title: Tamoxifen therapy in a murine model of myotubular myopathy (TAM4MTM)

status: Public on Sep 23 2018

city: Toronto

first: James

last: Dowling

state: Ontario

address: 686 Bay Street

institute: Hospital for Sick Children

summary:
Purpose: The goal of this study was to investigate the transcriptional profile of genes expressed in the quadriceps muscle of myotubularin deficient (Mtm1-/-) mice, and determine whether improvements in the pathophysiology of tamoxifen treated Mtm1-/- mice are a consequence of ER-dependent transcriptional modulation.
Methods: Muscle mRNA profiles from quadriceps of 36-day-old wild-type (WT), myotubularin deficient (Mtm1-/-) mice, and tamoxifen treated WT and Mtm1-/- mice were generated by deep sequencing, in triplicate or quadruplicate, using Illumina HiSeq 2500. Read sets from each of the 14 samples across the four conditions were aligned to the reference genome (GRCm38/MM10 version of the Mus musculus genome) and transcriptome using STAR (Dobin et al. Bioinformatics 2013 PMID: 23104886) two-step alignment to generate a Binary Alignment Map file (BAM file). Coordinate sorted BAM files were used to quantify transcript abundance (count data) using HTSeq (Anders et al. Bioinformatics 2014, PMID: 25260700). Raw read counts generated were used as input for differential gene expression analysis, carried out using both DESeq (Anders and Huber 2010) and edgeR (Robinson, McCarthy, and Smyth 2010) R/Bioconductor packages. This was carried out in a pair-wise manner between any two conditions that were considered. FDR adjusted p-values from both edgeR and DESeq was used to determine genes that are significantly differentially expressed between the conditions tested. Finally, we used the GoSeq R/Bioconductor package (Young MD, et al Genome Biology, 11, pp. R14) to identify pathways that were significantly enriched for differentially expressed genes between any two conditions.
Results: Using an established data analysis workflow, 65 million reads were aligned per sample (>90% exonic). We observed 849 differentially expressed transcripts in untreated mtm1-/-mice (p< 0.01) in comparison to wild-type (WT) controls. Furthermore, we identified 29 differentially expressed genes (p<0.01) between mtm1-/- mice and their TAM-treated mtm1-/- mice. In particular, we observed that the transcriptional profiles of mtm1 -/- mice and tamoxifen-treated mtm1-/- mice cluster together and are distinct from wild-type contros. Moreover, no significant changes were observed in the expression of estrogen-response genes that are known gene targets of tamoxifen; no significant transcriptional changes were observed in well-known MTM-related genes.This strongly indicates that, contrary to its well-established function as a transcriptional modulator, tamoxifen improves the pathophysiology of myotubular myopathy in a post-transcriptional manner.
Concusions: Our study represents the first comprehensive analysis of the whole transcriptome of the Mtm1-/-  and tamoxifen treated Mtm1-/-  mouse, generated by RNA-seq technology. The data reported here provides a framework a comparative investigation of the expression profiles in Mtm1-/- mice and tamoxifen treated Mtm1-/- mice. Importantly, our results demonstrate that in our MTM murine model, tamoxifen does not appear to alter the transcriptional profile of many estrogen-receptor (ER) related genes, and moreover does not appear to alter the transcriptional profile of genes that are abnormally expressed in Mtm1-/- mice alone. This suggests that tamoxifen is acting to improve the pathophysiology of the MTM mouse model in a transcriptionally-indepedent manner.

overall_design: Muscular mRNA profiles of 36-day old wild type (WT) and Mtm1-/- mice and WT and Mtm1-/- mice treated with high-dose (40mg/kg/day) of Tamoxifen were generated by deep sequencing, in triplicate or quadruplicate using Illumina HiSeq 2500.

