title: Hippocamus of SAMR1 and SAMP8 mice [microRNA]

overall_design: miRNA expression profiling of 84 mature miRNAs in the hippocampus of SAMR1 and SAMP8 mice using miScript miRNA PCR Array-Neurological Development & Disease miRNA PCR Array (Qiagen).

first: Marta

last: Cosín-Tomás

last: Griñán-Ferré


title: The genetic signature of variability in drug response in Drosophila melanogaster

status: Public on Oct 24 2018

city: Tjele

first: Palle

middle: Duun

last: Rohde

address: Blichers Alle 20

department: Department of Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary:
Knowledge of the genetic mechanisms underlying among-individual variation in response to environmental variables or treatment is important in many research areas; for example, acquaintance of the set of causal genetic variants for drug responses could revolutionize the field of personalized medicine. We used Drosophila melanogaster to investigate the genetic signature underlying variability in response to methylphenidate (MPH), a drug used in treatment of ADHD. We exposed a wild type D. melanogaster population to MPH or a control treatment and observed an increase in locomotor activity in individuals exposed to MPH. Whole-genome transcriptomic analyses revealed that the behavioral response to MPH was associated with abundant gene expression alterations.
To confirm these patterns in a different genetic background, and to further advance knowledge on the genetic signature of drug response variability, we used a system of sequenced inbred lines, the Drosophila Genetic Reference Panel. Utilizing an integrative genomic approach we incorporated the transcriptomic data as well as gene interactions into the genomic analyses, from which we identified putative candidate genes for drug response variability. We successfully validated 70% of the investigated putative candidate genes by gene expression knockdown. Furthermore, we showed that MPH has cross generational behavioral- and transcriptomic effects.

overall_design: In total, we obtained whole genome transcriptomic data of 12 Drosophila melanogaster samples. Six of the samples were males exposed to either methylphenidate or sucrose  for 24 hours (eight males per sample). The other six samples are male offspring from a cross between males exposed to sucrose and females exposed to mephylphenidate (eight males per sample).

middle: D

first: Iben

middle: R

last: Jensen

first: Pernille

middle: M

last: Sarup

first: Michael

last: Ã˜rsted

first: Ditte

last: Demontis

first: Peter

middle: S

last: ¸rensen

first: Torsten

middle: N

last: Kristensen


title: A mechanistic classification of clinical phenotypes in neuroblastoma (TERT expression threshold cohort)

status: Public on Oct 25 2018

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

country: Germany

institute: University Children’s Hospital of Cologne

summary: Our study proposes a precise mechanistic classification of clinical neuroblastoma phenotypes that is based on telomere maintenance mechanisms and RAS or p53 pathway mutations. A crucial factor in telomere maintenance is overexpression of TERT. We therefore determined a TERT expression threshold to identify MYCNWT TERTWT tumors whose TERT mRNA levels are comparable to those of tumors bearing MYCN or TERT alterations.

overall_design: Single-color gene expression profiles from 186 neuroblastoma tumors were generated using 44K oligonucleotide microarrays. Stages were classified according to the International Neuroblastoma Staging System.

first: Christoph

last: Bartenhagen


title: Stickleback genome-wide replication timing from whole embryo

status: Public on Oct 20 2018

city: Stanford

first: David

last: Kingsley

state: CA

address: 279 Campus Drive

department: Developmental Biology

country: USA

institute: Stanford University

summary: Developing stickleback embryos were dissociated and sorted for S-phase and G0/G1-phase cell populations. DNA was extracted from each population and sequenced. In a mixed S-phase population, regions that replicate earlier are at higher copy number (up to 2x) than regions that replicate later. The read depth in S-phase, normalized to the read depth in G-phase, thus represents replication timing.

overall_design: Replication timing (G0/G1-phase and S-phase cells) from 9 different stickleback populations

first: Kathleen

middle: T

last: Xie


title: Ribosomal protein S5b is essential for oogenesis and is required to maintain mitochondrial integrity and function in Drosophila melanogaster

city: Montreal

first: Eric

last: Lecuyer

state: Quebec

address: 110 Pine Ave W

department: RNA biology

country: Canada

institute: IRCM

summary: Increasing evidence indicates that ribosomes are heterogeneous and perhaps dynamic, in contrast to the classical view of them as constitutive machinery for protein synthesis [1-11]. In Drosophila melanogaster, nine ribosomal protein genes are each present in two paralogs, and in many of these cases one of the paralogs is primarily expressed in germline tissues [12-14]. Among these are two genes encoding ribosomal protein S5, called RpS5a and RpS5b. We demonstrate that RpS5b is specifically required for oogenesis. Females lacking RpS5b produce ovaries with polarity defects, fused egg chambers, and over-proliferation of posterior follicle cells.  Oogenesis ceases at stage 8-9, and widespread apoptosis follows.  Females lacking germline RpS5a are fully fertile, but germline expression of interfering RNA targeting RpS5a in an RpS5b mutant background worsens the RpS5b phenotype and causes complete germline lethality. A broad spectrum of mRNAs co-purified in immunoprecipitations with RpS5a, while RpS5b-associated mRNAs were specifically enriched for GO terms related to mitochondrial electron transport and cellular metabolic processes. Consistent with this, proteome comparison of wildtype and RpS5b ovaries revealed that RpS5b mitochondria were depleted for proteins linked to oxidative phosphorylation and mitochondrial respiration. As observed by immunohistochemical staining and transmission electron microscopy, RpS5b nurse cell mitochondria tended to form large clusters and had more heterogeneous morphology than those from controls. We also observed that RpS5b ovaries have elevated ROS, consistent with mitochondrial dysfunction. We conclude that RpS5b-containing ribosomes preferentially associate with mRNAs encoding mitochondrial components and serve an essential function in oogenesis.

overall_design: The mRNAs associated to either RpS5b and RpS5a were identified by co-IP followed by deep sequencing. The mRNAs enriched to either of the two parologs of RpS5, when applicable, were analyzed in three genetic backgrounds, wildtype, RpS5b-null and the ovary with germline RpS5a knocked down by RNAi.

first: Jian

last: Kong

first: Hong

last: Han

first: Julie

last: Bergalet

first: Louis

middle: P

last: Benoit Bouvrette

first: Hana

last: Antonicka

first: Nam-Sung

last: Moon

last: Shoubridge

first: Hojatollah

last: Vali

last: Lécuyer

first: Paul

last: Lask


title: New insights of polyamine metabolism in testicular physiology: a role of ornithine decarboxylase antizyme inhibitor 2 (AZIN2) in the modulation of testosterone levels and sperm motility

city: Murcia

first: Ana

last: Lambertos

address: Campus Espinardo

country: Spain

institute: Universidad de Murcia

summary:
The specific role of polyamines in the testis physiology is not fully understood.  Antizymes (OAZs) and antizyme inhibitors (AZINs) are modulators of ornithine decarboxylase (ODC), a key enzyme in polyamine biosynthesis and polyamine uptake. Although the three known OAZs are expressed in the testis, only OAZ3 is testis specific and has been proven to have an essential role in male fertility. Regarding the two existing AZINs, AZIN2 is the most abundantly expressed member in this gonad. Whereas previous studies suggested that AZIN2 might participate in mouse spermatogenesis, immunohistological analysis of human testicular sections revealed that AZIN2 is also detected in the steroidogenic Leydig cells but not in the germinal epithelium. In the present study, we found a close ontogenic similarity in the mRNA levels of OAZs and AZINs between mice and rats, but an opposite expression pattern of ODC activity. Further analysis of AZIN2 and OAZ3 in the testis of mice with different alterations in spermatogenesis and fertility, induced either genetically or pharmacologically, corroborated that both AZIN2 and OAZ3 are mainly expressed in the haploid germinal cells. Finally, by using transgenic mice with a truncated Azin2 gene fused to the bacterial lacZ gene, we studied the expression of Azin2 in testes, epididymides and spermatozoa. AZIN2 was detected in spermatids and spermatozoa, as well as in Leydig cells, and in epithelial epidydimal cells. Azin2 knock-out male mice were fertile; however, they showed marked decreases in testicular putrescine and plasma and testicular testosterone levels, and a dramatic reduction in the sperm motility. These results suggest an important role for AZIN2 in testicular cells by modulating polyamine concentrations, testosterone synthesis and sperm function. Overall, our data corroborate the relevance of polyamine regulation in spermatogenesis, where both AZIN2 and OAZ3 play fundamental roles.
We used microarrays in order to detect how the disruption of Azin2 could affect overall gene expression in testis.

overall_design: Homogeneous populations of male adult mice were selected for testis RNA extraction and hybridization on Affymetrix microarrays. For this analysis, we used two samples from Azin2 KO mice (KO1 and KO2) and two samples from Azin2 WT mice (WT1 and WT2)

first: Rafael

last: Peñafiel

first: Bruno

last: Ramos-Molina

first: Andrés

middle: J

last: López-Contreras

first: Asunción

last: Cremades


title: The aryl hydrocarbon receptor pathway defines the time frame for restorative neurogenesis

status: Public on Oct 18 2018

city: Planegg

first: Jovica

last: Ninkovic

address: Grosshaderner strasse 9

institute: LMU Munich

type: Expression profiling by high throughput sequencing

summary: We compared transcriptomes of two ependymoglial populations isolated from adult zebrafish telencephalon.

overall_design: Ependymoglial cells are acutely isolated from the adult zebrafish brains form 3 months old transgenic gfap:GFP animals. GFP is experssed in all ependymoglial cells and two populations are separated using GFP intensity in FACS.

first: Rossella

last: DiGiaimo


title: Transcriptome analysis of tubular tissues of focal segmental glomerulosclerosis patients

status: Public on Oct 15 2018

city: Nanjing

first: Hao

last: Bao

state: Jiangsu

address: 305 East Zhong Shan Road

department: National Clinical Research Center of Kidney Diseases, Jinling Hospital

country: China

institute: Nanjing university

summary:
Transcriptome comparison of tubular tissues from kidneys with focal segmental glomerulosclerosis (FSGS) and tubular tissues from the unaffected portion of tumor nephrectomies.
High-density Affymetrix Human Transcriptome Arrays (HTA) 2.0 were used for the gene expression analysis.

overall_design: Focal segmental glomerulosclerosis (FSGS) is a common podocytopathy. Renal tubular tissues from 5 focal segmental glomerulosclerosis patients and 5 controls were manually isolated under a stereomicroscope using 2 dissection needle holders in RNAlater at 4°C.Affymetrix HTA 2.0 microarray was used to perform a global analysis of the gene expression pattern in the tissues.

first: Zhihong

last: Liu


title: ArrayCGH on a cohort of pediatric T-ALLs to investigate the mechanism of primary chemotherapy resistance

status: Public on Oct 16 2018

city: Gent

first: Sofie

last: Peirs

address: De Pintelaan 185

country: Belgium

institute: Ghent University

type: Genome variation profiling by genome tiling array

summary:
ArrayCGH was performed on a cohort of 36 specimens collected from children with newly diagnosed T-ALL treated on contemporary clinical trials.
The data was used to investigate mechanisms of primary chemotherapy resistance in T-ALL.

