title: Delineating the Transcriptional Network of Prognostic Gene Signatures Refines Treatment Recommendations for Lymph Node-negative Breast Cancer Patients

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

institute: Trinity College Dublin

summary: We performed Chip-Seq analyses of several DNA binding transcription factors predicted to function as "master transcriptional regulators" (MTRs) of breast cancer prognostic gene signatures in primary human mammary epithelial cells (HMECs). These analyses demonstrated that these factors frequently co–bind the promoters of genes, the expression of which is associated with a proliferative phenotype and poor patient outcome. These data suggest that these predicted MTRs do indeed drive the expression of gene signatures associated with poor patient outcome in breast cancer.

overall_design: Examination of the genome–wide binding of breast cancer prognostic/proliferative transcription factors in proliferating breast cells.

first: Adrian

middle: P

last: Bracken

first: Gerard

last: Brien


title: APOBEC3B facilitates a functional and necessary link between oestrogen receptor mediated transcription and DNA repair

status: Public on Sep 30 2015

city: London

first: Luca

last: Magnani

address: DuCane road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College London

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Oestrogen receptor-α (ER) is the principal transcription factor in the majority of breast cancers, driving expression of genes that control cell growth and endocrine response. Understanding the mechanisms of ER action is crucial for improving response to endocrine treatments. Recent studies show that cytosine deaminase (CD) activity is an important source of cancer mutations. In particular, APOBEC3B (A3B) promotes mutagenesis in breast cancer cells1. Our analysis of breast cancer expression datasets showed that A3B expression predicts for poor survival in ER-positive, but not in ER-negative patients, indicative of a link with ER activity. Chromatin immunoprecipitation coupled to deep sequencing (ChIP-seq) used to map global A3B binding sites showed a remarkable oestrogen-stimulated recruitment of A3B to ER binding sites. Functionally, A3B was critical for ER transcriptional activity and regulated breast cancer cell proliferation. We show that A3B regulates ER transcription by promoting cytosine deamination and activation of DNA strand break repair at ER binding regions. We propose that cytosine deamination and DNA strand break generation by A3B facilitates gene expression by aiding chromatin remodeling at ER target genes. Our findings also suggest a mechanism by which subversion of transcription factor mediated recruitment of cytosine deaminases promotes cancer mutations.

overall_design: Hormone-depleted MCF-7 breast cancer cell line was treated with estrogen (100 nM) or vehicle for 45 minutes. APOBEC3B ChIP-seq was performed using Illumina methodology.

first: Simak

last: Ali


title: Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: First brain methylome and transcriptomic data of two simple eusocial insects: Polistes canadensis paper wasp and Dinoponera quadriceps dinosaur ant

sample_organism:
Polistes canadensis
Dinoponera quadriceps

overall_design: Bisulfite and RNA sequencing method on single brain

first: Solenn

last: Patalano

first: A

middle: V

last: Vlasova

first: C

last: Wyatt

first: P

middle: A

last: Ewels

first: F

last: Camara

middle: G

last: Ferreira

last: Asher

first: T

last: Jurkowski

last: Segonds-Pichon

first: M

last: Bachman

first: I

last: Gonzales

middle: E

last: Minoche

first: E

last: Lowy Gallego

last: Marcet-Houben

first: J

middle: L

last: Rodriguez-Ales

last: Nascimiento

first: S

last: Balsubramanian

last: Gabaldon

last: Tarver

last: Andrews

first: H

last: Himmelbauer

first: WO

middle: H

last: Hughes

first: R

last: Guigó

first: W

last: Reik

last: Sumner


title: mRNA- and RISC-sequencing of mouse hearts overexpressing miR-378a

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

country: USA

institute: Eli Lilly and Company

summary: Rationale: MicroRNAs play key roles in hypertrophic stress responses. miR-378(-3p) is a highly abundant, cardiomyocyte-enriched microRNA whose downregulation in pressure-overload has been suggested as detrimental to the heart. Previous studies have utilized systemic anti-miR or microRNA-encoding virus administration, and thus questions regarding the cardiomyocyte-autonomous roles of miR-378 remain.  Objective: To examine whether persistent overexpression of miR-378 in cardiomyocytes alters the phenotype of the unstressed heart, whether its overexpression is beneficial or deleterious in the setting of pressure-overload, and to comprehensively identify its cardiomyocyte-specific effects on mRNA regulation.  Methods and Results: Cardiac function was compared in young (10-12 week-old) mice overexpressing miR-378 in the heart under the control of the Myh6 promoter (alphaMHC-miR-378 mice), in older (40 week-old) mice and their age-matched wild-type controls. Older alphaMHC-miR-378 mice exhibited decreased fractional shortening and modest chamber dilation with an increase in cardiomyocyte length. When subjected to pressure-overload, cardiomyocyte length was increased in young alphaMHC-miR-378 mice, but fractional shortening declined precipitously over two weeks. Transcriptome profiling of wild-type and alphaMHC-miR-378 hearts in unstressed and pressure-overload conditions revealed dysregulation of several upstream metabolic and mitochondrial genes in alphaMHC-miR-378 hearts, compromising the reprogramming that occurs during early adaptation to pressure overload. Ago2 immunoprecipitation with mRNA sequencing revealed novel miR-378 cardiac mRNA targets including Akt1 and Epac2 and demonstrated the contextual nature of previously described miR-378 targeting events.  Conclusions: Long-term upregulation of miR-378 levels in the heart is not innocuous and exacerbates contractile dysfunction in pressure-overload hypertrophy through numerous signaling mechanisms.

overall_design: Cardiac polyadenylated RNA (mRNA) or RISC-seq (total RNA-seq of Ago2 immunoprecipitate) profiles were generated from nontransgenic and transgenic mouse hearts of FVB/N background, on Illumina HiSeq 2000 instruments.  Male mice 8-12 weeks of age were used in these studies, and subjected to sham surgery or 2 weeks of pressure-overload via transverse aortic constriction (TAC). 3 nontransgenic sham, 3 transgenic sham, 7 nontransgenic TAC, 7 transgenic TAC, each with mRNA-seq and RISC-seq data.

first: Gerald

middle: W

last: Dorn


title: Burkitt lymphoma cells vs. Lymphoblastoid B cells

city: Madrid

first: Miguel

middle: R

last: Campanero

address: Calle Arturo Duperier 4

department: Instituto de Investigaciones Biomedicas Alberto Sols

country: Spain

institute: Consejo Superior de Investigaciones Cientificas

summary: To identify genes mediating tumor transformation we compared the transcriptome of five Burkitt lymphoma (BL) cell lines (tumor cells) with that of a pool of three lymphoblastoid B-cell lines (LCL; immortal, but not tumor cells). Each BL cell line was considered as a biological replicate. BL cell lines: DG-75, Ramos, BL2, Mutu-I and Akata. LCL cell lines: X50-7, IB4 and Dana.

overall_design: Two-condition experiment, BL vs. pool of LCL. Biological replicates: 5 BL cell lines, 1 pool of LCL cell lines, independently grown and harvested. One replicate per array.


title: Transcriptome Profiling of Chinese White Pear (Pyrus bretschneideri Rehd.) During Fruit Development and Maturation

city: Hefei

first: cong

middle: bing

last: fang

state: Anhui

address: No. 130 Changjiang West Road

department: School of Horticulture

country: China

institute: Anhui Agricultural University

summary: Although pear is an important edible fruit species, the current available genomic information is limited. Combining the Solexa/ Illumina RNA-seq high-throughput sequencing approach with Digital Gene Expression (DGE) analysis results in a powerful transcriptomic study. This publication reports the transcriptome profiling analysis of Pyrus bretschneideri Rehd. using RNA-seq and DGE in order to better understand the molecular mechanisms underlying biological aspects of pear, especially fruit development and maturation.Using high-throughput Illumina RNA-seq combined with a tag-based Digital Gene Expression (DGE) system, de novo transcriptome assembly and gene expression analysis of P. bretschneideri were performed at an unprecedented depth (5.47 gigabase pairs). Approximately 60.77 million reads were obtained, trimmed, and assembled into 90,227 unigenes.  The unigenes comprised 17,619 contig clusters and 72,608 singletons and were an average length of 508 bp and had an N50 of 635 bp. Sequence similarity analyses against six public databases (Uniprot, NR and COGs at NCBI, Pfam, InterPro and KEGG) found 61,636 unigenes that could be annotated with gene descriptions, conserved protein domains, or gene ontology terms. 34.6% of the unigenes (31,215) were annotated against KEGG into 121 known metabolic or signaling pathways. DGE libraries of five different developmental fruit stages were constructed and analyzed, and the gene expression variations between two consecutive stages were compared. Thousands of genes showed significantly different expression levels based on the various comparisons. Extensive transcriptome and DGE profiling data have been obtained from the deep sequencing of the Chinese white pear, which can serve as an important public information platform for gene expression, genomic, and functional genomic studies in P. bretschneideri and which provides comprehensive gene expression information at the transcriptional level that could facilitate understanding of the molecular mechanisms in fruit development and maturation.

overall_design: 5 samples examined:pear fruit developmental stage 1(fs1),pear  fruit developmental stage 2(fs2),pear fruit developmental stage 3(fs3),pear fruit developmental stage4(fs4),pear fruit developmental stage 5(fs5).

first: Congbing

last: Fang


title: Neutrophils oppose uterine epithelial carcinogenesis via debridement of hypoxic tumor cells

status: Public on Sep 29 2015

city: New York

first: Adam

last: Blaisdell

state: New York

address: 522 First Avenue, SRB 307

institute: NYU School of Medicine

summary:
Our study demonstrates that neutrophils infiltrate early-stage PTEN-deficient uterine tumors and oppose tumor growth and malignant progression by inducing detachment and ultimately promoting cell death of tumor cells.
This RNA-seq study examined the expression profiles of these uterine epithelial tumor cells in the presence versus absence of neutrophil infiltration.

overall_design: Tumor cells from 4-week-old tumor-bearing neutrophil-sufficient versus -deficient mice were isolated by fluorescence activated cell sorting, RNA was isolated, and expression profiles were analyzed by deep sequencing.

