title: Serial Inversions Induce Tissue-specific Architectural Stripes, Gene Misexpression and Congenital Malformations [RNA-Seq]

overall_design: We used RNAseq to study the effects of the repositioning of an enhancer cluster, previously located in the Epha4 TAD, into a gene-dense region. We analyzed five biological replicates of wild type and at least 2 biological replicates of the CRISPR/Cas9-engineered mouse mutants (five mutants in total) featuring structural variations. Embryonic E11.5 distal forelimb tissue was used for these experiments.


title: Genetic and scRNA-seq Analysis Reveals Distinct Cell Populations that Contribute to Salivary Gland Development and Maintenance

status: Public on Nov 19 2018

city: Buffalo

first: Rose-Anne

last: Romano

state: New York

address: 3435 Main Street

department: Department of Oral Biology

country: USA

institute: State University of New York at Buffalo

type: Expression profiling by high throughput sequencing

summary: Through a combination of scRNA-Seq analysis and in-vivo genetic-lineage tracing, we generated a detailed a detailed map of the cell fate trajectories and branch points of the basal and myoepithelial of the mouse SMG during embryonic development and in adults.

overall_design: 10x scRNA-Seq of submandibular gland postnatal day 8 mice.

first: Eun-Ah

middle: C

last: Song

first: Sangwon

last: Min

first: Akinsola

last: Oyelakin

first: Kirsten

last: Smalley

first: Johnathan

middle: E

last: Bard

first: Lan

last: Liao

first: Jianming

last: Xu


title: Transcriptome-wide binding sites of mutually exclusive exon junction complexes

city: Columbus

first: Guramrit

last: Singh

state: OH

address: 484 W 12th Ave, BioSci, B211

department: Molecular Genetics

institute: Ohio State University

summary: The exon junction complex (EJC) deposited upstream of mRNA exon junctions shapes structure, composition and fate of spliced mRNA ribonucleoprotein particles (mRNPs). To achieve this, the EJC core nucleates assembly of a dynamic shell of peripheral proteins that function in diverse post-transcriptional processes. In this study we show that EJC exists in two mutually exclusive compositions characterized by peripheral proteins RNPS1 and CASC3. We identified transcriptome-wide binding sites of the two alternate EJCs via RNA:protein immunoprecipitation in tandem followed by deep sequencing (RIPiT-Seq). We show that RNPS1-EJC, which is an SR-rich mega-dalton sized RNP, is the major EJC form in the nucleus. After mRNP export to the cytoplasm and before translation, the EJC undergoes a remarkable compositional and structural remodeling into an SR- and RNPS1-devoid monomeric complex that contains CASC3. The CASC3-EJC is enriched on cytoplasmic RNAs and is the main EJC form that encounters ribosome and undergoes disassembly during translation.

overall_design: Analysis of exon junction complex footprints using RIPiT-Seq

first: Robert

last: Patton


title: Plant Extracellular Vesicles Contain Diverse Small RNA Species and Are Enriched in 10 to 17 Nucleotide "Tiny" RNAs.

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (sRNAs) are small non-coding RNAs of 20 to 24 nucleotides in size found across a wide range of eukaryote organisms, from plants to animals. sRNAs are master regulators of a wide range of biological functions, including development, reproduction and stress responses. They typically function via the control of the stability and translation of target mRNAs. sRNAs can be divided in two major classes, according to their biogenesis and mode of action: microRNAs (miRNAs) and small interfering RNAs (siRNAs). As a silencing signal, several different types of sRNAs have also the ability to move short distances, like cell-to-cell, or much longer distances like root to shoot. They are even trafficked between different species and organisms. However, the mechanisms by which sRNAs move remain unknown.   Extracellular vesicles (EVs) are mobile lipid compartments that participate in intercellular communication; they are able to carry proteins, lipids, nucleic acids and metabolites. Despite the fact that very little is known about the origin, formation or function of EVs in plants, recent results suggest that they participate in both long distance movement and immune responses. In this study, we analysed the small RNA content of EVs, and we identified miRNAs and siRNAs that are preferentially loaded into the EVs. This EV enrichment of certain RNAs supports hypotheses for long-distance RNA movement and for RNA-based communication between species, including host-pathogen interactions.

overall_design:
[Col-0] 3 different biological replicates of small RNA seq from Arabidopsis leaf total RNA, Extracellular vesicles and supernatant are included in this study.
[dcl234 triple mutant] 2 different biological replicates of small RNA seq from dcl234 triple mutant Arabidopsis leaf total RNA, Extracellular vesicles and supernatant are included in this study.

last: Baldrich

first: Brian

middle: D

last: Rutter

first: Ran

last: Podicheti

first: Roger

middle: W

last: Innes

first: Blake

last: Meyers


title: Differential epigenetic profiling of human aortic endothelial cells (HAEC) in response to shear stress forces using ATAC-Seq

city: Chicago

first: Matthew

last: Krause

state: Illinois

address: 5841 S. Maryland Ave

department: Medicine

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Biomechanical cues dynamically control major cellular processes but whether genetic variants actively participate in the mechano-sensing mechanisms remain unexplored. Vascular homeostasis is tightly regulated by hemodynamic forces. Exposure to disturbed blood flow at arterial sites of branching and bifurcation causes constant activation of vascular endothelium contributing to the development of atherosclerosis, the major cause of coronary artery disease (CAD). Conversely, unidirectional flow promotes the anti-inflammatory and anti-permeable endothelial phenotype resistant to atherogenesis. Genome-wide association studies (GWAS) have identified chromosome 1p32.2 as one of the loci most strongly associated with CAD susceptibility; however, the causal mechanism related to this CAD locus remain unknown. PhosphoLipid PhosPhatase 3 (PLPP3) is located at 1p32.2 and encodes a phosphatase that suppresses endothelial inflammation and promotes monolayer integrity by hydrolyzing lysophosphatidic acid. Our previous studies demonstrated that PLPP3 is significantly reduced in vascular endothelium exposed to disturbed flow while unidirectional flow significantly increases endothelial PLPP3 expression in vitro and in vivo. In addition, CAD protective allele at 1p32.2 locus is associated with increased PLPP3 in an endothelium-specific manner, shown by expression quantitative trait locus (eQTL). Using Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-Seq), H3K27ac ChIP-Seq, H3K4me2 ChIP-Seq, and luciferase assays, here we identified a mechano-sensitive endothelial enhancer in PLPP3 intron 5 that is dynamically activated by unidirectional flow. Deletion of this enhancer by CRISPR/Cas9-based genome editing causatively reduces endothelial PLPP3 expression and promotes endothelial activation, and moreover, impairs endothelial PLPP3 induction by unidirectional flow. Chromatin accessibility quantitative trait locus (caQTL) mapping, allelic imbalance assay, and luciferase assays further demonstrated that CAD protective allele at rs17114036 in the PLPP3 intron 5 confers an increased enhancer activity. ChIP-PCR and luciferase assays showed that CAD protective allele C at rs17114036 creates a binding site (CACC) for mechano-sensitive transcription factor KLF2, leading to increased enhancer activity under unidirectional flow. These results elucidate the contributory role of CAD genetic predisposition in critical endothelial mechano-transduction mechanisms and suggest that human genetic variants provide a previously unappreciated layer of regulatory control in cellular mechano-sensing mechanisms.

overall_design: 12 total samples. ATAC-seq of commercial HAEC under static conditions was performed in biological duplicate. 5 different donors were chosen to be subjected to unidirectional and disturbed flow for allele-specific and differential analyses.

first: Yun

last: Fang


title: Differential epigenetic profiling of human aortic endothelial cells (HAEC) in response to shear stress forces using ChIP-Seq of H3K27ac

overall_design: 20 samples. In five independent experiments HAEC were subjected to unidirectional and disturbed flow and ChIP was performed for H3K27ac. Inputs for each sample are included to control for background.


title: Lung transcriptomes of wild type, β-arrestin 1 -/-, and  β-arrestin 2 -/- mice exposed to normoxia or chronic hypoxia

city: Durham

first: Sudarshan

last: Rajagopal

state: North Carolina

address: 303 Research Drive

department: Department of Medicine

institute: Duke University Medical Center

summary: We found that β-arrestin 1 -/- mice were more sensitive to hypoxia-induced pulmonary arterial hypertension with increased right ventricle hypertrophy and higher right ventricle systolic pressure, while β-arrestin 2 -/- mice developed right ventricle hypertrophy comparable to wild type mice. Moreover, β-arrestin 1 -/- mice had worse right ventricle function than wild type mice in response to chronic hypoxia, whereas β-arrestin 2 -/- mice relatively preserved right ventricle function compared to wild type mice. To investigate the molecular mechanisms responsible for the worse PAH in β-arrestin 1 -/- mice, we performed lung transcriptome analysis of wild type, β-arrestin 1 -/-, and β-arrestin 2 -/- mice using high-throughput RNA-seq.

overall_design: Deep sequencing of lung transcriptomes from wild type, β-arrestin 1 -/-, and  β-arrestin 2 -/- mice exposed to normoxia or chronic hypoxia in triplicate.

first: Zhiyuan

last: Ma


title: Breast tumor from Pik3caH1047R/+ mammary gland transduced with single or pooled lentivirus.

status: Public on Nov 18 2018

city: Seattle

first: Slobodan

last: Beronja

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: RNA-seq of breast tumor from Pik3caH1047R/+ mammary gland transduced with single or pooled lentivirus.

overall_design: Tumor from Pik3caH1047R/+ mammary gland transduced with single or pooled lentivirus.

first: Zhe

last: Ying


title: Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats VI.

city: Ottawa

first: Nasrin

last: Khan

state: ON

address: 50 Colombine Driveway

country: Canada

institute: Health Canada

summary: The notion that adverse health effects produced by exposure to environmental contaminants (EC) may be modulated by the presence of non-chemical stressors is gaining attention. Previously, our lab demonstrated that cross-fostering (adoption of a litter at birth) acted as a non-chemical stressor that amplified the influence of developmental exposure to EC on the glucocorticoid stress-response in adult rats. Using liver from the same rats, the aim of the current study was to investigate whether cross-fostering might also modulate EC-induced alterations in hepatic gene expression profiles. During pregnancy and nursing, Sprague-Dawley dams were fed cookies laced with corn oil (control, C) or a chemical mixture (M) composed of polychlorinated biphenyls (PCB), organochlorine pesticides (OCP), and methylmercury (MeHg), at 1 mg/kg/day. This mixture simulated the contaminant profile reported in maternal human blood. At birth, some control and M treated litters were crossfostered to form two additional groups with different biological/nursing mothers (CC and MM). The hepatic transcriptome was analyzed by DNA microarray in male offspring at postnatal days 21 and 78–86. Mixture exposure altered the expression of detoxification and energy metabolism genes in both age groups, but with different sets of genes affected at day 21 and 78–86. Cross-fostering modulated the effects of M on gene expression pattern (MM vs M), as well as expression of energy metabolism genes between control groups (CC vs C). In conclusion, while describing short- and long-term effects of developmental exposure to EC on hepatic transcriptomes, these cross-fostering results further support the consideration of non-chemical stressors in EC risk assessments.

