title: Chloroplast signalling gates thermotolerance in Arabidopsis

city: Cambridge

first: Patrick

middle: James

last: Dickinson

address: The Sainsbury Laboratory , Bateman Street

department: Sainsbury Laboratory University of Cambridge

institute: University of Cambridge

summary: Temperature has a major role in plant growth and survival, for example wheat yields decrease by about 6% for every 1°C rise in global temperature [1]. High temperatures induce the expression of protective chaperones and modulate growth responses. Key players in the heat protection response are transcription factors of the HEAT SHOCK FACTOR A1 (HSFA1) family [2]. However the pathways that activate the HSFA1 class TFs, and how these perceive temperature and integrate it with other environmental signals are not clear. Plants are exposed to considerable diurnal temperature variation, and have evolved pathways to anticipate likely future conditions. For example, the cold response pathway is gated by the circadian clock, enabling the degree of responsiveness to cold to be controlled in the context of the environment [3, 4] and genes promoting elongation growth and flowering in response to warm temperature are induced during the night via thermosensory phytochromes [5 ,6]. It is not known in Arabidopsis if the warm temperature protective pathways are gated. In this study we find that there is strong diurnal variation in the heat stress response of Arabidopsis, and we show that this correlates with the expression of HSP70 in the day night cycle. The dark to light transition is in fact sufficient to robustly induce expression of warm temperature protective genes such as HSP70. A forward genetic screen with a HSP70-Luciferase reporter line revealed genes necessary for controlling this process and identified a central role for chloroplast signalling in the warm temperature response that accounts for diurnal variation in thermotolerance.

overall_design: RNA-seq was generated in duplicate for an ss4 mutant and WT at 17°C, ss3/4, pgm, ss3/4/pgm at 17°C ZT0 and ZT2, and DCMU and DBMIB treated seedlings at 22°C and 27°C. A WT timecourse at 22°C and 27°C has a single replicate.

first: Philip

last: Wigge


title: HoxC5 and Pbx4 repress hTERT to limit telomerase activity

status: Public on Feb 13 2018

city: Singapore

first: Wen Fong

last: Ooi

address: 60 Biopolis

country: Singapore

institute: Genome Institute of Singapore

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Telomere elongation by telomerase is critical for the proliferation of human stem cells and >85-90% of cancer cells. The repression of telomerase activity during cellular differentiation promotes replicative aging and function as a physiological barrier for tumorigenesis in long-lived mammals, including humans. However, the underlying mechanisms remain unclear. We found that HoxC5 repressed hTERT, via a previously uncharacterized upstream enhancer element. HoxC5 interacts with co-repressors Pbx4 and Meis3, and recruits Class I histone deacetylases, to mediate repression of hTERT. The upstream enhancer element are conserved in long-lived primates, and HOXC5 are activated upon differentiation, consistent with diminished telomerase activity. Thus, HoxC5/Pbx4/Meis3 together constitute a developmental-controlled regulatory loop that coordinates transcriptional repression of hTERT.

overall_design: Endogenous and overexpressed Hoxc5 and PBX4 ChIP-seq in prostate cancer cell line (PC-3)

first: Li

last: Shang

first: Tingdong

last: Yang

first: Xu

last: Chang

first: Wen

middle: F


title: Quiescent thymic epithelial cells contribute to regeneration following induced acute involution

city: Montréal

first: Maude

last: Dumont-Lagacé

state: Quebec

address: 2950 chemin de la polytechnique

country: Canada

institute: IRIC - Université de Montréal

type: Expression profiling by high throughput sequencing

summary: This study aims at isolate a subpopulation of thymic epithelial cells (TECs) enrich in thymic epithelial progenitors. While recent studies have shown that bipotent TEC progenitors exist in adults, the identity of thymic epithelial progenitors (TEPCs) is still debated. Using an exclusively in vivo approach, we show that quiescent UEA1– TECs actively proliferate during thymic regeneration in 6-month-old mice and possessed a MHCIIlo Sca1hi CD49fhi CD24lo Plet1– phenotype. We then performed RNA sequencing of UEA1- quiescent (label-retaining cells, called LRCs) cells and compared them to UEA1- GFP- (nonquiescent, NonLRCs) TECs.

overall_design: We analyzed 2 samples with one replicate each. Each sample contains pooled cells isolated from 11 mice to reach a minimum of 10000 cells/replicate.

first: Hervé

last: Gerbe

first: Étienne

last: Gagnon

first: Claude

last: Perreault


title: A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells

city: New York

first: Zhidong

last: Tu

state: New York

address: 1 Gustave L. Levy Place

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary:
Purpose: Exosomes and other extracellular vesicles (EVs) have emerged as an important mechanism of cell-to-cell communication. In this work, we present a novel next generation of sequencing (NGS) based approach to identify EV mediated mRNA exchanges between co-cultured adipocyte and macrophage cells.
Methods:We performed molecular and genomic profiling and jointly considered data from RNA sequencing (RNA-seq) and genotyping to track the ‘sequence varying mRNAs’ transferred between cells.
Results: We identified 8 mRNAs being transferred from macrophages to adipocytes and 21 mRNAs being transferred in the opposite direction. These mRNAs represented biological functions including extracellular matrix, cell adhesion, glycoprotein, and signal peptides.
Conclusions: Our study sheds new light on EV mediated RNA communications between adipocyte and macrophage cells, which may play a significant role in developing insulin resistance in diabetic patients. This work establishes a new method that is widely applicable to examining genetic material exchanges in many other cellular systems.

overall_design:
Our main experiment was performed on an in-vitro co-culture cellular system, in which two types of human cells (adipocytes and macrophages) were cultured in the same dish but separated by a porous membrane to prevent them from being mixed together (see Methods). The porous membrane allows small particles (size less than 0.4 µm) to pass through, making EV mediated mRNA exchanges between the two cell lines possible.
ADMO_qc_GRCH38.txt contains genotypes of genotype of Adipocytes and Macrohpages

first: Carmen

middle: A

last: Argmann

first: Jialiang


title: RNA-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 in mice at P0

city: Boston

first: Dong Feng

last: Chen

state: Massachusetts

address: 20 Staniford St

institute: Schepens Eye Research Institute

summary: Epigenetic mark deposition during embryonic development contribute to postnatal homeostasis and tissue stability. Previously, we found out that Ezh2 contributes critically to the function and postnatal cell survival in bipolar cells in the retina. (Yan et al. Postnatal onset of retinal degeneration by loss of embryonic Ezh2 repression of Six1. Sci Report. doi:10.1038/srep33887) In this study, we used RNA-seq to define up- and down regulated genes in Math5CreEzh2f/f mice which express a selective deletion of Ezh2 in retinal ganglion cells (RGC). Gene expression was compared to wild type murine retinal cells.

overall_design:
mice pups (Math5Cre+;Ezh2f/f or wild type) were sacrificed at P0 and the retina was harvested immediately. After enzymatic digestion, retinal ganglion cells (RGC) were purified from other retinal cells using magnetic labelling with anti-CD90-antibody which binds specifically to RGC. After elution, samples were immediately proceed to RNA extraction.
We collected triplicates for each cell samples. Library was prepared with NEBNext Poly A, Sequencing was done with Mid-Output single read 75 cycles flow cell.
Lucy, J, Wong

first: Dong


title: Transcriptome analysis of p16/p21-dependent monocytic myeloid-derived suppressor cells accumulation.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: p16 and p21 act as tumor suppressors through induction of cellular senescence.  However, senescence-independent roles of these CDK inhibitors are not known.  To identify the mechanism responsible for the failure of Mo-MDSCs (monocytic myeloid-derived suppressor cells) infiltration into tumor allografts in p16/p21-double knockout (DKO) mice, we searched for chemokine receptors that were highly expressed in Mo- but not PMN-MDSCs (polymorphonuclear myeloid-derived suppressor cells) and were downregulated in p16/p21-DKO as compared to WT Mo-MDSCs. Ccr2, Ccr5, and Cx3cr1 were identified by RNA-seq analysis.

overall_design: RNA sequencing was performed using PMN-MDSCs derived from wild-type mice (WT), Mo-MDSCs derived from WT mice and Mo-MDSCs derived from p16/p21 DKO mice in triplicates, respectively.

first: Atsushi

last: Okuma

first: Eiji

last: Hara


title: Evaluating and comparing the Transcriptome of (human) Hek 293 based cells, expressing either CHD3 or CHD4

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

country: Germany

institute: University of Regensburg

summary:
Purpose: Identifying target genes of the two human chromatin remodeling enzymes CHD3 and CHD4
Methods: see below in protocols
Results: Libraries were sequenced on Illumina HiSeq2000 platform resulting in 37-71 Mio 50 bp paired-end reads per sample. We identified 16 (i) and 115 (ii) distinctly regulated genes when CHD3-GFP (i) or CHD4-GFP (ii) were overexpressed. Nine  genes seem to be commonly regulated by CHD3 and CHD4. We successfully validated four genes from our RNA-seq via qPCR with two new (independent from those, used for RNA-seq) biological replicates.
Conclusion: CHD3 and CHD4 regulate distinct genes.

overall_design: Total RNA was prepared from 24 hours induced (1 ng/µl Dox) and non-induced Flp-In™ T-REx™ 293 cells, expressing GFP, hCHD3-GFP (UniProt: Q12873) or hCHD4-GFP(UniProt Q14839). Library preparation and Illumina Sequencing was perfprmed by EMBL GeneCore facility in Heidelberg (Germany: Dr. Vladimir Benes)

first: Helen

last: Hoffmeister

first: Andreas

last: Fuchs

first: Gernot

last: Längst


title: Foxp1 expression in forebrain pyramidal neurons controls gene expression required for spatial learning and synaptic plasticity

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Genetic perturbations of the transcription factor, Forkhead Box P1 (FOXP1), occur in patients with autism spectrum disorder who have an increased risk for comorbidity with intellectual disability. Recent work has begun to reveal an important role for Foxp1 in brain development, but the brain region-specific contribution of Foxp1 to autism and intellectual disability phenotypes has yet to be fully determined. Here, we characterize Foxp1 conditional knockout (Foxp1cKO) mice with loss of Foxp1 in the pyramidal neurons of the neocortex and the CA1/CA2 subfields of the hippocampus. Foxp1cKO mice exhibit behavioral phenotypes that are relevant to autism spectrum disorder, including hyperactivity, increased anxiety, and decreased sociability. In addition, Foxp1cKO mice have gross deficits in learning and memory tasks that are relevant to intellectual disability. Using a genome-wide approach, we identified genes differentially expressed in the hippocampus of Foxp1cKO mice that are associated with synaptic function and physiology that could represent molecular networks related to the observed behavioral deficits. Finally, we observed reduced maintenance of long-term potentiation in the CA1 subfield of these animals. Together, these data suggest that expression of Foxp1 in pyramidal neurons of the forebrain is important for regulating gene expression pathways that contribute to specific behaviors relevant to autism and intellectual disability. In particular, Foxp1 regulation of gene expression in the hippocampus appears to be crucial for normal CA1 physiology and spatial learning.

