title: Deep RNA Sequencing of Pectoralis Muscle Transcriptomes during Late-term Embryonic to Neonatal Development in Indigenous Chinese Duck Breeds

city: Yangzhou

first: Li

middle: hui

last: fang

state: Jiangsu

address: No.58 Cangjie Rd

institute: Jiangsu Institute of Poultry Science

summary: In this project we try to character potential candidate genes and signaling pathways related to PM development during late-term embryonic to neonatal development in indigenous chinese duck breeds. We use RNA-seq to analyse PM samples selected at embryonic days (E) 21 and 27 and 5 days post-hatch (dph) in Gaoyou and Jinding ducks. There were about 45 million clean reads, the total mapped rate was 58.58%–64.82%, and the uniquely mapped rate was 56.21%–63.55%.The results of cluster analysis of DEGs are shown that with the same developmental time nodes superimposed. There were 522 DEGs between Gaoyou and Jinding ducks at E21, including 146 novel genes. There were 299 DEGs and 81 novel genes at E27, and 510 DEGs and 118 novel genes at 5 dph. A total of 43 DEGs were shared by both breeds at all time points, including 19 novel genes.We further considered the 393 genes with expression patterns in line with the muscle development curve in both breeds. these DEGs may be involved in the mechanisms responsible for the phenomenon of static or decreased breast muscle growth in duck breeds during the late embryonic period.

overall_design: Constructed eighteen polyA mRNA-seq libraries, including nine from Gaoyou duck PM at E21 and E27, and at 5 days post-hatching (dph) (three libraries at each developmental stage), and nine libraries from Jinding duck PM at the same time points (three libraries at each developmental stage). We performed an integrated analysis of the DEGs detected in this work to identify key genes affecting early PM development in ducks.

first: Huifang


title: Exercise-induced modification of skeletal muscle transcriptome in Arabian horses

status: Public on Oct 21 2016

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

type: Expression profiling by high throughput sequencing

summary:
Purpose: RNA-seq method was used to select genes expressed in muscle tissue and are potentially associated with exercise adaptation in Arabian horses.
Methods: Whole transcriptomes between three time points of muscle tissue collection were compared: T0 (untrained horses),  T1 (horses after intense gallop phase) and T2 (at the end of the racing season), in total 23 samples.  The biopsy of gluteus medius muscle was performed by using minimally invasive ProMag™ Ultra Automatic Biopsy Instrument with a 2 mm diameter biopsy needle. The total RNA was isolated using by TriReagent and 300ng was used to  cDNA libraries preparation.  The NGS sequencing was performed on HiScan SQ (Illumina). The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes were detected by DESeq2. The RNA-seq results were validated using by qPCR.
Results: To detected differentially expressed genes during training preparing to the flat racing, whole transcriptomes between three time points of muscle tissue collection were compared: T0 (untrained horses),  T1 (horses after intense gallop phase) and T2 (at the end of the racing season). We identified 1168 DEGs between T0 vs T1; 1593 between T1 vs T2 and 763 between T2 vs T0. The analysis for all DEGs allow to detect 11 pathways which ale significant over represented between at last two training periods. The numerous group of exercise-regulated DEGs was related with muscle cell structure and signaling (‘focal adhesion’, ‘adherens juntion’ and ‘PI3-ATK signaling’) and included insulin-like growth factor 1 receptor (IGF1R); insulin receptor (INSR); transforming growth factor beta receptors 1 and 2 (TGFBR1; TGFBR2); vascular endothelial growth factor B (VEGFB);  epidermal growth factor (EGF); hepatocyte growth factor (HGF) and vascular endothelial growth factor D (FIGF). Our results showed that in Arabian horses exercise modified the expression of genes belonging to the  ‘PPAR signaling pathway’ (e.g. PPARA; PPARD; PLIN2); ‘calcium signaling pathway’ (e.g. PLN; PLCD1; TNNC1; TNNC2) as well as pathways associated with metabolism processes - ‘oxidative phosphorylation’; ‘fatty acid metabolism’; ‘glycolysis/gluconeogenesis’ and ‘citrate cycle’.
Conclusions: Our research allowed to identify the group of exercise-regulated genes which was related with muscle cell structure as well as signaling and pinpointed the significant metabolic processes critical for adaptive response during training. We confirmed that in Arabians, the exercise switch energy generation towards fatty acid utilization, enhance glycogen transport and calcium signaling. The sequencing of skeletal muscle transcriptome allowed to propose the panel of new candidate genes (such as SLC16A1; ME3; ACTN3; PPARα; SH3RF2; TPM3; TNNC1; TNNI3; TGFBR1; TGFBR2; FABP3) potentially related with body homeostasis maintenance and race performance in Arabian horse.

overall_design: The muscle (gluteus medius) transcriptome sequencing was performed for 23 samples collected form Arabian horses , using Illumina HiScan SQ in50 single-end cycles and in 6 technical repetitions repetitions.

first: Katarzyna

last: Ropka-Molik

first: Monika

last: Stefaniuk-Szmukier

last: Żukowski

last: Piórkowska

last: Bugno-Poniewierska


title: Maintenance of Leukemic Cell Identity by the Activity of the Polycomb Complex PRC1 (RNA-seq_2)

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

country: Italy

institute: IFOM-IEO

summary: These data include RNA Seq data generated from wild type and Ring1a Ring1b dKO Cdkn2a-/- MLL-AF9 Leukemic cells

overall_design: mRNA library preparation from Ring1a-/-;Ring1bf/f Cdkn2a-/- MLL-AF9 leukemic cells treated with OHT or EtOH

first: Alessandra

last: Rossi

first: Sri

middle: G

first: Diego

last: Pasini


title: Effects of pH on the transcriptional profile of adenylate cyclase (cyr1) mutants

city: Hanover

first: Deborah

middle: A

last: Hogan

state: NH

department: Microbiology and Immunology

country: Germany

institute: Dartmouth College

summary:
Purpose : To determine the role played by CaCYR1 in the transcriptional response to differences in medium pH
Methods : RNA was extracted from cells subjected to RNA seq

overall_design: mRNA profiles of C. albicans cells grown for four hours at 37C in YNB medium/.2% glucose/5mM GlcNAc/50 mM citrate at the indicated pH

first: Jeffrey

middle: M

last: Hollomon

first: Nora

last: Grahl

first: Katja

last: Koeppen

first: Sven

middle: D

last: Willger


title: Maintenance of Leukemic Cell Identity by the Activity of the Polycomb Complex PRC1 (ChIP-seq_2)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: These data include the genome wide occupancy of H2AUbq and H3K27me3 by ChIP sequencing in  Ring1a-/-;Ring1bf/f Cdkn2a-/- MLL-AF9 leukemic cells treated with OHT or EtOH

overall_design: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from  Ring1a-/-;Ring1bf/f Cdkn2a-/- MLL-AF9 leukemic cells treated with OHT or EtOH using H2AK119Ubq and H3K27me3 antibody.


title: The DNA modification is dynamic during the conversion from fibroblasts to neurons [Hydroxymethylation]

city: Beijing

first: J

last: Z

address: 1 Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Expression level of 5mC during the conversion from fibroblasts to neurons

overall_design: Examination of methylated level during the process of fibroblasts to neurons.

first: Jianwei

last: Jiao


title: The DNA modification is dynamic during the conversion from fibroblasts to neurons

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

overall_design: Refer to individual Series


title: The DNA modification is dynamic during the conversion from fibroblasts to neurons [Methylation]


title: Expression changes following conditional deletion of SMARCA4 (Brg) in mouse embryonic stem cells [RNA-seq]

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

country: USA

institute: Baylor College of Medicine

summary: We performed RNA-seq 72 h after acute deletion of Smarca4 in a line of conditional knockout mouse embryonic stem cells to examine altered gene expression.

overall_design: Examination of mRNA in mouse embryonic stem cells expressing conditional knockout of the mSWI/SNF ATPase Smarca4. For these studies, mRNA was harvested from Smarca4-CreER (Smarca4flfl) conditional knockout cells 72 h after treatment with either ethanol (EtOH) or 0.8 uM 4-hydroxytamoxifen (Tam).

first: Courtney

first: Benjamin

middle: Z

last: Stanton

first: Wai

middle: L

last: Ku

first: Gerald

middle: R

last: Crabtree

first: Keji

last: Zhao


title: AP-1 and TEAD4 co-operatively promote the vascular program during hemangioblast specification [DNase-Seq]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: Embryonic blood cell development occurs via well-defined developmental stages which are recapitulated in vitro by differentiation of embryonic stem cells. This process is tightly regulated by the interaction of tissue- specific and ubiquitous transcription factors with the chromatin landscape in response to outside signals. We previously identified binding motifs for the commonly expressed AP-1 transcription factor family in open chromatin regions specific for early stages of blood specification and thus aimed to study the role of AP-1 for hemangioblast differentiation. Here we show that FOS and JUN together bind to and activate a core set of vascular genes in the hemogenic endothelium and that upon global inhibition of AP-1 by expression of a dominant negative FOS peptide the balance between endothelial and hematopoietic fate is shifted towards blood. Moreover, we demonstrate that in the hemogenic endothelium AP-1 is required for de novo binding of TEAD4, a transcription factor connected to Hippo signaling, to vascular genes. Notably, after the endothelial-to-hematopoietic transition TEAD4 binding is no longer persisting. These findings provide novel mechanistic insights into vascular and hematopoietic development.

overall_design: High-resolution DNaseI accessibility in hemogenic endothelium and hematopoietic progenitors

first: Nadine

last: Obier

first: Salam

last: Assi

first: Jane

last: Gilmour

first: Michael

last: Lie-A-Ling

first: Maarten

last: Hoogenkamp

first: Monika

last: Lichtinger

first: Laura

last: Noailles

first: Peter

last: Cockerill

first: Georges

last: Lacaud

first: Valerie

last: Kouskoff

first: Constanze

last: Bonifer


title: AP-1 and TEAD4 co-operatively promote the vascular program during hemangioblast specification


title: N6-methyladenosine in Flaviviridae viral RNA genomes regulates infection

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

country: Switzerland

institute: University of Zurich

summary: We use MeRIP-seq and PAR-CLIP in liver cell lines to detail the role of m6A in positive strand RNA virus infection. We find that hepatitis C virus, dengue virus, West Nile virus, yellow fever virus, and Zika virus all contain m6A within their genomes, with some conservation between viruses in methylation sites.

