title: Alternative splicing factor hnRNPA1 induces U2AF2 association with Alu-derived RNA

city: Santa Cruz

first: Jonathan

middle: Michael

last: Howard

address: 1154 High Street

department: Molecular, Cell, and Developmental Biology

institute: University of California-Santa Cruz

summary: Alternative splicing drives transcriptome and proteome diversification. While splicing regulatory proteins govern this process, their global mechanisms remain enigmatic. We generated high resolution transcriptome-wide protein-RNA interaction maps to determine how the splicing repressor hnRNPA1 influences the global association of spliceosome assembly factor U2AF2 and SRSF1 with pre-mRNA. We observed changes in the distribution of U2AF2 crosslinking sites relative to the 3’ splice sites of cassette exons but not constitutive exons upon hnRNPA1 overexpression. By contrast, SRSF1 crosslinking patterns relative to splice sites are independent of hnRNPA1 expression levels. We also observed an hnRNPA1-dependent increase in U2AF2 but not SRSF1 crosslinking to exon proximal antisense Alu elements. Thus Alu elements can serve as splicing factor-responsive sinks for U2AF2. These results not only demonstrate a novel mechanism for alternative splicing regulation but also implicate retrotransposon-derived sequences in the evolution of species-specific alternative splicing.

overall_design: Perform iCLIP and RNA-seq from cells expressing endogenous or overexpressed levels of hnRNP A1.  iCLIP was performed on hnRNP A1 and two splicing factors seen to be influenced by modulation of hnRNP A1 levels in vitro, SRSF1 and U2AF2. RNA-seq was performed to determine splicing changes between two conditions for comparison to changes seen between iCLIP datasets under same conditions. These changes are summarized globally, as well as at observed splicing changes, and on representative examples.

first: Hai

last: Lin

first: Sol

last: Katzman

first: Jeremy

last: Sanford


title: PfAP2-I-GFP anti-GFP and anti-IgG ChIP-seq

status: Public on Jun 01 2017

city: University Park

first: Manuel

last: Llinas

state: Pennsylvania

address: Millennium Science Complex

department: Biochemistry and Molecular Biology

country: USA

institute: Pennsylvania State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To determine the genome-wide occupancy of the Plasmodium falciparum transcriptional regulator of invasion PfAP2-I (PfDd2_100013100/PF3D7_1007700), we used chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq). Synchronized, schizont stage, 40 hours post-invasion, cultures of parasites expressing the AP2-I-GFP fusion protein were treated with formaldehyde to crosslink proteins to DNA and harvested. After shearing the DNA, the chromatin was incubated with anti-GFP antibody or IgG (as control) for immunoprecipitation. This material was used to generate Illumina sequencing libraries. The final libraries were multiplexed with fourteen barcoded samples per lane on an Illumina HiSeq 2500 system to generate 150 base pair single-end reads.

overall_design: ChIP-seq libraries were prepared using three independently collected chromatin immunoprecipitated DNA samples from Plasmodium falciparum Dd2 parasites expressing AP2-I-GFP. ChIP was performed using a polyclonal anti-GFP antibody or, as a control, the same amount of anti-IgG, resulting in 3 total samples for each chromatin sample: 1 AP2-I-GFP anti-GFP ChIPed DNA, 1 AP2-I-GFP anti-IgG ChIPed DNA, and 1 sample of input DNA. Barcoded libraries for Illumina TruSeq single-end sequencing were then prepared for each ChIPed or input DNA.

first: Joana

middle: M

last: Santos

first: Gabrielle

last: Josling

first: Philipp

last: Ross

first: Preeti

last: Joshi

first: Lindsey

last: Altenhofen

first: Tracey

last: Campbell

first: Ariel

last: Schieler

first: Ileana

last: Cristea


title: Transcriptome analysis of condensin II knockdown cells

city: Kansas City

first: Jennifer

last: Gerton

state: Missouri

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

type: Expression profiling by high throughput sequencing

summary: Condensin complexes are highly conserved for chromosome compaction to ensure their faithful segregation in mitosis. Condensin II is present in the nucleus throughout the cell cycle, including interphase. The aim of these experiments is to investigate the changes of gene expression in knockdown of NCAPH2, a condensin II subunit, in mouse embryonic stem cells compared to their control cells.

overall_design: Examination of gene expression of controls and NCAPH2 knockdown cells by RNA-seq

first: Kobe

middle: C

last: Yuen

middle: L


title: Natural DNA methylation variation in Lotus japonicus

city: Vienna

first: Manu

last: Dubin

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute, Austrian Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Natural DNA methylation variation was examined in a population of wild Lotus japonicus accessions from Japan

overall_design: Whole genome DNA methylation data for 18 wild Lotus japonicus accessions (two with replicates) grown at 20C


title: Genome-wide binding of condensin II and TFIIIC upon respective knockdown of a TFIIIC and condensin II subunit

summary: Condensin complexes are highly conserved for chromosome compaction to ensure their faithful segregation in mitosis. However, little is known about the role of condensin complexes in interphase. Condensins exists in two complexes, condensins I and II, in higher eukayotic cells. During interphase, condensin II is predominantly localized in the nucleus throughout the cell cycle, whereas condensin I is localized at the cytoplasm in interphase. The distinct localization patterns suggest that condensin II, but not condensin I, may contribute to genome organization in interphase. Our results suggest that condensin II is associated with TFIIIC complex in vivo. The aim of these experiments is to unravel the dependency of each other on binding to chromatin.

overall_design: Examination of binding of condensin II and TFIIIC complexes upon TFIIIC and condensin II knockdown by ChIP-seq


title: Condensin II complex mediates interactions of histone gene loci

summary: Condensin complexes are known for their importance in chromosome condensation during mitosis. However, condensin II binds to the geome during interphase as well. The role of condensin II in genome organization in mammalian interphase nuclei is not characterized. Since condensin II binds to the promoters of the transcriptionally active promoters in interphase genome, the aim of this study is to uncover its role in mediating chromatin interactions between active gene promoters such as histone gene loci.

overall_design: Examination of interactions between histone gene loci in control and condensin II knockdown cells by 4C-seq


title: Gene expression profiling of cultured embryonic rat cortical neurons

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Embryonic CNS neurons can differentiate in culture and provide a model for maturation-related changes. A transcriptome profile over the course of maturation was perform to investigate the underlying molecular mechanism that drives maturation and its related changes such as developmental loss of intrinsic regenerative capacity.

overall_design: Primary cortical neurons were excised from E18 rat embryos and were co-cultured with primary rat astrocytes from P0-2 rats.  RNA were then extracted on day 1, 4, 8, 16, and 24 after plating.

first: Hiroaki

last: Koseki

middle: Y

first: Giles

middle: S

last: Yeo

first: James

last: Fawcett


title: Genome-wide binding profiles of nuclear FGFR1 in Control and Schizophrenia hiPSC-dervied NPC [ChIP-seq]

city: Buffalo

first: Michal

last: Stachowiak

state: NY

address: 3435 Main Street

department: Pathology and Anathomical Sciences

institute: State University of New York at Buffalo

summary: We report the genome-wide binding patterns of nuclear FGFR1 in Control and Schizophrenia hiPSC-dervied NPC differntiated in neuronal media for two days.  We also report the genome-wide binding patterns of NOTCH in schizophrenia hiPSC-dervied NPC differntiated in neuronal media for 2 days

overall_design: Examination of nuclear FGFR1 binding in control and schizophrenia states.  Examination of NOTCH binding in schizophrenia state

middle: K


title: The role of condensin II in genome organization

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Hydra modifies bacterial quorum sensing signals for stabilizing host-microbe interactions

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

country: Australia

institute: The Australian National University

summary: This study looks at gene expression changes in Curvibacter sp. AEP1.3 in the presence of homoserine-lactones modified or unmodified by the host (Hydra)

overall_design: This study compares five biological replicates of the Curvibacter sp. AEP 1.3 strain for each condition. The conditions are: 3OC12-HSL 3OHC12-HSL and control (solvent).

first: C

last: Pietschke

last: Treitz

first: S

first: A

last: Schultze

last: Kunzel

last: Tholey

first: T

last: Bosch

last: Fraune


title: Transcriptome Profiling of Two Separatively Reproduced Arabidopsis Lines

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

summary: We profiled transcriptome of seedling samples derived from SALK Col-0 plants and a Col-0 plants reproduced in our lab for at least 10 generations. Using strand-specific RNA-seq analysis, we identified 32 genes were differentially expressed genes (fold-change > 2, DESeq2 P-value < 0.01), including 28 ones (88%) were up-regulated in the Col-0 plants reproduced in our lab. Of them, QUA-QUINE STARCH (QQS) ranked top 2 differentially expressed gene.

overall_design: 2 lines with 2 biological replicates

first: Choonkyun

last: Jung

first: Hui-Wen

last: Wu

first: Huan

last: Wang

first: Nam-Hai

last: Chua


title: MethlyC-Seq of Col-0 WT and mbd7-2(CS876032) mutant

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary:
In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3) as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation

Using MethylC-Seq to provide single-base resolution of DNA methylation status in Col-0 WT and mbd7-2(CS876032) mutant

overall_design: Whole genome methylation maps of mbd7-2(CS876032) and Col-0 WT were generated using BS-seq

first: Zhaobo

last: Lang

first: Mingguang

last: Lei

first: Xingang

first: Kai

last: Tang

first: Daisuke

last: Miki


title: Integration of RNA-seq transcriptomics with metabolomics in mouse model of cigarette smoke exposure

city: Denver

first: Irina

last: Petrache

state: CO

address: 1400 Jackson St, Molly Blank Building, J203

department: Division of Pulmonary, Critical Care and Sleep Medicine

institute: National Jewish Health

summary: Chronic obstructive pulmonary disease (COPD), a leading cause of morbidity and mortality, is primarily caused by prolonged exposures to cigarette smoke (CS) and the disease may persist or progress even after smoking cessation. To provide novel insight the mechanisms of COPD development we investigated temporal patterns of lung transcriptome expression in response to chronic CS exposure that also persist following CS cessation, using next generation sequencing techniques. Whole lung RNA-seq data was analyzed from C57Bl/6 mice exposed to CS for 1 day, 7 days, 1 month, 3 months, 6 months, and 9 months as well as for 6 months followed by 3 months of cessation. Age-matched littermate mice exposed to ambient air were used as control (AC).  Differential gene expression and pathway analyses revealed consistent upregulation of genes involved in glutathione metabolism, a pathway previously implicated in lung responses to chronic CS and in COPD, that was reversible upon cessation. In addition, novel patterns in mouse-model pathways such as pyrimidine metabolism and phosphatidylinositol signaling system and have been recognized. Genes in these pathways encoding for enzymes controlling metabolic functions were significantly altered by CS exposures and were associated with congruent abnormalities in contemporaneous plasma metabolomic profiles. The bioinformatics integration of lung tissue genomics and plasma metabolomics uncovered that changes in lung gene expression induced by CS exposures are translated in systemic metabolic signatures, with potential implication in the development of COPD.

