title: DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells

first: Kendell

last: Clement

state: MA

address: 7 Divinity Ave.

institute: Harvard University

summary: Blastocyst-derived embryonic stem cells (ESCs) and gonad-derived embryonic germ cells (EGCs) represent two classic types of pluripotent cell lines, yet their molecular equivalence remains incompletely understood. Here, we compare genome-wide methylation patterns between isogenic ESC and EGC lines to define epigenetic similarities and differences. Surprisingly, we find that sex rather than cell type drives methylation patterns in ESCs and EGCs. Cell fusion experiments further reveal that the ratio of X chromosomes to autosomes dictates methylation levels, with female hybrids being hypomethylated and male hybrids being hypermethylated. We show that the X-linked MAPK phosphatase DUSP9 is upregulated in female compared to male ESCs, and its heterozygous loss in female ESCs leads to male-like methylation levels. However, male and female blastocysts are similarly hypomethylated, indicating that sex-specific methylation differences arise in culture. Collectively, our data demonstrate the epigenetic similarity of sex-matched ESCs and EGCs and identify DUSP9 as a regulator of female-specific hypomethylation.

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design: Genetically matched mouse EGC and ESC lines were collected for DNA methylation analysis via mRRBS

first: Jiho

last: Choi

first: Jamie

last: Webster

first: Patrick

last: Boyle

first: Alexander

last: Meissner

first: Konrad

last: Hochedlinger

first: Hongcang

last: Gu


title: Sequencing the DNA and mRNA from the same single cell

status: Public on Apr 11 2017

city: ShenZhen

first: Zhoufang

last: Li

address: No 1088,xueyuan Rd., Xili, Nanshan District,Shenzhen,Guangdong,China

department: Department of Biology

country: China

institute: SUSTech

type: Expression profiling by high throughput sequencing

summary: Single-cell genome and transcriptome data can address many questions, including somatic variation, meiotic recombination and cell-to-cell heterogeneity of expression, and techniques for single-cell sequencing have developed rapidly in recent years. Here, we further adapted this technology by performing simultaneous single-cell exome and transcriptome profiling on individual mouse oocytes. In brief, we physically separated the oocyte nuclei and cytoplasm using a micromanipulator. We then conducted exome-sequencing on the isolated nuclei and mRNA-sequencing on the enucleated cytoplasm. Combined analysis of the simultaneously derived sequencing data disclosed a high heterozygous recombination rate during oocyte meiosis, and genomic and transcriptomic heterogeneity among individual oocytes. This approach provides unprecedented opportunities to study RNA editing of single oocytes.

overall_design: Sequencing the DNA and mRNA from 6 single mouse secondary oocytes

first: Lily-Yan

last: Wang

first: Jiajie

last: Guo

first: Wei

last: Cao

first: Meng

last: Zhang

first: Jiankui

last: He


title: JunB is essential for IL-23-dependent pathogenicity of Th17 cells.

city: Onna-son,Kunigami-gun

first: Hiroki

last: Ishikawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To understand molecular mechanisms by which JunB regulates Th17 differentiation, we performed ChIP-seq analyses of JunB-deficient and control Th17 cells.

overall_design: ChIP-Seq analysis of JunB,IRF4,BATF in in vitro generated TH17(β) and TH17(23) cells.

first: Daiki

last: Sasaki

first: Nana

last: Arakaki

first: Shin-ichi

last: Koizumi


title: Nicotinana tabacum cv. K326 long day diurnal timecourse: Root, Shoot, Shoot Apex

city: Cambridge

first: Kieron

middle: David

last: Edwards

state: Cambridgeshire

address: GR&D Cambridge, 210 Cambridge Science Park

department: Plant Biotechnology

country: United Kingdom

institute: British American Tobacco

summary: Measurement of gene expression over a diurnal timecourse in different tissues of N.tabacum. The primary aim of the collection of this data was to validate predicted gene models in the associated publication

overall_design: 36 samples covering 3 tissues and 4 timepoints. Each in triplicate

middle: D

first: Jennifer

middle: R

last: Bromley

first: Alan

last: Evans

first: Matthew

middle: E

last: Humphry


title: Clustering of Drosophila housekeeping promoters facilitates their expression

city: Scarborough

first: Guillaume

middle: J

last: Filion

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: UTSC

summary: In this study, using thousands of reporters integrated in parallel in Drosophila Kc167 cells, we identify chromosome conformation as the main driver of position effects along chromosome arms.

overall_design: Barcoded libraries for different reporter-promoters were generated by PCR. The libraries were electroporated to 20 Million KC167 cells populations. After non-integrated plasmid dilution was achieved, DNA and RNA were extracted. DNA was used to map the integrated reporters, to normalize for barcode abundance and RNA to assess the level of expression of every single integrated reporter.

first: Arantxa

last: Rosado

first: Marc

last: Corrales

first: Ruggero

last: Cortini


title: Genome-wide analysis of the toxic effect of Bortezomib on human esophageal carcinoma epithelial cells

status: Public on Apr 10 2017

city: Suzhou

first: Ming

last: Li

address: No. 199 Ren'ai Road

institute: Soochow University

summary: The objective was to investigate the toxic effect of Bortezomib on human esophageal carcinoma epithelial cells at gene expression level. Gene expression profilings between Bortezomib and vehicle treated cells were compared.

overall_design: TE-1 cells were seeded in 10-cm dishes and treated with 150 nM Bortezomib and equivalent volume of vehicle in triplicate. After 24 hours of incubation, cells were harvested. Total RNA were extracted and subjected to gene expression profiling assays.

first: Geng

last: Liu


title: Uncovering novel roles for thyroid hormones in teleost fishes: Differential transcriptome regulation in brain and liver by 3,5-T2 and 3’,3,5-T3

city: Querétaro

first: Aurea

last: Orozco Rivas

state: Querétaro

address: Boulevard Juriquilla 3001

department: Neurobiología Celular y Molecular

country: Mexico

institute: Instituto de Neurobiología, UNAM

summary: We used a RNA-seq approach to determine the effect of 3,5-di-iodothyronine (T2) and 3,5,3'-tri-iodothyronine (T3) exogenous treatment on the transcriptome of tilapia (Oreochromis niloticus) liver, cerebellum, and thalamus-pituitary. We identified a total of 169, 154 and 2863 genes that were Thyroid hormone-regulated (FDR < 0.05) in tilapia cerebellum, thalamus-pituitary and liver, respectively. Among those, 130, 96 and 349 genes were uniquely regulated by T3, whereas 22, 40 and 929 were only regulated by T2 in the cerebellum, thalamus-pituitary and liver.

overall_design: Juvenile tilapia were treated by immersion protocol using these  conditions: 25 nM of T2 or T3 for 12 h of exposure (n = 2 individuals for liver samples and 2 biological replicates of a pool of 4 individuals for the brain regions samples). Transcriptome sequencing was conducted using Genome Analyzer GAIIx (Illumina). A configuration for pair-end reads with a 72 bp read length was used.

first: Aurora

last: Olvera

first: Veronica

last: Jiménez

first: Christopher

last: Martyniuk

first: Alejandro

last: Sánchez

first: Nicolas

last: Buisine

first: Laurent

last: Sachs

last: Orozco


title: Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

institute: University of Edinburgh

summary: RNA-binding proteins play a key role in shaping gene expression profiles during stress, however, little is known about the dynamic nature of these interactions and how this influences the kinetics of gene expression. To address this, we developed kinetic χCRAC, a UV cross-linking method that enabled us to quantitatively measure the dynamics of protein-RNA interactions in vivo on a minute time-scale. Here, using kinetic χCRAC we measure the global RNA-binding dynamics of the yeast transcription termination factor Nab3 in response to glucose starvation. These measurement reveal rapid changes in protein-RNA interactions within one minute following stress imposition. Changes in Nab3 binding are largely independent of alterations in transcription rate during the early stages of stress response, indicating orthogonal transcriptional control mechanisms. We also uncover a function for Nab3 in dampening expression of stress-responsive genes. Kinetic χCRAC has the potential to greatly enhance our understanding of in vivo dynamics of protein-RNA interactions.

overall_design: kinetic CRAC experiments performed on Nab3 and RNA polymerase II. Glucose to no glucose experiments were performed in duplicate.


title: TCF21 and Aryl-hydrocarbon receptor gene cooperate to activate a pro-atherosclerotic gene expression program

status: Public on Apr 12 2017

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

country: USA

institute: Stanford University

summary: Genome-wide association studies (GWAS) for coronary artery disease (CAD, also termed coronary heart disease, CHD) have discovered and validated 48 loci genome-wide and recent 1000-Genomes based meta-analyses have discovered additional 8 loci with significant association, however, true follow-up studies on the mechanisms of association are still scarce. Here we analyze the relationship of two transcription factors, TCF21, one of the lead GWAS candidate genes for coronary artery disease and AHR, aryl hydrocarbon receptor, which previously was not implicated as fundamental for the atherosclerotic process. We show that both the predicted and in-vivo ChIP-Seq binding sites for TCF and AHR colocalize in the human genome with over 400 predicted sites and 119 ChIP-Seq sites directly overlapping. TCF and AHR-ARNT predicted binding sites longitudinal phasing was observed near the transcription start sites, outlining the position of +1 nucleosome. AHR-ARNT matrix was highly enriched in both TCF21 ChIP-Seq peaks and ATAC-Seq open chromatin regions in human coronary artery smooth muscle cells (HCASMC), implicating the role of AHR in this important cell type for vascular biology. Co-expression modules of TCF21 and AHR showed high degree of connectivity. Separation of rotationally phased and unphased predicted binding sites for TCF and AHR resolved the roles of direct and indirect TCF-AHR interactions, and implicated as highly-modulated various inflammatory, interleukin and cytokine related processes, while ChIP-Seq co-localization of TCF21 and AHR/ARNT emphasized the role of calcium related processes. We performed TCF21 overexpression analysis in human coronary artery smooth muscle cells (HCASMC) and obtained GO ontologies that recapitulate in vivo pathophysiology of the atherosclerotic vessel wall, and a set of chronic inflammatory ontologies was established with the colocalization of TCF21 and AHR ChIP-Seq sites as well as with the binomial testing of GWAS SNP overrepresentation. We experimentally confirmed that TCF21 binds to and regulates AHR gene expression in HCASMC, as well as to elements near AHR downstream genes, such as CYP1A1, using reporter assays. The functional relevance of AHR pathway in HCASMC is confirmed using AHR ligands TCDD and oxidized LDL. Finally, we show that AHR is elevated in atherosclerotic arteries using laser capture microdissection in mice in vivo and in human ex vivo. In conclusion, we extend GWAS results to functional assays and show that TCF21 and AHR functional connectivity provides a novel mechanism for diseased coronary vessel wall biology.

overall_design:
[RNA-Seq] HCASMC: TCF21 overexpression and control.