overall_design: Study of m6A methylation in HCV, dengue, WNV, YFV, and Zika virus with two replicates using a polyA prep (m6A antibody, Synaptic Systems; 202 003). Identification of YTHDF1, YTHDF2, YTHDF3 binding sites on the HCV RNA genome using PAR-CLIP

first: Nandan

middle: S

last: Gokhale

first: Alexa

middle: B

middle: J

last: McFadden

first: Allison

middle: E

last: Roder

first: Edward

last: Kennedy

first: Jorge

last: Gandara

first: Sharon

last: Hopcraft

first: Kendra

last: Quicke

first: Christine

last: Vasquez

first: Jason

last: Willer

first: Mariano

last: Garcia-Blanco

first: Matthew

last: Evans

first: Mehul

last: Suthar

first: Shelton

last: Bradrick

first: Christopher

last: Mason

first: Stacy

last: Horner


title: AP-1 and TEAD4 co-operatively promote the vascular program during hemangioblast specification [ChIP-Seq]

first: Pierre

last: Cauchy

overall_design: Examination of transcription binding patterns, gene expression patterns in developing hemogenic and hematopoietic cells with and without AP-1, high-resolution DNaseI accessibility in hemogenic endothelium and hematopoietic progenitors

first: Nadine

last: Obier

first: Salam

last: Assi

first: Jane

last: Gilmour

first: Michael

last: Lie-A-Ling

first: Maarten

last: Hoogenkamp

first: Monika

last: Lichtinger

first: Laura

last: Noailles

first: Peter

last: Cockerill

first: Georges

last: Lacaud

first: Valerie

last: Kouskoff

first: Constanze

last: Bonifer


title: RNA-seq analysis of Penicillium oxalicum transcription factor mutant strains in response to cellulose

city: Jinan

first: Guangshan

last: Yao

address: No 27 ShanDa nan road

department: School of life science

institute: Shandong university

summary: RNA-seq was used to analyze the responses of Penicillium oxalicum strains to cellulose. The transcription facor (PoflbC, CA and PoClrC) mutants were studied.

overall_design: A total of 9 samples were analzyed, which include biological triplicates.

first: Yunfeng

last: Lei

first: Zhonghai

last: Li

first: Ruimei

last: Wu

first: Liwei

last: Gao

first: Qinbiao

last: Kan

first: Guodong

last: Liu

first: Yinbo

last: Qu


title: Hydroxychloroquine inhibits responses to group A streptococcus in peripheral blood mononuclear cells

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Immune responses to group A streptococcus in humans can lead to the development of acute rheumatic fever and rheumatic heart disease. Immune pathways that are activated by group A streptococcus are potential targets for inhibiting autoimmune responses to group A streptococcus. This experiment tests the impact of the drug hydroxychloroquine on immune responses to group A streptococcus in peripheral blood mononuclear cells

overall_design: Peripheral blood mononuclear cells from three healthy participants were stimulated with rheumatogenic, heat-killed group A streptococcus for 24 hours, MOI 10. The effect of hydroxychloroquine (20 µM) (HCQ) was measured, both alone and in combination with group A streptococcus (GAS).

first: Willy-John

last: Martin

first: Guido

last: Pacini


title: Maintenance of Leukemic Cell Identity by the Activity of the Polycomb Complex PRC1 (ChIP-seq)

first: Sri Ganesh

last: Jammula

summary: These data include the genome wide occupancy of H2AUbq by ChIP sequencing in Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa.

overall_design: Immuno-precipitation of formaldehyde cross-linked chromatin prepared from Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa using H2AK119Ubq antibody.

first: Alessandra

last: Rossi

first: Sri

first: Diego

last: Pasini


title: Quant Seq analysis of primary stretched rat alveolar type I-like epithelial (AEC-I) cells

status: Public on Oct 22 2016

city: Philadelphia

first: Tamas

last: Dolinay

state: PA

address: 220 S. 33rd St., Towne building, Room 390

department: Bioengineering

institute: University of Pennsylvania

summary: Rat AEC-I cell monolayers were generated from primary isolated type-II pneumoncytes by plating them on fibronectin-coated silastic membranes. After 4 days of culturing, type-II pneumocytes trasform into AEC-I cells and form monolayers.

overall_design:
Monolayers were randomized in the following four conditions:
1) unstretched monolayers (NS).
2) Monolayers exposed to 25% surface area change with custom built biaxial cyclic (15/min) stretcher for 6 hours (S).
3) Unstretched monolayers pretreated with 1microM GSK2606414 PERK kinase inhibitor for 18 hours (NS_PI).
4) Stretched monolayers pretreated with 1micro M GSK2606414 for 18 hours (S_PI).

first: Maya

last: Shumyatcher

first: Blanca

last: Himes


title: MOF acetyl transferase regulates transcription and respiration in mitochondria

first: Aindrila

last: Chatterjee

state: BW

address: Stübeweg 51

institute: Max Planck Institute of Immunbiology and Epigenetics

summary: Histone acetylation is sensitive to metabolic cues, however interplay between histone acetyl transferases and cellular metabolism remains poorly understood. Here we report the localization of a classical nuclear HAT- MOF and members of Non-Specific Lethal complex in mitochondria. MOF regulates expression of oxidative phosphorylation (OXPHOS) genes, residing in both nuclear and mitochondrial genomes, selectively in aerobically respiring cells. Furthermore, MOF/KANSL1 depletion causes impaired mitochondrial translation and reduced respiration. MOF loss is catastrophic for tissues with high-energy consumption. In mouse hearts, Mof knockout causes hypertrophic cardiomyopathy, compromised ventricular contractility/ stroke volume and ultimately leads to cardiac failure within three weeks of birth. RNA-seq analysis of the cardiomyocytes revealed deregulation of mitochondrial nutrient metabolism and OXPHOS pathways. Consistently, electron microscopy on affected tissues revealed mitochondrial deterioration with high tissue heterogeneity, commonly observed in mitochondrial diseases. Thus, we reveal a novel function of MOF in mitochondrial homeostasis and propose MOF as a sensor connecting epigenetic regulation to metabolism.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We generated mRNA-seq profile of Mof depleted HeLa cells adapted in glucose or galactose media. We also present nuclear RNA seq profile from Mof deleted cardiomyocytes.

first: Ralf

last: Gilsbach


title: RNAseq analysis of heart tissue from mice treated with atenolol and isoproterenol reveals a reciprocal transcriptional response

city: Lausanne

first: Fabienne

last: Maurer

address: Bugnon 27

department: Service of genetic medicine

institute: CHUV

summary: The transcriptional response to many widely used drugs and its modulation by genetic variability is poorly understood. Here we present an analysis of RNAseq profiles from heart tissue of 18 inbred mouse strains treated with the β-blocker atenolol (ATE) and the β-agonist isoproterenol (ISO). Differential expression analyses revealed a large set of genes responding to ISO (n=1770 at FDR=0.0001) and a comparatively small one responding to ATE (n=23 at FDR=0.0001). At a less stringent definition of differential expression, the transcriptional responses to these two antagonistic drugs are reciprocal for many genes, with an overall anti-correlation of r= -0.3. This trend is also observed at the level of most individual strains even though the power to detect differential expression is significantly reduced. The inversely expressed gene sets are enriched with genes annotated for heart-related functions. Modular analysis revealed gene sets that exhibited coherent transcription profiles across some strains and/or treatments. Correlations between such modules and a broad spectrum of cardiovascular traits are stronger than expected by chance. This provides evidence for the overall importance of transcriptional regulation for these organismal responses and explicits links between co-expressed genes and the traits they are associated with. Gene set enrichment analysis of differentially expressed groups of genes pointed to pathways related to heart development and functionality. Our study provides new insights into the transcriptional response of the heart to perturbations of the β-adrenergic system, implicating several new genes that had not been associated to this system previously.

overall_design: Cardiac mRNA expression profiles of the various inbred mouse strains were examined either under baseline condition (control) or in response to chronic administration of isoproterenol or atenolol at 10 mg/kg per day for 2 weeks. Expression data were produced by RNA-sequencing, in triplicates, using the HiSeq 2000 Illumina platform. Only males, aged ten to twelve weeks on average, were included in the experimental protocol. Mouse ID numbers refer to those described in Berthonneche C. et al. PLoS One. 2009 Aug 12;4(8):e6610 (doi: 10.1371/journal.pone.0006610. PMID: 19672458). Corresponding individual phenotypic values, in particular heart rate, systolic blood pressure, electrocardiogaphic measurements and heart weight are available in dataset "maurer1" of the Mouse Phenome Database (http://phenome.jax.org/). Preparation of the sequencing libraries, RNA-sequencing and RNA expression quantitations were performed by the BGI.


title: Lipocalin-2 protects the brain during inflammatory conditions

status: Public on Oct 20 2016

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary: Sepsis is a prevalent health issue that can lead to central nervous system (CNS) inflammation with long-term behavioral and cognitive alterations. Using unbiased proteomic profiling of over 100 different cytokines, we found that Lipocalin-2 (LCN2) was the most substantially elevated protein in the CNS after peripheral administration of lipopolysaccharide (LPS). To determine whether the high level of LCN2 in the CNS is protective or deleterious, we challenged Lcn2-/- mice with peripheral LPS and determined effects on behavior and neuroinflammation. At a time corresponding to peak LCN2 induction in WT mice injected with LPS, Lcn2-/- mice challenged with LPS had exacerbated levels of pro-inflammatory cytokines and exhibited significantly worsened behavioral phenotypes. To determine the extent of global inflammatory changes dependent upon LCN2, we performed an RNAseq transcriptomic analysis. Compared to WT mice injected with LPS, Lcn2-/- mice injected with LPS had unique transcriptional profiles and significantly elevated levels of multiple pro-inflammatory molecules. Several LCN2-dependent pathways were revealed with this analysis including, cytokine and chemokine signaling, NOD-like receptor signaling, and Jak-STAT signaling. These findings demonstrate that LCN2 serves as a potent protective factor in the CNS in response to systemic inflammation and may be a potential candidate for limiting sepsis-related CNS sequelae.

overall_design: RNAseq transcriptomic analysis was conducted from PBS perfused hemi-brain samples of WT and Lcn2-/- mice at 8 hours post LPS or saline injection. 3-4 replicates were used for each genotype-injection combination,

first: Silvia

last: Kang

first: Yingxue

last: Ren

first: Chia-Chen

first: Aishe

last: Kurti

first: Kelsey

last: Baker

first: Guojun

last: Bu

first: John

last: Fryer


title: SMARCA4 ATPase mutations disrupt direct eviction of PRC1 from chromatin

first: H. Courtney

last: Hodges


title: Th2 responses are primed by skin dendritic cells with distinct transcriptional profiles

city: Wellington

first: Franca

last: Ronchese

address: Kelburn Parade

department: Immune Cell Biology

country: New Zealand

institute: Malaghan Instititute of Medical Research

summary: Dendritic cell subsets purified from skin-draining lymph nodes of C57BL/6J mice following intradermal injection of  non-viable Nippostrongylus brasiliensis (Nb) or topical application of Dibutyl Phthalate-FITC. Results provide insight into the genetic programme induced in DC exposed to Th2 stimuli.