overall_design: Whole transcriptome profiling of air control vs cigarette smoke-exposed mice at each of 6 timepoints from 1 day to 9 months of exposure, including a stop smoking group exposed to 6 months of CS followed by 3 months of ambient air recovery.  Each treatment-by-time experimental group contains 5 biological replicates. 3 samples were discarded for quality reasons.

first: Mikaela

last: Miller

first: Thomas

last: Danhorn

first: Charmion

last: Cruickshank-Quinn

first: Sonia

last: Leach

first: Matthew

last: Strand

first: Nichole

middle: A

last: Reisdorph

first: Russell

middle: P

last: Bowler

first: Irinia

first: Katerina

last: Kechris


title: Genome-wide analysis of histone modifications H3K4me3, H3K4me1, and H3K27ac in primary human corneal epithelial cells

city: Irvine

first: Bogi

last: Andersen

state: CA

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

summary: The corneal epithelium is a stratified squamous epithelium that protects the eye from mechanical and toxic stress. In this system, cells are continually being sloughed off from the surface of the eye, and replenished by proliferation from corneal stem cells in the limbus, which migrate in and differentiate. During tissue development and homeostasis, distal regulatory regions called enhancers, which contain binding sites for numerous transcription factors, help to control and coordinate gene expression in a temporal and spatial specific manner. To identify enhancers in cornea epithelia, we performed ChIP-Seq with antibodies to the histone marks H3K4me3, H3K4me1, and H3K27ac in primary human corneal epithelial cells. Active enhancers were defined as having high levels of H3K4me1 and H3K27ac, and low levels of H3K4me3: 12,900 such regions were identified in the corneal epithelial cells. In combination with primary cell histone modification ChIP-Seq data from BROAD, 2946 active enhancer regions were identified that are unique to the corneal epithelial cells: 1551 of theses 2946 also overlie regions of high evolutionary constraint. Motif enrichment analysis of these regions has revealed binding sites for a number of transcription factors, highlighting their roles as key regulators of corneal epithelial development.

overall_design: ChIP experiments for histone modifications H3K4me1, H3K4me3, and H3K27ac were performed on primary human corneal epithelial cells, and were sequenced on the Hi-Seq 2000.

first: Rachel

middle: H

last: Klein


title: Small RNA sequencing: EVs and the producing cells

status: Public on May 31 2017

city: Gainesville

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the high-throughput profiling of small RNA in extracellular vesicles (EVs) and their producing mammalian cells using Illumina small RNA sequencing platform. By obtaining over 2190 miRNA expression from 18 samples, the miRNA profile in EVs and their producing cells were compared. Results provide insight into gene profile difference between EV loading and the producing cells.

overall_design: Profile of small RNA expression in EVs and the producing cells with small RNA sequencing method.


title: mRNA sequencing analysis of zebrafish embryos, Dcp2 inhibition

city: Kita-ku

first: Yuichiro

last: Mishima

state: Kyoto

address: Motoyama, Kamigamo,

department: Department of Frontier Life Sciences

country: Japan

institute: Kyoto Sangyo University

summary: we determined the contribution of the decapping enzyme Dcp2 to maternal mRNA clearance in zebrafish embryos by overexpressing a dominant-negative form of Dcp2.

overall_design: zebrafish embryonic mRNA profile at 6 hpf in mock-inejcted or Dcp2-DN expressing embryos. Experiments are performed as triplicates.


title: Signature of coevolution between determinants of defense and life span in Arabidopsis thaliana

city: Münster

first: Shirin

last: Glander

state: Deutschland (DEU)

address: Domagkstraße 3

country: Germany

institute: University Münster

summary: The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits, which arbitrates the evolution of host defenses. Their impact, however, has seldom been documented. Here, we show with a simple mathematical model that the selective advantage of the defense system is expected to decrease with decreasing life span. We further document that, in natural populations of the model plant system Arabidopsis thaliana, the expression level of defense genes correlate positively with flowering time, a proxy for the length of vegetative life span. Using a genetic strategy to partition life span-dependent and –independent defense genes, we demonstrate that this positive co-variation is not explained by the pleiotropic action of major regulatory genes controlling both defense and life span. In agreement with our model, this study reveals that natural selection has likely assembled alleles promoting lower expression of defense genes with alleles decreasing the duration of vegetative life span in natural populations of A. thaliana. This is the first study demonstrating that life history evolution has a pervasive impact on the evolution of host immunity.

overall_design: Seeds of Bur-0, Col-0 and 278 Bur-0xCol-0 Recombinant Inbred Lines (RIL) obtained after 8 generations of selfing were provided by the Arabidopsis Stock Center at INRA Versailles (France). We selected the 40 RIL in the 15% and 85% quantiles of flowering time for RNA sequencing. Each RIL and the two parental lines were planted in 20 replicates in the conditions described above. At days 14 and 28, the oldest leaf was flash-frozen in liquid nitrogen. Three pools, each combining 13 RIL, were produced at each time point for early and late lines, for a total of 3 biological replicates, 2 pool types (early and late RIL) and 2 time points (14 and 28 days). For each of the two parental lines, leaves of 12 replicates were pooled for each time point.

first: Fei

last: He

first: Gregor

last: Schmitz

first: Anika

last: Witten

first: Arndt

last: Telschow

first: Juliette

last: de Meaux


title: Identification of super-enhancers in colorectal cancer cell lines

city: Chuo-ku

first: Naoko

last: Iida

state: Tokyo

address: 5-1-1 Tsukiji

institute: National Cancer Center in Japan.

summary: H3K27 acetylation statuses were analyzed in four colon cancer cell lines (RKO, Caco2, SW48, and SW620), and colorectal cancer-specific super-enhancers were identified.

overall_design: H3K27 acetylation statuses in four colon cancer cell lines were analyzed using Illumina HiSeq4000.

first: Yoshiaki

last: Nakamura

last: Hattori

first: Toshikazu

last: Ushijima


title: Distinct H4-K20 methylation states time DNA replication initiation in mammalian cells

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

summary: The role of histone modifications in DNA replication remains poorly understood. Here, we show that histone H4K20 monomethylation (me1) favors the assembly of the pre-replication complex on chromatin, an association that is increased when H4K20me1 is converted to trimethylation (H4K20me3). Remarkably, these histone methylations enhance origin activity, indicating a positive role in both origin licensing and activation. Genome-wide approaches revealed that H4K20me1 and H4K20me3 are enriched in distinct GC-rich regions, where their presence correlates with early-replicating and late-firing origins respectively. Accordingly, depletion of H4K20me1 at early origins delays the replication of active chromatin. Conversely, loss of H4K20me2/3 causes a drop in the licensing and activity of late-firing origins, slowing down the replication of heterochromatin. Altogether, these results suggest that the concerted activity of mammalian H4K20 methyltransferases and the resulting distribution of H4K20me states are essential to ensure the order and replication timing of different chromatin states.

overall_design: H4K20me1 and H4K20me3 profile on the whole genome in U2OS cell line

first: Nizar

last: Batada

first: Eric

last: Julien


title: Activation of Parathyroid Hormone 2 Receptor Induces Decorin Expression and Promotes Wound Repair

city: San Diego

first: Christopher

last: Adase

address: 2525 John Hopkins Ct

department: Dermatology

institute: UCSD

summary: TIP39 is an specific agonist of PTH2R. In this paper, we investigated the TIP39-PTH2R response on extracellular matrix which is produced by fibroblasts and adipocytes.

overall_design: Each sample's RNA was isolated form a single biological source of P3 human preadipocytes. In total there are 4 samples (non-replicates); Control + differentiation media (shRNA), PTH2R knockdown + differentiation media (shRNA against PTH2R), Control + non-differentiation media (shRNA), PTH2R knockdown +non- differentiation media (shRNA against PTH2R)

first: Emi

last: Sato

first: Ling-juan

last: Zhang

first: Robert

last: Dorschner

first: Biswa

last: Choudhury

first: Richard

last: Gallo


title: Role of DNA methylation in the dietary restriction mediated cellular memory

status: Public on May 30 2017

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Dietary restriction (DR) appears to create a cellular memory, which persists even after DR is discontinued.DNA methylation seems a logical mechanism by which a cellular memory could be established.we first examined the effect of short-term DR on gene expression and DNA methylation, then determined whether the changes  persisted after DR was discontinued and mice returned to ad libitum (AL) feeding.We show that DR can induce substantial changes in gene expression within one month of its implementation in various tissues, and  ~15-50% of these changes in gene expression persist even when DR is discontinued. We then determined whether DR induced changes in DNA methylation in the promoter of three candidate genes (Pomc, Hsph1 and Nts1) that were correlated with the changes in the expression of these genes.

overall_design: mRNA profiles in 5 tissues (Liver, Epididymal fat, Colon, Hypothalamus, Hippocampus) of mice under three feeding diets (ad libitum (AL), diet restricted, ad libitum after diet restricted)

first: Archana

last: Unnikrishnan

first: Arlan

last: Richardson


title: In vitro expansion of mouse primordial germ cell‐like cells recapitulates an epigenetic blank slate [RNA-Seq]

city: Kyoto

first: Yukihiro

last: Yabuta

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: The expansion of primordial germ cells (PGCs), the precursors for the oocytes and spermatozoa, is a key challenge in reproductive biology/medicine. Using a chemical screening exploiting PGC‐like cells (PGCLCs) induced from mouse embryonic stem cells (ESCs), we here identify key signaling pathways critical for PGCLC proliferation. We show that the combinatorial application of Forskolin and Rolipram, which stimulate cAMP signaling via different mechanisms, expands PGCLCs up to ~50‐fold in culture. The expanded PGCLCs maintain robust capacity for spermatogenesis, rescuing the fertility of infertile mice. Strikingly, during expansion, PGCLCs comprehensively erase their DNA methylome, including parental imprints, in a manner that precisely recapitulates genome‐wide DNA demethylation in gonadal germ cells, while essentially maintaining their identity as sexually uncommitted PGCs, apparently through appropriate histone modifications. By establishing a paradigm for PGCLC expansion, our system reconstitutes the epigenetic “blank slate” of the germ line, an immediate precursory state for sexually dimorphic differentiation.

