title: Gene expression profiling of long non-coding RNAs between rainbow trout strains on plant-based diets

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Rainbow trout (Oncorhynchus mykiss) and other salmonids are piscivorous fish. In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. Total replacement of fishmeal with plant proteins causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we have developed a strain of rainbow trout that does not develop distal intestine enteritis when reared on a high soy plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a major role in dietary alterations, liver RNA was examined for differential expression of long non-coding RNAs (lncRNAs) between commercial and selected trout strains when fed an alternative diet. These types of non-coding RNA have been previously shown to have a potential role in regulation of gene expression; however, most identified lncRNAs have not been functionally characterized and/or lack definition in many non-model organisms. Their roles in gene regulation and their responsiveness to dietary changes in trout are to be explored. After three months of rearing on a plant protein-based (PM) diet, liver tissues from a domestic non-selected strain (House Creek; develops enteritis) and  the plant-diet tolerant selected strain (ARS-KO; no enteritis) were extracted and prepped for Illumina RNA-seq. Raw reads were screened for quality then assembled into transcripts using Trinity. Assembled transcripts were then submitted to the Annocript pipeline to determine their potential as lncRNAs. RNA-seq reads were mapped to putative lncRNAs. Read-counts were used to assess differential expression between strains.

overall_design: Rainbow trout strain selected for tolerance to plant-based diets (ARS-KO) and control fish strain (House Creek) were fed a plant meal (PM) based diet in replicate tanks over a 12-week period. After this time liver tissues were sampled. A total of 20 samples were taken: ten biological replicates, sampling liver tissue, with one treatment group, for each of the two trout strains.

first: Ken

last: Overturf


title: Early life diet conditions the molecular response to post-weaning protein restriction in the mouse

status: Public on Apr 09 2018

city: London

first: Amy

middle: Frances

last: Danson

state: Greater London

address: 2 Newark St

department: Centre for Genomics and Child Health

country: United Kingdom

institute: The Blizard Institute

type: Non-coding RNA profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: small RNA-seq analysis of mouse sperm exposed to protein restriction during different critical time windows

summary: Background: Environmental influences fluctuate throughout the life course of an organism. It is therefore important to understand how the timing of exposure impacts the molecular response. Here we examine the responses of two key molecular markers of dietary stress – variant-specific methylation at ribosomal DNA (rDNA) and small RNA distribution including tRNA fragments – in a mouse model of protein restriction (PR) with exposures pre- and/or post-weaning. Results: We first confirm that pre-weaning PR exposure modulates the methylation state of rDNA in a genotype-dependent manner whereas post-weaning PR exposure has no such effect. Conversely, post-weaning PR induces a shift in small RNA distribution, but there is no effect in the pre-weaning PR model. Intriguingly, mice exposed to PR throughout their lives show neither of these two dietary stress markers, similar to controls.

overall_design: sperm small RNA from four different diet groups (CTCT, CTPR, PRCT and PRPR) with one individual from each litter in each diet group being represented

middle: F

first: Vardhman

middle: K

last: Rakyan

first: Robert

last: Lowe


title: BisPCRSeq analysis of ribosomal DNA in mouse sperm exposed to protein restriction during different critical time windows

summary:
Background: Environmental influences fluctuate throughout the life course of an organism. It is therefore important to understand how the timing of exposure impacts the molecular response. Here we examine the responses of two key molecular markers of dietary stress – variant-specific methylation at ribosomal DNA (rDNA) and small RNA distribution including tRNA fragments – in a mouse model of protein restriction (PR) with exposures pre- and/or post-weaning.
Results: We first confirm that pre-weaning PR exposure modulates the methylation state of rDNA in a genotype-dependent manner whereas post-weaning PR exposure has no such effect. Conversely, post-weaning PR induces a shift in small RNA distribution, but there is no effect in the pre-weaning PR model. Intriguingly, mice exposed to PR throughout their lives show neither of these two dietary stress markers, similar to controls.

overall_design: sperm DNA from four different diet groups (CTCT, CTPR, PRCT and PRPR) with all males from each litter being represented


title: A blood RNA signature for tuberculosis disease risk in household contact study - GC6 cohort.

status: Public on Apr 10 2018

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

country: USA

institute: Regeneron

type: Expression profiling by high throughput sequencing

summary: Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis  infection to tuberculosis disease might lead to interventions that combat the tuberculosis epidemic in the context of house hold contacts.

overall_design: Samples are collected from subjects in a household contact study after a person comes back to the household, diagnosed with TB. Samples are collected every 6 months upto, 18 months. Some people go on to develop TB (cases)  where as some others do not (controls). Here we are trying to establish a gene signature to predict the occurance of TB.

first: Ethan

last: Thompson

first: Sara

last: Suliman

middle: E

first: Smitha

last: Shankar

first: Thomas

middle: J

last: Scriba


title: The DNA methylation landscape of enhancers in the guinea pig hippocampus

status: Public on Apr 11 2018

city: Montreal

first: Lisa

last: Boureau

state: QC

address: Sir William Osler Promenade

department: Pharmacology

country: Canada

institute: McGill University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Aim: To determine the state of methylation of DNA molecules that are physically engages with either poised or active enhancers.

Methods: We used  ChIP-bisulfite-sequencing with H3K4me1 antibody to map the methylation of DNA bound to enhancer. We used ChIP-sequencing with RNApolII-PS5 antibody to map actively transcribing transcription start sites. We used reduced representation bisulfite sequencing (RRBS) to map total DNA methylation.

Results - conclusion: DNA molecules that are physically found in H3K4me1 chromatin are hypomethylated while DNA found in enhancers that are associated with active transcription is further demethylated.

overall_design: ChIP bisulfite sequencing (H3K4me1 antibody), ChIP sequencing (RNApolII-PS5 antibody) and and RRBS were performed on hippocampus of 3 different wild type 12-week old guinea pig animals.

first: Andrea

last: Constantinof

first: Vasilis

middle: G

last: Moisiadis

first: Stephen

last: Matthews

first: Moshe

last: Szyf


title: Genome wide map of High-salt Recovered Sequences (HRS) in mouse embryonic stem cells (ESC)

city: Montpellier

first: Thierry

last: Forné

address: 1919, Route de Mende

country: France

institute: CNRS

summary: We have developed the HRS-seq method (High-salt Recovered Sequences-sequencing), a straightforward genome-wide approach whereby we isolated and sequenced genomic regions associated with large high-salt insoluble RNP complexes. Using mouse embryonic stem cells (ESC), we showed that HRS are over-represented into the active A chromosomal compartment. The vast majority of HRS-associated genes are very highly expressed. They include both cell type-specific genes, like pluripotency genes, and housekeeping genes, like histone and snRNA genes that are central components of Histone Locus Bodies and Cajal bodies. We conclude that large, high-salt insoluble, RNP complexes including nuclear bodies are associated to the active A chromosomal compartment.

overall_design: We perform a triplicate HRS-seq experiment in mouse E14Tg2a ESC

first: Marie-Odile

last: Baudement


title: HC2091 kills Mycobacterium tuberculosis by targeting the MmpL3 mycolic acid transporter

city: East Lansing

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

summary: The purpose of this study was to characterize the mechanism of action of the small molecule HC2091

overall_design: Mtb strain CDC1551 was grown at 37ºC in T-25 vented, standing tissue culture flasks in 8 mL of buffered 7H9 medium to an OD600 of 0.1. Cultures were subsequently treated with 10 µM HC2091 ro SQ109. For the control, cultures treated with an equal amount of DMSO. Following a 24 h incubation period, total bacterial RNA was extracted, quality controlled and sequenced. Each treatment was repeated with two independent (biological) replicates.

first: Huiqing

last: Zheng

first: John

middle: T

last: Williams

first: Garry

middle: B

last: Coulson

first: Elizabeth

middle: R

last: Haiderer


title: FAIRE-seq in PBMCs

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: Three independent repeats of FAIRE-seq from PBMCs obtained before and 1 and 2 days after an oral dose of 2,000 µg (80,000 IU) of vitamin D3

overall_design: A participant of the VitDbol study (NCT02063334, ClinicalTrials.gov) ingested a vitamin D bolus of 2,000 µg (80,000 IU) of vitamin D3. Blood was taken before and 1 and 2 days afterwards and PBMCs were isolated.

first: Sabine

last: Seuter

first: Antonio

last: Neme


title: Endothelial Transcriptome Remodeling in a Mouse Model of Chronic Hypertension

city: Portland

first: Jessica

last: Minnier

state: OR

address: 3181 SW Sam Jackson Park Rd, UHN62

institute: Oregon Health & Science University

summary: Aims: Hypertension poses a significant challenge to vasculature homeostasis and stands as the most common cardiovascular disease in the world.  Its effects are especially profound on vasculature-lining endothelial cells that are directly exposed to the effects of excess pressure. Here, we characterize the in vivo transcriptomic response of cardiac endothelial cells to hypertension using the spontaneous hypertension mouse model BPH/2J.    Methods and results: Verification of defective endothelial function in the BPH/2J hypertensive mouse strain was followed by acute isolation of cardiac endothelial cells and transcriptional profiling using RNA sequencing. Gene profiles from normotensive BPN/3J mice were compared to hypertensive animals. We observed over 3000 transcriptional differences between groups including pathways consistent with the cardiac fibrosis found in hypertensive animals. Importantly, many of the fibrosis-linked genes also differ between juvenile pre-hypertensive and adult hypertensive BPH/2J mice, suggesting that these transcriptional differences are hypertension-related. We also show that blood pressure normalization with amlodipine resulted in a subset of genes reversing their expression pattern, supporting the hypertension-dependency of altered gene expression. Yet, other transcripts were recalcitrant to therapeutic intervention illuminating the possibility that hypertension may irreversibly alter some endothelial transcriptional patterns.   Conclusions: Hypertension has a profound effect on both function and transcription of endothelial cells, the latter of which was only partially restored with normalization of blood pressure. This study represents one of the first to quantify how endothelial cells are reprogrammed at the molecular level in cardiovascular pathology and advances our understanding of the transcriptional events associated with endothelial dysfunction.

overall_design: Endothelium from hypertensive mice were acutely extracted at two different ages (4 weeks and 22 weeks) and compared to endothelium from 22 week old normotensive mice.

