last: Carballar

first: Maria

middle: d

last: Canyelles

first: Claudia

last: Fernández

first: Yasmina

last: Martí

first: Sarah

last: Bonnin

first: Esther

last: Castaño

first: Eduard

last: Montanya

first: Noèlia

last: Téllez


title: Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003

first: Francesca

last: Bottacini

type: Expression profiling by genome tiling array

summary: The recognition specificity and associated affinity of the RNA polymerase sigma subunit towards its cognate promoter sequence is one of the elements contributing to the modulation of gene expression in bacteria. In the present study we identified and assessed vegetative promoters of the bifidobacterial prototype Bifidobacterium breve UCC2003 employing a combination of tiling array analysis and RNA sequencing. By combining and comparing the outputs of these two distinct technologies we were able to identify a number of transcriptional units, including their initiation and termination signals, which correspond to promoters and terminators, respectively. Canonical -10 (TATAAT) and -35 (TTGACA) sequences were identified upstream of transcribed genes or operons, where deviations from this consensus correspond to transcription level variations. Using a Random Forest approach, we were able to define promoter characteristics that most substantially impact on transcription in B. breve. We observed that constitutively transcribed genes frequently encode house keeping functions that are part of the core and essential genome of this species. A comparative analysis between the tiling array-based and RNA-seq technologies allowed us to evaluate their performance and applicability for investigations on (regulation of) bifidobacterial gene expression.

overall_design: Complete genome tiling arrays containing oligonucleotide primers of 60 bp (designed on a 22nt sliding window) across the forward and reverse strand of the genome sequence of B. breve UCC2003 (O'Connell Motherway et al., 2011). Probes were obtained from Agilent Technologies (Palo Alto, Ca., USA). Overnight culture of B. breve UCC2003 was inoculated into 2 % glucose MRS (Difco) medium until reaching mid-log phase (OD600 of 0.5). Following growth, total bifidobacterial DNA and RNA was isolated as described previously (O' Connell Motherway et al., 2011). Labelling was performed using the Kreatech ULS labelling kit according to the manufacturer’s instructions (Kreatech, Amsterdam, The Netherlands). Labelled total gDNA and mRNA was hybridized as described in the Agilent manual Two-Color Microarray-Based Gene Expression Analysis (v4.0) (publication no. G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data sets were processed as previously described (Garcia De La Nava et al., 2003). Differential signal intensity between gDNA (baseline) and mRNA (transcriptome)  were analyzed using the Limma package implemented in the statistical environment R (https://cran.r-project.org)

first: Aldert

last: Zomer

first: Douwe

last: van Sinderen


title: Arid1a promotes tumor initiation but restrains progression and metastasis in liver cancer [ChIP-Seq]

city: shanghai

first: Xuxu

last: Sun

address: 227 south chongqing road

department: school of medicine

institute: shanghai jiao tong university

summary: ARID1A is hypothesized to be one of the most common tumor suppressors in human cancer.  However, the functional consequences of ARID1A gain and loss are not clear. We report that  mice with complete liver-specific Arid1a deficiency were resistant to MYC induced  liver carcinogenesis, indicating a requirement during tumor initiation. Mechanistically, Arid1a loss  constrained tumor formation by reducing Cytochrome P450 expression, which in turn mitigated  oxidative stress. We also examined the heterozygous state and found it potentiated metastasis formation and heterozygous has similar gene accessibility pattern with homozygous compared to WT.

overall_design: Liver tumor tissues were collected from LAP-MYC; Arid1a WT,Arid1a Het and Arid1a Homo knockout mice, then fixed and genomic DNA were isolated. Analysis of genomic occupancy of c-MYC in the cells from LAP-MYC;Arid1a WT,Arid1a Het and Arid1a Homo liver tumors by Chip-seq.