overall_design: 3' RNAseq analyses for d4c3, d4c5, and d4c7 PGCLCs (BVSC+), PGCs at E9.5, and male/female germ cells at E12.5 (Stella-EGFP+)

first: Hiroshi

last: Ohta

first: Kazuki

last: Kurimoto

first: Ikuhiro

last: Okamoto

first: Tomonori

first: Hidetaka

last: Miyauchi

first: Takuya

last: Yamamoto

first: Yukiko

last: Okuno

first: Masatoshi

last: Hagiwara

first: Kenjiro

last: Shirane

first: Hiroyuki

last: Sasaki

first: Mitinori

last: Saitou


title: Transcriptome analysis revealed impaired cAMP responsiveness in PHF21A-deficient human cells

city: Ann Arbor

first: Robert

middle: Scott

last: Porter

state: MI

address: 1241 E. Catherine St, Med Sci II, Rm. 5815

department: Human Genetics

institute: University of Michigan

summary: We performed RNA-Seq on PHF21A-deficient patient-dervied lymphoblasts as well as two unaffected individuals.

overall_design: We performed RNA-Seq from patient-derived lymphoblast cells. Libraries were polyA-selected and strand-specific according to the protocol described in PMID: 25607527

first: Shigeki

last: Iwase


title: Reduced representation bisulfite sequencing of equine sarcoid and tumor distant skin samples

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary: The aim of the project was to identify sites undergoing changes in methylation level in cancer cells of equine sarcoid. The comparative analysis of DNA methylation patterns of the genome fraction rich in CpG dinucleotides was investigated using Reduced Representation Bisulfite Sequencing (RRBS) technique. In this study, for the first time we report the genome-wide DNA methylation profile of skin tumour in horses and describe differentially methylated genomic regions with respect to healthy skin.

overall_design: One-condition experiment, sarcoid vs. tumour-distant skin. Biological replicates: 1 sarcoid replicate, 1 control tissue replicate.

last: Semik

first: Tomasz

last: Szmatoła

first: Artur

last: Gurgul

last: Ząbek


title: In vitro expansion of mouse primordial germ cell‐like cells recapitulates an epigenetic blank slate [ChIP-Seq]

first: Yukihiro

last: Yabuta

overall_design: H3K4me3, H3K27ac, H3K27me3 ChIP-seq analyses for d4c7 PGCLCs

last: Ohta

last: Nakamura


title: Capicua-dependent transcriptional changes in human cancer cell lines treated with trametinib

city: Boston

first: William

middle: C.

last: Hahn

state: MA

address: 450 Brookline Avenue; D1538

department: Medical Oncology

institute: Dana Farber Cancer Institute

summary: We performed a genome-scale CRISPR screen in a KRAS-mutant pancreatic cancer cell line treated with the MEK inhibitor trametinib, and found that loss of the transcriptional repressor CIC confers resistance to MEK inhibition. We determined that CIC loss also confers resistance to MEK or BRAF inhibition in lung cancer, colorectal cancer, and melanoma cell lines with mutant RAS or BRAF. CIC is a transcriptional repressor that is phosphorylated and inhibited by the MAPK pathway. We hypothesized that inhibition of the MAPK pathway would lead to activation of CIC and repression of CIC target genes. Loss of CIC would therefore restore expression of these genes, conferring drug resistance. To identify the relevant CIC target genes that mediate trametinib resistace, we generated 4 Cas9-expressing cell lines from different lineages and with different RAS or RAF mutations, and generated control (gGFP) or CIC-knockout (gCIC) cell lines. We treated cells with DMSO or trametinib for 24 hours, and performed NRA-seq. We found that trametinib treatment reduces expression of at least one member of the PEA3 family of ETS transcription factors (ETV1, ETV4, and ETV5) in all cell lines assessed, and that loss of CIC results in maintained expression of these genes despite MEK inhibition. We further validated that ETV1, 4, and 5 expression was necessary for resistance mediated by CIC loss; and that ETV1, 4, or 5 expression was sufficient to confer trametinib resistance.

overall_design: 4 Cas9-expressing human cancer cell lines (A549, CALU1, HCT116, PATU8902) were used to generate 3 isogenic cell lines with intact CIC (gGFP-1) or knocked out CIC (gCIC-1 or gCIC-2). Each of these 12 cell lines were treated with DMSO or trametinib for 24 hours (duplicates)

first: Belinda

last: Wang

first: Elsa

middle: B

last: Krall

first: Andrew

middle: J

last: Aguirre


title: Transcriptome profiling and histology change of juvenile blunt snout bream (Megalobrama amblycephala) liver tissue in response to acute thermal stress

city: Wuxi

first: sun

last: shengming

state: Jiangsu

address: No.9, Shanshui Rd East

institute: Freshwater Fisheries Research Center (FFRC) of Chinese Academy of Fishery Sciences (CAFS),

summary: The set of genes identified showed regulatory modulation at different temperature, and these genes are possible specific candidates that may be investigated, in addition to liver histology examinations, for further studies aimed at determining how M. amblycephala livers exhibit damage under high temperature stress and the possible roles of reactive oxygen species in this process.

overall_design: Previous studies have investigated the physiological responses to acute thermal stress in fish; however, little information is available for the underlying molecular mechanisms to changing temperatures in aquatic ecosystems. In an effort to understand the underlying mechanisms and the pathways activated by high temperature, we sampled livers from juvenile Megalobrama amblycephala exposed to control (25 °C) and test (35 °C) condition and performed short read (100 bp) next generation RNA sequencing (RNA-seq). The RNA-seq reads from all the exposures were assembled into unigenes datasets according to an available reference transcriptome. Using reads from each nitrite concentration, we performed RNA-seq based gene expression analysis that identified total 440 differentially expressed genes. The differentially expressed genes were related to oxidative stress, apoptosis, immune responses and the metabolism of proteins and fats. The differential mRNA expression of selected genes involved in antioxidant enzymes, apoptosis gene and heat shock proteins in response to stress was verified by quantitative real-time reverse transcriptase polymerase chain reaction.

first: Shengming

last: Sun


title: Functional and Technical Validation of SL-seq, a method for RNA-seq in Trypanosomatids

city: Antwerpen

first: Bart

last: Cuypers

state: Antwerp

address: Middelheimlaan 1

department: Computer Science

country: Belgium

institute: Adrem Data Lab

summary: We developed a novel method for RNA-seq in Trypanosomatids called ‘Spliced-Leader Sequencing’ (SL-seq). The method is based on the fact that the 5’ end of Trypanosomatid mRNA is starts with a SL-sequence, and specifically enriches SL-containing RNA prior to sequencing. In this study we compared the performance and functional results obtained with SL-seq to those generated with conventional Illumina Stranded mRNA prep. Therefore we sequenced mRNA of Leishmania donovani logarithmic phase promastigotes, stationary phase promastigotes and intracellular amastigotes with both methods. We also sequenced controlled dilutions of Leishmania RNA with human RNA.

sample_organism:
Leishmania donovani
Homo sapiens

platform_organism:
Leishmania donovani
Homo sapiens

overall_design: 37 samples


title: A Memory for Obesity in Adipose Tissue

city: Stockholm

first: Niklas

last: Mejhert

address: Hälsovägen 7

country: Sweden

institute: Karolinska Institutet

summary: To identify transcriptional alterations in subcutaneous human white adipose tissue of post-obese subjects, global gene expression measurements were performed. Three groups, obese before and after bariatric surgery as well as never-obese controls, were compared to dissect candidate genes.

overall_design: Based on high quality total RNA isolated from human subcutaneous white adipose tissue, gene expression profiles were generated using Affymetrix Human Gene 1.1 ST arrays (Affymetrix, Inc., Santa Clara, CA). Obese subjects before (n=16) and after bariatric surgery (n=16) as well as never-obese controls (n=16) were included in the study. Data were preprocessed with the Robust Multichip Average method.

first: Peter

last: Arner

first: Mikael

last: Rydén


title: ARF5/MP responsive genes in the vascular cambium of Arabidopsis

status: Public on May 29 2017

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

summary: 15-20 cm tall PXY:GR-MPΔIII/IV plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously  (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes

overall_design: RNA from three samples was pooled and analyzed by RNAseq.

first: Klaus

last: Brackmann

first: Virginie

last: Jouannet


title: Transcriptome analysis of CD4+ T cells infected with Ebolavirus

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building, 960 Republican St

institute: University of Washington

summary: Evaluating the transcriptome profiles of CD4+ T cells that were cultured with mock, LPS, or recombinant Ebolavirus strain Mayinga (EBV) with a particular interest in characterizing the T lymphocyte cell death-associated pathways.

overall_design: Transcriptome profiles of CD4+ T cells cultured with three treatments, mock, LPS, and Ebolavirus.  For each treatment, samples were taken from four donors on two separate days, day 1 and day 4 post-infection.

first: Mathieu

last: Iampietro

first: Patrick

last: Younan

last: Nishida

first: Alexander

last: Bukreyev


title: Transcriptom analyses of Arabidopsis altered meritem program1-32 (amp1-32) mutant as well as wild-type Columbia-0 plants via next-generation sequencing (NGS).

city: Busan

first: Ho Won

last: Jung

address: 37 Nakdong-Daero 550beon-gil, Saha-gu

department: Molecular Genetics

country: South Korea

institute: Dong-A University

summary:
Purpose:The goals of this study are to compare transcriptome of amp1-32 mutant with that of wild-type Columbia-0 plant and to identify genes whose expression are tightly regualted by AMP1 in Arabidopsis.
Methods: mRNA profiles of 3-week-old wild-type Col-0 and amp1-32 mutant plants were generated by deep sequencing, in duplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method : TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 30~53 million sequence reads per sample to the Arabidopsis genome (TAIR10). From the 2 biological replicates, we detected 135 up-regulated genes, and 36 down-regulated genes, in the amp1-32 mutant plant.
Conclusions: Our study represents the first detailed analysis of transcriptome of amp1 mutant plants, with biologic replicates. Our results show that AMP1 protein had weak, but significant, effects on transcription of genes important for plant development and responses to stresses.

overall_design: mRNA profiles of 3-week-old wild-type Col-0 and amp1-32 mutant were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.

first: Ri

middle: R

last: Seo

first: Ho

middle: W


title: Transcriptome-wide identification and target analysis of the Pumilio family of RNA binding proteins

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

summary: In this study, we identified the transcriptome-wide direct RNA target sites of the entire family of Pumilio proteins in the budding yeast Saccharomyces cerevisiae by deep sequencing of RNA regions bound by each of six Pumilio proteins. As a family, the Pumilio proteins of yeast interact with over half of the entire transcriptome. Computational analysis of Pumilio target sites reveal striking differences in mRNA stability, gene set categories, and response to nutrient deprivation conditions based on features of Pumilio binding. Some of these features include variations in primary sequence motif and presence of predicted structured RNA hairpins. Puf6p also binds snoRNAs.