The ChIP-Seq data are submitted under GSE61369 and the ATAC-Seq data are submitted under GSE72696.

first: Milos

last: Pjanic

first: Brian

last: Kim


title: RNA Analysis for Modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments, and its impact on gene expression

city: Antwerp

first: Hideo

last: Imamura

state: Antwerp

address: Nationalestraat 155

country: Belgium

institute: Institute of Tropical Medicine, Antwerp

summary:
Purpose: Monitor modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments, and its impact on gene expression
Importance: Aneuploidy is usually detrimental in multicellular organisms, but in several micro-organisms (fungi being the best-studied) it can be tolerated and even beneficial. Leishmania – a protozoan parasite killing more than 30,000 persons each year – is emerging as a new model for aneuploidy studies: unexpectedly high levels of aneuploidy are found in clinical isolates. Leishmania lacks classical regulation of transcription through inducible promoters, so aneuploidy could represent a major adaptive strategy of this parasite to modulate gene dosage in response to stressful environments. For the first time, we document the dynamics of aneuploidy throughout the life cycle of the parasite, in vitro and in vivo. We show its adaptive impact on transcription and its intertwinement with regulation. Besides offering a new model for aneuploidy studies, we show that further genomic studies should be done directly in clinical samples (without parasite isolation) and that adequate methods should be developed for this.

overall_design:
RNA profiles of Leishmania donovani strains in different environments.

ENA Study accession ERP017437 and BioProject accession PRJEB15610.

first: F

last: Dumetz

first: H

first: M

last: Sanders

first: J

last: Myskova

middle: A

last: Cotton

last: Berriman

first: P

last: Volf

middle: C

last: Dujardin

last: Domagalska


title: Etv4 and Etv5 binding sites in EpRas mouse mammary gland epithelial cell line [ChIP-seq]

city: Tokyo

first: Daizo

last: Koinuma

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

department: Pathology

institute: University of Tokyo

summary: We searched for roles of Etv4 and Etv5 during EMT through genome-wide analysis of their binding sites in Ras-transformed mammary gland epithelial cells.

overall_design: Etv4 and Etv5 binding sites in TGF-beta-stimulated EpRas cells were determined by ChIP-seq.

first: Mayu

last: Arase

first: Yusuke

last: Tamura

first: Natsumi

last: Kawasaki

first: Kazunobu

last: Isogaya

first: Ryo

last: Nakaki

first: Anna

last: Mizutani

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: Genome-wide analysis of histone modifications H3K27ac, H3K4me3, and H3K4me1 in migrating primary human epidermal keratinocytes (NHEK)

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

summary: The epidermis is a stratified squamous epithelium that serves to protect the body from dehydration, absorption of chemicals, and invasion of pathogens. It derives from the surface ectoderm during the later stages of mammalian embryonic development. In a stratified squamous epithelium cells of the basal layer contain proliferative potential. As they divide and move upward in the tissue, they progressively differentiate, and activate the gene expression program required to create a barrier; eventually, cells in the uppermost layer are sloughed off from the surface of the epidermis. This system requires continual replacement of differentiating cells from the basal layer. Such a process requires very precise regulation of gene expression to balance proliferation and differentiation and maintain a functioning epithelium. A number of transcription factors are known to be crucial to maintaining this balance; among these are p63, Notch, c-myc, Klf4, and Grhl3. These factors interact in a complex epidermal differentiation network, where the contributions of each factor provide balance and precision to the process of differentiation. When the epidermal barrier is breached due to wounding, a cascade of cytokines and other signaling molecules activate a wound healing program of gene expression, inducing everything from blood clotting, immune cell infiltration of the skin, regrowth of blood and lymph vessels, and the coordinated keratinocyte migration into the center of the wound followed by stratification, all of which is required to regenerate the lost tissue.

overall_design: ChIP experiments for histone modifications H3K27ac, H3K4me1, and H3K4me3 were performed on primary human epidermal keratinocyte cells that had been grown to 95% confluency and scratched with a pipet tip to induce migration, cells were collected for ChIP after 12 hours.

first: Rachel

middle: H

last: Klein


title: Rapid molecular profiling of defined cell types using viral TRAP

city: New York

first: Eric

middle: F

last: Schmidt

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Translational profiling methodologies enable the systematic characterization of cell types in complex tissues such as the mammalian brain, where neuronal isolation is exceptionally difficult. Here, we report a versatile strategy to profile CNS cell types in a spatiotemporally-restricted fashion by engineering a Cre-dependent adeno-associated virus expressing an EGFP-tagged ribosomal protein (AAV-FLEX-EGFPL10a) to access translating mRNAs by TRAP. We demonstrate the utility of this AAV to target a variety of genetically and anatomically defined neural populations expressing Cre recombinase and illustrate the ability of this viral TRAP (vTRAP) approach to recapitulate the molecular profiles obtained by bacTRAP in corticothalamic neurons across multiple serotypes. Furthermore, spatially restricting AAV injections enabled the elucidation of regional differences in gene expression within this cell type. Taken together, these results establish the broad applicability of the vTRAP strategy for the molecular dissection of any CNS or peripheral cell type that can be engineered to express Cre.

overall_design: Polysome-bound mRNAs from TRAP IPs were compared to whole tissue mRNAs. Data was collected from MCH neurons in hypothalamus using vTRAP, cortical layer 6 Ntsr1 neurons using vTRAP, and cortical layer 6 Ntsr1 neurons using bacTRAP. We include vTRAP data from three AAV serotypes for the cortical Ntsr1 cells. We collected three replicates for IP and inputs for vTRAP experiments, while bacTRAP data was collected in duplicate.

first: Alexander

last: Nectow

first: Jeffrey

middle: M

last: Friedman

first: Nathaniel

last: Heintz


title: Sap130 ChIP-seq on Mouse E12.5 heart

status: Public on Apr 13 2017

city: Pittsburgh

first: Cecilia

middle: W

last: Lo

state: PA

address: 530 45th St., 8120 Rangos Research Center

department: Developmental Biology

institute: University of Pittsburgh

summary: Congenital heart disease (CHD) is a prevalent birth defect affecting up to 1% of live births.  While a genetic etiology is indicated by increased recurrence risk and association with chromosomal abnormalities, the genetics of CHD is poorly understood and likely complex.  Here we show hypoplastic left heart syndrome (HLHS), a severe CHD with high morbidity/mortality, has a multigenic etiology.  Analysis of 8 HLHS mutant mouse lines recovered from a large-scale mutagenesis screen showed no mutations are shared in common. In the *Ohia* mouse line, mutations in 2 genes, *Pcdha9*/*Sap130*, act synergistically to cause HLHS. Cardiomyocyte proliferation and differentiation defects likely act in concert with valve abnormalities to cause HLHS.  Network analysis of mutations recovered in HLHS mice and 68 HLHS patients point to Notch signaling disruption, a pathway previously implicated in HLHS. These findings demonstrate large-scale mutagenesis is an effective systems approach for interrogating the complex genetics of human diseases.

overall_design: Examination of Sap130 targets in a mouse heart from E12.5, with 1 Sap130-antibody ChIP and 1 Input control.

first: Hisato

last: Yagi

first: Abha

middle: S

last: Bais


title: Cell Cycle-Targeting MicroRNAs as Therapeutic Tools Against Refractory Cancers

city: Beijing

first: Cheng

last: Li

address: No.5 Yiheyuan Road

institute: Peking University

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

overall_design: Refer to individual Series


title: Gene expression profiling of sensory epithelium of cochleas and vestibules of the inner ears of wild-type C57Bl/6J mice at post-natal day 0 (P0)

city: Tel Aviv

first: Karen

middle: B

last: Avraham

address: Levanon St.

department: Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

summary: The sensory epithelium of cochleas and vestibules of mice were compared. The two tissues are quite similar in structure, but have distinct roles in hearing and balance. By comparing their gene expression, we hoped to identify key regulators of differentiation.

overall_design: Cochlear and vestibular sensory epithelium was dissected from 20 inner ears of 10 P0 C57Bl/6J mice, generating 2.4 and 1.5 μg of total RNA, respectively. 450 ng RNA from each sample was used to create libraries with the TruSeq Stranded mRNA Sample Prep Kit (Illumina), followed by high-throughput sequencing at 100 bp paired end (PE) at the Technion Genome Center, Haifa, Israel. Six samples were generated, 3 cochlear and 3 vestibular, for sequencing in triplicate.

first: Kobi

last: Perl

first: Kathy

last: Ushakov

first: Ofer

last: Yizhar-Barnea

first: Yoni

last: Bhonker

first: Shaked

last: Shivatzki

first: Ron

last: Shamir


title: Appropriately Differentiated ARPE-19 Cells Regain a Native Phenotype and Similar Gene Expression Profile

city: Bethesda

first: Cynthia

last: Jawoski

state: MD

address: bldg 6, room 136

department: NEI

institute: NIH

summary: The retinal pigment epithelial (RPE) cell line ARPE-19 provides a widely-used alternative to native RPE. However, retention of the native RPE phenotype becomes problematic after multiple passages. We wished to determine if suitable culture conditions and differentiation could restore RPE-appropriate gene expression to ARPE-19. ARPE-19 cells at passages p9 to p12, grown in DMEM containing high glucose and pyruvate with 1% fetal bovine serum, were differentiated for up to 4 months. Using RNA-Seq, we compared the transcriptome of ARPE-19 cells kept in long-term culture with those cultured for 4 days. The 4 month cells developed the classic native RPE phenotype with heavy pigmentation. RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of genes in the 4 month cells. Of the 16,757 genes with detectable signals, nearly 2435 genes were upregulated, and 931 genes were down-regulated with a fold change differences of 2 or more. Genes characteristic of RPE, including RPE65, RDH5 and RDH10, were greatly increased in ARPE-19 cells maintained at confluence for 4 months. Comparison with microarray data sets from human primary cell lines revealed important overall similarities in expression of "signature" genes. The results of this study demonstrate that ARPE-19 cells can express genes specific to native human RPE cells when appropriately cultured, and thus, can provide a relevant system to study differentiated cellular functions of RPE in vitro.

overall_design: RNA-Seq profiles of ARPE-19 cells grown for 4 days or 4 months; triplicate replicates were sequenced.

first: William

last: Samuel

last: Jaworski

first: R

middle: K

last: Kutty

first: Todd

last: Duncan

first: Eugenia

last: Poliakov

first: Li

middle: X

last: Tan

first: Aparna

last: Lakkaraju

first: T

last: Redmond


title: Transcriptomic difference between the wild type red-fruited tomato and its yellow-fruited mutant

city: Shanghai

first: Lei

last: Gao

address: Dongchuan Road No. 800

institute: Shanghai Jiao Tong University

summary:
Background: Fruit color is an important quality trait for nutrition value in tomato (Solanum lycopersicum) and has attracted huge attention for a long time. In order to dissect the yellow-fruit color of a novel tomato mutant n3122, we compared the dynamic transcriptome of the fruit pericarps from the mutant n3122 and its wild type red-fruited tomato cultivar M82.

