title: Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development [RNA-seq]

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

summary: H3K9me3-dependent heterochromatin is considered as one of the major barriers for cell fate changes, and must be reprogrammed during fertilization to reactivate highly specialized paternal and maternal genome to establish totipotency. However, the molecular details are lacked for early embryos due to the limited materials. Here we map the genome-wide distribution of H3K9me3 modification in the early embryo as well as in the cell fate determined embryonic tissues after implantation. We find that H3K9me3 exhibits distinct dynamic features in promoters and retro-transposons. Both maternal and paternal genome undergo large scale of H3K9me3 reestablishment after fertilization, and the imbalance of maternal H3K9me3 signal over paternal last until the blastocyst stage. The rebuilding of H3K9me3 on LTR retro-transposons maintains its repression state after the global DNA demethylation, and we further discover that Chaf1a is essential for the establishment of H3K9me3 on LTRs and the loss function of Chaf1a leads to embryo development failure. Finally, we find that lineage specific H3K9me3 is established after lineage commitment in post-implantation embryos. Thus, our data demonstrate that H3K9me3-dependent heterochromatin undergoes dramatic reprogramming during early embryo development and the establishment of H3K9me3 on LTRs is essential for proper embryo development.

overall_design:
We mapped the H3K9me3 modifications on embryos from zygote to 8.5 day stage (with separated ICM and TE, Epi and Exe). The mouse metaphase II (MII) oocytes, sperm, as well as mouse embryonic stem cells (mESCs) and mouse trophoblast stem cells (mTSCs) were also analyzed. In the ChIP-seq analysis on pre-implantation embryos, 500 cells were used for per reaction and two or three replicates were performed for each stage.

This series contains the RNA-seq data on embryos from embryos from zygote to 6.5 day stage (with separated ICM and TE, Epi and Exe) including morula stage with siRNA.

first: Chenfei

first: Xiaoyu

last: Liu

first: Yawei

first: Lei

last: Yang

first: Chong

last: Li

first: Wenqiang

first: Chuan

last: Chen

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Hong

first: Yong

last: Zhang


title: Kinetic microarray of hPSC-derived SCGB3A2+ airway epithelium

status: Public on Apr 12 2018

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

country: USA

institute: Boston University

summary: We sought to better understand the kinetics of differentiation and the global transcriptomic programs of these labeled cells as they emerge over prolonged culture periods

overall_design: We performed whole transcriptome microarray profiling of cells at various stages of RSC differentiation to proximal airway: undifferentiated cells (day 0), purified early lung progenitors (day 15 CD47hi), early airway progenitors (day 22),  and SC+ and SC- late airway populations (day 36, Figure 3c, Supplementary File 1).

first: Katherine

middle: B

last: McCauley

first: Darrell

last: Kotton


title: Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development [ChIP-seq]

status: Public on Apr 13 2018

country: China

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: We mapped the H3K9me3 modifications on embryos from zygote to 8.5 day stage (with separated ICM and TE, Epi and Exe). The mouse metaphase II (MII) oocytes, sperm, as well as mouse embryonic stem cells (mESCs) and mouse trophoblast stem cells (mTSCs) were also analyzed. In the ChIP-seq analysis on pre-implantation embryos, 500 cells were used for per reaction and two or three replicates were performed for each stage.

last: Wang


title: Expression analysis in Patl2-knock-out mouse oocytes (GV and MII stages)

status: Public on Apr 16 2018

city: La Tronche

first: Christophe

last: Arnoult

address: rond-point de la Chantourne

department: Institute for Advanced Biosciences

country: France

institute: INSERM U1209 CNRS UMR5309

summary: The oocyte maturation is a poorly understood process. Patl2 is involved in human bad egg syndrome and is a translation factor. The aim of this study was to assess the impact of the lack of Patl2 on the transcriptomes of GV and MII oocytes.

overall_design: Mouse oocytes from wild type and Patl2-knock-out mouse were collected at GV and MII stages. Total RNA were purified and analyzed on mouse ClariomD Affymetrix arrays. The experiment included five GV stage oocyte samples (two wild type and three Patl2-KO) and five GMII stage oocytes samples (two wild-type and three Patl2-KO).

first: Marie

last: Christou-Kent

first: Jean-Paul

last: Issartel

first: Pierre

last: Ray


title: The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome Virus (total RNA)

status: Public on Apr 14 2018

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

institute: INRA

summary: Porcine alveolar macrophages were challenged in vitro with a low virulent strain of the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) to identify and characterize the population of host genes subjected to miRNA post-transcriptional regulation durign early viral infection.  We employed a high-throughput biochemical assay, i.e. the immunoprecipitation of RISCs followed by microarray analysis of the RISC-bound miRNA targets (RIP-Chip). qPCR analyses were carried out to validate the resolution of the microarray and to determine levels of expression of a panel of eight miRNAs (ssc-miR-142-3p, ssc-miR-142-5p, ssc-let-7f, miR-146a-5p, miR-155-5p, ssc-miR-181a, ssc-miR-21 and ssc-miR-335).

overall_design: Lung alveolar macrophages were obtained by lung lavage from 4 animals. Cells were infected in vitro with the strain Finistère at multiplicity of infection of 2, or mock infected.  Infected cells were harvested at 7 and 10 hours post-infection; control (mock infected) cells were collected at the same times. Total RNAs were extracted from total cell contents and from RISC (RNA-induced Silencing Complex) immunoprecipitates. RNAs were hybridized on microarrays and transcripts analyzed for relative enrichment in RISC (RIP-Chip technology).

first: Sophie

last: Dhorne-Pollet

first: Nuria

last: Mach

first: Patricia

last: Renson

first: Florence

last: Jaffrézic

first: Guillemette

last: Marot

first: Tatiana

last: Maroilley

first: Jérôme

last: Lecardonnel

first: Olivier

last: Bourry

first: Elisabetta

last: Giuffra


title: Reprogramming of H3K9me3-dependent heterochromatin during mammalian early embryo development

first: Shaorong

last: Gao

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary:
H3K9me3-dependent heterochromatin is considered as one of the major barriers for cell fate changes, and must be reprogrammed during fertilization to reactivate highly specialized paternal and maternal genome to establish totipotency. However, the molecular details are lacked for early embryos due to the limited materials. Here we map the genome-wide distribution of H3K9me3 modification in the early embryo as well as in the cell fate determined embryonic tissues after implantation. We find that H3K9me3 exhibits distinct dynamic features in promoters and retro-transposons. Both maternal and paternal genome undergo large scale of H3K9me3 reestablishment after fertilization, and the imbalance of maternal H3K9me3 signal over paternal last until the blastocyst stage. The rebuilding of H3K9me3 on LTR retro-transposons maintains its repression state after the global DNA demethylation, and we further discover that Chaf1a is essential for the establishment of H3K9me3 on LTRs and the loss function of Chaf1a leads to embryo development failure. Finally, we find that lineage specific H3K9me3 is established after lineage commitment in post-implantation embryos. Thus, our data demonstrate that H3K9me3-dependent heterochromatin undergoes dramatic reprogramming during early embryo development and the establishment of H3K9me3 on LTRs is essential for proper embryo development.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Chenfei

first: Xiaoyu

last: Liu

first: Yawei

first: Lei

last: Yang

first: Chong

last: Li

first: Wenqiang

first: Chuan

last: Chen

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Hong

first: Yong

last: Zhang


title: Quaking dysregulation contributes to demyelination and functional decline of the mouse auditory nerve after noise exposure

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Myelinating glia in the auditory system enclose auditory nerve fibers, providing an insulating effect that facilitates rapid transfer of auditory information from the ear to the brain.  Here we show that noise exposure at the levels sufficient for inducing hearing loss cause a rapid cellular and molecular response on myelinating glia that precedes neuron degeneration.  The response is characterized by inflammatory response, myelin dysmorphology and widespread changes in myelin-related gene expression.  Another characteristic was change in expression of the quaking gene (QKI), which encodes a group of RNA binding proteins that are enriched in myelinating glia.  Changes in QKI were accompanied by changes in numerous known and potential QKI target genes, including many genes associated with myelination.  Our results implicate QKI as a critical early component in the noise response, influencing glia dysfunction that leads to auditory nerve demyelination and, ultimately, sensorineural hearing loss.

overall_design: Analysis was done on control adult mice and on noise-exposed adults at four different times after noise exposure: immediately following, 1 day after, 7 days after, and 14 days after. Animals of both gender were used in the study. Auditory nerve tissue from both ears of a single animal were combined to generate an independent sample. All sample types were done in experimental triplicate (n=3).

first: Hainan

last: Lang

middle: L


title: Systematic discovery of RNA binding proteins that control microRNA processing

status: Public on Apr 11 2018

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the modulation of miRNA processing by several RNA binding proteins through the implementation of a high-throughput computational screen of eCLIP data

overall_design: Examinaiton of eCLIP data for enrichment at miRNA loci, modulation of candidate RBPs and small RNA-seq and biochemical validation

first: J

middle: K

last: Nussbacher

first: E

middle: W


title: Whole mitochondrial genome bisulfite sequencing (WmGBS) analysis for the mouse brain, liver, and embryonic stem cells

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary: Whilst 5-methylcytosine (5mC) is a major epigenetic mark in the nuclear DNA in mammals, whether or not mitochondrial DNA (mtDNA) receives 5mC modification remains controversial. Herein, we exhaustively analysed mouse mtDNA using three methods that are based upon different principles for detecting 5mC. Next-generation bisulfite sequencing did not give any significant signatures of methylation in mtDNAs of liver, brain and embryonic stem cells (ESCs). Also, treatment with methylated cytosine-sensitive endonuclease McrBC resulted in no substantial decrease of mtDNA band intensities in Southern hybridisation. Furthermore, mass spectrometric nucleoside analyses of highly purified liver mtDNA preparations did not detect 5-methyldeoxycytidine at the levels found in the nuclear DNA but at a range of only 0.3–0.5% of deoxycytidine. Taken together, we propose that 5mC is not present at any specific region(s) of mtDNA and that levels of the methylated cytosine are fairly low, provided the modification occurs. It is thus unlikely that 5mC plays a universal role in mtDNA gene expression or mitochondrial metabolism.

overall_design: Cytosine modification in the mitochondrial DNA was examined by bisulfite shotgun sequencing, restriction enzyme analysis, and mass spectrometry.

first: Takehiro

last: Yasukawa

first: Shigeru

last: Matsuda


title: MicroRNA profiling of demyelination and remyelination areas in corpus callosum of cuprizone-treated mice

city: Budapest

first: Viktor

last: Molnár

address: Nagyvárad tér 4.

