title: Structural basis for spumavirus GAG tethering to chromatin

city: London

first: Peter

middle: P

last: Cherepanov

address: 1 Midland Road

institute: The Francis Crick Institute

summary: The interactions between a retrovirus and host cell chromatin that underlie integration and provirus expression are poorly understood. The prototype foamy virus (PFV) structural protein GAG associates with chromosomes via a chromatin-binding sequence (CBS) located within its C-terminal region. Here, we show that the PFV CBS is essential and sufficient for a direct interaction with nucleosomes, and present a crystal structure of the CBS bound to a mono-nucleosome. The CBS interacts with the histone octamer, engaging the H2A-H2B acidic patch, in a manner similar to other acidic patch binding proteins such as herpesvirus latency-associated nuclear antigen (LANA). Substitutions of the invariant arginine anchor residue in GAG result in global re-distribution of PFV and macaque simian foamy virus (SFVmac) integration sites towards centromeres, dampening the resulting proviral expression without affecting the overall efficiency of integration. Our findings underscore the importance of retroviral structural proteins for integration site selection and the avoidance of genomic junkyards.

overall_design: Integration sites obtained by infection of cells with single-cycle prototype foamy virus (PFV) or macaque simian foamy virus (SFV) or by incubation of deproteinised human DNA with recombinant PFV intasome were amplified by linker-mediated PCR and sequenced using Illumina technology.

first: Erik

last: Serrao

first: Paul

last: Lesbats

first: Daniel

last: Maskell

first: Dirk

last: Lindemann

first: Alan

middle: N

last: Engelman


title: DNA methylation analysis of fibroblasts isolated from 5- and 16-month Holstein cows

status: Public on May 11 2017

city: Worcester

first: Filiz

last: Korkmaz

state: MA

address: 364 Plantation St.

country: USA

institute: UMass Chan Medical School

type: Methylation profiling by high throughput sequencing

summary: Background: Differences in DNA methylation are known to contribute to the development of immune-related disorders in humans but relatively little is known about how methylation regulates immune function in cattle. Utilizing whole-transcriptome analyses of bovine dermal fibroblasts, we have previously identified an age and breed-dependent up-regulation of genes within the toll-like receptor 4 (TLR4) pathway that correlates with enhanced fibroblast production of IL-8 in response to lipopolysaccharide (LPS). Age-dependent differences in IL-8 production are abolished by treatment with 5-aza-2-deoxycytidine and Trichostatin A (AZA-TSA), suggesting epigenetic regulation of the innate response to LPS. In the current study, we performed reduced representation bisulfite sequencing (RRBS) on fibroblast cultures isolated from the same animals at 5- and 16-months of age to identify genes that exhibit variable methylation with age. To validate the role of methylation in gene expression, six innate response genes that were hyper-methylated in young animals were assessed by RT-qPCR in fibroblasts from animals at different ages and from different breeds.   Results: We identified 14,094 differentially methylated CpGs (DMCs) that differed between fibroblast cultures at 5- versus 16-months of age. Of the 5065 DMCs that fell within gene regions, 1117 were located within promoters, 1057 were within gene exons and 2891 were within gene introns and 67% were more methylated in young cultures. Transcription factor enrichment of the 752 promoters hyper-methylated in young cultures revealed significant regulation by the key pro-inflammatory regulator, NF-κB. Additionally, five out of six chosen genes (PIK3R1, FES, NFATC1, TNFSF13 and RORA) that were more methylated in young cultures showed a significant reduction in expression post-LPS treatment in comparison with older cultures. Two of these genes, FES and NFATC1, were similarly down-regulated in Angus cultures that also exhibit a low LPS response phenotype.  Conclusions: Our study has identified immune-related loci regulated by DNA methylation in cattle that may contribute to differential cellular response to LPS, two of which exhibit an identical expression profile in both low-responding age and breed phenotypes. Methylation biomarkers of differential immunity may prove useful in developing selection strategies for replacement cows that are less susceptible to severe infections, such as coliform mastitis.

overall_design: DNA methylation assessment of cultured fibroblasts isolated from cows at 5- and 16-months of age. Six cultures per age group. Paired samples - taken from the same animal at 2 different ages.

middle: T

first: David

middle: E

last: Kerr


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Msx1-/- tooth mesenchyme Transcriptomes

city: Salt Lake City

first: Shihai

last: Jia

state: ut

address: 20 South 2030 East, Room 320 BPRB

department: Department of Neurobiology

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: Mutations in MSX1 cause craniofacial developmental defects, including tooth agenesis, in humans and mice. Previous studies suggest that Msx1 activates Bmp4 expression in the developing tooth mesenchyme to drive early tooth organogenesis. Whereas Msx1−/− mice exhibit developmental arrest of all tooth germs at the bud stage, however, mice with neural crest-specific inactivation of Bmp4 (Bmp4ncko/ncko), which lack Bmp4 expression in the developing tooth mesenchyme, showed developmental arrest of only mandibular molars. We recently demonstrated that deletion of Osr2, which encodes a zinc finger transcription factor expressed in a lingual-to-buccal gradient in the developing tooth bud mesenchyme, rescued molar tooth morphogenesis in both Msx1−/− and Bmp4ncko/ncko mice. In this study, through RNA-seq analyses of the developing tooth mesenchyme in mutant and wildtype embryos, we found that Msx1 and Osr2 have opposite effects on expression of several secreted Wnt antagonists in the tooth bud mesenchyme. Remarkably, both Dkk2 and Sfrp2 exhibit Osr2-dependent preferential expression on the lingual side of the tooth bud mesenchyme and expression of both genes was up-regulated and expanded into the tooth bud mesenchyme in Msx1−/− and Bmp4ncko/ncko mutant embryos. We show that pharmacological activation of canonical Wnt signaling by either lithium chloride (LiCl) treatment or by inhibition of Dkk in utero was sufficient to rescue mandibular molar tooth morphogenesis in Bmp4ncko/ncko mice. Furthermore, whereas inhibition of Dkk alone was insufficient to rescue tooth morphogenesis in Msx1−/− mice, pharmacological inhibition of Dkk in combination with genetic inactivation of Sfrp2 and Sfrp3 rescued maxillary molar morphogenesis in Msx1−/− mice. Together, these data reveal a novel mechanism that the Bmp4-Msx1 pathway drives tooth organogenesis by activating Wnt signaling via regulation of the secreted Wnt antagonists.

overall_design: E14 mouse embryos tooth germs were micro-dissceted by LCM, mandibular molar and maxillary molar were seperated, 3 pairs of control and mutant samples were pooled for the RNA extraction

first: Rulang

last: Jiang

first: Hyuk-Jae

last: Kwon


title: Ehmt2/G9a controls placental vascular maturation by activating the Notch Pathway

status: Public on May 10 2017

city: Toronto

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: G9a mediates a transcriptional switch, and activates the Notch pathway to coordinate endothelial cell and trophoblast proliferation to promote vascular maturation in the placenta.

overall_design: Examination of global transcriptional profiles in control and mutant placenta labyrinth at 2 developmental stages (E12.5 and 13.5).

first: Lijun

last: Chi

first: Abdalla

last: Ahmed

first: Anna

middle: R

last: Roy

first: Sandra

last: Vuong

first: Lindsay

middle: S

last: Cahill

first: Laura

last: Caporiccio

first: John

middle: G

last: Sled

first: Isabella

last: Caniggia

first: Michael

middle: D

last: Wilson


title: A quantitative and multiplexed approach to uncover the fitness landscape of tumor suppression in vivo

city: Menlo Park

first: Christopher

middle: Dennis

last: McFarland

state: CA

address: 2647 Alpine RD

department: Cancer Systems Biology

institute: Stanford University

summary: New method to measure tumor growth with programmable multiplexed CRISPR/Cas9-induced genotypes via ultra-deep sequencing of DNA barcoded tumors

overall_design: Ultra-deep sequencing of DNA barcode amplicon

first: Zoë

last: Rogers

first: Ian

last: Winters

first: Santiago

last: Naranjo

first: Chen-Hua

last: Chuang

first: Dmitri

last: Petrov

first: Monte

middle: M

last: Winslow


title: Total RNAseq of human putamen and caudate nucleus tissues in healthy control and Bipolar Disorder individuals

city: Jupiter

first: Courtney

last: MacMullen

state: FL

address: 130 Scripps Way

department: Neuroscience

institute: The Scripps Research Institute

summary: A multitude of genes have been associated with bipolar disorder via SNP genotyping studies.  However, many of these associated SNPs are found within intronic or intergenic regions of the human genome.  We were interested in studying transcriptional profiles/splice variation of genes associated with bipolar disorder within the human striatum. Understanding how these associated genes are transcribed in the human brain may help to guide the development of therapeutic agents for the treatment of bipolar disorder and other neuropsychiatric illnesses.

overall_design: NEBNext Ultra Directional RNAseq libraries were generated from putamen and caudate nucleus tissues from 4 healthy control individuals and 4 individuals with bipolar disorder.  These libraries were then multiplexed and run on an Illumina HiSeq platform using single read 100bp chemistries.

first: Ronald

middle: L

last: Davis

first: Mohammad

last: Fallahi


title: POLR3G Dependent PolyA+ and smallRNA Transcriptomes in Human Pluripotent Stem Cells

city: Turku

first: Riikka

last: Lund

address: Tykistökatu 6

country: Finland

institute: Turku Centre for Biotechnology, University of Turku

type: Non-coding RNA profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: POLR3G is expressed at high levels in human pluripotent stem cells (hPSCs) and is required for maintenance of stem cell state through mechanisms, which are not known in detail. In order to explore how POLR3G regulates stem cell state, we have carried out deep sequencing analysis of polyA+ and smallRNA transcriptomes present in hPSCs and regulated in POLR3G dependent manner. Our data reveals that POLR3G regulates a specific subset of the hPSC transcriptome, including multiple transcripts types, such as protein coding genes, lincRNAs, miRNAs and snoRNAs. The primary function of POLR3G is in the maintenance rather than repression of transcription. The majority of POLR3G polyA+ transcriptome is regulated during differentiation and the key pluripotency factors bind to the promoters of at least 30 % of the POLR3G regulated transcripts. The POLR3G transcriptome is functionally linked to embryonic development and important tasks in cellular maintenance and function. #!/bin/bash

overall_design: Transcriptome profiles of wild type and POLR3G siRNA knockdown hESC samples, in replicate and Chip-seq with antibodies for H3K4me3, POLR3G, and Input, in replicate.