overall_design: Dams (Sprague Dawley, rats) were treated during the gestation and lactation period, and eight male pups per treatment group were investigated.  RNA from pairs of rats in the same treatment group was randomly pooled together and thus each treatment group was represented by four microarrays.  To investigate mixture effects, five treatment groups were not cross-fostered and remained with their birth mothers (C, 0.5M, M, AhR, and 0.5MAhR), whereas four groups were compared to investigate effects of cross-fostering (CC vs C, and MM vs M).  The effects of developmental exposure to the chemical mixtures and effects of cross-fostering were investigated in rats at two time points, at 21 days of age, and at 78-86 days of age.  There were 72 samples included in the final analysis using a two-colour experiment (e.g., Cy5/Cy3) microarray design.

first: Daniel

last: Desaulniers

first: Cathy

last: Cummings-Lorbetskie

first: Karen

last: Leingartner

first: Gong

middle: H

last: Xiao

first: Andrew

last: Williams

first: Carole

middle: L

last: Yauk


title: Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats IV.

first: karen


title: Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats III.


title: Human immunodeficiency reveals the Zn2+-dependence of B cell development

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Despite the known importance of zinc for human immunity, molecular insights into its roles remain limited. Here we report a novel autosomal recessive disease characterised by early-onset infections, absent B cells and agammaglobulinaemia in five unrelated families. The immunodeficiency results from a series of hypomorphic and null alleles of SLC39A7, which encodes the endoplasmic-reticulum-to-cytoplasm zinc transporter, ZIP7. Using CRISPR-Cas9 editing and homologous recombination we have modelled ZIP7 deficiency in mice. Homozygosity for a null allele caused embryonic lethality, but hypomorphic alleles reproduced the block in B cell development seen in patients. B cells from mutant mice exhibited increased phosphatase activity and decreased phosphorylation of signalling molecules that lie downstream of the pre-B and B cell receptors. Our findings highlight a specific role for Zn2+ in modulating B cell receptor signal strength and positive selection, and suggest how Zn2+ could modulate outcome in a variety of signalling contexts.

overall_design: We constructed 40 RNA-seq libraries; 4 stages of B cells, 2 conditions (WT and mutant), 5 replicates. 5 WT and 5 P198A/P198A mutant staight chimeras mice were stained and sorted for FrB,C,D,E in BM. 100 cells each sample, processed by Smartseq2. Sequenced by HiSeq4000.

middle: P

first: Xijin

last: Xu

first: Consuelo

last: Anzilotti

first: Richard

middle: J

last: Cornall


title: Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats II.


title: Differential epigenetic profiling of human aortic endothelial cells (HAEC) in response to shear stress forces

first: Matthew

last: Krause

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

overall_design: Refer to individual Series


title: Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats I


title: Over expression of Receptor Activity Modifying Protein 2 in HEK293T cells

status: Public on Nov 17 2018

city: New York

first: Shahar

last: Barbash

state: NY

address: 1230 York Ave

institute: The Rockefeller University

summary: HEK293T cells were transfected with pcDNA3.1 vector containing codon optimized sequence for (Receptor Activity Modifying Protein 2) RAMP2. Control samples include both non-transfected cells and cells transfected with empty vector. There are three technical replications for each condition. RNA was extracted after 24 h, checked for quality and RNA integrity and profiled with whole exome RNA sequencing.

overall_design: HEK293T cells were cultured in cell medium and 300,000 cells were seeded onto poly-D-lysine mol wt 70,000-150,000 (Sigma-Aldrich) coated cover glasses (18-mm, thickness No. 1.5H, Marienfeld Superior) placed in 60-mm tissue culture dishes. The next day, cells were transfected with 2 µg plasmid DNA for RNA sequencing, using Lipofectamine 2000 (Thermo Fisher Scientific) according to manufacturer’s protocol. Plasmid DNA included RAMP2 with a FLAG-tag epitope sequence following the signal peptide, OLLAS-epitope, tag on the C-terminus in pcDNA3.1, codon optimized for expression in human cell lines. After 24 h incubation at 37°C, RNA was extracted using the miRneasy kit (QIAGEN) for RNA sequencing. Extracted RNA samples were examined with Bioanalyzer for RNA integrity and concentration before sequencing. RNA integrity number was 9.62 with 0.98 standard deviation. 100 ng of total RNA was used to generate RNA-Seq libraries using Illumina TruSeq stranded mRNA LT kit (Cat# RS-122-2101).   Libraries prepared with unique barcodes were pooled at equal molar ratios. The pool was denatured and sequenced on Illumina NextSeq 500 sequencer using high output V2 reagents and NextSeq Control Software v1.4 to generate 75 bp single reads, following manufactures protocol (Cat# 15048776 Rev.E). For read alignment after adaptor cutting we used STAR software. Quality control was verified with qualilmap.

first: Torbjörn

last: Persson

first: Emily

last: Lorenzen

first: Manija

last: Kazmi

first: Thomas

last: Huber

last: Sakmar


title: RORγt inhibition selectively targets IL-17 producing human iNKT and γδ-T cells enriched in Spondyloarthritis while preserving IL-22 responses

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

summary: Dysregulated IL-23/IL-17 responses have been linked to psoriatic arthritis and other forms of spondyloarthritides (SpA). RORγt, the key Thelper17 (Th17) cell transcriptional regulator, is also expressed by subsets of innate-like T cells, including invariant natural killer T (iNKT) and γδ-T cells, but how they contribute to disorders such as SpA is still unclear. Here we describe the presence of particular RORγt+T-betloPLZF- iNKT and γδ-hi T cell subsets in healthy peripheral blood. RORγt+ iNKT and γδ-hi T cells showed profound IL-23 mediated Th17-like immune responses and were clearly enriched within inflamed joints of SpA patients where they act as major IL-17 secretors. SpA derived iNKT and γδ-T cells showed a unique Th17 skewed phenotype and gene expression profile. Strikingly, RORγt inhibition blocked γδ17 and iNKT17 cell function while selectively sparing IL-22+ subsets. Overall, these findings highlight a unique diversity of human RORγt+ T cells and underscore the potential of RORγt antagonism to modulate aberrant type 17 responses.

overall_design: iNKT (CD3+TCRVb11+6B11+), γδ-T (CD3+TCRγδ+) cells and Tconv (CD3+CD161-; negative for iNKT and γδ-T markers) cells were sorted from peripheral blood samples of SpA patients (n=7) and RA patients (n=5). Sequence-libraries of each sample were sequenced on a NextSeq500 system (Illumina).

first: Koen

last: Venken

first: Peggy

last: Jacques

first: Céline

last: Mortier

first: Mark

last: Labadia

first: Tine

last: Decruy

first: Julie

last: Coudenys

first: Kathleen

last: Hoyt

first: Anita

last: Wayne

first: Robert

last: Hughes

first: Michael

last: Turner

first: Sofie

last: Van Gassen

first: Dustin

last: Smith

first: Christian

last: Harcken

first: Joseph

last: Wahle

first: Chao-Ting

last: Wang

first: Eveline

last: Verheugen

first: Nadia

last: Schryvers

first: Gaëlle

last: Varkas

first: Heleen

last: Cypers

first: Ruth

last: Wittoek

first: Yves

last: Piette

first: Lieve

last: Gyselbrecht

first: Serge

last: Van Calenbergh

first: Filip

last: Van Den Bosch

first: Yvan

last: Saeys

first: Gerald

last: Nabozny

first: Dirk

last: Elewaut


title: T-ALL Leukemia Stem Cell “stemness” is Epigenetically Controlled by the Master Regulator PU.1

city: Beijing

first: Bingjie

last: Dong

address: No.5, Yiheyuan Street, Haidian District

country: China

institute: Peking University

type: Methylation profiling by high throughput sequencing


title: T-ALL Leukemia Stem Cell “stemness” is Epigenetically Controlled by the Master Regulator PU.1 [scRNA-seq]

summary: Leukemia stem cells (LSCs) are regarded as the origins and key therapeutic targets of leukemia, but limited knowledge is available on the key determinants of LSC “stemness”. Using single cell RNAseq analysis, we identify a master regulator PU.1, whose LSC-specific expression determines the molecular signature and activity of LSC in the Pten-null T-ALL model. Although initiated by PTEN controlled β-catenin activation, PU.1 expression and LSC “stemness” are maintained by a β-catenin-PU.1-TIM-3 feedback loop, independent of the leukemogenic driver mutation. Perturbing any component of this loop, either genetically or pharmacologically, can prevent LSC formation or eradicate existing LSCs. LSCs lose their “stemness” when PU.1 expression is silenced by DNA methylation, which can be reactivated by 5-AZ. Importantly similar regulatory mechanisms are also present in human T-ALLs.

overall_design: Here we performed single cell RNA-seq analysis for different subpopulation cells from thymus  in PTEN null T-ALL mouse model.

first: Haichuan

last: Zhu

first: Liuzhen

last: Zhang

first: Yilin

last: Wu

first: Weilong

last: Guo

first: Mei

first: Lu

last: Yang

first: Xiaoying

last: Fan

first: Yulinag

last: Tang

first: Ningshu

last: Liu

first: Xiaoguang

last: Lei

first: Hong


title: Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats

first: Nasrin

last: Khan


title: Serial Inversions Induce Tissue-specific Architectural Stripes, Gene Misexpression and Congenital Malformations

city: Berlin

first: Andreas

last: Magg

state: Berlin

address: Ihnestraße 63-73

department: Development and Disease

country: Germany

institute: Max-Planck-Institute for Molecular Genetics


title: LXR Suppresses Inflammatory Gene Expression and Neutrophil Migration through cis-Repression and Cholesterol Efflux

first: David

middle: G

last: Thomas

institute: Columbia University


title: T-ALL Leukemia Stem Cell “stemness” is Epigenetically Controlled by the Master Regulator PU.1 [bulkRNA]

overall_design: Here we performed Bulk RNA-seq analysis for LSCs and Blast cells from BM, thymus and spleen in PTEN null T-ALL mouse model.

last: Wang


title: T-ALL Leukemia Stem Cell “stemness” is Epigenetically Controlled by the Master Regulator PU.1 [BiSulfite-seq]

overall_design: Here we performed RRBS-seq analysis for different subpopulation cells from BM,thymus and spleen  in PTEN null T-ALL mouse model.


title: Dominant roles of B cells in the initiation of CD4 T cell response to a virus-derived nanoparticle antigen

status: Public on Nov 16 2018

first: Zhuqiang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

summary: Nanoparticles, including virus-like particles (VLP), are attractive candidates as carriers for vaccines and drug delivery. However, little is known about how they are targeted to the immune system in vivo.  Using RNA phage Qb-derived VLP (Qb-VLP) as a model antigen, we found surprisingly that antigen-specific B cells, instead of dendritic cells (DCs), were the dominant antigen presenting cells that initiate the naïve CD4 T cell activation, and were sufficient to induce T follicular helper cell development in the absence of DCs. Qb-specific B cells promoted CD4 T cell proliferation by providing cognate interactions and cell differentiation by generating cytokine milieu which depended on the Toll-like receptor signaling in B cells. Moreover, antigen-specific B cells were also involved in initiating CD4 T cell response to influenza virus. The mechanism revealed here will advance the rational design of nanoparticles as vaccine candidates, especially for therapeutic vaccines that aim to break immune tolerance.