department: Department of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
Mouse cuprizone (CPZ ) model of experimental de- and remyelination was applied to mimic demyelination pathology of multiple sclerosis. In order to identify differentially expressed microRNAs involved in de- and remyelination, the affected areas of corpus callosum were isolated from mice exposed to CPZ and conducted an Agilent microarray analysis. To induce demyelination, CPZ was administrated for four weeks. Spontaneous remyelination occurs as mice returned to the regular diet after four weeks feeding with CPZ (DEM_4w). Remyelination was examined at two time points: acute remyelination induced by four weeks CPZ feeding followed by two days of regular diet (two days remyelination: REM_2d), and full remyelination induced by four weeks CPZ feeding followed by two weeks of regular diet (two weeks remyelination: REM_2w). Control mice (C) were kept on a normal diet.
The following groups representing de- and remyelinisation pathology in corpus callosum of CPZ-treated mice were compared: Demyelination: 4weeks CPZ: DEM_4w; Acute remyelination: 4 weeks CPZ +2 days UNTREATED: REM_2d; Full remyelination: 4 weeks CPZ +2 weeks UNTREATED: REM_2w; and UNTREATED control (C). The experiments were performed using 2-4 animals per groups.

overall_design: Nellie, A,Martin

last: Molnar

first: Gabor

middle: T

last: Somogyi

first: Maria

last: Elkjaer

first: Arkadiusz

last: Nawrocki

first: Justyna

last: Okarmus

first: Agnieszka

last: Wlodarczyk

first: Eva

last: Thygesen

first: Miklos

last: Palkovits

first: Ferenc

last: Gallyas

first: Martin

middle: R

last: Larsen

first: Hans

last: Lassmann

first: Eirikur

last: Benedikz

first: Trevor

last: Owens

first: Asa

middle: F

last: Svenningsen

first: Zsolt

last: Illes


title: Gene expression analysis of tumour xenografts after injection of breast cancer cells treated with axolotl oocyte extracts

status: Public on Apr 10 2018

city: Nottingham

first: Cinzia

last: Allegrucci

state: Notts

address: Science Road

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

summary: Analysis of genes that were differentially expressed in axolotl extract reprogrammed tumour xenografts compared to untreated controls. The study provided insight into the biological processes, signalling pathways and gene networks affected by the oocyte extract treatment which resulted in halted tumour growth in mice.

overall_design: Total RNA obtained from tumour xenografts collected at 12 weeks after injection of untreated or axolotl oocyte extract-treated MCF-7 cells.


title: Sex reversal following the deletion of a single far upstream enhancer of Sox9.

city: Chicago

first: Christopher

last: Futtner

state: Il

address: 303 E. Superior St, Lurie 7-220

department: Endocrinology

institute: Northwestern University

summary:
Purpose: In this study we employed unbiased, genome wide techniques to identify novel enhancers of Sox9 that may cause Disorders of Sex Development (DSDs) when disrupted in the mouse.
Methods: We performed ATAC-seq on 60K FACS-purified gonadal cells before and after sex determination to map nucleosome depleted regions (NDRs) indicative of regulatory elements. We then selected 16 putative enhancers present in Sertoli cells. To determine whether these are active enhancers, we performed ChIP-seq for H3K27ac, a histone modification that marks active enhancers. Transient transgenics was performed on select enhancers to determine whether they drive Sertoli-specific expression in vivo. Finally, we selected a single active Sertoli-specific enhancer to delete with CRISPR.
Results: We identified a single enhancer upstream of Sox9 that causes complete male-to-female sex reversal in mice when deleted.
Conclusions: Our study is the first to identify a single enhacer supstream of Sox9 which drives Sertoli-specific expression in vivo and causes complete male-to-female sex reversal when deleted in the mouse. Furthermore, this enhancer overlaps a region in humans (XY SR) associated to DSDs.

overall_design: ATAC-seq was performed in triplicate on FACS-sorted XX and XY gonadal supporting cells from E10.5 and E13.5 mouse embryonic gonads. ChIP-seq for H3K27ac was performed in duplicate on FACS-sorted  XX and XY gonadal suuported cells from E13.5 mouse embryonic gonads.

first: S

middle: A

last: Garcia-Moreno


title: Meg3 non-coding RNA expression controls imprinting by preventing transcriptional up-regulation in cis

city: Montpellier

first: Ildem

last: Sanli

address: 1919 Route de Mende

institute: IGMM - CNRS

summary: Although many long non-coding RNAs (lncRNAs) are controlled by genomic imprinting, their roles often remain unknown. The Dlk1-Dio3 imprinted domain expresses the lncRNA Meg3 (also called Gtl2) and multiple microRNAs and snoRNAs from the maternal chromosome. This locus constitutes an epigenetic model for pluripotency and development, particularly for neurogenesis. The domain’s Dlk1 (Delta-like-1) gene encodes a ligand that inhibits Notch1 signalling and regulates diverse developmental processes. Using a hybrid embryonic stem (ES) cell system, we find that Dlk1 becomes imprinted during neural differentiation and that this involves chromatin activation and transcriptional up-regulation on the paternal chromosome. On the maternal chromosome, the Dlk1 gene remains poised. This allelic protection against gene activation is controlled in cis by Meg3 expression and also involves the H3-lysine-27 methyltransferase Ezh2. Maternal Meg3 expression additionally protects against de novo DNA methylation at its promoter. Concordantly, we find that the lncRNA Meg3 is nuclear, accumulates onto the imprinted locus and overlaps in cis with Dlk1 in embryonic cells. Our data evoke an imprinting model in which a mono-allelic lncRNA prevents chromatin and gene activation in cis during development.

overall_design: RNA-Seq profiles of NPCs generated from WT ES cells (line BJ-WT3) and 2 different Meg3 KO ES lines (ES lines promoter-/- and intron1-/- derived from ES BJ-WT3) using Illumina HiSeq 2500 as 2 technical replicates.

first: Robert

last: Feil


title: A conserved transcriptional response to intranasal Ebola virus exposure in nonhuman primates before onset of fever

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

summary: Ebola Virus Disease (EVD), caused by the Ebola virus (EBOV), recently made headlines as it cause a large outbreak in West Africa killing more than 11,000 individuals. One aspect of an outbreak of this scale is understanding disease transmission and differences in the host response to infection. In animal models for disease, particularly non-human primate models of disease, a large infectious dose of 1000PFU through intramuscular injection results if a fairly uniformly lethal disease were the animals die after 6-9 days. However, this is not representative of actual transmission routes of infection as humans tend to have variable exposures through cuts and mucosal surfaces and have variable times to death. To determine if a low dose infection through a mucosal surface results in a different host response to infection, we infected 12 cynomologus macaques with 100PFU of EBOV-Makona (EBOV-Mak). To follow the host response to infection, we utilized RNA-Sequencing and a newly developed NanoString codeset to monitor changes in RNA transcripts. We found that despite different onset of disease and some animals presenting with delayed time to death, there was a highly conserved and predictable host response to infection. When animals were aligned based on onset of fever, the first clinical sign of severe disease, the host response to infection was able to be modeled showing a predictable pattern of gene expression with ISG appearing as early as 4 days before fever onset. Together, this shows that lethal EVD has a uniform and predictable response to infection and that expression of a subst of genes is present before the onset of fever.

overall_design: Whole blood RNA-Seq of 12 Cynomolgus Macaques infected through 2 routes (intranasal (IN) pipette (6) and IN MAD (6)) with EBOV Makona.

first: Sandra

last: Bixler

first: Louis

last: Altamura

first: Catherine

middle: E

last: Arnold

first: William

middle: D

last: Pratt

first: Cheryl

last: Taylor-Howell

first: Christina

last: Burrows

last: Aguilar

first: Franco

last: Rossi

first: Joshua

last: Shamblin

first: Suzanne

last: Wollen

first: Justine

middle: M

last: Zelko

first: Timothy

last: Minogue

first: Elyse

last: Nagle

first: Gustavo

last: Palacios

first: Arthur

middle: J

last: Goff

first: John

middle: H

last: Connor


title: Ligand-receptor co-evolution shaped the jasmonate pathway in land plants

city: Madrid

first: Gloria

middle: Garcia

last: Casado

state: Madrid

address: C/Darwin 3

department: Genomica

country: Spain

institute: CNB-CSIC

summary: Jasmonoyl-isoleucine regulates defence, growth and developmental responses in eudicots.  Bryophyte genomes have conserved sequences for all JA-Ile signalling pathway components, but in contrast to higher plants, the bioactive hormone has not been identified.  We show that the JA-Ile receptor COI1 is functionally conserved in the bryophyte Marchantia polymorpha, but responds to a different ligand.  Although Marchantia plants neither synthesize nor respond to JA-Ile, loss-of-function Mpcoi1 mutants have phenotypic defects reminiscent of COI1-dependent functions in Arabidopsis.  AtCOI1 functionally complements Mpcoi1 mutation and confers JA-Ile responsiveness on M. polymorpha, as does a single amino acid substitution in MpCOI1 that switches ligand specificity. Mass spectrometry quantification of cyclopentenone derivatives, bioactivity analysis and COI1-ligand interaction assays pinpointed two isomers of the JA-Ile precursor dinor-OPDA (dinor-cis-OPDA and dinor-iso-OPDA) as the natural MpCOI1 ligands.  Our results identify the ancestral jasmonate, confirm the functional conservation of its signalling pathway, and show that JA-Ile and COI1 emergence in higher plants from their ancestral counterparts required co-evolution of hormone biosynthetic complexity and receptor specificity.

overall_design: Six experimantal condition: 1_3 REPLICATES: Tak-2 treated 2 hours with OPDA 25µM (Experiment) vs Tak-2 mock (Control); 2_2 REPLICATES: Mutant Mpcoi1-2 treated 2 hours with OPDA 25µM (Experiment) vs mutant Mpcoi1-2 mock (Control); 3_3 REPLICATES: Mutant Mpcoi1-1 (Experiment) vs Tak-2 (Control)  treated both 2 hours with OPDA 25µM; 4_3 REPLICATES: Mutant Mpcoi1-2 (Experiment) vs Tak-1 (Control)  both treated  2 hours with OPDA 25µM; 5_3 REPLICATES: Tak-1 mechanical wounded (Experiment) vs Tak-1 Mock (Control); 6_3 REPLICATES: complemented line proMpEF:AtCOI1/Mpcoi1-1 treated  2 hours with 0.5 µMCOR (Experiment) vs Mutant Mpcoi1-1 (Control).

first: Isabel

last: Monte

first: Sakiko

last: Ishida

first: Angel

last: Zamarreño

first: Mats

last: Hamberg

first: José

last: Franco

last: García-Casado

first: Caroline

last: Gouhier-Nicolau

first: Philippe

last: Reymond

first: Kosaku

last: Takahashi

last: García-Mina

first: Ryuichi

last: Nishihama

first: Takayuki

last: Kohchi

first: Roberto

last: Solano


title: Gene expression biomarkers for neurobehavioral impairment from total sleep deprivation microarray data [D6]

city: Oklahoma City

first: Hilary

last: Uyhelji

state: OK

address: 6500 S. MacArthur Blvd.