first: Adrian

last: Erlebacher


title: Modulation of the ileal microbiota by green tea in broiler

city: hefei

first: xing

middle: yong

last: chen

state: anhui

address: 130 West Changjiang Road

department: School Of Animal Science And Technology

summary: The effects of increasing addition of green tea in dietary changes the bacterial populations in broiler ileum were evaluated. Four hundreds of AA broilers were randomly assigned to four groups with green tea addition of 0, 0.5, 1 and 2 percent in the diet. The body weight showed no difference but a digital increase positively correlated with addition of green tea. The content of green tea had a linear effect of lengthening the ileum villi. The barcoded DNA pyrosequencing method was used to reveal 15 phyla, 1157phylotypes and 3098 16S operational taxonomic units (OTUs). The most predominant bacterial phyla were Firmicutes (56.89%), Actinobacteria (30.58%), Proteobacteria (8.61%) and Bacteroidetes (2.72%). As the proportion of additional green tea increased, the abundance of phylum Actinobacteria (p=0.003) and Proteobacteria (p=0.049) almost linearly increased, while the proportion of Firmicutes (p=0.027) linearly decreased. Only 2 OTUs were significantly affected by the increased additive, Corynebacteriaceae (p=0.011) and Staphylococcaceae (p= 0.006). Triplot analysis suggested that the dominant phyla of Verrucomicrobia, TM7 and Actinobacteria were clearly related to the addition of green tea. Moreover, green tea addition influenced the construction of microbiota, and lengthened the villus in ileum by Monte Carlo permutation test. These findings provide a new understanding of the ileal microbial ecology, which may be useful in modulating the gut microbiome, and also the proper usage of powdered green tea.

overall_design: On  d 42 of the experiment, following a 12-h fast, 3 broilers from each group were randomly selected and weighted, then subjected to slaughter according to the Welfare of Animal Slaughter Regulations of China.

first: X

last: Chen

first: Q

last: Huang

first: Y

last: Zhou

first: Z

last: Geng

last: Wan


title: Global Epigenomic Analysis Indicates that Epialleles Contribute to Allele-specific Expression via Allele-specific Histone Modifications in Hybrid Rice

city: Wuhan

first: Zhibin

last: Guo

address: Luo Jia Shan

institute: Wuhan University

summary: We used chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) to investigate the global ASHM profiles of trimethylation on histone H3 lysine 27 (H3K27me3) and histone H3 lysine 36 (H3K36me3) in two rice F1 hybrids. A total of 522 to 550 allele-specific H3K27me3 genes and 428 to 494 allele-specific H3K36me3 genes were detected in GL×93-11 and GL×TQ, accounting for 11.09% and 26.13% of the total analyzed genes, respectively. The epialleles between parents were highly related to ASHMs. Further analysis indicated that 52.48% to 70.40% of the epialleles were faithfully inherited by the F1 hybrid and contributed to 33.18% to 46.55% of the ASHM genes. Importantly, 66.67% to 82.69% of monoallelic expression genes contained the H3K36me3 modification. Further studies demonstrated a significant positive correlation of ASE with allele-specific H3K36me3 but not with H3K27me3, indicating that ASHM-H3K36me3 primarily regulates ASE in this study.

overall_design: Examination of 2 different histone modifications in three rice indica varieties and two F1 hybrids

first: Gaoyuan

last: Song

first: Daichang

last: Yang


title: Single cell RNA_Seq in aging of hematopoietic stem and progenitor cells

first: Monika

middle: Sylwia

last: Kowalczyk

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Here, we use single-cell RNA-Seq to examine variation between individual hematopoietic stem and progenitor cells from two mouse strains (C57BL/6 and DBA/2) as they age. We prepared libraries from long-term (LT-HSCs) (LSK CD150+CD48-), short-term hematopoietic stem cells (ST-HSCs) (LSK CD150-CD48-) and multipotent progenitors (MPPs) (LSK CD150+CD48+) from young (2-3 months) and old mice (22 months for C57BL/6 and 20 months for DBA/2). Population controls for each cell type and age were isolated by sorting processed in parallel.

overall_design: RNA seq libraries from single cells and population controls. All prepared with SMARTer protocol for cDNA and amplification followed by Nextera protocol for library preparation.

middle: S


title: RNA-seq analysis of transcriptome changes upon Erk knockout, or Mek inhibition in WT and Erk KO ESCs.

city: Tianjin

first: Lingyi

address: 94 Weijin Road

institute: Nankai University

summary: RNA-seq were performed with six samples, WT KH2 ESCs treated with or without PD0325901 for 48 hours (KH2_PD and KH2, respectively), iErk1; Erk KO ESCs cultured in the presence Dox (P0), 48 and 96 hours after Dox withdrawal (P1 and P2, respectively), and iErk1; Erk KO ESCs cultured without Dox for 96 hours, and treated with PD0325901 in the last 48 hours (P2_PD).  iErk1; Erk KO ESCs cultured without Dox does not express Erk, thus mimicking Erk KO.

overall_design: Paired comparisons of KH2+PD and KH2, P2+PD and P2, and P1 and P0, allow us to analyzed the effects of Mek inhibition in WT ESCs, Mek inhibition in Erk KO ESCs, and Erk KO in ESCs, respectively.

first: Haixia


title: Transcriptional profiling of the ovine abomasal lymph node reveals a role for timing of the immune response in gastrointestinal nematode resistance

city: Mosgiel

first: Kathryn

last: McRae

address: Puddle Alley

department: Animal Productivity

country: New Zealand

institute: AgResearch

summary:
Background: Gastrointestinal nematodes are a serious cause of morbidity and mortality in grazing ruminants. The major ovine defence mechanism is acquired immunity, which develops over time in response to infection. Nematode resistance varies both within and between breeds and is moderately heritable (h ~ 0.3). A detailed understanding of the genes and mechanisms involved in protective immunity, and the factors that regulate this response, is required to aid future breeding strategies as well as the development of effective and sustainable nematode control methods. The aim of this study was to compare the abomasal lymph node transcriptome of resistant and susceptible lambs in order to determine biological processes differentially expressed between resistant and susceptible lambs.
Results: Scottish Blackface lambs, with divergent phenotypes for resistance, were challenged with 30,000 Teladorsagia circumcincta larvae (L3), and abomasal lymph node recovered at 7 and 14 days post-infection (dpi). High-throughput sequencing of abomasal lymph node cDNA was used to quantitatively sample the transcriptome with an average of 32 million reads per sample. A total of 194 and 144 genes were differentially expressed between resistant and susceptible lambs at 7 and 14 dpi respectively. Differentially expressed networks and biological processes were identified using Ingenuity Pathway Analysis. Resistant animals appear to generate a more rapid immune response as at 7 dpi processes relating to homing of lymphocytes, leukocyte migration and migration of antigen presenting cells were up-regulated. In susceptible animals this response appears to be delayed until approximately 14 dpi. Twenty-four Single Nucleotide Polymorphims (SNP), within 11 differentially expressed genes were tested for association with gastrointestinal nematode resistance in the Scottish Blackface lambs. Four SNPs in two genes (SLC30A2, and ALB) were suggestively associated with faecal egg count.
Conclusions: A large number of genes were differentially expressed in the abomasal lymph node of resistant and susceptible lambs responding to gastrointestinal nematode challenge. Resistant Scottish Blackface lambs appear to generate a more rapid immune response to T. circumcincta. In susceptible lambs this response appears to be delayed until approximately 14 days post infection. SNP in two differentially expressed genes were suggestively associated with faecal egg count indicating that differentially expressed genes can be considered as candidate loci for mediating nematode resistance.

overall_design: Scottish Blackface lambs, selected for divergent phenotypes for nematode resistance, were challenged with 30,000 Teladorsagia circumcincta larvae (L3) and abomasal lymph node recovered at 7 and 14 days post-infection for transcriptome sequencing.

middle: M

first: Barbara

last: Good

first: James

last: Hanrahan

first: Matthew

last: McCabe

first: Paul

last: Cormican

first: Torres

last: Sweeney

first: Mary

last: O'Connell

first: Orla

last: Keane


title: New roles for DNA cytosine modification, eRNA, anchors and super-anchors in developing B cell progenitors

status: Public on Sep 28 2015

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

summary: B cell fate is orchestrated by a series of well-characterized developmental regulators. Here we found that the onset of B cell development was accompanied by large-scale changes in DNA cytosine modifications associated with promoters, enhancers and anchors. These changes were tightly linked to alterations in transcription factor occupancy and eRNA transcription.  We found that the pre-pro-B to the pro-B cell transition was associated with a global exchange of DNA cytosine modifications for polycomb-mediated repression at CpG islands. Hypomethylated regions were found exclusively in the active/permissive compartment of the nucleus and were predominantly associated with regulatory elements or anchors that orchestrate the folding patterns of the genome. We identified super-anchors, characterized by clusters of hypomethylated CTCF-bound elements, which were predominantly located at boundaries that define topological domains (TAD). A particularly prominent hypomethylated super-anchor was positioned down-stream of the immunoglobulin heavy chain (Igh) locus. Analysis of global formaldehyde-cross linking studies indicated that the Igh locus super-anchor interacts with the VH region repertoire across vast genomic distances. We propose that the Igh locus super-anchor sequesters the VH and DHJH regions into a spatial confined geometric environment to promote rapid first-passage times. Collectively, these studies demonstrate how DNA cytosine modifications associated with regulatory and architectural elements affects patterns of gene expression, folding patterns of the genome and antigen receptor assembly in developing B-lineage cells.

overall_design: DNA cytosine methylation profiling of mouse pre-pro-B (E2A-/-) and pro-B (Rag1-/-) cells by whole genome bisulfite sequencing

first: Takeshi

last: Isoda

first: Cornelis

last: Murre


title: Differential regulation of alternatively polyadenylated isoforms

city: Oxford

first: Jonathan

last: Neve

address: South Parks Road

department: Biochemistry

institute: Oxford University

summary: Alternative Cleavage and Polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we employed a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This comparison allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape the APA profiles in the subcellular locations. Subsequently, we depleted these cells of Dicer to compromise the miRNA biogenesis pathway to isolate the differentially regulated APA events that were regulated by miRNA.

overall_design:
Two biological replicates of Dicer-depleted and non-depleted HEK293 subcellular fractions were analysed using 3'region extraction and deep sequencing to quantitatively measure the usage of each cleavage and polyadenylation site transcriptome-wide. In addition, 3'READS was performed on the subcellular RNA fractions of HBL melanocyte cells to see if the pattern of differential APA regulation holds between cell lines. Furthermore, standard RNA-seq was performed using the Ion Proton system on HEK293 subcellular RNA fractions.