first: Sam

last: Wang

first: Luo

last: Xin

first: Hao

last: Zhu


title: An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus

city: Stockholm

first: Kristina

last: Jonas

address: Svante Arrheniusväg 20 C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

institute: Stockholm University

summary: Hsp70 chaperones are well known for their important functions in maintaining protein homeostasis during thermal stress conditions. In many bacteria the Hsp70 homolog DnaK is also required for growth in the absence of stress. The molecular reasons underlying Hsp70 essentiality remain in most cases unclear. Here, we demonstrate that DnaK is essential in the α-proteobacterium Caulobacter crescentus due to its regulatory function in gene expression. Using a suppressor screen we identified mutations in genes coding for different components of the transcriptional machinery as well as an ATP dependent protease that allow growth in the absence of DnaK. These mutations reduced the activity of the heat shock sigma factor σ32 by different mechanisms, suggesting that DnaK's sole essential function in the absence of stress is the inactivation of σ32. We found that σ32 inhibits growth and that its unleashed activity leads to an extensive reprogramming of global gene expression, which re-allocates cellular resources from proliferative to maintenance functions. While this re-allocation provides an advantage during heat stress, it leads to detrimental growth defects under favorable conditions. We conclude that Caulobacter has co-opted the DnaK chaperone system as an essential regulator of gene expression under conditions when its folding activity is dispensable.

overall_design: RNA-sequencing was performed to determine gene expression changes after 6 and 9 h of depletion of DnaKJ in the PxylX-dnaKJ and PxylX-dnaKJ, rpoHD252G background, after 6 h of depletion in the PxylX-dnaKJ, ∆rpoH background as well as 2 h of overexpression of rpoH(V56A) in a PdnaK::Tn background. The RNA abundance of each sample was compared to undepleted PxylX-dnaKJ cells.

first: Frederic

last: Schramm


title: BCG reprogramming of hematopoietic stem cells generates protective innate immunity against tuberculosis (RNA-Seq)

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

summary: The dogma that adaptive immunity is the only arm of the immune response with memory capacity has been recently challenged by several studies demonstrating evidence for memory-like innate immune training. However, the underlying mechanisms and location for generating such innate memory responses in vivo remains unknown. Here we show that access of Bacillus CalmetteGuérin (BCG) to the bone marrow (BM) following intravenous immunization induced local hematopoietic stem cell (HSC) expansion and enhanced myelopoiesis at the expense of lymphopoiesis. Importantly, HSC reprogramming led to the generation of epigeneticallymodified macrophages that provided significantly better protection against virulent M. tuberculosis infection than naïve macrophages. By using parabiotic and chimeric mice as well as adoptive transfer approaches, we demonstrate that training of the monocyte/macrophage lineage via BCGinduced HSC reprogramming is sustainable in vivo. Our results indicate that targeting the HSC compartment provides a novel approach for vaccine development.

overall_design: Expression profiles in non-infected and MTB-infected bone marrow-derived macrophages from Control vs BCGiv vaccinated mice

first: Eva

last: Kaufmann

first: Jonathan

middle: L

last: Dunn

first: Joaquin

last: Sanz

first: Nargis

last: Khan

first: Alain

last: Pacis

first: Fanny

last: Tzelepis

first: Erwan

last: Pernet

first: Anne

last: Dumaine

first: Jean-Christophe

last: Grenier

first: Eisha

last: Ahmed

first: Jad

last: Belle

first: Rickvinder

last: Besla

first: Bruce

last: Mazer

first: Irah

last: King

first: Anastasia

last: Nijnik

middle: B

first: Maziar

last: Divangahi


title: BCG reprogramming of hematopoietic stem cells generates protective innate immunity against tuberculosis (ChIP-Seq)

first: Luis

last: Barreiro

overall_design: Examination of 3 types of histone modification in non-infected and MTB-infected bone marrow-derived macrophages, from control vs BCGiv vaccinated mice.


title: Rheostatic Chromatin Control of Promiscuous Transcription by Aire and Brg1 [Affymetrix]

city: Stanford

first: Andrew

middle: S.