overall_design: We measured expression profiles by RNA-seq in naïve B cells and Qb-VLP-activated B cells including plasma cells (PC).

first: Sheng

last: Hong

first: Zhimin

first: Hongtao

first: Meijie

last: Tian

first: Xiping

first: Weihong

first: Bing

first: Xuyu

last: Zhou

first: Fuping

first: Qing

last: Ge

first: Zhaolin

last: Hua

first: Baidong

last: Hou


title: Dissection of Metabolic Reprogramming in Polycystic Kidney Disease Reveals Coordinated Rewiring of Bionergetic Pathways

city: Baltimore

first: Feng

last: Qian

address: 655 W. Baltimore Street

department: School of medicine, Department of medicine

institute: University of Maryland

summary: Analysis of genome-wide transcriptional changes in cystic kidneys in the hypomorphic Pkd1V/V mouse model at postnatal day 10. The hypothesis tested in the present study was that metabolism is reprogrammed in polycystic kidney disease (PKD) in this model. Results provide important information of metabolic changes that affect glycolysis, mitochondrial metabolism, and fatty acid synthesis in the pathogenesis of PKD.

overall_design: Total RNA obtained from kidneys harvested from Pkd1V/V mouse mutants of 10 days of age compared to the wild-type littermates

first: Hyunho

last: Kim

first: Roberto

last: Pagliarini


title: Dynamic expression of Id3 defines the stepwise differentiation of tissue-resident regulatory T cells

first: Daniel

last: Campbell

state: Washington

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

summary: Foxp3+ regulatory T (TR) cells are phenotypically and functionally diverse, and broadly distributed in lymphoid and non-lymphoid tissues. However, the pathways guiding the differentiation of tissue-resident TR populations have not been well defined. By regulating E-protein function, Id3 controls the differentiation of CD8+ effector T cells and is essential for TR maintenance and function. We show that dynamic expression of Id3 helps define three distinct mouse TR populations, Id3+CD62LhiCD44lo central (c)TR, Id3+CD62LloCD44hi effector (e)TR and Id3- eTR. Adoptive transfer experiments and transcriptome analyses support a stepwise model of differentiation from Id3+ cTR to Id3+ eTR to Id3- eTR. Furthermore, Id3- eTR have high expression of functional inhibitory markers and a transcriptional signature of tissue-resident TR. Accordingly, Id3- eTR are highly enriched in non-lymphoid organs, but virtually absent from blood and lymph. Thus, we propose that tissue-resident TR develop in a multi-step process associated with Id3 downregulation.

overall_design: Biological triplicates from three different populations in lymph node and spleen.

first: Jenna

middle: M

last: Sullivan

first: Barbara

last: Höllbacher


title: LXR Suppresses Inflammatory Gene Expression and Neutrophil Migration through cis-Repression and Cholesterol Efflux [RNA-Seq]

first: David

summary: The activation of Liver X Receptor (LXR) promotes cholesterol efflux and repression of inflammatory genes with anti-atherogenic consequences. The mechanisms underlying repressive activity of LXR are controversial and have been attributed to cholesterol efflux or to transrepression of Activator Protein-1 (AP-1) activity. Here, we find that cholesterol efflux contributes to LXR repression, while direct repressive functions of LXR also play a key role but are independent of AP-1. We use ATAC-seq to show that LXR reduces chromatin accessibility in cis at inflammatory gene enhancers containing LXR binding sites. Targets of this repressive activity are associated with leukocyte adhesion and neutrophil migration, and LXR agonist treatment suppresses neutrophil recruitment in a mouse model of sterile peritonitis. These studies suggest a model of repression in which liganded LXR binds in cis to canonical nuclear receptor binding sites and represses pro-atherogenic leukocyte functions in tandem with induction of LXR targets mediating cholesterol efflux.

overall_design: mRNA profiling of BMDM treated with LXR agonist T0901317 and LPS

first: Alan

last: Tall


title: Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells (RNA-Seq)

city: Yangzhou

first: Zhen

last: Sun

address: Wenhui

institute: Yangzhou University

summary:
Aim: To study the biological function of NSUN2 in regulating gene expression and cell proliferation.
Materials & methods: The NSUN2 gene was knocked down in HEK293 cells via CRISPR/Cas9 system. Gene expression were assessed using RNA-Seq.
Results: A total of 790 differentially expressed genes (DEGs) were identified.

overall_design: mRNA profiles of wild type (WT) and NSUN2-/- HEK293 cells were generated by deep sequencing, in triplicate.

first: Hengmi

last: Cui


title: Hormone Control Regions mediate steroid receptor-dependent genome organizations

city: Barcelona

first: François

last: Le Dily

address: Dr Aiguader, 88

country: Spain

institute: CRG

summary: In breast cancer cells, some topologically associating domains (TADs) behave as hormonal gene regulation units, within which genes transcription is coordinately regulated in response to steroid hormones. Here we further described that responsive TADs contain 20-100 kb-long clusters of intermingled estrogen receptor (ER) and progesterone receptor (PR) binding sites, hereafter called Hormone-Control Regions (HCRs). In T47D cells, we identified more than 200 HCRs, which are frequently bound by unliganded ER and PR. These HCRs establish steady long-distance inter-TAD interactions between them and organize characteristic looping structures with promoters even in the absence of hormones in ER+-PR+ cells. This organization is dependent on the expression of the receptors and is further dynamically modulated in response to steroid hormones. HCRs function as platforms integrating different signals resulting in some cases in opposite transcriptional responses to estrogens or progestins. Altogether, these results suggest that steroid hormone receptors act not only as hormone-regulated sequence-specific transcription factors, but also as local and global genome organizers.

overall_design: Three dimensional structural differences between ER+/PR+ and ER-/PR- cells were analysed by in situ Hi-C.

first: Enrique

last: Vidal

first: Yasmina

last: Cuartero

first: Javier

last: Quilez

first: Silvina

last: Nacht

first: Guillermo

last: Vicent

first: José

last: Carbonell

first: Priyanka

last: Sharma

first: José Luis

last: Villanueva-Cañas

first: Lara

middle: I

last: De Llobet

first: Gaetano

last: Verde

first: Roni

last: Wright

first: Miguel

last: Beato


title: LXR Suppresses Inflammatory Gene Expression and Neutrophil Migration through cis-Repression and Cholesterol Efflux [ATAC-Seq]

first: David

last: Thomas

overall_design: Chromatin accessbility profiling by ATAC-Seq of BMDM treated with LXR agonist T0901317 and LPS


title: Effects of cross-fostering and developmental exposure to mixtures of environmental contaminants on hepatic gene expression in prepubertal 21 days old and adult male Sprague-Dawley rats V.

first: Nasrin

last: Khan

overall_design: Dams (Sprague Dawley, rats) were treated during the gestation and lactation period, and eight male pups per treatment group were investigated.  RNA from pairs of rats in the same treatment group was randomly pooled together and thus each treatment group was represented by four microarrays.  To investigate mixture effects, five treatment groups were not cross-fostered and remained with their birth mothers (C, 0.5M, M, AhR, and 0.5MAhR), whereas four groups were compared to investigate effects of cross-fostering (CC vs C, and MM vs M).  The effects of developmental exposure to the chemical mixtures and effects of cross-fostering were investigated in rats at two time points, at 21 days of age, and at 78-86 days of age.  There were 72 samples included in the final analysis using a two-colour experiment (e.g., Cy5/Cy3) microarray design

first: Daniel

last: Desaulniers

first: Cathy

last: Cummings-Lorbetskie

first: Karen

last: Leingartner

first: Gong

last: Xiao

first: Andrew

last: Williams

first: Carole

last: Yauk


title: Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells

first: Zhen

last: Sun

summary:
Aim: To study the biological function of NSUN2 in regulating gene expression and cell proliferation.
Materials & methods: The NSUN2 gene was knocked down in HEK293 cells via CRISPR/Cas9 system. mRNA m5C modification and gene expression were assessed using RNA-BisSeq and RNA-Seq.
Results: NSUN2 deficiency could inhibit proliferation and migration of HEK293 cells. A total of 1185 differentially methylated genes (DMGs) and 790 differentially expressed genes (DEGs) were identified. Bioinformatics analysis revealed the DMGs were mainly involved in regulating gene expression. Some pathways associated with cell proliferation were significantly enriched by the DEGs. Additionally, GRB2 and CD44 may be key regulators in NSUN2-mediated cell proliferation.
Conclusion: These findings help to elucidate the molecular mechanisms by which NSUN2 affects cell proliferation, migration and other cell phenotypes.

overall_design: Examination of mRNA 5-methylcytosine modifications in 2 cell types.

first: Hengmi

last: Cui


title: Expression data from Huh7 cells after 1,2,3,4,6-penta-O-galloyl-beta-D-glucopyranoside (PGG) treatment

city: Kaohsiung City

first: Yi-Ming

middle: Arthur

last: Chen

state: Taiwan

address: No. 100, Shih-Chuan Ist Rd

country: Taiwan

institute: Kaohsiung Medical University

summary:
PGG is a natural product exhibits anti-cancer effects on different type of cancers including liver cancer cell lines. In present study we identified a set of genes affected by PGG treatment in Huh7 cells. Some of them, for example, control cell cycle and cell proliferation.
We used microarrays to delineate the mechnism of action of PGG on GNMT expression in HCC. We identified distinct classes of up-regulated and down-regulated genes after PGG treatment in Huh7 cells.

overall_design: Huh7 cells were seeded for 24 hours. Cells were then treated with PGG 6 hr, PGG 48 hr and PBS 48 hr. Cells were harvested for RNA extraction and hybridization on Affymetrix Microarray. Differentially expression genes between PGG treatment and PBS control were identified for functional study.