department: Civil Aerospace Medical Institute

institute: Federal Aviation Administration

summary:
Healthy human adults were recruited to a sleep lab at Washington State University and remained there 7 consecutive days. Six received a well-rested Control condition of 10 h Time-In-Bed (TIB) nightly.
Another 11 subjects underwent Sleep Deprivation. They had a Baseline with 10 h TIB, followed by an Experimental phase of 62 h continued wakefulness, and finally two nights of 10 h TIB before dismissal. Blood draws on one Baseline day, one Experimental day, and one Recovery day were used for gene expression microarrays.

overall_design: Blood gene expression microarray data was compared between well-rested Control human subjects and a Sleep Deprived subject group. Furthermore the expression data was related to attention lapses as measured by the Psychomotor Vigilance Test. Three of the Sleep Deprivation subjects were characterized as fatigue resistant based on their PVT lapse profile; resistance was not determined for Control subjects.

first: Doris

last: Kupfer

first: Vicky

last: White

first: Dennis

last: Burian


title: HDAC1 and HDAC2 regulates TGF-b during Endothelial-to-Hematopoietic Transition

city: Manchester

first: Roshana

middle: S

last: Thambyrajah

address: Wilmslow Road

department: Stem Cell Biology

institute: CRUK Manchester

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


title: RNA sequencing (RNA-SEQ) of PSPC1 Knockout in A549 cells with TGFb1 stimulation

city: Taipei

first: HSI-Wen

last: Yeh

state: TAIWAN

address: Academia Sinica, No. 128

department: Institute of biomedical  science

country: Taiwan

institute: Academia Sinica

summary: We show that PSPC1 is required for cancer cell motilities and stemness properties in vitro and lung metastasis in vivo. We used high throughput sequencing to analyze the PSPC1 regulated gene expression. Loss of PSPC1 results in significant gene expression level changes in thousands of individual transcripts in key regulators of the EMT, CSCs and TGFb signaling.

overall_design: Methods: Gene expression profiles of PSPC1 knockout A549 cells were generated by Illumna RNA sequencing and compared to profiles derived from control cells with or TGFb1 stimulation  .

first: Hsi-Wen

first: Yuh-Shan

last: Jou


title: HDAC1 and HDAC2 regulates TGF-b during Endothelial-to-Hematopoietic Transition [ChIP-Seq]

summary: The first hematopoietic stem cells originate from hemogenic endothelium (HE), that trans-differentiate into the lumen to form hematopoietic clusters. The molecular mechanisms driving this transition are only poorly understood. Here, we present a complete and comprehensive study that shows the requirement for Transforming Growth Factor beta (Tgfbeta) signalling as the master regulator of triggering EHT from HE, including Runx1-/- HE. We employed RNA-Seq data on Hdac deficient HE, together with ChIP-Seq for HDAC1 and HDAC2 and on wild type HE that indicated its importance in EHT. We tested our findings extensively on HE derived from different sites/origin. In all instances we observed an increase in the frequency of EHT by decreasing Tgfbeta levels.

overall_design: ChIP-sequencing for Hdac1 and Hdac2 in HE populations derived from three different cell lines

first: Muhammad

middle: Z

last: Fadlullah

first: Martin

last: Proffitt

first: Shaun

last: Cowley

first: Valerie

last: Kouskoff

first: Georges

last: Lacaud


title: Chromatin accessibility based characterization of gene regulatory network of P. falciparum blood stage development

city: Nijmegen

first: Christa

last: Toenhake

state: Netherlands

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

summary: We present ATAC-seq combined with direction RNA seq data for eight time points across the intraerythorcytic development cycle of Plasmodium falciparum 3D7. ATAC peaks were called by MACS2 using ATAC-seq libraries generated with genomic DNA as a control. The majority of identified ATAC peaks were located in intergenic regions and captured most (95%) of previously identified binding sites of the transcription factor required for the expression of most invasion-related genes PfAP2-I (Santos et al., 2017).  The robustness of the ATAC-seq dataset was confirmed with a second biological replicate both in terms of peak location and relative peak accessibility pattern. Peaks were assigned to the closest gene and the majority of peaks showed a clear positive correlation between chromatin accessibility pattern and relative mRNA abundance (Pearson correlation > 0.6). In addition, they were sufficient to drive the stage-specific expression of a reporter gene, demonstrating their functionality. Motif searches restricted to accessible regions showed enrichment of several predicted Plasmodium motifs while also predicting several novel regulatory elements.

overall_design: ATAC-seq and RNA-seq at 8 time points across the intraerytrocytic development cycle of  P. falciparum 3D7 .

first: Richárd

last: Bártfai

middle: G

first: Sabine

last: Fraschka


title: Gene expression biomarkers for neurobehavioral impairment from total sleep deprivation microarray data [D9]


title: Effect of low-dose sorafenib and alkylating agents in inflammation and angiogenesis in breast cancer

status: Public on Apr 25 2018

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Molecular targeted compounds are emerging as important component to improve the efficacy of classical chemotherapeutics. In this study, we tested whether using low dose sorafenib to reduce off target inhibitions of kinases impacts the antitumor effect of alkylating agents in breast cancer models.

overall_design: MDA-MB231 cells were treated with 1 μM sorafenib, 40 μg/mL MMS, or pre-incubated with 1 μM sorafenib for 12 h followed by 40 μg/mL MMS, each in two independent experiments. RNA was harvested 8 and 24 h, or post MMS treatment for combination treatment.

first: Alfeu

last: Zanotto-Filho

first: Aparna

last: Gorthi

first: Alexander

last: Bishop


title: Preclinical studies on Orientin, as a countermeasure against radiation injury

city: Columbus

first: NADUPARAMBIL

middle: Korah

last: JACOB

state: Ohio

address: 410 W 12th Ave

department: Radiation Oncology

institute: The Ohio State University

type:
Expression profiling by array
Other

summary: Effects of radiation and Orientin in expression genes in bone marrow.

overall_design: Radiation Treatment:C57BL/6 male mice (8-10 weeks old) were divided into four groups: Irradiated control (IR); Orientin+Irradiated (ORI+IR);Vehicle treated and unirradiated (CT) mice and Orientin alone treated mice (ORI). Unanesthesized mice were exposed to 6Gy TBI (gamma rays) at a dose rate of 0.95Gy/min. Orientin was administered subcutaneously at 5mg/kg body weight in 150µl volume/mouse 24h and 3h pre irradiation while untreated control animals received PBS alone. Gene expression: An amplification-free, hybridization based direct digital counting method developed by NanoString Technologies was used for gene expression analysis using mouse cancer immune panel (NS_Mm_CancerImm_C3400). RNA was extracted from bone marrow cells on day 9 after irradiation using Ambion miRVANA kit and a digital multiplexed Nanostring nCounter gene expression assay was performe. Raw data from the NanoString assays were technically normalized followed by biological normalization with a set of 20 housekeeping genes.

first: Marshleen

last: Yadav

first: Feifei

last: Song

first: Arnab

last: Chakravarti

first: Naduparambil

last: Jacob


title: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons

city: London

first: Alex

last: de Mendoza

address: Mile End Road. Fogg Building 5.14

department: School of Biological and Behavioural Sciences

institute: Queen Mary University of London

summary: Transposable elements are entangled in a constant evolutionary arms race with their host genomes, constantly evolving ways to evade host silencing mechanisms. One silencing mechanism used by many distantly related eukaryotes is dependent on cytosine methylation, an epigenetic mark deposited by C5 cytosine methyltransferases (CMTs). Therefore, it is expected transposable elements would acquire mechanisms to escape from being targeted by cytosine methylation. Here we report how two distantly related eukaryotic lineages have incorporated CMTs into the coding regions of distinct retrotransposon classes. Three of these events have occurred in the dinoflagellates of the genus Symbiodinium, where these CMT-encoding retrotransposons show hundreds of insertions. In a case of convergent evolution, the charophyte Klebsormidium nitens shows an independent expansion of CMT encoding retrotransposons. Concomitantly, we find that Symbiodinium genomes show cytosine methylation patterns unlike any other eukaryote with most of the genome hypermethylated in CpGs, while targeted CH methylation accumulates on transposable elements. Similarly, K. nitens shows CHH and CHG targeted methylation on repressed transposable elements, while CpG methylation is concentrated in gene bodies and transposable elements. Furthermore, we demonstrate the ability of retrotransposon CMTs to de novo methylate CpGs, indicating a putative role in mimicking retrotranscribed DNA as host active genomic DNA. Our results show an unprecedented example of how retrotransposons incorporate host-derived genes involved in DNA methylation as a source of adaptation to their host epigenomic environments.

sample_organism:
Saccharomyces cerevisiae
Symbiodinium kawagutii
Klebsormidium nitens
Symbiodinium sp. clade B

overall_design: Profiling of gene expression and cytosine methylation of Symbiodinium kawagutii and Symbiodinium minutum in two temperature treatments. Profiling of cytosine methylation of Klebsormidium nitens in vegetative growth. Profiling of cytosine methylation of transformant budding yeast lines in duplicates.

first: Ryan

last: Lister


title: Comprehensive Analysis of RDR1/2/6-independent Small RNAs in Arabidopsis thaliana

status: Public on Apr 09 2018

city: University Park

first: Michael

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

summary: Plant small RNAs (sRNAs) regulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. sRNAs fall into two major categories: those that are reliant on RNA Dependent RNA Polymerases (RDRs) for biogenesis and those that aren’t. Known RDR-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR-independent sRNAs are primarily microRNAs (miRNAs) and other hairpin-derived sRNAs. In this study, we produced and analyzed sRNA-seq libraries produced from rdr1/rdr2/rdr6 triple mutant plants.  We found 58 previously annotated MIRNA loci that were dependent on RDR function, casting doubt on their classification as MIRNAs.  We also found 38 RDR-independent sRNA clusters that were not MIRNAs or otherwise hairpin-derived. These 38 sRNA loci have novel biogenesis mechanisms, and frequently arise from protein-coding genes.  Altogether, our analysis suggests that these 38 sRNA loci represent one or more new types of sRNA loci in Arabidopsis thaliana.

overall_design: Small RNA sequencing from Arabidopsis thaliana wild-type (Col-0 ecotype) and rdr1-1/rdr2-1/rdr6-15 triple mutant inflorescences

first: Seth

last: Polydore

first: Ceyda

last: Coruh


title: Gene expression biomarkers for neurobehavioral impairment from total sleep deprivation microarray data [D8]

first: Hilary

last: Uyhelji

first: Doris

last: Kupfer

first: Vicky

middle: L

last: White

first: Dennis

last: Burian


title: DNA accessibility in reactive and non-reactive CMV specific CD8+ lymphocytes