overall_design: 36 DNA samples from pediatric T-ALL patients at diagnosis were analyzed on the Agilent SurePrint G3 Human CGH microarrays (G4449A, design ID: 022060). For every sample, the gender-matched control was labeled in parallel and hybridized together

first: Pieter

last: Van Vlierberghe

first: Alejandro

last: Gutierrez

first: Ingrid

last: Aries

first: Melissa

last: Burns

first: Gayle

last: Pouliot


title: RNA-Seq of adult chicken sickle feather tissues between male and female

city: Los Angeles

first: Randall

middle: B.

last: Widelitz

state: California

address: 2011 Zonal Ave HMR 305

department: Department of Pathology

institute: University of Southern California

summary: Many animals can change their coats in response to different ages, sexes, or seasonal environmental changes. The hormones can also alter the size, shape, texture and color of the regenerated coat. Here we propose feather core branching morphogenesis module can be modulated by sex hormone or other environmental factors to change the form, texture or colors, thus generate a large spectrum of complexity for adaptation. We use sexual dimorphisms of the feather coat to explore the role of hormones in in coat morphogenesis and regeneration.  A long-standing question is whether the sex-dependent feather morphologies are autonomously controlled by the male or female cell types, or extrinsically controlled and reversible. We have recently identified core feather branching molecular modules which control the anterior-posterior (BMP, Wnt gradient), medio-lateral (retinoic signaling, gremlin), and proximo-distal (sprouty, BMP) patterning of feathers. We hypothesize that modulatory signaling modules can be added upon these core branching modules to topologically tune the dimension of each parameter. Here we explore the involvement of hormones in generating sexual dimorphisms using exogenously delivered hormones. Our strategy is to mimic androgen levels by applying exogenous dihydrotestosterone and aromatase inhibitors to adult females and injecting exogenous estradiol to adult males. We also examine differentially expressed genes in the feathers of wildtype male and female chickens to identify potential downstream modifiers of feather morphogenesis. The data show male and female feather morphology and their color patterns can be modified extrinsically through molting and reseting the stem cell niche during regeneration.

overall_design: Six kinds of adult chicken sickle feather tissues between male (M) and female (F), including lower follicle sheath (LFS), upper follicle sheath (UFS), pulp (PP), epithelium (EPi), papilla ectoderm (PE), and dermal papilla (DP)

middle: B

first: Cheng-Ming

last: Chuong


title: Prenatal alcohol exposure: profiling developmental DNA methylation patterns in central and peripheral tissues

status: Public on Oct 23 2018

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

type: Methylation profiling by high throughput sequencing

summary: Prenatal alcohol exposure (PAE) alters the development of neurobiological systems, leading to lasting neuroendocrine, neuroimmune, and neurobehavioral deficits. Although the etiology of this reprogramming remains unknown, emerging evidence suggests DNA methylation as a potential mediator and biomarker for the effects of PAE due to its responsiveness to environmental cues and relative stability over time. Here, we utilized a rat model of PAE to examine the DNA methylation profiles of rat hypothalami and leukocytes at four time points during early development to assess the genome-wide impact of PAE on the epigenome and identify potential biomarkers of PAE. Our model of PAE approximates to 1-2x the legal limit of drunk driving in most jurisdictions (blood alcohol 80-150 mg/dl) throughout the equivalent of the first two trimesters of human pregnancy. Hypothalami were analyzed on postnatal (P) days 1, 8, 15, 22 and leukocytes at P22 to compare central and peripheral markers. Genome-wide DNA methylation analysis was performed by methylated DNA immunoprecipitation followed by next-generation sequencing.  PAE resulted in lasting changes to DNA methylation profiles across all four ages, with 118 differentially methylated regions (DMRs) displaying persistent alterations across the developmental profile at a false-discovery rate (FDR) <0.05. By contrast, 299 DMRs showed the same direction of change in the hypothalamus and leukocytes of P22 pups at an FDR<0.05, with some genes overlapping with the developmental profile findings. The majority of these DMRs were located in intergenic regions, which contained several computationally-predicted transcription factor binding sites. Differentially methylated genes were generally involved in immune function, epigenetic remodeling, metabolism, and hormonal signaling, as determined by gene ontology analyses.  Persistent DNA methylation changes in the hypothalamus may be associated with the long-term deficits observed in PAE. Furthermore, correlations between epigenetic alterations in peripheral tissues and those in the brain will provide a foundation for the development of biomarkers of fetal alcohol spectrum disorder (FASD). Finally, findings from studies of PAE provide important insight into the etiology neurodevelopmental and mental health disorders, as they tend to share numerous symptoms and comorbidities.

overall_design: DNA methylation data from meDIP-seq of 60 rat samples, spanning three prenatal treatment groups (control, pair-fed, prenatal alcohol exposed), four ages (postnatal days 1, 8, 15, 22), and two tissues (hypothalamus [all ages], white blood cells [P22 only]). WBC and hypothalamic samples were  obtained from the same animal on P22. Each group/tissue/age had n= 4. Two sequencing runs were performed for each sample (120 aligned bam files) and DNA methylation peaks were called using MACS2 following DNA processed (peak files).

first: Alexandre

middle: A

last: Lussier

first: Tamara

last: Bodnar

first: Matthew

last: Mingay

first: Alexander

last: Morin

first: Martin

last: Hirst

first: Joanne

last: Weinberg


title: RNASeq analysis of untreated versus treated

city: St. Lucia

first: Lisa

last: Bohlmann

address: University of Queensland

country: Australia

institute: University of Queensland

summary: We report differential regulated genes in three pathogenic bacterial strains after treatment with a new antimicrobial.

sample_organism:
Staphylococcus aureus
Streptococcus pyogenes
Enterococcus faecium

overall_design: Bacteria were grown in triplicates to mid-log phase in the presence or anbsence of PBT2+zinc and RNA was isolated for RNASeq analysis.

first: Mark

last: Walker


title: Integrative genomic analyses revealed colorectal cancer susceptibility genes in risk loci identified in genome-wide association studies

city: Hangzhou

first: Weiqiang

last: Lin

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Genome-wide association studies (GWAS) have identified approximately 50 loci associated with colorectal cancer (CRC) risk. However, the target genes and underlying mechanisms are largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using data from the Genotype-Tissue Expression (GTEx), The Cancer Genome Atlas (TCGA), and the Colonomics projects. We identified 24 putative target genes for 17 index SNPs at Benjamini-Hochberg adjusted P < 0.05 in at least one of the datasets. By analyzing functional genomic data, our result further indicated that 18 genes (75%) showed evidence of cis-regulation by putative functional SNPs via promoter or enhancer-promoter interactions. We next performed in vitro functional assays for three genes, TMBIM1, AAMP, and CABLES2, and confirmed that they play a vital role in colorectal carcinogenesis via disruption of cell behavior. Furthermore, our results indicate that silencing CABLES2 can promote the PI3K/AKT pathway. Our study reveals new candidate susceptibility genes and provides novel insight into the biological mechanisms for CRC development.

overall_design: We conducted RNA-sequencing in the CABLES2 shRNA-1 and control vehicle cells with two technical replicates

first: Xingyi

last: Guo


title: Transcriptional profiling of Mms21 deleted (mms21Δ/Δ) mutant Candida albicans strains

city: London

first: Vanessa

last: Dumeaux

state: Ontario

address: Elgin Dr

department: Anatomy and Cell Biology

institute: Western University

summary: Mms21 deletion in Candida albicans resulted in invasveness and filamentatation in YPD media at 30 degrees Celsius. Wild type SN148 do not make any Filaments in YPD at 30 degrees Celsius. The aim was to look for transcription profiling mms21 dleleted mutant against wild type to find genes up and down regulated in the mutant especially thoseones critical for filamentation

overall_design: 2 samples were analyzed. Cells were grown in YPD media at 30 degrees celcius to OD 0.8. MMS21 deleted strain (mms21Δ/Δ) vs wild type (SN148)

first: Amjad

last: Islam


title: Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heterochromatin is a tightly packed form of DNA, which is associated with histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2 binding protein, Agenet domain (AGD)-containing protein 1 (AGDP1), in Arabidopsis thaliana. Our biochemical studies revealed that the AGDP1 can specifically recognize the H3K9me2 marks by the three pairs of tandem-AGDs. We determined the crystal structure of the AGD12 of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 employs a newly defined interacting interface to specifically recognize the H3K4me0 and H3K9me2 marks. In addition, we found that AGDP1 is required for transcriptional gene silencing, non-CG DNA methylation, and H3K9 dimethylation. Our ChIP-seq data showed that AGDP1 is enriched in TE regions and associated with the heterochromatin marks. Our findings suggest that, as a heterochromatin binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions.

overall_design: MethylC-Seq: 2 samples examined, Col-0 and agdp1-1; mRNA-Seq: 3 samples examined, Col-0 (5 replicates), agdp1-1 (5 replicates), and  suvh4/suvh5/suvh6 (suvh456)  triple mutant; ChiP-Seq: proAGDP1::3xFlag-gAGDP1 transgenic plants and wild-type control were used for ChIP-seq with two biological replicates; ChIP-Seq: H3K9me2 and H3 in Col-0 and agdp1 mutant (each with two replicates).

first: Cuijun

last: Zhang

first: Kai

last: Tang


title: DNA methylation of two triple-negative patient-derived breast cancer xenografts

status: Public on Oct 22 2018

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: PO Box 15000

department: Pathology

institute: Dalhousie University

type: Methylation profiling by genome tiling array

summary: All-trans retinoic acid (atRA) regulates gene expression and is used to treat acute promyelocytic leukemia. Attempts to use atRA for breast cancer treatment without a stratification strategy have resulted in limited overall effectiveness. To identify biomarkers for the treatment of triple-negative breast cancer (TNBC) with atRA, we characterized the effects of atRA on the tumor growth of 13 TNBC cell lines. This resulted in a range of tumor growth effects that was not predictable based on the levels of retinoid signaling molecules and transcriptional responses that were mostly independent of retinoic acid response elements. Given the importance of DNA methylation in regulating gene expression, we hypothesized that differential DNA methylation could predict the response of TNBCs to atRA. We identified over 1400 CpG sites that were differentially methylated between atRA resistant and sensitive cell lines. These CpG sites predicted the response of four TNBC patient-derived xenografts to atRA treatment and we utilized these xenografts to refine the profile to 6 CpGs. We identify as many as 17% of TNBC patients who could benefit from atRA treatment. These data illustrate that differential DNA methylation of specific sites may predict the response of patient tumors to atRA treatment.

overall_design:
Two independent PDXs were propagated in mice prior to DNA isolation and DNA methylation determination
2 samples analyzed, 1 replicate.

first: Krysta

last: Coyle

first: Cheryl

last: Dean

first: Margaret

middle: L

last: Thomas

first: Dejan

last: Vidovic

first: Carman

last: Giacomantonio

first: Lucy

last: Helyer


title: TCR sequencing of Treg and Tconv subsets from murine spleen

city: New York

first: Alexander

middle: Y

last: Rudensky

state: New York (NY)