overall_design: We carried out RNA-sequencing on adult male mouse hippocampal tissue and neocortical tissue. We compared gene expression profiles from Foxp1cKO mice to littermate controls, using four independent replicates per genotype.

first: Daniel

middle: J

last: Araujo

first: Kazuya

last: Toriumi

first: Christine

middle: O

last: Escamilla

first: Ashwinikumar

last: Kulkarni

first: Ashley

middle: G

last: Anderson

first: Matthew

last: Harper

first: Noriyoshi

last: Usui

first: Shari

last: Birnbaum

first: Haley

last: Tucker

first: Craig

last: Powell


title: Alterations of DNA methlation in oral cavity of mice induced by dibenzo[def,p]chrysene

first: Anna

last: Salzberg

state: MA

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

type: Methylation profiling by high throughput sequencing

summary: Despite advances in treatment modalities, 5-year survival of OSCC has remained at ~50% for the past decades, mostly due to the high risk of developing secondary primary tumors.  Early detection of OSCC represents one of the most promising approaches to improving survival.  In this study, we examined the alterations of DNA methylation in  early stage of oral carcinogenesis in mice induced by carcinogen dibenzo[def,p]chrysene.  We identified 30 differentially methylated sites and canonical pathways that may be served as potential biomarkers for early detection of OSCC.

overall_design: We analyzed the DNA methylomes from oral tissues of mice treated with dibeno[def,p]chrysene (24 nmol, 3 times per week, 5 weeks) or vehicle DMSO (n=3 per group).  This animal protocol was selected based on our previous study showing maximum DNA damage induced by carcinogen while the tissues were histologically normal .  Genomic DNA were extracted from oral tissues and subjected to Enhanced Reduced Representation Bisulfite Sequencing (ERRBS).

first: Yuan-Wan

last: Sun

middle: C


title: Transcriptome analysis of ruminal epithelia revealed that potential regulatory mechanisms involved in host adaptation to rapid high fermentable dietary transition in beef cattle

city: Edmonton

first: Ke

last: Zhao

institute: University of Alberta

summary: An abrupt transition from high forage to high fermentable diet may induce digestive disorders in the rumen. To date, the host mechanisms regulate the adaption to such dietary transition are largely unknown. To understand the molecular mechanisms involved in such phenomena, RNA-sequencing was performed to identify the changes in the transcriptomes of ruminal epithelia during a rapid high grain transition from 3% to 92% grain. In total, the expression of 11,044, 11,322 and 11,282 genes was detected in ruminal epithelia of beef heifers (n=15) fed 3%, 75% and 92% barley grain diet, respectively. When diet was changed from 75% to 92% grain, a significant difference was observed in the mean ruminal pH change among the individuals with five heifers decreased (DG; pH from 6.30 ± 0.09 to 5.87 ± 0.15, P < 0.01) and five other ones increased (UG; pH from 5.84 ± 0.42 to 6.35 ± 0.37, P < 0.05). In the ruminal epithelia of DG animals, the expression of genes involved in ketogenesis (HMGCL, P < 0.1) and lipid synthesis (SREBF2, P < 0.1; FABP4, P < 0.05) was increased, the abundance of genes involved in short chain fatty acid transporters (SMCT1, P < 0.1) and monocarboxylate transporters (MCT4, P < 0.1) was decreased. The function of “Concentration of lipid” was activated after 75% to 92% grain diet transition. Comparing to DG animals, the expression of ketogenesis (ACAT2, P < 0.05; HMGCS P < 0.1) and cholesterol synthesis related genes (HMGC and FDPs, P < 0.1) was deceased, while the expression of proton and cholesterol efflux related genes NHE3 and ABCA1 were increased (P < 0.05), and the function of “Storage of lipid” was inhibited in the ruminal epithelial of UG heifers. In addition, the function of differentially expressed (DE) genes in DG were involved in “T cell receptor signaling” and “complement and coagulation cascades” pathways, while the functions “metabolism of xenobiotics by cytochrome P450” and “p53 signaling pathway” were enriched for DE genes in UG animals. Furthermore, the single nucleotide polymorphisms (SNP) discovery by RNA-seq was performed, and SNP (g.46834311A > G) in FABP4 identified between two groups of animals (P < 0.1). The expression of genes involved in regulating lipid transport and fatty acid metabolism varied between DG and UG heifers during rapid 75% to 92% grain transition. The identified genes and SNP could be potential markers and may account for the varied ruminal pH responses between DG and UG heifers, which can be potentially applied in breeding and selecting beef cattle with more tolerance in dietary transition stress.

overall_design: Forty five rumen papillae samples were collected from fifteen heathy beef heifers (15 samples were collected when fed 3%, 75% and 92% grain diet, respectively). Using Trizol reagent to extract the total RNA, and the mRNA expression was profiled.

first: Yanhong

last: Chen


title: Bazedoxifene and conjugated estrogen combination improves gut-liver axis health [mouse liver]

city: Urbana

first: Karen

state: IL

address: 1201 W Gregory St

department: Division of Nutritional Sciences

institute: University of Illinois at Urbana-Champaign

summary: Bazedoxifene and conjugated estrogens (CE+BZA) combination has been shown to prevent visceral adiposity and weight gain after menopause. However, its interaction with the microbiota has yet to be examined. In the present study, we use several –omics technologies to characterize the effects of various estrogens on the health of gut-liver axis. As reported in previous studies, CE+BZA combination is very effective at preventing ovariectomy-induced weight gain in mice fed a high-fat diet. Additionally, CE+BZA induces unique liver transcriptomic and blood metabolite profiles compared to estradiol, conjugated estrogens alone, and bazedoxifene alone. Several pathways and metabolites influenced are associated with lower rates of inflammation and overall benefits to gut and liver health. Finally, microbiome analysis shows that several bacterial species that potentially metabolize estrogens and affect their half-life in the body were significantly changed in CE+BZA treated mice. Our findings indicate a possible link between certain estrogens and gut microbiome and suggest a metabolic benefit of estrogens through manipulation of the gut-liver axis.

overall_design: Liver samples treated with Bazedoxifene, estrogens, and vehicle control.

first: Zeynep

last: Madak-Erdogan


title: RNA-sequencing of GmPHD6 over-expression and RNAi transgenic hairy roots and the control samples of K599

city: Beijing

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No.2

department: State Key Lab of Plant Genomics

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Plant homeodomain (PHD) finger proteins are ‘histone code readers’. They recognize and bind to epigenetically modified histone H3 ‘tail’. Here we reported that an Alfin1-like soybean protein, GmPHD6, read H3K4me0/1/2 but not H3K4me3 with the N-terminal instead of the PHD finger. GmPHD6 does not possess transcriptional regulatory ability. Through the PHD finger, GmPHD6 interacts with its co-activator, LHP1-1/2. Using a transgenic hairy root system, we demonstrated that over-expression of GmPHD6 improved stress tolerance in transgenic soybean composites. Perhaps due to the excessive amount of LHP1 compared to that of GmPHD6, over-expression of LHP1-1/2 failed to do so. The integrity of the complex is essential in stress response, for the abrogation of DNA binding activity of GmPHD6 or the decrease of LHP1 content leads to stress sensitivity in soybean. GmPHD6 influences expression of dozens of stress-related genes to confer stress tolerance. Among these genes, we identified three direct targets of GmPHD6, ASR (ABA-stress-ripening induced), CYP71A22 (cytochrome P450) and CYP82C4. Our study reveals significant findings in stress response. GmPHD6 and LHP1 are recruited to H3K4me0/1/2 marks, where several stress-related genes may locate in, to form a transcriptional activation complex. GmPHD6 locates target sites through recognizing the G-rich elements in their promoters; LHP1 enhances expression levels of these targets. Genetically engineering of GmPHD6/LHP1 complex should improve stress tolerance in crop plants.

overall_design: Three samples were chosen, GmPHD6 over-expression, GmPHD6 RNAi and the control sample (K599).Downstream genes are defined as the common genes that are up-regulated in GmPHD6-OE sample and down-regulated in RNAi sample.

first: Jian-Jun

last: Tao

first: Hao-Wei

first: Qing-Tian

last: Li

first: Wan-Ke

last: Zhang

first: Biao

last: Ma

first: Qing

last: Lin

first: Jin-Song

first: Shou-Yi


title: Transcriptome profiling and digital gene expression analysis of sweet potato challenged with Fusarium oxysporum f. sp.batatas.

city: Fuzhou

first: Xuanyang

address: 15,Shangxiadian road,cangshan district

institute: Fujian Agriculture and Forestry University

summary: we performed de novo transcriptome assembly and digital gene expression (DGE) profiling analyses of sweet potato challenged with Fob using Illumina Hiseq technology. A total of 89,944,188 clean reads were generated and were assembled into 101,988 unigenes with an average length of 666bp, 62,605(61.38%) of them were functional annotated in the non-redundant(nr) protein database from NCBI by using BLASTX with a cut-off E-value of 10-5, and COG,GO and KEGG annotations were examined for better understand their functions. Five DGE libraries were constructed from the sweet potato cultivar JS57 (high resistance) and XZH (high susceptible) challenged with pathogenic and Nonpathogenic Fob. The differentially expressed genes including up- and down-regulation in five libraries were identified and calculated based on comparisons of transcriptomes, showing differences in gene expression profiles among the samples. A set of differentially expressed genes involved disease response were identified, including 40 WRKY and seven NAC transcription factors, four resistance genes, 22 pathogenesis-related genes, and six genes involved in SA signal pathway. Our study is the first to provide the transcriptome sequence resource of sweet potato challenged with pathogenic and non-pathogenic Fob and demonstrate its digital expression profiling. We discovered a set of genes involved in disease resistance. These data provides comprehensive sequence resource of sweet potato for genetic and genomic studies and will accelerate the understanding of molecular mechanism of disease resistance.

overall_design:
There were five sample groups were prepared in this experiment:
(1) JS57 inoculated with Fob-07 (JS57-F07); (2) JS57 inoculated with Fob-04 (JS57-F04); (3) JS57 in water (JS57-CK); (4) XZH inoculated with Fob-07 (XZH-F07); (5) XZH in water(XZH-CK).
Total RNAs were isolated and mixed equally to create a RNA pool for cDNA library, then the transcriptome was generated using Illumina HiSeq 2500 sequencing.