first: Jonathan

last: Nelson

first: Mohammed

last: Ferdaus

first: James

last: McCormick

first: Sanjiv

last: Kaul

first: David

last: Ellison

first: Anthony

last: Barnes


title: Changes in chromatin accessibility in mouse liver following TCPOBOP exposure

city: Boston

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: This work is part of a larger study where we investigated activation of the nuclear receptor and transcription factor CAR (Nr1i3) by its specific agonist ligand TCPOBOP (1,4-bis[2-(3,5-dichloropyridyloxy)]benzene), which dysregulates hundreds of genes in mouse liver and is linked to male-biased hepatocarcinogenesis. We used DNase-seq and DNase hypersensitivity site (DHS) analysis to identify several thousand genomic regions (∆DHS) where short-term exposure to TCPOBOP induces localized changes (increases or decreases) in mouse liver chromatin accessibility, many of which cluster together with TCPOBOP-responsive genes. Sites of chromatin opening were highly enriched nearby genes induced by TCPOBOP and chromatin closing was highly enriched nearby genes repressed by TCPOBOP, consistent with TCPOBOP-responsive ∆DHS serving as enhancers and promoters that positively regulate CAR-responsive genes. Gene expression changes lagged behind chromatin opening or closing for a subset of TCPOBOP-responsive ∆DHS. DHS that were specifically responsive to TCPOBOP in male liver were significantly enriched for genomic regions with a basal male bias in chromatin accessibility; however, the male-biased response of hepatocellular carcinoma-related genes to TCPOBOP was not associated with a correspondingly male-biased ∆DHS response. These studies elucidate the genome-wide organization of CAR-responsive genes and of the thousands of associated genomic sites where TCPOBOP exposure induces both rapid and persistent changes in chromatin accessibility.

overall_design: Nuclei were isolated from male and female CD1 mouse liver following exposure to TCPOBOP for either 3 h or 27 h, followed by limited DNase-I digestion. Two biological replicate pools, comprised of  DNase fragments released from n=3-5 individual mouse liver nuclei, were sequenced per control orTCPOBOP treatment group.

first: Nicholas

last: Lodato

first: Andy

last: Rampersaud


title: Tumor evolution and drug response in patient-derived organoid models of bladder cancer

city: New York

first: Suk Hyung

last: Lee

state: NY

address: 1130 St. Nicholas Ave, ICRC rm 208A

department: Medicine

institute: Columbia University

summary: Bladder cancer is the fifth most prevalent cancer in the U.S., yet is understudied and relatively lacking in suitable models. Here we describe a biobank of patient-derived organoid lines that recapitulates the spectrum of human bladder cancer at the histopathological and molecular levels. Organoid lines can be established efficiently from patient biopsies, including from patients before and after disease recurrence, and are interconvertible with orthotopic xenografts. Notably, these organoid lines often retain tumor heterogeneity and exhibit changes in their mutational profiles that are consistent with tumor evolution in culture. Analyses of drug response using bladder tumor organoids show partial correlations with mutational profiles as well as changes associated with treatment resistance, and specific responses can be validated using xenografts in vivo. Overall, our studies indicate that patient-derived bladder tumor organoids represent a model system for studying tumor evolution and treatment response in the context of precision cancer medicine.

overall_design: We generated organoids from bladder tumor tissue. The organoids were trypsinized, plated in matrigel and overlaid with medium. The medium was changed every 3 days. After 14 days of plating, Organoids were harvested and processed for RNA isolation and transcriptome analysis using Ambion MagMAX RNA isolation kit.

first: Suk

middle: H

first: Michael

last: Shen


title: Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G3E) on the berry transcriptome [RNA-seq]

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

summary: Changes in the performance of genotypes in different environments are defined as genotype 3 environment (G3E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect the basis of grapevine G3E interactions we characterized berry transcriptome plasticity, the genome methylation landscape and within-genotype allelic diversity in two genotypes cultivated in three different environments over two vintages. We identified, through a novel data-mining pipeline, genes with expression profiles that were: unaffected by genotype or environment, genotype-dependent but unaffected by the environment, environmentally-dependent regardless of genotype, and G3E-related. The G3E-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabolism categories. Our study unraveled the mutual relationships between genotypic and environmental variables during G3E interaction in a woody perennial species, providing a reference model to explore how cultivated fruit crops respond to diverse environments. Also, the pivotal role of vineyard location in determining the performance of different varieties, by enhancing berry quality traits, was unraveled.

overall_design: Vitis vinifera berries from Sangiovese and Cabernet Sauvignon cultivars were harvested at four different developmental stages (i.e., pea size (PS), pre-veraison (PV), mid-ripening (MR) and fully ripe (FR)), in three central Italian locations (i.e., Bolgheri in the Tuscany coast, Montalcino in the Tuscany Appennines and Riccione in the Adriatic coast) (Fig. 1, Supplementary Tables 1-3) during two consecutive growing seasons (2011 and 2012) in biological triplicates for a total of 144 samples. RNAseq analyses were performed on PV and MR samples, thus the high troughput sequencing derived sataset entailed 72 samples.

first: Sara

last: Zenoni

first: Marco

last: Sandri

first: Gabriella

last: De Lorenzis

first: Gabriele

last: Magris

first: Emanuele

last: DePaoli

last: Di Gaspero

first: Cristian

last: Del Fabbro

first: Michele

last: Morgante

first: Lucio

last: Brancadoro

first: Mara

last: Rossoni

first: Marianna

last: Fasoli

first: Paola

last: Zuccolotto

first: Mario

last: Pezzotti


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

city: Beijing

first: Xiaowei

last: Chen

address: 15 Datun Road, Chaoyang District

country: China

institute: Institute of Biophysics, CAS

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

overall_design: RNA-seq in Jurkat with MAPS strategy (Control shRNA VS SLEAR shRNA)

first: Zhen

last: Fan


title: Hepatic gene expression analysis between low and high growing hybrid striped bass

first: Jason

last: Abernathy

summary: Aquaculture is one of the fastest growing sectors of US food production, with hybrid striped bass (HSB) considered a major species. A significant issue in HSB aquaculture stems from the large amount of variation in growth observed when growing-out these hybrids to market size adults. The goal of this study was therefore to determine if significant differences in metabolic gene expression might play a role in observed growth differences in HSB. The objective of this study was to use RNAseq on liver tissue of superior and inferior performing HSB representatives to identify global expression differences in HSB adults.

overall_design: Domesticated F8 white bass and F4 striped bass were bred in a partial diallel breeding design to create hybrid striped bass (HSB) and reared in replicate family tanks until large enough to tag with a PIT tag. Thirty-two fish from each of 44 half-sib families were tagged and initial length and weight was recorded before being randomly assigned to one of four 0.04 hectare communal ponds resulting in 5632 individually tagged fingerlings. Fish were allowed to grow for 115 days prior to harvest. At harvest tags were scanned to reveal family of origin, final length and weight were taken. The largest and smallest HSB were sacrificed and liver samples taken. Equimolar amounts of total RNA were pooled from the extreme fish for RNA sequencing.

first: S

middle: A

last: Fuller


title: NANOG is required for the long-term establishment of avian somatic reprogrammed cells

status: Public on Apr 08 2018

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

institute: U1208, INSERM

sample_organism:
Anas platyrhynchos
Gallus gallus

platform_organism:
Anas platyrhynchos
Gallus gallus


title: DNA-binding pluripotency factors and DNA demethylases can cooperate to maintain pluripotent stem cell identity even in the absence of Brd4 [ATAC-seq]

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: The relative contributions of sequence-specific transcription factors and DNA/histone modifications to stem cell maintenance remains controversial. For example, the acetyllysine reader Brd4 has been implicated in stem cell maintenance, but how absolute the role of Brd4 is in maintaining pluripotency remains unclear. Here we show that Brd4 is dispensable for the proliferation, self-renewal and pluripotency of embryonic stem cells. In naive, ground state pluripotent stem cells, Mediator recruitment and transcription factor binding to stem cell-specific genes are maintained in the absence of Brd4 function or expression. Even in metastable embryonic stem cells poised for differentiation, Brd4 independence can be maintained by overexpression of pluripotency transcription factors so long as the DNA methylcytosine oxidases, Tet1 and Tet2, are present to facilitate chromatin accessibility. These data reveal that Brd4 is not essential for self-renewal of embryonic stem cells. Rather, Brd4 contributes to stem cell maintenance only under conditions where the expression of pluripotency transcription factors and/or DNA demethylation machinery is compromised.

overall_design: ATAC-seq of mouse ESCs under control and treatment conditions.

first: Lydia

middle: W

last: Finley

first: Santosha

last: Vardhana

middle: P

first: C

middle: D

last: Allis

first: Craig

last: Thompson


title: Transcription factors and Tet1/2 enable Brd4-independent maintenance of stem cell identity

summary: Histone acetylation and the acetyl-lysine reader Brd4 have recently been implicated in embryonic stem cell (ESC) proliferation and self-renewal. We found that na•ve pluripotent ESCs exhibit increased incorporation of glucose-derived carbons onto acetylated histones and elevations in H3K9ac and Brd4 recruitment at pluripotency gene promoters. Surprisingly, both H3K9 acetyltransferases, GCN5 and PCAF, and Brd4 recruitment were dispensable for proliferation, self-renewal and pluripotency of na•ve ESCs. Na•ve ESCs maintain gene expression by stabilizing Mediator at core pluripotency genes in a Brd4-independent manner. Brd4-independent proliferation could also be achieved in metastable ESCs by overexpression of pluripotency transcription factors. Under all conditions, self-renewal required the DNA methylcytosine oxidases Tet1 and Tet2. These data reveal that there is minimal dependence on Brd4 for self-renewal of na•ve ESCs. Instead, the relative levels of DNA methylation and transcription factor abundance determine the requirement for bromodomain recognition of histone acetylation to the maintenance of stem cell identity.

overall_design: ChIP-sequencing data of Brd4 and Med1 in mouse ESCs under control and treatment conditions.


title: NANOG is required for the long-term establishment of avian somatic reprogrammed cells [chicken]

summary:
Purpose: the goal of this study is to analyse various chicken stem cell lines and to compare them with both primary somatic fibroblasts and blastodermal cells derived from pre-gastrulating embryos
Methods: NGS RNA-sequencing was performed on chicken primary embryonic fibroblasts (CEF), embryonic stem cells (cESC), on blastodermal cells of EGK-X EGK-XII stages embryos (BCs), long term in vitro cultured primordial germ cells (PGCs) as specific chicken stem cells and reprogrammed cells (1A, 1D, 3E, 3F) derived from CEF by somatic reprogramming process. The librairies were prepared using the TruSeq R Stranded mRNA sample preparation kit (Illumina). The paired-end sequencing was performed on the NextSeq 500 sequencer (Illumina) and controlled by the Seqencing Analysis viewer software (Illumina). The quality control of the Sample-ID.fastq files was performed with the FasQC software (Babraham Institute).
Results: the total number of reads ranges from was of 80 millions to 145 millions.