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: While unique subsets of Treg cells have been described in some non-lymphoid tissues, their relationship to Treg cells in secondary lymphoid organs and circulation remains unclear. We have identified a recirculating and highly suppressive effector Treg cell subset that expresses the α2 integrin, CD49b, and exhibits a unique tissue distribution. We used TCR sequencing to ask whether CD49b+ activated Treg cells and CD49b− activated Treg cells represent stable states of Treg cell differentiation instructed by distinct TCR repertoires. We did not find a pattern of clonotypes that was specific to either subset, suggesting that essentially all CD49b− Treg cells could give rise to CD49b+ cells. These results shed light on the identity and development of a functionally potent subset of mature effector Treg cells that recirculate through and survey peripheral tissues.

overall_design: Tcra cDNA libraries were prepared from FACS-purified splenic Tconv and Treg cells from Foxp3GFP Tcra+/− DO11.10tg mice. In these mice, the presence of the DO11.10 TCRβ transgene inhibits the recombination of the endogenous Tcrb loci, thus restricting TCR repertoire variability to TCRα chains. Further limitation of the TCR repertoire was achieved by the presence of only one functional Tcra gene. 2 CD4+ T-cell lineages x 3 activation states x 4 replicates = 24 samples.

first: Xiying

last: Fan

first: Bruno

last: Moltedo

first: Alexey

last: Davydov

first: Dmitriy

last: Chudakov


title: Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability

status: Public on Oct 19 2018

first: Sigurd

last: Braun

address: Großhaderner Str. 9

department: BMC

institute: LMU

summary: Telomeres and the shelterin complex cap and protect the ends of chromosomes. Telomeres are flanked by the subtelomeric sequences that have also been implicated in telomere regulation, although their role is not well defined. Here we show that, in Schizosaccharomyces pombe, the telomere-associated sequences (TAS) present on most subtelomeres are hyper-recombinogenic, have metastable nucleosomes, and unusual low levels of H3K9 methylation. Ccq1, a subunit of shelterin, protects TAS from nucleosome loss by recruiting the heterochromatic repressor complexes CLRC and SHREC, thereby linking nucleosome stability to gene silencing. Nucleosome instability at TAS is independent of telomeric repeats and can be transmitted to an intrachromosomal locus containing an ectopic TAS fragment, indicating that this is an intrinsic property of the underlying DNA sequence. When telomerase recruitment is compromised in cells lacking Ccq1, DNA sequences present in the TAS promote recombination between chromosomal ends, independent of nucleosome abundance, implying an active function of these sequences in telomere maintenance. We propose that Ccq1 and fragile subtelomeres co-evolved to regulate telomere plasticity by controlling nucleosome occupancy and genome stability.

overall_design: Examination of genome-wide H3 levels in S. pombe.

first: Thomas

last: van Emden

first: Cornelia

last: Broenner

first: Mario

last: Halic


title: Expression profiles in circRHOT1-deficient or control HCC cells.

city: Guilin

first: b

last: Li

address: Lequn road No.15

department: Gastrointestinal Department

institute: Affiliated Hospital of Guilin Medical University

summary:
RNA-sequencing of Human hepatocellular carcinoma (HCC) cells
We analyzed two circRNA profiles expressed in human HCC tissues and identified circRHOT1 as a conserved and dramatically upregulated circRNA in HCC tissues. HCC patients displaying high circRHOT1 level possessed poor prognosis. We demonstrated circRHOT1 significantly promoted HCC growth and metastasis. In order to investigate the mechansim of circRHOT1, we constructed circRHOT1-deficient HCC cell lines. Through RNA-sequencing, we sough to identify the key gene regulated by circRHOT1 in HCC.

first: Bin

first: Liyan

last: Wang


title: Exon Level Expression Profiling of focal segmental glomerulosclerosis

first: Hao

last: Bao

summary:
Transcriptome comparison of glomeruli from kidneys with focal segmental glomerulosclerosis (FSGS) and glomeruli from the unaffected portion of tumor nephrectomies.
High-density Affymetrix Human Transcriptome Arrays (HTA) 2.0 were used for the gene expression analysis.

overall_design: Focal segmental glomerulosclerosis (FSGS) is a common podocytopathy. Renal glomerular tissues from 5 focal segmental glomerulosclerosis patients and 5 controls were manually isolated under a stereomicroscope using 2 dissection needle holders in RNAlater at 4°C.Affymetrix HTA 2.0 microarray was used to perform a global analysis of the gene expression pattern in the tissues.

first: Zhihong

last: Liu


title: Laminin-directed fate determination of human induced pluripotent stem cells (hiPSCs) during ocular cell differentiation

status: Public on Oct 17 2018

city: Suita

first: Shun

last: Shibata

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

summary: The extracellular matrix plays a crucial role in stem cell maintenance, expansion and differentiation. Laminin, a basement membrane protein, is effective in supporting cultures of human pluripotent stem cells. To furhter investigate the effects of different isoforms of laminin on  ectodemral differentiation of hiPSCs, we performed gene expression analysis  of differentiated human iPS cells on E8 fragments of laminin isoforms (LN111E8, LN211E8, LN332E8, LN411E8, and LN511E8).

overall_design: We performed global gene expression analysis of differentiated hiPSCs on E8 fragment of laminin isoforms (111, 211, 332, 411, and 511) and vitronectin (VN) on day 3 of differentiation culture.

first: Ryuhei

last: Hayashi

first: Kiyotoshi

last: Sekiguchi

first: Kohji

last: Nishida


title: Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [ATAC-seq]

status: Public on Oct 11 2018

city: Heidelberg

first: Fanny

last: Gatzmann

address: Im Neuenheimer Feld 580

department: A130 Epigenetics

institute: DKFZ

summary: The marbled crayfish (Procambarus virginalis) is a unique freshwater crayfish characterized by genetic uniformity, phenotypic variability, and substantial invasive potential. As invasion into different habitats occurs in the absence of genetic variation, epigenetic mechanisms have been suggested to mediate phenotypic adaptation. However, epigenetic regulation has not been analyzed in this organism yet. Here we show that the recently published P. virginalis draft genome sequence encodes a conserved DNA methylation system. Whole-genome bisulfite sequencing of multiple replicates and different tissues revealed a methylation pattern that is characterized by gene body methylation of housekeeping genes. Interestingly, this pattern was largely tissue-invariant, suggesting a function that is unrelated to cell-fate specification. Indeed, integrative analysis of RNA-seq datasets showed that gene body methylation correlated with stable gene expression, while unmethylated genes often showed a high degree of inter-individual expression variation. Our findings thus establish the methylome of an emerging model organism and suggest that methylation-dependent regulation of gene expression variability may facilitate the phenotypic adaptation and invasive spread of this animal.

overall_design: ATAC-seq data of hemocytes from marbled crayfish.

first: Frank

last: Lyko

first: Cassandra

last: Falckenhayn

first: Julian

last: Gutekunst

first: Katharina

last: Hanna

first: Guenter

last: Raddatz

first: Vitor

middle: C

last: Carneiro


title: Transcriptional profile of 786O cells with ERCC6L knockdown treatment

city: Shenyang

first: Zi

last: Yu

state: Liaoning

address: Shenyang North New Area, Shenyang, Liaoning Province, P.R. China

institute: China Medical University

summary: To explore which regulatory pathway of ERCC6L functioned, we down-regulated the expression of ERCC6L and performed the micro-array analysis

overall_design: 786O cells were transfected with lentivirus with shRNAs (negative control or shRNA targeting ERCC6L). All of these samples were prepared in three replicates.

first: Yu

last: Zeng

first: Gejun

last: Zhang


title: Genome-wide function of MCM-BP in Trypanosoma brucei DNA replication and transcription

city: Cleveland

first: Hee-Sook

last: Kim

state: OH

address: 2399 Euclid Ave

institute: Cleveland State University

summary: In Trypanosoma brucei, genes are arranged in Polycistronic Transcription Units (PTUs), which are demarcated by transcription start and stop sites. Transcription start sites are also binding sites of Origin Recognition Complex 1 (ORC1). These suggest that transcription and replication in trypanosomes must occur in highly ordered and cooperative manners. Not coincidently, our previous genetic screen, a LOss of transcription Silencing (LOS) screen, identified a T. brucei MCM-BP, which forms a complex with subunits of the replicative helicase MCM. Here, I show that TbMCM-BP is required for DNA replication and transcription. TbMCM-BP depletion causes a significant reduction of replicating cells in S phase and genome-wide impairments of replication origin activation. Moreover, levels of sense and antisense transcripts increase at boundaries of PTUs in the absence of TbMCM-BP. TbMCM-BP is also important for transcriptional repression of the specialized subtelomeric PTUs, the Bloodstream-form Expression-Sites (BESs), which house the gene of antigenic importance, VSG. In the absence of TbMCM-BP, expression of silent VSGs is elevated, silent promoter regions are derepressed, and antisense transcription increases downstream of the silent promoters.  This study reveals that TbMCM-BP, a replication initiation protein, guides transcription to properly start and stop, and also helps it move in the correct direction.

overall_design:
For RNAseq, sample for each time point have four replicates. For MFAseq, one sample per each time point was used, and FACS sorted at G1, early S (S1), late S (S2) and G2.

Please note that the associated processed data files are indicated in the corresponding sample description field and the readme.txt contains a brief description of the data content for each file.


title: Analysis of gene expression in brains of DO1 treated and untreated 5xFAD and control mice using a microarray technology

city: Berlin

first: Erich

last: Wanker

state: Berlin

address: Robert-Rössle-Str. 10

institute: MDC Berlin

summary: Transcripts of 4 groups of treated and untreated mice (TG+DO1, TG, WT+DO1 and WT) were systematically investigated. Results revealed a clear separation of data obtained from AD and non-AD brains (Figure 6A), confirming previous observations (Landel et al., 2014). Furthermore, we observed that the compound DO1 alters the transcriptional profiles in brains of 5xFAD and wild-type control mice.

overall_design: Group of transgenic (B6SJL-Tg(APPSwFlLon,PSEN1*M146L*L286V 6799Vas/jax) and wildtype mice were treated with DO1. As control untreated mice were used. 500 ng of total RNA in 11 µl RNase free water was used as starting material for the generation of biotin-labeled cRNA with the Illumina® TotalPrep™ RNA Amplification Kit (ThermoFisher Scientific, Dreieich,  Germany), following supplier instructions. cRNA was cleaned up with cRNA filter cartridges before use for subsequent hybridization on Illumina® Sentrix BeadChips (Illumina, San Diego, USA).

