title: Genome-wide binding of Lola in S2 cells

status: Public on Sep 07 2019

city: Shanghai

first: Wentao

last: Yu

address: 320 Yue Yang Road

department: Center for Excellence in Molecular Cell Science,Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary:
Purpose: The transcription fact Lola is identified as a conponent acting downstream of Hippo signaling to restrict ISC proliferation and regulate midgut homeostasis. To further elucidate the mechanism of Lola regulating ISC proliferation and midgut homeostasis,Chromatin immunoprecipitation assay followed by sequencing (ChIP-seq) was performed to identify genes suppressed directly by Lola.
Methods: Chromatin lysates were clarified from homogenized and sonicated S2 cells; protein-DNA complexes were isolated with antibody. Genomic DNA fragments were purified with a DNA purification kit (QIAGEN) and subjected to high throughput sequencing using  Illumina HiSeq2500.
Process: After the genomic DNA segments were sequenced using Illumina HiSeq2500. After quality control with fastqc (version 0.11.8), we built genome index from Drosophila melanogaster genome(BDGP6)with bowtie2-build. Reads were aligned to Drosophila genome BDGP6 index with bowtie2. Then we converted sam files to bam files with samtools. Peaks were called from the aligned reads using MACS2 callpeak, and peaks annotation using R package ChIPseeker.
Conclusion: Thousands of Lola-associated chromatin binding sites were identified in cultured S2 cells. Analysis of the Lola binding profiles revealed that Lola mainly binds to the regions around transcription start sites (TSS) and promoters.

overall_design: Identification of the transcription factor Lola binding region in S2 cells.

first: Xue

last: Hao

first: Lei

last: Zhang


title: PML2‐mediated thread‐like nuclear bodies mark late senescence in Hutchinson–Gilford progeria syndrome [RNA-seq]

status: Public on Sep 10 2019

city: Shenzhen

first: Baohua

last: Liu

address: No.1066 Xueyuan Av. Nanshan District

country: China

institute: Shenzhen University

type: Expression profiling by high throughput sequencing

summary: Regular nuclear structure is critical for genome maintenance and proper gene expression, disorder of which has a causal role in aging. Accumulation of Progerin in Hutchinson-Gilford progeria syndrome (HGPS) disrupts the integrity of nuclear lamina and causes nuclear structure abnormalities, leading to premature aging. However, the nuclear structure/function relationships in HGPS cells have not been well addressed, and roles of nuclear sub-compartments for HGPS pathogenesis are rarely reported. Here, evidence reveals that classical dot-like PML nuclear bodies (PML NBs) are reorganized into thread-like morphology in HGPS cells, and these irregular NBs are strongly associated with cell senescence. We demonstrate that farnesylated Progerin interacts with PML isoform 2 specifically, which accounts for the formation of thread-like PML NBs. Moreover, our findings uncover that irregular PML NBs perturb NBs-associated DNA repair and gene transcription, thereby promoting HGPS cell senescence. Thus, our work helps to clarify the roles of nuclear structure and sub-compartments such as PML NBs in cell aging, and evidence presented in this study strongly support that thread-like PML NBs could be a novel biomarker of human cell senescence.

overall_design: Normal human dermal fibroblasts (NHDF) were transfected with control siRNA (NFcon) or pan-PML siRNA (NFsi) to analyze the expression of PML NBs-associated genes in NHDF cells. Fibroblasts from the Hutchinson-Gilford progeria syndrome (HGPS) patient were treated with control siRNA (HGcon), pan-PML siRNA (HGsi), PML2 siRNA (HGI2si), or FTI (2 uM of farnesylation inhibitor lonafarnib combined with 1 uM of zoledronate, HGFTI) for 3 days. High-throughput RNA sequencing were performed to analyze the differential gene expression between HGPS and NHDF, and to examine the 'rescue effect' of pan-PML siRNA, PML2 siRNA or FTI treatment on expression of PML NBs-associated genes in HGPS cells. Thus, there are total 6 groups of samples for RNA-seq, ie., NFcon, NFsi, HGcon, HGsi, HGI2si and HGFTI. Each group contains 3 replications, and siRNA sequence information was described in the supporting data of the manuscript.

first: Ming

last: Wang


title: Non-functioning pituitary adenomas AmpliSeq data

status: Public on Sep 04 2019

city: Warsaw

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular Oncology Department

country: Poland

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

summary: This dataset contains high throughput sequencing data from Non-functioning pituitary adenomas (NFPAs) together with associated control sections of healthy pituitary which was obtained from formalin-fixed paraffin embeded samples. All of the samles come from patients of Maria Sklodowska-Curie Memorial Cancer Center in Warsaw. All the samples were sequenced using Ion Torrent technology in Maria Sklodwoska-Curie Memorial Cancer Center in Warsaw. They were further processed and used to perform complex analyses using other high-throughput data.

overall_design: 42 freshly frozen samples from patients with non-functioning pituitary adenomas were used together with 4 formalin-fixed paraffin embeded controls – ie. healthy pituitary section.

first: Joanna

last: Boresowicz

first: Paulina

last: Kober

first: Natalia

last: Rusetska

first: Maria

last: Maksymowicz

first: Agnieszka

last: Paziewska

first: Michalina

last: Dabrowska

first: Jacek

last: Kunicki

first: Wiesław

last: Bonicki


title: Microarray profile of CD19+ B cells from Graves' disease patients reveals potential molecular mechanisms associated with the proliferation of B cell

status: Public on Sep 02 2019

first: Bingbing

last: Zha

address: 801Heqing   Rd

institute: Fifth People's Hospital of Shanghai Fudan University

summary: Hyperthyroidism is a kind of common autoimmune disease. It is widely accepted that B lymphocytes play a significant role in GD as they are the source of autoantibodies (TRAb) against the thyroid-stimulating hormone receptor (TSHR). We previously observed B cells infiltrated in the thyroid tissue from GD patients was significantly higher than that in healthy controls.In this study, our flow cytometry results indicated that the proportion of B cells in GD patients is much higher than that in control. To explore the underlying pathological function of B cells in GD, a microarray profiles was performed in these isolated B cells.

overall_design: Peripheral blood was obtained from newly diagnosed GD patients (n = 34) and age matched healthy individuals (n = 34) who were recruited in a parallel group trial. Microarrays were performed to compare the differences in long non-coding RNA (lncRNA) and mRNA expression profiles of purified B cells in newly diagnosed GD patients with healthy individuals. Gene Ontology (GO)and Pathway analysis showed the potential function and pathway involved in the differentially expressed genes, some were validated by qRT-PCR. Two independent algorithms were used to predict the lncRNAs that regulate target gene. The Protein-protein interaction (PPI) network present the underlying interaction of these differentially expressed genes.

first: Xuechao

last: Jiang

first: Yonghui

first: Xiaoying

last: Li

first: Leqi

last: He

first: Wei

first: Jun


title: PML2‐mediated thread‐like nuclear bodies mark late senescence in Hutchinson–Gilford progeria syndrome [ChIP-seq]

first: Baohua

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Analyze PML nuclear bodies associated gene loci

first: Ming


title: PML2-mediated thread-like nuclear bodies mark late senescence in Hutchinson–Gilford progeria syndrome

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

overall_design: Refer to individual Series


title: ChIP-seq of beta-catenin and TCF4 in mouse marrow derived MSCs

city: Rochester

first: Andre

middle: J

last: van Wijnen

state: MN

address: 200 First Street SW

department: Orthopedic Surgery & Biochemistry and Molecular Biology

country: USA

institute: Mayo Clinic

overall_design: Marrow derived MSC cells were treated with vehicle or LiCL for 3 hours to ChIP assay, library creation and sequencing.

first: Mark

middle: B

last: Meyer

first: Nancy

middle: A

last: Benkusky

first: J

middle: W

last: Pike


title: Oligomeric human Aβ1-42 inhibits antigen presentation

status: Public on Sep 16 2019

city: Schlieren

first: Anna

last: Mallone

state: Zurich

address: Wagistrasse 12

department: Institute for Regenerative Medicine

country: Switzerland

institute: University of Zurich

summary: The goal of this study is to investigate the involvement of inflammation in Alzheimer’s disease (AD) and to clarify the signaling pathways involved in the presence of beta-amyloidosis, a hallmark of AD pathogenesis, to help identifying potential targets for therapy. To do that, we isolated bone marrow-derived progenitor cells from femurs, tibiae and hip bones of non-transgenic C57BL/6 mice according to established protocols , and we maturated them with LPS. To obtain an unbiased view of gene regulation in mouse bone marrow-derived dendritic cells (BM-DCs) exposed to pre-aggregated beta-amyloid peptide (Aβ) oligomers, we analyzed the transcriptome of untreated immature control BM-DCs (‘Ctrl’), LPS-treated BM-DCs (’LPS’), Aβ1-42 oligomer-treated BM-DCs (‘Aβ‘) and BM-DCs treated with Aβ1-42 oligomers and LPS (‘Aβ+LPS‘) via explorative RNA-sequencing.

overall_design: Relative comparison of mRNA profile of mouse bone marrow-derived dendritic cells with different treatments: (1) control bone marrow-derived dendritic cells (‘Ctrl’), (2) LPS-treated bone marrow-derived dendritic cells (’LPS’), (3) Aβ1-42 oligomer-treated bone marrow-derived dendritic cells (‘Aβ‘), (4) and bone marrow-derived dendritic cells treated with Aβ1-42 oligomers and LPS (‘Aβ+LPS‘). The RNA sequencing was performed in single reads of 100bp length using Illumina HiSeq3000 (Illumina), data were generated in triplicate.

first: Christoph

last: Gericke

first: Britta

last: Engelhardt

first: Roger

middle: M

last: Nitsch

first: Maria

middle: T

last: Ferretti


title: A Molecular Signature Predicts 2-Year Outcome of Biliary Atresia and Identifies a Treatment Target to Suppress Fibrosis

status: Public on Aug 20 2019

city: Cincinnati

first: Zhenhua

last: Luo

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Background & Aims: Age at diagnosis and response to surgery have been correlated with an improved survival with the native liver in children with biliary atresia. However, biological predictors of outcome are largely undefined. We investigated if gene expression profiles at diagnosis predict clinical outcome.  Methods: Global gene expression was quantified by RNAseq of liver biopsies from 171 infants with BA at diagnosis and randomly assigned into discovery (N=121), validation (N=50) cohorts and 7 normal  controls.

overall_design: mRNA profiles of 171 livers from patients with biliary atresia and 7 livers from normal controls by deep sequencing using Hiseq 2500

first: Jorge

last: Bezerra


title: Expression profile of select glucose and lipid metabolic genes mediated by STIM1-Snail1 circuit in SMMC7721 cells

status: Public on Aug 17 2019

city: Chongqing

first: Huakan

last: Zhao

state: State...

