title: The B-type cyclin gene, SlCycB2, is essential to multicellular trichome-mediated defense against herbivores and reproductive organ development in tomato

city: wuhan

first: Yanna

last: Gao

address: hongshan area, shizishan street

institute: Huazhong agricultural university

summary:
Purpose: Plant trichomes are hair-like protuberances developing from epidermal cells of most terrestrial plants, serve as an excellent system for analyzing the molecular mechanisms underlying cell fate choices, cell cycle control, and cell morphogenesis. Regulation of trichomes in arabidopsis has been well characterized. However, the mechanisms of multicellular trichomes is unclear. To further identify the genes responsible for the SlCycB2-mediated phenotype change, we compared the gene expression profiles of SlCycB2-OE and RNAi plants by RNA-seq.
Methods: The transcriptomes of between SlCycB2-OE and RNAi in tomato (Solanum lycopersicum) cultivar Ailsa Craig (AC) by RNA-seq analysis were evaluated using the Illumina HiSeq™ 2500 sequencing platform. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by Hisat2 and DEGseq software. qRT-PCR validation was performed using SYBR Green assays.
Results: In this study, we determined that SlCycB2 encodes a nuclear localized protein, which is highly expressed in trichomes, stigmas, hypocotyls and stems, and induced by the light, suppressed under the dark. Transgene analysis showed that suppression of SlCycB2 could promote type III and type V trichomes formation. On the contrary, overexpression of SlCycB2 could result in nearly disappearance of all non-glandular trichomes (including type III and V), as well as the glandular ones of type I and type VI. Detection of secondary metabolites indicated that the production of monoterpene and sesquiterpene were significantly decreased in SlCycB2-OE plants, which thus caused the reduction of the defense against Prodenia litura. Transcriptome profile demonstrated that the differential expressed genes mainly participate in the biosynthesis of terpenes, cutin, suberine and wax. Furthermore, we identified several homologs of this gene in many plants, SlCycB3 in tomato, NtCycB2 in tobacco, AtCycB2 in Arabidopsis, which have similar regulatory functions in trichome formation. SlCycB2 overexpression also led to abnormal flower with the unclosed stamen, shortened style and aberrant pollen.
Conclusions: The results demonstrate that SlCycB2 play a critical role in multicellular trichome formation, secondary metabolite biosynthesis, Prodenia litura defense and reproductive organ development in tomato. The similar roles of its homologs in multicellular trichome formation suggest that Solanaceous species may share common regulatory pathway.

overall_design: The transcriptomes of between SlCycB2-OE and RNAi in tomato (Solanum lycopersicum) cultivar Ailsa Craig (AC) by RNA-seq analysis were evaluated, using the Illumina sequencing platform.

first: Zhibiao

last: Ye

first: Shenghua

first: Changxian

last: Yang


title: Comparative transcript profiling of a male sterile cybrid pummelo and its fertile type revealed altered gene expression related to flower development

status: Public on Dec 02 2016

city: Wuhan

first: Zheng

last: Beibei

state: Hubei

address: Shizi shan street No. 1

country: China

institute: Huazhong Agricutural University

type: Expression profiling by high throughput sequencing

summary: To gain new insight into the underlying mechanism, we compared, by RNA-Seq analysis, the nuclear gene expression profiles of floral buds of the cybrid with that of fertile pummelo. Gene expression profiles which identified a large number of differentially expressed genes (DEGs) between the two lines were captured at both petal primordia and stamen primordia distinguishable stages. For example, nuclear genes involved in nucleic acid binding and response to hormone synthesis and metabolism, genes required for floral bud identification and expressed in particular floral whorls.

overall_design: Total four sample pools (petal primordia and stamen primordia development stages of G1+HBP and HBP)

first: Beibei

last: Zheng

first: Wenwu

last: Guo


title: Key regulators in two different colorectal cancer cell lines 1638N-T1 vs. CMT-93

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

country: Germany

institute: Institute of Bioinformatics

summary: In this dataset, we present RNA-Seq data of two colorectal cancer (CRC) cell lines, namely 1638N-T1 and CMT-93.

overall_design: Two colorectal cancer cell lines in 3 replicates

first: Annalen

last: Bleckmann

first: Jetcy

last: Malayil

first: Tim

last: Beissbarth


title: DNA methylation in the gene body influences MeCP2-mediated gene repression

status: Public on Dec 01 2016

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

country: USA

institute: Harvard Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Rett syndrome is a severe neurodevelopmental disorder caused by loss-of-function mutations in the methyl-CpG-binding protein gene, MECP2. MeCP2 is a methyl-cytosine binding protein that is proposed to function as a transcriptional repressor. However, multiple gene expression studies comparing wild-type and MeCP2-deficient neurons have failed to identify gene expression changes consistent with loss of a classical transcriptional repressor. Recent work suggests that one function of MeCP2 in neurons is to temper the expression of the longest genes in the genome by binding to methylated CA dinucleotides (mCA) within transcribed regions of these genes. In the present study, we explore the mechanism of mCA and MeCP2 in fine-tuning the expression of long genes. We find that mCA is not only highly enriched within the body of genes normally repressed by MeCP2, but also enriched within extended megabase-scale regions surrounding MeCP2-repressed genes. While enrichment of mCA exists in a broad region around these genes, mCA within gene bodies appears to be the primary driver of gene repression by MeCP2. Disruption of methylation at CA sites within the brain results in depletion of MeCP2 across genes that normally contain a high density of gene-body mCA. We further find that the degree of gene repression by MeCP2 is proportional to the total number of methylated cytosine MeCP2 binding sites across the body of a gene. These findings suggest a model in which MeCP2 tunes gene expression in neurons by binding within the transcribed regions of genes to impede the elongation of RNA polymerase.

overall_design: MeCP2 ChIP-seq from the cerebral cortex of Dnmt3a knockout and wild-type mice

first: Benyam

middle: Z

last: Kinde

first: Dennis

middle: Y

last: Wu

first: Michael

middle: E

last: Greenberg

middle: W


title: Dynamic enhancer landscape in postmitotic motor neurons

status: Public on Dec 05 2016

city: New York

first: Hynek

last: Wichterle

state: NY

address: 630 West 168th Street

department: Departments of Pathology and Cell Biology, Neurology, and Neuroscience

institute: Columbia University Medical Center

summary: Generic spinal motor neuron identity is specified by cooperative binding of selector transcription factors to motor neuron specific enhancers. Whether these enhancers remain active to maintain the motor neuron expression program following downregulation of selector factors in maturing motor neurons remains unknown. We demonstrate that enhancers established by selector genes are highly transient during motor neuron differentiation. The chromatin immunoprecipitation-exonuclease (ChIP-exo) assay reveals that Isl1 is anchored to nascent motor neuron enhancers through protein-protein interaction. Stage-specific recruitment of transcription factors correlates with active enhancer marks. The majority of genes contain distinct early and late enhancers suggesting that the motor neuron expression program is maintained by a dynamic regulatory landscape.

overall_design: Examination of ChIP-seq profiles of 5 transcription factors and 1 histone modification, chromatin accessibility profiles using ATAC-seq, and total RNA profiles during differentiation of mouse ES cell-derived spinal motor neurons by deep sequencing.

first: Ho-Sung

last: Rhee

last: Closser

first: Yuchun

first: Elizaveta

middle: V

last: Bashkirova

first: G

middle: C

last: Tan

first: David

middle: K

last: Gifford


title: Genome-wide use of high and low affinity Tbrain transcription factor binding sites during echinoderm development

city: Pittsburgh

first: Gregory

last: Cary

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

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

sample_organism:
Strongylocentrotus purpuratus
Patiria miniata

overall_design: Refer to individual Series


title: Genome-wide detection of Tbrain binding sites during early development in both sea urchin (S. purpuratus) and sea star (P. miniata)

summary: Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs).  While cis regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low affinity, secondary  binding motif, although the primary, high affinity motif is conserved. To date, however, no genome-wide comparisons have been performed in order to provide an unbiased assessment of the evolution of GRNs between these taxa; and no study has attempted to determine the interplay between transcription factor binding motif evolution and GRN topology.  The study here measures genome-wide binding of Tbrain orthologs using ChIP-seq, and associates these with putative target genes to assess global function. Targets of both factors are enriched for other regulatory genes, although non-overlapping sets of functional enrichments in the two datasets suggest a much diverged function. The number of low affinity binding motifs are significantly depressed in sea urchins compared to sea star, but both motifs types are associated with genes from a range of functional categories.  Only a small fraction (~10%) of genes are predicted to be orthologous targets. Collectively these data indicate that Tbr has evolved significantly different developmental roles in these echinoderms, and that the maintained and unique targets, and their associated binding motifs are dispersed throughout the hierarchy of the GRN, rather than being biased towards terminal process or discrete functional blocks suggesting extensive evolutionary tinkering.

platform_organism:
Strongylocentrotus purpuratus
Patiria miniata

overall_design: Chromatin immunoprecipiation was performed using custom antibodies raised against either the sea urchin or the sea star protein. One biological replicate each, prepared by pooling chromatin from 2-3 independently fertilized cultures prior to immunoprecipitation, was used. Input and immunoprecipitated chromatin was sequenced for each species.

middle: A

first: Veronica

middle: F

last: Hinman


title: Targeted intron retention and excision for rapid gene regulation in response to neuronal activity

city: Basel

first: oriane

last: mauger

address: Klingelbergstrasse 50/70

country: Switzerland

institute: Biozentrum of University of Basel

summary: A substantial population of intron retentions are stably maintained in poly-adenylated transcripts and a subset of them are excised upon neuronal stimulation. These regulated intron retention events in fully transcribed RNAs represent a mechanism to rapidly mobilize a pool of mRNAs in response to neuronal activity.

overall_design: Examination of intron retention events in the mouse neocortex and their regulation upon neuronal activity. We first identified intron retention events in the mouse neocortex from developing brain (post-natal day 10, P10) and adult brain (P49) as well as in primary neocortical cultures. We then assessed the stability of the retained introns by looking how evolve their retention levels two hours after DRB-mediated transcription inhibition (primary culture samples). Finally, we investigated whether some intron retention events are regulated by neuronal activity. For that, we analysed in a transcription-inhibited context (mediated by DRB), levels of intron retention in primary neocortical cultures treated with bicuculline to increase the overall network activity.

