title: Naked mole rat cells show resistance to iPSC reprogramming and signs of more stable epigenome

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

summary: Naked mole rat (NMR) is a valuable model for aging and cancer research due to its exceptional longevity and resistance to tumorigenesis. In an effort to generate NMR induced pluripotent stem cells (iPSCs) we observed that reprogramming efficiency of NMR fibroblasts in repsonse to OSKM overexpression was drasticaly lower than that of mouse fibroblasts. To understand the cause of NMR resistance to reprogramming we screened for factors that improve reprogramming effciency. We identified that expression of SV40 Large T (LT) dramatically improved reprogramming of NMR fibroblasts. Inactivation of Rb alone, but not p53, was suffcient to improve reprogramming effciency suggesting that NMR chromatin structure is refractory to reprogramming. Analysis of global histone landscape using quantitative mass spectrometry revealed that NMR fibroblasts had higer levels of repressive H3K27 methylation marks, and lower levels of activating H3K27 acetylation mark than the mouse fibroblasts. Furthermore, the NMR cells had lower levels of permissive H2A.Z acetylation marks. ChIP showed that of E-cadherin had repressive H3K9me3 histone mark in the NMR, but was poised with a bivalent H3K4me3/H3K27me3 in the mouse. Expression of LT reduced the levels of H3K9me3 mark on E-cadherin promoter. ATAC-seq revealed that NMR had more open chromatin globally, however, NMR promoters were more closed than mouse promoters. Expression of LT antigen led to massive opening of the NMR promoters including gene promoters required for reprogramming. Cumulatively, these data suggest that NMR has more stable epigenome than mouse, which resists reprogramming and may contribute to NMR longevity and cancer resistance.

sample_organism:
Mus musculus
Heterocephalus glaber

platform_organism:
Mus musculus
Heterocephalus glaber

overall_design: ATAC-seq in mouse and naked mole rate fibroblast cell lines.

first: Vera

last: Gorbunova

first: Li

last: Tan

last: Lv


title: Multilineage communication regulates human liver bud self-organization from pluripotency II

status: Public on Jun 21 2017

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

type: Expression profiling by high throughput sequencing

summary: Conventional 2-D differentiation from pluripotency fails to recapitulate cell interactions occurring during organogenesis. 3-D organoids generate complex organ-like tissues, however it is unclear how heterotypic interactions impact lineage identity. Here we use single-cell RNA-seq to reconstruct hepatocyte-like lineage progression from pluripotency in 2-D culture. We then derive 3-D liver bud (LB) organoids by reconstituting hepatic, stromal, and endothelial interactions, and deconstruct heterogeneity during LB development. We find that LB hepatoblasts diverge from the 2-D lineage, and express epithelial migration signatures characteristic of organ budding. We benchmark 3-D LBs against fetal and adult human liver scRNA-seq data, and find a striking correspondence between the 3-D LB and fetal liver cells. We use a receptor-ligand pairing analysis and a high-throughput inhibitor assay to interrogate signaling in LBs, and show that VEGF crosstalk potentiates endothelial network formation and hepatoblast differentiation. Our molecular dissection reveals interlineage communication regulating organoid development, and illuminates previously inaccessible aspects of human liver development.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell transcriptomes from multiple time points during hepatocyte-like lineage progression from pluripotency in 2-D culture, from 3-D liver bud (LB) organoids that self-organized after reconstituting hepatic, stromal, and endothelial interactions, and from adult, fetal, and mouse primary liver tissue.

first: J

middle: G

first: Barbara

last: Treutlein


title: Field cancerized fibroblasts in primary culture, P2

status: Public on Jun 22 2017

city: Albuquerque

first: Kristina

middle: Antonia

last: Trujillo

state: New Mexico

address: 915 Camino de Salud NE

department: Cell Biology and Physiology

country: USA

institute: University of New Mexico

summary: Fibroblasts cultured from human breast cancer and adjacent normal tissues at 1cm and 5cm from the margin.

overall_design: 3 patient sets of fibroblasts from tumor, and patient matched adjacent normal at 1cm and 5cm from tumor.


title: Innate immune sensing of cytosolic chromatin fragments through cGAS promotes senescence

status: Public on Jun 20 2017

city: Lausanne

first: Selene

last: Glück

address: Station 19

department: SV-GHI

country: Switzerland

institute: EPFL

summary: Cellular senescence is triggered by various distinct stresses and characterized by a permanent cell cycle arrest. Senescent cells secrete a variety of inflammatory factors, collectively referred to as the senescence-associated secretory phenotype (SASP). The mechanism(s) underlying the regulation of the SASP remains incompletely understood. Here we define a role for innate DNA sensing in the regulation of senescence and the SASP. We find that cyclic GMP-AMP synthase (cGAS) recognizes cytosolic chromatin fragments (CCFs) in senescent cells. The activation of cGAS, in turn triggers the production of SASP factors via Stimulator of interferon genes (STING), thereby promoting paracrine senescence. We demonstrate that diverse stimuli of cellular senescence engage the cGAS-STING pathway in vitro and we show cGAS-dependent regulation of senescence upon irradiation and oncogene activation in vivo. Our findings provide insights into the mechanisms underlying cellular senescence by establishing the cGAS-STING pathway as a crucial regulator of senescence and the SASP.

overall_design: Primary WT MEFs and cGAS KO MEFs were passaged for three weeks under 20% oxygen; their RNA was isolated at three different time points (day 33, 36, 42) and processed for RNA sequencing.

first: Baptiste

last: Guey

first: Muhammet

middle: F

last: Gulen

first: Katharina

last: Wolter

first: Tae-Won

last: Kang

first: Anne

last: Bridgeman

first: Niklas

middle: A

last: Schmacke

first: Jan

last: Rehwinkel

first: Lars

last: Zender

first: Andrea

last: Ablasser


title: Flt3-ITD-induced extrinsic depletion of the normal hematopoietic stem cell reservoir

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

summary: Gene expression analysis of purified  endothelial cells (Ecs), mesenchymal stem cells (MSCs) and mononuclear cells (MNCs) from wild-type and Flt3-ITD knock-in mice.

overall_design: Differentially expressed genes analysis of haematopoietic and niche cell populations from Flt3-ITD mice

first: A

last: Mead

first: S

last: Thongjuea

last: Giustacchini

first: Sten

middle: E

last: Jacobsen


title: Assessing the developmental and malignant potential of human pluripotent stem cells by RNA-seq analysis of Teratomas

city: Sheffield

first: Paul

last: Gokhale

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary: The International Stem Cell Initiative compared three common approaches for assessing pluripotent stem cells (PSC).  The formation of teratomas in vivo, or embryoid bodies (EB) in vitro, provide direct tests of differentiation, whereas PluriTest predicts pluripotency through bioinformatic analysis of transcriptomes of undifferentiated cells.  We studied the teratomas by histology and TeratoScore, which analyzes gene expression in each tumor.  For the EB assay, we assessed differentiation under neutral conditions and under conditions promoting differentiation to ectoderm, mesoderm, or endoderm lineages.  Comparison of each method showed that all assays predict pluripotency, but they have different endpoints that provide different insights.  For example, tumors from a subset of lines also contained undifferentiated cells and yolk sac elements that indicate possible malignant potential.  This characteristic was not detected by the other two methods.  Our results highlight the need for multiple assays to assess both pluripotency and potential malignancy in clinical applications of PSCs.

overall_design: RNA-seq analysis of human pluripotent stem cell-derived teratomas obtained from 15 human pluripotent stem cells lines from 4 laboratories with 2-3 replicates each, 37 samples in total.

last: Robson


title: Yorkie is required to restrict the injury responses in planarians

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: Regeneration requires the precise integration of cues that initiate proliferation, direct differentiation, and ultimately re-pattern tissues to the proper size and scale. Yet how these processes are integrated with wounding cues remains relatively unknown. The freshwater planarian, Schmidtea mediterranea, is an ideal model to study the stereotyped proliferative and transcriptional responses to injury due to its high capacity for regeneration. Here, we characterize the effector of the Hippo signalling cascade, yorkie, during planarian regeneration and its role in restricting early injury responses. In yki(RNAi) regenerating animals, wound responses are hyper-activated; the bimodal proliferation kinetics are heighted and prolonged, while the transcriptional injury responses are similarly augmented with dysregulated temporal patterns. We also uncovered novel wound-induced genes by RNAseq that are primarily associated with tissue patterning. Indeed, a high proportion of non-wound- and wound-induced patterning molecules are mis-expressed in yki(RNAi), which we demonstrate is in part due to an expanded muscle cell population. These altered injury responses have consequential effects on regenerative outcomes, specifically sensing the size of a given injury and appropriately scaling organ and tissue sizes. Taken together, our results suggest that yki functions as a key node to integrate the injury responses of proliferation, apoptosis, injury-induced transcription, and patterning to coordinate regeneration.

overall_design: control(RNAi) and yki(RNAi) animals at 1 day post-60Gy irradiation were amputated or not (intact). RNA was collected from intact animals and tail fragments at 6, 12, and 24 hours post-amputation. Samples were sequenced to a depth of >20 million reads.

first: Alexander

middle: Y

last: Lin


title: The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly [RNA-seq]

city: Cold Spring Harbor

first: Robert

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

summary: RNAi factors and their catalytic activities are essential for heterochromatin assembly in S. pombe. This has led to the idea that siRNAs can promote H3K9 methylation by recruiting the Cryptic Loci Regulator Complex (CLRC), also known as Recombination In K Complex (RIKC), to the nucleation site. The conserved RNA-binding protein Rct1 (AtCyp59/SIG-7) interacts with splicing factors and with RNA polymerase II.  Here we show that Rct1 promotes processing of pericentromeric transcripts into siRNAs, via the RNA recognition motif. Surprisingly, loss of siRNA in rct1 mutant cells has no effect on H3K9 di- or tri-methylation, resembling other splicing mutants, and suggesting post-transcriptional gene silencing per se is not required to maintain heterochromatin. Splicing of the Argonaute gene is also defective in rct1 mutants, and contributes to loss of silencing but not to loss of siRNA. Our results suggest that Rct1 guides transcripts to the RNAi machinery by promoting splicing of elongating non-coding transcripts.

overall_design: rRNA-depleted RNA expression profiling of WT, rct1 KO, rct1-RRM, clr3 KO, ago1 KO, dcr1 KO and rct1 clr3 double KO cells. Two biological replicates are included for all except ago1 KO and dcr1 KO. 12 samples in total.

first: An-Yun

last: Chang

first: Stephane

last: Castel

first: Evan

last: Ernst

first: Hyun

middle: S

last: Kim


title: Generational Comparisons (F1 versus F3) of Vinclozolin Induced Epigenetic Transgenerational Inheritance of Sperm Differential DNA Methylation Regions (Epimutations) Using MeDIP-Seq

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: The agricultural fungicide vinclozolin exposure of a gestating female rat has previously been shown to promote transgenerational disease and epimutations in F3 generation (great-grand-offspring) animals. The current study was designed to investigate the actions of direct fetal exposure on the F1 generation rat sperm DMRs compared to the F3 transgenerational sperm DMRs. The F1 generation DMRs were found to be fewer in number and for the most part distinct from the F3 generation epimutations. Therefore, the direct exposure induced F1 generation DMRs appear to promote alterations in germ cell development that lead to the programming of the F3 generation epimutations, but are distinct between the generations.

overall_design:
F0 generation gestating female rats were treated with either vinclozolin or dimethyl sulfoxide (vehicle). The rats were then raised and bred to the F3 generation. Genome wide methylation levels were assessed for both the F1 and F3 generation rats. This was done by pooling three rat individual samples into a single sample pool. Three pools for each treatment in each generation were collected. The methylation for each pool was measured using MeDIP-seq on an Illumina HiSeq 2500.