overall_design: CD11b+, TN and CD103+ (Nb only) migratory DC subsets were flow sorted from skin-draining lymph nodes following treatment with Th2 stimuli or respective controls. Three independent replicates were generated for each DC population from pooled lymph nodes in three independent flow cytometry sorting experiments.

first: Melanie

last: McConnell

first: Lisa

last: Connor

first: Shiau-Choot

last: Tang

first: Sotaro

last: Ochiai

first: Olivier

last: Lamiable

first: David

last: Eccles

first: Adam

last: Smith


title: ChIP-Seq analysis C57BL/6 thymocytes

city: Boston

first: Kenzie

last: MacIsaac

state: MA

address: 33 Avenue Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck Research Labs

summary: In this study, we show that in addition to regulating DP thymocytes survival, RORgT also controls genes that regulate thymocyte migration, proliferation, and T cell receptor (TCR) selection. Strikingly, pharmacological inhibition of RORg skews TCR gene rearrangement, limits T cell repertoire diversity, and inhibits development of autoimmune encephalomyelitis. Thus, targeting RORgT not only inhibits Th17 cell development and function but also fundamentally alters thymic-emigrant recognition of self and foreign antigens.

overall_design: Examination of RORgT-bound genomic sites in C57BL/6 mouse thymocytes.

first: Yanxia

last: Guo

first: Abbas

last: Hawwari


title: High-Throughput Screening of Human Induced Pluripotent Stem Cell Cardiomyocytes Predicts Tyrosine Kinase Inhibitor Cardiotoxicity

city: Stanford

first: Jared

last: Churko

state: CA

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

overall_design: day 30 hiPSC-CMs from TKI project control lines treated with/without 1uM Sorafenib (TKI) for 72 hours

first: Arun

last: Sharma


title: Genome-wide expression profiling and phenotypic evaluation of European maize inbreds at seedling stage in response to heat stress

city: Köln

first: Felix

middle: Peter

last: Frey

address: Carl-von-Linné-Weg 10

department: Quantitative Genetics

institute: Max-Planck Institute for Plant Breeding Research

summary:
BACKGROUND:
Climate change will lead in the future to an occurrence of heat waves with a higher frequency and duration than observed today, which has the potential to cause severe damage to seedlings of temperate maize genotypes.
In this study, we aimed to (I) assess phenotypic variation for heat tolerance of temperate European Flint and Dent maize inbred lines, (II) investigate the transcriptomic response of temperate maize to linearly increasing heat levels and, (III) identify genes associated with heat tolerance in a set of genotypes with contrasting heat tolerance behaviour.
RESULTS:
Strong phenotypic differences with respect to heat tolerance were observed between the examined maize inbred lines on a multi-trait level.
We identified 607 heat responsive genes as well as 39 heat tolerance genes.
CONCLUSION:
Our findings indicate that individual inbred lines developed different genetic mechanisms in response to heat stress.
We applied a novel statistical approach enabling the integration of multiple genotypes and stress levels in the analysis of abiotic stress expression studies.

overall_design: Identifcation of differentially expressed genes between 8 genotypes and 3 heat levels

middle: P

first: Claude

last: Urbany

first: Bruno

last: Hüttel

first: Richard

last: Reinhardt

first: Benjamin

last: Stich


title: Lymphocyte activation gene3 and coronary artery disease.

city: Farmington

first: Annabelle

last: Rodriguez

state: CT

address: 263 Famington Ave, MC-3501

department: Center for Vascular Biology

institute: UCONN Health

summary:
Purpose: Utilized Next-generation sequencing (NGS) to profile transcriptional differences between two populations, carriers (CC) of rs10846744 SNP associated with cardiovascular disease (CVD) and non-carriers (GG) who are disease free.
Methods: Total RNA was isolated from three subjects homozygous for the rs10846744 reference (GG) allele and three subjects homozygous for the rs10846744 risk (CC) allele and then subjected to full transcriptome sequencing using the Perkin Elmer next gen sequencing  platform (Perkin  Elmer,  Branford, CT). Bioinformatics was performed using Perkin Elmer GeneSifter software program. The data was adjusted by selecting total map reads, quality reads >20, log transformation, and using Benjamini Hochberg to correct for multiple testing. RNA targets of interest were validated by qRT–PCR using TaqMan assays and western blotting using standard methodologies.
Results: Using Perkin Elmer's Genesifter Analysis Edition Software, we mapped about 100 million sequence reads per sample to the human genome (build 37.2), normalized the raw read count by total mapped million reads and identified 937 upregulated and 587 downregulated transcripts in the EBV (Epstein Barr Virus)-transformed B lymphocyte cells isolated from 3 carriers of the risk (CC) allele and 3 non-carriers of the (GG) reference allele with BWA workflow. RNA-seq data confirmed differential expression of LAG3 and this was validated with qRT–PCR.
Conclusions: Our study represents the first detailed analysis of differential LAG3 expression, contributing to CVD, with biologic replicates, generated by RNA-seq technology.

overall_design: mRNA transcriptional profiles from EBV (Epstein Barr Virus)-transformed B lymphocyte cells, isolated from 3 carriers of the risk (CC) allele and 3 non-carriers of the (GG) reference allele, were generated by deep sequencing, in triplicate, using Illumina platform technology.

first: Diana

last: Golden


title: Zebrafish microglia transcriptome

city: Rotterdam

first: Tjakko

last: van Ham

address: Westzeedijk 353

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

summary:
Purpose: Identify zebrafish microglia transcriptome in the healthy and neurodegenerative brain.
Methods: RNA sequencing was performed on FACS-sorted microglia (3x), other brain cells (3x) and activated microglia (4x). Microglia activation was induced using nitroreductase-mediated cell ablation. 10-20 million reads per sample were obtained. Reads were mapped to zebrafish genome GRC10.
Results: We identified the zebrafish microglia transcriptome, which shows overlap with previously identified mouse microglia transcriptomes. Transcriptomes obtained 24h and 48h after treatment appeared highly similar. Therefore, these datasets were pooled. Additionally, we identified an acute proliferative response of microglia to induced neuronal cell death.

overall_design: Zebrafish microglia transcriptomes of homeostatic microglia (triplicate), other brain cells (triplicate), activated microglia 24h (duplo), activated microglia 48h (duplo). In data analysis all activated microglia samples were pooled.

first: Nynke

last: Oosterhof

first: Inge

last: Holtman

first: Laura

last: Kuil

first: Herma

middle: C

last: van der Linde

first: Hendrikus

middle: W

last: Boddeke

first: Bart

last: Eggen


title: SMARCA4 (Brg) ATPase mutations induce increased occupancy and activity of Polycomb repressive factors on chromatin

first: H. Courtney

last: Hodges

summary: We generated a library of Brg variants with mutations in conserved regions of the N-terminal ATPase domain based on mutants observed in primary tumors and cancer cell lines. Heterozygous expression of ATPase mutants leads to increased occupancy of Polycomb Repressive Complex 1 (PRC1) at bivalent CpG-island promoters. Increased PRC1 binding was accompanied by increases in H3K27me3, the mark left by the Polycomb Repressive Complex 2 (PRC2) ~2 kbp away.

overall_design: Examination of PRC1 subunits Ring1b and Cbx7, PRC2 subunit Suz12, H3K27me3 in mouse embryonic stem cells expressing conditional knockout or heterozygous mutations of mSWI/SNF subunits. For both Smarca4-CreER (Smarca4flfl) and Arid1a-CreER (Arid1aflfl) conditional knockout cells, ChIP was performed 72 h after treatment with either ethanol (EtOH) or 0.8 uM 4-hydroxytamoxifen (Tam). Cells expressing V5-tagged mutants of Smarca4 (Smarca4V5) were untreated.

first: Courtney

last: Stanton

first: Wai

last: Ku

first: Gerald

last: Crabtree

first: Keji

last: Zhao


title: Genome-wide hepatic miRNAome profiling in chronic hepatitis C patients using next-generation sequencing [miRNA-seq]

city: Lahore

first: Azeem

middle: Mehmood

last: Butt

address: 87-West Canal Bank Road, Thokar Niaz Baig

department: Centre of Excellence in Molecular Biology (CEMB)

country: Pakistan

institute: University of the Punjab

type: Non-coding RNA profiling by high throughput sequencing

summary:
Although several dysregulated miRNAs have been reported in liver diseases of different etiologies, no genome-wide analyses of hepatic miRNAs from patients with chronic hepatitis C (CHC) of HCV genotype 3 have been reported. With the aim of determining miRNAs associated with CHC pathogenesis, we present a comprehensive catalogue of the hepatic miRNAome of CHC-infected and control liver tissues obtained using next-generation sequencing.
The study design was divided into discovery and validation phases. In the initial NGS-based discovery phase, 10 liver tissues (CHC-positive: 8, controls: 2) were subjected to miRNA-sequencing, using illumina HiSeq 2000. The expression of selected deregulated miRNAs was validated using qRT-PCR in a validation cohort comprising of 123 treatment-naive CHC patients of the HCV genotype 3 and 60 healthy controls. Furthermore, a comprehensive computational workflow incorporating miRNA–mRNA interaction analysis, was established to determine the functional significance of dysregulated miRNA–mRNA pairs in CHC infection.

first: Leandro

last: Castellano

first: Muhammad

last: Idrees

first: Yigang

last: Tong


title: HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_small_rnaseq]

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: HnRNPA2B1 encodes an RNA binding protein associated with neurodegenerative disorders. However, its function in the nervous system is unclear. Transcriptome-wide cross-linking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ~2,500 hnRNP A2/B1 binding sites and an unexpected role for hnRNP A2/B1 in alternative polyadenylation. Loss of hnRNP A2/B1 results in alternative splicing, including skipping of an exon in amyotrophic lateral sclerosis (ALS)-associated D-amino acid oxidase (DAO) that reduces D-serine metabolism. Inclusion of the DAO exon is also reduced in transgenic ALS mice models. ALS-associated hnRNP A2/B1 D290V mutant patient fibroblasts and motor neurons differentiated from induced pluripotent stem cells demonstrate gain-of-mutant-dependent splicing differences. Mutant motor neurons also exhibit increased hnRNP A2/B1 localization to cytoplasmic granules during stress, which are abrogated by a small molecule CA43.  Our findings and cellular resource identify RNA networks affected in loss of normal and mutated hnRNP A2/B1 with broad relevance to neurodegeneration.