Results: The transcriptomes of fruits from M82 35 DPA (Days Post Anthesis), M82 47 DPA, M82 54 DPA, n3122 35 DPA, n3122 47 DPA, n3122 54 DPA and n3122 60 DPA were sequenced using an Illumina Hiseq 2000 sequencing platform. A total of 5568 differentially expressed genes (DEGs) were commonly identified in the four pairwise comparisons of M82_35 DPA vs n3122_35 DPA, M82_47 DPA vs n3122_47 DPA, M82_54 DPA vs n3122_54 DPA and M82_47 DPA vs n3122_60 DPA. Further Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that carotenoids biosynthesis, ethylene biosynthesis and signaling transduction, and transcription factors associated fruit ripening were different between M82 and n3122 which might be the underlying mechanisms for the yellow-fruit color of tomato.

Conclusions: This research provided a global data set of dynamic transcriptomic changes during fruit development and ripening for the wild type red-fruited tomato cultivar M82 and its yellow-fruited mutant n3122, and offered a base for elucidating the molecular mechanisms underlying tomato red/yellow fruit color mutation.

overall_design: Compareing transcriptomic difference between  the wild type red-fruited tomato and its yellow-fruited mutant

first: Lingxia

last: Zhao


title: Dynamics of chromatin accessibility during TGF-beta-induced EMT of Ras-transformed mammary gland epithelial cells

first: Daizo

last: Koinuma

summary:
This SuperSeries is composed of the SubSeries listed below.
Epithelial-mesenchymal transition (EMT) is induced by transforming growth factor (TGF)-beta stimulation and facilitates tumor progression. We here performed global mapping of accessible chromatin in the mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) using formaldehyde-assisted isolation of regulatory element (FAIRE)-sequencing (seq). We also searched for differentially expressed transcription factors by RNA-seq and found that Etv4, an ETS family oncogenic transcription factor, was strongly expressed in EpRas cells. Moreover, chromatin immunoprecipitation (ChIP)-seq showed that Etv4 bound to more than one-third of the accessible chromatin regions in EpRas cells treated with TGF-beta. We found by gene ontology analysis that genes encoding extracellular proteins are the most strongly down-regulated genes by Etv4 and Etv5 siRNAs. These findings suggest a mechanism of transcriptional regulation during TGF-beta-induced EMT that involves alterations of accessible chromatin.


title: FAIRE-seq analysis of Ras transformed mouse mammary gland epithelial cells transfected with Etv4 and Etv5 siRNAs and stimulated with TGF-beta.

summary: We performed global mapping of accessible chromatin in mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) using formaldehyde-assisted isolation of regulatory element (FAIRE)-sequencing (seq) to analyze the mechanisms of transcriptional regulation during TGF-beta-induced EMT.

overall_design: FAIRE-seq was perfomed using EpRas cells transfected with Etv4 and Etv5 siRNAs and stimulated with 1 ng/ml TGF-beta or left untreated for 4 days.

first: Mayu

last: Arase

first: Kazunobu

last: Isogaya

first: Ryo

last: Nakaki

first: Anna

last: Mizutani

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses

first: Liang

last: Liu

address: 1150 St. Nicholas Avenue

institute: Columbia University

summary: In this study, we performed integrative multi-omics studies to understand the complex mechanisms underlying UV photobiological effects. While H3K27ac and genetic mutations can both contribute to UV-induced transcriptomic changes, additional omics-based studies on other histone modifications, DNA methylation, and whole genome mapping of genetic mutations will provide a thorough understanding of UV-gene interactions in skin disease pathogenesis. The new UV target genes that we identified have important clinical implications in skin carcinogenesis..

overall_design: In this study, we performed RNA-Seq, Chip-Seq and Exome-seq studies to elucidate the molecular mechanisms underlying the photobiological effects of UV radiation on gene regulation in skin homeostasis

first: Yao

last: Shen


title: Dynamics of chromatin accessibility during TGF-beta-induced EMT of Ras-transformed mammary gland epithelial cells [FAIRE-Seq]

overall_design: FAIRE-seq was perfomed using EpH4 and EpRas cells stimulated with 1 ng/ml TGF-beta or left untreated for 8 days.


title: Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

city: Vienna

first: Roman

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

summary: We analysed the effect on the genomic localisation of cohesin (Stag1 and Scc1) and CTCF in CTCF, Smc3 and Wapl single depleted as well as CTCF Wapl double depleted mouse embryonic fibroblasts. Furthermore, we addressed the effect of CTCF and Smc3 depletion on gene expression as measured by RNA-Seq and the transcriptional activity in CTCF and Wapl double depleted cells by GRO-Seq.

overall_design: ChIP-Seq profiles of CTCF, H3K4me2, H3K9ac, Nipbl, Scc1, Stag1 in wild-type mouse embryonic fibroblasts (MEFs, E13.5d), CTCF, Smc3 and Wapl depleted or CTCF Wapl double depleted MEFs; mRNA-seq profiles of wild-type MEFs as well as CTCF and Smc3 depleted MEFs; GRO-seq profiles of wild-type MEFs as well as CTCF Wapl double depleted MEFs.

first: Georg

last: Busslinger

first: Petra

last: van der Lelij


title: Cell Cycle-Targeting MicroRNAs as Therapeutic Tools   Against Refractory Cancers [SW900 cells]

first: Cheng

last: Li

summary: Cyclins and cyclin-dependent kinases (CDKs) are hyperactivated in nearly all human tumor types. To identify new approaches for interfering with cyclins/CDKs, we systematically searched for microRNAs (miRNAs) regulating these proteins. We uncovered a group of miRNAs that target nearly all cyclins and CDKs, and demonstrated that these miRNAs are very effective in shutting off cancer cell expansion. By profiling the response of over 120 human cancer cell lines representing 12 tumor types to these cell-cycle-targeting miRNAs, we identified miRNAs particularly effective against triple-negative breast cancers and KRAS-mutated cancers. We also derived expression-based algorithm that predicts response of primary tumors to cell-cycle-targeting miRNAs. Using systemic administration of nanoparticle-formulated miRNAs, we halted tumor progression in seven mouse xenograft models, including three highly aggressive and treatment-refractory patient-derived tumors, without affecting normal tissues. Our results highlight the utility of using cell-cycle-targeting miRNAs for treatment of refractory cancer types.

overall_design: RNA-seq for SW900 cells transfected with 25 nM of miR-193a-3p mimic or 25 nM of negative miRNA control (Negative control #2, Ambion).

first: Per

last: Hydbring

first: Piotr

last: Sicinski


title: Transcriptomic changes in response to different carbon sources in Neurospora crassa

status: Public on Apr 09 2017

city: Berkeley

first: Yi

last: Xiong

state: California

address: 341A Koshland Hall

department: Plant and Microbial Bioloby

institute: UC berkeley

summary:
Purpose: We explore gene expression changes when Neurospora crassa wild type responds to different carbon sources in Vogel's medium.
Method: We obtained mRNA samples of Neurospora crassa WT in Vogel's minimal medium (VMM) with different carbon source and used RNA-seq technique to measure the trancriptome changes.
Results: We identified many genes of transcription factors and enzymes that were up regulated or down regulated in response to the different carbon stimulation.
Conclusion: Our data represents a systematic transcriptome profiling of filamentous fungi on different carbon source and identify COL-26 as a critical regulator in degradation of starch components.

overall_design: mRNA profiles of cultures of WT after 4 hours of exposure to media of interest were generated by deep sequencing, in triplicate, using Illumina HiSeq2000. Soluble carbon sources are 2 mM and insoluble carbon source are 2% (w/v).

first: Vincent

last: Wu

first: Igor

middle: V

last: Grigoriev

first: N

middle: L

last: Glass


title: Role of SMARCAD1 and H3R26Cit in Maintenance of the Naïve Pluripotent State

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Drive MC 0412

department: Bioengineering

institute: University of California, San Diego

summary: Genome-wide maps of SMARCAD1 binding and histone modification H3R26Cit in mouse ES cells, histone modification H3K9me3, H3K4me3, H3K27Ac in Smarcad1 KD mouse ES cells, and histone modification H3K9me3 in mouse ES cells after PADI inhibition. Together with RNA-seq data for mouse ICM, blastocyst, embryonic stem cells and Smarcad1 KD cells.

overall_design:
We used the strategies of ChIP-Seq to detect the epigenetic pattern of SMARCAD1 and H3R26Cit in E14 cells to describe the colocalization of the two.
We also used the strategies of ChIP-Seq to detect the epigenetic pattern in E14 and Smarcad1-knock down cells. Together with RNA-seq data for mouse ES cells, Smarcad1 KD cells, mouse ICM and blastocyst, we described the fuction of Smarcad1 in switch pluripotent states.

first: Shu

last: Xiao

first: Jia

last: Lu

first: Bharat

last: Sridhar

first: Xiaoyi

last: Cao

first: Tianyi

last: Zhao

first: Pengfei

last: Yu

first: Chieh-Chun

last: Chen

first: Darina

last: McDee

first: Laura

last: Sloofman

first: Yang

last: Wang

first: Marcelo

last: Rivas-Astroza

first: Bhanu

middle: P

last: Telugu

first: Dana

last: Levasseur

first: Kang

last: Zhang

first: Jing

first: Tetsuya

last: Tanaka

first: Gary

last: Stormo


title: A Fungal Transcription Factor Essential for Starch Degradation Regulates Primary Carbon and Nitrogen Metabolism and Amino Acid Biosynthesis

first: Yi

last: Xiong

summary:
Purpose: The ∆col-26 mutant cannot utilize starch components and many other simple sugars efficiently. We employed RNA-seq based transcriptome profiling to reveal genes under the control of col-26.
Method: We first obtained transcriptional data of Neurospora crassa WT on Vogel's minimal medium (VMM) without carbon source, on VMM with 2% sucrose, and on VMM with starch component, and transcriptional data of the ∆col-26 mutant on VMM with maltose or amylose.
Results: We identified a starch-regulon of 322 genes and found that 255 of the starch-regulon were down regulated in in absence of col-26. We also found that genes with functions in primary carbon and nitrogen metabolism and amino acid biosynthesis were also down regulated in the mutant.
Conclusion: Our data represents a systematic transcriptome profiling of filamentous fungi on different starch components and identify COL-26 as a critical regulator in both starch degradation and primary carbon and nitrogen regulation.

overall_design: mRNA profiles of cultures of WT and the ∆col-26 mutant after 4 hours of exposure to media of interest were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Vincent

last: Wu

first: Igor

last: Grigoriev

first: N

last: Glass


title: Modeling Trilateral Retinoblastoma using Human Embryonic Stem Cells

city: Jerusalem

first: Yishai

last: Avior

state: Israel

address: Edmond J. Safra Campus, Givat Ram

department: Genetics

institute: Hebrew University of Jeursalem

summary: Human embryonic stem cells (hESCs) provide a platform for understanding mechanisms underlying diseases and finding ways to treat them. Trilateral retinoblastoma (TRb) is a condition in which retinoblastoma, the most common congenital intraocular malignancy, is associated with an intracranial neural tumor. This mostly fatal disease is caused by biallelic inactivation of the retinoblastoma-1 (RB1) gene, transcribing pRB. Using CRISPR-Cas9 we generated RB1-null hESCs, an embryonic lethal condition. These cells display distinct gene expression patterns with alterations in pRB targets, and mitochondrial phenotypes similar to those of poorly differentiated retinoblastomas. RB1–/– hESC produce extremely large teratomas, with neural expansions similar to those of TRb tumors. Analysis of these tumors revealed a potentially novel role of pRB in ectoderm differentiation, acting through ZEB1. Lastly, RB1–/– cells are significantly sensitive to carboplatin, a chemotherapy used to treat TRb, suggesting our model can be used to screen novel treatments for the disease.