first: P

last: Scheiffele

first: O

last: Mauger

first: F

last: Lemoine


title: Genome-wide analysis of DNA methylation Metarhizium robertsii

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

type: Methylation profiling by high throughput sequencing

summary: Genome-wide analysis of DNA methylation for different stages of  Metarhizium robertsii

overall_design: Metarhizium robertsii is a well-characterized entomopathogenic fungus that used as an important alternative to chemical insecticides in programs of agricultural pest and disease vector control. Metarhizium conidia are involved in fungal propagation and also are responsible for host infection. Despite their importance, several aspects of conidial biology, including their DNA methylome, are still unknown. Here, we performed a comparative DNA methylomic analysis of the conidia and mycelia of an M. robertsii strain at single-base resolution. The results showed that approximately 0.39 % of cytosines are methylated in conidia, lower than the DNA methylation level (0.42 %) in mycelia. DNA methylation in M. robertsii undergoes genome-wide reprogramming during fungal development. Gene Ontology (GO) analysis and KEGG analysis of DMR-associated genes revealed that amino acid, carbohydrate, fatty acid metabolism and ATP synthase were involved in energy synthesis and metabolism in M. robertsii. Intriguingly, transcription is influenced by genic methylation: genes with moderately methylated in promoter regions are likely to be enhanced transcription, whereas genes at either extreme are least likely. These patterns contrast with those found previously in other eukaryotes. Especially, some differentially methylated genes which are essential for energy synthase and metabolism have been found in this study, such as acetyl-CoA acetyltransferase and ATP synthase H chain. We propose that genes involved in energy synthesis and metabolic activity are developmentally regulated primarily by promoter DNA methylation.

first: Yu-long

first: Bo

last: Huang


title: Genome-wide analysis of SRC-1/NCOA1 and Erα/ESR1 binding in chromatin obtained from the ERα stably transfected U2OS osteosarcoma cell line (U2OS-ERα) with ChIP-SEQ.

status: Public on Dec 04 2016

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

summary: To better understand the role of SRC-1 in estrogen signaling in bone, a genome-wide analysis of ERα and SRC-1 binding sites in the absense and presence of E2 was conducted.

overall_design: Cells were grown in CSS media for 3 days, and treated with vehicle (EtOH) or estrogen (10^-8M) for 45 minutes and immediately harvested for chomatin immunoprecipitation (ChIP)

first: Kaifu

last: Chen


title: A neural basis for melanocortin-4 receptor-regulated appetite.

status: Public on Dec 03 2016

city: Boston

first: John

middle: N

last: Campbell

address: Center for Life Science, room 7-717

department: Medicine

institute: Beth Israel Deaconess Medical Center

summary: Pro-opiomelanocortin (POMC)- and agouti-related peptide (AgRP)-expressing neurons of the arcuate nucleus of the hypothalamus (ARC) are oppositely regulated by caloric depletion and coordinately stimulate and inhibit homeostatic satiety, respectively. This bimodality is principally underscored by the antagonistic actions of these ligands at downstream melanocortin-4 receptors (MC4R) in the paraventricular nucleus of the hypothalamus (PVH). Although this population is critical to energy balance, the underlying neural circuitry remains unknown. Using mice expressing Cre recombinase in MC4R neurons, we demonstrate bidirectional control of feeding following real-time activation and inhibition of PVH(MC4R) neurons and further identify these cells as a functional exponent of ARC(AgRP) neuron-driven hunger. Moreover, we reveal this function to be mediated by a PVH(MC4R)→lateral parabrachial nucleus (LPBN) pathway. Activation of this circuit encodes positive valence, but only in calorically depleted mice. Thus, the satiating and appetitive nature of PVH(MC4R)→LPBN neurons supports the principles of drive reduction and highlights this circuit as a promising target for antiobesity drug development.

overall_design:
Single-neuron mRNA-seq was performed on fluorescently-labeled or -unlabeled cells that were manually isolated from dissociated adult mouse paraventricular and arcuate hypothalamus: Mc4r-2a-Cre::L10-GFP+ or Mc4r-2a-Cre::AAV-XFP+ or Mc4r-2a-Cre::AAV-XFP-negative PVH neurons; Agrp-IRES-Cre::L10-GFP+ ARC neurons; Pomc-hrGFP+ ARC neurons; and vGLUT2-IRES-Cre::AAV-XFP+ ARC neurons

Note:  Raw files unavailable for samples GSM2413312 GSM2413313 GSM2413314 GSM2413346 GSM2413347

first: Alastair

middle: S

last: Garfield

first: Chia

last: Li

first: Joseph

last: Madara

first: Bhavik

middle: P

last: Shah

first: Emily

last: Webber

first: Jennifer

last: Steger

first: Oksana

last: Gavrilova

first: Charlotte

last: Lee

last: Olson

first: Joel

last: Elmquist

first: Bakhos

last: Tannous

first: Michael

middle: J

last: Krashes

first: Bradford

middle: B

last: Lowell


title: Quantitative Analysis of PPARD Transcriptomes  in Colon Cancer Cells by Next Generation Sequencing (NGS)

first: Xiaofeng

last: Zheng

state: TX

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary:
Purpose: NGS has revolutionized systems-based analysis of cell signaling pathways. The goal of this study is to determine the effects of PPARD in colon cancer cell transcriptomes in relation to the metastatic potential.
Methods: NGS-derived colon cancer cell mRNA transcriptome profiles of HCT116 WT (HCT116) and HCT116 with genetic PPARD-knockout (KO1) cells were generated by deep sequencing, in quadruplicate, using Illumina  HiSeq2000 .The transcriptomes of HCT116 and KO1 cells will be compared to determine the differentially expressed genes between HCT116  and KO1 cells. Differentially expressed genes will be examined in relation to the metastatic potential  and  validated by qRT-PCR.
Results: Using an optimized data analysis workflow Tophat2, we mapped about 25 million sequence reads per sample to the human genome. Out of 22229 genes, we identified 12118 transcripts  with >50 reads in at least one sample of HCT116 and KO1 cells with edgeR package and identified 6668 differentailly expressed genes with FDR 0.001 and P value cutoff  0.0022 using GLM tests fitted with BUM model. We further fltered the genes with both p-value and fold change and identified 416 genes  with FDR 0.001 and fold change larger than 2.  Among the differentially expressed genes, 311 were downregulated and 105 were upregulated in the KO1 cells compared with the WT cells. Twenty-three of the differentially expressed genes had significant association (i.e., a tendency towards co-occurrence) with PPARD expression (P < 0.05; log odds ratio > 1.5) in the TCGA colorectal adenocarcinoma database. Of these 23 genes, 7 were linked to metastasis by PubMed literature searches: GJA1, VIM, SPARC, NRG1, CXCL8 (IL-8), STC1, and  SNCG, which were validated by q-RT-PCR.
Conclusions: Our study represents the detailed analysis of PPARD transcriptomes in colon cancer cells, generated by mRNA-seq technology. Our results  show that NGS offers a comprehensive and  accurate quantitative and qualitative evaluations of mRNA contents in cells. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: The transcriptome profiles of HCT116 WT and KO1 colon cancer cells were generated by deep sequencing, in quadruplicate, using Illumina HiSeq2000.

first: Imad

last: Shureiqi

first: Xiangsheng

last: Zuo

first: Jing

last: Wang


title: RNA-seq of GDF15 or TGF-β stimulated NIH3T3 fibroblasts.

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: Transcriptome analysis revealed that GDF15 and TGF-β stimulation displayed similar expression patterns in differentially expressed genes.

overall_design: GDF15 or TGF-β stimulated NIH3T3 fibroblasts transcriptomes were analyzed by RNA-sequencing.

first: Takayuki

last: Ishige

first: Atsushi

last: Kaneda

first: Fumio

last: Nomura


title: Transcriptomics and metabolomics assisted molecular characterization of novel ERF transcription factors involved in the regulation of specialized metabolism in Ophiorrhiza pumila

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

summary: In this study, the genes that encode AP2/ERF transcription factors, namely OpERF1 to OpERF5, were isolated from HR of O. pumila. Phylogenetic analysis of AP2/ERF protein sequences suggested the close evolutionary relationship of OpERF1 with stress-responsive ERF factors in Arabidopsis and of OpERF2 with ERF factors reported to regulate alkaloid production, such as ORCA3 in Catharanthus roseus, NIC2-locus ERFs in tobacco, and JRE4 in tomato. We generated the HR lines of O. pumila, ERF1i and ERF2i, in which the expression of OpERF1 and OpERF2, respectively, was suppressed using RNA interference technique. The transcriptome and metabolome of these suppressed HR were analyzed for functional characterization of OpERF1 and OpERF2.

overall_design: De novo transcriptome assembly used in this study for transcriptome expression analysis was based on previously published  and characterization O. pumila transcriptome assembly by Rohanin et al., 2016 (doi: 10.5511/plantbiotechnology.15.1117a). Illumina based paired-end RNA-seq profiling for transgenic lines were created, and differential expression analysis was performed to identify contigs affected in response to the down-regulation of OpERF1 and OpERF2

first: Nirin

last: Udomsom

first: Amit

last: Rai

first: Hideyuki

last: Suzuki

first: Ryo

last: Nakabayashi

first: Jun

last: Okuyama

first: Miki

last: Tokoro

first: Ryosuke

last: Imai

first: Kazuki

last: Saito


title: Novel MicroRNA Signature to Differentiate Ulcerative Colitis from Crohn Disease: A Genome-Wide Study Using Next Generation Sequencing

city: Indianapolis

first: Jingmei

last: Lin

state: IN

address: 350 West 11th Street, Room 4048

department: Department of Pathology and Laboratory Medicine

institute: Indiana University School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: USeq software package identified 44 microRNAs with altered expression (fold change ≥2 and false discovery rate ≤0.10) compared to controls. Among them, a panel of 11 microRNAs was aberrantly expressed between UC and CD. qRT-PCR validation assays performed on frozen tissue from additional samples of UC (n=20) and CD (n=10) confirmed specific differential expression of miR-147b, miR-194-2, miR-383, miR-615 and miR-1826 (P<0.05). In addition, pathway analysis identified target genes of epithelial adhesion junction, integrin, glycolysis and cell cycle that involve in signaling pathways of TGF-β, STAT3, IL-8 and PI3L/AKT/mTOR. Conclusion: Identification of differentially expressed microRNAs in UC and CD supports the hypothesis that UC and CD are regulated by distinct pathophysiologic mechanisms. MicroRNA panels show promise as diagnostic biomarkers for the subtyping of inflammatory bowel disease.

overall_design: Illumina next generation sequencing was performed on nondysplastic fresh-frozen colonic mucosa of the distal-most colectomy from 19 patients (10 UC and 9 CD) and 18 patients with diverticular disease serving as controls.

first: Xinjun

last: Zhang

first: Zijin

last: Zhao

first: Noah

last: Welker

first: Yong

last: Li

first: Yunlong

last: Liu

first: Mary

last: Bronner


title: Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly-dividing de-differentiated state

first: Mohammad

last: Fallahi-Sichani

address: 200 Longwood Ave.

