title: The genetic legacy of continental scale admixture in Indian Austroasiatic speakers

status: Public on Mar 07 2019

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

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

summary: We combined new data with previously published data to characterize admixture patterns of Austroasiatic speaking populations of India in the context of their geographic neighbours across Eurasia

overall_design: 39 samples were analysed with the Illumina Human660W-Quad and HumanOmniExpress 24 Genotyping BeadChips and are described herein.

first: Kai

last: Tätte

first: Mait

last: Metspalu

first: Toomas

last: Kivisild

first: Gyaneshwer

last: Chaubey

first: Richard

last: Villems


title: The role of topical containing camellia sinensis in the cosmetic management of skin scars in healthy human volunteers

status: Public on May 01 2019

city: Manchester

first: Ardeshir

last: Bayat

address: Oxford Road

country: United Kingdom

institute: University of Manchester

type: Expression profiling by high throughput sequencing

summary: Epigallocatechin-3-gallate (EGCG), a polyphenol, influences cutaneous wound healing due to its anti-angiogenic, anti-inflammatory and anti-oxidant properties. We previously demonstrated the role of EGCG in scarring in ex vivo human scar models. A double-blind randomised-controlled trial. Here, we evaluated application of topical EGCG compared with placebo in 62 healthy human volunteers, over 8 weeks, in scars created in their upper inner arms using skin punch biopsies. RNA sequencing was used here based on 45 samples: day 0 (n=3), week 1 (n=3 placebo, n=3 EGCG), week 2 (n=3 placebo, n=3 EGCG), week 3 (n=3 placebo, n=3 EGCG), week 4 (n=3 placebo, n=3 EGCG), week 5 (n=3 placebo, n=3 EGCG), week 6 (n=3 placebo, n=3 EGCG), week 8 (n=3 placebo, n=3 EGCG). The common differentially expressed genes identified between treated (EGCG) and placebo samples were grouped according to time point (Zonal priming: weeks 1 and 2; Direct application post scar formation (2 weeks post-biopsies): weeks 1, 2, 3, 4, 6). Further exploration of these genes using Gene Ontology and Ingenuity Pathway Analysis revealed gene signatures of relevant biological processes and pathways. Here, RNA sequencing revealed a number of angiogenic, inflammatory and antioxidant genes that were significantly downregulated with EGCG particularly at week 1 including; TPSAB1, VEGFA, EDF, IL17F, IL1A, IL1RL1, IL36A, IL36G, SOD3.

overall_design: mRNA profiles of human skin scars over 8 weeks (treatment EGCG versus placebo) were generated by sequencing, in triplicate, using Illumina PE150 Platform.

first: Sara

last: Ud-Din


title: Lineage-specific super-enhancer activates genes in a promoter-selective manner

status: Public on Mar 01 2019

city: Haining

first: Chaochen

last: Wang

address: 718 East Haizhou Rd

department: ZJU-UoE Institute

country: China

institute: Zhejiang University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Lineage-specific genetic programs rely on cell-restricted super-enhancers but it is not clear whether they selectively engage with their associated promoters to attain maximum activity. Exploiting the highly expressed Wap gene, we investigate the relative contributions of the super-enhancer and promoter in mammary tissue during lactation. Employing ChIP-seq profiling and mouse genetics, we uncover a selective lineage-specific promoter-enhancer synergy. Mechanistically, a chromatin platform permissive for high level expression develops in the native promoter-enhancer configuration but not with a heterologous promoter. While this promoter-enhancer synergy permits the induction of gene expression during pregnancy, post-transcriptional mechanisms need to be invoked to account for the high levels of Wap mRNA during lactation. Taken together, our data reveal that lineage-specific enhancer-promoter synergy and post-transcriptional regulation are critical for mammary gene regulation during pregnancy and lactation.

overall_design: Wap super-enhancer or super-enhancer-promoter was fused to gene Tbrg4 by CRISPR/Cas9-mediated genomic deletion. Therefore mouse lines seTbrg4,ΔE/wTbrg4 and WT/wTbrg4 were generated. ChIP-seq of histone modifications, STAT5, Pol II and RNA-seq were performed in mammary glands at lactation day 10 (L10) from the mice.

first: Xianke

last: Zeng

first: Precious

last: Achikeh

first: Chengyu

last: Liu

first: Lothar

last: Hennighausen


title: RNA-sequencing and bioinformatics analysis of long non-coding RNAs and mRNAs in the prefrontal cortex of mice following repeated social defeat stress

status: Public on Mar 05 2019

city: NanJing

first: Feng

last: Zhang

state: JiangSu

address: Weigang NO.1

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA-sequencing was used to screen all differentially expressed (DE) lncRNAs and mRNAs between the RSD and control groups. In mice experiencing RSD, 373 and 454 lncRNAs, along with 1142 and 654 mRNAs were significantly upregulated and downregulated, respectively.Available informatics evidence highlighted the likely role of synapse dysfunction and abnormal synaptic neurotransmission in these behaviors. Thus, our findings provide potential candidate biomarkers or intervention targets for chronic psychological stress-induced neuropsychiatric disorders.

overall_design: Total RNA obtained from prefrontal cortex of mice subjected to repeated social defeat stress compared to untreated control mice.

first: Xian

first: Shaolei

last: Ma

first: Mao

last: Mao

first: Caijuan

last: Li

first: Xiaofeng

last: Shen

first: Shiqin

last: Xu

first: Jianjun

last: Yang


title: An extracellular Argonaute protein mediates export of repeat-associated small RNAs into vesicles in parasitic nematodes

status: Public on Feb 21 2019

city: Irapuato

first: Cei

last: Abreu-Goodger

state: Guanajuato

address: Km. 9.6 Libramiento Nte Carr Leon-Irapuato

country: Mexico

institute: Langebio - Cinvestav

summary: Mobile small RNAs are an integral component of the arms race between plants and fungal parasites, and several studies suggest microRNAs could similarly operate between parasitic nematodes and their animal hosts. However, whether and how specific sequences are selected for export by parasites is unknown. Here we describe a specific Argonaute protein (exWAGO) that is secreted in extracellular vesicles (EVs) released by the gastrointestinal nematode Heligmosomodies bakeri, at multiple copies per EV. Phylogenetic and gene expression analyses demonstrate exWAGO is highly conserved and abundantly expressed in related parasites, including the human hookworm and proteomic analyses confirm this is the only Argonaute secreted by rodent parasites. In contrast, exWAGO orthologues in species from the free-living genus Caenorhabditis are highly diverged. By sequencing multiple small RNA libraries, we determined that the most abundant small RNAs released from the nematode parasite are not microRNAs but rather secondary small interfering RNAs (siRNAs) that are produced by RNA-dependent RNA Polymerases. We further identify distinct evolutionary properties of the siRNAs resident in free-living or parasitic nematodes versus those exported in EVs by the parasite and show that the latter are specifically associated with exWAGO. Together this work identifies an Argonaute protein as a mediator of RNA export and suggests rhabditomorph nematode parasites may have co-opted a novel nematode-unique pathway to communicate with their hosts.

sample_organism:
Caenorhabditis elegans
Heligmosomoides polygyrus bakeri

overall_design: A total of 20 small RNA samples from two nematodes (H. bakeri and C. elegans), adults and extracellular vesicles (from H. bakeri), with and without polyphosphatase treatment to detect sRNAs with 5' tri-P, with biological replicates.

first: Franklin

middle: W

last: Chow

first: Georgious

last: Koutsovoulos

first: Cesare

last: Ovando-Vazquez

first: Dominik

middle: R

last: Laetsch

first: Jose

last: Bermudez-Barrientos

first: Elaine

last: Robertson

first: Sujai

last: Kumar

first: Julie

middle: M

last: Claycomb

first: Mark

last: Blaxter

first: Amy

middle: H

last: Buck


title: MiR-145 antagonist effect in house dust mite model of asthma

status: Public on Feb 16 2019

city: Reno

first: William

middle: T

last: Gerthoffer

state: Nevada

address: 1440 N Virginia St

department: Pharmacology

country: USA

institute: University of Nevada, Reno

summary:
Purpose:  Identify whole lung gene expression patterns modified by nanoparticle delivery of an antisense LNA/DNA oligonucleotide targeting mmu-miR145a-5p and nontargeting oligonucleotides

Methods: Lung gene expression profiles of 10 week old BALB/c female mice were generated by polyA RNA-seq with Illumina HiSeq v4. Sequence reads that passed quality filters after timming were analyzed at the gene level with RNA STAR, featureCounts and Deseq2 . qRT–PCR validation was performed using TaqMan and SYBR Green methods.

Results: 10-15 million sequence reads per sample were mapped to the mouse genome (build mm10). Pathway analysis of differentially expressed genes identified upregulation of gene sets for human asthma, mouse lung allergic inflammation, Muc5ac regulated genes and smooth muscle genes after allergic sensitization. Gene level exppression in each asthma-related pathway was reduced by the miR-145 antagonist. The miR-145 antagonist and several nontargeting oligos also upregulated interferon signaling pathways suggesting a general antiinflammatory effect of LNA/DNA oligos in the lung.

Conclusions: Lung-directed delivery of LNA/DNA oligonucleotides with cationic lipid nanoparticles is an efffective means to prevent inflammatory gene expression in a house dust mite model of asthma

overall_design: Lung gene expression in unsensitized, house dust mite sensitized, antimiR-145 treated and nontargeting oligonucleotide treated mice

first: Sabrina

middle: C

last: Ramelli


title: Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue

status: Public on Feb 15 2019

city: Stockholm

first: Marcus

last: Buggert

state: PA

address: C2:94; Karolinska Universitetssjukhuset Huddinge

department: Microbiology

country: Sweden

institute: Karolinska Institutet

summary:
We investigate the role of resident memory T cells in protective immunity in HIV infection

Funding sources:

Michael R. Betts: NIH/NIAID R01 AI076066 and R01 AI118694

Marcus Buggert: Swedish Research Council (Dnr 537-2014-6829), Karolinska Institutet, Magnus Bergvall and Lars Hiertas Stiftelse

overall_design:
Examination of resident memory T cell transcriptome and chromatin accessibility in lymph nodes. Examination of single-cell transcriptome and T cell receptor sequences of HIV-specific resident memory CD8+ T cells in lymph nodes.
Bulk RNASeq and ATAC-Seq were performed on CD69+ and CD69- CD8+ T cells from human lymph nodes. Single cell RNASeq was performed on CD69+ and CD69- CD8+ T cells from human mesenteric lymph nodes.

first: Michael

last: Betts


title: Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity

status: Public on Mar 12 2019

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

summary: We discovered potent small molecule inhibitors against the WIN site of WDR5. These inhibitors selectively block the proliferation of mammalian cells carrying fusions of the MLL1 oncogene. Here, we show that these inhibitors result in the rapid displacement of WDR5 from chromatin in both sensitive (MV4:11) and non-sensitive (K562) cell lines, induce early changes in the distribution of active polymerases at a subset of WDR5-bound genes, and induce global transcript changes that are consistent with induction of the tumor suppressor p53.