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

summary: Poor immune reconstitution following haematopoietic stem cell transplantation (HSCT) can cause unwanted and harmful sequelae in recipients with chronic cytomegalovirus (CMV) infection. To understand the molecular mechanisms underlying poor reconstitution, we profiled the transcriptome-chromatin accessibility landscape of CMV-specific CD8+ memory lymphocytes from HCST recipients with different reconstitution efficiencies. Although the transcriptional and epigenomic signatures in non-reactive lymphocytes were not naïve or classic ‘exhaustion’ profiles, some gene expression was common to lymphocytes from other non-resolving infections. Reactive lymphocytes expressed higher levels of interferon/defence response and cell cycle genes in an interconnected network involving PI3KCG, STAT5B, NFAT, RBPJ, and NR3C1, increasing chromatin accessibility at the enhancer regions of immune and T cell receptor signalling pathway genes. We propose that increased HDAC6 expression in non-reactive lymphocytes decreases accessibility at particular enhancers including PI3KCG. Non-reactive cells also expressed higher levels of EGR and KLF factors that, along with lower expression of JARID2, maintained higher accessibility at promoter and CpG-rich regions of genes associated with apoptosis. Together, transcription factors and chromatin modulators create a different chromatin accessibility landscape in reactive and non-reactive cells that not only affects immediate gene expression but differentially primes the cells for responses to additional signals.

overall_design: 3 (each pooled from 4 donors) biological samples were analysed by FAIRE-seq with a mixed total input.

first: Candice

last: Lee

first: Wen

last: Tu

first: Sudha

last: Rao

first: Corey

last: Smith

first: Rajiv

last: Khanna


title: Next Generation Sequencing upon siRNA-mediated knockdown of EIF5A in MCF-7 cells.

city: Copenhagen N

first: Imke

last: Tiessen

address: Ole Maaløes Vej 5

department: Biotech Research and Innovation Centre (BRIC)

country: Denmark

institute: University of Copenhagen

summary: The goal of this study is to examine the effect of EIF5A knockdown on the MCF-7 transcriptome.

overall_design: MCF-7 total RNA profiles upon siRNA-mediated knockdown of EIF5A or using a control siRNA (siCTRL) were generated by deep sequencing, in triplicate, using the Illumina TruSeq kit (RPHMR12126). Library products were sequenced on the Illumina NextSeq500 platform.


title: Transcriptomic profile of the retinal ganglion cell type J-RGC

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: The goal of this experiment was to identify markers and potential regulators of J-RGC development.

overall_design: J-RGCs were labeled with Green Fluorescent Protein using a J-RGC specific transgenic line and isolated by magnetic beads and flow cytometry. Two biological replicates from different litters, consisting of 5-6 animals each, were collected. RNA was extracted and libraries prepared for illumina sequencing.

first: Joshua

last: Sanes


title: Molecular Signature of Hepatitis D Virus-Associated  Hepatocellular Carcinoma

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

country: Italy

institute: University of Cagliari

summary: To investigate the role of viral and host factors in HDV-associated HCC we carried out an integrated clinicopathological and gene expression study of tissue specimens and laser microdissected hepatocytes obtained at the time of liver transplantation from livers with HDV-HCC, HDV-cirrhosis without HCC, HCV-HCC and HBV-HCC. References to GSM series of HDV and HBV livers, already deposited in GEO, are included in this series. Part of data of HCV livers are a re-analysis of GSE series GSE69715 and GSE78737, the re-analyzed GSM is indicated in the 'description' column and with a link at the bottom of the page.

overall_design:
Multiple liver specimens and serum were obtained from   5 male patients, aged 57.2 ± 3 years (mean ± SEM) with HDV-HCC, who underwent liver transplantation for tumor (re-used from GSE98383);   7 patients, aged of 55.8 ±1 years, with HDV non-HCC cirrhosis who underwent liver transplantation for end-stage liver disease (re-used from GSE98383);  11 patients, 1 female and 10 males, aged 56.7 ± 4 years with HCV-HCC, who underwent liver transplantation for tumor;   11 male patients aged 59.6 ± 2 years with HBV-HCC , who underwent liver transplantation for tumor, and were the object of a recent study (Melis et al., 2014. J Transl Med, 12, 230. doi: 10.1186/s12967-014-0230-1; reused from GEO accession GSE55092).

A data matrix with the log2 RMA data for all 307 samples is available on the series record.

first: Ronald

last: Engle

first: Ashely

last: Tice

first: Marta

last: Melis

first: Stefania

last: Montenegro

first: Jaime

last: Rodriguez-Canales

first: James

last: Hanson

last: Emmert-Buck

first: Ian

middle: N

last: Moore

first: Kevin

last: Bock

first: Fausto

last: Zamboni

first: Sugantha

last: Govindarajan

first: David

last: Kleiner

first: Patrizia

last: Farci


title: Interaction of neutrophils and hepatic stellate cells promotes fibrosis in a mouse model of steatohepatitis

city: Rockville

first: Ming-Jiang

last: Xu

state: MD

address: 5625 Fishers LN, 2S12

department: NIAAA

institute: NIH

summary: Our current study proved a synergistic effect of obesity and binge drinking on liver fibrosis, which is partially mediated via the interaction of neutrophils and HSCs. Controlling the infiltration of neutrophils as well as the interplay between neutrophils and HSCs may be a novel therapeutic intervention to prevent liver fibrosis in steatohepatitis.

overall_design: Four-condition experiment, Chow+maltose, Chow+one binge, HFD+maltose, HFD+one binge

first: Zhou

last: Zhou

first: Xu

last: Mingjiang

first: Cai

last: Yan

first: Gao

last: Bin


title: Differentially expressed miRNA in biological premature ovarian insufficiency (bPOI)

city: Jinan

first: Yujie

last: Dang

address: 157 Jingliu Road

institute: Center for Reproductive Medicine, Shandong University.

summary: We first examined changes of miRNAs and expression using microarrays ( Exiqon miRCURY™ microarray LNA v.18.0) of GCs from 10 bPOI and 10 age and BMI matched normal control women. Seventy-five miRNAs (Fold Change [FC]>2, P<0.05) were identified differentially expressed between bPOI patients and control women.

platform_organism:
Homo sapiens
Human alphaherpesvirus 1
Human alphaherpesvirus 2
Cytomegalovirus
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: Our study is designed to demonstrate altered profiles of miRNAs in the granulosa cells from patients with bPOI. Functional studies will be further confirmed. This study will provide new viewpoint for understanding the roles of non-coding RNA for GCs function, as well as potential etiologic mechanism for POI.


title: SLEAR predisposes to systemic lupus erythematosus by regulating apoptosis [ChIRP-Seq]

city: Beijing

first: Xiaowei

last: Chen

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, CAS

summary: Systemic lupus erythematosus (SLE) is an autoimmune disease, and affects all parts of the human body. Genome-wide association studies have been employed to identify susceptibility genes of SLE. However, most of the SLE associated variants are located in the noncoding regions of the human genome.We characterized SLE risk variants in Chinese populations. One of the most significant validated SNP was located in a gene which we named SLEAR. We found SLEAR was enriched in the nucleus and could regulate apoptosis. Apoptosis is a highly regulated process. And misregulation of the process could lead to autoimmune diseases, especially SLE. Our results suggest that the SLEAR plays a key role in apoptosis regulation and is associated with SLE predisposition.

overall_design: ChIRP-seq in Jurkat (input, lacZ, odd and even libraries)

first: Zhen

last: Fan


title: Differential effects of estrogen receptor beta isoforms on glioblastoma progression

first: Yidong

summary: We examined the transcriptional changes modulated by knocking out ERβ and reintroduction of ERβ1 and ERβ5 isoforms by perfroming global transcriptome analysis. ERβ was knocked out in U87 cells using CRISPR/Cas9 system and reintroduced the ERβ1 and ERβ5 isoforms in knockout background. RNA was isolated from control U87, U87-ERβ-KO, U87-ERβ1 and U87-ERβ5 cells and utilized for RNA-seq analysis. Our results demonstrated that ERβ-KO, ERβ1 and ERβ5 modulated unique pathways  including NF-κB singaling, Jak/STAT pathway and mTOR signaling.

overall_design: Total RNA was isolated from U87 control, U87-ERβ-KO, U87-ERβ1 and U87-ERβ5 cells. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicates. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

last: Sareddy

first: Ratna

middle: K

last: Vadlamudi


title: Pseudouridylation of tRNA-derived fragments steers translation control in stem cells [Polysome-Seq]

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Pseudouridylation (pseudouridine) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of pseudouridine remains poorly understood. Here, we show that a pseudouridine-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the pseudouridine ‘writer’ PUS7 modifies and activates a network of tRNA-derived fragments (tRFs) targeting the translation initiation complex. PUS7 inactivation in embryonic stem cells impairs tRF-mediated translational regulation leading to high protein biosynthesis and abnormal germ layer specification. Dysregulation of PUS7 and tRFs in myeloid malignancies associates with altered translation rates, suggesting a role of pseudouridine in tumorigenesis. Our findings unveil a critical function of pseudouridine in directing translational control in stem cells with promisingly broad implications for human disease.

overall_design: Polysome Profiling of samples

first: Nicola

last: Guzzi

first: Maciek

last: Cièsla

first: Stefan

last: Lang

first: Marios

last: Dimitriou

first: Roberto

last: Munita

first: Michal

last: Lubas

first: Kazuki

last: Okuyama

first: Anders

last: Lund

first: Göran

last: Jonsson

first: Jörg

last: Cammenga

first: Shamit

last: Soneji

first: Mikael

last: Sigvardsson

first: Eva

last: Hellström-Lindberg

first: Andrew

last: Hsieh

first: Cristian

last: Bellod


title: MINIYO and QUATRE-QUART 2 Are Required for the Assembly of RNA Polymerase V in Arabidopsis

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

summary: RNA polymerases IV and V (Pol IV and Pol V) are plant-specific polymerases required for the generation of noncoding RNAs in RNA-directed DNA methylation (RdDM) and transcriptional gene silencing. Their subunit compositions largely resemble that of Pol II. However, the mechanism and accessory factors involved in their assembly remain largely unknown. In this study, we performed a forward genetic screen and identified novel mutant alleles of MINIYO (IYO), QUATRE-QUART 2 (QQT2) and NUCLEAR RNA POLYMERASE B/D/E 11 (NRPB/D/E11) that are defective in RdDM. We found that Pol IV-dependent small interfering RNAs (siRNAs) and Pol V-dependent transcripts were greatly reduced in the mutants. NRPE1, the largest subunit of Pol V, dissociated from other Pol V subunits in the iyo and qqt2 mutants, suggesting the involvement of IYO and QQT2 in Pol V assembly. Furthermore, we found that IYO and QQT2 were mutually dependent for their binding to the NRPE3 subassembly to facilitate the assembly of Pol V holoenzyme. Our findings reveal IYO and QQT2 as cofactors for Pol V assembly and provide mechanistic insights into how RNA polymerases are assembled in Arabidopsis.