last: Koh

address: 279 Campus Drive B203

institute: Stanford University

summary: Gene Expression Profiles of mTECs from Aire-/- and Brg1-/- mice and their littermate controls.

overall_design: DAPIneg, CD45neg, Epcam+, UEA+, Ly51lo, MHCIIhi and MHCIIlo mTECs were sorted from respective mice.  Total RNA was prepared using Trizol, cleaned-up with Qiagen RNeasy MicroKit, followed by amplification and cDNA preparation. cDNA was hybridized to Affymetrix 2.0 ST microarrays.

first: Erik

last: Miller

first: Jason

last: Buenrostro

first: David

last: Moskowitz

first: William

last: Greenleaf

first: Howard

last: Chang

first: Gerald

last: Crabtree


title: BCG reprogramming of hematopoietic stem cells generates protective innate immunity against tuberculosis

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

overall_design: Refer to individual Series


title: Arid1a promotes tumor initiation but restrains progression and metastasis in liver cancer

first: Xuxu

last: Sun


title: Capturing the Interactome of Newly Transcribed RNA (PAR-CLIP)

status: Public on Dec 12 2017

city: Guangzhou

first: Xiangpeng

last: Guo

address: 190 Kaiyuan Avenue, Science Park, Guangzhou , China

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

summary: Key features of gene transcription, such as transcriptional pausing, divergent transcription, and enhancer RNA production can be explored using techniques based on the incorporation of synthetic nucleoside analogs into RNA, followed by pull-down and high-throughput sequencing. Whether these approaches can be adapted to expand our knowledge of the RNA-bound proteome is, however, unexplored. Here, we have designed a methodology (isolation of the newly transcribed RNA Interactome using ClicK reaction; RICK) based on the incorporation of 5-ethynyluridine (EU) into newly transcribed RNAs to systematically capture proteins bound to RNAs of wide scope including traditionally neglected non-polyadenylated RNAs. Amongst the novel RNA-binding proteins identified by RICK, we found mitotic regulators, components of the DNA damage response pathway, and epigenetic regulators. Because the protocol can be easily modified to include variations such as labeling time or transcriptional interference, RICK will enable an in depth and global interrogation of the RNA-bound proteome.

overall_design: Perform 2 independent PAR-CLIP sequencing experiments for CDK1 and METTL1 in HEK293T cells

first: X

last: Bao

first: M

last: Yin

last: Esteban


title: Capturing the Interactome of Newly Transcribed RNA (RICK)

overall_design: Perform RICK sequencing in HeLa cells


title: Capturing the Interactome of Newly Transcribed RNA


title: Single-Cell Analysis of Sensory Experience Regulated Gene Expression in Mouse Visual Cortex

status: Public on Dec 11 2017

city: Boston

first: Mark

middle: Aurel

last: Nagy

state: Massachusetts

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

summary: Single-cell (inDrops) analysis of primary visual cortex in visually stimulated mice

overall_design: 6-8 week old C57BL6/J mice were dark-reared for 7 days and exposed to light for 1h or 4h. Control mice were kept in the dark. V1 was dissected and single cell RNASeq performed.

first: Sinisa

last: Hrvatin

first: Daniel

last: Hochbaum

first: Bernardo

last: Sabatini

first: Michael

middle: E

last: Greenberg


title: Chromatin Open/Close Logic in Cellular Reprogramming [ChIP-Seq]

