title: Sex chromosome complement defines diffuse versus focal angiotensin II-induced aortic pathology

status: Public on Jul 22 2018

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary: Objective-Aortic pathologies exhibit sexual dimorphism, with aneurysms in the ascending, thoracic and abdominal aorta (AAA) exhibiting higher prevalence in males. Despite lower incidence of aortic vascular disease in women, aneurysms progress rapidly. Mechanisms for these sex differences are unclear. We defined the role of sex chromosome complement and testosterone in regional development and progression of angiotensin II (AngII)-induced vascular pathologies. Approach and Results-We used transgenic male mice expressing Sry on an autosome to create low density lipoprotein receptor (Ldlr) deficient male mice with an XY or XX sex chromosome complement. Subjects were then sham operated or orcheictomized. Transcriptional profiling on abdominal aortas from XY or XX males demonstrated1746 genes influenced by sex chromosomes, sex hormones, or an interaction. A second cohort of animals was then infused with AngII for 28 days. Diffuse aortic aneurysm pathology developed in XY AngII-infused males, while XX males developed discrete AAAs. Castration reduced all AngII-induced aortic pathologies in XY and XX males. Thoracic aortas from AngII-infused XY males, but not XX males exhibited adventitial thickening. We infused male XY and XX mice with saline or AngII and quantified mRNA abundance of key genes in thoracic versus abdominal aortas. Regional differences in mRNA abundance existed before AngII infusions, which were differentially influenced by AngII between genotypes. Prolonged AngII infusions resulted in AAA aortic wall thickening in XY males with diffuse aortic pathology, while XX males had dilated focal AAAs. Conclusions-An XY sex chromosome complement mediates diffuse aortic pathology, while an XX sex chromosome complement contributes to discrete AngII-induced AAAs.

overall_design: All studies using mice were approved by the institutional Animal Care and Use Committee at the University of Kentucky and conformed to the Guide for the Care and Use of Laboratory Animals published by the NIH.  Male transgenic mice with deletion of Sry from the Y-chromosome expressing Sry on autosomes (8-12 weeks of age) were backcrossed 10 times on a C57BL/6J background (Stock#010905, The Jackson Laboratories, Bar Harbor MA) and bred to low density liproprotein receptor deficient (Ldlr-/-) females (Stock# 002207, The Jackson Laboratories, Bar Harbor MA) to generate Ldlr-/- male mice with an XY or an XX sex chromosome complement. DNA was extracted from ear or tail clips and subjected to PCR using a commercial PCR mix (Promega 2X Master Mix, cat#m7123, Fitchburg WI) and specific primers. Mice were fed a western diet (TD88137, Harlan Teklad, Indianapolis, IN) for the duration of the experiment and randomly assigned to sham and orchiectomized (ORC) groups. Two weeks later, anesthetized mice were implanted subcutaneously with osmotic micropumps (Alzet model 1004, Durect Co., Cupertino, CA) for infusion of AngII for 28 days (1,000 ng/kg/min, Bachem, Torrance, CA).  At the end of the experiment, mice were euthanatized under anesthesia (ketamine/xylazine, 100:10 mg/kg, i.p.) and blood was collected via cardiac puncture.   Orchiectomy.  Male (8-12 weeks of age) XX and XY Ldlr-/- mice were orchiectomized under isoflurane anesthesia (2-3%) and given pre and post-operative analgesic (24 hr. after surgery; flunixin; 2.5 mg/kg). Mice were shaved in the scrotum region and a depilatory cream (Nair, Inc.) applied to the area to remove hair, followed by sterilizing with povidone-iodine/ethanol (three times). A small incision was made in this region. Vas deferens were collapsed using a hemostat and the testes were removed. The vascular supply was ligated by cauterization using a high-temperature fine-tip loop cauterizer and the hemostat was released. The wound site was monitored for bleeding, and the skin was closed by wound clips (Autoclip stapler). The site was then treated with povidone-iodine, and mice were allowed to recover. The testes were manipulated but left intact in anesthetized sham-operated mice.  All mice were allowed to recover from surgery and to clear their endogenous testicular hormones for two weeks. After two weeks, mice were placed on Western diet (TD88137, Harlan Teklad, Indianapolis, IN) for one week. RNA from abdominal aortas was extracted using the RNeasy fibrous tissue mini kit (Qiagen, cat # 74704). Harvested abdominal aortic RNA quality and quantity were measured by Agilent 2100 Bioanalyzer using RNA 6000 Nano Labchip kits (Agilent Technologies, Cat # 5067-151). One RNA sample (subject #9) was excluded due to poor quality. The remaining 17 samples had excellent quality and did not differ significantly by treatment group (RNA Integrity Number [RIN]: 9.64 ± 0.03; RNA concentration (ng/ul): 55.7 ± 7.4; 28s:18s ratio: 3.00 ± 0.07; all p-values for main effects of gene and surgery, as well as of interaction terms were n.s. [p > 0.1]). Extracted RNA was labeled and hybridized to Affymetrix Mouse Transcriptome Assay 1.0 arrays (one array per subject; N = 17). Signal intensities were calculated using the RMA algorithm (Bolstad et al., 2003) at the transcript level using Genomics Suite software (Partek, St Louis). Data were transferred to flat files in Excel and associated with vendor-provided annotation data. Pre-statistical filtering retained unique, annotated probe sets with adequate signal intensity (signal intensity ≥ 4.2 on at least 3 arrays in the study). Filtered signal intensities were analyzed by two-way ANOVA to identify significant main effects of genotype (XX versus XY), surgery (Sham vs ORC), as well as interaction. The False Discovery Rate (FDR) procedure (Hochberg and Benjamini, 1990) was used to estimate the error of multiple testing.

first: Yasir

last: Alsiraj

first: Sean

middle: E

last: Thatcher

first: Bradley

last: Fleenor

first: Alan

last: Daugherty

first: Lisa

last: Cassis


title: Comparison of gene expression between Ftx KO eyes and wild type eyes

status: Public on Jul 29 2018

city: Bunkyo-ku

first: Yusuke

last: Hosoi

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

summary: Gene expression of embryonic eye (e13.5) in Ftx KO females, Ftx KO males, WT females and WT males.

first: Shin

last: Kobayashi


title: SAMHD1 is recurrently mutated in T-cell prolymphocytic leukemia

status: Public on Jul 23 2018

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: We identified novel recurrent genetic lesions in T-PLL affecting genes involved in JAK/STAT signaling (PTPRC), epigenetic regulation (PRDM2), or DNA damage repair (SAMHD1, PARP10, HERC1, HERC2). Mutations of the tumor suppressor gene SAMHD1 causing amino-acid exchanges or protein truncations as well as copy number variations in SAMHD1 were seen in 20% of cases.

overall_design: Copy number variation analysis (Affymetrix SNP 6.0 and CytoHD Arrays) of 14 T-PLL patients.

first: Patricia

last: Johansson


title: Inherited disorders of cobalamin metabolism disrupt nucleocytoplasmic transport of mRNA through impaired methylation/phosphorylation of HuR

status: Public on Jul 20 2018

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

country: France

institute: INSERM

summary: Molecular mechanisms underlying the neurological disorders of inherited diseases of cobalamin metabolism remain obscure. Transcriptome data from a cell model with impaired cobalamin metabolism implicated dysregulated RNA metabolism and endoplasmic reticulum stress. Evidence from the cell model, Cd320 knockout mice, and fibroblasts with inborn errors of cobalamin metabolism indeed supported the findings of transcriptome. These models allowed the demonstration of RNA binding proteins (RBP) mislocalized subcellularly due to failed nucleocytoplasmic shuttling. In the case of HuR, decreased RBP interaction with nuclear receptor CRM1/exportin accounted for the failure, and HuR hypomethylation and dephosphorylation were the causes of this. Our evidence further indicated that decreased SAM and CARM1 level and increased PP2A expression were partly responsible for the post translational modifications of HuR. The consequent HuR mislocalization to the nucleus in turn reduced the expression of SIRT1 and other genes involved in brain development, neuroplasticity, myelin formation, and brain aging. This mislocalization was reversible upon treatment with siPpp2ca, cobalamin, S-adenosylmethionine, or PP2A inhibitor okadaic acid. In conclusion, our data highlight the key roles of cobalamin metabolism on HuR-mediated mRNA stability, which when disrupted produce genomic changes consistent with the effects of inborn errors of cobalamin on brain development, neuroplasticity and myelin formation.

overall_design: The N1E-115 cells are neuroblastoma cells chosen here as a neuronal model. Chimeric proteins were produced by the fusion of either N-terminal (TO) or C-terminal (OT) of transcoblamin (TCN2) to oleosin. Expressed TO fusion protein has high binding affinity toward Cbl whereas OT fusion protein has no detectable Cbl binding activity. Cells were cultured in a proliferation or a differentiation medium. Biological replicates were used to obtain samples from proliferated control (WT-p ; n=4), proliferated TO (TO-p ; n=4), proliferated OT (OT-p ; n=4), differentiated control (WT-d ; n=4), differentiated TO (TO-d ; n=4) and differentiated OT cells (OT-d ; n=4). WT samples represent non-transfected N1E-115 cells. TO and OT cells were transfected with the TO and OT chimeric constructs, respectively.

first: Shyue-Fang

middle: F

last: Battaglia-Hsu

first: Rose

last: Ghemrawi

first: Sébastien

first: Jean-Louis

middle: L

last: Guéant


title: Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage [single-cell RNA-seq]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

type: Expression profiling by high throughput sequencing

summary: T cell development and selection is orchestrated in the thymus by a specialized niche of diverse stromal populations. By transcriptional single cell sorting, we de novo characterize the entire stromal compartment of the thymus. We identified dozens of cell states within the thymic stroma, with thymic epithelial cells (TEC) showing the highest degree of heterogeneity. Our analysis highlights four major medullary TEC (mTEC I-IV) populations, with distinct molecular functions, epigenetic landscapes and lineage regulators. Specifically, mTEC-IV constitutes a new and highly divergent TEC lineage with molecular characteristics of the gut chemosensory epithelial tuft cells. Mice deficient of Pou2f3, a tuft cells master regulator, resulted in complete and specific depletion of mTEC-IV, without affecting other TEC populations. Overall, our study comprehensively defines all stroma cells in the thymus and identifies a new TEC lineage associated with chemosensory properties that may potentially link the adaptive immune system to environmental and neurological signals.

overall_design: Transcriptional profiling of single cells from the stroma of mouse thymus, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500

first: Jakub

last: Abramson

first: Chamutal

last: Bornstein

first: Shir

last: Nevo

first: Amir

last: Giladi

first: Noam

last: Kadouri


title: RNA-seq analysis of emf1, lhp1, ebs shl and ebs shl lhp1 transcriptomes in Arabidopsis thaliana