overall_design: To investigate the effects of iyo-4, qqt2-2 and nrpb/d/e11-1 mutations on Arabidopsis DNA methylome, we carried out whole genome bisulfite sequencing. The destabilization of AGO4 in the iyo-4, qqt2-2 and nrpb/d/e11-1 mutants suggests that IYO, QQT2 and NRPB/D/E11 could be required for the production of 24-nt siRNAs. To test this, we performed small RNA deep sequencing analysis.

first: Yaoxi

last: Li

first: Yuxiang

last: Yuan

first: Xiaofeng

last: Fang

first: Xiuli

last: Lu

first: Bi

last: Lian

first: Gaozhan

last: Zhao

first: Andrzej

last: Wierzbicki


title: SLEAR predisposes to systemic lupus erythematosus by regulating apoptosis

first: Xiaowei

last: Chen

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

overall_design: Refer to individual Series


title: Exploring gene expression biomarker candidates for neurobehavioral impairment from total sleep deprivation

city: Oklahoma City

first: Hilary

last: Uyhelji

address: 6500 S. MacArthur Blvd.

institute: Federal Aviation Administration


title: Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma

first: Giacomo

last: Diaz

summary: To investigate the role of viral and host factors in HDV-related HCC we analyzed the serum, tissue specimens and laser microdissected hepatocytes obtained at the time of liver transplantation from five patients with HDV-HCC. Livers of seven patients with HDV-cirrhosis without HCC were also analyzed. We carried out an integrated clinicopathological analysis and gene expression profiling,

overall_design: Multiple liver specimens and serum were obtained from 5 male patients, aged 57.2 ± 7.8 years (mean ± SD) who underwent liver transplantation for HDV-associated HCC, and 7 patients, aged of 55.8 ± 2.1 years, with HDV non-HCC cirrhosis who underwent liver transplantation for end-stage liver disease. The study also included data of 11 male patients with HBV-associated HCC, aged 59.6 ± 8.0 years, that were the object of a recent investigation (Melis et al., 2014. J Transl Med, 12, 230. doi: 10.1186/s12967-014-0230-1; GSE accession no.55092).

first: Ronald

last: Engle

first: Ashely

last: Tice

first: Marta

last: Melis

first: Stefania

last: Montenegro

first: Jaime

last: Rodriguez-Canales

first: James

last: Hanson

first: Mike

last: Emmert-Buck

first: Kevin

middle: W

last: Bock

first: Ian

last: Moore

first: Fausto

last: Zamboni

first: Sugantha

last: Govindarajan

first: David

last: Kleiner

first: Patrizia

last: Farci


title: Genotype x Environment approaches provide insights into genotype-specific grapevine transcriptomic plasticity

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

institute: University of Udine

summary:
A dissection of Genotype x Environment interactions in grapevine berry using a multi-layered -omics approach
Grapevine, the most widely-cultivated perennial fruit crop, is also considered a very environmentally sensitive crop. It is characterized by remarkable phenotypic plasticity which in turn is believed to effectively buffer environmental extremes especially through transcriptomic and epigenomic reprogramming. Thus, the final phenotype (P) of a given vine is the result of the close interaction between its genetic composition (G) and the environment (E).  Here we analyzed Genotype x Environment (GxE) interactions in two grapevine varieties by characterizing their transcriptome plasticity when cultivated in different environments. Specifically, two genotypes (Sangiovese and Cabernet Sauvignon) were cultivated in three different locations in Italy (Bolgheri -littoral Tuscany-, Montalcino – Appennine Tuscany- and Romagna -foothill area-), trained in an almost identical manner, and sampled at four developmental stages over two grapevine growing seasons, 2011 and 2012, for a total of 144 samples that were analyzed by hybridization to a whole-genome microarray and by Reduced Representation Bisulfite Sequencing (RRBS-seq).  In order to study the relationships among differential gene expression profiles and environmental cues, we have developed a new statistical data mining tool based on  data reduction approaches which allowed a dissection of the transcriptomic data into stage-specific, cultivar-related and GxE important clusters of gene expression.  This deep inspection of inner relationships between the different dataset variables allowed the identification of several candidate genes that could represent putative markers of berry quality traits in grapevine GxE interactions. Moreover, the methods used to establish our model provide a framework for the analysis of transcriptome plasticity in other crops as they respond to diverse environments.

overall_design: Vitis vinifera berries from Sangiovese and Cabernet Sauvignon cultivars were harvested at four different developmental stages (i.e., pea size (PS), pre-veraison (PV), mid-ripening (MR) and fully ripe (FR)), in three central Italian locations (i.e., Bolgheri in the Tuscany coast, Montalcino in the Tuscany Appennines and Riccione in the Adriatic coast) (Fig. 1a, Supplementary Tables 1-2) during two consecutive growing seasons (2011 and 2012) in biological triplicates for a total of 144 samples. Forty-eight of these samples, corresponding to two developmental stages (i.e. pre-veraison (PV) and mid-ripening) and two biological replicates were analyzed by Reduced Representation Bisulfite Sequencing (RRBS-seq) to provide genome-wide DNA methylation data.

first: Silvia

last: Dal Santo

first: Sara

last: Zenoni

first: Marco

last: Sandri

first: Gabriella

last: De Lorenzis

first: Gabriele

last: Magris

last: DePaoli

last: Di Gaspero

first: Cristian

last: Del Fabbro

first: Michele

last: Morgante

first: Lucio

last: Brancadoro

first: Mara

last: Rossoni

first: Marianna

last: Fasoli

first: Paola

last: Zuccolotto

first: Mario

last: Pezzotti


title: Screening for lincRNAs in C2C12 cells [array_differentiation]

status: Public on Apr 06 2018

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

institute: Aalborg University

summary: We screened for long intergenic non-coding RNAs (lincRNAs) that are highly and specifically expressed in the murine myoblast cell line C2C12 during the differentiation process.

overall_design: Using C2C12 cells, we performed microarray experiments (n=1) for 4 time points.

first: Yuliya

last: Ponomareva


title: A New Family of Vertebrate Specific Polycomb Proteins Encoded by the LCOR and LCORL Gene Loci Reveal Antagonism Between PRC2 Subtypes

status: Public on Apr 05 2018

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: The Polycomb Repressive Complex 2 (PRC2) is composed of core subunits SUZ12, EED, RBBP4/7 and EZH1/2, which together are responsible for all di- and tri- methylation of lysine 27 on Histone H3 (H3K27me2/3) in higher eukaryotes. While two distinct forms, PRC2.1 (containing one Polycomb-like protein) and PRC2.2 (containing AEBP2 and JARID2) exist, little is known about their differential functions or interplay. Here we report the discovery of a new family of vertebrate specific PRC2.1 associated proteins; ‘PRC2 associated LCOR isoform 1’ (PALI1) and PALI2, encoded by the LCOR and LCORL gene loci, respectively. PALI1 promotes PRC2 methyltransferase activity in vitro and in vivo and is essential for mouse development. We uncover an antagonistic relationship between the PALI-PRC2.1 and AEBP2-PRC2.2 subtypes and establish that both are required for balanced regulation of Polycomb target genes during differentiation. This discovery links the Polycomb epigenetic system with co-repressors and nuclear receptors in the regulation of cellular identity.

overall_design: RNA seq analysis of Pali WT, Pali1 KO, Pali1/2 double KO, C129 WT and Aebp2 gene trap mouse embryonic stem cells at three time points (Day 0, Day 4 and Day 8) during embryoid body differentiation (EB). 30 samples are included. Biological duplicates are present.

first: Eric

last: Conway

first: Emilia

last: Jerman

first: Evan

last: Healy

first: Shinsuke

last: Ito

first: Daniel

last: Holoch

first: Orla

last: Deevy

first: Eleanor

last: Glancy

first: Giorgio

last: Oliviero

first: Ariane

last: Watson

first: Alan

last: Rice

first: Marlena

last: Mucha

first: Indigo

last: Pratt-Kelly

first: Yoko

last: Koseki

first: Manabu

last: Nakayama

first: Tomoyuki

last: Ishikura

first: Gundula

last: Streubel

first: Kieran

last: Wynne

first: Karsten

last: Hokamp

first: Aoife

last: McLysaght

first: Luciano

last: Di Croce

first: Raphael

last: Margueron

first: Gerard

last: Cagney

first: Haruhiko

first: Adrian

middle: P

last: Bracken


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and o11 mutant Transcriptomes

city: Shanghai

first: Fan

last: Feng

address: 333 Nanchen Road

institute: Shanghai University

summary: Analysis of gene expression level. The hypothesis tested in the present study was that o11 mutant affects nutrient metabolism and stress response.

overall_design: Endosperm mRNA profiles of 15 DAP wild type (WT) and o11 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

first: Weiwei

last: Qi


title: Viral shRNA Knockdown of INS Promotor Activity in EndoC-βH1 Cells

city: Bethesda

first: Gary

last: Felsenfeld

address: 5 Memorial Drive, Room 212

department: NIDDK

institute: National Institutes of Health

summary: To inhibit INS expression, we used shRNA to target the INS promoter. We find that knocking down INS expression with such an shRNA targeting the INS promoter significantly affects expression of 259 genes.

overall_design: mRNA profiles of EndoC βH1 with or without shRNA targetting INS promoter were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

first: Xing

last: Jian


title: Genome-wide maps of chromatin state in EndoC-βH1 Cells

summary: We report the actively transcribed chromatin regions in EndoC-βH1 Cells that are associated with histone H3 lysine 27 acetylation mark.

overall_design: Examination the histone modification H3K27Ac in EndoC-βH1 Cells by deep sequencing, in triplicate, using Illumina Hiseq 2500.


title: 4C-seq of insulin promoter, knockdown of INS promoter activity and Genome-wide maps of chromatin state in EndoC-βH1 Cells


title: 4C-seq of insulin promoter

summary: We report the 4C (Circularized Chromosome Conformation Capture)-seq data of insulin promoter in EndoC βH1 and HeLa cells.

overall_design: 4C-seq data from 2 cell lines with three biological replicates each

last: felsenfeld


title: SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

city: Vienna

first: Matthias

last: Muhar

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute for Molecular Pathology


title: NGS of virus derived small RNAs as a diagnostics method used to determine viromes of Hungarian vineyards