first: Wilfried

last: Nietfeld

first: Miguel

last: Andrade


title: Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [RNA-seq]

sample_organism:
Procambarus fallax
Procambarus virginalis

overall_design: RNA-seq data of different tissues (hepatopancreas, abdominal musculature) from 6 different P. virginalis individuals and 2 different P. fallax individuals


title: Transcriptome analysis of Xenopus orofacial tissues deficient in retinoic acid receptor function

city: Richmond

first: Amanda

last: Dickinson

state: VA

address: 1000 W. Cary St. Rm 339

department: Biology

institute: Virginia Commonwealth University

summary:
Xenopus laevis embryos were treated with a retinoic acid inhibitior during early orofacial development. The facial tissues were dissected, removing eye and brain tissue from the analysis.
RA regulates midface development, we sought to determine global changes in gene expression when RA function is pharmacologically disrupted

overall_design: We utilized a pharmacological inhibtior to reduce RA funciton during early orofacial development, dissected the facial region (omitting the eyes and brain), isolated total RNA, and performed a microarray analysis

first: Stacey

last: Wahl


title: Nut directs p300-dependant genome-wide H4 hyperacetylation in male germ cells: transcriptomic data

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

summary: NUT, nuclear protein in testis, is a universal oncogenic driver in the highly aggressive NUT Midline Carcinoma whose physiological function in male germ cells had so far remained unknown. Here we show that Nut’s expression is normally restricted to post-meiotic spermatogenic cells, where its presence triggers the p300-dependant genome-wide histone H4 hyperacetylation, which is essential for the completion of histone-to-protamine exchange. Accordingly, the inactivation of Nut induces male sterility with spermatogenesis arrest at the histone removal stage. Molecular investigations show that Nut uses CBP/p300 to enhance acetylation of H4 at both K5 and K8 providing binding sites for the first bromodomain of Brdt, the testis-specific member of the BET family, which subsequently mediates genome-wide histone removal. Altogether, our data reveal the detailed molecular basis of the global histone hyperacetylation wave, which has long been known to occur prior to the final compaction of the male genome.

overall_design: Total RNA were obtained from meiotic and post meiotic male germ cells (respectively spermatocytes and round spermatids) from adult mice either wild-type or with a knock down of Nut. In each experiments, 6 replicates of each genotype and cell type were used.

first: Saadi

last: Khochbin

first: Thierry

last: Buchou

first: Hitoshi

last: Shiota

last: Barral

first: Florent

last: Chuffart

first: Guillaume

last: Charbonnier

first: Ekaterina

last: Bourova-Flin


title: Functional difference in the HTLV-1 subgroup specific viral transcriptional regulators Tax

status: Public on Oct 13 2018

city: Kurashiki

first: Tadasuke

last: Naito

state: Okayama

address: 577 Matsushima

department: Microbiology

institute: Kawasaki Medical School

summary: Among HTLV-1-infected individuals, the lifetime risk of developing HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is associated with the HTLV-1 gene subgroup (i.e., subgroup-A or -B) in Japan. The purpose of this study is to understand the molecular mechanism responsible for this association.

overall_design: Jurkat Tet-On 3G cells were transfected with each indicated plasmids (i.e., pTRE3G-IRES-empty, pTRE3G-Tax-A, pTRE3G-Tax-B) using an electroporator and then cultured at 37ºC in RPMI1640 without antibiotics. After 24 h transfection, Tax protein expression were induced by adding Dox (final concentration: 3 ng/ml) to the culture medium. After 24 h induction, cells were collected, and total RNA was extracted with the RNeasy Mini Kit (QIAGEN) following the manufacture’s instructions. We synthesize cDNA and performed microarray analysis according to the manufacturer's instructions (Agilent Tecnologies). Data were analyzed using GeneSpring GX (Agilent Technologies).

first: Mineki

last: Saito


title: RNA sequencing of cell-specific profile of AVK

status: Public on Oct 14 2018

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: We report the transcriptome profile of the AVK neuron in L1 C. elegans

overall_design: AVK was isolated using FACS sorting

first: Rebecca

last: McWhirter

first: Sierra

last: Palumbos


title: Expression Profiling of Fibroblasts in Chronic and Acute Disease Models

city: Ann Arbor

first: Greg

last: Dressler

state: MI

address: 109 Zina Pitcher Drive

institute: University of Michigan

summary: Gene expression patterns among populations of kidney fibroblasts at different stages of injury or repair were analyzed by Affymetrix arrays.

overall_design: PDGFra-positive fibroblasts were FACS sorted from mouse kidneys at various times post injury and RNA extracted for gene expression comparisons.

first: Gregory

first: Atsuko

last: Higashi


title: microRNA expression signature in estrogen receptor-positive and -negative breast cancers

city: Kamogawa City, Chiba

first: Yuko

last: Tsunoda

address: 929 Higashi-cho

institute: Kameda Medical Center

summary: Micro RNA (miRNA) profiling of breast cancer subtype was demonstrated using RT-PCR. We present herein two cases with miRNA profiling in estrogen receptor (ER)-positive and -negative breast cancer. The level of miR-181a expression in ER-positive cancer was higher than in ER-negative cancer, while expression of miR-27a, -107 and -195 was lower in ER-positive when compared with ER-negative cancer.

overall_design: qPCR-micro RNA expression profiling. Six samples (triplicate, sample1: reference, sample2; control)


title: Maternal Western-style diet alters the transcriptome of chemically induced mammary tumors in female offspring rats

status: Public on Oct 12 2018

city: Barretos

first: Lucas

middle: Tadeu

last: Bidinotto

state: SP

address: Antenor Duarte Vilela, 1331

country: Brazil

institute: Barretos Cancer Hospital

summary: Some previous experimental studies have shown that early in life intake of high-fat or Western-style diets did alter the development of mammary cancer in adulthood female rats. Thus, the present study investigated the distinct gene expression patterns of chemically induced mammary tumors derived from female offspring whose dams intake control diet (CD) or Western-style diet (WD). During gestational days (GD) 12-21 and post-natal days (PND) 1-21, pregnant Sprague-Dawley (SD) rats were fed a CD diet or WD (high-fat and low-fiber and oligoelements) diet. On postnatal day (PND) 21, the female offspring received a single dose of carcinogen N-Methyl-N-Nitrosourea (MNU, 50 mg/kg) and CD diet for 12 weeks. Latency, incidence and tumor burden were registered. Mammary tumors samples were collected and histopathology and gene expression analysis were performed.

overall_design: Pregnant Sprague-Dawley (SD) rats received control diet (CD) or Western-style diet (WD) from gestational days (GD) 12-20 and post-natal days (PND) 1-21. At weaning, the female offspring received CD until the end of the tumor bioassay. Female offspring 3 weeks old from both CD and WD groups received a single intraperitoneal dose of 50 mg/kg of N-Methyl-N-Nitrosourea (MNU) dissolved in phosphate-buffered saline acidified with acetic acid. At the end of study, the animals were euthanized and mammary tumors were removed and kept at -80°C for molecular analysis.

first: Tony

middle: F

last: Grassi

first: Gisele

last: Lopes

first: Maria

last: Rodrigues

first: Luís

last: Barbisan


title: PanCancer Immune panel on treated tumors

status: Public on Oct 10 2018

city: Baltimore

first: Evanthia

middle: Theodosiou

last: Roussos Torres

state: Maryland

address: 1650 Orleans Street, CRB1 4M

department: Oncology

institute: Johns Hopkins University

summary: Our data showed that ENT broadly impacted multiple populations of immune cells within the TME. Thus, we performed general immune transcriptome profiling on whole tumors isolated from the neu-N model using a PanCancer immune-profiling gene panel for the NanoString platform.

overall_design: To identify all immune cell types infiltrating the tumors and associated functions, we utilized NanoString transcript profiling to evaluate broad changes in the transcriptome of whole tumors following treatment with various different drug combinations.

first: Brian

last: Christmas

first: Alexander

last: Hopkins

first: Christine

middle: I

last: Rafie

first: Elizabeth

last: Jaffee


title: Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons [SPAR-seq]

city: Toronto

first: Ulrich

last: Braunschweig

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

summary: Alternative splicing has critical roles in diverse cellular, developmental and pathological processes. However, the full repertoires of factors that control individual splicing events are not known. We describe a CRISPR-based screening strategy for the systematic identification of genes that control 3-27 nt microexons with functions in nervous system development and that are commonly disrupted in autism. Besides known regulators including nSR100/Srrm4, Rbfox and Ptbp1, approximately 200 additional genes impact microexon splicing. These genes are enriched in genetic links to autism. Two of the screen hits, Srsf11 and Rnps1, preferentially regulate Srrm4-dependent microexons relative to other exons. These factors form mutually stabilizing interactions with Srrm4 that bridge upstream intronic enhancer elements and exonic sequences to activate microexon splicing. Our study thus presents a system for the genome-wide definition of splicing regulatory networks and further reveals a mechanism for the recognition of microexons with critical roles in nervous system development and disorders.

overall_design: Alternative splicing of selected endogenous genes was monitored in 24 siRNA-mediated knockdowns, including controls, in N2A mouse neuroblastoma cells in duplicate.

first: Thomas

last: Gonatopoulos-Pournatzis

first: Mingkun

last: Wu

first: Jonathan

last: Roth

first: Hong

last: Han

first: Andrew

last: Best

first: Bushra

last: Raj

first: Michael

last: Aregger

first: Dave

last: O'Hanlon

middle: D

last: Ellis

first: John

last: Calarco

first: Jason

last: Moffat

first: Anne-Claude

last: Gingras

first: Benjamin

last: Blencowe


title: Kdm3a in mouse promotes pressure overload induced cardiac hypertrophy

status: Public on Oct 09 2018

city: Dalals

first: zhi-ping

last: liu

state: TX

address: 6000 Harry Hines Blvd

department: internal medicine

institute: ut southwestern

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

overall_design: Refer to individual Series


title: Kdm3a in mouse promotes pressure overload induced cardiac hypertrophy [WT vs. Tg]

summary: Heart disease and failure is a leading cause of mortality worldwide. Left ventricular hypertrophy (LVH) and myocardial fibrosis are the major risk factor for cardiovascular morbidity and mortality and the development of heart failure. Pathological LVH induced by sustained pressure-overload engages transcriptional programs including reactivation of canonical fetal genes and those inducing fibrosis. Histone lysine demethylases (KDMs) are emerging potent regulators of transcriptional reprogramming in cancer, though their potential role in abnormal growth and fibrosis in heart disease remains little understood. Here, we investigated gain and loss of function of an H3K9me2 specific demethylase, Kdm3a, in myocytes and in vivo, and show it promotes LVH and myocardial fibrosis in response to pressure-overload. Cardiomyocyte KDM3A activates the transcription of tissue-inhibitor of MMP type 1 (Timp1) with pro-fibrotic activity.  By contrast, a pan-KDM inhibitor, JIB-04, suppresses TAC-induced LVH and fibrosis. JIB-04 inhibits KDM3A and suppresses the transcription of fibrotic genes that overlap with genes downregulated in Kdm3a-KO mice versus WT controls. Our study provides genetic and biochemical evidence for a pro-hypertrophic function of KDM3A and proof-of principle for pharmacological targeting of KDMs as an effective strategy to counter LVH and pathological fibrosis.