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

summary: By RNA deep sequencing, around 11,000 genes were found to be differentially expressed in ebs shl lhp1 compared with wild type, and SHL and EBS, together with LHP1 and EMF1, co-regulate the expression of thousands of gene in Arabidopsis

overall_design: Total RNAs were extracted from wild type, lhp1, ebs shl, ebs shl lhp1 and emf1 3-week old seedings with three biological repeats and mRNA were deep sequencing by Hi-Seq 2500 (Illumina).

first: Zicong

last: Li

first: Yuehui

last: He


title: Genome-wide mapping of EARLY BOLTING IN SHORT DAYS (EBS) binding sites in Arabidopsis thaliana

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A total of 2,356 genes were identified as EBS target loci by ChIP-seq

overall_design: EBS-binding regions were immunoprecipitated by ChIP from Arabidopsis seedlings, and sequenced on an Illumina Hi-seq 2500.


title: Genome-wide mapping of SHORT LIFE (SHL) binding sites in Arabidopsis thaliana

summary: A total of 1,942 loci were identified as SHL targets

overall_design: SHL-binding regions were immunoprecipitated by ChIP from Arabidopsis seedlings, and sequenced on an Illumina Hi-seq 2500.

first: Yizhong

last: Wang


title: Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage

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

overall_design: Refer to individual Series


title: Cxcl12a/cxcr4b and myca signaling override collective cell migration to repair zebrafish pronephros injuries

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Injuries of the zebrafish kidney are rapidly repaired by a migratory response in two to three day-old embryos. While this migratory repair process re-establishes the integrity of the pronephric tubules independently of proliferation, fluid flow, intact cilia, or Wnt signaling, pronephros injuries before 36 hours post fertilization were repaired by a purse string-like mechanism that irreversibly occluded the pronephric tubules. Comparing the gene expression profiles between these two developmental stages and focusing on up-regulated zebrafish pronephros genes, we identified cxcl12a and myca as potential candidates orchestrating the migratory repair process. Zebrafish lines with either cxcl12a or cxcr4b mutations displayed striking repair abnormalities, confirming the requirement for cxc12a/cxcr4b signaling to override the ongoing collective cell migration and repair the pronephros injury. However, in contrast to the collective cell migration of the posterior lateral line primordium, cxc12a/cxcr4b signaling was dispensable for normal pronephros development. Zebrafish myca, the pronephros-specific homologue of human MYC, was also increased in cells participating in the repair response. The defective repair response caused by knockdown of myca resembled the abnormalities observed in cxcx12a/cxcr4b-deficient zebrafish, and was partially rescued by cxcr4b mRNA, suggesting that myca acts in part through up-regulating cxcr4b expression during the migration-based repair process. Kidney-specific knockout of Cxcl12 and Myc suppressed mitochondrial functions, reduced retinoic acid receptor signaling, and delayed the recovery after ischemic/reperfusion injury in mice. Tretinoin, known to stimulate Cxcr4 expression and mitochondrial metabolism, accelerated renal recovery. Thus, the zebrafish pronephros injury mode provides a systematic approach to identify molecules involved in the immediate repair response after kidney injury, and to design strategies to ameliorate this severe complication of human disease.

overall_design: Whole kidney gene expression of was measured after ischemia for 22.5 minutes 12 hour reperfusion in WT C57BL/6 mice as well as conditional KO mice for Cxcl12 and Myc.

first: Toma

middle: A

last: Yakulov

first: Abhijeet

middle: P

last: Todkar

first: Krasimir

last: Slanchev

first: Martin

last: Groß

first: Anne

last: Bunjes

first: Florian

last: Grahammer

first: Tobias

last: Huber

first: Virginie

last: Lecaudey

first: Alexandra

last: Bona

first: Jochen

last: Hochrein

first: Melanie

last: Boerries

first: Albrecht

last: Kramer-Zucker

first: Gerd

last: Walz


title: Single-cell RNA-seq analysis reveals the progression of human osteoarthritis

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: Understanding the molecular mechanisms underlying human cartilage degeneration and regeneration is helpful for improving therapeutic strategies for treating osteoarthritis (OA). Here, we report the molecular programmes and lineage progression patterns controlling human OA pathogenesis using single-cell RNA sequencing (scRNA-seq). We performed unbiased transcriptome-wide scRNA-seq analysis, computational analysis and histological assays on 1464 chondrocytes from 10 patients with OA undergoing knee arthroplasty surgery. We investigated the relationship between transcriptional programmes of the OA landscape and clinical outcome using severity index analysis and correspondence analysis. We identified seven molecularly defined populations of chondrocytes in human OA cartilage, including three novel phenotypes with distinct functions. We presented gene expression profiles and transcriptional networks among chondrocytes at different OA stages at single-cell resolution. We found a potential transition among proliferative chondrocytes, prehypertrophic chondrocytes and hypertrophic chondrocytes (HTCs) and defined a new subdivision within HTCs. We revealed novel markers for cartilage progenitor cells (CPCs) and demonstrated a relationship between CPCs and fibrocartilage chondrocytes using computational analysis. Notably, we derived predictive targets with respect to clinical outcomes and clarified the role of different cell types for the early diagnosis and treatment of OA.

overall_design: 34 Samples

first: Quanbo

last: Ji

first: Guoqiang

last: Zhang

first: Yuqiong

last: Hu

first: Xiaoying

last: Fan

first: Yu

last: Hou

first: Lu

last: Wen

first: Li

last: Li

first: Yameng

last: Xu

first: Yan

first: Fuchou

last: Tang


title: DOWNREGULATION OF SPLICING REGULATOR RBFOX1 COMPROMISES VISUAL DEPTH PERCEPTION

status: Public on Jul 19 2018

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

country: USA

institute: UCLA

summary: Rbfox1 is a splicing regulator that has been associated with various neurological conditions such as autism spectrum disorder, mental retardation, epilepsy, attention-deficit/hyperactivity disorder, and schizophrenia. We show that in adult rodent retinas, Rbfox1 is expressed in all types of retinal ganglion cells (RGCs) as well as in certain subsets of amacrine cells (ACs) within the inner nuclear and ganglion cell layers. In developing retinas, Rbfox1 can be detected as early as E12. At that age, Rbfox1 is localized in the cytoplasm of differentiated RGCs. Between P0 and P5, strong expression of Rbfox1 in the inner plexiform layer was observed. This coincided with switching of Rbfox1 localization in RGC somas from cytoplasmic to a predominantly nuclear. Dynamic changes in Rbfox1 expression during first 10 postnatal days are correlated with the stage II spontaneous retinal waves of excitation, which in mice begins around the time of birth and continues for as long as two weeks. By P10, dendritic staining of Rbfox1 was dramatically reduced and remained so in the fully developed retina. In Rbfox1 knockout (KO) animals no detectable changes in retinal gross morphology were observed two months after Rbfox1 downregulation. However, the visual cliff test revealed marked abnormalities of depth perception of these animals. Retinal transcriptome analysis of Rbfox1 KO mice identified a number of genes that are involved in establishing neural circuits and synaptic transmission, including Vamp1, Vamp2, Snap25, Trak2, and Slc1A7, suggesting a role of Rbfox1 in the regulation of genes that facilitate AC and RGC synaptic communication.

overall_design: Retinal RNRetinal RNA-seq analysis was performed with 3 biological replicates representing Rbfox1-/- and 3 biological replicates representing control animals to identify differentially expressed and alternatively spliced genes. Rbfox1-/- animals were generated by crossing Rbfox1loxP/loxP(B6.129S2-Rbfox1tm1.1Dblk/J) mice with Tg(UBC-cre/ERT2)1Ejb mice. Cre expression was induced with tamoxifen in adult homozygous Rbfox1loxP/loxP; UBC-Cre+/- mice. Mice used in this study were maintained on the C57BL/6J background.

first: Lei

last: Gu

first: Dean

last: Bok

first: Fei

last: Yu

first: Joseph

last: Caprioli

first: Natik

last: Piri


title: Gene and microRNA expression data from neuroendocrine transdifferentiated and untreated prostate cancer cell line LNCaP

first: Ludger

last: Klein-Hitpass

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

summary:
Prostate tumors contain foci of neuroendocrine transdifferentiation (NETD), resulting in an increase of androgen-independent neuroendocrine-like (NE) tumor cells, whose number significantly correlates with tumor aggressiveness and a lower survival rate. The mechanisms leading to NETD and the exact role of NE-like tumor cells in disease progression are not fully understood yet.
We used microarrays to analyze mRNA and microRNA expression during NE-transdifferentiation and we identified wide changes in both expression profiles including several genes and microRNAs with potential roles in NETD of prostate carcinoma.

platform_organism:
Homo sapiens
synthetic construct

overall_design: LNCaP prostate cancer cells were differentiated to NE-like cancer cells by androgen deprivation or cultivated in control medium for RNA extraction and hybridization on Affymetrix microarrays. Succesful NE differentiation was confirmed by qRT-PCR analysis of three marker genes (PSA, AR, NSE). Total RNA from three independent NETDs and control cells was pooled for gene and miRNA expression analysis.

first: Dankert

last: Jaroslaw


title: The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham


title: System-wide Dissection of the Transcriptional Response to RUNX1 During Hematopoietic Specification [ChIP-seq]

summary: The specification of hematopoietic cells in the developing embryo occurs in specific stages and is regulated by the successive establishment of specific transcriptional networks. However, the molecular mechanisms of how the different stages switch from one to another are still not well understood. Hematopoietic cells arise from endothelial cells within the dorsal aorta which transit into hematopoietic cells by a process called the endothelial-hematopoietic transition (EHT) which does not involve DNA replication. The transcription factor RUNX1 is essential for this process. Using the differentiation of mouse embryonic stem cells carrying an inducible version of RUNX1, we have previously shown that hematopoietic genes are primed prior to the EHT by the binding of transcription factors required to form both endothelial and hematopoietic cells (FLI-1 and SCL/TAL1). We demonstrated that after induction RUNX1 reshapes the transcription factor binding landscape by causing a relocation of these factors and pulling them towards its binding sites. In the study presented here, we employed the same system to globally dissect the transcriptional processes that underlay the EHT. We demonstrate that the RUNX1-mediated movement of FLI-1 involves the recruitment of the basal transcription components CDK9 and BRD4 to promoters. The looping factor LDB1 to binds to distal elements and after induction relocates towards RUNX1/FLI-1 to form a co-localizing complex in chromatin. This entire process is blocked by treatment with the BRD4 inhibitor JQ1. Our study constitutes a paradigm for transcriptional processes driving transitions in cellular shape and function which are widely observed in development and disease.

overall_design: ChIP-seq expreiments have been used to study RUNX1 transcription factor during Hematopoietic specification

first: Jane

last: Gilmour

first: Laura

last: Noailles

first: Monika

last: Lichtinger

first: Nadine

last: Obier

first: Constanze

last: Bonifer


title: Expression data from heart tissue after induction of ischemic stroke (occlusion of the middle cerebral artery)