overall_design: MV4:11 or K562 cells were treated with one of two WIN site inhibitors (C3 or C6), a negative control compound (C6nc), or DMSO. ChIP-Seq was used to track interaction of WDR5 with chromatin; PRO-Seq was used to track early changes in the distribution of active RNA polymerases, and RNA-Seq was used to monitor long-term transcriptional changes. RNA-Seq was also performed on MV4:11 cells treated with the HDM2 inhibitor nultin.

middle: P

last: Tansey

first: Erin

last: Aho

first: Gregory

last: Howard

first: Qi

last: Liu

first: Pankaj

last: Acharya


title: Multiomics Analyses of Vesicular Transport Pathway-Specific Transcripts and Proteins in Ovine Amnion: Responses to Altered Intramembranous Transport

status: Public on Mar 30 2019

city: Portland

first: Cecilia

middle: Y

last: Cheung

state: Or

address: 3181 SW Sam Jackson Park Road

department: Obstetrics & Gynecology

institute: Oregon Health & Science University

summary: Amniotic fluid (AF) volume (AFV) is determined primarily by the rate of intramembranous (IM) transport of AF across the amnion.  Intramembranous transport is characterized as vesicular endocytotic and transcytotic processes regulated by fetal urine-derived stimulators and AF inhibitors.  Our objectives were to utilize a large-scale multiomics approach to decipher the vesicular transport pathways in the amnion and to identify potential transport regulators in AF and fetal urine.  We utilized fetal sheep to experimentally induce alterations in IM transport rate and analyze the expression profiles of transcripts and proteins in amnion, AF and fetal urine.  Four experimental groups were studied: control (C), urine drainage with reduced IM transport rate and AFV (UD), urine drainage and fluid replacement with decreased IM transport rate but increased AFV (UDR), and intra-amniotic fluid infusion with augmented IM transport rate and AFV (IA).  Amnion and fluid samples were subjected to transcriptomics (RNA-Seq) and proteomics studies followed by bioinformatics analyses using Ingenuity Pathway Analysis software.  The analyses revealed 9 functional transport pathways and a panel of differentially expressed transcripts and proteins that are known mediators of vesicular transport and energy metabolism.  During UD, expressions of endocytosis and trafficking mediators were reduced as compared to controls.  Under UDR, expressions of energy metabolism activators increased while trafficking mediators decreased.  During IA, expressions of vesicular uptake and transcellular trafficking regulators were enhanced.  Co-expression of the motor protein, cytoplasmic dynein light chain-1, in both AF and fetal urine suggest that this molecule may function as a urine-derived stimulator of IM transport.

overall_design: Transcriptome and proteome in amnion and fetal fluids in four experimental groups. Utilized fetal sheep to experimentally induce alterations in IM transport rate and analyze the expression profiles of transcripts and proteins in amnion, AF and fetal urine.

first: Debra

middle: F

last: Anderson

first: Robert

middle: A

last: Brace


title: RNA-sequencing facilitates Quantitative Analysis of Wild Type and Tsg101 Transgenic cardiac transcriptomes

status: Public on Feb 27 2019

city: Cincinnati

first: Kobina

last: Essandoh

state: OH

address: 231 Albert Sabin Way

institute: University of Cincinnati

summary: Tumor susceptibilty gene 101 (Tsg101) is a key member of the endosomal sorting complex required for transport (ESCRT), that has divergent roles in carcinogenesis, ubiquitination, endosomal trafficking, virus budding, cytokinesis, cell survival and proliferation. The goal of this study is to compare cardiac transcriptome profiles of wild-type (WT) and cardiac-specific Tsg101 Transgenic (TG) mice.

overall_design: Cardiac mRNA profiles of 8-week old wild-type (WT) and Tsg101 Transgenic mice were generated by RNA sequencing  using standard Illumina

first: Guo-Chang

last: Fan

first: Shan

last: Deng


title: Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment [Microarray]

status: Public on Feb 13 2019

city: Minneapolis

first: Tania

last: Incitti

state: Minnesota

address: 2231 6th Street SE

institute: University of Minnesota

summary: Optimal cell-based therapies for the treatment of muscle degenerative disorders should not only regenerate fibers, but provide a quiescent satellite cell pool ensuring long-term maintenance and regeneration. Conditional expression of Pax3/Pax7 in differentiating pluripotent stem cells (PSC) allows the generation of myogenic progenitors endowed with satellite cell-like abilities.  To identify the molecular determinants underlying their regenerative potential, we performed transcriptome analyses of these cells along with primary myogenic cells from several developmental stages. Here we show that in vitro generated PSC-derived myogenic progenitors possess a molecular signature similar to embryonic/fetal myoblasts. However, compared to fetal myoblasts, following transplantation they show superior myofiber engraftment and ability to seed the satellite cell niche, respond to multiple re-injuries and contribute to long-term regeneration. Upon engraftment, the transcriptome of Pax3/Pax7-induced PSC-derived myogenic progenitors changes dramatically, acquiring similarity to that of satellite cells, particularly in genes involved in extracellular matrix remodeling. Single cell profiling reveals that these changes are induced, not selected, by the in vivo environment.  These findings demonstrate that Pax3/Pax7-induced PSC-derived myogenic progenitors possess proliferative and migratory abilities characteristic of earlier developmental stages, and an intrinsic ability to respond to environmental cues upon skeletal muscle regeneration.

overall_design: Three replicates of each sample (iPax3 and iPax7 mononucleated cells) were analyzed and compared to reference developmental samples adult satellite cells (three rep each). Transcriptome profiling of iPax3/7 cells injected in vivo and re-isolated was then compared to adult satellite cells (3 reps each).

first: Radbod

last: Darabi

first: Yuan

last: Ce

first: Rita

last: Perlingeiro


title: m6A-RIP-seq of mRNA in HeLa cells undergoing EMT

status: Public on Mar 25 2019

city: Guangzhou

first: Guoshi

last: Chai

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: SUN YAT-SEN UNIVERSITY

summary: We report the application of m6A-RIP-seq to indentify the m6A modifications variation in genes invovled in EMT. Briefly, total polyadenylated RNA was isolated from HeLa cells treated with or without 10 ng/ml TGF-β for 3 days by use of TRIZOL reagent followed the using of FastTrack MAGMaxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed according to instructions of manufacture and the previously published protocol (Wang et al., 2015). NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) was used for library preparation. Each experiment was conducted in two biological replicates. m6A-seq data were analyzed according to the protocols described before (Wang et al., 2015). Significant peaks with FDR < 0.05 were annotated to RefSeq database (hg19). Sequence motifs were identified by using Homer. Gene expression was calculated by Cufflinks using the sequencing reads from input samples. Cuffdiff was used to find the DE genes.

overall_design: Examination of m6A modification variation in HeLa cells undergoing EMT or not.

first: Hongsheng

first: Guanzheng

last: Luo


title: Expression data from healthy and diastolic heart failure rats

status: Public on Feb 05 2019

city: Beijing

first: Wenxi

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: Heart failure (HF) with preserved ejection fraction (HFpEF) is rising, whose morbidity, mortality and healthcare costs are similar to HF with reduced ejection fraction (HFrEF). Although substantial molecular pathways lead to the changes in organ and tissue levels, there are still lack of successful treatments for HFpEF given the complexity molecular networks remaining unknown. Here we report that the significantly changed genes of HFpEF rats associates positively with inflammatory processes and immune responses while negatively with calcium ion transport into cytosol. GSEA analysis shows several KEGG pathways are significantly enriched in HFpEF rats including p53 signaling pathway, Toll like receptor signaling pathway and so on.   Our study provides new insights into HFpEF pathogenesis and a new therapeutic against HFpEF.

overall_design: Total RND of hearts from healthy and HFpEF rats was obtained, and RNA quantity and quality were measured by NanoDrop ND-1000. RNA microarray were performed.

first: Weijuan

last: Yao


title: Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment [RNA-seq]

overall_design: Three replicates of each sample (iPax3 and iPax7 myogenic progenitors) were analyzed and compared to reference developmental samples embryonic and fetal myoblasts, and neonatal satellite cells (three rep each). Transcriptome profiling of iPax3/7 cells injected in vivo and re-isolated was then compared to adult satellite cells (3 reps each); finally, iPax3 cells were subjected to single-cell RNA-Seq and compared to single-cell RNA-Seq of adult satellite cells.

first: Incitti

last: Tania

first: Magli

last: Alessandro

first: Ce

last: Yuan

first: Perlingeiro

last: Rita


title: Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment

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

overall_design: Refer to individual Series


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

status: Public on Mar 19 2019

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

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) white males above and below poverty.

first: Nicole

last: Noren Hooten

first: Michele

middle: K

last: Evans


title: Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single Cell RNA Sequencing

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

country: Germany

institute: University of Tuebingen

summary:
A single cell RNA sequencing atlas of the Arabidopsis root distinguishes cells both by developmental fate and time, revealing defining expression features that depict a complex cascade of developmental progressions from stem cell through differentiation supported by mirroring waves of transcription factor expression.
Methods: mRNA profiles of 6-day-old wild-type (WT) and shortroot-knockout Arabidopsis thaliana roots were generated by deep sequencing of single cell (all) and bulk RNA libraries (wild type only), in duplicate (bulk & wild-type single cell) and singlicate (shr-3), using Illumina NextSeq. The sequence reads that passed quality filters were analyzed at the transcript level. Single Cell libraries were processed and analysed using Cell Ranger, STAR, Seurat. Bulk libraries were processed using Trimmomatic, STAR, HTSeq and DEseq2.
Results: For Single Cell - Using an optimized data analysis workflow, we mapped ~87k sequence reads per wild-type cell to the Arabidopsis genome (TAIR10) and identified a median of 4,276 genes and 14,758 transcripts per cell. In total, transcripts for 16,975 genes were detected (RPM ≥1) from wild-type cells. After correction for read depth, this represents ~90% of genes detected by bulk RNA-seq of protoplasted root tissue. Bulk RNA-seq data identified genes induced by protplasting of the Arabidopsis root which could be discounted from single cell analysis. The global gene expression profiles of pooled scRNA-seq and bulk RNA-seq are highly correlated (r = 0.9) indicating that plant scRNA-seq is highly sensitive.
Conclusions: Our high-resolution single cell RNA sequencing atlas of the Arabidopsis root captures precise temporal information for all major cell types, revealing new regulators and defining features foreach. Developmental trajectories derived from pseudotime analysis depict a finely resolved cascade of developmental progressions between stem cell and final differentiation supported by mirroring waves of transcription factor expression.

overall_design: Single cell RNA sequencing for 5,767 cells (total) from Arabidopsis (2x wild-type root replicate, 1x shr-3 mutant root replicate). Bulk RNA sequencing for Arabidopsis 2x replicates unprotoplasted roots and 2x replicates protoplasted roots.

first: Tom

last: Denyer

first: Xiaoli

last: Ma

first: Simon

last: Klesen


title: RNA-seq 2-cell Suv391 injected

status: Public on Feb 07 2019

city: Munich

first: Adam

last: Burton

address: Marchioninistr. 25

department: IES

institute: Helmholtz Munchen

summary: Determine whole genome RNA sequence information from 2-cell stage mouse embryos (20 embryos per sample). To use Ovation RNA-Seq System V2 kit for cDNA preparation of both mRNA and non-polyadenylated transcripts. Paired-end sequencing.

overall_design: Injected at 18h phCG with 0.6 ug/ul Suv39h1wt or Suv39h1mut mRNA


title: Differential expression between epithelium and mesenchyme in embryonic mouse lung

status: Public on Jan 25 2019

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Identification of genes differentially expressed between epithelium and mesenchyme of embryonic lung. Embryonic lung are harvested from time pregnant mice

overall_design:
Epithelium and mesenchyme were isolated from 4 embryonic mice (BALb/c, E12.5) and hybridized in a two-color design (epithelium vs. mesenchyme).