overall_design: Sequencing of RNAs bound by Puf1/2/4/5/6.

first: Ting

last: Han

first: John

last: Kim


title: Specification and Diversification of Pericytes and Smooth Muscle Cells from Mesenchymoangioblasts

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

summary: Recently, we identified mesenchymoangioblast (MAB), as a clonal mesodermal precursor for mesenchymal and endothelial cells. Here we show, that MABs have the capacity to produce mesenchymal progenitors, which can be differentiated into pericytes or smooth muscles cells under the influence of PDGF-BB or TGFβ plus sphingosylphosphorylcholine (SPC), respectively. Based on these studies we established the hierarchy of vasculogenic progenitors that provides the platform for interrogation of molecular mechanisms regulating vasculogenic cell specification and diversification from primitive posterior mesoderm.

overall_design: Vasculogenic cells generated under specific culture conditions. Primary cells were used as control.

first: Igor

last: Slukvin

first: Akhilesh

last: Kumar

first: Scott

last: Swanson


title: Retinal degeneration triggers the activation of YAP/TEAD in reactive Müller cells

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

institute: CNRS-Universite Paris Sud

summary: PURPOSE. During retinal degeneration, Müller glia cells respond to photoreceptor loss by undergoing reactive gliosis, with both detrimental and beneficial effects. Increasing our knowledge of the complex molecular response of Müller cells to retinal degeneration is thus essential for the development of new therapeutic strategies. The purpose of this work was to identify new factors involved in Müller cell response to photoreceptor cell death.   METHODS. Whole transcriptome sequencing was performed from wild-type and degenerating rd10 mouse retinas at P30. The changes in mRNA abundance for several deregulated genes were assessed by RT-qPCR. Protein expression level and retinal cellular localization were determined by western-blot and immunohistochemistry, respectively.  RESULTS. Pathway-level analysis from whole transcriptomic data revealed the Hippo/YAP pathway as one of the main signaling pathways altered in response to photoreceptor degeneration in rd10 retinas. We found that downstream effectors of this pathway, YAP and TEAD1, are specifically expressed in Müller cells and that their expression, at both the mRNA and protein levels, is increased in rd10 reactive Müller glia after the onset of photoreceptor degeneration. The expression of Ctgf and Cyr61, two target genes of the transcriptional YAP/TEAD complex, is also upregulated following photoreceptor loss.  CONCLUSIONS. This work reveals for the first time that YAP and TEAD1, key downstream effectors of the Hippo pathway, are specifically expressed in Müller cells. We also uncovered a deregulation of the expression and activity of Hippo/YAP pathway components in reactive Müller cells under pathological conditions.

overall_design: Retinal samples were harvested from C57Bl6/J and rd10 mouse retina at postnatal days 30 for whole transcriptome sequencing (RNAseq).  Each sample included 2 frozen retina and experiments were performed in triplicate. RNA-seq transcriptome libraries were constructed from 1 ug of total RNA.

first: Annaïg

last: Hamon

first: Christel

last: Masson

first: Juliette

last: Bitard

first: Linn

last: Gieser

first: Jérôme

middle: E

first: Muriel

last: Perron


title: Combining RNA-Seq and Somatic CRISPR Mutagenesis to Study Mouse Neural Development in vivo

city: Los Angeles

first: Yerbol

middle: Z.

last: Kurmangaliyev

address: 675 Charles E. Young Drive South

institute: University of California, Los Angeles

summary: We used RNA sequencing to identify candidate regulators of interactions between photoreceptor axons and bipolar cell (BCs) dendrites in developing mouse retina. We chose three time points: P7, just after the OPL forms and synaptogenesis with BCs begins; P13, as synaptogenesis nears completion and sublamination begins; and P30, when the OPL is mature. We purified cone and rod photoreceptors separately by fluorescence activated cell sorting (FACS) using transgene markers: Rhoicre;Ai9 for rods and HRGPcre;Ai9 for cones. We purified ON BCs, which include ON cone bipolars plus rod bipolars using Grm6:GFP. As appropriate transgenic lines to separate RBCs from CBCs were not available, we performed RNAseq on cells from Grm6:GFP mice that were fixed and immunostained prior to FACS, allowing us to purify RBCs (GFP+PKC+) and CBCs (GFP+PKC-) from the same retinas. As PKC is not highly expressed at P7, profiling of developing rod bipolars separate from developing ON cone bipolars was restricted to P13.

overall_design: RNA sequencing of purified rods, cones and ON-bipolar cells at three time points (P7, P13, P30).

first: Elizabeth

middle: Z

last: Sanchez

first: Lawrence

last: Zipursky


title: H2AZ Orchestrates Neural Progenitor Cell Proliferation and Differentiation via Setd2-mediated H3K36me3 Modification [ChIP-seq]

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We report the genomic characterization of H2AZ binding at E13 brain. ChIP experiment was performed with antibody against H2AZ. we generated genome-wide characterization of H2AZ occupancy and find that H2AZ was prone to bind the promoter and the intergenic regions. The genomic localization of H2AZ might reveal its essential role during early neurogenesis. Gene ontology (GO) analysis, revealing that these genes occupied by H2AZ play roles in the cellular metabolic process, DNA replication, cell cycle, and neuron development and so on. Detailed investigation of the binding profiles show that direct binding of NkX2-4 by H2AZ. This study provides a framework for the epigenetic regulation of H2AZ in embryonic neurogenesis.

overall_design: Genomic characterization of H2AZ binding at E13 brain

first: Tianjin

last: Shen


title: E3 SUMO ligase PIAS3 fine-tunes dorsoventral patterning and visual response of cones in the mouse retina but is not essential for photoreceptor cell fate specification

summary: Differentiation of distinct neurons in the developing retina is controlled by combinatorial action of a small subset of transcription factors and signalling molecules. Protein inhibitor of activated STAT3 (PIAS3) has been implicated in guiding the specification of both rod and cone photoreceptors through posttranslational modification of key retinal transcription factors. To investigate its role during retinal development, we deleted exon 2-5 of the mouse Pias3 gene, which resulted in complete loss of the PIAS3 protein. Pias3-/- mice did not exhibit any overt phenotype, and retinal lamination appeared normal by histology even at 18 months. We detected reduced photopic b-wave amplitude by electroretinography (ERG) analysis following green light stimulation of Pias3-/- retina at postnatal day (P) 21, suggesting a compromised visual response of medium wavelength (M) cones. No change was evident in response of short wavelength (S) cones or rod photoreceptors until 7 months. Immunohistochemistry demonstrated altered distribution of cone photoreceptors as revealed by increased S-opsin expression in the M-cone dominant dorsal retina. Transcriptome profiling of P21 and 18-month old Pias3-/- retina revealed aberrant expression of genes associated with photoreceptor function. Our studies suggest redundancy in SUMOylation-associated transcriptional control mechanisms and identify a specific though limited role of PIAS3 in modulating spatial patterning and optimal function of cone photoreceptor subtypes in the mouse retina.

overall_design: Retinal samples were harvested from PIAS3+/+ and PIAS3-/- retina at postnatal days 21 and at 18 months for whole transcriptome sequencing (RNAseq).  Each sample included 2 frozen retina and experiments were performed in triplicate. RNA-seq transcriptome libraries were constructed from 100 ng of total RNA.

first: Christie

last: Campla

first: Hannah

last: Breit

first: Lijin

last: Dong

first: Jessica

last: Gumerson

first: Anand

last: Swaroop


title: The Genetic and Transcriptional Basis of Short and Long Term Adaptation across Multiple Stresses in Escherichia coli

city: davis

first: Ilias

last: Tagkopoulos

state: CALIFORNIA

address: 2063 kemper hall, 1 shields avenue

institute: university of california at davis

summary: Microbes exhibit short and long term responses when exposed to challenging environmental conditions. To what extent these responses are correlated, what their evolutionary potential is and how they translate to cross-stress fitness is still unclear. In this study, we comprehensively characterized the response of Escherichia coli populations to four abiotic stresses (n-butanol, osmotic, acidic, and oxidative) and their combinations by performing genome-scale transcriptional analysis and growth profiling. We performed an analysis of their cross-stress behavior which identified 15 cases of cross- protection and one case of cross vulnerability. To elucidate the evolutionary potential of stress responses to individual stresses and stress combinations, we re-sequenced E. coli populations evolved in those four environments for 500 generations. We developed and applied a network-driven method that integrates mutations and differential expression to identify core and stress-specific gene communities that are likely to have a phenotypic impact. Our results suggest that beyond what is expected from the general stress response mechanisms, cross-stress behavior arises both from common pathways, several including metal ion binding and glycolysis/gluconeogenesis, and stress-specific expression programs. The stress-specific dependences uncovered, argue that cross-stress behavior is ubiquitous and central to understanding microbial physiology under stressful conditions.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Examination of the differential expression under exposure to different stresses

first: Violeta

last: Zorraquino-Salvo

first: Minseung

last: Kim

first: Navneet

last: Rai


title: Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Translational control of gene expression plays essential roles in cellular stress responses and organismal development by enabling rapid, selective, and localized control of protein production. Translational regulation depends on context-dependent differences in the protein output of mRNAs, but the key mRNA features that distinguish efficiently translated mRNAs are largely unknown. Here we comprehensively determined the RNA-binding preferences of the initiation factor eIF4G to assess whether this core translation initiation factor has intrinsic sequence preferences that contribute to preferential translation of specific mRNAs.