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Stroke is frequently associated with cardiac troponin increase and cardiac complications. 24h and 72h after experimental ischemic stroke of the brain, we harvested the heart to investigate pathways and target genes, involved in cardiac dysfunction after acute ischemic stroke

overall_design: We induced ischemic stroke (middle carebral artery occlusion) in wildtype animals. After 24 and 72 hours, we sacrificed the animals and isolated the cardiac RNA for expression analysis. For both timepoints, we generated and analyzed sham operated control animals.

first: Lorenz

middle: H

last: Lehmann

first: Roland

last: Veltkamp


title: System-wide Dissection of the Transcriptional Response to RUNX1 During Hematopoietic Specification [RNA-seq]

overall_design: RNA-seq expreiments have been used to study RUNX1 transcription factor during Hematopoietic specification


title: miRNA-145 signalling in TFK-1 cells

summary:
Gallbladder carcinoma (GBC) is a rare cancer entity in Western Europe and the US with an incidence of less than 3/100.000 and a survival rate <10%. Radical surgery is the only potentially curative treatment option but most patients diagnosed with GBC are not resectable. Thus, there is a great need for the development of new treatment options, including targeted therapy for GBC.
To dissect the epigenetic regulation during GBC development, we performed global miRNA profiling of 40 GBC and 8 normal gallbladder tissues. MiRNAs that are associated with survival were functionally analysed by cell proliferation and colony formation assays. In addition, we performed whole genome gene expression analysis of cells expressing miRNA mimics or control and performed biochemical assays to dissect miR-145 signalling.
The GBC miRNA profiles exhibited large differences compared to normal gallbladder tissues with 49% of miRNAs being differentially expressed (FDR<0.001). In addition, 8 miRNAs were found to be down- and 16 to be up-regulated in the GBCs with poor outcome (p<0.05). The most down-regulated miRNA was miR-145-5p and the top up-regulated miRNA was miR-575. Overexpression of miR-145 led to a significant reduction of cell proliferation and colony formation, whereas opposite effects were observed for miR-575. Gene expression profiling of cells overexpressing miR-145 revealed activation of the STAT1 signalling pathway by inhibition of PTPRF in cholangiocellular but not hepatocellular carcinoma cells. Thereby, PTPRF directly bound to STAT1 and reduced STAT1 phosphorylation.
This study identified pro- and anti-tumorigenic miRNAs in GBC and provides new mechanistic insight in the tumour suppressive function of miR-145 loss leading to active STAT1 signalling.

overall_design: To study the function of miR-145 in biliary tract carcinomas, we performed whole genome gene expression analysis of cells expressing miR-145-5p mimics or AllStars control.

first: Stephanie

last: Roessler


title: An OMIC approach to elaborate the antibacterial mechanisms of different alkaloids

status: Public on Jul 17 2018

city: İstanbul

first: Fatma

middle: Gizem

last: Avci

address: Marmara Uni, Bioengineering  Dep., No:404  Kadıköy

department: Bioengineering

country: Turkey

institute: Marmara University

summary: In the current study, RNA sequencing was used to comparatively elaborate the activities and the effects of the alkaloids, boldine, bulbocapnine, and roemerine along with the well-known antibacterial alkaloid berberine on Bacillus subtilis cells.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Comparison of one-hour alkaloid treated (berberine,boldine,bulbocapnine,roemerine) cells with the control (DMSO treated) cells

middle: G

first: Nihat

last: Sayar

first: Berna

last: Sarıyar-Akbulut


title: Overall expression of genes in CRYM overexpressed Prostate cancer cell line LNCaP

city: Vienna

first: Olaf

last: Merkel

address: Waehringer Guertel 18-20

department: Clinical Institute of Pathology

country: Austria

institute: Medical University of Vienna

summary: RNA sequencing was employed to profile the entire mRNA transcripts. Total RNA from LNCaP transfected with control vector or CRYM bearing vector was isolated. RNA and samples were subjected to the sequencing on illumina's HiSeq 4000 platform. RNA-seq revealed the expression of 58,540 transcripts and of 34,878 (59.6 %) genes were expressed in LNCaP cells. 3226 (9.25 %) genes were altered by CRYM and 2.72 % were upregulated and 6.53 % were downregulated.

overall_design: Cells were in transiently transfected cells with CRYM vector vs control in duplicate. GFP expression was monitored and total RNA was isolated at 48 hours upon transfection.

first: Osman

last: Aksoy


title: Transcriptome analysis of C2C12 cells (WT and MYOD KO) overexpressing MUNC: proliferating and differentiating conditions.

status: Public on Jul 18 2018

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

summary: To check global changes of genes expression correlating with induction of MUNC, we stably overexpressed MUNC in WT cells and in MYOD KO cells. We compared transcriptomes of control cells and cells overexpressing MUNC and distinguished genes that are differentially expressed in different conditions

overall_design: C2C12 WT cells were stably transfected with control vector (EV) and vector coding for MUNC spliced  (ovMUNC). MYOD-/- cells were generated by CRISPR-Cas9 method, and after single cell screeening and deletion confirmation, MYOD-/- cells were transfected with control vector (EV) or the vector coding for MUNC spliced (ovMUNC). RNA samples were isolated from proliferating or differentiating (DM3) cells. 1 ug of RNA per sample was enriched for polA tailed mRNA molecules and RNA-Seq libraries were made. Pooled libraries were sequenced using paired-end protocol on Illumina platform

first: Magdalena

last: Cichewicz

first: Manjari

last: Kiran

first: Roza

middle: K

last: Przanowska


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and transgenic DgWRKY5 Chrysanthemum  Transcriptomes

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary: We generated 12 Gb of high-quality sequencing data (~6 Gb per sample) to clarify the molecular mechanism of salt tolerance between wild tipe and transgenic DgWRKY5 chrysanthemum under normal condition. A total of 1078 differentially expressed genes (DEGs) (593 up-regulated and 485 down-regulated) were identified between CK and DgWRKY5, including genes encoding transcription factors and protein kinases. We identified numerous differentially expressed genes that exhibited distinct expression patterns, and stress-related genes that were highly differentiated in wild tipe and transgenic DgWRKY5 chrysanthemum. These genes have known or potential roles in stress tolerance relative and were enriched in functional gene categories potentially responsible for chrysanthemum resistance. Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to stress response .

overall_design: Chrysanthemum leaves mRNA profiles of  of wild type and transgenic DgWRKY5  were generated by deep sequencing, in two or triplicate, using Illumina HiSeq4000.

first: L

last: Yu


title: Innate immune activity differentiate subtypes in new onset Type 1 diabetes that predict duration of the post-onset partial remission and correlate with responsiveness to CTLA4-Ig treatment

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: New measures are needed to predict type 1 diabetes disease trajectory.  We have developed a sensitive array-based bioassay whereby patient plasma is used to induce transcription in healthy “reporter” leukocytes.  Here we report a refined gene ontology-based inflammatory index (I.I.359) that is based upon expression levels of 359 transcripts identified in cross-sectional studies of new onset Type 1 diabetes patients and controls, where higher scores reflect greater inflammatory bias.  We examined the relationship between I.I.359 measured at onset and the post-onset disease course in local patients as well as participants of the TrialNet CTLA4-Ig trial.  In untreated patients, I.I.359 at baseline was highly variable and exhibited a significant inverse relationship with stimulated C-peptide AUC at 3, 6, 12, 18 and 24 months post-onset.  Further, duration of the post-onset partial remission was negatively related to baseline I.I.359 and positively associated with the peripheral abundance of activated regulatory T cells (CD4+/CD45RA-/FoxP3high).

overall_design: UPN727 cells were stimulated with CTLA4 treated patients (n=54) and placebo patients (n=20) plasma at baseline (BL), 3 month, 12 month and 24 month (total n=294 samples w/ 2 missing 3 month samples). Plus stimulated with our local  Recent onset T1DM plasma (n=26). Gene expression analysis was perfromed in order to evaluate the transcriptional signature associated with T1D.

first: Mary

last: Kaldunski

first: Shuang

last: Jia

first: Rhonda

last: Geoffrey

first: Aniko

last: Szabo

first: Cate

last: Speake

first: Carla

middle: J

last: Greenbaum

first: Yi-Guang

last: Chen


title: High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [WGBS]

status: Public on Jul 15 2018

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

type: Methylation profiling by high throughput sequencing

summary: Reprogramming of somatic cells to induced pluripotent stem cells provoke immense interest both for clinical applications in regenerative medicine, and in understanding the regulation of cell identity. Previous characterization of the molecular events that underlie this process were limited by the low yield and by the stochastic dynamics of this process. Here we present an in-depth mapping of the molecular events that underlie an efficient and successful reprogramming, covering transcriptional, epigenetic and translational changes in a single day resolution.

overall_design: Mbd3f/- and Gatad2a-/- MEFs that carry DOX-inducible OKSM cassette were used,  and iPSC reprogramming was initiated by addition of DOX in FBS/LIF medium in 5% pO2 conditions. On day 3.5 after DOX initiation, medium was changed to LIF/KSR-based with the addition of two small molecule inhibitors for MEK/ERK and GSK3 signaling (2i). Cells were harvested every 24 hours until day 8, and processed for library preparation followed by high-throughput sequencing. Mbd3f/- and Gatad2a-/- established iPSC line (after 3 passages or more) WGBS was measured in each time point. A wildtype cell line, WT-2, isogenic to Gatad2a-/- was used as a control.

first: Asaf

last: Zviran

first: Yoach

last: Rais

first: Nofar

last: Mor

first: Elad

last: Chomsky

first: Jacob

last: Hanna


title: High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [ChIP-Seq]

overall_design:
Mbd3f/- or Gatad2a-/- (P66) MEFs that carry DOX-inducible OKSM cassette were used,  and iPSC reprogramming was initiated by addition of DOX in FBS/LIF medium in 5% pO2 conditions. On day 3.5 after DOX initiation, medium was changed to LIF/KSR-based with the addition of two small molecule inhibitors for MEK/ERK and GSK3 signaling (2i). Cells were harvested every 24 hours until day 8, and processed for library preparation followed by high-throughput sequencing. Mbd3f/-, Gatad2a-/- and WT established iPSC line (after 3 passages or more), and WT V6.5 mouse ESCs were used as positive controls. ChIP-seq of the following proteins was measured in each time point: Oct4/Pou5f1, c-Myc, Klf4, Sox2, PolII, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3, H3K9me2, H3K9me3.