These are dual channel arrays but analyzed like single channel.

first: Saverio

last: Bellusci


title: FGFR2b/ßcatenin signalling pathway in embryonic mouse lungs

summary: FGFR2b signalling interacts with ßcatenin signalling to regulate early branching morphogenesis. Earlier, we identified a set of genes regulated in the epithelium of the developing lung by the global inhibition of FGFR2b signalling after 6 and 9 hours, in vivo. In this experiment, we used a pharmacological inhibitor of ßcatenin signalling, IQ1, to block ßcatenin signalling in isolated E12.5 wildtype lungs for 9 and 24 hrs, in vitro. We intend to assess the overlap between genes regulated in our in vivo experiment with those regulated in our in vitro, IQ1 experiment. In so doing, we hope to identify genes regulated by the FGFR2b/ßcatenin signalling pathway. Samples were obtained by isolating E12.5 lungs from C57bl/6J mice. Isolated lungs were then cultured on filters with culture medium supplied with 10 uM IQ1 (experimental) or vehicle (control), for 9 and 24 hrs. After these times, the experiments were stopped, and samples were prepared for RNA isolation.

overall_design: 4 groups, each with 1 to 3 biological replicates


title: Expression profiling of histone deacetylase (HDAC) family member genes in human synovial sarcoma cells

status: Public on Feb 06 2019

city: Birmingham

first: Yanfeng

state: AL

address: Kaul Human Genetics Building 720 20th St S

department: Department of Genetics

institute: University of Alabama at Birmingham

summary: We applied RNA sequencing to generate gene expression profiles for human synovial sarcoma SYO-1 and Yamato-SS cells. We particularly focused on eleven histone deacetylase (HDAC) family genes, and found that HDAC1 and -2 are consistently expressed at relatively higher levels in both two cell lines.

overall_design: RNA sequencing analysis of two human synovial sarcoma cell lines, SYO-1 and Yamato-SS

first: Le

last: Su


title: Identifying and targeting angiogenesis-related microRNAs in ovarian cancer

status: Public on Feb 28 2019

city: Houston

first: Lingegowda

middle: Selanere

last: Mangala

state: TX

address: 1881 East Rd

department: Gynecological Oncology

institute: M.D. Anderson Cancer Center

summary:
The deregulation of microRNAs (miRNAs) has been demonstrated to be involved in tumor angiogenesis and offers opportunities for a new therapeutic approach. However, effective miRNA delivery systems are needed for such approaches to be successful. In this study, miRNA profiling of patient data sets, along with in vitro and in vivo experiments, revealed that miR-204-5p could promote angiogenesis in ovarian tumors through THBS1.
To identify potential molecular mechanisms by which miR-204-5p exerts its pro-angiogenic effects, we performed a gene expression microarray of HeyA8-MDR cells following treatment with miR-204-5p-inh.

overall_design: Total RNA from control miR-inh- or miR-204-5p-inh-treated HeyA8-MDR cells was collected to assess global gene changes following miR-204-5p loss by gene expression assay. The array was analyzed using the Affymetrix Human Clariom S Assay.

first: Xiuhui

last: Chen

middle: S


title: Lhx8 ablation leads to massive autophagy of mouse oocytes associated with DNA damage

status: Public on Jan 22 2019

summary: Following proliferation of oogonia inmammals, great numbers of germ cells are discarded, primarily by apoptosis, while the remainder form primordial follicles (the ovarian reserve) that determine fertility and reproductive lifespan. More massive, rapid, and essentially total loss of oocytes, however, occurs when the transcription factor Lhx8 is ablated—though the cause and mechanism of germ cell loss from the Lhx8-/- ovaries has been unknown. We found that Lhx8−/− ovaries maintain the same number of germ cells throughout embryonic development; rapid decrease in the pool of oocytes starts shortly before birth. The loss results from activation of autophagy, which becomes overwhelming within the first postnatal week, with extracellular matrix proteins filling the space previously occupied by follicles to produce a fibrotic ovary. Associated with this process, as early as a few days before birth, Lhx8-/- oocytes failed to repair DNA damage—which normally occurs when meiosis is initiated during embryonic development; and DNA damage repair genes were downregulated throughout the oocyte short lifespan. Based on gene expression analyses and morphological changes, we propose a model in which lineage-restricted failure of DNA repair triggers germ cell autophagy, causing premature depletion of the ovarian reserve in Lhx8-/- mice

overall_design: Gonadal tissue was obtained from postnatal day 0 (P0) and P7 wildtype (WT) and Lhx8 knockout (KO) mice, with three biological replicates per genotype and time point.

first: Emanuele

last: Pelosi

first: Laura

last: D'Ignazio

first: Marc

last: Michel

first: Melissa

last: Beyer

first: Kassimier

last: Thompson

first: Antonino

last: Forabosco

first: David

last: Schlessinger


title: Single-cell RNA-sequencing analysis of Arabidopsis roots

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

summary: We report the use of high-throughput single-cell RNA sequencing (scRNA-seq) to analyze gene expression in wild-type and mutant Arabidopsis root cells.  We demonstrate that using a commercially available platform for droplet-based scRNA-seq (10X Genomics Chromium) enables transcriptional profiling of individual protoplasts representing all of the major cell/tissue types of the root.  Furthermore, rare cell types and subtypes have been identified.  These single-cell transcriptomes were also used to generate a pseudotime series for the root hair and non-hair cell differentiation pathways.  In addition, scRNA-seq was used to define and compare transcriptomes from root epidermis mutants, which enabled a detailed molecular analysis of the mutant phenotype.  This study demonstrates the feasibility and usefulness of scRNA-seq in plants and provides a gene expression map at single-cell resolution for the Arabidopsis root.

overall_design: Analysis of gene expression among WT(Col-0), hairless mutant(rhd6-1) and hairy mutant(gl2) at the single cell level

first: Kook

last: Ryu

first: Ling

last: Huang

first: Hyun

last: Kang


title: A comprehensive analysis of fibroblast growth factor receptor 2b signalling on epithelial tip progenitor cells during early mouse lung branching morphogenesis

first: Jochen


title: Genetic ablation of miR-33 increases food intake, enhances adipose tissue expansion, and promotes obesity and insulin resistance

first: Supriyo

last: De

summary: While therapeutic modulation of miRNAs provides a promising approach for numerous diseases, the promiscuous nature of miRNAs raises concern over detrimental off-target effects. miR-33 has emerged as a likely target for treatment of cardiovascular diseases. However, the deleterious effects of long-term anti-miR-33 therapies, and predisposition of miR-33-/- mice to obesity and metabolic dysfunction, exemplify the possible pitfalls of miRNA based therapies. Our work provides an in-depth characterization of miR-33-/- mice, and explores the mechanisms by which loss of miR-33 promotes insulin resistance in key metabolic tissues. Contrary to previous reports, our data do not support a direct role for SREBP-1 mediated lipid synthesis in promoting these effects. Alternatively, in adipose tissue of miR-33-/- mice we observe increased pre-adipocyte proliferation, enhanced lipid uptake, and impaired lipolysis. Moreover, we demonstrate that the driving force behind these abnormalities is increased food intake, which can be prevented by pair feeding with wild-type animals.

overall_design: Wild-type (WT) and mir-33 knockout (KO) male mice were fed a standard chow diet for 8-10 weeks after which they were either switched to a high fat diet (HF, 60% calories from fat: Research Diets D12492) for 20 weeks or maintained on chow diet (CHOW). For fasting-refeeding experiments, mice were either sacrificed at 8:00am after overnight feeding (FED), after being fasted for 24 h beginning at 8:00am (FAST), or after being fasted for 24 h beginning at 8:00pm followed by 12 h of feeding overnight (FED2X). Each group is represented by four biological replicates.

first: Nathan

middle: L

last: Price

first: Abhishek

last: Singh

first: Noemi

last: Rotllan

first: Leigh

last: Goedeke

first: Allison

last: Wing

first: Alberto

last: Canfrán-Duque

last: Diaz-Ruiz

first: Elisa

last: Araldi

first: Ángel

last: Baldán

first: Joao-Paulo

last: Camporez

first: Yajaira

last: Suárez

first: Matthew

last: Rodeheffer

first: Gerald

middle: I

last: Shulman

first: Rafael

last: de Cabo

first: Carlos

last: Fernández-Hernando


title: Primary target of Fgf10 in embryonic mouse lung

last: Wilhelm

summary: We performed this experiment to identify the primary target of Fgf10 in lung development. We used a double transgenic system to either attenuate FGFR2b ligands Rosa26rtTAtet(O)solubleR2b based on the use of doxycycline we generated the samples after 6 and 9 hours of doxycyline induction, or to increase Fgf10 using Rosa26rtTAtet(O)fgf10 double transgenic system we generated samples after 9 of doxycycline induction, controls lungs are provided

overall_design: 4 groups with 3 independent replicates each

first: Saverio

last: Bellusci


title: CRISPR-based multimodal genetic screens in human iPSC-derived neurons

status: Public on Jan 07 2019

city: San Francisco

first: Ruilin

last: Tian

state: CA

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California, San Francisco

summary: CRISPR/Cas9-based functional genomics have transformed our ability to elucidate mammalian cell biology. Most previous CRISPR-based screens were implemented in cancer cell lines, rather than healthy, differentiated cells. Here, we describe a CRISPR interference (CRISPRi)-based platform for genetic screens in human neurons derived from induced pluripotent stem cells (iPSCs). We demonstrate robust and durable knockdown of endogenous genes in such neurons, and present results from three complementary genetic screens. A survival-based screen revealed neuron-specific essential genes and a small number of genes that improved neuronal survival upon knockdown. A screen with a single-cell transcriptomic readout uncovered several examples for genes knockdown of which had dramatically different cell-type specific consequences. A longitudinal imaging screen detected distinct consequences of gene knockdown on neuronal morphology. Our results highlight the potential of interrogating cell biology in iPSC-derived differentiated cell types and provide a platform for the systematic dissection of normal and disease states of neurons.

