title: CFP1/SET1 complex occupancy and H3K4me3 profile in CFP1 fl/fl ES cells and rescue lines. [mESC_ChIPseq]

overall_design: CFP1 fl/fl mouse embryonic stem cells were treated with tamoxifen (TAM) for 96h to ablate CFP1 protein levels. ChIP-seq experiments were performed to determine the genome-wide occupancy of CFP1 and SET1A, the catalytic subunit of the SET1 complex. Since SET1A occupancy is altered upon deletion of CFP1, we used a calibrated ChIP-seq approach to assess the changes in H3K4me3 in this cell line. Moreover, we generated additional ES cell lines with CFP1 fl/fl background expressing exogenous GFP-tagged forms of CFP1 to analysed the effects of different CFP1 mutantions on H3K4me3 profile. We generated a GFP control line (EV), a wild type CFP1 line, a PHD and CxxC domains (PC) double point mutant line, and a SET1 interaction domain (SID) mutant line.   Calibrated experiments were performed when possible mixing mouse cells with a Drosophila S2 line (SG4) prior to chromatin extraction.


title: A hyperdynamic H3.3 nucleosome marks promoter regions in pluripotent embryonic stem cells

status: Public on Sep 05 2017

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone variants and their chaperones are key regulators of eukaryotic transcription, and are critical for normal development. The histone variant H3.3 has been shown to play important roles in pluripotency and differentiation, and although its genome-wide patterns have been investigated, little is known about the role of its dynamic turnover in transcriptional regulation. To elucidate the role of H3.3 dynamics in embryonic stem cell (ESC) biology, we generated mouse ESC lines carrying a single copy of a doxycycline (Dox)-inducible HA-tagged version of H3.3, and monitored the rate of incorporation of the HA-tagged variant by ChIP-seq at varying time points following Dox induction. Active H3K4me3-enriched genes display high turnover dynamics in transcription start sites (TSS); H3K27me3-enriched genes have a lower turnover dynamics in the TSS, but higher turnover rates in gene bodies; developmental bivalent genes marked by both H3K4me3 and H3K27me3 show a mixed behavior with high TSS dynamics and high gene body dynamics, especially in genes bound by both PRC1 and PRC2. In contrast, genes proximal to super-enhancers show the most reduced gene-body turnover dynamics, while genes proximal to other enhancers show no unique pattern. In RA-treated cells, while the overall profile in expressed genes remains largely unaltered over the TSS and gene body, a significant and dramatic decrease in turnover occurs at the -1 nucleosome position immediately before the TSS, revealing a hyperdynamic nucleosome in promoters of genes expressed in ESCs. We suggest that histone turnover dynamics provides an additional mechanism involved in expression regulation, that gene-body turnover dynamics is distinct from that of promoter regions, and that a hyperdynamic -1 nucleosome marks promoters in ESCs. Our data provide evidence for regional regulation of H3.3 turnover in ESC promoters, and calls for testing, in high resolution, the dynamic behavior of additional histone variants and other structural chromatin proteins.

overall_design: Examination of genome-wide H3.3 incorporation in mouse ESC.

first: Sharon

last: Schlesinger

first: Shai

last: Melcer

first: Eran

last: Meshorer


title: Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers [RNA-seq]

city: Berlin

first: Tommaso

last: Mari

address: Robert-Rössle-Str. 10

country: Germany

institute: Max-Delbrück-Centrum für Molekulare Medizin

summary: The activity of enhancers and promoters fine-tunes the transcriptional program of mammalian cells through the recruitment and interplay between cell type-specific and ubiquitous transcription factors. Despite their key role in modulating transcription, the identification of enhancers is challenged by their limited sequence conservation and highly variable distance from target genes. Although enhancers are characterised by the strong enrichment of mono-methylation at lysine 4 of histone H3, mirrored by low tri-methylation at the same residue, a comprehensive list of enhancers-associated histone post-translational modifications (PTMs) is still lacking. We undertook a proteomics investigation, based on chromatin immunoprecipitation combined with mass spectrometry (MS), to identify histone marks specifically associated to cis-regulatory elements in macrophages, focusing on enhancers. We also profiled their plasticity during the transcriptional activation induced by an inflammatory stimulus. The proteomic analysis suggested novel PTM associations, which were validated by analysis of ChIP- and RNA-seq data, whose intersection revealed the existence of novel sub-populations of enhancers marked by specific signatures: the dual mark H3K4me1/K36me2 labels transcription at enhancers, whereas H3K4me1/K36me3 and H3K4me1/K79me2 tag distinct intronic enhancers. While demonstrating that analyzing restricted genomic regions can disclose the combinatorial language of histone modifications, this study highlights the potential of MS-based proteomics in addressing fundamental questions in epigenetics.

overall_design: Total RNA was extracted from 5x10^6 untreated RAW 264.7 cells using RNAeasy kit (Qiagen). Libraries were then prepared using TruSeq RNA sample preparation Kit (Illumina) after depleting ribosomal RNA

first: Monica

last: Soldi

first: Luciano

last: Nicosia

first: Daniele

last: Musiani

first: Gianluca

last: Sigismondo

first: Alessandro

last: Cuomo

first: Giulio

last: Pavesi

first: Tiziana

last: Bonaldi


title: CFP1 engages in multivalent interactions with CpG island chromatin to recruit the SET1 complex and regulate gene expression.

city: Oxford

first: Vincenzo

last: Di Cerbo

address: South Parks Road

country: United Kingdom

institute: University of Oxford

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

overall_design: Refer to individual Series


title: An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets [iPCR/BC-PCR]

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: Clonal cellular variance often confounds reproducibility of forward and reverse genetic studies. We developed combinatorial approaches for whole genome saturated mutagenesis using haploid murine ES cells to permit induction and reversion of genetic mutations. Using these systems, we created a biobank with over 100000 individual ES cell lines with repairable and genetically bar coded mutations targeting 16950 genes. This biobank termed “Haplobank” is freely available. In addition, we developed a genetic color coding system for rapid repair of mutations and direct functional validation in sister clones. Using this system, we report functional validation of essential ES cell genes. We also identified phospholipase16G as a key pathway for cytotoxicity of human rhinoviruses, the most frequent cause of the common cold.  Moreover, we derived 3D blood vessel organoids from haploid ES cells, combining conditional mutagenesis in haploid ES cells with tissue engineering. We identified multiple novel genes, such as Connexin43/Gja1, in blood vessel formation and tip cell specification in vitro and also in vivo. Taken together, we develop a conditional homozygous ES cell resource for the community to empower controlled genetic studies in murine ES cells and tissues derived from it.

overall_design:
Genomic integration sites of mutagens were mapped by inverse PCR
Please note that [1] this study is used to create a biobank of clones which have a specific insertion and are uniquely identifieable. Due to the huge amount of clones the processed data would be very large and difficult to interpret without the context of the database. Therefore, the processed data will be made accessible to everyone at https://www.haplobank.at (upon acceptance of the manuscript) [2] the barcodes are used to identify the clones/wells in "4D" which are rows/columns/slices/towers [3] The protocols used for the samples are found in great detail at https://www.haplobank.at/ecommerce/control/haplobank_resource

first: Ulrich

last: Elling

first: Andreas

last: Leibbrandt


title: An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets [RNA-Seq]

overall_design:
RNA-Seq was carried out using standard protocols.
https://www.haplobank.at/ecommerce/control/haplobank_resource


title: An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets


title: Transcriptome analysis of ECFCs treated with GSK-343 and Panobinostat

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

summary: Human endothelial colony-forming cells (ECFCs) represent one of the most promising sources of adult stem cells for vascular regeneration after ischemia. Yet, the molecular mechanism underlying the unique properties of these cells to repair damaged blood vessels remains unclear, and new strategies to improve their regenerative function are needed. Here, we demonstrate that ex vivo treatment of ECFCs with a combination of epigenetic drugs (i.e. the histone H3K27 demethylase inhibitor GSK-343 and the histone deacetylase inhibitor panobinostat) improves the migration of these cells and their capacity to form capillary-like networks while also increasing their resistance to serum starvation-induced apoptosis. Furthermore, the kinetic of blood flow recovery is significantly increased upon transplantation of drug-treated ECFCs in a pre-clinical model of hind-limb ischemia. Gene expression profiling by RNA-sequencing reveals that these effects are mediated through the simultaneous activation of several major pro-angiogenic signaling pathways including VEGFR, CXCR4, WNT, NOTCH and SHH. At the molecular level, we provide evidence that the two drugs work through complementary mechanisms that entail the resolving of bivalently marked genes characterized by the presence of both negative (H3K27me3) and positive (H3K4me3 and H3-Ac) histone modifications to create a transcriptionally permissive chromatin environment. Thus, ex vivo treatment with epigenetic drugs increases the vascular repair properties of ECFCs through transient activation of major pro-angiogenic signaling pathways.

overall_design: ECFCs mRNA profile after treatment with GSK-343 and panobinostat epigenetic drug combiantion

first: Sylvain

last: Fraineau

first: Alphonse

last: Chu


title: A Complex Association between DNA Methylation and Gene Expression in Human Placenta at First and Third Trimesters

city: Wenzhou

first: Chunming

last: Ding

address: Wenzhou Medical University, University Town, Chashan, Wenzhou, Zhejiang, P.R China

country: China

institute: Wenzhou Medical University

type: Methylation profiling by high throughput sequencing

summary: We performed DNA methylome analysis by reduced representation bisulfite sequencing (RRBS) and gene expression analysis by RNA-Seq for both first and third trimester human placenta tissues.The correlation between DNA methylation and gene expression was non-linear and complex, depending on the genomic context (promoter or gene body) and gene expression levels. A wide range of DNA methylation and gene expression changes were observed at different gestational ages. The non-linear association between DNA methylation and gene expression indicates that epigenetic regulation of placenta development is more complex than previously envisioned.

overall_design:
[RRBS] DNA methylation comparison in human placenta between 6 first trimester and 5 third trimester samples
[RNA-Seq] Comparison of RNA expression in human placenta between 5 first/second trimester and 4 third trimester samples

first: Yen

middle: C

last: Lim


title: Transcriptomics analysis of gene expressions and DNA 5mC enrichment levels in control and dnmt1 morphants zebrafish embryos

city: Beijing

first: Lu

last: WANG

address: 1 Beichen West Road, Chaoyang District

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

summary: RNA and whole-genome DNA were isolated from control and dnmt1 morphants zebrafish cells using the TRIzol (Tiangen) reagent and phenol-chloroform extraction by following the  manual, respectively. The cDNA library for RNA-seq and DNA library for MeDIP-seq were sequenced using HiSeq2000 (Illumina) in single-end read and paired-read mode, reapectively.