overall_design: Chicken stem cells and somatic cells mRNA profiles were generated by Next-generation sequencing (NGS) using Illumina kits

first: Valérie

last: Sylvain-Vidal

first: Véronique

last: Vidal

first: Christian

last: Jean

last: Pain


title: Cse4 ChIP seq of Cryptococcus amylolentus to identify centromeres

city: Durham

first: Robert

middle: Blake

last: Billmyre

state: North Carolina

address: 312 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

summary: Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing about one million infections globally each year. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large MAT locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with two MAT loci (P/R and HD) located on different chromosomes. Thus, studying C. amylolentus will shed light on the origin and evolution of pathogenesis, as well as the transition from tetrapolar to bipolar mating systems in the pathogenic Cryptococcus species. In this study, we sequenced, assembled, and annotated the genomes of two C. amylolentus isolates, CBS6039 and CBS6273, which are sexual and interfertile. Genome comparison between the two C. amylolentus isolates identified the boundaries and the complete gene contents of the P/R and HD MAT loci. Also, bioinformatics and ChIP-seq analyses showed that C. amylolentus has regional centromeres that are enriched with species-specific transposable and repetitive elements, similar to the centromeric structures in the pathogenic Cryptococcus species. Additionally, we found that while neither of the P/R and HD loci in C. amylolentus is physically linked to its centromere, both MAT loci exhibit centromere linkage in meiosis, suggesting the presence of recombinational suppressors and/or epistatic gene interactions in the inter MAT-CEN regions. Furthermore, genomic comparison between C. amylolentus and pathogenic Cryptococcus species provides evidence that chromosomal rearrangements mediated by intercentromeric recombination have occurred after the two lineages split from their common ancestor. We propose a model in which the evolution of the bipolar mating system was initiated by an ectopic recombination event mediated by repetitive elements located within the centromeric regions and shared between chromosomes. This translocation brought the P/R and HD loci onto the same chromosome, and was followed by chromosomal rearrangements that resulted in the two MAT loci becoming physically linked and eventually fused to form the single contiguous MAT locus that is now extant in the pathogenic Cryptococcus species.

overall_design: Examination of centromere location using ChIP sequencing of CBS6039 Cryptococcus amylolentus

first: Sheng

last: Sun

first: Vikas

last: Yadav

first: Blake

first: Christina

last: Cuomo

first: Minou

last: Nowrousian

first: Joshua

last: Granek

first: Liuyang

last: Wang

first: Jean-Luc

last: Souciet

first: Teun

last: Boekhout

first: Betina

last: Porcel

first: Patrick

last: Wincker

first: Kaustuv

last: Sanyal

first: Joseph

last: Heitman


title: DNA-binding pluripotency factors and DNA demethylases can cooperate to maintain pluripotent stem cell identity even in the absence of Brd4

first: Richard

last: Koche

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

overall_design: Refer to individual Series


title: Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia [LPS]

status: Public on Apr 07 2018

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

summary: Peripherally derived macrophages infiltrate the brain after bone marrow transplantation and during central nervous system (CNS) inflammation. It was initially suggested that these engrafting cells were newly derived microglia and that irradiation was essential for engraftment to occur. However, it remains unclear whether brain-engrafting macrophages (beMφs) acquire a unique phenotype in the brain, whether long-term engraftment may occur without irradiation, and whether brain function is affected by the engrafted cells. In this study, we demonstrate that chronic, partial microglia depletion is sufficient for beMφs to populate the niche and that the presence of beMφs does not alter behavior. Furthermore, beMφs maintain a unique functional and transcriptional identity as compared with microglia. Overall, this study establishes beMφs as a unique CNS cell type and demonstrates that therapeutic engraftment of beMφs may be possible with irradiation-free conditioning regimens.

overall_design: Microglia were isolated from the brains of adult male c57BL/6 mice given bone marrow tranplants (BMT) with or without head shield. All mice received PLX5622 for 2 weeks, then placed and normal chow to recoever. Some mice were then challenged with LPS. Cells were isolated by MACS using CD11b magnetic beads.

first: James

middle: C

last: Cronk

first: Anthony

last: Filiano

first: Antoine

last: Louveau

first: Ioana

last: Marin

first: Rachel

last: March

first: Emily

last: Ji

first: Dylan

last: Goldman

first: Igor

last: Smirnov

first: Nicholas

last: Geraci

first: Scott

last: Acton

first: Jonathan

last: Kipnis


title: The genetic landscape of a physical interaction

status: Public on Apr 06 2018

city: Barcelona

first: Guillaume

last: Diss

address: C/ Dr. aiguader, 88

country: Spain

institute: CRG

summary: A key question in human genetics and evolutionary biology is how mutations in different genes combine to alter phenotypes. Efforts to systematically map genetic interactions have mostly made use of gene deletions.  However, most genetic variation consists of point mutations of diverse and difficult to predict effects.  Here we provide the first comprehensive view of how point mutations in two genes combine to alter a molecular phenotype. Using a new sequencing-based protein interaction assay – deepPCA – we quantified the effects of >100,000 pairs of point mutations on the formation of the AP-1 transcription factor complex between the products of the FOS and JUN proto-oncogenes.  We then compared how mutations interact in cis (within one protein) and in trans (between the two molecules). Genetic interactions are abundant and consist of two classes –interactions driven by thermodynamics and captured by a global model that explains ~90% of the double mutant data in both cis and trans, and structural interactions that are enriched between proximally located residues.  There are more structural interactions between mutations within one gene than between the two genes.  These results reveal how physical interactions generate abundant and quantitatively predictable genetic interactions, even in the absence of complex regulatory dynamics.

overall_design: Epistasis between mutations in two interacting proteins

first: Ben

last: Lehner


title: Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia

overall_design: Mice were given 1000rad whole body irradiation, followed by bone marrow transplant with UBC-GFP bone marrow at 8 weeks of age. Engraftment was allowed to occur for 8 months, then engrafting macrophages and microglia were isolated from whole brains for RNA-Seq.


title: Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia [GFP]

overall_design: Microglia were isolated from the brains of adult male Cx3cr1CreER/+::Csf1rFlox/Flox  c57BL/6 mice fed tamoxifen chow for 12 weeks then placed back on control chow for 4 weeks. Cells were isolated by MACS using CD11b magnetic beads then FAC sorted for GFP.


title: An Evolutionarily-Conserved Long Noncoding RNA Myolinc Regulates muscle differentiation [ChIP-seq]

city: Copenhagen SV

first: Shizuka

last: Uchida

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

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

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

summary: Myogenesis is a complex process required for skeletal muscle formation during embryonic development and for regeneration and growth of myofibers in adults. Accumulating evidence suggests that long non-coding RNAs (lncRNAs) play key roles in regulating cell fate decision and function in various tissues. However, the role of lncRNAs in the regulation of myogenesis remains poorly understood. In this study, we identified a novel muscle-enriched lncRNA called "Myolinc (AK142388)", which we functionally characterized in the C2C12 myoblast cell line. Myolinc is predominately localized in the nucleus, and its levels increase upon induction of the differentiation. Knockdown of Myolinc impairs the expression of myogenic regulatory factors and formation of multinucleated myotubes in cultured myoblasts. Myolinc also regulates the expression of Filip1 in a cis-manner. Similar to Myolinc, knockdown of Filip1 inhibits myogenic differentiation. Furthermore, Myolinc binds to TAR DNA-binding protein 43 (TDP-43), a DNA/RNA-binding protein that regulates the expression of muscle genes (e.g. Acta1 and MyoD). Knockdown of TDP-43 inhibits myogenic differentiation. We also show that Myolinc-TDP-43 interaction is essential for the binding of TDP-43 to the promoter regions of muscle marker genes. Finally, we show that silencing of Myolinc inhibits skeletal muscle regeneration in adult mice. Altogether, our study identifies a novel lncRNA that controls key regulatory networks of myogenesis.

overall_design: To elucidate the function of Myolinc, we conducted loss-of-function experiments to show that Myolinc–TDP-43 interaction is essential for the expression of muscle-specific genes by direct binding of TDP-43 at their promoter regions.

first: Giuseppe

last: Militello


title: Suppression of asthmatic phenotype and altered lipid metabolism in mice lacking zona pellucida binding protein 2

status: Public on Apr 05 2018

first: Anna

middle: K.

last: Naumova

state: Quebec

address: 1001 Decarie Blvd, Bloc E, Room EM03226

department: Department of Obstetrics and Gynecology

summary: The human chromosomal region 17q12-q21 is associated with childhood asthma.  It harbors 5 protein-coding genes, of which ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3) and gasdermin B (GSDMB) are the top causal gene candidates.  Emerging evidence suggests that the promoter region of another gene, the zona pellucida binding protein 2 (ZPBP2), located more than 50kb proximal to ORMDL3 may be critical for its transcriptional regulation influencing susceptibility to asthma.  To test this hypothesis, we examined the lung phenotypes, liver transcriptomes and lipid metabolism of Zpbp2 knock-out (KO) mice. We found that in comparison to wild type (WT) mice, Zpbp2 KO mice sensitized with allergen ovalbumin (OVA) had reduced bronchial reactivity.  The Zpbp2 KO mice also had altered lipid metabolism with a 3-fold decrease in the levels of docosahexaenoic acid (DHA), increased body weight and changes in the expression of the adipocytokine signaling pathway gene peroxisome proliferator activated receptor alpha (Pparα).  The Zpbp2 deletion was also associated with increased DNA methylation at the Zpbp2 promoter/enhancer region, reminiscent of the methylation of the orthologous region in humans, and reduced expression of Ormdl3 in liver.  The sum of our results implies that the Zpbp2 gene is involved in the regulation of airway hypersensitivity and lipid metabolism, either directly or through a cis-regulatory effect on Ormdl3.

overall_design: RNA-sequencing assays were conducted on RNA from livers of 3 C57BL/6J and 3 B6.Zpbp2-/- males.

first: Cynthia

last: Kanagaratham

first: Victoria

last: Chiwara

first: Bianca

last: Ho

first: Mina

last: Youssef

first: David

last: Venuto

first: Lucie

last: Jeannotte

first: Sanny

last: Moussette

last: Bourque

first: Juan

last: Bautista de Sanctis

first: Danuta

last: Radzioch

middle: K


title: Estrogen receptor ChIP-seq in response to mTOR inhibition

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

summary: We have used ChIP-seq to profile binding of the estrogen receptor (ER) to chromatin in response to two mTOR inhibitors, i.e. everolimus (RAD001) and vistusertib (AZD2014). Two hours of treatment with these inhibitors significantly affected mTOR signaling, but surprisingly did not affect binding of ER to chromatin. This suggests that these mTOR inhibitors work through largely ER-independent mechanisms.

overall_design: Estrogen receptor ChIP-seq was performed on chromatin from asynchronous MCF7 cells in full estrogenic media treated for 2 hours with vehicle, everolimus, or vistusertib.

first: Chrysiis

last: Michaloglou

first: Claire

last: Crafter

first: Rasmus

last: Siersbaek

first: Oona

last: Delpuech

first: Jon

last: Curwen

first: Larissa

last: Carnevalli

last: Staniszewska

first: Ursula

last: Polanska

first: Azadeh

last: Cheraghchi-Bashi

first: Mandy

last: Lawson

first: Igor

last: Chernukhin

first: Rob

last: McEwen

first: Sabina

last: Cosulich


title: Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

institute: Aalto University

summary:
Background: Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tregs is of great interest, and first-in-man trials of Treg transfer achieved promising outcomes. Yet, the mechanisms governing induced Treg (iTreg) differentiation and the regulation of FOXP3 are incompletely understood.