overall_design: #444 is a WT mouse under sham surgery as control; #445 and #17 are WT mice under TAC surgery to show the change of gene expression induced by pressure overload; #454 is a Kdm3a-Tg mouse under sham surgery used to show the gene expression change induced by Kdm3a overexpression at basal level; #446 and #18 are Kdm3a-Tg mice under TAC surgery to show the gene expression change induced by Kdm3a under pressure overload condition.

first: Qing-jun

last: Zhang

first: Zhi-ping

last: Liu


title: The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [small RNA]

city: Shenzhen

first: Xuemei

last: Chen

state: Guangdong

address: Nanhai Road 3688

institute: Shenzhen University

type: Non-coding RNA profiling by high throughput sequencing

summary: Plants evolved an array of disease resistance genes (R genes) to fight pathogens. In the absence of pathogen infection, NBS-LRR genes, which comprise a major subfamily of R genes, are suppressed by a small RNA cascade involving microRNAs (miRNAs) that trigger the biogenesis of phased siRNAs (phasiRNAs) from R gene transcripts. However, whether or how R genes influence small RNA biogenesis is unknown. In this study, we isolated a mutant with global defects in the biogenesis of miRNAs and phasiRNAs in Arabidopsis thaliana and traced the defects to the over accumulation and nuclear localization of an R protein SNC1. We showed that nuclear SNC1 represses the transcription of miRNA and phasiRNA loci, probably through the transcriptional corepressor TPR1. Intriguingly, nuclear SNC1 reduces the accumulation of phasiRNAs from three source R genes and concomitantly, the expression of a majority of the ~170 R genes was up-regulated. Taken together, this study reveals a new R gene-miRNA-phasiRNA regulatory module that regulates plants' growth-defense trade-off.

overall_design:
For library construction, 30 µg total RNA was resolved on a 15% polyacrylamide gel with 8 M urea. Small RNAs in the 15~40 nt size range were recovered as described 48. Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Libraty Prep Set for Illumina (New England Biolabs, E7300), and sequenced with an Illumina HiSeq2500 platform at BerryGenomics, China. Raw reads (SE50) were trimmed using Perl scripts to remove adapters. The clean reads were mapped to the Arabidopsis thaliana genome TAIR10 using the Bowtie program 49. The small RNA reads were calculated and normalized in RPM (reads per million mapped reads). The comparison between samples was conducted with the R package edgeR 50.

For analysis of miRNA levels, small RNA reads were mapped to annotated miRNAs in miRBase v21. For analysis of tasiRNAs levels, small RNA reads were mapped to each of the eight annotated TAS genes (TAS1A/1B/1C, TAS2, TAS3A/3B/3C and TAS4). For the analysis of phasiRNAs from protein coding genes, such as R genes and PPR genes, small RNA reads were mapped to the genes known to produce phasiRNAs and only uniquely mapped reads were included in subsequent analyses.

first: Qiang

last: Cai

first: Chao

last: Liang

first: Suikang

last: Wang

first: Yingnan

last: Hou

first: Lei

last: Gao

first: Li

first: Wenrong

last: He

first: Wenbo

last: Ma

first: Beixin

last: Mo


title: The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs [mRNA]

overall_design: Total RNAs extracted from 15-day-old seedlings of wild type and mutants were sent to Novogene, China, for mRNA-seq library construction and the libraries were sequenced on an Illumina Hiseq X10 platform to generate single-end reads of 150 bp in length.


title: A multi-omics analysis of the regulatory changes induced by miR-223 in a monocyte/macrophage cell line

city: AMIENS

first: Laurent

last: METZINGER

address: Avenue René Laënnec

institute: INSERM U1088

summary:
We used a multi-omics approach to study the impact of miR-223 in the RAW cell line. We evidenced changes linked to cell death, histone acetylation, bone remodeling, RNA regulation.
Changes in miR-223 expression altered the metabolic profile of cells including nucleotides. miR-223 impacted NF-kB levels, macrophage differentiation and osteoclastogenesis.

overall_design: Cell culture was performed in the same conditions for all techniques used. First, RAW 264.7 cells were seeded in 6-well culture plates (Corning) or Petri Dish (10 mm2) at 10,000 cells/cm2, grown until confluency, and transfected for 48 h with irrelevant scramble (Sbl), anti-miR-223 or pre-miR-223 (Qiagen).

first: M

middle: E

last: Mbaya

first: L

last: Louvet

first: R

last: Molinié

first: C

last: Guerrera

last: Cerutti

first: O

last: Fourdinier

first: V

last: Nourry

last: Gutierrez

first: S

last: Guénin

first: P

last: Morlière

first: F

last: Mesnard

first: Z

last: Massy

last: Metzinger-Le

last: Metzinger


title: The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs in Arabidopsis

first: Xuemei

last: Chen


title: Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [RNA-seq II]

first: Fanny

last: Gatzmann

summary: The marbled crayfish (Procambarus virginalis) is a unique freshwater crayfish characterized by genetic uniformity, phenotypic variability, and substantial invasive potential. As invasion into different habitats occurs in the absence of genetic variation, epigenetic mechanisms have been suggested to mediate phenotypic adaptation. However, epigenetic regulation has not been analyzed in this organism yet. Here we show that the recently published P. virginalis draft genome sequence encodes a conserved DNA methylation system. Whole-genome bisulfite sequencing of multiple replicates and different tissues revealed a methylation pattern that is characterized by gene body methylation of housekeeping genes. Interestingly, this pattern was largely tissue-invariant, suggesting a function that is unrelated to cell-fate specification. Indeed, integrative analysis of RNA-seq datasets showed that gene body methylation correlated with stable gene expression, while unmethylated genes often showed a high degree of inter-individual expression variation. Our findings thus establish the methylome of an emerging model organism and suggest that methylation-dependent regulation of gene expression variability may facilitate the phenotypic adaptation and invasive spread of this animal.

overall_design: RNA-seq data of hemocytes from marbled crayfish

first: Frank

last: Lyko

first: Cassandra

last: Falckenhayn

first: Julian

last: Gutekunst

first: Katharina

last: Hanna

first: Guenter

last: Raddatz

first: Vitor

last: Carneiro


title: IG-MYC-positive neoplasms with precursor B-cell phenotype are molecularly distinct from Burkitt lymphomas

status: Public on Oct 08 2018

city: Ulm

first: Rabea

last: Wagener

address: Albert-Einstein-Allee 11

department: Ulm University and Ulm University Medical Center

institute: Institute of Human Genetics

summary: Genome wide DNA methylation profiling of Burkitt lymphoma subsets. The Illumina Infinium HumanMethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 85,000 CpGs in B-cell lymphoma samples. Samples included 2 primary IG-MYC-positive B-cell neoplasms with precursor B-cell phenotype and 5 Burkitt lymphoma.

overall_design: Bisulphite converted DNA from the 7 samples were hybridised to the Illumina Infinium HumanMethylationEPIC BeadChip

first: Siebert

last: Reiner

first: Wagener

last: Rabea


title: Kdm3a in mouse promotes pressure overload induced cardiac hypertrophy [WT vs. KO]

first: zhi-ping

last: liu

summary: Heart disease and failure is a leading cause of mortality worldwide. Left ventricular hypertrophy (LVH) is a major risk factor for cardiovascular morbidity and mortality and the development of heart failure. Pathological LVH induced by sustained pressure-overload engages transcriptional programs including reactivation of canonical fetal genes and those inducing fibrosis. Histone lysine demethylases (KDMs) are emerging potent regulators of transcriptional reprogramming in cancer, though their potential role in abnormal growth and fibrosis in heart disease remains little understood. Here, we investigated gain and loss of function of an H3K9me2 specific demethylase, Kdm3a, in myocytes and in vivo, and show it promotes LVH and myocardial fibrosis in response to pressure-overload. Cardiomyocyte KDM3A activates the transcription of tissue-inhibitor of MMP type 1 (Timp1) with pro-fibrotic activity.  By contrast, a pan-KDM inhibitor, JIB-04, suppresses TAC-induced LVH and fibrosis. JIB-04 inhibits KDM3A and suppresses the transcription of fibrotic genes that overlap with genes downregulated in Kdm3a-KO mice versus WT controls. Our study provides genetic and biochemical evidence for a pro-hypertrophic function of KDM3A and proof-of principle for pharmacological targeting of KDMs as an effective strategy to counter LVH and pathological fibrosis.

overall_design: The expression profile of WT Sham serve as baseline control for WT mice; the expression change of genes in WT TAC rep1 and WT TAC rep2 indicating pressure overload induced change; the expression change of genes in Kdm3a-KO indicating the change induced by loss of function of Kdm3a; the expression change of genes in Kdm3a-KO rep1 and Kdm3a-KO rep2 indicating the change induced by pressure overload under Kdm3a-KO background.

first: Qing-jun

last: Zhang

first: Zhi-ping

last: Liu


title: Genome-wide mapping and functional analysis of DNA methylation in clonal invasive crayfish [WGBS]

city: Heidelberg

address: Im Neuenheimer Feld 580

institute: DKFZ

platform_organism:
Procambarus fallax
Procambarus virginalis

overall_design: Methylome data of different tissues (including hepatopancreas, abdominal musculature, embryos, and hemocytes) from 6 different P. virginalis individuals and 2 different P. fallax individuals


title: Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions

city: Paris

first: Angela

last: Taddei

address: 26 rue d'Ulm

institute: Institut Curie

type: Genome binding/occupancy profiling by array

summary: The eukaryotic genome is divided into chromosomal domains of heterochromatin and euchromatin. Transcriptionally silent heterochromatin is found at subtelomeric regions, leading to the telomeric position effect (TPE) in yeast, fly and man. Heterochromatin generally initiates and spreads from defined loci, and diverse mechanisms prevent the ectopic spread of heterochromatin into euchromatin. Here, we overexpressed the silencing factor Sir3 at various levels in yeast, and found that Sir3 spreading into Extended Silent Domains (ESD) eventually reached saturation at subtelomeres. We observed that Sir3 spreading into ESDs covered zone associated with specific histone marks in wild-type cells and stopped at zones of histone mark transitions including H3K79 tri-methylation levels. The conserved enzyme Dot1 deposits H3K79 methylation, and we found that it is essential for viability upon overexpression of Sir3, but not of a spreading-defective mutant Sir3A2Q. These data suggest that H3K79 methylation actively blocks Sir3 spreading. Lastly, we demonstrate that our work uncovers previously uncharacterized discrete subtelomeric domains associated with specific chromatin features, that offers a new viewpoint on how to separate subtelomeres from the core chromosome.

overall_design: Comparison of Sir3 spreading on chromatin in different strains : WT (yAT191, in duplicates), different levels of SIR3 ovexpression (pADH,pTEF and pGPD) with duplicates and different strain background for the pGPD-SIR3 strains. We also studied the influence of Sir2 on Sir3 spreading by studying Sir3 spreading in strains overexpressing SIR2(yAT1667) and co-overexpressing Sir2 and Sir3. Strains overexpressing the SIR3-A2Q point mutant were used to study the influence of telomere clustering on the genome (yAT1256). Lastly Sir3 binding in strains overexpressing SIR3 or in dot1 mutant strains overexpressing SIR3 was studied on release from a 5mM NAM YPD medium to a fresh YPD medium ( 8hours of growth).