overall_design: Ribosome footprint profiling of eIF4G depleted yeast cells

first: Maria

middle: F

last: Rojas-Duran

first: Wendy

middle: V

last: Gilbert


title: Profiling of CD34+ hair follicle stem cells

city: South San Francisco

first: Robert

last: Piskol

state: CA

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

summary:
RNA was isolated from fluorescence activated cell sorted (FACS) CD49f+/CD34+/GFP- hair follicle stem cells after hair follicle keratinocyte isolation from the skin of age matched saline or diphtheria toxin (DT) treated Lgr5-DTReGFP mice.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is PRJ0009986

overall_design: Gene expression profiling of CD49f+/CD34+/GFP- hair follicle stem cells from saline or DT treated Lgr5-DTReGFP mice

first: Joerg

last: Hoeck


title: Auxin responses in the Arabidopsis stem and cambium

status: Public on May 28 2017

first: Thomas

last: Greb

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

overall_design: Refer to individual Series


title: Transcriptional profiling of Mycobacterium tuberculosis Rv3852 (hns) knockout mutant

city: Bern

first: Andrej

last: Benjak

address: Murtenstrasse 24-28

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary: A handful of nucleoid-associated proteins (NAPs) regulate the vast majority of genes in a bacterial cell. H-NS, the Histone-like Nucleoid-Structuring protein, is one of these NAPs and protects Escherichia coli from foreign gene expression. Though lacking any sequence similarity with E. coli H-NS, Rv3852 was annotated as the H-NS ortholog in Mycobacterium tuberculosis, as it resembles human histone H1. The role of H-NS was thoroughly investigated by immunoblotting, subcellular localization, construction of an unmarked hns deletion in the M. tuberculosis genome and subsequent analysis of the resulting Δhns strain. We found that H-NS was predominantly present in the logarithmic growth phase with a decrease in protein abundance in stationary phase. Furthermore, it was strongly associated with the cell membrane and not detected in the cytosolic fraction, nor was it secreted. The Δhns strain displayed no growth defect or morphological abnormalities. Quantitative measurement of nucleoid localization in Δhns compared to the parental H37Rv strain showed no difference in nucleoid position or spread. Infection of macrophages as well as severe combined immunodeficient (SCID) mice demonstrated that loss of H-NS had no detectable influence on the virulence of M. tuberculosis. Only few genes wre differentially expressed in the Δhns strain. We thus conclude that M. tuberculosis H-NS is not involved in pathogenesis and is not a typical NAP.

overall_design: The hns knockout mutant (named Δhns) was constructed using a two-step allelic exchange method based on the suicide vector pJG1100. Phenotypic properties and transcriptional profile of Δhns was compared to the parental wild-type strain (H37Rv). Since hns was reported to be part of an operon with the downstream gene rraA, we first mapped the 5’-end of the bicistronic mRNA to ensure that the promoter region was not deleted and rraA expression was not affected in the mutant.

first: Nina

middle: T

last: Odermatt

first: Claudia

last: Sala

first: Andréanne

last: Lupien

first: Anthony

last: Vocat

first: Gaëlle

middle: S

last: Kolly

first: Stewart

last: Cole


title: Dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator in Arabidopsis

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

institute: Ghent University

summary: Since its discovery over two decades ago as an important cell death regulator in Arabidopsis thaliana, the role of LESION SIMULATING DISEASE 1 (LSD1) has been studied intensively within both biotic and abiotic stress responses as well as with respect to plant fitness regulation. However, its molecular mode of action remains enigmatic. Here we demonstrate that nucleo-cytoplasmic LSD1 interacts with a broad range of other proteins that are engaged in various molecular pathways such as ubiquitination, methylation, cell cycle control, gametogenesis, embryo development and cell wall formation. The interaction of LSD1 with these partners is dependent on redox status, as oxidative stress significantly changes the quantity and types of LSD1-formed complexes. Furthermore, we show that LSD1 regulates the number and size of leaf mesophyll cells and affects plant vegetative growth. Importantly, we also reveal that in addition to its function as a scaffold protein, LSD1 acts as a transcriptional regulator. Taken together, our results demonstrate that LSD1 plays a dual role within the cell by acting as a condition-dependent scaffold protein and as a transcription regulator.

overall_design: 4 genotypes x 3 replicates

first: Weronika

last: Czarnocka

first: Katrien

last: Van Der Kelen

first: Magdalena

last: Szechyńska-Hebda

first: Sara

last: Shahnejat-Bushehri

first: Salma

last: Balazadeh

first: Anna

last: Rusaczonek

first: Bernd

last: Mueller-Roeber

first: Frank

last: Van Breusegem

first: Stanislaw

last: Karpinski


title: NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation

first: Hu

last: Jin

address: 10 Shattuck St

department: Biomedical Informatics

institute: Harvard Medical School

summary: While years of investigation have elucidated many aspects of embryonic stem cell (ESC) regulation, the contributions of post-transcriptional and translational mechanisms to the pluripotency network remain largely unexplored. In particular, little is known in ESCs about the function of RNA binding proteins (RBPs), the protein agents of post-transcriptional regulation. We performed an unbiased RNAi screen of RBPs in an ESC differentiation assay and identified two related genes, NF45 (Ilf2) and NF90/NF110 (Ilf3), whose knockdown promoted differentiation to an epiblast-like state. Characterization of NF45 KO, NF90+NF110 KO, and NF110 KO ESCs showed that loss of NF45 or NF90+NF110 impaired ESC proliferation and led to dysregulated differentiation down embryonic lineages. Additionally, we found that NF45 and NF90/NF110 physically interact and influence the expression of each other at different levels of regulation. Globally across the transcriptome, NF45 KO ESCs and NF90+NF110 KO ESCs show similar expression changes. Moreover, NF90+NF110 RNA immunoprecipitation (RIP)-seq in ESCs suggested that NF90/NF110 directly regulate proliferation, differentiation, and RNA-processing genes. Our data support a model in which NF45, NF90, and NF110 operate in feedback loops that enable them, through both overlapping and independent targets, to help balance the push and pull of pluripotency and differentiation cues.

overall_design: We performed RNA-seq in NF45 KO and NF45 WT mouse embryonic stem cells (ESCs) with 2 biological replicates for each condition. We also performed NF90/NF110 RNA immunoprecipitation and sequencing (RIP-seq) in NF110 KO, NF90+NF110 KO, and NF90/NF110 WT mouse ESCs. Each NF90/NF110 RIP-seq experiment contains paired input (total RNA) and IP samples; and RIP-seq experiments were repeated in biological triplicate.

first: Julia

last: Ye

first: Aleksandr

last: Pankov

first: Jun

last: Song

first: Robert

last: Blelloch


title: Stabilization of c-Myc protein by CAMKIIγ promotes T-cell lymphoma

status: Public on May 27 2017

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: Although high c-Myc protein expression is observed alongside c-Myc gene amplification in some cancers, in most cases protein overexpression occurs while the amplified gene is largely absent, e.g. T-cell lymphoma (TCL). Here, Ca2+/calmodulin-dependent protein kinase II γ (CAMKIIγ) was shown to stabilize c-Myc protein by directly phosphorylating at serine 62 (S62), which represents a hitherto unknown mechanism of c-Myc protein overexpression. Further, CAMKIIγ was shown to be essential for tumor maintenance. Inhibiting CAMKIIγ with a potent CAMKIIγ-specific inhibitor destabilized c-Myc and reduced tumor burden dramatically. Importantly, high CAMKIIγ in clinical patient specimens positively correlated with increased c-Myc / pS62-c-Myc expression. Together, the CAMKIIγ:c-Myc axis critically influences the development and maintenance of TCL, and represent a novel therapeutic target for TCL.

overall_design: We investigated how deleting CAMKIIγ suppressed the development of MNU-induced TCL in mice. Through RNA-sequencing, we analyzed the gene expression profiles of the thymuses of both wild-type and CAMKIIγ-/- mice, under either malignant (with MNU) or normal (without MNU) conditions.

first: Wendong

last: Huang

first: Ying

last: Gu

first: Jiawei

last: Zhang

first: Xiaoxiao

last: Ma

first: Rongzhen

last: Xu


title: miR-34a and miR-34b/c suppress intestinal tumorigenesis in ApcMin/+ Mice

city: Munich

first: Longchang

last: Jiang

address: Thalkirchner Strasse 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University München

summary: miR-34a and miR-34b/c genes are frequently epigenetically silenced in primary CRCs. However, the in vivo relevance of miR-34a/b/c for suppression of intestinal tumor formation has not been analyzed by genetic approaches. ApcMin/+ mice with deletion of the miR-34a and miR-34b/c genes were generated and analyzed. The mRNA expression profiles of intestinal adenomas with and without functional miR-34a/b/c genes were compared.

overall_design: miR-34a/b/c deficient ApcMin/+ mice and wild-type ApcMin/+ mice were sacrificed at 18 weeks of age. 3 tumor RNA samples were obtained for each genotype; each tumor RNA sample represented a pool of 3 tumors isolated from the same mouse.

first: Heiko

last: Hermeking


title: Ataxin-2 modulates mRNA levels of proteins in ribosomal large and small subunit and in translation initiation complex

city: Frankfurt am Main

first: GenXPro

last: GenXPro

address: Altenhöferallee 3

institute: GenXPro GmbH

summary: Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disorder, caused by an unstable CAG-repeat expansion in the SCA2 gene, which encodes a polyglutamine (polyQ) domain expansion in the protein ataxin-2 (ATXN2). The RNA-binding protein ATXN2 interacts with the poly(A)-binding protein PABPC1, localizing to ribosomes in the rough endoplasmic reticulum or in polysomes. Under cell stress ATXN2 and PABPC1 are relocated to stress granules where mRNAs are protected from translation and from degradation. It is unknown whether ATXN2 associates preferentially with specific mRNAs or how it modulates their processing. Here, we investigated the RNA profile of liver and cerebellum from adult Atxn2 knock-out (Atxn2-/-) mice, employing oligonucleotide microarrays for screening and RNA deep sequencing for validation. We consistently observed modest upregulations for the level of many mRNAs encoding proteins of the ribosomal large and small subunit as well as the translation initiation complex. Quantitative reverse transcriptase PCR in liver tissue confirmed these upregulations for the ribosomal components Rpl14, Rpl18, Rps10, Rps18, Gnb2l1, the translation initiation factors Eif2s2, Eif3s6, Pabpc1, and the ribosomal biogenesis modulator Nop10. Quantitative immunoblots substantiated the effects for PABPC1. Thus, the physiological role of ATXN2 modifies the abundance of cellular translation factors.

overall_design: Examination of 3 tissues (cerebellum, hippocampus, liver) for consistent expression changes

first: Georg

last: Auburger

first: Björn

last: Rotter

first: M

last: Fittschen

first: I

last: Lastres-Becker


title: Methylation DNA mediated KLF4 binding activity in glioblastoma cells

first: Shuli

last: Xia

address: 707 N Broadway

institute: Kennedy Krieger Institute

summary: RNA-seq, ChIP seq and Whole genome bisulfite seq for KLF4-mCpG binding in GBM cells

overall_design: We engineered two doxycycline-inducible U87 cell lines to express KLF4 wild type and mutant (R458A), and examined KLF4 binding, gene regulation and whole genome bisulfite seq in U87 cells

last: Wan

first: Yijing

last: Su

first: Qifeng

first: Brian

last: Tung

first: Olutobi

last: Oyinlade

first: Sheng

last: Liu

first: Mingyao

last: Ying

first: Guo-li

last: Ming

first: Hongjun

first: Jiang

last: Qian

first: Heng

last: Zhu


title: The effect on anthelmintic drugs on Brugia malayi gene expression in vivo

status: Public on May 26 2017

city: Athens

first: Adrian

middle: J.