first: Yuli

first: Weikun

last: Zou

first: Zhaojuan

first: Dennis

last: Onofua

first: Shiqiang

first: Songliang

last: Wang

first: Zhijian

last: Yang


title: Genetic Model of  iron deficiency in the Mouse Liver

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary: Iron overload causes the generation of reactive oxygen species, which can lead to lasting damage to the liver and other organs.  We studied the effects of iron deficiency and iron overload on the hepatic transcriptional and metabolomic profile in mouse models.

overall_design: We studied effect of different iron  deficiency by HJV gene knockout mice on liver transcriptome using whole genome transcriptome profiling.

first: Paula

last: Fraenkel


title: A cell cycle-based functional screen to identify lncRNA-based cancer biomarkers

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

type: Non-coding RNA profiling by high throughput sequencing

summary: We report S-phase cancer associated lncRNAs which were identified using nascent RNA capture assay in HeLa cells. Coupling high throughput RNA sequencing with clinical investigation across TCGA datasets we identified a number of lncRNAs that act as prognostic biomarkers for survival in different cancer types

overall_design: The differential expression levels of S-phase specific lncRNAs across TCGA datasets were assessed. The clinical values of the differentially expressed lncRNAs were predicted using Kaplan-Meir, univariate and multivariate Cox regression analysis. Functional characterization for different lncRNAs was done using knockdown strategies followed by RNA-seq

first: Chandrasekhar

last: Kanduri

first: Mohamad

middle: M

last: Ali

middle: T

last: Kosalai

first: Santhilal

last: Subhash


title: Genetic vs Dietary Models of Iron Overload in the Mouse Liver

overall_design: We studied effect of different iron overloads (High, medium and Low) on liver transcriptome using whole genome transcriptome profiling.


title: Evaluation of the immunogenicity of live-attenuated influenza vaccines in nasal epithelial cells in primary differentiated human nasal epithelial cells [RNA-Seq]

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

summary: The host innate immune response to influenza virus is a key determinant of pathogenic outcomes and long-term protective responses against subsequent exposures. Comparison of the transcriptional profiles obtained 24 and 36 hrs post-infection showed that the magnitude of gene expression was greater in LAIV infected cells relative to that observed in WT infected cells. Functional enrichment analysis revealed that the antiviral and inflammatory responses was largely driven by type III IFN induction in both WT and LAIV infected cells. However, the enrichment of biological pathways involved in the recruitment of mononuclear leukocytes, antigen presenting cells, and T lymphocytes was uniquely observed in LAIV infected cells. These findings indicate that cell-intrinsic type III IFN-mediated innate immune responses in the nasal epithelium are not only crucial for viral clearance and attenuation, but may also play an important role in the immunogenicity of live-attenuated vaccines

overall_design: Differentiated hNECs were infected at a multiplicity of infection (MOI) of 5 50% tissue culture infectious dose per cell.  Prior to infection, cells were apically washed and the basolateral media was refreshed with 500 μl of fresh LHC Basal Medium.  The virus inoculum was added to the apical compartment and incubated for 2 hours, after which the inoculum was aspirated and the apical chamber was washed three times.  The plates were then returned to the incubator. RNA was isolated from Trizol homogenates from samples harvested at 24hpi and 36hpi.  Gene expression microarray analysis was conducted on these samples.

first: Adriana

last: Forero

first: Katherine

last: Fenstermacher

first: Nicholas

last: Wohlgemuth

first: Victoria

last: Carter

first: Elise

last: Smith

first: Andrew

last: Nishida

first: Xinxia

last: Peng

first: Melissa

last: Hayes

first: Doreen

last: Francis

first: John

last: Treanor

first: Juliet

last: Morrison

first: Sabra

middle: L

last: Klein

last: Lane

last: Pekosz


title: Methylation of Transcription Factor YY2 Regulates its Transcriptional Activity and Cell Proliferation

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

summary: Yin Yang 1 (YY1) is a multifunctional DNA-binding transcription factor shown to be critical in a variety of biological processes, and its activity and function have been shown to be regulated by multitude of mechanisms, which include but are not limited to post-translational modifications (PTMs), its associated proteins and cellular localization. YY2, the paralog of YY1 in mouse and human, has been proposed to function redundantly or oppositely in a context specific manner compared to YY1. Despite its functional importance, how YY2’s DNA binding activity and function is regulated, particularly by PTMs, remains completely unknown. Here we report the first PTM with functional characterization on YY2, namely lysine 247 mono-methylation (K247me1), which was found to be dynamically regulated by SET7/9 and LSD1 both in vitro and in cultured cells. Functional study revealed that SET7/9-mediated YY2 methylation regulated its DNA-binding activity in vitro and association with chromatin examined by ChIP-seq (chromatin immunoprecipitation coupled with sequencing) in cultured cells. Knockout of YY2, SET7/9 or LSD1 by CRISPR (clustered, regularly interspaced, short palindromic repeats) /Cas9-mediated gene editing followed by RNA-seq revealed that a subset of genes was positively-regulated by YY2 and SET7/9, but negatively-regulated by LSD1, which were enriched with genes involved in cell proliferation regulation. Importantly, YY2-regulated gene transcription, cell proliferation and tumor growth were dependent, at least partially, on YY2 K247 methylation. Finally, somatic mutations on YY2 found in cancer, which are in close proximity to K247, altered its methylation, DNA binding activity and gene transcription it controls. Our findings revealed the first PTM with functional implications imposed on YY2 protein, and linked YY2 methylation with its biological functions.

overall_design: The YY2 ChIP-seq in this study was designed to reveal YY2 genomic binding sites in HeLa cells.

first: Wen

last: Liu

first: Wen-juan

first: Jian-cheng

last: Ding


title: Evaluation of the immunogenicity of live-attenuated influenza vaccines in nasal epithelial cells in primary differentiated human nasal epithelial cells

first: Michael

last: Katze

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

overall_design: Refer to individual Series


title: Methylome Analysis of Esophageal Squamous Cell Carcinoma by using Next Generation Sequencing

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

institute: Axiohelix Co. Ltd.

summary: We obtained methylome profiling (MeDIP-seq) of esophageal squamous cell carcinoma (ESCC) and normal tissue specimens by using next generation sequencing.

overall_design: Comparison of DNA methylation pfofiles between ESCC and normal mucosa.

first: Takeshi

last: Otsubo

first: Kenshiro

last: Oshima

first: Kei

last: Iida

first: Koro

last: Nishikata

first: Tetsuro

last: Toyoda

first: Masahira

last: Hattori

first: Taeko

last: Dohi

first: Yuki

middle: I

last: Kawamura


title: Transcriptome Analysis of Esophageal Squamous Cell Carcinoma by using Next Generation Sequencing

summary: We obtained transcriptome profiling (SAGE-seq) of esophageal squamous cell carcinoma (ESCC) and normal tissue specimens by using next generation sequencing.

overall_design: Comparison of expression pfofiles between ESCC and normal mucosa.


title: Integrated analysis of methylome and transcriptome of Esophageal Squamous Cell Carcinoma by using Next Generation Sequencing


title: A requirement for dual-specificity phosphatase 6 in zebrafish gametogenesis

status: Public on Feb 12 2018

city: Worcester

first: Jennifer

last: Maurer

address: 364 Plantation Street, LRB 870D

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

summary: Identification of genes that are differentially-expressed in dusp2um287/um287;dusp6um286/um286 mutant embryos compared to wildtype

overall_design: Total RNA was extracted from pools of dechrionated, deyolked wildtype and dusp2um287/um287;dusp6um286/um286 embryos at 18hpf using the RNeasy Mini Kit (Qiagen). Three libraries from wildtype embryos and three libraries from dusp2um287/um287;dusp6um286/um286 embryos were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). All libraries were analyzed for quality on a bioanalyzer prior to sequencing (Agilent 2100 BioAnalyzer).

first: Charles

last: Sagerstrom


title: Expression data from liver sinusoidal endothelial cells in Wild Type and NICeCA

city: Xi'an

first: Bai

last: Ruan

state: Shannxi

address: No.169, Changle Road

institute: Fourth Military Medical University

summary: The Notch pathway plays a critical role in regulating the proliferation and differentiation of endothelial cells during liver homeostasis,so we used EC-specific Notch activation flox-Notch1-ICD mice, and compare the gene expression profiles of LSEC in wild type and NICeCA

overall_design: liver sinusoidal endothelial cells mRNA profiles of 7-8 weeks old wild type (WT) and NICeCA mice were generated by RNA sequencing, in triplicate, using Illumina HiSeq 3000

first: Lin

last: Wang

first: Juanli

last: Duan


title: Highly multiplexed and quantitative cell surface protein profiling using genetically barcoded antibodies

city: South San Francisco

first: Samuel

last: Pollock

state: CA

address: 1 DNA way

department: MPL

institute: Genentech

summary: Next generation sequencing (NGS) allows for sensitive quantification of DNA and RNA. It would be highly desirable to have a systematic equivalent for assaying cellular protein levels on living cells. We present a highly multiplexed, quantitative, and inexpensive sequencing-based proteomic method using genetically barcoded antibodies called Phage-antibody Next Generation Sequencing (PhaNGS). We demonstrate the utility of PhaNGS by showing how a set of 144 targeted Fab-phage can reliably detect changes in 44 targeted cell surface proteins in drug sensitive and resistant B-cells, or upon induction of the Myc oncogene.

overall_design: We examined profiling of Fab-phage against parental and surface GFP over-expression conditions with 2 replicates each for HeLa cells; we examined diagnosis and relapse conditions with 4 replicates each for LAX7 cells; we examined induction of expression or control conditions with 3 replicates each in surface-CDCP1-expressing T-REx cells; we examined control (MycON), MycOFF, and wash-out (MycBACKON) conditions with 4 replicates each for P493-6 cells; we examined 72 single T-REx cells over-expressing surface GFP; and we examined 95 single P493-6 cells. Each individual group comes with an input mixture against which the outputs are compared.

middle: B

first: Amy

last: Hu

first: Yun

last: Mou

first: Alexander

last: Martinko

first: Olivier

last: Julien

last: Hornsby

first: Lynda

last: Ploder

first: Jarrett

last: Adams

first: Huimin

last: Geng

first: Markus

last: Müschen

first: Sachdev

last: Sidhu

first: Jason

last: Moffat

first: James

last: Wells


title: Burden- driven feedback control of gene expression

city: Siena

first: Simone

last: Furini

address: viale Mario Bracci, 16

department: Department of Medical Biotechnologies

country: Italy

institute: University of Siena

summary:
RNAseq analysis was performed on 90 E. coli samples in order to identify the transcriptional cellular response to the burden of heterologous gene expression
Early responsive promoters that are upregulated in response to burden were identified. The htpG1 early responsive promoter was selected to guide the activation of a burden- responsive feedback controller able to decrease heterologous gene expression while rescuing cellular capacity and growth

overall_design: E. coli DH10B/MG1655, previously modified to bear a GFP expressing cassete integrated in the genome [Ceroni et al Nat Methods 2015], were transformed with 4 synthetic constructs and their empty plasmids. RNAseq analysis was performed at 15 and 60 min after induction of gene expression to capture the very first response to burden in these systems.