overall_design: Analysis of RB1–/– human embryonic cell lines and teratomas initiated from them

first: Nissim

last: Benvenisty


title: Dynamic Landscape of Alternative Polyadenylation during Retinal Development

city: Guangzhou

first: Zhi

last: Xie

address: 54 South Xianlie Road, Guangzhou, China

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

summary: The development of the central nervous system (CNS) is a complex process that must be exquisitely controlled at multiple levels to ensure the production of appropriate types and quantity of neurons. RNA alternative polyadenylation (APA) contributes to transcriptome diversity and gene regulation and has recently been shown to be widespread in the CNS. However, previous studies have been primarily focused on the tissue specificity of APA and developmental APA change of whole model organisms, a systematic survey of APA usage is lacking during CNS development. Here we conducted global analysis of APA during mouse retinal development, and identified stage-specific polyadenylation (pA) sites that are enriched for genes critical for retinal development and visual perception. Moreover, we demonstrated 3’UTR lengthening and increased usage of intronic pA sites over development that would result in gaining many different RBP (RNA binding protein) and miRNA target sites. Furthermore, we showed that a considerable number of polyadenylated lncRNAs are co-expressed with protein-coding genes involved in retinal development and functions. Together, our data indicate that APA is highly and dynamically regulated during retinal development and maturation, suggesting that APA may serve as a crucial mechanism of gene regulation underlying the delicate process of CNS development.

overall_design: PA-seq of mouse retina tissues at embryonic day E13.5, E15.5, E18.5 and postnatal day P0, P6, P21

first: Mengqing

last: Xiang


title: Transcriptome analysis of the shoot apical meristem (SAM) of WT tomato and the late termination (ltm) mutant

status: Public on Apr 08 2017

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

institute: Weizmann Institute of Science


title: Transcriptome of tung tree sees with emphasis on genes from lipid metabolism

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

summary: Tung oil, the major product of tung tree (Vernicia fordii) seeds, is one of the highest quality oils for industrial applications and has been considered to the production of biodiesel. Because of the poor agronomical traits of this crop, efforts have been made to breed tung tree for higher fruit yield and for modification of oil properties to be used as biodiesel, or to engineer higher yielding plants to produce tung oil. However, these efforts have been hampered by the lack of molecular information since there is no available genome and the identified and characterized transcripts of tung are scarce. Furthermore, there are still many knowledge gaps regarding tung oil biosynthesis. To provide a comprehensive and accurate foundation for molecular studies of tung tree, herein we present the reference transcriptome dataset of tung mature seeds. A set of 43,081,927 ESTs were assembled into 47,585 unigenes. The homology search using blastx against the GenBank non-redundant protein database and the Swiss-Prot database resulted in the annotation of 96 % and 81% of the unigenes, respectively. We also systematically arranged the series of transcripts potentially associated with oil biosynthesis and breakdown and examined the expression profile of a subset of those genes in samples from different stages of seed development, providing a valuable source of genes and transcriptional information related to these pathways. This study represents the first large-scale transcriptome annotation of tung tree seeds and will be useful to breed tung for oil properties and other agronomical traits.

overall_design: Transcriptome analysis in a mature seed library of Vernicia fordii by deep sequencing (Illumina HiSeq2000).

first: Vanessa

last: Galli

first: Frank

last: Guzman

first: Rafael

last: Messias

first: Ana

last: Körbes

first: Sérgio

middle: D

last: Silva

first: Márcia

last: Margis-Pinheiro

first: Rogério


title: Transcriptome analysis of the shoot apical meristem (SAM) of WT tomato and the late termination (ltm) mutant [exp2]

summary: Enlargement and doming of the shoot apical meristem (SAM) is a hallmark of the transition from vegetative growth to flowering. While this change is widespread, its role in the flowering process is unknown. The late termination (ltm) tomato mutant shows severely delayed flowering and precocious doming of the vegetative SAM. LTM encodes a kelch domain-containing protein, with no link to known meristem maintenance or flowering time pathways. LTM interacts with the TOPLESS (TPL) corepressor and with several transcription factors, providing specificity for its repressive functions. A sub-group of flowering-associated genes are precociously upregulated in vegetative stages of ltm SAMs, among them, the antiflorigen gene SELF PRUNING (SP). A mutation in SP restored the structure of vegetative SAMs in ltm sp double mutants and late flowering was partially suppressed, suggesting LTM functions to suppress SP in the vegetative SAM. In agreement, SP-overexpressing wild type plants exhibited precocious doming of vegetative SAMs combined with late flowering, as found in ltm plants. Strong flowering signals can result in termination of the SAM, usually by its differentiation into a flower. We propose that activation of a floral antagonist that promotes SAM growth in concert with floral transition protects it from such terminating effects.

overall_design: The tomato ltm mutant SAM was compared to WT SAM at the same vegetative stage. WT SAM at floral transition was compared to vegetative WT SAM. Experiments were done in two repeats for each condition.

first: Lior

last: Tal

first: Yuval

last: Eshed


title: Transcriptome analysis of the shoot apical meristem (SAM) of WT tomato and the late termination (ltm) mutant [exp1]


title: Quantitative Analysis of cortical transcriptomes through Next Generation Sequencing from wild-type mice, wild-type mice treated with IL1b, IL-1R8-/-  mice and IL-1R8-/- mice treated with IL1b antagonist Anakinra

city: San Joan d'Alacant

first: Jose

last: Lopez-Atalaya

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias

country: Spain

institute: CSIC-UMH

summary:
Quantitative Analysis of cortical transcriptomes through Next Generation Sequencing (RNA-Seq) from wild-type mice, wild-type mice treated with IL1b (200 ng/mouse, 14h), IL-1R8-/-  mice and IL-1R8-/- mice treated with IL1b antagonist Anakinra (25 mg/kg per day for 3 consecutive days, i.p. administration).
mRNA profiles of cortical tissue from adult wild-type mice, wild-type mice treated with IL1b (200 ng/kg, 14h), IL-1R8-/- mice (Garlanda et al., 2004), and IL-1R8-/- mice treated with Anakinra (25 mg/kg per day for 3 consecutive days, i.p. administration) were generated by next-generation sequencing (RNA-seq) using Illumina HiSeq 2500 apparatus in paired-end configuration (2x125bp). Each condition was assessed in triplicate (12 mRNA-seq libraries) and, to reduce biological variability, each mRNA library was generated from pooled total RNA isolated from cortical tissue of 3 individual mice. In total, 9 mice per condition were used. Libraries were stranded and multiplexed. To increase sequencing depth, libraries were sequenced in two different lanes. All the libraries were loaded in each of the two lanes. Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Libraries were trimmed for adapter removal using Trimmomatic (Bolger et al., 2014) and mapped to reference genome (Ensembl GRCm38) using TopHat2 (Kim et al., 2013) and Bowtie2 (Langmead et al., 2009). Library sizes of primary mapped reads were between 70 and 96 million reads. Samtools was used to manipulate BAM files (Li et al., 2009). For calling of differentially expressed genes (DEG), mapped reads were counted with HTSeq v0.6.1 (Anders et al., 2014) and count tables were analysed using DeSeq2 v1.10.1 R-package (Love et al., 2014) with a design of one factor with four levels (“wild-type”, “wild-type + IL1”, “IL-1R8-/-”, “IL-1R8-/- + Anakinra"), and differences between groups were tested using contrasts for wild-type + IL1b versus wild-type; IL-1R8-/- versus wild-type; IL-1R8-/- + Kineret versus wild-type. For consideration of differentially regulated genes between conditions, we used adjusted p-value < 0.1 or adjusted p-value < 0.05 as indicated in the manuscript.

overall_design: mRNA profiles in adult mouse cerebral cortex of wild type (WT), WT mice treated with IL1b (200 ng/kg, 14h), IL-1R8-/- mice, and IL-1R8-/- mice treated with IL1b antagonist Anakinra (25 mg/kg per day for 3 consecutive days, i.p. administration) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. Each sample was prepared by pooling cortical tissue from 3 idenpendent mice.

first: Romana

last: Tomasoni

first: Angel

last: Barco

first: Michela

last: Matteoli


title: Transcriptional deregulation in EZH2-deficient lymphocyte progenitors

status: Public on Apr 07 2017

city: Chicago

first: Barbara

last: Kee

state: Illinois

address: 924 E57th st

institute: The University of Chicago

summary: This goal of this study was to identify genes that are deregulated in the absence of EZH2 in early lymphocyte progenitors.  We examined gene expression by RNA-sequencing in sorted CLPs (Lin-CD117int CD127+ CD135+), pro-B cells (B220+CD19+CD43+), DN3 cells (Lin- CD25+ CD117-), splenic NK cells (Lin-NK1.1+DX5+) and bone marrow ILC2 cells (Lin- Sca1+CD127+) from Ezh2fl/fl Il7racre/+  and Il7racre/+ control mice.  Reads were aligned to the mm10 reference genome by Tophat2.1.0.   Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78.   Differential expression was calculated across 2-3 independent replicates by EdgeR.  We found that CLPs, ILC2s, and splenic NK cells maintained their normal transcriptional programs despite loss of EZH2.  In contrast, loss of EZH2 caused over 1000 genes to be deregulated in pro-B and DN3 cells indicating that EZH2 is required for transcriptomic stability in adaptive, but not innate lymphocyte progenitors.

overall_design: Expression profiling analysis of CLPs, pro-B, DN3, splenic NK, and ILC2 in Ezh2fl/fl Il7racre/+ mice and Il7racre/+ controls generated by RNA-sequencing. 2-3 independent replicates per sample.

first: Jennifer

last: Jacobsen

first: Mikael

last: Sigvardsson

first: Elizabeth

last: Bartom


title: The role of Ng2/Cspg4 in soft tissues sarcoma

city: Durham

first: Claire

last: Hsu

address: 305 research drive

institute: Duke University

summary: NG2/CSPG4 is expressed in soft tissue sarcomas, however, its function in this tumor type, and its capacity to serve as a therapeutic target are unknown. Here, we used genetically engineered mice and cells from human tumors to determine the function of Ng2/Cspg4 in soft tissue sarcoma initiation and growth.  We also investigated the potential for NG2/CSPG4 mAb immunotherapy to target human sarcomas established as xenografts in mice. Inhibiting Ng2/Cspg4 expression in established soft tissue sarcomas is associated with a smaller tumor volume and a reduction in cell proliferation. Intriguingly, deleting Ng2/Cspg4 at the time of tumor initiation has the opposite effect. Gene profiling found that Igfbp3/5 are substantially downregulated when Ng2/Cspg4 is depleted at the time of tumor initiation, but upregulated or only minimally downregulated when Ng2/Cspg4 is depleted after tumor initiation. Furthermore, the normal regulation of Igfbp is blunted when Ng2/Cspg4 is deleted at the time of tumor initiation. Our data show a difference in NG2/CSPG4 function in tumor initiation and maintenance, and provides pre-clinical evidence supporting NG2/CSPG4 as a therapeutic approach in soft tissue sarcoma.

overall_design: RNA samples isolated from 2 tumors derived from KrasG12D/+; p53f/f; Ng2/Cspg4f+/+ mice and 3 tumors derived from KrasG12D/+; p53f/f; Ng2/Cspg4f/f mice were used for RNA-seq analysis

first: Shu-Hsuan

first: Benjamin

last: Alman


title: Translational contributions to tissue-specificity in rhythmic and constitutive gene expression

city: Lausanne

first: David

last: Gatfield

address: Genopode

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary:
BACKGROUND: The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We have used ribosome profiling to explore the contribution of translation efficiency to temporal gene expression in kidney, and contrasted our findings with liver data available from the same mice.