first: Antoine

last: Hocher


title: The Trihelix Transcription Factor GT2-like 1 (GTL1) promotes salicylic acid metabolism and regulates basal and bacterial effector-triggered Immunity

status: Public on Oct 05 2018

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

summary: We report the transcriptome composition of gtl1-2 compared to Columbia wild-type plant without treatment and after flg22-application

overall_design: Illumina high-sequencing plateform was used to analyse the transcriptome composition of gtl1-2 under treated and untreated conditions

first: Ronny

last: Voelz

first: Soon-Kap

last: Kim

first: Jianing

last: Mi

first: Kiruthiga

middle: G

last: Mariappan

first: Xiujie

last: Guo

first: Jean

last: Bigeard

first: Naganand

last: Rayapuram

first: Salim

last: Al-Babili

first: Heribert

last: Hirt


title: Gene expression in Arabidopsis leaves after P. brassicae egg deposition

status: Public on Oct 04 2018

city: Berlin

first: Vivien

last: Firtzlaff

address: Haderslebener Str. 9

department: Applied Zoology/Animal Ecology

institute: Freie Universität Berlin

summary: Characterization of Arabidopsis thaliana`s transcriptional response to Pieris brassicae eggs

overall_design: Arabidopsis thaliana Col-0 wild type plants were grown under short day conditions at 20°C for seven weeks (6 weeks: 10 h/14 h light/dark + 1 week: 8 h/ 16 h light/dark). Seven week old plants were (i) deposited with eggs (one egg cluster with about 40 eggs was deposited onto the lower surface of a rosette leaf within position 14-17) or were (ii) left untreated. Six days after egg deposition, leaf tissue was harvested from egg-deposited and untreated plants. The tissue was harvested from a leaf region proximal to the egg deposition site.

first: Monika

last: Hilker

first: Reinhard

last: Kunze


title: Gene expression in Arabidopsis leaves after P. brassicae egg deposition and/or herbivory by P. brassicae larvae

summary: Plants can prepare their defense of impending herbivory, when they previously perceived  eggs deposited by herbivores insect which reliably indicates that larvae will soon hatch and feed on the plants. Using Arabidopsis thaliana and Pieris brassicae we addressed the question whether  prior egg deposition affects transcriptional changes in feeding-damaged plants. We determined the transcriptomes of Arabidopsis leaves that (i) were for six days deposited with eggs and suffered larval feeding for two days, (ii) suffered larval feeding for two days without prior egg deposition or (iii) were left untreated.

overall_design: Arabidopsis thaliana Col-0 wild type plants were grown under short day conditions at 20°C for seven weeks (6 weeks: 10 h/14 h light/dark + 1 week: 8 h/ 16 h light/dark). Seven week old plants were (i) deposited with eggs (one egg cluster with about 40 eggs was deposited onto the lower surface of a rosette leaf within position 14-17) or were (ii) left untreated. Six days after egg deposition a defined number of larvae was allowed to feed for two days on the leaf which carried the former egg cluster or on leaf with corresponding position of the untreated plants. Control plants were left untreated. From treated and untreated plants, tissue from a leaf region proximal to the egg deposition and/or feeding site was harvested for transcriptome analysis

first: Jana

last: Oberländer


title: Mouse Myeloid panel on G-MDSCs from treated tumors

first: Evanthia

last: Roussos Torres

summary: Immune checkpoint inhibition (ICI) has revolutionized treatment in cancers that are naturally immunogenic by enabling infiltration of T cells into the tumor microenvironment (TME) and promoting cytotoxic signaling pathways. Tumors possessing complex immunosuppressive TME’s such as breast and pancreatic cancers present unique therapeutic obstacles as response rates to ICI remain low. Such tumors often recruit myeloid-derived suppressor cells (MDSCs) whose functioning prohibits both T-cell activation and infiltration. We attempted to sensitize these tumors to ICI using epigenetic modulation to target MDSC trafficking and function to foster a less immunosuppressive TME. We showed that combining a histone deacetylase inhibitor, entinostat (ENT), with anti–PD-1, anti–CTLA-4, [A1]   [A2]  or both, significantly improved tumor-free survival in both the HER2/neu transgenic breast cancer and the Panc02 metastatic pancreatic cancer mouse models. Using flow cytometry, gene expression profiling, and ex vivo functional assays, we characterized populations of tumor-infiltrating lymphocytes (TILs) and MDSCs, as well as their functional capabilities. We showed that addition of ENT to checkpoint inhibition led to significantly decreased suppression by granulocytic-MDSCs in the TME of both tumor types. We also demonstrated an increase in activated granzyme-B–producing CD8+ T effector cells in mice treated with combination therapy. Gene expression profiling of both MDSCs and TILs identified significant changes in immune-related pathways. In summary, addition of ENT to ICI significantly altered infiltration and function of innate immune cells, allowing for a more robust adaptive immune response. These findings provide a rationale for combination therapy in patients with immune-resistant tumors, including breast and pancreatic cancers.

overall_design: To identify possible mechanisms for their impaired function, we utilized NanoString transcript profiling to evaluate broad changes in the transcriptome of isolated G-MDSCs induced by treatment.

middle: T

first: Brian

last: Christmas

first: Alexander

last: Hopkins

first: Christine

last: Rafie

first: Elizabeth

middle: M

last: Jaffee


title: Expression data from HeLa cell line transfected with TIPE1 or control vector

city: Zibo

first: Peiqing

last: Zhao

address: 54# Gongqingtuan Road

department: Center of Translational Medicine

institute: Zibo Central Hospital

summary:
HeLa cells transfected with an empty vector or a TIPE1 lentiviral vector were collected for gene expression detection. Some of them, for instance, the expression of genes induced by p53 was dramatically decreased.
We used microarrays to detail the gene expression after transfection with TIPE1 and identified distinct classes of changed genes during this process.

overall_design: HeLa cells transfected with an empty vector or a TIPE1 lentiviral vector were collected for RNA extraction and hybridization on Affymetrix microarrays, and then the data were analysed.

first: Wenlin

last: Xu


title: A longitudinal model of human neuronal differentiation for functional studies of schizophrenia polygenic risk

city: Los Angeles

first: Anil

last: Ori

state: Verenigde Staten van Amerika

address: 695 Charles E Young Drive South

department: Center for Neurobehavioral Genetics

institute: University of California, Los Angeles

summary: Human neural stem cells were differentiation to a neuronal lineage over 30 days. Genome-wide gene expression was collected at seven time points in at least triplicates. We used these expression profiles to identify longitunal gene clusters that are expressed over time and map GWAS disease risk onto this. We show that schizophrenia disease is enriched in specific clusters across in vitro neuronal differentiation, which could make this an applicable model to study this disease.

overall_design: A longitudinal experimental design with seven time points and at least three replicates per time point. All samples come from the same genetic background (H9/WA09 NSC)

middle: P

first: Merel

middle: H

last: Bot

first: Remco

last: Molenhuis

first: Loes

last: Olde Loohuis

first: Roel

last: Ophoff


title: Molecular characterization of a precision-cut rat lung slice model for the evaluation of anti-fibrotic drugs

status: Public on Oct 02 2018

city: Pennington

first: Ron

last: Ammar

state: New Jersey

address: 311 Pennington Rocky Hill Road

institute: Bristol-Myers Squibb

summary: The translation of novel pulmonary fibrosis therapies from preclinical models into the clinic represents a major challenge demonstrated by the high attrition rate of compounds that showed efficacy in preclinical models but demonstrated no significant beneficial effects in clinical trials. Precision-cut lung tissue slice (PCLS) contains all major cell types of the lung and preserves the original cell-cell and cell-matrix contacts. It represents a promising ex vivo model to study pulmonary fibrosis. In this study, using RNA sequencing, we demonstrated that TGFβ1 induced robust fibrotic responses in the rat PCLS model as it changed the expression of genes functionally related to extracellular matrix remodeling, cell adhesion, epithelial-to-mesenchymal transition and various immune responses. Nintedanib, pirfenidone and sorafenib each reversed a subset of genes modulated by TGFβ1 and of those genes we identified 229 genes whose expression was reversed by all three drugs. These genes define a molecular signature characterizing many aspects of pulmonary fibrosis pathology and its attenuation in the rat PCLS fibrosis model. A panel of 12 genes and 3 secreted biomarkers including procollagen I, HA and WISP1 were validated as efficacy endpoints for the evaluation of anti-fibrotic activity of experimental compounds.  Finally, we showed that blockade of αV integrins suppressed TGFβ1-induced fibrotic responses in the rat PCLS fibrosis model. Overall, our results suggest that the TGFβ1-induced rat PCLS fibrosis model may represent a valuable system for target validation and to determine the efficacy of experimental compounds.

overall_design: TGFb-treated rat precision-cut lung tissue slices (PCLS) were treated with drug and profiled with RNA-Seq

first: Xinqiang

last: Huang


title: Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury

city: Vancouver

first: Jordan

middle: W

last: Squair

state: BC

address: 818 West 10th Avenue

institute: University of British Columbia

summary: Spinal cord injury (SCI) is a devastating neurological condition for which there are currently no effective treatment options to restore function. A major obstacle to the development of new therapies is our fragmentary understanding of the coordinated pathophysiological processeses triggered by damage to the human spinal cord. An additional challenge to translation of preclinical therapies is the reliance of clinical trials on standardized neurological assessments to enrol and stratify patients, rather than objective injury biomarkers. Here, we describe a systems biology approach to integrate decades of small-scale experiments with unbiased, genome-wide gene expression from the human spinal cord, revealing a gene regulatory network signature of the pathophysiological response to SCI. Our integrative analyses converge on an evolutionarily conserved gene subnetwork enriched for genes associated with the response to SCI by small-scale experiments, and whose expression is upregulated in a severity-dependent manner following injury and downregulated in functional recovery. We validate the severity-dependent upregulation of this subnetwork in prospective transcriptomic and proteomic studies. Our analysis provides a systems-level view of the coordinated molecular processes activated in response to SCI. Further, our results nominate quantitative biomarkers of injury severity and functional recovery, with the potential to facilitate development and translation of novel therapies.

overall_design: Examination of rat spinal cord transcriptome after spinal cord injuries of different severities; The T9 spinous process was identified and a laminectomy was performed to expose the T10 spinal segment. Following this the animal was transferred to the IH impactor stage, where the T8 and T10 spinous processes were securely clamped using modified Allis forceps. The animal was stabilized on the platform and the impactor tip (2.0 mm) was properly aligned using a 3-dimensional coordinate system moving platform. The position of the impactor was confirmed as midline by two separate experimenters. The IH system was set to deliver an impact of 0 (control), 100, or 200 kdyn of pre-defined force.