overall_design: small RNA-seq in mouse spinal after injection with ASO against hnRNP A2/B1 or saline. Three or four replicates per condition

first: Fernando

last: Martinez

first: Gabriel

middle: A

last: Pratt

first: Eric

last: Van Nostrand

first: Ranjan

last: Batra

first: Stephanie

last: Huelga

first: Katannya

last: Kapeli

first: Mark

last: Fang

first: Peter

last: Freese

first: Seung

last: Chun

first: Chelsea

last: Gelboin-Burkhart

first: Layla

last: Fijany

first: Harrison

last: Wang

first: Julia

last: Nussbacher

first: Hong-joo

last: Kim

first: Rea

last: Lardelli

first: Shibing

last: Tang

first: Balaji

last: Sundararaman

first: John

last: Donohue

first: Jens

last: Lykke-Andersen

first: Sheng

last: Ding

first: Shuo-Chien

last: Ling

first: Frank

last: Bennett

first: Manuel

last: Ares Jr

first: Christopher

last: Burge

first: J

last: Taylor

last: Rigo


title: HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_eCLIP_human_iPSC_MN]

first: Gene

last: Yeo

overall_design: eCLIP-seq in human iPSC-MNs

first: Fernando

last: Martinez

first: Gabriel

last: Pratt

first: Eric

last: Van Nostrand

first: Ranjan

last: Batra

first: Stephanie

last: Huelga

first: Katannya

last: Kapeli

first: Peter

last: Freese

first: Seung

last: Chun

first: Karen

last: Gelboin-Burkhart


title: HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_RNA-seq_mouse_SC]

overall_design: RNA-seq in mouse spinal after injection with ASO against hnRNP A2/B1 or saline. Three or four replicates per condition

first: Chelsea

first: Layla

last: Fijany

first: Harrison

last: Wang

first: Julia

last: Nussbacher

first: Hong-joo

last: Kim

first: Rea

last: Lardelli

first: Balaji

last: Sundararaman

first: John

last: Donohue

first: Jens

last: Lykke-Andersen


title: Reciprocal Regulation between the Circadian Clock and Hypoxia Signaling at the Genome Level in Mammal

city: Beijing

first: xiong

middle: will

last: wei

address: 7 Science Park Road ZGC Life Science Park

institute: NIBS,Beijing

summary: we propose that the clock plays an important role in fine-tuning the hypoxic response under pathophysiological conditions, which can serve as a strategy to reduce the severity of fatal hypoxia-related diseases.

overall_design: BMAL1 and HIF1a Chip-seq in U2OS cells at circadian peak and trough with DMOG or DMSO

first: wei

last: xiong


title: HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [iCLIP-seq]

first: Gene

last: Yeo

overall_design: iCLIP-seq in mouse spinal cord for hnRNP A2/B1. one replicate

first: Fernando

last: Martinez

first: Gabriel

last: Pratt

first: Eric

last: Van Nostrand

first: Ranjan

last: Ling

first: Frank

last: Bennett

first: Manuel

last: Ares Jr

first: Christopher

last: Burge

first: J

last: Taylor

last: Rigo


title: Maintenance of Leukemic Cell Identity by the Activity of the Polycomb Complex PRC1 (RNA-seq)

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

institute: IFOM-IEO

summary: These data include RNA Seq data generated from  Ring1b wild type and Ring1b KO Ring1a-/- Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa.

overall_design: Total RNA extracted from Ring1b wild type and Ring1b KO Ring1a-/- Cdkn2a-/- Lin- HSC cells non-transduced or transduced with MLL-AF9, HOXA9 and PML-RARa.

first: Alessandra

last: Rossi

first: Sri

middle: G

first: Diego

last: Pasini


title: Maintenance of Leukemic Cell Identity by the Activity of the Polycomb Complex PRC1

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

overall_design: Refer to individual Series


title: Base-resolution analysis of cisplatin-DNA adducts at the genome scale

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

summary: Cisplatin, one of the most widely used anticancer drugs, crosslinks DNA and ultimately induces cell death. However, the genomic pattern of cisplatin-DNA adducts remains unknown, due to the lack of a reliable and sensitive genome-wide method. Here we present “cisplatin-seq” to identify genome-wide cisplatin crosslinking sites at base-resolution. Cisplatin-seq reveals that mitochondrial DNA is a preferred target of cisplatin. For nuclear genome, cisplatin-DNA adducts are enriched within promoters and regions harboring transcription termination sites. While the density of GG dinucleotide determines the initial crosslinking of cisplatin, binding of proteins to the genome largely contributes to the accumulative pattern of cisplatin-DNA adducts.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Developing a method "Cisplatin-seq" to profile cisplatin-crosslinking site in human genome, using cells treated with cisplatin for 3h, 12h, 24h respectively.

first: Xiaoting

last: Shu

first: Chengqi

last: Yi


title: Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: Mediator is a conserved, essential transcriptional coactivator complex, but its in vivo functions have remained unclear due to conflicting data regarding its genome-wide binding pattern obtained by genome-wide ChIP. Here, we used ChEC-seq, a method orthogonal to ChIP, to generate a high-resolution map of Mediator binding to the yeast genome. We find that Mediator associates with upstream activating sequences (UASs) rather than the core promoter or gene body under all conditions tested. Mediator occupancy is surprisingly correlated with transcription levels at only a small fraction of genes. Using the same approach to map TFIID, we find that TFIID is associated with both TFIID- and SAGA-dependent genes and that TFIID and Mediator occupancy is cooperative. Our results clarify Mediator recruitment and binding to the genome, showing that Mediator binding to UASs is widespread, partially uncoupled from transcription, and mediated in part by TFIID.

overall_design: We used ChEC-seq to map the genome-wide binding of Mediator and its relationship to TFIID in budding yeast. ChEC-seq was performed as described in PMID 26490019.

first: Sebastian

last: Gruenberg

first: Steven

last: Hahn

last: Zentner


title: High-throughput sequencing identify miRNAs of Tribolium castaneum

city: Nanjing

first: Wei

last: Wu

address: Nanjing Normal University, #1 Wenyuan Road, Qixia District, Nanjing, China

institute: Nanjing Normal University

summary: To identify miRNAs of Tribolium castaneum, one small RNA libraries for mix samples of eight development stage (including 1-day-old early embryo, 3-day-old late embryo, 1-day-old early larva, 20-day-old late larva, 1-day-old early pupa, 6-day-old late pupa, 1-day-old early adult, 7-day-old late adult) were constructed.  Totally, 12,259,974 raw reads were obtained, 7,116,806 mappable reads were remained and 2,175,311 high-quality miRNA reads were identified after the small RNA digitalisation analysis. At last, 1,447 unique miRNAs which contained 274 conserved miRNAs, 245 known candidate miRNAs and 927 novel miRNAs were identified.

overall_design: Examination of small RNA in Tribolium castaneum lifecycle development

first: Bin

last: Li


title: HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons

first: Gene

last: Yeo


title: Reciprocal Regulation between the Circadian Clock and Hypoxic Signaling in Mammals

first: xiong

last: wei

address: 5 Yiheyuan Rd, Haidian, Beijing, China

institute: peking university

summary: We propose that the clock plays an important role in fine-tuning the hypoxic response under pathophysiological conditions, which can serve as a strategy to reduce the severity of fatal hypoxia-related diseases.

overall_design: RNA-seq  between wildtype and mutant MEF cells and Chip-seq in U2OS cells

first: wei

last: xiong


title: Temporal transcriptome analysis of control and Zeb2 knockout mESC in pluripotency and in neural differentiation

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

summary: To capture the Zeb2-dependent transcriptional changes in early cell state/fate decisions we performed RNA-seq on Zeb2 control and Zeb2 knockout cells. We chose three stages, which correspond in control ESCs to the naive pluripotent state (d0; very low amounts of Zeb2 mRNA), multipotent progenitors (d4, low Zeb2 mRNA/protein) and early neural progenitors (d6, high Zeb2 mRNA/protein), respectively.

overall_design: Three biological replicates of Zeb2 control (Ctrl) and Zeb2 knockout (KO) samples on day 0, day 4 and day 6 of neural differentiation were used in this study (18 samples in total)

first: Agata

last: Stryjewska

first: Danny

last: Huylebroeck


title: Temporal DNA methylation analysis (RRBS) for differentiating mouse embryonic stem cells deficient for Zeb2

summary: In this study we performed temporal profiling of DNA methylation by RRBseq of differentiating mouse embryonic stem cells using an embryoid body protocol. Analysis at d0, d4 and d6 revealed that Zeb2 deficient mESC lose their initially acquired DNA methylation at d6.

overall_design: DNA methylation analysis using RRBseq was performed on Zeb2 KO and Ctrl (fl/fl) samples at 3 consecutive time-points - corresponding to ground-state mESC (d0), multi-potent progenitor (d4) and neural progenitor (d6) - in 2 independent experiments.


title: Impact of RNA degradation on fusion detection by RNA-seq

city: Rochester

first: Numrah

middle: Mohammadali

last: Fadra

state: Minnesota

address: 200 2nd Street SW

department: Health Sciences Research

summary:
Purpose: Popular methods for library preparation in RNA-seq such as Illumina TruSeq® RNA v2 kit use a poly-A pulldown strategy. Such methods can cause loss of coverage at the 5’ end of genes, impacting the ability to detect fusions when used on degraded samples. The goal of this study was to quantify the effects RNA degradation has on fusion detection when using poly-A selected mRNA and to identify the variables involved in this process
Methods: Total RNA was extracted from solid tumor tissue and whole blood using the Qiagen® miRNeasy Micro and Mini kits, respectively. The KU812 cell line was purchased from Sigma-Aldrich (St. Louis, MO) and UHR (Universal Human Reference RNA) was purchased from Agilent (Santa Clara, CA). UHR is a mixture of cell lines derived from breast adenocarcinoma, hepatoblastoma, cervix adenocarcinoma, testis embryonal carcinoma, gliobastoma, melanoma, liposarcoma, histiocytic lymphoma, lymphoblastic leukemia and plasmocytoma. For Degradation experiments, two micrograms of human universal reference RNA (UHR) (Agilent Technologies, Santa Clara, CA) and 1ug of RNA extracted from KU812 cell line (purchased from ATCC) were degraded at 74oC from 1 to 11 minutes in 1 minute intervals, using the NEBNext® Magnesium RNA Fragmentation Module Kit (NEB, Ipswich, MA). RNA was then purified and concentrated with RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA).
Results: In this study, we designed experiments using artificially degraded RNA from cell lines as well as naturally degraded RNA from tissue samples to quantify the effect RNA degradation has on fusion detection when using poly-A selected RNA libraries We found that both the RNA degradation level and the distance from the 3’ end of a gene, negatively impact the read coverage profile in RNA-seq. Furthermore, the median transcript coverage decreases exponentially as a function of the distance from the 3’ end and there is a linear relationship between the coverage decay rate and the RNA integrity number (RIN).
Conclusions: we found that when using poly-A pulldown techniques for library preparation in RNA-seq, the fusion sensitivity is negatively impacted by both sample degradation and distance of the fusion breakpoint from the 3’ end and developed graphs that show such effect. Such graphs can be useful in assessing the fusion sensitivity of RNA-seq in both research and clinical settings

overall_design: Sequencing data was generated using Hiseq 2500 with a library of 101 paired end reads in the rapid run mode

first: Jaime

last: Davila

first: Asha

last: Nair

first: Eric

last: Klee

first: Kevin

last: Halling

first: Amber

last: McDonald

first: Lisa

middle: M

last: Peterson

first: Barbara

last: Crusan

first: Xianglin


title: The development of Drosophila melanogaster during space flight

status: Public on Oct 19 2016

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

summary: In prospective human exploration of outer space, the need to maintain a species over several generations under changed gravity conditions may arise. This paper reports the analysis of the third generation of fruit fly Drosophila melanogaster obtained during the 44.5-day space flight (Foton-M4 satellite, 2014, Russia), followed by the fourth generation on Earth and the fifth generation under conditions of a 12-day space flight (2014, in the Russian Segment of the ISS). The obtained results show that it is possible to obtain the third-fifth generations of a complex multicellular Earth organism under changed gravity conditions (in the cycle “weightlessness – Earth – weightlessness”), which preserves fertility and normal development. However, there were a number of changes in the expression levels and content of cytoskeletal proteins that are the key components of the spindle apparatus and the contractile ring of cells.