first: Francesca

last: Ceroni

first: Tom

last: Gorochowski

first: Alice

last: Boo

last: Borkowski

first: Yaseen

last: Ladak

first: Ali

last: Awan

first: Charlie

last: Gilbert

first: Guy-Bart

last: Stan

last: Ellis


title: Sequencing of matched pair samples (diagnosis and relapse) in human B-cell acute lymphoblastic leukemia cells (ALL)

city: San Francisco

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: The experiment focused on how B-cells respond transcriptionally to drug treatment in acute lymphocytic leukemia (ALL). We obtained B-cell samples from a patient at diagnosis (LAX7) and after the development of resistance (LAX7R) following a standard 3-week chemotherapy regimen (vincristine, dexamethasone, L-asparaginase and doxorubicin). The resistance sample possessed a KRASG12V mutation not present at diagnosis.  Cells obtained from the patient were directly engrafted into NOD/SCIDγc-/- mice, and later frozen as stocks.

overall_design: Genome-wide profiling of total RNA transcript levels in human B-cell acute lymphoblastic leukemia cells (ALL)

last: Muschen

first: Sam

last: Pollock

first: Jim


title: A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [RNA-Seq, HiC_C2C12, ChIP-Seq]

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

summary: The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here, we tested the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~15 CTCF binding sites, and located at the long non-coding RNA (lncRNA) locus Firre. Specifically, this TAD boundary is invariant across evolution, tissues, and temporal dynamics of X-chromosome inactivation. We demonstrate that neither the deletion of this locus, nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter TADs in a sex-, or allele-specific manner. In contrast, Firre’s deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms can play roles in establishing TAD boundary formation.

overall_design: Hi-C in C2C12 mouse muscle cells, RNAseq in wildtype and Firre lncRNA knockout male and female mouse embryonic fibroblasts (MEFs), CTCF ChIP-seq in wildtype, Firre lncRNA kncokout and transgene MEFs

first: A

middle: R

first: Philipp

last: Maass

first: Jordan

middle: P

last: Lewandowski

first: Catherine

last: Weiner

first: John

last: Rinn


title: Role of SKN-1 in dpy-7 and osmotic gene induction

city: Gainesville

first: Keith

last: Choe

state: Florida

address: 876 Newell Dr, 321 Bartram Hall

institute: University of Florida

summary: We report the use of mRNA sequencing to analyze the role of SKN-1 in regulation of genes under two conditions, dpy-7 mutants and high osmolarity.

overall_design: Total RNA was prepared from gravid young adult Caenorhabditis elegans with three biological replicates and sent to the Yale Center for Genome Analysis for 75 nucleotide single-end sequencing in an Illumina HiSeq 2000.  Sequence files were processed with Kallisto to quantify transcripts and Sleuth for differential adundance analysis.

first: Cheng-Wei

last: Wu


title: A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [HiC_MEF]

overall_design: Allele-specific and traditional Hi-C in Firre lncRNA loss and gain of function mouse embryonic fibroblasts


title: Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture (human)

city: Berlin

first: Darío

last: Lupiáñez

address: Ihnestrasse 73

institute: Max Planck Institute for Molecular Genetics

summary: Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and consecutive disease. However, the prediction of such effects remains a challenge. Here we present a polymer physics based approach (PRISMR) to model chromatin folding and to predict enhancer-promoter contacts. Using the Epha4 locus as a model, the effects of pathogenic SVs were predicted in-silico and compared to published Hi-C and capture Hi-C data generated from mouse limb buds and patient-derived fibroblasts. PRISMR deconvolutes the folding complexity of the studied locus, and identifies SV-induced alterations of 3D genome organization in the homozygous as well as the heterozygous state. Our method accurately predicts the specific sites of ectopic chromatin contacts that produce extensive rewiring of regulatory interactions, causing disease by gene misexpression. PRISMR can be used to predict interactions in silico thereby providing a tool for analyzing the disease causing potential of SVs.

overall_design: Capture Hi-C experiments at the EPHA4 locus in human skin fibroblasts from patients (heterozigous mutations) and healthy controls.

first: Robert

last: Schöpflin

first: Katerina

last: Kraft

first: Guillaume

last: Andrey

first: Stefan

last: Mundlos


title: Transcriptome analysis of mRNA and microRNAs of the intramuscular fat tissues from castrated and intact male Chinese Qinchuan cattle

city: Shanghai

first: zhang

middle: ying

last: ying

state: Shanghai

address: Beidi Road No.2901

department: Institute of Animal Husbandry & Veterinary Science

institute: Shanghai Academy of Agricultural Sciences

summary:
We report the application of the second-generation sequencing technology for microRNA and mRNA gene expression profiling of intramuscular fat (IMF) in castrated male (CM) and intact male 24 months old Qinchuan cattle (IM) to explore the regulation of intramuscular fat deposition. By comparing the mRNA expression profiles of IMF between CM and IM, 580 upregulated and 1120 downregulated genes were identified as differentially expressed genes correlated with castration.
The upregulated genes were mainly associated with lipid metabolism, lipogenesis and fatty acid transportation signaling pathway, and the downregulated genes were correlated with immune response, intracellular signal transduction. Concurrently, the DE miRNAs, which are the important player in adipose tissue accumulation induced by castration, were also examined in IMF tissues, and 52 DE miRNAs were identified. Additionally, the expression profiles of selected genes and miRNAs were confirmed by using quantitative real-time PCR (qRT-PCR) assays. Furthermore, by means of integrated analysis, a total of 951 differentially expressed miRNA-Mrna pairs including 103 DE miRNAs and 535 DE mRNAs were found to show a negative correlation and a pair bovine known microRNA-target network was constructed which were supported by targets validation using dual luciferase reporter system. Moreover, the Ingenuity Pathway Analysis (IPA) software was used to construct a molecular interaction network which might involve in regulating IMF after castration. This molecular network is closely associated with lipid metabolism and adipocyte differentiation, which is supported by the functional identification results of bta-let-7i on bovine preadipocytes. These results provided valuable insights into the molecular mechanisms resulting in the IMF phenotype difference between CM and IM cattle.

overall_design: Intramuscular fat mRNA and microRNA profiles of castrated male (CM) and intact male (IM) 24 monthes old cattle were respectively generated by using Ion ProtonTM Sequencer and Illumina HiSeq 2500. Two cDNA libraries representing CM and IM groups (coming from a pooling of 6 CM and 6 IM IMF) were constructed for mRNA transcriptome analysis. A total of four small RNA libraries (CM1, CM2, IM1, and IM2, a pooling of 3 CM or IM IMF for each library) were constructed for microRNA transcriptome analysis.

first: Zhang

last: Yingying

first: Wang

last: Hongbao

last: Yaning

last: Hongcheng

last: Song

first: Hong

last: Jieyun

first: Guo

last: Hongfang

first: Chen

last: dai

first: Yang

last: Yang

first: Zan

last: Linsen


title: Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture (mouse)

overall_design: Capture Hi-C experiments at the Epha4 locus in developing distal limbs of homozigous mutants and WT mice at E11.5


title: Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP pathways in macrophages

city: La Jolla

first: Jenhan

last: Tao

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: UC San Diego

summary: Activation of liver X receptors (LXRs) with synthetic agonists promotes reverse cholesterol transport and protects against atherosclerosis in mouse models.  Most synthetic LXR agonists also cause marked hypertriglyceridemia by inducing the expression of SREBP1c and downstream genes that drive fatty acid biosynthesis.  Recent studies demonstrated that desmosterol, an intermediate in the cholesterol biosynthetic pathway that suppresses SREBP processing by binding to SCAP, also binds and activates LXRs and is the dominant LXR ligand in macrophage foam cells.    Here, we explore the potential of increasing endogenous desmosterol production or mimicking its activity as a means of inducing LXR activity while simultaneously suppressing SREBP1c induced hypertriglyceridemia.  Unexpectedly, while desmosterol strongly activated LXR target genes and suppressed SREBP pathways in mouse and human macrophages, it had almost no activity in mouse or human hepatocytes in vitro.   We further demonstrate that sterol-based selective modulators of LXRs have biochemical and transcriptional properties predicted of desmosterol mimetics and selectively regulate LXR function in macrophages in vitro and in vivo.     These studies thereby reveal cell-specific discrimination of endogenous and synthetic regulators of LXRs and SREBPs, providing a molecular basis for dissociation of LXR functions in macrophages from those in liver that lead to hypertriglyceridemia.

overall_design: Primary mouse hepatocytes (in duplicate) and thioglycollate elicited mouse macrophages (in triplicate) were treated in vitro with various ligands for 18-20 hours prior to RNA isolation and RNA-Seq library preparation

first: Christopher

middle: K

last: Glass

first: Evan

middle: D

last: Muse

first: Nathan

last: Spann


title: Ezh2 and Runx1 Mutations Targeted to Early Lymphoid Progenitors Collaborate to Promote Early Thymic Progenitor Leukemia

city: Oxford

first: Adam

last: Mead

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford


title: Transcriptome-wide measurement of ribosomal occupancy by ribosome profiling

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

summary: Experiments for optimization of the ribosome profiling protocol using C. elegans lysates. We report that optimizing the cutting accuracy to a narrow window of 28-30 nucleotides when PAGE-purifying the ribosome-protected fragments (RPFs) significantly improves the quality of the RPF library. In addition, we find that purifying monosomes by sucrose gradient fractionation clearly removed more contaminating ribosomal RNA from the samples compared to the purification by gel filtration columns.

overall_design: Experiment 1 (samples 1-4): Comparison between different methods to isolate monosomes and between different library preparations. Experiment 2 (samples 5-8): Optimization of the cutting accuracy to PAGE purify ribosome-protected fragments.