overall_design: Examination of gene expressive levels and 5mC enrichment levels in normal and dnmt1 morphants zebrafish cells

last: Wang

first: Feng

last: Liu


title: Expression of long non-coding RNAs during spermatogenesis

status: Public on Sep 04 2017

city: Cleveland

first: Ahmad

middle: M

last: Khalil

state: OH

address: 2109 Adelbert Rd

department: Genetics and Genome Sciences

country: USA

institute: Case Western Reserve University

summary: Total RNA from purified stages of spermatogenesis were subjected to next generation RNA-seq (100bp, paired-end, strand-specific). The expression of mRNAs and lncRNAs was calculated as FPKM values.

overall_design: Three biological replicates of spermatogonia, pachytene and round spermatids were utilized for RNA isolation.

first: Saigopal

last: Somasundaram


title: Reduced expression of ABCB4 is linked to an inflammatory phenotype of biliary atresia in mice and men

city: Cincinnati

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Purpose: to identify differentially regulated pathways and processes in the livers of neonatal  Mdr+/- compared to Mdr+/+ mice and correlate these transcriptomics with hepatic lipdomics data
Methods: Mdr2+/- mice were mated. There offspring with +/+, +/-,  and -/- mdr2 genotypes were kept as litter mates until harvest of livers at 10 days of life. Lobe 1 and 2 were dissected and snap frozen in liquid nitrogen for subsequent RNA isolation and lipid extraction, respectively. RNA-seq libraries were prepared using Illumina TruSeq RNA prep kits and sequenced on the Illumina Hi-Seq 2000.
Results: Approximately 20 million reads were mapped to the mm10 mouse genome build using attotations produced by the Ensembl project, which corresponded to 36,400 transcripts.  Of these, over 600 transcripts exhibited differential regulation between Mdr+/+ and Mdr+/- samples.
Conclusions:  Our study supports a pro-inflammatory microenvironment in neonatal, non-infected mdr2+/- compared with wild type mice.

overall_design: Hepatic mRNA profiles of Mdr2+/+ and +/- neonatal, BALB/C mice were generated through RNAsequencing.

first: Alex

last: Miethke


title: Analysis of the common and respective roles of CBP and p300 co-activators in human primary myoblast differentiation.

city: Toulouse

first: Laurence

last: Vandel

address: 118 ROute de Narbonne

department: CBD

country: France

institute: CNRS

summary: We used Affymetrix microarrays to detail the global programme of gene expression regulated by CBP and/or p300 during human primary myoblast differentiation.

overall_design: Human Primary Myoblasts (HPM) were used to assess the respective roles of CBP and p300 in myogenesis. To this aim, HPM were grown in proliferation medium and cells were transfected at conflunce with 5nM of siRNAs (siCBP, siP300, siCBP+P300) before being inducing 24 hours later later for diffrentiation. Cells were then harvested at 24, 48, 72 and 96hrs after transfection before RNA extraction and hybridization on Affymetrix microarrays.

first: Lucas

last: Fauquier


title: Comprehensive molecular phenotypic effects of the large deletion on chromosome 22q11.2

city: Thousand Oaks

first: Xianglong

last: Zhang

state: CA

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

summary:
Purpose: 22q11 Deletion Syndrome (22q11DS) is a disorder caused by a heterozygous deletion of 3 million base pairs containing approximately 50 known genes on chromosome 22q.  It occurs in around 1 in 4,000 live births. The common phenotypes of 22q11DS include a large spectrum of congenital anomalies, most notably of the cardiovascular system as well as several developmental neuropsychiatric disorders, in particular schizophrenia and autism spectrum disorders.Here we are testing the hypothesis that, in addition to changing the gene dosage of genes located within the CNV boundaries, large CNVs may have an effect on long-range chromosome interactions and epigenetic profiles.
Methods: We generated Hi-C contact maps for 11 human lymphoblastoid cell lines and performed RNA-Seq on 14 cell lines and ChIP-seq of H3K27ac, H3K27me3 and CTCF for some of the cell lines.
Results: We found dosage effects of 22q11del on chromosome contacts, epigenetic profiles and gene expressions. Extensive changes on these levels caused by 22q11del are global instead of confined to the deletion region only.
Conclusions: Our results shed light on the comprehensive effects of 22q11del on different molecular levels in lymphoblastoid cell lines.

overall_design: Hi-C data of 6 control and 5 22q11DS cell lines were generated. RNA-seq were performed for 9 control and 5 22q11DS cell lines. ChIP-seq of H3K27ac, H3K27me3 and CTCF were performed for 2 or 3 controls and 3 22q11DS cell lines. All the sequencing was performed using Illumina HiSeq.

first: Ying

first: Xiaowei

last: Zhu

first: Carolin

last: Purmann

last: Ward

first: Michael

last: Haney

first: Sherman

last: Weissman

first: Alexander

last: Urban


title: Next Generation Sequencing of β-cat lox(ex3) (Ctrl) mouse and β-cat lox(ex3);Nex-Cre (β-cat overexpression, β-cat Ovp) mouse Transcriptomes

status: Public on Sep 02 2017

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 320 Yueyang Rd

institute: Institute of Neuroscience, Chinese Academy of Sciences

summary: Using RNA-seq to sequence the transcriptomes of β-cat lox(ex3) (Ctrl) and β-cat lox(ex3);Nex-Cre (β-cat Ovp) mice, we did not find significant change in the expression level of classical Wnt target genes.

overall_design: mRNA profiles of 14-day old β-cat lox(ex3) (Ctrl) and β-cat lox(ex3);Nex-Cre (β-cat Ovp) mice were generated by deep sequencing, in triplicate, using Illumina Hiseq.

first: M

last: Li

first: X


title: Chromatin binding of CFP1 mutants in C127 mouse cell lines. [C127_ChIPseq]

first: Vincenzo

last: Di Cerbo

summary: Chromatin modifications and the promoter associated epigenome are thought to be important for the regulation of gene expression. However, the mechanisms by which chromatin modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed target gene promoters through CFP1 which engages in a unique form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). CFP1 defines SET1 complex occupancy on chromatin and its multivalent interactions are required for the SET1 complex to place H3K4me3. In the absence of CFP1, gene expression is perturbed suggesting that the normal targeting and function of SET1 complex is central to creating an appropriately functioning vertebrate promoter associated epigenome.

overall_design: C127 mouse cell line was used to investigate the occupancy of variuos chromatin binding proteins, including CFP1, KDM2B and RNA PolII, as well as the genome-wide distribution of H3K4me3. In addition, novel C127 cell lines were generated that expressed different forms of a GFP-tagged CFP1 protein to compare the binding properties of wild-type CFP1 with single point mutants within its binding domains. The cell lines generated include GFP-CFP1 wild-type , GFP-CFP1 CXXC mutant, GFP-CFP1 PHD mutant, a double GFP-CFP1 PHD and CXXC mutant, GFP-CPF1 SID mutant, along with a GFP control.

first: David

middle: A

last: Brown

first: Angelika

last: Feldmann

first: Rob

last: Klose


title: An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets [ATAC-Seq, ChIP-Seq]

first: Thomas

last: Burkard

overall_design:
We correlated the genome-wide insertion frequency of different lentiviral-, retroviral- and transposon (Tol2 and Sleeping beauty-SB)-based mutagenesis vectors to DNA accessibility and the distribution pattern of active and repressive histone modifications.
https://www.haplobank.at/ecommerce/control/haplobank_resource

first: Jorge

last: Zepeda-Martínez

first: Oliver

last: Bell


title: Amplification of mutant BRCA2 gene confers resistance to PARP inhibitor

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Breast cancer gene 2 (BRCA2) deleterious mutations confer sensitivity to poly(ADP-ribose) polymerase (PARP) inhibition due to its critical role in DNA repair.   PARP inhibitor Olaparib is now approved and several other PARP inhibitors are now in different stages of clinical trials.  Development of resistance to PARP inhibitors limits their clinical utility.  The mechanism of resistance remains not fully understood.  Here we show that amplification of mutant BRCA2 confers PARP inhibitor resistance.  The amplification of mutant BRCA2 gene copies correlates with an increase in mutant BRCA2 expression and an increase in the levels of its interacting proteins PALB2 and RAD51. In addition, homologous recombination mediated DNA repair is rescued in these cells as evidenced by the formation of RAD51 focus formation.   The overexpressed mutant BRCA2 is essential for the observed PARP inhibitor resistance because knockdown of its expression is sufficient to re-sensitize these cells to PARP inhibition.  Collectively, our results indicate a new mechanism of resistance to PARP inhibitor in BRCA2 mutant cancer cells

overall_design: RNA-seq profiling of parental CAPAN1 cell line and PARP resistant cell line.

first: Pyoung

middle: H

last: Park

first: Rugang


title: RNAseq to determine whether bidirectional transcription occurs over transposable elements following depletion of SETDB1 in THP-1 AML Cells

status: Public on Sep 06 2017

city: Princeton

first: Trinna

middle: L.

last: Cuellar

state: New Jersey

address: Lewis Thomas Lab, Washington Rd/MOF223C

department: Molecular Biology

institute: Princeton University

summary:
SETDB1 disruption leads to an increase in the expression of transposable elements as determined by our standard RNAseq, where bidirectional transcription has been reported. We repeated RNA seq on our samples with a stranded prep to determine whether bidirectional transcription occurs of transposable elements following depletion of SETDB1 in THP-1 AML Cells
Methods: THP-1 cells were treated with two different SETDB1 sgRNAs (6, and 9) or Non-targeting control sgRNA (NTC) for 4 and 7 days. RNA was isolated and prepared for RNAseq with Qiagen RNeasy kits.
Results: Consensus sequences for elements for upregulated TEs were downloaded from the Dfam database (Hubley et al., 2016). Stranded RNA-seq data was then aligned to consensus sequences using BWA-MEM and quantified using HTseq-count(Anders et al., 2015; Li, 2013). Reads were visualized using the IGV genome browser, using a custom pseudogenome that was generated from the Dfam consensus sequences (Robinson et al., 2011; Thorvaldsdottir et al., 2013).
Conclusions: Our data determined that following the disruption of SETDB1, there is increased bidirectional transcription over a subset of transposable elements.

overall_design: THP-1 RNA samples treated with 2 different SETDB1 sgRNAs (6, and 9) or NTC sgRNAs and collected at days 4 and 7 in triplicate for a total of 12 samples.

middle: L

first: Steffen

last: Durinck


title: CHD1 regulates cell fate determination by activation of  differentiation-induced genes

status: Public on Sep 03 2017

city: Göttingen

first: Simon

middle: Joschka

last: Baumgart

state: Lower Saxony

address: Justus-von-Liebig Weg 11

department: Allgemeine und Viszeralchirurgie - Surgery

institute: Göttingen Medical Center

summary: We describe here a novel role for CHD1 in regulating the osteoblast cell fate by studying the effect of CHD1 depletion on the epigenetic landscape and on mRNA expression in mesenchymal stem cells (MSC) (Simonsen et al. 2012) and fetal Osteoblast (hFOB 1.19) (Harris et al. 1995) during osteoblast differentiation.