Results: To gain a comprehensive and unbiased molecular understanding of FOXP3 induction, we performed time-series RNA sequencing (RNA-Seq) and proteomics profiling on the same samples during human iTreg differentiation. To enable the broad analysis of universal FOXP3-inducing pathways, we used five differentiation protocols in parallel. Integrative analysis of the transcriptome and proteome confirmed involvement of specific molecular processes, as well as overlap of a novel iTreg subnetwork with known Treg regulators and autoimmunity-associated genes. Importantly, we propose 37 novel molecules putatively involved in iTreg differentiation. Their relevance was validated by: a targeted shRNA screen confirming a functional role in FOXP3 induction; discriminant analyses classifying iTregs accordingly; and comparable expression in an independent novel iTreg RNA Seq data set.

Conclusion: The data generated by this novel approach facilitate understanding the molecular mechanisms underlying iTreg generation as well as the concomitant
changes in the transcriptome and proteome. Our results provide a reference map exploitable for future discovery of markers and drug candidates governing control of Tregs, which has important implications for the treatment of cancer, autoimmune and inflammatory diseases

overall_design: Comparing the gene expression in activated CD4+ cells and iTreg differentiated cells in human. 10 time points, 3 biological replicates for each time point.

first: Riitta

last: Lahesmaa

first: Heinz

last: Wiendl


title: Deep Sequencing of brain Transcriptome Reveals difference in immune response between domesticated pigs and wild boars

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

summary:
Purpose:  The goal of this study was to perform a transcriptome-wide analysis of variation in brain gene expression between domesticated pig and wild boars using illumina sequencing strategy.
Methods: Brain mRNA profiles of wild boars and Rongchang pigs were generated by deep sequencing, in triplicate, using Illumina Hiseq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: We identified 808 widely-expressed conserved and 697 species-specific novel miRNAs in two species. In addition, although two organs showed similar high expression miRNAs, larger differentiation was present in lung than heart between two species. In addition, miRNAs with significantly differentiated patterns of expression in two organs exhibited obvious co-operation effect in high altitude adaptation in form of miRNA family and cluster. Functional analysis revealed that a large amount of differentially expressed miRNAs were enriched in hypoxia-related pathways, such as VEGF signaling pathway, HIF-1α signaling pathway, insulin signaling pathway, DNA damage response, apoptosis, fatty acid metabolism and glucose metabolism. These results suggested the diverse degrees of epigenetic variation in different tissues between yak and cattle, and revealed extensive roles of miRNAs in high altitude adaptation.
Conclusions: First, we totally identified 20,805 genes in two groups, of which 18,904 in wild boar and 17,980 in Rongchang pigs, respectively. Second, we detected substantial variation in expression profiles between wild boar and Rongchang pig, including substantial wild boar/Rongchang specifically expressed genes and differentially expressed genes. The functional enrichment analysis revealed immune response was enriched for genes upregulated in wild boars. Finally, we compared our results against previous study and identified seven genes that were associated with domestication.The work performed here will provide a typical demonstration for future deciphering the mechanism of pig domestication.

overall_design: Brain mRNA profiles of wild boars and Rongchang pigs were generated by deep sequencing, in triplicate , using Illumina Hiseq2000 .

first: Keren

last: Long

first: Jideng

last: Ma


title: Tracing the temporal-spatial transcriptomic landscapes of the human fetal digestive tract by single cell RNA-seq analysis

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University


title: Parental allele specific single-cell transcriptome dynamics reveal incomplete epigenetic reprogramming in human female germ cells

city: Utrecht

first: Abel

last: Vertesy

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: In contrast to mouse, human female germ cells develop asynchronously. Germ cells transition to meiosis, erase genomic imprints, and reactivate the X chromosome. It is unknown if these events all appear asynchronously, and how they relate to each other. Here we combine exome sequencing of human fetal and maternal tissues with single-cell RNA-sequencing of five donors.  We reconstruct full parental haplotypes and quantify changes in parental allele specific expression, genome-wide. First we distinguish PGC, pre-meiotic, and meiotic transcriptional stages. Next we demonstrate that germ cells from various stages monoallelically express imprinted genes from e.g. the SNURF-SNRPN cluster and confirm it by methylation patterns.  Finally we show that ±30% of the PGCs, are still reactivating their inactive X chromosome and that this is related to transcriptional stage, and not to embryonic age. Altogether, we reveal the complexity and cell-to-cell heterogeneity of transcriptional and epigenetic remodelling in female human germ cells.

overall_design: RNA sequences from human gonadal (N=73) and adrenal cells (N=35) from the mentioned fetuses 8.1-14.4wk of development (equivalent to 10.1-16.4 weeks of gestation) using SMART-seq2.

first: Ábel

last: VÉRTESY

first: Wibowo

last: ARINDRARTO

first: Matthias

middle: S

last: ROOST

first: Björn

last: REINIUS

first: Vanessa

last: TORRENS-JUANEDA

first: Monika

last: BIALECKA

first: Ioannis

last: MOUSTAKAS

first: Yavuz

last: ARIYUREK

first: Ewart

last: KUIJK

first: Leon

last: MEI

first: Rickard

last: SANDBERG

first: Alexander

last: van OUDENAARDEN

first: Susana

middle: M

last: CHUVA DE SOUSA LOPES


title: H2A.Z acetylation fine-tunes gene expression dynamics by regulating H2A.Z degradation

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: University of Cambridge

summary: H2A.Z acetylation has been suggested to regulate genes but effects on gene expression globally have not been reported. We find that the H2A.Z acetylation sites are required for normal growth in the presence of caffeine and therefore examined the gene expression response to caffeine when H2A.Z can’t be acetylated. Surprisingly we found little or no change in gene induction but a marked failure to remove H2A.Z from activated promoters. Caffeine causes a proteasome-dependent degradation of H2A.Z that is impaired in the absence of the H2A.Z acetylation sites. The proteasomal regulator Blm10 that has previously been implicated in acetylation-dependent histone degradation is required for H2A.Z degradation, revealing a novel role for acetylation in regulating H2A.Z protein levels. When H2A.Z levels are raised, either through loss of the acetylation sites or overexpression of the protein, a shared set of genes aberrantly retains H2A.Z at their 5’ ends during the caffeine response. As a result, expression of these genes fails to return to normal levels. H2A.Z is therefore subject to post-translational proteasomal regulation that controls protein levels, and the fine-tuning of gene expression during a stress response requires the normal function of this pathway. This regulation of H2A.Z degradation by acetylation is a previously unrecognised aspect of gene regulation.

overall_design: H2A.Z occupancy and gene expression of wild-type, lysine-to-arginine and overexpression mutants of H2A.Z at 0, 30 and 120 minutes during response to caffeine

first: Yanin

last: Naiyachit

first: Catherine

last: Millar


title: Tracing the temporal-spatial transcriptomic landscapes of the human fetal digestive tract by single cell RNA-seq analysis [adult tissues]

first: Rui

last: WANG

summary: Here, using a modified STRT-seq protocol, we analyzed the large intestine (LI) from two adults.In detail, the total 1891 single cells were picked from two adults LI. After the same rigorous filtration as fetal, 1463 individual cells were used for subsequent analysis. We identified 18 cell types including all main cell types existed in intestine such as enterocyte, goblet cell, enteroendocrine, Paneth cell, stem cell and immune cell. Take advantage of single cell RNA sequencing, we found that there were subtypes existed in some cell types. Subsequently, combined with our previous fetal data, we investigate the transcriptomic similarity and difference between human from fetal to adult. The transcriptome feature and development process from fetal to adult were revealed for the first time at single-cell resolution.

overall_design: Single cell transcriptome profiles of two human adult large intestine were generated by next generation suquencing using Illumina HiSeq X Ten

first: Shuai

last: Gao

first: Liying

last: Yan

last: Wang

first: Jingyun

last: Li


title: Time-course RNA-sequencing of human induced regulatory T cell (iTreg) differentiation

city: Stockholm

first: Francesco

last: Marabita

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

summary:
Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tregs is of great interest, and first- in-man trials of Treg transfer achieved promising outcomes. Yet, the mechanisms governing induced Treg (iTreg) differentiation and the regulation of FOXP3 are incompletely understood.
To gain a comprehensive and unbiased molecular understanding of FOXP3 induction, we performed time-series RNA sequencing (RNA-Seq) and proteomics profiling on the same samples during human iTreg differentiation. To enable the broad analysis of universal FOXP3-inducing pathways, we used five differentiation protocols in parallel. Integrative analysis of the transcriptome and proteome confirmed involvement of specific molecular processes, as well as overlap of a novel iTreg subnetwork with known Treg regulators and autoimmunity-associated genes. Importantly, we propose 37 novel molecules putatively involved in iTreg differentiation. Their relevance was validated by: a targeted shRNA screen confirming a functional role in FOXP3 induction; discriminant analyses classifying iTregs accordingly; and comparable expression in an independent novel iTreg RNA-Seq data set.
The data generated by this novel approach facilitate understanding the molecular mechanisms underlying iTreg generation as well as the concomitant changes in the transcriptome and proteome. Our results provide a reference map exploitable for future discovery of markers and drug candidates governing control of Tregs, which has important implications for the treatment of cancer, autoimmune and inflammatory diseases.