first: Florian

last: Aeschimann

first: Andreas

last: Arnold

first: Christoph

last: Dieterich

first: Helge

last: Grosshans


title: Ezh2 and Runx1 Mutations Targeted to Early Lymphoid Progenitors Collaborate to Promote Early Thymic Progenitor Leukemia [RNA-Seq 1]

summary: Understanding the specific cell populations responsible for propagation of leukemia is an important step for development of effective targeted therapies. Recently, the lymphoid-primed multipotent progenitor (LMPP) has been proposed to be a key propagating population in acute myeloid leukemia (AML; PMID 21251617). We have also shown that LMPPs share many functional and gene expression properties with early thymic progenitors (ETPs; PMID 22344248). This finding is of particular interest as ETP leukemias have recently been described: a distinct and poor prognostic disease entity with a transcriptional profile reminiscent of murine ETPs, showing co-expression of hematopoietic stem cell (HSC) and myeloid markers (PMID 19147408). Together, this raises the question whether ETPs can act as a leukemia-initiating/propagating cell population; however, relevant disease models to test this hypothesis are currently lacking. Analysis of the genetic landscape of ETP leukemias has revealed frequent coexistence of inactivating mutations of EZH2 and RUNX1 (PMID 22237106). We therefore generated mice with deletions of Ezh2 and Runx1 specifically targeted to early lymphoid progenitors using Rag1Cre (Ezh2fl/flRunx1fl/flRag1Cre+; DKO mice). As anticipated, HSCs lacked significant recombination in DKO mice whereas close to 100% of purified ETPs (Lin-CD4-CD8-CD44+CD25-Kit+Flt3+) showed deletion of Ezh2 and Runx1. Strikingly, despite a 16-fold reduction in thymus cellularity caused by a block in thymocyte maturation at the DN2-DN3 transition, absolute numbers of ETPs within the thymus of DKO mice were markedly expanded (12-fold; p<0.0001). In contrast, Ezh2 or Runx1 deletion alone had no impact on numbers of ETPs. RNA-sequencing of the expanded ETPs in DKO mice revealed upregulation of HSC- and myeloid-associated transcriptional programs, reminiscent of ETP leukaemia e.g. Pbx1 (log2FC=3.0; p<0.0001) and Csf3r (log2FC=1.9; p=0.0038). Single-cell gene expression analysis confirmed co-expression of HSC and myeloid programs with lymphoid genes within individual DKO ETPs. Further, some key regulators of T-cell maturation which are aberrantly expressed in ETP leukemia were also disrupted in DKO ETPs e.g. Tcf7 (log2FC=-9.5; p<0.0001). Gene expression associated with aberrant Ras signalling was also present. However, despite a continued expansion of the ETP population with age, we did not observe leukemia in DKO mice with over 1 year of follow-up. Since ETP leukemias frequently feature activating mutations in genes regulating RAS signaling, we hypothesised that the expanded “pre-leukemic” ETPs in DKO mice would be primed for leukemic transformation by signalling pathway mutation. We therefore crossed DKO mice with a Flt3ITD/+ knock-in mouse line, as internal tandem duplications (ITD) of FLT3 are frequent in ETP leukemias. Ezh2fl/flRunx1fl/flRag1Cre+Flt3ITD/+ (DKOITD) mice showed dramatically reduced survival (median 9.3 weeks) resulting from an aggressive, fully penetrant acute leukemia showing a predominantly myeloid phenotype (e.g. Mac1) but with co-expression of some lymphoid antigens (e.g. intracellular CD3). Crucially, this leukaemia could be propagated in wild-type recipients upon transplantation of the expanded ETPs. DKOITD ETPs were transcriptionally very similar to DKO ETPs, retaining expression of lymphoid alongside HSC- and myeloid-associated genes. Finally, in a lympho-myeloid cell line model (EML cells) we demonstrated that Ezh2 inactivation-induced loss of H3K27me3 is associated with a corresponding increase in H3K27Ac, a transcriptional activating signal that recruits bromodomain proteins. As such, we reasoned that our ETP leukemia model might be sensitive to bromodomain inhibitors such as JQ1. Indeed, we observed high sensitivity of expanded DKOITD ETPs to JQ1, raising the possibility of a new therapeutic approach for ETP leukemias. This novel mouse model of ETP-propagated leukemia, driven by clinically relevant mutations, provides intriguing evidence that leukemias with a predominant myeloid phenotype, but co-expressing lymphoid genes, may initiate within a bona fide early lymphoid progenitor population. Since the functional characteristics of the cell of origin of a leukaemia may direct its progression and response to therapy, these findings could have important implications for future stratification and treatment of both AML and ETP leukemias.

overall_design: mRNA-sequencing of mouse early thymic precursors from three genotypes

last: Booth

first: Nikolaos

last: Barkas

first: Wen

middle: H

last: Neo

first: Elizabeth

last: Soilleux

first: Hanane

last: Boukarabila

first: Alice

last: Giustacchini

first: Thomas

last: Milne

first: Neil

last: Ashley

first: Joana

last: Carrelha

first: Lauren

last: Jamieson

first: Deborah

last: Atkinson

first: Tiphaine

last: Bouriez-Jones

first: Sten

middle: E

last: Jacobsen


title: Ezh2 and Runx1 Mutations Targeted to Early Lymphoid Progenitors Collaborate to Promote Early Thymic Progenitor Leukemia [RNA-Seq 2]

first: Adam

last: Mead

overall_design: mRNA-sequencing of mouse Mac1+ bone marrow cells from three genotypes

first: Christopher


title: Distribution of transcription elongation complex in the PTPRN2 gene

city: beijing

first: XiaLu

last: Li

address: 105 Xisanhuan Beilu

institute: Capital Normal University

summary: Analysis of RNA polymerase II (RNAP II) binding data in HCT116-C52-tTA cells provides insight into the stalling site of RNAP II in the human PTPRN2 gene.

overall_design: We established a stable HCT116 cell line, HCT116-C52, in which a tetracycline (tet)-repressible promoter was integrated into the second intron of the PTPRN2 gene by homologous recombination. An EGFP-tagged tTA (EGFP-tTA) expression cassette was then introduced into the HCT116-C52 cells by virus transduction to generate HCT116-C52-tTA cells. RNAP II binding sites in HCT116-C52-tTA cells were determined by RNAP II ChIP-seq, using an antibody targeting the YSPTSPS repeats in the C-terminal domain (CTD) of the largest subunit of RNAP II.

first: Yi

last: Wei

first: Fan

last: Yang

first: Juchuanli

last: Tu

first: Peihua

last: Zhao

first: Yonggong

last: Zhai

first: Ying

last: Tao

first: Xialu


title: Genome-wide maps of Brd7 binding sites in control and BRD7 overexpressed cells.

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: We applied Chromatin immunoprecipation and massively parallel DNA sequencing technique, ChIP-seqencing, to identify the binding sites of Brd7 protein in human cells. ChIP-seq was applied to HEK293 cell line in control and BRD7 overexpressed cells.

overall_design: Map binding sites of Brd7 in the genome of HEK293 cells

first: K

last: Xu

first: W


title: Gene expression profiling of HEK293 in control and BRD7 overexpression cells (DGE)

summary: We applied digital gene expression profiling to HEK293 cell line in control and BRD7 overexpressed cells, to investigate the globle differently gene expression.

overall_design: Examination of differentially expressed genes in control and BRD7 overexpressed HEK293 cell line


title: High technical resolution transcriptomics analysis for CHO cells

city: Brisbane

first: Camila

middle: Antonia

last: Orellana

state: Queensland

address: Crn College and Cooper Rds (Bldg 75)

department: Australian Institute for Bioengineering and Nanotechnology

country: Australia

institute: The University of Queensland

summary: The development of next-generation sequencing technologies has opened new opportunities to better characterize complex eukaryotic cells. Chinese hamster ovary (CHO) cells play a primary role in therapeutic protein production, with currently five of the top ten blockbuster selling drugs produced in CHO. However, engineering superior CHO cells with improved production features has had limited results to date and cell lines are still developed through generation and screening of large strain pools. Here, we applied RNA sequencing to contrast a high and a low monoclonal antibody producing cell line. Rigorous experimental design achieved high reproducibility between biological replicates, remarkably reducing variation to less than 10%. More than 14,000 gene-transcripts were identified and surprisingly 58% were classified as differentially expressed, including 2,900 with a fold change higher than 1.5. The largest differences were found for gene-transcripts belonging to regulation of apoptosis, cell death and protein intracellular transport GO term classifications, which were found to be significantly enriched in the high producing cell line. RNA sequencing was also performed to lower producing subclones, where down-regulation of genes encoding secreted glycoproteins was found to be the most significant change. The large number of significant differences even between subclones suggests a substantial genetic fluidity in CHO lines and challenges the notion of identifying and manipulating a few key genes to generate high production CHO cell lines.

overall_design: Two Illumina RNA-Seq comparisons were performed: high producer (3 biological replicates) versus low producer (3 biological replicates) and subclone high producer (3 biological replicates) versus subclone low producer (3 biological replicates)

middle: A

first: Esteban

last: Marcellin

first: Robin

middle: W

last: Palfreyman

first: Trent

last: Munro

first: Peter

last: Gray

first: Lars

last: Nielsen


title: RNA-seq of MCF10A cells and CAF

status: Public on Feb 11 2018

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

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

overall_design: Refer to individual Series


title: Ezh2 and Runx1 Mutations Targeted to Early Lymphoid Progenitors Collaborate to Promote Early Thymic Progenitor Leukemia [ChIP-Seq]

first: Adam

last: Mead

overall_design: Examine the distribution of H3K27me3 mark and binding sites of Ezh2 and Runx1 in EML_C1 cells.

first: Christopher

last: Booth

first: Nikolaos

last: Barkas

first: Wen

last: Neo

first: Elizabeth

last: Soilleux

first: Hanane

last: Boukarabila

first: Alice

last: Giustacchini

first: Thomas

last: Milne

first: Neil

last: Ashley

first: Joana

last: Carrelha

first: Lauren

last: Jamieson

first: Deborah

last: Atkinson

first: Tiphaine

last: Bouriez-Jones

first: Sten

last: Jacobsen

middle: J


title: RNA-seq of cancer-associated fibroblasts (CAF) treated with PBS or extracellular vesicles (EV) from MCF10A or MDA-MB-231 cells

summary: To identify gene expression changes associated with treatment of EV that carry high levels of miR-105 (from MDA-MB-231 and MCF10A/miR-105 cells) in human breast tumor derived CAF, we analyzed RNA isolated from PBS- or EV-treated CAF.  Gene expression in CAF treated with EV from MDA-MB-231 or MCF10A/miR-105 cells was compared to cells treated with PBS or EV from MCF10A cells, both of which served as controls in this experiment.

overall_design: RNA was extracted from PBS- and EV-treated CAF, and subjected to library construction and RNA sequencing.

first: Shizhen

last: Wang


title: RNA-seq of MCF10A cells stably expressing empty vector, GFP, miR-105, or MYC

summary: To identify gene expression changes associated with overexpression of miR-105 or MYC in MCF10A non-cancerous human mammary epithelial cells, we analyzed RNA isolated from engineered MCF10A cell lines that stably express empty vector, GFP, miR-105, or MYC by RNA-seq.  Gene expression in cells overexpressing miR-105 or MYC was compared to cells expressing the empty vector or GFP, both of which served as controls in this experiment.