overall_design: In this study we performed ChIP-seq and RNA-seq experiments in two different cell lines namely MSC and FOB in undifferentiated (Und), osteoblast (Ob) or adipocyte differentiated (Ad) condition. ChIP-seq was done for H2A.Z, H2Bub1, H3.3, RNAPII and CHD1 in osteoblast differentiated FOB with control or CHD1 siRNA treatment (siCON, siCHD1 respectively). In MSC ChIP-seq was performed for H3K4me3, H3K27me3, H3K27ac and CHD1.

first: Steven

last: Johnsen


title: Transcriptomic analysis of brainstem samples from mutants with Hoxa5 postnatal inactivation versus controls at postnatal day 21

city: Louvain-le-Neuve

first: Françoise

last: Gofflot

address: Croix du Sud, 4-5, Bte L7.07.02

department: Institut des Sciences de la Vie

country: Belgium

institute: Université catholique de Louvain

summary: After inactivation of Hoxa5 at postnatal days (P)1-P4, we established RNA-seq profiling with RNA extracted from P21 brainstem of tamoxifen-treated Hoxa5flox/flox;CMV-CreERT2+/- (Hoxa5 cKO) pups and  tamoxifen-treated Hoxa5flox/flox;CMV-CreERT2-/-(Hoxa5 control) pups

overall_design: To explore HOXA5 downstream target genes in the postnatal brainstem, we carried out transcriptomic analyses by RNA-Seq using a model of postnatal Hoxa5 loss-of-function. We induced Hoxa5 inactivation after birth (P1 to P4) using the tamoxifen-inducible CMV-CreERT2 mice and conditional Hoxa5 floxed allele mice (Hoxa5flox). RNA was extracted from the brainstem of P21 tamoxifen-treated Hoxa5flox/flox;CMV-CreERT2+/- pups and from tamoxifen-treated Hoxa5flox/flox;CMV-CreERT2-/- littermates (see extract protocol).

first: Benoit

last: Hennuy

last: Lizen

last: Charloteaux


title: Hoxa5 dependent transcriptional regulation and RA-mediated Hox PG5 chromatin organization

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

overall_design: Refer to individual Series


title: Gene expression changes  upon deletion of CFP1 in mouse ES cells. [mESC_RNAseq]

first: Vincenzo

last: Di Cerbo

overall_design: CFP1 fl/fl mouse embryonic stem cells were treated with tamoxifen (TAM) for 96h to ablate CFP1 protein levels. Calibrated nuclear RNA-seq (nucRNA-seq) was performed to evaluate gene expression changes (4 biological replicates). 4-thiouridine-seq (4sU-seq) was used to measure the expression level of nascent transcripts in untreated CFP1 fl/fl cells (3 biological replicates).

last: Brown


title: An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets [iPCR]

overall_design:
Genomic integration sites of mutagens were mapped by inverse PCR
https://www.haplobank.at/ecommerce/control/haplobank_resource

first: Ulrich

last: Elling

first: Andreas

last: Leibbrandt


title: Investigating putative RPS4-chromatin associations during Arabidopsis plant disease resistance, using a temperature-inducible system which resembles pathogen-infection

city: Koeln

first: Servane

last: Baufume

state: Germany (DEU)

address: Carl-von-Linné-Weg 10

department: Plant Microbe Intreractions

institute: Max Planck Institute for Plant Breeding Research

summary: Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. The Arabidopsis Toll-related intracellular receptor RPS4 operates inside nuclei to trigger resistance and defence gene reprogramming through the stress response regulator, EDS1. In order to test a role for RPS4 at the chromatin level during Effector-Triggered Immunity (ETI), we undertook a ChIP-seq approach.

overall_design:
We used transgenic Arabidopsis plants constitutively expressing RPS4 in EDS1 WT or eds1-2 mutant backgrounds. In the EDS1 WT background, an immune response can be turned on rapidly and synchronously in leaf cells after a switch from high to moderate temperature. In order to substract defense-unrelated artifacts due to the temperature stimulus, we used Col-0 WT plants in parallel as negative control.
This Series represents the ChIP-Seq data only. The related gene expression microarray data are available in GSE40143, and RNA-Seq data in GSE40216.

last: Blanvillain-Baufumé

first: Jane

last: Parker

first: Nahal

last: Ahmadinejad

first: Barbara

last: Kracher

first: Janine

last: Altmueller

first: Susanne

last: Motameny


title: DNA 5-hydroxymethylcytosines from cell-free circulating DNA as diagnostic biomarkers for human cancers

city: Chicago

first: Xu

last: Zhang

state: Illinois

address: 820 South Wood St

institute: University of Illinois at Chicago

summary: DNA modifications such as 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) are epigenetic marks known to affect global gene expression in mammals. Given their prevalence in the human genome, close correlation with gene expression, and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology, we report here genome-wide 5hmC profiling in circulating cell-free DNA (cfDNA) and paired tumor/adjacent tissues collected from a cohort of 90 healthy individuals and 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver, or thyroid cancer. 5hmC was mainly distributed in transcriptionally active regions coincident with open chromatin and permissive histone modifications. Robust cancer-specific epigenetic signatures in cfDNA were identified in different cancers. 5hmC-based biomarkers demonstrated highly accurate predictive value for patients with colorectal and gastric cancers versus healthy controls, superior to conventional biomarkers, and comparable to epigenetic biomarkers from tissue biopsies. This new strategy could lead to the development of an effective blood-based, minimally-invasive cancer diagnosis and prognosis approach.

overall_design: A total of 421 + 11 individual (90 healthy individuals, 260 cancer patients, 71 patients with benign disease from China; 6 healthy individuals, 5 caner patients  from the United States).

first: Chuan

last: He

first: Jie

last: Liu

first: Wei


title: Gene expression analysis between rainbow trout strains with different susceptibility to enteritis when reared on plant-based diets

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

summary: Rainbow trout (Oncorhynchus mykiss) and other salmonids are piscivorous fish. In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. Total replacement of fishmeal with plant proteins causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we have developed a strain of rainbow trout that does not develop distal intestine enteritis when reared on a high soy plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a major role in dietary alterations, and as growth was a major factor in the selection program, both muscle and liver gene expression were examined for differential regulation between commercial and selected trout strains when fed alternative diets. After three months of rearing on either a fishmeal (FM) or plant protein-based (PM) diet, muscle and liver tissues from a domestic non-selected strain (House Creek; develops enteritis) and  the selected strain (ARS-KO; no enteritis) were extracted and prepped for Illumina RNA-seq. Raw reads were screened for quality then aligned to the rainbow trout transcriptome. Read-counts were used to assess differential expression between strains and treatments. Significant differentially expressed genes between comparisons were assessed.

overall_design: Rainbow trout strain selected for tolerance to plant-based diets (ARS-KO) and control fish strain (House Creek) were fed either a fish meal (FM) or plant meal (PM) based diet in replicate tanks over a 12-week period. After this time, muscle and liver tissues were sampled. A total of 80 samples were taken: ten biological replicates, sampling two tissues, with two treatment groups, for each of the two trout strains.

first: Ken

last: Overturf


title: Three Dimensional (3D) conformational change of chromatin organization upon RA mediated Hox PG5 induction

last: Roloff

summary: Changes in the transcriptional status of developmentally regulated genes, including Hox genes, go along with changes in the chromatin organisation as shown in cultured cells as well as in the developing embryo. The signals that affect the 3D structure of the genome are less understood. The tight regulation of Hox PG5 genes by RA might be accompanied by the physical separation of active and inactive Hox genes in the r5-6 and r8 domains in the hindbrain. To examine the role of RA on higher order chromatin conformation, we employed high-resolution circular chromosome conformation capture followed by high throughput sequencing (4C-Seq). We performed 4C-seq at E14.5, using the Hoxa5 and b5 promoters as view-points on Hox PG5 negative (rhombomers 5-6) and positive domains (rhombomer 8). 4C-seq was also performed with cortex as an entirely Hox negative control tissue.

overall_design: 12 samples were analysed. Two replicates for each tissue and treatment. The raw data for all samples in this series are contained in three fastq files associated with sample GSM1868848.

first: Sjored

last: Holwerda

first: Sophie

last: Dessus-Babus

first: Michael

middle: B

last: Stadler

first: Filippo

last: Rijli


title: Hoxa5 dependent transcriptional regulation of pontine nuclei subset formation

first: Tim

summary: Cortico-ponto-cerebellar topographic circuit formation requires patterned expression of chemotropically active molecules as well as differential expression of axon guidance molecules within the pontine nuclei. We carried out RNA-sequencing experiments on different sets of genetically identified or manipulated pontine nuclei neurons followed by comparative transcriptome analysis to identify genes which are potentially involved in controlling PN circuit formation and are regulated by Hoxa5.

overall_design: 6 control samples were compared to 3 12 samples in total; 6 reference samples were compared to 2 conditions with 3 samples each

first: Stephane

last: Thiry

first: Dominik

last: Kraus


title: An efficient method for generation of bi-allelic null mutant mouse embryonic stem cell lines and its application for investigating epigenetic modifiers

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

summary: Mouse embryonic stem (ES) cells are a popular model system to study biological processes, though uncovering recessive phenotypes requires inactivating both alleles. Building upon resources from the International Knockout Mouse Consortium (IKMC), we developed a targeting vector for second allele inactivation in conditional-ready IKMC ‘knockout-first’ ES cell lines. We applied our technology to several epigenetic regulators, recovering bi-allelic targeted clones with a high efficiency of 60%, and used Flp recombinase to restore expression in two null cell lines to demonstrate how our system confirms causality through mutant phenotype reversion. We designed our strategy to select against re targeting the ‘knockout-first’ allele, and identify essential genes in ES cells, including the histone methyltransferase Setdb1. For confirmation, we exploited the flexibility of our system, enabling tamoxifen inducible conditional gene ablation while controlling for genetic background and tamoxifen effects. Setdb1 ablated ES cells exhibit severe growth inhibition, which is not rescued by exogenous Nanog expression or culturing in naive pluripotency ‘2i’ media, suggesting that the self-renewal defect is mediated through pluripotency network independent pathways. Our strategy to generate null mutant mouse ES cells is applicable to thousands of genes and repurposes existing IKMC Intermediate Vectors.