overall_design: The Quant-seq experiments were performed using iPSC-derived neurons at Day 14, Day 21 and Day 28 of differentiation with 2 replicates for each sample. The CROP-seq experiments were performed using iPSCs and Day 7 neurons infected by a library of sgRNAs. Two lanes of 10X platform were used for each CROP-seq sample.

first: Connor

last: Ludwig

first: Martin

last: Kampmann


title: High salt intake exacerbates aortic dissection through IL-17 pathway

status: Public on Dec 31 2018

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

country: Japan

institute: Kurume University

summary: Rationale— Aortic dissection (AD) is a fatal disease that occurs suddenly without preceding clinical signs or symptoms. It is desirable to prevent AD before the onset. Although high salt intake is an established risk factor for cardiovascular diseases, the relationship between high salt intake and AD has not been clarified. Although recent studies have shown that high salt intake promotes interleukin (IL)-17-dependent inflammation, it is unknown whether this mechanism is involved in the pathogenesis of AD. Objective— The purpose of this study was to investigate the effect of high salt challenge on AD and involvement of IL-17.  Methods and Results— We used a mouse AD model that was induced by continuous infusion of -aminopropionitrile and angiotensin II. High salt challenge exacerbated AD lesion length compared to the mice without high salt challenge, which was abolished in IL-17 knockout mice. Unexpectedly, deletion of IL-17 resulted in the activation of Smad pathway, induction of synthetic phenotype of smooth muscle cells, remodeling of extracellular matrix in aortic tunica media, reduced stiffness of aortic walls, and less stress-induced activation of NFkB. Conclusions— These findings establish the worsening effect of high salt intake on AD that involves IL-17 pathway through the extracellular matrix metabolism. Salt restriction may represent a low-cost and practical way to reduce AD risk.

overall_design: Wild type C57BL/6 mice or IL-17-deicient mice were with or without high salt challenge by 1% NaCl as drinking water prior to and during 3 days of continuous infusion of BAPN and angiotensin II or vehicle. Three biological replicates were made in each of 8 experimental groups.

first: Satoko

last: Ohno-Urabe

first: Michihide

last: Nishihara

first: Aya

last: Furusho

first: Saki

last: Hirakata

first: Makiko

last: Hayashi

first: Sohei

last: Ito

first: Hiroshi

last: Yamada

first: Hideo

last: Yasukawa

first: Tsutomu

last: Imaizumi

first: Yoshihiro

last: Fukumoto


title: Transcriptional profiling by 4SU-seq in mouse ESCs and ESC-derived neural progenitor cells.

status: Public on Jan 12 2019

city: Edinburgh

first: Rob

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

summary: Nascent RNA was metabolically labelled with 4SU in undifferentiated and ESC-derived neural progenitor cells (NPCs). 4SU incorporated RNA was isolated and deep-sequenced at day 0 (ESCs), 3, 5 and 7 of differentiation. NPC differentiation was monitored through expression of a GFP reporter insereted into the Sox1 locus (46C reporter ESC line; PMID: 12524553). The aim was to monitor changes in transcription as ESCs differentiate into NPCs and relate this to enhancer activity.

overall_design: For each of the 4 differentiation time points, two independent biological replicates were prepared and sequenced. For each assayed time point, both merged and individual replicate 4SU-seq profiles were generated.

first: Nezha

last: Benabdallah

first: Iain

last: Williamson

first: Robert

first: Shelagh

last: Boyle

first: Dipta

last: Sengupta

first: Pierre

last: Therizols

first: Wendy

last: Bickmore


title: Comparative toxicity of Aflatoxin B1, Patulin and their biosynthetic precursors:  A human intestinal microarray analysis

city: TOULOUSE

first: Olivier

last: PUEL

address: 180 chemin de Tournefeuille

department: TOXALIM UMR 1331

country: France

institute: INRAE

summary: Patulin (PAT) and Aflatoxin B1 (AFB1) are frequent mycotoxins contaminating food and feed which demonstrate multiple toxic effects. These mycotoxins represent final product in cascades of enzymatic reactions. In order to limit the risk generated by food contamination, approaches aiming to block the biosynthesis pathway of these mycotoxins can be considered, provided that their precursors are devoid of toxicity. The aim of this study was to compare the toxicity of two precursor compounds (Versicolorin A (VERA), sterigmatocystin (STG)) to AFB1 and the precursor compound (ascladiol) to PAT. Human intestinal Caco-2 cells were exposed to 1 µM AFB1, VERA, STG or 3 µM PAT or ascladiol for 24 hours and transcription analysis was performed using an “Agilent Sureprint 63 Human GE 8x60k microarray.

overall_design: Human intestinal Caco-2 cells were exposed in vitro to different molecules at 1µM for AFB1, VERA, STG and 3 µM for PAT and ascladiol during 24 h. Then RNAs were extracted.

first: Joanna

last: Tannous

first: Selma

last: Snini

first: Yannick

last: Lippi

first: Imourana

last: Alassane-Kpembi

first: Ting

last: Zhou

first: Claire

last: Naylies

first: Souraia

last: Tadrist

first: Isabelle

last: Oswald

last: Puel


title: EGFR-targeted therapy-induced resistance mechanism in glioblastoma

status: Public on Jan 01 2019

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

summary:
Analysis of mouse glioma tumors (in RAG1-/- mouse host) overexpressing Control(C) or Slug(S) viruses, and treated with doxycyclin(D) to turn off EGFRviii expression. Results provide insight into molecular basis of EGFRviii targeted therapy-induced resistence in GBM.

By utilizing animals engineered with doxycycline (dox)-off oncogenic EGFRvIII transgene and conditional Ink4a/Arf and Pten alleles (Nestin-CreERT2; Ink4aL/L; PtenL/L; hGFAP_tTA; tetO-EGFRvIII, designated iEIP), we previously demonstrated that sustained oncogenic EGFR signaling was required for maintenance of EGFR-driven glioma progression and suppression of oncogenic EGFRvIII transgene expression induces tumor regression. But despite of a robust initial response, the regressed tumors relapsed inevitably. The finding that relapsed tumors had escaped oncogenic EGFR signaling addiction promoted our search for potential genetic events that might fuel the resistance development. Three relapse and two matched treatment-naïve tumors derived from the same parental line were analyzed by whole exome sequencing.

overall_design:
Glioma mRNA profiles of Control, ControlDox, Slug, SlugDox were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

To examine potential changes in mutation and copy number landscapes in replased tumors recovered from oncogenic EGFR suppression, we performed exome sequencing on three cultured tumor cells from relapsed tumors (147, 175, relapse 8) as well as two untreated glioma samples (QX, 2QX).

first: Hwanhee

last: Oh

first: Tuo

last: Zhang

first: Hongwu

last: Zheng

first: Jun

last: Yao


title: Gene expression and ChIP-seq analysis of hematopoetic progenitors

first: Supriyo

last: De

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

overall_design: Refer to individual Series


title: Gene expression analysis of hematopoetic progenitors

summary: Bivalency has been postulated to be a ‘poised’ state from which removal of one or the other mark permits gene activation or repression. To determine whether gene expression changes accompanied resolution of bivalent genes, we first obtained the expression pattern of hematopoietic stem cells (HSC), lymphoid-primed multipotent progenitors (LMPP), common lymphoid progenitors (CLP) , early thymic precursors (ETP), double negative 2 (DN2) and double negative 3 (DN3) cells using Affymetrix arrays. Consistent with trends noted in earlier studies, K4+ genes were, on average, expressed at higher levels compared to K4+K27+ or K27+ genes in all subsets.

overall_design: Hematopoietic stem cells (HSC), lymphoid-primed multipotent progenitors (LMPP) and common lymphoid progenitors (CLP) were purified from bone marrow of C57BL/6J mice; early thymic precursors (ETP), double negative 2 (DN2) and double negative 3 (DN3) cells were purified from C57BL6 thymus and used to obtained an expression pattern of each cell subset using Affymetrix arrays.

first: Amalendu

last: Ghosh

first: Jeremiah

last: Bell

first: Brittany

middle: N

last: Weber

first: William

last: Wood

first: Kevin

middle: G

last: Becker

first: Jyoti

last: Sen

first: Avinash

last: Bhandoola

first: Ranjan


title: Treatment of melanoma cell lines with CCG-222740

status: Public on Dec 30 2018

city: East Lansing

first: Sean

middle: Alexander

last: Misek

state: MI

address: 1355 Bogue Street

institute: Michigan State University

summary: The Ras/MEK/ERK pathway has been the primary focus of targeted therapies in melanoma, given that it is aberrantly activated in almost 80% of human cutaneous melanomas (~50% BRAFV600 mutations and ~30% NRAS mutations). While targeted therapies have yielded success in BRAFV600 mutant melanoma patients, such therapies have been ineffective in NRAS mutant melanomas in part due to their cytostatic effects and primary resistance in this patient population. Here, we demonstrate that increased Rho/MRTF-pathway activation correlates with high intrinsic resistance to trametinib, a MEK inhibitor, in a panel of NRAS mutant melanoma cell lines. Combination of trametinib with the Rho/MRTF-pathway inhibitor, CCG-222740, synergistically reduced cell viability in NRAS mutant melanoma cell lines in vitro. Furthermore, the combination of CCG-222740 with trametinib induced apoptosis and reduced clonogenicity in the highly trametinib-resistant SK-Mel-147 cells. These findings suggest a role of the Rho/MRTF-pathway in high intrinsic trametinib resistance to a subset of NRAS mutant melanoma cell lines and highlights the potential of concurrently targeting the Rho/MRTF-pathway and MEK in NRAS mutant melanomas.

overall_design: mRNA profiles of various melanoma cell lines treated with 10 uM CCG-222740 for 0, 2, 6, or 24 hours.

first: Richard

last: Neubig


title: ChIP-seq analysis of hematopoetic progenitors

summary: Bivalent chromatin refers to the simultaneous occurrence of transcription activation (H3K4me3)- and repression (H3K27me3)-associated histone modifications at gene promoters.  This mark was first identified in ES cells and proposed to maintain genes in a poised state for future resolution to fully-active (H3K4me3-only) or fully-repressed (H3K27me3-only) states.  In this report we rigorously test the poising hypothesis using a well-established developmental paradigm of hematopoietic stem cell differentiation to T lymphoid lineage committed cells.  We show that bivalent chromatin is generated and resolved at specific stages of hematopoiesis.  The epigenetic states from which it is generated and the states to which it is resolved vary with developmental stage, suggesting that bivalency serves different functions at each stage.  Moreover, singly-marked genes do not transition to the opposing univalent state via a bivalent intermediate.