summary: Treatment of BRAF-mutant melanomas with MAP-kinase pathway inhibitors is paradigmatic of the promise of precision cancer therapy but also highlights problems with drug resistance that limit patient benefit. We use live-cell imaging, single-cell analysis and molecular profiling to show that exposure of tumor cells to RAF/MEK inhibitors elicits a heterogeneous response in which some cells die, some arrest and a remaining fraction adapts to drug. Drug-adapted cells up-regulate markers of the neural crest (e.g. NGFR), a melanocyte precursor, and grow slowly. To identify genes associated with acquisition of the slowly-cycling, vemurafenib-adapted state, we performed RNA sequencing (RNA-seq) on COLO858 cells (that show the slowly-cycling phenotype) exposed to drug for 24 and 48 h; drug-treated MMACSF cells served as a control. Transcriptional profiling implicates a c-Jun/ECM/FAK/Src cascade in adaptive resistance to RAF inhibition.

overall_design: Gene expression analysis of the response of two melanoma cell lines to 24 and 48 h treatment with RAF inhibitor vemurafenib

first: Sarah

last: Boswell

first: Peter

last: Sorger


title: Regionally distinct astrocyte interferon signaling promotes blood-brain barrier integrity and limits immunopathology during neurotropic viral infection

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: The role of astrocytes in innate immunity during viral infections of the central nervous system (CNS) remains to be fully elucidated. Here, we demonstrate that type I interferon (IFN) receptor (IFNAR) signaling in astrocytes regulates blood-brain barrier permeability and protects the cerebellum from infection and immunopathology. Mice with astrocytes lacking IFNAR signaling showed decreased survival after West Nile virus infection that was not due to expanded viral tropism or increased replication. Pattern recognition receptors and IFN-stimulated genes (ISGs) had higher basal and IFN-induced expression in human and mouse cerebellar astrocytes compared to cerebral cortical astrocytes. Our data identify cerebellar astrocytes as key responders to viral infection and highlight distinct innate immune programs in astrocytes from evolutionarily disparate regions of the CNS.

overall_design: Primary human astrocytes were maintained on collagen-coated tissue culture plates in a complete astrocyte medium (ScienCell Laboratories) in 2% FBS. Prior to isolation of RNA, cells were treated for 4 hours with 10U/ml recombinant human IFN-β or a PBS vehicle. Cells were then lysed in buffer RLT (Qiagen).

first: Brian

last: Daniels

first: Harsha

last: Jujjavarapu

first: Douglas

middle: M

last: Durrant

first: Jessica

middle: L

last: Williams

first: Richard

middle: R

last: Green

first: James

last: White

first: Helen

last: Lazear

last: Gale Jr.

last: Diamond

first: Robyn

last: Klein


title: Characterization of genetic loss-of-function of Fus in zebrafish

city: Mainz

first: René

last: Ketting

address: Ackermannweg 4

institute: Institute of Molecular Biology

summary: The RNA-binding protein FUS is implicated in transcription, alternative splicing of neuronal genes and DNA repair. Mutations in FUS have been linked to human neurodegenerative diseases such as ALS (amyotrophic lateral sclerosis). We genetically disrupted fus in zebrafish (Danio rerio) using the CRISPR-Cas9 system. The fus knockout animals are fertile and did not show any distinctive phenotype. Mutation of fus induces mild changes in gene expression on the transcriptome and proteome level in the adult brain. We observed a significant influence of genetic background on gene expression and 3’UTR usage, which could mask the effects of loss of Fus. Unlike published fus morphants, maternal zygotic fus mutants do not show motoneuronal degeneration and exhibit normal locomotor activity.

overall_design: We performed paired-end sequencing (100bp reads) of the polyA+ transcriptome from brains of five individuals with Fus-/- genotype and four with Fus wild type genotype. Note on RNA-Seq replicates: after performing first RNA sequencing on four replicates of Fus-/- and WT (labeled with the prefix "Sample_imb_ketting_2014_13_") we received a notice from Illumina stating a problem with the library preparation kit lot that was used to prepare the libraries. Due to that, we performed RNA sequencing a second time, using the same input RNA, except for the Fus knockout replicate #3, because there was not enough input RNA left. Instead, a different Fus knockout replicate (#1) was sequenced. However, we compared the mapped reads from sequencing run 1 and sequencing run 2 using plotCorrelaction from DeepTools, and the samples are highly correlated (at least 0.97 and 0.95, Spearman and Pearson correlation respectively). Therefore, we considered first ("Sample_imb_ketting_2014_13_") and second sequencing runs as technical replicates.

first: Svetlana

last: Lebedeva

first: António

last: de Jesus Domingues

first: Falk

last: Butter


title: RNA-seq assessment of morpholino knockdown of the sea star (Patiria miniata) Pm-Tbr transcription factor in early embryos

first: Gregory

last: Cary

summary:
Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star and sea urchin orthologs. We sought to identify targets of sea urchin and sea star orthologs of Tbr. Because less is known about the function of Tbr during sea star development, we used RNA-seq in conjuction with ChIP-seq studies (GEO:xxxx) to determine the targets of sea star Tbr in early development.
Methods: Sea star (Patiria miniata) embryos were injected with translation-blocking morpholino antisense oligonucleotides to knock-down PmTbr expression, as described previously. Control morpholinos were injected into sibling embryos. Embryos were allowed to develop until hatching (30-36 hpf) at which point injected embryos were collected and RNA was extracted. RNA-seq libraries were prepared, sequenced, and analyzed using standard protocols.
Results: There are 2,562 genes that are significantly differentially expressed relative to control morpholino inected embryos (FDR < 0.05). There are roughly equivalent numbers of genes down-regulated (1,041) and up-regulated (1,521) by Pm-tbr knockdown, suggesting that PmTbr may act as both a transcriptional activator and repressor. 1,165 differentially expressed genes are located within 75 kb of a PmTbr binding site determined using ChIP-seq, and this set is used as a basis for comparison between sea star and sea urchin binding sites.
Conclusions: 1,165 targets of the PmTbr transcription factor were identified based on differential expression following knockdown and the presence of transcription factor binding sites proximal to differentially expressed genes. There are an equal number of up- and down-regulated targets, suggesting Tbr may function as a transcriptional activator and repressor, depending on context and target gene. There was no clear association of motif utilization with either the direction of differential expression or ontological category of the target gene. There are only a small fraction of target genes (approximately 10%) that are in common between the sea star and sea urchin sets.

overall_design: mRNA sensitive to PmTbr knockdown were determined by measuring RNA from blastula embryos injected with either anti-Pm-Tbr morpholino antisense oligonucleotides or a control MASO, in triplicate, followed by sequencing using Illumina HiSeq 2500

first: Veronica

last: Hinman


title: Transcriptional profiling of cortex and striatal tissue following chronic dosing of PDE10A inhibitor PF-02545920 in a Q175 homozygous knock-in mouse model of Huntington’s disease

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: Huntington’s disease (HD) symptoms are driven to a large extent by dysfunction of the basal ganglia circuitry. HD patients exhibit reduced striatal phoshodiesterase 10 (PDE10) levels. Using HD mouse models that exhibit reduced PDE10, we demonstrate the benefit of pharmacologic PDE10 inhibition to acutely correct basal ganglia circuitry deficits. PDE10 inhibition restored corticostriatal input and boosted cortically driven indirect pathway activity. Cyclic nucleotide signaling is impaired in HD models and PDE10 loss may represent a homeostatic adaptation to maintain signaling. Elevation of both cAMP and cGMP by PDE10 inhibition were required for rescue. Phosphoproteomic profiling of striatum in response to PDE10 inhibition highlighted plausible neural substrates responsible for the improvement. Early chronic PDE10 inhibition in Q175 mice showed improvements beyond those seen with acute administration after symptom onset, including partial reversal of striatal deregulated transcripts and the prevention of the emergence of HD neurophysiological deficits.

overall_design: Transcriptional profiling of cortex and striatal tissue following chronic dosing of either vehicle or the  PDE10A inhibitor PF-02545920 (0.32, 1 and 3.2 mg/kg po qd) in the Q175 homozygous knock-in mouse model of Huntington’s disease (dosing from 5-weeks to 9 months of age).

first: Jim

last: Rosinski


title: Field systems biology of grapevine red blotch reveals the impact of viral infections on the transcriptional and hormonal regulation of berry ripening

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

summary: Red blotch disease causes major reprogramming of grape berry metabolism and development leading to the inhibition of ripening pathways and stress responses

overall_design: Red-skinned grape berries naturally infected with the Grapevine Red Blotch associated Virus and healthy controls at four stages of ripening (pre-veraison, veraison, post-veraison and harvest) and collected from two independent vineyards (Healdsburg and Oakville)

first: Rosa

last: Figueroa-Balderas

first: Dario

last: Cantu


title: Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle

city: Reykjavik

first: Benjamin

last: Sigurgeirsson

address: Sturlugata 7

country: Iceland

institute: Reykjavik University

summary: mRNA, sncRNA and lncRNA show a clear difference in expression between proliferative phase and 7–9 days after ovulation, thorough described together with lncRNA, snoRNA and snRNA not previously reported in healthy human endometrium

overall_design: 7 small RNA and 7 total RNA samples sequenced from endmometrial tissue from two time points of the menstrual cycle. Gene expression from the two time points compared. Additionally 12 small RNA from stromal cells was sequenced.

first: Hanna

last: Åmark

first: Anders

last: Jemt

first: Dorina

last: Ujvari

first: Magnus

last: Westgren

first: Joakim

last: Lundeberg

first: Sebastian

last: Gidlöf


title: CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells

city: SAN FRANCISCO

first: John

last: Liu

state: California

address: 35 Medical Center Way

institute: UCSF

summary: The human genome produces thousands of long non-coding RNAs (lncRNAs) – transcripts >200 nucleotides long that do not encode proteins. While critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. Here, we developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in 7 diverse cell lines including 6 transformed cell lines and human induced pluripotent stem cells (iPSCs). Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth modifying function exclusively in one cell type. We further found that lncRNA knockdown can perturb complex transcriptional networks in a cell type-specific manner. These data underscore the functional importance and cell type-specificity of many lncRNAs.

overall_design: 96 RNA-seq samples; 16 ChIP-seq samples

first: S

first: Max

last: Horlbeck

first: Jonathan

last: Weissman

first: Daniel

last: Lim


title: Whole transcriptome analysis of lung squamouse cell carcinoma

city: Maebashi

first: Susumu

last: Rokudai

state: Gunma

address: Showa-machi 3-39-22

department: Molecular Pharmacology and Oncology

institute: Gunma University Graduate School of Medicine

summary: Discovery of novel diagnostic and/or prognostic biomarkers of lung squamous cell carcinoma based on a whole transcriptome analysis using RNA sequencing (RNA-seq). Transcriptomic profiles of 12 available samples, out of 87 recruited patients with lung squamous cell carcinoma (SCC) were generated using Ion Proton system.