address: Xinqiao Street 183, Shapingba district

department: Clinical Medicine Research Center

institute: Xinqiao Hospital, Third Military Medical University

summary: To investigate the altered glucose and lipid metabolic genes after Snail1 overexpression, Snail1 plus STIM1 double overexpression in SMMC7721 cells. Snail1 overexpression (Snail1 OE)- and Snail1 plus STIM1 double overexpression(Snail1+STIM1 dOE)- SMMC7721 cells were established via lentiviral Infection. The cells mentioned above were cultured in DMEM supplemented with 10% (v/v) FBS at 37°C in 5% CO2. When the cells grow to 60~70% confluent, Total RNA was extracted by using Trizol (TAKARA, Japan). Reverse transcription was performed from 1μg total RNA using PrimeScript™ RT reagent Kit with gDNA Eraser (TAKARA), Quantitative real-time PCR were performed (CFX386, BioRad) with 40 cycles at 95 oC for 10 seconds, 59 oC for 20seconds and 72 oC for 30 seconds.

overall_design: In the study presented here, Widetype (WT), STIM1 knockout (STIM1-KO), Mock, Snail1 overexpression (Snail1 OE) and Snail1 plus STIM1 double overexpression (Snail1+STIM1 dOE)-SMMC7721 cells were used to acquire expression profiles of a total of 48 unique genes related to glucose and lipid metabolism.

first: Yongsheng


title: 3’ Uridylation Expands miRNA Target Repertoire

status: Public on Aug 15 2019

city: Frederick

first: Shuo

last: Gu

state: MD

address: 1050 Boyles Str. Building 560 Room 11-6B

institute: National Cancer Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Many microRNAs (miRNAs) exist alongside abundant miRNA isoforms (isomiRs), most of which arise from post-maturation sequence modifications, such as 3’ uridylation. However, the ways in which these sequence modifications affect miRNA function remain poorly understood. Here, using human miR-27a in cell lines as a model, we have discovered that a nonfunctional target site unable to base pair extensively with the miRNA seed sequence can regain function when an upstream adenosine is able to base-pair with a post-transcriptionally added uridine in the miR-27a tail. This Tail-U-Mediated Repression (TUMR) is abolished in cells lacking the uridylation enzymes TUT4 and TUT7, indicating that uridylation alters miRNA function by modulating target recognition. We identified a set of non-canonical targets in human cells that are specifically regulated by uridylated miR-27a. We provide evidence that TUMR expands the targets of other endogenous miRNAs. Our study reveals a function for uridylated isomiRs in regulating non-canonical miRNA targets.

overall_design: HEK293T cells and TUT4/7 Double Knockout (DKO) cells with or without ectopic expression of miR-27a or specific depletion of miR-148b were subjected to miRNA-Seq and isomiR profile analyses. In parallel, mRNA profiles were measured by RNA-seq to monitor miR-27a and miR-148b mediated repressions.

first: Acong

last: Yang

first: Xavier

last: Bofill-De Ros


title: Dynamic changes of muscle insulin sensitivity after metabolic surgery

status: Public on Aug 14 2019

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

type: Methylation profiling by genome tiling array


title: NAD+ repletion inhibits accelerated aging in Werner syndrome through the restoration of mitophagy

status: Public on Aug 16 2019

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Metabolic dysfunction is a primary feature of the premature aging Werner syndrome (WS), a heritable human disease caused by mutations in the gene encoding the DNA helicase Werner (WRN). However, the relationship between WRN mutation and its severe metabolic phenotypes is unclear. Here we report mitochondrial dysfunction and depletion of NAD+, a fundamental ubiquitous cofactor, in WS patient samples and WS animal models. NAD+ repletion restores NAD+ metabolic profiles and improves mitochondrial quality through DCT-1 and ULK-1-dependent mitophagy. At the organismal level, NAD+ repletion remarkably delays accelerated aging, including stem cell dysfunction in both C. elegans and Drosophila models of WS. Mechanistically, WRN physically binds to a key NAD+ biosynthetic enzyme nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) and facilitates its NAD+ production. Our findings reveal an unprecedented anti-aging mechanism of WRN that integrates its new function of NAD+ synthesis to coordinate mitochondrial maintenance and energy expenditure, and suggest therapeutic potential.

overall_design: Two C. elegans strains were used: the N2: wild type Bristol isolate was from Caenorhabditis Genetics Center (CGC) and the wrn-1(gk99), a C. elegans model of WS with a 196bp deletion mutation resulting in the complete absence of the WRN-1 protein, was a gift from Dr. Hyeon-Sook Koo (Yonsei University, Korea). Both strains were treated with vehicle control, NAD+ precursor nicotinamide riboside (NR, 1 mM), a SIRT1 activator (SRT1720, 10 µM), or a PARP inhibitor (Olaparib, 500 nM) from the L4 stage, followed by changing to fresh drug plate on adult Day 4, and collection for transcriptomic analysis on adult D7. Approximately 500 worms were used for each experiment, with four biological repeats per condition.   (N=4 per group, total N=32 microarray samples)

first: Evandro

middle: F

last: Fang

first: Yujun

last: Hou

first: Martin

last: Jensen

first: Henok

last: Kassahun

first: Marya

last: Morevati

first: Jesse

middle: S

last: Kerr

first: David

last: Figueroa

first: Beimeng

first: Ho-Joon

last: Lee

first: Hisaya

last: Kato

first: Tanima

last: SenGupta

first: Tyler

middle: G

last: Demarest

first: Jong-Hyuk

first: Domenica

last: Caponio

first: Tomasz

last: Kulikowicz

first: Aswin

last: Mangerich

first: Deborah

middle: L

last: Croteau

first: Yoshiro

last: Maezawa

first: Costas

last: Lyssiotis

middle: P

last: Mattson

first: Heinrich

last: Jasper

first: Hilde

last: Nilsen

first: Vilhelm

last: Bohr


title: MeCP2 regulates gene expression through direct interaction with H3K27me3 [Targeted_BS_seq: DMSO_vs_GSK343]

status: Public on Aug 22 2019

city: Gwangju

first: Wooje

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

country: South Korea

institute: Chosun University

type: Methylation profiling by high throughput sequencing

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: To analyze the effect of GSK343 treatment on DNA methylation, targeted bisulfite sequencing was performed using the SureSelectXT Methyl-Seq Target Enrichment System of Illumina Multiplexed Sequencing (Agilent Technologies).

first: Qizhi

last: Gong


title: MeCP2 regulates gene expression through direct interaction with H3K27me3 [ChIP_human: HCT116_vs_DKO1]

overall_design: To determine whether MeCP2 binding to H3K27me3 is independent of DNA methylation, we examined MeCP2-chromatin interactions in DKO cells, which have reduced  DNA methylation, and compared with parental HCT116 cell line.


title: Dynamic changes of muscle insulin sensitivity after metabolic surgery I

first: Heike

last: Vogel

summary: The mechanisms underlying improved insulin sensitivity after surgically-induced weight loss are still unclear. We monitored skeletal muscle metabolism in obese individuals before and over 52 weeks after metabolic surgery. Initial weight loss occurs in parallel with a decrease in muscle oxidative capacity and respiratory control ratio. Persistent elevation of intramyocellular lipid intermediates, likely resulting from unrestrained adipose tissue lipolysis, accompanies the lack of rapid changes in insulin sensitivity. Simultaneously, alterations in skeletal muscle expression of genes involved in calcium/lipid metabolism and mitochondrial function associate with subsequent distinct DNA methylation patterns at 52 weeks after surgery. Thus, initial unfavorable metabolic changes including insulin resistance of adipose tissue and skeletal muscle precede epigenetic modifications of genes involved in muscle energy metabolism and the long-term improvement of insulin sensitivity.

overall_design: This study includes 6 controls and 16 obese participants. Gene expression from obese persons was measured 3 times: before, 2 weeks and 52 weeks after metabolic surgery

first: Meriem

last: Ouni

first: Markus

last: Jähnert

first: Sofiya

last: Gancheva

first: Michael

last: Roden

first: Annette

last: Schürmann


title: Dynamic changes of muscle insulin sensitivity after metabolic surgery III

overall_design: This study includes 32 obese participants. Gene expression from obese persons was measured 2 times: 12 weeks and 24 weeks after metabolic surgery.


title: Dynamic changes of muscle insulin sensitivity after metabolic surgery II

overall_design: This study includes 1 control and 7 obese participants. Gene expression from obese persons was measured 3 times: before, 2 weeks and 52 weeks after metabolic surgery


title: A novel reprogramming strategy to generate functionally competent human hepatocytes

city: Beijing

first: Bingqing

last: Xie

address: Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

summary: Cell fate can be directly converted between differentiated cells by lineage reprogramming, thus generating multiple cell types across developmental lineages. However, lineage reprogramming is hindered by incomplete cell-fate conversion with residual initial cell identity and partial functions compared with the native counterparts. Here, we develop a high-fidelity reprogramming strategy, by mimicking the natural cell-fate changing route, thus permitting the production of functionally competent human hepatocytes from another cell type. We first converted fibroblasts into plastic hepatic progenitor-like cells (hHPLCs) and chemically induced them into mature hepatocytes. The molecular identity of human induced hepatocytes (hiHeps) are suggested a terminally differentiated state, resembling primary human hepatocytes (PHHs). Functionally, hiHeps were competent to replace PHHs for equivalent drug-metabolizing activities, toxicity prediction and hepatitis B virus infection. Remarkably, the stably robust expansion of hHPLCs allowed large-scale generation of mature hepatocytes. Our results demonstrate the necessity of taking a reprogramming step for plastic progenitors for efficient cell-fate conversion. This strategy is promising for the generation of other mature human cell types.

overall_design: Total of 47 samples were analyzed, which included human embryonic fibroblasts, primary human hepatocytes, human hepatic progenitor-like cells, human induced hepatocytes and human fetal liver cells.Global transcriptional profiles of these cells were analyzed by RNA-seq.

first: Da

last: Sun

first: Hongkui

last: Deng


title: Molecular profiling demonstrates modulation of immune cell function and matrix remodeling during luteal rescue

status: Public on Aug 04 2019

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

summary: The corpus luteum (CL) is essential for maintenance of pregnancy in all mammals and luteal rescue, which occurs around day 16-19 in the cow, is necessary to maintain luteal progesterone production. Transcriptomic and proteomic profiling were performed to compare the day 17 bovine CL of the estrous cycle and pregnancy. Among mRNA and proteins measured, 140 differentially abundant mRNA and 24 differentially abundant proteins were identified. Pathway analysis was performed using four programs.  Modulated pathways included T cell receptor signaling, vascular stability, cytokine signaling, and extracellular matrix remodeling. Two mRNA that were less in pregnancy were regulated by prostaglandin (PG) F2A in culture, while two mRNA that were greater in pregnancy were regulated by interferon tau (IFNT). To identify mRNA that could be critical regulators of luteal fate, the mRNA that were differentially abundant during early pregnancy were compared to mRNA that were differentially abundant during luteal regression. Eight mRNA were common to both datasets, including mRNA related to regulation of steroidogenesis and gene transcription. A subset of differentially abundant mRNA and proteins, including those associated with extracellular matrix functions, were predicted targets of differentially abundant microRNA (miRNA). Integration of miRNA and protein data, using miRPath, revealed pathways such as extracellular matrix-receptor interactions, abundance of glutathione, and cellular metabolism and energy balance. Overall, this study has provided a comprehensive profile of molecular changes in the corpus luteum during maternal recognition of pregnancy and has indicated that some of these functions may be miRNA-regulated.