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

institute: HUN-REN Institute of Experimental Medicine

summary: As virus diseases cannot be controlled by traditional plant protection methods the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomics approaches used for virus diagnostics, offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, why their usage can reduce the risk of using infected material for a new plantation. Here we used a special field, deep sequencing of virus derived small RNAs, of this high throughput method for virus diagnostics and determined viromes of vineyards in Hungary. With NGS of virus derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which have never been described in Hungary before. Virus presence didn’t correlated with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections mostly caused by the usage of infected propagating material. Our results, validated by other molecular methods, highlighted further questions to be answered before these method can be introduced as a routine, reliable test for grapevine virus diagnostics.

overall_design: Samples were collected from 14 vineyards representing 18 different varieties and 9 wine growing-regions at different locations of Hungary. Shoots of 1-10 randomly chosen individual plants per plantation were collected on the field or from forced canes. RNA was extracted from different organs: shoot tips, young leaves (until the 3rd internodes from the soot apex), older leaves (lower than the 3rd internodes), tendrils and flowers by CTAB method (Gambino, 2008). RNA pools representing each plant were generated mixing equal content of RNA originated from different organs. This individual plant RNA pools (library 14-18) or a plantation pool generated by the same strategy, representing all of the sampled plant from the same plantation (library 1-13), was used for small RNA library preparation (18 libraries in total

first: Nikoletta

last: Czotter

first: Janos

last: Molnar

first: Emese

last: Szabo

last: Demian

first: Levente

last: Kontra

first: Ivett

last: Baksa

first: Gyorgy

last: Szittya

first: Laszlo

last: Kocsis

first: Tamas

last: Deak

last: Bisztray

first: Gabor

last: Tusnady

first: Jozsef

last: Burgyan

first: Eva

last: Varallyay


title: Influence of deficiency in mevalonate kinase (MVK) on wide gene expression in Saccharomyces cerevisiae

city: Recife

first: Marcos

middle: Antonio

last: Morais

state: Pernambuco

address: Av. Moraes Rego, 1235

department: Department of Genetics

country: Brazil

institute: Federal University of Pernambuco

summary: Periodic fever syndrome is a disease that affects children mainly in the Mediterranean region, which has as one of the typical conditions of inflammation generalized by the body that can spontaneously regress. It has already been established that this pattern is presented by individuals carrying a mutant allele of the gene encoding the enzyme mevalonate kinase (MVK). This gene has an ortholog in the yeast Saccharomyces cerevisiae (ERG12) and mutations in this genes show phenotype that resemble those of the cells of these individuals. The present work aims to use this yeast as a biological model to analyze the role of the ERG12 gene (MVK) in the development of the disease. In this experiment, we used a wild type strain for the enzyme Erg12 (wt) and a genetically modified strain that decreases the activity of this enzyme (erg12-d) to 10%. The cells were cultured in synthetic medium containing glucose (reference medium) and each was re-inoculated and synthetic medium containing glucose or glycerol (erg12-d cells have growth deficiency in glycerol). By attaining D.O. value around 0.5 (600nm), the cells were collected for total RNA extraction and this was subjected to double-labeled microarray analysis in four combinations: erg12-d/wt and glycerol/glucose.

overall_design:
A MVK-positive parental strain and a MVK-deficient Damp mutant (showing 10% of parental enzyme activity) were cultivated in synthetic YNB medium containing glucose to mid-exponential growth phase, collected, washed and suspended in YNB containing glucose or glycerol as carbon source. After one hour of incubation, cells were collected for total RNA extraction. Following cRNA synthesis and labelling by two-color method, slides were hybridised and scanned. Two arrays, corresponding to biological duplicate, were used for each sample combination: parental glycerol (Cy5, test) x parental glucose (Cy3, reference); Damp glycerol (Cy5, test) x Damp glucose (Cy3 reference); Damp glucose (Cy5, test) x parental glucose (Cy3, reference); Damp glycerol (Cy5, test) x parental glycerol (Cy3, reference). Internal reference included RNA spike.

Please note that there are two biological replicates for each sample comparison (ie.g. two raw data files per sample). However, the replicate data were combined and normalized together, resulting in 4 sample records.

first: Manuela

last: Santos

first: Rafael

middle: B

last: deSouza

first: Carolina

last: Elsztein

first: Sérgio

last: Paiva Jr

first: Will

last: de Barros Pita

first: Jaqueline

middle: A

last: SIlva

last: de Morais Jr


title: SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis [SLAM-seq]

first: Matthias

last: Muhar

summary: Defining direct targets of transcription factors and regulatory pathways is key to understanding their role in physiology and disease. Here we combine SLAM-seq, a novel method for direct quantification of newly synthesized mRNAs, with pharmacological and rapid chemical-genetic perturbation to interrogate primary transcriptional targets of BRD4 and MYC and define the response to BET bromodomain inhibitors (BETi). While BRD4 acts as a global co-activator of Pol2-dependent transcription in a BET bromodomain-dependent manner, therapeutic BETi doses deregulate a small set of hypersensitive target genes. In contrast to BRD4, MYC primarily acts as a selective transcriptional activator that controls basic metabolic processes such as ribosome biogenesis and de-novo purine synthesis across diverse cancer contexts. Beyond defining primary regulatory functions of BRD4 and MYC in cancer, our study establishes a simple, robust and scalable approach to dissect direct transcriptional targets of any gene or pathway.

overall_design: Baseline gene expression profiling of clonal cell lines engineered to express AID-tagged proteins and unedited controls by 3'mRNA sequencing.

first: Anja

last: Ebert

first: Tobias

last: Neumann

first: Christian

last: Umkehrer

first: Corinna

last: Wieshofer

first: Anna

middle: C

last: Obenauf

first: Johannes

last: Popow

first: Stefan

last: Ameres

last: Zuber


title: Comprehensive immunoproteogenomic analyses of malignant pleural mesothelioma

city: HOUSTON

first: Hyun-Sung

last: Lee

state: TX

address: One Baylor Plaza

department: Surgery

institute: BAYLOR COLLEGE OF MEDICINE

summary: We characterized tumor and immune microenvironment (TiME) of malignant pleural mesothelioma (MPM) using immunoproteomic approach to comprehensively understand the landscape to affect prognosis and possibly to predict response to immunotherapy.  Time-of-Flight Mass Cytometry (CyTOF) was performed on the tumors of 12 MPM patients. We comprehensively analyzed TiME by developing intuitive models for visualizing single-cell data with statistical inference and performed unsupervised clustering of cell frequency. A clinically relevant protein signature through mass spectrometry and mRNA transcriptome array was tested for its ability to reflect prognosis in three independent cohorts (n=330) and to predict response to immune checkpoint inhibitor therapy in publicly available data and in 10 patients of MPM treated with anti-PD1 therapy. A systematic understanding of antitumor immunity by immunoproteomic characterization of TiME envisions significant progress in developing rational immunotherapeutic strategies in MPM.

overall_design: Pre-clinical study

first: Hee-Jin

last: Jang

first: Bryan

last: Burt


title: Identification of  target genes of Arabidopsis NIGT1 subfamily members  (AtNIGT1s)

city: Yokohama

first: Takatoshi

last: Kiba

state: Kanagawa

address: Suehiro 1-7-22

department: CSRS

institute: RIKEN

summary:
Nitrogen (N) is a key nutrient that is often the limiting factor in plant growth. However, the molecular mechanisms underlying transcriptional regulation of N-starvation-responses remain largely unknown.
AtNIGT1s are putative regulators of nitrogen-starvation responsive transcriptome in arabidopsis. We aimed to identify AtNIGT1s target genes by microarray experments.

overall_design: AtNIGT1.2 overexpressor and AtNIGT1.2-VP overepxressor were subjected to microarray analysis to identify Direct Target genes.

first: Hitoshi

last: Sakakibara


title: Gene expression profiling in Hepa1c1c7 transfected Mst1r or Slpi

status: Public on Apr 04 2018

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

institute: National Institute for Environmental Studies

summary: To analysis Mst1r and slpi function as a tumor associated gene, we carried out overexpression analysis of Mst1r or Slpi to Hepa1c1c7 and  investigated downstream genes expression by microarray.

overall_design: We measured gene expression levels of Hepa1c1c7 transfected Mst1r or Slpi.  We identified Il33 that increasing in Hepa1c1c7 overexpressed Mst1r.


title: Single cell RNA sequencing data of bone marrow lymphoid progenitors

city: Freiburg im Breisgau

first: Josip

middle: Stefan

last: Herman

address: Stuebeweg 51

department: Quantitative Single Cell Biology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Using different surface markers it has been possible to isolate lymphoid lineage-biased progentors and test their potential in vivo and in vitro. Here we apply single cell sequencing of lymphoid progenitors to obtain further insights into differentiation and commitment to the lymphoid lineage.

overall_design: Single cells  from the bone marrow from various stages during lymphoid differentiation were sorted into 384-well plates based on their surface marker expression of Flt3, Sca-1 and c-Kit  and processed using a modified version of the CEL-Seq2 protocol (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8). In addition the original version of the CEL-Seq2 protoco and thel modified versions with different volume reductions and were compared using murine embryonic stem cells.

last: Sagar

first: Dominic

last: Grün


title: TP53INP2 knockout in perigonadal and inguinal white adipose tissue

status: Public on Apr 03 2018

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)


city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

country: USA

institute: Baylor College of Medicine

summary: To determine if ERG expression and PTEN loss were sufficient to transform prostate epithelial cells we constructed cell lines with expression of the TMPRSS2/ERG fusion gene (TE), stable knockdown of PTEN with shRNA (PTEN KD) or both alterations (PTEN KD/TE) using the PNT1A cell line. To determine what gene expression changes are associated the phenotypic changes between the cell line experimental groups, we carried expression microarray studies using Agilent 60K expression microarrays. RNAs from all four cell lines were analyzed in duplicate and probes with ≥ 1.4-fold or ≤0.7-fold relative to control cells identified. Our results demonstrated that PTEN loss and expression of the TMPRSS2/ERG fusion gene transform prostatic epithelial cells via enhanced FGF signaling.

overall_design: Microarray analyses of four cell lines (PA, PA-TE, PA-PTEN KD and PA-TE+PTEN KD).

first: Longjiang

last: Shao

first: Jianghua

last: Wang

first: Yiqun

last: Zhang

first: Michael

last: Ittmann


title: PTCD1 is required for 16S rRNA maturation complex stability and mitochondrial ribosome assembly

city: Bentley

first: Irina

last: Kuznetsova

address: Building 304, Kent Street

department: The Centre for Crop and Disease Management

institute: Curtin University

summary: Differential gene expression as a consequence of PTCD1 loss

overall_design: We used RNA from control and PTCD1 knockout mice to investigate changes at the RNA level in response to PTCD1 loss

first: Kara

last: Perks

first: Giulia

last: Rossetti

first: Laetitia

last: Hughes

first: Judith

last: Ermer

first: Nicola

last: Ferreira

first: Jakob

middle: D

last: Busch

first: Danielle

last: Rudler

first: Henrik

last: Spahr

first: Thomas

last: Schöndorf

first: Ann-Marie

middle: J

last: Shearwood

first: Helena

middle: M

last: Viola

last: Siira

first: Livia

last: Hool

first: Dusanka

last: Milenkovic

first: Nils-Göran

last: Larsson

first: Oliver

last: Rackham

first: Aleksandra

last: Filipovska


title: TP53INP2 knockout in inguinal white adipose tissue

first: Antoni

last: Berenguer-LLergo

summary: Excessive fat accumulation is a major risk factor for the development of type 2 diabetes.To determine the mechanisms by wich TP53INP2 regulates adipogenesis, gene expression profile was performed in inguinal white adipose tissue fromTP53INP2-deficient mice.