status: Public on Dec 09 2017

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: The reprogramming of fibroblasts into pluripotent stem cells by Oct4, Sox2, Myc and Klf4 represents a unique system to understand the logic of cell fate decisions. The reprogramming process can be divided into initial, middle and maturation phases that are coupled to the ordered execution of multiple biological processes, of which one of the earliest is a mesenchymal to epithelial transition (MET). Yet, despite these critical insights, less is known about how the reprogramming factors alter the chromatin state to convert somatic cells back to pluripotent cells. Here we report the global chromatin accessibility dynamics as cells reprogram from a somatic to a pluripotent state as assessed by assay for transposase-accessible chromatin with sequencing (ATAC-seq). We show that chromatin changes during reprogramming are defined by a fast initial wave of chromatin changes from accessible/open to inaccessible/closed (OC), which is followed by a slower opening up of chromatin from closed to open (CO), and ends with a climactic wave of CO. The initial OC wave includes loci enriched with motifs for AP-1, TEAD, RUNX and ETS-family transcription factors. Consistently, over-expression of one of the AP-1-family members c-Jun, c-Fos and Fra1blocked reprogramming. c-Jun inhibits reprogramming by preventing OSK-driven OC and skewing the overall OC-CO dynamics.  Paradoxically, we show that Sox2 and to a less extent Oct4 and Klf4 are CO-, not OC-, mediators , suggesting that they must first activate potent OC factors to remodel chromatin. Indeed, we show that Sap30, a component of the Sin3 complex8, functions as such an OC factor. Together, our results reveal the chromatin accessibility logic during reprogramming and identify Sap30 as one of the first responders that help silence somatic genes.

overall_design: chromatin accessible profile of reprogramming cell were generated by ATAC-seq, in two replicates, using illumina nextseq 500

first: Dongwei


title: Osteoblasts remotely supply lung tumors with cancer-promoting SiglecFhigh neutrophils

status: Public on Dec 08 2017

city: Richard B. Simches Research Center

first: Mikael

last: Pittet

state: 185 Cambridge Street

address: Center for Systems Biology, Massachusetts General Hospital

institute: CSB

summary: RNAseq (3'DGE) profiles of osteoblasts from four lung cancer-bearing mice and three tumor-free mice.

overall_design: Osteoblasts were FACS-sorted using the following markers: CD45-CD31-Terr119-GFP+ from lineage depleted bone and bone marrow tissue of lung tumor-bearing or tumor-free age-, sex- and litter-matched KrasLSL-G12D/WT;p53Flox/Flox (KP)-Ocn GFP mice. Total RNA was prepared using the Trizol method followed cDNA preparation, amplification, Illumina adapter ligation and 3'end sequencing by Illumina HiSeq 2500

last: Zemmour

first: Camilla

last: Engblom

first: Christina

last: Pfirschke


title: Arabidopsis MOS4-associated complex promotes microRNA biogenesis and pre-mRNA splicing [ncRNA-seq]

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

summary: The evolutionarily conserved, putative RNA helicase MAC7 exists in both animals and plants. The human MAC7 homolog, Aquarius, is part of the spliceosome and plays a role in pre-mRNA splicing in vitro. In Arabidopsis, MAC7 was shown to be part of the MOS4-associated complex (MAC), which is required for plant defense and development. Here through RNA-seq analysis we discover that down-regulated genes in MAC subunit mutants are mostly involved in plant defense and stimulus response, confirming a role of MAC in the regulation of biotic and abiotic stress responses. We also discover global intron retention defects in mutants in three members of MAC, thus linking the functions of MAC to splicing in Arabidopsis. In addition, we show that mac7-1, a partial loss-of-function mutant in MAC7, and two other MAC subunit mutants, mac3a mac3b and prl1 prl2, exhibit reduced microRNA levels in general, indicating that MAC promotes microRNA biogenesis. The mac7-1 mutant shows reduced primary miRNA (pri-miRNA) levels without affecting MIR promoter activity or the degradation of pri-miRNA transcripts, implicating functions of MAC7 during transcription elongation or maturation of pri-miRNAs. As a nuclear protein, MAC7 is not localized in dicing bodies, but it affects the localization of HYL1 to dicing bodies. We propose that MAC acts to link MIR transcription to pri-miRNA processing.