overall_design: Eight holstein heifers were used. Four heifers were bred and four were left unbred. On day 17 following estrus, all heifers were slaughtered and pregnancy was confirmed in bred heifers. CL were snap frozen and RNA was isolated and sequenced by next generation sequencing.

middle: H

first: Samar

last: Maalouf

first: Wansheng

last: Liu

first: Joy

last: Pate


title: Dynamic changes of muscle insulin sensitivity after metabolic surgery IV

overall_design: This study includes 7 controls and 16 obese participants. Genome-wide DNA methylation was peroformed with EPIC Chip from lean and obese persons, For Obese participant DNA methylation was measured 3 times: before, 2 week, and 52 weeks after metabolic surgery


title: Next Generation Sequencing of Loxp (Rxratm1Krc/J,Rxra loxP), Hetero(Nex-cre;Rxratm1Krc/J,Rxra cKO-Het) and cKO (Nex-cre;Rxratm1Krc/J,Rxra cKO) mouse Transcriptomes

first: Huateng

last: Cao

state: Shanghai

address: 320 Yueyang Road

institute: Institute of Neuroscience, CAS, China

summary: When compared with Loxp, both Hetero and cKO mice showed reduced expression of immediate early genes

overall_design: mRNA profiles of S1BF tissues from 17-day old Loxp, Hetero and cKO mice were generated by deep sequencing using Illumina Hiseq.

first: Xiang

last: Yu


title: Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation

status: Public on Aug 06 2019

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H=A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. CMT3 expression reconstituted gbM through a progression of de novo CHG methylation on expressed genes, followed by the accumulation of CG methylation that could be inherited even following loss of the CMT3 transgene. Thus, gbM originates from the simultaneous targeting of loci by pathways that promote euchromatin and heterochromatin, which primes genes for the formation of stably inherited epimutations in the form of CG DNA methylation.

overall_design: MethylC-seq, RNA-seq, and ChIP-seq


title: RBMX preferentially associates with repetitive DNAs along with RPA

status: Public on Jul 27 2019

city: Guangzhou

first: Tian

last: Zheng

address: No. 135 West Xingang Road

institute: Sun Yat-sen University

summary: To characterize the binding sites of RBMX and RPA on chromatin, 293T cells were treated with CPT and binding profiles were obtained by ChIP-seq assay. RBMX ChIP-seq profile was highly correlated with RPA ChIP-seq profile, both showing strong peaks at centromeres. To characterize the occupancy sites bound by both RBMX and RPA, we annotated their shared peaks. The results showed that these sequences are mostly enriched on repetitive DNAs including rRNA, simple repeats and satellite DNAs.

overall_design: Examination of RBMX and RPA1 binding profiles in 293T cells.

first: Yong

last: Zhao


title: Maternal antibiotic use in sows affects microbiota and gut development in offspring

status: Public on Jul 29 2019

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

summary: We demonstrated that a maternal antibiotic treatment can change intestinal development of the offspring piglets permanently by showing that maternal gestational antibiotic treatment affects intestinal development in offspring piglets for a period of at least seven weeks after the antibiotic treatment in the sows was finished. It was shown that immediately after birth the piglets from amoxicillin treated sows, showed upregulation of genes involved in processes related to ‘tight junctions’ and ‘immunoglobulins’. In addition, these piglets had significantly lower number of goblet cells. Together, this may lead to a gut wall that is more rapidly closed in piglets from amoxicillin treated sows, affecting the uptake of immunoglobulins and the intestinal development. Later in life, around weaning, gene expression and morphological data indicate that the crypts of piglets from amoxicillin treated sows deepen around weaning as an effect of the amoxicillin treatment which in combination with the upregulation of genes involved in cell cycle processes, ribosomal activity and protein degradation might imply that the intestinal development, the subsequent differentiation of cells or the timing of these processes was delayed by the maternal antibiotic treatment.

overall_design: In total 43 samples remained for analysis, 23 controls and 20 antibiotic treated piglets

first: Astrid

last: de Greeff


title: MicroRNA and mRNA profiling in the idiopathic inflammatory myopathies

status: Public on Jul 31 2019

city: Johnson City

first: Joanna

last: Parkes

state: NY

address: Pharmacy Building

department: School of Pharmacy and Pharmaceutical Sciences

institute: Binghamton University

summary:
Objectives: The idiopathic inflammatory myopathies (IIMs) are heterogeneous autoimmune conditions of skeletal muscle inflammation and weakness. MicroRNAs (miRNAs) are short, non-coding RNA which regulate gene expression of target mRNAs. The aim of this study was to profile miRNA and mRNA in IIM and identify miRNA-mRNA relationships which may be relevant to disease.
Materials and methods: mRNA and miRNA in whole blood samples from 7 polymyositis (PM), 7 dermatomyositis (DM), 5 inclusion body myositis (IBM) and 5 non-myositis controls was profiled using next generation RNA sequencing. Gene ontology and pathway analyses were performed using GOseq and Ingenuity Pathway Analysis. Dysregulation of miRNAs and opposite dysregulation of predicted target mRNAs in IIM subgroups was validated using RTqPCR and investigated by transfecting human skeletal muscle cells with miRNA mimic.
Results Analysis of differentially expressed genes showed that interferon signalling and anti-viral response pathways were upregulated in PM and DM compared to controls. An anti-Jo1 autoantibody positive subset of PM and DM (n=5) had more significant upregulation and predicted activation of interferon signalling and highlighted T-helper (Th1 and Th2) cell pathways. In miRNA profiling miR-96-5p was significantly upregulated in PM, DM and the anti-Jo1positive subset. RTqPCR replicated miR-96-5p upregulation and predicted mRNA target (ADK, CD28 and SLC4A10) downregulation.  Transfection of a human skeletal muscle cell line with miR-96-5p mimic resulted in significant downregulation of ADK.
Conclusion: MiRNA and mRNA profiling identified dysregulation of interferon signalling, anti-viral response and T-helper cell pathways, and indicates a possible role for miR-96-5p regulation of ADK in pathogenesis of IIM.

overall_design: Whole blood microRNA and mRNA profiles of idiopathic inflammatory myopathy patients compared to controls generated by RNA sequencing, using Illumina HiSeq 4000

middle: E

first: Janine

last: Lamb

first: Hector

last: Chinoy

first: Philip

last: Day


title: Transcriptome data of B cells in patients with primary Sjögren's syndrome

status: Public on Sep 03 2019

city: Shinjuku-ku

first: Jun

last: Inamo

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University School of Medicine

summary:
We compared subsets of B cells as follows: Bm1 cells; CD38-IgD+, naïve B cells; CD38+IgD+, pre-germinal centre B cells; CD38highIgD+ and memory B cells; CD38±IgD that were collected from patients with primary Sjögren's syndrome.
As a result, list of 623 differentially expressed genes was created. We found  interferon signature genes and HLA genes were mostly up-regulated in patients compared to healthy controls.

overall_design: Examination between patients with primary Sjögren's syndrome and healthy controls

first: Katsuya

last: Suzuki

first: Masaru

last: Takeshita

first: Yoshiaki

last: Kassai

first: Maiko

last: Takigchi

first: Rina

last: Kurisu

first: Yuumi

last: Okuzono

first: Shinya

last: Tasaki

first: Akihiko

last: Yoshimura

first: Tsutomu

last: Takeuchi


title: RNASeq whole blood of Dutch 500FG cohort

status: Public on Jul 11 2019

city: Groningen

first: Raul

last: Aguirre-Gamboa

address: Antonius Deusinglaan 1

department: Department of Genetics

institute: University of Groningen, University Medical Center Groningen

summary: Expression levels from bulk whole blood  from 96 individuals within the 500FG cohort. The aim of the 500FG project is to characterize the interaction between the genetic background of the host, the microbiome composition of different niches, and the consequences on an array of physiological functions: the immune response against important human pathogens, thrombocyte function, and in a subgroup of individuals the cognitive function of the brain. These aims are approached by a combination of advanced -omics technology, cutting edge functional tests (immune tests, functional brain MRI, etc) and systems biology-based bioinformatics.

overall_design: Quantification of gene expression in bulk whole blood using paired end RNA Sequencing

first: Raúl

first: Niek

last: de Klein

first: Yang

last: Li


title: Transcriptomic analysis of probable asymptomatic and symptomatic Alzheimer Brains

status: Public on Jul 22 2019

city: London

first: Hamel

last: Patel

address: De Crespigny Park

department: Biostatistics and health informatics

country: United Kingdom

institute: King's College London

summary:
Objectives:
Individuals with intact cognition and neuropathology consistent with Alzheimer’s disease (AD) are referred to as asymptomatic AD (AsymAD). These individuals are highly likely to develop AD, yet transcriptomic changes in the brain which might reveal mechanisms for their AD vulnerability are currently unknown.
Methods:
Differential and co-expression analysis was performed on microarray profiled human brains of 27 control , 33 AsymAD and 52 AD subjects. Tissues known to be affected by AD neuropathology (entorhinal cortex, temporal cortex, frontal cortex) and tissue partially spared by the disease (cerebellum).
Results:
The AsymAD subjects exhibited significant changes in transcriptomic activity in the frontal cortex when compared to AD and control subjects. Fourteen genes (GPM6B, ANKEF1, NPC2, ALDH2, FBLN2, METTL7A, FLCN, ASPHD1, ARL5A, GPR162, HBA2, PCID2, BEND3 and RAP1Gap) were highly associated with AD neuropathology   with overall disturbances in the “glutamate-glutamine cycle”, “oxidative phosphorylation”, “innate immune system”, “TYROBP network”, “neutrophil degranulation” and “amino acid metabolism” in both the AsymAD and AD subjects.
Conclusions:
Transcriptomic activity in AsymAD subjects suggests fundamental changes in AD brains may begin within the frontal cortex region.  In addition, we provide new insight into the earliest biological changes occurring in the brain prior to clinical AD diagnosis which offers new avenues for therapeutic interventions for preventing AD.