Please note that the raw data from two replicates of Dicer-depleted and non-depleted HEK293 subcellular fractions samples were merged to generate processed data, which is linked to the first replicate sample record (i.e. *rep1.1). For example, the processed data files, C0d.p.bw and C0d.m.bw, were generated from both 3'READs cyto_rep1.1 and 3'READs cyto_rep1.2 sample data and linked to the  '3'READs cyto_rep1.1' sample records as supplementary data file.

first: Kaspar

last: Burger

first: Wencheng

last: Li

first: Mainul

last: Hoque

first: Radhika

last: Patel

first: Bin

last: Tian

last: Gullerova

first: Andre

last: Furger


title: Papilio machaon developmental transcriptomes by RNAseq

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: Papilio machaon developmental transcriptomes from egg to adult

overall_design: 10 samples from egg to adult

first: Xue

middle: Y

first: Ding

middle: D

last: Fan


title: m6A-CLIP identified major presence of m6A in last exons

city: Bar Harbor

first: Shengdong

last: Ke

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: By adapting UV cross-linking immune precipitation for m6A (m6A-CLIP), we developed several novel genomic approaches with single-nucleotide resolution to accurately locate tens of thousands of m6A residues in human cells and mouse brain mRNAs. We found over 70% of these residues in the last exon with a very sharp rise (six-fold) within 150-400 nucleotides of the last exon, which overlaps the beginning of many 3′ untranslated region (UTRs).  The 3′ UTRs contain ~two-thirds of the last exon m6A and 40 to 45% of the total of this base modification in mRNA.  Contrary to earlier studies, we found no preference for location of m6A sites in the coding sequences around STOP codons.  Many mRNA 3′ UTRs contain multiple polyA sites at least some of which are subject to regulated choices when cells change growth rate or differentiation state. The m6A density is at a peak early in the 3′ UTR and gradually diminishes in the more distal region of the last exon suggesting a possible inhibitory role of the proximal m6A residues to allow polyA choice of more distal polyA sites. This possibility was supported by finding that a main switch from distal to proximal polyA site choice is associated with m6A loss after triple knockdown of the m6A methylase complex. There is a significant overlap of m6A with identified binding sites for Ago complexes that carry microRNAs known to regulate mRNA stability which might possibly represent cooperation in function.  With higher accuracy of m6A identification it is now more realistic to engage in highly localized mutagenesis to more definitively identify m6A function.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Precise mapping m6A sites in mouse brain and liver tissues, human CD8 T cells and A549 cells by m6A-CLIP/IP; PolyA sites mapping by PolyA-Seq (Derti et al., 2012) in the same tissues and cells

first: James

last: Darnell

first: Robert

middle: B


title: RNA-Seq atopic dermatitis transcriptome profiling provides insights into novel disease mechanisms with potential therapeutic implications

first: Joel

last: Correa da Rosa

address: 1230 York Avenue

department: CTSA

institute: Rockefeller University

summary:
Purpose: provide evidence that RNA-seq can add information to transcriptome profiling already discovered by other technologies for atopic dermatitis
Methods: mRNA profiles of 20 atopic dermatitis were analyzed to compare lesional and non-lesional skin, then transcriptomes found by reads were compared to Microarray and RT-PCR
Results:RNA-seq provided complementary genes to AD transcriptome IL-36 and TREM-1
Conclusions: Our study represents the first analysis of lesional AD tissue by RNA-seq and comparison to microarray and RT-PCR

overall_design: paired biopsies from lesional and non-lesional tissue of 20 patients sequenced by RNA-seq

first: Mayte

last: Suárez-Fariñas


title: Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology (RNA-seq_RiboZero)

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: We present a more extensive and yet precise assessment to elucidate differences and similarities in performance at numerous aspects including signal range, sensitivity to fold-change, and fidelity with TaqMan qRT-PCR. There were three levels of data examined: entire data sets, data derived from gene name annotation oriented subset of 15442 RefSeq genes, and data derived from transcript pattern defined subset of 7034 RefSeq genes.  Our results showed a fair degree of overall correlation between all 6 platforms evaluated; but, to varying degrees, two RNA-seq protocols outperformed three of the microarray platforms in most categories.  Notably, a fourth microarray platform, Agilent, was comparable, or marginally superior, to the RNA-seq protocols within these same assessments.  Furthermore, 3 platforms (Agilent and two RNA-seq methods) demonstrated over 80% concordance with the gold standard TaqMan assay in terms of fold-change accuracy.  Our study suggests that the use of transcript patterns can enhance a number of the observed cross-platform correlations, indicating a potential usefulness for similar evaluations.

overall_design: The study assessed differences and similarities in performance at numerous aspects including signal range, sensitivity to fold-change, and fidelity with TaqMan qRT-PCR. There were three levels of data examined: entire data sets, data derived from gene name annotation oriented subset of 15442 RefSeq genes, and data derived from transcript pattern defined subset of 7034 RefSeq genes.

first: Richard

last: Head


title: Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

overall_design: 5 samples, 2 replicates

first: Philip

last: Wolff

first: Hua

last: Jiang

first: Guifeng

last: Wang

first: Claudia

last: Köhler


title: Transcriptome-wide analysis of the response of the thecosome pteropod Clio pyramidata to short-term moderate CO2 exposure

status: Public on Sep 27 2015

city: Woods Hole

first: Amy

middle: Elizabeth

last: Maas

address: 266 Woods Hole Road

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Ocean acidification, resulting from the dissolution of excess CO2 produced by humans into the ocean, is predicted to impact a broad variety of marine taxa, particularly calcifying animals such as the thecosome (shelled) pteropods. To achieve a better understanding of the mechanisms of pteropod calcification and physiological compensation for high CO2 exposure, we investigated the transcriptomic responses of Clio pyramidata, a cosmopolitan diel migratory thecosome. Individuals were sampled from the Northwest Atlantic in the fall of 2011 and were exposed to ambient (~380 ppm) and end of the century predicted CO2 levels (~800 ppm) and their oxygen consumption was measured. We then used RNA-seq technology to assess transcriptome-wide effects of exposure to elevated CO2. We conducted a de novo assembly of the transcriptome of C. pyramidata, annotated the genes associated with biomineralization, and assessed the differential gene expression patterns. This assembly reveals a number of similarities with other molluscan transcriptomes, and some similar biomineralization genes such as perlucin, calmodulin, regucalcin and SPARC. The results of the differential expression indicate that there is a great deal of natural variability in gene expression and suggest that a few genes putatively associated with biomineralization, particularly perlucin, were up-regulated in the high CO2 treatment. This is the first experiment employing gene expression analysis to investigate the effects of CO2 on a planktonic open-ocean species, providing the first insights into the effects of acidification on these important planktonic calcifiers and suggesting interesting gene families which may prove useful in further ecophysiological, biomaterials and phylogenetic studies.

overall_design: Four discrete individuals of Clio pyramidata were exposed to either ambient (~380 ppm) or high (~800 ppm) CO2 for a period of 9-11 hours, for a total of eight samples.

first: Gareth

last: Lawson

first: Ann

last: Tarrant


title: Neonatal naïve CD8+ T cells have effector-like gene expression that prevents memory cell formation [miRNA-Seq]

status: Public on Sep 26 2015

city: Ithaca

first: Andrew

last: Grimson

state: NY

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Neonates are intrinsically defective at creating memory CD8+ T cells in response to infection with intracellular pathogens. Here we investigated differential of small RNAs, transcription factors, and chemokine receptors regulation in neonates as compared to adults before and during infection. We found that prior to infection, naïve cells have a different expression profile for many microRNAs, and gene targets of these microRNAs show widespread expression differences. These targets and other changes in gene expression in naïve cells result in neonatal cells that get activated more easily, express chemokine receptors that home to sites of infection, and are less protected from apoptosis during contraction. As a result, changes in neonatal naïve cells drive effector cell terminal differentiation at the expense of creating long-lived memory cells.

overall_design: Small RNAs were sequenced from adult and neonatal CD8+ T cells before and during infection

first: Erin

last: Wissink


title: TG-interacting factor1 (Tgif1) maintains the identity of mouse ES cells by counterbalancing the expression of core pluripotency factors and ES cell core factors

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

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

overall_design: Refer to individual Series


title: Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology


title: TG-interacting factor1 (Tgif1) maintains the identity of mouse ES cells by counterbalancing the expression of ES cell core factors

summary: TG-interacting factor1 (Tgif1) is well-known as a transcriptional repressor in transforming growth factor beta (TGFβ) signaling pathway. Target mapping of ES cell core factors in mouse embryonic stem (ES) cells revealed that Tgif1 is occupied by Oct4 and Nanog. Moreover, recent interactome study of mouse gene regulatory regions showed a preferential regulation of Tgif1 by mouse ES cell specific enhancers. However, the detailed role and mode of actions of Tgif1 in stem cell maintenance and development remains elusive. We show that Tgif1 is indispensable for self-renewal and pluripotency of mouse embryonic stem (ES) cells. Aberrant expression of Tgif1 promotes differentiation of ES cells even in the presence of LIF in part by deregulation of pluripotency factors. Intriguingly, we find that Tgif1 level is a critical factor to determine specific lineage commitment in a dosage-dependent manner. We further show that Tgif1 interacts with ES cell core factors and co-localizes at their binding sites, which eventually restricts expression of ES cell core factors including Oct4, Sox2, and Nanog. Taken together, we provide new insights into the roles of Tgif1 in maintenance as well as differentiation of ES cells.

overall_design: ChIP sequenicngs were performed for 5 transcription factors (Tgif1, Tgif2, Nanog, Hdac1 and Smad3) in mouse ES cells. Nanog ChIP was performed using bioChIP-seq.  Control ChIP-seq was performed using BirA cells.

first: Jonghwan

last: Kim


title: Search for Meis1 target genes in embryonic sympathetic neurons

city: LYON

first: MARMIGERE

last: FREDERIC

address: 32/34 Av. Tony Garnier

department: Institut de génomique fonctionelle de Lyon

country: France

institute: CNRS

summary: To uncover Meis1 functions during the embryonic development of sympathetic neurons, we perfomed a ChIP-seq analysis from mouse E16 embryonic superior cervical ganglia (SCG) using an antibody against Meis1. We identified 309 potential target genes with a particular enrichment in genes involved in vesicles formation, function and trafficking, leading to the hypothesis that Meis1 participate in late sympathetic neurons differentiation by coordinating target-field innervation, synaptogenesis and survival through the transcriptional control of the machinery necessary for endocytosis and exocytosis. We further confirmed that the expression of some of these genes was lost and/or modified in E16 SCGs of a HtPACRE/Meis1LoxP/LoxP mouse strain compared to wild type littermates. We additionaly confirmed that endocytosis and synaptogenesis is impaired in those mutants.