DOI:  10.1093/eep/dvx016

first: Daniel

last: Beck

first: Ingrid

last: Sadler-Riggleman


title: The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly [small RNA]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Small RNA expression profiling of WT, rct1 KO, rct1-RRM, clr3 KO, rrp6 KO and double KOs. 17 samples in total.


title: The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq of H3K9me2, H3K9me3, nonspecific RNAPII (8WG16), initiating RNAPII (phospho S5), and elongating RNAPII (phospho S2). Whole cell extract (DNA input) samples are included for each experiment. 38 samples in total.


title: The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly

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

overall_design: Refer to individual Series


title: Molecular role of RNA helicases MVH and TDRD9 in PIWI slicing-triggered mammalian piRNA biogenesis and function

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: PIWI-interacting RNAs (piRNAs) function in the nucleus and cytoplasm of animal germ cells to suppress mobile genetic elements. In the mouse male germline, biogenesis of MIWI2-bound nuclear piRNAs depends on endonuclease activity of cytosolic MILI, but the process is poorly understood. Here we use a mouse model expressing an artificial piRNA precursor to show that MILI slicing of the precursor generates a 16-nt by-product and a  pre-piRNA intermediate that requires 3ʹ end processing to mature as a new piRNA. The ability to use the slicer products requires ATPase activity of the RNA helicase MVH, as the catalytic-dead Mvh mutant mice (Mvh-/KI) fail to  convert the intermediate into piRNAs, abrogating biogenesis of MIWI2 piRNAs. This results in an early arrest in spermatogenesis and de-repression of transposons. Furthermore, the mutant MVH protein is dominant-negative (Mvh+/KI) as it causes a late-spermatogenic arrest by trapping complexes containing the mysterious pachytene piRNAs and slicer products, uncovering a role for the protein beyond the embryonic germline. In contrast, we find that the ATPase activity of TDRD9 is dispensable for piRNA biogenesis, but is essential for silencing by MIWI2. Our studies implicate distinct RNA helicases in specific steps along the mammalian nuclear piRNA pathway.

overall_design: Testicular piRNAs and longer RNA species associated with MVH, MILI, MIWI or MIWI2 were immunoprecipitated and sequenced. The  effect of TDRD9 and MVH mutation on piRNA pathway was investigated.

first: Joanna

middle: M

last: Wenda

first: David

last: Homolka

first: Zhaolin

last: Yang

first: Pietro

last: Spinelli

first: Ravi

last: Sachidanandam

first: Radha

middle: R

last: Pandey


title: Profiling of Ileal Transcriptome in Pediatric Crohn Disease

city: Atlanta

first: Urko M.

last: Marigorta

state: Georgia

address: 950 Atlantic Drive

department: School of Biosciences

institute: Georgia Institute of Technology

summary: We report ileal gene expression at diagnosis in a cohort of 210 treatment-naïve patients of pediatric Crohn's disease and 35 non-IBD controls from the RISK study. After three years of follow-up after diagnosis, 27 of the CD patients progressed to complicated disease (B2 and/or B3). We aim to test whether Transcriptional Risk Scores helps to distinguish between patient subgroups, improving the predictive power gained from Genetic Risk Scores.

overall_design: Ileal biopsies were obtained during diagnostic colonoscopies of children and adolescents (<17 years) who presented with symptoms of IBD. Non-IBD control label corresponds to those with suspected IBD, but without inflammation and normal endoscopic findings. Biopsies were stored at -80 degrees.

first: Urko

first: Greg

last: Gibson

first: Subra

last: Kugathasan

first: Lee

last: Denson


title: Comparative transcriptome profiling of zebrafish and medaka hearts following cardiac cryoinjury

city: Bad Nauheim

first: Shih-Lei

middle: Ben

last: Lai

state: Hessen

address: Ludwigstraße 43

department: Developmental Genetics

institute: Max Planck Institute for Heart and Lung Research

summary: Heart failure results from the inability of the human heart to replenish damaged tissue after myocardial infarction (MI), forming an unresolved scar which leads to functional impairment and tissue remodeling.  Unlike humans, many animals, including certain fish and amphibians, are able to regenerate their hearts.  Comparative analyses have been performed in many model systems including zebrafish (Danio rerio), with the goal to identify factors that could promote cardiac regeneration in humans.  However, profound physiological differences between regenerative and non-regenerative models often make it difficult to extract informative data that are directly relevant to cardiac regeneration.  Recently, medaka (Oryzias latipes), another fresh water teleost, has been reported to lack activation of neovascularization and cardiomyocyte (CM) proliferation post cardiac injury, and to display excessive fibrosis and an unresolved scar.  This finding constitutes a unique opportunity to directly compare reparative responses to cardiac injury between regenerative (zebrafish) and non-regenerative (medaka) models with common physiological condition and anatomical structures, as well as phylogenetically close orthologous genes.  Here we investigate potential triggers that promote heart regeneration using a comparative transcriptomic analysis between zebrafish and medaka.  We generated a detailed dataset containing more than 15000 orthologous genes, covering multiple time points in the first week after cardiac injury.  Analyses based on gene ontology revealed that differential responses in processes such as the immune response and angiogenesis exist between the two models.  Pathway analyses further suggested potential candidates accounting for these differential responses including the Toll-like receptor agonist poly I:C.  Altogether, these data provide further insight into the complex role of the immune response during regeneration, and serve as a platform to identify and test additional regulators of cardiac repair.

sample_organism:
Danio rerio
Oryzias latipes

platform_organism:
Danio rerio
Oryzias latipes

overall_design: Zebrafish: We pooled hearts from 4 fish to represent one biological sample. This was done for each combination of timepoint (0h=untreated, 6h, 1d, 2d, 3d, 5d) and treatment (post sham operation [ps],  post cardiac injury [pci]) resulting in 11 samples.  Medaka: We pooled hearts from 4 fish to represent one biological sample and repeated this once. This was done for each combination of timepoint (0h=untreated, 6h, 2d, 3d, 6d) and treatment (post sham operation [ps],  post cardiac injury [pci]) resulting in 18 samples.

first: Rubén

last: Marín-Juez

first: Pedro

last: Moura

first: Carsten

last: Kuenne

first: Kuan

middle: H

first: Ayele

middle: T

last: Tsedeke

first: Stefan

last: Guenther

first: Mario

last: Looso

first: Didier

last: Stainier


title: Differential impact of Dicer deficiency on microglia of the developing and adult brain (Bulk RNA-Seq)

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

summary: Microglia seed the embryonic neuro-epithelium, expand and actively sculpt neuronal circuits in the developing CNS, but eventually adopt relative quiescence and ramified morphology in the adult. Here we probed the impact of post-transcriptional control by microRNAs (miRNAs) on microglial performance during development and adulthood by generating mice lacking microglial dicer expression at these distinct stages. RNA seq of conditional dicer ablation in adult microglia revealed that miRNAs were required to limit microglial responses to challenge but had only minor changes on non-challenged microglia. Specifically, following peripheral endotoxin exposure of the animals (LPS), Dicer-deficient microglia either from total brain or hippocampus overexpressed pro-inflammatory cytokines and as a result compromised hippocampal neuronal functions. In contrast, prenatal ablation resulted in spontaneous microglia activation and revealed Dicer involvement in DNA repair and preservation of genome integrity. Overall, our study shows miRNA and Dicer regulation of inflammatory response either following challenge in the adult or spontaneously in the newborn microglia. Moreover, Dicer is required for preservation of microglia DNA integrity required for their proliferation, longevity and radioresistance.

overall_design: Adult Microglia (defined as CD45intCD11b+F4/80+Ly6C-Ly6G- cells) were sorted from nontreated control (Cx3cr1CreER:Dicer+/-, n=4) and Dicer deficient (Cx3cr1CreER:Dicer+/-, n=3) microglia in order to examine steady state changes in adult microglia in response to Dicer deficiency. Next, control and Dicer deficient adult microglia were examined at 6h following LPS  challenge from either total brain (Steady state WT, n=3; Steady state Dicer, n=3; LPS WT, n=4; LPS Dicer, n=3) or hippocampus (Steady state WT, n=2; Steady state Dicer, n=3; LPS WT, n=2; LPS Dicer, n=2).                                                                                In addition, we examined control (Dicerfl/fl) and Dicer deficient microglia at developmental stages. This analysis included control microglia (dicerfl/fl) from different stages (Adult, n=5; P0 (newborn), n=5; E14, n=4) followed by a P0 stage comparison between control (dicerfl/fl, n=3) and Dicer deficient (Cx3cr1Cre:Dicerfl/fl, n=2) microglia.                                                                                RNA-seq based transcriptomic profiling was performed to deliniate the effect of Dicer deficiency on microglia inflammatory response and proliferation at developmental and adult stages.