overall_design: Examination of drosophila genes expression change during space flight by RNA-Seq technique

first: Irina

middle: V

last: Ogneva

first: Stepan

middle: N

last: Belyakin

first: Svetlana

last: Sarantseva


title: Escape from X-Inactivation Tumor Suppressor (EXITS) genes contribute to sex bias

first: Andrew

last: Lane

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: In this manuscript, we described male-biased mutations in chrX genes in cancer. In this RNA-seq experiment we tested the transcriptional consequences of shRNA knockdown of one of those genes, CNKSR2

overall_design: Murine NIH 3T3 cells were infected with and selected for expression of lentiviruses expressing shRNAs targeting Cnksr2 (2 independent shRNA sequences) or a control shRNA (targeting RFP, a gene not present in these cells). Each was performed in biological triplicate independent cultures for n=9 total samples


title: A ribosome profiling study of mRNA cleavage by the endonuclease RelE

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Implicated in persistence and stress response pathways in bacteria, RelE shuts down protein synthesis by cleaving mRNA within the ribosomal A site. Structural and biochemical studies have shown that RelE cuts with some sequence specificity, which we further characterize here, and that it shows no activity outside the context of the ribosome. We obtained a global view of the effect of RelE on translation by ribosome profiling, observing that ribosomes accumulate on the 5’-end of genes through dynamic cycles of mRNA cleavage, ribosome rescue, and initiation. Moreover, the addition of purified RelE to cell lysates shows promise as a method for generating ribosome footprints. In bacteria, profiling studies have suffered from relatively low resolution and have yielded no information on reading frame due to problems inherent to MNase digestion, the method used to degrade unprotected regions of mRNA. In contrast, we find that RelE yields precise 3’-ends that for the first time reveal reading frame in bacteria. Given that RelE has been shown to function in all three domains of life, RelE has potential to improve reading frame and shed light on A-site occupancy in ribosome profiling experiments more broadly.

overall_design: Ribosome profiling and RNAseq of E. coli MG1655, both WT and overexpressing RelE.


title: Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

city: Davis

first: Luca

last: Comai

state: Calif

address: 451 Health Sciences Dr

department: Genome Center

institute: UC Davis

summary: We report the binding profile of A. thaliana CENH3, L. oleraceum CENH3 and Z. mays CENH3 in the genetic background of A. thaliana Col ecotype. The L. oleraceum CENH3 and Z. mays CENH3 ChIP was performed in a cenh3 homozygous mutant background expressing CENH3 homologs as transgenes.

overall_design: Examination of 3 different centromeric histone H3 (CENH3) variants in 3 different A. thaliana genotypes.

first: Shamoni

last: Maheshwari


title: RNA-seq analysis of Hypoxia and Normoxia cultured cancer cells

city: HOUSTON

first: anil

middle: k

last: sood

state: TEXAS

address: 7777 knight road, unit 173

department: Gyn Oncology and Rep Medicine

institute: UT MD Anderson Cancer Center

summary: Purpose: To study differential mRNA and precursor miRNA expression under hypoxia exposure in cancer cells. We treated ovarian cancer cell line A2780 under hypoxia condition at different time points. Normoxi acultured cells at corresponding time point were used as controls.

overall_design: A2780 cancer cells, cultured under hypoxia and normoxia. Time points tested: 6hr, 48hr, 6days.

first: Anil

last: Sood

first: Rajesha

last: Rupaimoole


title: Differential RNA-Seq (dRNA-seq)  of Escherichia coli O104:H4

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: We performed a high-throughput mapping of the 5’ end transcriptome of the pAA plasmid of the clinical Escherichia coli O104:H4 (E. coli O104:H4) isolate LB226692. We employed differential RNA-sequencing (dRNA-seq), a terminator exonuclease (TEX)-based RNA-seq approach allowing for the discrimination of primary and processed transcripts. This method has proven to be a powerful tool for the mapping of transcription start sites (TSS) and detection of non-coding RNAs (ncRNAs) in bacteria. We catalogued pAA-associated TSS and processing sites on a plasmid-wide scale and performed a detailed analysis of the primary transcriptome focusing on pAA virulence gene expression.

overall_design: Exponentially growing E. coli O104:H4 isolate LB226692 was subjected to dRNA-seq. A detailed analysis of the pAA plasmid primary transcriptome focusing on virulence gene expression was performed

first: Petya

last: Berger

middle: U


title: Hypoxia Mediated Downregulation of miRNA Biogenesis Leads to Increased Tumor Progression


title: Genome-wide uniformity of human “open” pre-initiation complexes

city: University Park

first: Bongsoo

last: Park

address: 453 North Frear Building

institute: Penn State University

summary: Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. Their sites of initiation are generally inferred from transcript 5’ ends, and are thought to be either locally dispersed or focused. How these two modes of initiation relate is unclear. Here, we apply permanganate treatment and chromatin immunoprecipitation (PIP-seq) of initiation factors to identify the precise location of melted DNA separately associated with the pre-initiation complex (PIC) and the adjacent paused complex (PC). This approach revealed the two known modes of transcription initiation. However, in contrast to prevailing views they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. PIP-seq allowed transcriptional orientation of Pol II to be determined, which may be useful near promoters where sufficient sense/anti-sense transcript mapping information is lacking. PIP-seq detected divergently oriented Pol II at both coding and noncoding promoters, as well as at enhancers.  Their occupancy levels were not necessarily coupled in the two orientations. DNA sequence and shape analysis of initiation complex sites suggest that both sequence and shape contribute to specificity, but in a context-restricted manner. That is, initiation sites have the locally “best” initiator (INR) sequence and/or shape. These finding reveal a common core to pervasive Pol II initiation throughout the human genome.

overall_design: Genome-wide analysis of pre-initiation complex using PIP-seq

first: William

middle: K

last: Lai

first: B

middle: F

last: Pugh


title: Independent roles of switching and hypermutation in the development and persistence of B lymphocyte memory [Nurr77]

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

summary: Somatic hypermutation (SHM) and class switch recombination (CSR) increase the affinity and diversify the effector functions of antibodies during immune responses. Although SHM and CSR are fundamentally different, their independent roles in regulating B cell fate have been difficult to uncouple because a single enzyme, activation-induced cytidine deaminase (encoded by Aicda), initiates both reactions. Here, we used a combination of Aicda and antibody mutant alleles that separate the effects of CSR and SHM on polyclonal immune responses. We found that class-switching to IgG1 biased the fate choice made by B cells, favoring the plasma cell over memory cell fate without significantly affecting clonal expansion in the germinal center (GC). In contrast, SHM reduced the longevity of memory B cells by creating polyreactive specificities that were selected against over time. Our data define the independent contributions of SHM and CSR to the generation and persistence of memory in the antibody system.

overall_design: IgG1 and IgM light zone (LZ) germinal center (GC) B cells that were Nurr77-GFP+ or Nurr77-GFP- were compared in immunized AIDcre/- IgH-96K/+ Nurr77-GFP mice.

first: Alexander

middle: D

last: Gitlin

first: Lotta

last: von Boehmer

first: Anna

last: Gazumyan

first: Ziv

last: Shulman

first: Michel

last: Nussenzweig


title: Interplay between RNA interference and heat shock response systems in Drosophila melanogaster

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

institute: Institute of Molecular Genetics

summary: The genome expression pattern is strongly modified during the heat shock response (HSR) to form an adaptive state. This may be partly achieved by modulating microRNA levels that control the expression of a great number of genes that are embedded within the gene circuitry. Here, we investigated the cross-talk between two highly conserved and universal house-keeping systems, the HSR and microRNA machinery, in Drosophila melanogaster. We demonstrated that pronounced interstrain differences in the microRNA levels are alleviated after heat shock (HS) to form a uniform microRNA pattern. However, individual strains exhibit different patterns of microRNA expression during the course of recovery. Importantly, HS-regulated microRNAs may target functionally similar HS-responsive genes involved in the HSR. Despite the observed general downregulation of primary microRNA precursor expression as well as core microRNA pathway genes after HS, the levels of many mature microRNAs are upregulated. This indicates that the regulation of miRNA expression after HS occurs at transcriptional and post-transcriptional levels. It was also shown that deletion of all hsp70 genes had no significant effect on microRNA biogenesis but might influence the dynamics of microRNA expression during the HSR.

overall_design: Time-course analysis of miRNA expression after heat-shock treatment of three strain of Drosophila by deep-sequencing

middle: S

first: Sergey

last: Funikov

first: Michael

middle: B

last: Evgen'ev


title: DNA methylation profile for male SD Rats upon fructose and DHA treatment by RRBS

city: Los Angeles

first: Xia

last: Yang

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

institute: UCLA

summary: To investigate the beneficial effects of DHA (omega-3) on affecting fructose induced brain dysfunction and metabolic disorders by sequencing the methylome (RRBS) in the hypothalamus and hippocampus of male SD rats.

overall_design: Male Sprague–Dawley (SD) rats of 2 months old were randomly assigned to an omega-3 fatty acid diet (n-3 diet) with or without fructose added in the drinking water (15%) for six weeks. The rats were sacrificed by decapitation. Hypothalamus and hippocampus were dissected out, flash frozen, and stored at -70°C for later transcriptome and DNA methylome sequencing experiments. All experiments were performed in accordance with the United States National Institutes of Health Guide for the Care and Use of Laboratory Animals and were approved by the University of California at Los Angeles Chancellor’s Animal Research Committee.