overall_design: H3K9me3 ChIP-Seq profiling of Setdb1 depleted mouse ES cells

first: Cynthia

last: Fisher

first: Lily

middle: T

last: Cho

first: Rob

last: Andrews

first: Sam

last: Wormald

first: Tom

last: Carroll

first: Vivek

last: Iyer

first: Peri

last: Tate

first: Barry

last: Rosen

middle: G

last: Stunnenberg

first: Amanda

first: William

last: Skarnes


title: Genome-wide miRNA turnover profile in HDMYZ cells after transcription inhibition

city: New Haven

first: Mei

last: Zhong

address: 10 Amistad Street

department: Stem Cell Center

institute: Yale University

type: Non-coding RNA profiling by high throughput sequencing

summary: HDMYZ cells were treated with 2ug/ml ActD for 0, 4 and 12 hours. Small RNAs of 15-40 bases were gel-purified from 10 ug total RNA, and subjected to multiplex Illumina small RNA library preparation. Small RNA libraries were sequenced on a HiSeq2000 (Illumina) with 3 samples per lane. To quantify miRNA and isoform abundance, sequence reads were processed by the miRDeep2 package, with the following modifications. First, to remove adaptor sequence, we removed both the main adaptor sequence present in the sequencing reads, as well as the second most abundant adaptor variant. In addition, we did not restrict the size of small RNAs during adaptor removal. Second, we used miRBase v18 for mapping the reads. Third, for quantifying miRNA and isoform frequency, we limited reads to more or equal to 15 bases in length with zero mis-match during mapping. The number of reads that were mapped to known miRNAs was used to normalize read frequencies for each miRNA or each miRNA isoform. For quantification purposes, we only considered miRNAs or isoforms that had frequency >= 1x10e-6 in samples without ActD treatment, which correspond to ~21-30 reads in raw count. These miRNAs or isoforms were referred to as reliably quantifiable.To analyze mapping to the genome, we removed reads that mapped to miRNA precursors. The rest of the reads were then mapped to the genome with Bowtie.

overall_design: Measure miRNA expression level at 0, 4, 12 hours post ActinomycinD treatment to examine miRNA turnover pattern.

first: Yanwen

last: Guo

first: Sarah

last: Elfenbein

first: Jun

last: Lu


title: Identifying targets for RNAi in Sclerotinia sclerotiorum using RNA sequencing

status: Public on Sep 01 2017

city: Winnipeg

first: Michael

middle: G.

last: Becker

state: Manitoba

address: 66 Chancellors Circle

department: Biological Sciences

institute: University of Manitoba

overall_design: Three biological replicates of in vitro grown (PDA media) Sclerotinia sclerotiorum.

first: Mark

middle: F

last: Belmonte

first: Steve

last: Whyard


title: Comparison of gene expression between control and Panobinostat treated Notch1-driven T-ALL

city: Melbourne

first: Stephin

last: Vervoort

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: T-cell acute lymphoblastic leukaemia (T-ALL) is a disease characterized by the uncontrolled clonal proliferation of immature lymphoid cells. Despite improvement in remission rates using conventional chemotherapeutics, the prognosis for T-ALL remains poor due to disease relapse associated with intrinsic, or acquired tumor cell resistance to the initial therapies. Although T-ALL is a genetically heterogenous disease, mutations resulting in activation of the Notch-1 signaling pathway are present in over 50% of patients, thus defining Notch signaling as a central player in T-ALL onset and progression. Studies also defined an oncogenic c-MYC gene signature as a key characteristic of these T-ALL and connectivity map experiments implicated histone deacetylase inhibitors (HDACi) as potential modifiers of pathways de-regulated by Notch. Recently, studies have shown that panobinostat, an FDA-approved HDACi shows efficacy against human T-ALL cell lines in-vitro, but the molecular mechanism that underpin the therapeutic efficacy of panobinostat is poorly understood. To investigate this, we performed 3'mRNA-seq analysis on T-ALL cells treated for 2 hours with panobinostat in vitro.

first: R

middle: W

last: Johnstone

first: S


title: Transcriptional profiling of a mouse model of Uromodulin Associated Kidney Disease (UAKD)

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

summary: Uromodulin (UMOD) is a secreted glycoprotein exclusively expressed by the cells lining the thick ascending limb of the loop of henle and the early distal tubule of the kidney nephron. Mutations in UMOD that interfere with proper folding of the protein are responsible for a progressive form of interstitial fibrotic kidney disease that leads to end stage renal disease, referred to as Uromodulin Associated Kidney Disease (UAKD). To assess key transcriptional changes associated with the progression of UAKD, we generated a knock-in mouse model harboring the mouse equivalent of the human mutation C148W. We profiled both the whole kidney tissue, as well as the specific UMOD+ cell populaitons in mutant and wild type mice. Analysis of differentially expressed genes in whole tissue and UMOD+ cells revealed a strong TNF-signaling signature, as well as TRIB3 upregulation, which is a key mediator of the intrinsic ER-stress mediated cell death pathway.

overall_design: Uromodulin mutant and wild type littermate controls were aged to 6, 12, 24, and 30 weeks of age. Total RNA was isolated from whole kidney tissue and from isolated, Uromodulin positive cells at each timepoint.

first: Bryce

last: Johnson

first: Lan

last: Dang

first: Graham

last: Marsh

first: Allie

last: Roach

first: Zebulon

last: Levine

first: Anthony

last: Monti

first: Deepak

last: Reyon

first: Lionel

last: Feigenbaum

first: Jeremy

middle: S

last: Duffield


title: Probing the Roles of SUMOylation in Cancer Cell Biology Using a Selective SAE inhibitor

first: Pooja

last: Shah

address: 40 Landsdowne Street

institute: Takeda Pharmaceuticals

summary: Small ubiquitin-like modifier (SUMO) family proteins regulate target protein functions by post-translational modification. However, a potent and selective inhibitor to target the SUMO pathway has been lacking.  Here we describe ML-792, the first mechanism-based SUMO-activating enzyme (SAE) inhibitor with nanomolar potency in cellular assays. ML-792 selectively blocks SAE enzyme activity and total SUMOylation, which leads to reduced cancer cell proliferation. Moreover, induction of the MYC oncogene increased the ML-792 mediated viability effect in cancer cells, indicating potential application of SAE inhibitors in MYC-amplified tumors. Using ML-792, we further explored the critical roles of SUMOylation in mitotic progression and chromosome segregation. Furthermore, expression of an SAE catalytic subunit (UBA2) mutant S95N/M97T rescued SUMOylation loss and the mitotic defect induced by ML-792, confirming the selectivity of ML-792. As a potent and selective SAE inhibitor, ML-792 provides rapid loss of endogenously SUMOylated proteins allowing for novel insights into SUMO biology.

overall_design: RNA-SEQ was used to analyze changes in mRNA profiles of human colon and breast cancer cells treated with ML00754792 SAEi

first: Xingyue

last: He


title: Chromatin assembly factor-1 (CAF-1) chaperone regulates Cse4 deposition at active promoter regions in budding yeast

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

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


title: Generation of mouse haploid somatic cells by small molecules for genome-wide genetic screening

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

summary: Using piggyBac transposon based insertional mutagenesis, we have generated a haploid neural cell library harboring genome-wide mutations for genetic screening, and identified Park2 gene as a proof-of-concept in screening for Mn2+-mediated toxicity.

overall_design: To identify the trapping sites of piggyBac transposon in a pool of cells, the splinkerette PCR was performed and the PCR products were sequenced with on HiSeq 2500

first: Zheng-Quan

first: Bao-Long

last: Xia

first: Yu-Kai

last: Wang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Control and FoxM1-knockdown C2C12 Transcriptomes

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

summary:
Purpose:To identify FoxM1-dependent genes and the molecular pathways involved in the regulation of muscle stem cells function, we performed RNA-Sequence of C2C12 from shControl and shFoxM1 cells.
Methods: C2C12 mRNA and lncRNA profiles of shControl and shFoxM1 cells (quiescent or activated states) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
Results:Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm10) and identified 49,586 transcripts in the control C2C12 and FoxM1-knockdown C2C12 with BWA workflow.
Conclusions: Our results represents the first detailed analysis of C2C12 transcriptomes and found that knockdown of FoxM1 perturbed multiple mRNA pathways, as well as for novel lncRNA pathways.

first: Yu

last: Hou


title: Analysis of gene expression by RNA Seq in mutants of Psh1, Cac2, or the double mutant relative to WT upon overexpression of Cse4 in Saccharomyces cerevisiae.

summary: Correct localization of the centromeric histone variant CenH3/CENP-A/Cse4 is an important part of faithful chromosome segregation. Mislocalization of CenH3 could lead to ectopic centromere formation and missegregation, and could affect DNA replication and transcription. CENP-A is often overexpressed and mislocalized in cancer genomes, but the underlying mechanisms are not understood. One major regulator of Cse4 deposition is Psh1, an E3 ubiquitin ligase that controls levels of Cse4 to prevent deposition into noncentromeric regions. We present evidence that Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved histone H3/H4 chaperone shown previously to interact with CenH3 in flies and human cells, regulates Cse4 deposition in budding yeast. Yeast CAF-1 (yCAF-1) is a heterotrimeric protein complex consisting of CAC1, CAC2, and CAC3, which interacts with Cse4, and can assemble Cse4 nucleosomes in vitro. yCAF-1 regulates the stability of both soluble and chromatin associated Cse4. Loss of yCAF-1 can rescue growth defects and changes in gene expression associated with Cse4 deposition that occur in the absence of Psh1-mediated proteolysis. Incorporation of Cse4 into promoter nucleosomes at transcriptionally active genes depends on yCAF-1. Overall our findings suggest CAF-1 can act as a CenH3 chaperone, regulating levels and incorporation of CenH3 in chromatin. Furthermore, the misincorporation of CenH3 at promoter regions may have negative consequences for gene expression.

overall_design: Examination of gene expression by RNA Seq in yeast mutants of Psh1, Cac2, or the double mutant relative WT in duplicate using Illumina sequencing

first: Geetha

last: Hewawasam

first: Karthik

last: Dhatchinamoorthy

first: Mark

last: Mattingly

first: Jennifer

last: Gerton


title: mRNA sequencing of whole 15 d old Oryza sativa shoots

city: Raleigh

first: Anna

last: Locke

state: NC

address: 4112 Williams Hall, 101 Derieux Place

summary: The rice gene SUB1A-1 confers flooding tolerance restricting shoot growth during submergence.  Rice with SUB1A also show more rapid recovery after submergence ends, but mechanisms by which SUB1A improves recovery from submergence had not been examined.  In this study, the transcriptome was sequenced at five time points over a 24 hour submergence recovery period in near-isogenic rice genotypes with and without SUB1A.

overall_design: 36 samples, 2 genotypes:  M202 and 202(Sub1), 2 conditions:  unsubmerged and 3d whole shoot submergence, 5 time points:  desubmergence (at midday following 3d submergence), dusk, midnight, dawn, midday (24 hours after desubmergence). 3 bioreplicates.  Unsubmerged plants only sequenced for at desubmergence time point.