overall_design: ChIP-seq analysis of Meis1 target genes in neurons from the superior cervical ganglion of E16 wild type embryos

first: F

last: Bouilloux

last: Marmigère


title: Histone Deacetylase 3

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

institute: Vanderbilt University


title: The cis-regulatory code of Hox function in Drosophila

city: Heidelberg

first: Ingrid

last: Lohmann

address: Im Neuenheimer Feld 230

country: Germany

institute: COS, University Heidelberg

summary: Precise gene expression is a fundamental aspect of organismal function and depends on the combinatorial interplay of transcription factors (TFs) with cis‐regulatory DNA elements. While much is known about TF function in general, our understanding of their cell type‐specific activities is still poor. To address how widely expressed transcriptional regulators modulate downstream gene activity with high cellular specificity, we have identified binding regions for the Hox TF Deformed (Dfd) in the Drosophila genome. Our analysis of architectural features within Hox cis‐regulatory response elements (HREs) shows that HRE structure is essential for cell type‐specific gene expression. We also find that Dfd and Ultrabithorax (Ubx), another Hox TF specifying different morphological traits, interact with non‐overlapping regions in vivo, despite their similar DNA binding preferences. While Dfd and Ubx HREs exhibit comparable design principles, their motif compositions and motif‐pair associations are distinct, explaining the highly selective interaction of these Hox proteins with the regulatory environment. Thus, our results uncover the regulatory code imprinted in Hox enhancers and elucidate the mechanisms underlying functional specificity of TFs in vivo.

overall_design: ChIP-seq analysis for the Hox TF Deformed (Dfd) was performed in Drosophila embryos to identify Dfd-bound and regulated regulatory regions. One replicate was analysed and activity of bound regions was assessed in vivo with Enhancer-Reporter contructs (as shown in Sorge et al, 2012).

first: Sebastian

last: Sorge

first: Nati

last: Ha

first: Maria

last: Polychronidou

first: Jana

last: Friedrich

first: Daniela

last: Bezdan

first: Petra

last: Kaspar

first: Martin

last: Schäfer

first: Stephan

last: Ossowski

first: Stefan

last: Henz

first: Juliane

last: Mundorf

first: Jenny

last: Rätzer

first: Fani

last: Papagiannouli


title: Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology (RNA-seq_ClonTech)

first: Jinsheng

last: Yu

first: Richard

last: Head


title: Transcriptional Signatures of Hypoxic and Inflammatory Renal Epithelial Injury

city: New York

first: Chenyi

last: Xue

institute: Columbia University

summary: To identify RNA transcripts involved in acute and chronic renal epithelial injury, we performed unbiased whole transcriptome profiling of human proximal tubular epithelial cells (PTECs) in hypoxic and inflammatory conditions. RNA sequencing (RNA-seq) revealed that the protein-coding and noncoding transcriptomic landscape differed between hypoxia-stimulated and cytokine-stimulated human PTECs.

overall_design: Examination of transcriptomic response of human PTECs to hypoxic or inflammatory injury

first: Reilly

last: Muredach

first: Xue

last: Chenyi


title: Arrested replication forks guide retrotransposon integration

status: Public on Sep 25 2015

city: Piscataway

first: Miguel

last: Zaratiegui

state: NJ

address: 604 allison rd

department: Molecular Biology and Biochemistry

institute: Rutgers, the State University of New Jersey

summary: Long Terminal Repeat (LTR) Retrotransposons are an abundant class of genomic parasites that replicate by insertion of new copies into the host genome. LTR retrotransposons prevent mutagenic insertions through diverse targeting mechanisms that avoid coding sequences, but a universal set of principles guiding their target site selection hasn’t been established. Here we show that insertion of the fission yeast LTR retrotransposon Tf1 is guided by the DNA binding protein Sap1, and that the efficiency and location of the targeting depend on the activity of Sap1 as a replication fork barrier. We propose that Sap1 guides insertion of Tf1 by blocking the progression of the replication fork, and that the Tf1 transposon uses features of arrested forks to insert into the host genome. These observations point to a universal mechanism for determination of LTR retrotransposon target site selection.

overall_design: High throughput sequencing of Tf1 insertions

first: Mikel

first: Jake

last: Jacobs


title: Estimating mRNA lengths from Plasmodium falciparum genes by virtual northern RNA-seq analysis

city: Pathumthani

first: Philip

middle: James

last: Shaw

state: Pathumthani

address: 113 Phahonyothin Road

department: National Center for Genetic Engineering and Biotechnology

country: Thailand

institute: National Science and Technology Development Agency

summary: Accurate gene models are essential for understanding parasite biology. However, transcript structure information is lacking for most parasite genes. Here, we describe “virtual northern” analysis of the malaria parasite Plasmodium falciparum to address this issue. RNA-seq libraries were made from size-fractionated RNA. Transcript sizes for 3052 genes were inferred from the abundance signals in each library. The data show that for almost half of the transcripts, the combined untranslated regions are more than twice the length of the open reading frame. Furthermore, we identified novel polycistronic, or gene overlapping transcripts that suggest revisions to current gene models are needed.

overall_design: mRNA profiles of from 8 size-fractions of RNA were compared with unfractionated mRNA; sequence data were obtained from TruSeq stranded RNA-seq libraries sequenced on an Illumina MiSeq  instrument

first: Pavita

last: Kaewprommal

first: Jittima

last: Piriyapongsa

first: Chayaphat

last: Wongsombat

first: Sumalee

last: Kamchonwongpaisan

first: Yongyuth

last: Yuthavong


title: Decrease in EZH2 histone methyltransferase mediates the effects of fluid shear stress (FSS) in endothelial cells

city: Cologne

first: Monika

last: Maleszewska

address: Joseph-Stelzmann-Strasse 9b

institute: Max Planck Institute for Biology of Ageing

summary: High uniform fluid shear stress (FSS) is atheroprotective and preserves the endothelial phenotype and function through activation of downstream mediators such as MAPK7 (Erk5). Endothelial cells respond to FSS thanks to mechanotransduction. However, how the resulting signaling is integrated and resolved at the epigenetic level, remains elusive. We hypothesized that Polycomb methyltransferase EZH2 is involved in the effects of FSS in human endothelial cells. We showed that FSS decreases the expression of the Polycomb methyltransferase EZH2. Despite simultaneous activation of MAPK7, MAPK7 pathway does not directly influence the transcription of EZH2. Interestingly though, the knock down of EZH2 activates the protective MAPK7 signaling in endothelial cells, even in the absence of FSS. To understand the influence of the FSS-decreased expression of EZH2 on endothelial transcriptome, we performed RNA-seq and differential gene expression analysis. We identified candidate groups of genes dependent on both EZH2 and FSS. Among those, Gene Ontology overrepresentation analysis revealed highly significant enrichment of the cell cycle-related genes, suggesting changes in proliferation. Indeed, the depletion of EZH2 strongly inhibited endothelial proliferation, indicating cell cycle arrest. The concomitant decrease in CCNA expression suggests the transition of endothelial cells into a quiescent phenotype. Further bioinformatical analysis suggested TXNIP as a possible mediator between EZH2 and cell cycle-related gene network. Our data show that EZH2 is a FSS-responsive gene. Decreased EZH2 levels enhance the activation of the atheroprotective MAPK7 signaling. Decrease in EZH2 under FSS mediates the decrease in the expression of the network of cell cycle-related genes, which allows the cells to enter quiescence. EZH2 is therefore important for the protective effects of FSS in endothelium.

overall_design: Puromycin-selected HUVEC (Human Umbilical Vein Endothelial Cells, Lonza, Switzerland) cells, expressing either scrambled control (SCR) or anti-EZH2 short-hairpin (shEZH2) constructs (at total 7 days after the first viral transduction), were used in FSS experiments (72h of control static culture or exposure to 20 dynes/cm2 of fluid shear stress, using Ibidi pump system (in µ-Slides I 0.4 Luer, Ibidi, Planegg/Martinsried, Germany)). Each replicate experiment consisted of viral transductions and puromycin selection of a separate HUVEC batch, followed by the FSS experiment. Two FSS experimental sets of the same HUVEC batch were run every time in parallel and lysed at the same end time point, one in RNAse-free conditions with RNA-Easy Mini Plus kit RLT Plus lysis buffer (QIAGEN, Venlo, The Netherlands), and one with RIPA buffer. The RIPA-lysates were analyzed with Western blotting and confirmed the complete (no protein present) knock-down of EZH2. From the RNA-lysates, RNA was isolated using the RNA-Easy Mini Plus kit (QIAGEN, Venlo, The Netherlands). High quality RNA samples (pre-assessed by Nanodrop measurements) were further processed in the Genome Analysis Facility of the University Medical Center Groningen. The RNA quality and integrity were verified using PerkinElmer Labchip GX with a cut-off value of 9 (scale 1 to 10, where 9 is very high quality RNA). RNA library was created in accordance with the TruSeqTM RNA Sample Preparation v2 Guide (Illumina, San Diego, CA, USA), using the PerkinElmer Sciclone liquid handler, resulting in 330bp cDNA fragments. The paired-end sequencing (100bp reads) was performed using the Illumina HiSeqTM 2500. (Quoted from the Materials and Methods of the related manuscript, with adjustments).


title: Identification of the Thermoproteus tenax small Rnome

city: Marburg

first: Michael

last: Daume

state: Hessen

address: Karl-von-Frisch-Strasse 10

department: Prokaryotic Small RNA Biology

institute: Max Planck Institute for Terrestrial Microbiology

summary: Small RNAs were isolated from the hyperthermophilic archaeon Thermoproteus tenax and subjected to Illumina Hiseq2000 sequencing. The RNA reads revealed significant abundance of constitutively transcribed CRISPR RNAs and a plethora of C/D box sRNAs. The presence of a rare RNase P RNA variant was verified. Circular RNA molecules could be identified.

overall_design: A T. tenax small RNA isolate was applied to Illumina HiSeq2000 sequencing.

first: André

last: Plagens

first: Lennart

last: Randau


title: The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways

city: Vienna

last: Tscherner

address: Dr. Bohr Gasse 9/2

department: Max F. Perutz Laboratories, Department for Medical Biochemistry

country: Austria

institute: Medical University of Vienna

summary: Transcriptome analysis of wild type, Hat1-deficient, Cac2-deficient and Rtt109-deficient Candida albicans cells prior to and after treatment with hydrogen was done to determine the transcriptional changes in these three mutatns in logarithmically growing cells as well as under oxidative stress conditions.

overall_design: RNA Sequencing was performed of wild type, Hat1-deficient, Cac2-deficient and Rtt109-deficient Candida albicans strains prior to and after treatment with hydrogen peroxide. Cells were grown to the exponential phase in YPD at 30oC. Aliquots were harvested for RNA isolation and to the remaining culture hydrogen eproxide was added to a final concentration of 1.6 mM. After 30 min incubation at 30°C cells were harvested for RNA isolation. Five biological replicates were done for the wild type and Hat1-deficient cells and three biological replicates were done for Cac2-deficient and Rtt109-deficient strains.