first: Diana

last: Varol

first: Alexander

last: Mildner

first: Eyal

last: David


title: The RNAi Inheritance Machinery of Caenorhabditis elegans

city: Worcester

first: George

last: Spracklin

state: Massachusetts

address: 368 Plantation Street

department: Systems Biology

institute: University of Massachusetts Medical School

summary: Gene silencing mediated by dsRNA (RNAi) can persist for multiple generations in C. elegans (termed RNAi inheritance). Here we describe the results of a forward genetic screen in C. elegans that has identified six factors required for RNAi inheritance: GLH-1/VASA, PUP-1/CDE-1, MORC-1, SET-32, and two novel nematode-specific factors that we term here (heritable RNAi defective) HRDE-2 and HRDE-4. The new RNAi inheritance factors exhibit mortal germline (Mrt) phenotypes, which we show is likely caused by epigenetic deregulation in germ cells. We also show that HRDE-2 contributes to RNAi inheritance by facilitating the binding of small RNAs to the inheritance Argonaute (Ago) HRDE-1. Together, our results identify additional components of the RNAi inheritance machinery whose sequence conservation provides insights into the molecular mechanism of RNAi inheritance, further our understanding of how the RNAi inheritance machinery promotes germline immortality, and show that HRDE-2 couples the inheritance Ago HRDE-1 with the small RNAs it needs to direct RNAi inheritance and germline immortality.

overall_design: Examine small RNA populations after feeding oma-1 or l4440 dsRNA in control and hrde-2 mutant animals.

first: Scott

last: Kennedy


title: Aneuploidy triggers an immune response

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Aneuploidy, a state of karyotype imbalance, is a hallmark of cancer. Changes in chromosome copy number have been proposed to drive disease by modulating the dosage of cancer driver genes and by promoting cancer genome evolution. Given the potential of cells with abnormal karyotypes to become cancerous, do pathways exist that limit the prevalence of such cells? By investigating the immediate consequences of aneuploidy on cell physiology, we identified mechanisms that eliminate aneuploid cells.  We find that chromosome mis-segregation leads to replication stress, generating further genomic instability, increased karyotype complexity, and ultimately cell cycle arrest. Cells with complex karyotypes exhibit features of senescence and a pro-inflammatory response that promotes their clearance by the immune system. We propose that cells with abnormal karyotypes generate a signal for their own elimination that might well be a source of cancer cell immunosurveillance that must be overcome during malignant transformation.

overall_design: Assay the transcriptional impact of aneuploidy by comparing the transcriptomes Euploid control RPE-1 cells in Aneuploid cycling RPE-1 cells and Aneuploid arrested RPE-1 cells using RNA-Seq.

first: Stefano

last: Santaguida

first: Amelia

last: Richardson

first: Divya

last: Iyer

first: Ons

last: M'Saad

first: Lauren

last: Zasadil

first: Kristin

last: Knouse

first: Yao

last: Wong

first: Nick

last: Rhind

first: Arshad

last: Desai

first: Angelika

last: Amon


title: Mouse pooled LNEPs, pre- and post-influenza - Local lung hypoxia determines epithelial fate decisions during alveolar regeneration

city: PHILADELPHIA

first: Andrew

last: Vaughan

state: United States

address: 3800 Spruce Street

institute: University of Pennsylvania

summary: Flow sorted mouse LNEP cells isolated from normal lungs and influenza-infected lungs (day 17 PR8)

overall_design: Highly purified quiescent LNEPs (EpCAMposb4posCC10negFoxJ1neg) and activated LNEPs (Krt5-CreERT2 traced cells 17 days post infection) were flow sorted and extracted for RNA using ReliaPrep™ RNA Tissue Miniprep kit (Promega).

first: Hal

last: Chapman

first: Ying

last: Xi


title: Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

city: Chicago

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

institute: University of Chicago

summary: Gaining insights into the regulatory mechanisms that underlie the pervasive transcriptional variation observed between individual cells necessitates the development of methods that measure chromatin organization in single cells. Nucleosome Occupancy and Methylome-sequencing (NOMe-seq) employs a GpC methyltransferase to detect accessible chromatin and has been used to map nucleosome positioning and DNA methylation genome-wide in bulk samples. Here I provide proof-of-principle that NOMe-seq can be adapted to measure chromatin accessibility and endogenous DNA methylation in single cells (scNOMe-seq). scNOMe-seq recovered characteristic accessibility and DNA methylation patterns at DNase Hypersensitive sites and enabled direct estimation of the number of accessible DHS sites within an individual cell. In addition, scNOMe-seq provided high resolution of chromatin accessibility within individual loci which was exploited to detect footprints of CTCF binding and to estimate the average nucleosome phasing distances in single cells.

overall_design: Single cell study of chromatin organization using GpC methyltransferase in 19 GM12878 cells (inlcuding 7 controls without GpC methyltransferase treatment) and 11 K562 cells.


title: Local lung hypoxia determines epithelial fate decisions during alveolar regeneration


title: Human Single Cells - Local lung hypoxia determines epithelial fate decisions during alveolar regeneration

summary: Single human lung epithelial cell transcriptomes, isolated and processed via Fluidigm C1

overall_design: Flow sorted cells from digested human lungs were captured on the Fluidigm C1 chip.


title: Germinal-center development of memory B cells driven by IL-9 from follicular helper T cells

city: Beijing

first: Hai

last: Qi

state: Beijing

address: Tsinghuayuan Street

department: School of Medicine

country: China

institute: Tsinghua University

summary: A subset of GC B cells that have stopped cycling, upregulated CD38 and downregulated BCL-6 is functionally verified as GC-derived memory B cell precursors (GC-MPs). RNA-seq analyses of the transcriptome were used to probe the developmental trajectory of these cells and their responses to IL-9, a cytokine that is found to drive the memory development from the GC.

overall_design: Differential gene expression analyses between GC-MP cells and regular GC B cells in G1 phase (GC-MPP cells); Gene expression profiling of different GC subsets in comparison to memory B cells and plasma cells; acute effects of in vivo IL-9 or anti-IL-9 treatment on GC-MP or GC-MPP cells.

first: Yifeng

last: Wang

first: Jingwen

last: Shi

first: Jiacong

last: Yan

first: Zhengtao

last: Xiao

first: Xiaoxiao

last: Hou

first: Peiwen

last: Lu

first: Shiyue

first: Tianyang

last: Mao

first: Yuanwu

last: Ma

first: Lianfeng

last: Zhang

first: Xuerui

last: Yang


title: RNA-sequencing of Fes KO and WT melanomas

city: Leuven

first: Sara

last: Aibar

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

summary: Publication abstract: An incomplete view of the (epi)genetic events that drive melanoma initiation and progression has been a major barrier to rational development of effective therapeutics and prognostic diagnostics for melanoma patients. Recent approaches that integrate human melanoma genomic and transcriptomic data provide unprecedented opportunities to discover oncogenic melanoma drivers. One limitation, however, is that human melanoma genome exhibits a radically altered cytogenetic profile. There is therefore the need for biologically-meaningful approaches to identify and validate lesions that drive melanomagenesis. We combined comparative oncogenomic approaches with mouse modeling to identify new cancer genes/pathways that drive melanoma progression. Spontaneously acquired genetic alterations such as copy-number alterations and specific mutations in mouse tumors of defined genetic origin were identified and used to prioritize relevant lesions from the complex human melanoma genomes. This integrated effort confirmed the importance of several genes and pathways previously implicated in melanoma and identified new putative melanoma tumor suppressor genes. Genetic ablation of one such gene, c-Fes, cooperated with BRafv600E to accelerate melanomagenesis in mice. This comparative oncogenomic approach has therefore helped discover a series of novel melanoma tumor suppressor genes, including c-FES, with prognostic and therapeutic relevance in human melanoma.

overall_design: RNA extracted from 5 Tyr::CreERT2/+;BRafV600E/+;Ptenl/l;Fes-/- and 5 Tyr::CreERT2/+;BRafV600E/+;Ptenl/l;Fes+/+ melanomas

first: Michael

last: Olvedy

first: Julie

last: Tisserand

first: Flavie

last: Luciani

first: Bram

last: Boeckx

first: Jasper

last: Wouters

first: Sophie

last: Lopez

first: Florian

last: Rambow

first: Jasmine

last: Barra

first: Corinna

last: Köhler

first: Enrico

last: Radaelli

last: Tartare-Deckert

first: Joost

last: van den Oord

first: Stein

last: Aerts

first: Patrice

last: Dubreuil

first: Diether

last: Lambrechts

first: Paulo

last: De Sepulveda

first: Jean-Christophe

last: Marine


title: Endoplasmic reticulum–mitochondria junction is required for iron homeostasis

city: Los Angeles

first: Siavash

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

summary: The Endoplasmic Reticulum–Mitochondria Encounter Structure (ERMES) is a protein complex that tethers the two organelles and creates the physical basis for communication between them. ERMES functions in lipid and calcium exchange between the ER and mitochondria, mitochondrial protein import and maintenance of mitochondrial morphology and genome. Here we report that ERMES is also required for iron homeostasis. Loss of ERMES components activates an Aft1-dependent iron deficiency response even in iron-replete conditions, leading to accumulation of excess iron inside the cell. This function is independent of ERMES known roles in calcium regulation, phospholipid biosynthesis or mitochondrial biology. A mutation in the vacuolar protein sorting 13 (VPS13) gene that rescues the glycolytic phenotype of ERMES mutants suppresses the iron deficiency response and iron accumulation. Our study reveals that proper communication between the ER and mitochondria is required for appropriate maintenance of cellular iron levels.

overall_design: various mutants

first: Yong

last: Xue


title: Identification of Amino Enhancer of Split (AES) and DDX21 binding snoRNAs by RIP-Seq.