This series includes re-analyzed samples from GSE49766.


title: The promoter interactome of cardiomyocytes differentiated from human embryonic stem cells links regulatory elements to cardiac gene promoters

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: Long-range chromosomal interaction is an important mechanism by which differentiating cells organise three dimensional promoter-enhancer networks to regulate lineage-specifying, developmental, regulatory genes1,2. Distal promoter contacts in pluripotent stem and specialised cell types, such as foetal liver cells, form co-regulated gene networks correlated with their biological functions1. Promoter interactomes of 17 primary blood cell types also reflect high cell-type specificity3. The lineage-specifying promoter interactions can be constrained by polycomb repressive complexes and genes with specialised functions will be selectively released from this poised network during cell fate specification or differentiation2. The cis-regulatory contact upon lineage commitment is also a dynamic process that includes acquisition and loss of specific promoter interactions4. We characterise 5126 promoter-enhancer interactions specific to cardiomyocytes differentiated from human embryonic stem cells (hESC-CM) by performing a differential promoter capture Hi-C (PCHi-C)5 approach that allows physical promoter-enhancer contacts in hESC-CM to be identified against the background level of embryonic stem cells’ interactions. This approach enables us to extract key genomic regulators and their target genes highly specific to the cardiovascular development and functions.

overall_design: Performed capture Hi-C on cardiomyocytes differentiated from human embryonic stem cells (hESC-CM).  There were three biological replicates.

first: Mun-Kit

last: Choy

first: Biola

last: Javierre

first: Stephanie

last: Baross

first: Yingjuan

last: Liu

first: Simon

last: Williams

middle: W

first: Artur

last: Akbarov

first: Chris

last: Wallace

first: Mikhail

last: Spivakov

first: Peter

last: Fraser

first: Bernard

middle: D

last: Keavney


title: Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability

city: Durham

first: Nahid

last: Iglesias

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

summary: Histone H3 lysine 9 methylation (H3K9me) mediates heterochromatic gene silencing and is important for genome stability and the regulation of gene expression. The establishment and epigenetic maintenance of heterochromatin involve the recruitment of H3K9 methyltransferases to specific sites on DNA, followed by the recognition of pre-existing H3K9me by the methyltransferase and methylation of proximal histone H3. This positive feedback loop must be tightly regulated to prevent deleterious epigenetic gene silencing. Extrinsic anti-silencing mechanisms involving histone demethylation or boundary elements help limit the spread of inappropriate H3K9me. However, how H3K9 methyltransferase activity is locally restricted or prevented from initiating random H3K9me—which would lead to aberrant gene silencing and epigenetic instability—is not fully understood. Here we reveal an autoinhibited conformation in the conserved H3K9 methyltransferase Clr4 (Suv39h) of the fission yeast Schizosaccharomyces pombe that has a critical role in preventing aberrant heterochromatin formation. Biochemical and X-ray crystallographic data show that an internal loop in Clr4 inhibits the catalytic activity of this enzyme by blocking the histone H3K9 substrate-binding pocket, and that automethylation of specific lysines in this loop promotes a conformational switch that enhances the H3K9me activity of Clr4. Mutations that are predicted to disrupt this regulation lead to aberrant H3K9me, loss of heterochromatin domains, and growth inhibition, demonstrating the importance of the intrinsic inhibition and auto-activation of Clr4 in regulating the deposition of H3K9me and in preventing epigenetic instability. Together, conservation of the Clr4 autoregulatory loop in other H3K9 methyltransferases and the automethylation of a corresponding lysine in the human SUV39H2 homologue suggest that the mechanism described here is broadly conserved.

overall_design: ChIP-seq analysis of histone modifications (H3K9me2 and H3K9me3)

first: Gloria

middle: T

last: Jih

first: Danesh

last: Moazed


title: Single-base resolution DNA methylome maps of different organs in chickpea

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

summary: In this study, we have elucidated the DNA methylation patterns in different organs of a cultivated chickpea genotype ICC 4958 (leaf, root, flower and young pod) and leaf of wild chickpea PI 489777 using bisulphite sequencing. Approximately 108 million read pairs were analyzed per sample. The extent of methylation along-with the context and genomic location of methylated Cs was identified. Further processing was performed to identify the differentially methylated regions among samples with leaves of ICC 4958 as the reference sample. The high resolution methylome maps of different organs and differentially methylated regions will serve as reference for understanding the epigenetic regulation in chickpea.

sample_organism:
Cicer arietinum
Cicer reticulatum

platform_organism:
Cicer arietinum
Cicer reticulatum

overall_design: Whole-genome bisulphite sequencing was performed using HiSeq 2000 Illumina platform after isolating genomic DNA from different organs of ICC 4958 and PI 489777.

first: Rohini

last: Garg

first: Himanshi

last: Bhatia

first: Niraj

last: Khemka


title: G-quadruplex structures moulds the DNA methylome

status: Public on Jul 16 2018

first: Avazeh

last: Ghanbarian

address: Robinson Way

department: Cancer Research UK, Cambridge Inst

institute: University of Cambridge

summary: Control of DNA methylation level is critical for gene regulation, and the factors that govern hypomethylation at CpG islands (CGIs) are still being uncovered. Here, we provide evidence that G-quadruplex (G4) DNA secondary structures are genomic features that influence methylation at CGIs. We show that the presence of G4 structure is tightly associated with CGI hypomethylation. Surprisingly, we find that these G4 sites are enriched for DNA methyltransferase 1 (DNMT1) occupancy, which is consistent with our biophysical observations that DNMT1 exhibits higher binding affinity for G4s as compared to duplex, hemi-methylated or single-stranded DNA. The biochemical assays also show that the G4 structure itself, rather than sequence, inhibits DNMT1 enzymatic activity. Based on these data, we propose that G4 formation sequesters DNMT1 thereby protecting certain CGIs from methylation and inhibiting local methylation.

overall_design: G4 ChIP-seq perform on asynchronous K562 cells to detect the presence of DNA G-Quadruplexes. Experiment performed in 2 biological replicatest with 2 and 3 technical replicates, respectively. WGBS was done in entinostat treated HaCaT cells and control cells.

first: Jochen

last: Spiegel

first: Giovanni

last: Marsico

first: Dario

last: Beraldi

first: Robert

last: Hänsel-Hertsch

first: Shiqing

last: Mao

first: David

last: Tannahill

first: Shankar

last: Balasubramanian


title: High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems

first: Noa

last: Novershtern

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: High-Resolution Dissection of Conducive Somatic Cell Reprogramming to Naïve Ground State Pluripotency in Mbd3/NuRD and Gatad2a/NuRD Depleted Systems [ATAC-Seq]

overall_design: Mbd3f/- and Gatad2a-/- MEFs that carry DOX-inducible OKSM cassette were used,  and iPSC reprogramming was initiated by addition of DOX in FBS/LIF medium in 5% pO2 conditions. On day 3.5 after DOX initiation, medium was changed to LIF/KSR-based with the addition of two small molecule inhibitors for MEK/ERK and GSK3 signaling (2i). Cells were harvested every 24 hours until day 8, and processed for library preparation followed by high-throughput sequencing. Mbd3f/- and Gatad2a-/- established iPSC line (after 3 passages or more), and WT V6.5 mouse ESCs were used as positive controls. ATAC-seq was measured in each time point.

first: Asaf

last: Zviran

first: Yoach

last: Rais

first: Nofar

last: Mor

first: Jacob

last: Hanna


title: Small RNA sequencing in wild chickpea

first: Mukesh

last: Jain

summary: We report small RNA data from the leaves of wild chickpea PI 489777. Small RNA library was prepared and sequencing was performed using Illumina platform. A total of 23 million reads were generated, which represented 0.95 million unique reads. These were mapped to the chickpea genome using Bowtie to obtain the non-redundant set of unique small RNA sequences.

overall_design: In this study, RNA was isolated from the leaves of PI 489777 and small RNA library was prepared using TruSeq Small RNA Sample Prep Kit (Illumina Technologies) according to the manufacturer's instructions. Data obtained in FASTQ files was pre-processed to remove low-quality reads. Unique reads from each sample were mapped to the chickpea genome using Bowtie.Only the non-redundant set of uniquely mapped small RNA reads were retained.


title: METTL3-mediated m6A modification is required for cerebellar development m6A modification and cerebellar development

city: Beijing

first: Xiuying

last: Liu

address: Yard 28, Science Park Road, Changping District

institute: Changping Laboratory

summary: N6-methyladenosine (m6A) RNA methylation is the most abundant modification on mRNAs and plays important roles in various biological processes. The formation of m6A is catalyzed by a methyltransferase complex including methyltransferase like 3 (METTL3) as a key factor. However, the in vivo functions of METTL3 and m6A modification in mammalian development remain unclear. Here we show that specific inactivation of Mettl3 in mouse nervous system causes severe developmental defects in the brain. Mettl3 conditional knockout mice manifest cerebellar hypoplasia caused by drastically enhanced apoptosis of new born cerebellar granule cells (CGCs) in the external granular layer (EGL). METTL3 depletion induced loss of m6A modification causes extended RNA half-lives and aberrant splicing events, consequently leading to dysregulation of transcriptome-wide gene expression and premature CGC death. Our findings reveal a critical role of METTL3-mediated m6A in regulating the development of mammalian cerebellum.

overall_design: The mRNA expression and m6A modification were analyzed in wildtype and Mettl3 conditional knockout (Nestin-Cre) mice using postnatal day 7 and day 14 mouse cerebellums.

first: Chen-Xin

last: Wang

first: Guan-Shen

last: Cui

first: Kai

last: Xu

first: Meng

first: Xin-Xin

last: Zhang

first: Li-Yuan

last: Jiang

first: Ang

last: Li

first: Ying

last: Yang

first: Wei-Yi

last: Lai

first: Bao-Fa

last: Sun

first: Gui-Bing

first: Hai-Lin

first: Wei-Min

last: Tong

first: Wei

first: Xiu-Jie

first: Yun-Gui

first: Qi

last: Zhou


title: A bivalent histone reader is an epigenetic switch regulating floral phase transition

status: Public on Jul 14 2018

city: Madison

first: Christine

last: Wooddell

address: 502 S Rosa Rd

institute: Arrowhead Pharmaceuticals

summary: EBS and CLF genome-wide binding sites were investigated by ChIP sequencing,

overall_design: Arabidopsis wild-type Col (containing no FLAG-tagged transgene), EBS-FLAG (containing FLAG-tagged transgenic EBS), EBSΔC-FLAG (containing FLAG-tagged transgenic EBSΔC), and CLF-FLAG (containing FLAG-tagged transgenic CLF) plants were subject to ChIP-sequecing analysis using the FLAG beads. H3K4me3 ChIP-seq was also performed in Col-0, EBS-FLAG, and EBSΔC-FLAG.

first: Xuehua

last: Zhong

first: Shuiming

last: Qian


title: Whole genome bisulphite sequencing using the Illumina X system [Illumina HumanMethylation450 BeadChip]

status: Public on Jul 12 2018

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

summary: While Illumina X technology has helped to reduce the cost of whole genome sequencing substantially, its application for bisulphite sequencing is not straightforward.  We describe the optimization of a library preparation and sequencing approach that maximizes the yield and quality of sequencing, and how to eliminate a previously unrecognized artefact affecting several percent of bisulphite sequencing reads.