overall_design: RNA was extracted from MCF10A cells stably expressing pBabe vector, pBabe-GFP, pBabe-miR-105, or pBabe-MYC; RNA was then subjected to library construction and RNA sequencing.


title: Tumor suppressor REST/NRSF controls genome stability by preventing R-loop formation

first: XiaLu

last: Li

summary: Analysis of HeLa cell with overexpression of an EGFP-tagged dominant-negative truncation (73- 563 a.a.) of human REST/NRSF. RNA polymerase II and DNA damage repair factor γ-H2AX binding data provide insight into the molecular bases of how REST/NRSF perturbation impairs genome stability.

overall_design: Identification of RNA polymerase II and γ-H2AX binding sites in normal and REST-disrupted HeLa cells. An antibody targeting the YSPTSPS repeats in the C-terminal domain (CTD) of the largest subunit of RNAP II was utilized to immunoprecipitate RNAP II, regardless of its phosphorylation status.

first: Yi

last: Wei

first: Fan

last: Yang

first: Juchuanli

last: Tu

first: Peihua

last: Zhao

first: Yonggong

last: Zhai

first: Ying

last: Tao

first: Xialu


title: Temporally-regulated tRNA-derived small RNAs are associated primarily with non-polysomal fractions in Drosophila

city: Urla

first: Bunyamin

last: Akgul

state: izmir

address: Gulbahcekoyu

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

summary: Eukaryotic genomes contain various types of small non-coding RNAs such as microRNAs (miRNAs), silencing RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). Recent studies point to the presence of a more diverse array of uncharacterized small regulatory RNAs including those that are generated from mRNAs, rRNAs and tRNAs. To explore the possible involvement of tRNA-derived fragments (tRFs) in translational regulation, we fractionated 1 and 8h Drosophila embryos on sucrose density gradients and quantitatively measured by deep-dequencing the expression levels of the tRFs in the fractionated and unfractionated Drosophila embryonic cytosolic extracts. Analysis of 9,007,661 reads has revealed that tRFs, which are produced mainly from the 5’ends of a subset of tRNAs, are mostly associated with the non-polysomal fractions in Drosophila embryos. Quantitative analysis indicates that the expression levels of a subset of tRFs change temporally following the maternal-tozygotic transition in embryos. We detected non-polysomal association of tRFs in S2 cells as well. When transfected into S2 cells, the biotinylated tRFgly:GCC:5 co-fractionated with the non-polysomal complexes similar to the endogenous tRFgly:GCC:5 in embryos and S2 cells. These results suggest that the tRFs, which are much smaller in size than the stres-induced tRNA fragments, are generated selectively from a fraction of tRNAs and that they associate primarily with the non-polysomal complexes in Drosophila embryos and S2 cells.

overall_design: Examination of small RNAs from 10 (mRNP, 60S, 80S, Polysome and Total RNA) samples of 0-1h and 7-8h embryos

first: Hatice

last: Yigit

first: Mehmet

last: Cosacak


title: Neurogenomic Profiling Reveals Distinct Gene Expression Profiles between Brain Parts that are Consistent in  Ophthalmotilapia Cichlids

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

institute: Genomics Core Leuven

summary: The detection of external and internal cues alters gene expression in the brain which in turn may affect neural networks that underly behavioral responses. Previous studies have shown that gene expression profiles differ between major brain regions within individuals and between species with different morphologies, cognitive abilities and/or behaviors. A detailed description of gene expression in all macroanatomical brain regions and in species with similar morphologies and behaviors is however lacking. Here, we dissected the brain of two cichlid species into six macroanatomical regions. Ophthalmotilapia nasuta and O. ventralis have similar morphology and behavior and occasionally hybridise in the wild. We use 3’ mRNA sequencing and a stage-wise statistical testing procedure to identify differential gene expression between females that were kept in a social setting with other females. Our results show that gene expression differs substantially between all six brain parts within species: out of 11 577 assessed genes, 8 748 are differentially expressed (DE) in at least one brain part compared to the average expression of the other brain parts. At most 16 % of these DE genes have |log2FC| significantly higher than two. Functional differences between brain parts were consistent between species. The majority (61 – 79 %) of genes that  are DE in a particular brain part were shared between both species. Only 32 genes show significant differences in fold change across brain parts between species. These genes are mainly linked to transport, transmembrane transport, transcription (and its regulation) and signal transduction. Moreover, statistical equivalence testing reveals that within each comparison, on average 89 % of the genes show an equivalent fold change between both species. The pronounced differences in gene expression between brain parts and the conserved patterns between closely related species with similar morphologies and behavior suggest that unravelling the interactions between genes and behavior will benefit from neurogenomic profiling of distinct brain regions.

sample_organism:
Ophthalmotilapia ventralis
Ophthalmotilapia nasuta

overall_design: 5 females O. nasuta and 5 females O. ventralis; 6 brain parts (cerebellum, olfactory bulbs, telencephalon, diencephalon, brainstem, optic tectum) from each of the ten fish; the five specimens per species were kept in one tank (so we had two tanks).

first: Álvaro

last: Cortés-Calabuig


title: A Histone Deacetylase 3-Dependent Pathway Delimits Peripheral Myelin Growth and Functional Regeneration

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: A Histone Deacetylase 3-Dependent Pathway Delimits Peripheral Myelin Growth and Functional Regeneration [ChIP-Seq]

summary: Schwann cell remyelination defects impair functional restoration after nerve damage, contributing to peripheral neuropathies. The mechanisms that mediate remyelination block remain elusive. Upon small-molecule epigenetic screening, we identified HDAC3, a histone-modifying enzyme, as a potent inhibitor of peripheral myelinogenesis. Inhibition of HDAC3 markedly enhances myelin growth and regeneration, and improves functional recovery after peripheral nerve injury. HDAC3 antagonizes myelinogenic neuregulin/PI3K/AKT signaling axis. Moreover, genome-wide profiling analyses reveal that HDAC3 represses pro-myelinating programs through epigenetic silencing, while coordinating with p300 histone acetyltransferase to activate myelination-inhibitory programs that include HIPPO signaling effector TEAD4 to inhibit myelin growth. Schwann-cell-specific deletion of either Hdac3 or Tead4 results in a profound increase in myelin thickness in sciatic nerves. Thus, our findings identify the HDAC3-TEAD4 network as a dual-function switch of cell-intrinsic inhibitory machinery that counters myelinogenic signals and maintains peripheral myelin homeostasis, highlighting the therapeutic potential of transient HDAC3 inhibition for improving peripheral myelin repair.

overall_design: 8 ChIP-seq samples from in vritro cultured rat Schwann cells

first: Xuelian

last: He

first: Liguo

last: Zhang


title: A Histone Deacetylase 3-Dependent Pathway Delimits Peripheral Myelin Growth and Functional Regeneration [RNA-seq]

overall_design: 4 RNA-Seq samples from P6 sciatic nerves of Ctrl and Hdac3-cKO mice (Cnpcre-Ctrl, Cnpcre-cKO, Dhhcre-Ctrl, Dhhcre-cKO)


title: The RNA sequencing of microglia repopulated retina

status: Public on Feb 10 2018

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

summary: The RNA sequencing of retina after microglial depletion and repopulation

overall_design: Retinal mRNA profiles of adult wild type C57BL/6J mice, after treatment for PLX5622, LPS, vechcle control or microglial repopulation

first: Guangrong

last: Qin


title: RNA-seq data of mouse cerebral cortex in control and UTX conditional knockout groups

city: Beijng

first: Xuepei

last: Lei

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We demonstrate that UTX deficiency increases neural progenitor cells (NPCs) proliferation, decreases terminal mitosis and neuronal differentiation. Furthermore, we discover that impairment of cortex development caused by lack of UTX is less significant in males than in females. And further knockdown of UTY in male UTX-deficient cortex makes the phenotype consistent with the female’s. In order to understand the amount of gene expression, gene expression differences, as well as differences in gene patterns and functional clustering and other aspects of the situation after UTX conditional knockout in cortex, we conducted RNA-seq.

overall_design: There are two samples: one is control and the other one is UTX conditional knockout cortex, both of the samples are harvested from female.

first: Jianwei

last: Jiao


title: Three-dimensional analysis of regulatory features reveals functional enhancer-associated loops

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: To gain insight into the relationship between chromatin structure and gene expression, we conducted a Tethered Chromatin Capture (TCC) analysis using MCF7 breast cancer and PANC1 pancreatic cancer cells. We applied a novel Hi-C analysis algorithm and identified hundreds of thousands of Interacting Loci Pairs (ILPs) in each of the two cell types. We classified ILPs according to location with respect to gene structure, gene expression, different histone modifications, DNase hypersensitivity, and RNA polymerase II and CTCF binding, identifying distinct classes of ILPs. Interestingly, we found that only 5% of the ILPs involved promoter regions, with even fewer promoter-enhancer loops. We find that genes associated with promoter-enhancer loops have cell type-specific functional annotations. We then tested the impact of pharmacological inhibition of histone acetylation on genes having promoter-enhancer ILPs in PANC1 cells. We found that genes with promoter-enhancer ILPs show reduced expression in response to drug treatment, suggesting that the chromatin loops we identified are functional.

overall_design: We analyzed two datasets, TCC in MCF7 and PANC1 cells. We then correlated them with histone modification data and gene expression data.  Anti-CTCF ChIP-Seq was performed on PANC1 cells.

first: Victor

middle: X

last: Jin

first: Peggy

last: Farnham


title: BRD7 overexpression cells

first: Wei

last: Xiong


title: Differential gene expression in IDH1-R132H low grade glioma animal brain tumors brain in response to 20 Gy of radiation

city: Ann Arbor

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: IDH1-R132H is expressed in Low Grade Glioma (LGG) in combination with loss of function mutation in ATRX and TP53 genes. IDH1-R132H results in gain of function with production of 2-hydroxygluatrate, that in turn generates a hypermethylated phenotype in DNA and histone with consequences in epigenetic regulation of gene expression. Here we will compare the gene expression profile between IDH1-R132H and IDH1 Wt LLG moribund animal brain tumors and identify key genes responsible for the phenotype of this subtype of glioma.

overall_design: Evaluate differential gene expression between Brain IDH1-R132H and IDH1 wt in response to 20Gy of ionizing radiation (IR) at time that animals become moribunds.