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

institute: Heidelberg University

summary: We studied AES and DDX21 binding RNAs in Kasumi-1 cells stably expressing V5-tagged AES. RNA immunoprecipitation was performed with V5 antibody (for AES), DDX21 antibody and control IgG. We found that AES as well as DDX21 RIP samples showed enrichment for small nucleolar RNAs (snoRNAs) compared to control IgG. We also showed that AES and DDX21 binding snoRNAs showed significant overlap. Our studies provide mechanisms how AES regulates snoRNAs and rRNA modification.

overall_design: RIP followed by small RNA sequencing in Kasumi-1 cells

first: Fengbiao

last: Zhou

first: Christoph

last: Bartenhagen

first: Carsten

last: Müller-Tidow


title: Expression profile of small nucleolar RNA (snoRNA) in human acute myeloid leukemia with different leukemia stem cell frequency

summary: Leukemogenesis requires enhanced self-renewal activity, which is induced by specific oncogenes. The underlying molecular mechanisms remain incompletely understood. We measured snoRNA expression in human primary AML samples that contained determined leukemia stem cells frequency. We identified that expression of C/D box snoRNAs was closely associated with leukemia stem cell frequency.

overall_design: We used small RNA-Seq to determine the expression profile of small nucleolar RNA (snoRNA) in 20 primary AML patient samples with determined leukemia stem cell frequency (n=4 samples with high frequency, n=6 with medium and n=10 with low frequency).  Stem cell frequency and further sample information can be obtained from the following publication: Pabst, C. et al. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo. Blood (2016). doi:10.1182/blood-2015-11-683649

first: Marcel

last: Köhn

first: Caroline

last: Pabst


title: Ptbp2 controls an alternative splicing network required for cell communication during spermatogenesis

city: Cleveland

first: Donny

middle: D

last: Licatalosi

state: Ohio

address: 10900 Euclid Avenue

department: Center for RNA Molecular Biology

institute: Case Western Reserve University


title: Expression profile of small nucleolar RNA (snoRNA) in acute myeloid leukemia.

summary: Leukemogenesis requires enhanced self-renewal activity, which is induced by specific oncogenes. The underlying molecular mechanisms remain incompletely understood. We transduced mouse lineage negative bone marrow cells (enriched for hematopoietic stem and progenitor cells) with retrovirus expressing leukemic oncogene AML1-ETO9a, MYC and MLL-AF9 as well as empty vector (MIG). We found that all three oncogenes enhanced snoRNA formation. High abundance of snoRNAs was observed in primary human AML specimens with the notable exception of NPM1 mutant AML. Leukemogenesis by AML1-ETO required expression of the groucho related Amino Enhancer of Split (AES). AES functioned by inducing snoRNA/RNP formation via interaction with the RNA helicase DDX21. Similarly, loss of C/D box snoRNAs with concomitant loss of rRNA 2’-O-methylation resulted in decreased leukemia self-renewal potential.In summary, we identified C/D box snoRNAs and rRNA 2’-O-methylation as critical determinants of leukemic stem cell activity.

overall_design: We used small RNA-Seq to determine the expression profile of small nucleolar RNA (snoRNA) in 63 primary AML patient samples. To further investigate the role of AES and DDX21 in snoRNA formation we also analyzed kasumi-1 cell lines with shRNA based downregulation of AES or DDX21. Furthermore, we show that mouse snoRNAs are induced by leukemia oncogene AML-ETO9a, MLL-AF9 and MYC in mouse lineage negative bone marrow cells.


title: Ptbp2 controls an alternative splicing network required for cell communication during spermatogenesis [HITS-CLIP]

summary: Alternative splicing (AS) plays key roles in the specialization of cell functions in different tissues and stages of development.  In spermatogenic cells, the complexity of AS isoforms exceeds that of most whole tissues, but the regulation, dynamics, and functions of AS in spermatogenesis have remained poorly defined. We previously demonstrated that the RNA binding protein Ptbp2 is essential for cell survival during spermatogenesis; however, the underlying mechanisms were not explored.  Here, we demonstrate that Ptbp2 is a critical AS regulator in spermatogenic cells, and controls a functionally-related network of genes involved in germ cell adhesion and protein trafficking to and from the plasma membrane.  In parallel, we identify distinct AS programs in different stages of spermatogenesis, and demonstrate an important role for Ptbp2 in stage-specific AS regulation.  Collectively, the data provide new insights into the temporal dynamics and importance of AS in mammalian germ cell development, and demonstrate a central role for Ptbp2 in its regulation.

overall_design: Three Ptbp2 HITS-CLIP libraries generated from 8 week old CD1 mouse testes (3 biologic replicate animals).

first: Molly

last: Hannigan


title: AR-13, a celecoxib derivative, directly kills Francisella in vitro and aids clearance and mouse survival in vivo

status: Public on Jun 19 2017

city: Columbus

first: John

last: Gunn

address: 700 Children’s Drive

department: Center for Microbial Pathogenesis

institute: Abigail Wexner Research Institute at Nationwide Children’s Hospital

summary: The goal of this study is to compare transcriptomics between wild type LVS vs AR-13 isogenic resistant mutant

sample_organism: Francisella tularensis subsp. holarctica LVS

overall_design: Total RNA from the wild type and isogenic mutant were purified and subjected for sequencing

first: Ky

middle: V

last: Hoang

first: Haley

last: Adcox

first: James

last: Fitch

first: David

last: Gordon

first: Heather

last: Curry

first: Larry

last: Schlesinger

first: Peter

last: White


title: Transcriptomic analysis of two 14-3-3 proteins Bmh1 and Bmh2 under osmotic and oxidative stresses in the entomopathogen fungus Beauveria bassiana by using RNA sequencing

city: Tianjin

first: Liu

last: Qian

address: Xi 7 Dao No.32 Airport Economic Area

institute: TIB CAS

summary: Bmh1 and Bmh2 contribute equally to mediating fungal stress tolerance of Beauveria bassiana , a determinant to the biocontrol potential of fungal entomopathogens. We characterize their functionsfor the first time and interaction by multi-phenotypic analyses of single-gene deletion mutants and double-gene mutants by RNAi, and to probe possible mechanisms involved in multi-phenotypic changes by analysis of Bmh1- and Bmh2-specific transcriptomes constructed under osmotic and oxidative stresses versus wild-type (BbWT) through using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which were many more effectors and signaling factors likely involved in morphogenesis and asexual development, multidrug resistance, transcription, transduction, cell rescue, defense and virulence, and carbohydrate metabolism , were significantly down-regulated in expression level by Bmh-delection.

overall_design: Total RNA obtained from Bmh1 and Bmh2 disruption mutant subjected to 0.5 M NaCl and 40 mM H2O2 at  25°C for 1-h response compared to the wild type strain under the same stress treatment.

first: Qian

last: Liu

first: Ming-Guang

last: Feng


title: Ptbp2 controls an alternative splicing network required for cell communication during spermatogenesis [RNA-Seq]

summary: Alternative splicing (AS) plays key roles in the specialization of cell functions in different tissues and stages of development. In spermatogenic cells, the complexity of AS isoforms exceeds that of most whole tissues, but the regulation, dynamics, and functions of AS in spermatogenesis have remained poorly defined. We previously demonstrated that the RNA binding protein Ptbp2 is essential for cell survival during spermatogenesis, however the underlying mechanisms were not explored. To investigate this, we generated paired-end RNA-Seq data from wild type (WT) and Ptbp2 conditional knockout (cKO) testes at postnatal day 25 (p25) using Illumina ScriptSeq™ v2 RNA-Seq library preparation kits and sequenced at the CWRU Sequencing Core. Our resulting analyses demonstrate that Ptbp2 is a critical AS regulator in spermatogenic cells, where it controls a functionally-related network of genes involved in germ cell adhesion and protein trafficking to and from the plasma membrane. In parallel, we identified distinct AS programs in different stages of spermatogenesis, and defined a role for Ptbp2 in stage-specific AS regulation. Collectively, the data provide new insights into the importance of AS in mammalian germ cell development and demonstrate a central role for Ptbp2 in its regulation.

overall_design: Transcriptome profiling of testes in wild type (WT) and Ptbp2-deficient (cKO) mice at postnatal day 25 (p25) by deep sequencing, in duplicate using Illumina HiSeq 2500.


title: Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants

city: Louisville

first: Kevin

last: Sokoloski

state: KY

address: 505 S. Hancock St.

department: Microbiology and Immunology

institute: University of Louisville

summary: Alphaviruses are arthropod-borne viruses that represent a significant threat to public health at a global level. While the formation of alphaviral nucleocapsid cores, consisting of cargo nucleic acid and the viral capsid protein, is an essential molecular process of infection, the precise interactions between the two partners are ill-defined. A CLIP-seq approach was used to screen for candidate sites of interaction between the viral Capsid protein and genomic RNA of Sindbis virus (SINV), a model alphavirus. The data presented in this report indicates that the SINV capsid protein binds to specific viral RNA sequences in the cytoplasm of infected cells, but its interaction with genomic RNA in mature extracellular viral particles is largely non-specific in terms of nucleotide sequence. Mutational analyses of the cytoplasmic viral RNA-capsid interaction sites revealed a functional role for capsid binding early in infection. Interaction site mutants exhibited decreased viral growth kinetics; however, this defect was not a function of decreased particle production. Rather mutation of the cytoplasmic capsid-RNA interaction sites negatively affected the functional capacity of the incoming viral genomic RNAs leading to decreased infectivity. Furthermore, cytoplasmic capsid interaction site mutants are attenuated in a murine model of neurotropic alphavirus infection. Collectively, the findings of this study indicate that the identified cytoplasmic interactions of the viral capsid protein and genomic RNA, while not essential for particle formation, are necessary for genomic RNA function early during infection. This previously unappreciated role of capsid protein during the alphaviral replication cycle also constitutes a novel virulence determinant.

sample_organism:
Homo sapiens
Sindbis virus

platform_organism:
Homo sapiens
Sindbis virus

overall_design: 5 CLIP-Seq samples in TOTAL- 2 Control Samples (Input and Empty), 2 Cytoplasmic Capsid IPs, and 1 Virion Capsid IP Library.

first: Lauren

last: Nease

first: Nicholas

last: May

first: Natasha

middle: N

last: Gebhart

first: Claire

last: Jones

first: Thomas

last: Morrison

first: Richard

middle: W

last: Hardy


title: Colonic Organoids Derived from Human Pluripotent Stem Cells for Modeling Colorectal Cancer and Drug Discovery

city: Houston

first: Eduardo

last: Vilar

state: TX

address: 1515 Holcombe Blvd., Unit 1360

department: Clinical Cancer Prevention

institute: The University of Texas MD Anderson Cancer Center

summary: mRNA expression from tubular adenomas of patients with Familial Adenomatous Polyposis

overall_design: 3 tubular adenoma samples analyzed


title: TCF7L1 knockdown in pancreatic cancer

last: Dawson

state: California

address: 650 Charles E Young Dr South

department: Pathology

summary: RNAi mediated depletion of TCF7L1 increases activity of a Wnt-based reporter and imparts more aggressive tumor phenotypes in vitro in pancreatic cancer cell lines that express TCF7L1. We sought to determine what changes in transcription ocurred after RNAi mediated knockdown of TCF7L1 in these cells by RNA-sequencing

overall_design: 12 samples, 4 different conditions with 3 replicates each

first: Dawson

last: David

first: Kershaw

last: Kathleen


title: Nascent RNA-seq in Kasumi-1 cells

first: Christian

last: Rohde

summary: Amino Enhancer of Split (AES) is essential for AML1-ETO induced self-renewal and leukemogenesis. To study the effect of AES on transcription regulation in AML1-ETO expressing Kasumi-1 cells, nascent transcripts in control (shctr) and AES knockdown (shAES) Kasumi-1 cells were labelled with uridine analogue 4-thioduridine with subsequent nascent RNA purification and next generation sequencing (Nascent RNA-seq).