overall_design: We performed a time-course experiment including six time points and four iTreg differentiation conditions. We included also a control time series and unstimulated nTregs. Three biological replicates were included. The total sample count is 81. In detail, human naïve CD4+ T cells were magnetically negatively isolated from peripheral blood. Cells were stimulated in serum-free medium with anti-CD3/anti-CD28 antibodies plus IL-2, and samples were taken at 2h, 6h, 24h, 48h and 6d of stimulation. Mock stimulation control cells (sample group G02) received no further compounds, whereas induced regulatory T cells (iTregs) were either differentiated under addition of TGF-b (sample group G03), TGF-b + retinoic acid (sample group G04), TGF-b + retinoic acid + rapamycin (sample group G05) or TGF-b + butyrate (sample group G06). As control, naïve CD4+ T cells were left unstimulated (0h; sample group G01). Ex vivo isolated CD25-high cells were included as positive control for the Treg signature (“nTreg”; sample group G07). Tregs were defined by expression of FOXP3, the “master” transcription factor of Tregs.

first: Angelika

last: Schmidt


title: Coordinated control of mRNA and rRNA processing regulates early mammalian embryogenesis [ChIP-Seq_PolII]

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: Stem cells are regulated by transcriptional networks controlling pluripotency and differentiation. How basic cellular processes like splicing or protein synthesis regulate stem cell function is less well understood. Here, we show that the RNA binding protein HTATSF1 controls protein synthesis by controlling several independent RNA processing steps during ribosome biogenesis. In a complex with ribosomal RNA transcription and processing factors, HTATSF1 regulates ribosomal RNA abundance. By binding to the U2snRNP complex, HTATSF1 also controls intron removal specifically in ribosomal protein transcripts. HTATSF1-mediated control of protein synthesis is essential for the transition from the naïve pre-implantation epiblast to the primed post-implantation epiblast, a stage of low protein synthesis levels, and during further differentiation towards neuroectoderm. Our results identify coordinated regulation of ribosomal RNA and protein biosynthesis by HTATSF1 as an essential mechanism to mediate protein synthesis control during early stages of mammalian embryogenesis.

overall_design: Comparison of Polymerase II chromatin occupancy in mouse ESCs with or without RNA-binding protein HTATSF1

first: Nina

last: Corsini

first: Angela

last: Peer

first: Paul

last: Moeseneder

first: Hans-Christian

last: Theussl

first: Juergen

last: Knoblich


title: Electromagnetic field-mediated direct lineage reprogramming into induced dopamine neurons in vivo for Parkinson’s disease therapy [ChIP-Seq]

city: Goyang-si

first: Junghyun

last: Jung

state: Gyeonggi-do

address: Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu

department: Life Science

country: South Korea

institute: Dongguk Uvi.

summary: Electromagnetic fields (EMF) are physical energy generated by electrically charged objects that can influence numerous biologic processes, including control of cell fate and plasticity. In this study, we show that magnetic gold nanoparticles in the presence of EMF can facilitate efficient direct lineage reprogramming to induced dopamine neurons both in vitro and in vivo. Remarkably, electromagnetic stimulation leads to the specific activation of the histone acetyl transferase Brd2, resulting in H3K27 acetylation and robust activation of neuronal-specific gene expression. In vivo reprogramming in conjunction with EMF stimulation efficiently alleviated symptoms in a mouse model of Parkinson’s disease (PD) in a noninvasive and controllable manner. These studies provide a proof of principle that EMF-based approaches may represent a viable and safe therapeutic strategy facilitating in vivo lineage conversion for neurodegenerative disorders.

overall_design: Genome binding/occupancy profiling of H3K27 acetylation was performed in mouse embryonic stem cells by ChIP sequencing.

first: Junsnag

last: Yoo

first: Wonhee

last: Jang

first: Jongpil

last: Kim


title: Coordinated control of mRNA and rRNA processing regulates early mammalian embryogenesis [ChIP-Seq_HTATSF1]

overall_design: Identification of Chromatin regions bound by HTATSF1


title: Coordinated control of mRNA and rRNA processing regulates early mammalian embryogenesis

overall_design: Refer to individual Series


title: Innate immune memory in the brain shapes neurological disease hallmarks [RNA-seq]

city: Tübingen

first: Jonas

middle: J

last: Neher

address: Otfried Mueller Str. 23

department: Experimental Neuroimmunology

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE) Tübingen

summary: Innate immune memory is a vital mechanism of myeloid cell plasticity that occurs in response to environmental stimuli and alters subsequent immune responses. Two types of immunological imprinting can be distinguished—training and tolerance. These are epigenetically mediated and enhance or suppress subsequent inflammation, respectively. Whether immune memory occurs in tissue-resident macrophages in vivo and how it may affect pathology remains largely unknown. Here we demonstrate that peripherally applied inflammatory stimuli induce acute immune training and tolerance in the brain and lead to differential epigenetic reprogramming of brain-resident macrophages (microglia) that persists for at least six months. Strikingly, in a mouse model of Alzheimer’s pathology, immune training exacerbates cerebral beta-amyloidosis and immune tolerance alleviates it; similarly, peripheral immune stimulation modifies pathological features after stroke. Our results identify immune memory in the brain as an important modifier of neuropathology.

overall_design: mRNA was isolated from FACS-purified microglia and prepared for RNA-sequencing.

first: Andre

last: Fischer

last: Ulas


title: Coordinated control of mRNA and rRNA processing regulates early mammalian embryogenesis [RNA-Seq]

overall_design: Comparison of mouse ESCs with or without RNA-binding protein HTATSF1

middle: R


title: Abnormal interneuron development in a new humanized mouse model of Arx dup24 which recapitulates the patients’ behavioural and fine motor alterations

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

summary: The Aristaless-related homeobox (ARX) gene is a transcription factor involved in the development of GABAergic and cholinergic neurons in the forebrain. ARX mutations have been associated with a wide spectrum of neurodevelopemental disorders in humans, among which the most frequent, the 24 bp duplication in the protein polyalanine tract 2 (c.428_451dup24), gives rise to intellectual disability (ID), fine motor defects with or without epilepsy. To understand the physiological and functional consequences of this mutation, we generated and characterized a humanized mouse model carrying the c.428_451dup24 duplication (Arxdup24/0). Arxdup24/0 males presented with hyperactivity, enhanced stereotypies and altered contextual fear memory. Specific fine motor skills were also affected in Arxdup24/0 males, with reaching and grasping abilities alteration and fine motor coordination and balance defect. Transcriptome analysis of Arxdup24/0 forebrains at E15.5 showed a down-regulation of genes specifically expressed in interneurons associated with an up-regulation of interneuron silenced genes, suggesting abnormal interneuron development. Accordingly, interneuron migration and development were altered particularly in the cortex and the striatum between stages E15.5, P0 and adult. We also revealed a perturbation of the inhibitory/excitatory balance in Arxdup24/0 basolateral amygdala. Altogether, we showed that the c.428_451dup24 mutation modifies Arx function with a direct consequence on interneuron development, leading to hyperactivity and defects in precise motor movement control and in associative memory. Finally, we presented a new review of the clinical features of 33 male patients with ARX c.428_451dup24 mutation and showed striking similarities between their clinical features and the mouse phenotype.

overall_design: Total of 6 sequenced samples. RNA-seq (3 replicates) for ARX wt/0 and ARX dup24/0 in embryonic forebrain E15.5.

first: Aline

last: Dubos

first: Hamid

last: Meziane

first: Giovanni

last: Iacono

first: Gaëlle

last: Friocourt

first: Yann

last: Herault


title: Tracing the temporal-spatial transcriptomic landscapes of the human fetal digestive tract by single cell RNA-seq analysis [fetal tissues]

first: Rui

last: WANG

summary: The development of digestion tract is critical for proper digestion of food and absorbance of nutrient for an individual. It includes the spatial segregation into esophagus, stomach, small and large intestine. The temporal-spatial gene expression profiles of human digestion tract in vivo have never been analyzed at single-cell resolution.Here we analyzed esophagus, stomach, small intestine (SI) and large intestine (LI) from multiple human embryos between 6 and 25 weeks of gestation by single cell RNA-seq analyses.We firstly identified 51 clusters of different types of cells using t- Distributed Stochastic Neighbor Embedding (t-SNE) analysis.Moreover,cell type of each organ were identified according to the known marker genes and new cell types were further analyzed.The dynamic change of each cell type were tracked during the human embryonic digestive tract development.We found HOX family geens paly different roles in the regulation of digestion tract developemnt. In addition, Hedgehog,TGFβ and BMP signaling pathway are essential for SI and LI development in human fetal. The function of nutrient digestion and absorption was increased as the SI development in human fetal.Finally, we demonstrated that the immune system was established at late stage of human fetal and verified the immune-like cells,such as T cell, B cells and macrophage. In summary, by using single cell RNA seq technique, we identified the waves of signaling pathways and critical cell types for the human digestion tract development.

overall_design: Single cell transcriptome profiles of four main human organs (esophagus, stomach, small and large intestine) from 6 week to 25 week gestation of digestion system were generated by next generation sequencing using Illumina HiSeq X Ten

first: Shuai

last: Gao

first: Liying

last: Yan

last: Wang

first: Jingyun

last: Li


title: Innate immune memory in the brain shapes neurological disease hallmarks [ChIP-seq]

overall_design: Chromatin from FACS sorted microglia was pooled from 8-10 animals per treatment and two replicates were processed independently. H3K4me1 and H3K27ac Chip-Seq experiments were then performed, using input DNA for background measurements.


title: Gene expression profiles of rat hypertrophic zone after treatment of CNP53 or U0126 [CNP53]

status: Public on Apr 04 2018

city: Kobe

first: Kazunori

last: YOSHIKIYO

state: Hyogo

address: 6-4-3, Minatojima-Minamimachi, Chuo-ku

country: Japan

institute: Asubio Pharma Co., LTD.

summary: To investigate the similarity of gene expression profile of CNP53 and U0126 treatment in growth plate.

overall_design: Tibiae from E18.5 embryonic rat were isolated and pre-cultured in BGJb media for 1 day, followed by culturing in the presence of vehicle or CNP53 (100 ng/mL) for 1 day. The tibiae (12 bones) were micro-dissected into the hypertrophic zone and pooled, from which RNA was isolated by using Qiagen RNeasy micro Kit, then microarray analyses were performed by using Agilent array system.