middle: J

first: Nelly

last: Rahkonen

first: Maia

last: Malonzo

first: Leni

last: Kauko

first: Maheswara

last: Emani

first: Virpi

last: Kivinen

first: Elisa

last: Närvä

first: Asta

last: Laiho

first: Heli

last: Skottman

first: Outi

middle: H

last: Rasool

first: Matti

last: Nykter

first: Harri

last: Lähdesmäki

first: Riitta

last: Lahesmaa


title: HAND2 Target Gene Regulatory Networks Control Cardiac Valve Development

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

summary: The HAND2 transcriptional regulator controls cardiac development and we uncover addition essential functions in the endothelial to mesenchymal transition (EMT) underlying cardiac cushion development in the atrioventricular canal (AVC). In Hand2-deficient mouse embryos, the EMT underlying AVC cardiac cushion formation is disrupted and we combined ChIP-Seq of embryonic hearts with transcriptome analysis of wild-type and mutants AVCs to identify the functionally relevant HAND2 target genes. The HAND2 target gene regulatory network (GRN) includes most genes with known functions in EMT processes and AVC cardiac cushion formation. One of these is Snai1, an EMT master regulator whose expression is lost from Hand2-deficient AVCs. Re-expression of Snai1 in mutant AVC explants partially restores this EMT and mesenchymal cell migration. Furthermore, the HAND2-interacting enhancers in the Snai1 genomic landscape are active in embryonic hearts and other Snai1-expressing tissues. These results show that HAND2 directly regulates the molecular cascades initiating AVC cardiac valve development.

overall_design: Atrioventricular canals (AVCs) were dissected from wild-type and Hand2 d/d (null-mutant) mouse embryos between E9.0-E9.25 (18-23 somites) and total RNA was analyzed.

first: F

last: Laurent

first: A

last: Girdziusaite

first: J

last: Gamart

first: I

first: M

last: Osterwalder

last: Lopez-Rios

last: Lincoln

first: JA

last: Akiyama

last: Visel

last: Zuniga

first: R

last: Zeller


title: RNA Sequencing of Pinometostat Sensitive and Resistant Paired Cell Lines

city: Cambridge

first: Carly

last: Campbell

state: Massachusetts

address: 400 Technology Sq, 4th Fl

institute: Epizyme

summary: MLL-r cell lines KOPN-8 and NOMO-1 were cultured with pinometostat to derive treatment emergent resistant pools. RNA sequencing was performed on the resistant pools to generate hypotheses around mechanisms of resistance

overall_design: RNA-sequencing of KOPN-8 and NOMO-1 cell lines treated long term (ie resistant) and short term (sensitive) with pinometostat, along with DMSO matched controls

first: Scott

last: Daigle


title: Macrophage function in tissue repair and remodeling requires IL-4/IL-13 with apoptotic cells

city: New Haven

first: Lidia

last: Bosurgi

state: Connecticut

address: 300 Cedar street

department: Immunobiology

institute: Yale University

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

overall_design: Refer to individual Series


title: Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation reveals in moso bamboo (Phyllostachys edulis)

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

country: China

institute: Fujian Agriculture and Forestry University

summary: Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to their well-developed rhizomes system. However, the post-transcriptional regulation mechanism has not been comprehensively studied for the development of rhizome system in bamboo. We therefore used single-molecule long-read sequencing technology to re-annotate the bamboo genome, and genome-wide identify alternative splicing (AS) and alternative polyadenylation (APA) in the rhizomes system. In total, 145,522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2,241 mis-annotated genes and identification of 8,091 previously unannotated loci. Markedly, more than 42,280 contiguous exon connectivity were derived from full-length splicing isoforms, including a large number of AS events that associated with rhizome systems. In addition, we characterized 25,069 polyadenylation sites from 11,450 genes, 6,311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements (TEs) within the intronic polyadenylation region. Furthermore, this study provided a quantitative altas of poly(A) usage and identified several hundreds of differential poly(A) sites in rhizome-root system using a combination of polyadenylation site sequencing (PAS-seq) and PacBio reads. Taken together, these results suggest that posttranscriptional regulation may potentially play vital role in the underground rhizome-root system.

overall_design: Single-molecule long-read sequencing, PAS-seq and RNA-seq of leptomorph rhizome tip, new shoot tip and bud

first: Huiyuan

last: Wang

first: Yubang

last: Gao

first: Hangxiao

last: Zhang

first: Liuyin

last: Ma


title: Transcriptomic data for splenic neutrophils isolated from female NZBWF1/J lupus mice

city: Rochester

first: Anna

middle: Kathleen

last: Bird

state: New York

address: 601 Elmwood Ave, Box 695

institute: University of Rochester

summary: Recent literature has shown that neutrophils exert significant influence on the course of disease progression in lupus, but there is currently controversy in the lupus field regarding a) whether neutrophils are predominantly protective or deleterious toward the propagation of auto-reactivity, b) the specific mechanism of neutrophil influence on adaptive immune dysregulation, and c) identity and origin of functionally abnormal neutrophil subsets in lupus. Here we used RNA sequencing of splenic neutrophils isolated from a murine lupus model (NZB/W) to characterize changes in the transcriptional program of neutrophils over the course of lupus progression. We find that the transcription of immunologically relevant genes change over the course of disease, and that lupus neutrophils early in disease show enrichment for transcripts associated with neutrophil precursors. These data provide the first detailed profile of the splenic neutrophil transcriptional program changes during the progression of lupus.

overall_design: UltraLoInput RNA sequencing of neutrophils isolated from the spleens of female NZBWF1/J lupus mice at three stages of disease (Ages: 14 weeks, 20 weeks, 26 weeks).

middle: K

first: Jennifer

last: Anolik


title: Environment-dependent regulation of spliceosome activity by the LSM2-8 complex in Arabidopsis

city: Madrid

first: Julio

last: Salinas

address: Ramiro de Maeztu, 9

department: Departamento de Biologia Medioambiental

country: Spain

institute: Centro de Investigaciones Biologicas

summary: We report the role of LSM2-8 complex in the Arabidopsis tolerance to abiotic stresses. LSM2-8 controls gene expression reprogramming at the post-transcriptional level by promoting the splicing of pre-mRNA. This function is selectively achieved over selected transcripts depending on stress nature.

overall_design: Transcriptomic profiling through RNA-seq of Col-0 and lsm8-1 plants exposed to low temperatures (4ºC, 24h) or high salt conditions (150 mM NaCl, 10h).

first: Cristian

last: Carrasco-López

first: Tamara

last: Hernández-Verdeja

first: Carlos

last: Perea-Resa

first: David

last: Abia

first: Rafael

last: Catalá


title: H3K36me3 ChIP-seq

city: Wageningen

first: Alice

last: Pajoro

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

summary: Plants developed a plasticity to eviromental conditions, such as temperaure, that allows their adaptation. A change in ambient temperature leads to changes in the transcriptome in plants, such as the production of different splicing isoforms. Here we study temperature induced alternative splicing events in Arabidopsis thaliana wild-type and two epigentic mutants, sdg8-2 and sdg26-1 using an RNA-seq approach.

overall_design: We performed 4 biological replicates of H3K36me3 ChIP-seq for each condition (16°C and 25°C day 1).  Anti-He ChIP-seq was used as a control.

first: Richard

last: Immink


title: Target enrichment followed by high throughput sequencing of telomeric DDRNAs in telomere-deprotected mouse cells

city: Milan

first: Fabrizio

last: d'Adda di Fagagna

state: Mi

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

summary: Telomeres are the nucleoprotein complexes located at the tips of eukaryotic chromosomes, composed of repetitive DNA (TTAGGG in vertebrates), and coated by a set of proteins collectively known as the shelterin complex. Dysfunctional telomeres resemble DSBs and they have been observed during ageing and cancer and a number of pathological conditions. Apart from telomeric repeat-containing RNA (TERRA), a non-coding UUAGGG-rich transcript starting from promoters located in the subtelomeric region, in mammals no other transcripts at telomeres have been characterized so far.  Here we show that in mammals telomere dysfunction (analysed using TRF2+/- and TRF2-/- mouse embryonic fibroblasts) induces the transcription of telomeric DDRNAs (tDDRNAs) from both DNA strands. To characterize the length and sequence of tDDRNAs, we devised and employed an innovative method for target enrichment of RNA, based on in solution capture of low abundance small RNA species followed by next generation sequencing, developed in our laboratories. By this approach, we observed that telomere deprotection induced the accumulation of small RNA species generated from the transcription of both telomere strands and including the expected DDRNA size range products. Importantly, 20-23 nucleotide RNAs displayed a base bias at both 5’ and 3’ ends significantly different from the telomeric locus suggesting a regulated processing.

overall_design: RNA extracted from mouse embryonic fibroblasts, induced or uninduced for TRF2 knock out, were used for target enrichment and MiSeq sequencing. The experiment was carried out in 3 replicates

first: Fabio

last: Iannelli

first: Quan

last: Nguyen

last: Aguado

first: Francesca

last: Rossiello

first: Piero

last: Carninci


title: H3K36me3 histone modification and regulation of ambient temperature-induced alternative splicing in Arabidopsis


title: Temperature induced alternative splicing is affected in sdg8 and sdg26.

summary: Plants developed a plasticity to environmental conditions, such as temperature, that allows their adaptation. A change in ambient temperature leads to changes in the transcriptome in plants, such as the production of different splicing isoforms. Here we study temperature induced alternative splicing events in Arabidopsis thaliana wild-type and two epigenetic mutants, sdg8-2 and sdg26-1 using an RNA-seq approach.

overall_design: We generate 3 biological replicates for each genotype (wild-type, sdg8-2 and sdg26-1) at each condition (16°C and 25°C day 1), for a total of 18 samples.

first: Severing

last: Edouard


title: Integrative analysis of DNA methylation, mRNAs, and small RNAs during maize embryo dedifferentiation

city: Wenjiang,Chengdu

first: hongjun

last: liu

state: Sichuan

address: 211 Huimin Road

institute: Sichuan Agricultural University

summary:
Background: Maize (Zea Mays) is an important model crop for transgenic studies. However, genetic transformation of maize requires embryonic calli derived from immature embryo, and the impact of utilizing tissue culture methods on the maize epigenome is poorly understood. Here, we generated whole-genome MeDIP-seq data examining DNA methylation in dedifferentiated and normal immature maize embryos.
Results: We observed that most of the dedifferentiated embryos exhibited a methylation increase compared to normal embryos. Increased methylation at promoters was associated with down-regulated protein-coding gene expression; however, the correlation was not strong. Analysis of the callus and immature embryos indicated that the methylation increase was induced during induction of embryonic callus, suggesting phenotypic consequences may be caused by perturbations in genomic DNA methylation levels. The correlation between the 21-24nt small RNAs and DNA methylation regions were investigated but only a statistically significant correlation for 24nt small RNAs was observed.
Conclusions: These data extend the significance of epigenetic changes during maize embryo callus formation, and the methylation changes might explain some of the observed embryonic callus variation in callus formation.