first: Julia

last: Bailey-Serres


title: Study of expression changes and alternative splicing events during RPS4-mediated resistance in Arabidopsis using a temperature-inducible system which mirrors pathogen-infection

first: Servane

last: Baufume

summary: Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. The Arabidopsis Toll-related intracellular receptor RPS4 operates inside nuclei to trigger resistance and defence gene reprogramming through the stress response regulator, EDS1. Using a combinaison of ChIP-seq and gene expression microarray profiling, we found that RPS4 associates with the genomic coding sequence of (mainly) defense-associated genes whose expression is subsequently strongly upregulated. Using RNA-seq, we tested wether the association pattern of RPS4 to its targets correlates with alternative splicing of similar sets of genes.

overall_design:
We used transgenic Arabidopsis plants over-expressing RPS4, a genetic background in which an immune response can be turned on rapidly and synchronously in leaf cells after a switch from high to moderate temperature. In order to substract defense-unrelated artifacts due to the temperature stimulus, we used Col-0 WT plants in parallel as negative control.
This Series represents the RNA-Seq data only. The related gene expression microarray data are available in GSE40143, and ChIP-Seq data in GSE40329.

last: Blanvillain-Baufumé

first: Jane

last: Parker

first: Bruno

last: Huettel

first: Arunkumar

last: Srinivasan

first: José

last: Jimenez-Gomez


title: RNA-Seq of the Spodoptera frugiperda ascovirus-1a (SfAV-1a) infecting 3rd instar Spodoptera frugiperda caterpillars in vivo

city: Riverside

first: Heba

middle: A. H. M.

last: Zaghloul

address: 900 University Ave

department: Entomology

institute: University of California, Riverside

summary: Purpose: we targeted the transcription profile of two types of SfAV-1a genes, first, we targeted, core genes that occur in several ascovirus species, second, we targeted, genes predicted by in silico analysis to have metabolic functions likely involved in synthesizing viral vesicle membranes, the distinguishing feature of ascovirus cytopathology.

overall_design: Method: we used a wild type strain of the Spodoptera frugiperda ascovirus-1a (SfAV-1a), the type species for the family Ascoviridae. This strain was used to infect 3rd instar caterpillars of Spodoptera frugiperda, and all transcriptome data were derived from this developmental stage using the HiSeq2500 sequencer (Illumina) in the UCR Core Facility in the Institute for Integrative Genome Biology, in duplicate. The RT-qPCR used for validation using the iQ™ SYBR® Green Supermix (BIORAD).

first: Robert

last: Hice

first: Peter

last: Arensburger

first: Brian

last: Federici


title: Transcriptomic response to 24-hour food deprivation in four hypothalamic nuclei

city: Box 289, Addenbrooke’s Hospital

first: Joseph

last: Polex-Wolf

state: Cambridgeshire

address: Wellcome Trust-MRC Institute of Metabolic Science

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: The hypothalamus has an established role in the central control of energy homeostasis.  In this study, we examine the gene expression changes in four discrete hypothalamic nuclei across 24-hour food deprived versus ad libitum fed mice.

overall_design: Using wild-type fed or 24-hour fasted male mice, we laser-capture microdissected four hypothalamic nuclei for RNA sequencing: the ventromedial hypothalamus (VMH), arcuate nucleus (ARC), dorsomedial hypothalamus (DMH) and paraventricular nucleus (PVN).

middle: Y

last: Lam

first: Rachel

last: Larder

first: Anthony

middle: P

last: Coll

first: Giles

last: Yeo


title: ChIP Seq analysis of Cse4 in mutants of Psh1, Cac2, the double mutant, and WT upon overexpression of Cse4 in Saccharomyces cerevisiae.

first: Chris

last: Seidel

overall_design: Global localization of Cse4 by ChIP Seq in yeast mutants of Psh1, Cac2, the double mutant, and WT in duplicate or triplicate using Illumina paired-end sequencing.

first: Geetha

last: Hewawasam

first: Karthik

last: Dhatchinamoorthy

first: Mark

last: Mattingly

last: Gerton


title: miRNA profiles within lean and obese adipose tissue macrophages-derived exosomes

city: La Jolla

first: Wei

last: Ying

address: 9500 Gilman Dr, Stein Clinical Research Building, Room 225

institute: UC San Deigo

summary: Small RNA deep sequencing analysis on the microRNA components within exosomes secreted from adipose tissue macrophages of lean and obese mice

overall_design: Total RNA extracted from exosomes secreted from adipose tissue macrophages (CD11b+F4/80+) and subjected to small RNA seq analysis.

first: Jerrold

last: Olefsky


title: Intestinal mRNA profiles of 2-month old control (APCmin) and APCmin; Setd2IEC-/- mice generated by deep sequencing

city: Shanghai

first: Ni

last: Li

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

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

summary: Setd2 catalyzes trimethylation of lysine 36 on histone H3. H3K36me3 is deposited mainly in the gene body and has recently been demonstrated to play a role in regulating transcriptional elongation and alternative splicing. We conduct deep sequencing in 2-month old control (APCmin) and APCmin; Setd2IEC-/- mice intestinal cells to understand the splicing events regulated by Setd2.

overall_design: Intestinal mRNA profiles of 2-month old control (APCmin) and APCmin; Setd2IEC-/- mice were generated by deep sequencing. Each RNA sample was from 3 littermates RNA mixture.

first: Jun

last: Qin

first: Huairui

last: Yuan


title: Expression data from control and Setd2 IEC-deficient mice intestine [RNA-seq]

summary: We conduct transcriptome comparison of APCmin and APCmin; Setd2IEC-/- mice intestine to gain genomic insights on the biological processes that Setd2 is involved in colon cancer cells. More than 3000 known genes were found changed in the Setd2 depleted cells. Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA) show that the prominent altered pathways in the Setd2 depleted cells are related to Wnt signaling pathway and cell stemness.

overall_design: Intestinal mRNA profiles of 2-month old control (APCmin) and APCmin; Setd2IEC-/- mice were generated by sequencing. Each RNA sample was from 3 littermates RNA mixture.


title: Differential programming of intestinal tissues in SETD2-/- mice

overall_design: Refer to individual Series


title: H3K36me3 occupancy profiling by high throughput sequencing from control(APCmin) and APCmin; Setd2IEC-/- mice intestinal cells [ChIP-seq]

summary: Setd2 catalyzes trimethylation of lysine 36 on histone H3. We conduct ChIP sequencing in chromatin landscape induced by Setd2 depleted in mouse intestinal cells to understand the H3K36me3 genome-wide alterations.

overall_design: Samples were from control(APCmin) and APCmin; Setd2IEC-/- mice intestinal cells. The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K36me3(abcam).


title: Transcriptome profiling of individual rhesus macaque oocytes and preimplantation embryos

city: Davis

first: Pablo

middle: Juan

last: Ross

address: 1 Shields Ave, 2239 Meyer Hall

department: Animal Science

institute: University of California Davis

summary: Early mammalian embryonic transcriptomes are dynamic throughout the process of preimplantation development. Cataloging of primate transcriptomics during early development has been accomplished in humans, but global characterization of transcripts is lacking in the rhesus macaque: a key model for human reproductive processes. We report here the systematic classification of individual macaque transcriptomes using RNA-Seq technology from the germinal vesicle stage oocyte through the blastocyst stage embryo. Major differences in gene expression were found between sequential stages, with the 4- to 8-cell stages showing the highest level of differential gene expression. Analysis of putative transcription factor binding sites also revealed a striking increase in key regulatory factors in 8-cell embryos, indicating a strong likelihood of embryonic genome activation occurring at this stage. Furthermore, clustering analyses of gene co-expression throughout this period resulted in distinct groups of transcripts significantly associated to the different embryo stages assayed. The sequence data provided here along with characterizations of major regulatory transcript groups presents a comprehensive atlas of polyadenylated transcripts that serves as a useful resource for comparative studies of preimplantation development in humans and other species.

overall_design: RNA-seq analysis in single oocytes/embryos at different stages of development including 2-3 replicates per stage.

first: James

last: Chitwood


title: RNA-Sequencing Reveals Genome-Wide  LncRNAs Profiling Associated with Early Development of Diabetic Nephropathy

city: Xi'an

first: Xiaoke

last: Ma

state: Shaanxi

address: No.2 South TaiBai Road

institute: Xidian University

summary: In early development of diabetic nephropathy (DN), pathogenesis remains largely unknown. We used RNA-sequencing to profile protein-coding and long non-coding RNA (lncRNA) gene transcriptome of mouse kidney proximal tubular cells during early stage of DN at various time points. Over 7000 protein-coding and lncRNA genes were differentially expressed, and most of them were time-specific. Nearly 40% of lncRNA genes overlapped with functional element signals using CHIP-Seq data from ENCODE database. Disease progression was characterized by lncRNA expression patterns, rather than protein-coding genes, indicating that the lncRNA genes are potential biomarkers for DN. For gene ontologies related to kidney, enrichment was observed in protein-coding genes co-expressed with neighboring lncRNA genes. Based on protein-coding and lncRNA gene profiles, clustering analysis reveals dynamic expression patterns for kidney, suggesting that they are highly correlated during disease progression. To evaluate translation of mouse model to human conditions, we experimentally validated orthologous genes in human cells in vitro diabetic model. In mouse model, most gene expression patterns were repeated in human cell lines. These results define dynamic transcriptome and novel functional roles for lncRNAs in diabetic kidney cells; these roles may result in lncRNA-based diagnosis and therapies for DN.

overall_design: Examination of genomewide RNAs in PTCs at 4 timepoints in early DN

first: Wanxin

last: Tang

first: Dongmei

last: Zhang

first: Zaiyi

last: Liu

first: Di

last: Dong

first: Jie

last: Tian


title: ESRP1 mutations cause hearing loss due to defects in alternative splicing that disrupt cochlear development

city: Philadelphia

first: Douglas

last: Epstein

state: Pennsylvania

address: 415 Curie Blvd

department: Genetics

institute: University of Pennsylvania

summary: Alternative splicing contributes to gene expression dynamics in many tissues, yet its role in auditory development remains unclear. We performed whole exome sequencing in individuals with sensorineural hearing loss (SNHL) and identified pathogenic mutations in Epithelial Splicing Regulatory Protein 1 (ESRP1).  Patient derived induced pluripotent stem cells showed alternative splicing defects consistent with impaired ESRP1 function. To determine how mutations in ESRP1 cause hearing loss we evaluated Esrp1-/- mouse embryos and uncovered alterations in cochlear morphogenesis, auditory hair cell differentiation and cell fate specification. Transcriptome analysis revealed impaired expression and splicing of genes with essential roles in inner ear development and auditory function. In particular, aberrant splicing of Fgfr2 blocked stria vascularis formation due to erroneous ligand usage, which was corrected by reducing Fgf9 gene dosage. These findings implicate mutations in ESRP1 as a novel cause of SNHL and demonstrate the complex interplay between alternative splicing, inner ear development, and auditory function.