last: Wolstenholme

state: GA

address: 501 DW Brooks Dr.

department: Infectious Diseases

institute: University of Georgia

summary: Lymphatic filariasis (LF) threatens nearly 20% of the world’s population and has handicapped one-third of the 120 million people currently infected. Current control and eventual elimination of LF rely on mass drug administration (MDA) programs with three drugs: ivermectin (IVM), albendazole (ALB), and diethylcarbamazine (DEC). Only the mechanism of action of albendazole is well-understood.  . To gain a better insight into antifilarial drug action, we treated gerbils with patent B. malayi infections with 6 mg/kg DEC, 1 mg/kg ALB, or 0.15 mg/kg IVM to mirror the doses used in human MDA programs. These treatments had no effect on the numbers of worms present in the peritoneal cavity of infected animals. Adults and Mf were collected 1 and 7 days post-treatment and RNA was isolated for transcriptomic analysis. The experiment was repeated three times. Preliminary analysis of the effects of IVM, ALB, and DEC on adult males and females revealed treatment-specific changes in transcripts related to collagen expression, reproduction, embryogenesis, larval development, and lifespan determination. Similar data are currently being collected for the microfilariae.

overall_design: Three biological replicates were performed. For each replicate, B. malayi-infected gerbils were treated with either albendazole, DEC or ivermectin, or left untreated. One and seven days post-treatment, parasites were isolated from the peritoneal cavity. Males, females and microfilariae were separated and RNA isolated from each sample.


title: Cell intrinsic changes in transcription of naïve CD4 T cells upon S1pr1 deletion

city: new york

first: Susan

last: Schwab

state: NY

address: 540 First Avenue

department: Immunology

institute: new york university

summary: Naïve CD4 cells (CD45.2+CD4+,CD62L high,CD44 low) isolated from lymph nodes of mixed bone marrow chimeras 5 days after induced S1pr1 deletion.

overall_design: CD45.1+ mice were reconstituted with a mix of BM from WT UBC:GFP mice and BM from S1pr1f/fUBC-CreERT2 CD45.2+ mice or littermate controls. S1pr1 was deleted by tamoxifen injection for 5 days. Naïve CD4+ CD62L high CD44 low CD45.2+ GFP- cells were sorted 5 days after last tamoxifen injection.

first: Alejandra

last: Mendoza

first: Olivier

last: Elemento

first: Akanksha

last: Verma


title: Rhinovirus infection results in stronger and more persistent genomic dysregulation: evidence for altered innate immune response in asthmatics at baseline, early in infection, and during convalescence

city: Cincinnati

first: Gurjit

last: Khurana Hershey

state: Ohio

address: 3333 Burnet Avenue

department: Division of Asthma Research

institute: Cincinnat Children's Hospital Medical Center

summary:
Background: Rhinovirus (HRV) is associated with the large majority of virus-induced asthma exacerbations in children and young adults, but the mechanisms remain poorly defined.
Methods: Asthmatics and non-asthmatic controls were inoculated with HRV-A16, and nasal epithelial samples were obtained 7 days before, 36 hours after, and 7 days after viral inoculation. RNA was extracted and subjected to RNA-seq analysis.
Results: At baseline, 57 genes were differentially expressed between asthmatics and controls, and the asthmatics had decreased expression of viral replication inhibitors and increased expression of genes involved in inflammation. At 36 hours (before the emergence of peak symptoms), 1329 genes were significantly altered from baseline in the asthmatics compared to 62 genes in the controls. At this time point, asthmatics lacked an increase in IL-10 signaling observed in the controls. At 7 days following HRV inoculation, 222 genes were significantly dysregulated in the asthmatics, whereas only 4 genes were dysregulated among controls. At this time point, the controls but not asthmatics demonstrated upregulation of SPINK5.
Conclusions: As judged by the magnitude and persistence of dysregulated genes, asthmatics have a substantially different host response to HRV-A16 infection compared with non-asthmatic controls. Gene expression differences illuminate biologically plausible mechanisms that contribute to a better understanding of the pathogenesis of HRV-induced asthma exacerbations.

overall_design: Comparison of gene dysregulation in adult asthmatics and healthy controls at baseline and following human Rhinovirus inoculation.

middle: K

first: Peter

last: Heymann

first: Huyen

last: Nguyen

first: John

last: Steinke

first: Ronald

last: Turner

first: Judith

middle: A

last: Woodfolk

first: Thomas

last: Platts-Mills

first: Lisa

last: Martin

first: Hua

last: He

first: Jocelyn

last: Biagini-Myers

first: Mark

last: Lindsey

first: Umasundari

last: Sivaprasad

first: Mario

last: Medvedovic

first: Naim

last: Mahi

first: Holliday

last: Carper

first: Deborah

middle: D

last: Murphy

first: James

last: Patrie


title: Auxin responsive genes in the Arabidopsis stem

city: Heidelberg

last: Greb

address: Im Neuenheimer Feld 360

institute: Heidelberg University

summary: 15-20 cm tall 35S::Myc-GR-bdl plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously  (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes

overall_design: RNA from three samples was pooled and analyzed by RNAseq.

first: Klaus

last: Brackmann

first: Virginie

last: Jouannet


title: MicroRNA-183 cluster continuously scales mechanical pain sensitivity by regulating basal and neuropathic pain gene pathways.

status: Public on May 25 2017

city: Stockholm

first: Patrik

last: Ernfors

address: Solnavägen 9

department: Medical Biochemestry and Biophysics

institute: Karolinska Institutet

summary:
Nociception is protective and prevents tissue damage but can also facilitate chronic pain. If a general principle governs these two types of pain is unknown. Here, we show that both basal mechanical and neuropathic pain are controlled by microRNA-183 cluster in mice. This single cluster controls more than 80% of neuropathic pain-regulated genes and scales basal mechanical sensitivity and mechanical allodynia by regulating auxiliary voltage-gated calcium channel subunits a2d.
Basal sensitivity is controlled in nociceptors and allodynia involves TrkB+ light-touch mechanoreceptors. These light-touch sensitive neurons that normally do not elicit pain produce pain during neuropathy that is reversed by gabapentin. Thus, a single miRNA cluster continuously scales acute noxious mechanical sensitivity in nociceptive neurons and suppresses neuropathic pain transduction in a specific, light-touch sensitive neuronal type recruited during mechanical allodynia.

overall_design: Bulk DRG RNA sequencing of control and tissue-specific knock-out animals, naive and after nerve injury

first: Changgeng

last: Peng


title: Splicing Modulators Act at the Branch Point Adenosine Binding Pocket Defined by the PHF5A-SF3b Complex

city: Cambridge

first: Silvia

last: Buonamici

address: 300 Technology Square #5

institute: H3 Biomedicine

summary: Developing small-molecule splicing modulators represents a promising therapeutic approach for various diseases.  Natural products such as pladienolide, herboxidiene, and spliceostatin have been identified as potent splicing modulators that target SF3B1 in the SF3b subcomplex. Using integrated chemogenomic, structural and biochemical approaches, we show that PHF5A, another core component of the SF3b complex, is also targeted by these compounds. Mutations in PHF5A-Y36, SF3B1-K1071, SF3B1-R1074, and SF3B1-V1078 confer resistance to these modulators, suggesting a common site of interaction.  Whole-transcriptome RNA-seq analysis reveals that PHF5A-Y36C has minimal effect on basal splicing but alters the action of splicing modulators from inducing intron-retention to exon-skipping.  Relative intron strength to splicing inhibition correlates with the differential in GC content between adjacent introns and exons, leading to this differential global splicing pattern. We determine the crystal structure of human PHF5A and find that Y36 is located on the surface in a region of high sequence conservation. Structural analysis of the cryo-EM spliceosome Bact complex shows that these mutations cluster in a well-defined pocket surrounding the branch point adenosine suggesting a possible competitive mode of action for these splicing modulators, which interact with the aromatic side-chain of PHF5A-Y36. Collectively, we propose that PHF5A-SF3B1 forms a central node for binding to these small-molecule splicing modulators, offering insights to modulate splicing.

overall_design: 24 samples, including HCT-116 cells +/- treatment with E7107 with and without PHF5A Y36C mutation. Each condition has 6 replicates.

first: Michael

last: Seiler

first: Ping

last: Zhu


title: Guided self-organization recapitulates tissue architecture in a bioengineered brain organoid model

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

institute: IMBA

summary: Engineered brain organoids (enCORs) exhibit reproducible neural differentiation and forebrain regionalization.

overall_design: Comparison of transcriptomes from bioengineered micropatterned enCORs and spheroids at 20 days and 60 days

first: Madeline

last: Lancaster

first: Nina

last: Corsini

first: Juergen

last: Knoblich


title: Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells [RNA-seq]

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: Precise spatiotemporal regulation of genetic programs, driven by cellspecific super-enhancers, is paramount for the function of cell lineages. Studies have suggested that insulated neighborhoods, formed by the zincfinger protein CTCF, sequester genes and their associated enhancers thus preventing them from trespassing on off-target genes. Although this could explain the enhancer-gene-specificity conundrum, there is limited genetic evidence that the search space of cell-specific super-enhancers is constrained by CTCF. We have addressed this question in the Wap locus with its exceptional mammary-specific super-enhancer, which is separated by five CTCF sites from neighboring genes. Three of these sites are positioned between the Wap super-enhancer and the widely expressed Ramp3. Enhancer deletions demonstrated that the Wap super-enhancer controls Ramp3 expression despite the presence of three parting CTCF sites. Individual and combinatorial deletions of these CTCF sites revealed cell-specific functions of the conserved anchor site. Although unable to block super-enhancer activity, it muffled its impact on Ramp3 in mammary tissue. Unexpectedly, this CTCF site was obligatory for Ramp3 expression in cerebellum, suggesting the coinciding presence of regulatory elements. While our results suggest a surprisingly limited in vivo role for a CTCF anchor in blocking a mammary-specific super-enhancer, they also implicate this site in cerebellum-specific gene activation. Our study illustrates additional complexities of CTCF sites supporting tissue-specific functions.

overall_design: Total RNA-seq was done for mammary tissue at pregnancy day 18.

first: Kyung-Hyun

last: Yoo

first: Fabian

last: Reinisch

first: Tyler

middle: M

last: Kuhns

first: Chaochen

last: Wang

first: Lothar

last: Hennighausen


title: Revealing global translational reprogramming as a fundamental layer of immune regulation in plants

city: Durham

first: Xinnian

last: Dong

state: NC

address: 124 Science Drive

department: Biology

institute: Duke University

overall_design: RNA-seq and ribosome footprint profiling (Ribo-seq) of mock or elf18-treated Arabidopsis leaves.