first: Hongjun

last: Liu

first: Langlang

last: Ma

first: Xuerong

last: Yang

first: Lin

last: Zhang

first: Xing

last: Zeng

first: Shupeng

last: Xie

first: Huanwei

last: Peng

first: Shibin

last: Gao

first: Haijian

last: Lin

first: Guangtang

last: Pan

first: Yongrui

last: Wu

first: Yaou

last: Shen


title: Histone variant H2A.L.2 guides transition protein - dependent protamine assembly in male germ cells

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

summary: Histone replacement by small basic proteins, transition proteins (TPs) and protamines (Prms) constitutes an essential step for the successful production of male gametes, yet nothing is known on the underlying functional interplay between histones, TPs and Prms. By studying spermatogenesis in the absence of H2A.L.2, a spermatid-specific histone variant, we identify a new step essential for the "metamorphosis" of nucleosomes to nucleoprotamines. H2A.L.2 plays the role of a "Trojan horse" histone, which induces dramatic structural changes that enables the invasion of nucleosomes by TPs, themselves driving the processing and incorporation of Prms. H2A.L.2 incorporation initiates a series of rapidly changing transitional states that ultimately shift to a more stable state characterized by nucleoprotamine assembly and histone-TP Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporationdisplacement, leading to the generation of mature spermatozoa. The textbook view of histone-to-nucleoprotein transition needs to be revisited to include a new step with H2A.L.2 assembly prior to the action of TPs and Prms.

overall_design: MNase-seq analysis on WT and H2A.L.2-less mouse during three stages of spermiogenesis: Spermatocyte, Round Spermatid and Condensing Spermatid). MNase produces two distinct fragment size populations for condensing spermatid samples: nucleosome-like fragments (approximately 130 to 170 bp) and smaller structure fragments (approximately 40 to 80 bp). These populations are separated by electrophoresis prior to sequencing. The eight samples have been sequenced in three runs on Illumina NextSeq500 to achieve higher coverage. Runs for each sample are merged before downstream analysis and after quality control and alignment. Total read counts from all sequencing runs ranged from 207 to 753 million reads per sample.

last: Barral

first: Yuichi

last: Morozumi

first: Hiroki

last: Tanaka

first: Emilie

last: Montellier

first: Jérôme

last: Govin

first: Maud

last: de Dieuleveult

first: Guillaume

last: Charbonnier

first: Yohann

last: Couté

first: Denis

last: Puthier

first: Thierry

last: Buchou

first: Fayçal

last: Boussouar

first: Takashi

last: Urahama

first: François

last: Fenaille

first: Sandrine

last: Curtet

first: Patrick

last: Héry

first: Nicolas

last: Fernandez-Nunez

first: Hitoshi

last: Shiota

first: Matthieu

last: Gérard

last: Kurumizaka

first: Saadi

last: Khochbin


title: Transcriptional profiling reveals monocyte signature associated with JIA patient poor response to methotrexate

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: The mechanisms that determine the efficacy or inefficacy of methotrexate in juvenile idiopathic arthritis (JIA) are ill-defined.  The objective of this study was to identify a gene expression transcriptional signature associated with poor response to MTX in patients with JIA. RNA sequencing was used to measure gene expression in peripheral blood mononuclear cells (PBMC) collected from 47 patients with JIA prior to MTX treatment and 14 age-matched controls. Biological differences between all JIA patients and controls were explored by constructing a signature of differentially expressed genes. Unsupervised clustering and pathway analysis was performed. Transcriptional profiles were compared to a reference gene expression database representing sorted cell populations, including B and T lymphocytes, and monocytes. A signature of 99 differentially expressed genes (Bonferroni-corrected p<0.05) capturing the biological differences between all JIA patients and controls was identified. Unsupervised clustering of samples based on this list of 99 genes produced subgroups enriched for MTX response status. Comparing this gene signature to reference signatures from sorted cell populations revealed high concordance between the expression profiles of monocytes and of MTX non-responders. CXCL8 (IL-8) was the most significantly differentially expressed gene transcript comparing all JIA patients to controls (Bonferroni-corrected p=4.12E-10). Variability in clinical response to methotrexate in JIA patients is associated with differences in gene transcripts modulated in monocytes.  These gene expression profiles may provide a basis for biomarkers predictive of treatment response.

overall_design: Peripheral blood mononuclear cells (PBMC) collected from 47 patients with JIA prior to MTX treatment and 14 age-matched controls

first: Halima

last: Moncrieffe

first: Mark

middle: F

last: Bennett

first: Monica

last: Tsoras

first: Lorie

last: Luyrink

first: Anne

last: Johnson

first: Huan

last: Xu

first: Jason

last: Dare

first: Mara

last: Becker

first: Sampath

last: Prahalad

first: Margalit

last: Rosenkranz

first: Kathleen

last: O’Neil

first: Peter

middle: A

last: Nigrovic

first: Thomas

last: Griffin

first: Daniel

last: Lovell

first: Alexei

last: Grom

first: Susan

last: Thompson


title: Genes that mediate leptomeningeal metastasis from breast and lung solid tumor primaries

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake University

summary: Little is understood about the gene expression changes that underlie cancer spread to the cerebrospinal fluid, or leptomeningeal metastasis. Using four cancer cell line models, we empolyed iterative in vivo selection to generate subpopulations of these cell lines able to access the leptomeningeal space and grow once there. We compared the gene expression profile of the terminally selected cells or "Lep" cells with that of the parental or "Par" cells, as well as that of an intermediate stage of in vivo selection or "Int" cells. Analyses for brain parenchymal metastatic derivatives or "BrM" cells were included for comparison.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Four different models were employed: Two human breast cancer cell lines, MDA-MB-231 and HCC1954 as well as one human lung cancer cell line, PC9 and a mouse non-small cell lung cancer cell line, Lewis lung carcinoma. Three technical replicates of each Par cell line, two or three biological replicates and two technical replicates of each of the Int and Lep cells were all subjected to analysis.

first: Adrienne

last: Boire

first: Joan

last: Massague


title: Flower development and sex determination in Vernicia fordii

status: Public on May 09 2017

city: Hefei

first: Lifang

last: Wu

state: Anhui

address: 350 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China

institute: Hefei Institutes of Physical Science, Chinese Academy of Sciences

summary: To further elucidate the molecular mechanism underling sex determination at the divergence stage of male and female flowers, the comparative transcriptome analysis was performed. In total, 56,065 unigenes were generated 24,567 transcripts were identified. Among 608 differential expression genes (DEGs), 310 DEGs showed significant expression in males and 298 DEGs in females. The data showed that the sexual dimorphism of female flowers was affected by jasmonic acid, transcription factors and some genes related with activity of floral meristem, which were considered as the candidate sex determination genes. In this study, interesting information will be provided in  understanding the development of unisexual flower and the regulatory networks hidden the sex determination in V. fordii, which is useful for the practice of improving its yield.

overall_design: In order to investigate the molecular mechanisms responsible for establishment of unisexual flower in V. fordii, the divergence of male and female developmental stage 7 were sequenced with three biological replicates, respectively.

first: Yingji

last: Mao


title: RNA-seq Analysis of Wild Type and Ptpn11-deficient cerebellar Transcriptomes

city: Farmington

first: James

middle: YH

last: Li

state: CT

address: 263 Farmington Ave

department: Genetics and Genome Sciences

institute: UCHC

summary:
We have recently discovered that deletion of Ptpn11, which codes for protein tyrosine phosphatase Shp2, blocks Bergmann glia (BG) formation and cerebellar foliation, whereas expressing a constitutively active Mek1 (Map2k1), Mek1DD, reverses the Ptpn11-deficient phenotypes, uncovering a previously unappreciated role of BG in folding of the cerebellar cortex. Relatively little is known regarding to the BG induction. The goal of the study was to determine molecular features of newly generated BG.
To identify transcripts enriched in nascent BG, we performed RNA-seq of microdissected cerebellar tissues from wild type (WT), En1cre/+;Ptpn11F/F (Ptpn11-cKO), and En1cre/+;Ptpn11F/F;R26Mek1DD/+ (Ptpn11-cKO;MEK) embryos at E12.5, E13.5, and E14.5.
As BG are initially formed at E13.5, we reasoned that BG-enriched transcripts should be increased from E12.5 to E14.5, decreased in Ptpn11-cKO cerebella, and restored in Ptpn11-cKO;MEK cerebella. By intersecting differentially expressed (DE) genes based on the above-mentioned assumptions, we wanted to identify genes that are specifically expressed in BG and affected by Ptpn11 deletion.
Conclusions: though RNA-seq and subsequent validation, we have successfully identified genes that enriched in nascent BG in the developing mouse cerebellum.

overall_design: The transcriptome of the cerebellum of mid-gestation stage mouse embryos were generated by deep sequencing.


title: Tailing and degradation of Argonaute-bound small RNAs protect the genome from uncontrolled RNAi

city: Munich

first: Mario

last: Halic

department: Biochemistry - Gene Center

country: Germany

institute: Ludwig-Maximilians-Universität

summary: RNAi is a conserved mechanism in which small RNAs induce silencing of complementary targets. How Argonaute-bound small RNAs are targeted for degradation is not well understood. We show here that the adenyl-transferase Cid14, a member of the TRAMP complex, and the uridyl-transferase Cid16 add non-templated nucleotides to Argonaute-bound small RNAs in fission yeast. The tailing of Argonaute-bound small RNAs in vitro recruits the 3’-5’ exonuclease Rrp6 to degrade small RNAs. Failure in degradation of Argonaute-bound small RNAs results in accumulation of “noise” small RNAs on Argonaute and targeting of diverse euchromatic genes by RNAi. To protect themselves from uncontrolled RNAi, cid14Δ cells exploit the RNAi machinery and silence genes essential for RNAi itself, which is required for their viability. Our data indicate that surveillance of Argonaute-bound small RNAs by Cid14/Cid16 and the exosome protects the genome from uncontrolled RNAi and reveal a rapid RNAi-based adaptation to stress conditions.

overall_design: RNA, siRNA and ChIP sequencing in wild type cells and different mutants of S. pombe

first: P

last: Pisacane

first: M


title: Controlling a Necessary Evil: Quorum Sensing Attenuates Virulence in Sodalis praecaptivus.

city: Salt Lake City

first: Shin

last: Enomoto

state: Utah

address: 201 South Biology, 257 S 1400 E

department: Biology

institute: University of Utah

summary: Sodalis praecaptivus is a close relative and putative environmental progenitor of the widely distributed, insect-associated, Sodalis-allied symbionts. Mutant strains of S. praecaptivus, lacking critical components of a quorum sensing (QS) apparatus acquire a rapid and potent killing phenotype following microinjection into an insect host. Transcriptomic and genetic analyses indicate that insect killing occurs as a consequence of virulence factors, including insecticidal toxins and enzymes that degrade the insect integument that are normally repressed by QS at high infection densities. This unorthodox method of regulation ensures that virulence factors are only utilized to initiate the insect-bacterial association. Once bacteria reach a sufficient infection density in host tissues, the QS circuit represses the expression of these harmful genes, facilitating a long-lasting and benign association. We discuss the implications of the functionality of this QS system in the context of the establishment and evolution of mutualistic relationships involving these bacteria.