first: Seth

last: Tigchelaar

first: Kyung-Mee

last: Moon

first: Jie

last: Liu

first: Wolfram

last: Tetzlaff

first: Brain

middle: K

last: Kwon

first: Andrei

middle: V

last: Krassioukov

first: Christopher

middle: R

last: West

first: Leonard

middle: J

last: Foster

first: Michael

last: Skinnider


title: Impact of two reoviruses and their coinfection on the rice RNAi system and vsiRNA production

status: Public on Oct 03 2018

city: Guangzhou

first: Zhanbiao

last: Li

address: NO.382 Wushan Road, Tianhe District

institute: South China Agricultural University

summary: Both Southern rice black-streaked dwarf virus (SRBSDV) and Rice ragged stunt virus (RRSV) belong to the family Reoviridae, and synergistic infection of these two viruses commonly occurs in the field. This study revealed that both SRBSDV and RRSV affect the RNA interference (RNAi) pathway and form different virus-derived interfering RNA (vsiRNA) profiles in rice. Co-infection of rice by SRBSDV and RRSV up-regulated the expression of rice Dicer and DICER-like (DCL) proteins but down-regulated the expression of rice RNA-dependent RNA polymerases (RDRs), and the accumulation of vsiRNAs of either RBSDV or RRSV was decreased compared with that in singly infected plants. The majority of SRBSDV vsiRNAs were 21 nt or 22 nt in length, whether plants were singly infected with SRBSDV or co-infected with RRSV. On the other hand, the majority of RRSV vsiRNAs were 20 nt, 21 nt, or 22 nt in length, among which those 20 nt in length accounted for the largest proportion; co-infection with SRBSDV further increased the proportion of 20 nt vsiRNAs and decreased the proportion of 21 nt vsiRNAs. Co-infection had no effects on the strand favoritism and hot spots of the vsiRNAs, but changed the bias of the 5' terminal nucleotide significantly. This study provides a reference for further study on the pathogenesis and synergistic mechanism of SRBSDV and RRSV.

overall_design: 3 samples

first: Tong

last: Zhang

first: Xiuqin

first: Guohui

last: Zhou


title: The effect of inhibition of arginine methylation in human FOXP3-transduced T cells

status: Public on Oct 07 2018

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

institute: Keio University

summary:
The forkhead box transcription factor 3 (FOXP3) plays a pivotal role in the suppressive function of regulatory T cells.  Protein function is diversely controlled by posttranslational mechanisms as well as mRNA expression levels.  In this study, we demonstrate that FOXP3 undergoes arginine methylation by interacting with the protein arginine methyltransferase 1 (PRMT1).
The inhibition of arginine methylation conferred gene expression profiles representing type I helper T cells to FOXP3+ T cells, which resulted in attenuated suppressive activity.  A methylation-defective mutant of FOXP3 displayed less potent activity to suppress xenogeneic graft-versus-host disease in vivo.

overall_design: Human CD4+ T cells derived from three different donors were transduced with control DNGFR or FOXP3-DNGFR and cultured in the presence of DMSO or MS023 (type I PRMT inhibitor).  The DNGFR+ cells were isolated on day 7, and the gene expression profiles were analyzed using the Affymetrix PrimeView™ Human Gene Expression Array.

first: Naoto

last: Hirano


title: Littorina saxatilis Comparative Genomics Hybridization (CGH) study with NimbleGen 090824_L_saxatilis_expr_HX12

city: Vigo

first: Humberto

last: Quesada

address: Campus As Lagoas-Marcosende

department: Departamento de Bioquímica, Genética e Inmunología,

institute: Universidad de Vigo

summary: Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel local adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that phenotypic divergence followed complex evolutionary paths, affecting multiple loci, and including the parallel recruitment of the same genes as well as completely different genes in distinct ecotype pairs. The majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously, providing evidence for a decoupled evolution among regulatory and coding regions. Overall, our findings suggest that gene expression and coding sequences may evolve independently as a result of being distinctly targeted by evolutionary constraints, and that divergent selection significantly contributed to the process of molecular differentiation among ecotype pairs.

overall_design: Expression array for 25,205 (from which 17,431 satsified the quality criteria) transcripts from Littorina saxatilis with five 60 nt probes per transcript. A full description of the microarray features can be found in Panova et al. (2006). Mol Ecol. 15: 4021-4031. Data correspond to crab (ridged-banded, RB) and wave (sheltered-unbanded, SU) ecotype pooled samples from three Spanish localities. The whole experiment included samples of 72 Galician snails (12 samples per ecotype and locality, 69 samples satisfied quality criteria) for which genomic DNA extracts were individually hybridized to the array.

first: M

last: Rivas

last: Saura

first: A

last: Pérez-Figueroa

last: Panova

first: T

last: Johannesson

first: C

last: Andre

last: Caballero

first: E

last: Rolán-Álvarez

first: K

first: H


title: Epigenetic Enhancer Marks and Transcription Factor Binding Influence Vk Gene Rearrangement in Pre-B Cells and Pro-B Cells [VDJ-seq]

status: Public on Oct 01 2018

city: La Jolla

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

summary: There has been no study to date that has examined genomic DNA (gDNA) and RNA Igkappa repertoires directly from the same set of cells.  In this study we performed deep sequencing on Igkappa repertoire library preparations from both gDNA and RNA from the same sorted cells.  This was done for both pre-B cells, where most Igkappa rearrangement takes places as well as pro-B cells where some B cells undergo early Igkappa rearrangement.  In addition, we perfored gDNA repertoire analysis on iEkappa-/- pre-B cells.  We find that some Vk genes display skewed DNA or RNA representiation relative to the other.  We also find that pro-B cell Igkappa rearrangement is skewed to Jkappa-distal Vkappa genes.  Lastly, we find that iEkappa-/- pre-B cells are not capable of rearranging to the most proximal Vkappa family genes.

overall_design: gDNA (DNeasy, Qiagen) or RNA (RNeasy, Qiagen) was prepared from C57BL/6 pre-B cells, C57BL/6 pro-B cells, and iEkappa-/- pre-B cells.  gDNA was sonicated to 500 to 1000 bp fragments, end repaired, A-tailed and adapter ligated.  Jkappa gene biontinylated primer extended products were pulled out with streptavidin.  Sequential PCRs added index, barcode and flow cell binding sequences.  The last PCR utilized NEBNext Dual indexing primers.  RNA was converted to cDNA with Transcriptor high-fidelity reverse transcriptase (Roche).  RNase treatments removed unwanted RNA.  cDNA was then adapter ligated using bridge adapters.  Sequential PCRs was performed as in gDNA.  Libraries were sequenced using Illumina MiSeq 2x300 read length.

first: Eden

last: Kleiman

first: Ann

last: Feeney


title: MicroRNAs and histone deacetylase inhibition-mediated protection against inflammatory β-cell damage

city: Gentofte

first: Flemming

last: Pociot

address: Niels Steensens Vej 2

department: T1D Biology

institute: Steno Diabetes Center Copenhagen

summary: Inflammatory b-cell failure contributes to type 1 and type 2 diabetes pathogenesis. Proinflammatory cytokines cause b-cell dysfunction and apoptosis, and lysine deacetylase inhibitors (KDACi) prevent b-cell failure in vitro and in vivo, in part by reducing NFkB transcriptional activity. Here we investigated the hypothesis that the protective effect of KDACi involves transcriptional regulation of microRNAs (miRs), potential new targets in diabetes treatment. Insulin-producing INS1 cells were cultured with or without the broad-spectrum KDACi Givinostat prior to exposure to the proinflammatory cytokines IL-1-b and IFN-g for 6h or 24h, and miR expression was profiled with miR array. A shortlist of ten miRs (miR-7a-2-3p, miR-29c-3p, miR-96-5p, miR-101a-3p, miR-140-5p, miR-146a-5p, miR-146b-5p, miR-340-5p, miR-384-5p, and miR-455-5p) regulated by both cytokines and Givinostat was verified by qRT-PCR. MiR-146a-5p was strongly regulated by cytokines and KDACi and analyzed further. MiR-146a-5p expression was induced by cytokines in rat and human islets. Cytokine-induced miR-146a-5p expression was specific for INS1 and β-TC3 cells, whereas α-TC1 cells exhibited a higher basal expression. Transfection of INS1 cells with miR-146a-5p reduced the activity of NFκB and iNOS promoters, decreased NO production, and decreased protein levels of iNOS and its own direct target TNF receptor associated factor 6 (TRAF6). MiR-146a-5p was elevated in diabetes-prone BB-DP rat pancreas at diabetes onset, suggesting that miR-146a-5p could play a role in type 1 diabetes development. The miR array of cytokine-exposed INS1 cells rescued by KDACi revealed several other miRs potentially involved in cytokine-induced b-cell apoptosis, demonstrating the strength of this approach.

overall_design: miRNA gene expression in INS1 cells was measured at 6 and 24 hours with or without exposure to  Givinostat and proinflammatory cytokines IL-1β and IFNγ. Eight independent experiments were performed with three technical replicates at each time (6 or 24 hours).

first: Thomas

last: Mandrup-Poulsen


title: RNA-seq of Drosophilaembryos with Lim3knockdown and normal expression of Lim3

city: Moscow

first: Olga

last: Rybina

state: Moskva

address: Kurchatov sq.,2

country: Russia

institute: IMG RAS

summary: Understanding the molecular mechanisms underlying variation in lifespan is central to ensure long life and postpone aging. There is growing evidence that changes in expression of key lifespan regulators during early development are crucially important for lifespan determination.To study the early developmental impact of Lim3on Drosophila lifespan we performed a Lim3knockdown at early stages of Drosophiladevelopment. We detected the significant decrease of lifespan both in Drosophila males and females with depleted Lim3expression and revealed it to be associated with mitochondriala activity.

overall_design: Two biological samples were analyzed. Each biological sample contained 100–200 mkg embryos of 0- to 16-hour from flies obtained by crossing a Drosophila line (y1 w*; P{en2.4-GAL4}e22c; P{tGPH}4/TM3, Ser1) that was used to induce the expression of transgenic constructs during early Drosophila development and a fly line (y1 v1; P{TRiP.JF02125}attP2) that was used to provide Lim3 RNAi knockdown or a line (y1 v1; P{y+t7.7=CaryP}attP2) that was used as a control.

middle: Y

first: Mikhail

last: Schelkunov

first: Elena

last: Pasyukova


title: C. elegans DLC-1 is a component of diverse ribonucleoprotein complexes

city: Missoula

first: Ekaterina

last: Voronina

state: MT

address: 32 Campus Drive

department: Division of Biological Sciences

institute: University of Montana

summary: Ribonucleoprotein complexes, which contain mRNAs and their regulator proteins, carry out post-transcriptional control of gene expression. The function of many RNA-binding proteins depends on their association with cofactors. Here we use a genomic approach to identify transcripts associated with DLC-1, a protein previously identified as a cofactor of two unrelated RNA-binding proteins that act in the C. elegans germline. Among the 2732 potential DLC-1 targets, most are germline mRNAs. Removal of DLC-1 affects expression of its targets, meg-1 and meg-3. We propose that DLC-1 acts as a cofactor for multiple ribonucleoprotein complexes, thus making diverse contributions to RNA regulation in the germline.