overall_design: Small RNAs were isolated from total RNA extracted from 12-day-old seedlings of Col-0, mac7-1, prl1 prl2 with 1 biological replicate for Col-0 and two biological replicates for mac7-1 and prl1 prl2.

first: Tianran

last: Jia

first: Xuemei

last: Chen


title: RNA-seq of the lacrimal gland mesenchymal tissue in control vs Shp2-deleted neural crest mouse embryos

city: New york

first: Xin

last: Zhang

state: New york

department: Ophthalmology

institute: Columbia University

summary: The goal of the study is to find the transcriptional targets downstream of Shp2-mediated signaling regulating Fgf10 production in the lacrimal gland mesenchyme. In order to look for the potential targets, we performed laser capture microdissection of the lacrimal gland mesenchyme tissue at embryonic day E14.5 from control embryos as well as mutant embryos containing neural crest-specific deletion of Shp2. After tissue harvest, RNA was extracted and conversion to cDNA as well as amplification was performed by NUGEN’s ovation kit v2. After preparation of cDNA library, each sample was sequenced using Illumina platform.

overall_design: For this experiment, one control sample and one mutant sample were analysed.

first: Ankur

last: Garg


title: BCG reprogramming of hematopoietic stem cells generates protective innate immunity against tuberculosis (ATAC-Seq)

first: Luis

last: Barreiro

overall_design: Examination of open chromatin profiles in non-infected bone marrow-derived macrophages, in control vs BCGiv vaccinated mice

first: Eva

last: Kaufmann

first: Jonathan

last: Dunn

first: Joaquin

last: Sanz

first: Nargis

last: Khan

first: Alain

last: Pacis

first: Fanny

last: Tzelepis

first: Erwan

last: Pernet

first: Anne

last: Dumaine

first: Jean-Christophe

last: Grenier

first: Eisha

last: Ahmed

first: Jad

last: Belle

first: Rickvinder

last: Besla

first: Bruce

last: Mazer

first: Irah

last: King

first: Anastasia

last: Nijnik

first: Maziar

last: Divangahi


title: Chromatin Open/Close Logic in Cellular Reprogramming [ATAC-Seq]

first: dongwei

last: Li

first: Dongwei


title: The Adenovirus E1A C Terminus Suppresses a Delayed Antiviral Response and Modulates RAS Signaling [Pol2_H3K18ac_H3K27ac_ChIP]

first: Bing

last: Ren

overall_design: Examination of Pol2, H3K18ac, H3K27ac, IRF3 and mRNA by ChIP-seq and mRNA-seq

first: Nathan

last: Zemke

first: Arnold

last: Berk


title: Chromatin Open/Close Logic in Cellular Reprogramming


title: Polymerases IV and V affect Pol II transcription termination

status: Public on Dec 10 2017

city: Bloomington

first: Ram

last: Podicheti

state: IN

institute: Indiana University

summary: Nuclear run-on assays reveal that in the absence of Pol IV or Pol V, Pol II occupancy downstream of poly A sites increases for approximately 12% of protein-coding genes.

overall_design: Analysis of nascent and steady-state RNA levels in pol IV (nrpd1-3) and pol V (nrpe1-11) mutant plants

last: McKinlay

first: Douglas

last: Rusch

first: Ross

last: Cocklin


title: 4sU-seq analysis for tethering hnRNPK to Xist lacking of XR-PID

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Xist lacking of XR-PID (B-repeat and part of C-repeat) can't  recruit the polycomb during X chromsome inactivation. The majoring of Xist-mediated chromosomal silencing wouldn’t be achieved. We found that hnRNPK was the one of main contributors for binding B-repeat of Xist. When we tethered hnRNPK to Xist which lacks of XR-PID region, the silencing and polycomb recruitment are restored.

overall_design: Cell lines were generated by randomly integrating Xist lakcing of XR-PID (mainly B-repeat) but with bgl sequence. The fused hnRNPK with bglG were engineered and consitutely expressed. After 3 days of Dox induced Xist RNA expression, 4sU were incorperated into the medium and incubated for 12 minutes, and 4sU-RNAs were isolated and then library preped for sequencing.