first: Rajni

last: Kant

first: Chia-Hung

last: Yen

first: Chien-Yi

last: Tung

first: YiMing


title: Gene expression data of glioblastoma patients from GAPVAC trial (Glioma Actively Personalized Vaccine Consortium)

status: Public on Nov 15 2018

city: Heidelberg

first: Wolfgang

last: Wick

address: Im Neuenheimer Feld 400

department: Neurooncology

institute: Ruprecht-Karls University Heidelberg

summary:
Patients with glioblastoma (GB) so far do not sufficiently benefit from recent breakthroughs with checkpoint inhibitors (CPI), for which high mutational load and responses to neo-epitopes are regarded essential. GB tumours show limited intra-tumoral immune cell infiltration and carry 30-50 non-synonymous mutations only. Exploitation of the full repertoire of tumour antigens - non-mutated and neo-epitopes – may offer more effective immunotherapies, especially for tumours with low mutational load. In the first-in-human trial GAPVAC-101, the Glioma Actively Personalized Vaccine Consortium (GAPVAC) integrated both tracks highly individualized into standard treatment to optimally exploit the limited target space for patients with newly diagnosed GB. Fifteen HLA-A*02:01+ or -A*24:02+ patients were treated with a warehouse-based vaccine (APVAC1) targeting non-mutated antigens followed by APVAC2, targeting preferentially neo-epitopes. Personalization was based on mutations, transcriptome, and immunopeptidome of the individual tumours. The GAPVAC approach was feasible and vaccinations adjuvanted by poly-ICLC and GM-CSF displayed favourable safety and excellent immunogenicity: Non-mutated APVAC1 antigens induced sustained central memory CD8+ T-cell responses. APVAC2 induced predominantly TH1 CD4+ T-cell responses against predicted neo-epitopes.
www.GAPVAC.eu

overall_design:
mRNA of 16 patients were analyzed and normalized against a normal kidney sample used as reference
contributor: GAPVAC (Glioma Actively Personalized Vaccine Consortium)

first: J

last: Fritsche


title: Deregulated expression of mammalian lncRNA through loss of SPT6 induces R-loop formation, replication stress and cellular senescence

first: Nicholas

last: Proudfoot

address: South Parks Road

institute: Sir William Dunn School of Pathology,  University of Oxford

summary: Extensive tracts of the mammalian genome that lack protein-coding function are still transcribed into long noncoding RNA. While these lncRNA are generally short-lived, length-restricted and non-polyadenylated, how their expression is distinguished from protein-coding genes remains enigmatic. Surprisingly depletion of the ubiquitous Pol II associated transcription elongation factor SPT6, promotes a redistribution of H3K36me3 histone marks from active protein coding to lncRNA genes which correlates with increased lncRNA transcription. SPT6 knockdown also impairs the recruitment of Integrator complex to chromatin which results in a transcriptional termination defect for lncRNA genes. This leads to the formation of extended, polyadenylated lncRNA that are both chromatin restricted and form increased levels of RNA:DNA hybrid (R-loops) that are associated with DNA damage.  Additionally, these deregulated lncRNA overlap with DNA replication origins leading to localized DNA replication stress and a cellular senescence phenotype. Overall our results underline the importance of restricting lncRNA expression.

overall_design: Directional R-loop occupancy was conducted by sequencing the RNA moeity of the R-loop fragments which were immunoprecipitated by mouse monoclonal S9.6 antibody.

first: S

last: Tan-Wong

first: Somdutta

last: Dhir

first: Nick


title: Bud13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7

city: Pasadena

first: Luke

last: Frankiw

state: California

address: 1200 E California Blvd

institute: Caltech

summary: Intron retention (IR) has emerged as an important mechanism of gene expression control. Despite this, the factors that control IR events remain poorly understood. We observed consistent IR in one intron of the Irf7 gene and identified Bud13 as an RNA-binding protein that acts at this intron to increase the amount of successful splicing. Deficiency in Bud13 led to increased IR, decreased mature Irf7 transcript and protein levels, and consequently to a dampened type I interferon response. This impairment of Irf7 production in Bud13 deficient cells compromised their ability to withstand VSV infection. Global analysis of Bud13 knockdown and BUD13 cross-linking to RNA revealed a subset of introns that share many characteristics with the one found in Irf7 and are spliced in a Bud13-dependent manner. Deficiency of Bud13 led to decreased mature transcript from genes containing such introns. Thus, by acting as an antagonist to IR, Bud13 facilitates the expression of genes at which IR occurs.

overall_design:
mRNA profiles of mouse bone-marrow derived macrophages (BMDMs) expressing either knockdown shRNA or control.  Stimulations performed with TNFa, Poly(I:C), and CpG.
Please note that the -Cyto and -Nuc (in the sample titles) indicates the fraction that was sequenced; '-Cyto' is mRNA from the cytoplasm and '-Nuc' is from the Nucleus.
For the TNFa 0 mins - IFNa 120 mins samples, the raw data was simply mapped to generate the splicing data (provided in .tdf files).


title: RAT-seq mapping of the FLI1 exonic circular RNA FECR1 target gene network in MDA-MB231 breast cancer cells

city: Palo Alto

first: Jifan

last: Hu

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

summary: FECR1 is an exonic circular RNA of the proto-oncogene FLI1. FECR1 is identified as a molecular component in the FLI1 promoter chromatin complex. To study its function in breast cancer, we utilized a RNA reverse transcription-associated trap sequencing (RAT-Seq) approach to map the DNA binding targets in MDA-231 cells.

overall_design: RAT-Seq was utilized to generate the database to map the regulatory element network of FECR1.

first: Naifei

first: Jiuwei

first: Ji-Fan


title: E14.5 pancreatic islet single-cell RNA-seq [ngn3ko1]

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: pancreas islet single-cell RNA-seq

overall_design: isolated from 2 Ngn3 negative mice

first: Guoqiang

last: Gu

first: Alan

last: Simmons


title: Comparative RNA-Seq in mouse prelimbic cortex (PL)

first: yongqing

last: liu

address: 38 Xue Yuan Road

department: Department of Biochemistry and Molecular Biology

institute: Peking University Health Science Center

summary: Major depressive disorder (MDD) is a prevalent and life-threatening illness in modern society. The susceptibility to MDD is profoundly influenced by environmental factors, such as stressful lifestyle or traumatic events, which could impose maladaptive transcriptional program through epigenetic regulation. However, the underlying molecular mechanisms remain elusive. Here we report that stress-susceptible rodents exhibit lower levels of histone crotonylation in the medial prefrontal cortex (mPFC), concurrent with regional upregulation of chromodomain Y-like (CDYL), a crotonyl-CoA hydratase and histone methyllysine reader. Overexpression of CDYL in the prelimbic cortex (PL), a sub-region of mPFC, increases microdefeat-induced social avoidance behaviors and anhedonia in mice. Conversely, knockdown of CDYL in PL prevents chronic social defeat stress-induced depression-like behaviors. Mechanistically, we show that CDYL inhibits structural synaptic plasticity mainly by transcriptional repression of neuropeptide VGF, and this activity is dependent on its dual effect on regional histone crotonylation and H3K27 tri-methylation on the VGF promoter. Together, our data indicate CDYL plays a critical role in regulating stress-induced depression-like behaviors, providing a potential therapeutic target for MDD.

overall_design: PL tissues mRNA profiles of 8-week old Control and Susceptible mice, and AAV-GFP or AAV-CDYL virus expressed mice were generated by deep sequencing, using Illumina HiSeq 2500.

first: Yongqing

last: Liu

first: Zhuo

last: Huang


title: RASA3 regulates the balance of pTh17-Th2 reciprocal programs.

city: Chapel Hill

first: Di

last: Wu

address: 385 S. Columbia Street

department: Periodontics

institute: University of North Carolina, Chapel Hill

summary: Total RNAof pTh17 cells from wild type (WT) and RASA3 KO (RASA3KO) mouse (C57BL/6) was extracted and RNA-seq libraries were generated. Reads (32-45 Million reads per sample) were analyzed with Salmon software to align and quantify the transcript expression. R packages in Bioconductor, tximport and tximportData  were used to aggregate transcript-level quantifications to the gene level, with the R package biomaRt for gene and transcripts mapping. The option "lengthScaledTPM" for countsFromAbundance in tximport was used to obtain the estimated counts at the gene level using abundance estimates scaled based on the average transcript length over samples and the library size. R function voom in limma package was used to transform the estimated count data into log2 scale and estimate the mean-variance relationship so that it can be used to compute appropriate observation level weights, followed by linear modelling. For gene-level differential expression analysis, a linear model was fitted to the log scaled expression data with the genotypes (knockout and wild-type) as one covariate using empirical Bayes moderated t-statistics. The false discovery rate (FDR) was controlled using the Benjamini and Hochberg algorithm. Probes with FDR < 0.05 and fold-change > 2 were judged to be differentially expressed. 317 and 35 genes were identified to be significantly up- and down-regulated respectively. The R function CAMERA was used to determine whether each gene set was differentially expressed in the comparisons as a set. The differential expression patterns and to calculate the enrichment scores of Th1/Th2 (KEGG mmu04658) and Th17 (KEGG mmu04659) related genes in the knockout vs. wild-type comparisons. Our analysis demonstrated that increase of Th2 program and decrease Th17 program in RASA3 KO pTh17 cells, with no change of Th1 related genes. This study indicated that RASA3 is vital for the balance of pTh17-Th2 reciprocal programs.

overall_design: Examination of differential gene expression in WT and RASA3 KO pTh17 cells at 6hr after differentiatoin.

first: Bing

first: Yisong

last: Wan

first: Jitong

last: Lou


title: Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (MeCP2 ChIP-seq)

city: Boston

first: Will

last: Renthal

state: MA

address: 60 Fenwood Rd.

institute: Brigham and Women's Hospital

summary: In females with X-linked genetic disorders, wild-type and mutant cells coexist within brain tissue because of random X-chromosome inactivation. This cellular mosaicism leads to phenotypic variability and poses significant challenges for interpreting the effects of X-linked mutant alleles on gene expression. We present a single-nucleus RNA sequencing approach that resolves mosaicism by using single nucleotide polymorphisms in genes that are expressed in cis with the X-linked mutation to determine whether individual nuclei express the wild-type or mutant allele even when the mutant gene is not directly detected. This approach enables genome-wide comparisons of gene expression between mutant and wild-type cells within the same individual and eliminates the variability introduced by comparisons to controls with different genetic backgrounds. We apply this approach to mosaic female mouse models and humans with Rett syndrome, an X-linked neurodevelopmental disorder caused by mutations in the methyl-DNA-binding protein MECP2, and reveal that cell-type-specific DNA methylation patterns largely predict the degree of gene upregulation by MECP2 in specific neuronal subtypes. The approach described here can be broadly applied to the characterization of gene expression in additional mosaic X-linked conditions.

overall_design: MeCP2 ChIP and input experiments in CamkIIa-positive neurons.

first: William

first: Lisa

last: Boxer

first: Michael

last: Greenberg


title: Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (Single-cell or single-nuclei RNA sequencing)

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell or single-nuclei RNA sequencing was performed on male and female MeCP2 mutant mice or human occipital cortex from Rett syndrome brain donors.


title: Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing

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

overall_design: Refer to individual Series


title: Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (Total RNA sequencing)

overall_design: Total RNA sequencing was performed on human occipital cortex from Rett syndrome brain donors


title: SLE PBMC RNA-seq

status: Public on Nov 14 2018

city: New Haven

first: Maria

last: Tokuyama

state: CT

address: 300 Cedar Street TAC S640

institute: Yale University

summary: RNA sequencing of systemic lupus erythematosus (SLE) and healthy PBMCs to measure transcriptional changes in gene and endogenous retrovirus expression

overall_design: RNA sequencing using RNA obtained from PBMCs of SLE patients and healthy controls

first: Akiko

last: Iwasaki


title: Methylome assays of E14.5 pancreatic progenitor cells

address: 2213 Garland Avenue, MRB4, Rm 9415

summary: pancreatic endocrine progenitor methylome

overall_design: Ngn3-expressing cells were FACS-enriched in Ngn3eGFP/eGFP and Ngn3eGFP/+ panreata

first: Emily

last: Hodges

first: Jonathan

last: Attalla


title: RNA-seq in wild type and dCAP-D3 mutant tissues

city: Cleveland

first: Michelle

middle: Suzanne

last: Longworth

address: 9500 Euclid Ave NE20

institute: Cleveland Clinic Foundation

summary: The goal of this experiment was to identify transcripts that are differentially expressed in dCAP-D3 mutant tissues.