overall_design: Tumoral mRNA profiles of 12 patients with lung SCC were generated by deep sequencing, using Ion Proton system.

first: Yukihiro

last: Otaka

first: Ikuko

last: Horikoshi

first: Shinji

last: Yoshiyama

first: Reika

last: Kawabata

first: Masahiko

last: Nishiyama


title: The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation

city: Odense M

first: Ann-Sofie

middle: Bøgh

last: Brier

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark, Odense

summary: Here we have characterized the role of KDM5 family during adipocyte differentiation of 3T3-L1 preadipocytes. Notably, our study represents the first to simultaneously knock down all the KDM5 family members thereby avoiding interference from redundancy between KDM5 subtypes. Using a combination of knockdown and genome-wide ChIP-seq and RNA-seq analyses we uncover the underlying mechanisms of the inhibition of adipogenesis as well as basic aspects of KDM5 function.

overall_design: Genome-wide profiling of KDM5A binding in 3T3-L1 preadipocytes and differentiating adipocytes, and profiling of H3K4me3 and gene expression in 3T3-L1 cells depleted for KDM5 family members

first: Anne

last: Loft

first: Jesper G.

last: Madsen

first: Thomas

last: Rosengren

first: Ronni

last: Nielsen

first: Søren

last: Schmidt

first: Zongzhi

first: Qin

last: Yan

first: Hinrich

last: Gronemeyer

first: Susanne

last: Mandrup


title: Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade [ATAC-Seq]

city: Philadelphia

first: Yu

last: Qiu

address: 421 Curie Blvd

department: Radiation Oncology

institute: University of Pennsylvania

summary: The goal of this study is to investigate if interferon signaling regulates immune checkpoint blockade in mouse melanoma model.

overall_design: ATAC-seq for B16, B16 after chronic interferon treatment, B16 derived checkpoint blockade resistant strain 499, coupled with RNA-seq data.

first: Joseph

last: Benci

first: Bihui

last: Xu

first: Tony

last: Wu

first: Hannah

last: Dada

first: Christina

last: Twyman-Saint Victor

first: Lisa

last: Cucolo

first: David

last: Lee

first: Kristen

last: Pauken

first: Alexander

last: Huang

first: Tara

last: Gangadhar

first: Ravi

last: Amaravadi

first: Lynn

last: Schuchter

first: Michael

middle: D

last: Feldman

first: Hemant

last: Ishwaran

first: Robert

middle: H

last: Vonderheide

first: Amit

last: Maity

first: E

last: Wherry

first: Andy

last: Minn


title: A MOUSE MODEL OF ALCOHOLIC LIVER FIBROSIS-ASSOCIATED ACUTE KIDNEY INJURY IDENTIFIES KEY MOLECULAR PATHWAYS

city: College Station

first: Ivan

last: Rusyn

address: 4458 TAMU

institute: TEXAS A&M UNIVERSITY

summary: We reported this study established a mouse model of fibrosis- and alcohol-associated AKI and identified key mechanistic pathways.

overall_design: kidney mRNA profiles of Olive oil, CCl4, EtOH, and CCl4+EtOH treatment in C57BL/6 mice were generated by deep sequencing.

first: Shinji

last: Furuya

first: Ramon

last: Bataller

first: Grace

last: Chappell


title: Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade [RNA-Seq]

first: Yu

last: Qiu

overall_design: Transcription profiling for B16, B16 after chronic interferon treatment, B16 derived checkpoint blockade resistant strain 499 and various knockout from 499, coupled with ATA-seq data.

first: Joseph

last: Benci

first: Bihui

last: Xu

first: Tony

last: Wu

first: Hannah

last: Dada

first: Christina

last: Twyman-Saint Victor

first: Lisa

last: Cucolo

middle: E


title: Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade

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

overall_design: Refer to individual Series


title: Widespread and dynamic translational control of red blood cell development

city: Cambridge

first: Juan

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: Cell development requires tight yet dynamic control of protein production. Here, we use murine erythropoiesis as a model to study translational regulatory dynamics during mammalian cell differentiation. We uncover pervasive translational control of protein synthesis, including widespread alternative translation initiation and termination, stoichiometric synthesis, and dynamic use of upstream reading frames. We thus unravel translational regulatory programs during erythropoiesis, comprising hundreds of mRNAs with dynamic translation efficiencies and their cell type-specific regulators. A major such program involves enhanced decoding of specific mRNAs depleted in terminally differentiating/enucleating cells with decreasing transcriptional capacity. Rbm38, an erythroid-specific RNA-binding protein, promotes translation of many such genes by recruiting the translation initiation factor eIF4G. Inhibiting Rbm38 blocks red cell production, and mice lacking Rbm38 develop anemia, demonstrating an essential role for Rbm38-mediated enhanced translation of irreplaceable mRNAs. These findings reveal critical roles for dynamic translational control in supporting specialized mammalian cell formation.

overall_design: Matched RNA-seq and Ribo-seq profiles of erythroid progenitors purified from E14.5 mouse fetal livers after 0, 24, 33, and 48 hours of ex vivo differentiation, generated by deep sequencing, in duplicate, using the Illumina HiSeq2000 platform.

first: Wenqian

last: Hu


title: RNA Seq analysis of gene expression during Schmidtea mediterranea embryogenesis, including yolk and adult samples

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Planarian neoblasts are pluripotent, adult somatic stem cells and lineage-primed progenitors required for the production and maintenance of all differentiated cell types, including the germline. Neoblasts, originally defined by Harriet Randolph as undifferentiated, embryonic-like cells residing in the adult parenchyma, are frequently compared to embryonic stem cells yet their developmental origin remains obscure. We investigated the provenance of neoblasts during S. mediterranea embryogenesis, and report that neoblasts arise from an anarchic, cycling piwi-1+ population that is wholly responsible for production of all temporary and definitive organs during embryogenesis. Early embryonic piwi-1+ cells are molecularly and functionally distinct from neoblasts: they express unique cohorts of early embryo enriched transcripts and the cells behave differently than neoblasts in cell transplantation assays.  Neoblast lineages, established as organogenesis commences, persist into adulthood, where they act as agents of tissue homeostasis and regeneration.

overall_design: Examine gene expression in single staged embryos of flatworm from yolk through adult. Four replicates were performed for each stage: Yolk, Stages 2-8, sexually mature adults (SX) and asexual adults (CIW4), for a total of 40 samples.

first: Erin

last: Davies

first: Kai

last: Lei

first: Amanda

last: Kroesen

first: Sean

last: McKinney

first: Longhua

last: Guo

first: Eric

last: Ross

first: Kirsten

last: Gotting

first: Alejandro

last: Sanchez Alvarado


title: mTor inhibition induces a paused pluripotent state

city: Urbana

first: Miroslav

last: Hejna

state: Illinois

address: 1110 West Green Street

department: Department of Physics

institute: University of Illinois

summary: Cultured pluripotent stem cells are a cornerstone of regenerative medicine due to their ability to give rise to all cell types of the body. While pluripotent stem cells can be propagated indefinitely in vitro, pluripotency is paradoxically a very transient state in vivo, lasting 2-3 days around the time of blastocyst implantation. The exception to this rule is embryonic diapause, a reversible state of suspended development triggered by unfavorable conditions. Diapause is a strategy widely employed across the animal kingdom, including in mammals, but its regulation remains poorly understood. Here we report that inhibition of mechanistic target of rapamycin (mTor), a major nutrient sensor and promoter of growth, induces reversible pausing of mouse blastocyst development and allows their prolonged culture ex vivo. Paused blastocysts remain pluripotent and competent to give rise to embryonic stem (ES) cells and mice. We show that both natural diapause blastocysts in vivo and paused blastocysts ex vivo display pronounced reductions in mTor activity, translation and transcription. In addition, pausing can be induced directly in cultured ES cells and sustained for weeks in the absence of cell death or deviations from cell cycle distributions. We show that paused ES cells remain pluripotent, display a remarkable global suppression of transcription, and maintain a gene expression signature of diapaused blastocysts. These results allow for the first time the sustained suspension of development of a mammalian embryo in the laboratory, and shed light on the regulation of diapause and the origins of ES cells. Our findings have important implications in the fields of assisted reproduction, regenerative medicine, cancer, metabolic disorders and aging.

overall_design: Examination of RNA expression profiles of embryonic stem cells in serum, 2i and paused states by RNA-seq

first: Miguel

last: Ramalho-Santos

first: Aydan

last: Bulut-Karslioglu

first: Jun

last: Song

first: Hu

last: Jin


title: Role of H3.3 residues in chromatin assembly and cell fate at the maternal-to-embryo transition

city: Bethesda

first: Bertram

last: Canagarajah

state: Maryland

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: HISRainbow mice were used to obtain mosaic ovaries for transcriptome analysis of MII eggs expressing H3.3-eGFP, H3.3R26K-eCFP, or H3.3K27R-mCherry. Results provide comparison of eggs with different genotypes and insight into mechanism of how resting oocytes are selected for ovulation.

overall_design: Transcriptome profiling of eggs expressing H3.3-eGFP, H3.3R26K-eCFP, or H3.3K27R-mCherry by deep sequencing in duplicates.

first: Liquan

last: Zhou

first: Jurrien

last: Dean


title: Renal Fanconi syndrome and hypoposphatemic rickets in mice deficient for retroviral receptor XPR1 in the nephron

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

institute: UNI Lausanne

summary: Tight control of both extracellular and intracellular inorganic phosphate (Pi) levels is critical to the normal functioning of virtually all biochemical and physiological processes. The kidney participates in Pi homeostasis by controlling Pi reabsorption from the primary urine. Pi is freely filtered at the kidney glomerulus and is reabsorbed in the renal tubule by the action of the apical sodium-dependent phosphate transporters NaPi-IIa/NaPi-IIc/Pit2. The molecular identity of transporter(s) involved in the basolateral Pi efflux remains unknown. Recent evidence has suggested that the retroviral receptor XPR1 might be a candidate for this role. Here we show that conditional inactivation of Xpr1 in the renal tubule in mice results in impaired renal Pi reabsorption associated with a generalized proximal tubular dysfunction, or Fanconi syndrome, characterized by glycosuria, aminoaciduria, calciuria and albuminuria. Bone histomorphometry showed that the Xpr1-deficient mice develop hypophosphatemic osteomalacia secondary to the renal dysfunction. The analysis of Pi transport in primary culture of the proximal tubular cells revealed that the Pi efflux was significantly affected in cells devoid of Xpr1. These results identify XPR1 as a major player in Pi homeostasis and as a potential therapeutic target in bone and kidney disorders.