first: G

last: Pintacuda

first: N

last: Brockdorff


title: RNAseq in control and shQk KD mouse neural stem cells, and Qki5 CLIP in E14.5 mouse brain

city: Niigata

first: Masato

last: Yano

address: 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,

department: Division of Neurobiology and Anatomy

institute: Niigata University


title: RNAseq in control and shQk KD mouse neural stem cells

summary: We sequenced mRNA from mouse primary cultured neural stem cells infected with control or shQk lentivirus to compare gene expression level and alternative splicing events between 3 control and 3 shQk.

overall_design: mRNA profiles obtained from 3 different control and 3 shQk treated neural stem cells were generated by deep sequencing using Illumina Hiseq2500.

first: Yoshika

last: Hayakawa-Yano

first: Hideyuki

last: Okano


title: Qki5 CLIP in E14.5 mouse brain

summary: Mouse brains at E14.5 wild-type were subjected to HITS-CLIP to identify Qki5-binding positions on RNA.

overall_design: UV-irradiated mouse brain samples obtained from 3 different mouse brains were subjected to HITS-CLIP to identify in vivo Qki5-binding sites by using Illumina MiSeq.


title: Transcription Pausing Regulates Mouse Embryonic Stem Cell Differentiation [ATAC-seq]

city: Dallas

first: Xiaoying

last: Bai

state: Texas

address: 5323 Harry Hines Blvd., J7.130

department: Department of Obstetrics and Gynecology

institute: UT Southwestern Medical Center

summary: The pluripotency of embryonic stem cells (ESCs) relies on appropriate responsiveness to developmental cues. Promoter-proximal pausing of RNA polymerase II (Pol II) has been suggested to play a role in keeping genes poised for future activation. To identify the role of Pol II pausing in regulating ESC pluripotency, we have generated mouse ESCs carrying a mutation in the pause-inducing factor SPT5. Consistent with previous in vitro studies showing the pausing deficiency of this mutant SPT5, our genomic analysis reveals genome-wide reduction of paused Pol II in mutant mESCs. Furthermore, we find that genes differentially regulated by mutant SPT5 correlates with distinct chromatin states. Functionally, this pausing-deficient SPT5 disrupts ESC differentiation without affecting self-renewal.  Thus, our study uncovers an important role of Pol II pausing in regulating ESC differentiation and also suggests that Pol II pausing can both positively and negatively influence transcription depending on the local chromatin environment.

overall_design: using ATAC-seq to analyze chromatin accessibility in mouse ESCs in serum-free media

first: Melodi

last: Tastemel

first: Aishwarya

last: Gogate

first: Venkat

last: Malladi

first: Courtney

last: Mitchell

first: Laura

last: Banaszynski


title: Transcription Pausing Regulates Mouse Embryonic Stem Cell Differentiation


title: Transcription Pausing Regulates Mouse Embryonic Stem Cell Differentiation [GRO-seq]

overall_design: using Gro-seq to analyze transcription in wild-type and Spt5 mutant (Spt5V1008D) ESCs


title: 4sU-seq analysis of Xist-mediated chromosomal silencing

summary: The Polycomb repressive complexes PRC1 and PRC2 play a key role in chromosome silencing by Xist RNA. Previously we have shown that initation of Polycomb recruitment is mediated by the PCGF3/5-PRC1 complex, which catalyses chromosome-wide H2A ubiquitylation (H2AK119u1), signalling recruitment of other PRC1 complexes, and PRC2. However, the molecular basis for PCGF3/5-PRC1 recruitment by Xist RNA remains unknown. Here we define the Xist RNA Polycomb Interaction Domain (XR-PID), a 600 nt element encompassing the Xist B-repeat element. XR-PID is required for Polycomb recruitment by Xist RNA, Xist-mediated chromosome silencing. We identify the RNA-binding protein hnRNPK as the principal XR-PID binding factor required to recruit PCGF3/5-PRC1. Accordingly, synthetically tethering hnRNPK to Xist RNA lacking the B-repeat is sufficient for Xist-dependent Polycomb recruitment. Our findings resolve the molecular mechanism for Polycomb recruitment by Xist RNA, providing key insights into chromatin modification by non-coding RNA.