overall_design: mRNA profiles of exponential growing bacterial culutres in rich media for wild type (WT), ∆ypeI, ∆ypeR, ∆yenR were generated by deep sequencing, in triplicate, using Illumina TruSeq method on a HiSeq instrument.

first: Shinichiro

first: Abhishek

last: Chari

first: Adam

last: Clayton

first: Colin

last: Dale


title: Integrative analysis unveils new functions for the Drosophila Cutoff protein in non-coding RNA biogenesis and gene regulation

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: Piwi-Interacting RNAs (piRNAs) are central components of the piRNA pathway, which directs transposon silencing and guarantees genome integrity in the germ cells of several metazoans. In Drosophila, piRNAs are produced from discrete regions of the genome termed piRNA clusters, whose expression relies on the RDC complex comprised of the core proteins Rhino, Deadlock and Cutoff. To date, the RDC complex has been exclusively implicated in the regulation of the piRNA loci. Here we further elucidate the function of Cutoff and the RDC complex by performing genome-wide ChIP-seq and RNA-seq assays in the Drosophila germline and analyzing these data together with other publicly available data sets. In agreement with previous studies, we confirm that Cutoff is involved in the transcriptional regulation of piRNA clusters and in the repression of transposable elements in germ cells. Surprisingly, however, we find that Cutoff is enriched at and affects the expression of other non-coding RNAs, including spliceosomal RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). At least in some instances, Cutoff appears to act at a transcriptional level in concert with Rhino and perhaps Deadlock. Finally, we show that mutations in Cutoff result in the deregulation of hundreds of protein-coding genes in germ cells. Our study uncovers a broader function for the RDC complex in the Drosophila germline development.

overall_design: Cutoff ChIP-seq (2 replicates with ChIP, 3 replicates with control), Pol2 ChIP-seq (3 replicates in WT, 3 replicates in cuff mutant), RNA-seq (3 replicates in WT, 3 replicates in cuff mutant)

first: Tarcisio

last: Brito

first: Trudi

last: Schupbach

first: Mona

last: Singh

first: Attilio

last: Pane


title: Human RELA haploinsufficiency results in autosomal dominant chronic mucocutaneous ulceration: the transcriptional profile of RelA haploinsufficient patients

city: Boston

first: Janet

last: Chou

address: 1 Blackfan Circle, Karp 10007D

department: Immunology

institute: Boston Children's Hospital

summary: The treatment of chronic mucocutaneous ulceration is challenging and only some patients respond selectively to inhibitors of tumor necrosis factor-alpha (TNF-a). TNF-a activates opposing pathways leading to caspase-8-mediated apoptosis as well as NF-kB-dependent cell survival. We investigated the etiology of autosomal dominant mucocutaneous ulceration in a family whose proband was dependent on anti-TNF-a therapy for sustained remission. A heterozygous mutation in RELA (NM_021975: c.559+1G>A), encoding the NF-kB subunit RelA (p65), segregated with the disease phenotype and resulted in RelA haploinsufficiency. The patients’ fibroblasts exhibited increased apoptosis in response to TNF-a, impaired NF-kB activation, and defective expression of NF-B-dependent anti-apoptotic genes. We show that Rela+/- mice have similarly impaired NF-kB activation, develop cutaneous ulceration from TNF-a exposure, and exhibit severe dextran sodium sulfate-induced colitis ameliorated by TNF-a inhibition. These findings demonstrate an essential contribution of biallelic RELA expression in protecting stromal cells from TNF-a-mediated cell death, thus delineating the mechanisms driving the effectiveness of TNF-a inhibition in this disease.

overall_design: Total RNA was obtained from human dermal fibroblasts from two patients with RelA haploinsufficiency  (in duplicates) as well as three healthy controls after they were treated with TNF-α for 24 hours and the transcriptional profile of the samples was determined.

first: Raif

last: Geha

first: Jeffrey

last: Goldsmith

first: Athos

last: Bousvaros

first: Toshiro

last: Ohsumi

first: Wayne

last: Bainter

first: Juan

last: Castillo

first: Fatma

last: Dedeoglu

first: Yousef

last: Badran


title: Comparative transcriptomics of the virulence regulons of enteropathogenic Escherichia coli from diverse phylogenomic lineages

city: Baltimore

first: Sean

last: Daugherty

state: Maryland

address: 801 W. Baltimore St.

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Global transcriptional analysis of eleven EPEC strains, including the most frequently studied strains used in laboratory studies investigating EPEC virulence mechanisms.

sample_organism:
Escherichia coli
Escherichia coli E110019
Escherichia coli B171
Escherichia coli O127:H6 str. E2348/69
Escherichia coli C581_05
Escherichia coli 100329
Escherichia coli 103385
Escherichia coli 300059
Escherichia coli 302053
Escherichia coli 401140
Escherichia coli 402290

overall_design: RNA sequencing was performed on the four EPEC prototype strains during growth in laboratory media and conditions that have been previously demonstrated to induce expression of EPEC virulence factors.

first: Tracy

last: Hazen

first: Amol

last: Shetty

first: Anup

last: Mahurkar

first: Owen

last: White

first: James

last: Nataro

last: Kaper

first: David

last: Rasko


title: Compute the Significant Interactions of Hi-C data through HOMER

city: Beijing

first: hebing

last: chen

address: taiping road 27

institute: Institute of Health Service  and Transfusion Medicine

type:
Third-party reanalysis
Other

summary:
Purpose: We can explain the related biological significance from the enhanced proximity in the Hi-C data.
Methods: 1. Look for pairs of regions that have more Hi-C reads between them than would be expected by chance.  2.The expected number of reads is calculated using the background model.
Result: We found 261,758 significant interactions from H1 cell line and 133,169 significant interactions from IMR90 cell line.

overall_design: Significant interactions of Hi-C data from two cell lines. Hi-C data are used from GSE43070.

first: Hebing

last: Chen

first: Shuai

last: Jiang

first: Zhuo

last: Zhang


title: 12hr 5-FU treatment vs. DMSO in SJSA cells (from 'A kinase independent role for CDK19 in p53 response')

city: Boulder

first: Dylan

last: Taatjes

state: Colorado

address: 3415 Colorado Ave.

department: Molecular and Cell Biology

institute: University of Colorado, Boulder

summary: The human Mediator complex regulates RNA Polymerase II transcription genomewide. A general factor that regulates Mediator function is the four-subunit Mediator kinase module, which contains either CDK8 or CDK19. Whereas CDK8 has been linked to specific signaling cascades and oncogenesis, the cellular roles of its paralog, CDK19, are poorly studied. To define cellular roles for CDK19, we used osteosarcoma cells (SJSA) that naturally lack endogenous CDK8 protein. Although stable CDK19 knockdown was tolerated in SJSA cells, it caused reduced proliferation vs. control shRNA cells. Global gene expression analyses (RNA-Seq) suggested that defects in cholesterol biosynthesis contributed to reduced proliferation in CDK19 knockdown cells (vs. shCTRL). Notably, proliferation defects were rescued with transient expression of wild-type or kinase-dead CDK19. Using RNA-Seq and other assays, we established a general role for CDK19 in the transcriptional response to 5-fluorouracil (5-FU), an inducer of genotoxic and metabolic stress. These experiments also implicated CDK19 in activation of p53 target genes during 5-FU treatment. To further probe a potential role for CDK19 in the p53 response, SJSA cells (shCDK19 vs. shCTRL) were treated with the p53 activator Nutlin-3. Remarkably, CDK19 was required for SJSA cells to return to a proliferative state following Nutlin-3 treatment, and this effect was kinase-independent. These results implicate CDK19 as a regulator of p53 stress responses and suggest a manifestation of CDK19 knockdown—potentially reduced levels of cholesterol metabolites—blocks cellular resistance to Nutlin-3.

overall_design: SJSA cells were treated with either 375uM 5-FU or DMSO in biological duplicate for each population (4 samples total). Treatment was for 12h for compound and vehicle.

first: Katherine

last: Audetat


title: The transcription factor Gli3 promotes B cell development in the fetal liver through repression of Shh

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

country: United Kingdom

institute: UCL

summary: Before birth B-cells develop in the fetal liver (FL).  Here we show that Gli3 activity in the FL stroma is required for B-cell development. In the Gli3-deficient FL B-cell development was reduced at multiple stages, whereas the Sonic hedgehog (Shh)-deficient FL showed increased B-cell development, and Gli3 functioned to repress Shh transcription. Use of a transgenic Hedgehog (Hh)-reporter mouse showed that Shh signals directly to developing B-cells, and that Hh pathway activation was increased in developing B-cells from Gli3-deficient fetal liver. RNAsequencing confirmed that Hh-mediated transcription is increased in B-lineage cells from Gli3-deficient FL, and showed that these cells expressed reduced levels of B-lineage transcription factors and BCR/pre-BCR-signalling genes. We showed that expression of the master regulators of B-cell development, Ebf1 and Pax5, is reduced in developing B-cells from Gli3-deficient FL and increased in Shh-deficient FL, and that in vitro Shh-treatment or neutralisation can repress or induce their expression respectively.

overall_design: Wildtype and Gli3 mutant (Gli3+/- and Gli3-/-) (n=2) embryonic day 17.5 fetal livers were sorted for CD19+B220+ cells. RNA extracted from these cells was sequenced to help understand the transcriptional changes governing B cell development in the Gli3 mutants.

first: Anisha

last: Solanki


title: Transposon mutagenesis of the Zika virus genome highlights regions essential for RNA replication and restricted for immune evasion

city: New York

first: Peter

last: Palese

address: 1 Gustave L. Levy Place, Box 1124

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: RNA-seq of Zika virus libraries

overall_design: To investigate Zika virus (ZIKV) genetic flexibility, we used transposon mutagenesis to add 15-nucleotide insertions throughout the MR766 ZIKV genome and deep sequenced the viable genomes. The ZIKV transposon library was constructed and rescued as described before: Heaton, N.S., Sachs, D., Chen,C.J., Hai, R., and Palese, P. (2013). Genome-wide mutagenesis of influenza virus reveals unique plasticity of the hemagglutinin and NS1 proteins. PNAS. 110, 20248-20253, and Fulton, B.O., Sachs, D., Beaty, S.M., Won, S.T., Lee, B., Palese, P., and Heaton, N.S. (2015). Mutational Analysis of Measles Virus Suggests Constraints on Antigenic Variation of the Glycoproteins. Cell Rep. 1(9): 11331–1338.