overall_design: NA12878 and IMR90 cell lines assayed with Illumina Infinium MethylationEPIC BeadChip for comparison against whole genome bisulphite sequencing using BS-tagging protocol

first: Masako

last: Suzuki

first: Will

last: Liao

first: Frank

last: Wos

first: Justin

last: DeGrazia

first: Jennifer

last: Ishii

first: Toby

last: Bloom

first: Michael

middle: C

last: Body

first: Soren

last: Germer

first: John

last: Greally


title: Whole genome bisulphite sequencing using the Illumina X system [Bisulfite-Seq]

overall_design: Whole genome bisulphite sequencing of NA12878 and IMR90 cell lines using BS-tagging protocol

last: Zody

middle: M


title: Whole genome bisulphite sequencing using the Illumina X system


title: ILC1 lineage identity is determined by a cis-regulatory element marked by a novel lncRNA [RNA-seq]

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

summary: Innate lymphoid cells (ILCs) comprise three groups of recently identified tissue resident immune cell lineages that play critical roles in protective immune responses and tissue homeostasis. While significant progress has been made in defining the key protein mediators of ILC development and function, how cis-acting epigenetic regulatory elements or long non-coding RNAs (lncRNAs) regulate ILCs is unknown. Herein, we describe a cis-regulatory element demarcated by a novel lncRNA that controls the maturation, function and lineage identity of group 1 ILCs while being dispensable for early ILC development and homeostasis of mature ILC2s and ILC3s. We named this ILC1-restricted lncRNA Rroid. The Rroid locus controls the functional specification and lineage identity of ILC1 by promoting chromatin accessibility and STAT5 deposition at the promoter of its neighboring gene, Id2, in response to the ILC1-specific cytokine IL-15.

overall_design: RNA-seq for gene expression in mouse NK cells

first: Walter

last: Mowel

first: Sam

last: McCright

first: Jonathan

last: Kotzin

first: Magalie

last: Collet

first: Xin

last: Chen

first: Alexandra

last: DeLaney

first: Sean

last: Spencer

first: Anthony

last: Virtue

first: Enjun

last: Yang

first: Alejandro

last: Villarino

first: Makoto

last: Kurachi

first: Margaret

last: Dunagin

first: Gretchen

last: Harms Pritchard

first: Judith

last: Stein

first: Cynthia

last: Hughes

first: Diogo

last: Fonseca-Pereira

first: Henrique

last: Veiga-Fernandes

first: Arjun

last: Raj

first: Taku

last: Kambayashi

first: Igor

middle: E

last: Brodsky

last: O’Shea

first: E

last: Wherry

first: Loyal

last: Goff

last: Rinn

first: Adam

last: Williams

first: Richard

last: Flavell

first: Jorge

last: Henao-Mejia


title: Transcriptome analysis reveals important alkali-responsive genes and key pathways in rice under alkaline stress

city: Harbin

first: Ning

last: Li

address: No.600 Changjiang Road

department: College of Agriculture

institute: Northeast Agricultural University

summary: Soil alkalinity greatly affects plant growth and crop productivity. Although RNA-Seq analyses have been conducted to investigate genome-wide gene expression in response to alkaline stress in many plants, the expression of alkali-responsive genes in rice has not previously investigated. In this study, the transcriptomic data were compared between an alkaline-tolerant [WD20342 (WD)] and an alkaline-sensitive [Caidao (CD)] rice cultivar under control and alkaline stress conditions. A total of 962 important alkali-responsive (IAR) genes from highly differentially expressed genes (DEGs) were identified, including 28 alkaline-resistant cultivar-related genes, 771 alkaline-sensitive cultivar-related genes and 163 cultivar-non-specific genes. Gene ontology (GO) analysis suggested the enrichment of IAR genes involved in response to various stimuli or stresses. According to KEGG pathway analysis, the IAR genes were related primarily to plant hormone signal transduction and biosynthesis of secondary metabolites. Additionally, among these 962 IAR genes, 74 were transcription factors and 15 occurred with differential alternative splicing between the different samples after alkaline treatment. Our results provide a valuable resource on alkali-responsive genes and should benefit the improvement of alkaline stress tolerance in rice.

overall_design: Rice leaves mRNA profiles of physcion and chrysophanol alone treatment and combination treatment were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Detang

last: Zou


title: Whole genome bisulphite sequencing using the Illumina X system [Infinium MethylationEPIC]

first: Andrew

last: Johnston

overall_design: NA12878 and IMR90 cell ines assayed with Illumina Infinium MethylationEPIC BeadChip for comparison against whole genome bisulphite sequencing using BS-tagging protocol

first: Masako

last: Suzuki

first: Will

last: Liao

first: Frank

last: Wos

first: Justin

last: DeGrazia

first: Jennifer

last: Ishii

first: Toby

last: Bloom

first: Michael

last: Zody

first: Soren

last: Germer

first: John

last: Greally


title: Whole genome bisulphite sequencing using the Illumina X system [ATAC-Seq]

overall_design: The accessible regions of chromatin from ENCODE tier 1 cell line GM12878 were assayed from two different cultures; thus, producing two biological replicates.


title: Transcriptional response to a prime/boost vaccination of chickens with three vaccine variants based on HA DNA and Pichia-produced HA protein

city: Warsaw

first: Barbara

last: Kalenik

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: Broilers were immunized with three variants of subunit vaccines, based on the hemagglutinin (HA) DNA and Pichia-produced HA protein from H5N1 virus, in comparison to the control group, which was administered an empty vector (pCI).  Gene expression changes in the spleens of chickens were investigated at 7 day post booster dose.

overall_design: Chickens were divided into four groups: 'pCI/pCI' group was a negative control; 'Protein/protein' group was vaccinated twice with Pichia-produced  hemagglutinin (HA) protein from H5N1 virus; 'DNA/DNA' group was vaccinated twice with HA DNA on pCI vector and 'DNA/protein' group gained one dose of HA DNA  on pCI vector and one dose of Pichia-produced HA protein. At least three independent biological replicates of total RNA were isolated for each group at 7 day post booster dose. Two biological replicates from 'pCI/pCI' group; two biological replicates from 'DNA/DNA' group; three biological replicates from  'DNA/protein' group and four biological replicates from 'Protein/protein' group were selected for final analysis. Totally eleven samples of RNA were analysed.

first: Anna

last: Gora-Sochacka

last: Stachyra

first: Maria

last: Pietrzak

first: Edyta

last: Kopera

last: Fogtman

first: Agnieszka

last: Sirko


title: ILC1 lineage identity is determined by a cis-regulatory element marked by a novel lncRNA

first: Asli

last: Uyar


title: Genome-wide copy number variation analysis identifies novel candidate loci associated with pediatric obesity [CytoScanHD_Array]

city: Toronto

first: Stephen

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

summary: Purpose: Obesity is known to be a multifactorial condition that is highly heritable. There have been ~60 susceptibility loci identified, but they only account for a fraction of cases. As copy number variations (CNVs) have been implicated in the etiology of a multitude of human disorders including obesity, here, we investigated the contribution of rare CNVs (<0.1% population frequency) in pediatric cases of obesity.   Methods: We genotyped 67 pediatric patients presenting with obesity, including 22 with co-morbid developmental delay and prioritized rare CNVs at known associated loci, as well as, those impacting genes involved in energy homeostasis or related processes.  Results: We identified clinically relevant or potentially clinically-relevant CNVs in 15% (10/67) of individuals. Of these, 4% (3/67) had 16p11.2 microdeletions encompassing the known obesity risk gene SH2B1. Notably, we identified two unrelated probands harboring different 6p22.2 microduplications encompassing SCGN, a potential novel candidate gene for obesity. Further, we identified other biologically relevant candidate genes for pediatric obesity including ARID5B, GPR39, PTPRN2, and HNF4G.   Conclusion: We found previously reported candidate loci for obesity, and new ones, suggesting CNV analysis may assist in the diagnosis of pediatric obesity.

overall_design:
DNA was genotyped using the Affymetrix CytoScan HD array at TCAG using the manufacturer's protocol
We identified CNVs using Affymetrix Chromosome Analysis Suite, iPattern, Nexus, and Partek. CNVs were classified as stringent when called by at least two algorithms.

first: Thanuja

last: Selvanayagam

first: Susan

last: Walker

first: Matthew

last: Gazzellone

first: Rosanna

last: Weksberg


title: Genome-wide copy number variation analysis identifies novel candidate loci associated with pediatric obesity [GenomeWideSNP_6]

summary: Purpose: Obesity is known to be a multifactorial condition that is highly heritable. There have been ~60 susceptibility loci identified, but they only account for a fraction of cases.. As copy number variations (CNVs) have been implicated in the etiology of a multitude of human disorders including obesity, here, we investigated the contribution of rare CNVs (<0.1% population frequency) in pediatric cases of obesity.   Methods: We genotyped 67 pediatric patients presenting with obesity, including 22 with co-morbid developmental delay and prioritized rare CNVs at known associated loci, as well as, those impacting genes involved in energy homeostasis or related processes.  Results: We identified clinically relevant or potentially clinically-relevant CNVs in 15% (10/67) of individuals. Of these, 4% (3/67) had 16p11.2 microdeletions encompassing the known obesity risk gene SH2B1. Notably, we identified two unrelated probands harboring different 6p22.2 microduplications encompassing SCGN, a potential novel candidate gene for obesity. Further, we identified other biologically relevant candidate genes for pediatric obesity including ARID5B, GPR39, PTPRN2, and HNF4G.   Conclusion: We found previously reported candidate loci for obesity, and new ones, suggesting CNV analysis may assist in the diagnosis of pediatric obesity.

overall_design:
DNA was genotyped using the Affymetrix Genome-wide Human SNP Array 6.0 array at TCAG using the manufacturer's protocol
We identified CNVs using Birdsuite, iPattern, and Genotyping Console. CNVs were classified as stringet when called by at least two algorithms.


title: Gene Expression Profiling reveals a close relationship between Follicular lymphoma Grade 3A and 3B, but distinct profiles of Follicular Lymphoma Grade 1 and 2

city: Regensburg

first: Christian

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

institute: University of Regensburg

summary:
Since follicular lymphoma (FL) grade 3A often coexist with a FL1/2 component a linear progression model of FL1, FL2 and FL3A has been developed. FL3B, on the other hand, is supposed to be more closely related to diffuse large B-cell lymphoma (DLBCL) and both FL3B and DLBCL are often simultaneously present in one tumor (DLBCL/FL3B).
To obtain more detailed insight into FL progression, comprehensive analysis of a well-defined set of FL1/2 (n=22), FL3A (n=16), FL3B (n=6), DLBCL/FL3B (n=9) and DLBCL (n=45) was performed using gene expression profiling, immunohistochemical staining and genetic analysis by fluorescence in situ hybridization (FISH).