first: Qingying

last: Meng

first: Fernando

last: Gomez-Pinilla


title: DNA methylation profile for male SD Rats upon fructose treatment by RRBS

overall_design: male SD Rats were feed with fructose for 6 weeks


title: A Dynamic Model for the Function of Mediator Modules In Vivo

first: Alain

middle: Roger

last: Bataille

address: 453 North Frear

department: BMB

summary: Mediator is a highly conserved transcriptional coactivator organized into four modules, namely Tail, Middle, Head and Kinase (CKM). Previous work suggests regulatory roles for Tail and CKM, but an integrated model for these activities is lacking. Here, we analyzed the genome-wide distribution of Mediator subunits in wild-type and mutant yeast cells in which RNA polymerase II promoter escape is blocked allowing detection of transient Mediator forms.  We found that while all modules are recruited to upstream activated regions (UAS), assembly of Mediator within the pre-initiation complex is accompanied by the release of CKM. Surprisingly, our data show that CKM regulates Mediator-UAS interaction rather than Mediator-promoter association. In addition, while Tail is required for Mediator recruitment to UAS, Tail-less Mediator nevertheless interacts with core promoters. Collectively, our data suggest that the essential function of Mediator is mediated by Head and Middle at core promoters, while Tail and CKM play regulatory roles.

overall_design: ChIP-exo of 2 subunits of mediator (MED15 and MED7) in Saccharomyces cerevisiae using MYC epitope tag in kin28as strains. Samples are done in replicates. 2 combined No-Tag samples were process and used to normalize the combined experiment sample (by subtraction). ChIP-exo of Sua7 (TFIIB) in Saccharomyces cerevisiae using TAP epitope tag. Samples are done in replicates. 4 combined No-Tag samples were process and used to normalize the combined experiment sample (by subtraction).

first: Celia

last: Jeronimo

first: Marie-France

last: Langelier

first: John

last: Pascal

first: Francois

last: Robert


title: Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis

status: Public on Oct 18 2016

city: London

first: Nuria

last: Andreu

address: Keppel Street

country: United Kingdom

institute: LSHTM

summary: Macrophages play an essential role in the early immune response to Mycobacterium tuberculosis and are the cell type preferentially infected in vivo. Primary macrophages and macrophage-like cell lines are commonly used as infection models, although the physiological relevance of cell lines, particularly for host-pathogen interaction studies, is debatable. Here we use high-throughput RNA-sequencing to analyse transcriptome dynamics of two macrophage models in response to M. tuberculosis infection. Specifically, we study the early response of bone marrow-derived mouse macrophages and cell line J774 to infection with live and -irradiated (killed) M. tuberculosis. We show that infection with live bacilli specifically alters the expression of host genes such as RSAD2, IFIT1/2/3 and RIG-I, whose potential roles in resistance to M. tuberculosis infection have not yet been investigated. In addition, the response of primary macrophages is faster and more intense than that of J774 cells in terms of number of differentially expressed genes and magnitude of induction/repression. Our results point to potentially novel processes leading to immune containment early during M. tuberculosis infection, and support the idea that important differences exist between primary macrophages and cell lines, which should be taken into account when choosing a macrophage model to study host-pathogen interactions.

overall_design: J774 and BMDM infected with live and dead (gamma-irradiated) bacteria compared to uninfected control. Two time-points (4 and 24 hpi) and 3 replicates.

first: Martin

middle: L

last: Hibberd


title: Macrophage Epithelial Reprogramming Underlies Mycobacterial Granuloma Formation and Promotes Infection

city: Durham

first: Steve

last: Taylor

state: NC

address: 303 Research Dr

department: Division of Infectious Diseases

institute: Duke University School of Medicine

summary: Mycobacterium tuberculosis infection in humans triggers formation of granulomas, tightly organized immune cell aggregates that are the central structure of tuberculosis. Infected and uninfected macrophages interdigitate, assuming an altered, flattened appearance. Although pathologists have described these changes for over a century, the molecular and cellular programs underlying this transition are unclear. We find that mycobacterial granuloma formation is accompanied by macrophage induction of canonical epithelial molecules and structures. Using the zebrafish-Mycobacterium marinum model, we identify fundamental macrophage reprogramming events that parallel E-cadherin-dependent mesenchymal-epithelial transitions. Macrophage-specific disruption of E-cadherin function results in disordered granuloma formation, enhanced immune cell access, decreased bacterial burden and increased host survival, suggesting that the granuloma can also serve a bacteria-protective role.  In humans, we find that granuloma macrophages are similarly transformed. Long considered largely through the prism of immune signaling pathways, granuloma macrophages are reprogrammed by epithelial modules that alter the trajectory of mycobacterial infection.

overall_design: We found that mycobacterial granuloma formation was accompanied by epithelialization within the granuloma. To further assess the epithelial reprogramming within granuloma macrophages, granulomas were microdissected from 2 week post infection zebrafish infected with 400 CFU M. marinum. Dissected granulomas were compared to matched macrophage samples sorted from the kidney of infected animals. Control cell populations were also derived from mixed larval cell populations specifically depleted for macrophages. Data was analyzed from 5 granuloma samples, 4 kidney macrophage samples and 3 control cell populations. Granuloma samples were derived from 2-7 granuloma dissected from a single animal. Macrophage populations were derived from matched kidneys of the granuloma-containing animals.

first: Mark

last: Cronan

first: Rebecca

middle: W

last: Beerman

first: Allison

last: Rosenberg

first: Joseph

last: Saelens

first: Matthew

middle: G

last: Johnson

first: Stefan

middle: H

last: Oehlers

first: Dana

last: Sisk

first: Kristen

last: Jurcic Smith

first: Neil

middle: A

last: Medvitz

first: Sara

middle: E

last: Miller

first: Le

last: Trinh

first: Scott

last: Fraser

last: Madden

first: Joanne

last: Turner

first: Jason

last: Stout

first: Sunhee

last: Lee

first: David

last: Tobin


title: Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers

city: Chapel Hill

first: Daniel

middle: J

last: McKay

address: 3344 Genome Sciences Building

department: Biology, Genetics

institute: The University of North Carolina at Chapel Hill

summary: Transcriptional analysis of Drosophila CNS midline cells provides a useful system for studying transcriptional regulation at the genomic level due to a well-characterized set of midline-expressed genes and in vivo-validated enhancers. To investigate how access to regulatory information is controlled during midline cell development, we performed FAIRE-seq on FACS-purified midline cells. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak (“midline-enriched”) often correspond to midline enhancers near a midline-expressed gene and provides a useful predictive tool. Analysis of a large collection of midline enhancers revealed that those with a midline-enriched peak were located near midline-expressed genes, as were about half of the midline enhancers that overlapped a midline FAIRE peak that was not statistically "midline-enriched". There is a substantial fraction of midline enhancers that do not have a midline FAIRE peak and these tend to reside in chromatin regions that are not transcriptionally active and thus, unlikely to drive midline activity in vivo. This study emphasizes the utility of combining chromatin analysis of purified cell populations with gene expression and enhancer datasets to determine an experimentally useful chromatin profile that identifies biologically relevant enhancers and genes.

overall_design: We performed two FAIRE-seq replicates on purified populations of midline cells from 6-8hr embryos, two FAIRE-seq replicates from 6-8hr whole embryos, and one genomic DNA input.

middle: C

last: Pearson

last: Lieb

first: Stephen

middle: T

last: Crews


title: Temporal transcriptome and methylome analysis of differentiating mouse embryonic stem cells deficient for Zeb2

city: Boston

first: Ruben

last: Dries

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

overall_design: Refer to individual Series


title: RNA-seq analyses of JMJD3c-MYOD1-induced myogenic cells and human skeletal myotubes

city: Tokyo

first: Tomohiko

last: Akiyama

address: 35 Shinanomachi

department: School of Medicine

country: Japan

institute: Keio University

summary: We generated the human ES lines, in which the genome-wide reduction of H3K27me3 can be induced by the ectopic expression of catalytic domain of histone demethylase JMJD3 with doxycycline treatment (JMJD3c-hESCs). The overexpression of JMJD3c enhances MYOD1-mediated myogenic differentiation of hESCs. We compared the gene expression patterns of the generated myogenic cells with those of human skeletal myotubes.

overall_design: Doxycycline-treated JMJD3c-hESCs were differentiated into myogenic cells by MYOD1 overexpression. Human myoblast HSMM cells were differentiated into myotubes with 2% horse serum.

first: Shunichi

last: Wakabayashi

first: Mayumi

last: Oda

first: Miki

last: Sakota


title: A herpesvirus protein selectively inhibits cellular mRNA nuclear export

city: los angeles

first: Danyang

last: Gong

address: 650 Charles Young Dr. So.

department: pharmacology

summary: Nuclear export of mRNA is essential for eukaryotic cells to establish the flow of genetic information in the nucleus to protein synthesis in the cytoplasm. This transport process is highly regulated to ensure efficient and accurate gene expression. Viruses are well known for their ability to manipulate host gene expression. Here, we report that ORF10 of Kaposi’s sarcoma associated herpesvirus (KSHV), a nuclear DNA virus, inhibits mRNA export in a transcript-selective manner to control cellular gene expression. This export inhibitory effect of ORF10 requires the interaction with an RNA export factor, Rae1. Genome-wide analysis by RNA sequencing revealed the subset of cellular mRNAs whose nuclear export is blocked by ORF10. The 3’ untranslated regions (3’ UTRs) of ORF10-targeted transcripts confer their sensitivity to nuclear export inhibition by ORF10. In the context of KSHV replication, the interaction of ORF10 with Rae1 is important for the virus to express viral genes and produce infectious virions. Our results suggest that a nuclear replicating DNA virus can selectively interfere with RNA export through Rae1 to restrict host gene expression for optimal viral replication.

overall_design: 1. Study lytic replication profile of KSHV WT and KSHV ORF10 mutant. 2. Study role of ORF10 on host mRNA nuclear export

first: Yushen

last: Du


title: Identification of ParB binding sites in vivo in Pseudomonas aeruginosa

city: Gif sur Yvette

first: isabelle

last: Vallet-Gely

address: avenue de la Terrasse

country: France

institute: CNRS

summary: To identify ParB binding sites in vivo, we performed ChIP experiments followed by high throughput sequencing using a 3xflag tagged version of ParB, in different genetic backgrounds. This allowed us to show that ParB binds in vivo mostly to 4 parS sites, located within 15 kb of oriC. We also identify 9 secondary ParB binding sites.

overall_design: A functional ParB-3xflag was used for ChIP-seq experiments.