overall_design: Mice with doxycycline (DOX)-inducible, Pax8-rtTA-driven conditional deletion of Xpr1 in the renal tubule (Xpr1lox/lox/Pax8-rtTA/LC1 mice) were treated with DOX for two weeks (2 mg/ml in drinking water). Littermate Xpr1lox/lox mice were used as Controls.

first: Camille

last: Ansermet

first: Gabriel

last: Centeno

first: Matthias

last: Moor

first: Muriel

last: Auberson

first: Svetlana

last: Nikolaeva

first: Ivan

last: Gautschi

first: Olivier

last: Bonny

first: Dmitri

last: Firsov


title: Influence of chitin on the transcriptome of Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753 (V. coralliilyticus)

city: Kgs. Lyngby

first: Sonia

last: Giubergia

address: Matematiktorvet 301

institute: Technical University of Denmark

summary: Members of the Vibrionaceae family are often found associated with chitin-containing organisms and they are thought to play a major role in chitin degradation. The purpose of the present study was to determine how chitin affected the transcriptome and metabolome of two bioactive Vibrionaceae strains, Vibrio corallilyticus and Photobacterium galatheae. We focused on chitin degradation genes and secondary metabolites based on the assumption that these molecules in nature confer an advantage to the producer. Growth on chitin caused up-regulation of genes related to chitin metabolism and of genes potentially involved in host colonization and/or infection. The expression of genes involved in secondary metabolism was also significantly affected by growth on chitin, in one case being thirty-four folds upregulated. This was reflected in the metabolome, where the antibiotics andrimid and holomycin were produced in higher amounts on chitin. Interestingly, in cultures of P. galatheae grown on chitin we detected high amounts of the biogenic amine phenylethylamine. Overall, these results suggest that both V. coralliilyticus and P. galatheae have a specific lifestyle for growth on chitin, and that the secondary metabolites they produce are likely to play a crucial role during chitin colonization.

overall_design: Each strain was grown on two carbon sources (glucose G and chitin C). RNA was extracted at two time points: late exponential phase (1*10^8 CFU/ml) and stationary phase (24 hours from inoculation). For each strain in each condition, at 3 biological replicates were analyzed, unless the QC led us to discard one replicate (so at least two biological replicates were analyzed for each strain in each condition)

first: Lone

last: Gram


title: Next Generation Sequencing Analysis of human embryonic stem cells derived MESP1-mTomato reporter cells

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary:
Purpose: To compare the transcriptome of MESP1-mTomato reporter cells at undifferentiated state, mesoderm differentiation day 3 mTomato+ and mTomato- cells and MESP1+ cells undergoing endothelial differentiation in 2D and 3D.
Methods: total RNA from sorted MESP1+, MESP1- and hESCs (in biological duplicates) was extracted using RNeasy Plus Mini Kit (Qiagen) and treated with RNase free DNase. Libraries prepared following the instruction of TruSeq™ RNA Sample Preparation kit (Illumina) and sequenced on Illumina HiSeq 2000.
Results: genes differentially expressed in MESP1-mTomato+ and mTomato- cells were identified.
Conclusions: the gene expression profile of MESP1-mTomato cells indicates that they are cardiovascular progenitor cells.

overall_design: Perform RNA-seq of undifferentiated hESCs,  mesoderm differentiating MESP1+, MESP1- cells, and endothelial differentiating MESP1+ cells in 2D and 3D.

first: Fengzhi

last: Zhang


title: Influence of chitin on the transcriptome of Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753 (P. galatheae)


title: Influence of chitin on the transcriptome of Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753

sample_organism:
Vibrio coralliilyticus
Photobacterium galatheae


title: Genome-wide association of Geminin and Zic1 during neuroectodermal cell specification

city: Saint Louis

first: Kristen

last: Kroll

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

type: Genome binding/occupancy profiling by genome tiling array


title: Restoration of mesenchymal RPE by transcription factor-mediated reprogramming

city: Santa Barbara

first: Monte

middle: J.

last: Radeke

address: Neuroscience Research Institiute

department: Neuroscience Research Institute

institute: University of California, Santa Barbara

summary: TGFbeta-mediated epithelial-to-mesenchymal transition (EMT) is a major component of the wound healing response and a negative determinant of retinal pigment epithelial (RPE) differentiation after periods of sustained sub-confluent culture or repetitive passage. Inhibition of TGFbeta signaling using receptor kinase inhibitors forestalls the onset of passage-dependent EMT and can restore the capacity to differentiate to cells that previously underwent the mesenchymal switch [Radeke et al., 2015, Genome Med. 7:58]. However, even with the sustained inhibition of mesenchymal gene expression using  TGFbeta signaling inhibitors the cells eventually lose the capacity to attain a characteristic phenotype. This suggests that there are additional mechanisms at play that contributeto the prevention of RPE differentiation after protracted periods of wound stimulus and mitosis. In this study we investigate the non-TGFbeta-mediated processes that contribute to the demise of the RPE phenotype after extended periods of proliferative wound response. Using comparative transcriptomics, we show that with increasing passage there is a downregulation of RPE genes, misregulation of cell cycle genes, a decline in proliferative potential that cannot be prevented or reversed by inhibition of TGFbeta signaling using the TGFbeta receptor kinase inhibitor A-83-01. Importantly, among the RPE genes with decreased expression are several transcription factors known to be critical for RPE development. Exogenous expression of MYCN and OTX2 in conjunction with A-83-01 treatment restored the ability of passage 7 RPE  to differentiate. Taken together, these results demonstrate that the loss of capacity to differentiate as a result of chronic wound stimulus is a product of both TGFbeta pathway-dependent increases in mesenchymal gene expression and a TGFbeta pathway-independent loss of RPE programming.

overall_design: PolyA+ RNA-Seq analysis of primary fetal RPE donor lines as a function of passage with and without treatment with A-83-01 or after transcription factor-mediated reprogramming were done in triplicate using cells obtained from different donors. PolyA+ RNA-Seq analysis of the adult RPE cell line ARPE-19 was carried out in triplicate using independent experimental replicates obtained on different days. In two instances the reads from duplicate sequencing runs were carried out on the same seqeuncing libraries and the sequence files were combined prior to analysis.

first: Ying-Hsuan

last: Shih

first: Carolyn

first: Pete

last: Coffey


title: A network of paralogous stress response transcription factors in the human pathogen Candida glabrata

city: Paris

first: Gaëlle

last: LELANDAIS

address: 15, rue Hélène Brion

country: France

institute: IJM/University Paris Diderot

summary: We conducted a network-based analysis of the seven transcription factors belonging to the Yap (Yeast AP1) family in Candida glabrata.

overall_design: We performed ChIPseq experiments using myc-tagged versions of each factor. For CgYap1, CgYap2, CgYap3, CgYap4/6 and CgYap5, we submitted the corresponding tagged strains to stress conditions known to induce full activity of their S. cerevisiae orthologues, i.e. oxidative stress cause by metalloide for Yap1, cadmium for Yap2, salt excess for Yap4/6 and iron excess for Yap5.

first: F

last: Devaux

first: J

last: Merhej

first: G

last: Lelandais


title: Genome-wide chromatin binding profiles for Zic1 and Geminin during neuroectodermal cell specification

summary: Cell intrinsic factors that control neuroectoderm specification of early embryonic cells include the nucleoprotein Geminin (Gmnn) and the Zic family of zinc finger transcription factors. Gmnn modulates chromatin state to activate neural gene expression during neural cell fate acquisition, while Gmnn deficiency in the forming neural plate disrupts transcriptional programs that control neural cell specification, neural plate patterning and neurogenesis, resulting in neural tube defects. Likewise, Zic1 over-expression promotes neural gene expression, while heterozygous deletion of Zic1/4 leads to Dandy-Walker malformation, the most common congenital cerebellar malformation. During embryonic development, Geminin and Zic1 expression is enriched in neuroectoderm from gastrula stages, with broad expression in the forming CNS during post-gastrula stages, when neural tube closure and neurogenesis are initiated. To gain a greater understanding of the molecular events that regulate neural cell specification, here we used ChIP-seq to define genome-wide chromatin binding profiles for Gmnn in embryonic stem cells (ESCs) and for Gmnn and Zic1 during specification of ESCs into neuroectoderm.

overall_design: Genome engineering of the mouse embryonic stem cell line ES-E14TG2a (ATCC #CRL-1821) was used to generate clonal embryonic stem cell (ESC) lines with knock-in of a 3XTy1 epitope tag sequence at the Gmnn or Zic1 genomic locus. Clonal ESC lines expressing 3XTy1-tagged Gmnn or Zic1 proteins under the control of endogenous Gmnn or Zic1 regulatory sequences were used for ChIP-seq analysis. Two independent biological replicates per clone and two clones for each sample type were sequenced after Ty1 ChIP for the following sample types: (1) Ty1-Gmnn ChIP-seq in ESCs (clones 3.4 and 66), (2) Ty1-Gmnn ChIP-seq in ESC-derived neuroectoderm after 3 days of N2B27 monolayer culture (clones 3.4 and 66), and (3) Ty1-Zic1 ChIP-seq in ESC-derived neuroectoderm after 3 days of N2B27 monolayer culture (clones 6.8 and 8.9). Control samples sequenced for both ESCs and ESC-derived neuroectoderm included input and Ty1 ChIP from the original E14TG2a ESC line that does not express a Ty1-tagged fusion protein. Subtraction of these control samples (E14TG2a Ty1 ChIP and input) after sequencing was used to define specific peaks of ChIP enrichment.

first: Bo

first: Bryan

last: Teets

first: Savita

last: Sankar


title: Polycomb Repressive Complex-2 (PRC2) regulates intestinal homeostasis.

city: Tampere

first: Mikko

last: Oittinen

address: Arvo Ylpön katu 34

department: Tampere Center for Child Health Research

country: Finland

institute: Tampere University

summary: Differential GRO-Seq and ChIP-Seq (H3K27me3) was performed on mouse mini-gut model cells.

overall_design: GRO-Seq and ChIP-Seq

first: Minna

middle: U

last: Kaikkonen

first: Keijo

last: Viiri


title: Isoform switch of TET1 regulates DNA demethylation and mouse development

city: Boston

first: Wenhao

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

institute: Harvard Medical School

summary: The methylcytosine oxidase TET proteins play important roles in DNA demethylation and development. However, it remains elusive how exactly they target substrates and execute oxidation. Interestingly, we found that in mice, the full-length TET1 isoform (TET1e) is restricted to early embryos, ESCs and PGCs. By contrast, a short isoform (TET1s) is preferentially expressed in somatic cells which lacks the N-terminus including the CXXC domain, a DNA-binding module that often recognizes CpG islands (CGIs) where TET1 predominantly occupies. Unexpectedly, TET1s can still bind CGIs, despite the fact that its global chromatin binding is significantly reduced. Interestingly, the global chromatin binding, but not the targeted binding at CGIs, is correlated with TET1 mediated demethylation. Finally, mice with exclusive expression of Tet1s failed to erase imprints in PGCs and displayed developmental defects in progeny. These data show that isoform switch of TET1 regulates epigenetic memory erasure and mouse development.