title: Modulation of the microRNA cluster miR-183-96-182 expression by the Epstein-Barr virus latent membrane protein 1

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: Epstein-Barr virus (EBV) is an oncogenic human herpesvirus involved in the pathogenesis of Burkitt’s lymphoma (BL) and various other lymphoproliferative disorders. In BL, EBV protein expression is restricted to the EBNA-1, but small non-coding RNAs such as the EBERs and micro (mi)RNAs can also be detected. miRNAs play major roles in crucial processes such as proliferation, differentiation and cell death. It has recently become clear that alteration in the expression profile of miRNAs contribute to the pathogenesis of a number of malignancies. During latent infection, EBV expresses 25 viral pre-miRNAs and modulates the expression of specific cellular miRNAs, such as miR-155 and miR-146, which potentially play a role in oncogenesis. Here, we established the small RNA expression profiles of three BL cell lines. Using large-scale sequencing coupled to northern blot and real-time RT-PCR analysis validation, we demonstrated the differential expression of some cellular and viral miRNAs. High-level expression of the miR-183-96-182 cluster and EBV miR-BART cluster was significantly associated with EBV type I latency. This expression was not affected by viral reactivation since TGF-ß1 stimulation did not significantly change the miRNA profiles. However, the expression of latent membrane protein (LMP)-1 triggered down-regulation of the expression of the miR-183-96-182 cluster. We further show that this effect involves the AKT signaling pathway.

overall_design:
Cellular and viral miRNA profiling of the EBV-positive Burkitt's lymphoma (BL) cell lines Mutu, Kem and Sav treated (2h and 24h post-treatment) or not (0h) with TGF-β1

Please note that EBV-positive BL cell lines can be classified into 3 different latency types, termed latency I to III, based on the expression pattern of several EBV latent genes. Our Mutu and Kem cells were in latency I as expected, and are therefore referred to as Mutu-I and Kem-I in our study. However, our Sav cells appeared to have derived from a type I latency to a latency type not yet characterized. Therfore, the Sav cells were refered as Sav* cells and the '*' value was provided in the corresponding characteristics field.

first: Lassad

last: Oussaief

first: Ali

last: Fendri

first: Béatrice

last: Chane-Woon-Ming

first: Rémy

last: Poirey

first: Henri

last: Delecluse

first: Irène

last: Joab


title: Effect of 4hr cortistatin A treatment on gene expression in SET2 cells.

city: Cambridge

first: Matthew

middle: D.

last: Shair

address: 12 Oxford Street

department: Chemistry and Chemical Biology

institute: Harvard University

summary:
We characterized the marine natural product cortistatin A (CA) as an inhibitor of CDK8 to determine whether pharmacologic inhibition of CDK8 regulates super-enhancer function and inhibits AML proliferation.
In this series, we examine the transcriptional effect on SET2 cells of 4hrs exposure to CA to identify immediate effects.

overall_design: SET2 cells were treated in triplicate with either DMSO or CA for 4hrs after which RNA was harvested and prepared for RNA sequencing to assess transcriptional changes.

first: Henry

middle: E

last: Pelish

first: Brian

last: Liau

first: Ioana

middle: I

last: Nitulescu

first: Madeleine

last: Lemieux


title: RNA-seq data of intestinal epithelial cells

status: Public on Sep 24 2015

city: Shinjuku-ku

first: Koji

last: Atarashi

state: TOKYO

address: 35 Shinanomachi

department: Dept of Microbiology and Immunology

country: Japan

institute: Keio University School of Medicine

summary: We report that adhesion of microbes to intestinal epithelial cells is a critical cue for Th17 induction. SFB colonized in the intestine of mice can adhere to mouse small intestinal epithelial cells and induce intestinal Th17 cells. However, SFB colonized in rats cannot adhere to mouse intestinal epithelial cells and induce Th17 cells. Likewise, Citrobacter rodentium (WT) can adhere to mouse colonic epithelial cells and induce Th17 cells, but non-adherent mutant of C. rodentium (Δeae) cannot induce Th17 cells. To examine the influence of adherent bacteria on intestinal epithelial cells, we performed RNA seq. Germ free mice were orally inoculated with M-SFB or R-SFB and total RNA was isolated from small intestinal epithelial cells 1 week after inoculation. Alternatively, germ free mice were orally inoculated with C. rodentium WT or eae mutant and total RNA was isolated from colonic epithelial cells 5 days after inoculation.

overall_design: The gene expression of small intestinal epithelial cells isolated from small intestine of germ free mice (2 mice), mice monocolonized with M-SFB (2 mice) or R-SFB (3 mice), and colon of germ free mice (3 mice), mice monocolonized C. rodentium WT (3 mice) or eae mutant (3 mice).

first: Takeshi

last: Tanoue

first: Yuji

last: Nagano

first: Yoshinori

last: Umesaki

first: Kenya

last: Honda


title: Role of the Small Subunit Processome in the Maintenance of Pluripotent Stem Cells

city: Seoul

first: Joha

last: Park

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: RNA-binding proteins (RBPs) play integral roles in gene regulation, yet only a small fraction of RBPs has been studied in the context of stem cells. We here apply RNA interference screen for RBPs in mouse embryonic stem cells (ESCs) and identify 16 RBPs involved in pluripotency maintenance. Interestingly, six identified RBPs including Krr1 and Ddx47 are part of a complex called Small Subunit Processome (SSUP) that mediates 18S rRNA biogenesis. The SSUP components are preferentially expressed in stem cells and enhance global translational rate, which is critical to sustain the protein levels of labile pluripotency factors such as Nanog and Esrrb. Furthermore, the SSUP proteins are required for efficient reprogramming of induced pluripotent stem cells. Our study uncovers the role of SSUP and the importance of translational control in stem cell fate decision.

overall_design: R1 cells were transfected with 3 different control siRNAs and 3 different siRNAs targeting Krr1 for 48 hrs. Transcriptome profiles were generated by deep sequencing using illumina HiSeq 2000.

first: Kwon

middle: T

last: You


title: Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization [RNA-Seq]

city: Boston

first: Mary-Lee

last: Dequeant

email: mdequeant@genetics.med.harvard.edu, fagegalt@cshl.edu, Greg.Hannon@cruk.cam.ac.uk, perrimon@receptor.med.harvard.edu

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: To characterize the sequence of events associated with RasV12 immortalization of Drosophila embryonic cells, we generated transcriptional time series during cell line establishment, from primary cultures until passage (P) 19.

overall_design: We generated three transcriptional time series from three cell lines (R1, R4 and R5) by sampling the cultures at successive stages, early (P2-4), intermediate (P4-11), and late (P16-19), characterized by different passage times. Time points for the R1 time-series were: P2, P3, P4, P5, P7, P8, P10, P11, P16, P17 and P19; for the R4 time-series: P2, P3, P4, P5, P6, P7, P9, P11, P12, P16, P17 and P19; and for the R5 time-series: P2, P3, P4, P6, P7, P8, P16, P17 and P19

last: Dequéant

first: Delphine

last: Fagegaltier

first: Yanhui

last: Hu

first: Kerstin

last: Spirohn

first: Amanda

last: Simcox

first: Gregory

middle: J

last: Hannon

first: Norbert

last: Perrimon


title: Discovery of progenitor signatures by time series synexpression analysis during Drosophila cell immortalization


title: Engrailed homeoprotein protects mesencephalic dopaminergic neurons from oxidative stress

city: Paris

first: Hocine

last: Rekaik

address: 11, Place Marcelin Berthelot

department: CIRB

institute: College de France

summary: Engrailed homeoproteins are expressed in adult dopaminergic neurons of the substantia nigra. In Engrailed1 heterozygous mice, these neurons start dying at 6 weeks, are more sensitive to oxidative stress and progressively develop traits similar to those observed following an acute and strong oxidative stress inflected to wild-type neurons. These changes include DNA strand breaks and the modification (intensity and distribution) of several nuclear and nucleolar heterochromatin marks. Engrailed1 and Engrailed2 are biochemically equivalent transducing proteins previously used to antagonize dopaminergic neuron death in Engrailed heterozygous mice and in mouse models of Parkinson disease. Accordingly, we show that, following an acute oxidative stress, a single Engrailed2 injection restores all nuclear and nucleolar heterochromatin marks, decreases the number of DNA strand breaks and protects dopaminergic neurons against apoptosis.

overall_design: RNA-seq data for differentially expressed genes in the SNpc of En1+/- mice, En2 infused mice and 6-OHDA/En2 injection experiments.

first: François-Xavier

last: Blaudin de Thé

first: Julia

last: Fuchs

first: Olivia

last: Massiani-Beaudoin

first: Alain

last: Prochiantz

first: Rajiv

middle: L

last: Joshi


title: PTEN suppresses neoplastic transformation of human neural stem cells by transcriptional repression of Pax7

city: Beijing

first: xiaomeng

last: liu

state: Beijing

address: Yiheyuan Road No.5

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

summary: Our data throw light upon the effect of PTEN deficiency on gene expression, epigenomic modifications(H3K4me3, H3K27me3, 5-Hydroxymethylcytosine and 5-methylcytosin).

overall_design: RNA-seq of NSCs-PTEN+/+ and NSCs-PTEN-/-; RRBS and TA-RRBS of NSCs-PTEN+/+, NSCs-PTEN-/-; H3K4me3 ChIP-seq of NSCs-PTEN+/+ and NSCs-PTEN-/-; H3K27me3 ChIP-seq of NSCs-PTEN+/+ and NSCs-PTEN-/-.

first: Shunlei

last: Duan

first: Guohong

last: Yuan

first: Xiaomeng

last: Liu

first: Jingyi

last: Li

first: Guanghui

first: Fuchou

last: Tang


title: Genome-wide maps of PBX3-binding sites and Quantitative Analysis of PBX3-Regulated Transcriptomes

city: Peiking

first: haibo

last: Han

address: 52 Fucheng Road, Haidian District

department: Department of Cell Biology

institute: Peking University School of Oncology

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

overall_design: Refer to individual Series


title: Genome-wide maps of PBX3-binding site

summary: We report the high-throughput profiling of PBX3-binding sites under liver cancer stem cell reprogramming driven by PBX3 overexpression. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide PBX3-binding maps of SMMC-7721 cells. This study provides a prediction of regulated genes by the PBX3.

overall_design: Examination of PBX3-binding sites in SMMC-7721 cell with overexpression PBX3. The fragmented DNA was precipitated with a PBX3 antibody.

first: Zhiqian

last: Zhang

first: Haibo


title: Next Generation Sequencing Facilitates Quantitative Analysis of PBX3 Regulated Transcriptomes

summary: The goals of this study are to analyze the transcriptome profiling (RNA-seq) after PBX3 overexpression in SMMC-7721 cells.