We provide access of gene-level results to the broader research community through a publicly available R SHINY web-application accessible at: https://phidatalab-shiny.rosalind.kcl.ac.uk/ADbrainDE

overall_design: Total RNA obtained from entorhinal cortex, temporal cortex, frontal cortex and cerebellum brain region from controls, asymptomatic AD and AD subjects.

first: Stephen

last: Newhouse


title: Hippocampal transcriptome analysis following maternal separation in a mouse model of fetal alcohol spectrum disorder

status: Public on Jun 27 2019

first: Shiva

last: Singh

state: ON

address: 1151 Richmond Street

department: Biology

country: Canada

institute: Western University

summary: Fetal alcohol spectrum disorders (FASD) are common, seen in 1-5% of the population in the United States and Canada. Regrettably, children diagnosed with FASD are not likely to remain with their biological parents, facing early maternal separation and foster placements throughout childhood. We have modeled FASD in mice via prenatal alcohol exposure and further induce early life stress through maternal separation. We report an association between adult hippocampal gene expression and prenatal and postnatal treatment that is related to behavioral changes. Clustering of expression profiles through weighted gene co-expression network analysis (WGCNA) identifies a set of transcripts associated with anxiety-like behavior as well as treatment group. Genes in this module are overrepresented by genes involved in transcriptional regulation and other pathways related to neurodevelopment. Interestingly, one member of this module, Polr2a, polymerase (RNA) II (DNA directed) polypeptide A, is downregulated by the combination of prenatal ethanol and postnatal stress in an RNA-Seq experiment and qPCR validation. Together, transcriptional control is implicated as a potential underlying mechanism leading to anxiety-like behavior via environmental insults. Greater understanding of the role of prenatal alcohol exposure and postnatal stress in altering the hippocampal transcriptome in the hippocampus is warranted. Further research is required to elucidate the mechanism involved and use this insight towards early diagnosis and amelioration strategies involving children born with FASD.

overall_design: Hippocampal RNA profiles of adult mice that had been prenatally exposed to alcohol and/or postnatal maternal separation stress as well as non-exposed controls were generated by sequencing, using Illumina HiSeq.

first: Bonnie

last: Alberry

first: Christina

last: Castellani


title: Identification of novel ETn insertions in KRAB-ZFP cluster depleted mice

city: Bethesda

first: Gernot

last: Wolf

address: 6 Center Drive

department: NICHD

institute: NIH

summary: Genetic deletion of a large KRAB-ZFP gene cluster on chromosome 4 (Chr4-cl) leads to transcriptional reactivation of retrotransposons (mainly ETn elements) in ES cells. We therefore wanted to test whether ETn elements retrotranspose in Chr4-cl KO mice at higher frequency. For this we purified genomic DNA from WT and KO mice, enriched gDNA libraries using ETn capture probes and sequenced those libraries as paire-end reads. These reads were then used to identify novel ETn insertions that are not annotated in the reference genome or present in the germ line of their progenitors.

overall_design: Identification of novel retrotransposon insertons in mice by capture sequencing

first: Todd

last: Macfarlan


title: Genome-wide maps of chromatin state and KAP1 occupancy in KRAB zinc finger protein (KRAB-ZFP) gene cluster KO ES cells and testis

summary: We have shown that many mouse KRAB-ZFPs target retrotransposons which are generally marked by H3K9me3 and KAP1 in ES cells. To test whether these KRAB-ZFPs are require to establish and maintain repressive chromatin marks at these elements, we performed ChIP-seq with antibodies against KAP1 (2 KRAB-ZFP cluster KOs) and H3K9me3 (5 KRAB-ZFP cluster KOs). We show that KRAB-ZFP targeted retrotransposons show reduced KAP1 binding and  H3K9me3 in these KO ES cells. Furthermore, we performed ChIP-seq with antibodies against histone modifications typical for promoters and enhancers in Chr4-cl KO ES cells and testis. We show that, in ES cells, ETn retrotransposons gain signatures of active enhancers which acts on earby gene expression. In testis,  a handful of different retrotransposons gain enhancer marks, although to a lesser degree. In conclusion, our data shows that KRAB-ZFPs are required to maintain H3K9me3 at retrotransposons in ES cells and to prevent some retrotransposons of becoming enhancers that affect gene expression patterns.

overall_design: Native or cross-linked chromatin was prepared from ES cells or testis and immunoprecipitated with antibodies against KAP1 or various histone modifications

first: Alberto

last: De Iaco

first: Matthew

last: Tinkham

first: Didier

last: Trono


title: Retrotransposon reactivation and mobilization upon deletions of megabase-scale KRAB zinc finger gene clusters in mice

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

overall_design: Refer to individual Series


title: Integrated epigenome, exome and transcriptome analyses reveal molecular subtypes and homeotic transformation in uterine fibroids

status: Public on Aug 07 2019

city: Houston

first: Katayoun

last: Rezvani

state: Texas

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

institute: The University of Texas MD Anderson Cancer Center

summary: Uterine fibroids are benign myometrial smooth muscle tumors of unknown etiology that when symptomatic are the most common indication for hysterectomy in the USA.  We conducted an integrated analysis of fibroids and adjacent normal myometria by whole exome sequencing, DNA methylation (Human Methylation EPIC) array, and RNA-sequencing.  Unsupervised clustering by DNA methylation segregated normal myometria and fibroids, and further separated the fibroids into subtypes marked by MED12 mutation, HMGA2 activation (HMGA2hi) and HMGA1 activation (HMGA1hi). Upregulation of HMGA2 expression in HMGA2hi fibroids did not always appear to be dependent on translocation, as has been historically described, and was associated with hypomethylation in the HMGA2 gene body.  Furthermore, we found that expression of HOXA13 was highly upregulated in fibroids and that overexpression of HOXA13 in a myometrial cell line induced expression of genes classically associated with uterine fibroids. Transcriptome analyses of the most differentially expressed genes between cervix and myometrium also showed that uterine fibroids and normal cervix clustered together and apart from normal myometria. Together, our integrated analysis shows a role for epigenetic modification in fibroid biology and strongly suggests that homeotic transformation of myometrium cells to a more cervical phenotype is important for the etiology of the disease.

overall_design: Matched fibroid, normal myometrium, and stromal cervix from the same individual (n=8) are analyzed.

first: Hui

last: Shen

first: Jose

last: Teixeira


title: Indicated that null segregants lacking transgene have been obtained from the progeny of the backcross of transformants

status: Public on Jul 30 2019

city: Shizuoka

first: Hiroshi

last: Fujii

state: Shizuoka

address: 485-6 Okitsunakacho, Shimizu

department: Division of Citrus Research

institute: Institute of Fruit Tree Science, NARO

type: Genome variation profiling by genome tiling array

summary:
Citrus disease resistance breeding has been advanced to introduce CTV resistance of trifoliate orange to citrus.   Because the quality of the fruit of trifoliate ogate was low, backcross with citrus was necessary. In the case of citrus, it takes several years from flowering to obtaining next-generation seeds.   Therefore, we generated transformants for the early flowering genes (citrus FLOWERING LOCUS T: CiFT) using CiFT co-expression vector construct and promoted generation.
In Japan, it is difficult to plant transformants in the field. Therefore, it was decided to select null segregant lacking transgene from backcross progenies. In order to prove that the transgene has been completely removed, it is necessary to prove that no vector conract is present on the genome.    Tthis matter was proved by CGH analysis.

overall_design: Wild type of trifoliate orange vs. wild type of trifoliate orange as control, wild type of trifoliate orange and vector contract as control, transgenic torifoliate orange by vector construct (T0), two null segregant lacking transgene in back cross generation 2nd, one transgenic segregant with transgene inserted in the genome in back cross generation 2nd, one null segregant lacking transgene in back cross generation 3rd, one transgenic segregant with transgene inserted in the genome in back cross generation 3rd

first: FUJII

last: Hiroshi

first: ENDO

last: Tomoko

first: SHIMADA

last: Takehiko


title: De novo DNA methylation at imprinted loci during reprogramming into naïve and primed pluripotency

status: Public on Jun 18 2019

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

summary: CpG islands (CGIs) including those at imprinting control regions (ICRs) are protected from de novo methylation in somatic cells. However, many cancers often exhibit CGI hypermethylation, implying that the machinery is impaired in cancer cells. Here, we conducted a comprehensive analysis of CGI methylation during the somatic cell reprogramming. Although most CGIs remain hypomethylated, a small subset of CGIs, particularly at several ICRs, were often de novo methylated in reprogrammed pluripotent stem cells (PSCs). Such de novo ICR methylation was linked with the silencing of reprogramming factors, which occurs at a late stage of reprogramming. The ICR-preferred CGI hypermethylation was similarly observed in human PSCs. Mechanistically, ablation of Dnmt3a prevented PSCs from de novo ICR methylation. Notably, the ICR-preferred CGI hypermethylation was observed in pediatric cancers, while adult cancers exhibit genome-wide CGI hypermethylation. These results may have important implications in the pathogenesis of pediatric cancers and the application of PSCs.

overall_design: Analyzing DNA methylation profiles and transcriptional profiles by Methylseq and RNA-seq in ESCs, EpiSCs, iPSCs and iEpiSCs with F1 genetic background between 129/SvJ and MSM/Ms and various tissues obtained from E14.5 embryos.

first: Masaki

last: Yagi

first: Mio

last: Kabata

first: Takuya

last: Yamamoto


title: Coordinating Tissue Regeneration through TGF-β Activated Kinase 1 (TAK1) In-activation and Re-activation

status: Public on Jun 10 2019

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

summary: Our study reveals up-regulation of the TAK1 pathway when compared with the uninjured hindlimb in our model of trauma-induced heterotopic ossification (tHO) consisting of hindlimb Achilles’ tendon transection with dorsal burn injury.

overall_design: Using a model of musculoskeletal injury, we sought to determine the role that TGF-β activated kinase 1 (TAK1) signaling has on MSC cellular differentiation and inappropriate tissue formation (heterotopic ossification).

first: Amanda

last: Huber

first: Benjamin

last: Levi


title: Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals cancer-associated fibroblasts expressing MHC class II

status: Public on Jun 19 2019

city: Cold Spring Harbor

first: David

middle: A.

last: Tuveson

address: 1 Bungtown Rd.

department: Cancer Center

institute: Cold Spring Harbor Laboratory

summary: This study used 10X Genomics, single-cell RNA-sequencing to examine the cell types present in the KrasLSL-G12D; Trp53LSL-R172H; Pdx1-Cre (KPC) mouse model for pancreatic ductal adenocarcinoma. The study analyzed tumors from 4 different mice. For each tumor, we performed flow sorting to isolate all viable cells, and to isolate a fibroblast-enriched population of cells for single-cell RNA-seq to determine the transcriptomes of individual cells in KPC pancreatic ductal adenocarcinoma tumors.

overall_design: Single-cell RNA-sequencing analysis (10X Genomics and Illumina sequencing) of the viable and fibroblast-enriched cell populations taken from 4 replicate mice of the KPC mouse model of pancreatic ductal adenocarcinoma

first: Lindsey

last: Baker


title: RNA-seq Analysis of GPCRs expressed in mouse inguinal white adipocytes (iWAT), epididymal white adipocytes (eWAT) and brown adipose tissues (BAT) after high fat diet treatment.