overall_design: ChIP-seq was conducted in mESCs where Tet1 variants were overexpressed. MethylC-seq was performed in WT, Tet1 KO, Tet2 KO, Tet1/2 DKO, and Tet1cs/cs mESCs. RNA-seq was conducted in WT and Tet1cs/cs mESCs. DNA methylome and transcriptome were also profiled in WT and Tet1cs/cs E13.5 PGCs.

first: Weikun

last: Xia

first: Wei

last: Xie


title: RNA-Seq of the undifferentiated and differentiated SH-SY5Y cells

city: Palo Alto

first: Jingjing

last: Li

address: 3165 Porter Drive

institute: Stanford University

summary: We performed RNA-Seq for the SH-SY5Y cells before and after neuronal differentiation

first: Zhihai

last: Ma

first: Michael

last: Snyder


title: Single cell transcriptome dynamics and subpopulation heterogeneity in radiation treated recurrent glioma

city: New York

first: Sheng

state: New York

address: 525 East 68th Street

department: Neurological Surgery

institute: Weill Cornell Medical College

summary: Radiation is the frontline treatment for malignant gliomas.  Intra-tumoral heterogeneity has been proposed to grant cancer cells a superior trajectory and survival advantage to avoid therapeutic interventions including radiation. However, direct evidence to support the hypothesis via the transcriptome dynamics of glioma during radiation therapy is limited. The current study aim to measure the functional subpopulation dynamics before and after radiation treatment that assist the radiation resistance at single cell resolution. We investigate the single cell transcriptome and biological pathways of primary glioma mouse model and post-radiation early/late time point. Specifically, we used the RCAS mouse model for gliomas, which overexpress PDGFRA as the model. Using single cell transcriptome, for the first time, we confirmed the proneural classification of PDGFRA RCAS glioma mouse model and its heterogeneity. We found that recurrent dominant subpopulations are featured with elevated proliferation rate and hypoxia. In addition, we identified a subpopulation of radiation resistant cells in at early time points with elevated stemness. Lastly, the subpopulations composition undergoes large changes at late time point when the tumor recurred. Single cell transcriptome profiling of radiation treated mouse glioma mouse model identified tumor cell subpopulations dynamics. It provides novel insights into the molecular phenotype and biological functions of radiation resistant tumor cell population.

overall_design: To study mechanism of glioma relapse posterior to therapeutic dose irradiation, we have used PDGF-driven murine RCAS-tva glioma model as described in Methods. These mice develop high-grade glioma at approximately week 6. The tumors mimic pathological radiological and characteristics of glioblastoma. Since tumors in the RCAS-tva mice were driven by enhanced PDGF signaling and tumor cells were potentially derived from oligodendritic progenitor cells, majority of transformed cells were are abundantly expressing PDGFRa. Once we detected the radiographic primary high-grade tumor in RCAS-tva mice, we started to irradiate mice’s brain at 2 Gy every other day for five times. During week one post-radiation, we observed complete regression of primary tumors after radiation, confirmed by both MRI and histology. Thereafter, we had followed up the recurrence of tumors by MRI every week by MRI. We demonstrated that the mice had developed secondary high-grade tumors from week 4 to week 8 post-irradiation. We collected tumor samples from three time points: primary glioma (T1, primary stage), early phase of relapse post-radiation (T2, early stage), and late phase of relapse post-radiation (T3, late stage). Tumor samples were dissociated and subjected for FCAS. The stromal cell including immune cells and endothelial cells were removed and PDGFRa positive cells were isolated for subsequent analysis. To examine the transcriptome level heterogeneity of tumor cells of these three stages, we performed bulk RNA-seq and single cell RNA-seq experiments for the FCAS sorted tumor cells using Fluidgm C1 system.

first: Yujie

last: Huang

first: Jeffrey

last: Greenfield


title: Transcriptomic analysis of human neural progenitor cells differentiation into astrocytes

city: Miami

first: Marco

last: Magistri

state: FL

address: 1501 NW 10th Ave

department: Psychiatry

institute: University of Miami

summary: In this study we isolated and cultured neural progenitor cells (NPCs) from human fetal brain collected during the gliogenic phase (second trimester) of aborted fetuses, we differentiated NPCs into astrocyte using different protocols (FBS or CNTF/BMP4) and utilized RNA sequencing to analyze transcriptomic changes underlying the differentiation process

overall_design: Neural progenitor cells (NPCs) isolated from 4 different donors  (91, 103, 110 and 114 days embryos) were differentiated for 1 week using 2.5% FBS, while 3 NPCs lines (two from 103 and one from 110 days embryo) were differentiated for 1 week in the presence of CNTF/BMP4. RNA was extracted from NPCs before and after differentiation and submitted for sequencing on the Illumina HiSeq 2000 platform

first: Nathalie

last: Khoury

first: Emilia

last: Mazza

first: Dmitry

last: Velmeshev

first: Silvio

last: Bicciato

first: Pantelis

last: Tsoulfas

first: Mohammad

middle: A

last: Faghihi


title: Functional Genomic Analyses of Hep-G2 Cell Line after FTO knockdown

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

summary: To explore the molecular mechanism underlying glucose regulation by hepatic FTO, we used the human hepatocyte Hep-G2 cell line as an experimental platform and analyzed transcriptome changes following FTO knock-down.

overall_design: Examination of three Hep-G2 cell lines: FTO is knocked down more efficiently in sh7 and less efficiently in sh2. The control is the scramble.

first: Shiming

last: Peng

first: Dapeng

last: Ju

first: Niu

first: Eric

last: Zhang

first: Huanwei

first: Tao

last: Cai


title: Methylome of Lotus japonicus accession 'Gifu'

city: Vienna

first: Manu

last: Dubin

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute, Austrian Academy of Sciences

summary: Whole genome DNA methylation data for the  the Lotus japonicus accession 'Gifu'

overall_design: Whole genome bisulfite sequencing on arial tissue from Lotus japonicus grown at 20C


title: Unique Transcriptional Programs Identify Subtypes of AKI

first: Paolo

last: Guarnieri

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

summary: Two metrics, a rise in serum creatinine concentration and a decrease in urine output, are considered tantamount to the injury of the kidney tubule and the epithelial cells thereof (AKI).Yet neither  criterion emphasizes the etiology or the pathogenetic heterogeneity of acute decreases in kidney excretory function. In fact, whether decreased excretory function due to contraction of the extracellular fluid volume (vAKI) or due to intrinsic kidney injury (iAKI) actually share pathogenesis and should be aggregated in the same diagnostic group remains an open question. To examine this possibility, we created mouse models of iAKI and vAKI that induced a similar increase in serum creatinine concentration. Using laser microdissection to isolate specific domains of the kidney, followed by RNA sequencing, we found that thousands of genes responded specifically to iAKI or to vAKI, but very few responded to both stimuli. In fact, the activated gene sets comprised different, functionally unrelated signal transduction pathways and were expressed in different regions of the kidney. Moreover, we identified distinctive gene expression patterns in human urine as potential biomarkers of either iAKI or vAKI, but not both. Hence, iAKI and vAKI are biologically unrelated, suggesting that molecular analysis should clarify our current definitions of acute changes in kidney excretory function.

overall_design: Examining transcriptional profiles of two models of "acute kidney injury" (iAKI and pAKI), compared to controls, in different microanatomic regions of the kidney using laser capture microdissection

first: Katherine

last: Xu

first: Paul

last: Rosenstiel

first: Jonathan

last: Barasch


title: Transcriptome analyses of continuous cultures of Pseudomonas aeruginosa growing slowly under oxygen and nitrate limitation

city: Seattle

first: Caroline

last: Harwood

state: WA

address: 1705 NE Pacific St.

department: Microbiology

institute: University of Washington

summary: Chemostats have been used for decades in studying cell growth under controlled environments. Whole transcriptome sequencing by RNA-seq is a relatively new method for gene expression analysis. We utilized both tools for expression analysis of Pseudomonas aeruginosa growing slowly in synthetic cystic fibrosis medium under growth-limiting nitrate and oxygen levels. We established steady-state cultures under two divergent growth rates and found that during slower growth at a doubling time of 9.8 h, 76 known quorum genes were up-expressed while just 11 were down-expressed. Quorum-controlled genes were also more expressed in response to oxygen limitation. 21% of up-expressed genes under slow, oxygen-limited growth are quorum controlled while just 6% are up-expressed under slow, nitrate-limited growth. We found that the autoinducer for regulator RhlR, C4-HSL, is ~3.4 times higher when cells are growing slowly under oxygen limitation while the concentration of the autoinducer for LasR remained unchanged. Experiments with deletion mutants show the importance of rhlR for expression of quorum-controlled genes under slow, oxygen-limited conditions. This is an intriguing observation since P. aeruginosa is likely growing in similar environments in the cystic fibrosis lung, and lasR mutations are known to arise during chronic infection.

overall_design: RNA-seq analysis of continuously grown cultures grown in duplicate per growth rate tested (2.4 h and 9.8 h doubling times) per conditions tested (anaerobic and microaerobic)

first: Sandy

last: Thao

first: Yasu

last: Oda

first: Kyle

last: Hager

first: Matthew

last: Radey

first: Mitchell

last: Brittnacher

first: Hillary

last: Hayden


title: Marginal zone B cells control follicular helper T cell response to high cholesterol diet

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary: Splenic innate-like marginal zone B (MZB) cells are strategically positioned at the interface between the circulating blood and lymphoid tissue, where they initiate rapid immune responses to blood-borne antigens. Here, we find that selective genetic deletion of MZB cells substantially increases the follicular helper T (Tfh) cell and germinal center (GC) response to high cholesterol diet (HCD), which leads to T cell-dependent acceleration of atherosclerosis. We show that MZB cells activate a homeostatic program in response to HCD, in which upregulation of the transcription factor Atf3 plays a determinant regulatory role. Shuttling of MZB cells to the follicle is dispensable for their regulatory properties on Tfh cells. Instead, HCD promotes increased interaction between MZB and (pre-)Tfh cells outside the follicle, and upregulates MZB cell expression of Cd274 in an Atf3-dependent manner. Interaction between MZB and Tfh cells leads to Cd274-mediated suppression of Tfh cell motility, limits Tfh cell accumulation in the follicle and suppresses the pro-atherogenic Tfh/GC response. Our findings reveal a previously unsuspected role for MZB cells in the control of Tfh/GC response to a cholesterol diet, and uncover a new mechanism through which MZB cells can couple their unique metabolic and innate immune properties and use them to maintain a tolerogenic state. The results may have broad (patho)physiological implications.