overall_design: RNA was isolated from wing discs and salivary glands of wild type (w1118) or dCap-D3 homozygous mutant (dCap-D3c07081/c07081) larvae. Directional (wing disc) or nondirectional (salivary gland) cDNA libraries (50 bp, paired end) were made at the University of Chicago Genomics Core and sequenced on an Illumina HiSeq2500, according to standard protocols.

middle: S


title: Virus Infection Induces Expression of Novel RNAs in Human Cells

city: Evanston

first: Roli

last: Mandhana

address: 2205 Tech Drive

institute: Northwestern University

summary: Innate antiviral immune responses are driven by virus-induced changes in host gene expression.  In this study, RNA-sequencing of mock-infected and Sendai virus-infected cells was performed to characterize the virus-inducible transcriptome and identify novel virus-inducible RNAs in human cells.

overall_design: RNA-sequencing of mock-infected and Sendai virus-infected for 6 hours Namalwa cells in duplicate using Illumina HiSeq2000

first: Curt

last: Horvath


title: Loss of Sirt2 increase and prolongs a chemically induced pancreatitis permissive phenotype and induces spontaneous oncogenic Kras mutations in mouse

city: Chicago

first: Nobuo

last: Horikoshi

state: IL

address: 303 E Superior St

department: Radiation Oncology

summary: Transcriptome analysis by RNA-seq in pancreas identified 529 differentially expressed genes between wild-type and Sirt2-deficient mice 2 days after injury and confirmed continuous inflammention and tissue regeneration, as well as delayed tissue reorganization.

overall_design: Pancreas mRNA profiles of 2-day post cerulein-induced pancreatitis of wild type (WT) and Sirt2-/- mice were generated by deep sequencing, in triplicate, using lllumina NextSeq 500 Sequencer.

first: David

last: Gius


title: Foxo signaling declines with age

city: Shanghai

first: Xiaofen

address: 345 Lingling Rd

department: Shanghai Institute of Organic Chemistry

institute: Chinese Academy of Sciences

summary:
We performed RNA-seq for WT and foxo mutant flies, by combining with Dr. Baihua's foxo chip-seq data, we found 101 foxo-repressed and 300 foxo-activated genes.
By analyzing expression change of these genes during age, we found foxo-repressed genes became activated, while foxo-activated genes became repressed, suggesting foxo signaling declines with age.

overall_design: Find potential foxo-regulated genes by comparing transcriptome differences between WT and foxo mutant flies, analyze their changes with age using RNA-sequencing data performed at 3d, 15d, 30d and 45d age of WT flies.

last: Liu


title: Six3 and Six6 are jointly required for the   maintenance of multipotent retinal progenitors   through both positive and negative regulation

city: BRONX

first: Wei

address: 1300 Morris Park Avenue

department: Ophthalmology

institute: Albert Einstein College of Medicine

summary:
Purpose: the goal of this experiment was to identify differentially expressed genes in Six3 null, Six6 null and Six3;Six6 compound null retinas by RNAsequencing.
Method: Retinas were dissected out from the following E13.5 mouse embryos: 1) WT (Six3F/F; Six6+/+); 2) Six3 KO (Six3F/F; CAGGCre-ERTM; Six6+/+); 3) Six6 KO (Six3F/F; Six6–/–); 4) DKO (Six3F/F; CAGGCre-ERTM; Six6–/–). RNA was then extracted from the retinas and profiled using RNAsequencing.
Results: RNA isolated from three pairs of retinas for each genotype group (181.2-792 ng, RIN>9) was used for library preparation using KAPA RNA HyperPrep Kit with RiboErase. Sequencing was run on Illumina HiSeq 2500 in 100-bp single-end high-output mode in the Einstein Epigenomics Core Facility. About 30 million reads were generated for each sample. Each genotype group initially had three biological replicates, but one Six6 KO replicate was later removed due to over duplication. After trimming adapters with Trim Galore (v. 0.3.7), RNA-Seq reads were aligned back to mouse genome mm10 using Tophat (v. 2.0.13). The number of reads mapped back to each gene was calculated with HTseq (v.0.6.1)  using Refseq gene annotation (downloaded from the UCSC genome browser in 03/17). The Cuffdiff in Cufflinks package (v. 2.2.1) was used to generate FPKM values. We identified 13498 transcripts with FPKM value >1 in at least one of samples. Deseq2 was used to determine the differentially expressed genes (DEGs) with FDR less than 0.05 as a cutoff.

overall_design: Three pairs of retinas from each genotype were analyzed (n=3 biological replicates). One Six6 KO sample was later removed due to high duplication. Six3KO, Six6KO and DKO samples were compared to WT Controls (Six3F/F) using DESeq2, respectively .

first: Raven

last: Diacou

first: Yilin

last: Zhao

first: Deyou

last: Zheng

first: Ales

last: Cvekl


title: SETDB1 compacts the inactive X chromosome in part through silencing an enhancer in the IL1RAPL1 gene

city: Tallahassee

first: Brian

last: Chadwick

state: FL

address: 319 Stadium Drive, King 3076

department: Biological Science

institute: Florida State University

summary: The product of dosage compensation in human females is the compacted inactive X chromosome (Xi). Here we show that loss of SET domain bifurcated 1 (SETDB1) results in decompaction of the Xi territory coupled with reactivation on the Xi of a powerful enhancer within the 1.4 Mb interleukin-1 receptor accessory protein like 1 (IL1RAPL1) gene at Xp21.2. The enhancer is centrally located in a 0.5 Mb region corresponding to the 3’ third of the IL1RAPL1 locus that transitions from a heterochromatic territory to a euchromatic configuration on the Xi in the absence of SETDB1. This same region showing chromatin instability is part of a common chromosome fragile site that is frequently deleted or rearranged in patients afflicted with intellectual disability and other neurological ailments. Immediately adjacent to the enhancer is an ERVL-MaLR element that drives bi-directional transcription of novel long sense and antisense transcripts. Deletion of the enhancer from the Xa (but not Xi), resulted in detection of bi-directional expression from the Xi coupled with decompaction of the chromosome territory, supporting a critical role for SETDB1 in maintaining this interval in a silent state to facilitate Xi compaction.

overall_design: Examination of three different histone modifications in parental and knock out cells, as well as rRNA-depleted total-RNA-Seq in the parental cells and two independent knock-out clones.

first: Zhuo

last: Sun


title: Gene Expression in COP1-ETV1-ETV5-cJun deficient mouse brain

city: South San Francisco

first: Sarah

middle: K

last: Kummerfeld

address: 1 DNA Way

institute: Genentech

summary:
Total RNA was extracted from E18.5 brains with the olfactory bulbs removed using the MirVana miRNA isolation kit (Invitrogen).  RNA concentration was determined in a NanoDrop 8000 (ThermoFisher) and RNA integrity using both 2100 Bioanalyzer and 2200 TapeStation (Agilent). Libraries were prepared from 1 μg of total RNA with TruSeq RNA Sample Preparation Kit v2 (Illumina).  Library size was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent) and concentration was determined by Library quantification kit (KAPA). Libraries were multiplexed five per lane and then sequenced in a HiSeq2500 (Illumina) to generate 50 million paired end 75 bp reads.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0013017

overall_design: RNA from brain of mice with the following genotypes: COP1 het control, COP1 KO, COP1/cJun DKO, COP1/cJun/ETV1 TKO, COP1/cJun/ETV1/ETV5 QKO

first: Kim

last: Newton

first: Debbi

last: Becker


title: Single cell RNA-seq from cortical cells from e16.5 HET and COP1 KO mice

summary: This study investigates the changes in gene expression with COP1 loss. Single cell reoslution allowed idetnfication of changes in cell populations and in particular an increase in the number of oligodendrocytes in the COP1 KO mice.

overall_design: Cortical cells from four mice (two HET and two COP1 KO) at day e16.5 were dissociated into single cells and sequenced.


title: ACE-inhibition induces a cardioprotective transcriptional response in the metabolic syndrome heart.

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

institute: Genomics Core Leuven

summary:
The goal of the current study was to characterize the cardiac transcriptional signature of the metabolic syndrome (MetS) murine model relative to the healthy, control heart and the differential changes induced by ACE-inhibition, a frequent intervention in MetS subjects, at the transcriptomic level in control and MetS hearts.

Methods - LDLR-/-;ob/ob (DKO, MetS model) and C57Bl6/J (WT) mice were injected with ACE-inhibitor captopril (10 mg/kg/day) between 12 and 24 weeks of age, or NaCl 0,9% as controls. Transcriptome analysis (RNA-seq) from the whole heart RNA samples was performed. Differential gene expression was analysed with Cufdiff. Ingenuity Pathway Analysis (IPA) was used to determine functional enrichment, and analyse pathways, networks, and upstream regulators. Transcription factor motif enrichment analysis was performed with i-cisTarget.

Results – 288 genes implicating 72 pathways were differentially expressed between DKO and WT hearts. The hallmarks of MetS in the heart were an increase in activity of the following pathways: ILK, Rho, dendritic cell maturation, production of nitric oxide and reactive oxygen species in macrophages, atherosclerosis, LXR-RXR, cardiac hypertrophy, and acute phase response. ACE-inhibition resulted in a limited transcriptional effect in WT hearts and in a decrease in activity of Rho-associated signalling pathways. In contrast, a more prominent transcriptional effect was observed in DKO hearts. Similar to WT, Rho-associated pathways were affected, but ACE-inhibition further displayed a counteracting effect on the pathways affected by MetS in the heart

Conclusion –MetS and control mouse hearts have unique transcriptional profiles, with characteristic baseline gene expression landscapes prior to ACE-inhibition, and a partially specific transcriptional response to ACE-inhibition. The Rho-associated signalling pathways and Rho, Rock, Myl, and Fos genes represent potential therapeutic targets.

overall_design: Experimental animal models: DKO; LDLR-/- and ob/ob)18. C57BL/6 (WT); RNA Extraction and Sequencing; RNA-Seq Data Analysis; Pathway and Regulatory Network Analysis; Ethical committee approval.

first: Aziza

last: Yakubova

first: Lieven

last: Thorrez

first: Dmitry

last: Svetlichnyy

first: Liesbeth

last: Zwarts

first: Griet

last: Laenen

first: Wouter

last: Oosterlinck

first: Yves

last: Moreau

first: Luc

last: Dehaspe

first: Jeroen

last: Van Houdt

first: Bart

last: De Moor

first: Patrick

last: Callaert

first: Paul

last: Herijger


title: Comparing the Transcriptomes of Marf1 wildtype (WT) oocytes with those of  Marf1-genetrap (GT-Mut) and Marf1-D272 mutant(D272-Mut) oocytes by RNA-Seq Analysis