overall_design: FLAG-tagged DLC-1 was  immunoprecipitated from worm extracts to capture DLC-1/RNP complexes and the RNA was sequenced

first: Nicholas

last: Day

first: Mary

last: Ellenbecker


title: Untreated vs. QR-110 treated retinal organoids

city: Leiden

first: kalyan

last: dulla

address: Zernikedreef 9

country: Netherlands

institute: ProQR Therapeutics

summary: CEP290 c.2991+1655 homozygous retinal organoids were treated with 1 µM QR-110 for 28 days

overall_design: two untreated organoids and two treated organoids

first: Kalyan

last: Dulla


title: RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis

status: Public on Sep 30 2018

first: Zhicheng

last: Dong

address: 230 Wai Huan Xi Road,Guangzhou Higher Education Mega Center

department: School of Life Sciences

institute: Guangzhou University

summary: RNA polymerase II (Pol II) play an essential role in gene expression. Here, we adapted plant Native Elongation Transcript sequencing and Global Run On sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site and pausing at proximal promoter is an important regulatory step for Pol II transcription although loosely controlled. Furthermore, the Pol II with unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream the TSS, while the Ser5P CTD Pol II associates with spliceosome, and the Ser2P CTD Pol II presents a sharp peak 250 base pair downstream of polyadenylation site indicating a stringent control of termination for protein coding genes; whilst the termination of noncoding genes is not. Active expressed genes can be classified into three clusters according to the distribution patterns of different Pol II isoforms. In summary, we demonstrated the modified plant GRO-seq and pNET-seq are suitable to study RNA Pol II dynamics in planta. Although transcription is conserved among high eukaryotes, Pol II has its feature in Arabidopsis.

overall_design: Transcriptional profiling by  GRO-seq and pNET-seq

first: Jiafu

last: Zhu

first: Min

last: Liu

first: Xiaobin


title: Comparative gene array analyses of severe elastic fiber defects in late embryonic and newborn mouse aorta

status: Public on Sep 26 2018

city: St. Louis

first: Jessica

last: Wagenseil

state: Missouri

address: One Brookings Dr., CB 1185

institute: Washington University

summary: Elastic fibers provide reversible elasticity to the large arteries and are assembled during development when hemodynamic forces are increasing. Mutations in elastic fiber genes are associated with cardiovascular disease. Mice lacking expression of the elastic fiber genes elastin (Eln-/-), fibulin-4 (Efemp2-/-), or lysyl oxidase (Lox-/-) die at birth with severe cardiovascular malformations. All three genetic knockout models have elastic fiber defects, aortic wall thickening, and arterial tortuosity. However, Eln-/- mice develop arterial stenoses, while Efemp2-/- and Lox-/- mice develop ascending aortic aneurysms. We performed comparative gene array analyses of these three genetic models for two vascular locations and developmental stages to determine differentially expressed genes and pathways that may explain the common and divergent phenotypes. We first examined arterial morphology and wall structure in newborn mice to confirm that the lack of elastin, fibulin-4, or lysyl oxidase expression provided the expected phenotypes. We then compared gene expression levels for each genetic model by three-way ANOVA for genotype, vascular location, and developmental stage. We found three genes upregulated by genotype in all three models, Col8a1, Igfbp2, and Thbs1, indicative of a common response to severe elastic fiber defects in developing mouse aorta. Genes that are differentially regulated by vascular location or developmental stage in all three models suggest mechanisms for location or stage specific disease pathology. Comparison of signaling pathways enriched in all three models shows upregulation of integrins and matrix proteins involved in early wound healing, but not of mature matrix molecules such as elastic fiber proteins or fibrillar collagens.

overall_design: Three genetic models of elastin fibers defects, two genotypes, two vascular locations, two developmental stages, N = 2 of 8 pooled aortic samples each


title: Littorina saxatilis Expression study with NimbleGen 090824_L_saxatilis_expr_HX12

first: Humberto

last: Quesada

overall_design: Expression array for 25,205 (from which 17,431 satsified the quality criteria) transcripts from Littorina saxatilis with five 60 nt probes per transcript. A full description of the microarray features can be found in Panova et al. (2006). Mol Ecol. 15: 4021-4031. Data correspond to crab (ridged-banded, RB) and wave (sheltered-unbanded, SU) ecotype pooled samples from three Spanish localities. It includes four replicate samples from each ecotype and locality (24 samples in total, from which 22 satisfied the quality criteria), each including 15 pooled female specimens with an equimolar RNA contribution of each specimen to the pool.

first: M

last: Rivas

last: Saura

first: A

last: Pérez-Figueroa

last: Panova

first: T

last: Johannesson

first: C

last: Andre

last: Caballero

first: E

last: Rolán-Álvarez

first: K

first: H


title: Identification of potential metastasis associated miRNAs in colorectal cancer

status: Public on Sep 22 2018

first: Zeng

last: zhicheng

department: Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology

institute: Southern Medical University

summary: To identify potential metastasis associated miRNAs in colorectal cancer (CRC), we performed miRNA array on  normal mucosa, CRC tissues without metastasis and CRC tissues with distant metastasis.

overall_design: The miRNA expression in normal mucosa, CRC tissues without metastasis and CRC tissues with distant metastasis were analyzed using human miRNA Paraflo™ array (LC Sciences, CA, USA). Five clinical samples were pooled in each group.

first: L

last: Liang


title: Changes of gene expression in adrenal gland after Ephb6 gene knockout in mice

city: Montreal

first: Wei

last: Shi

state: Quebec

address: 1855 Boulevard René-Lévesque O, 303

institute: University of Montreal

summary: Eph kinases constitute the largest receptor tyrosine kinase family, and their ligands, ephrins (Efns), are also cell surface molecules. Our purpose is to compare the expression levels of genes in adrenal gland chromaffin cells in EphB6 KO and WT male/female/castrated mice.

overall_design: Total RNA was extracted from adrenal gland of male, female and castrated male Ephb6 KO mice and their WT counterparts.

first: Jiangping

last: Wu

first: Yujia

last: Wang


first: Zhicheng

last: Dong

summary: RNA polymerase II (Pol II) play an essential role in gene expression. Here, we adapted mammalian Native Elongation Transcript sequencing and Global Run On sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site and pausing at proximal promoter is an important regulatory step for Pol II transcription although loosely controlled. Furthermore, the Pol II with unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream the TSS, while the Ser5P CTD Pol II associates with spliceosome, and the Ser2P CTD Pol II presents a sharp peak 250 base pair downstream of polyadenylation site indicating a stringent control of termination for protein coding genes; whilst the termination of noncoding genes is not. Active expressed genes can be classified into three clusters according to the distribution patterns of different Pol II isoforms. In summary, we demonstrated the modified plant GRO-seq and mNET-seq are suitable to study RNA Pol II dynamics in planta. Although transcription is conserved among high eukaryotes, Pol II has its feature in Arabidopsis.

overall_design: Transcriptional profiling by  GRO-seq and mNET-seq

first: Jiafu

last: Zhu


title: Vav proteins maintain epithelial traits in breast cancer cells using miR-200c-dependent and independent mechanisms

status: Public on Sep 21 2018

city: Salamanca

first: L. Francisco

last: Lorenzo-Martín

state: Castilla y León

address: Campus Miguel de Unamuno

institute: University of Salamanca (USAL) – Centro de Investigación del Cáncer (CIC)

summary:
Here, we report that the Rho GTPase activators Vav2 and Vav3 utilize a new, miR-200c-dependent mechanism that maintains the epithelial state by limiting the abundance of the Zeb2 transcriptional repressor in breast cancer cells. In parallel, Vav proteins engage an expression program that maintains epithelial cell traits in 3D culture.
Depletion of Vav proteins triggers EMT in epithelioid breast cancer cells and, conversely, expression of constitutively active Vav2 restores both miR-200c expression and epithelial traits in mesenchymal breast cancer cells. In silico analyses suggest that the negative Vav-Zeb2 axis is operative in human luminal breast tumors.

overall_design: 4T1 cells were transduced with empty pLKO lentiviral vector (3 replicates included) and lentiviral shRNAs to Vav2 and Vav3 transcripts (2 independent experiments, 3 replicates each). Knockdown cells were then rescued by reexpressing either Vav2 (3 replicates) or Vav3 (3 replicates).

first: Carmen

last: Citterio

first: Mauricio

last: Menacho-Márquez

first: Romain

last: Larive

first: Ramón

last: García-Escudero

first: Javier

last: Robles-Valero

first: Myriam

last: Cuadrado

first: María

last: Fernández-Pisonero

first: Mercedes

last: Dosil

middle: A

last: Sevilla

last: Montero

first: Pedro

last: Fernández-Salguero

first: Jesús

last: Paramio

first: Xosé

last: Bustelo


title: Cytokinin modulates chromatin accessibility in a context-dependent manner through the type-B response regulators

status: Public on Sep 27 2018

city: Chapel Hill

first: Joseph

last: Kieber

state: NC

address: 4144 Genome Sciences Building

department: Biology

institute: University of North Carolina

summary: The plant hormone cytokinin regulates diverse aspects of plant growth and development, likely through context-dependent transcriptional regulation that relies on a dynamic interplay between regulatory proteins and chromatin. We employed the Assay for Transposase Accessible Chromatin (ATAC-Seq) to profile changes in the chromatin landscape of Arabidopsis roots and shoots in response to cytokinin. Our results reveal differentially accessible chromatin regions indicative of dynamic regulation in response to cytokinin. These changes in chromatin occur preferentially upstream of genes whose expression changes in response to cytokinin and largely overlap with binding sites for the type-B ARRs, transcription factors that mediate the primary response to cytokinin. Further, the type-B ARRs were found to be necessary for the changes in chromatin state in response to cytokinin. Lastly, we find context-dependent responses by comparing root and shoot profiles. These datasets provide new insights into the transcriptional regulatory mechanisms involved in the cytokinin response and how cytokinin mediates its pleiotropic effects.

overall_design: Harvested plants were treated with BA for 45 minutes. For ATAC analyses, four biological replicates of root samples (-/+ cytokinin), two biological replicates of shoot samples (-/+ cytokinin), two biological replicates of arr1,10,12 root samples (-/+ cytokinin). For RNA analyses, three biological reps of root and shoots samples (-/+ cytokinin) was performed.

first: Kevin

middle: C

last: Potter

first: Judy

last: Wang

first: Eric

last: Schaller


title: Exosomal miRNA expression derived from colon cancer cells in the TP53 deficiency of cancer cells

status: Public on Sep 17 2018

city: Suita

first: Shunsuke

last: Yoshii

state: Osaka

address: 2-2, Yamadaoka

department: Gastroenterology and Hepatology

institute: Osaka University Graduate School of Medicine

summary: TP53 deficiency within colon cancer cells can affect surrounding stromal cells by modifying of miRNAs expression profiling in the exosomes.

overall_design: In the study presented here, miRNA profiling in exosomes derived from TP53-wild colon cancer cells and TP53-deficiency colon cancer cells was compared. Exosomes were collected from culture supernatant using sequential ultracentrifugation method.

first: Yoshito

last: Hayashi