overall_design: Examination of nascent transcription in Kasumi-1 cells under two conditions with duplicate.

first: Fengbiao

last: Zhou

first: Hans-Ulrich

last: Klein

first: Carsten

last: Müller-Tidow


title: Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer [HNSCC]

city: La Jolla

first: Vijay

last: Pandurangan

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

summary: Therapies that boost the anti-tumor responses of cytotoxic lymphocytes (CTLs) have shown promise in the clinic. However, clinical responses to currently available immunotherapeutic agents vary considerably, for which the molecular basis is unclear. To date, unbiased transcriptomic studies of CTLs in human cancers have been performed in whole tumors or cells obtained from peripheral blood or metastatic sites of heavily pre-treated patients. We performed global transcriptional profiling of CTLs in tumors and adjacent non-tumor tissue from treatment-naïve patients with early stage lung cancer to define the molecular features associated with robustness of anti-tumor immune responses. We observed major differences in the transcriptional program of tumor-infiltrating CTLs that are shared across tumor subtypes. Pathway analysis revealed enrichment of genes in cell cycle, T cell receptor (TCR) activation and co-stimulation pathways, indicating tumor-driven expansion of presumed tumor antigen-specific CTLs. We also observed marked heterogeneity in the expression of molecules associated with TCR activation and immune checkpoints such as 4-1BB, PD1, TIM3, and their expression was positively correlated with the density of tumor-infiltrating CTLs. Interestingly, transcripts linked to tissue-resident memory cells (TRM), such as CD103, were enriched in tumors containing a high density of CTLs, and CTLs from CD103high tumors displayed features of enhanced cytotoxicity, implying better anti-tumor activity. In an independent cohort of 689 lung cancer patients, we confirmed that patients with CD103high (TRM rich) tumors survived significantly longer. In summary, we define the molecular fingerprint of tumor-infiltrating CTLs at the site of primary tumor and identify a number of novel targets that may be important in modulating the magnitude and specificity of anti-tumor immune responses in lung cancer.

overall_design: Analysis of  purified populations of CD8 T cells (isolated from primary head and neck squamous cancer tumors from patients) at the transcriptomic level by RNA sequencing.

first: Anusha-Preethi

last: Ganesan

first: Divya

last: Singh

first: Grégory

last: Seumois

last: Ottensmeier

first: Pandurangan

last: Vijaynand


title: Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer [NSCLC]

overall_design: Analysis of  purified populations of CD8 T cells (isolated from primary lung tumors and matched adjacent lung tissue of lung cancer patients) at the transcriptomic level by RNA sequencing.


title: Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer

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

overall_design: Refer to individual Series


title: AML1-ETO induces leukemia via C/D box snoRNA/RNPs.


title: Identification of Tfcp2l1 target genes in the mouse kidney

city: New York

first: Max

last: Werth

address: 1150 St. Nicholas Ave.

department: Medicine

institute: Columbia University

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: RNA-Seq Gene Expression Analysis in Rat Metanephric Mesenchyme overexpressing Transcription Factor Tfcp2l1

summary: We identified genes regulated by Tfcp2l1 overexpression in Rat Metanephric Mesenchyme

overall_design: Rat E13.5 metanephric mesenchyme was microdissected and transduced with Tfcp2l1 or GFP adenoviruses,  48 hours later RNA was isolated and analyzed by RNA-Seq

first: Jonathan

last: Barasch


title: Gene expression profiles of mouse long term repopulating hematopoietic stem cells treated with p300/catenin antagonist YH250 vs control

first: Kahn

last: Michael

address: NRT 4501, 1450 Biggy Street

department: Department of Biochemistry and Molecular Biology

institute: University of Southern California

summary: We report a single dose administration of p300/catenin antagonist YH250 can up-regulate ID2 gene expression and promote long term HSC non-differenciative proliferation.

overall_design: It is expected that some genes playing roles in maintenance of stemness and symetyric expansion will be upregulated by the treatment of YH250 compared with control.

first: Michael

last: Kahn

first: Yi

last: Zhao

first: Kaijin

last: Wu

first: Cu

last: Nguyen

first: Goar

last: Smbatyan

first: Chen

last: Yibu

first: Yusuke

last: Higuchi

first: Elisabeth

last: Melendez


title: Total RNA sequencing of WT intestinal orgaonids.

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: We report elevated expression levels of genes involved in small intestine or colon regional identity. hESCs were differentiated to colonigc organoids, where the total RNA was extracted from.

overall_design: Comparison of the expression profiles of colonic and small intestinal organoids

first: Miguel

last: Crespo


title: RNAseq study of synovial biopsies

city: Spring House

first: Alice

last: Walsh

state: PA

address: Welsh & McKean Roads

department: Immunology

institute: Janssen R&D

summary: Total RNA sequencing was performed on samples isolated from joint synovial biopsies from subjects with and without rheumatoid arthritis

overall_design: One biopsy sample per subject was analysed without replicates

first: A

first: Y

last: Guo


title: Comparison of translational profiles in Motor Neurons (CHAT), to all neurons (Snap25) in the spinal cord.

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: Translating ribosome affinity purification (TRAP) was performed on spinal cord dissections pooled from 3-4 mice 21 days post birth that were positive for the eGFP-L10A fusion ribosomal marker protein under the expression of either the Chat promoter (Tg(Chat-EGFP/Rpl10a)DW167Htz) or the Snap25 promoter (Tg(Snap25-EGFP/Rpl10a)JD362Jdd). RNA-sequencing was performed on both TRAP and pre-immunoprecipitation (PreIP) control RNA samples.

overall_design: Three replicates of PreIP and TRAP for two transgenic lines.

first: Rebecca

last: Ouwenga

first: Allison

last: Lake


title: Genome-wide profiling of the nascent transcription of non-coding RNAs in porcine heart after myocardial infarction

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

summary: Very little information is available about non-coding(nc)RNAs and their role in regulating tissue responses in myocardial ischemia and acute infarction. We measured for the first time nascent RNA transcription of protein coding genes, primary(pri)-miRNAs, long non-coding(lnc)RNAs and enhancer(e)RNAs in healthy myocardium, border zone to ischemia and infarction area in pig hearts using GRO-seq. The gene expression analysis indicated a gradient of induction of inflammatory mediators, and repression of PPAR-signaling and oxidative phosphorylation. An exception to rule was A1 adenosine receptor, which exhibited induced gene expression in the border zone, where it might increase myocardial resistance to ischemia, but repression in the ischemic zone. In addition, we interrogated for the first time the transcriptional regulation of pri-miRs and provide evidence that several arrhythmia-related target genes are further repressed at post-transcriptional level. We identified 450 lncRNAs which were differently regulated by ischemia including novel lncRNAs expressed in antisense orientation to major myocardial transcription factors GATA4, GATA6 and KLF6. Finally, characterization of enhancers exhibiting differential expression of eRNAs, pointed a central role for KLF, MEF2C, ETS, NFY, ATF, E2F2 and NRF1 transcription factors in determining tissue-specific responses to ischemic insult. In conclusion, GRO-Seq allowed us to follow the gradient of gene expression occurring in the ischemic heart and identify novel ncRNAs regulated by oxygen deprivation. These findings have identified potential new targets for diagnosis and treatment of myocardial ischemia based on acute changes in eRNA, lncRNA and miRNA expression in the affected heart.

overall_design: GRO-Seq from pig myocardium

first: Paavo

last: Halonen

first: Tiia

last: Husso


title: Total RNA sequencing of APC mutant and wt colonic organoids

summary: We report elevated expression levels of genes involved in colon cancer in samples that carry mutations in the APC gene. Mutated skin fibroblasts were reprogrammed to iPSCs and then differentiated to colonigc organoids, where the total RNA was extracted from.

overall_design: Comparison of the expression profiles of APC mutant and WT colonic organoids


title: Genome-wide mapping of MAT2A-associsted regions in bovine blastocysts

city: Kyoto

first: Shuntaro

last: Ikeda

address: Kitashirakawa Oiwake-cho, Sakyo-ku

department: Graduate School of Agriculture

country: Japan

institute: Kyoto University

summary: Methionine adenosyltransferase (MAT), that catalyzes the synthesis of S-adenosylmethionine (SAM) from ATP and methionine, is involved in folate-mediated one-carbon metabolism (OCM) that is essential for preimplantation embryos in terms of both short-term periconceptional development and long-term phenotypic programming beyond the periconceptional period. SAM is the universal methyl donor for epigenetic methylation of DNA and histones. In the context of the long-term phenotypic programming by the modulation of OCM during periconceptional period, possible interactions between MAT2A and epigenetic status of specific genes during this period are of particular interest. MAT2A has been proposed to interact with many chromatin-related proteins and be recruited to their specific target genes to constitute gene-regulatory complexes. Thus, in the aim of addressing the possible interaction of MAT2A with specific genomic DNA regions in periconceptional period, we performed a ChIP-seq analysis using MAT2A antibody against bovine blastocysts.

overall_design: In vitro produced bovine blastocysts were processed to ChIP-Seq using MAT2A antibody with corresponding Input and IgG control. The same procedures were duplicated using total of 669 and 677 blastocysts, respectively, for each replicate.

first: Ryouka

last: Kawahara-Miki

first: Hisataka

last: Iwata

first: Miki

last: Sugimoto

first: Shinichi

last: Kume


title: Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

summary: Polyadenylation of nascent RNA by poly(A) polymerase (PAP) is important for 3’ end maturation of almost all eukaryotic mRNAs. Most mammalian genes harbor multiple polyadenylation sites (PASs), leading to expression of alternative polyadenylation (APA) isoforms with distinct functions. How poly(A) polymerases may regulate PAS usage and hence gene expression is poorly understood. Here we show that the nuclear canonical (PAPalpha and PAPgamma) and non-canonical (Star-PAP) PAPs play diverse roles in PAS selection and gene expression. Deficiencies in the PAPs resulted in perturbations of gene expression, with Star-PAP impacting lowly expressed mRNAs and long-noncoding RNAs to the greatest extent. Importantly, different PASs of a gene are distinctly regulated by different PAPs, leading to widespread relative expression changes of APA isoforms. The location and surrounding sequence motifs of a PAS appear to differentiate its regulation by the PAPs. We show Star-PAP-specific PAS usage regulates the expression of the eukaryotic translation initiation factor EIF4A1, the tumor suppressor gene PTEN, and the long non-coding RNA NEAT1. The Star-PAP-mediated APA of PTEN is essential for DNA damage-induced increase of PTEN protein levels. Together, our results reveal a PAS-guided and PAP-mediated paradigm for gene expression in response to cellular signaling cues.