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

summary: The goal of this study is to reveal the globle changes of oocyte transcriptome after mutations of Marf1 either by gene trap or knockin of point mutation by comparing the corresponding transcriptomes via RNA-Seq Analysis.

overall_design: Marf1 wildtype (WT), Marf1-genetrap (GT-Mut), and Marf1-D272 mutant(D272-Mut) GV-stageFGOs were collected in RLT lysis buffer for RNA-Seq analysis. 4 replictates of each treatment, with 80 oocyte per  samples, were collected for the experiment. Total RNA was extracted with RNeasy Micro Kit (Qiagen, Germantown, MD, USA) according to manufacturer's instructions, and the mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment. The oocyte mRNA libraries were sequenced on an Illumina HiSeq X Ten platform with 150bp pair-end reads. All reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads were then aligned to the mm10 reference genome using tophat2 (v2.0.13), and FPKMs were calculated and normalized using cufflinks (v2.2.1). The differentially expressed genes were calculated using default parameter of cuffdiff (v2.2.1). Hierarchical clustering was carried on log2(FPKM+1) across samples. Genes used for clustering were selected by maximum FPKM≥1 and with top 10% standard deviation of log2(FPKM+1).


title: The expression profiles of CD4low(HLA-G+) T cells

city: ShangHai

first: Chao

last: Wang

address: 1954HuaShan road

institute: Shanghai Jiao Tong University

summary: The aim of the dataset was to demonstrate that CD4low T cells were murine homolog of CD4lowHLA-G+ T cells by comparing the expression profiles of CD4lowHLA-G+ T cells in prostate cancer (PCa) patients to those of CD4low T cells in PCa mouse models.

overall_design: mRNA profiles of CD4lowHLA-G+ T cells isolated from PCa patients with androgen deprivation therapy (ADT) and naïve CD4+ T cells derived from healthy donors (HD) as controls were generated by deep sequencing, in duplicate, using Illumina HiSeq X Tten. mRNA of CD4low T cells isolated from castrated TRAMP mice and naive CD4+ T cells derived from wild-type mice as controls were sequenced, in duplicate,using Illumina HiSeq X Tten.To determine whether CD4low T cells were murine homolog of CD4lowHLA-G+ T cells,the expression profiles of CD4lowHLA-G+ T cells and CD4low T cells were compared.

first: Yan

last: Zhang

first: Wei

middle: Q

last: Gao


title: Development of Specific Covalent MALT1 Inhibitors and Biomarkers for B-cell Lymphomas

city: New York

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: The MALT1 paracaspase plays an essential role in Activated B-cell like Diffuse Large B-cell Lymphoma (ABC DLBCL) downstream of B-cell and Toll-like receptor pathway genes mutated in these tumors. Although MALT1 is considered to be a compelling therapeutic target, development of tractable and specific MALT1 protease inhibitors has thus far been elusive. Herein, we developed a target engagement assay that provides a quantitative readout for specific MALT1 inhibitory effects in living cells. This enabled a structure-guided medicinal chemistry effort culminating in a novel class of substrate-mimetic compounds that bind MALT1 active site and, constitute the first pharmacologically tractable irreversible MALT1 inhibitor. We confirmed MALT1 targeting is effective at suppressing ABC DLBCL cells in vitro and in vivo. We show that reduction in serum IL10 levels exquisitely correlates with drug PK and degree of MALT1 inhibition in vitro and in vivo and constitutes a useful pharmacodynamic biomarker to evaluate these compounds in clinical trials. Our new inhibitor revealed insights into the biology of MALT1 in ABC DLBCL, such as driving JAK-STAT signaling and suppressing type I interferon (IFN) response and MHC class II expression, suggesting that MALT1 inhibition could prime lymphomas for immune recognition by cytotoxic immune cells.

overall_design: ABC-DLBCL cell lines treated with MALT1 inhibitor compound #3

first: Lorena

last: Fontán

first: Ari

last: Melnick


title: Assessing the effect of D272A-mutation of MARF1 on oocyte transcriptome


title: Comparing the Transcriptomes of Marf1-genetrap (GT) oocytes with those microinjected with mRNAs for wild type MARF1 (GTWT) or D272-mutated MARF1 (GTD272) by RNA-Seq Analysis

summary: The goal of this study is to reveal the globle effect of supplementation with either wild type MARF1or D272-mutated MARF1 on the steady-state levels of mRNAs in Marf1-gene trap GV-stage fully-grown oocytes(FGOs) by comparing the corresponding transcriptomes via RNA-Seq Analysis.

overall_design: Marf1-genetrap (GT)  GV-stageFGOs were microinjected with mRNAsencoding wild type MARF1 or D272-mutated MARF1, and cultured for 48 h in milrinone supplemented medium. Then the oocytes were collected in RLT lysis buffer for RNA-Seq analysis. 4 replictates of each treatment, with 80 oocyte per  samples, were collected for the experiment. Total RNA was extracted with RNeasy Micro Kit (Qiagen, Germantown, MD, USA) according to manufacturer's instructions, and the mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment. The oocyte mRNA libraries were sequenced on an Illumina HiSeq X Ten platform with 150bp pair-end reads. All reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads were then aligned to the mm10 reference genome using tophat2 (v2.0.13), and FPKMs were calculated and normalized using cufflinks (v2.2.1). The differentially expressed genes were calculated using default parameter of cuffdiff (v2.2.1). Hierarchical clustering was carried on log2(FPKM+1) across samples. Genes used for clustering were selected by maximum FPKM≥1 and with top 10% standard deviation of log2(FPKM+1).


title: Distinct Adaptive Mechanisms Drive Recovery from Aneuploidy Caused by Loss of the Ulp2 SUMO Protease [WGS]

status: Public on Nov 13 2018

first: Hong-Yeoul

last: Ryu

address: 266 Whitney Ave

department: MB&B

institute: Yale

summary: In response to acute loss of the Ulp2 SUMO-specific protease, yeast become disomic for chromosome I (ChrI) and ChrXII. Here we report that ChrI disomy, which creates an adaptive advantage in part by increasing the dosage of the Ccr4 deadenylase, was eliminated by extended passaging. Loss of aneuploidy is often accompanied by mutations in essential SUMO-ligating enzymes, which reduced polySUMO-conjugate accumulation. The mRNA levels for almost all ribosomal proteins increases transiently upon initial loss of Ulp2, but elevated Ccr4 levels limit excess ribosome formation. Notably, extended passaging leads to increased levels of many small nucleolar RNAs (snoRNAs) involved in ribosome biogenesis, and higher dosage of three linked ChrXII snoRNA genes suppressed ChrXII disomy in ulp2Δ cells. Our data reveal that aneuploidy allows rapid adaptation to Ulp2 loss, but long-term adaptation restores euploidy. Cellular evolution restores homeostasis through countervailing mutations in SUMO-modification pathways and regulatory shifts in ribosome biogenesis.

overall_design: aneuploid ulp2Δ yeast undergo an analogous evolutionary process using whole genome DNA sequencing (DNA-seq) to identify potential gene mutations arising during repeated cell passaging. WT, ulp2Δ and ulp2Δ reintroduced with pULP2 strains that had been passaged for 500 generations.

first: Mark

last: Hochstrasser


title: Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [proB RNA-Seq]

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recapitulated the transcriptional changes seen with triplication of a “Down syndrome critical region” on distal chromosome 21. Absolute exogenous normalized ChIP-seq (ChIP-Rx) also revealed a global increase in histone 3 lysine 27 acetylation caused by HMGN1. Genes most amplified downstream of HMGN1 were enriched for tumor- and developmental stage-specific programs of B-cell acute lymphoblastic leukemia dependent on the cellular context. These data offer a mechanistic explanation for DS transcriptional patterns, and suggest that further study of HMGN1 and RNA amplification in diverse DS phenotypes is warranted.

overall_design: ERCC spike in RNA-Seq in mouse proB_Ts1Rhr cells

first: Cody

middle: T

last: Mowery

first: Andrew

middle: A

last: Lane


title: Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [ChIP-Seq]

overall_design: ChIP-RX in NALM6 B-ALL cell lines for H3K27ac, H3K4me3, H3K27me3, and H3 in DOX treated and untreated cells


title: Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [SLAM-Seq]

overall_design: SLAM-seq in NALM6 human pre-B cells with engineered HMGN1 overexpression

first: Charles

middle: Y

last: Lin

first: Jarey

first: Kristen

last: Karlin

first: Thomas

middle: F

last: Westbrook


title: scRNAseq of aging dermal fibroblasts

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

institute: Centro Nacional de Análisis Genómico

summary: Transcriptomic analysis of murine aging dermal fibroblasts at single cell level.

overall_design: Comparative study of dermal fibroblasts at 3 different ages: 1.5/2.5-days-old (newborn), two-months-old (young) and 18-months-old (old) mice. C57Bl/6

first: Holger

last: Heyn

last: Rodríguez-Esteban


title: Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [NALM6 RNA-Seq]

overall_design: ERCC spike-in RNA-Seq in NALM6 B-ALL cell line


title: Circulating lymphoid committed progenitors after allogeneic stem cell transplantation in humans

city: Paris

first: Emmanuel

last: Clave

state: Paris

address: INSERM

country: France

institute: UMRS 1160

summary: Lymphoid committed CD34+lin-CD10+CD24- progenitors undergo a rebound at month 3 after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in the absence of acute graft-versus-host disease (aGVHD). Here, we analyzed transcriptional programs of cell-sorted circulating lymphoid committed progenitors and CD34+Lin-CD10- non lymphoid progenitors in 11 allo-HSCT patients having (n=5) or not developed (n=6) grade 2 or 3 aGVHD and in 7 age-matched healthy donors. Major deregulated pathways included protein synthesis, energy production, cell cycle regulation and cytoskeleton organization. Notably, genes from protein biogenesis, translation machinery and cell cycle (CDK6) were over-expressed in progenitors from patients in the absence of aGVHD compared with healthy donors and patients affected by aGVHD. Expression of many genes from the mitochondrial oxidative phosphorylation metabolic pathway leading to ATP production were more specifically increased in lymphoid committed progenitors in absence of aGVHD. This was also the case for genes involved in cell mobilization such as those regulating Rho GTPases activity. In all, we show that circulating lymphoid committed progenitors undergo profound changes in metabolism favoring cell proliferation, energy production and cell mobilization after allo-HSCT in humans. These mechanisms are abolished in case of aGVHD or its treatment, indicating a persistent cell-intrinsic defect after exit from bone marrow.

overall_design: Transcriptome analysis of 2 cell populations CD34+lin-CD10+CD24-(TSP) and CD34+lin-CD10- (CD10) from peripheral blood of 11 patients that underwent Hematopoietic transplantation (5 with acute Graft versus Host Disease) and 7 Healthy controls,

first: Salomé

last: Glauzy

first: Régis

last: Peffault de Latour

first: Joël

last: Lachuer

first: Sophie

last: Servais

first: Gérard

last: Socié

first: Antoine

last: Toubert


title: TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma

city: Cold Spring Harbor

first: Tim

middle: D D

last: Somerville

address: 1 Bungtown Road

department: CSHL

institute: Cold Spring Harbor Laboratory

summary: The aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative trans-differentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 (ΔN isoform) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human PDA cells. In addition, we demonstrate that TP63-driven enhancer reprogramming promotes aggressive tumor phenotypes, including enhanced cell motility and invasion and an accelerated growth of primary PDA tumors and metastases in vivo. Conversely, we provide evidence that squamous PDA remains addicted to TP63 to sustain the growth of primary tumors and metastases. Taken together, our study validates the functional significance of squamous trans-differentiation in PDA, and reveals TP63-based reprogramming of PDA cells as an experimental tool for investigating vulnerabilities linked to this cell fate transition.