status: Public on Jul 26 2019

first: LEI

last: WANG

address: Building 8A, Room B1A05 8 Center Dr , MD 20814

summary:
Purpose: The goals of this study are to identify GPCRs that are endogenously expressed by high fat diet fed mouse adipose tissue, we subjected RNA prepared from isolated mouse adipocytes (iWAT and eWAT) and BAT tissue to RNA-seq analysis.
Methods: Total RNA extracted from mature adipocytes (iWAT and eWAT) and BAT tissue of C57BL/6 mice maintained on high fat diet for 12 weeks were used to construct high throughput sequencing libraries. RNAs with RIN >8 (assessed by the Agilent 2100 Bioanalyzer system) were used to prepare transcriptome libraries using the NEBNext Ultra RNA library prep kit (New England Biolabs). High throughput RNA-sequencing was performed using a Illumina HiSeq 2500 at the NIDDK Genomic Core Facility (NIH, Bethesda, MD). Raw reads were mapped to the mouse (mm9) genome.
Results: Our study demonstrated that mouse adipocytes/BAT tissue from HFD-fed mice express several GPCRs.

overall_design: Inguinal white adipocytes (iWAT), epididymal white adipocytes (eWAT), and brown adipose tissues (BAT) were isolated from male C57BL/6 mice consuming high fat diet for 12 weeks (n=6)

first: Lei

last: Wang


title: Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [scRepli-seq]

status: Public on Jun 26 2019

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

summary: In mammals, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which correspond to early (E) and late (L) replicating timing (RT) domains, respectively. Here, we show that RT changes are tightly correlated with A/B compartment changes during mouse embryonic stem cell (mESC) differentiation. A/B compartments changed mostly by a “boundary shift,” frequently causing compartment switching of single TADs, which coincided with or preceded RT changes. Upon differentiation, mESCs acquired an A/B compartment organization that closely resembled EpiSCs (epiblast-derived stem cells), suggesting that accumulation of compartment boundary repositioning eventually led to naïve-to-primed pluripotency transition in A/B compartment organization. We propose that large-scale reorganization of A/B compartments, which is reflected in RT domain reorganization, represents major cell fate changes. Collectively, our data provides valuable insights into the regulatory principles of 3-dimensional (3D) genome organization during early embryonic stages.

overall_design:
scRepli-seq: Single-cell Repli-seq experiments in G1 and S-phase cells (total 884 cells) of 7-day differentiation (d0~d7) of female mouse embryonic stem cells (CBMS1 mESCs) and epiblast stem cells (EpiSCs) incorporating our previous scRepli-seq data (under GSE108556). We also selected the sample sets from our previous scRepli-seq data (under GSE108556) to obtain additional sequence reads for analyzing the resolution at 40kb (28 Mid-S single cells for mESCs, and 15 Mid-S single cells for 7-day differentiated mESCs).

Please note that, as most (49 out of 51 [GSM3142337 to GSM3142387]) of the re-analyzed GSE108556 samples/data include additional raw data, duplicated sample records (e.g. GSM3142338 for GSM2904979 in GSE108556) were created to link all associated raw data and re-analyzed processed data, as described in the corresponding sample description field.

first: Hisashi

last: Miura

first: Saori

last: Takahashi

first: Rawin

last: Poonperm

first: Akie

last: Tanigawa

first: Shin-ichiro

last: Takebayashi


title: Expression profile of stromal vascular fraction during would healing

status: Public on Jul 23 2019

city: Tochigi

first: Ken-ichi

last: INOUE

address: 880 Kitakobayashi, Mibu-machi, Shimotsuga-gun

institute: Dokkyo Medical University

summary:
Stromal cells rapidly reorganize cell composition during would healing. Resident stromal cells secrete systemic ligands and mobilize immune cells from bone marrow. Subsequently resident cells and mobilized immune cells cooperate together for efficient wound healing.
We term such phenomena as "stromal priming for wound healing" and investigated the intercellular communications among heterogeneous populations through comrehensive expression analysis.

overall_design: Subcutaneous fat was surgically injured and stromal vascular fraction was purified during healing process. Total RNA from day zero, one or three after injury was purified and expression profile was investigated by Affimetrix microarray.

first: Satoko

last: Kishimoto


title: Global identification of retinoic acid regulated genes

status: Public on May 22 2019

city: San Diego

first: Brian

middle: Patrick

last: James

state: CA

address: 10901 North Torrey Pines Road

department: Genomics

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Retinoic acid (RA) signaling plays a major role in controlling several developmental processes in vertebrate embryos. RA repression of caudal Fgf8 has emerged as a crucial mechanism through which RA controls body axis extension, somitogenesis, and spinal cord neurogenesis.  The role of RA in Fgf8 repression is supported by mechanistic studies demonstrating direct RA repression through a nearby RA response element that recruits NCOR in an RA-dependent manner.  RA is also required for balanced neuromesodermal progenitor differentiation needed for coordinated generation of mesodermal progenitors for somites and neural progenitors for spinal cord.  As many pathways are controlled by RA, we performed RNA-seq analysis comparing wild-type embryos with Aldh1a2 mutants that lack the ability to produce RA. This analysis identified a few hundred genes whose expression is significantly altered when RA is absent, thus providing candidate genes for further analysis to discover RA-regulated genes essential for development.

overall_design: 2 samples were analyzed: one control and one test.

first: Gregg

last: Duester


title: Diminished OPA1 expression and impaired mitochondrial morphology and homeostasis are prominent features of aprataxin-deficient cells

status: Public on May 21 2019

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Ataxia with oculomotor apraxia type 1 (AOA1) is an early onset progressive spinocerebellar ataxia caused by mutation in aprataxin (APTX). APTX removes 5´-AMP groups from DNA, a product of abortive ligation during DNA repair and replication. APTX deficiency has been suggested to compromise mitochondrial function; however, a detailed characterization of mitochondrial homeostasis in APTX-deficient cells is not available. Here we show that cells lacking APTX undergo mitochondrial stress and display significant changes in the expression of the mitochondrial inner membrane fusion protein OPA1, and components of the oxidative phosphorylation complexes. At the cellular level, APTX deficiency impairs mitochondrial morphology and network formation, and autophagic removal of damaged mitochondria by mitophagy. Thus, our results show that aberrant mitochondrial function is a key component of AOA1 pathology. This work corroborates the emerging evidence that impaired mitochondrial dynamics and mitophagy are at the hub of an increasing number of genetically diverse neurodegenerative disorders.

overall_design: Three biological replicates of normal control (U2OS_N1-3) and CRISPR-mediated aprataxin (APTX) knock-out (APTX_KO1-3) U2OS cells were employed for this comparison.

first: Jin

last: Zheng

first: Deborah

last: Croteau

first: Vilhelm

last: Bohr

first: Mansour

last: Akbari


title: Transcriptome of Tribolium castaneum in different climatic conditions

status: Public on Jul 02 2019

city: Zurich

first: Eva

last: Koch

address: Winterthurerstrasse 190

department: IEU

institute: University of Zurich

summary: We combined fitness and whole-transcriptome data of Tribolium castaneum to investigate gene expression and fitness responses to drought, heat and their combination. Fitness was reduced by both stressors and their combined effects were nearly additive. Accordingly, expression data showed that both stressors were acting mostly independently and did not interfere physiologically.  Response to heat stress resulted in a much higher number of differentially expressed genes compared to drought stress. Responses to heat and heat-drought combination were similar.

overall_design: We used the Tribolium castaneum Cro1 strain collected from a wild population in 2010 and adapted to lab standard conditions (33°C, 70% relative humidity) for more than 20 generations. The conditions in the treatments were: Hot: 37°C and 70% r. h., Dry: 33°C and 30% r. h., Hot-Dry: 37°C and 30% r. h.  RNA was extracted from the whole body of reproducing females at the age of eight weeks. mRNA was used for library preparation (using LEXOGEN kit) and single end sequencing was performed on Illumina NextSeq (75 cycles).

first: Frédéric

last: Guillaume


title: Genome-wide analysis of DNA methylation in KRAB-ZFP cluster KO ES cells

first: Gernot

last: Wolf

summary: We report a retrotransposon-specific loss of CpG methylation in chromosome 4 KRAB-ZFP cluster (Chr4-cl) KO ES cells that are cultivated in conditions that induce DNA hypomethylation. The retrotransposon groups with the strongest DNA methylation loss are the main targets of the KRAB-ZFPs within the deleted gene cluster indicating that these KRAB-ZFPs prevent complete DNA demethylation at retrotransposons during global DNA demethylation.

overall_design: Analysis of CpG methylation status in WT and Chr4-cl KO ES cells in serum and 2i + vitamin C growth condition,

first: Todd

last: Macfarlan

first: Ming-An

last: Sun


title: Genome-wide analysis of differential transcription in KRAB-ZFP cluster knock-out ES cells and mouse tissues

summary: Mammalian genomes encode several hundred Krüppel-associated box zinc finger proteins (KRAB-ZFPs) that bind DNA in a sequence-specific manner through tandem arrays of C2H2-type zinc fingers and repress transcription via KRAB-dependent recruitment of the silencing cofactor KAP1. The KRAB-ZFP family rapidly amplified and diversified in mammals by segmental gene duplications, mutations, and zinc finger rearrangements likely in response to continued transposable element invasions, but the biological functions and in vivo requirement of these proteins has gone largely unexplored. We determined the genomic binding sites of 61 murine KRAB-ZFPs and genetically deleted five large KRAB-ZFP gene clusters encoding more than 100 of the approximately 360 mouse KRAB-ZFPs. We demonstrate that most KRAB-ZFPs bind to specific retrotransposon families and that many of these retrotransposons are transcriptionally activated in KRAB-ZFP cluster KO ESCs, licensing retrotransposon-derived enhancers to activate nearby genes.

overall_design: RNA-seq analysis of KRAB-ZFP cluster KO ES cells and tissues.

first: Alberto

last: De Iaco

first: Matthew

last: Tinkham

first: Didier

last: Trono


title: Genome-wide binding patterns of murine KRAB zinc finger proteins

summary: Mammalian genomes encode several hundred Krüppel-associated box zinc finger proteins (KRAB-ZFPs) that bind DNA in a sequence-specific manner through tandem arrays of C2H2-type zinc fingers and repress transcription via KRAB-dependent recruitment of the silencing cofactor KAP1. The KRAB-ZFP family rapidly amplified and diversified in mammals by segmental gene duplications, mutations, and zinc finger rearrangements likely in response to continued transposable element invasions, but the biological functions and in vivo requirement of these proteins has gone largely unexplored. Here we report the identification of the genome-wide binding profiles of 61 mouse KRAB-ZFPs by overexpression of epitope-tagged transgenes. We found that 51 of these KRAB-ZFPs target at least one retrotransposon group. Interestingly, evolutionary young and still active retrotransposons such as IAP and ETn elements are targeted by several KRAB-ZFPs which are mainly encoded within two gene clusters that are not conserved in any other sequenced species. This indicated that an evolutionary arms race drives the rapid expansion of KRAB-ZFP genes in order to restrict active retrotransposons.