overall_design: 3'READS of siStar-PAP, siPAPα, siPAPγ and siCtrl samples in HEK293 cells

first: Weimin

first: Rakesh

last: Laishram

first: Zhe

last: Ji

first: Mainul

last: Hoque

first: Bin

last: Tian

first: Richard

middle: A

last: Anderson


title: Epigenetic activation of the prostaglandin receptor EP4 promotes resistance to endocrine therapy for breast cancer [Methyl-MAPS]

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

summary: Approximately 75% of breast cancers express estrogen receptor α (ERα) and depend on estrogen signals for continued growth. Aromatase inhibitors (AIs) prevent estrogen production and inhibit estrogen receptor signaling, resulting in decreased cancer recurrence and mortality. Advanced tumors treated with AIs almost always develop resistance to these drugs via the up-regulation of alternative growth signals. The mechanisms that drive this resistance—especially epigenetic events that alter gene expression—are however not well understood. Here we performed a genome-wide DNA methylation and expression analysis of cell line models to find epigenetically regulated genes involved in acquired aromatase inhibitor resistance. We discovered that prostaglandin E2 receptor 4 (PTGER4) is up-regulated after demethylation and promotes phosphorylation and activation of ERα. Knockdown and inhibitor studies demonstrate that PTGER4 promotes AI resistance via ligand independent activation of the ERα-cofactor CARM1. We believe that we have discovered a novel epigenetic mechanism for altering cell signaling and acquiring endocrine therapy resistance. Our findings indicate that PTGER4 is a potential drug target in AI resistant cancers. Additionally, the epigenetic component of PTGER4 regulation suggests that further study of PTGER4 may yield valuable insights into how DNA methylation-targeted diagnoses and/or treatments can improve AI resistant breast cancer treatment.

overall_design:
Methyl-MAPS was used to generate genome-wide DNA methylation profiles for MCF7-LTED (long-term estrogen deprived) cells grown in charcoal stripped serum. McrBC and RE libraries were each sequenced on two slides.

Please note that the slide1 and slide2 are the same library loaded on two slides.


title: Epigenetic activation of the prostaglandin receptor EP4 promotes resistance to endocrine therapy for breast cancer


title: RNA-seq of C. elegans worms treated with RNAi toward daf-2 or cav-1 or left untreated (EV) to compare gene expression profiles

city: Jerusalem

first: Ehud

last: Cohen

address: Ein Karem

institute: The Hebrew University of Jerusalem

summary: We observed functional outcomes of cav-1 knockdown and wanted to characterize changes in gene expression profiles following this manipulation. To address this, we treated nematodes with daf-2 or cav-1 RNAi and compared gene expression profiles to these of untreated worms. The knockdown of cav-1 resulted in modulation in the expression of 92 genes, and some of them overlapped with genes which were affected by knockdown of daf-2.

overall_design: We performed two biological repeats. Each repeat we had 3 samples: (1) worms that were left untreated (EV), (2) worms that were treated with RNAi toward daf-2, and  (3) worms that were treated with RNAi toward cav-1.

first: Noa

last: Roitenberg


title: Maize transcriptional responses to specialist and generalist spider mite herbivores

status: Public on Jun 17 2017

city: Salt Lake City

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

summary: Spider mites, including the two-spotted spider mite (Tetranychus urticae, TSSM) and the Banks grass mite (Oligonychus pratensis, BGM), are becoming increasingly important agricultural pests. The TSSM is an extreme generalist documented to feed on more than 1100 plant hosts. In contrast, the BGM is a grass specialist, with hosts including important cereal crops like maize, wheat, and sorghum. Historically, studies of plant-herbivore interactions have focused largely on insects. As such, far less is known about plant responses to spider mite herbivores, especially in grasses, and whether responses differ between generalist and specialist mites. To identify plant defense pathways responding to spider mites, we collected time course RNA-seq data from maize (Zea mays) infested with TSSMs and BGMs. Additionally, and as a comparison to the physical damage caused by spider mite feeding, a wounding treatment was also included. In total, four biological samples were generated per treatment.

overall_design: The experiment was performed with four biological replicates across each of the following (28 samples in total): no infestation (C, control), 2hr after wounding (W2), 24hr after wounding (W24), 2hr after TSSM infestation (T2), 24hr after TSSM infestation (T24), 2hr after BGM infestation (B2), and 24hr after BGM infestation (B24).

first: Huyen

last: Bui

first: Robert

last: Greenhalgh

first: Ricardo

last: Ramirez


title: Epigenetic activation of the prostaglandin receptor EP4 promotes resistance to endocrine therapy for breast cancer [RNA-seq]

summary: Approximately 75% of breast cancers express estrogen receptor α (ERα) and depend on estrogen signals for continued growth. Aromatase inhibitors (AIs) prevent estrogen production and inhibit estrogen receptor signaling, resulting in decreased cancer recurrence and mortality. Advanced tumors treated with AIs almost always develop resistance to these drugs via the up-regulation of alternative growth signals. The mechanisms that drive this resistance - especially epigenetic events that alter gene expression - are however not well understood. Here we performed a genome-wide DNA methylation and expression analysis of cell line models to find epigenetically regulated genes involved in acquired aromatase inhibitor resistance. We discovered that prostaglandin E2 receptor 4 (PTGER4) is up-regulated after demethylation and promotes phosphorylation and activation of ERα. Knockdown and inhibitor studies demonstrate that PTGER4 promotes AI resistance via ligand independent activation of the ERα-cofactor CARM1. We believe that we have discovered a novel epigenetic mechanism for altering cell signaling and acquiring endocrine therapy resistance. Our findings indicate that PTGER4 is a potential drug target in AI resistant cancers. Additionally, the epigenetic component of PTGER4 regulation suggests that further study of PTGER4 may yield valuable insights into how DNA methylation-targeted diagnoses and/or treatments can improve AI resistant breast cancer treatment.

overall_design: RNA-Seq was used to generate mRNA expression profiles of MCF7-LTED (long-term estrogen deprived) cells grown in charcoal stripped serum. Two replicates were performed.


title: IGF-1 gene therapy in aging rats modulates hippocampal genes relevant to memory function

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: In rats, learning and memory performance decline during normal aging, which makes this rodent species a suitable model to evaluate therapeutic strategies. In aging rats, insulin-like growth factor-I (IGF-I), is known to significantly improve spatial memory accuracy as compared to control counterparts. A constellation of gene expression changes underlie the hippocampal phenotype of aging but no studies on the effects of IGF-I on the hippocampal transcriptome of old rodents have been documented. Here, we assessed the effects of IGF-I gene therapy on spatial memory performance in old female rats and compared them with changes in the hippocampal transcriptome.

overall_design: Hippocampal RNA-Seq profiles of 28 months old rats intracerebroventricularly injected with an adenovector expressing rat IGF-I was compared with placebo adenovector-injected counterparts (4 samples each group)

first: Rodolfo

last: Goya

first: Tiago

last: Outeiro


title: Developmentally-Faithful and Effective Human Erythropoiesis in Immunodeficient and Kit Mutant Mice

status: Public on Jun 16 2017

city: Boston

first: Vijay

last: Sankaran

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Immunodeficient mouse models have been valuable for studies of human hematopoiesis, but high-fidelity recapitulation of erythropoiesis in most xenograft recipients remains elusive. Recently developed immunodeficient and Kit mutant mice, however, have provided a suitable background to achieve higher-level human erythropoiesis after long-term hematopoietic engraftment. While there has been some characterization of human erythropoiesis in these models, a comprehensive analysis of various developmental stages has not yet been reported. Here, we have utilized cell surface phenotypes, morphologic analyses, and molecular studies to fully characterize human erythropoiesis from multiple developmental stages in immunodeficient and Kit mutant mouse models following long-term hematopoietic stem and progenitor cell engraftment. We show that human erythropoiesis in such models demonstrates complete maturation and enucleation, as well as developmentally appropriate globin gene expression. These results provide a framework for future studies to utilize this model system for interrogating disorders affecting human erythropoiesis and for developing improved therapeutic approaches.

overall_design: (mRNA-seq) RNA-seq of human CD235a+ cells isolated 14-16 weeks post-implantation from mouse bone marrow were performed for three biological replicates each of mice xenograted with adult bone marrow-derived human CD34+ cells and cord blood-derived CD34+ cells.

first: Sean

last: McFarland

middle: G


title: Role of JunB in Th17 cell effector stability [RNA-seq]

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

institute: Duke University School of Medicine

summary: Here we identify the activator protein-1 (AP-1) factor JunB as an essential regulator of Th17 cell identity. JunB activates the expression of Th17 lineage-specifying genes, and coordinately represses genes controlling Th1 and Treg fate. Through regulatory analysis, we find that JunB is a core regulator of global transcriptional programs that promote Th17 cell identity and restrict alternative CD4+ T cell potential.

overall_design: Examination of differential gene expression in Junb+/+CD4cre and Junbfl/flCD4cre 48 hour in vitro polarized Th17 cell cultures

first: Tiffany

last: Carr

first: Joshua

last: Wheaton


title: Next Generation Sequencing Facilitates Quantitative Analysis of Differentially Expressed Genes and Transcriptional Regulation Induced by Salt Stress in  Upland Cotton

status: Public on Jun 18 2017

city: Anyang

first: Du

last: Xiongming

state: Henan

address: 38# Huanghe Avenue

institute: Institute of cotton research of CAAS

summary:
Purpose:Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology. And quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods:We investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics approach was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions.
Results:During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype.
Conclusions:Our comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance.

overall_design: Leaf mRNA and miRNA profiles of  14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive during a 72-h NaCl exposure were generated by deep sequencing, using Illumina HiSeq 2000 system.