overall_design: SMMC-7721 cells were transfected by PBX3 expression lentivirus and blank lentivirus as control. Total RNA was extraced by Qiagen kit and the mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000.


title: Genome-wide maps of nuclear lamina interactions in single human cells (CEL-seq)

city: Utrecht

first: Siddharth

middle: Subhas

last: Dey

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, single-cell gene expression and chromatin accessibility analysis shows that loci with consistent NL contacts are expressed at lower levels and are more consistently inaccessible than loci with lower contact frequencies. These results highlight fundamental principles of single cell chromatin organization.

overall_design: In this dataset, single-cell mRNA sequencing results from 96 single KBM7 cells have been deposited

first: Jop

last: Kind

first: Alexander

last: van Oudenaarden

first: Bas

last: van Steensel


title: RNA-Seq analysis of human neutrophils isolated by different protocols (Polymorphprep and negative selection) and incubated with and without in vitro cytokine stimulation

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

institute: University of Liverpool

summary: We report gene expression in human neutrophils isolated by two methods: Polymorphprep (~95% purity) and negative selection (~99% purity) from two healthy donors - one donor with low eosinophil contamination of neutrophils and one donor with high eosinophil contamination of neutrophils.  We report the effect of the presence of contaminating leukocytes in neutrophil preparations, and in reponse to inflammatory cytokines TNF-alpha and GM-CSF.

overall_design: Healthy human neutrophils were isolated using Polymorphprep or negative selection, and incubated for 1h in the absence or presence of TNF-alpha or GM-CSF.  RNA was analysed by Illumina HiSeq 2000.  The results from n=2 donors were analysed as biological replicates for differential expression analysis.

first: Huw

last: Thomas

first: Robert

last: Moots

first: Steven

middle: W

last: Edwards


title: Mediator kinase inhibition further activates super-enhancer-associated genes in AML

first: Matthew

last: Shair

summary:
Super-enhancers (SEs), which are composed of large clusters of enhancers densely loaded with the Mediator complex, transcription factors and chromatin regulators, drive high expression of genes implicated in cell identity and disease, such as lineage-controlling transcription factors and oncogenes. BRD4 and CDK7 are positive regulators of SE-mediated transcription. By contrast, negative regulators of SE-associated genes have not been well described. Here we show that the Mediator-associated kinases cyclin-dependent kinase 8 (CDK8) and CDK19 restrain increased activation of key SE-associated genes in acute myeloid leukaemia (AML) cells. We report that the natural product cortistatin A (CA) selectively inhibits Mediator kinases, has anti-leukaemic activity in vitro and in vivo, and disproportionately induces upregulation of SE-associated genes in CA-sensitive AML cell lines but not in CA-insensitive cell lines. In AML cells, CA upregulated SE-associated genes with tumour suppressor and lineage-controlling functions, including the transcription factors CEBPA, IRF8, IRF1 and ETV6. The BRD4 inhibitor I-BET151 downregulated these SE-associated genes, yet also has anti-leukaemic activity. Individually increasing or decreasing the expression of these transcription factors suppressed AML cell growth, providing evidence that leukaemia cells are sensitive to the dosage of SE-associated genes. Our results demonstrate that Mediator kinases can negatively regulate SE-associated gene expression in specific cell types, and can be pharmacologically targeted as a therapeutic approach to AML.

This SuperSeries is composed of the SubSeries listed below.


title: Neonatal naïve CD8+ T cells have effector-like gene expression that prevents memory cell formation [RNA-seq]

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotechnology Building

institute: Cornell University

summary: Neonates are intrinsically defective at creating memory CD8+ T cells in response to infection with intracellular pathogens. Here we investigated differential of small RNAs, transcription factors, and chemokine receptors regulation in neonates as compared to adults before and during infection. We found that prior to infection, naïve cells have a different expression profile for many microRNAs, and gene targets of these microRNAs show widespread expression differences. These targets and other changes in gene expression in naïve cells result in neonatal cells that get activated more easily, express chemokine receptors that home to sites of infection, and are less protected from apoptosis during contraction. As a result, changes in neonatal naïve cells drive effector cell terminal differentiation at the expense of creating long-lived memory cells.

overall_design: total RNAs were sequenced from adult and neonatal CD8+ T cells before and during infection

first: Erin

last: Wissink


title: Genome-wide maps of nuclear lamina interactions in single human cells. (DamID; LaminB1, clone-14, diploid)

city: Amsterdam

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

overall_design: 52 single cell LaminB1 DamID samples

first: Ludo

last: Pagie

first: Sandra

last: de Vries


title: Genome-wide maps of nuclear lamina interactions in single human cells. (DamID; LaminB1, clone-14, haploid)

overall_design: 124 single cell LaminB1 DamID samples


title: Genome-wide maps of nuclear lamina interactions in single human cells. (DamID; LaminB1, clone-5-8, haploid)

overall_design: 124 single cell DamOnly DamID samples


title: Effect of cortistatin A (CA) on enhancer occupancy in CA-sensitive and -insensitive human cell lines

summary:
We characterized the marine natural product cortistatin A (CA) as an inhibitor of CDK8 to determine whether pharmacologic inhibition of CDK8 regulates super-enhancer function and inhibits AML proliferation.
In this series, we use ChIP-seq of H3K27ac, H3K4me1, MED1, CDK8, BRD4, and RNA polymerase II (PolII) to examine enhancer occupancy and transcriptional response to CA in human cells lines.

overall_design: ChIP-seq was carried out in CA-sensitive: MOLM-14 cells (H3K27Ac, H3K4me1, MED1, CDK8, BRD4, and PolII), MV4;11(H3K27Ac, CDK8), SET2 (H3K27Ac, CDK8), and in CA-insensitive cells: K562 (CDK8).

first: Henry

last: Pelish

first: Brian

last: Liau

first: Ioana

last: Nitulescu

first: Madeleine

last: Lemieux


title: Neonatal naïve CD8+ T cells have effector-like gene expression that prevents memory cell formation [human miRNA-seq]

overall_design: Small RNAs were sequenced from adult and neonatal CD8+ T cells before infection.


title: Genome-wide maps of nuclear lamina interactions in single human cells. (DamID; LaminB1, clone-5-5, diploid)


title: Neonatal naïve CD8+ T cells have effector-like gene expression that prevents memory cell formation


title: Genome-wide maps of nuclear lamina interactions in single human cells. (DamID; LaminB1, clone-5-5, haploid)

overall_design: 172 single cell LaminB1 DamID samples


title: The menu of features that define primary microRNAs and enable  de novo design of microRNA genes

first: Wenwen

last: Fang

state: Massachusetts

address: Room 625, 455 Main Street

institute: Whitehead Institute

summary: MicroRNAs (miRNAs) are small regulatory RNAs processed from stem-loop regions of primary transcripts (pri-miRNAs), with the choice of stem-loops for initial processing largely determining what becomes a miRNA. To identify sequence and structural features influencing this choice, we determined cleavage efficiencies of >50,000 variants of three human pri-miRNAs, focusing on the regions intractable to previous high-throughput analyses. Our analyses revealed a mismatched motif in the basal stem region, a preference for maintaining or improving base-pairing throughout the remainder of the stem, and a narrow stem-length preference of 35±1 base pairs. Incorporating these features with previously identified features, including three primary-sequence motifs, yielded a unifying model defining mammalian pri-miRNAs, in which motifs help orient processing and increase efficiency, with the presence of more motifs compensating for structural defects. This model enables generation of artificial pri-miRNAs, designed de novo, without reference to any natural sequence, yet processed more efficiently than natural pri-miRNAs.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Three major experiments are included in the submitted data. 1) Pools of synthetic DNA containing barcodes and pri-miRNA variants were sequenced to infer the barcode-pri-miRNA linkages, and the pri-miRNA variants were assayed for their cleavage efficiency ("selection"), which can be quantified by comparing their representations in the input and after cleavage. 2) Artificial miRNAs produced in HEK293T cells were sequenced.  3) Transcriptomes of artificial miRNA-expressed cells were sequenced to quantify mRNA changes.

first: David

middle: P

last: Bartel


title: Genome-wide maps of nuclear lamina interactions in single human cells

type: Genome binding/occupancy profiling by genome tiling array


title: hTERT promotes cell adhesion and migration independent of telomerase activity

status: Public on Sep 22 2015

city: Guangzhou

first: Qi

last: Zhao

state: Guangdong

address: No. 651, Dongfengdong Road

department: Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: We sequenced mRNA from 6 human cell lines stably over-expressed specific gene or empty vector, and searched for differently expressed genes after gene over-expression as compared to empty vector.

overall_design: mRNA levels were compared as following pairs: U2OS+hTERT vs U2OS+vector; U2OS+hTERTmut vs U2OS+vector; VA-13+hTERT vs VA-13+vector; VA-13+hTERTmut vs VA-13+vector.

first: Haiying

last: Liu

first: Qianqian

first: Yuanlong

last: Ge

first: Xiaohui

last: Zheng

first: Yong


title: A comprehensive epigenome map of Plasmodium falciparum reveals unique mechanisms of transcriptional regulation

status: Public on Sep 23 2015

city: Pune

first: Krishanpal

last: Karmodiya

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Center of Excellence in Epigenetics

country: India

institute: Indian Institute of Science Education and Research

summary: Epigenetic mechanisms have been poorly understood in Plasmodium falciparum, the causative agent of malaria. To elucidate stage specific epigenetic regulations in P. falciparum, we performed genome-wide mapping of various histone modifications, nucleosomes and RNA Polymerase II. Our comprehensive analysis suggest that transcription initiation and elongation are distinct in Plasmodium. In this study, by analyzing histone modifications, nucleosome occupancy and RNA Polymerase II (Pol II) at three different IEC developmental stages of Plasmodium; ring, trophozoite and schizont, we tried to unravel the epigenetic mechanism associated with gene regulation.