first: Guoyong

last: Xu

first: George

middle: H

last: Greene

first: Heejin

first: Liijing

last: Liu

first: Jorge

last: Marques

first: Jonathan

last: Motley


title: Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells [ChIP-seq]

overall_design: ChIP-seq for CTCF in wild type and mutant mice ΔAB, ΔC, ΔD were done in mammary tissue. ChIP-seq for CTCF in mutant ΔCDE was done in liver tissue. ChIP-seq for H3K27ac in mutant mice ΔC, ΔD, ΔE were done in mammary tissue. All tissues were from lactation day one (L1).


title: Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells

overall_design: Refer to individual Series


title: Airway epithelial cells obtained via bronchoscopy from high risk subjects with and without bronchial premalignant lesions

city: Boston

first: Jennifer

last: Beane

address: 72 East Concord Street, E6

department: School of Medicine

institute: Boston University


title: Airway epithelial cells from high-risk subjects obtained via multiple bronchoscopy procedures to follow bronchial premalignant lesions as part of lung cancer screening

summary: While lung cancer is the leading cause of cancer death in the US, we have a limited understanding of the earliest molecular events preceding the onset of disease. Prior work has demonstrated that cigarette smoke creates a molecular “field of injury” throughout the airway epithelium and that there are distinct alterations in the airway transcriptome among smokers who have lung cancer. Molecular characterization of this airway “field of injury” in current and former smokers with premalignant lesions (PMLs) could provide novel insights into the earliest molecular events associated with lung carcinogenesis and identify relatively accessible biomarkers to guide lung cancer detection and early intervention. Using mRNA sequencing (mRNA-Seq), we profiled cytologically normal bronchial airway epithelial cells collected during autofluorescence bronchoscopy from high-risk smokers (n=75) with and without bronchial PMLs. We identified 280 genes differentially expressed in the “field of injury” between subjects with (n=50)  and without (n=25) PMLs (FDR<0.002), 81 of which were up-regulated in subjects with PMLs. Oxidative phosphorylation (OXPHOS), the electron transport chain (ETC), and mitochondrial protein transport pathways were strongly enriched among these up-regulated genes (FDR<0.05). We next demonstrated that OXPHOS activation is shared between the “field” and the PMLs with increased oxygen consumption and increased staining for mitochondrial markers in biopsies of PMLs from patients as well as an animal model of lung squamous cell carcinoma (SCC) premalignancy. The 280-gene signature also has a significant concordant relationship to gene expression changes identified in PMLs adjacent to lung SCC tumors, in lung SCC tumors, and in the cytologically normal airway of individuals with lung cancer (FDR<0.05).  These findings suggest that these expression changes are reflective of early cancer-associated changes occurring throughout the respiratory tract, and that pathways such as OXPHOS may be targets for chemoprevention.  We subsequently developed an airway gene expression biomarker that predicts the presence of PMLs (AUC=0.92, n=17 samples in test set) and show that changes in the biomarker score are associated with progression and regression of PMLs in an independent cohort (AUC=0.75, n=51 samples). The biomarker results indicate that molecular alterations in the field of injury are dynamic with progression or regression of PMLs, suggesting that these changes may be leveraged to stratify high-risk smokers with progressive disease into early intervention trials and monitor disease progression or recurrence.

overall_design: 51 mRNA-Seq samples from 23 subjects obtained via bronchscopy (18 subjects with 2 procedures, 5 subjects with 3 procedures).

first: Anna

last: Tassinari


title: Airway epithelial cells from smokers with and without bronchial premalignant lesions

summary: While lung cancer is the leading cause of cancer death in the US, we have a limited understanding of the earliest molecular events preceding the onset of disease. Prior work has demonstrated that cigarette smoke creates a molecular “field of injury” throughout the airway epithelium and that there are distinct alterations in the airway transcriptome among smokers who have lung cancer. Molecular characterization of this airway “field of injury” in current and former smokers with premalignant lesions (PMLs) could provide novel insights into the earliest molecular events associated with lung carcinogenesis and identify relatively accessible biomarkers to guide lung cancer detection and early intervention. Using mRNA sequencing (mRNA-Seq), we profiled 82 cytologically normal bronchial airway epithelial cells collected during autofluorescence bronchoscopy from high-risk smokers with and without bronchial PMLs, 75 of which were used in downstream analyses. We identified 280 genes differentially expressed in the “field of injury” between subjects with (n=50)  and without (n=25) PMLs (FDR<0.002), 81 of which were up-regulated in subjects with PMLs. Oxidative phosphorylation (OXPHOS), the electron transport chain (ETC), and mitochondrial protein transport pathways were strongly enriched among these up-regulated genes (FDR<0.05). We next demonstrated that OXPHOS activation is shared between the “field” and the PMLs with increased oxygen consumption and increased staining for mitochondrial markers in biopsies of PMLs from patients as well as an animal model of lung squamous cell carcinoma (SCC) premalignancy. The 280-gene signature also has a significant concordant relationship to gene expression changes identified in PMLs adjacent to lung SCC tumors, in lung SCC tumors, and in the cytologically normal airway of individuals with lung cancer (FDR<0.05).  These findings suggest that these expression changes are reflective of early cancer-associated changes occurring throughout the respiratory tract, and that pathways such as OXPHOS may be targets for chemoprevention.  We subsequently developed an airway gene expression biomarker that predicts the presence of PMLs (AUC=0.92, n=17 samples in test set) and show that changes in the biomarker score are associated with progression and regression of PMLs in an independent cohort (AUC=0.75, n=51 samples). The biomarker results indicate that molecular alterations in the field of injury are dynamic with progression or regression of PMLs, suggesting that these changes may be leveraged to stratify high-risk smokers with progressive disease into early intervention trials and monitor disease progression or recurrence.

overall_design: 82 mRNA-Seq samples from 25 smokers without PMLs, 50 smokers with PMLs, and 7 smokers with metaplasia.


title: Signatures of positive selection in germinal center B cells

city: New York

first: Luka

last: Mesin

address: 1230 York Ave

institute: The Rockefeller University

summary: We used RNA sequencing to characterize gene expression of Ly75+/+ B1-8hi and Ly75-/- B1-8hi B cells from the germinal center light zone (LZ) 12 h after forcing positive selection of the Ly75+/+ population with anti-DEC205-OVA.

overall_design: We primed C57BL/6 hosts with OVA-alum i.p. and after 2 weeks we adoptively transferred a mixture of B1-8hi B cells in which 15% were Ly75+/+ CD45.1 (DECP) and 85% were Ly75-/- CD45.1/2 (DECN). We then immunized the animals with NP-OVA in the footpads and after 6 days we injected anti-DEC205-OVA.  12 h or 24 h after anti-DEC205-OVA injection we sorted B220+ CD38- CD95+ CD45.1+ CD45.2- CD83hi CXCR4lo (DECPLZ) and B220+ CD38- CD95+ CD45.1+ CD45.2+ CD83hi CXCR4lo (DECNLZ) cells for whole transcriptome analysis by mRNA sequencing.

first: Jonatan

last: Ersching

first: Gabriel

last: Victora


title: An environment-dependent transcriptional network regulates human microglia phenotypes

city: La Jolla

first: Dylan

middle: Derik

last: Skola

address: 9500 Gilman Dr.

department: Cellular and Molecular Medicine

institute: UCSD

summary: Microglia play essential roles in central nervous system (CNS) homeostasis and influence diverse aspects of neuronal function. Although dysregulation of microglia activity is genetically linked to neurodegenerative and behavioral diseases, the transcriptional mechanisms that specify human microglia phenotypes are largely unknown.  We report here on the transcriptomes and epigenetic landscapes of human microglia isolated from surgically resected brain tissue, revealing broad similarities but also significant differences with mouse microglia. Many genes associated with risk alleles for neurodegenerative diseases are preferentially or highly expressed in human microglia.  The transition of human and mouse microglia from the brain to a tissue culture environment results in rapid and extensive downregulation of genes that are induced in primitive mouse macrophages following migration into the fetal brain. These findings reveal an environment-dependent transcriptional network specifying microglia-specific programs of gene expression and will facilitate efforts to better understand the roles of microglia in human disease.

overall_design: We isolated microglia ex vivo from mouse brains using FACS. We also cultured isolated mouse microglia in vitro for varying lengths of time, both with and without TGFB. Various subsets of these cells were assayed with RNA-seq, ATAC-seq, as well as ChIP-seq for the transcription factor PU.1 and the histone marks H3K4me2 and H3K27ac.

first: David

last: Gosselin

first: Nicole

last: Coufax

first: Inge

middle: R

last: Holtman

first: Johannes

middle: C

last: Schlachetzki

first: Carolyn

last: O’Connor

first: Martina

middle: P

last: Pasillas

first: Monique

last: Pena

first: Amy

last: Adair

first: Baptiste

last: Jaeger

middle: G

last: Gonda

first: Michael

middle: L

last: Levy

first: Richard

last: Ransohoff

first: Fred

last: Gage

first: Christopher

last: Glass

first: Eniko

last: Sajit


title: RNA-seq analysis of mitochondrial stress

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

institute: École Polytechnique Fédérale de Lausanne

summary: Expression analysis in HeLa cells upon treatment with doxycycline, actinonin, FCCP and MitoBloCK-6

overall_design: HeLa cells treated with different mitochondrial stressors for 24 hours

first: Pedro

last: Quiros


title: miR-seq to define mature miRNAs in human HEK293T cells that are targeted for degradation by the endonuclease Tudor-SN (i.e. by TumiD).

city: Rochester

first: Lynne

last: Maquat

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

summary: We report that human Tudor-SN degrades particular miRNAs that contain CA or UA dinucleotides located more than five nucleotides from miRNA ends.

overall_design: We defined miRNAs that are degraded by Tudor-SN by performing miR-seq on RNA isolated from HEK293T cells transiently transfected with Tudor-SN siRNA or, as a control, Control (Ctl) siRNA.

first: Peicheng

last: Du

first: Bin

last: Tian

first: Reyad

last: Elbarbary

first: Keita

last: Miyoshi

first: Jason

last: . Myers

first: John

last: Ashton


title: A Trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling

city: Carlsbad

first: Joanne

last: Yeakley

address: 1945 Camino Vida Roble Ste i

institute: BioSpyder Technologies, Inc.

summary: The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0.9) for 20,629 targets. Unlike many expression assays, TempO-Seq does not require RNA purification, cDNA synthesis, or capture of targeted RNA, and lacks a 3′ end bias. To investigate the sensitivity of the TempO-Seq assay to identify significantly modulated compound-responsive genes, we derived whole transcriptome profiles from MCF-7 cells treated with the histone deacetylase inhibitor Trichostatin A (TSA) and identified more than 9,000 differentially expressed genes. The TSA profile for MCF-7 cells overlapped those for HL-60 and PC-3 cells in the Connectivity Map (cMAP) database, suggesting a common TSA-specific expression profile independent of baseline gene expression. A 43-gene cell-independent TSA signature was extracted from cMAP and confirmed in TempO-Seq MCF-7 data. Additional genes that were not previously reported to be TSA responsive in the cMAP database were also identified. TSA treatment of 5 cell types revealed 1,136 differentially expressed genes in common, including 785 genes not previously reported to be TSA responsive. We conclude that TSA induces a specific expression signature that is consistent across widely different cell types, that this signature contains genes not previously associated with TSA responses, and that TempO-Seq provides the sensitive differential expression detection needed to define such compound-specific, cell-independent, changes in expression.

sample_organism:
Homo sapiens
synthetic construct
unidentified

overall_design:
Commercially available human reference and tissue RNAs, unpurified cell lysates from MCF-7 and MDA MB 231 cells, and synthetic ERCC RNAs were used to assess performance of a targeted whole transcriptome expression profiling method. In addition, MCF-7 cells, PC3 cells and HL60 cells were exposed to Trichostatin A, then lysed and profiled, to define a novel TSA-specific expression signature.