overall_design: Fresh ex vivo cells were used from mice to study dynamics of bivalent chromatin during hematopoietic differentiation to the T lymphoid lineage. Hematopoietic stem cells (HSC), lymphoid-primed multipotent progenitors (LMPP) and common lymphoid progenitors (CLP) were purified from bone marrow of C57BL/6J mice; early thymic precursors (ETP), double negative 2 (DN2) and double negative 3 (DN3) cells were purified from C57BL6 thymus.  We analyzed at least two independent cell preparations for each subset, obtained from approximately 25 mice per preparation.  Purified cells were subjected to micro-chromatin immunoprecipitation (micro-ChIP) using antibodies directed against H3K4me3 and H3K27me3. Immunoprecipitated DNA was sequenced using standard Illumina platform


title: Mitophagy ameliorates Aβ and p-Tau pathologies, and cognitive deficits, in experimental models of Alzheimer’s disease

status: Public on Nov 26 2018

summary: Accumulation of damaged mitochondria is a hallmark of human aging and age-related neurodegenerative pathologies, including Alzheimer’s disease (AD). However, the molecular mechanisms of the impaired mitochondrial homeostasis and their relationship to AD are still elusive. Here we provide evidence that mitophagy, a cellular process mediating selective clearance of dysfunctional mitochondria, is impaired in AD patient hippocampus, in iPSC-derived human neurons and in animal AD models. In C. elegans models of AD, pharmacological stimulation of mitophagy reverses memory impairment through a PINK-1, PDR-1 and DCT-1 dependent pathway. Mitophagy induction diminishes the levels of insoluble amyloid-β (Aβ)1-42 and Aβ1-40 peptide isoforms and prevents cognitive impairment in AD mice by a mechanism involving microglial phagocytosis of extracellular Aβ plaques and suppression of neuroinflammation. Furthermore, mitophagy abolishes AD-related Tau hyperphosphorylation in human neuronal cells and reverses memory impairment in transgenic Tau nematodes. Our findings suggest that impaired removal of defective mitochondria is a pivotal event in AD pathogenesis. Interventions that stimulate mitophagy therefore have therapeutic potential in the prevention and treatment of AD.

overall_design: APP/PS1 mice were treated with either vehicle (DMSO, N=7) or Urolithin A (UA, 200 mg/kg/day, N=6) by gavage from 6 months until 8 months of age, while wild-type (WT) littermates (N=6) were treated with vehicle in the same manner.

first: Evandro

last: Fang

first: Yujun

last: Hou

first: Konstantinos

last: Palikaras

first: Bryan

last: Adriaanse

first: Jesse

last: Kerr

first: Beimeng

last: Yang

first: Sofie

last: Lautrup

first: Xiuli

last: Dan

first: Deborah

last: Croteau

first: Mansour

last: Akbari

first: Nigel

last: Greig

first: Tormod

last: Fladby

first: Hilde

last: Nilsen

first: M

middle: Z

last: Cader

first: Mark

last: Mattson

first: Nektarios

last: Tavernarakis

first: Vilhelm

last: Bohr


title: Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

status: Public on Oct 26 2018

city: Berkeley

first: Alejandro

last: Padron

address: University of California, Berkeley

department: MCB

institute: UC Berkeley

summary: Stress granules are dynamic non-membrane bound organelles made up of untranslating messenger ribonucleoproteins (mRNPs) that form when cells integrate stressful environmental cues resulting in stalled translation initiation complexes. Although stress granules dramatically alter mRNA and protein localization, understanding these complexes has proven to be challenging through conventional imaging, purification, and crosslinking approaches. We therefore developed an RNA proximity labeling technique, APEX-Seq, which uses the ascorbate peroxidase APEX2 to probe the spatial organization of the transcriptome. We show that APEX-Seq can resolve the localization of RNAs within the cell and determine their enrichment or depletion near key RNA-binding proteins. Matching both the spatial transcriptome using APEX-seq, and the spatial proteome using APEX-mass spectrometry (APEX-MS) provide new insights into the organization of translation initiation complexes on active mRNAs, as well as revealing unanticipated complexity in stress granule contents, and provides a powerful approach to explore the spatial environment of macromolecules.

overall_design: APEX-eIF4E, APEX-eIF4A, APEX-GFP, C1-APEX, and APEX-CBX1 under Naive conditions were used to assess within and between compartment differnces were performed in duplicate with their corresponding input samples using a Hiseq4000. RNA from APEX-eIF4A under heatshock or hippuristanol samples were performed in duplicate using a Hiseq4000

first: Shintaro

last: Iwasaki

first: Nicholas

last: Ingolia


title: Integrative analysis of the einkorn (Triticum monococum) grain reveals new mechanisms of response to sulfur deficiency

status: Public on Dec 01 2018

city: Clermont-Ferrand

first: Titouan

last: Bonnot

address: 5 chemin de Beaulieu

institute: INRA

summary: In wheat, the main staple crop in many regions of the word, one major challenge is to improve the yield potential while maintaining the grain quality, which is mainly defined by its protein concentration and composition. To achieve this goal, it is essential to considerate the nitrogen (N) and sulfur (S) nutrition, which strongly influences the grain storage protein (GSP) composition. Nowadays, the limitation of nitrogen inputs and the sulfur deficiency recently observed in soils represent major difficulties to control the grain quality. Thus, identification of the molecular mechanisms that control the accumulation of GSP in response to N and S supply is necessary. In this study, we applied four post-anthesis N and S treatments to an einkorn (Triticum monococcum) culture. Effects of the treatments on the grain transcriptome and metabolome were evaluated at different times during grain development. From the 386 differentially expressed genes and the 21 metabolites differentially accumulated, our results have revealed a strong impact of a high-N supply without any added S. A large majority of genes were transiently influenced by the treatments while others showed strong modifications of their kinetics of expression during grain filling. We hypothesized the role of several genes (e.ge.g. sulfate transporters, transcriptional regulators) in the adjustment of the N-to-S ratio in response to a S deficiency. These genes could coordinate the amino acid pool necessary for GSP synthesis. These new results contribute in facing the challenge of maintaining wheat grain quality for the development of more sustainable agriculture.

overall_design: Transcriptome comparisons between four N and S treatments and between six grain develomental stages in three replicates

first: Pierre

last: Martre

first: Victor

last: Hatte

first: Emmanuelle

last: Bancel

first: Mireille

last: Dardevet

first: Philippe

last: Leroy

first: Julie

last: Boudet

first: Marie

last: Pailloux

first: Catherine

last: Ravel


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

status: Public on Nov 10 2018

city: Gwangju

first: Wooje

last: Lee

address: 309, Pilmun-daero, Dong-gu

department: Cellular and Molecular Medicine

country: South Korea

institute: Chosun University

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: MIR100 host gene-encoded lncRNAs promote cell proliferation by modulating the interaction between HuR and its target mRNAs

status: Public on Oct 22 2018

first: Supriyo

last: De

summary: Long non-coding RNAs (lncRNAs) regulate vital biological processes, including cell proliferation, differentiation and development. A subclass of lncRNAs is synthesized from microRNA host genes (MIRHGs) due to pre-miRNA processing, and is categorized as miRNA-host gene lncRNAs (lnc-miRHGs). Presently, it is not clear whether lnc-miRHG perform additional functions.  We demonstrate a miRNA-independent role for a nuclear-enriched lnc-miRHG in cell cycle progression. MIR100HG produces spliced and stable lncRNAs (lnc-MIR100HG) that display elevated levels during the G1 phase of the cell cycle. Depletion of lnc-MIR100HG in human cells results in aberrant cell cycle progression with out altering the levels of miRNA encoded within MIR100HG. Notably, lnc-MIR100HG interacts with the HuR/Elav as well as with several of HuR-target mRNAs. Further, lnc-MIR100HG-depleted cells show reduced interaction between HuR and its target mRNAs, indicating that lnc-MIR100HG facilitates interaction between HuR and target mRNAs. Our studies have unearthed novel roles played by miRHG-encoded lncRNAs in regulating RNA binding protein activity, thereby underscoring the importance of determining the function of several hundreds of miRHG lncRNAs that are present in human genome.

overall_design: Cell cycle synchronized U2OS (osteosarcoma) cells were transfected with either control siRNA or miR-100HG siRNA, and RNA immunoprecipitated using either IgG and HuR antibodies, using four biological replicates for each of the four conditions.

first: Qinyu

last: Sun

first: Vidisha

last: Tripathi

first: Je-Hyun

last: Yoon

first: Deepak

last: Singh

last: Hao

first: Kyung-Won

last: Min

first: Sylvia

last: Davila

first: Richard

middle: W

last: Zealy

first: Xiao

last: Li

first: Maria

last: Polycarpou-Schwarz

first: Dawood

last: Dudekula

first: Elin

last: Lehrmann

first: Yongqing

last: Zhang

first: Kevin

last: Becker

first: Susan

middle: M

last: Freier

first: Sven

last: Diederichs

first: Supriya

last: Prasanth

first: Ashish

last: Lal

first: Myriam

last: Gorospe

first: Kannanganattu

middle: V


title: Transcription factor activity and nucleosome organisation in mitosis

status: Public on Dec 04 2018

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

summary: Mitotic bookmarking transcription factors (BFs) maintain the capacity to bind to their targets during mitosis, despite major rearrangements of the chromatin. While they were thought to propagate gene regulatory information through mitosis by statically occupying their DNA targets, it has recently become clear that BFs are highly dynamic in mitotic cells. This represents both a technical and a conceptual challenge to study and understand the function of BFs: first, formaldehyde has been suggested to be unable to efficiently capture these transient interactions, leading to profound contradictions in the literature; second, if BFs are not permanently bound to their targets during mitosis, it becomes unclear how they convey regulatory information to daughter cells. Here, comparing formaldehyde to alternative fixatives we clarify the nature of the chromosomal association of previously proposed BFs in embryonic stem cells: while ESRRB can be considered as a canonical BF that binds at selected regulatory regions in mitosis, SOX2 and OCT4 establish DNA sequence independent interactions with the mitotic chromosomes, either throughout the chromosomal arms (SOX2) or at pericentromeric regions (OCT4). Moreover, we show that ordered nucleosomal arrays are retained during mitosis at ESRRB bookmarked sites, whereas regions losing transcription factor binding display a profound loss of order. By maintaining nucleosome positioning during mitosis, ESRRB might ensure the rapid post-mitotic re-establishment of functional regulatory complexes at selected enhancers and promoters. Our results provide a mechanistic framework that reconciles dynamic mitotic binding with the transmission of gene regulatory information across cell division.

overall_design: Examination of binding of Esrrb, Nanog, Sox2 and Oct4 in mouse ES cells in interphase and mitosis by ChIP-seq with differing fixatives: FA and DSG+FA. Examination of chromatin accessibility and nucleosome positioning in mouse ES cells in interphase and mitosis by ATAC-seq and MNase-seq. Examination of the consequences of potential Sox2 bookmarking by cell-cycle resolved RNA-seq of Sox2-AID line.

first: Nick

last: Owens


title: Metabolic reprogramming with the induction of toxin production of Clostridioides difficile during the stationary phase

status: Public on Oct 01 2018

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

institute: Technische Universtität Braunschweig

summary: Systems biology approach of Clostridioides difficile to analyze the temporal changes in the intracellular and extracellular metabolme, transcriptome and proteome along the growth curve in casamino acids medium and the connection to toxin production.

overall_design:
Clostridioides difficile 630∆erm (DSM28645) were grown in a casamino acids medium (CDMM) containing 2 g/L glucose. Samples were taken at five time points along the growth curve (exponential growth: 14.5 h of cultivation, transient phase: 17.25 h, stationary phase 1: 19.25 h, stationary phase 2: 24.25 h, stationary phase 3: 29.25 h). The cultivation was performed with four biological replicates. Reference in transcriptomic acid proteomic measurement was the exponential phase samples.