overall_design: Epitope tagged KRAB zinc finger proteins were overexpressed in F9 EC or B6 ES cells and ChIP-seq was performed to identify their genomic binding sites


title: Small molecule-mediated reprogramming of human hepatocytes into bipotent progenitor cells

status: Public on May 08 2019

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

summary: Currently, much effort is directed to the development of new cell sources for clinical therapy using cell fate conversion approaches by small molecules. Direct lineage reprogramming to a progenitor state has been reported in terminally differentiated rodent hepatocytes, yet remains a challenge in human hepatocytes. Human hepatocytes were isolated from healthy and diseased donor livers and reprogrammed into progenitor cells by two small molecules, A83-01 and CHIR99021 (AC), in the presence of EGF and HGF. The stemness properties of human chemically derived hepatic progenitors (hCdHs) were tested by standard in vitro and in vivo assays and transcriptome profiling. We developed a robust culture system for generating hCdHs with therapeutic potential. The use of HGF proved to be an essential determinant of fate conversion process. Based on functional evidence, activation of HGF/MET signal transduction system collaborated with A83-01 and CHIR99021 to allow a rapid expansion of progenitor cells through activation of ERK pathway. hCdHs expressed hepatic progenitor marker genes and proteins, and could self-renew for at least 10 passages while retaining normal karyotype and potential to differentiate into functional hepatocytes and biliary epithelial cells in vitro. RNASeq gene expression profiling confirmed transcriptional reprogramming of hCdHs toward a progenitor state and suppression of mature hepatocyte transcripts. Upon intrasplenic transplantation into immunocompromised mice with acute liver injury, hCdHs effectively repopulated damaged parenchyma. Our study is a first report of successful reprogramming of human hepatocytes to a population of proliferating bipotent cells with regenerative potential. hCdHs may provide a nove tool that permits expansion and genetic manipulation of patient-specific progenitors to study regeneration and repair of diseased liver.

overall_design: Transcriptome analysis for reprogrammed progenitor like cells

first: Jaemin

last: Jeong

first: Dongho

last: Choi


title: Identifying RNAs bound by Drosophila Zn72D

city: Stanford

middle: Billy

last: Li

address: 300 Pasteur Dr, Alway M341

department: Genetics

institute: Stanford University

summary: Zn72D is an RNA binding protein that alters A-to-I RNA editing and splicing in the fly brain. We performed RNA immunoprecipitation and sequencing (RIP-seq) to identify the RNAs that are bound by Zn72D.

overall_design: We immunprecipitated Zn72D using an  anti-GFP antibody in Zn72D-GFP(BDSC50830) fly heads. We extracted RNA from 5% of input lysates and after immunoprecipitation from three replicates total.

first: Anne

last: Sapiro


title: Zfr regulates ADAR-mediated RNA editing in mouse primary neurons

summary: We used RNA-seq of mouse primary cortical neurons transfected with control shRNAs or shRNAs targeting ADAR1, ADAR2, or Zfr to test for A-to-I RNA editing level differences between control and knockdown neurons.

overall_design: To determine RNA editing sites controlled by ADAR1 and ADAR2, we compared editing levels in two biological replicates of mouse primary neurons transfected with shControl#1, shADAR1, and shADAR2. shADAR2 biological replicate 1 has three technical replicates, which are different RNA-seq libraries prepared from RNA extracted from the same neurons. We compared editing levels between shControl#1 and shADAR1 and shADAR2 to determine which editing sites are regulated by each ADAR. We compared editing levels between shControl#2 and shZfr to determine which editing sites were regulated by Zfr.

first: Emily

last: Crane


title: Measuring the influence of RNA binding proteins on A-to-I RNA editing in the Drosophila brain

first: Jin

summary: A-to-I RNA editing levels differ across tissues and cell types, but regulators of the editing process are largely unknown. We used RNA-seq on whole fly brains with different RNA binding proteins knocked down to test for A-to-I RNA editing level differences between controls and knockdowns.

overall_design: To screen for editing regulators in the Drosophila brain, we crossed a pan-neuronal Gal4 driver, C155-Gal4, to different UAS-shRNA lines targeting individual RNA binding proteins, extracted RNA and made RNA-seq libraries. We sequenced four total replicates of shGFP controls and two replicates of all RNA binding protein knockdowns.

first: Huan-Huan

last: Qiao

first: Jian-Quan

last: Ni


title: ChIP-sequencing of mouse HPC7 cells

status: Public on Jun 20 2019

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: We have expressed mouse Snai1, mutant Snai1 or empty vector in the HPC7 cell line and performed ChIP sequencing analysis of Snai1, H3K4me1 and H3K4me2

overall_design: HPC7 cells were engineered to express either wildtype Snai1, a mutant version of Snai1 that cannot bind Lsd1 or an empty vector control using retroviral transduction. GFP+ cells were sorted after 1 week in culture and expanded for ChIP-sequencing. 2x10^7 cells were used for each IP condition (Snai1, H3K4me1, H3K4me2 or IgG control).

first: Catherine

last: Carmichael

first: Soroor

last: Hediyeh-zadeh


title: Profiling of mRNA, lncRNA and circRNA in Apoptotic Bodies during Osteoclastogenesis by RNA-seq

status: Public on Jun 06 2019

city: Chongqing

first: Ce

last: Dou

state: Chongqing

address: Gaotanyan Street No.30

institute: Third Military Medical University

summary:
Purpose: The goals of this study are to describe the RNA contents in apoptotic bodies (ABs) derived from osteoclasts at different stages and to compare the differences among those ABs from difference cell stages. The biological function of these ABs are also predicted and evaluated.
Methods: Primary bone marrow cells were isolated and treated with M-CSF (30ng/mL) to generate bone marrow macrophages (BMMs). BMMs were then used to generate preosteoclast (pOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 24 h and mature osteoclast (mOC) stimulated by M-CSF (30ng/mL) together with RANKL (100ng/mL) for 72 h or more. RNA profiles of BMM, pOC and mOC were generated by deep sequencing, using Illumina NovaSeq 6000.
Results: After acquiring of clean reads, we used Hisat2 for spliced mapping. We mapped about 40 million sequence reads per sample to the mouse genome (GRCm38). Saturation rate analysis was then performed evaluating the gene coverage rate along with read depth increase. The transcripts mapping to difference functional region of the genome was then analyzed. Circos software was used to map the consistency of samples with mouse genome on a chromosomal level. The quantification of transcript intensity was analyzed using Fragments Per Kilobase of exon modelper Million mapped fragments (FPKM).
Conclusions: Our study represents the first high-throughput deep RAN sequencing data of cell derived apoptotic bodies. The biological prediction and analysis also revealed that ABs derived from osteoclast of different stages have distinct biological role. Followed by low throughput validation and detailed experiments, we identified that pOC derived ABs are more pro-angiogenic while mOC derived ABs are more pro-osteogenic.

overall_design: Apoptotic bodies derived from ostoeclast at distinct differentiation stages were isolated and undergo with deep RNA-seq to reveal their inner RNA content.

first: Qinyu

last: Ma


title: Identification of trans regulators of ADAR and A-to-I RNA editing using RNA-seq

status: Public on May 07 2019

summary: A-to-I RNA editing levels differ across tissues and cell types, but regulators of the editing process are largely unknown. We performed RNA-seq on M17 and HeLa cells with overexpression of different candidate Adar regulators and GFP as a control to assay editing level differences between overexpression and control.

overall_design: To assay the effects of overexpressing candidate Adar regulators on A-to-I RNA editing levels, we transiently overexpressed ILF2, IL3, and STRBP in H293T cells and H293T cells stably overexpressing Adar2. We extracted RNA and made RNA-seq libraries. We sequenced two biological replicates of GFP overexpression (OE) controls and two replicates of  ILF2, ILF3, and STRBP overexpression.

last: Freund

first: Qin


title: The influence of WWOX gene on cellular pathways in neuronal differentiation of human neural stem cells

status: Public on Jun 01 2019

city: Lodz

first: Andrzej

middle: K.

last: Bednarek

address: Zeligowskiego St. 7/9

department: Department of Molecular Carcinogenesis

institute: Medical University in Lodz

summary: The aim of presented study was to investigate in detail how depletion of WWOX gene disturbs signaling pathways pivotal in neuronal differentiation and CNS organogenesis. We conducted a global transcriptome analysis using CAGE method.

overall_design: Human neural stem cells (H9 hESC-Derived, Gibco, cat. No. N7800-100) with native and silenced (by shRNA lentiviral system) WWOX expression were compared before and after differentiation into neurons.

middle: K

first: Katarzyna

last: Kośla


title: Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization

first: Ichiro

last: Hiratani

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

overall_design: Refer to individual Series


title: Global identification of retinoic acid regulated enhancers and silencers

status: Public on May 23 2019

first: Brian

last: James

summary: Retinoic acid (RA) is known to regulate many genes during development by acting as a ligand for nuclear RA receptors that bind RA response elements (RAREs). However, identification of RAREs required to activate or repress specific genes during development has been quite difficult. Here, we focused on identification of RAREs in the developing trunk of vertebrate embryos during the early stages of body axis extension when RA controls neuromesodermal progenitor differentiation, spinal cord neurogenesis, somitogenesis, and forelimb bud initiation. Trunks from wild-type and Aldh1a2-/- mutants lacking RA synthesis were compared using ChIP-seq analysis for H3K27ac (a marker of gene activation) and H3K27me3 (a marker of gene repression) as well as RNA-seq analysis.  We identified numerous RAREs, defined as elements displaying differential deposition of H3K27ac and/or H3K27me3 marks in Aldh1a2-/- vs wild-type that contain a canonical RARE sequence and are near genes that have altered expression when RA is missing.  Our findings were able to differentiate genes likely to be directly regulated by RA via a RARE versus genes regulated by another factor further downstream. We identified several RA-regulated genes associated with changes in both H3K27ac and H3K27me3 near a RARE, providing new insight into how RAREs function in vivo.

overall_design: 10 samples were analyzed: 4 samples each with replicates plus two input controls.

first: Gregg

last: Duester


title: Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria [pacbio_DnmA2]

status: Public on May 04 2019

first: Taylor

last: Nye

address: 1105 N University Ave

department: MCDB

summary: We used Pacific Biosciences Single Molecule Real-Time sequencing platform to identify m6A modifications and putative methyltransferases in Bacillus subtilis

overall_design: Examination of genomic m6A in Bacillus subtilis

first: Lyle

middle: A

last: Simmons


title: Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria

sample_organism:
Bacillus subtilis
Bacillus subtilis PY79


title: Genomic N6-methyladenosine promotes expression of genes important for chromosome maintenance in bacteria [pacbio_DnmA]


title: Transcriptome data of temporal and cingulate cortex in the Rett syndrome brain

status: Public on May 01 2019

city: Seattle

first: Kimberly

last: Aldinger

state: WA

address: 1900 Nineth Ave

institute: Seattle Children's Research Institute

summary: Rett syndrome is an X-linked neurodevelopmental disorder caused by mutation in the methyl-CpG-binding protein 2 gene in the majority of cases. We describe an RNA sequencing dataset of postmortem brain tissue samples from four females clinically diagnosed with Rett syndrome and four age-matched female donors. The dataset contains transcriptomes from two brain regions, temporal and cingulate cortex, for each individual, providing a valuable resource to explore the biology of the human brain in Rett syndrome.