first: Benjamin

middle: O

last: Fulton

first: Matthew

last: Evans


title: Gene expression of  thyroid cancer cell lines

status: Public on May 08 2017

city: Lund

first: Kajsa

last: Paulsson

address: Sölvegatan 19

department: Department of Clinical Genetics

country: Sweden

institute: Lund University

summary:
Purpose: The primary goal of this study was to identify gene-expression profiles of  anaplastic thyroid cancer and  to identify some novel in-frame gene fusions that could result in translated protein products affecting the development of  anaplastic thyroid cancer.
Methods: RNAseq Data was processed with TCGA UNC V2 RNAseq protocol and different expressed genes were identify by using DESeq2, limma-voom, and edgeR. Potential fusion genes were identified by using SOAPfuse, Chimerascan and TopHat-Fusion. Potential fusion genes were confirmed by cDNA PCR and Sanger sequencing.
Results: A total of 21 fusion genes were detected, including six predicted in-frame fusions; none were recurrent. Global gene expression analysis showed 661 genes to be differentially expressed between anaplastic thyroid cancer and papillary thyroid cancer cell lines, with pathway enrichment analyses showing downregulation of TP53-signaling as well as cell adhesion molecules in anaplastic thyroid cancer .
Conclusions: Our study represents the first detailed analysis of anaplastic thyroid cancer cell lines and found several novel in-frame gene fusions that could result in translated protein products affecting the development of anaplastic thyroid cancer. These data provide novel insights into the tumorigenesis of  anaplastic thyroid cancer and may be used to identify new therapeutic targets.

overall_design: Gene expression profiles of anaplastic thyroid cancer cell lines and papillary thyroid cancer cell lines were generated by deep sequencing by using Illumina HiSeq2000 platform.


title: Temperature induced changes in the Arabidopsis transcriptome

city: Wageningen

first: Alice

last: Pajoro

address: Droevendaalsesteeg 1

institute: Wageningen University

summary: Plants developed plasticity to environmental conditions, such as temperature, that allows their adaptation. A change in ambient temperature leads to changes in the transcriptome in plants. Here we study changes in the splicing of Arabidopsis thaliana using an RNA-seq approach. Plants were growing in short day conditions (8h light/16h dark) at 16°C for 5 weeks and then moved to 25°C. We monitor changes in the transcriptome in the time, material was harvested 24h, 3 days and 5 days after the temperature change.

overall_design: We generate 3 biological replicates for each condition, for a total of 12 samples.

first: Severing

last: Edouard

first: Richard

last: Immink


title: A Network Approach of Gene Co-Expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways

city: Carbondale

first: Bryan

middle: Manyasi

last: Musungu

state: IL

address: 1125 Lincoln Dr.

department: Plant Biology

institute: Southern Illinois University Carbondale

summary: A gene co-expression network was generated using a dual RNA-seq study with the fungal pathogen A. flavus and its plant host Z. mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection.  This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS).  For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network.  There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays, and 1942 A. flavus genes.  This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of reactive oxygen species.  In addition to the ROS from Z. mays, there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus. Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire gene expression network for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus.

sample_organism:
Zea mays
Aspergillus flavus

platform_organism:
Zea mays
Aspergillus flavus

overall_design: Maize B73 was grown in Clayton, NC during the years 2011 and 2013.  Seeds were planted on April 16.  Ears were hand pollinated from July 5-8 and covered with a paper bag. On July 23, a time course study was performed by pin bar inoculating one ear (per time point) of maize B73 with A. flavus NR3357 and harvesting at 0, 6, 12, 18, 24, 30, 36, 42, 48 and 72 hours post inoculation.  Biological replicates were done for samples 12,24,48,72 hours post inoculation.  Samples were frozen in liquid nitrogen, placed on dry ice and stored at -80°C until RNA was isolated.

first: Matt

last: Geisler

first: Ahmad

last: Fakhoury

first: Gary

last: Payne

first: Robert

last: Brown

first: Deepak

last: Bhatnagar


title: Cooperation between a hierarchical set of recruitment sites specifically targets the C. elegans dosage compensation complex to the X chromosomes.

first: Sarah

middle: Elizabeth

last: Albritton

state: NY

address: 100 Washington Square East

institute: New York University

summary: The genetic mechanisms that allow specific targeting of large chromosomal domains by various gene regulatory complexes remain unclear. Here, we used the C. elegans dosage compensation system to study how binding of a condensin-like dosage compensation complex (DCC) is specifically targeted to the X chromosomes. Previous work established that the DCC is first recruited to a small number of recruitment sites before subsequently spreading in cis along the X chromosome. To understand X-specificity of DCC recruitment, we examined the genomic properties of the recruitment sites and analyzed DCC binding upon ectopic insertion and deletion of recruitment site sequence. We find that X-specificity of DCC recruitment is the combined result of hierarchical recognition of and long-distance cooperation between the recruitment sites.

overall_design: Included are ChIP-seq profiles from C. elegans mixed stage embryos. Data was collected from at least two and up to five replicates. N2 ChIP-seq data sets were generated using antibodies against four dosage compensation complex proteins (SDC-2, SDC-3, DPY-30, and DPY-27), the histone modification H3K4me3, and the histone protein H3. TY1072 (sdc-2 null) ChIP-seq data was generated using antibodies against SDC-2 and histone H3. TY2205 (sdc-3 null) ChIP-seq data was generated using antibodies against SDC-2. New strains generated in this study include recruitment site deletions (ERC38, ERC54, and ERC64) and recruitment site insertions (ERC51); ChIP-seq data from these strains was generated using antibodies against DPY-27. We additionally include ERC38 ChIP-seq data from SDC-3 antibodies and matching RNA-seq data. Paired-end input data from ERC08 and ERC09 were used to map recruitment site insertions.

middle: E

first: Anna-Lena

last: Kranz

first: Lara

last: Winterkorn

first: Lena

last: Street

first: Sevinc

last: Ercan


title: Substrate and oxygen dependent citric acid production by Yarrowia lipolytica: Insights through transcriptome and fluxome analysis

city: Newcastle upon Tyne

first: Rajesh Reddy

last: Bommareddy

address: Ellision building

department: Health Sciences

institute: Northumbria University

summary: The goal of the study is to use Next generation sequencing (RNA-seq) and 13C based flux analysis to study the underlying regulation of citric acid metabolism in mixed culture fermentation (glucose and glycerl) of Yarrowia lipolytica. We  sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) under oxygen excess and limited conditions with 2 replicates each . Transcriptional profiles showed that under oxygen limited conditions, due to deficient mitochondrial activity, citric acid is being consumed back after glycerol exhaustion eventhough glucose is present in excess. Transcriptome and fluxome profiles showed that glucose is mainly directed towards the Pentose phosphate pathway in the dual substrate fermentations.

overall_design: Total 4 phases (pO2-1, pO2-2, pO2-UN-2, pO2-UN-3) were choosen and 2 replicates for each phase were paired-end sequenced using Illumina True seq kit on Illumina Hiseq 2000 platform.

first: Wael

last: Sabra

first: Rajesh

middle: R

first: An-Ping

last: Zeng


title: Genomewide poly(A) site mapping for YJR141W and related mutants

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

institute: ScilifeLab - Karolinska Institutet

summary: Genomewide characterization of  YJR141W role in mRNA polyadenylation.

overall_design:
Poly(A) site usage was quantified using the 3'T-fill aproach for 3 mutants and a control (BY4741) S. cerevisiae strain. Biological duplicates were analyzed for tsa685 (pcf11-2::KanR; his3^1 leu2^0 ura3^0 met15^0 pcf11-2 BY4741) and tsa801 (CFT2-1::KanR; his3^1 leu2^0 ura3^0 met15^0 cft2-1 BY4741). Only one replicate was analyzed for tsa1248 (YJR141W-PH::KanR; his3^1leu2^0 ura3^0 met15^0 yjr141w-ph BY4741) and BY4741 (Mata; his3^1leu2^0 ura3^0 met15^0).
A second batch of libraries (marked as "B") the same starting RNA was performed. The second batch contains biological triplicates for BY4741 and tsa801; and biological duplicates for tsa685 and tsa1248. Samples sharing the same biological origin are labeled with the same roman numeral.

first: Michael

last: Costanzo

first: Charles

last: Boone

first: Lars

last: Steinmetz


title: MiR31 increases CD8 T cell sensitivity to type I interferon

status: Public on May 07 2017

first: Kai

middle: W

last: Wucherpfennig

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology and Virology

institute: Dana Farber Cancer Institute

summary:
We report that the microRNA (miR)-31 confers CD8 T cell sensitivity to type I interferon (IFN) stimulation following CD3/CD28 engagement.
Method: miR31 WT and KO CD8 T cells were stimulated with anti-CD3/CD28 beads for two days, then maintained in 10ng/mL IL-2 for a further 5 days. CD8 T cells were then stimulated with 20ng/mL IFN-beta for 0, 4, or 18h. Total RNA was isolated at each time point and sequenced.
Results: Prior to IFN-beta stimulation, miR-31 KO CD8 T cells had a slightly increased effector program (cytotoxic granzymes) and decreased inhibitory program (Mt1/Maf). Stimulation with IFN-beta further enhanced this difference increasing a number of granzymes, Prf1 and Spp1 whilst also decreasing inhibitory genes (Mt1, Mt2, Maf, Ptger2).
Conclusion: This study shows that miR-31 may lead to decreased effector function and increased inhibitory programs in CD8 T cells during chronic viral infections, in particular due to continued type I interferon stimulation.

overall_design: RNA profiles of miR31 WT or KO CD8 T cells were generated in triplicate following a 7 day TCR/IL-2 stimulation followed by 0, 4, or 18 hours IFN-beta stimulation.

first: Howell

last: Moffett

first: Adam

middle: N

last: Cartwright


title: Lmx1b ChIP-seq dataset in embryonic day 12.5 (e12.5) wild type mouse limb buds

status: Public on May 06 2017

city: Loma Linda

first: Kerby

middle: C

last: Oberg

state: CA

address: 24785 Stewart St

department: Pathology

institute: Loma Linda University

summary: Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct downstream gene targets in the limb have been confirmed. To determine direct targets of Lmx1b during limb dorsalization (E12.5), we performed chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq).  Nearly 84% (n=617) of the Lmx1b-bound genomic fragments or intervals (LBIs) identified by two Lmx1b-ChIP-seqs overlap with chromatin regulatory marks indicative of potential cis-regulatory modules (PCRMs).  In addition, 73 LBIs mapped to known cis-regulatory modules (CRMs) active during limb development.  We compared Lmx1b-bound PCRMs to genes differentially expressed by Lmx1b at E12.5 and found 292 PCRMs within 1 Mb of 254 Lmx1b-regulated genes.  Gene ontology analysis of these associated genes suggests that Lmx1b mediates dorsalization through the regulation of extracellular matrix production, bone/joint formation, axonal guidance, vascular development, cell proliferation and cell movement.  We validated the functional activity of 2 PCRMs associated to Lmx1b-regulated genes, demonstrating activity and overlap with the associated gene during limb development. This is the first report to describe the genome-wide distribution of Lmx1b binding during limb development, directly linking Lmx1b to targets that accomplish limb dorsalization.