first: Felipe

last: Nunez

first: Maria

middle: G

last: Castro

first: P

last: Lowenstein


title: Single-cell RNA-Seq reveals a developmental atlas of human prefrontal cortex

city: Beijing

first: Shu

state: Beijing

address: Peking University, No.5 Yiheyuan Road Haidian District

institute: BIOPIC

summary: Mammalian prefrontal cortex contains billions of cells, some of which are known as neurons to play critical roles in memory, cognitive ability, decision making, social behavior etc. through participating into complex neural circuits. Although neural circuits build up in the late stage of human embryo development and even after birth, the diverse and functional cells start to generate and migrate to the appropriate location play essential roles as basis for developing future circuits. However, it remains challenging to identify cell types of developing human PFC and distinguish their developmental features. Here, to address these challenges, single cells from human embryos PFC were carried out for RNA-seq.  Detailed analysis of neural progenitor cells (NPCs) illustrated a developmental feature of intermediate progenitor (IP) cells and revealed new marker genes of IP cells. We also mapped the neurogenesis timeline of PFC excitatory neurons and intrinsic singles regulating neuron maturation and circuit formation. Our screening and characterization approach provides a blueprint of human PFC development in early and mid embryonic stages, with which to systematically discover the cellular basis and molecular regulation of PFC function in humans.

overall_design: Here we performed single cell RNA-seq analysis for prefrontal cortex (PFC), covering the developmental stages of gestational weeks 8-26.

first: Suijuan

last: Zhong

first: Xiaoying

last: Fan

first: Qian

last: Wu

first: Xiaoqun

last: Wang

first: Fuchou

last: Tang


title: Pof8 is a La-related protein and a constitutive component of telomerase in fission yeast

status: Public on Feb 09 2018

city: Kansas City

first: Peter

last: Baumann

state: MO

institute: Stowers Institute for Medical Research

summary: Telomerase reverse transcriptase (TERT) and the noncoding telomerase RNA (TR) subunit constitute the core of telomerase.  We now report that the putative F-box protein Pof8 is also a constitutive component of active telomerase in fission yeast.  Pof8 functions in a hierarchical assembly pathway by promoting the binding of the Lsm2-8 complex to telomerase RNA, which in turn promotes binding of the catalytic subunit.  Loss of Pof8 reduces TER1 stability, causes a severe assembly defect and results in critically short telomeres.  Structure profile searches identified similarities between Pof8 and telomerase subunits from ciliated protozoa, making Pof8 next to TERT the most widely conserved telomerase subunits identified to date.

overall_design: Differential gene expression of pof8 deletion (strain PP1723) versus wildtype (strain PP138). There are 3 replicates for the pof8 deletion samples and 3 replicates for the isogenic control samples. RNA libraries from Lsm8 and control immunoprecipitations were prepared following instructions for Solexa mRNA sequencing and each sample was sequenced on a single lane of the Illumina GAIIx sequencer producing 40bp single-end unstranded reads.

first: Diego

last: Páez-Moscoso

first: Lili

last: Pan

first: Rutendo

middle: F

last: Sigauke

first: Morgan

last: Schroeder

first: Wen


title: KSHV oral shedding and plasma viremia result in significant changes in the extracellular tumorigenic miRNA expression profile in patients exposed to malaria

city: seattle

first: Serge

last: Barcy

address: 1900 Ninth Avenue

department: SCRI

institute: Seattle Children's

summary:
Purpose: The goal of this study is to compare the small RNA expression profile in exosomes isolated from plasma samples from KSHV+/HIV- and KSHV+/HIV+ patients
Methods: Total RNA was isolated from plasma exosomes obtained from Ugandan patients with different viral status. A small RNA fraction was gel purified and was used to make sequencing libraries. At least 14 million read sequences were obtained from each library. Non-redondant sequences were then aligned to genomic (hg19) and and mRNA sequence (hg19) using bowtie 2; sequences with perfect-match and 1bp mismatch alignments were retained for further analysis using DEseq2
Methods: Total RNA was isolated from plasma obtained from KSHV-infected patients with or without HIV co-infection. A small RNA fraction was gel purified and was used to make sequencing libraries. At least 14 million read sequences were obtained from each library. Non-redondant sequences were then aligned to genomic (hg19) and and mRNA sequence (hg19) using bowtie 2; sequences with perfect-match and 1bp mismatch alignments were retained for further analysis using DEseq2
Results:Plasma exosomes isolated from either KSHV-infected or KSHV/ HIV co-infected patients exposed to malaria are overwhelmingly populated with YRNAs instead of miRNAs
Results: KSHV oral sheeding correlated with the detection of a pro-tumorigenic cellualr miRNA profile in plasma. KSHV plasma viremia is associated with the detec tion of KSHV encoded miRNA in plasma
Conclusions: Ugandan patients exposed to Plasmodium falciparum show an unusual repertoire of small RNAs in plasma exosomes, as the exosomal RNA is mostly composed of small RNA from the YRNA biotype
Conclusions: Our study represents the first detailed analysis of the small RNA biotypes present in plasma from KSHV infected and KSHV/HIV co-infected patients without clinical sign of KSHV associated malignancies.

overall_design:
Examine:the small RNA expression repertoire in total RNA isolated from plasma exosomes obtained from KSHV infected patients with or without HIV co-infection
Examine the small RNA expression repertoire including miRNA in total RNA isolated from plasma obtained from KSHV infected patients with or without HIV co-infection

first: Minako

last: Ikoma

first: Soren

last: Gantt

first: Corey

last: Casper

first: Yuko

last: Ogata

first: Qing

last: Zhang

first: Ryan

last: Basom

first: Michael

last: Dyen


title: Rev-erbα Dynamically Modulates Chromatin Organization to Control Circadian Gene Transcription

city: Toronto

first: Sajid

last: Marhon

state: ON

address: 101 College Street

institute: Princess Margaret Cancer Centre

summary: Much of mammalian physiology exhibits 24-hour cyclicity due to circadian rhythms of gene expression controlled by transcription factors (TF) that comprise molecular clocks. Core clock TFs bind to the genome at non-coding enhancer sequences to regulate circadian gene expression, but not all binding sites are equally functional. Here we demonstrate that circadian gene expression in mouse liver is controlled by rhythmic chromatin interactions between enhancers and promoters within topologically associating domains (TAD). Rev-erbα-, a core repressive TF of the clock, opposes functional loop formation between Rev-erbα-regulated enhancers and circadian target gene promoters by recruitment of the NCoR-HDAC3 corepressor complex, histone deacetylation, and eviction of the elongation factor BRD4 and the looping factor MED1. These loops are stronger and functionally active in the physiological or genetic absence of Rev-erbα.Thus, a repressive arm of the molecular clock operates by rhythmically interrupting enhancer-promoter loops to control circadian gene transcription.

overall_design: We performed in situ Hi-C and ChIP-seq  on C57BL/6J mouse livers harvested 12 hours apart, at zeitgeber time 22 (ZT22, 5 AM) and ZT10 (5 PM) and in genetic absence of Rev-erbα to examine whether chromatin interactions and the binding of looping factors change in a circadian manner.

first: Yong

last: Kim

first: Kyoung-jae

last: Won

first: Mitchell

last: Lazar


title: PRC2 mediates paternal epigenetic inheritance

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

institute: Monash University

overall_design: Refer to individual Series


title: Coupling shRNA screening with single-cell RNA-Seq identifies mechanisms regulating senescence during reprogramming

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

summary: Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. Cellular senescence is one of these barriers, which is mediated through activation of the tumour suppressors p53/p21CIP1, p15INK4b and p16INK4a.   In this study, we have screened for shRNAs blunting reprogramming-induced senescence. We integrated single-cell RNA sequencing (scRNA-Seq) with shRNA screening to investigate the mechanism of action of the identified candidates.

overall_design: 376 samples: 280 IMR90 cells expressing OSKM and shRNA library derived from the shRNA screen (bypassing senescence), 64 OSKM-expressing IMR90 cells (senescent), 32 IMR90 cells expressing control vector

first: Marieke

last: Aarts

first: Jesus

last: Gil

first: Thomas

last: Carroll


title: PRC2 mediates paternal epigenetic inheritance: comparison of heterozygous mutant embryos

summary: Determining the mechanisms that establish and regulate the transmission of non-genetic (i.e. epigenetic) information from parent to offspring is critical for understanding disease heredity. Using an innovative model to assess transmission of epigenetic effects, we provide evidence that Polycomb Repressive Complex 2 (PRC2) mediates inheritance through the male germline. This study reveals a novel role for histone modifying complexes in epigenetic inheritance, with important implications for understanding disease inheritance.

overall_design: Comparison of gene expression in E8.5 embryos with the same heterozygous genotype, produced from heterozygous (n=4) and homozygous (n=4) Eedl7Rn5-1989SB fathers reveal differences in gene expression possibly due to altered epigenetic patterning in the sperm.

first: Jessica

middle: M

last: Stringer

first: Samuel

first: Patrick

middle: S

last: Western


title: Single-cell RNA-Sequencing of IMR90 fibroblasts bypassing reprogramming-induced senescence

summary: Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. Cellular senescence is one of these barriers, which is mediated through activation of the tumour suppressors p53/p21CIP1, p15INK4b and p16INK4a.   In this study, we have investigated the feasibility of coupling single-cell RNA sequencing (scRNA-Seq) to functional shRNA screening. To this end, we performed scRNA-Seq of OSKM-expressing IMR90 cells infected with shRNAs targeting the top candidates identified in the screen.

overall_design: 310 samples: scRNA-Seq libraries of OSKM-expressing IMR90 cells infected individually with shRNAs targeting p53 (40 cells) or shRNAs against the top candidates identified in the screen: p21 (three different shRNAs; 40 cells), MTOR (three different shRNAs; 40 cells), MYOT (two different shRNAs; 40 cells) and UBE2E1 (two different shRNAs; 40 cells). Control samples were: cells expressing OSKM (40 cells) or control vector (40 cells) with empty shRNA vector, 10 positive controls (RNA from IMR90 cells expressing control vector as input) and 10 negative control samples.


title: Single-cell RNA Sequencing as a tool for simultaneous shRNA detection and transcriptome analysis in the context of functional shRNA screens

summary: Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. Cellular senescence is one of these barriers, which is mediated through activation of the tumour suppressors p53/p21CIP1, p15INK4b and p16INK4a.   In this study, we have screened for shRNAs blunting reprogramming-induced senescence. To evaluate the feasibility of using single-cell RNA Sequencing (scRNA-Seq) in functional screens for simultaneous transcriptome and shRNA identification, we first assessed the accuracy of detecting shRNAs in single cells. To this end we performed a pilot experiment on a pool of OSKM-expressing IMR90 cells infected with the shRNA library.

overall_design: 460 samples: 300 IMR90 cells expressing OSKM and shRNA library, 50 IMR90 cells expressing control vector, 50 K562 myeloid leukemia cells, 30 positive controls (RNA from IMR90 cells expressing control vector as input; RNA used as a control for the single cell processing, coming from RNA isolation of a bulk population of IMR90 cells expressing the control vector), 30 negative controls


title: Transcriptome analysis of OSKM- or RAS-induced senescent IMR90 fibroblasts treated with Rapamycin.