overall_design: 36 follicular lymphoma samples were hybridized to HGU133A Affymetrix GeneChips. In addition, this study contains 99 already published samples whereas 51 of them contribute to GSE4475, 36 contribute to GSE22470, 9 to GSE44164 and 3 to GSE48097. No re-normalisation of published samples was performed.

first: Heike

last: Horn

first: Raphael

last: Witzig

first: Markus

last: Kreuz

first: Ellen

last: Leich

last: Loeffler

first: Lorenz

last: Trümper

first: Rainer

last: Spang

first: Andreas

last: Rosenwald

first: German

last: Ott


title: Genome-wide copy number variation analysis identifies novel candidate loci associated with pediatric obesity [Omni2.5M Beadchip]

overall_design: We detected CNVs using iPattern, PennCNV, QuantiSNP, and CNVPartition. We defined a stringent set of variants when each variant was called by at least by two algorithms.


title: Genome-wide copy number variation analysis identifies novel candidate loci associated with pediatric obesity


title: Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos[RNA-Seq]

city: Shanghai

first: Jian

last: Hu

address: 1239,Siping Road

institute: Tongji University

summary: Expression profiles of in after egg laying (AEL)  3-4 hours (hr) and 14-15hr Drosophila melanogaster embryos (W1118)

overall_design: Expression profiles were generated from  AEL 3-4hr and 14-15hr D. melanogaster embryos.. We examined the changes in gene expression during D.melanogaster embryonic differentiation.

first: Cizong

last: Jiang


title: Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos

overall_design: Refer to individual Series


title: Effect of TGFB on primary human alveolar cells type 2 (hAEC2)

status: Public on Jul 11 2018

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

institute: Research Center Borstel - Leibniz Lung Center

summary: Investigating the effect of TGFB stimulation and/or inhibition on the transcriptome of primary human alveolar cells type 2

overall_design: hAECII from 4 different donors were stimulated with each 5ng/ml TGFB1, 10µM SB431542, 5ng/ml TGFB+10µM SB31542 or left untreated for 48h. Each experimental parameters has 4 biological replicates as paired observations

first: Torsten

last: Goldmann


title: Dynamic placement of the linker histone H1 regulates nucleosome arrangement and coordinates gene transcription in early Drosophila embryos[ChIP-Seq]

summary: H1 ChIP-seq profiling and nucleosome MNase-seq profiling were performed in after egg laying (AEL)  3-4 hours (hr) and 14-15hr Drosophila melanogaster embryos (W1118).

overall_design: Nucleosome and H1 maps were generated from AEL 3-4hr and 14-15hr D. melanogaster embryos. We determinated nucleosome occupancy in embryo by micrococcal nuclease sequencing (MNase-Seq). We also performed ChIP-Seq (chromatin immunoprecipitation and sequencing) for H1 genome wide profiles. Sequencing was performed on Illumina HiSeq 2000 using signle end protocol.


title: Characterization of imprinted methylation using the Illumina Infinium MethylationEPIC array platform

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

type: Methylation profiling by genome tiling array

summary: Bisulphite (BS) converted DNA from 2 paternal uniparental diploidies (pUPDs), one maternal (mUPD) and 5 control leukocytes samples were hybridized to the Infinium HumanMethylationEPIC BeadChip (Illumina), obtaining the BS DNA methylation profiles across approximately 850,000 CpGs. In addition, the 5 control leukocyte samples were also coverted using oxidative bisulphite (oxBS) treatment. The selective chemical oxidation of 5-hydroxymethylcytosine (5hmC) to 5-formylcytosine (5fC) and the deamination of the latter to uracil during the BS conversion allowed the quantification of independent 5-methylcytosine (5mC) and 5hmC methylation levels at every single CpG.

overall_design: Bisulphite converted DNA from 3 reciprocal uniparental diplodies were hybridised to the Infinium HumanMethylationEPIC BeadChip (Illumina) together with bisulphite and oxidative bisulphite converted DNA from 5 control leukocytes.

first: Jose

middle: R

first: David

last: Monk


title: Gene expression analysis of IDH1 wild type and IDH1 R132H mutated U87 cells

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: U87 cells were transduced with IDH1 WT or IDH1 R132H and stable clones were selected.

overall_design:
Human U87 glioblastoma cells either wild-type IDH1 or mutant IDH1.

Note: the processed data was generated using RMA normalization with other samples not included in this submission and can therefore not be fully reproduced from these two CEL files.

first: Georg

last: Karpel-Massler

last: Siegelin


title: Gene expression profiling of murine plasmocytes isolated from the spleen of IL-10eGFP mice infected with Salmonella

status: Public on Jul 10 2018

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary: The goal of this study was to identify the molecular characteristics and putative markers distinguishing IL-10eGFP+CD138hi and IL-10eGFP-CD138hi plasmocytes. To this end, IL-10eGFP B-green mice were challenged intravenously with Salmonella typhimurium (strain SL7207, 10e7 CFU), and IL-10eGFP+CD138hi as well as IL-10eGFP-CD138hi plasmocytes were isolated from the spleen on the next day. For this, single cell suspensions were prepared, cells were treated with Fc block (10 µg/ml, anti-CD16/CD32, clone 2.4G2), and then stained with an antibody against CD138 conjugated to PE (1/400; from BD Pharmingen) followed by incubation with anti-PE microbeads (Miltenyi Biotech). CD138+ cells were then enriched on Automacs (Miltenyi Biotech) using the program possel_d2. Cells were then stained with anti-CD19-PerCP, anti-CD138-PE, and antibodies against CD11b, CD11c, and TCR conjugated to APC as a dump channel to exclude possible contaminants. DAPI was added to exclude dead cells. Live IL-10eGFP+CD138hi and IL-10eGFP-CD138hi cells were subsequently isolated on a cell sorter. The purity of the samples was always above 98%. This led to the identification of LAG-3 as a cell surface receptor specifically expressed on IL-10eGFP+CD138hi cells but not on IL-10eGFP-CD138hi cells.

overall_design: Gene expression profiles of IL-10eGFP+CD138hi and IL-10eGFP-CD138hi cells. The experiment contains 2 groups. One group corresponds to IL-10eGFP+CD138hi cells, and the other group corresponds to IL-10eGFP-CD138hi cells. These cells were isolated from the spleen of IL-10eGFP mice (C57BL/6 genetic background) on day 1 after intravenous challenge with Salmonella typhimurium (strain SL7207, 10e7 CFU). The experiment was done in triplicates so there were three samples for each group. After total RNA extraction, reverse transcription, cDNA extraction, and in vitro transcription the biotinylated cRNA was fragmented, and hybridized on Affymetrix mouse genome 430 2.0 whole genome arrays. To obtain genes differentially expressed when comparing expression profiles of IL-10eGFP+CD138hi and IL-10eGFP-CD138hi cells group-wise comparisons were performed.

first: Lampropoulou

last: Vicky

first: Schliemann

last: Heidi

first: Boudinot

last: Pierre

first: Fillatreau

last: Simon


title: Key role of piRNAs in telomeric chromatin maintenance and telomere nuclear positioning in Drosophila germline

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

summary:
Background.
Telomeric small RNAs related to PIWI-interacting RNAs (piRNAs) have been described in various eukaryotes; however, their role in germline-specific telomere function remains poorly understood. Using a Drosophila model, we performed an in-depth study of the biogenesis of telomeric piRNAs and their function in telomere homeostasis in the germline.

Results
To fully characterize telomeric piRNA clusters, we integrated the data obtained from analysis of endogenous telomeric repeats, as well as transgenes inserted into different telomeric and subtelomeric regions. The small RNA-seq data from strains carrying telomeric transgenes demonstrated that all transgenes belong to a class of dual-strand piRNA clusters; however, their capacity to produce piRNAs varies significantly. Rhino, a paralog of heterochromatic protein 1 (HP1) expressed exclusively in the germline, is associated with all telomeric transgenes, but its enrichment correlates with the abundance of transgenic piRNAs. It is likely that this heterogeneity is determined by the sequence peculiarities of telomeric retrotransposons. In contrast to the heterochromatic non-telomeric germline piRNA clusters, piRNA loss leads to a dramatic decrease in HP1, Rhino, and trimethylated histone H3 lysine 9 in telomeric regions. Therefore, the presence of piRNAs is required for the maintenance of telomere chromatin in the germline. Moreover, piRNA loss causes telomere translocation from the nuclear periphery toward the nuclear interior but does not affect telomere end capping. Analysis of the telomere-associated sequences (TASs) chromatin revealed strong tissue specificity. In the germline, TASs are enriched with HP1 and Rhino, in contrast to somatic tissues, where they are repressed by Polycomb group proteins.

Conclusions
piRNAs play an essential role in the assembly of telomeric chromatin, as well as in nuclear telomere positioning in the germline. Telomeric arrays and TASs belong to a unique type of Rhino-dependent piRNA clusters with transcripts that serve simultaneously as piRNA precursors and as their only targets. Telomeric chromatin is highly sensitive to piRNA loss, implying the existence of a novel developmental checkpoint that depends on telomere integrity in the germline.

overall_design: The fractions of small RNAs (19-29 nt) from ovaries of four transgenic strains of Drosophila melanogaster were sequenced using Illumina HiSeq 2000.

first: Elizaveta

last: Radion

first: Valeria

last: Morgunova

first: Natalia

last: Akulenko

first: Sergey

last: Lavrov

first: Yuri

last: Abramov

first: Pavel

last: Komarov

last: Glukhov

first: Ivan

last: Olovnikov

first: Alla

last: Kalmykova


title: Transcriptomic analysis of heat stress transcriptional memory in Arabidopsis seedling

status: Public on Jul 09 2018

city: Taipei

first: Yee-yung

last: Charng

address: 128, Academia Rd. Sec. 2

department: Agric. Biotech. Res. Center

country: Taiwan

institute: Academia Sinica

summary:
Plants can be primed by a stress cue to mount a faster and stronger activation of defense mechanisms upon a subsequent stress. A crucial component of such stress priming is the modified reactivation of genes upon recurring stress, a phenomenon known as transcriptional memory. The transcriptional memory in response to heat stress is not clear at the genome scale.
We used microarrays to identify genes that showed transcriptional memory in response to recurring heat stress.

overall_design: Arabidopsis thaliana 7-d-old wild-type (Col-0) seedlings subjected to four different treatments were collected for RNA extraction.  Naïve: 7-d-old seedlings kept at normal growth condition without heat stress; Primed: 4-d-old seedlings were treated at 37 °C for 1 h then at normal growth condition for 3 d before sample collection; Triggered: 7-d-old seedlings were treated at 37 °C for 1 h before sample collection; Primed and triggered: 4-d-old seedlings were treated at 37 °C for 1 h, transferred to normal growth condition for 3 d, treated at 37 °C for 1 h again before sample collection. The heat treatment was performed around 10 am of the day. For HSFA2 knockout mutant (SALK_008978), the same treatments were conducted except the primed. The experiment contained at least two biological replicates for each treatment.