overall_design: pooled  limbs from embryonic day 12.5  (both fore and hind limbs -  2 runs,48 limb buds each

first: Endika

last: Haro

first: Billy

last: Watson

first: Jennifer

last: Feenstra

first: Luke

last: Tegeler

first: Charmaine

middle: U

last: Pira

first: Subburaman

last: Mohan


title: Ribosome footprints sequencing from Arabidopsis thaliana roots during Pi starvation

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

institute: CNRS

summary: Post-transcriptional gene regulation plays a significant role in the response to Pi starvation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, RNA association with translating ribosomes in 14-day-old Arabidopsis seedlings subjected to 7 days of Pi starvation.

overall_design: 14 samples, 2 conditions 500uM NaH2PO4,  0uM NaH2PO4. 2 bioreplicates of 4 RNA pools (total mRNA, ribosome footprints, small RNA, double stranded RNA)

first: Julia

last: Bailey-Serres


title: Mouse lung transcriptome response to infection with H1N1, H3N2, and H5N1 influenza virus.

status: Public on May 05 2017

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: The cellular transcriptome of C57BL/6 mouse lungs was profiled by mRNA-Seq analysis at multiple time points in response to infection with influenza A/California/04/09 (H1N1), A/Wyoming/03/03 (H3N2), and A/Vietnam/1203/04 (H5N1) HALo virus. The Influenza A/Vietnam/1203/04 (H5N1) HALo mutant virus is an attenuated H5N1 virus generated from wild-type Influenza A/Vietnam/1203/04 (H5N1) virus as described in Steel, J., et al. J Virol. 2009 Feb; 83(4):1742-53. A/Wyoming/03/03 (H3N2) influenza virus replicates poorly in mice and lung tissue collected from mice inoculated with this virus did not carry viral loads detectable by plaque assay.

overall_design: Six to eight week-old female C57BL/6 mice were infected with influenza A/California/04/09 (H1N1), A/Wyoming/03/03 (H3N2), or A/Vietnam/1203/04 (H5N1) HALo virus. Lungs from 3 infected mice per experimental group were collected at 12h, 1d, 2d, 3d and 4d post infection. Lungs of mice treated with PBS, collected after 4 d, served as mock control.

first: Giorgi

last: Metreveli

first: Sven

last: Heinz

first: Chris

last: Benner

last: Pache

first: Randy

last: Albrecht

first: Adolfo

last: Garcia-Sastre


title: Albugo-imposed immunosuppression by compromised salicylate-triggered immunity and altered tryptophan-derived anti-microbial metabolite biosynthesis and bioavailability

city: Norwich

first: Ghanasyam

last: Rallapalli

address: Norwich Research Park

institute: The Sainsbury Laboratory

summary: Infection by Albugo species, resulting in white rust disease, suppresses host plant immunity, and can even enable Albugo laibachii-infected Arabidopsis to support growth and reproduction of the non-host potato late blight pathogen Phytophthora infestans.  However, the mechanisms involved in non-host resistance remain to be elucidated. Here, we investigate specific host defense mechanisms that are suppressed by A. laibachii and A. candida infection, and compare the resistance contributed by indole glucosinolates and camalexin to that resulting from other components of defense induced by salicylic acid. We conclude a broad repertoire of host defense components contributes to non-host resistance in Arabidopsis to P. infestans, with a particular role for tryptophan-derived anti-microbial metabolites. Identifying the mechanisms involved in non-host resistance to pathogens such as P. infestans is necessary in the development of strategies to ensure future food security.

overall_design: 4-5 weeks old Arabidopsis (MAGIC-107: a multi-parent recombinant inbred line) plants were spray inoculated with either Mock or Albugo candida strain Nc2 or Albugo laibachii strain Nc14 , and infected plants were harvested at 0, 2, 4, 6 and 8 days post-inoculation (dpi) for total RNA extraction. mRNA profiles were generated by deep sequencing on Illumina GAIIx using EXPRSS tag-seq protocol. Four biological replicates were collected. Samples of Nc2 and Nc14 infections from 2, 4, 6 and 8 dpi were sequenced each in a separate lane. Samples of 2 and 4 dpi are sequenced 3 times and 6 dpi samples are 2 times to generate higher depth of sequencing data. Samples of Mock, Nc2 and Nc14 infections from 0 dpi were sequenced in one lane. Mock samples from 2, 4, 6 and 8 dpi were sequenced in one lane.

first: David

last: Prince

first: Shuta

last: Asai

first: Eric

middle: M

last: Kemen

first: Jonathan

middle: D

last: Jones


title: ERRa/ERRg KO heart gene expression analysis

city: Philadelphia

first: Liming

last: Pei

state: PA

address: 3501 Civic Center Blvd. CTRB 6018

department: Pathology and Laboratory Medicine

institute: Children's Hospital of Philadelphia/University of Pennsylvania

summary: ERRa and ERRg are essential transcriptional regulators of cardiac metabolism and functions.  Here we extend our previous studies by analyzing the transcriptome changes in ERRa/ERRg KO hearts

overall_design: RNA from 16-day-old mouse hearts were used.  2-3 mice per sample, 2 samples per genotype, 4 genotypes (aHetgWT, aHetgKO, aKOgWT, aKOgKO)

first: Ting

last: Wang


title: RNA-seq analysis of Kdm6a deficient brains in mice

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

summary: Kdm6a is an X-linked histone demethylase that activates gene expression via removal of the repressive methylation mark at histone H3 lysine 27 (H3K27). In humans, KDM6A mutations cause Kabuki syndrome, a disorder characterized by intellectual disability and motor coordination deficits. To assess the role of Kdm6a in brain development and behavior, we generated a neuron-specific Kdm6a deficient mouse model using Cre-LoxP recombination. The mutant mice exhibited an adult-onset deficit in motor coordination. We then performed RNA-seq analysis to determine the mis-regulated genes that are listed in this dataset.

overall_design: Genome-wide gene expression was determined in the brain between 3 adult male Kdm6a deficient and 3 wild type littermate mice.

first: Jun

last: Xu


title: Genome-wide identification of eggplant (Solanum melongena L.) miRNAs and their targets reveals differential regulation of heterostyly [Seq]

city: Nanning

first: Wang

last: Yikui

address: north road

institute: Institute Of Vegetable Research, Guangxi Academy Of Agricultural Sciences

summary: MicroRNAs (miRNAs), a class of endogenous, non-coding, ~21 nucleotide RNAs, regulate the expression of their target genes by mRNA cleavage or translation inhibition. In plants, miRNAs have been demonstrated to play crucial roles in regulating diverse cellular, physiological, and developmental processes. The identification of all the miRNAs is not yet complete; there are no studies on their possible links with the difference in heterostyly observed in eggplant (Solanum melongena L.).

overall_design: In the present study, small RNAs and their targets were identified in S-morph and L-morph styles during the development of eggplant pistil, using high-throughput small RNA microarray and degradome sequencing. Most of the miRNAs were found to be highly conserved in comparison to other plants. Among the 686 miRNAs on the microarray chip, 10 were demonstrated to be differentially expressed, among which ten were identified as pistil development-related miRNAs. The expression profiles of the eggplant miRNAs obtained through the microarray assays were validated by quantitative real-time polymerase chain reaction (qRT-PCR) for randomly selected miRNAs. We also annotated the target genes for differentially expressed miRNAs taking advantage of GO annotations and KEGG pathway analysis. And the pathway Cysteine and methionine metabolism, with a minimal P value, involved the largest number of miRNA target genes. The profiling of the miRNAs and their target genes described in the present study provides new information on the miRNA network during the development of eggplant pistil.

first: Yikui


title: Protein Kinase CK2 Controls the Fate Between Th17 Cell and Regulatory T Cell Differentiation

city: Birmingham

first: Sara

middle: Ann

last: Gibson

state: AL

address: MCLM 313 1918 University Blvd

department: Cell, Developmental and Integrative Biology

institute: University of Alabama at Birmingham

summary: We report that CK2 inhibition with CX-4945 broadly suppresses Th17-associated effector and metabolic gene expression.  CD4+ T cells were cultured in IL-6, IL-23 and TGFb1 for 72 h, in the absence of presence of 2 mM CX-4945, RNA-seq was performed and gene expression compared between the control and treatment groups.

overall_design: RNA-seq was performed on 3 biological replicates in the control and treatment groups.

first: Hongwei

last: Qin

first: Etty

last: Benveniste


title: Genome-wide identification of eggplant (Solanum melongena L.) miRNAs and their targets reveals differential regulation of heterostyly

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

platform_organism:
Macrobrachium nipponense
Solanum virginianum

overall_design: Refer to individual Series


title: Dynamic Profiles of MicroRNAome in Developing Porcine Liver

city: Chengdu

first: Yihui

last: Liu

address: Wen jiang district, Hui Min road #211

department: College of Animal Science & Technology

institute: Sichuan Agricultural University

summary: To evaluate the roles of miRNA in porcine liver, dynamic profiles of microRNAome were investigated using liver tissue from pigs at embryonic period  (Embryonic 90 days), weaning stage (postnatal 30d) and adult stage (7 years old). In this study, we identified 503 miRNAs sequences corresponding to 472 unique miRNAs sequences, and 353 unique miRNAs were differentially expressed during liver development. We also identified that 17, 13 and 6 miRNAs were specific abundant at embryonic day 90, postnatal day 30 and year 7, respectively. Besides regulating basic cellular roles in the development and function maintain, miRNAs expressed at E90, 30d and 7 y, also participated in the regulating of “embryonic liver development”, “early hepatic growth and generating a functioning liver” and “energy metabolic processes” ,respectively. Our study indicates that miRNAs are extensively involved in liver development and provides a valuable resource for further elucidation of regulatory role of miRNAs in liver development.

overall_design: Using high-throughput sequencing technology to reveal the characteristic of microRNAome during porcine liver development.

first: Xuewei


title: The impacts of the Spx regulator and H2O2 stress on the transcriptome of Streptococcus mutans

city: Gainesville

first: Jessica

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: As a resident of the oral cavity, Streptococcus mutans must withstand a variety of stresses, including oxidative stress.  Previously, we reported the identification of two Spx homologues (SpxA1 and SpxA2) in Streptococcus mutans that appear critical in the ability of the microbe to tolerate oxidative stresses; SpxA1 was shown to play a primary role in activation of detoxification strategies whereas SpxA2 served as a secondary activator.  Here, we used RNA deep sequencing (RNA-Seq) to examine the transcriptional changes associated with H2O2 stress in the parent S. mutans strain UA159 and to compare the peroxide-stress transcriptome of UA159 with its Δspx derivatives. The transcriptome data confirmed the relationship between SpxA1 and genes typically associated with oxidative stress responses, but also identified new genes and metabolic pathways that are activated during peroxide stress, also in an SpxA1-dependent manner.