overall_design: Transcriptomic comparision between high-fat diet and standard chow in  LDLr -/- splenic marginal zone B cells

first: Meritxell

last: Nus

middle: Y

first: Giles

last: Yeo

first: Ziad

last: Mallat


title: Identification of Volatile and Softening-Related Genes Using Digital Gene Expression Profiles in Peach

city: Hangzhou

first: Xiong-wei

last: Li

state: Zhejiang

address: Yuhangtang Road866

department: Department of Horticulture

institute: Zhejiang University

summary: Digital gene expression (DGE) profiles based on Illumina RNA-seq technology were applied to investigate the different gene expression patterns in peach fruit mesocarp of four commercial cultivars (‘Hu Jing Mi Lu’-‘HJ’, ‘Yu Lu’-‘YL’, ‘Zhong Hua Shou Tao’-‘ZH’ and ‘Jin Xiu Huang Tao’-‘JX’) and at three ripening stages of ‘HJ’. The aim was to identify the key candidate genes related to the formation of volatile compounds and fruit softening, and to get an insight into molecular mechanisms associated with these two traits from a full transcriptome view. The large set of differentially expressed genes (DEGs), and the annotation of each gene provides valuable information for research on other fruit traits

overall_design: Twelve digital gene expression profiles based on Illumina RNA-seq technology were applied to investigate the gene expression pattern in peach fruit mesocarp of four commercial cultivars (‘Hu Jing Mi Lu’-‘HJ’, ‘Yu Lu’-‘YL’, ‘Zhong Hua Shou Tao’-‘ZH’ and ‘Jin Xiu Huang Tao’-‘JX’) and at three ripening stages of ‘HJ’. The firmness and the content of seven volatile compounds especially lactone and linalool was assessed to detect candidate genes which are associated with these two traits

first: Xiongwei

first: Zhongsha

last: n Gao


title: Epigenetic characteristics and gene-expression analysis of a de novo centromere in maize

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

summary: De novo centromeres originate occasionally from non-centromeric regions of chromosomes, providing an excellent model system to study centromeric chromatin. The maize mini-chromosome Dp3a contains a de novo centromere, which was derived from a euchromatic site on the long arm of chromosome 3 that lacks traditional centromeric repeat sequences. Our previous study found that the CENH3 binding domain of this de novo centromere is only 350 kb with a high-density gene distribution with low-density of transposons. Here we analyzed the kinetochore complex assembled on the de novo centromere, which revealed that it resembles the native centromeres. Meiotic analyses showed that the Dp3a mini-chromosome formed bi-orientation during meiosis I and could stably transmit through meiosis. We applied next generation sequencing technology to analyze gene transcription, DNA methylation and histone modifications for this region. Our RNA-seq data revealed that active chromatin is not a barrier for de novo centromere formation. The gene expression level within the Dp3a breakpoints of native chromosome 3 indicated a gene dosage effect due to the additional copy of Dp3a mini-chromosome region in chromosome 3. Bisulfite-ChIP-seq results indicate a slightly increased DNA methylation level after de novo centromere formation, reaching the level of a native centromere. No strand-specific bias of DNA methylation was found at maize native and Dp3a de novo centromeres. H2A-T133 phosphorylation occurs in the CENH3 nucleosome. These results provide insight into the mechanism of de novo centromere formation and subsequent consequences.

overall_design: RNA-seq was carried out using material from seedling and young leaves between control and Dp3a.  Bisulfite-ChIP-seq was carried out with anti-CENH3 and ph-H2A-T133 antibodies using material from young leaves in Dp3a.

first: Fangpu

last: Han

first: James

last: Birchler


title: Naïve iPSCs Generated from β-thalassemia Fibroblasts Allow Efficient Gene Correction with CRISPR/Cas9

city: Shanghai

first: Xiaobai

last: Zhang

address: 1239 Siping Road

institute: Tongji University

summary: We used a modified 5i/L/FA system to generate transgene-free naïve iPSCs directly from the fibroblasts of a patient suffering from β-thalassemia and further demonstrated efficient gene correction with a CRISPR/Cas9 system, which provides an improved strategy for personalized treatment of β-thalassemia.

overall_design: A modified 5i/L/FA system was used to generate transgene-free naïve iPSCs directly from the fibroblasts of a patient suffering from β-thalassemia.

first: Yuanyuan

last: Yang

first: Li

last: Yi

first: Zhenzhen

last: Hou

first: Jiayu

last: Chen

first: Xiaochen

last: Kou

first: Yanhong

last: Zhao

first: Hong

last: Wang

first: Xiaofang

last: Sun

first: Cizhong

last: Jiang

first: Yixuan

first: Shaorong

last: Gao


title: A ChIP-seq spike-in method enables detection of global histone modification changes across the genome

first: Barbara

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

summary: This study outlines a method that dramatically alters the interpretation of ChIP-seq data and will improve the quantitative comparison of histone modification maps across biological contexts or across various conditions within a given biological context.

overall_design: We introduced a small fraction of Drosophila chromatin into human ChIP samples and added a Drosophila-specific antibody as a means to consistently precipitate Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 levels is observed across the genome upon EZH2 inhibitor treatment.

first: Brian

last: Egan

first: Paul

last: Labhart

first: Chih-Chi

last: Yuan

first: Feng

first: Charlie

last: Hatton

first: Patrick

last: Trojer


title: Functional roles of Aves class specific cis-regulatory elements on macroevolution of bird-specific features

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

summary: We carried out a comparative genomic analysis of 48 avian species to identify avian-specific highly conserved elements (ASHCEs). We performed genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) for three enhancer-associated histone modifications (H3K4me1, H3K27ac, H3K27me3), to investigate dynamic regulatory roles of ASHCEs in chicken development. We found that all three enhancer-associated histone marks are enriched in ASHCEs compared to the whole genome background.

overall_design: ChIP-seq analyses for three known enhancer-associated histone modifications (H3K4me1, H3K27ac and H3K27me3) with samples from developing chicken embryos at stages HH16, HH21 and HH32 respectively and samples from developing limbs at stages HH21 and HH32 respectively with two biological replicates.

first: Cai

last: Li

first: Ryohei

last: Seki

first: Naoki

last: Irie

first: Koji

last: Tamura

first: Guojie

last: Zhang


title: Deep sequencing identifies small molecule modulated microRNAs in the J1 mESCs

city: Lanzhou

first: Y

address: Xujiaping 1

institute: LVRI

summary: Many small molecular compounds reported were involved in improving reprogramming efficiency during inducing pluripotent stem cells (iPSC) or maintain a blastocyst-like state in embryonic stem cells (ESC), including BIO, CHIR99021 (CHIR), and vitamin C et al. However, the knowledge about these small molecules regulating miRNAs in ESC was limited. To understand the role of miRNAs during small molecules induced ESC maintenance and gain an insight how these small molecules regulates miRNAs expression; we performed small RNA sequencing using Illumina HiSeq 2000 under the compounds treatment. Retinoic acid (RA), a stimulus molecule for cellular differentiation, is set as negative control. The data show the miRNAs regulated by BIO, CHIR, vitamin C and RA.

overall_design: J1 mESCs maintained in medium containing 1000 U/mL LIF and supplemented with BIO, CHIR99021, vitamin C or RA for 24 hours, J1 treated with DMSO or ddH2O were set as control of BIO, CHIR99021, RA and vitamin C respectively. Then total RNA was extracted for analysis.

first: Yongyan

last: Wu

first: Xiaoyan

last: Shi

first: Zhiying

last: Ai

first: Zekun

last: Guo


title: Genome-wide transcriptional regulation by RBP-J

first: Baohong

last: Zhao

address: 535 E70th ST

institute: Hospital for Special Surgery

summary: We sequenced mRNAs from bone borrow derived macrophages derived from the control (WT) and RBP-J conditional knockout mice (RBP-J KO; Rbpj f/f;LysM cre).

overall_design: Examination of differential mRNA levels regulated by RBP-J in bone marrow derived macrophages.

first: Lionel

last: Ivashkiv


title: Identification of NAD+ capped mRNAs in S. cerevisiae

status: Public on Nov 30 2016

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

summary: We report the identification of NAD-RNA in the yeast Saccharomyces cerevisiae under two distinct growth mediums.

overall_design: RNA-seq libraries (in triplicate) were generated from total RNA that was treated with ADP-ribosylcyclase to select for NAD-RNAs and compared to mock-treated samples.  After ADPRC treatment, RNA was biotinylated using click chemistry and a pull down using streptavidin beads was performed.

first: Robert

last: Walters

first: Tyler

last: Matheny

first: Laura

middle: S

last: Mizoue

first: Bhalchandra

last: Rao

first: Denise

last: Muhlrad


title: GRO-Seq analysis of in vitro activated B cells in early G1

city: Stanford

first: Ansuman

middle: T

last: Satpathy

address: 240 Pasteur Drive

summary:
Purpose: To detect the on-going transcription in early G1 B cells
Methods: Primary B cells were isolated and in vitro activated by LPS, IL4 and Rp105, followed by nocodazole arrest and release. The early G1 population was then sorted and the nuclei was isolated for GRO-Seq. The sequenced reads were processed using Burrows–Wheeler Aligner (BWA) followed by HOMER.
Results: The nascent transcription and the convergent transcription were determined in both unsynchronized and sorted early G1 population
Conclusions: Convergent transcription is detected at Igh switch regions in early G1 cells.

overall_design: Two samples for unsynchronized B cells, and two samples for sorted early G1 cells.

first: Qiao

last: Wang

first: Kyong-Rim

last: Kieffer-Kwon

first: Thiago

last: Oliveira

first: Marei

last: Dose

first: Joy

last: Pai

first: Davide

middle: F

last: Robbiani


title: DNA demethylation is initiated in the central cells of Arabidopsis and rice

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

summary: Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extra-embryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell prior to fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Downregulation of the MET1 DNA methyltransferase has also been proposed to contribute to demethylation in the central cell. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice, as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared to non-sexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm.

sample_organism:
Arabidopsis thaliana
Oryza sativa

platform_organism:
Arabidopsis thaliana
Oryza sativa

overall_design: Examination of DNA methylation in Arabidopsis central cell, and rice egg and central cell

first: Kyunghyuk

last: Park

first: M

last: Kim

first: Martin

last: Vickers

first: Jin-Sup

first: Youbong

last: Hyun

first: Takashi

last: Okamoto

first: Daniel

last: Zilberman

last: Fischer

first: Yeonhee

last: Choi

first: Stefan

last: Scholten


title: RNAseq analysis of thymic CD4-CD8- double-negative (DN) invariant NKT cells from CD4+CD8+ double-positive (DP)-specific Rag2-conditional knock-out mice