Please not that the sample data tables have been updated with the correct values on Sep 27th, 2019.

first: Julia

middle: D

last: Hofmann

first: Andreas

last: Otto

first: Mareike

last: Berges

first: Annika-Marisa

last: Michel

first: Dörte

last: Becher

first: Dieter

last: Jahn

first: Meina

last: Neumann-Schaal


title: ImmGen ULI: Deep RNA-seq data

status: Public on Nov 16 2018

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: Primary RNAseq data for five highly purified immunocyte populations (splenic NK, Follicular B, Naïve CD4+ abT, gdT cells and peritoneal macrophages) profiled to unusual depth as multiple biological replicates, using the ImmGen ULI pipeline.

overall_design:
RNAseq datasets generated routinely by ImmGen using the ULI (ultra-low-input) pipeline are somewhat shallow, and not suitable for exploration of genes expressed at very low levels. Here, an average of 16 replicates were generated for each of 5 reference cell-types and sequenced using ImmGen's standard RNA-seq pipeline

contributor: Immunological Genome Project Consortium


title: IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner [IGF2BP1 and SRF KD in ES-2 (total RNA)]

status: Public on Oct 10 2018

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: The oncofetal mRNA-binding protein IGF2BP1 and the transcriptional regulator SRF modulate gene expression in cancer. In cancer cells, we demonstrate that IGF2BP1 promotes the expression of SRF in a conserved and N6-methyladenosine (m6A) dependent manner by impairing the miRNA-directed decay of the SRF mRNA. This results in enhanced SRF-dependent transcriptional activity and promotes tumor cell growth and invasion. At the post-transcriptional level, IGF2BP1 sustains the expression of various SRF-target genes. The majority of these SRF/IGF2BP1-enhanced genes, including PDLIM7 and FOXK1, shows conserved upregulation with SRF and IGF2BP1 synthesis in cancer. PDLIM7 and FOXK1 promote tumor cell growth and were reported to enhance cell invasion. Consistently, 35 SRF/IGF2BP1-dependent genes showing conserved association with SRF and IGF2BP1 expression indicate a poor overall survival probability in ovarian, liver and lung cancer. In conclusion, these findings identify the SRF/IGF2BP1-, miRNome- and m6A-dependent control of gene expression as a conserved oncogenic driver network in cancer.

overall_design: total RNA-Seq of ES-2 cells transfected with either control siRNAs (siC) or siRNAs directed against IGF2BP1 or SRF. Three replicates per condition.

first: Simon

last: Müller

first: Anurag

last: Singh

first: Jacob

last: Haase

first: Nadine

last: Bley

first: Tommy

last: Fuchs

first: Marcell

last: Lederer

last: Dahl

first: Huilin

last: Huang

first: Jianjun

last: Chen

first: Guido

last: Posern

first: Stefan

last: Hüttelmaier


title: Loss of TET2 results in DNA methylation changes in mouse GC B-cells

status: Public on Oct 08 2018

city: Farmington

first: Sheng

last: Li

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory


title: Integrated transcriptional regulatory network of quorum sensing, replication, and SOS response in Dinoroseobacter shibae

status: Public on Nov 03 2018

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: Transcriptional response of the QS-negative D. shibae strain ∆luxI1 towards externally added 500nM autoinducer (AI) 3-oxo-C14-HSL over a time period of 3 hours.

overall_design: Samples from three independent cultures were withdrawn. Each of the three replicate cultures were split and treated with either autoinducer or DMSO as control. Samples from AI treated cultures were taken 10, 20, 40, 60, 120 and 180 minutes after treatment, Samples from DMSO treated cultures were taken 60 and 180 minutes after treatment

first: Sonja

last: Koppenhöfer

first: Hui

last: Wang

first: Maren

last: Scharfe

first: Volkhard

last: Kaever

first: Irene

last: Wagner-Döbler


title: Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation [ChIP-seq]

status: Public on Sep 17 2018

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

institute: NIA-IRP, NIH

summary: Transcription factor NF-κB regulates cellular responses to environmental cues.  For many stimuli NF-κB resides only transiently in the nucleus.  Consequently, time-dependent transcriptional outputs are a fundamental feature of NF-κB activation.  Here we identify mechanisms that direct kinetic patterns of NF-κB-dependent gene expression and transcriptional outcomes in response to a transient NF-κB-inducing stimulus in B cells.  By combining RELA binding, RNA polymerase II (Pol II) recruitment, and perturbation of NF-κB activation, we demonstrate that kinetic differences amongst early- and late-activated RELA target genes can be understood based on chromatin configuration prior to cell activation and RELA-dependent priming, respectively.  Additionally, we identified genes that were repressed by RELA activation and others that responded to RELA-activated transcription factors.  Cumulatively, our studies define an NF-κB-responsive inducible gene cascade in activated B cells.

overall_design: kinetic patterning of direct and indirect  NF-κB targets

first: Ranjan

last: Sen

first: Mingming

last: Zhao

first: Ken

last: Zhou

first: William

middle: H

last: Wood

first: Kevin

last: Becker

first: Hongkai

last: Ji


title: Rec114 ChIP-seq

status: Public on Sep 12 2018

city: New York

first: Hajime

last: Murakami

address: 1275 york ave

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: To segregate accurately during meiosis, homologous chromosomes in most species must recombine. Very small chromosomes would risk missegregation if recombination were randomly distributed, so the double-strand breaks (DSBs) that initiate recombination are not haphazard. How this nonrandomness is controlled is not understood. Here we demonstrate that Saccharomyces cerevisiae integrates multiple, temporally distinct pathways to regulate chromosomal binding of pro-DSB factors Rec114 and Mer2, thereby controlling duration of a DSB-competent state. Homologous chromosome engagement regulates Rec114/Mer2 dissociation late in prophase, whereas replication timing and proximity to centromeres or telomeres influence timing and amount of Rec114/Mer2 accumulation early. A distinct early mechanism boosts Rec114/Mer2 binding quickly to high levels specifically on the shortest chromosomes, dependent on chromosome axis proteins and subject to selection pressure to maintain hyperrecombinogenic properties of these chromosomes. Thus, an organism’s karyotype and its attendant risk of meiotic missegregation influence the shape and evolution of its recombination landscape.

sample_organism:
Saccharomyces cerevisiae
Saccharomyces mikatae

overall_design: Sixty samples total: 3 time points (each time points contains ChIP and input samples) from Rec114-myc wild type, zip3, hop1, red1, rec8, hop1 red1, hop1 red1 rec8 strains, strains with reciprocal translocation (between chr1 and chr4, or chr8 and chr9) in S. cerevisiae, and Rec114-myc wild type in S. mikatae.

first: Scott

last: Keeney


title: Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation [ChIA-PET]


title: Mer2 ChIP-seq

overall_design: Twenty-four samples total: 12 time points (each time points contains ChIP and input samples) from Mer2-myc ars∆ strain


title: Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation [RNA-seq]


title: Topoisomerase 3β Interacts with RNAi Machinery to Promote Heterochromatin Formation and Transcriptional Silencing in Drosophila


title: Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation


title: The mechanistic basis of diverse, environmentally dependent genetic interaction in a metabolic pathway

status: Public on Sep 15 2018

city: Paris

first: Harry

middle: E.

last: Kemble

address: UMR 1137 – UFR de Médecine Paris 7 Denis Diderot,  16 rue Henri Huchard

institute: IAME, INSERM

summary: Metabolic imbalances underlie a large spectrum of diseases, spanning congenital and chronic conditions and cancer. Our ability to explain and predict such imbalances remains severely limited by the diversity of underlying mutation effects and their dependence on the genetic background and environment, but it is unclear whether these complicating factors can be reduced to simple quantitative rules. To characterise their interplay in determining cell physiology and fitness, we systematically quantified almost 4,000 interactions between expression variants of two genes of a well-known sugar-utilisation pathway containing a toxic metabolite in the model bacterium, Escherichia coli, in different environments. We detect a remarkable variety of types and trends of intergenic interaction in this linear pathway, which cannot be reliably predicted from the effects of each variant in isolation, along with a dependence of this epistasis on the environment. Despite this apparent complexity, the fitness consequences of interactions between alleles and environment are explained by a mechanistic model accounting for catabolic flux and toxic metabolite concentration. Our findings reveal how, contrary to a common assumption, the nature of fitness interactions is governed by more than just the topology of the molecular network underlying a selected trait. Our prospects of predicting disease and evolution will therefore improve by expanding our knowledge of the links among proteome, metabolome and physiology.

overall_design: The experimental system consists of 2 combinatorially mutagenised promoters (each driving expression of a metabolic gene) carried on a plasmid. Plasmids are barcoded with 20 randomised nucleotide tags, so that every gentoype is associated to multiple different barcodes. Sequencing thus consisted of two steps: first, MiSeq was used to uncover which barcodes were attached to which genotypes (one sample - "pTet-pLac-BC-linked"); second, the library was grown together and barcodes tracked over time with HiSeq in 4 independent experiments. A preliminary experiment consisted of 6 time-points (6 samples). The 3 others were performed in 3 different experimental environments, one of which replicated the preliminary experiment, and consisted of 4 time-points each (3x4=12 samples).