first: Siou-ying

last: Lin

first: Hsiang-chin

last: Liu

first: Jörn

last: Lämke

first: Isabel

last: Bäurle


title: Host response and prevention of avian pathogenic Escherichia coli following vaccination with an attenuated Salmonella expressing E. coli common pilus in chickens

city: Ames

first: Angelica

last: Van Goor

state: Iowa

address: 1221 Kildee Hall

institute: USDA-NIFA

summary: Avian pathogenic Escherichia coli (APEC) is a subset of extraintestinal pathogenic E. coli that causes detrimental losses to the poultry industry. Vaccines to reduce APEC in chickens have been partially successful, but many lack protection against multiple serotypes of APEC. Recombinant attenuated Salmonella vaccine (RASV) strains have been used to induce immunity against Salmonella in production chickens and can be modified to deliver foreign antigens as well. This study evaluated the transcriptome of chicken spleens and assessed prevention of APEC infection following vaccination with RASV strains, including a RASV carrying an E. coli antigen. Four-day-old White Leghorn chicks were orally vaccinated with RASV c8025(pYA3337) carrying an empty plasmid, c8025(pYA4428) carrying genes for E. coli common pilus (ECP), a combination of RASVs c8025(pYA3337) and c8025(pYA4428), or PBS (unvaccinated). To assess the host response to vaccination, antibody titers were measured by ELISA and spleen samples (n = 5) were collected from combination vaccinated and unvaccinated groups of four-week-old chickens for RNA sequencing. Five-week old chickens were challenged via air sac with APEC strains APEC-O2 and c7122 (O78). Blood was obtained 24 hours post-challenge, heart, liver, lung, and spleen were collected 48 hours post-challenge for enumeration of E. coli, and gross colibacillosis lesions were scored at necropsy. Chickens vaccinated with RASV strains elicited anti-E. coli EcpA, as well as cross reactive anti-E. coli IutA and IroN IgY antibodies. IgA results. In some organs, bacterial loads and lesions scores were numerically reduced, but no significant differences were detected for vaccinated compared to unvaccinated chickens. Transcriptome results. This data indicates that RASVs could be used to stimulate the immune system and is an initial step toward developing improved therapeutics to combat APEC infections in chickens.

overall_design: Chickens were evaluated for the spleen transciptomic response to vaccination with either PBS (non-vaccinated) or RASV  chi8025(pYA4428) carrying genes for E. coli common pilus (ECP) (vaccinated). Four spleens from each non-vaccinated and vaccinated chickens were used for library construction and sequenced on the HiSeq 3000. Differential

first: Zach

last: Stromberg


title: Trac-looping measures genome structure and chromatin accessibility

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

summary: Interaction between different chromatin regions plays critical roles in genome organization and regulation of transcription. Existing technologies of analyzing genome-wide chromatin interactions rely on in vitro proximity-based ligation of interacting chromatin fragments and thus are prone to potential artifacts. We now report a novel technique, Transposase-mediated Analysis of Chromatin loops (TrAC-loop), for detection of genome-wide chromatin interactions between regulatory regions. With this technique, a bivalent oligonucleotide linker is inserted between two interacting chromatin regions such that the distant interacting chromatin regions can be directly amplified by PCR and thus avoids the prior chromatin fragmentation and subsequent error-prone re-ligation steps. TrAC-loop selectively targets accessible regions, which effectively reduces the sequencing cost for detecting promoter-enhancer interactions at high resolution. Application of TrAC-loop to human CD4+ T cells reveals a substantial reorganization of enhancer-promoter interaction associated with changes in gene expression upon TCR stimulation.

overall_design: Examination of enhancer-promoter interaction associated with changes in gene expression upon TCR stimulation.

first: Binbin

last: Lai

first: Qingsong

last: Tang

first: Wenfei

last: Jin

first: Gangqing

last: Hu

first: Darawalee

last: Wangsa

first: Kairong

last: Cui

first: Benjamin

middle: Z

last: Stanton

first: Gang

last: Ren

first: Yi

last: Ding

first: Ming

first: Jiuzhou

last: Song

first: Thomas

last: Ried


title: RAP2 Mediates Mechanotransduction to Hippo pathway

city: La Jolla

first: Bing

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

institute: University of California, San Diego School of Medicine

summary: Mammalian cells are surrounded by the extracellular matrix (ECM), which regulates intercellular signal transduction and provides structural support to cells. Mechanical forces generated by ECM play a key role in regulating cell behaviors including survival, growth, mobility, and differentiation. However, it is unclear how mechanical forces are sensed by cells and transmit biochemical signals to cell fate-determining transcription factors such as YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif). Here we show the identification of Ras-associated protein 2 (RAP2) as an intracellular signal transducer that senses ECM rigidity and modulates cell survival and growth by negatively regulating YAP/TAZ. Activation of RAP2 by low ECM stiffness or contact inhibition triggers YAP/TAZ phosphorylation. Deletion of RAP2 leads to sustained YAP/TAZ activation in cells that grow on soft matrix or undergo contact inhibition, alters transcription programs initiated by low matrix stiffness, and results in cell transformation and malignant growth. Mechanistically, RAP2 can directly bind to Mitogen-activated protein kinase kinase kinase kinase 4/6/7 (MAP4K4/6/7) or Rho GTPase activating protein 29 (ARHGAP29), both of which lead to LATS1/2 activation and YAP/TAZ inhibition. These findings define a new molecular pathway that transmits mechanical cues to their effectors in the nucleus.

overall_design: The overall goal is to examine expression changes in response to ECM stiffness. mRNA profiles of wild type (WT), RAP2A/B/C-tKO, LATS1/2-dKO, and YAP/TAZ-dKO HEK293A cells were generated using deep sequencing with three biological replicates.

first: Zhipeng

last: Meng

first: Yunjiang

last: Qiu


title: The changed piRNA profiles of GC-1 cells exposure to 500 nM MC-LR.

city: Nanjing

first: Ling

last: Zhang

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

summary: We treated GC-1 cells with 500 nM or 0 nM of MC-LR for 24 h.Next, total RNA from GC-1 cells of these two groups were extracted using TRIzol Reagent. The two small RNA libraries were prepared using the Illumina small RNA preparation kit and were deep-sequenced. After adapter sequences were trimmed, 10,824,057, and 11,566,902 small RNA reads that were smaller than 45 nucleotides were obtained from control group and MC-LR group, respectively. The sequences that correspond to known piRNAs were determined by perfect sequence matching to the NCBI database (http://www.ncbi.nlm.nih.gov). We identified 244066 reads of piRNAs and 220 unique piRNA sequences in control group and 359871 reads of piRNAs and 230 unique piRNA sequences in MC-LR group

overall_design: The piRNA profiles of GC-1 cells exposure to 500 nM or 0 nM MC-LR were generated by Illumina high-throughput sequencing.

first: Xiaodong

last: Han


title: P68-associated lncRNA LOC284454 is differentially expressed in human cancers and modulates gene expression

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

summary: DDX5/p68 RNA helicase protein which is involved in splicing of precursor mRNAs also interacts with lncRNAs like, SRA and mrhl, to modulate gene expression. We performed RIP-seq analysis in HEK293T cells to identify the complete repertoire of DDX5/p68 interacting transcripts including 75 single exonic (SE) lncRNAs. The LOC284454 lncRNA is the second top hit of the list of SE lncRNAs which we have characterized in detail for its molecular features and cellular functions. The RNA is located in the same primary transcript harboring miR-23a~27a~24-2 cluster.  LOC284454 is a stable, nuclear restricted and chromatin associated lncRNA. The sequence is conserved only in primates and is expressed in multiple human tissues. Expression of LOC284454 is significantly reduced in breast, prostate, uterus and kidney cancer and also in breast cancer cell lines. Global gene expression studies upon loss and gain of function of LOC284454 revealed perturbation of genes related to cancer-related pathways. Focal adhesion and cell migration pathway genes are downregulated under overexpression condition, and these genes are significantly upregulated in breast cancer cell lines as well as breast cancer tissue samples suggesting a functional role of LOC284454 RNA in breast cancer pathobiology.

overall_design: We investigated the global effect of LOC284454 lncRNA on gene expression by transcriptome analysis in HEK293Tcells after siRNA mediated silencing of LOC284454 lncRNA.

first: Monalisa

last: Das

first: Arun

last: Renganathan

first: Shrinivas

middle: N

last: Dighe

first: Utsa

last: Bhaduri

first: Abhijith

last: Shettar

first: Geetashree

last: Mukherjee

first: Paturu

last: Kondaiah

last: Rao


title: circRNA expression in breast cancer cell lines

status: Public on Jul 07 2018

city: Shantou

first: Jianzhen

last: Xu

address: No.22 Rd Xinling

institute: Shantou University Medical College

summary: Use of circRNA array to examine the circRNA expression profile in breast cancer cell lines

overall_design: Arraystar Human circRNAs chip (Arraystar) were used to determine the circRNA expression in four breast cancer cell lines.

first: Min

last: Chen


title: Skeletal muscle Nr4a1 hypomethylation and gene induction reduce insulin sensitivity in sedentary maternal high-fat offspring

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Maternal high-fat consumption has negative effects on the offspring’s obesity/diabetes susceptibility and we hypothesize that epigenetic modifications in the skeletal muscle are partly responsible for this phenotype. To detect genes affected by maternal nutrition, offspring of low-fat (LF) and high-fat (HF) diet fed dams (C57BL/6 mice) received LF diet upon weaning and were sacrificed at an age of 6 or 25 weeks. M. quadriceps gene expression was investigated by microarray analysis revealing upregulation of the nuclear receptor Nr4a1 by maternal HF feeding. This was accompanied by promoter hypomethylation of CpG‑1408 which correlated with higher Nr4a1 gene expression at both ages. Offspring voluntary exercise training normalized Nr4a1 methylation/expression and ameliorated the negative effects of maternal HF feeding on insulin sensitivity. Overall, Nr4a1 expression correlated with higher insulin levels during oral glucose tolerance test and could, therefore, be involved in the programming offspring’s diabetes susceptibility.

overall_design: Starting three days prior to mating, female C57BL/6J mice (8 weeks old) received either a semisynthetic low-fat (LF; 10% energy from fat, 23% energy from protein, 67% energy from carbohydrates) or HF diet (40% energy from fat, 23% energy from protein, 37% energy from carbohydrates) diet during pregnancy and lactation (mLFD and mHFD, resp.). For mating, two females were introduced to one male for two weeks and subsequently individually caged. The litter size was adjusted to 5–7 pups, with no more than four siblings finally present in one group. Mice were kept in a light- and temperature-controlled facility at 22°C with a 12 h light-12 h dark cycle. After weaning, mLF and mHF male offspring were single caged and received LF until the end of the study at 6 weeks of age. All mice were sacrificed after 2 h of fasting using isoflurane and cervical dislocation.

first: Sara

last: Schumann

first: Inge

last: van der Stelt

first: Dorien

last: van Dartel

first: Susanne

last: Klaus


title: circRNA expression in breast cancer and non-tumor breast tissues

summary: Use of circRNA array to examine the circRNA expression profile in breast cancers,non-tumor breast tissues

overall_design: Eight breast cancers tissues and three non-tumor breast tissues from surgery were used as comparation group.Then circRNAs chips by Arraystar Human circRNAs chip (Arraystar) were used to determine the circRNA expression in all the samples.


title: Open chromatin in somatic cells transplanted into Xenopus oocytes

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: Active gene transcription is associated with an open chromatin configuration at gene regulatory regions. However, the relationship between chromatin architecture of somatic cells and transcriptional activation during nuclear reprogramming in oocytes is unclear. We therefore examined changes in open chromatin states before and after transplantation of mouse somatic nuclei into Xenopus laevis oocytes by using the Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq).