RESULTS: Rhythmic translation of constantly abundant mRNAs affects largely nonoverlapping transcript sets with distinct phase clustering in the two organs. Moreover, tissue differences in translation efficiency modulate the timing and amount of protein biosynthesis from rhythmic mRNAs, consistent with organ-specificity in clock output gene repertoires and rhythmicity parameters. Our comprehensive datasets provided insights into translational control beyond temporal regulation. Between tissues, many transcripts show differences in translation efficiency, which are, however, of markedly smaller scale than mRNA abundance differences. Tissue-specific changes in translation efficiency are associated with specific transcript features and, intriguingly, globally counteracted and compensated transcript abundance variations, leading to higher similarity at the level of protein biosynthesis between both tissues.

CONCLUSIONS: We show that tissue-specificity in rhythmic gene expression extends to the translatome and contributes to define the identities, the phases and the expression levels of rhythmic protein biosynthesis. Moreover, translational compensation of transcript abundance divergence leads to overall higher similarity at the level of protein production across organs. The unique resources provided through our study will serve to address fundamental questions of post-transcriptional control and differential gene expression in vivo.

overall_design: A total of 48 mice were entrained under 12hours light:dark conditions for 2 weeks and also collected under 12hours light:dark. Mice were sacrificed every two hours during the 24 hours daily cycle. Two replicates per time point, each replicate is a pool of livers or kidneys from 2 animals.

first: Violeta

last: Castelo-Szekely

first: Alaaddin

last: Arpat

first: Peggy

last: Janich


title: Ribosome profiling study of eIF5A depletion strain

city: Frederick

first: Colin

last: Wu

department: RNA Biology Laboratory

institute: NCI

summary: The eukaryotic translation factor eIF5A, originally identified as an initiation factor, was later shown to promote translation elongation of iterated proline sequences. Using a combination of ribosome profiling and in vitro biochemistry, we report a much broader role for eIF5A in elongation and uncover a substantial function for eIF5A in termination. Ribosome profiling of an eIF5A-depleted strain reveals a global elongation defect, with abundant ribosomes stalling at many sequences, not limited to proline stretches. Our data also show accumulation at stop codons and in the 3’-UTR, suggesting a global defect in termination in the absence of eIF5A. Using an in vitro reconstituted translation system, we find that eIF5A strongly promotes the translation of novel stalling sequences and increases the rate of peptidyl-tRNA hydrolysis more than 17-fold. We conclude that eIF5A functions broadly in elongation and termination, rationalizing its great cellular abundance and essential nature.

overall_design: 8 biological samples are included in the study (8 ribosome footprinting samples). These include wild-type and eIF5A depletion strains (with biological replicates). Also included are ribosome footprint profiling after high salt treatment.

first: Rachel

last: Green


title: Extensive rewiring of the Calcineurin-Crz1 stress response network in the human fungal pathogen Cryptococcus neoformans

first: Joshua

middle: Aaron

last: Granek

state: NC

address: Box 3568, 213 Research Drive

department: Department of Biostatistics and Bioinformatics

institute: Duke University School of Medicine

summary: Calcineurin is a highly conserved Ca2+/calmodulin-dependent serine/threonine-specific protein phosphatase that orchestrates cellular Ca2+ signaling responses. In Cryptococcus neoformans, calcineurin is activated by multiple stresses including high temperature, and is essential for stress adaptation and virulence. The transcription factor Crz1 is a major calcineurin effector in Saccharomyces cerevisiae and other fungi. Calcineurin dephosphorylates Crz1, thereby enabling Crz1 nuclear translocation and transcription of target genes. Here we show that Crz1 is dephosphorylated by calcineurin, and crz1Δ mutants display phenotypes intermediate between wild-type and calcineurin mutants. RNA-sequencing revealed 102 genes that are regulated in a calcineurin/Crz1-dependent manner at 37°C.  99 genes were down-regulated in cna1Δ and crz1Δ mutants, indicating these genes are normally activated by the calcineurin/Crz1 pathway at high temperature. About 58% of calcineurin-Crz1 target genes have unknown functions, while genes with known or predicted functions are involved in cell wall remodeling, calcium transport, and pheromone production.  Surprisingly, only five genes have orthologs known to be calcineurin/Crz1-dependent in S. cerevisiae. 393 genes are independently regulated by calcineurin, and Crz1 regulates 59 genes independently of calcineurin. Taken together, these results indicate that the calcineurin/Crz1-dependent pathway controls a transcriptional circuit that has been extensively rewired in C. neoformans compared to S. cerevisiae. Given the intermediate crz1Δ mutant phenotype, and our recent evidence for a calcineurin regulatory network impacting mRNA in P-bodies and stress granules independently of Crz1, calcineurin likely acts on factors beyond Crz1 that govern mRNA expression/stability to operate a branched transcriptional/post-transcriptional stress response network necessary for fungal virulence.  Taken together, our findings reveal the core calcineurin-Crz1 stress response cascade is maintained from ascomycetes to a pathogenic basidiomycete fungus, but its output has been extensively rewired to promote fungal virulence.

overall_design: mRNA expression profiles of Cryptococcus neoformans of WT, cna1Δ, crz1Δ, and knockout-complemented strains in the H99 background, grown at 24C and 37C (temperature stress).


title: The Biotagging toolkit for analysis of specific cell populations in zebrafish reveals gene regulatory logic encoded in the nuclear transcriptome

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

summary: Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types, as well as robust methods for tissue-specific labeling and biochemical profiling of target proteins. By exploiting multiple transgenesis strategies, we have developed a tissue-specific binary in vivo biotinylation system in zebrafish termed "biotagging", a versatile methodology that uses genetically-encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. Using tissue-specific transgenic drivers and individual cell compartment effector lines from our "biotagging" toolkit, we demonstrate the specificity of our approach at the biochemical, cellular and transcriptional levels. By characterizing the in vivo transcriptional landscape of migratory neural crest and myocardial cells in two different cellular compartments (ribosomes and nucleus), we identify a comprehensive network of protein-coding and non-coding RNAs and uncover cis-regulatory modules and regulatory logic conferring cell-specific identity, embedded in the complexity of the non-coding nuclear transcriptomes. Our study demonstrates that "biotagging" eliminates background inherent to complex embryonic environments and allows analyses of molecular interactions in any cellular context at highest resolution.

overall_design: Examination of RNA-seq and ATAC-seq using in vivo biotinylated nuclei and polysomes.

first: Le

last: Trinh

first: Vanessa

last: Chong

first: Daria

last: Gavriouchkina

first: Tatiana

last: Hochgreb-Hagele

first: Upeka

last: Senanayake

first: Scott

middle: E

last: Fraser


title: PRC2 represses transcriptionally competent genes on the inactive X-chromosome

city: Ann Arbor

first: Emily

last: Maclary

state: MI

address: 1241 Catherine St., 3710 Med Sci-II

department: Human Genetics

institute: University of Michigan

summary: Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which characterizes many silenced genes including those on the inactive X-chromosome.  Here we interrogate the role of core PRC2 protein EED in X-linked gene silencing by assessing allele-specific X-linked gene expression in WT and Eed-/- hybrid mouse trophoblast stem cells (TSCs) harboring a 129/S1-derived maternal X-chromosome and a JF1/Ms-derived paternal X-chromosome. This study generates mRNA-seq data for WT and Eed-/- TSCs, which undergo imprinted inactivation of the paternal X-chromosome. RNA-seq data was mapped allele-specifically to in silico strain-specific maternal and paternal reference genomes, generated based on known single nucleotide polymorphisms. We find that EED loss abrogates H3K27me3 and expression of Xist lncRNA, which is required for X-inactivation, however, despite the absence of H3K27me3 and Xist, only a subset of PRC2 target genes are derepressed in Eed-/- TSCs.

overall_design: RNA-seq profiles of four WT (Eed +/+ and Eed fl/fl) and three EED null (Eed -/-) female TS cell lines were generated through strand-specific 100 bp paired-end sequencing on the Illumina HiSeq2000

first: Sundeep

last: Kalantry


title: Genome-wide analysis of the differentially expressed genes between a butanol-producing wild type strain and a pykA mutant during fermentation

city: Beijing

first: Chunhua

last: Zhao

address: No.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: To analyze the change of transcription pattern and differentially expressed genes caused by pykA inactivation as the pykA mutant showed a longer growth cycle, increased butanol titer and less pyruvate accumulation. Some new target genes may be used for further metabolic engineering.

overall_design: The total RNA of strain EB216 and EB216-∆pykA (EB222) was isolated in different time points in the fermentation process at 6 h, 12 h, 24 h, and 48 h. Samples of strain EB216 were used as control samples for strain EB216-∆pykA at the respective time. Illumina Hiseq2000 platform was employed for RNA-Seq.

first: Zhao

last: Lin

first: Hongjun

last: Dong

first: Yanping

last: Zhang

first: Yin

last: Li


title: Transcriptome changes during the differentiation of myoblasts into myotubes

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

summary: This study aimed to interrogate the interrelationship between 3D genome organization and global gene expression during muscle development using a mouse C2C12 cell line as an in vitro model. The C2C12 cell line is a well-established and extensively studied in vitro model derived from serial passage of myoblasts cultured from the thigh muscle of C3H mice after a crush injury. C2C12 cells divide when mitogens are present in the culture medium and spontaneously differentiate into muscle-like multinucleated (myotubes) cells if the medium is depleted of mitogens (i.e. serum; (Bischoff 1986)). C2C12 cells were either harvested as: 1) proliferating myoblasts (Myoblasts); 2) myotubes that were not treated with AraC (as such these myotubes contained myoblasts) - Myotubes(Day3); or 3) myotubes which were treated with AraC (myoblasts were largely depleted from these myotube cultures; Myotubes(Day7+AraC).