last: Yoshikiyo


title: High-resolution RNA 3’-ends mapping of bacterial rho-dependent transcripts

city: Rehovot

first: Daniel

last: Dar

address: 234 Herzl St

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Transcription termination in bacteria can occur either via Rho-dependent or independent (intrinsic) mechanisms. Intrinsic terminators are composed of a stem-loop RNA structure followed by a uridine stretch and are known to terminate in a precise manner. In contrast, Rho-dependent terminators have more loosely defined characteristics and are thought to terminate in a diffuse manner. While transcripts ending in an intrinsic terminator are protected from 3’-5’ exonuclease digestion due to the stem-loop structure of the terminator, it remains unclear what protects Rho-dependent transcripts from being degraded. In this study, we mapped the exact steady-state RNA 3’ ends of hundreds of E. coli genes terminated either by Rho-dependent or independent mechanisms. We found that transcripts generated from Rho-dependent termination have precise 3’-ends at steady state. These termini were localized immediately downstream of energetically stable stem-loop structures, which were not followed by uridine rich sequences. We provide evidence that these structures protect Rho-dependent transcripts from 3’-5’ exonucleases such as PNPase and RNase II, and present data localizing the Rho-utilization (rut) sites immediately downstream of these protective structures. This study represents the first extensive in-vivo map of exact RNA 3’-ends of Rho-dependent transcripts in E. coli.

overall_design: Three replicates

first: Rotem

last: Sorek


title: Gene expression profiles of rat hypertrophic zone after treatment of CNP53 or U0126

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


title: Gene expression profiles of rat hypertrophic zone after treatment of CNP53 or U0126 [U0126]

overall_design: Tibiae from E18.5 embryonic rat were isolated and pre-cultured in BGJb media for 1 day, followed by culturing in the presence of vehicle or U0126 (0.02mM) for 1 day. The tibiae (12 bones) were micro-dissected into the hypertrophic zone and pooled, from which RNA was isolated by using Qiagen RNeasy micro Kit, then microarray analyses were performed by using Agilent array system.


title: Global dynamics of stage-specific transcription factor binding during thymocyte development

city: Ann Arbor

first: Tomonori

last: Hosoya

address: 109 Zina Pitcher Place

department: CDB

institute: University of Michigan

summary: ATAC-seq in DN, DP, CD4 SP and CD8 SP thymocytes isolated from 9 weeks-old wild type C57BL/6J mouse

overall_design: Anlysis of 4 mice in 4 different stages

first: Ricardo

last: D’Oliveira Albanus

first: James

last: Engel

first: Stephan

last: Parker


title: Dissociable structural and functional hippocampal outputs via distinct subiculum cell classes

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: University of British Columbia

summary: Here, we profile gene expression from subiculum pyramidal cells in the mouse.

overall_design: RNA-seq was performed in bulk (3 biological replicates/sample) and single cell (96 cells/plate x 4 plates) resolution, with deep sequencing on Illumina HiSeq 2500

first: Nelson

last: Spruston


title: Impaired chloroplast biogenesis causes color variation between two varieties/cultivars of Chinese orchid (Cymbidium longibracteatum)

status: Public on Apr 03 2018

city: Chengdu

first: Yu

middle: NMN

last: Jiang

address: Shizishan road 4#

institute: Institute of Horticulture, Sichuan Academy of Agricultural Sciences

summary: To explore the mechanisms governing the leaf color variations in Chinese orchids, we analyzed  gene expression differences between a wild-type and an albino-type cultivar of Cymbidium longibracteatum

overall_design: The youngest five leaves from each plant were collected and mixed into one sample for RNA-seq

first: Jun-rong

last: He

first: Jia

last: Liu


title: RbFox1-Nestin hippocampus

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

summary: Dysregulation of the brain-enriched RNA binding protein Rbfox1 has been linked to neurologic diseases such as epilepsy and autism spectrum disorders. However, it remains unexplored how distinct neuronal populations might contribute to neurologic dysfunction resulting from Rbfox1 loss. To examine these issues we profiled gene expression specifically in the hippocampus of wildtype and Rbfox1-/- mice. We identified transcripts whose expression was strongly Rbfox1-dependent and exhibited significant Rbfox1 binding in their 3’UTRs. One prominent target, Vamp1, was found to be specifically expressed in GABAergic interneurons. Both Vamp1 knockdown and Rbfox1 loss led to decreased synaptic transmission, and altered E/I balance in the Rbfox1-/- hippocampus, indicating that Vamp1 loss is a major component of the Rbfox1-/- physiological phenotype. The cytoplasmic isoform of Rbfox1 was sufficient to rescue Vamp1 expression in Rbfox1-/- neurons. We show that Rbfox1 binding in the Vamp1 3’UTR promotes its expression in part by antagonizing the brain-enriched microRNA-9. These results demonstrate that inhibitory neurons maintain specialized synaptic vesicle release machinery containing Vamp1 that is critically regulated by Rbfox1.

overall_design: We performed RNA-seq to profile gene expression and splicing changes. Adult (P60-P70)  hippocampal tissue was dissected from 3 pairs of male wildtype (Rbfox1 fl/fl; +/+) and Nes-cKO (Rbfox1 fl/fl; Nes/+) mice. Gene expression and splicing profiles were compared between wildtype and Nes-cKO. 6 total samples were analyzed.

first: Celine

last: Vuong

first: Chia-Ho

first: Douglas

last: L Black


title: Analysis of differential gene expression in the Streptococcus sanguinis SK36 treated with heat shock for 3 periods of time

city: Richmond

first: Fadi

middle: Elias

last: El-Rami

state: VA

address: 521 N 11th Str, wood bldg, room 424

department: Microbiology & Immunology

institute: Virginia Commonwealth University

summary: Gene expression profile of the Streptococcus sanguinis SK36 exposed to heat (43 C) for three time periods compared to the untreated strain SK36.

overall_design: Experiment: SK36 strains were treated with heat shock (43 C) for 10, 20, or 30 minutes. Control strain was untreated. Three biological replicates independently grown and prepared for each time period and control.

middle: E

first: Ping

last: Xu


title: Transcriptome Analysis of Tendon Derived Stem Cells (TDSCs) Isolated from WT and CFTRΔF508 Mice

city: Hong Kong

first: Gang

last: LI

address: Shatin

department: Department of Orthopaedics & Traumatology

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: We performed RNA-sequencing to compare the gene expressions of TDSCs isolated from the WT and CFTRΔF508 (DF508) mice.

overall_design: Examination of mRNA levels in TDSCs isolated from 10-week old WT and DF508 mice by deep sequencing, using Illumina HiSeqTM 2000.

first: Liu

last: Yang

last: Li


title: Deciphering the dynamic transcriptional and post-transcriptional networks of macrophages in the healthy heart and after myocardial injury [RNA-seq]

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

institute: CNIC

summary: Macrophage plasticity has been studied in vitro, but transcriptional regulation upon injury is poorly understood.  In this study, we generated a data set for genome-wide transcriptome and miRNome analysis of macrophages in the healthy heart and after myocardial injury.

overall_design: Cardiac macrophages GFP+ cells were isolated from Cx3cr1GFP/+ knock-in mouse hearts in steady-state and at different post-injury stages.

first: Mercedes

last: Ricote

first: Fátima

last: Sánchez-Cabo


title: Deciphering the dynamic transcriptional and post-transcriptional networks of macrophages in the healthy heart and after myocardial injury


title: BEARscc: robustness of single-cell clusters determined using simulated technical replicates

city: Durham

first: David

last: Severson

address: 2301 Erwin Road

department: Department of Surgery

institute: Duke University Health System

summary: Technical variance is a major confounding factor in single-cell RNA sequencing, not least because measurements on the same cell are not replicable. We developed BEARscc, a tool that simulates experiment-specific technical replicates based on a probabilistic model of technical variance trained on RNA spike-in measurements. We demonstrate that the tool improves the unsupervised classification of cells and aids the interpretation of single-cell RNA-seq experiments.

sample_organism:
Homo sapiens
other sequences

platform_organism:
Homo sapiens
other sequences

overall_design: scRNA-seq was performed on dilute whole brain tissue and water samples in order to assess BEARscc as cluster robustness tool.

middle: T

first: Benjamin

last: Schuster-Böckler

first: Xin

last: Lu

first: Richard

last: Owen

first: Michael

last: White


title: Global transcriptional changes in U87MG glioblastoma cells upon shRNA-mediated TRIM52 knockdown

status: Public on Apr 01 2018

first: Stefan

last: Benke

state: Vienna

address: Dr. Bohr-Gasse 9

institute: Max F. Perutz Laboratories, University of Vienna

summary: shRNA-mediated ablation of the RING-finger protein TRIM52 from multiple glioblastoma cell lines reduces proliferation and tumorigenesis. To identify gene signatures underlying this phenomenon, transcritional profile of TRIM52 knockdown cells was compared to control cells. Upon TRIM52 ablation, we find 278 differentially regulated genes. Gene ontology analysis reveals that many of the upregulated genes are associated with glycolysis and biosynthetic processes.

overall_design: U87MG glioblastoma cells were stably transduced with doxycycline-inducible shRNA constructs targeting TRIM52 (two different shRNAs) or controls (two different non-targeting shRNAs). Knockdown was induced for five days using 2µg/ml doxycycline. shRNA expressing cells were sorted based on shRNA-coupled GFP expression via flow cytometry. mRNA sequening was performed in duplicate per shRNA cell line.

first: Gijs

middle: A

last: Versteeg


title: Genome-wide identification of miRNAs associated with alcoholism endophenotypes

status: Public on Apr 02 2018

city: Aurora, CO

first: Katerina

last: Kechris

state: CO

address: Mail Stop B119, 13001 E. 17th Place

department: Colorado School of Public Health

institute: University of Colorado Anschutz Medical Campus

summary: Innate sensitivity to ethanol can be an important first step towards understanding alcohol use disorders. We investigated miRNA-modulated transcriptional expression in brain associated with a predisposition to the hypnotic effect of ethanol, as measured by Loss of Righting Reflex (LORR). Expression of miRNAs and mRNAs in brain were independently analyzed for an association with LORR in mice from the LXS recombinant inbred panel.  These results were then integrated via a meta-analysis for miRNA-mRNA target pairs identified in miRNA target interaction databases.  We found 112 significant miRNA-mRNA pairs where a large majority of miRNAs and mRNAs were highly inter-connected. Most pairs indicated a pattern of increased levels of miRNAs and reduced levels of mRNAs being associated with more alcohol sensitive strains. For example, CaMKIIn1 was targeted by multiple miRNAs associated with LORR. CAMK2N1 is an inhibitor of CAMK2, which among other functions, phosphorylates or binds to GABAA and NMDA receptors. Our results suggest a novel role of miRNA-mediated regulation of an inhibitor of CAMK2 and its downstream targets including the GABAA and NMDA receptors, which have been previously implicated to have a role in ethanol-induced sedation and sensitivity.