overall_design: Refer to individual Series


title: PPARg-K107 SUMOylation regulates insulin sensitivity but not adiposity in mice

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Homozygous K107R mutation of PPARg in mice alters the expression of its downstream target genes and increases insulin sensitivity but not adiposity.

overall_design: RNA-seq was performed using inguinal and epididymal white adiose tissue from high fat diet-fed WT and PPARg-K107R mutant adipose administered either rosiglitazone or vehicle.

first: Takeshi

last: Katafuchi

first: Rahul

last: Kollipara

first: David

last: Mangelsdorf

first: Steven

last: Kliewer


title: TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma (ChIP-seq)

overall_design: H3K27ac ChIP-seq was performed using antibody recognizing endogenous protein with input genomic DNA as control with/without transduction of sgNEG/sgTP63#2/sgTP63#4 (BxPC3 cells) or MTV/TP63ΔN (SUIT2 cells). TP63 ChIP-seq in BxPC3 cells was performed using antibody recognizing endogenous protein with input genomic DNA as control. FLAG-TP63 ChIP-seq in SUIT2 cells was performed in FLAG-TP63 expressing cells with input genomic DNA as control.

middle: D

first: Christopher

middle: R

last: Vakoc


title: Gene expression profiles of PD1-high, PD1-intermediate, and PD1-negative tumor-infiltrating CD8 T cells in hepatocellular carcinoma

city: Daejeon

first: Su-Hyung

last: Park

address: 291 Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: We report the gene expression profiles of FACS-sorted PD1-high, PD1-intermediate, and PD1-negative tumor-infiltrating CD8 T cells in hepatocellular carcinoma.

overall_design: Examination of gene expression profiles in 3 distinct subpopulations of tumor-infiltrating CD8 T cells in hepatocellular carcinoma.


title: Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression

city: Boston

first: James

last: Bradner

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


title: TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma (RNA-seq)

overall_design: For RNA-seq performed in cells transduced with control empty, one or two technical repeats were used. For RNA-seq performed in cells transduced in experimental sgRNAs/cDNA two sgRNAs/cDNAs were treated as repeats.


title: Robust hematopoietic stem cell activity is derived from pre-circulation embryos but not yolk sacs

city: Memphis

first: Shannon

last: McKinney-Freeman

state: Tennessee

address: MS 341, Room D3007E, 262 Danny Thomas Place Memphis, TN

institute: st jude children's research hospital

summary: The embryonic site of definitive hematopoietic stem cell (dHSC) origination has been debated for decades. Although an intra-embryonic origin is supported, recent data suggest that a large fraction of adult blood derives from the yolk sac (YS). Investigating the origins of hematopoiesis before heartbeat onset (i.e. 5-7 somite pairs (sp)) is precluded by a lack of assays that can distinguish dHSC precursors in early embryos. Here, we report robust, multi-lineage and serially transplantable dHSC activity from cultured 2-7sp murine embryonic explants (Em-Ex). dHSC were undetectable in 2-7sp YS explants (YS-Ex).  Our work supports a model in which the embryo, not the YS, is the major source of lifelong hematopoiesis.

overall_design: Single cell global gene expression analysis of Em-Ex- and YS-Ex-CD31+CD45+c-Kit+CD41- cells.

first: Miguel

last: Ganuza

first: Ashley

last: Chabot

first: Xing

last: Tang

first: Wenjian

last: Bi

first: Sivaraman

last: Natarajan

first: Robert

last: Carter

first: Charles

last: Gawad

first: Guolian

last: Kang

first: Yong

last: Cheng


title: A CHAF1B-dependent molecular switch in hematopoiesis and leukemia pathogenesis

status: Public on Nov 12 2018

first: Elizabeth

middle: Thomas

last: Bartom

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

summary: CHAF1B is the p60 subunit of the chromatin assembly factor (CAF1) complex, which is responsible for assembly of H3.1/H4 heterodimers at the replication fork during S phase. Here we report that CHAF1B is required for normal hematopoiesis while its overexpression promotes leukemia. CHAF1B has a pro-leukemia effect by binding chromatin at discrete sites and interfering with occupancy of transcription factors that promote myeloid differentiation, such as CEBPA. Reducing Chaf1b activity by either heterozygous deletion or overexpression of a CAF1 dominant negative allele was sufficient to suppress leukemogenesis in vivo without impairing normal hematopoiesis.

overall_design: Examination of the function of CHAF1B in maintaining undifferentiated state of leukemic cells. We used Chaf1b-floxed MLL-AF9 leukemic cell clones which were transduced with CreERT2. Knockout was induced by treatment with B-estradiol, and cells were lysed 48 hours after induction for analysis. Floxed cells expressing CreERT2 treated with EtOH were used as clonal controls.

first: Andrew

last: Volk

first: John

last: Crispino


title: Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-thioguanisine

city: West Haven

first: Matthew

last: Simon

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

summary: RNA-sequencing (RNA-seq) measures RNA abundance in a biological sample but does not provide temporal information about the sequenced RNAs. Metabolic labeling can be used to distinguish newly made RNAs from pre-existing RNAs. Mutations induced from chemical recoding of the hydrogen bonding pattern of the metabolic label can reveal which RNAs are new in the context of a sequencing experiment. These nucleotide recoding strategies have been developed for a single uridine analogue, 4-thiouridine (s4U), limiting the scope of these experiments. Here we report expansion of TimeLapse sequencing (TimeLapse-seq) to the guanosine analogue, 6-thioguanosine (s6G), which can be recoded under RNA-friendly nucleophilic-aromatic substitution conditions to produce adenine analogues (substituted 2-aminoadenosines). We demonstrate the first use of s6G recoding experiments to reveal transcriptome-wide RNA population dynamics.

overall_design: Distinguishing newly made from preexising RNA using RNA-sequencing of 6-thioguanosine containing RNA, which was subjected to TimeLapse chemistry to induce G to A mutations in newly-made RNA.

first: Lea

last: Kiefer

first: Jeremy

last: Schofield


title: Gut Adaptation of Ahr Expression Cell-intrinsically Restricts Group 2 Innate Lymphoid Cell Function

city: Gainesville

first: Liang

last: Zhou

department: Department of Infectious Diseases and Immunology

institute: University of Florida

summary: Innate lymphoid cells (ILCs) are important for mucosal immunity. The intestine harbors all ILC subsets; however, how these cells orchestrate each other to achieve immune homeostasis and mount appropriate immunity during infection remains elusive. Here, we show that the adaptation of the aryl hydrocarbon receptor (Ahr) expression in the gut is a key regulatory mode for the host to keep the ILC balance. Among ILCs, Ahr is most highly expressed by gut ILC2, and controls in a positive feedback manner, chromatin accessibility at the Ahr gene locus. Ahr suppresses Gfi1-mediated ST2 expression in ILC2 and expression of ILC2 effector molecules IL-5, IL-13 and amphiregulin in a cell-intrinsic manner. Ablation of Ahr enhances anti-helminth immunity in the gut, while genetic or pharmacological activation of Ahr suppresses ILC2 but enhances ILC3 to protect the host from Citrobacter rodentium infection. Thus, the host regulates the gut ILC2-ILC3 balance by engaging the Ahr pathway to mount appropriate immunity against various pathogens.

overall_design: RNA-seq (8 samples) and ATAC-seq  (24 samples) analysis of small and large intestine ILC2s from Ahr wildtype and knockout mice.

first: Shiyang

last: Li

middle: W

last: Bostick

first: Jian

last: Ye

first: Ju

last: Qiu

first: Bin

last: Zhang

first: Joseph

last: Urban

first: Dorina

last: Avram


title: MLL4 establishes super-enhancers and broad H3K4me3 for tumor-suppressive function

first: JIE

last: Lv

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

summary: Clusters of enhancers called super-enhancers are associated with gene activation. Broad trimethyl histone H3 lysine 4 (H3K4me3) often defines actively transcribed tumor suppressor genes. However, how these epigenetic signatures are regulated for tumor suppression is poorly understood. Here, we show that brain-specific knockout of the H3K4 methyltransferase MLL4 (aka KMT2D) in mice spontaneously induces cerebellar tumors in brain while indirectly increasing expression of oncogenic programs, such as Ras activators and Notch pathway components. Mll4 loss caused widespread impairment of super-enhancers and broad H3K4me3. Notably, Mll4 loss reduced super-enhancer and broad H3K4me3 signals in tumor suppressor genes co-marked by both signatures, including Dnmt3a and Bcl6. MLL4 upregulates DNMT3A-mediated DNA methylation to downregulate expression of Ras activators and increases Bcl6 expression to suppress the Notch pathway. These findings suggest an unanticipated epigenetic tumor-suppressive mechanism in which MLL4 is required for establishing super-enhancers and broad H3K4me3 for anti-tumor programs in normal cells.

overall_design:
Expression profiling by RNA-seq, profiling of Mll4f/f (Mll4_WT) and Mll4 BSKO (Mll4 KO) from one month and 4 months mice cerebellum, and histone modifications (H3K4me1/3, H3K27ac, and Mll4) by ChIP-seq, at four months cerebellum. ChIP assays were performed as a modification of the previously described methods (Dhar et al., 2016; Dhar et al., 2012). In brief, cerebellar (4-month-old) tissues were isolated. DNA was purified from chromatin immunoprecipitates for MLL4 or IgG using the phenol/chloroform extraction. IgG was used as a negative control for ChIP (samples not included here). Then, DNA was amplified by quantitative PCR and normalized to input. To compare H3K4me1, H3K27ac, and H3K4me3 levels between Mll4f/f and Mll4 BSKO cerebellum, ChIP with reference exogenous genome (ChIP-Rx) was carried out as previously described (Li et al., 2016; Orlando et al., 2014).