overall_design: 3 biological replicates of whole E16.5 cochlear epithelium from individual Esrp1+/+ (Control) and Esrp1-/- (E1-KO) embryos (2 cochlea pooled from each embryo) were analyzed by RNA-seq

first: Alex

middle: M

last: Rohacek

first: Thomas

last: Bebee

first: Richard

middle: K

last: Tilton

first: Caleb

last: Radens

first: Yoseph

last: Barash

first: John

middle: A

last: Germiller

first: Ian

middle: D

last: Krantz

first: Russ

last: Carstens

first: Doug


title: Excretory/secretory microRNAs from the gastrointestinal nematode Trichuris muris in culture

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

institute: McGill University

summary: We report analyses of the types and amounts of microRNAs found in culture media recovered after incubating approximately 3000 T. muris adult worms for 48 hours.

sample_organism:
Mus musculus
Trichuris muris

platform_organism:
Mus musculus
Trichuris muris

overall_design: Examination of excretory/secretory miRNAs of the mouse gastrointestinal nematode parasite Trichuris muris released in culture media.

first: L

first: T

last: Geary


title: Development of a selective CDK9 degrader from a multi-targeted CDK inhibitor [ChIP-seq]

city: Boston

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Cyclin dependent kinase 9 (CDK9), a key regulator of transcriptional elongation, has long been considered a promising target for cancer therapy, particularly for cancers driven by transcriptional dysregulation.  However, despite promising early clinical data in blood cancers using pan-CDK inhibitors that potently inhibit CDK9 such as Dinaciclib and Flavopiridol, no selective CDK9 inhibitors have been clinically approved.  Here we show that a multi-targeted CDK inhibitor can be used to develop a selective CDK9 degrader exemplified by THAL-SNS-032, a hetero-bifunctional molecule composed of SNS-032, a CDK2,7,9 inhibitor conjugated to thalidomide, a small molecule binder of Cereblon.  We demonstrate that THAL-SNS-032 can recruit the E3 ubiquitin ligase Cereblon to CDK9 and induce its proteasome-mediated degradation.  Treatment of cells with low nanomolar concentrations of THAL-SNS-032 resulted in rapid and efficient CDK9 degradation but did not affect levels of other SNS-032 targets, including CDK2 and CDK7.  Consistent with this selective degradation phenotype, transcriptional profiling of THAL-SNS-032 indicated that its transcriptional effects were more similar to that of a selective CDK9 inhibitor, NVP2, than that of the nonselective SNS-032 parent compound. Moreover, THAL-SNS-032, in contrast to traditional CDK9 inhibitors, retained potent pro-apoptotic activity even after compound removal from cells.  This suggests that degradation of CDK9 leads to prolonged cytotoxic effects as compared to CDK9 inhibition.  Thus, our findings suggest that thalidomide conjugation may be a promising strategy for converting multi-targeting inhibitors into selective degraders, and that the pharmacological effects of kinase degradation can be distinct from kinase inhibition.

overall_design: ChIP-seq of MOLT4 cells treated with DMSO, SNS-032, THAL-SNS-032, or NVP-2 for 2 hours

first: Calla

last: Olson

first: Nathanael

last: Gray


title: Crucial gene networks for fatty acid metabolism during lactation revealed by RNA-Sequencing of the goat mammary gland

city: Chengdu

first: Jiangjiang

last: Zhu

state: Sichuan

address: #16, South Section, 1st Ring Road

department: Institute of Qinghai-Tibetan Plateau

institute: Southwest Uniersity for Nationalities

summary: Milk fatty acids secreted by the mammary glands are one of the most important determinants of the nutritional value of goat milk. However, there are few data available on the transcriptome-wide changes across lactation in the goat. In this study, goat mammary tissue from the periods encompassing lactation, cessation of milking and involution were used for digital gene expression sequencing (DGE) using the goat transcriptome as reference sequence. A total of 51299 unigenes were identified and annotated to 12763 genes, of which 9131 genes were differentially expressed (DEG) among the various stages of lactation. Functional classification through KOG, GO, and KEGG was used for selection of the top expressed genes and the differentially expressed genes (DEG). DEG series-cluster analysis revealed 16 possible expression patterns. Using co-expression analysis, within the lipid transport and metabolism KOG categories, PLA2, CPT1, PLD had the most number of correlated genes. GGA, SRPRB and AP4S1 were the top 3 with the highest number of correlated genes associated with intracellular trafficking, secretion, and vesicular transport. These data may provide candidate genes with a high probability of having functional roles in regulating of goat fatty acid metabolism during the various stages of lactation.

overall_design: Examination of the crucial genes associated with fatty acid metabolism in mammary gland during lactation in dairy goat. SRP089750, PRJNA342566.

first: Jun

last: Luo


title: Peptide-signaling and miRNA regulation of transmitter switching affecting social preference

first: Giordano

last: Lippi

state: CA

address: 9500 Gilman Drive

department: Neurobiology

institute: University of California, San Diego

summary: Sensory circuit activation can induce neurotransmitter respecification. To understand the consequences and mechanisms of this neuroplasticity we investigated the effects of olfactory system activation on transmitter expression in interneurons of the accessory olfactory bulb (AOB) during development. Frog larvae use olfactory-mediated kin recognition to distinguish siblings from non-siblings. Prolonged exposure to kin (sibling) or non-kin (non-sibling) odorants changed the number of neurons expressing dopamine or GABA compared to odorant deprivation (orphan condition). To identify signaling molecules mediating this behavior we performed mass spectrometry of kin-conditioned water samples. Vitellogenin-derived peptides, uniquely present in kin-conditioned samples of one genotype, were sufficient to elicit aversion behavior in non-kin larvae. RNA profiling identified AOB microRNAs (miRs) differentially regulated across conditions. Inhibition of miR-375 and miR-200b revealed that they regulate the dopaminergic and GABAergic phenotypes by targeting Pax6 and Bcl11b. Altering the ratio of dopamine/GABA AOB interneurons or locally introducing receptor blockers reversed kinship preference.

overall_design: The AOBs of 15 larvae (stage 45) raised in sibling, orphan, or non-sibling conditions were frozen, cryosectioned at 50 μm and neuronal tissue was harvested with scalpels for clean dissection. Total RNA was extracted from tissue with the “Recover All Total Nucleic Acid” isolation kit. RNA quality was assessed on a Bioanalyzer and degraded samples excluded from RNA sequencing. Library preparation and RNA sequencing were performed at the UCSD Biogem core.

first: Davide

last: Dulcis

first: Christiana

middle: J

last: Stark

first: Long

middle: H

last: Do

first: Darwin

last: Berg

first: Nicholas

middle: C

last: Spitzer


title: Search for genes affected by mgtC leader expression in Salmonella enterica serovar Typhimurium 14028s

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: A set of genes are highly downregulated in the presence of extra copy of the mgtC leader. Provide a hint of potental target of the leader RNA

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu

overall_design: RNA expression profile of cells harboring a plasmid with the mgtC leader versus the empty vector, grown in minimal media, using Illumina HiSeq 2500

first: Eun-Jin

last: Lee

first: Daesil

last: Nam


title: RNA-Seq Analysis of Gfi1b KO Hematopoietic Stem Cells

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

institute: Insititut de Recherches Cliniques

summary: The zinc finger protein and SNAG domain transcription factor Gfi1b is highly expressed in hematopoietic stem cells (HSC) and in megakaryocytes (MKs). Deletion of Gfi1b in mice leads to a drastic expansion of both cell types, suggesting that Gfi1b controls their proliferation. Here we present evidence that Gfi1b exerts this control by modulating the Wnt/beta-catenin signaling pathway. We can show that Gfi1b binds to beta-catenin and is part of a larger complex that contains β-catenin co-factors. Gfi1b activates beta-catenin/TCF mediated transcription and is required for the activity of beta-catenin target gene promoter driven reporter genes in vivo. This is dependent of the ability of Gfi1b to recruit the histone modifying enzyme lysine demethylase 1 (LSD1) to β-catenin containing complexes. Moreover, LSD1 enhances the Gfi1b-mediated activation of beta-catenin/TCF dependent transcription. Both Gfi1b deficient HSCs and MKs show de-regulation of expression of many sets on Wnt/β-catenin target genes and Gfi1b and β-catenin co-occupy the promoters of many common target genes. Finally, activating the Wnt/β-catenin signaling pathway in Gfi1b deficient HSCs and MKs significantly reduces their expansion, which confirms that Gfi1b is a critical factor controlling the cellularity of HSCs and MKs and exerts this function by regulating the Wnt/β-catenin pathway in these cells.

overall_design: Hematopoietic Stem Cells isolated from Gfi1b flox/flox mice carrying ROSA-Cre or not, were analysed for differential expression by RNA-Seq. A sample of each Gfi1b wild-type and Knock-Out from each model was analyzed.

first: Peiman

last: Shooshtarizadeh

first: Tarik

last: Möröy

first: Charles

last: Vadnais


title: Development of a selective CDK9 degrader from a multi-targeted CDK inhibitor

first: James

last: Bradner

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


title: RNA-Sequencing of HDLEC treated with siRNA targeting PROX1 and TIE2

city: Irvine

first: Hosung

last: Bae

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

summary: We analyzed genome-wide transcriptional changes induced by siPROX1 and siTIE2, using RNA-seq analysis of HDLECs in order to highlight the importance of Ang-Tie2 system in SC and lymphatic development. Here, we report that coordination between both Ang1- and Ang2-signaling via Tie2 and Prox1 activity are essential for the appropriate formation of SC during development and maintenance of SC integrity.

overall_design: Examination of 3 differenct siRNAs treated to HDLEC to analyze the effect of PROX1 and TIE2 knockdown.

first: Gou

last: Koh


title: Dnmt3a haploinsufficiency transforms Flt3-ITD myeloproliferative disease into a rapid, spontaneous, and fully-penetrant acute myeloid leukemia

city: Miami

first: Maria

middle: E

last: Figueroa

state: FL

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

summary: Cytogenetically normal acute myeloid leukemia (CN-AML) represents nearly 50% of human acute myeloid leukemia (AML) cases with a 5-year overall survival of approximately 30%. In CN-AML with poorer prognosis, mutations in the de novo DNA methyltransferase (DNMT3A) and the FMS-like tyrosine kinase 3 (Flt3) commonly co-occur (1-3). We demonstrate that mice with Flt3-internal-tandem duplication (Flt3ITD) and inducible deletion of Dnmt3a spontaneously develop a rapidly-lethal, completely-penetrant, and transplantable AML of normal karyotype. These murine AML retain a single Dnmt3a floxed allele, revealing the oncogenic potential of Dnmt3a haploinsufficiency. FLT3-ITD/DNMT3A-mutant primary human and murine AML demonstrate a similar pattern of global DNA methylation. In the murine model, rescuing DNMT3A expression was accompanied by DNA re-methylation and loss of clonogenic potential, suggesting that Dnmt3a-mutant oncogenic effects are reversible.  Differentially methylated genomic regions were associated with changes in the expression of nearby genes. Moreover, dissection of the cellular architecture of the AML model using single-cell RNA-Seq, flow cytometry and colony assays identified clonogenic subpopulations that differentially express genes that are sensitive to the methylation of nearby genomic loci and varied in response to Dnmt3a levels. Thus, Dnmt3a haploinsufficiency transforms Flt3ITD myeloproliferative disease by modulating methylation-sensitive gene expression within a clonogenic AML subpopulation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To identify the DNA methylation changes associated with Dnmt3a loss of function in human and murine Flt3-ITD and Dnmt3a-mutant AML.