overall_design: This dataset includes small RNA NGS sequencing data from 12 ILS/IbgTejJ and ISS/IbgTejJ mouse RNA samples. Six mice (3 from each strain) were saline treated (SAL) 8 hours before tissue extraction. The remaining 6 were untreated (NVE). The saline-treated mouse samples were provided by Richard Radcliffe and the naive samples were provided by Boris Tabakoff. All analysis was done by the Kechris Group

first: Boris

last: Tabakoff

last: Radcliffe


title: Viral targeting of TFIIB impairs de novo polymerase II recruitment and affects antiviral immunity

city: Martinsried

first: Andreas

last: Pichlmair

state: Bayern

address: Am Klopferspitz 18

department: Mann

institute: Max-Planck Institut für Biochemie

overall_design: Refer to individual Series


title: Trnascriptome analysis of HeLa cells infected with rTHOV-wt, -dML, -SW mutant or mock-treated

summary: The goal of the study was to compare transcriptome changes in HeLa cells after infection with recombinant Thogoto virus (wild-type, ML deletioin mutant or ML SW mutant not able to interact wiith TFIIB. While wild-type virus is able to inhibit inflammatory genes, ML deletion mutant and TFIIB-non-interacting mutant lose this effect on gene transcription.

overall_design: Examination of transcriptome changes in HeLa cells under steady state or after THOV infection using Illumina HiSeq.

first: Darya

last: Haas

first: Arno

last: Meiler


title: Transcriptome of TNF-a-treated and untreated HeLa cells before and after TFIIB knockdown

summary: The goal of this study was to compare transcriptome of HeLa cells with or without TFIIB knockdown for gene expression changes in steady state or after TNF-a treatment. Although a broad effect on gene expression would be anticipated, TFIIB depletion led only to an altered expression of a limited number of genes.

overall_design: Examination of transcriptome changes in HeLa cells under steady state or TNF-a treatment before and after TFIIB knockdown using Illumina HiSeq.


title: Single-cell RNA-seq of fibroblasts from recessive dystrophic epidermolysis bullosa patients and wild-type controls

city: Minneapolis

first: Jakub

last: Tolar

state: MN

address: 420 Delaware St SE

department: Pediatrics

institute: University of Minnesota, Twin Cities

summary: The goal of this study is to discover fibroblast subpopulations relevant to recessive dystrophic epidermolysis bullosa

overall_design: Cultured fibroblasts from recessive dystrophic epidermolysis bullosa patients and wild-type controls were captured using the C1 Fluidigm and sequenced on an Illumina MiSeq

first: Catherine

last: Lee


title: DNA methylation in the placentas of typically developing and autistic children

city: Davis

first: Janine

last: LaSalle

address: Medical Microbiology and Immunology

institute: UC Davis

summary: Epigenetic perturbations in the early embryo could have later effects during development.  For a disease such as autism, where a diagnosis is hard before two years of age but earlier intervention is correlated with better outcomes, finding a molecular signature of the disease at birth could have a significant impact of the quality of life.  Since placenta also derives from the early embryo, is a readily-available tissue at birth, and has a unique DNA methylation pattern, we tested whether disruptions in placental DNA methylation was predictive of autism.  As part of the MARBLES study, parents that already had an autistic child and were therefore at much greater risk to have another autistic child were followed as they planned another pregnancy.  Biological samples were collected at birth and the children followed for several years to determine the diagnosis.  “Typical” children in this study were those that did not later develop autism.

overall_design: MethylC-seq was performed on the placentas of 23 typical and 24 autism placentas from the MARBLES study.  In addition, MethylC-seq was performed on four regions in a normal placenta to assess heterogeneity within the tissue.

first: Diane

middle: I

last: Schroeder


title: A novel hybrid two-component system Lvr mediates virulence and global regulation in pathogenic Leptospira

city: New Haven

first: Sameet

last: Mehta

state: CT

address: 300 Cedar St.

institute: Yale University

summary: Transmission of leptospirosis requires that the spirochete pathogen adapts rapidly to the mammalian host milieu during infection and the external environment upon shedding from the renal tubules of animal reservoirs. The pathogenic Leptospira genomes encode a notably large number (≥76) of putative two-component system (TCS) proteins, which presumably play a key role in switching the ecological niches. Yet to date, the regulatory networks that govern virulence and environmental adaptation have not been elucidated in Leptospira. We identified seven ORFs encoding putative TCS proteins that are exclusively conserved in all the pathogenic Leptospira species. Two of these ORFs (LMANv2_670020, LMANv2_670019), juxtaposed in an operon, are predicted to encode a cytoplasmic hybrid histidine kinase and response regulator. Corresponding transposon mutants ΔlvrA/B and ΔlvrB demonstrated a loss-of-virulence in a hamster model of leptospirosis and aberrant motility phenotype. RNA sequencing revealed the differential expression of transcripts on a global scale in ΔlvrA/B (8.13%), ΔlvrB (5.06%) and ΔlvrA/B∩ΔlvrB (8.24%). In vitro transcriptomes provided insights into the role of Lvr dyad in regulating virulence, motility, signal transduction and metabolism related genes. Phosphotransfer assays indicated that LvrA interacts with LvrB in a branched signaling pathway. Phylogenetic analyses indicated that Our findings suggest that a novel, hybrid two-component system Lvr plays a key role in governing virulence and mediating global regulation in pathogenic Leptospira.

overall_design: To study the impact of two transposon mutants in signal transduction genes in Leptospira and study their role in virulence.

first: Haritha

last: Adhikarla

first: Elsio

last: Wunder

first: Albert

last: Ko


title: Comparative expression data between the epidermis and dermis of wild-type (Pparb/d^fl/fl) and fibroblast-selective knockout Pparb/d (FSPCre-Pparb/d^fl/fl) mice

city: Singapore

first: Ming Keat

last: Sng

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary:
The role of PPARβ/δ in maintaining skin homeostasis during skin injury or inflammation has been widely studied. However, the majority of these reports based their studies in PPARβ/δ found in keratinocytes, which is the major cell type of the skin epidermis. The skin is mainy made up of the epidermis and dermis, and skin homeostasis is tightly regulated by complex crosstalks between epidermis and dermis. The dermis is predominantly made up of fibroblasts, and the predominant PPAR subtype in dermal fibroblasts is PPARβ/δ. Knowledge in the role of fibroblasts PPARβ/δ in skin homeostasis is lacking.
To identify gene changes leading to phenotypical and biological functions alterations upon deletion of fibroblasts PPARβ/δ, we performed a comparative microarray gene expression analysis between Pparb/d^fl/fl and FSPCre-Pparb/d^fl/fl mice.

overall_design: Pparb/d^fl/fl mice, having the exon 4 of their Pparb/d gene flanked by loxP sites, were mated with mice harbouring the Cre transgene under the control of the FSP promoter. FSPCre-Pparb/d^fl/+ progenies were then bred with Pparb/d^fl/fl mice to obtain FSPCre-Pparb/d^fl/fl mice and the wild-type control mice. To sustain this genotype, we bred FSPCre-Pparb/d^fl/fl progenies with Pparb/d^fl/fl mice. Mice were housed in a specific-pathogen free facility with a 12 h/12 h light/dark cycle. Food and water were provided ad libitum. Animal experiments were carried out in accordance to the guidelines of the University Institutional Animal Care and Use Committee (IACUC, ARF-SBS/NIE-A0216AZ), Singapore. Mice in the telogen phase of their hair cycle were anaesthetized and depilated on their dorsal back before being subjected to a biopsy punch (~4 mm). The skin biopsy was then treated with 3.8% ammonium thiocyanate (Sigma, USA) in 1X PBS for 30 min at 37 oC. Subsequently, the epidermis was mechanically separated from the dermis with a pair of forceps. The dermis was then curetted with a 30-gauge needle. RNA was extracted from the epidermis and dermis with Trizol according to the manufacturer’s protocol. Further sample processing of the RNA was carried out using Applause® WT-Amp ST System (NuGEN), and microarray experiments were performed on GeneChip® Mouse Gene 1.0 ST arrays according to the manufacturer’s instructions.


title: Next Generation Sequencing of Wild Type and AtSRT1 transgene plants Transcriptomes

city: Wuhan

first: Xiaoyun

last: Liu

state: Hubei

address: Economic and Technological Development Zone, Sanjiaohu Road, No. 8

institute: Jianghan university

summary: To study genome-wide gene expression regulated by AtSRT1, we analyzed transcriptomes of wild type and AtSRT1 RNAi-1 (R) and overexpression OX-SRT1-1(OX)   line by RNA-sequencing using the Illumina Hiseq-2000 sequencing system. Three biological replicates for each genotype were tested.The data suggest that AtSRT1 plays an important role in regulation of genes involved in stress responses and in carbon and energy metabolism in Arabidopsis.

overall_design: Arabidopsis mRNA profiles of 14-day old wild type (WT) and RNAi-SRT1 and OX-SRT1 were generated by deep sequencing, in triplicate, using Illumina.

first: Dao-xiu

last: Zhou


title: Transcriptome profile of wildtype and Ret homozygote null male mouse guts at E10.5

city: Baltimore

first: Sumantra

last: Chatterjee

state: MD

address: 733 N Broadway, Room 572

department: Institute of Genetic Medicine

country: USA

institute: Johns Hopkins University School of Medicine

summary: Total mRNA seq was perfomed on widtype and Ret null male mouse embryonic gut at E10.5

overall_design: Total RNA from 3 replicates each of wildtype and Ret null homozygous male emryonic gut was converted to cDNA  and run on HiSeq 2000 (75 bp paired end)

first: Aravinda

last: Chakravarti


title: Total RNAseq of intestinal stem cells (ISCs) and progenitor cells (EBs) with expression of Lamin Dm0 and/or UPD

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary:
Purpose: To determine the effect of Lamin Dm0 expression on the transcription profile of ISCs/EBs with and without activated Jak/Stat signalling.