middle: E

first: Olivier

last: Tenaillon


title: RNAseq for finding splicing events in Arabidopsis prefoldin and lsm8 mutants in different environmental conditions

status: Public on Jan 09 2019

city: Valencia

first: Javier

last: Forment

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (UPV-CSIC)

summary: This GEO submission includes RNAseq raw data (fastq) and processed data (using ASpli 1.6.0) from samples obtained in the wild type and the single prefoldin4 and lsm8 mutants in three different environmental conditions as well as in the triple prefoldin2 prefoldin4 prefoldin6 mutant growth in standard conditions.

overall_design: 28 biological samples from 10 different conditions and genopypes, including the Col-0 WT in each condition (standard, cold and salt conditions)

first: David

last: Esteve-Bruna

first: Cristian

last: Carrasco-López

first: Noel

last: Blanco-Touriñán

last: Iserte

first: Marcelo

middle: J

last: Yanovsky

first: Miguel

middle: A

last: Blázquez

first: Julio

last: Salinas

last: Alabadí


title: Topoisomerase 3β Interacts with RNAi Machinery to Promote Heterochromatin Formation and Transcriptional Silencing in Drosophila [RNA-Seq]

first: Supriyo

last: De

department: Laboratory of Genetics and Genomics

summary: Topoisomerases solve topological problems during DNA metabolism, but whether they participate in RNA metabolism remains unclear. Top3b represents a family of topoisomerases carrying activities for both DNA and RNA. Here we show that in Drosophila, Top3b interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) containing AGO2, p68 RNA helicase, and FMRP. Top3b and RISC mutants are similarly defective in heterochromatin formation and transcriptional silencing by position-effect variegation assay. Moreover, both Top3b and AGO2 mutants exhibit reduced levels of heterochromatin protein HP1 in pericentric heterochromatin. Furthermore, expression of several genes and transposable elements in heterochromatin is increased in the Top3b mutant. Notably, Top3b mutants defective in either RNA binding or catalytic activity are deficient in promoting HP1 recruitment and silencing of transposable elements. Our data suggest that Top3b may act as an RNA topoisomerase in siRNA-guided heterochromatin formation and transcriptional silencing.

overall_design: We examined the RNA expression profile in RNA/DNA topoisomerase (Top3b) mutant flies as compared to w1118 control flies. We isolated the head of each fly and extracted the total RNA for RNA-seq.

first: Seung

middle: K

last: Lee

first: Yutong

last: Xue

first: Weiping

last: Shen

first: Yongqing

last: Zhang

first: Yuyoung

last: Joo

first: Muzammil

last: Ahmad

first: Madoka

last: Chinen

first: Yi

last: Ding

first: Wai

last: Ku

first: Elin

last: Lehrmann

first: Elissa

last: Lei

first: Keji

last: Zhao

first: Sige

last: Zou

first: Alexei

last: Sharov

first: Weidong

last: Wang


title: Effect of lifelong carnitine supplementation on plasma and tissue carnitine status, hepatic lipid metabolism and stress signaling pathways and skeletal muscle transcriptome in mice at advanced age

status: Public on Sep 19 2018

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

summary: Despite this large body of evidence from clinical studies that an improvement of carnitine status has beneficial effects on metabolic health, serious safety concerns with carnitine supplementation have been raised based on the recent observation that longterm carnitine supplementation (from weaning to 5 mo of age) in a transgenic mouse model of atherosclerosis (Apoe-/- mice) promotes atherosclerosis through gut microbiota-dependent formation of trimethylamine (TMA) and subsequent hepatic conversion into proatherogenic TMA-N-oxide (TMAO) (Koeth et al., 2013). In addition, Lu et al. (2017) found that carnitine supplementation to normal mice for 3 mo induces oxidative stress, liver inflammation, liver lipid accumulation and even liver damage as well as hypercholesterinemia. However, it has to be mentioned that the carnitine dose administered to the mice in the abovementioned studies was extremely high. In order to address whether safety concerns are founded under conditions of longterm supplementation of a carnitine dose used in clinical trials, the present study aimed to investigate the effect of almost lifelong daily administration of a carnitine-supplemented diet (1 g/kg diet) to mice from weaning to 18 mo of age. Considering a body weight of 50 g for an adult mice and a daily feed intake of 5 g, the daily intake of this diet results in a daily carnitine dose of 100 mg/kg body weight which better reflects the dose used in clinical trials. In order to evaluate possible detrimental effects of carnitine supplementation, we investigated parameters of lipid metabolism and stress signaling pathways in the liver and performed a genome-wide transcriptome analysis of skeletal muscle in the mice at advanced age.

overall_design: For microarray analysis of skeletal muscle, n = 5 skeletal muscle total RNA samples were randomly selected each from the control group and the carnitine group. RNA samples were processed at the “Kompetenzzentrum Fluoreszente Bioanalytik” (Regensburg) using Affymetrix GeneChip Mouse Gene 2.0 Sense Target arrays as described.

first: Uzman

middle: B

last: Cheema

first: Erika

last: Most

first: Klaus

last: Eder


title: Spo11-oligo mapping in wild type S. cerevisiae strain

status: Public on Sep 09 2018

first: Hajime

last: Murakami

overall_design: Four samples total: two biological replicate Spo11-oligo maps generated at 4 and 6 h in meiosis

first: Megan

last: van Overbeek

first: Scott

last: Keeney


title: Hydroxyurea protects hippocampal neurons against oxidative, metabolic and excitotoxic stress, and improves spatial memory in a mouse model of Alzheimer’s disease (Rat)

status: Public on Sep 10 2018

first: Supriyo

last: De

summary: Alzheimer’s disease (AD) is an age-related neurodegenerative disorder characterized by accumulation of amyloid β-peptide (Aβ) plaques in the brain and decreased cognitive function leading to dementia. We determined if hydroxyurea (HU), a ribonucleotide reductase inhibitor known to activate adaptive cellular stress responses in fibroblasts, could protect rat hippocampal neurons against oxidative-, excitatory-, mitochondrial-, and Aβ-induced stress and if HU treatment could improve learning and memory in a mouse model of AD (APP/PS1 double mutant transgenic mice). HU treatment attenuated the loss of cell viability induced by treatment of hippocampal neurons with hydrogen peroxide, glutamate, rotenone, and Aβ1-42. HU treatment also attenuated reductions of mitochondrial reserve capacity, maximal respiration, and cellular ATP content induced by hydrogen peroxide treatment. In vivo, treatment of APP/PS1 AD mice with HU (45 mg/kg/day) improved spatial memory performance in the hippocampus-dependent Morris water maze task. In summary, HU provides neuroprotection against toxic insults, improves mitochondrial bioenergetics, and improves spatial memory in a mouse model of AD. HU may offer a new therapeutic approach to delay cognitive decline in AD.

overall_design: Embryonic Day 18 rat hippocampal neurons were cultured for 6-9 days before treatment with hydroxyurea (HU, 5 µM) for 2, 6, 12, or 24 hours or left untreated (UT), with three replicates (#1,2,3) for each condition for a total of 15 samples.

first: Rebecca

last: Brose

first: Yongqing

last: Zhang

first: Kirby

last: Smith

first: Mark

middle: P

last: Mattson


title: Hydroxyurea protects hippocampal neurons against oxidative, metabolic and excitotoxic stress, and improves spatial memory in a mouse model of Alzheimer’s disease (Mouse)

overall_design: RNA extracted from hippocampi from four APP/PS1 mice nontransgenic control littermates treated with HU (45 mg/kg/day) for 2.5 months were compared to that of four untreated control animals.

first: Elin

last: Lehrmann


title: Next Generation Sequencing Facilitates Quantitative Analysis of mesoderm posterior bHLH transcription factor 1(MESP1)+ and MESP1- cells' Transcriptomes

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary:
Purpose: To compare the transcriptome of MESP1-mTomato reporter cells at undifferentiated state, cardiac differentiation day 3 and day 5.

Methods: total RNA from sorted MESP1+, MESP1- and HESCs (in biological duplicates) was extracted using RNeasy Plus Mini Kit (Qiagen) and treated with RNase free DNase. RNA library was prepared following the instruction of TruSeq™ RNA Sample Preparation kit (Illumina) and sequenced on Illumina HiSeq 2000.

Results: genes differentially expressed in MESP1-mTomato+ and mTomato- cells were identified.

Conclusions: the gene expression profile of MESP1-mTomato cells indicates that they are cardiovascular progenitor cells.

overall_design: Through RNA-seq of MESP1+, MESP1- and undifferentiated cells, perform bioinformatics analysis to identify differentially expressed genes,  then perform functional study.


title: Hydroxyurea attenuates oxidative, metabolic, and excitotoxic stress in rat hippocampal neurons and improves spatial memory in a mouse model of Alzheimer’s disease

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Topoisomerase 3β Interacts with RNAi Machinery to Promote Heterochromatin Formation and Transcriptional Silencing in Drosophila [ChIP-Seq]

overall_design: We determined the profiles of HP1, Top3b, and FLAG-AGO2 binding on chromatin, and methylation of H3K9 level in RNA/DNA topoisomerase mutant (Top3b) as compared to w1118 control using the Drosophila model. The chromatin complex was isolated from fly heads, then immunoprecipitated by the above antibodies.

first: Seung

last: Lee

first: Yutong

last: Xue

first: Weiping

last: Shen

first: Yuyoung

last: Joo

first: Muzammil

last: Ahmad

first: Madoka

last: Chinen

first: Yi

last: Ding

first: Wai

middle: L

last: Ku

first: Kevin

last: Becker

first: Elissa

last: Lei

first: Keji

last: Zhao

first: Sige


title: Topoisomerase 3B Interacts with RNAi Machinery to Promote Heterochromatin Formation and Transcriptional Silencing

status: Public on Aug 29 2018

first: Supriyo

last: De

summary:
Topoisomerases solve topological problems during DNA metabolism, but whether they participate in RNA metabolism remains unclear. Top3b represents a new family of topoisomerases carrying activities for both DNA and RNA. Here we show that in Drosophila, Top3b interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) containing AGO2, p68 RNA helicase, and FMRP. Top3b and RISC mutants are defective in heterochromatin formation and transcriptional silencing by position-effect variegation assay; and this defect is suppressed in their double mutants. Moreover, both Top3b and AGO2 single mutants exhibit reduced heterochromatin protein HP1 in pericentric heterochromatin; and this reduction is also suppressed in their double mutant. Furthermore, expression of several genes and transposable elements (TEs) in heterochromatin is increased in the Top3b mutant. Notably, Top3b mutants defective in either RNA binding or catalytic activity are deficient in promoting HP1 recruitment and silencing of TEs. Our data suggest that Top3b acts as an RNA topoisomerase in siRNA-guided heterochromatin formation and transcriptional silencing.