first: Xiongming

last: Du

first: Zhen

last: Peng


title: Genome wide map of Tfcp2l1 binding sites from mouse kidney

first: Max

last: Werth

state: NY

summary: We identified Tfcp2l1 binding sites in mouse kidney using Chromatin Immunoprecipitation followed by high-throughput sequencing (ChiP-Seq)

overall_design: Analysis of Chromatin Immunoprecipitation by Tfcp2l1 antibody vs. IgG control

first: Jonathan

last: Barasch


title: Histone lysine-to-methionine mutation reprograms the histone methylation landscape and contributes to pleiotropic development in Arabidopsis

city: Madison

first: Christine

last: Wooddell

state: WI

address: 502 S Rosa Rd

institute: Arrowhead Pharmaceuticals

summary: This study investigated the effect of expressing transgenic H3 with K36M missense mutations. We uncovered pleiotropic phenotypic defects and a strong loss of endogenous H3K36 methylation in all forms (me1,me2,me3)

overall_design: Arabidopsis WT (containing non-mutated transgenic H3) and K36M (containing transgenic H3 K36M) plants were subject to ChIP-sequecing analysis using the H3K36me3 antibody (ab 9050) upon noting global losses of endogenous H3K36me3. Similarly grown samples were also subject to RNA-seq to investigate transcriptional changes associated with H3K36 methylation loss

first: Xuehua

last: Zhong

first: Dean

last: Sanders


title: The islet resident macrophage is in an inflammatory state and senses microbial products in blood

first: Javier

last: Carrero

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

summary: We examined the transcriptional profiles of macrophages that reside in the islets of Langerhans of NOD, NOD.Rag1-/-, and B6.g7 mice at three weeks of age. Islet macrophages expressed an activation signature with high expression of Tnf, Il1b, and MHC-II both at the transcript and protein levels. These features are common with barrier macrophages of the lung and gastrointestinal tract. Moreover, injection of lipopolysaccharide induced a rapid inflammatory gene expression, indicating that blood stimulants are accessible to the macrophages and that these macrophages can sense them. In NOD mice, the autoimmune process imparted an increased inflammatory signature, including elevated expression of chemokines, chemokine receptors, and an oxidative response. The elevated inflammatory signature indicates that the autoimmune program was active at the time of weaning. Thus, the macrophages of the islets of Langerhans are poised to mount an immune response even at steady state, while the presence of the adaptive immune system elevates their activation state.

overall_design: We examined the transcriptional profiles of macrophages that reside in the islets of Langerhans of NOD, NOD.Rag1-/-, and B6.g7 mice at three weeks of age.  Lung macrophages and pancreatic LN dendritic cells of NOD mice were also examined.

first: Pavel

last: Zakharov

first: Stephen

last: Ferris


title: RNA-sequencing in MDA-231-D cells transfected with ZEB1 or ZEB2 siRNAs

city: Tokyo

first: Daizo

last: Koinuma

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

institute: University of Tokyo

summary: We searched for roles of ZEB1and/or ZEB2 during EMT by RNA-seq in breast cancer cells.

overall_design: Expression of mRNA in a basal type breast cancer cell line MDA-231-D transfected with ZEB1 or ZEB2 siRNAs.

first: Akihiro

last: Katsura

first: Yusuke

last: Tamura

first: Masato

last: Morikawa

first: Tsubasa

last: Sakurai

first: Anna

last: Mizutani

first: Yasuyuki

last: Morishita

first: Kohei

last: Miyazono


title: RNA-sequencing in TGF-beta treated MDA-231-D cells transfected with ZEB1/ZEB2 siRNAs [RNA-seq]

summary: We searched for roles of ZEB1 during EMT by RNA-seq in breast cancer cells.

overall_design: Expression of mRNA in a basal type breast cancer cell line MDA-231-D transfected with ZEB1/ZEB2 siRNAs and stimulated with TGF-beta for 24 h.


title: ZEB1 binding sites in TGF-beta-stimulated MDA-231-D and Hs578T basal type breast cancer cell lines [ChIP-seq]

summary: We searched for roles of ZEB1 during EMT through genome-wide analysis of its binding sites in breast cancer cells.

overall_design: ZEB1 binding sites in TGF-beta-stimulated MDA-231-D and Hs578T cells were determined by ChIP-seq.


title: Hit-and-run' programing of CAR-T cells using mRNA nanocarriers

city: Seattle

first: Matthias

last: Stephan

state: WA

address: 1100 Fairview Ave. N.

department: Program in Immunology

institute: Fred Hutchinson Cancer Research Center

summary: RNAseq of ex vivo CD8 T cell lineages and in vitro differentiated CD8 T cells treated with nanocarriers encapsulating control or Foxo1-3A transcription factor mRNA

overall_design: Gene expression in central memory CD8 and in vitro Foxo1-3A nanoparticle treated CD8 were compared to control cells cultured in vitro with eGFP mRNA encapsulating nanoparticles.

first: Howell

middle: F

last: Moffett


title: Developmental transcription factor NFIB is a putative target of oncofetal miRNAs and is associated with tumour aggressiveness in lung adenocarcinoma

city: Vancouver

first: Daiana

middle: D.

last: Becker-Santos

state: BC

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: British Columbia Cancer Research Centreb

summary: Genes involved in fetal lung development are thought to play crucial roles in the malignant transformation of adult lung cells.  Consequently, the study of lung tumour biology in the context of lung development has the potential to reveal key developmentally relevant genes that play critical roles in lung cancer initiation/progression.  Here, we describe for the first time a comprehensive characterization of miRNA expression in human fetal lung tissue, with subsequent identification of 37 miRNAs in non-small cell lung cancer (NSCLC) that recapitulate their fetal expression patterns. Nuclear Factor I/B (NFIB), a transcription factor essential for lung development, was identified as a potential frequent target for these “oncofetal” miRNAs.

overall_design: We performed a comprehensive characterization of miRNA expression in human fetal lung tissues, NSCLC tumours and patient-matched non-malignant lung parenchymal tissues by miRNA sequencing. The miRNA-sequencing data for other NSCLC samples used in this study  (i.e. all the ones with the adenocarcinoma subtype) were previously deposited in GEO (GSE62182).


title: Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance

status: Public on Jun 15 2017

city: Shanghai

first: yiwen

last: Deng

state: Shanghai

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

institute: Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

summary: Crop breeding aims to balance disease resistance with yield; however, single resistance (R) genes can lead to resistance breakdown, and R gene pyramiding may affect growth fitness. Here we report that the rice Pigm locus contains a cluster of genes encoding nucleotide-binding leucine-rich repeat (NLR) receptors that confer durable resistance to the fungus Magnaporthe oryzae without yield penalty. Among these NLR receptors, PigmR confers broad-spectrum resistance, whereas PigmS competitively attenuates PigmR homodimerization to suppress resistance. PigmS expression, and thus PigmR-mediated resistance, are subjected to tight epigenetic regulation. PigmS increases seed production to counteract the yield cost induced by PigmR Therefore, our study reveals a mechanism balancing high disease resistance and yield through epigenetic regulation of paired antagonistic NLR receptors, providing a tool to develop elite crop varieties.

overall_design: The small RNA profiles of the leaves of two-weeks seedling of rice variety NIL-Pigm were generated by deep sequence dependent on Illumina Hiseq2000.

first: Yiwen

first: Xudong

last: Zhu

first: Qun

last: Li

first: Zuhua

last: He


title: Determination of tRNA aminoacylation levels by high throughput sequencing

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

summary: Here we develop a high throughput sequencing method that enables accurate determination of charged tRNA fractions at single base resolution (Charged tRNA-seq). Our method takes advantage of the recently developed DM-tRNA-seq method, but includes additional chemical steps that specifically remove the 3'A residue in the uncharged tRNA. Charging fraction is obtained by counting the fraction of A-ending reads versus A+C-ending reads for each tRNA species. In HEK293T cells, most cytosolic tRNAs are charged at >90% levels, whereas tRNASer and tRNAThr are generally charged at lower levels. These low charging levels were validated using acid denaturing gels. Our method should be widely applicable for investigations of tRNA charging as a parameter for biological regulation.

overall_design: 3 biological replicates of tRNA from HEK293T cells are analyzed; each biological replicate is also demethylase treated/untreated

first: Molly

last: Evans

first: Wesley

last: Clark

first: Guanqun

last: Zheng


title: Gene expression profiling in Ciona TVCs with FGF-MAPK perturbation [bulk RNA-seq]

city: New York

first: wei

last: wang

address: 100 washington square east

department: Biology

institute: New York University

summary:
Dynamic gene expression programs determine multipotent cell states and fate choices during development. Multipotent progenitors for cardiomyocytes and branchiomeric head muscles populate the pharyngeal mesoderm of vertebrate embryos, but the mechanisms underlying cardiopharyngeal multipotency and heart vs. head muscle fate choices remain elusive. The tunicate Ciona emerged as a simple chordate model to study cardiopharyngeal development with unprecedented spatio-temporal resolution. We analyzed the transcriptome of single cardiopharyngeal lineage cells isolated at successive time points encompassing the transitions from multipotent progenitors to distinct first and second heart, and pharyngeal muscle precursors. We reconstructed the three cardiopharyngeal developmental trajectories, and characterized gene expression dynamics and regulatory states underlying each fate choice. Experimental perturbations and bulk transcriptome analyses revealed that ongoing FGF/MAPK signaling maintains cardiopharyngeal multipotency and promotes the pharyngeal muscle fate, whereas signal termination permits the deployment of a full pan-cardiac program and heart fate specification. We identified the Dach1/2 homolog as a novel evolutionarily conserved second-heart-field-specific factor and demonstrate, through lineage tracing and CRISPR/Cas9 perturbations,  that it operates downstream of Tbx1/10 to actively suppress the first heart lineage program. This data indicates that the regulatory state of multipotent cardiopharyngeal progenitors determines the first vs. second heart lineage choice, and that Tbx1/10 acts as a bona fide regulator of cardiopharyngeal multi potency.
We performed bulk RNAseq to profile the FACS purified Ciona Robusta Truck Ventral Cells (TVCs) with FGF-MAPK perturbation conditions to address the question- What is the role of FGF signaling pathway during early cardiopharyngeal specification.  we performed bulk RNA sequencing of FACS-purified cardiopharyngeal lineage cells isolated from embryos and larvae expressing either a dominant negative form the fibroblast growth factor receptor (dnFGFR), or a constitutively active form of M-Ras (caM-Ras), the sole Ras homolog in Ciona, under the control of TVC-specific enhancers.