first: Sara

last: Meyer

first: Tingting

last: Qin

first: David

last: Muench

first: Kohei

last: Masuda

first: Meenakshi

last: Venkatasubramanian

first: Emily

last: Orr

first: Elisabeth

last: Paietta

first: Martin

last: Tallman

first: Hugo

last: Fernandez

first: Ari

last: Melnick

first: Michelle

last: Le Beau

first: Scott

last: Kogan

first: Nathan

last: Salomonis

first: H

middle: L

last: Grimes


title: Transcriptome Profiling of Testis Tissue from Boars with Good and Bad Sperm DNA Fragmentation Index

city: Hamar

first: Maren

last: van Son

address: Storhamargata 44

country: Norway

institute: Norsvin

summary: Chromatin packaging in sperm protects it against DNA fragmentation, and the importance of proper chromatin packaging for boar fertility outcome has become increasingly evident. Little is known however about the molecular mechanisms underlying differences in sperm DNA fragmentation and an understanding of the genes controlling this sperm parameter could help in selecting the best boars for AI use. The aim of this study was to identify differentially expressed genes in testis of Norsvin Landrace and Duroc boars with good and bad sperm DNA fragmentation using transcriptome sequencing and to use the data for polymorphism search. RNA sequence reads were obtained using Illumina technology and mapped by TopHat using the Ensembl pig database. Differentially expressed genes and pathways were analyzed using the R Bioconductor packages edgeR and goseq respectively. Using a false discovery rate of 0.05, 309 and 375 genes were found displaying significant differences in expression level between the good and bad condition in Landrace and Duroc respectively. Of the differentially expressed genes, 72 were found in common for the two breeds. Gene ontology analysis revealed that terms common for the two breeds included extracellular matrix, extracellular region and calcium ion binding. Additionally, different metabolic processes were enriched in Landrace and Duroc, whereas immune response ontologies were found to be important in Landrace. SNP detection in Landrace/Duroc identified 53182/53931 variants in 10924/10748 transcripts and of these, 1573/1827 SNPs occurred in 189/241 unique genes that were also differentially expressed. Possible high impact variants were detected using SnpEff. Transcriptome sequencing identified differentially expressed genes and nucleotide variants related to differences in sperm DNA fragmentation, and functional annotation of the genes pointed towards important biochemical pathways. This study provides insights into the genetic network underlying this trait and is a first step towards using sperm DNA fragmentation for predicting boar fertility.

overall_design: Nine Landrace, five low and four high, and eleven Duroc, five low and six high, boars were selected for transcriptome profiling based on their extreme DFI values. The biological replicates within the high and low groups were compared.

first: Nina

last: Hårdnes Tremoen

first: Ann

last: Gaustad

first: Else-Berit

last: Stenseth

first: Teklu

last: Zeremichael

first: Frøydis

last: Myromslien

first: Dag

middle: I

last: Våge

first: Eli

last: Grindflek


title: Next-generation sequencing analysis of Piwi-interacting RNAs (piRNAs) in Drosophila wild-type and bel mutant ovaries

city: Tallahassee

first: Wu-Min

last: Deng

state: Florida

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

summary: Belle has been known to be co-localized with piRNA-related proteins at the nuage of germline cells during Drosophila oogenesis. However, its role in piRNA biogenesis remains unclear. To reveal whether Belle is involved in regulating piRNA expression, we performed next-generation sequencing analysis of small non-coding RNAs on ovaries harvested from the wild type (W1118) and trans-heterozygous bel[74407/neo30] mutant. Small RNA-seq experiments were performed on three individual ovary samples with the same genotype. For piRNA expression analysis, we performed mapping of three sets of small RNA sequencing reads for each genotype to previously identified eight distinct piRNA clusters located in four different Drosophila chromosomes (from X to 4). Analysis of the piRNA expression profiling from these piRNA cluster loci indicates that some specific piRNA populations were either upregulated or downregulated in bel mutant ovaries compared with wild-type ovaries. Furthermore, we performed systematic analysis by mapping piRNA sequencing reads to sequences of all identified Drosophila transposable elements (TEs) to classify and measure piRNA reads based on their TE targets. Among 124 TE-classified piRNA populations, 9 and 20 of them were upregulated and downregulated (≥2 folds), respectively, in bel74407/neo30 mutant ovaries compared with those from wild-type ovaries. To examine the effect of the bel[74407/neo30] mutation on the ping-pong cycle for secondary piRNA biogenesis, analysis of the ping-pong signature of piRNAs specifically mapped to the retro-element Burdock was performed. The ping-pong signature for the generation of secondary piRNAs was not significantly altered in bel mutants compared with the wild type. These results, taken together, indicate that Bel is not required for primary and secondary piRNA biogenesis, but it is involved in regulating expression of specific subsets of piRNA populations.

overall_design: The fractions of small RNAs (19-29 nt) from ovaries of wild type and bel mutants of Drosophila melanogaster were sequenced using Illumina HiSeq 2500.

first: Pang-Kuo

last: Lo

first: Yi-Chun

last: Huang


title: Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV

city: Hangzhou

first: Heng-Mu

last: Zhang

address: 198 Shiqiao Road

department: Institute of Virology and Biotechnology

institute: Zhejiang Academy of Agricultural Sciences


title: Genome-wide single-molecule sequencing of 6-methyladenine in eukaryotes

city: Walnut Creek

first: Denis

last: Tolkunov

address: 2800 Mitchell Dr

institute: DOE Joint Genome Institute

summary: Mapping 6mA at single-base resolution across multiple eukaryotic genomes reveals its genomic distribution patterns, indicating a function in transcriptional regulation.

sample_organism:
Chlamydomonas reinhardtii
Arabidopsis thaliana
Saccharomyces cerevisiae
Caenorhabditis elegans
Drosophila melanogaster
Nannochloropsis oceanica
Auricularia delicata

overall_design: Using genome-wide methylation detection by single-molecule sequencing, we mapped 6mA at single-base resolution in seven eukaryotic species including the model plant Arabidopsis thaliana, the green alga Chlamydomonas reinhardtii, the marine alga Nannochloropsis oceanica, and the wood-degrading fungus Auricularia delicata.  We also performed methylation mapping of publicly available raw SMRT sequencing data from two animal models, Drosophila melanogaster and Caenorhabditis elegans, and budding yeast, Saccharomyces cerevisiae.

first: Chia-Lin

last: Wei

first: Chew

last: Ngan


title: Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV (miRNA-Seq)

summary: To investigate how rice responds to RSV infection, we integrated miRNA expression with parallel mRNA transcription profiling by deep sequencing. A total of 570 miRNAs were identified of which 69 miRNAs (56 up-regulated and 13 down-regulated) were significantly modified by RSV infection. Digital gene expression (DGE) analysis showed that 1274 mRNAs (431 up-regulated and 843 down-regulated genes) were differentially expressed by RSV infection. The differential expression of selected miRNAs and mRNAs was confirmed by qRT-PCR. Gene ontology (GO) and pathway enrichment analysis showed that a complex set of miRNA and mRNA networks were selectively regulated by RSV infection. In particular, 63 differentially expressed miRNAs were found to be significantly and negatively correlated with 160 target mRNAs. Interestingly, 22 up-regulated miRNAs were negatively correlated with 24 down-regulated mRNAs encoding disease resistance-related proteins, indicating that the host defense responses were selectively suppressed by RSV infection. The suppression of both osa-miR1423-5p- and osa-miR1870-5p-mediated resistance pathways was further confirmed by qRT-PCR. Chloroplast functions were also targeted by RSV, especially the zeaxanthin cycle, which would affect the stability of thylakoid membranes and the biosynthesis of ABA. All these modifications may contribute to viral symptom development and provide new insights into the pathogenicity mechanisms of RSV.

overall_design: Examination of microRNAome and trascriptome in mock and RSV-infected rice plants.

first: Jian

last: Yang


title: Integrative analysis of microRNAome and transcriptome elucidates the response of susceptible rice plants to rice stripe virus RSV (RNA-Seq)


title: Tau exacerbates excitotoxic brain damage in an animal model of stroke

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

summary: Neuronal excitotoxicity induced by aberrant excitation of glutamatergic receptors contributes to brain damage in stroke. Here, we show that tau-deficient (tau-/-) mice are profoundly protected from excitotoxic brain damage and neurological deficits following experimental stroke, using a middle cerebral artery occlusion (MCAO) with reperfusion model. Mechanistically, we show that this protection is due to site-specific inhibition of glutamate-induced and Ras/ERK-mediated toxicity by accumulation of Ras-inhibiting SynGAP1, which resides in a post-synaptic complex with tau. Accordingly, reducing SynGAP1 levels in tau-/- mice abolished the protection from pharmacologically induced excitotoxicity and MCAO-induced brain damage. Conversely, over-expression of SynGAP1 prevented excitotoxic ERK activation in wild-type neurons. Our findings suggest that tau mediates excitotoxic Ras/ERK signaling by controlling post-synaptic compartmentalization of SynGAP1.

overall_design: Total RNA was extracted from control and Tau -/- primary neurons from PTZ treated and untreated C57Bl/6 mice. Mice treated with PTZ were injected intraperitoneally at 6 weeks of age. The final libraries were paired end sequenced on Illumina HiSeq 2000.

first: Amadeus

last: Gladbach

first: Janet

middle: V

last: Eersel

first: Mian

last: Bi

first: Ernesto

last: Guccione

first: Yazi

last: Ke

first: Lars

last: Ittner


title: RNAseq of FACS Drd1 and Drd2 receptor expressing medium spiny neurons (direct and indirect medium spiny neurons) from 5-6 month BACHD Huntington's disease model mice, compared to WT littermates

status: Public on Aug 31 2017

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary:
mRNAseq for baseline transcriptional profiling of D1 and D2 receptor-expressing medium spiny neurons from 5-6 month BACHD mice, compared to respective WT littermates.
BACHD iSPN and dSPN RNAseq data has been described in "Impaired TrkB receptor signaling underlies corticostriatal dysfunction in Huntington's disease"; Plotkin et al; 2014; PMID accession number 24991961.