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary: We report the identification of DN NKT cells developed from DN stage thymocytes. We analyzed the gene expression profiles of NKT cells that have developed from DN stage thymocytes isolated from DP-specific E8III-Cre transgenic Rag2-floxed mouse strain, and NKT cells developed from DP thymocytes sorted as YFP-reporter positive NKT cells that were isolated from E8III-Cre transgenic Rosa26-loxP-STOP-loxP mouse.

overall_design: Next generation sequencing of total transcriptomes using total RNA isolated from FACS sorted ex vivo thymic and liver NKT cells. DN-origin NKT cells were obtained from DP-specific E8III-Cre transgenic Rag2-floxed mice, and DP-origin NKT cells were obtained from E8III-Cre transgenic Rosa26-loxP-STOP-loxP mouse. The sorting gate was determined as: 7AAD-CD45R-CD4-CD8-CD1d dimer+TCRb+ cells.

first: Nyambayar

last: Dashtsoodol


title: Mutations in EBF3 disturb transcriptional profiles and cause intellectual disability, ataxia and facial dysmorphism

city: Huntsville

first: Richard

middle: M

last: Myers

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: From a GeneMatcher-enabled international collaboration, we identified ten individuals with intellectual disability, speech delay, ataxia and facial dysmorphism carrying a deleterious variant in the EBF3 (Early B-cell Factor 3) gene detected by whole-exome sequencing. Five missense, two nonsense, one 9-bp duplication, and one splice-site variant in EBF3 were found; the mutation occurred de novo in eight individuals, and the missense variant c.625C>T [p.(Arg209Trp)] was inherited by two affected siblings from their healthy mother who is a mosaic. EBF3 belongs to the early B-cell factor family (also known as Olf, COE, or O/E) and encodes a transcription factor involved in neuronal differentiation and maturation. Structural assessment predicts damaging effects of the five amino acid substitutions on DNA-binding of EBF3. Transient expression of EBF3 mutant proteins in HEK 293T cells revealed mislocalization of all but one mutant in the cytoplasm in addition to nuclear localization. By transactivation assays, all EBF3 mutants showed significantly reduced or no ability to activate transcription of the CDKN1A reporter gene, and EBF3 mutant proteins were less tightly associated with chromatin as demonstrated by in situ subcellular fractionation experiments. Finally, RNA-seq and ChIP-seq experiments demonstrate that EBF3 acts as a transcriptional regulator and EBF3 mutant protein had reduced genome-wide DNA binding and gene regulatory activity. Our findings demonstrate that variants that disrupt EBF3-mediated transcriptional regulation cause intellectual disability and developmental delay, and are present in ~0.1% of individuals with unexplained neurodevelopmental disorders.

overall_design:
RNA-sequencing and ChIP-sequencing were performed on SK-N-SH cells stably expressing wild-type EBF3 or mutant (p.P177L) EBF3.
We measured the transcriptome of 3 untransfected Control, 3 EBF3 wild-type expressing and 4 EBF3 p.P177L expressing SK-N-SH replicates, and measured genome-wide binding of two replicates each for EBF3 wild-type and EBF3 p.P177L.

first: Frederike

middle: L

last: Harms

first: Katta

last: Girisha

first: Andrew

last: Hardigan

first: Gregory

last: Cooper

first: Kerstin

last: Kutsche


title: Next Generation Sequencing for Quantitative Analysis of transcriptome of follicular compared to non-follicular CD8 T cells from  HIV+ Lymph nodes

city: BETHESDA

first: Jianfei

last: Hu

state: MD

address: 40 CONVENT DR

department: Vaccine Research Center

institute: NIH

summary: The goal of the study was to characterize the molecular signatures of CD8 T cell subpopulations sorted from HIV+ lymph nodes and HIV- tonsils. We compared the transcriptome profiles of follicular and non -foliccular CD8 T cells (sorted based on the surface expression fo CCR7 and CXCR5, chemokine receptors that govern the intratissue trafficking of T cells). This is the first study addressing this question. We found several genes differentially expressed in these two CD8 T cell populations. Our pathway analysis revealed that several pathways related to costimulation/activation as well as to beta-catenin pathway were differentially expressed in these two CD8 t cell populations too.

overall_design: CD8 T cell populations were sorted and whole transcriptome analysis was performed using an Illumina machine

first: Constantinos

last: Petrovas


title: Age-Related Gene Expression Changes in Prostate Cancer Patients [RNA-Seq]

city: Duarte

first: Susan

last: Neuhausen

state: California

address: 1500 E duarte road

department: Population Sciences

institute: City of hope

summary: Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

overall_design: Gleason-score matched tumor and adjacent normal samples were collected to compare gene expression differences in early-onset versus late-onset prostate cancer patients

first: Neuhausen

last: Susan

first: Ding

last: Chun


title: A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan

city: Providence

first: Jason

middle: G

last: Wood

state: RI

address: 185 Meeting St.

department: MCB

institute: Brown University

summary: In gonadal tissues, the Piwi-interacting (piRNA) pathway preserves genomic integrity by employing 23-29nt small RNAs complexed with argonaute proteins to suppress parasitic mobile sequences of DNA called transposable elements (TEs). While recent evidence suggests that the piRNA pathway may be present in select somatic cells outside the gonads, the role of a non-gonadal somatic piRNA pathway is not well characterized. Here we report a functional somatic piRNA pathway in the adult Drosophila fat body including the presence of the piRNA effector protein Piwi and canonical 23-29nt long TE-mapping piRNAs. piwi mutants exhibit depletion of fat body piRNAs, increased TE mobilization, increased levels of DNA damage, and reduced lipid stores. These mutants are starvation-sensitive, immunologically compromised, and short-lived, all phenotypes associated with compromised fat body function. These findings demonstrate the presence of a functional non-gonadal somatic piRNA pathway in the adult fat body that impacts normal metabolism and overall organismal health.

sample_organism:
Drosophila melanogaster
Drosophila simulans
Drosophila yakuba

overall_design:
RNA-seq: 18 samples total, 6 tissues/genotypes (wild-type head, thorax, abdomen, ovary; piwi2/CyO fat body; and piwi2/piwi2 fat body), 3 replicates each.
Small RNA-seq: 6 samples total (wild-type, D. simulans, D. yakuba, ovoD1 mutant, piwi2/CyO, and piwi2/piwi2; all fat body).

first: Brian

middle: C

last: Jones

first: Stephen

last: Helfand


title: Age-Related Gene Expression Changes in Prostate Cancer Patients

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

overall_design: Refer to individual Series


title: Comparative analysis of citrus polyembryonic and monoembryonic ovule transcriptomes identifies candidate transcripts related to nucellar embryony initiation

first: Liu

last: Zheng

summary: Next-generation sequencing was employed to compare transcriptomic profiling of ovules at and prior to the appearance of nucellar embryony initial cells. To exclude the unwanted genetic background noise and variations among years, two biological replicates for each sample were set by sampling in two consecutive years from two pairs of polyembryonic and monoembryonic cultivars, i.e. one pair of mandarin and the other of grapefruit/pummelo. In that manner, 71 embryo-type enriched transcripts were determined by overlaying differentially expressed transcripts, derived from pairwise comparisons between polyembryonic and monoembryonic cultivars in each basic taxa, which revealed commonly genes that indeed regulated nucellar embryogenesis. Transcriptome profiling indicated that cell wall remodelling transcripts, such as pectinesterase, endochitinase, glucan endo-1,3-β-glucosidase precursor, UDP-glucosyltransferase and laccase were significantly enriched in the polyembryonic cultivars. The expression of transcription factors containing AP2/ERF and WRKY domains were also up-regulated in polyembryonic cultivars compared with monoembryonic cultivars. In addition, the embryo-type enriched transcripts were associated with hormone regulation and signal transduction, as well as carbohydrate metabolism.

sample_organism:
Citrus maxima
Citrus x paradisi
Citrus reticulata
Citrus x clementina

overall_design: A total of 16 mRNA-Seq libraries were constructed, for the ovules of the two paired citrus varieties PK/CM and GF/PU at pre-NEI and NEI stages, with  biological replicates. For each stage, trancriptomes were compared between the poly- and mono-embryonic genotype within each pair. The overlapped differentially expressed genes between the two pairs were identified as factors involved in nucellar embryogenesis of citrus

first: Guo

last: Wenwu


title: Ailanthone targets p23 to overcome MDV3100 resistance in castration-resistant prostate cancer

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: Anti-androgen therapies including the new androgen receptor (AR) antagonist MDV3100 are the first therapeutic approach in treating prostate cancer (PCa). However, tumors frequently become castration resistant through multiple mechanisms including alternative expression of AR splice variants. To identify new inhibitors which block both full-length AR (AR-FL) and constitutively-active truncated AR splice variants (AR-Vs), a library of natural compounds was screened for molecules that could inhibit AR-driven transcription in PCa cells expressing AR-FL or AR-Vs. We identified the small-molecule Ailanthone (AIL) as a potent inhibitor of both AR-FL and AR-Vs. AIL down-regulates both AR itself and its target genes in PCa cell lines as well as orthotopic animal tumors. Moreover，AIL directly binds to the co-chaperone protein p23 and prevents AR’s interaction with HSP90, which results in the disruption of the AR-chaperone complex followed by Ubiquitin/proteasome-mediated degradation of AR as well as other p23 clients including AKT and Cdk4. Meanwhile, overexpression of p23 dose-dependently rescued AIL-mediated cell proliferation inhibition, suggesting that p23 might be a critical target of AIL. Furthermore, treatment of MDV3100-resistant 22RV1 xenografts with AIL reduced tumor volume by 77.5% (2 mg/kg/day AIL, intraperitoneal) and 79.2% (5 mg/kg/day AIL, oral) compared with the control group.  Finally, AIL possesses favorable drug-like properties such as good bioavailability (25.7% F), high solubility, lack of CYP inhibition, and low hepatotoxicity, although signs of gastrointestinal toxicity were observed at high doses. In conclusion, AIL overcomes MDV3100 resistance in castration resistant prostate cancer (CRPC) with excellent absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) properties, thus suggesting that AIL is a potential candidate for the clinical treatment of CRPC.

overall_design: Retinal mRNA profiles of LNCaP cells treated with or without AIL in the absence or presence of AR1-651 were generated by deep sequencing using Illumina HiSeq2000

first: Yundong

last: He

first: Mingyao

last: Liu


title: Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals

city: Jena

first: Friedrich

last: Becker

state: Thuringia

address: Beutenberg Strasse 11

department: Stem cell aging

institute: Leibniz Institute on Aging - Fritz Lipmann Institute