overall_design: Examination of H3K27me3, H3K4me3, H3K9me3, H3K14ac, H3K4me1, H3K79me3, H3K27ac, H3K4me2, H3K9ac, H4ac, RNA Pol II and Histone H3 at three different stages of Plasmodium falciparum


title: Neonatal naïve CD8+ T cells have effector-like gene expression that prevents memory cell formation [3'UTR-seq]

first: Andrew

overall_design: PolyA RNA was selected and sequenced from adult and neonatal CD8+ T cells before and during infection


title: Ectomycorrhizal fungi decompose humus-rich litter material using oxidative mechanisms adapted from saprotrophic ancestors

city: Lund

first: Anders

last: Tunlid

address: Sölvegatan 37

department: Biology

institute: Lund University

summary: Decomposition of soil organic matter in forest soils is thought to be controlled by the activity of saprotrophic fungi, while biotrophic fungi including ectomycorrhizal fungi act as vectors for input of plant carbon. The limited decomposing ability of ectomycorrhizal fungi is supported by recent findings showing that they have lost many of the genes that encode hydrolytic plant cell-wall degrading enzymes in their saprophytic ancestors. Nevertheless, here we demonstrate that ectomycorrhizal fungi representing at least four origins of symbiosis have retained significant capacity to degrade humus-rich litter amended with glucose. Spectroscopy showed that this decomposition involves an oxidative mechanism and that the extent of oxidation varies with the phylogeny and ecology of the species. RNA-Seq analyses revealed that the genome-wide set of expressed transcripts during litter decomposition has diverged over evolutionary time. Each species expressed a unique set of enzymes that are involved in oxidative lignocellulose degradation by saprotrophic fungi. A comparison of closely related species within the Boletales showed that ectomycorrhizal fungi oxidized litter material as efficiently as brown-rot saprotrophs. The ectomycorrhizal species within this clade exhibited more similar decomposing mechanisms than expected from the species phylogeny in concordance with adaptive evolution occurring as a result of similar selection pressures. Our data shows that ectomycorrhizal fungi are potential organic matter decomposers, yet not saprotrophs. We suggest that the primary function of this decomposing activity is to mobilize nutrients embedded in organic matter complexes and that the activity is driven by host carbon supply.

sample_organism:
Suillus luteus
Laccaria bicolor
Paxillus involutus
Hebeloma cylindrosporum
Coniophora puteana
Piloderma croceum
Serpula lacrymans
Leucogyrophana pinastri
Jaapia argillacea

overall_design: Comparative transcriptomics of ectomycorrhizal (ECM) versus brown-rot (BR) fungi while degrading soil-organic matter

first: Firoz

last: Shah

first: César

last: Nicolás

first: Johan

last: Bentzer

first: Magnus

last: Ellström

first: Mark

last: Smits

first: Francois

last: Rineau

first: Björn

last: Canbäck

first: Rober

last: Carleer

first: Gerald

last: Lackner

first: Jana

last: Braesel

first: Dirk

last: Hoffmeister

first: Bernard

last: Henrissat

middle: S

last: Hibbet

first: Francis

last: Martin

first: Dag

last: Ahrén

first: Tomas

last: Johansson

first: Per

last: Persson


title: A transcriptomic study of maternal thyroid adaptation to pregnancy in rats

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

summary: To identify potential regulators of late pregnancy-dependent thyroid weight increase, thyroid gene expression profiles of non-pregnant (NP) and late pregnant (LP, day 18) rats was analyzed using the RNA-seq approach.

overall_design: Identifying global gene changes in the maternal thyroid in rats


title: Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle

first: miaomiao

last: Zhou

department: fungal physiology

institute: centre of fungal biodiversity, Utrecht, KNAW

summary: The common edible mushroom Agaricus bisporus is a basidiomycete that thrives on decaying plant material in the forests and grasslands of North America and Europe. It is adapted to forest litter and contributes to global carbon recycling, degrading cellulose, hemicellulose and lignin in plant biomass to oligomers and monomers. A. bisporus is also an edible mushroom that is widely cultivated and economically important. However, relatively little is known about how A. bisporus grows in this controlled environment and utilizes its substrate. Using transcriptomics and proteomics, we showed that changes in plant biomass degradation by A. bisporus occur throughout its life cycle. Ligninolytic genes were highly expressed during the spawning stage day 16 and had low expression during all the other growth stages which could indicate that lignin is not modified after the spawning stage. Our results also revealed differences in gene expression involved in cellulose and hemicellulose degradation between the first and second flushes. This could partially explain the reduction in the number of mushrooms during the second flush.

overall_design: This study compares the gene expression of A. bisporus A15 at different stages of its life cycle using the controlled environment of indoor commercial cultivation. The samples were taken at the spawning stage,  primordial stage, first flush, after first flush, second flush and after second flush, respectively

first: Miaomiao

first: Aleksandrina

last: Patyshakuliyeva

first: Harm

last: Post

first: Edita

last: Jurak

first: Albert

last: Heck

first: Kristiina

last: Hildén

first: Mirjam

middle: A

last: Kabel

first: Miia

middle: R

last: Mäkelä

first: A

middle: F

last: Altelaar

first: Ronald

last: de Vries


title: Cell fate determination by ubiquitin-dependent regulation of translation

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

summary: Metazoan development depends on accurate execution of differentiation programs that allow pluripotent stem cells to adopt specific fates. Differentiation is brought about by global changes to chromatin architecture and transcriptional networks, yet whether other regulatory events support cell fate determination is less well understood. Using human embryonic stem cell and Xenopus models, we identified the vertebrate-specific ubiquitin ligase Cul3KBTBD8 as an essential regulator of neural crest specification. Cul3KBTBD8 monoubiquitylates NOLC1 and its paralog TCOF1, whose mutation underlies the craniofacial disorder Treacher Collins Syndrome that is characterized by a loss of cranial neural crest cells. Ubiquitylation of NOLC1 and TCOF1 drives formation of a platform that connects RNA polymerase I with ribosome modification enzymes, thereby altering the translational program of differentiating cells to support the generation of neural crest cells. We conclude that the dynamic regulation of ribosome function is an important feature of cell fate determination.

overall_design: Ribosome profiling and mRNA-Seq

first: Achim

last: Werner

first: Nia

last: Teerikorpi

first: Indro

last: Fedrigo

first: Nicholas

last: Ingolia

first: Michael

last: Rape


title: Expression analysis of CsMYBF1 overexpressing tomato fruit

city: Wuhan

first: chaoyang

last: Liu

state: Hubei

address: Huazhong Agricultural University, Wuhan, 430070, China.

department: Huazhong Agricultural University

institute: Key Laboratory of Horticultural Plant Biology (Ministry of Education)

summary: To investigate global genome expression changes caused by the ectopic expression of CsMYBF1, we compared the gene expression profiles of the transgenic and wild type tomato fruits by RNA-seq analysis.Fruit samples from at least five plants of each genotype, which were harvested between 7 and 10 days after breaker stage, were pooled for total RNA isolation.A total of 3296 genes were differentially expressed between the transgenic and wild type fruits, and most of them were significantly induced, indicating the widespread influence on the expression of the endogenous tomato genes.

overall_design: Two lines of the tomato transgenic fruits expressing citrus gene CsMYBF1 were compared with two of that from the wild type.

first: Chaoyang

first: Xiuxin

last: Deng


title: High salt primes a specific activation state of macrophages, M(Na)

city: Shanghai

first: WUCHANG

last: ZHANG

state: Shanghai

address: 115 Jinzun Road

department: School of stomatology

institute: Shanghai Jiao Tong University

summary:
Purpose: Investigate effects of high salt on human macrophage activation
Methods: Human monocytes-derived macrophages were treated by additional 51mM NaCl for 24 hours (NaCl groups) or not (Control groups). mRNA profiles were generated by RNA-Seq, in triplicate, using Ion proton（Life tech). qRT–PCR validation was performed using SYBR Green assays.
Results: High salt significantly promotes pro-inflammatory gene expressions,while suppresses the expressions of anti-inflammatory genes and pro-endocytic genes in human macrophages.
Conclusions: Our results identify a novel macrophage activation state, M(Na), and high salt as a potential environmental risk factor for lung inflammation through the induction of M(Na)

first: Wuchang

last: Zhang

first: Shengzhong

last: Duan


title: Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

summary: ATP6AP2 is an essential accessory component of the vacuolar H+ ATPase (V-ATPase) and has been associated with intellectual disabilities (ID) and Parkinsonism. ATP6AP2 has been implicated in several signaling pathways, but little is known about its role in the nervous system. To decipher its function in behaviour and cognition, we generated and characterized conditional ATP6AP2 Drosophila and mouse models in the nervous system. In Drosophila, knockdown of ATP6AP2 induced defective phototaxis and vacuolisation of photoreceptor neurons and pigment cells when deleted in eyes and alteration of short- and long-term memory when deleted in the mushroom body. In mouse, conditional Atp6ap2 deletion in glutamatergic neurons (Atp6ap2Camk2aCre/0 mice) caused increased spontaneous locomotor activity and altered memory for fear. Both Drosophila ATP6AP2 knockdown and Atp6ap2Camk2aCre/0 mice presented with presynaptic transmission defect, abnormal number and morphology of synapses, and alteration of axonal transport in fly. In addition, Atp6ap2Camk2aCre/0 mice showed autophagy defect leading to axonal and neuronal degeneration in the cortex and the hippocampus. Surprisingly, myelinisation of axons was affected in our mutant mice. In accordance with the identified phenotypes across species, genome-wide transcriptome profiling of Atp6ap2Camk2aCre/0 mouse hippocampi revealed dysregulated genes involved in myelination, action potential, membrane bound vesicles and adult behaviour. In summary, disruption of ATP6AP2 in mouse and fly leads to cognitive impairment and neurodegeneration, mimicking aspects of the neuropathology associated with ATP6AP2 mutations in humans. Our results identify ATP6AP2 as an essential gene for the nervous system.

overall_design: 4 samples, 2 wt and 2 Atp6ap2Camk2aCre/0

first: Iacono

last: Giovanni


title: Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis [ATAC-Seq]

status: Public on Sep 21 2015

first: James

last: Bradner

state: MA

address: 450 Brookline

institute: Dana-Farber Cancer Institute

summary: Cohesin complex members have recently been identified as putative tumor suppressors in hematologic and epithelial malignancies. The cohesin complex guides chromosome segregation, however cohesin-mutant leukemias do not show genomic instability. We hypothesized reduced cohesin function alters chromatin structure and disrupts cis-regulatory architecture of hematopoietic progenitors.  We investigated the consequences of Smc3 deletion in normal and malignant hematopoiesis. Bi-allelic Smc3 loss induced bone marrow aplasia with premature sister chromatid separation, and revealed an absolute requirement for cohesin in hematopoietic stem cell function. In contrast, Smc3 haploinsufficiency increased self-renewal in vitro and in vivo including competitive transplantation. Smc3 haploinsufficiency reduced coordinated transcriptional output, including reduced expression of transcription factors and other genes associated with lineage commitment.  Smc3 haploinsufficiency cooperated with Flt3-ITD to induce acute leukemia in vivo, with potentiated Stat5 signaling and altered nucleolar topology.  These data establish a dose-dependency for cohesin in regulating chromatin structure and hematopoietic stem cell function.