overall_design:
Hemizygous BACHD (FVB) × Drd2 -EGFP BAC (FVB) and BACHD (FVB) × Drd1-EGFP BAC (FVB) mice were generated. Both D2BAC-EGFP (FVB) and D1BAC-EGFP (FVB) were obtained from Gensat/MMRRC. HD model BACHD (FVB) mice, a bacterial artificial chromosome (BAC)-mediated transgenic mouse model expressing full length -mHtt with 97 glutamine repeats under the control of endogenous Htt regulatory machinery on the BAC (Grey et al, 2008 PMID: 18550760) were obtained from CHDI Foundation (CHDI-81001010).
Fluorescence activated cell sorting (FACS) for GFP was used to isolate BACHD and WT  - indirect pathway medium spiny neurons (iMSNs) and direct pathway medium spiny neurons (dMSNs) from the D2BAC-EGFP or D1BAC-EGFP x HD model crosses, respectively. Cells were pooled from four animals (150,000 cells/animal) to create iSPN and dSPN pools for sequencing. RNA was extracted, and sequencing was performed by Expression Analysis on an Illumina Hi-seq 2000. Paired-end sequencing was performed, 4-plexed across lanes for a total of around 38 million 50mer paired reads per sample.

first: Jim

last: Rosinski


title: Development of a selective CDK9 degrader from a multi-targeted CDK inhibitor [RNA-seq]

first: James

last: Bradner

overall_design:
RNA-seq of MOLT4 cells treated with DMSO, SNS-032, THAL-SNS-032, or NVP-2 for 6 hours
Please note that the data column headers (and their order) in the in the 'molt4_cdk9_all_fpkm_exprs_norm.txt' file are different from the Sample title. The corresponding data column for each sample is indicated in the sample description field.

first: Calla

last: Olson

first: Nathanael

last: Gray


title: A Crop Plant Integrates and Coordinates its Defenses to Cope with the Attack by Begomovirus and Whitefly

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

institute: Zhejiang University

summary: We analyzed the global defense responses in common tobacco against a begomovirus Tomato yellow leaf curl China virus, an invasive whitefly species Middle East-Asia Minor 1, and their co-infestation. The transcripts of defense related genes were both overlapping and divergent in response to virus and whitefly.

overall_design: Four treatments were conducted, and they include mock inoculated plants, TYLCCNV infected plants, whitefly infested plants, and plants co-infested with TYLCCNV and whitefly. Plants at the 3-4 true-leaf stage were inoculated with TYLCCNV and its DNA-beta and cultivated to the 6-7 true-leaf stage at 22 days post-inoculation. For the whitefly feeding treatment, approximately 6,000 adult whiteflies that emerged from the tobacco plants were allowed to distribute randomly onto the leaves of six mock inoculated plants in one cage, and 6,000 adult whiteflies that emerged from the tobacco plants were released onto the leaves of six virus infected plants in another cage. After 72 h of feeding, all the adult whiteflies were discarded. Then the comparable leaves from the six plants in each of four treatments were harvested, flash-frozen in liquid N2 and stored at -80 °C.

first: Jun-Bo

last: Luan

first: Shu-Sheng

last: Liu

first: Xiao-Wei


title: Structural and mechanistic insights into ATRX-dependent and –independent functions of the histone chaperone DAXX [RNA-seq]

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

summary: The histone variant H3.3 is incorporated in a replication-independent manner at heterochromatic regions by the ATRX-DAXX histone chaperone complex. Here, we present a high-resolution x-ray crystal structure of an interaction surface between ATRX and DAXX.  We used single amino acid substitutions in DAXX that abrogate formation of the complex to explore ATRX-dependent and -independent functions of DAXX. We found that  the repression of specific murine endogenous retroviruses is dependent on DAXX, but not on ATRX. In support, we reveal the existence of two biochemically distinct DAXX-containing complexes: The ATRX-DAXX complex involved in gene repression and telomere chromatin structure, and a DAXX-SETDB1-KAP1-HDAC1 complex that represses endogenous retroviruses independently of ATRX and H3.3 incorporation into chromatin.  We found that histone H3.3 stabilizes DAXX protein levels and affects DAXX-regulated genes independently of its incorporation into nucleosomes.  Our findings represent the first description of a nucleosome-independent function for the H3.3 histone variant.

overall_design: RNA-seq analysis of five embryonic stem cell lines in duplicate (Daxx-/- mESC, Daxx-/- mESC rescued with Daxx WT, H3.3 KO mESC, H3.3 KO mESC rescued with H3.3 WT and H3.3 L126A-L130A  mutant)

first: P

first: D

last: Hoelper

first: A

last: Jain


title: Gene expression response to glucose/fructose in WT vs. tps1-

first: David

middle: G

last: Hendrickson

address: 725 Parsons

institute: Harvard

summary: WT or tps1- yeast grown in galactose were subjected to addition of glucose/fructose; cells were collected for RNA extraction and sequencing to assess the gene expression responses between these treatments

overall_design: 2 strains (one wild type and one mutant); 2 treatments per strain; each treatment is an 8-point time-course

first: Patrick

last: Gibney

first: Andrea

last: Ireland

last: Botstein


title: A key regulator of the glycolytic and gluconeogenic central metabolic pathways in Sinorhizobium meliloti

city: Hamilton

first: Turlough

last: Finan

state: Ontario

address: 1280 Main St. W.

department: Department of Biology

institute: McMaster University

summary: The order Rhizobiales contains numerous agriculturally, biotechnologically, and medically important bacteria including the rhizobia, Agrobacterium, Brucella, and Methylobacterium, among others.  These organisms tend to be metabolically versatile, but there has been relatively little investigation into the regulation of their central carbon metabolic pathways.  Here, RNA-seq and promoter fusion data are presented to show that the PckR protein is a key regulator of central carbon metabolism in Sinorhizobium meliloti; during growth with gluconeogenic substrates, PckR represses expression of the complete Entner-Doudoroff glycolytic pathway and induces expression of the pckA and fbaB gluconeogenic genes.  Electrophoretic mobility shift assays (EMSA) indicate that PckR binds an imperfect palindromic sequence that overlaps the promoter or transcriptional start site in the negatively regulator promoters, or is present in tandem upstream the promoter motifs in the positively regulated promoters.  Genetic and in vitro EMSA experiments suggest that elevated concentrations of a PckR effector ligand results in the dissociation of PckR from its target binding site, and evidence is presented that suggests phosphoenolpyruvate (PEP) may function as the effector.  Characterization of missense pckR alleles identified three conserved residues important for increasing the affinity of PckR for its cognate effector molecule.  Bioinformatics analyses illustrates that PckR is limited to a narrow phylogenetic range consisting of the Rhizobiaceae, Phyllobacteriaceae, Brucellaceae, and Bartonellaceae families.  These data provide novel insights into the regulation of the core carbon metabolic pathways of this pertinent group of α-proteobacteria.

overall_design: There were a total 8 samples for the RNA-sequencing analysis: four conditions performed in biological duplicates.  Total RNA was isolated from S. meliloti RmG212 (pckR+) and from S. meliloti RmK124 (pckR::ΩSp), grown either in minimal medium with 15 mM glucose as the carbon source or in minimal medium with 15 mM succinate as the carbon source.  Sequencing was performed using Illumina HiSeq 1500 with 60 nt single reads.

first: George

last: diCenzo

first: Zahed

last: Muhammed

first: Magne

last: Østerås

first: Shelley

last: O'Brien


title: FOXP2's impact on the primate transcriptome

city: Mainz

first: Holger

last: Herlyn

address: Anselm-Franz-von-Bentzel-Weg 5

department: Institute of Organismic and Molecular Evolution

institute: University of Mainz

summary: The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In spite of its relevance, the FOXP2-controlled network and its functional implications are only partially understood. Therefore, we analyzed the transcriptomes of human neuroblastoma cells (SH-SY5Y) stably overexpressing human, chimpanzee, macaque, and marmoset FOXP2 cDNAs. Clones carrying empty vector served as a standard of baseline expression. All conditions were represented by two biological replicates (A, B), each. By comparing expression levels (bases which map per kb of exon model per million mapped bases) across the different conditions we were able to identify genes with differential expression in clones overexpressing human FOXP2 relative to each other condition.

overall_design: Examination of expression profiles in SH-SY5Y clones that were alternatively transfected with different primate FOXP2 cDNAs

first: Ulrich

last: Zechner

first: Franz

last: Oswald


title: Methyl-Spec-seq control data sets

city: St. Louis

first: Basab

last: Roy

address: 4515 Mckinley avenue

department: Department of Genetics

institute: Washington University School of Medicine

summary: We developed a novel in-vitro experimental method to characterize the protein-DNA interaction specificity and methylation sensitivity, we called Methyl-Spec-seq. In this data set, mouse ZFP57 (F1-F3) was used as a positive control example to show that Methyl-Spec-seq can determine the relative binding energy for variants with different methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated by either chemical synthesis or enzymatic treatment.

overall_design: Except different methylation types of DNA, the overall design is the same as conventional Spec-seq, which we have published work before.


title: Effects of dexamethasone and KLF15 on genome-wide occupancy of the glucocorticoid receptor (NR3C1) and RNA polymerase II (RNAPII) in human airway smooth muscle

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

summary: The objective of this study was to determine how dexamethasone and KLF15 modify GR and RNAPII occupancy in human airway smooth muscle on a genome-wide basis.

overall_design: This study utilized duplicate samples and the following conditions: A primary human airway smooth muscle cell line derived from a deceased donor without asthma was treated with ethanol or dexamethasone (dex) for one hour and ChIP was performed for each condition for GR and RNAPII.  The same airway smooth muscle cell line was also transduced with a KLF15 expressing adenovirus (Ad-KLF15)  or a GFP control (Ad-GFP) for 17 hours and treated with dex for one hour and ChIP was perfomed for each condtion for GR and RNAPII. In addition, RNAPII ChIP was performed on cells transduced with Ad-KLF15 for 17 hours and treated with ethanol for one hour. Input samples from ethanol treated cells (Sample 1D_input) and dex treated cells (Sample 2A_input) were used as additional controls.

first: Sarah

last: Sasse

first: Vineela

last: Kadiyala

first: Reynold

last: Panettieri

first: Tzu

first: Anthony

middle: N

last: Gerber


title: Every-other-day feeding extends lifespan but fails to prevent many symptoms of aging in mice

city: Bonn

first: Kan

last: Xie

address: Sigmund-Freud-Str. 25

institute: German Center for Neurodegenerative Diseases

summary: Dietary restriction is a well-known model to induce longevity across a variety of model organisms ranging from worms, flies to mammals. However, whether lifespan extension is associated with retardation of aging phenotypes still remains unclear. Here, we address whether every-other-day feeding affects age-related gene expression in the brain.

overall_design: RNA was extracted from whole brain tissue derived from young (3 months old) and aged (24 months old) mice which were kept on ad libitum (AL) or intermittent fasting (IF) dietary regimen, respectively.

first: Devon

last: Ryan

first: Dan

last: Ehninger