first: Nika

last: Maani

first: Nesrin

last: Sabha

first: Kamran

last: Rezai

first: Arun

last: Ramani

first: Linda

last: Groom

first: Nadine

last: Eltayeb

first: Faranak

last: Mavandadnejad

first: Andrea

last: Pang

first: Guilia

last: Russo

last: Brundho

first: Volker

last: Haucke

first: Robert

last: Dirksen


title: Effect of neuronal primary cilia on axonal tract development

status: Public on Sep 22 2018

city: Chapel Hill

first: Travis

last: Ptacek

state: NC

address: 5109 Neuroscience Research Building

country: USA

institute: UNC Neuroscience Center Bioinformatics Core

type: Expression profiling by high throughput sequencing

summary: This experiment aims to study the impact of primary cilia signaling on transcriptional programs relevant to axonal development in the mouse cerebral cortex.

overall_design: Transcriptional profiling of telencephalon from Arl13b-/- mutants and wild type controls

first: Eva

middle: S

last: Anton

first: Jiami

last: Guo

first: Jeremy

middle: M

last: Simon


title: Genome-wide DNA methylation analysis in peripheral blood of monozygotic twins informative for psychopathology

city: Barcelona

first: Lourdes

last: Fañanás

address: Av. Diagonal, 643, 2nd floor

department: Evolutionary Biology, Ecology and Environmental Sciences

country: Spain

institute: University of Barcelona

summary: Peripheral blood from thirty-four monozygotic twin subjects from the general population (n = 17 twin pairs) was collected for epigenomic analysis via Illumina Infinium HumanMethylation450 Beadchip. All subjects were screened for DSM-IV based criteria for both current and lifetime psychiatric disorders. Out of 17 twin pairs, there were: 7 healthy twin pairs where none of the twins of a pair met criteria for any DSM-IV disorder; 6 discordant twin pairs where only one of the twins of each pair met diagnostic criteria; and 4 concordant twin pairs where both twins of a pair met clinical DSM-IV based criteria.

overall_design: Bisulphite converted DNA from the 34 samples (17 twin pairs) were hybridised to the Illumina Infinium Human Methylation450 Beadchip

first: Helena

last: Palma-Gudiel

first: Aldo

last: Córdova-Palomera


title: Gene expression profiling in human nasal epithelial cells (HNEpCs) stimulated with eosinophil-derived neurotoxin (EDN)

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: The goal of this study is to evaluate the function of eosinophil-derived neurotoxin (EDN) in eosinophilic chronic rhinosinusitis (ECRS) pathogenesis and assess its potential as a disease activity marker.

overall_design: To determine the pathological role of eosinophil-derived neurotoxin (EDN) in eosinophilic chronic rhinosinusitis (ECRS), we performed RNA sequencing to analyze gene expression in human nasal epithelial cells (HNEpCs) stimulated with EDN.

first: Takeshi

last: Tsuda

first: Atsushi

last: Kumanogoh


title: Microtubule acetylation is required for mechanosensation in Drosophila

city: Seattle

first: Jay

last: Parrish

state: Washington

department: Department of Biology

institute: University of Washington

summary: At the cellular level, α-tubulin acetylation alters the structure of microtubules to render them mechanically resistant to compressive forces. How this biochemical property of microtubule acetylation relates to mechanosensation remains unknown, though prior studies have shown that microtubule acetylation influences touch perception. Here, we identify the major Drosophila α-tubulin acetylase (dTAT) and show that it plays key roles in several forms of mechanosensation. dTAT is highly expressed in the larval peripheral nervous system (PNS), but is largely dispensable for neuronal morphogenesis. Mutation of the acetylase gene or the K40 acetylation site in α-tubulin impairs mechanical sensitivity in sensory neurons and behavioral responses to gentle touch, harsh touch, gravity, and vibration stimuli, but not noxious thermal stimulus. Finally, we show that dTAT is required for mechanically-induced activation of NOMPC, a microtubule-associated transient receptor potential channel, and functions to maintain integrity of the microtubule cytoskeleton in response to mechanical stimulation.