overall_design: ATAC-seq in murine c-kit+ cells for the following genotypes: Smc3 fl/+, Smc3 del/+, Flt3-ITD, Smc3 fl/del Flt3-ITD

first: Christopher

last: Ott

first: Aaron

middle: D

last: Viny


title: Transcriptome profiling of the defense response following elicitation by a bacterial pathogen or flg22

city: Stanford

first: Elizabeth

middle: S.

last: Sattely

state: CA

address: 443 Via Ortega, Room 271

department: Chemical Engineering

institute: Stanford University

summary: Phytoalexins are abundant in edible crucifers and have important biological activities, yet no dedicated gene for their biosynthesis is known. Here, we report two new cytochromes P450 from the non-model plant Brassica rapa (Chinese cabbage) that catalyze unprecedented S-heterocyclizations in cyclobrassinin and spirobrassinin biosynthesis. Our results reveal the first genetic and biochemical insights into the biosynthesis of a prominent pair of dietary metabolites, and have important implications for pathway discovery across >20 recently sequenced non-model crucifers.

overall_design: Leaf mRNA profiles of four conditions (Pseudomonas syringae pv. maculicola, flg22, and their respective mock treatments) were tested in triplicate.

first: Andrew

last: Klein


title: Muscle transcriptome analysis of the large yellow croaker under fasting treatment by RNA-seq

city: Taizhou

first: Baoying

last: Qian

state: Zhejiang

address: 1139 Shifu Road, Jiaojiang, Taizhou, Zhejiang 318000, P. R. China

department: School of life science

institute: Taizhou University

summary: We sequenced mRNA from 2 muscle samples of the large yellow croaker (Larimichthys crocea) taken from normal feeding fish and fasting stress treatment fish, respectively, to investigate the transcriptome and comparative expression profiles of the large yellow croaker muscle undergoing fasting.

overall_design: Muscle mRNA profiles of control group (M7C) and 21-day fasting group (M7E) were generated by RNA-seq using Illumina HiSeq 2500.

first: Hongli

last: Huang

first: Liangyi

last: Xue


title: ACF chromatin remodeling complex mediates stress-induced depressive-like behavior through nucleosome repositioning and transcriptional regulation.

city: New York

first: Eric

last: Nestler

state: NY

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: Despite depression being one of the most prevalent and debilitating disorders worldwide, it has been difficult to understand its pathophysiology and to develop more effective treatments. Maladaptive transcriptional regulation within limbic neural circuits, including reward processing regions such as the nucleus accumbens (NAc), in response to chronic stress is thought to be a major contributor to the development of the syndrome. Epigenetic events?in particular, histone writers and erasers?that alter chromatin structure to regulate programs of gene expression have increasingly been associated with depression-related behavioral abnormalities in animal models and in depressed humans examined postmortem. However, very little is known about the ATP-dependent chromatin remodelers that control nucleosome positioning and the packing state of chromatin. Here we show that the ACF complex, part of the ISWI family of chromatin remodelers, is persistently and selectively upregulated in the NAc of mice that are susceptible to chronic social stress, as well as in the NAc of depressed human. We further establish that ACF induction is both necessary and sufficient for susceptibility to stress-induced depressive-like behaviors. Using ChIP-seq, we demonstrate that altered ACF binding after chronic stress is strongly correlated with altered nucleosome positioning, in particular, around the transcriptional start sites of affected genes. These alterations in ACF binding and nucleosome repositioning are associated with repressed expression of a subset of genes in animals that are susceptible to chronic stress. Together, these findings establish that active ATP-dependent chromatin remodeling by the ACF complex is a key regulator in the repression of genes that mediate susceptibility to social stress, and provide novel candidate targets for improved therapeutics of depression and other stress-related disorders.

overall_design: c57bl/6 mice underwent chronic social defeat stress (CSDS), and social interaction test was used to separate animals into control, susceptible and resilient groups. Nucleus accumbens (NAc) tissue was collected 48 hours after the last defeat session, and then Acf1, SNF2H ChIP-seq or H3 MNase-seq were performed based on the control, susceptible, and resilient groups. Three sequencing replicates were performed on each group.

first: HaoSheng

last: Sun

first: Ning-Yi

last: Shao

first: Li

last: Shen


title: Global DNA methylation changes and differential gene expression in Anaplasma phagocytophilum-infected human neutrophils

city: Baltimore

first: John

middle: Stephen

last: Dumler

state: MD

address: 685 W Baltimore St

department: Pathology and Microbiology & Immunology

institute: University of Maryland School of Medicine

summary:
Background: Anaplasma phagocytophilum is an obligate intracellular prokaryotic pathogen that both infects and replicates within human neutrophils. The bacterium represses multiple antimicrobial functions while simultaneously increasing proinflammatory functions by reprogramming the neutrophil genome. Previous reports show that many observed phenotypic changes are in part explained by altered gene transcription. We recently identified that large chromosomal regions of the neutrophil genome are differentially expressed during A. phagocytophilum infection. Because of this, we sought to determine whether gene expression programs altered by infection were the result of changes in the host neutrophil DNA methylome.
Results: Within 24 h of infection, marked increases in DNA methylation were observed genome-wide as compared with mock-infected controls and pharmacologic inhibition of DNA methyltransferases resulted in decreased bacterial growth. New regions of DNA methylation were enriched at intron and exon junctions; however, intragenic methylation did not correlate with altered gene expression. In contrast, intergenic DNA methylation was associated with A. phagocytophilum-induced gene expression changes. Within the major histocompatibility complex locus on chromosome 6, a region with marked changes in infection-induced differential gene expression, new regions of methylation were localized to boundaries of active and inactive chromatin.
Conclusions: These data strongly suggest that A. phagocytophilum infection, in addition to altering histone structure, alters DNA methylation and the epigenome of its host cell to promote survival and replication, providing evidence that such bacterial infection can radically alter the epigenome of its host cell.

overall_design: Examination of methylated DNA sites in 3 human donors' neutrophils with and without 24h infection by Anaplasma phagocytophilum.

first: Sara

middle: H

last: Sinclair

first: Srinivasan

last: Yegnasubramanian

first: J


title: Novel IDH1 Mutant Inhibitors for Treatment of Acute Myeloid Leukemia

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

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

overall_design: Refer to individual Series


title: RNA-sequencing elucidates the regulation of behavioural transitions associated with mating in honey bee queens

city: Egham

first: Fabio

last: Manfredini

state: Surrey

address: Bourne Lab Room 4-17

institute: Royal Holloway University of London

summary: Mating is a complex process, which is frequently associated with behavioural and physiological changes. However, understanding of the genetic underpinnings of these changes is limited. Honey bees are both a model system in behavioural genomics, and the dominant managed pollinator of human crops; consequently understanding the mating process has both pure and applied value. We used next-generation transcriptomics to probe changes in gene expression in the brains of honey bee queens, as they transition from virgin to mated reproductive status. In addition, we used CO2-narcosis, which induces oviposition without mating, as an experimental control for the mating process. Mating produced significant changes in the expression of vision, chemo-reception, metabolic, and immune-related genes. Differential expression of these genes maps clearly onto known behavioural and physiological changes that occur during the transition from being a virgin queen to a newly-mated queen. A subset of these changes in gene expression were also detected in CO2-treated queens, as predicted from previous physiological studies. In addition, we compared our results to previous studies that used microarray techniques across a range of experimental time-points. Changes in expression of immune- and vision-related genes were common to all studies, supporting an involvement of these groups of genes in the mating process. However, these comparisons also indicate the need to understand the temporal dynamics of gene expression across the entire mating and reproductive process.

overall_design: Brain RNA samples for 3 treatments: control (N=4), mated (N=4) and treated with carbon dioxide (N=4)

first: Mark

last: Brown

first: Vanina

last: Vergoz

first: Ben

last: Oldroyd


title: Neonatal naïve CD8+ T cells have effector-like gene expression that prevents memory cell formation [small-RNA seq]

first: Andrew

last: Grimson

address: 445 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

summary: Neonates are intrinsically defective at creating memory CD8+ T cells in response to infection with intracellular pathogens. Here we investigated differential of small RNAs, transcription factors, and chemokine receptors regulation in neonates as compared to adults before and during infection. We found that prior to infection, naïve cells have a different expression profile for many microRNAs, and gene targets of these microRNAs show widespread expression differences. These targets and other changes in gene expression in naïve cells result in neonatal cells that get activated more easily, express chemokine receptors that home to sites of infection, and are less protected from apoptosis during contraction. As a result, changes in neonatal naïve cells drive effector cell terminal differentiation at the expense of creating long-lived memory cells.

overall_design: Small RNAs were sequenced from adult and neonatal CD8+ T cells before and during infection

first: Erin

last: Wissink


title: Mouse ES cells expressing catalytically inactive Ring1B display impaired Ring1B and H3K27me3 deposition.

status: Public on Sep 20 2015

city: Edinburgh

first: Rob

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

summary: ChIP-seq for H3K27me3 and Ring1B was performed in WT mESCs and mESCs containing catalytically inactive Ring1B (I53A mutant). Cells expressing catalytically inactive Ring1B maintain the spatial distribution of Ring1B and H3K27me3 but at reduced levels. These findings support the notion that PRC2 recruitment is, in part, dependent on H2A ubiquitination (H2AK119ub).

overall_design: Two biological replicates were performed for Ring1B and H3K27me3 ChIPs in WT and Ring1B I53A/I53A mouse ESCs. Input chromatin was sequenced for each replicate as a control for ChIP enrichment.

first: Michael

last: Moffat

first: Robert

first: Abigail

last: Mann

first: David

last: Read

first: Pradeepa

middle: M

last: Marulasiddappa

first: Ian

last: Adams

first: Wendy

last: Bickmore


title: Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis

city: Boston

first: James

last: Bradner


title: Liver tissue HELP-tagging cytosine methylation data from C57BL/6J mice receiving high-fat diet with or without lingonberries

first: Lovisa

last: Heyman-Lindén

address: Klinikgatan 28

summary: The C57BL/6J mouse model develops obesity and pre-diabetes when fed a high-fat diet. In this experiment, DNA methylation was assessed globally at specific CpG sites in liver tissue from mice receiving high-fat diet (45E% from fat) for 13 weeks (Control) or high-fat diet supplemented with 20% (w/w) of freeze-dried lingonberries (n=4). Our findings show that lingonberries prevent development of high-fat induced obesity, hepatic steatosis and low-grade inflammation, and the DNA was hypermethylated in mice receiving lingonberries compared to control.

overall_design: Genome wide hepatic DNA methylation comparison between mice fed high-fat diet with or without a lingonberry supplement (n=4/group).

first: Maureen

last: Charron

first: Yoshinori

last: Seki