overall_design: Transcriptional profiling of Streptococcus mutans UA159 wild-type strain was performed before and after 5 minutes exposure to 0.5mM H2O2, and of mutant strains ∆spxA1, ∆spxA2, ∆spxA1/∆spxA2 after the same H2O2 exposure.  RNA was extracted from S. mutans cells after the desired treament using standard methods.  Following Dnase treatment and enrichment for mRNA, Deep RNA sequencing was performed by the University of Rochester Genomics Research Center using the Illumina platform

first: Jose

last: Lemos


title: Gene expression in BRAFV600E thyrocyte

city: swon

first: Tea jun

last: Park

address: 206, World cup-ro, Yeongtong-gu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Ajou University School of Medicine

summary: To evaluate SASP in an in vitro model, we analyzed the gene expression profile of BRAFV600E-induced OIS thyrocytes by RNA sequencing  and detected an increase in SASP expression.

overall_design: Examination of 2 different BRAFV600E-induced thyroctes, each compared with Control thyrocte.

first: Tae

middle: J

first: Young

middle: H

last: Kim


title: The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university


title: Posttranscriptional control of the neutrophil transcriptome by tristetraprolin promotes neutrophil apoptosis and compromises host antimicrobial defense

city: Vienna

first: Vitaly

last: Sedlyarov

address: Lazarettgasse 14, AKH BT 25.3

institute: Research Center for Molecular Medicine

summary: Posttranscriptional regulation of mRNA levels in neutrophils and its consequences for immune responses are unexplored. By employing profiling of the neutrophil transcriptome we show that the mRNA-destabilizing protein tristetraprolin (TTP) limits the expression of hundreds of genes, including genes negatively regulating apoptosis. Elicited TTP-deficient neutrophils exhibited reduced apoptosis and were increased in numbers. The anti-apoptotic protein Mcl-1 was elevated in TTP-deficient neutrophils and Mcl1 mRNA was bound and destabilized by TTP. Ablation of TTP in macrophages and neutrophils resulted in an improved defense and survival of mice during invasive infection with Streptococcus pyogenes. Mice lacking myeloid TTP prevented dissemination of bacteria and efficiently blunted systemic disease by massive but controlled neutrophil deployment. These data identify posttranscriptional control by TTP to restrict neutrophils and antimicrobial defense.

overall_design: WT and TTPKO peritoneal neutrophils stimulated with LPS for 4 h. Each condition analyzed in three replicates

first: Florian

last: Ebner

first: Nina

last: Gratz

first: Lukas

last: Kenner

first: Andreas

last: Villunger

first: Franz

last: Kratochvill

first: Pavel

last: Kovarik


title: The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status (smallRNA-seq)

summary: DNA methylation is a chromatin modification that is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation have been identified, relatively little is understood about how DNA methylation influences gene expression. Using complementary genetic and biochemical approaches we identified a protein complex that antagonizes the transcriptional gene silencing of two LUCIFERASE (LUC) reporters in a manner that requires DNA methylation. At its core, this complex contains LOW IN LUCIFERASE EXPRESSION (LIL), an α-crystallin domain protein, and METHYL-CpG-BINDING DOMAIN 7 (MBD7), a protein previously associated with DNA methylation. At the LUC reporters, loss of MBD7 or LIL resulted in decreased LUC expression concomitant with modest, but reproducible increases in DNA methylation that can be phenocopied by DNA demethylase mutants. These findings are consistent with other reports and reveal a genetic connection between MBD7, LIL and DNA demethylation. However, we found that the hyper-methylation and gene expression phenotypes at a LUC reporter can be genetically uncoupled, demonstrating that changes in DNA methylation alone are not sufficient to silence LUC expression, and suggesting a role for the MBD7-LIL complex downstream of DNA methylation. Consistent with this hypothesis, our more extensive analysis of DNA methylation in mbd7 and lil mutants revealed only a small number of hyper-methylated loci genome wide. Furthermore, these loci displayed minimal overlap with demethylase targets, suggesting that, in general, the DNA demethylation machinery does not function in a manner dependent on the MBD7-LIL complex. Taken together, our findings place the MBD7-LIL complex amongst a small number of factors that regulate gene expression without causing significant changes in DNA methylation. This complex, however, is unique in that it functions to suppress, rather than enforce the silencing effects of DNA methylation, enabling gene expression of several transgene reporters despite high levels of promoter methylation.

overall_design: 2 small RNA libraries were sequenced

first: Dongming

last: Li

first: Ana-Marie

middle: S

last: Palanca

first: So

middle: Y

last: Won

first: Ying

last: Feng

first: Ajay

last: Vashisht

first: Li

first: Yuanyuan

last: Zhao

first: Xigang

first: Xiuyun

last: Wu

first: Shaofang

first: Brandon

last: Le

first: Yun

first: Guodong

last: Yang

first: Shengben

first: Jinyuan

first: James

last: Wohlschlegel

first: Hongwei

last: Guo

first: Beixin

last: Mo

first: Xuemei

last: Chen

first: Julie

last: Law


title: mRNA sequence of individual Drosophila melanogaster (w1118) male and female flies fed with different concentrations of dimethyl sulfoxide (DMSO) over different time periods.

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary: To gain an understanding of the toxic effect of a commonly used solvent, flies were exposed to 0, 0.1, 0.2, or 0.4% v/v DMSO for 0, 2, 4, or 8 h. We performed compound exposure of 800 individual flies in 4 Whole Animal Feeding Flats (WAFFL), a novel 96 well system to house, feed, and harvest individual flies. This expression profiling was part of a set of the experiments performed to evaluate the suitability of the WAFFL for high throughput small compound screening in D. melanogaster. Treated flies and controls were used for poly A+ stranded mRNA library preparation and we performed high throughput RNA sequencing to determine the transcriptional changes due to DMSO treatment.

overall_design: Flies were anesthetized and transferred one fly per well to the WAFFL for treatment, with half of the plate bearing females and the other half bearing males. Flies were fed for 24 h with 8 m of chemically defined food (CDF) 400 kcal/L after which flies were starved for 6 h with 8 m of Phosphate Buffered Saline (PBS) pH 7.4. After starvation, flies were fed with DMSO (0, 0.1, 0.2 or 0.4% v/v in CDF with 0.5 mg/ml of sulforhodamine B sodium salt) for 0, 2, 4 or 8 h. To ensure that flies fed, we visually examined them for a bolus of dyed food in the abdomen. We used 96 samples for the RNAseq libraries with the following design: sex (n=2), concentration (n=4), time point (n= 4), and biological replicates (n=3). We prepared PolyA+ RNA and stranded libraries that were multiplexed both by using index adaptors and by RNAs from distantly related species [Hawaiian Drosophila species (GSE80124) and Anopheles stephensi (to be reported elsewhere)]. RNAseq was performed using a HiSeq2500 Illumina platform, to produce single-end, 75 bp reads.

first: Maria

last: Jaime

first: Justin

last: Fear

first: Haiwang


title: Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses

status: Public on May 04 2017

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: We perform massively parallel single cell RNA-seq (MARS-Seq) on non-lymphocytic immune cells sorted from a human stage IA lung adenocarcinoma lesion and from the adjacent non-involved lung. With an unbiased single cell transcriptomic analysis of non-lymphocyte cells accumulating in these tissues, we sought to capture the heterogeneity of the tumor-infiltrating myeloid (TIM) compartment. Using a previously described unbiased expectation-maximization algorith (Paul et al., 2015), we identified clusters that were then named according to literature-reported marker profiles. This revealed a CD141+ DC subets, a CD1c+ DC subset, and a macrophage subset that clustered separately and was found to be enriched in the lesion as compared to other macrophage subsets.

overall_design: Using singlet, CD45+ DAPI- CD3- CD19- gating, over 1100 cells from a human stage IA lung adenocarcinoma lesion and over 700 cells from the non-involved lung were sorted into individual wells of a 384-well plate, then processed by MARS-Seq.

first: Miriam

last: Merad


title: Distinct Chromatin States Define a Program Of Mesenchymal Stem Cell Commitment To Osteogenesis

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: Multipotent mesenchymal stromal cells (MSCs) from bone marrow are critical for regeneration and homeostasis of multiple tissues. As epigenetic mechanisms are a fundamental regulator of lineage specification and cell fate, we examined histone modification changes in MSCs at distinct stages osteogenic differentiation, including: proliferation, early commitment, matrix deposition, and mineralization. Temporal changes of multiple histone modifications along with several transcriptional regulators were assessed and correlated to gene expression, which revealed distinct epigenetic mechanisms that regulate transcriptional programs necessary for commitment and tissue-specific phenotype development. Patterns of stage-specific enrichment of histone modifications revealed distinct modes of repression and activation of gene expression that would not be detected using single endpoint analysis. In addition, we have defined dynamic enhancer regions that control tissue-specific genes. Our work provides a cornerstone to understand the epigenetic regulation of transcriptional programs that are important for MSC commitment, as well as insights to facilitate MSC-based therapeutic interventions.

overall_design:
ChIP-seq

Raw data are not available for sample GSM1973717.

first: Hai

first: Joseph

last: Boyd

first: Troy

last: Whitfield

first: Jane

last: Lian


title: bulk cell RNA-seq of Lgr5+ ISCs with in vivo Rspo GOF and LOF

city: Palo Alto

first: Xiao

last: Li

address: 3165 Porter Dr

institute: Stanford University

summary: sorted Lgr5-eGFP+ cells under conditions of in vivo Rspo manipulation in reporter mice,

overall_design: Ad Fc (control) vs Ad LGR5 ECD (LOF) vs Ad Rspo1 (GOF) treatment.  Two biological replicates were used for Ad Fc and three biological replicates were used for LOF and GOF conditions

first: Kelley

last: Yan

first: Michael

middle: P

last: Snyder

first: Calvin

last: Kuo


title: Transcriptional profiling of renal cells expressing wild type or mutant uromodulin isoforms.

city: Milan

first: Luca

last: Rampoldi

address: Via Olgettina 60

institute: San Raffaele Scientific Institute

summary: Uromodulin is the most abundant urinary protein. It is exclusively produced and released in the urine by renal epithelial cells lining the thick ascending limb of Henle’s loop (TAL). Mutations in UMOD, the gene encoding uromodulin, cause autosomal dominant tubulointerstitial kidney disease uromodulin-related (ADTKD-UMOD). While the primary effect of all mutations, retention in the endoplasmic reticulum (ER), is well established, its downstream effects are still unknown. The aim of this study was to gain insight into ADTKD-UMOD pathogenesis through transcriptional profiling of immortalised mouse TAL cells (mTAL) transduced with lentiviral vectors encoding wild type or mutant (C150S) GFP-tagged human uromodulin.