overall_design: Inguinal white adipose tissue from TP53INP2-deficient mice, and their respective controls were used in this study.

first: Antonio

last: Zorzano

first: Montserrat

last: Romero

first: Alba

last: Sabaté-Pérez


title: Gene Enrichment Analysis Reveals Major Regulators of Mycobacterium tuberculosis Gene Expression in Two Models of Antibiotic Tolerance

city: Baltimore

first: Petros

middle: Constantine

last: Karakousis

address: 733 North Broadway

department: Department of Infectious Diseases

institute: Johns Hopkins University School of Medicine

summary: The development of antibiotic tolerance is believed to be a major factor in the lengthy duration of current tuberculosis therapies. In the current study, we have modeled antibiotic tolerance in vitro by exposing Mycobacterium tuberculosis to two distinct stress conditions: progressive hypoxia and nutrient starvation [phosphate-buffered saline (PBS)]. We then studied the bacterial transcriptional response using RNA-seq and employed a bioinformatics approach to identify important transcriptional regulators, which was facilitated by a novel Regulon Enrichment Test (RET). A total of 17 transcription factor (TF) regulons were enriched in the hypoxia gene set and 16 regulons were enriched in the nutrient starvation, with 12 regulons enriched in both conditions. Using the same approach to analyze previously published gene expression datasets, we found that three M. tuberculosis regulons (Rv0023, SigH, and Crp) were commonly induced in both stress conditions and were also among the regulons enriched in our data. These regulators are worthy of further study to determine their potential role in the development and maintenance of antibiotic tolerance in M. tuberculosis following stress exposure.

overall_design: Samples from 4 different conditions (7H9, PBS, Hypoxia, Phosphate-depleted) and 2 different strains (CDC1551, CDC1551-rpoB). Strain CDC1551-rpoB contains the H526D SNP in the rpoB gene.  2, 3, or 4 replicates per condition.

first: Dalin

last: Rifat

first: William

last: Matern


title: Gene expression profiling in liver normal and tumor tissues in C3H mice

first: Keiko

last: Nohara

summary: We have employed microarray analysis to detect tumor-related genes of liver tissues in C3H mice

overall_design: We measured gene expression levels of normal liver and liver tumor tissues in C3H mice.  We identified Mst1r and slpi as a tumor-related genes increasing in gene expression in tumor tissues compared with normal tissues.


title: A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing

status: Public on Apr 02 2018

city: Wako

first: Masaki

last: Kato

state: Saitama

address: 2-1 Hirosawa

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

overall_design: Refer to individual Series


title: Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding  [uPBM_Elk1Ets1Gabpa_MycMaxMad]

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

summary: Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. Our finding was possible due to a unique combination of carefully designed high-throughput assays and rigorous computation modeling, integrated into a unified framework called iMADS. We used iMADS to quantity, model, and analyze specificity differences between 11 paralogous TFs from 4 distinct human TF families. Our finding of differential specificity between closely related TFs has important implications for the interpretation of the regulatory effects of non-coding genetic variants.

overall_design: Universal protein-binding microarray (PBM) experiments were performed for recombinant, full-length, human transcription factors c-Myc, Max, and Mad1. Briefly, universal PBMs involved binding of his-tagged transcription factor dimers to double-stranded 44K Agilent microarrays containing a DNA library designed to cover all possible 10-bp sequences, with every 8-mer occurring in at least 16 different spots on the array. This design allows comprehensive and unbiased characterization of the binding specificity of transcription factors for all possible 8-bp sequences.


title: A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing [ChIP-Seq]

summary: Subsets of endogenous retroviruses (ERVs) are derepressed in mouse embryonic stem cells (mESCs) deficient for Setdb1, which catalyzes histone H3 lysine 9 trimethylation (H3K9me3). Most of those ERVs, including IAPs, remain silent if Setdb1 is deleted in differentiated embryonic cells; however they are derepressed when deficient for Dnmt1, suggesting that Setdb1 is dispensable for ERV silencing in somatic cells. However, H3K9me3 enrichment on ERVs is maintained in differentiated cells and is mostly diminished in mouse embryonic fibroblasts (MEFs) lacking Setdb1. We find that distinctive sets of ERVs are reactivated in different types of Setdb1-deficient somatic cells, including the VL30-class of ERVs in MEFs, whose derepression is dependent on cell type-specific transcription factors (TFs). These data suggest a more general role for Setdb1 in ERV silencing, which provides an additional layer of epigenetic silencing through the H3K9me3 modification.

overall_design: Analyses of transcriptional profiles and chromatin state in Setdb1 WT and KO cells

last: Takemoto

first: Yoichi

last: Shinkai


title: A novel long non-coding RNA Myolinc regulates myogenesis through TDP-43 and Filip1

city: Copenhagen SV

first: Shizuka

last: Uchida

address: Frederikskaj 10B, 2. (building C)


title: Innate immune memory in the brain shapes neurological disease hallmarks

city: Tübingen

first: Jonas

last: Neher

address: Otfried Mueller Str. 23

department: Experimental Neuroimmunology

institute: German Center for Neurodegenerative Diseases (DZNE) Tübingen


title: Development of miRNA expression signatures for selective intrauterine growth restriction (sIUGR) in two fetus placenta tissues

city: Hangzhou

first: Jun

last: Lin

address: No. 1 Xueshi Road, Uptown District

country: China

institute: Department of Obstetrics, The Women’s Hospital, School of Medicine, Zhejiang University

summary: We investigated sIUGR-related placental miRNA expression

overall_design: miRNA profile analysis was performed on two sIUGR cases and one control

first: Hong

last: Wen


title: MALT1 Inhibition Is Efficacious in Both Naïve and Ibrutinib-Resistant Chronic Lymphocytic Leukemia.

city: New Orleans

first: Nakhle

last: Saba

state: LA

address: 1415 Tulane Ave, Room 118

department: Internal Medicine/Hematology

institute: Tulane University

summary: The clinical efficacy displayed by ibrutinib in chronic lymphocytic leukemia (CLL) has been challenged by the frequent emergence of resistant clones. The ibrutinib target, Bruton's tyrosine kinase (BTK), is essential for B-cell receptor signaling, and most resistant cases carry mutations in BTK or PLCG2, a downstream effector target of BTK. Recent findings show that MI-2, a small molecule inhibitor of the para-caspase MALT1, is effective in preclinical models of another type of BCR pathway-dependent lymphoma. We therefore studied the activity of MI-2 against CLL and ibrutinib-resistant CLL. Treatment of CLL cells in vitro with MI-2 inhibited MALT1 proteolytic activity reduced BCR and NF-κB signaling, inhibited nuclear translocation of RelB and p50, and decreased Bcl-xL levels. MI-2 selectively induced dose and time-dependent apoptosis in CLL cells, sparing normal B lymphocytes. Furthermore, MI-2 abrogated survival signals provided by stromal cells and BCR cross-linking and was effective against CLL cells harboring features associated with poor outcomes, including 17p deletion and unmutated IGHV Notably, MI-2 was effective against CLL cells collected from patients harboring mutations conferring resistance to ibrutinib. Overall, our findings provide a preclinical rationale for the clinical development of MALT1 inhibitors in CLL, in particular for ibrutinib-resistant forms of this disease. Cancer Res; 77(24); 7038-48. ©2017 AACR.

overall_design: To investigate the effect targeting MALT1 with MI-2 on tumor biology, 1 μg of total RNA from purified CLL cells treated for 8h with 2 µM MI-2 in vitro (N=3) was subject to RNA sequencing (by next-generation sequencing) and compared to untreated controls (N=3).

middle: S

first: Deanna

last: Wong

first: Georges

last: Tanios

first: Jessica

last: Iyer

first: Patricia

last: Lobelle-Rich

first: Eman

last: Dadashian

first: Delong

last: Liu

first: Lorena

last: Fontan

first: Erik

last: Flemington

first: Cydney

last: Nichols

first: Chingiz

last: Underbayev

first: Hana

last: Safah

first: Ari

last: Melnick

first: Adrian

last: Wiestner

first: Sarah

middle: E

last: Herman


title: Role of histone demethylase Kdm6a in pancreatic cancer - ChIP-Seq

status: Public on Apr 01 2018

city: Washington

first: Alexandros

last: Tzatsos

state: DC

address: 800 22nd St NW SEH 8850

department: GW Cancer Center

institute: George Washington University

summary: Loss-of-function mutations of KDM6A, an X chromosome encoded histone H3K27 demethylase, are frequent in a broad spectrum of epithelial and hematopoietic malignancies and contribute to oncogenesis with so far poorly characterized mechanisms. Pancreas specific ablation of Kdm6a in mice accelerated Kras-driven cell transformation and compromised survival in a gender specific manner. Female knockout animals were particularly vulnerable and developed aggressive squamous and quasi-mesenchymal tumors with metastatic potential, as opposed to the males which developed adenocarcinomas and exhibited a better prognosis. Integration of gene expression studies coupled to ChIP-seq profiling of chromatin modifications demonstrated that loss of Kdm6a caused genome-wide remodeling of bivalent promoters and rewiring of enhancer chromatin to repress endodermal fate by activating c-MYC and TP63 dependent transcriptional programs favoring squamous and quasi-mesenchymal differentiation.

overall_design: Cell lines established from K6A null murine pancreatic cancer were analyzed by ChIP-seq for epigentic regulators and histone modifications

first: Yan

last: Kai


title: Expression date from WT RAW264.7 and HuR-deficient RAW264.7 stimulated with poly(I:C) using lipofectamine

city: Ikoma, Takayama

first: Takuya

last: Sueyoshi

state: Nara

department: Biological Science

institute: Nara Institute of Science and Technology

summary:
HuR-deficient cells showed the decreased expression of genes involved in chemotaxis,  cell proliferation and signal transduction.
We used microarray to detail the global gene expression of HuR-deficient cell after poly(I:C) stimulation.

overall_design: WT and HuR-deficeint RAW264.7 cells were stimulated with poly(I:C) using lipofectamine. RNA was extracted and analyzed by Affymetrix microarrays.

first: Takumi

last: Kawasaki

first: Taro

last: Kawai


title: Cdk4 is a critical regulator of age-associated hepatic steatosis.