overall_design: Six neuronal and non-neuronal cell types of Drosophila melanogaster larvae, with 100 cells each and at least four biological replicates were profiled by mRNA-Seq

first: Claire

middle: R

last: Williams

middle: Z

first: Charles

middle: C

last: Kim


title: β-RA reduces DMQ/CoQ ratio and recues the encephalopathic phenotype in Coq9R239X mice

city: Granada

first: Mohammed

last: Bakkali

address: Facultad de Ciencias, Fuentenueva S/N

department: Genetics

institute: Universidad de Granada

summary: Coenzyme Q (CoQ) deficiency has been associated to primary defects in the CoQ biosynthetic pathway or to secondary events. In some cases, the exogenous CoQ supplementation has limited efficacy. In the Coq9R239X  mouse model of fatal mitochondrial encephalopathy due to CoQ deficiency, we have tested the therapeutic potential of β-Resorcylic Acid (β-RA), a structural analog of the CoQ precursor 4-hydroxybenzoic acid and the anti-inflammatory salicylic acid. β-RA noticeably rescued the phenotypic, morphological and histopathological signs of the encephalopathy, leading to a significant increase in the survival. Those effects were due to the decrease of the levels of demethoxyubiquinone-9 (DMQ9) and the increase of mitochondrial bioenergetics in peripheral tissues. However, neither CoQ biosynthesis and mitochondrial function changed in the brain after the therapy, suggesting that some endocrine interactions may induce the reduction of the astrogliosis, spongiosis and the secondary down-regulation of astrocytes-related neuroinflammatory genes. Because the therapeutic outcomes of β-RA administration were superior to those after CoQ10 supplementation, its use in the clinic should be considered in CoQ deficiencies.

overall_design: Physiological, biochemical and gene expression (RNA-Seq) analysis of the mitochondrial encephalopathy and the therapeutic effect of the β-Resorcylic Acid

first: Agustín

last: Hidalgo-Gutiérrez

first: Eliana

last: Barriocanal-Casado

first: M

middle: E

last: Díaz-Casado

first: Laura

last: Sánchez-Maldonado

first: Miguel

last: Romero

first: Ramy

last: Sayed

first: Cornelia

last: Prehn

first: Germaine

last: Escames

first: Juan

last: Duarte

first: Darío

last: Acuña-Castroviejo

first: Luis

last: López


title: Genome-wide SRF occupancy on chromatin in mouse heart ventricles

status: Public on Sep 24 2018

city: boston

first: Yuxuan

last: Guo

state: MA

address: 320 Longwood Ave, Enders 1250,

department: Department of Cardiology

institute: Boston childrens hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The goal of this study is to analyze genome-wide Srf binding to chromatin in mouse heart during heart maturation

overall_design:
Srf-fbio/+;Rosa-birA/+ hearts were collected at postnatal day 14 (P14) and P42 (adult). The apex of the hearts were dissected, homogenized and nuclei crosslinked and fragmented by sonication. Streptaviding pull down followed by sequencing (bioChIP-seq) analyzed SRF occupancy on chromatin.
At least two ventricles were pooled per sample. Two biological replicates were analyzed at each stage. Sequencing data aligned by bowtie2 and peaks called by MACS2.

first: William

last: Pu


title: MYC Targeted Long Noncoding RNA DANCR Promotes Cancer in Part by Reducing p21 Levels.

status: Public on Sep 21 2018

city: Philadelphia

first: Chi

middle: V

last: Dang

state: PA

address: 3601 Spruce

institute: wistar

summary: p493 RNA-seq in the MYC on and MYC off conditions

overall_design: For RNA-seq analysis of MYC-ON versus MYC-OFF states, the P493-6 cells, which were engineered to have tetracycline-repressible ectopic MYC, were supplemented with 0.1 μg/mL tetracycline (Sigma) for 48 hours before harvesting for the MYC-OFF state. The RNA from these cells were compared with MYC-ON cells that had continuously expressed MYC for 48 hours grown contemporaneously with the MYC-OFF cells.

first: Zachary

last: Stine


title: The Zmiz1-Notch1 interaction induces Myc expression to drive steady state and stress thymopoiesis [ETP and DN3]