overall_design: Transcriptional profiles for postmortem temporal and cingulate cortex from four females with Rett syndrome and four age-matched controls.


title: RNA-seq Analysis of Gs-linked GPCRs expressed in mouse inguinal white adipocytes (iWAT), epididymal white adipocytes (eWAT) and brown adipose tissues (BAT)

status: Public on May 29 2019

city: Bethesda

first: LEI

last: WANG

state: MD

institute: NIH

summary:
Purpose: The goals of this study are to identify Gs-linked GPCRs that are endogenously expressed by mouse adipose tissue, we subjected RNA prepared from isolated mouse adipocytes (iWAT and eWAT) and BAT tissue to RNA-seq analysis.
Methods: Total RNA extracted from mature adipocytes (iWAT and eWAT) and BAT tissue of C57BL/6J mice (16-week old males) maintained on regular chow were used to construct high throughput sequencing libraries. RNAs with RIN >8 (assessed by the Agilent 2100 Bioanalyzer system) were used to prepare transcriptome libraries using the NEBNext Ultra RNA library prep kit (New England Biolabs). High throughput RNA-sequencing was performed using a HiSeq 2500 instrument (Illumina) at the NIDDK Genomic Core Facility (NIH, Bethesda, MD). Raw reads were mapped to the mouse (mm9) genome. GPCRs were extracted from the RNA-seq data using R form. Gs-coupled GPCRs were identified using the IUPHAR/BPS Guide to Pharmacology Database (https://www.guidetopharmacology.org/).
Results: Our study demonstrated that mouse adipocytes/BAT tissue express several GPCRs that are selectively coupled to Gs, including the V2 vasopressin receptor, the glucagon receptor, and different melanocortin receptor subtypes.

overall_design: Inguinal white adipocytes (iWAT), epididymal white adipocytes (eWAT), and brown adipose tissues (BAT) were isolated from 16-week-old male C57BL/6J mice consuming regular chow (n=6)

first: Lei

last: Wang

first: Jaroslawna

last: Meister


title: Raptor determines β-cell identity and plasticity independent of metabolic state

city: Shanghai

first: Qinglei

last: Yin

address: Ruijin Second Road No.197

institute: Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: In this study, we employed RNA-seq technology to identify the  exact role of mTORC1 on β-cell identity and plasticity.

overall_design: β cell specific Raptor deficiency induced gene expression from purified β cells in mice with or without insulin pellets was measured at 4 weeks after the pellet implanted.  β cells from WT mice were set as controls.

first: Guang

last: Ning

first: Qidi


title: Disruption of miRNA Sequence by TALENs and CRISPR/Cas9 Induces Varied Length of miRNA Production [TALENs]

status: Public on Apr 25 2019

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
Purpose: MicroRNAs (miRNAs) have been recognized as crucial players in plant growth, development, production and responses to biotic and abiotic stresses, while only limited number of mutants can be used to dissect their roles. Here we used TALENs (Transcription Activator-Like Effector Nucleases) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) to introduce base pair mutations in MIRNA genes, resulting in creation of miRNA mutants and elucidating the effect of mutations on the miRNA biogenesis in rice and Arabidopsis.
Methods: Total RNAs were prepared using a Trizol reagent-based method. The plant materials were homogenized and reconstituted in Trizol solution. The solution in turn was extracted by chloroform. Isopropanol was used to precipitate the total RNA. The whole process was performed under RNase free environment. DEPC-treated water was used to dissolve RNA. The total RNA underwent miRNA isolation using Qiagen miRNA purification kit according to the manufacturer’s manual. Small RNA libraries were made using 5 µg total RNA with NEBNext Small RNA library Prep Set, as described, and sequenced on the Illumina HiSeq 2500 platform.

overall_design: To study rice miRNA abundance after TALENs induced mutations

first: Bi

last: Honghao

first: Liu

last: Bo

first: Xia

last: Rui

first: Yang

last: Bing

middle: C


title: Genomic profiling of yeast resistance to food carcinogens

status: Public on Apr 13 2019

city: Albany

first: Michael

middle: Thomas

last: Fasullo

state: New York

address: 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

summary: 96 genes were identified as conferring aflatoxin resistance and 114 genes were identified as conferring resistance to IQ.

overall_design: Two diploid yeast deletion collections expressing human CYP1A2 or human CYP1A2 and NAT2  was exposed to aflatoxin B1

first: Frank

last: Doyle


title: High-fat diet enhances food-seeking behavior via sensitizing hunger-sensing neurons in Drosophila II

status: Public on Apr 11 2019

city: hangzhou

first: Rui

last: Huang

address: Yu-hang-tang road 866

institute: Zhejiang University

summary: The function of the central nervous system to regulate food intake can be disrupted by sustained metabolic challenges such as high-fat diet (HFD), which may contribute to the development of various metabolic disorders. In the present study, we found that HFD specifically enhanced food-seeking behavior in fruit flies without altering flies’ baseline metabolism and food consumption. Mechanistically, HFD increased the excitability of a small group of octopaminergic (OA) neurons to a hunger hormone named adipokinetic hormone (AKH), via increasing the accumulation of AKH receptor (AKHR) in these neurons. Upon HFD, excess dietary lipids are transported by a lipoprotein LTP to enter these OA+AKHR+ neurons via the cognate receptor LpR1, which in turn activated AMPK-TOR signaling and suppressed autophagy-dependent degradation of AKHR. Taken together, we uncovered a mechanism that linked HFD, AMPK-TOR signaling, neuronal autophagy, and food-seeking behavior, providing insight in the reshaping of neural circuitry under metabolic challenges and the progression of metabolic diseases.

overall_design: Total RNA from fly heads was extracted from 5-day-old female flies using the Trizol reagent (Invitrogen, USA), subjected to poly(A) mRNA isolation, cDNA synthesization, library preparation (NEBNext Ultra RNA Library Prep Kit, NEB), and sequencing (Illumina Hiseq2500/4000 platform). Sequence data were subsequently mapped to Drosophila genome and uniquely mapped reads were collected for further analysis. Gene expression was calculated by the RPKM (Reads Per Kilobase of exon per Million reads mapped). The genes with p-value less 0.05 and fold change more than 2 were considered as the differentially expressed gene.

first: Liming


title: Zinc finger RNA binding protein Zn72D regulates ADAR-mediated RNA editing in neurons

first: Jin

last: Li

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus


title: High-fat diet enhances food-seeking behavior via sensitizing hunger-sensing neurons in Drosophila I

overall_design: As described previously (Yu et al., 2016), individual AKHR+ cells (visualized by GFP experession) were harvested from dissected fly brain under a fluorescence microscope with a glass micropipette pulled from thick-walled borosilicate capillaries (BF120-69-10, Sutter Instruments).  Individual cells were immediately transferred to lysate buffer and underwent reverse transcription and cDNA amplification (SMARTer Ultra Low RNA Kit for Sequencing, Clonetech). The amplified cDNA were sonicated to ~250 bp fragments by the Covaris S2 system and then subjected to end-repair, dA-tail, adaptor ligation, and 12 cycles of PCR amplification using the library preparation kit (NEBNext Ultra II DNA Library Prep Kit, NEB). The cDNA libraries were sequenced by Illumina Hiseq 2500 platform. The sequenced raw data were first pre-processed to remove low-quality reads, adaptor sequences and amplification primer. Reads were mapped to Drosophila genome and mapped reads were selected for further analysis. FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) was used to quantify gene expression.


title: Cdk8 is required for establishment of chromatin marks and gene repression by Xist and mouse embryonic lineage development

status: Public on Apr 05 2019

first: Andreas

last: Postlmayr

address: Otto-Stern-Weg 7

department: D-BIOL

institute: ETH

summary: We previously reported the cyclin dependent kinase Cdk8 as a putative silencing factor for Xist. Here we investigate the role of Cdk8 in X inactivation and embryo development. We engineered a Cdk8 mutation in mouse embryonic stem cells carrying an inducible system for studying Xist function. We find that Xist repressed X-linked genes to half the expression level of the active X chromosome in the absence of Cdk8, whereas near complete silencing was observed in cells with intact Cdk8. The reduced ability of Xist to repress genes is paralleled with reduced Ezh2 recruitment and establishment of histone H3 lysine 27 tri-methylation. Introduction of wild-type but not catalytically inactive Cdk8 transgenes restores efficient gene repression and PRC2 recruitment. Notably, mutation of the highly homologous kinase Cdk19 does not affect Xist function. Combined mutations of Cdk8 and Cdk19 resemble the Cdk8 single mutation. Analysis of a conditional Cdk8 mutation in mice reveals a post-implantation lethal phenotype with variable onset between day 8.5 and 10.5. A clear female specific phenotype is masked by requirements of Cdk8 for processes in addition to X inactivation.

overall_design: Differential Gene expression upon Xist expression in the presence and absence of Cdk8 in mouse embryonic stem cells

first: Anton

last: Wutz


title: Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1

status: Public on Apr 30 2019

city: Cambridge

first: Matthew

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: The mammalian cochlea loses its ability to regenerate new hair cells prior to the onset of hearing. In contrast, the adult vestibular system can produce new hair cells in response to damage, or by reprogramming of supporting cells with the hair cell transcription factor Atoh1. We used RNA-seq and ATAC-seq to probe the transcriptional and epigenetic responses of utricle supporting cells to damage and Atoh1 transduction. We show that the improved regenerative response of the utricle correlates with a more accessible chromatin structure in utricle supporting cells compared to their cochlear counterparts. We also provide evidence that Atoh1 transduction of supporting cells is able to promote increased transcriptional accessibility of some hair cell genes. Our study offers a possible explanation for regenerative differences between sensory organs of the inner ear, but shows that additional factors to Atoh1 may be required for optimal reprogramming of hair cell fate.