first: Valentine

last: Lagage

first: Frédéric

last: Boccard

first: Isabelle


title: Novel metastatic models of human esophageal adenocarcinoma highlight the importance of E-cadherin in cancer metastasis

city: Amsterdam

first: Sanne

last: Hoefnagel

state: Noord-Holland

address: Meibergdreef 9

department: Gastroenterology

institute: Academic Medical Centre Amsterdam

summary: We report the identification of FLO-1, and derivation of its isogenic companion FLO-1LM, as two spontaneously metastatic cell line models of human esophageal adenocarcinoma (EAC). We performed genome-wide RNAseq comparing FLO-1LM and FLO-1 parental cells to gain molecular insights into the phenotypic differences between these two cell lines. Using an adjusted p-value<0.05, a total of 375 (307 downregulated, 68 upregulated) genes were differentially regulated in FLO-1LM compared with parental cells. Genome-wide RNAseq profiling revealed significant enrichment of metastasis-related pathways in FLO-1LM cells, many of which are also evident in patient samples. Moreover, CDH1, which encodes the adhesion molecule E-cadherin, was the most significantly downregulated gene in FLO-1LM compared to FLO-1.

overall_design: Genome-wide RNAseq comparing FLO-1LM and FLO-1 parental cells

last: Liu

first: Oliver

middle: M

last: Fisher

first: Kausilia

last: Krishnadath

first: Karen

last: Montgomery

first: Rita

last: Busuttil

first: Andrew

last: Colebatch

first: Matthew

last: Read

first: Cuong

middle: P

last: Duong

first: Wayne

last: Philips

first: Nicholas

last: Clemons


title: ChIP-seq analyses of H3K27me3 and H3K4me3 in JMJD3c-hESCs

first: Tomohiko

last: Akiyama

summary: We generated the human ES lines, in which the genome-wide reduction of H3K27me3 can be induced by the ectopic expression of catalytic domain of histone demethylase JMJD3 with doxycycline treatment (JMJD3c-hESCs). Genome-wide changes in H3K27me3 and H3K4me3 after JMJD3c overexpression were examined by ChIP-seq analyses.

overall_design: JMJD3c-hESCs were cultured in StemFit AK-03 medium with or without doxycycline. The samples were collected at day 3 after doxycycline treatment.

first: Shunichi

last: Wakabayashi

first: Mayumi

last: Oda

first: Miki

last: Sakota


title: Whole RNA sequencing to identify targets of ETS-4 and REGE-1

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute


title: Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans

city: Princeton

first: Tess

last: Jeffers

state: NJ

address: 165 Carl Icahn Laboratory

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Nucleosomes have structural and regulatory functions in all eukaryotic DNA-templated processes. The position of nucleosomes on DNA and the stability of the underlying histone-DNA interactions affect the access of regulatory proteins to DNA. Both stability and position are regulated through DNA sequence, histone post-translational modifications, histone variants, chromatin remodelers, and transcription factors. Here, we explored the functional implications of nucleosome properties on gene expression and development in C. elegans embryos. We performed a time-course of micrococcal nuclease (MNase) digestion, and measured the relative sensitivity or resistance of nucleosomes throughout the genome. Fragile nucleosomes were defined by nucleosomal DNA fragments that were recovered preferentially in early MNase-digestion time points. Nucleosome fragility was strongly and positively correlated with the AT content of the underlying DNA sequence. There was no correlation between promoter nucleosome fragility and the levels of histone modifications or histone variants. Genes with fragile nucleosomes in their promoters tended to be lowly expressed and expressed in a context-specific way, operating in neuronal response, the immune system, and stress response. In addition to DNA-encoded nucleosome fragility, we also found fragile nucleosomes at locations where we expected to find destabilized nucleosomes, for example at transcription factor binding sites where nucleosomes compete with DNA-binding factors. Our data suggest that in C. elegans promoters, nucleosome fragility is in large part DNA-encoded, and that it poises genes for future context-specific activation in response to environmental stress and developmental cues.

overall_design: MNase digestion timecourses (MNase-seq) and (RNA-seq) expression in duplicate for control and heat-shocked C. elegans embryos


title: Whole RNA sequencing to identify targets of the RNase domain protein encoded by rege-1 (C30F12.1)

summary: The goal was to identify targets of the RNase REGE-1 by whole RNA sequencing.

overall_design: mRNA profiling of C.elegans young adults of rege-1 knockdown or mock RNAi control performed in N2 as well as glp-1 background

first: Cornelia

last: Habacher


title: Whole RNA sequencing to identify targets of ets-4 that are responsible for rege-1 (C30F12.1) phenotype

summary: Ets-4 was previously identified as a suppressor of rege-1(rrr13) phenotype. The goal of this experiment was to identify down-stream regulators of ETS-4, which facilitate this suppression.

overall_design: mRNA profiling of C.elegans young adults of ets-4 knockdown or mock RNAi control in the background of rege-1(rrr13)


title: RNA-seq analyses of JMJD3c-overexpressing human embryonic stem cells

summary: We generated the human ES line, in which the genome-wide reduction of H3K27me3 can be induced by the ectopic expression of catalytic domain of histone demethylase JMJD3 with doxycycline treatment (JMJD3c-hESCs). The forced-demethylation of H3K27me3 triggered the upregulation of many developmental genes. Overexpression of JMJD3c mutant, which lacked catalytic activity, did not induce these changes. These results suggest that H3K27me3 demethylase activity of JMJD3 is necessary and sufficient for upregulation of developmental genes in hESCs.

overall_design: RNA-seq analyses of JMJD3c-hESCs and JMJD3c mut-hESCs treated with or without doxycycline. The samples of JMJD3c-hESCs were collected at day 0, 1, 2, 3, and 4 after doxycycline treatment. The samples of JMJD3c mut-hESCs were collected at day 4 after doxycycline treatment.

first: Shun-ichi


title: Independent roles of switching and hypermutation in the development and persistence of B lymphocyte memory [IgM_IgG1]

first: Thiago

last: Oliveira

summary: Somatic hypermutation (SHM) and class switch recombination (CSR) increase the affinity and diversify the effector functions of antibodies during immune responses. Although SHM and CSR are fundamentally different, their independent roles in regulating B cell fate have been difficult to uncouple because a single enzyme, activation-induced cytidine deaminase (encoded by Aicda), initiates both reactions. Here, we used a combination of Aicda and antibody mutant alleles that separate the effects of CSR and SHM on polyclonal immune responses. We found that class-switching to IgG1 biased the fate choice made by B cells, favoring the plasma cell over memory cell fate without significantly affecting clonal expansion in the germinal center (GC). In contrast, SHM reduced the longevity of memory B cells by creating polyreactive specificities that were selected against over time. Our data define the independent contributions of SHM and CSR to the generation and persistence of memory in the antibody system.

overall_design: IgG1 and IgM light zone (LZ) and dark zone (DZ) germinal center (GC) B cells were compared in immunized AIDcre/- IgH-96K/+ R26-LSL-YFP mice.

first: Alexander

last: Gitlin

first: Lotta

last: von Boehmer

first: Anna

last: Gazumyan

first: Ziv

last: Shulman

first: Michel

last: Nussenzweig


title: Independent roles of switching and hypermutation in the development and persistence of B lymphocyte memory


title: Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression of Cdkn2a (RNA-Seq)

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

summary: Unlike clustered HOX genes, the role of non-clustered homeobox gene family members in hematopoiesis and leukemogenesis has not been extensively studied. Here we find that the Hematopoietically-expressed Homeobox gene, Hhex, is overexpressed in acute myeloid leukemia (AML) and is essential for the initiation and propagation of MLL-ENL induced AML, but dispensable for normal myelopoiesis, indicating a specific requirement for Hhex for leukemic growth. Loss of Hhex leads to upregulated expression of the tumor suppressors p16INK4a and p19ARF, which are required for growth arrest and myeloid differentiation following Hhex deletion. Mechanistically, we show that Hhex binds to the Cdkn2a locus and is required for H3K27Me3-mediated repression of this locus. Thus, Hhex is a novel therapeutic target that is specifically required for AML stem cells to repress tumor suppressor pathways and enable continued self-renewal.

overall_design: Transcriptional profiling of MLL-ENL Hhex-/fl and MLL-ENL Hhex+/fl leukemia cells using RNA sequencing

first: Benjamin

last: Shields

first: Alexandra

last: Garnham

first: Gordon

middle: K

last: Smyth

first: Matthew

last: McCormack


title: Genome-wide expression profiles  and identification of upregulated genes in larval Culex quinquefasciatus during exposure to permethrin

city: Auburn

first: Nannan

last: Liu

state: AL

address: 301 Funchess Hall

department: Entomology

institute: Auburn University

summary: The Southern house mosquito, Culex quinquefasciatus, is a vector of the causative agents of many diseases including West Nile Fever, St. Louis Encephalitis, and lymphatic filariasis. In order to manage the spread of these diseases, vector control efforts rely heavily on insecticides, including pyrethroids, namely permethrin. In our study we investigated the changes in the gene expression profiles of a highly-permethrin resistant strain of Cx. quinquefasciatus during constant exposure to permethrin at the LC-0, LC-50, and LC-70 rates, which killed 0, 50, and 70% of all larvae, respectively. Overall, we identified several genes that were up-regulated including detoxification genes such as cytochrome P450s as well as genes that were down-regulated.

overall_design: Analysis of gene expression in Cx. quinquefasciatus using RNASeq. Data were analyzed using the Tophat-Cufflinks-Cuffdiff pipeline from the Center for Bioinformatics and Computational Biology, Univ. Maryland College Park.

first: Lee

last: Zhang


title: Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression of Cdkn2a


title: H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans

status: Public on Oct 17 2016

city: Copenhagen

first: Anna Elisabetta

last: Salcini

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: The lysine 23 of histone H3 (H3K23me2) positively correlates with H3K9me3 and H3K27me3, marks enriched in heterochromatic regions (Ho, J.W. et al., 2014; Garrigues, J.M. et al., 2015; Liu, T. et al., 2015), and negatively correlates with H3K36me2/3 and H3K23/27ac, modifications enriched in actively transcribed regions. Similarly to the reported distribution of H3K9me3 (Ho, J.W. et al., 2014; Garrigues, J.M. et al., 2015), H3K23me2 is enriched on autosomal arms and is depleted from the central regions of the autosomes and from most of the lenght of the X chromosome.

overall_design: Genome-wide H3K23me2 distribution in wild type embryos.

first: Julien

last: Vandamme

first: Simone

last: Sidoli

first: Luca

last: Mariani

first: Carsten

last: Friis

first: Jesper

last: Christensen

first: Kristian

last: Helin

first: Ole

middle: N

last: Jensen


title: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant mRNA signatures

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary: Tumor-infiltrating macrophages, NK cells, CD8+ and CD4+ T cells sorted from clear cell renal cell carcinoma patient specimens.

overall_design: 4 macrophage samples (CD45+CD3-CD56-CD14+), 2 CD16+ NK cell samples (CD45+CD3-CD56+CD16+), 5 CD8+ T cell samples (CD45+CD3+CD8+), 3 CD4+ T cell samples (CD45+CD3+CD4+), and one non-immune cell sample (CD45-).