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: to identify the impact of cdk4 inhibition on genes and pathways involved in age-associated liver disorders using next generation sequencing on young and control- or PD0332991-treated aged mice.
Methods:  RNA was isolated from livers of young (2 month old) and old (20-22 month old) C57Bl6 mice.  Old mice were either either control-aged mice or PD-0332991 treated aged mice (450mg/dk for 2 weeks).  The three conditions were represented in triplicate.  Raw reads passing quality filtration were aligned to the mm10 mouse genome using UCSC annotations by pseudoalignment in Kallisto. All reasonably expressed transcripts were submitted for statistical analysis to identify age-altered transcripts corrected by cdk4 inhibition.
Results: We mapped a minimum of 20 million reads per sample, which corresponded to a total of 25,240 transcripts.  Of these, 12,551 were considered reasonably expressed and were included in analysis comparing control-aged v young and PD0332991-treated-aged v young.
Conclusion: Inhibition of cdk4 in ages wildtype mice by cdk4 inhibitor PD-0332991 reduces CEBPa-p300 and reduced aged-related alterations of hepatic structure and function.

overall_design: RNA from livers of young mice, untreated aged mice, and PD-0332991-treated mice was sequenced in triplicate using the Illumina HiSeq2500.

first: Nikolai

last: Timchenko


title: TP53INP2 knockout in perigonadal white adipose tissue

first: Antoni

last: Berenguer-LLergo

summary: Excessive fat accumulation is a major risk factor for the development of type 2 diabetes.To determine the mechanisms by wich TP53INP2 regulates adipogenesis, gene expression profile was performed in perigonadal white adipose tissue fromTP53INP2-deficient mice.

overall_design: Perigonadal white adipose tissue from TP53INP2-deficient mice, and their respective controls were used in this study.

first: Antonio

last: Zorzano

first: Montserrat

last: Romero

first: Alba

last: Sabaté-Pérez


title: Chemically Induced Paneth Cells Provide Superior In Vivo Mimic to Organoid-derived Analog

city: Cambridge

first: Jose

last: Ordovas-Montanes

state: MA

address: 77 Massachusetts Ave

department: IMES

institute: Massachusetts Institute of Technology

summary: Paneth cells (PCs) are post-mitotic secretory cells of the small intestine that produce antimicrobials, growth factors, and cytokines. Multiple diseases have been linked to alterations in PC function. Past studies of PCs have relied on in vivo models, and limited in vitro models, including organoids. While useful, whether the in vitro models recapitulate in vivo biology is an important, yet unanswered question. Here, we present a bona fide in vitro PC-enriched population derived via chemically-induced (CI) differentiation of primary murine adult stem cells. We define the identity of PCs in our system and compare to PCs of established organoid systems and those found in vivo. Importantly, we demonstrate stimulant-induced and microbe-responsive antimicrobial function of our CI-PCs – hallmark functions of PCs in vivo. Thus, we define and produce the most physiologically-relevant in vitro PC population to date, providing a superior tool to study cellular development, host-microbe interactions, and inflammatory disease.

overall_design:
Single-cell RNA sequencing experiments on Seq-Well platform of ENR (Control), ENR+CD (Paneth enriched), and ENR+CV (ISC-enriched) organoids.
Org_All_merged.txt: merged UMI file

first: Alex

last: Shalek


title: Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding

first: Raluca

last: Gordan

type: Genome binding/occupancy profiling by array

platform_organism:
Homo sapiens
synthetic construct


title: High level efficacy of lufenuron against sea lice (Lepeophtheirus salmonis) linked to rapid impact on moulting processes

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

summary: This study investigates the transcriptomic responses of salmon lice (L. salmonis) to five concentrations (30, 300, 700, 1000, and 1500 ppb) of lufenuron (Elanco Animal Health)

overall_design: Copepodid-staged larvae of L. salmonis were separated in to seven groups (n = 3 pools of approxximately 500 lice). Five of these groups were exposed to lufnuron at 30, 300, 700, 1000, or 1500 ppb lufenuron. Two control groups, one acetone only and one seawater only, were also used. The bioassay (exposures) lasted 3 h before all groups of lice were moved to a sea water holding container for 21 h. Lice were then stored at -80C for RNA extraction and microarray analyses.

first: Jordan

last: Poley.

first: Laura

last: Braden.

first: Amber

last: Messmer.

first: Okechukwu

middle: O

last: Igboeli.

first: Shona

last: Whyte.

first: Alicia

last: MacDonald.

last: Rodriguez.

first: Marta

last: Gameiro.

first: Lucien

last: Rufener.

first: Jaques

last: Bouvier.

first: Dorota

last: Wadowska.

last: Koop.

first: Barry

last: Hosking.

first: Mark

last: Fast.


title: Expression data from TNF-α treated chordoma cell lines U-CH1 and MUG-Chor1 (Long-term)

city: IStanbul

first: Sukru

last: Gulluoglu

address: Acibadem Mah. IStek vakfi binasi

country: Turkey

institute: Yeditepe University

summary:
TNF-α is an important inflammatory cytokine. Recent findings suggest tumor promoting inflammation could be a driving factor for chordoma progression.
We used microarray to monitor the global changes in gene expression after TNF-α treatment for 1 year in two chordoma cell lines

overall_design: Chordoma cell lines U-CH1 and MUG-Chor1 were treated 3 times a week with 10 ng/mL TNF-α. Cells were harvested and microarray was conducted

first: Mesut

last: Sahin

first: Emre

last: Tuysuz

first: Omer

last: Bayrak


title: Expression data from TNF-α treated chordoma cell lines U-CH1 and MUG-Chor1 (Short-term)

summary:
TNF-α is an important inflammatory cytokine. Recent findings suggest tumor promoting inflammation could be a driving factor for chordoma progression.
We used microarray to monitor the global changes in gene expression after TNF-α treatment for 1 week in two chordoma cell lines


title: Role of histone demethylase Kdm6a in pancreatic cancer (ChIP-Seq)

first: Alexandros

last: Tzatsos

overall_design: Cell lines estabished from K6A null murine pancreatic cancer were analyzed by ChIP-seq for H3K4me3, H3K27me3, and H3K27ac

first: Yan

last: Kai


title: Role of histone demethylase Kdm6a in pancreatic cancer (PrimeView)

summary:
Transcriptional profile of human pancreatic cancer cell lines trerated with JQ1 inhibitor.
Loss-of-function mutations of KDM6A, an X chromosome encoded histone H3K27 demethylase, are frequent in a broad spectrum of epithelial and hematopoietic malignancies and contribute to oncogenesis with so far poorly characterized mechanisms. Pancreas specific ablation of Kdm6a in mice accelerated Kras-driven cell transformation and compromised survival in a gender specific manner. Female knockout animals were particularly vulnerable and developed aggressive squamous and quasi-mesenchymal tumors with metastatic potential, as opposed to males which developed adenocarcinomas and exhibited a better prognosis. Integration of gene expression studies coupled to ChIP-seq profiling of chromatin modifications demonstrated that loss of Kdm6a caused genome-wide remodeling of bivalent promoters and rewiring of enhancer chromatin to repress endodermal fate by activating c-MYC and TP63 dependent transcriptional programs favoring squamous and quasi-mesenchymal differentiation.

overall_design: Human pancreatic cancer cell lines were treated with 500nM of JQ1 for 24 hours. Gene expression was analyzed with the Affymetrix platform to identify differentially regualted genes.


title: Exacerbating role of angiopoietin-2 in cardiac hypoxia and inflammation after myocardial infarction

city: Daejeon

first: Gou Young

last: Koh

address: 291  Daehak-ro

department: Center for Vascular Research

country: South Korea

institute: Institute for Basic Science

summary: To unveil the role of Angiopoietin-2 in regulating vascular remodeling after myocardial infarction

overall_design: Infarct border zone endothelial cells were sorted from myocardial infarction model mice deleting Angiopoietin-2 or Wild-type control.

first: Goh

middle: Y

first: Seung-Jun

last: Lee


title: Whole-transcript Expression data from skin of different coat color in Chinese Merion (Junken type)

city: Shihezi

first: dai

last: rong

state: Xinjiang

address: Wuyi Road No. 221

department: Animal husbandry and veterinary institute

institute: XinJiang Academy of Agricultural and Reclamation Science

summary:
Coat color mainly reflects pigmentation resulting from melanin. Wool color is one of the most visible and heritable traits in sheep. Although several detailed molecular mechanisms involved in coat color have been elucidated, our understanding of differences in gene expression patterns of wool color-related genes in Chinese Merino (Junken type) is limited. We employed the Affymetrix microarray to identify differentially expressed genes. 122 genes were differentially expressed, consisting of 117 upregulated and 5 downregulated genes that were related to black/brown skin. The expression level of the BMP2, BMP4, TYRP1, LEPR, DCT, BMPR1A, and TP45A genes was validated by qRT-PCR, and the results coincided with those of microarray. The expression level of ASIP in the black/brown group was significantly lower than that of the white group, suggesting that this plays a key role in the regulation of wool pigmentation. Some cloned color genes (MITF, MC1R, GPR143, and KIT) showed no significant differences in expression levels between the black/brown- and white-skinned sheep. Functional annotation by using Gene Ontology (GO) showed that the differentially expressed genes enriched specific GO terms, particularly those relating to melanin biosynthesis and metabolic processes. KEGG pathway analysis indicated that the categories of tyrosine metabolism and melanogenesis pathway were enriched with differentially expressed genes. Taken together, the present study has shown that the tyrosine metabolism pathway plays an essential role in regulating wool color. The findings of this study may also be utilized in the elucidation of the molecular mechanisms and relationship between genes and wool color in Chinese Merino (Junken type).
We used microarrays to detail the global programme of gene expression and identified distinct different expression genes of skin in different coat color Chinese Merino (Junken type).

overall_design: Six healthy adult Chinese Merino (Junken type) consisting of three white (A) and three black/brown (C) coat-colored were selected from the farm of Xinjiang Academy of Agricultural and Reclamation Science (Xinjiang, China) for sample collection. The skin samples (1 cm × 1 cm) from the body side were collected under local anesthesia and immediately stored in liquid nitrogen. Whole-transcript expression analysis was performed as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

first: Dai

last: Rong

first: Shi

middle: G

last: Qing

first: Shen

last: Jun

first: Wan

last: Cheng

first: Zhou

last: Ping

first: Guo

last: Hua


title: Role of histone demethylase Kdm6a in pancreatic cancer

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing [RNA-Seq]

first: Masaki

last: Kato

country: Japan

institute: RIKEN

first: Keiko

last: Takemoto

first: Yoichi

last: Shinkai