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design: ATAC-seq was performed using the following cell samples; (1) C2C12 cells, (2) mouse embryonic fibroblasts (MEFs) before and after nuclear transplantation into Xenopus laevis oocytes.

first: Kei

last: Miyamoto


title: Transcriptional profiling reveals no response of fungal pathogens to the durable, quantitative Lr34 disease resistance gene of wheat

city: Zürich

first: Coraline

middle: Rosalie

last: Praz

address: Zollikerstrasse 107

department: Institute of Plant and Microbial Biology

country: Switzerland

institute: University of Zürich

summary: We report the transcriptional analysis of the Blumeria graminis and Puccinia triticina biotrophic pathogen during their respective growth on Lr34 resistance and susceptible barley and wheat plants. No gene expression pattern has been observed suggesting that pathogen does not react to the presence of the resistance gene.

sample_organism:
Puccinia triticina
Blumeria hordei

platform_organism:
Puccinia triticina
Blumeria hordei

overall_design: RNA sequencing of three biological replicates for Blumeria graminis growing on Lr34 resistant and susceptible barley plants, at 48 h.p.i and 5 d.p.i, from a greenhouse infection. Three biological replicates of Puccinia triticina growing on Lr34 resistance and susceptible wheat have been sequenced from a late sporulation stage from field infection.

first: Justine

last: Sucher

first: Fabrizio

last: Menardo

first: Simon

last: Krattinger

first: Beat

last: Keller


title: Epididymal white adipose tissue expression data from WT and Abhd15-ko mice on normal chow diet at refed state

status: Public on Jul 06 2018

city: Graz

first: Juliane

last: Bogner-Strauss

address: Petersgasse 10-12/II

institute: Institute of Biochemistry, Graz University of Technology

summary:
Abhd15 is mainly expressed in white adipose tissues and highly upregulated upon adipogenesis. Abhd15 expression is correlated with insulin resistance in obese humans, however its physiological function remains unknown. We used the microarray technology to gain insight into ABHD15’s physiological function by identifying dysregulated genes in eWAT from Abhd15-ko mice in comparison to WT mice.
We used microarrays to detail the global programme of gene expression in epididymal white adipose tissue and identified distinct dysregulated genes in response to refeeding

overall_design: Male WT and Abhd15-ko mice on a clean C57BL/6J background were used. At 14 weeks of age, WT and Abhd15-ko mice were fasted overnight and refed with chow diet for 1 hour prior to harvesting. eWAT from WT and Abhd15-ko mice was collected and immediately snap frozen in liquid nitrogen. RNA was isolated for gene expression microarray analyses at the exon level (Affymetrix, Santa Clara, CA, USA). To isolate RNA, the frozen tissue samples were homogenized in TRIzol® reagent (Invitrogen/Life Technologies, Carlsbad, CA, USA) and processed based on the manufacturer’s instruction. Total RNA (200ng) from individual samples was then used for Affymetrix analysis. Terminal-labeled cDNA, hybridization to genome-wide Mouse Gene 2.0 ST Gene Chips and scanning of the arrays were carried out according to the manufacture’s indications (Affymetrix). Output primary row data was analyzed with Expression Console software (Affymetrix).

first: Wenmin

last: Xia

first: Ariane

last: Pessentheiner

first: Melina

last: Amor

first: Evelyn

last: Walenta

first: Hubert

last: Hackl

first: Thomas

last: Rülicke


title: miRNA expression profiling in malignant transformation of human bronchial epithelial cells induced by arsenite

city: Chengdu

first: shiyan

middle: Shi

last: Gu

state: Sichuan

address: Number 17 on the 3rd The people of South Road

department: Department of Environmental and Occupational Health

institute: Sichuan University

summary: miRNA Array was used to detect the expression level of miRNAs in human bronchial epithelial (HBE) cells that were transformed by a low-level arsenite exposure for 13 weeks. The transformed cells exhibited malignant phenotypes manifested by increased levels of cell proliferation, cell migration and high level of cell survival. Subsequently, 191 differentially expressed miRNAs are identified to be associated with arsenite-induced malignant transformation by employing miRNA Array. Among them, six miRNAs were chosen to validate their expression levels with qPCR and 17 miRNAs were further explored their target genes and the network. Three databases, TargetMiner, miRDB and TarBase, were used to predict the target genes of miRNAs and a total of 954 common genes were identified. Results of Gene Ontology (GO) analyses showed that these target genes were involved in diverse terms of GO categories, such as positive regulation of macroautophagy, epithelial cell maturation and synaptic vesicle clustering and so on. Moreover, results of KEGG pathway analyses demonstrated that most of these target genes were enriched in various cancer-related pathways including non-small cell lung cancer, Wnt signaling pathway, cell cycle, p53 signaling pathway and so forth. The miRNA-gene regulatory network, which was constructed by cytoscape software with miRNAs and their target genes, showed that the target genes were mainly regulated by miR-15b-5p, miR-106b-5p and miR-320d. Although more experimental verification is still needed to prove these predictions, our results may provide new insights into miRNA-mediated mechanisms underlying arsenite-induced malignant transformation.

overall_design: in this study,191 differentially expressed miRNAs are associated with arsenite-induced malignant transformation by using microRNA Array. Among them, 17 miRNAs were chosen to further investigate their target genes and regulatory network. Our results provided the first evidence that most of these target genes of arsenite-related miRNAs were involved in diverse terms of GO categories enriched in various cancer-related pathways. Also, the miRNA-gene regulatory network was firstly constructed demonstrated that the modulation of the malignant transformation by miRNAs is complex. Our results indicate a dysregulation in the expression level of a panel of miRNAs which specific for arsenite-induced malignant transformation cells. The findings might help to promote the understanding of mechanisms underlying arsenite-induced carcinogenesis and provide some new and meaningful candidate miRNAs and genes to be further investigated after arsenite exposure.

first: S

first: Z

last: Zhang


title: Genome-wide DNA methylation pattern changes in basal-like breast cancer patients

status: Public on Jul 05 2018

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Ten eleven translocation enzymes (TET1-3) convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), inducing DNA demethylation and gene regulation. They are often downregulated in cancer, yet the upstream cause of this event remains largely unknown. Here, we show increased TET1 expression in basal-like breast cancer (BLBC), specifically in tumors with low expression of immune markers and low infiltration by immune cells. Furthermore, we identify an anti-correlation between TET1 expression and NF-κB, a major immune regulatory family, in BLBC tissues. In vitro and in vivo, TET1 is downregulated in breast cells upon activation of NF-κB, through binding of p65 to its consensus sequence in the TET1 promoter. Moreover, we uncover genome-wide 5hmC changes related to TET1 regulation in BLBC. Finally, these findings are extended to other cancer types, including melanoma, lung and thyroid cancers. Collectively, our data suggest a novel mode of regulation for TET1, linking TETs and immunity, two major features of cancer.

overall_design: Genome-wide profiling of DNA methylation in 4 pairs of matched tumor and normal breast

first: Evelyne

last: Collignon

first: Annalisa

last: Canale

first: Clémence

last: Al Wardi

first: Emilie

last: Calonne

first: Dedeurwaerder

last: Sarah

first: Whitney

last: Barham

first: Soizic

last: Garaud

first: Céline

last: Naveaux

first: Sophie

last: Bouchat

first: Carine

last: Van Lint

first: Karen

last: Willard-Gallo

first: Christos

last: Sotiriou

first: Agnès

last: Noel

first: François

last: Fuks


title: Transcriptome analysis the citrus rootstocks of Ziyang xiangcheng (Citrus junos Sieb.) and Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) under saline-alkali stress

city: Wuhan

first: Juxun

last: Wu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

institute: Huazhong Agricultral University

summary: Salt stress, especially saline-alkali stress, has seriously negative effect on citrus production. Ziyang xiangcheng (Citrus junos Sieb.) (Cj) has been reported as a saline-alkali stress and iron deficiency tolerant citrus rootstock. However, the molecular mechanism of its saline-alkali stress tolerance is still not clear. Two citrus rootstocks and one navel orange scion, Cj, Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) (Pt) and ‘Lane Late’ navel orange (Citrus sinensis (L.) Osb.) (LL), were used in this study. The grafted materials Cj+LL and Pt+LL grown in calcareous soil were used to identify genes and pathways responsive to saline-alkali stress using RNA-seq. The seedlings of Cj and Pt grown in the solutions with different gradient pH value were used to perform a supplement experiment. Comprehensively analyzing the data of RNA-seq, physiology and biochemistry, agronomic traits and mineral elements of Cj+LL, Pt+LL, Cj and Pt, several candidate pathways and genes were identified to be highly regulated under saline-alkali stress. Here, we propose citrate is important for the tolerance to iron deficiency and the jasmonate (JA) biosynthesis and signal transduction pathway may play a crucial role in tolerance to saline-alkali stress in citrus by interacting with other plant hormones, calcium signaling, ROS scavenging system and lignin biosynthesis.

sample_organism:
Citrus sinensis
Citrus trifoliata
Citrus junos

overall_design: Two citrus rootstocks, Ziyang xiangcheng (Citrus junos Sieb.) (Cj) and Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) (Pt), one navel orange scion, ‘Lane Late’ navel orange (Citrus sinensis (L.) Osb.) (LL), were used in this study. LL was grafted on Cj and Pt, respectively. The grafted materials Cj+LL and Pt+LL (rootstock+scion) were planted in the same orchard in 2009, which was located in Changyang city, Hubei province, China. The root, stem and leaf samples of Cj+LL and Pt+LL were subjected to RNA-seq using BGISEQ-500 at Beijing Genomics Institute (Shenzhen) in 2015. Each sample performed two biological replicates.

first: Hualin

last: Yi