overall_design: RNA-seq of myoblasts, myotubes that were not treated with AraC (Day3) and myotubes which were treated with AraC (Day7). Two replicates per sample type.

first: J

last: O’Sullivan

first: M

last: Doynova

first: David

last: Cameron-Smith

last: Markworth


title: MicroRNA Expression Profiling in Porcine Muscle Identifies a Role for miR-27 in Mediating MYH7 Expression

first: Liu

last: Yihua

address: Wushan street, Tianhe

institute: South China Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Solexa/Illumina deep sequencing was used to obtain miRNA transcriptome profiles for control (basal diet, 14.49% crude protein, 13.73 MJ/kg digestible energy, 0.86% available lysine) and traditional Chinese medicine formula (basal diet+2.5 g/kg traditional Chinese medicine formula) groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis was performed using DAVID functional annotation to identify the biological process function of the miRNAs identified as being involved in muscle fiber regulation. We detected 269 mature miRNAs and 14 pre-miRNAs in the porcine muscle samples, of which 211 were previously unreported. Pathway analyses suggested that several independent signaling pathways were involved in the biological process, cellular component, and molecular function categories, with metabolic pathways showing the most enrichment and including some pathways involved in the regulation of muscle fiber phenotype such as mitogen-activated protein kinase (MAPK), mammalian target of rapamycin, and citrate cycle signaling pathways. Thirty-seven miRNAs exhibited normalized expression of over 10,000 reads per million, accounting for 85.91% of the overall counts of the total porcine mature miRNAs. Among these, 9 were muscle-related miRNAs involved in muscle development, including skeletal satellite cell (ssc)-miR-133a-3p, ssc-miR-486, ssc-miR-26a, ssc-miR-21, ssc-miR-1, ssc-miR-10b, ssc-miR-181a, ssc-miR-128, and ssc-miR-23a. In particular, miR-1 and miR-133 are muscle-specific miRNAs, termed myomiRs, which play an important role in muscle differentiation and development. Furthermore, porcine skeletal satellite cell transfection experiments indicated that overexpression or inhibition of ssc-miR-27a repressed or increased, respectively, MYH7 gene and protein expression through the PGC-1-MEF2C pathway, suggesting that miR-27a participated in the regulation of muscle fiber in skeletal muscle. In conclusion, these miRNAome profiles provide novel insight into the mechanism underlying muscle fiber regulation.

overall_design: To better understand the mechanism attributed to microRNA (miRNA) regulation of muscle fiber type transition, this study examined the miRNAs that regulate muscle fiber type after porcine dietary treatment using miRNA profiling.

first: Yihua

last: Liu

first: Jianjun

last: Zuo


title: RNA-sequencing of EpH4 and EpRas cells treated with Etv4 and Etv5 siRNAs and/or TGF-beta.

city: Tokyo

first: Daizo

last: Koinuma

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

institute: University of Tokyo

summary: We performed RNA-seq analysis in mouse mammary gland epithelial EpH4 cell line and its Ras-transformed derivative (EpRas) to analyze the mechanisms of transcriptional regulation during TGF-beta-induced EMT.

overall_design: RNA-seq was perfomed using EpH4 and EpRas cells transfected with Etv4 and Etv5 siRNAs and stimulated with 1 ng/ml TGF-beta or left untreated for 48 h.

first: Mayu

last: Arase

first: Yusuke

last: Tamura

first: Natsumi

last: Kawasaki

first: Kazunobu

last: Isogaya

first: Ryo

last: Nakaki

first: Anna

last: Mizutani

first: Shuichi

last: Tsutsumi

first: Hiroyuki

last: Aburatani

first: Kohei

last: Miyazono


title: Gene expression analysis (RNA-seq) of Arabidopsis thaliana roots in wild type and trm4b-1 mutants under control and oxidative stress conditions

city: Adelaide

first: Alice

middle: Louise

last: Burgess

state: SA

address: Frome road

department: Genetics and Evolution

country: Australia

institute: University of Adelaide

summary: To investigate why Arabidopsis trm4b mutants have short roots and increased sensitivity to oxidative stress, we investigated gene expression in wild type and trm4b-1 mutants under control and oxidative stress conditions

overall_design: RNA-seq analysis was performed on wild type and trm4b-1 mutants under controlled conditions and under oxidative stress (0.01 uM paraquat). Three biological replicates were performed for each sample.

first: Rakesh

last: David

first: Iain

middle: R

last: Searle


title: Transcriptome-wide RNA 5-methylcytosine methylation in roots of Arabidopsis thaliana

type: Methylation profiling by high throughput sequencing

summary: Here we use bisulfite conversion of rRNA depleted RNA combined with high-throughput Illumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites transcriptome-wide in Arabidopsis thaliana roots. m5C sites were analyzed in wild type (WT) and an Arabidopsis T-DNA KO mutant for the RNA methyltransferase TRM4B.

overall_design: RNA bisulfite sequencing was used to identify candidate m5C sites transcriptome-wide in Arabidopsis thaliana roots, using rRNA depleted RNA. Illumina sequencing was performed on a HiSeq platform. The two genotypes used are wild type and trm4b-1. All genotypes have three biological replicates with one technical replicate for each biological replicate.


title: Transcriptome-wide RNA 5-methylcytosine methylation in siliques of Arabidopsis thaliana

summary: Here we use bisulfite conversion of rRNA depleted RNA combined with high-throughput Illumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites transcriptome-wide in Arabidopsis thaliana siliques. m5C sites were also analyzed in an Arabidopsis T-DNA knockout for the RNA methyltransferase TRM4B.

overall_design: RNA bisulfite sequencing was used to identify candidate m5C sites transcriptome-wide in Arabidopsis thaliana siliques, using rRNA depleted RNA. Illumina sequencing was performed on a HiSeq platform. The two genotypes used are wild type and trm4b-1. For wild type (WT) there are two biological replicates. The first biological replicate for wild type siliques has only one technical replicate, while there are two technical replicates for the second wild type biological replicate. There are three biological replicates for trm4b-1


title: Effect of PKN1 inhibition on androgen responsive genes.

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: To study and compare the effect of siRNA-mediated PKN1 silencing and CEP701-mediated PKN1 inhibition on androgen-responsive genes.

overall_design:
1. Human LNCaP prostate cancer cells were transfected with siRNA SmartPools targeting PKN1 or a non-targeting siRNA SmartPool.  Forty hours after transfection, cells were treated with synthetic androgen R1881 (5nM) or vehicle.  Three biological replicates were generated per treatment group.  Forty-eight hours later, total RNA was isolated and processed for RNA-Seq analysis.
2. Human LNCaP prostate cancer cells were treated with synthetic androgen R1881 (5nM) or vehicle and CEP701 (50nM) or DMSO.  Three biological replicates were generated per treatment group.  Forty-eight hours later, total RNA was isolated and processed for RNA-Seq analysis.
PRJNA380418

first: Hannelore

last: Heemers

first: Song

first: Varadha

last: Venkadakrishnan


title: Transcriptome-wide RNA 5-methylcytosine methylation in siliques, shoots and roots and root gene expression profiling of Arabidopsis thaliana

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

overall_design:
Refer to individual Series

The SuperSeries record includes the processed data for GSE80050, GSE80051 and GSE80052. Processed data for GSE80053 is available on the GSE80053 record.


title: Linkages between 3D genome organization and transcriptome during muscle cell development

first: Justin

last: O'Sullivan

summary: This study aimed to interrogate the interrelationship between 3D genome organization and global gene expression during muscle development using a mouse C2C12 cell line as an in vitro model. The C2C12 cell line is a well-established and extensively studied in vitro model derived from serial passage of myoblasts cultured from the thigh muscle of C3H mice after a crush injury. C2C12 cells divide when mitogens are present in the culture medium and spontaneously differentiate into muscle-like multinucleated (myotubes) cells if the medium is depleted of mitogens (i.e. serum; (Bischoff 1986)).

overall_design: C2C12 cells were either harvested as: 1) proliferating myoblasts (Myoblasts); 2) myotubes that were not treated with AraC (as such these myotubes contained myoblasts) - Myotubes(Day3); or 3) myotubes which were treated with AraC (myoblasts were largely depleted from these myotube cultures; Myotubes(Day7+AraC).

first: J

last: O’Sullivan

first: M

last: Doynova

first: David

last: Cameron-Smith

last: Markworth


title: Gene expression in tissues from an immune challenged adult sea urchin (Strongylocentrotus purpuratus)

status: Public on Apr 06 2017

city: Washington

first: Katherine

middle: Michele

last: Buckley

state: DC

address: 800 22nd St NW

department: Department of Biological Sciences

institute: The George Washington University

summary: To induce an immune response, a single adult animal was injected intracoelomically with complex microbiota isolated from the gut of another adult animal (4.8 × 10^6 total bacteria). After 12 hours, phagocytic coelomocytes and gut tissue were collected for RNA-Seq experiments.

overall_design: A single immune-challenged animal was the source of the two tissues analyzed for gene expression (coelomocytes and gut).

first: Jonathan

last: Rast


title: Domestic chickens activate a piRNA defense against avian leukosis virus

city: Rochester

first: Xin

last: Li

address: 601 Elmwood Ave.

department: Biochemistry and biophysics

institute: University of Rochester Med Center

summary: PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry. Domestic fowl produced piRNAs targeting ALV from a genomic locus that was known to render its host ALV resistant. This genomic locus does not produce piRNAs in undomesticated wild chickens. Our findings uncover rapid piRNA evolution reflecting contemporary TE activity, identify a new piRNA acquisition modality by activating a pre-existing genomic locus, and extend piRNA defense roles to include the period when endogenous retroviruses are still infectious.

overall_design: Ribosome profiling and RNA sequencing of rooster testes

middle: Z

first: Yu

middle: H

last: Sun


title: Gene and transcript expression in a G1S Cell Cycle Phase Marker (G1S-CCPM) recombinant U2OS cell line that stably expresses the Cas9 nuclease from a CAG promoter

city: Lafayette

first: Matthew

last: Perkett

state: CO

address: 2650 Crescent Drive Suite 100

institute: Dharmacon, GE Healthcare

summary: The purpose of this experiment is to determine the gene/transcript expression levels in the G1S-CCPM-Cas9 cell line to help interpret gene editing experiments.

overall_design: Two replicate samples were sequenced from the G1S-CCPM-Cas9 cell line

first: Žaklina

last: Strezoska

first: Anja

last: van Brabant Smith


title: Novel BET protein Proteolysis Targeting Chimera (BET-PROTAC) exerts superior lethal activity than Bromodomain Inhibitor (BETi) against post-myeloproliferative Neoplasm (MPN) Secondary (s) AML Cells