overall_design: Stable cell lines were derived by transfecting the FLXist, XistDXEv or some truncated Xist into P4D7, a Mus domesticus (129S1) x Mus castaneus F1 hybrid mouse embryonic stem cell (mESC) line. Use of a hybrid genetic background facilitated analysis of Xist-mediated silencing. Xist expression was induced upon the Dox treatment. Due to high amount of SNPs located in intronic region, we isolated the nascent transcripts labelled by 4sU, to quantify the silencing efficiency among different Xist constructs.


title: hnRNPK recruits PCGF3/5-PRC1 to the Xist RNA B-repeat to establish Polycomb mediated chromosomal silencing

overall_design: Refer to individual Series


title: Dynamic transcriptome analysis of human erythroind progenetor cells infected by human Parvovirus B19

status: Public on Dec 07 2017

city: Kansas City

first: Jianming

last: Qiu

state: KS

address: 3901 rainbow blvd

department: Microbiology

institute: University of Kansas Medical Center

summary: Human parvovirus B19 (B19V) infection can cause transient aplastic crisis, persistent viremia, and pure red-cell aplasia. In fetuses, B19V infection can result in non-immune hydrops fetalis and fetal death. To systematically investigate the interaction between B19V and erythoid progenetor cells (EPC), microarray was applied to systematically analyze the dynamic transcriptome of CD36+ EPCs during B19V infection.

overall_design: The mock- and B19V-infected CD36+ EPCs were collected at 6, 12, 24, and 48 hpi. RNA samples were extracted using the miRNeasy Mini Kit by following the manufacturer’s instruction. At each time points, 3 repeat samples were prepared. All RNA samples were analyzed on an Agilent 2100 Bioanalyzer with an Agilent RNA 6000 Nano Kit to ensure an RNA Intergrity Number (RIN) ≥ 8.0. Microarray hybridization was performed on the GeneChip Human Genome U133A 2.0 Array using the Affymetrix GeneChip system (Affymetrix, CA).

first: Aaron

last: Chen

first: Min

last: Xiong


title: Arabidopsis MOS4-associated complex promotes microRNA biogenesis and pre-mRNA splicing [RNA-seq]

city: Shanghai

first: Chenjiang

last: You

overall_design: Polyadenylated RNA was isolated from total RNA extracted from 12-day-old seedlings of Col-0, mac7-1, mac3a mac3b, prl1 prl2,with 2 biological replicates for each genotype.

first: Tianran

last: Jia

first: Xuemei


title: Changes in Bone Marrow Innate Lymphoid Cell Subsets In Monoclonal Gammopathy: Target For IMiD Therapy

city: New Haven

first: Kavita

last: Dhodapkar

address: 333 Cedar Street

institute: Yale

summary: We report an alteration in subset composition and function of ILCs in monoclonal gammapthy.

overall_design: Examine ILC1s and NK cells

first: Madhav


title: Directed hydroxyl radical probing reveals Upf1 binds 80S ribosomal E site rRNA at L1 stalk

status: Public on Dec 06 2017

city: Cambridge

first: Anthony

last: Schuller

state: MA

address: 77 Massachusetts Avenue, 68-480

department: Biology

institute: Massachusetts Institute of Technology

summary: Fe-BABE probing of Upf1 binding site on yeast ribosome

overall_design: Purified ribosomes are probed with Fe-BABE conjugated Upf1 proteins to identify the binding site

first: Boris

last: Zinshteyn

first: Syed

last: Enam

first: Rachel

last: Green