summary: Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram somatic cells into induced pluripotent stem cells (iPSCs). These iPSCs are highly similar to embryonic stem cells and can be used for regenerative medicine, drug screening and disease modelling. Despite recent advances, reprogramming is a slow and inefficient process. This suggests that there are several safeguarding mechanisms to counteract cell fate conversion. Cellular senescence is one of these barriers, which is mediated through activation of the tumour suppressors p53/p21CIP1, p15INK4b and p16INK4a.   In this study, we have screened for shRNAs blunting reprogramming-induced senescence. We found that mTOR depletion bypasses OSKM-indced senescence but not RAS-induced senescence. To investigate the differences between the two types of senescence, we performed RNA-sequencing (RNA-Seq). Cells were transduced with OSKM or RAS expression and treated with 2 doses of the mTOR inhibitor Rapaycin for 10 days.

overall_design: 7 samples in triplicate: IMR90 + MSCV + DMSO (Prolif), IMR90 + OSKM + DMSO (OSKM), IMR90 + OSKM + 1nM Rapamycin (OSKM1nM), IMR90 + OSKM + 10nM Rapamycin (OSKM10nM), IMR90 + RAS + DMSO (RAS), IMR90 + RAS + 1nM Rapamycin (RAS1nM) and IMR90 + RAS + 10nM Rapamycin (RAS10nM).

first: Athena

last: Georgilis


title: The deregulated microRNAome contributes to the cellular response to aneuploidy [mRNA]

city: Martinsried

first: Milena

last: Dürrbaum

address: Am Klopferspitz 18

department: Maintenance of Genome Stability

institute: Max Planck Institute of Biochemistry

summary: Aneuploidy severely alters cell physiology and is widespread in cancers and other pathologies. In model cell lines, aneuploidy impairs proliferation, leads to proteotoxic as well as replication stress and triggers conserved transcriptome and proteome changes. In this study we analysed for the first time miRNAs and demonstrate that their expression is altered in response to chromosome gain.

overall_design: HiSeq Illumina sequencing of total RNA for four whole-chromosome aneuploid cell lines and their corresponding parental cell line.

first: Christine

last: Kruse

first: Karen

last: Nieken

first: Bianca

last: Habermann

first: Zuzana

last: Storchová


title: The deregulated microRNAome contributes to the cellular response to aneuploidy

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


title: m6A and YTHDF2, YTHDF3 mapping of SV40 RNA with PAR-CLIP and PA-m6A-seq

status: Public on Feb 08 2018

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: Polyomaviruses are a family of small DNA tumor viruses that includes several pathogenic human members, including Merkel cell polyomavirus, BK virus and JC virus. As is characteristic of DNA tumor viruses, gene expression in polyomaviruses is temporally regulated into an early phase, consisting of the viral regulatory proteins, and a late phase, consisting of the viral structural proteins. Previously, the late transcripts expressed by the prototypic polyomavirus simian virus 40 (SV40) were reported to contain several adenosines bearing methyl groups at the N6 position (m6A), although the precise location of these m6A residues, and their phenotypic effects, have not been investigated. Here, we first demonstrate that overexpression of the key m6A reader protein YTHDF2 induces more rapid viral replication, and larger viral plaques, in SV40 infected BSC40 cells, while mutational inactivation of the endogenous YTHDF2 gene, or the m6A methyltransferase METTL3, has the opposite effect, thus suggesting a positive role for m6A in the regulation of SV40 gene expression. To directly test this hypothesis, we mapped sites of m6A addition on SV40 transcripts and identified two m6A sites on the viral early transcripts and eleven m6A sites on the late mRNAs. Using synonymous mutations, we inactivated the majority of the m6A sites on the SV40 late mRNAs and observed that the resultant viral mutant replicated more slowly than wild type SV40. Alternative splicing of SV40 late mRNAs was unaffected by the reduction in m6A residues and our data instead suggest that m6A enhances the translation of viral late transcripts. Together, these data argue that the addition of m6A residues to the late transcripts encoded by SV40 plays an important role in enhancing viral gene expression and, hence, replication.

sample_organism:
Chlorocebus aethiops
Betapolyomavirus macacae

overall_design: PA-m6A-seq on SV40 RNA in BSC40 cells; GFP/YTHDF2/YTHDF3 PAR-CLIP of SV40 RNA in BSC40 cell; PA-m6A-seq validation of m6A removal by VPm mutations and corresponding WT SV40 control, in BSC40 cells; PA-m6A-seq validation of early transcript m6A mutants and WT control. The Early transcript m6A mutant validation WT control also acts as PA-m6A-seq repeat 2.

first: Bryan

middle: R

last: Cullen


title: The deregulated microRNAome contributes to the cellular response to aneuploidy [miRNA]

overall_design: HiSeq Illumina sequencing of total RNA including small RNAs for seven whole-chromosome aneuploid cell lines and their corresponding parental cell line.


title: Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

institute: Institute of Molecular Biology (IMB)

summary: VCP is an evolutionary conserved ubiquitin-dependent ATPase that mediates the degradation of proteins through the ubiquitin-proteasome pathway. Despite the central role of VCP in the regulation of protein homeostasis, identity and nature of its cellular substrates remain poorly defined. Here, we combined chemical inhibition of VCP and quantitative ubiquitin remnant profiling to assess the effect of VCP inhibition on the ubiquitin-modified proteome and to probe the substrate spectrum of VCP in human cells. We demonstrate that inhibition of VCP perturbs cellular ubiquitylation and increases ubiquitylation of a different subset of proteins compared to proteasome inhibition. VCP inhibition globally upregulates K6-linked ubiquitylation that is dependent on the HECT-type ubiquitin E3 ligase HUWE1. We report ~450 putative VCP substrates, many of which function in nuclear processes, including gene expression, DNA repair and cell cycle. Moreover, we identify that VCP regulates the level and activity of the transcription factor c-Myc.

overall_design: RNA profiling of U2OS cells in the response to VCP inhibition by NMS-873 (5 µM, 4 h) treatment


title: Genomewide screening for pectoral fin MN specific markers

city: New York

first: Jeremy

last: Dasen

state: NY

address: 522 First Avenue

department: Neuroscience Program

institute: NYU School of Medicine

summary: The goal of this study is to find skate pectoral fin motor neuron markers. Total RNA was extracted from manually sorted pectoral fin MNs, which were retrogradely labeled and tail spinal cord cells.  By comparing RNA expression profiles of pectoral fin MNs and tail spinal cord neurons, we could identity general MN, MN columnar, and subset MN pool markers for fin MNs.

overall_design: Examination of RNA expression profiles in two different samples: pectoral fin MNs and tail spinal cord cells.

first: Myungin

last: Baek

first: Stuart

last: Brown

first: Adriana

last: Heguy


title: Circuit design features of a stable two-cell system

city: Boston

first: Xu

last: Zhou

state: MA

address: 300 Longwood Ave

department: Pediatrics

institute: Boston Children's Hospital

summary: Cell communication within tissues is mediated by multiple paracrine signals including growth factors, which control cell survival and proliferation. Cells and the growth factors they produce and receive constitute a circuit, yet the design features of cell circuits involved in tissue homeostasis are unknown. Here we used computational and experimental approaches to characterize the features of cell circuits based on growth factor exchange between macrophages and fibroblasts, two cell types found in most mammalian tissues. We found that the macrophage-fibroblast cell circuit is stable and robust to perturbations. We employed analytical screening of all possible two-cell circuit topologies and defined the circuit features sufficient for stability, including environmental constraint and negative feedback regulation. Moreover, we discovered that cell-cell contact was essential for the stability of the macrophage-fibroblast circuit. These findings highlight general principles of cell circuit design, and provide a new perspective on quantitative understanding of tissue homeostasis.

overall_design: 1 sample of murine embryonic fibroblast and 1 sample murine bone marrow derived macrophages are analyzed for their expression of growth factors and growth factor receptors

first: Ruth

last: Franklin

first: Ruslan

last: Medzhitov


title: A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus [HiC_mESC]

city: Durham

first: Rasim

last: Barutcu

address: 6 Davis Drive

institute: ScitoVation

summary: The binding of the transcriptional regulator CTCF to the genome has been implicated in the formation of topologically associated domains (TADs). However, the general mechanisms of folding the genome into TADs are not fully understood. Here, we tested the effects of deleting a CTCF-rich locus on TAD boundary formation. Using genome-wide chromosome conformation capture (Hi-C), we focus on one TAD boundary on chromosome X harboring ~15 CTCF binding sites, and located at the long non-coding RNA (lncRNA) locus Firre. Specifically, this TAD boundary is invariant across evolution, tissues, and temporal dynamics of X-chromosome inactivation. We demonstrate that neither the deletion of this locus, nor the ectopic insertion of Firre cDNA or its ectopic expression are sufficient to alter TADs in a sex-, or allele-specific manner. In contrast, Firre’s deletion disrupts the chromatin super-loop formation of the inactive X-chromosome. Collectively, our findings suggest that apart from CTCF binding, additional mechanisms can play roles in establishing TAD boundary formation.

overall_design: Hi-C in wildtype and Firre lncRNA knockout mouse Embryonic Stem Cells

first: A

first: Philipp

last: Maass

first: Jordan

middle: P

last: Lewandowski

first: Catherine

middle: L

last: Weiner

first: John

last: Rinn


title: Global transcriptome comparison reveals stress adaptation between Russet Norkotah and its Clonal Selection, TXNS278

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

summary: The Texas Potato breeding program has been succesful at bringing several potato variety including somaclonal selection made in the field.  This genetic diversity is in part due to somaclonal variability that appears within potato selections for which tubers are used as seeds. However, nogenetic or molecular evidences were identified so far. In this investigation, we used RNA-seq, which allows genome-wide gene expression analysis to compare the transcriptomes of the subclonal Russet Norkotah selection TXNS278 with standard Russet Norkotah grown in commercial fields. Among the selections, TXNS278 appeared in a multi- year analysis as a top No 1 yielding variety. Russet Norkotah and TXNS278 leaf and root transcriptomes were compared at two time points. Results indicated that yield differences between Russet Norkotah and TXNS278 might possibly be linked to differences in responses to biotic and abiotic stresses and hormonal signaling

overall_design: Texas Somaclonal selection RN and TXNS278 mRNA profiles of 66-day old and 84-day old leaf and root tissue. The plant were grown in the field condition. Sequences were generated by deep sequencing, in triplicate, using Illumina Hiseq-2000 platform and CyVerse.

first: Julien

last: Levy

first: Giridhar

last: Athrey

first: Douglas

last: Scheuring

first: Jeffrey

last: Koym

first: J

last: Miller Jr.