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

summary: The PROTAC (proteolysis-targeting chimera) ARV-825 recruits bromodomain and extraterminal (BET) proteins to the E3 ubiquitin ligase cereblon, leading to degradation of BET proteins, including BRD4. Whereas the BET-protein inhibitor (BETi) OTX015 caused accumulation of BRD4, treatment with equimolar concentrations of ARV-825 caused sustained and profound depletion (>90%) of BRD4 and induced significantly more apoptosis in cultured and patient-derived (PD) CD34+ post-MPN sAML cells, while relatively sparing the CD34+ normal hematopoietic progenitor cells. RNA-Seq, Reversed Phase Protein Array and mass cytometry ‘CyTOF’ analyses demonstrated that ARV-825 caused greater perturbations in mRNA and protein expressions than OTX015 in sAML cells. Specifically, compared to OTX015, ARV-825 treatment caused more robust and sustained depletion of c-Myc, CDK4/6, JAK2, pSTAT3/5, PIM1 and Bcl-xL, while increasing the levels of p21 and p27. Compared to OTX015, PROTAC ARV-771 treatment caused greater reduction in leukemia burden and further improved survival of NSG mice engrafted with luciferase-expressing HEL92.1.7 cells. Co-treatment with ARV-825 and JAK inhibitor ruxolitinib was synergistically lethal against the established and PD-CD34+ sAML cells. Notably, ARV-825 induced high levels of apoptosis in the in vitro generated ruxolitinib-persister or ruxolitinib-resistant sAML cells. These findings strongly support the in vivo testing of the BRD4-PROTAC based combinations against post-MPN sAML.

overall_design: SET2 cells (biologic triplicates for control and ARV-825; biologic duplicates for OTX015-treated cells) and patient-derived, post-MPN secondary AML cells (biologic replicates).

middle: N

first: Warren

last: Fiskus


title: Role of CRP K100 positive charge on Escherichia coli global transcriptome

city: Maywood

first: Alan

middle: J

last: Wolfe

department: Microbiology and Immunology

institute: Loyola University - Chicago

summary: We hypothesized that the positive charge of CRP K100 is important for transcription of Class II CRP-dependent genes. These data show mutations that affect K100 charge status result in genome-wide changes in transcription of both CRP-dependent and -independent genes.

overall_design: Total RNA obtained from E.coli strains overexpressing WT CRP or a K100 variant (K100Q or K100R) grown in tryptone broth buffered to pH 7 (TB7) supplemented with 22 mM glucose. A strain overexpressing an AR1-/AR2- variant was used as a negative control.

first: Gina

last: Kuffel


title: Identify novel muscle fusogenic factors for reconstitution of plasma membrane fusion in non-fusogenic cells

city: Cincinnati

first: Douglas

last: Millay

state: OH

address: 240 Albert Sabin Way  MLC 7020

institute: Cincinnati Children's Hospital Medical Center

summary:
Overall goal: To identify genes that will cause non-fusogenic fibroblasts to become fusogenic.
Purpose of analysis: To generate transcriptional profile of non-fusogenic fibroblasts, using 10T1/2 fibroblasts transduced with empty retrovirus as model.
Experimental structure: The profile generated from the RNAseq analysis would be compared with transcriptional profile of MyoD-expressing fibroblasts (GEO DataSet GSE34907) to identify genes regulating fusion in muscle cells.

overall_design: RNAseq analysis of total RNA from 10T1/2 fibroblasts transduced with retrovirus carrying empty pBabe-X retroviral vector was carried out to generate a transcriptional profile of a model of non-fusogenic fibroblasts.

first: Vikram

last: Prasad


title: Transcriptomic approach for understanding molecular mechanisms of in situ environmental toxicity of Hg using an aquatic microalgae and a macrophyte

city: Geneva

first: Natacha

last: Civic

address: Rue Michel-Servet 1

department: iGE3 Genomics Platform

institute: University of Geneva

summary: The present study aimed to evaluate the use of transcriptomic analyses of two primary producers to assess the impact of Hg environmental pollution in aquatic primary producers.

sample_organism:
Chlamydomonas reinhardtii
Elodea nuttallii

overall_design: 2h exposure in situ.

first: Perrine

last: Dranguet

first: Claudia

last: Cosio


title: A double blinded, placebo-controlled pilot study to examine reduction of CD34+/CD117+ lymphoma progenitor cells and duration of remission induced by neoadjuvant valspodar in dogs with large B-cell lymphoma

city: Minneapolis

first: Milcah

last: Scott

state: MN

address: 2101 6th Street Se

department: Department of Microbiology and Immunology

institute: University of Minnesota

summary: We previously described a population of lymphoid progenitor cells (LPCs) in canine B-cell lymphoma defined by retention of the early progenitor markers CD34 and CD117 and slow proliferation molecular signatures that persist in the xenotransplantation setting. We examined whether valspodar, a selective inhibitor of the ATP-binding cassette B1 transporter (ABCB1, a.k.a., p-glycoprotein/multidrug resistance protein-1) used in the neoadjuvant setting would sensitize LPCs to doxorubicin and extend the length of remission in dogs with therapy-naive large B-cell lymphoma. Twenty dogs were enrolled into a double-blinded, placebo controlled study where experimental and control groups received oral valspodar (7.5 mg/kg) or placebo, respectively, twice daily for five days followed by five treatments with doxorubicin 21 days apart with a reduction in the first dose to mitigate the potential side effects of ABCB1 inhibition. Lymph node and blood LPCs were quantified at diagnosis, on the fourth day of the neoadjuvant period, and 1-week after the first chemotherapy dose. Valspodar therapy was well tolerated. There were no significant differences between groups in total LPCs in lymph nodes or peripheral blood, nor in event-free survival or overall survival. Overall, we conclude that valspodar can be administered safely in the neoadjuvant setting for canine B-cell lymphoma; however, its use to attenuate ABCB1+ cells does not appear to alter the composition of lymph node or blood LPCs, and it is not sufficient to prolong doxorubicin-dependent remissions in this setting.

overall_design: mRNA profiles of lymph node biopsy samples from dogs with newly diagnosed diffuse large B-cell lymphoma, before and after 4-days of  treatment with valspodar or placebo, were generated by deep sequencing using Illumina HiSeq 2000.

first: Daisuke

last: Ito

first: Michael

middle: O

last: Childress

first: Nicola

last: Mason

first: Amber

last: Winter

first: Kathleen

middle: M

last: Stuebner

first: Timothy

last: O'Brien

middle: S

last: Henson

first: Antonella

last: Borgatti

first: Mitzi

last: Lewellen

first: Erika

last: Krick

first: Jane

middle: C

last: Stewart

first: Sarah

middle: A

last: Lahrman

first: Bartek

last: Rajwa

first: Davis

last: Seelig

first: Joseph

last: Koopmeiners

first: Stephan

last: Ruetz

first: Jaime

middle: F

last: Modiano


title: The Granulocyte Progenitor Stage is a Key Target of IRF8-Mediated Regulation of Myeloid-Derived Suppressor Cell Production

first: Eduardo

last: Cortes

summary: Alterations in myelopoiesis are common across various tumor types, resulting in immature populations termed myeloid-derived suppressor cells (MDSCs). MDSC burden correlates with poorer clinical outcomes, credited to their ability to suppress antitumor immunity. MDSCs consist of two major subsets, monocytic and polymorphonuclear (PMN). Intriguingly, the latter subset predominates in many patients and tumor models, though the mechanisms favoring PMN-MDSC responses remain poorly understood. Ordinarily, lineage-restricted transcription factors regulate myelopoiesis that collectively dictate cell fate. One integral player is interferon regulatory factor-8 (IRF8), which promotes monocyte/dendritic cell differentiation while limiting granulocyte development. We recently showed that IRF8 inversely controls MDSC burden in tumor models, particularly the PMN-MDSC subset. However, where IRF8 acts in the pathway of myeloid differentiation to influence PMN-MDSC production has remained unknown. Here, we showed that: 1) tumor growth was strongly associated with a selective expansion of newly defined IRF8lo granulocytic progenitors (GPs); 2) tumor-derived GPs had an increased ability to form PMN-MDSCs; 3) tumor-derived GPs shared gene expression patterns with IRF8-/- GPs, suggesting that IRF8 loss underlies GP expansion; and 4) enforced IRF8 overexpression in vivo selectively constrained tumor-induced GP expansion. These findings support the hypothesis that PMN-MDSCs result from selective expansion of IRF8lo GPs, and that strategies targeting IRF8 expression may limit their load to improve immunotherapy efficacy.

overall_design: 3 groups of mice:  1) non-tumor-bearing  (NTB) control; 2) mice orthotopically implanted with 4T1 mammary tumor cells (4T1-TB); mice genetically deficient in IRF8 expression and function (KO-GP)

first: Colleen

last: Netherby

first: Michelle

last: Messmer

first: Lauren

last: Burkard-Mandel

first: Sean

last: Colligan

first: Austin

last: Miller

first: Jianmin

last: Wang

last: Nemeth

first: Scott

last: Abrams


title: Dynamic gene regulatory networks of human myeloid differentiation [ATAC-seq_siRNA]

city: Irvine

first: Ricardo

middle: Noel

last: Ramirez

address: 2300 Biological Sciences III

department: Developmental and Cell Biology

institute: University of California Irvine

summary: We utilize gene expression and open chromatin footprinting data to build a gene regulatory network of key transcription factors that capture the cell and time-specific regulatory programs specified during human myeloid differentiation.

overall_design: ATAC-seq profiling of undifferentiated HL-60, differentiating macrophage, neutrophil, monocyte, and monocyte-derived macrophage cells.

first: Ali

last: Mortazavi


title: GRHL3 binding and the enhancer landscape are reorganized during transitions between different functional states of epidermal keratinocytes [ChIP-seq]

first: Bogi

last: Andersen

state: CA

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

summary: The genomic mechanisms underlying progressive, irreversible cell lineage commitments and differentiation, which include large scale chromatin re-organization, transcription factor binding, and chromatin modifications, have been well defined. However, we know little about the chromatin changes during transitions between transient cell states such as cell migration. Here we demonstrate the formation of unique complements of typical enhancers and super-enhancers as human progenitor keratinocytes either differentiate or migrate. Unique super-enhancers for each cellular state are linked to gene expression that confer functions associated with each cell state, and sequence variants associated with skin diseases are enriched within super-enhancers. GRHL3, a factor that promotes both differentiation and migration, exhibits prominent super-enhancer interactions in differentiating keratinocytes, while during migration, it preferentially binds to promoters along with REST, repressing the expression of migration inhibitors. Key epidermal differentiation transcription factor genes, including GRHL3, are located within super-enhancers, and many of these transcription factors in turn bind to and regulate super-enhancers. Of note, GRHL3 also represses the formation of a number of progenitor and non-keratinocyte super-enhancers in differentiating keratinocytes.  Thus, coordinated GRHL3 binding and enhancer rearrangements regulate the functional states of keratinocytes.