Method: Lamin Dm0 and UPD were expressed in ISCs/EBs alone and in concert and the transcriptional changes compared with control flies.

Conclusions: We found that 49% of UPD induced Jak/Stat targets were normalized by Lamin Dm0 coexpression.

overall_design: ISC/EB specific expression of Lamin Dm0 and/or UPD for 5 days. Isolation of ISCs/EBs by FACS and total RNA isolation.

first: Roman

last: Petrovsky

first: Jörg

last: Großhans


title: Effect of Seven-up RNAi on wandering third instar larval fat body gene expression in Drosophila melanogaster

city: Binghamton

first: Laura

middle: Palanker

last: Musselman

state: New York

address: 4400 Vestal Parkway East

department: Biological Sciences

institute: Binghamton University

summary: We compared Seven-up-dependent gene expression in the Drosophila fat body on control and high-sugar diets in order to gain insight into the role of this gene during caloric overload. Phenotypic analyses showed an increased severity of Seven-up RNAi phenotypes with increasing dietary sugar concentration. Because Seven-up is a transcription factor, we performed RNA-seq studies to identify transcriptional targets that might underlie insulin resistance downstream of Seven-up RNAi. Our data support a model where Seven-up promotes insulin signaling by inhibiting ecdysone receptor target gene expression.

overall_design: Control and fat body-expressed Seven-up RNAi Drosophila were reared on control (0.15M sucrose) and high-sugar (0.7M sucrose) diets until the wandering stage. Fat bodies were isolated and RNA extracted to determine the effects of diet on gene expression using Illumina RNA-seq.

first: Thomas

last: Baranski

first: Ezekiel

last: Maier


title: Chromatin accessibility profiling identifies cis-regulatory modules in an early embryonic cell lineage

city: Pittsburgh

first: Charles

last: Ettensohn

state: PA

address: 4400 Fifth Avenue

institute: Carnegie Mellon University

summary: We used DNase-seq and ATAC-seq to identify a set of putative CRMs regulating skeletogenic gene expression during sea urchin embryogenesis. These CRMs, identified by differential chromatin accessibility, are likely to be regulated by two upstream TFs, Alx1 and Ets1, that are part of the skeletogenic GRN. 9/31 od these identified CRMs were validated by reporter gene assay. Our work demonstrates the value of using differential chromatin accessibility for the high-throughput identification of CRMs in embryonic tissues.

overall_design: DNase-seq performed on U0126-treated PMC(-) S. purpuratus embryos at 28 hpf and control whole embryos at 28 hpf. There are 2 samples and 3 replicates for each sample. ATAC-seq was performed on isolated PMCs at 24 hpf and other non-PMC cells of the embryo at 24 hpf. There were 2 samples and 2 replicates per sample.

first: Tanvi

last: Shashikant

first: Jian-Ming

last: Khor


title: MEK inhibition rewires enhancer landscapes in RAS-driven Rhabdomyosarcoma to unlock a myogenic differentation block

city: Bethesda

first: Javed

last: Khan

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

summary: Trametinib-treated rhabdomyosarcoma cells undergo transcriptional reprogramming akin to myogenic differentiation.   This reprogramming is induced by loss of ERK-mediated inhibition of MYOG expression.  Restoration of MYOG allows establishment of super-enhancers at genes expressed by terminally differentiated myotubes.  Our findings demonstrate that aberrant MAP kinase activity blocks differentiation in rhabdomyosarcoma and highlight trametinib as a potential therapeutic for RAS-mutated rhabdomyosarcoma.

overall_design: RNA-seq in 2 FN-RMS cell lines exposed to either DMSO or Trametinib treatment for various concentrations and timepoints, and siRNA against MEK1 or scramble.

first: Berkley

last: Gryder

first: Marielle

last: Yohe

first: Xinyu

last: Wen


title: MEK inhibition profoundly reprograms myogenic super enhancers in mutant-RAS driven Rhabdomyosarcoma

overall_design: Genome-wide profiles for histone marks, DNase hypersensitivity, transcription factors in mutant-RAS driven, Fusion-Negative Rhabdomyosarcoma (FN-RMS) cell lines and tissues


title: Epigenetic Reprogramming of mutant RAS-driven Rhabdomyosarcoma via MEK Inhibition

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Methylome analysis of colorectal cancer cell line DNA (HCT116) and colorectal cancer patient derived xenografts (PDXs) using MeDIP-seq and cfMeDIP-seq

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre

summary: Three separate experiments were carried out using MeDIP-seq and cfMeDIP-seq for methylome analysis. For the first experiment, different starting amounts of HCT116 cell line DNA, sheared to mimic cell-free DNA, were analyzed using MeDIP-seq and cfMeDIP-seq. In the second experiment the limit of detection of cfMeDIP-seq was tested using varying dilutions of colorectal cancer cell line DNA (HCT116) with multiple myeloma cell line DNA (MM1.S). For both cell line DNA samples, the DNA was sheared to mimic cell-free DNA. In the final experiment, we tested the enrichment of human ctDNA using cfMeDIP-seq performed on plasma collected from patient-derived xenografts (PDXs) generated in mice from two colorectal cancer patients.

overall_design:
The gold standard MeDIP-seq protocol using 100 ng of sheared cell line DNA and the cfMeDIP-seq protocol using 10 ng, 5 ng, and 1 ng of the same sheared cell line DNA was performed with two biological replicates. For the samples starting with less than 100 ng of DNA, as part of cfMeDIP-seq, the DNA starting amount prior to MeDIP was inflated to 100 ng using filler DNA in the form of unmethylated and artificially methylated PCR amplicons. For the second experiment, using HCT116 and MM1.S cell line DNA sheared to mimic cell-free DNA, a serial dilution was performed using a starting DNA amount of 60 ng with HCT116 DNA diluted with MM1.S DNA. The varying percentages of HCT116:MM1.S DNA included: 100% HCT116, 10% HCT116, 1% HCT116, 0.1% HCT116, 0.01% HCT116, 0.001% HCT116 and 100% MM1.S. These samples were subjected to cfMEDIP-seq, with the DNA starting amounts prior to MeDIP inflated to 100 ng using filler DNA as previously mentioned.  In both experiment 1 and 2, the sequenced reads were aligned to reference genome hg19. For the PDX-driven experiment, cfMeDIP-seq was performed on two plasma samples from mice engrafted with colorectal cancer patients-derived xenograft (PDXs). In this experiment, both the cfMeDIP-seq samples and their respective input controls were sequenced. The sequencing reads were aligned to both reference genome hg19, and reference genome mm9.

The PDX samples (GSM2422520 - GSM2422527) have no associated processed data. Conclusions for these samples were based solely on alignments. Raw data for these samples are represented by BAM files.

middle: D

first: Rajat

last: Singhania

first: Shu

middle: Y

last: Shen


title: Expanded Genomic Profiling of Circulating Tumor Cells in Metastatic Breast Cancer Patients to Assess Biomarker Status and Biology Over Time (CALGB 40502 and CALGB 40503, Alliance).

city: San Francisco

first: Mark

last: Magbanua

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

type: Genome variation profiling by genome tiling array

summary:
We developed a novel approach to isolate tumor cells with high purity from blood which was subjected to immunomagnetic enrichment using EpCAM beads followed by fluorescence activated cell sorting (IE/FACS) to isolate EpCAM-positive cells away from leukocytes (CD45+). Duplicate samples of 20 cells were isolated from the same enriched blood from  MBC patients and then subjected to DNA and RNA profiling in parallel.
For DNA profiling, sorted cells were subjected to BAC array comparative genomic hybridization analysis following whole genome amplification. For RNA profiling, QPCR analysis was performed on sixty four (64) cancer-related genes using Taqman® low density arrays.

overall_design: Differential gene expression analysis between EpCAM-positive cells and matched leukocytes confirmed the up-regulation of EPCAM and other genes including MUC1 and KRT19 (adjusted p <0.05). In addition, EpCAM-positive cells showed a significant down-regulation of the leukocyte-specific marker PTPRC (encodes CD45) as well as CD44 and VIM, markers associated with stem cellness and epithelial to mesenchymal transition, respectively. Unsupervised hierarchical clustering analysis of RNA profiles showed that EpCAM-positive cells clustered away from the leukocytes. Genome-wide copy number analysis of EpCAM-expressing cells revealed gains (e.g. 1q and 8q), losses (e.g. 8p and 16q), and focal amplifications (e.g. on 8q and 11q including CCND1) frequently seen in primary breast cancers.

first: Janet

middle: H

last: Scott

first: Louai

last: Hauranieh

first: Adam

last: Olshen

first: Eduardo

middle: V

last: Sosa

first: Dan

last: Pinkel

first: Ritu

last: Roy

first: Hope

last: Rugo

first: Lauren

last: Eisenbud

first: John

middle: W

last: Park


title: Effect of human pulmonary MSCs isolated from normal and tumor tissues on the expression profile of primary lung cancer cells

status: Public on Mar 31 2018

city: LAUSANNE

first: Mathieu

last: Quinodoz

state: Vaud

address: Rue du Bugnon 27

department: DBC

country: Switzerland

institute: Université de Lausanne

summary: Metastasis is a multi-step process that involves direct cross-talk between cancer cells and their microenvironment. Here we assessed the effect of paired mesenchymal stem cells (MSCs) isolated from the tumor tissue (T-) and normal lung adjacent tissue (N-) on the expression profile of primary lung cancer cells. We observed that MSCs induce the expression of genes in tumor cells associated with an aggressive phenotype and promote early tumor cell dissemination. Our observations provide new insight into mechanisms whereby MSCs promote lung cancer metastasis.

overall_design: We obtained sphere-forming primary cell cultures of lung tumor from two patients (21 and 32) diagnosed with squamous cell carcinoma (SCC) and isolated MSCs from normal lung tissues (N-) and paired tumor tissues (T-) from the same patients or from patient 29, also diagnosed with SCC. To investigate the effect of pulmonary N- and T-MSCs on the expression profile of primary lung cancer cells, we performed indirect tumor-MSC cell co-cultures for 5 days. Tumor cells cultured alone were considered as control. Two independent experiments were done, one with paired MSCs, one with MSCs from patient 29. RNA from tumor cells in the different culture conditions was sequenced and the genes modulated in presence of MSCs identified. As the gene modulation following co-culture with paired MSCs or MSCs from patient 29 was similar, we considered them as replicates and data were pooled together in "+N-MSCs" and "+T-MSCs" groups for subsequent analysis of the two tumor samples.

first: Giulia

last: Fregni