Samples GSM2429258 - GSM2429287 were purified reference RNAs and brain RNAs and mixtures between them that were run in the TempO-Seq assay in replicates of 6 each. Samples GSM2429258 - GSM2429287 have no associated raw data due to data loss.

The GSM2460368-GSM2460377 samples represent human reference RNA replicates that were processed in parallel, pooled in a single library and sequenced twice on the same instrument.

first: Peter

middle: J

last: Shepard


title: Small RNA-seq of ago4 null and slicing-defective mutant in Arabidopsis

city: State College

last: Axtell

address: 208 Mueller Lab

department: Department of Biology

institute: The Pennsylvania State University

summary: To investigate the effect of AGO4 upon small RNA accumulation in Arabidopsis, we analyzed small RNA accumulation in ago4, ago4/ago6/ago9 triple mutant, stable transgenic lines expressing wild-type AGO4 and slicing-defective AGO4 in ago4 and ago4/ago6/ago9 background.

overall_design: Three biological replicates each from indicated mutant and stable transgenic lines are analyzed on a HiSeq2500 platform.

first: Feng

last: Wang


title: Repurposing tofacitinib as an anti-myeloma therapeutic to reverse growth-promoting effects of the bone marrow microenvironment

city: San Francisco

first: Arun

middle: P.

last: Wiita

address: 185 Berry St., Suite 290

department: Laboratory Medicine

institute: University of California, San Francisco

summary: The myeloma bone marrow microenvironment promotes proliferation of malignant plasma cells and resistance to therapy. Interleukin-6 (IL-6) and downstream JAK/STAT signaling are thought to be central components of these microenvironment-induced phenotypes.  In a prior drug repurposing screen, we identified tofacitinib, a pan-JAK inhibitor FDA-approved for rheumatoid arthritis, as an agent that may reverse the tumor-stimulating effects of bone marrow mesenchymal stromal cells.  Here, we validated both in vitro, in stromal-responsive human myeloma cell lines, and in vivo, in orthotopic disseminated murine xenograft models of myeloma, that tofacitinib showed both single-agent and combination therapeutic efficacy in myeloma models.  Surprisingly, we found that ruxolitinib, an FDA-approved agent targeting JAK1 and JAK2, did not lead to the same anti-myeloma effects.  Combination with a novel irreversible JAK3-selective inhibitor also did not enhance ruxolitinib effects.  RNA-seq and unbiased phosphoproteomics revealed that marrow stromal cells stimulate a JAK/STAT-mediated proliferative program in myeloma plasma cells, and tofacitinib reversed the large majority of these pro-growth signals.  Taken together, our results suggest that tofacitinib specifically reverses the growth-promoting effects of the tumor microenvironment through blocking an IL-6-mediated signaling axis.  As tofacitinib is already FDA-approved, these results can be rapidly translated into potential clinical benefits for myeloma patients.

overall_design: Single-end 50 bp RNA-seq of MM.1S myeloma cell line either grown alone in monoculture, MM.1S isolated after 24 hr co-culture with immortalized HS5 bone marrow stromal cells, or HS5 bone marrow stromal cells grown alone

first: Lam

last: Christine

first: Wiita

last: Arun P.


title: NicE-seq: high resolution open chromatin profiling

status: Public on May 24 2017

city: Ipswish

first: V K Chaithanya

last: Ponnaluri

state: Massachusetts

address: 240 County Road, 3W031

department: Genome Biology

institute: New England Biolabs

summary: Mammalian chromatin is dynamic and contains structural information that leads to transcriptional regulation of genes by recruiting transcription factors and altering nucleosome positioning. Here, we describe open chromatin mapping using Nicking Enzyme assisted sequencing (NicE-seq) for integrative epigenomic analysis. NicE-seq captures open chromatin sites in both fixed and native cells and reveals the genomic location of open chromatin sites (OCS) and transcription factor occupancy at single nucleotide resolution, with as few as 250 HCT116 cells. In HCT116 cells a large percentage of the OCS were coincident with DHS (DNaseI hypersensitive site) and ATAC-seq sites. OCSs correlated well with RNA pol II occupancy and transcriptionally active chromatin marks, while displaying a pattern contrasting to CpG methylation.  ChIP CTCF peaks common to OCS and DHS displayed a strong correlation with H3K4me3 and H3K27ac marks. Further peaks unique to OCS and ChIP CTCF peaks also correlated strongly with H3K4me3, H3K27ac and higher transcription. Similar results were also obtained for Max and Sp1 transcription factors. Using NicE-seq we have demonstrated that HCT116 cells, treated with anti cancer drug decitabine, displayed time dependent accumulation of OCS coinciding with hypomethylation of the genome, particularly in SINE and satellite repetitive DNA. Differentially methylated regions (DMRs) were more pronounced in promoters, 5’UTR, CpG islands and exons. In summary, sequence specificity offered by a nicking enzyme allows a means to study open chromatin structure and hypomethylation of genomes, revealing the open chromatin landscape in cellular context.

overall_design: Examination of NicE-seq libraries on HCT116 cells (25 to 250,000 cells), MCF7 cells, Decitabine treated HCT116 cells, WGBS on Decitabine treated and untreated HCT116 cells and ATC-seq on HCT116 cells.

first: Sriharsa

last: Pradhan


title: The role and mechanism of erythrocyte invasion by Francisella tularensis

city: Huntington

first: Swanthana

last: Rekulapally

state: WV

address: 1 John Marshall Drive

department: Biomedical Sciences

institute: Marshall University

summary: Francisella tularensis, is an extremely virulent bacterium that can be transmitted naturally by blood sucking arthropods.  During mammalian infection, F. tularensis infects numerous types of host cells, including erythrocytes.  As erythrocytes do not undergo phagocytosis or endocytosis, it remains unknown how F. tularensis invades these cells.  Furthermore, the consequence of inhabiting the intracellular space of red blood cells has not been determined. Here, we provide evidence indicating that residing within an erythrocyte enhances the ability of F. tularensis to colonize ticks following a blood meal.

overall_design: mRNA profiles of F. tularensis with and without human erythrocyte exposure (5 replicates of each) were generated using high-throughput sequencing on an Illumina HiSeq 1500 in a 2X50 bp paired-end strategy

first: Joseph

last: Horzempa

first: Rebecca

last: Barnes

first: Taylor

last: Rogerson

first: Ashley

last: Haught

first: Leanne

last: Mazzella

first: Matthew

last: Ford

first: Tricia

last: Gilson

first: Anders

last: Sjöstedt

first: Douglas

last: Reed

first: Jonathan

last: Franks

first: Donna

last: Beer Stolz

first: James

last: Denvir

first: Jun

last: Fan

first: Donald

last: Primerano

first: Deanna

last: Schmitt


title: A Comparison of the Sexually Dimorphic Dexamethasone Transcriptome in Mouse Cerebral Cortical and Hypothalamic Embryonic Neural Stem Cells

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary: We used RNA-Seq analysis to identify the sexually dimorphic dexamethasone regulated gene expression profile in primary mouse embryonic cerebral cortical and hypothalamic neural progenitor/stem cells.

overall_design: RNAseq on primary E14.5 mouse cerebral cortical and hypothalamic (hypo) neurosphere cultures. 8 conditions - Male Cortex Dex, Male Cortex Ethanol vehicle (EtOH), Female Cortex Dex, Female Cortex EtOH, Male Hypo Dex, Male Hypo EtOH, Female Hypo Dex and Female Hypo EtOH. There are 3 biological replicates for each condition and all the 24 samples were run on two lanes (technical duplicates).

first: K

last: Frahm

first: S

last: Luthra

first: J

last: Waldman

first: A

last: Rudine

last: Monaghan-Nichols

first: U

first: D

middle: B

last: DeFranco


title: Genome-wide analysis of AR binding and comparison with transcript expression in primary human fetal prostate fibroblasts and cancer associated fibroblasts

city: Montréal

first: Claire

middle: Elizabeth

last: Nash

state: QC

address: 1001 Decarie Blvd

department: Urology

country: Canada

institute: Research Institute of McGill University Health Centre

summary: We applied ChIPseq to identify genomic AR binding sites for the first time in primary human fetal prostate fibroblasts and patient derived cancer associated fibroblasts, as well as the WPMY1 cell line overexpressing AR. We identified AR binding sites that were specific to fetal prostate fibroblasts (7534), cancer fibroblasts (629), WPMY1-AR (2561) as well as those common among all (783). Primary fibroblasts had a distinct AR binding profile versus prostate cancer cell lines and tissue, and showed a localisation to gene promoter binding sites 1kb upstream of the transcriptional start site, as well as non-classical AR binding sequence motifs. We used RNAseq to define transcribed genes associated with AR binding sites and derived cistromes for embryonic and cancer fibroblasts as well as a cistrome common to both. These were compared to several in vivo ChIPseq and transcript expression datasets; which identified subsets of AR targets that were expressed in vivo and regulated by androgens in order to define for the first time which cellular subpopulations might be the true source of AR-associated signals.

overall_design: Examination of AR binding profile in 3 cell types.

middle: E

first: Axel

last: Thomson