overall_design: GRHL3 ChIP was performed in duplicate on primary human keratinocytes (NHEK) 12 hours after induction of migration

first: Rachel

last: Klein


title: Dynamic gene regulatory networks of human myeloid differentiation [RNA-seq_siRNA]

overall_design: RNA-seq profiling of undifferentiated HL-60, differentiating macrophage, neutrophil, monocyte, following siRNA control and siPU.1 treatment for 24 hours.


title: Transcriptome changes in cultured mouse cortical neurons infected with lentivirus expressing shMeCP2

city: Shanghai

first: Zilong

last: Qiu

address: No.320, Rd. Yueyang

institute: Chinese Academic of Science

summary: Illumina RNA sequencing technology was used to determine transcriptome changes in cultured mouse cortical neurons infected with lentivirus expressing shMeCP2

overall_design: RNA-Seq comparing between cultured mouse cortical neurons infected with lentivirus expressing shMeCP2 and control group

first: Tian-Lin

last: Cheng


title: Transcriptome-wide RNA 5-methylcytosine methylation in shoots of Arabidopsis thaliana

first: Alice

last: Burgess

summary: Here we use bisulfite conversion of rRNA depleted RNA combined with high-throughput Illumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites transcriptome-wide in Arabidopsis thaliana seedlings. m5C sites were also analyzed in Arabidopsis trm4b-1 and trdmt1 T-DNA KO mutants for the RNA methyltransferases TRM4B and TRDMT1.

overall_design: RNA bisulfite sequencing was used to identify candidate m5C sites transcriptome-wide in Arabidopsis thaliana seedlings, using rRNA depleted RNA. Illumina sequencing was performed on a HiSeq platform. The genotypes used are wild type trm4b-1 and trdmt1. All genotypes have two biological replicates with two technical replicates for each biological replicate.

first: Rakesh

last: David

middle: L

first: Iain

last: Searle


title: Assessing the mechanism of action of BTK inhibitor, G7744

city: South San Francisco

first: Mark

last: McCreary

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

summary:
Purpose: to investigate the method of action (MOA) of BTK small molecule inhibitor, G7744, in a pre-clinical mouse lupus model (NZB/W F1).
Hypothesis: BTK inhibition will affect B cell and myeloid cell pathways.

overall_design: There are 5 mice per group. Sample groups: G1: Naive G2: Ad5 IFNa TD day 21 G3: Vehicle HPMC in citrate G4: BTK SMI G7744 100 mg/kg G5: SYK SMI G955 60 mg/kg G6: Anti ragweed IgG2a G7: mBR3 IgG2a G8: Cytoxan. Animals treated for 4 weeks. Samples: Spleen and kidney RNA from groups G1-G8.

first: Michael

last: Townsend

first: Nandhini

last: Ramamoorthi

first: Jason

last: Hackney


title: Genome-wide nucleosome occupancy and DNA methylation profiling in endometriosis cells

status: Public on Apr 05 2017

city: Los Angeles

first: Ranjani

last: Lakshminarasimhan

address: 1441 Eastlake ave NOR7336

department: Urology

institute: University of Southern California

summary: We show that knocking down ARID1A in an immortalized endometriosis cell line leads to phenotypic changes  in vitro.  Additionally, we find strong increases in the active H3K27ac mark in promoter regions but decrease of H3K27ac at potential enhancers with targeted DNA methylation-independent alterations in nucleosome occupancy.

overall_design: Simultaneous examination of nuclesome-occupancy and DNA methylation in endometriosis control and ARID1A knockdown cell lines.

first: Claudia

last: Andreu-Vieyra

first: Kate

last: Lawrenson

first: Chris

middle: E

last: Duymich

first: Simon

last: Gayther

first: Gangning

last: Liang

first: Peter

last: Jones


title: Genome-wide analysis of chromatin state in extended pluripotent stem cells, primed pluripotent stem cells, and naïve pluripotent stem cells

city: Beijing

first: Hongkui

last: Deng

address: this is for reviewer only

institute: Peking University

summary: Among all known cultured stem cell types, pluripotent stem cells (PSCs) sit atop the landscape of developmental potency and are characterized by their unrestricted developmental potential, able to generate all cell types of an adult organism. However, PSCs show limited contribution to the extraembryonic (ExEm) tissues, in particular, those giving rise to the placenta in vivo. To date, it remains unknown whether stem cells with both embryonic and extraembryonic developmental potency can be captured and maintained in vitro. Here, we identify a new chemical cocktail that allows for the generation of stem cells with extended developmental potency from mouse and human, designated as extended pluripotent stem (EPS) cells, which is capable of chimerizing both embryonic and extraembryonic tissues. Importantly, a single mouse EPS (mEPS) cell shows widespread contribution to both embryonic and extraembryonic lineages in chimeric mouse conceptuses at late-gestation stages, and permits generation of high-grade germline competent chimeras as well as single EPS-derived viable mice by tetraploid complementation. Furthermore, human EPS (hEPS) cells contribute to embryonic and extraembryonic tissues in interspecies chimeric mouse conceptuses. Compared to known PSCs, EPS cells show unique gene modules that upregulate in embryonic cells from early preimplantation development. Further analysis shows that PARP1 inhibition is required for maintaining EPS potency. Our findings constitute a first step towards capturing pluripotent stem cells with extraembryonic developmental potentials in culture, and open new avenues for generating mammalian PSCs with robust chimeric competency for basic and translational research.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of histone modifications H3K4me3 and H3K27me3 in extended pluripotent stem cells, primed pluripotent stem cells and naïve pluripotent stem cells.

first: Yang

last: Yang

first: Bei

last: Liu

first: Jun

last: Xu

first: Jinlin

last: Wang


title: The PIF4 controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana

city: Canberra

first: Li

state: ACT

address: North-Science Road, Acton ACT 2601

institute: CSIRO

summary: F1 hybrids in Arabidopsis and crops species are uniform and high yielding. The F2 generation loses much of the yield advantage and the plants have heterogeneous phenotypes. We generated pure breeding Hybrid Mimic lines by recurrent selection and also selected a pure breeding Small phenotype line. The Hybrid Mimics are almost completely homozygous with chromosome segments from each parent. Four particular chromosomal segments from C24 and eight from Ler were present in all of the Hybrid Mimic lines whereas in the F6 Small phenotype line the 12 segments were each derived from the alternative parent. Loci critical for promoting hybrid vigor may be contained in each of these 12 conserved segments. We have identified genes with similar altered expression in Hybrid Mimics and F1 plants but not in the Small phenotype line. These genes may be critical for the generation of hybrid vigour. Analysis of transcriptomes indicated that increased expression of the transcription factor PHYTOCHROME-INTERACTING FACTOR (PIF4) may contribute to hybrid vigor by targeting the auxin biosynthesis gene YUCCA8 and the auxin signalling gene IAA29. A number of auxin responsive genes promoting leaf growth were upregulated in the F1 hybrids and Hybrid Mimics suggesting increased auxin biosynthesis and signaling contribute to the hybrid phenotype. The Hybrid Mimic seeds had earlier germination as did the seeds of the F1 hybrids indicating co-segregation of the genes for rosette size and the germination trait. Early germination may be an indicator of vigorous hybrids.

overall_design: For the transcriptomes of two parents C24 and Ler, F1 hybrids and F6 plant lines at 15 DAS. 30 samples were sequenced in total. C24 (three biological replicates), Ler (three biological replicates), C24xLer F1 hybrids (three biological replicates), LerxC24 F1 hybrids (three biological replicates) and three F6 siblings of each of six F6 lines (HM-W, HM-S, HM-G, Med-E, Med-F, Sml-D) were grown in one experiment under the same conditions. The library preparation and mRNA sequencing were completed by the Australian Genome Research Facility (AGRF).

last: Wu

first: Ian

middle: K

last: Greaves

first: Anyu

last: Zhu

first: Elizabeth

last: Dennis

first: W

last: Peacock


title: Transcriptomic profiling of dorsal root ganglia of transgenic sickle and control mouse models for studying genetic signatures of pain in sickle cell disease

first: Kalpna

last: Gupta

address: 14-100 PWB, 516 Delaware Street SE

department: Medicine/HOT

summary: We sequenced mRNA from the dorsal root ganglion (DRG) of transgenic mouse models of sickle cell disease (SCD) and their transgenic controls. Each genotype (strains) were divided into two age groups and each age groups were subjected to two treatment conditions (each simulating acute and chronic pain respectively). Each of these 8 groups had 6 male mice (except one group had 7 mice) resulting into a total of 49 samples. The goal of mRNA sequencing of these samples is to identify genetic signatures associated with transition from acute to chronic pain in SCD.

overall_design: Examination of mRNA levels from dorsal root ganglion of transgenic mouse models of sickle cell disease and littermate controls under two dffiferent age groups and two different treatment conditions to find genetic targets that underly SCD pain and transition from acute to chronic pain.

first: Anupam

last: Aich


title: Analysis of WT and IRF1-deficient Th9 cell transcriptomes in the presence of IFN-gamma

city: Marburg

first: Lucia

last: Campos Carrascosa

address: Hans-Meerwein-Straße 2

country: Germany

institute: Institute of Medical Microbiology

summary: Goal of this study was to compare transcriptional changes in IFN-gamma-treated WT compared to IRF1-deficient Th9 cells

overall_design: mRNA profiles of Th9 cells cultured for 2 days in the presence of IFN-gamma in vitro were generated by deep sequencing using Illumina HiSeq2000

first: Magdalena

last: Huber

first: Matthias

last: Klein

first: Federico

last: Marini


title: Dynamic gene regulatory networks of human myeloid differentiation [RNA-seq]

first: Ricardo

last: Ramirez

overall_design: RNA-seq profiling of undifferentiated HL-60, differentiating macrophage, neutrophil, monocyte, and monocyte-derived macrophage cells.

first: Ali

last: Mortazavi


title: Dynamic gene regulatory networks of human myeloid differentiation [ATAC-seq]


title: Recognition memory-induced gene expression in the perirhinal cortex: a transcriptomics analysis.

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

institute: Cardiff University

summary: It is possible to identify the key genes and pathways involved in specific physiological processes using transcriptome analyses. However, these powerful new deep sequencing-based methods have rarely been applied to studies of memory function. We used the bow-tie maze to train rats by exposing them to highly familiar objects or to novel objects. Total RNA sequencing was then used to compare the transcriptome of the perirhinal cortices of naïve control rats and rats exposed to novel and familiar stimuli. Differentially expressed genes were identified between group Novel and group Familiar rats and these included genes coding for transcription factors and extracellular matrix-related proteins. Moreover, differences in alternative splicing were also detected between the two groups. To conclude, this study shows that RNA sequencing can be used as a tool to identify differences in gene expression in behaving animals undergoing the same task but encountering different exposures.

overall_design: RNA profiles of perirhinal cortex from rats exposed to novel objects (n=5) or familiar objects (n=5) in a recognition memory task were investigated using the Ion Proton System. Controls were naïve rats that had not undergone any behavioural testing (n=4).

first: Mark

last: Rogers

first: Helen

first: Colin

last: Campbell

last: Warburton

first: James

middle: B

last: Uney