overall_design: Transcriptional profiling performed in triplicate of mTAL cells expressing GFP-tagged wild type or C150S mutant uromodulin isoforms.

first: Céline

last: Schaeffer

first: Stefania

last: Merella

first: Dejan

last: Lazarevic


title: The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status (mRNA-seq)

first: Lei

last: Gao

overall_design: Examination of global RNA expression in 14-day-old Col, YJ , mbd7-4, mbd7-3, LUCH lil-2, LUCH, YJ lil-1 seedlings.

first: Dongming

first: Ana-Marie

last: Palanca

first: So

last: Won

first: Ying

last: Feng

first: Ajay

middle: A

last: Vashisht

first: Li

last: Liu

first: Yuanyuan

last: Zhao

first: Xigang

first: Xiuyun

last: Wu

first: Shaofang

first: Brandon

last: Le

first: Yun

last: Kim

first: Guodong

last: Yang

first: Shengben

first: Jinyuan

first: James

last: Wohlschlegel

first: Hongwei

last: Guo

first: Beixin

last: Mo

first: Xuemei

last: Chen

first: Julie

last: Law


title: Domains  of  methylated  CAC  and  CG  target  MeCP2  to  tune transcription in the brain

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh


title: Single-cell RNA-seq of Lgr5-eGFP+ intestinal stem cells upon Wnt and R-spondin modulation in vivo

city: New York

first: Kelley

last: Yan

department: Medicine

institute: Columbia University

summary: We report the transcriptomic alterations of Lgr5-eGFP+ intestinal stem cells upon Wnt and R-spondin gain-of-function and loss-of-function in vivo

overall_design:
Lgr5-eGFP+ intestinal stem cells were isolated by FACS following in vivo GOF and LOF Wnt and R-spondin.  Mice were treated with intravenous adenovirus encoding agonists and antagonists, then small intestine was harvested from these mice, the tissue was dissociated and cells were collected by FACS.  Sorted Lgr5-eGFP(-) cells and Lgr5-eGFP(+) cells following control Ad Fc treatment were used as controls.  Two technical replicates were generated for each treatment condition.
Please note that each mtx (processed data) file is accompanied with 2 files; a list of genes (i.e. mm10_genes.tsv linked as a Series supplementary file) and a list of cell ids (mm10_barcodes.tsv linked to the corresponding sample), which correspond to the rows and columns of the mtx file  (i.e. genes correspond to rows, and barcodes correspond to the columns).

first: Yan

last: Kelley

first: Kuo

last: Calvin

first: Zheng

last: Grace


title: Whole genome bisulfite sequencing of adult hypothalamus male mouse brain

summary: Mutations in the gene encoding the methyl-CG binding protein MeCP2 cause neurological disorders including Rett syndrome. The di-nucleotide methyl-CG (mCG) is the canonical MeCP2 DNA recognition sequence, but additional targets including non-methylated sequences have been reported. Here we use brain-specific depletion of DNA methyltransferase to show that DNA methylation is the primary determinant of MeCP2 binding in mouse brain. In vitro and in vivo analyses reveal that MeCP2 binding to non-CG methylated sites in brain is largely confined to the tri-nucleotide sequence mCAC. Structural modeling suggests that mCG and mCAC may be interchangeable as minimal structural perturbation of MeCP2 accompanies binding. MeCP2 binding to chromosomal DNA in mouse brain is proportional to mCG + mCAC density and defines domains within which transcription is sensitive to MeCP2 occupancy. The results suggest that MeCP2 interprets patterns of mCAC and mCG in the brain to negatively modulate transcription of genes critical for neuronal function.

overall_design: We have used 3 male wildtype Bl/6 adult dissected hypothalamus brain regions and performed whole genome bisulfite sequencing. We have generated this dataset to complement the RNA-seq and MeCP2 ChIP-seq datasets generated by Chen et al. PNAS 2015.

first: Sabine

last: Lagger

first: Adrian

last: Bird


title: Genome-wide location analysis of Abf1 and Reb1 in Saccharomyces cerevisiae

city: Parma

first: Giorgio

last: Dieci

address: Parco Area delle Scienze 23/A

department: Deparment of Life Sciences

institute: University of Parma

summary: Abf1 and Reb1, two general regulatory factors playing roles at promoters and other genome functional sites in budding yeast, were mapped genome-wide by ChIP-sequencing using strains expressing TAP-tagged versions of the proteins. As expected on the basis of previous in silico analysis of promoter regions, we found that these factors are enriched at the promoters of ribosome biogenesis (Ribi) genes, a large regulon of more than 200 genes required for ribosome biosynthesis and assembly, and known to be coordinately regulated in response to nutrient availability and cellular growth rate.

overall_design: The reported analysis was designed as a confirmative experiment. Chromatin immunoprecipitation of TAP-tagged Abf1 and Reb1 was carried out using logarithmically growing yeast cells, as described in Fermi et al (2016) Nucleic Acids Res, March 25, doi:10.1093/nar/gkw194

first: Maria

last: Bosio

first: Beatrice

last: Fermi

first: Gloria

last: Spagnoli

first: Elisabetta

last: Levati

first: Ludmilla

last: Rubbi

first: Roberto

last: Ferrari

first: Matteo

last: Pellegrini


title: Whole genome bisulfite and TAB-Sequencing from sorted neurons in the adult mouse brain

overall_design: WGBS and TAB-sequencing of wildtype Bl6 adult male mouse brains where neuronal cells were FACS sorted according to high NeuN expression.


title: Expression profiling of MCF-7 cells with treatment of TCDD

status: Public on May 03 2017

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine


title: De novo transcriptome analysis profiles gene expression in Vanessa cardui wing patterns

city: ithaca

first: Linlin

last: Zhang

address: 215 TOWER RD

department: Ecology and Evolutionary Department

institute: Cornell University

summary: Butterfly wing patterns are an important model for studying the genetic basis of morphological evolution. Here we used RNA-seq expression profiling in the butterfly Vanessa cardui to characterize the transcriptional basis of wing pigmentation. This approach identified numerous candidate genes including known and suspected components of the insect melanin and ommochrome biosynthetic pathways.

overall_design: mRNA profiling of hind wings from 5 developmental stages and Red/Black color regions in melanin stages of the painted lady butterfly (V. cardui), generated by deep sequencing with two replicates, using Illumina HiSeq 2500 for 150 bp paired end sequencing.

first: Robert

last: Reed


title: Modeling gene regulation from matched expression and chromatin accessibility data

city: Stanford

first: Zhana

last: Duren

address: 318 Campus Drive

institute: Stanford university

summary: We propose a statistical method to model gene regulation by paired expression and chromatin accessibility (PECA) data, which dissects the regulatory elements (RE) of the genome by modeling their interaction with general chromatin regulators (CR) and sequence-specific transcriptional regulators (TF) and consequent effects on transcriptional changes.

overall_design: To generate RNA-seq and ATAC-seq data on the retinoic acid-induced mESC differenation at Day 6.

first: Xi

last: Chen

first: Rui

last: Jiang

first: Yong

last: Wang

first: Wing

last: Wong


title: Contact-dependent killing by Caulobacter crescentus via cell surface-associated, glycine zipper proteins

city: Seattle

first: Monica

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

summary: Most bacteria are in fierce competition with other species for limited nutrients. Some bacteria can kill nearby cells by secreting bacteriocins, a diverse group of proteinaceous antimicrobials. However, bacteriocins are typically freely diffusible, and so of little value to planktonic cells in aqueous environments. Here, we identify an atypical two-protein bacteriocin in the gamma-proteobacterium Caulobacter crescentus that is retained on the surface of producer cells where it mediates cell contact-dependent killing. The bacteriocin-like proteins CdzC and CdzD harbor glycine-zipper motifs, often found in amyloids, and CdzC forms large, insoluble aggregates on the surface of producer cells. These aggregates can drive contact-dependent killing of other organisms, or Caulobacter cells not producing the CdzIE immunity protein. The Cdz system uses a type I secretion system and is unrelated to previously described contact-dependent inhibition systems. However, Cdz-like systems are found in many bacteria, suggesting that this form of contact-dependent inhibition is common.

overall_design: RNA-seq of Caulobacter crescentus NA1000 cells grown in PYE to early stationary phase to monitor changes in expression in stationary phase

first: Leonor

last: García-Bayona

first: Michael

middle: T

last: Laub


title: Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation

city: NEW YORK

first: Julide

middle: Tok

last: Celebi

state: New York

address: 1470 Madison Avenue

department: Tisch Cancer Institute

institute: Mount Sinai School of Medicine

summary: We set out to identify molecular underpinnings of high-risk melanomas, those that are likely to progress rapidly, metastasize, and result in poor outcomes. Gene expression changes unequivocally discriminated benign versus malignant states, and a dual epigenetic and immune signature emerged defining this transition. We discovered previously unrecognized melanoma subtypes. A high-risk primary melanoma subset was discriminated by a 122-epigenetic gene signature (‘epigenetic’ cluster) and TP53 family gene deregulation (TP53, TP63, and TP73). This subtype associated with poor overall survival and showed enrichment of cell cycle genes. Noncoding repetitive element transcripts (LINEs, SINEs, and ERVs) that can result in immunostimulatory signals recapitulating a state of ‘viral mimicry’ were significantly repressed. The high-risk subtype and its poor predictive characteristics were validated in several independent cohorts. Additionally, primary melanomas distinguished by specific immune signatures (‘immune’ clusters) were identified.  TP53 family of genes and genes regulating the epigenetic machinery demonstrate strong prognostic and biological relevance during progression of early disease. Gene expression profiling of RNA transcripts may be better predictors for disease course in melanoma. This study outlines the transcriptional interplay of the cancer cell’s epigenome with the immune milieu with potential for future therapeutic targeting.

overall_design: Examination of transcriptome changes from benign states to early-, intermediate-, and late-category tumors using a unique set of 78 treatment-naive melanocytic tumors consisting of primary melanomas of the skin and benign melanocytic lesions.

first: Brateil

last: Badal

first: Alexander

last: Solovyov

first: Serena

last: Di Cecilia

first: Joseph

last: Chan

first: Li-Wei

last: Chang

first: Ramiz

last: Iqbal

first: Iraz

last: Aydin

first: Geena

last: Rajan

first: Chen

first: Franco

last: Abbate

first: Kshitij

last: Arora

first: Antoine

last: Tanne

first: Stephen

middle: B

last: Gruber

first: Timothy

last: Johnson

first: Douglas

middle: R

last: Fullen

first: Leon

last: Raskin

last: Phelps

first: Nina

last: Bhardwaj

first: Emily

last: Bernstein

first: David

last: Ting

first: Georg

last: Brunner

first: Eric

middle: E

last: Schadt

first: Benjamin

last: Greenbaum

last: Tok Celebi