first: Yasin

last: Şenbabaoğlu

first: Ron

last: Gejman

first: Andrew

last: Winer

first: Ming

first: Emily

last: Cheng

first: David

last: Scheinberg

middle: O

last: Li

first: James

last: Hsieh

first: A

last: Hakimi


title: Acute myeloid leukemia requires Hhex to enable PRC2-mediated epigenetic repression of Cdkn2a (ChIP-Seq)

first: Wei

last: Shi

overall_design: Genome-wide profiling of histone modification and Hhex binding in leukemia cells.

first: Benjamin

last: Shields

first: Alexandra

last: Garnham

first: Gordon

last: Smyth

first: Matthew

last: McCormack


title: Transcriptomic Analysis of Instinctive and Learned Reward-Related Behaviors in Honey Bees

city: Urbana

first: Amy

last: Cash

state: IL

address: 1206 W. Gregory Dr

department: Biology

institute: University of Illinois

summary: We used transcriptomics to compare instinctive and learned, reward-based, honey bee behaviors with similar spatio-temporal components: mating flights by males (drones) and time-trained foraging flights by females (workers), respectively. Genome-wide gene expression profiling via RNA sequencing was performed on the mushroom bodies (MB), a region of the brain known for multi-modal sensory integration and responsive to various types of reward. Differentially expressed genes (DEGs) associated with the onset of mating (623 genes) were enriched for the Gene Ontology (GO) categories of Transcription, Unfolded Protein Binding, Post-embryonic Development, and Neuron Differentiation. DEGs associated with the onset of foraging (473) were enriched for Lipid Transport, Regulation of Programmed Cell Death, and Actin Cytoskeleton Organization. These results demonstrate that there are fundamental molecular differences between similar instinctive and learned behaviors. In addition, there were 166 genes with strong similarities in expression across the two behaviors -- a statistically significant overlap in gene expression, also seen in Whole Genome Coexpression Network Analysis. This finding indicates that similar instinctive and learned behaviors also share common molecular architecture. This common set of DEGs was enriched for Regulation of RNA Metabolic Process, Transcription Factor Activity, and Response to Ecdysone. These findings provide a starting point for better understanding the relationship between instincts and learned behaviors. In addition, because bees collect food for their colony rather than for themselves, these results also support the idea that altruistic behavior relies, in part, on elements of brain reward systems associated with selfish behavior.

overall_design: Mushroom body mRNA-enriched profiles from 48 individual honey bee brains, including 12 active drone bees collected in the afternoon just prior to taking flight, 12 inactive drone bees collected in the morning, 12 active worker bees collected in the afternoon as they prepared to forage, and 12 inactive worker bees collected in the morning

first: Gene

last: Robinson

first: Nick

last: Naeger

last: Cash Ahmed


title: Human liver RNA-seq and HELP-tagging data corresponding to uninfected non-malignant, HCV+ non-malignant, and HCV+ HCC tissue

city: Bronx

first: Neil

middle: Ari

last: Wijetunga

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

overall_design: Refer to individual Series


title: Human liver HELP-tagging cytosine methylation data corresponding to uninfected non-malignant, HCV+ non-malignant, and HCV+ HCC tissue

summary: We aimed to identify epigenetic regulators of transcription that may be involved in the development and the progression of HCV-associated HCC.  Using HELP-tagging, we performed the highest resolution DNA methylation profiling of HCV-associated HCC to date, testing ~2 million loci throughout the human genome in liver biopsies from 30 patients, identifying changes starting in infected liver and maintained through carcinogenesis.  We identified loci at which DNA methylation is consistently altered, beginning earlier in the course of neoplastic disease and progressing with disease advancement.

overall_design: HELP-tagging for 11 uninfected, 10 non-neoplastic infected and 9 HCV infected HCC samples

first: N

first: John

last: Greally


title: OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: MYC genes have both essential roles during normal development and exert oncogenic functions during tumorigenesis. Expression of a dominant-negative allele of MYC, termed OmoMYC, can induce rapid tumor regression in mouse models with little toxicity for normal tissues. How OmoMYC discriminates between physiological and oncogenic functions of MYC is unclear. We have solved the crystal structure of OmoMYC and show that it forms a stable homodimer and as such recognizes DNA in the same manner as the MYC/MAX heterodimer. OmoMYC attenuates both MYC-dependent activation and repression by competing with MYC/MAX for binding to chromatin, effectively lowering MYC/MAX occupancy at its cognate binding sites. OmoMYC causes the largest decreases in promoter occupancy and changes in expression on genes that are invaded by oncogenic MYC levels. A signature of OmoMYC-regulated genes defines subgroups with high MYC levels in multiple tumor entities and identifies novel targets for the eradication of MYC-driven tumors.

overall_design: Gene expression changes and DNA binding of MYC in a cancer cell line expressing OmoMYC.

first: Lisa

last: Jung

first: Anneli

last: Gebhardt

first: Wolfgang

last: Kölmel

first: Carsten

last: Ade

first: Susanne

last: Walz

first: Jochen

last: Kuper

first: Björn

last: von Eyß

first: Sebastian

last: Letschert

first: Cornelia

last: Redel

first: Luana

last: d'Artista

first: Andrew

last: Biankin

first: Lars

last: Zender

first: Markus

last: Sauer

first: Elmar

last: Wolf

first: Gerard

last: Evan

first: Caroline

last: Kisker


title: Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros

city: Parkville

first: Belinda

last: Phipson

state: VIC

address: 1G Royal Parade

department: Bioinformatics

institute: WEHI

summary: The production of definitive haematopoietic stem/progenitor cells from human pluripotent stem cells (hPSCs) remains a significant challenge. Using reporter lines to track the endothelial (SOX17) to haematopoietic (RUNX1C) transition, we found that hPSC differentiated in growth factor supplemented serum free medium generated RUNX1C+CD34+ clonogenic cells that homed to the bone marrow, but did not engraft. Compared to repopulation-competent cord blood CD34+ cells, RUNX1C+CD34+ progenitors lacked HOXA gene expression, indicating incorrect mesoderm patterning. This deficiency was ameliorated by a timed pulse of WNT activation combined with ACTIVIN antagonism. Significantly, these HOXA+ cultures now formed complex SOX17+ vessels that produced fetal liver-like haematopoietic cells, similar to the human aorta-gonad-mesonephros (AGM). Comparison of transcriptional profiles of these nascent haematopoietic stem/progenitors with cells isolated from human AGM confirmed significant similarities, consistent with the assignment of our in vitro generated cells to the definitive human haematopoietic lineage. Our findings argue that HOXA codes established early in differentiation predict cellular potential and provide correct cell patterning for the specification of definitive haematopoietic lineages from hPSCs.

overall_design: mRNA profiling of 9 samples for 9 different cell populations

last: Elefanty


title: Epigenetic targeting of immunocheckpoint PD-L1 by BET bromodomain inhibition

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

institute: The Wistar Institute

summary: Epigenetic regulators have emerged as exciting targets for cancer therapy.  Additionally, restoration of antitumor immunity by blocking the PD-L1 signaling using antibodies has proven to be beneficial in cancer therapy. Here we show that BET bromodomain inhibition suppresses PD-L1 expression and restores antitumor immunity in ovarian cancer. CD274 (encoding PD-L1) is a direct target of BRD4-mediated gene transcription.  In mouse models, treatment with the BET inhibitor JQ1 significantly reduced PD-L1 expression on tumor cells and tumor-associated dendritic cells and macrophages, which correlated with an increase in the activity of antitumor cytotoxic T cells. Together, these data demonstrate an epigenetic approach to block PD-L1 signaling to restore antitumor immunity. Given the fact that BET inhibitors have been proven safe with manageable reversible toxicity in clinical trials, our findings indicate that pharmacological BET inhibitors represent a novel treatment strategy for targeting PD-L1 expression.

overall_design: RNA-seq for JQ1 treated and shBRD4 knockdown cells with controls

first: Hengrui

last: Zhu

first: Rugang

last: Zhang


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


title: Pif1-family helicases cooperate to suppress widespread replication fork arrest at tRNA genes

first: Duncan

last: Smith

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

summary: Saccharomyces cerevisiae encodes two distinct Pif1-family helicases – Pif1 and Rrm3 – which have been reported to play distinct roles in numerous nuclear processes. Here, we systematically characterize the roles of Pif1 helicases in replisome progression and lagging- strand synthesis in S. cerevisiae. We demonstrate that either Pif1 or Rrm3 redundantly stimulate strand-displacement by DNA polymerase δ during lagging-strand synthesis. By analyzing replisome mobility in pif1 and rrm3 mutants, we show that Rrm3, with a partially redundant contribution from Pif1, suppresses widespread terminal arrest of the replisome at tRNA genes. Although both head-on and codirectional collisions induce replication fork arrest at tRNA genes, head-on collisions arrest a higher proportion of replisomes; consistent with this observation, we find that head-on collisions between tRNA transcription and replisome progression are under-represented in the S. cerevisiae genome. Further, we demonstrate that tRNA-mediated arrest is R-loop independent, and propose that replisome arrest and DNA damage are mechanistically separable.

overall_design: We enriched Okazaki fragments by depletion of DNA ligase I, and sequenced the resulting enriched single-stranded/nicked DNA

first: Joseph

middle: S

last: Osmundson

first: Jayashree

last: Kumar

first: Rani

last: Yeung


title: Deep Sequencing analysis of the total RNA state and the polyadenylation state of mRNAs in Scrambled or CNOT7 knockdown neurons

status: Public on Oct 15 2016

city: Worcester

first: Rhonda

middle: Leah

last: McFleder

state: MA

address: 373 Plantation st, Biotech II, S204

department: Molecular Medicine

institute: University of Massachussets Medical School

summary: Differential thermal elution over poly(U) agarose was used to identify mRNAs that underwent a change in their poly(A) tail following CNOT7 knockdown in cultured hippocampal neurons. Total RNA levels were also measured from both sets to identify changes in stability or expressions of mRNAs in the different cell types

overall_design: mRNA and poly(A) state profiles of 17-19 day old hippocampal neurons were generated by deep sequencing in duplicate.

first: Joel

middle: D

last: Richter


title: Expression profiles of innate and Th2 lymphocytes

city: San Francisco

first: Jesse

last: Nussbaum

state: California

address: 513 Parnassus Ave., Campus Box 0795

department: Medicine

institute: University of California San Francisco

summary: We compare the transcription profiles of IL-5-reporter marked ILC2s and Th2 cells sorted from mouse lung tissue after Nippostrongylus brasiliensis infection

overall_design: mRNA sequencing comparing material from 2 cell populations sorted from the lungs of 7 Red5/Red5 mice, comprising 2 independent infections, 14 days after N.b. infection

first: Steven

last: Van Dyken

first: Rich

last: Locksley