overall_design: ATAC profiles of 4-6 weeks old mice utricle endogenous hair cell, supporting cells, supporting cell cultured for 10 days, supporting cells with overexpression of Atoh1 cultured for 10 days and ATAC profiles of neontal cochlea hair cells and 21 days old mice cochlea supporting cells were generated by deep sequencing, in duplicate or triplicate, using Illumina Nextseq500 instrument

first: Hsin-I

last: Jen

first: Andrew

last: Groves

first: Neil

last: Segil


title: Multilevel modulation of light signaling by GIGANTEA regulates both the output and pace of the circadian clock

status: Public on May 16 2019

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

summary: Integration of environmental signals with endogenous biological processes is essential

overall_design: 11 ChIP-seq experiments

first: Maria

last: Nohales


title: Unbiased identification of trans regulators of ADAR and A-to-I RNA editing


title: Identification of trans regulators of ADAR and A-to-I RNA editing using mmPCR-seq

summary: A-to-I RNA editing levels differ across tissues and cell types, but regulators of the editing process are largely unknown. We performed mmPCRseq on H239T and H293TAdar2OE cells with overexpression of different candidate Adar regulators and GFP as a control to assay editing level differences between overexpression and control.

overall_design: To assay the effects of overexpressing candidate Adar regulators on A-to-I RNA editing levels, we transiently overexpressed ILF2, ILF3, and STRBP in H293T cells and H293T cells stably overexpressing Adar2. We extracted RNA and made mmPCR-seq libraries to measure editing levels at targeted sites. We sequenced two technical replicates of two biological replicates of GFP overexpression (OE) controls and of ILF2, ILF3, and STRBP overexpression. We then overexpressed an ILF3 mutant lacking double stranded RNA binding domains (ILF3RBDOE) and compared two biological replicates to two biological replicates of matched GFP overexpression controls (GFPOE reps 3 and 4).

first: Emily

last: Freund

first: Anne

last: Sapiro

middle: B


title: Gastric Lgr5+ cells are programmed by Rspo3 to shield the gland from infection

status: Public on Mar 25 2019

city: Berlin

first: Cornelius

last: Fischer

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary: R-spondin (Rspo) signaling is crucial for stem cell renewal and tissue homeostasis in the gastrointestinal tract. In the stomach, Rspo is secreted from myofibroblasts and controls epithelial gland regeneration by inducing proliferation of Wnt-responsive Axin2+ cells in the isthmus of the gland. Infection with H. pylori results in increased expression of stromal Rspo, leading to an expansion of Axin2+ isthmus stem cells and gland hyperplasia. Lgr5+ cells in the gland base are exposed to Rspo3 but the effects of this are not well understood. Here we demonstrate that apart from its activity as a mitogen, endogenous Rspo3 regulates gene expression of Lgr5+ cells in the gastric gland base. Surprisingly, Rspo3 induces differentiation within the Lgr5+ compartment towards secretory deep mucous cells. Moreover, the Rspo3-Lgr5 axis turns out to be a stimulus of epithelial antimicrobial defense. Infection with H. pylori induces a strong antimicrobial response, with Lgr5+ cells expressing antimicrobial compounds that are secreted into the lumen in an Rspo3-dependent manner. Depletion of Lgr5+ cells or knockout of Rspo3 in myofibroblasts leads to hyper-colonization of gastric glands, including the stem cell compartment, whereas systemic application of recombinant Rspo clears H. pylori from the glands. We provide an intriguing, unexpected feature of the Rspo3-Lgr5 axis in the stomach, exhibiting antimicrobial self-protection of the gland to protect the stem cell compartment from invading pathogens.

overall_design: Lgr5eGFP reporter mice were infected with H. pylori for 2 months, uninfected mice served as controls. Mice were sacrificed and isolated, sorted Lgr5eGFP+ cells from the stomach antrum were used for single cell RNAseq using the 10x genome platform.

last: Sigal

last: del Mar Reines

first: Stefanie

last: Müllerke

first: Marta

last: K.

first: Hilmar

last: Berger

first: Hans-Joachim

last: Mollenkopf

last: Rothenberg

first: Bertram

last: Wiedenmann

first: Sascha

last: Sauer

first: Thomas

middle: F

last: Meyer


title: Disruption of miRNA Sequence by TALENs and CRISPR/Cas9 Induces Varied Length of miRNA Production [CRISPR/Cas9]

first: Blake

last: Meyers

summary:
Purpose: MicroRNAs (miRNAs) have been recognized as crucial players in plant growth, development, production and responses to biotic and abiotic stresses, while only limited number of mutants can be used to dissect their roles. Here we used TALENs (Transcription Activator-Like Effector Nucleases) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) to introduce base pair mutations in MIRNA genes, resulting in creation of miRNA mutants and elucidating the effect of mutations on the miRNA biogenesis in rice and Arabidopsis.
Methods: Total RNAs were prepared using a Trizol reagent-based method. The plant materials were homogenized and reconstituted in Trizol solution. The solution in turn was extracted by chloroform. Isopropanol was used to precipitate the total RNA. The whole process was performed under RNase free environment. DEPC-treated water was used to dissolve RNA. The total RNA underwent miRNA isolation using Qiagen miRNA purification kit according to the manufacturer’s manual. Small RNA libraries were made using 5 µg total RNA with Illumina TruSeq Small RNA Library Prep Kit as described, and sequenced on the Illumina HiSeq 2500 platform.

overall_design: To study the change of Arabidopsis siRNAs by CRISPR/Cas9-mediated mutations.

first: Qili

last: Fei


title: Diagnostic value of a panel of plasma exosomal miRNAs as potential biomarkers for thyroid nodules

city: Harbin

first: Xiaoyi

last: Huang

state: Heilongjiang

address: Haping Road 150

institute: Harbin Medical University Cancer Hospital

summary: Exosomes and exosomal miRNAs from the plasma of volunteers were isolated from thyroid nodules and papillary tyriod cancer patients . Profiling of exosomal miRNA was performed using next-generation sequencing(NGS) to identify miRNA candidates for diagnosis.

overall_design: Sequencing small RNA libraries prepared from  8 benign thyroid nodules and 16 PTC patients with or without metastasis.

first: Meihua

last: Liang

first: Siming

last: Yu


title: MicroRNA-451a Regulates Myogenesis by Suppressing SPARC Expression Levels

status: Public on Apr 03 2019

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

institute: NIA-IRP, NIH

summary: MicroRNAs (miRNAs) are small noncoding RNAs that critically regulate gene expression.  Their abundance and function have been linked to processes such as senescence and aging.  In aged monkey muscle, miR-451a and miR-144-3p were highly upregulated compared to young animals. This led us to hypothesize that the miRNAs 451a/144-3p may be involved in muscle differentiation. We found that these miRNAs are downregulated during the differentiation of C2C12 myoblasts. Overexpression of miR-451a, but not miR-144-3p, robustly impeded the differentiation, suggesting an inhibitory role for miR-451a.  We further investigated the potential regulatory targets of miR-451a and identified Sparc mRNA, encoding a secreted protein acidic and rich in cysteine (SPARC), which is involved in wound healing and cellular differentiation. Interestingly, we found that miR-451a suppresses Sparc mRNA translation according to the analysis of polysome profile. Our findings show that miR-451a is downregulated in differentiated myoblasts and decreases C2C12 differentiation at least in part by the suppression of SPARC biosynthesis.

overall_design: C2C12 myoblasts were cultured and two time-points, Day 0 and Day 6 of exposure to differentiation medium, were examined by gene expression microarray analysis using five independent experiments per condition.

first: Rachel

last: Munk

first: Jennifer

last: Martindale

first: Xiaoling

last: Yang

first: Ioannis

last: Grammatikakis

first: Clara

last: Di Germanio

first: Sarah

last: Mitchell

first: Rafael

last: de Cabo

first: Elin

last: Lehrmann

first: Yongqing

last: Zhang

first: Kevin

middle: G

last: Becker

first: Kotb

last: Abdelmohsen

first: Amaresh

last: Panda

first: Myriam

last: Gorospe


title: Age and poverty status alter the coding and noncoding transcriptome [African American]

status: Public on Mar 19 2019

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

summary: Emerging evidence indicates that noncoding RNAs play important regulatory roles during aging and the development of chronic disease. The functional roles of long noncoding RNAs (lncRNAs) in physiology and disease are under intense examination. However, little is known about lncRNAs in the context of human aging and socio-environmental conditions. Microarray profiling of lncRNAs and mRNAs in young and old white and African American (AA) males living above or below poverty revealed robust changes in both lncRNAs and mRNAs with age and poverty status in white males, but not in AA males. We validated the changes in lncRNAs in an expanded cohort; CDT-3247F14.2, GAS5, H19, TERC and MEG3 changed significantly with age, whereas AK022914, GAS5, KB-1047C11.2, MEG3 and XLOC_003262 changed significantly with poverty. Pathway analysis revealed that mitochondrial function and response to DNA damage and stress were enriched in younger individuals. Pathways of response to stress, viral infection, and immune signals were enriched in individuals living above poverty. These data show that both human age and a marker of social adversity influence lncRNA expression patterns. These data may provide insight into the molecular pathways underlying aging and social factors that affect disparities in aging and disease.

overall_design: Long noncoding RNAs and mRNAs were analyzed by microarray from PBMCs from young (~30 yrs, n=8) and old (~64, n=8) African American males above and below poverty.

first: Nicole

last: Noren Hooten

first: Michele

last: Evans


title: Age and poverty status alter the coding and noncoding transcriptome

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

overall_design: Refer to individual Series


title: Stage-specific regulation of the WNT/β-catenin pathway enhances differentiation of hESCs into hepatocytes

status: Public on Mar 12 2019

city: La Jolla

first: Robert

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary:
Background & Aims
Hepatocytes differentiated from human embryonic stem cells (hESCs) have the potential to overcome the shortage of primary hepatocytes for clinical use and drug development. Many strategies for this process have been reported, but the functionality of the resulting cells is incomplete. We hypothesize that the functionality of hPSC-derived hepatocytes might be improved by making the differentiation method more similar to normal in vivo hepatic development.
Methods
We tested combinations of growth factors and small molecules targeting candidate signaling pathways culled from the literature to identify optimal conditions for differentiation of hESCs to hepatocytes, using qRT-PCR for stage-specific markers to identify the best conditions. Immunocytochemistry was then used to validate the selected conditions. Finally, induction of expression of metabolic enzymes in terminally differentiated cells was used to assess the functionality of the hESC-derived hepatocytes.
Results
Optimal differentiation of hESCs was attained using a 5-stage protocol. After initial induction of definitive endoderm (stage 1), we showed that inhibition of the WNT/β-catenin pathway during the 2nd and 3rd stages of differentiation was required to specify first posterior foregut, and then hepatic gut cells. In contrast, during the 4th stage of differentiation, we found that activation of the WNT/β-catenin pathway allowed generation of proliferative bipotent hepatoblasts, which then were efficiently differentiated into hepatocytes in the 5th stage by dual inhibition of TGF-β and NOTCH signaling.
Conclusion
Here, we show that stage-specific regulation of the WNT/β-catenin pathway results in improved differentiation of hESCs to functional hepatocytes.

overall_design: mRNA profiles of undifferentiated, definitive endoderm, stage 2-5 cell ines were generated by deep sequencing, in duplicate, as well as five liver samples.

first: Louise

last: Laurent

first: Cuong

last: To