This series includes H3K4me1, H3K27ac, and H3K4me3 ChIP-seq data of cerebellar neurospheres.

first: S

last: Dhar

first: D

last: Zhao

first: J

first: K

last: Chen

first: M

middle: G

last: Lee


title: Role of PAEP/glycodelin in NSCLC

city: Heidelberg

first: Michael

last: Meister

state: Select One

address: Roentgenstr. 1

department: STF

institute: Thoraxklinik-Heidelberg


title: The Transcription Factor ATF7 Controls Adipocyte Differentiation and Thermogenic Gene Programming

status: Public on Nov 10 2018

city: Tsukuba

first: Yang

last: LIU

state: Ibaraki.

address: 3-1-1 Koyadai, Tsukuba, Ibaraki

country: Japan

institute: Riken

summary:
The adipocytes functions as a central organ in the regulation of metabolic homeostasis. Factors which contribute to the adipocyte differentiation and function would be the promising targets to combat the obesity and associated metabolic disorders. The activating transcription factor 7 (ATF7), a stress-responsive chromatin regulator, has recently been shown to be involved in the energy metabolism; however, the underlying mechanisms are still unknown. Here, we show that ATF7 is required for adipocyte differentiation and it interacts with histone dimethyltransferase G9a in adipocyte to repress the interferon-stimulated genes (ISGs) expression, which suppresses adipogenesis. Ablation of ATF7 promotes the beige biogenesis and browning of inguinal white adipose tissue (iWAT). ATF7 binds to the transcription regulatory regions of Ucp1 gene, and silences it by maintaining the histone H3K9 dimethylation level. These results establish the multifunction of ATF7 in adipocyte and provide molecular insights into the epigenetic control of development and function of adipose tissues.
We used microarrays to identify the differentatial expression genes in the inguinal white adipose tissue of ATF7 KO mice.

overall_design: Three control replicates (wildtype) and three experimental replicates (ATF7 KO) mice were analyzed.

last: Liu

first: Toshio

last: Maekawa

first: Keisuke

last: Yoshida

first: Masafumi

last: Muratani

first: Bruno

last: Chatton

first: Shunsuke

last: Ishii


title: Gene expression profiling of two NSCLC cell lines treated with PAEP/glycodelin expression stimulating substances

summary:
We compared H1975 and 2106T cells treated with PAEP/glycodelin expression inducing substances and the corresponding contol treated cells.
Gene expression profiling of  H1975 and 2106T cells with induced PAEP/glycodelin expression might give hints on several pathways regulating this activated expression.

overall_design: PAEP/glycodelin expression stimulating substances in NSCLC cell lines were screened in previous qPCR and western blot analyses. Accordingly, H1975 cells were treated with PMA and 2106T cells were incubated with LPA, PMA, EGF and HB-EGF for 24 h. We compared these data with the corresponding control treatment in three independent experiments (named with 1, 2 and 3). Gene expression profile was analysed by using Affymetrix HG-U133 Plus 2.0 arrays.

first: Rebecca

last: Weber

first: Thomas

last: Muley

last: Thomas

first: Holger

last: Sültmann

first: Arne

last: Warth

first: Hauke

last: Winter

first: Felix

middle: J

last: Herth

first: Elizabeth

middle: C

last: Xu

first: Marc

last: Schneider


title: Gene expression profiling of NSCLC tumors with high and low PAEP expression

last: Meister

summary: Gene expression profiling of NSCLC tumors with distinct PAEP expression suggested several pathways, which might be involved in the regulation of PAEP/glycodelin expression.

overall_design: We compared lung squamous cell carcinomas (15 each) as well as lung adenocarcinomas (20 each) with high and low PAEP expression. Gene expression profile was analyzed using Affymetrix HG-U133 Plus 2.0 arrays.


title: Differential expression of miRNAs in mouse hearts of ADAR2 knockout mice.

city: Vienna

first: Cornelia

last: Vesely

address: Schwarzspanierstrasse 17

department: Anatomy

country: Austria

institute: Medical University of Vienna

summary: Using small RNA next generation sequencing, we report the differential expression of mature miRNAs in mice hearts in wildtype versus Adar2-/- (Adarb1-/-) knockout animals.

overall_design: Differential gene expression analysis in 3 replicates of 2 genotypes.

first: Aamira

last: Tariq


title: RNA-seq of Mus musculus: WT and MTCH2 KO Naïve & Primed mouse embryonic stem cells

city: Rehovot

first: Amir

last: Bahat

address: Herzel 234 st

department: Biological regulation

country: Israel

institute: Weizmann institute of science

summary: The role of mitochondria dynamics and its molecular regulators remains largely unknown during naïve-to-primed pluripotent cell interconversion. Here we report that mitochondrial MTCH2 is a regulator of mitochondrial fusion, essential for the naïve-to-primed interconversion of murine embryonic stem cells (ESCs). During this interconversion, wild-type ESCs elongate their mitochondria and slightly alter their glutamine utilization. In contrast, MTCH2-/- ESCs fail to elongate their mitochondria and to alter their metabolism, maintaining high levels of histone acetylation and expression of naïve pluripotency markers. Importantly, enforced mitochondria elongation by the pro-fusion protein Mitofusin (MFN) 2 or by a dominant negative form of the pro-fission protein dynamin-related protein (DRP) 1 is sufficient to drive the exit from naïve pluripotency of both MTCH2-/- and wild-type ESCs. Taken together, our data indicate that mitochondria elongation, governed by MTCH2, plays a critical role and constitutes an early driving force in the naïve-to-primed pluripotency interconversion of murine ESCs.

overall_design: Examination of WT and MTCH2 KO ESC and EpiLC mouse embryonic stem cells transcriptome


title: MeCP2 regulates genome-wide gene expression through recognition of H3K27me3 [ChIP_human]

city: Gwangju

first: Wooje

last: Lee

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

institute: Chosun University

summary: MeCP2 plays a multifaceted role in gene expression regulation and chromatin organization. Interaction between MeCP2 and methylated DNA to regulate gene expression is well established. However, the widespread MeCP2 distribution suggests its additional interactions with chromatin. Here we show, by both biochemical and ChIP-seq analyses, that MeCP2 directly binds to nucleosome subunit proteins and is recruited to distinct chromatin regions where H3K27me3 is enriched. We further observed that the impact of MeCP2 on transcriptional changes is correlated with histone post-translational modification patterns. Our findings indicate that MeCP2 can be recruited to genomic loci via indirect binding and that interaction between MeCP2 and histone proteins plays a significant role in gene expression regulation.

overall_design:
In order to perform genome-wide quantitative comparisons of histone modification difference between DMSO and GSK343 treatment, the drosophila S2 genome was added to each experiment. An exogenous genome-derived normalizing factor was used for normalization.
Please note that each processed data file was generated from both rep1 and rep2 samples, and is linked to the corresponding rep1 sample records.

first: Qizhi

last: Gong


title: MeCP2 regulates genome-wide gene expression through recognition of H3K27me3 [ChIP_mouse]

overall_design: Examination of three epigenetic markers from the olfactory epithelium in two biological samples


title: DNA microarray analysis of active- and inactive-adult Still disease (ASD)

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

summary: Objective: Adult Still’s disease (ASD) is a systemic disorder of unknown etiology characterized by high spiking fever, rash and arthritis. The purpose of this study was to determine the pathogenic roles of specific genes in ASD.  Methods: Differentially expressed genes (DEGs) were examined by DNA microarray and validated by quantitative PCR using monocytes isolated from patients with active-ASD, inactive-ASD and healthy controls. The correlation between validated DEGs and ASD activity was analyzed. After inflammasome activation with LPS and Nigericin, the production of IL-1β, IL-18, inflammasome and autophagy related proteins in DEGs-overexpressing THP-1 cells was carried out by ELISA or western blotting. DEGs-overexpressing THP-1 cells were treated with an inhibitor of autophagy followed by assessment of IL-1β and IL-18 production by ELISA and western blotting method.Conclusions: The overexpression of PLAC8 in monocytes might play a regulatory role in the production of IL-1β and IL-18 by the enhancement of autophagy, resulting in the suppression of ASD.  Results:A total of 68 genes were highly expressed in monocytes isolated from active-ASD patients, relative to their expression in inactive-ASD patients and healthy controls. After validation of expression of 13 genes (CLU, FCGR1B, PLAC8, TLR1, S100A12, CD55, PIM1, BCL2A1, SOD2, PLSCR1, CYP1B1, STEAP4, IL1RN), the expression of PLAC8 was significantly higher in active-ASD patients than the other groups. In ASD, PLAC8 expression level correlated with serum levels of CRP, ferritin and IL-18. Stimulation of monocytes with lipopolysaccharide resulted in PLAC8 upregulation. LPS or Nigericin stimulation of PLAC8-overexpressing THP-1, but not THP-1 cells< was associated with significant decrease in IL-1β and IL-18 production. PLAC8 overexpressing in THP-1 cells was associated with enhanced autophagy and suppression of IL-1β and IL-18 production.  Conclusions: PLAC8 upregulation in monocytes seemed to play a regulatory role in the production of IL-1β and IL-18 through enhanced autophagy, resulting in suppression of ASD. The results highlight the role of PLAC8 in the pathogenesis of ASD and suggest its potential suitability as a therapeutic target in ASD.

overall_design: All subjects were examined at the University of Tsukuba Hospital and each provided signed consent form for participation in the study. The study was approved by the ethics committee of the University of Tsukuba. In total, 9 active-ASD patients (3 males and 6 females, the mean±SD age; 51.2±17.0 years), 10 inactive-ASD patients (3 males and 7 females, the mean±SD age; 45.5±13.6 years), 8 rheumatoid arthritis (RA, 3 males and 5 females, the mean±SD age; 50.0±18.3 years) patients as a disease control and 8 healthy controls (HC, 3 males and 5 females, the mean±SD age; 50.1±8.4 years)  were included in present prospective study. All active-ASD patients satisfied Yamaguchi’s criteria [Yamaguchi M, et al.,  J Rheumatol. 1992; 19: 424-430], and all RA patients satisfied the American College of Rheumatology classification criteria [Arnett FC, et al., Arthritis Rheum. 1988; 31:315-324]. Healthy control subjects matched for sex and age were recruited as the control group. Monocytes (CD14+ cells) were isolated from HC (n=3, 1 males and 2 females, the mean±SD age; 51.0±7.9 years), inactive-ASD (n=3, 1 males and 2 females, the mean±SD age; 48.7±10.7 years) and active-ASD patients (n=3, 1 males and 2 females, the mean±SD age; 48.7±10.7 years) by magnetic-activated cell sorting (MACS, Miltenyi Biotec, Bergisch Gladbach, Germany). In ASD, monocytes were isolated from same patients on active and inactive stages.

first: Seiji

last: Segawa

first: Yuya

last: Kondo

first: Akira

last: Iizuka

first: Shunta

last: Kaneko

first: Masahiro

last: Yokosawa

first: Kotona

last: Furuyama

first: Hiroto

last: Tsuboi

first: Daisuke

last: Goto

first: Isao

last: Matsumoto

first: Takayuki

last: Sumida


title: Genome-wide identification of protein binding sites on RNAs in mammalian cells [PBS-R]

city: Beijing

first: Liu

last: Fenglin

address: Courtyard 1, Beichen West Road

institute: Chinese Academy of Sciences

summary: We develop a novel method, called protein binding sites on RNA (PBS-R) to identify genome-wide protein binding sites on RNAs without using antibodies. Double click strategy is used for the PBS-R assay. Proteins and RNAs are UV-crosslinked in vivo first, then the proteins are crosslinked to the magnetic beads. The protein binding RNA elements are captured, reverse transcribed and sequenced.

overall_design: Identification of RNA-protein binding patterns in Hela cells through high-throughput sequencing.

first: Fenglin

last: Liu

first: Yuxiang

last: Zhang