Grant title: An RNA topoisomerase complex interacts with Fragile X syndrome protein to promote neurodevelopment and maintain normal life-span. Grant ID: AG000689-08. Source: NIA/NIH

overall_design: Gene expression differences between Topoisomerase 3beta (TOP3B) wildtype (W1118) and mutant (TOP3B26) Drosophila melanogaster (D.m.) flies were assessed using three independent preparations of drosophila fly heads per condition.

first: Yongqing

last: Zou

first: Alexei

last: Sharov

first: Weidong

last: Wang


title: UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells

status: Public on Aug 23 2018

city: Shenzhen

first: Zengqi

last: Wen

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-sen University


title: UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells [ChIP-seq]

summary: In this study, we demonstrate that the UBN1 or UBN2 subunit is mainly responsible for specific recognition and direct binding of H3.3 by the HIRA complex, while the HIRA subunit can enhance the binding affinity of UBN1 toward H3.3, but Cabin1 subunit cannot. We also demonstrate that both Ala87 and Gly90 residues of H3.3 are required and sufficient for the specific recognition and binding by UBN1. ChIP-seq studies reveal that two independent HIRA complexes (UBN1-HIRA and UBN2-HIRA) can cooperatively deposit H3.3 to cis-regulatory regions, including active promoters and active enhancers in mouse embryonic stem (mES) cells. Importantly, disruption of histone chaperone activities of UBN1 and UBN2 by FID/AAA mutation results in the defect of H3.3 deposition at promoters of developmental genes involved in neural differentiation, and subsequently causes the failure of activation of these genes during neural differentiation of mES cells. Together, our results provide novel insights into the mechanism by which the HIRA complex specifically recognizes and deposits H3.3 at promoters and enhancers of developmental genes, which plays a critical role in neural differentiation of mES cells

overall_design: We first demonstrate the interaction between H3.3 and UBN1/2, then analysis how HIRA complex regulate H3.3 deposition genome-wide and the function of HIRA complex mediated H3.3 deposition to chromatin.


title: UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells [RNA-seq]

overall_design: We first demonstrate the interaction between H3.3 and UBN1/2, then analysis how HIRA complex regulate H3.3 deposition genome-wide.


title: Whole-genome mapping of RUNX1, FUBP1, H3K4me1, H3K4me3, H3K27me3 and H3K27ac in human pre-B lymphoblasts, and B cell precursor leukemia (BCP-ALL)

status: Public on Aug 21 2018

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

institute: University Rennes 1

summary: Genome binding/occupancy profiling of human Runt-related transcription factor 1 (RUNX1), Far Upstream Binding Protein 1 (FUBP1) and histone marks by high throughput sequencing. RUNX1 and FUBP1 are two key transcriptional regulators implicated in hematopoiesis, from the maintenance of HSC to lineage-specific differentiation. We hypothesized that both proteins could play a joint role in transcription regulation of hematologic lineages. Here, we investigated the molecular proximity between RUNX1 and FUBP1 proteins on chromatin and their common target genes in pre-B lymphoblasts and B cell precursor leukemia (BCP-ALL). Altogether, our data show that RUNX1 and a subset of FUBP1 colocalize on chromatin in transcriptionally active/accessible chromatin regions mainly in promoters and enhancers regions.

overall_design: RUNX1, FUBP1, H3K4me1, H3K4me3, H3K27me3 and H3K27ac genome-wide distributions were determined using ChIP-seq. Cells used in this study are human pre-B lymphoblast Nalm6 cell line and blasts from B-cell precursor acute lymphoblastic leukemia (BCP-ALL). ChIP samples and libraries were done by Sérandour A.A and Debaize L.

first: Marie-Bérengère

last: Troadec

first: Lydie

last: Debaize


title: Hepatic transcript profiling in early lactating dairy cows fed rumen-protected niacin during the transition from late pregnancy to lactation

status: Public on Jun 21 2018

first: Robert

last: Ringseis

summary: In dairy cows, administration of high dosages of niacin (NA) was found to cause anti-lipolytic effects, which are mediated by the NA receptor hydroxyl-carboxylic acid receptor 2 (HCAR2) in white adipose tissue (WAT), and thereby to an altered hepatic lipid metabolism. However, almost no attention has been paid to possible direct effects of NA in cattle liver, despite showing that HCAR2 is expressed also in the liver of cattle and is even more abundant than in WAT. Due to this, we hypothesized that feeding of rumen-protected NA to dairy cows influences critical metabolic and/or signaling pathways in the liver through inducing changes in the hepatic transcriptome. In order to identify these pathways, we applied genome-wide transcript profiling in liver biopsies obtained at 1 wk postpartum (p.p.) from dairy cows of a recent study (Zeitz et al., 2018) which were fed a total mixed ration without (control group) or with rumen-protected NA from 21 d before calving until 3 wk p.p. Hepatic transcript profiling revealed that a total of 487 transcripts were differentially expressed [filter criteria fold change (FC) > 1.2 or FC < -1.2 and P < 0.05] in the liver at 1 wk p.p. between cows fed NA and control cows. Substantially more transcripts were down-regulated (n = 338), while only 149 transcripts were up-regulated by NA in the liver of cows. Gene set enrichment analysis (GSEA) for the up-regulated transcripts revealed that the most enriched gene ontology (GO) biological process terms were exclusively related to immune processes, such as leukocyte differentiation, immune system process, leukocyte differentiation, activation of immune response and acute inflammatory response. In line with this, the plasma concentration of the acute phase protein haptoglobin tended to be increased in dairy cows fed rumen-protected NA compared to control cows (P < 0.1). GSEA of the down-regulated transcripts showed that the most enriched biological process terms were related to metabolic processes, such as cellular metabolic process, small molecule metabolic process, lipid catabolic process, organic cyclic compound metabolic process, small molecule biosynthetic process and cellular lipid catabolic process. In conclusion, hepatic transcriptome analysis shows that rumen-protected NA induces genes which are involved mainly in immune processes including acute phase response and stress response in dairy cows at wk 1 p.p. These findings indicate that supplementation of rumen-protected NA to dairy cows in the periparturient period may induce or amplify the systemic inflammation-like condition which is typically observed in the liver of high-yielding dairy cows in the p.p. period.

overall_design: For microarray analysis, n = 9 RNA samples each of the control group and the NA group were used for hybridization to the Affymetrix GeneChip Bovine Gene 1.0 ST array.

first: Johanna

middle: O

last: Zeitz

first: Alexandra

last: Weber

first: Christian

last: Koch

first: Klaus

last: Eder


title: Overexpression of CYB5R3 and NQO1, two NAD+ producing enzymes, mimics aspects of caloric restriction

status: Public on Jul 31 2018

summary: Calorie restriction (CR) is one of the most robust means to improve health and survival in model organisms. CR imposes a metabolic program that leads to increased stress resistance and delayed onset of chronic diseases, including cancer. In rodents, CR induces the upregulation of two NADH-dehydrogenases, namely NAD(P)H:quinone oxidoreductase 1 (Nqo1) and cytochrome b5 reductase 3 (Cyb5r3), which provide electrons for energy metabolism. It has been proposed that this upregulation may be responsible for some of the beneficial effects of CR, and defects in their activity are linked to aging and several age-associated diseases. However, it is unclear whether changes in metabolic homeostasis solely through up-regulation of these NADH-dehydrogenases have a positive impact on health and survival. We generated a mouse that overexpresses both metabolic enzymes leading to phenotypes that resemble aspects of CR including a modest increase in lifespan, greater physical performance, a decrease in chronic inflammation, and importantly, protection against carcinogenesis, one of the main hallmarks of CR. Furthermore, these animals showed an enhancement of metabolic flexibility and a significant upregulation of the NAD+/sirtuin pathway. The results highlight the importance of these NAD+ producers for the promotion of health and extended lifespan.

overall_design: A transgenic mouse overexpressing rat Nqo1 and rat Cyb5r3 reductases (RedTg), was created, and the liver transcriptomes of WT and RedTg mice (N=4 per condition) assayed.

first: A

last: Diaz-Ruiz

first: M

last: Lanasa

first: J

last: Garcia

first: H

last: Mora

first: F

last: Fan

last: Martin-Montalvo

last: Di Francesco

last: Calvo-Rubio

last: Salvador-Pascual

last: Aon

first: K

last: Fishbein

last: Pearson

last: Villalba

first: P

last: Navas

last: Bernier

first: R

last: de Cabo


title: Eda-activated RelB recruits an SWI/SNF (BAF) chromatin-remodeling complex and initiates gene transcription in skin appendage formation

status: Public on Jul 24 2018

first: Supriyo

last: De

summary: Skin-specific Eda signaling promotes skin appendage development through NF-kB mediated gene transcription. We find that Eda triggers the formation of a novel SWI/SNF complex in which RelB is recruited through a linker protein, Tfg, to interact with the BAF45d component in SWI/SNF (BAF) chromatin remodeling complex. BAF component BAF250a is particularly enriched in skin appendages, and epidermal knockout (cKO) of BAF250a impairs skin appendage development, resulting in phenotypes similar to those of Eda-deficient mouse models. We further reveal that Eda signaling is predominantly mediated by the p50/RelB subclass of NF-kB in both human keratinocytes and mouse skin. Consistent with the phenotype of BAF250a cKO mice, downregulation of RelB, Tfg, or BAF45d arrests the growth of Meibomian gland germs in organ cultures. Transcription profiling consistently identifies several target genes regulated by Eda, RelB and SWI/SNF. In particular, we show that both RelB and SWI/SNF are indispensable for transcription of Eda target Ltb. Chromatin remodeling SWI/SNF recruited to specific gene loci by Eda-activated RelB thus provides a mediation model between an initiation signal and gene activation in organogenesis.

overall_design: A human keratinocyte line that stably expresses Edar protein (Edar-HaCat) was created and cultured along with the original HaCaT cell line. HaCaT cells were transfected with scrambled siRNA (Empty), while Edar-HaCat cells were transfected with scrambled siRNA (EDAR), or SMARTpooled siRNAs against hRelB (RelBi) or hBRG1 (BRG1) for 48 h prior to extraction of RNA (N = 3 biological repeats per group).

first: Jian

last: Sima

first: Zhijiang

last: Yan

first: Yaohui

last: Chen

first: Elin

last: Lehrmann

first: Yongqing

last: Zhang

first: Ramaiah

last: Nagaraja

first: Weidong

last: Wang

first: Zhong

first: David

last: Schlessinger


title: Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources

status: Public on Jun 26 2018

city: Leuven

first: Abbas

last: Jariani

address: Gaston Geenslaan 1, box 2471

department: KU Leuven - VIB Centre for Microbiology

country: Belgium

institute: KU Leuven - VIB

summary: Transcriptome of S. cerevisiae in shifts between glucose and maltose media with different re-growth conditions

overall_design: Cells are pregrown in maltose, then grown for different durations in glucose and then washed back to maltose

first: Bram

last: Cerulus