overall_design: Examination of 2 different FGF-MAPK perturbation conditions in TVCs from 4 time points.

first: Wei

last: Wang

first: Xiang

last: Niu

first: Lionel

last: Christiaen

first: Rahul

last: Satija


title: RNA sequencing data from pigs with high and low intramuscular fat content.

city: Wanju

first: Kyung-Tai

last: Lee

state: JeonBuk

address: 1500 Kongjwipatjwi

department: Animal Genomics and Bioinformatics Division

country: South Korea

institute: National Institute of Animal Science

summary: Intramuscular fat (IMF) content in pork is an important element of consumer preference, and is positively correlated with meat quality, including tenderness and juiciness. With advances in RNA sequencing technologies, transcriptome-related differences can be associated with specific traits in animals. The objective of this study was to investigate the differentially expressed genes (DEG) closely related with IMF content in porcine longissimus muscle using RNA sequencing. A total of 107 Berkshire pigs were used for IMF content measurements and significant difference between extremely high (H, n=3) and low (L, n=3) IMF content groups was found (P < 0.0001). From multi-dimensional scaling analyses, it was observed that the relationships between H and L groups were similar to each other. Here, we identified a total of 134 genes that were differentially expressed between the groups (FDR < 0.05, and FC ≥ 2). Functional analyses with DEGs revealed that the lipid metabolism (SCD and FASN) was one of the significant biological processes related with IMF content determination. In addition, we also found that DEGs related with muscle regeneration (MYOG and VEGFA) and extracellular matrix (COL1A1, COL1A2, COL5A1, COL14A1, and COL15A1) were changed between individuals with the extreme IMF contents, interestingly. These results will aid in understanding the regulation of IMF contents in pigs.

overall_design: The mRNA profiles in longissimus muslce from pig with high (n=3) and low (n=3) intramuscular fat contents were generated by an Illumina HiSeq 2000 Sequencing System.

first: Tae

last: Kim

first: Kyu-Sang

last: Lim


title: Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells

city: Guangzhou

first: Lin

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

summary: Single-cell epigenome sequencing techniques have recently been developed. However, the combination of different layers of epigenome sequencing in an individual cell has not yet been achieved. Here, we developed a single-cell multi-omics sequencing technology (single-cell COOL-seq) that can analyze the chromatin state/nucleosome positioning, DNA methylation, copy number variation and ploidy simultaneously from the same individual mammalian cell. We used this method to analyze the reprogramming of the chromatin state and DNA methylation in mouse preimplantation embryos. We found that within < 12 h of fertilization, each individual cell undergoes global genome demethylation together with the rapid and global reprogramming of both maternal and paternal genomes to a highly opened chromatin state. This was followed by decreased openness after the late zygote stage. Furthermore, from the late zygote to the 4-cell stage, the residual DNA methylation is preferentially preserved on intergenic regions of the paternal alleles and intragenic regions of maternal alleles in each individual blastomere. However, chromatin accessibility is similar between paternal and maternal alleles in each individual cell from the late zygote to the blastocyst stage. The binding motifs of several pluripotency regulators are enriched at distal nucleosome depleted regions from as early as the 2-cell stage. This indicates that the cis-regulatory elements of such target genes have been primed to an open state from the 2-cell stage onward, long before pluripotency is eventually established in the ICM of the blastocyst. Genes may be classified into homogeneously open, homogeneously closed and divergent states based on the chromatin accessibility of their promoter regions among individual cells. This can be traced to step-wise transitions during preimplantation development. Our study offers the first single-cell and parental allele-specific analysis of the genome-scale chromatin state and DNA methylation dynamics at single-base resolution in early mouse embryos and provides new insights into the heterogeneous yet highly ordered features of epigenomic reprogramming during this process.

overall_design: In total, we analyzed 24 single embryonic stem cells as well as 4 bulk samples of embryonic stem cells and 223 single cells from the oocyte stage to the blastocyst stage as well as 9 bulk samples of sperm cells.

first: Fan

last: Guo

first: Jingyun

first: Fuchou

last: Tang


title: In vivo genome-wide chromatin immunoprecipitation for the chondrogenic transcription factors, Sox9, Sox5 and Sox6

city: Potsdam

first: Thomas

last: Lufkin

address: 8 Clarkson Avenue

institute: Clarkson University

summary: Tissue ChIP-seq was performed on transcription factor Sox5, Sox6 and Sox9 using limbs and tails from E13.5 mouse embryos to find their in vivo binding sites in the genome

overall_design: Sox9 and Sox6 ChIP-seq was performed on wildtype mice whereas Sox5 ChIP-seq was done using transgenic wildtype mice.

first: Sook-Peng

last: Yap

first: Wenqing-Jean

first: Petra

last: Kraus


title: Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (RNA-Seq)

status: Public on Jun 14 2017

city: Oxford

first: Jelena

middle: M

last: Telenius

address: MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington

department: Weatherall Institute of Molecular Medicine (WIMM)

institute: Oxford University

summary: The genome is organized via CTCF/cohesin binding sites, which partition chromosomes into 1-5Mb topologically associated domains (TADs), and further into smaller contact sub-domains within TADs (sub-TADs; 40-1000kb). Here we examined in vivo an ~80kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ~1Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF/cohesin sites which are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. Whereas the α-globin regulatory elements normally act solely on promoters downstream of the enhancers, removal of a conserved upstream CTCF/cohesin boundary extends the sub-TAD to the adjacent upstream CTCF/cohesin binding site. The α-globin enhancers now interact with the flanking chromatin, upregulating expression of genes within this extended sub-TAD. Rather than acting solely as a barrier to chromatin modification, CTCF/cohesin boundaries in this sub-TAD regulate both directionality and specificity of enhancer interactions with surrounding promoters.

overall_design: RNA-seq of globin-depleted polyA-isolated RNA libraries isolated from primary erythroid ter119+ cells obtained from the spleens of acetylphenylhydrazine treated mice. Wild-type C57BL/6 mice were comparied with mice containing deletions for HS-29 (D29) or HS-38 and HS-39 (D3839) CTCF binding sites. Biological triplicates are included for each mouse and are analysed compared to WT (C57)

first: Lars

middle: P

last: Hanssen

first: Douglas

last: Higgs


title: Heterogeneous ribosomes exist and selectively translate distinct subpools of mRNAs in stem cells

city: Stanford

first: Zhen

last: Shi

address: 279 Campus Drive

institute: Stanford

summary: Emerging studies have linked the ribosome to more selective control of gene regulation. However, an outstanding question is whether ribosome heterogeneity at the level of core ribosomal proteins (RPs) enables ribosomes to preferentially translate specific mRNAs genome-wide. Here, we measured the absolute abundance of RPs in translating ribosomes and profiled transcripts that are enriched or depleted from select subsets of ribosomes within embryonic stem cells. We find that heterogeneity in RP composition endows ribosomes with different selectivity for translating subpools of transcripts including those controlling metabolism, the cell cycle, and development. As a paradigm example, we show that mRNAs enriched in binding to RPL10A/uL1-containing ribosomes require RPL10A/uL1 for their efficient translation. Within several of these transcripts, we find this level of regulation is mediated, at least in part, by internal ribosome entry sites. Together, these results reveal a critical functional link between ribosome heterogeneity and the post-transcriptional circuitry of gene expression.

overall_design: To identify the transcripts specifically translated by ribosomes demarcated by RPL10A or RPS25, we enriched for RPL10A or RPS25-containing ribosomes by immunoprecipitation (IP), and performed RPL10A-Ribo-Seq and RPS25-Ribo-Seq (2 replicates each), with the control being total Ribo-Seq (2 replicates each). To further assess the translation efficiencies of mRNAs upon Rpl10a knockdown at genome-wide scale, we performed RNA-Seq (2 replicates each) of purified RNAs from combined medium and heavy polysome fractions containing the most actively translating ribosomes (>=4 ribosomes along a mRNA molecule), and from all other fractions containing the free ribonucleoproteins (RNPs), 40S/60S ribosomal free subunits, 80S/monosomes as well as light polysomes (2-3 ribosomes per mRNA molecule).

first: Kotaro

last: Fujii

first: Kyle

last: Kovary

first: Naomi

last: Genuth

first: Hannes

last: Röst

first: Maria

last: Teruel

last: Barna


title: Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (ChIP-Seq)

overall_design: ChIP-seq with indicated antibodies on chromatin isolated from primary erythroid ter119+ cells obtained from the spleens of acetylphenylhydrazine treated mice. Wild-type C57BL/6 mice were comparied with mice containing deletions for HS-29 (D29) or HS-38 and/or HS-39 (D38, D39,D3839) CTCF binding sites. Duplicate ChIP data is analysed for each antibody and genotype. (Third replicate of CTCF is provided, but was not used in the publication). Mutant data (Dxx) is compared to wild-type (C57) ChIP-seq.

middle: R


title: Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (Capture-C"

overall_design:
NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments; in this case promoters, enhancers and CTCF binding sites in the alpha-globin subTAD were used as viewpoints. The method was applied to wild type mouse erythroid and mES cells and to in vivo models in which CTCF sites -HS38 and -HS39 were deleted in combination.
-------------------------
A1_R1_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
A4_HS38_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
A5_CTCF48_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
mpg_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
rhbd_ESvsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
A1_R1_DEL3839vsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
A5_CTCF48_DEL3839vsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
mpg_DEL3839vsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
rhbd_DEL3839vsC57BL6.gfc: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

first: A

last: Oudelaar

first: Jim

last: Hughes


title: T Cell Expression of AhR Inhibits the Maintenance of pTreg Cells in the GI Tract in Acute GvHD

city: Chapel Hill

first: Jonathan

middle: S

last: Serody

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Transcriptome analysis of murine T cells pre- and post-transplant.

overall_design: Sorted CD4 and CD8 splenic T cells  where evaluated by RNA-seq either at the time of allogeneic transplant or 14 days after.

first: Trisha

last: Dant

first: Danny

last: Bruce

first: Jon


title: Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

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

overall_design: Refer to individual Series


title: Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (ATAC-Seq)

overall_design: ATAC-seq on chromatin isolated from primary erythroid ter119+ cells obtained from the spleens of acetylphenylhydrazine treated mice. Wild-type C57BL/6 mice were comparied with mice containing deletions for HS-29 (D29) or HS-38 and/or HS-39 (D38, D39,D3839) CTCF binding sites. Experiments are performed in duplicate in mutant and WT mice.