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Notch1 signaling ramps up to very high levels in order to drive CD4-CD8- double-negative (DN) thymocytes to the CD4+CD8+ double-positive (DP) stage. During this important phase of T-cell development, which is known as the DN-DP transition, it is unclear whether the Notch1 complex simply strengthens its signal output as an isolated unit or recruits cofactors to amplify its signals. We previously showed that the PIAS-like coactivator Zmiz1 is a direct and context-dependent cofactor of Notch1 in T-cell leukemia. Using conditional knockout mouse models, we show that like inactivation of Notch, inactivation of Zmiz1 impaired the DN-DP transition under steady state and stress conditions. To determine mechanism, we performed RNA-Seq on sorted early T-lineage progenitor (ETP) and DN3 cells that were deprived of Zmiz1 signals either acutely (DeltaTamCre) or chronically (DeltaMxCre). To differentiate Notch1-independent from Notch1-dependent target genes, we also performed RNA-Seq on ETP and DN3 cells that were deprived of Notch1 signals using the anti-NRR Notch1 antibody. Our data suggests that Zmiz1 selectively amplifies a subset of Notch1 target genes in DN3 cells, such as Myc. In contrast, Zmiz1 does not have these functions in ETP cells, thus indicating stage-specific roles of Zmiz1.

overall_design: RNA-Seq in murine ETP and DN3 thymocytes

first: Qing

last: Wang

first: Mark

last: Chiang


title: Targeted profiling of RNA translation reveals mTOR-4EBP1/2-independent translational regulation of mRNAs encoding ribosomal proteins

city: Boston

first: Jean

last: Zhao

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: The PI3K-Akt-mTOR signaling pathway is a master regulator of RNA translation. Pharmacological inhibition of this pathway preferentially and coordinately suppresses, in a 4EBP1/2-dependent manner, translation of mRNAs encoding ribosomal proteins. However, it remains unclear whether mTOR-4EBP1/2 is the exclusive translational regulator of this group of genes, and furthermore, systematic searches for novel translational modulators have been immensely challenging due to difficulties in scaling existing RNA translation profiling assays. Here, we developed a rapid and highly scalable approach for gene-specific quantitation of RNA translation, termed Targeted Profiling of RNA Translation (TPRT). We applied this technique in a chemical screen for novel translational modulators, and identified numerous preclinical and clinical therapeutic compounds, with diverse nominal targets, that preferentially suppress translation of ribosomal proteins. Surprisingly, some of these compounds act in a manner that bypasses canonical regulation by mTOR-4EBP1/2. Instead, these compounds exert their translational effects in a manner that is dependent upon GCN2-eIF2α, a central signaling axis within the integrated stress response. Furthermore, we were also able to identify metabolic perturbations that also suppress ribosomal protein translation in an mTOR-independent manner. Together, we describe a novel translational assay that is directly applicable to large-scale RNA translation studies, and that enabled us to identify a non-canonical, mTOR-independent mode for translational regulation of ribosomal proteins.

overall_design: Examination of translation changes in 2 cell lines under 3 conditions

first: Ben

middle: B

last: Li

first: Changli

last: Qian

first: Paulo

middle: A

last: Gameiro

first: Chin-Chih

last: Liu

first: Tao

last: Jiang

first: Thomas

last: Roberts

first: Kevin

last: Struhl

middle: J


title: mRNA circularization by METTL3-eIF3h enhances translation

first: Shuibin

last: Lin

address: 1 Blackfan Circle

institute: Boston Childrens Hospital

summary: N6-methyladenosine (m6A) modification of mRNA catalyzed by METTL3 is enriched at a subset of stop codons. METTL3 can promote translation but the mechanism and widespread relevance remain unknown. Here we show that METTL3 enhances translation only when tethered to reporter mRNA at sites close to the stop codon supporting a mRNA looping mechanism for ribosome recycling and translational control. Electron microscopy revealed the topology of individual polyribosomes with single METTL3 foci found in close proximity to 5’ cap-binding proteins. We identify a direct physical and functional interaction between METTL3 and the eukaryotic translation initiation factor 3 subunit h (eIF3h). METTL3 promotes translation of a large subset of oncogenic mRNAs, including BRD4 that are also m6A-modified in human primary lung tumors. The METTL3-eIF3h interaction is required for enhanced translation, formation of densely packed polyribosomes, and oncogenic transformation. METTL3 depletion inhibits tumorigenicity and sensitizes lung cancer cells to BRD4 inhibition. These findings uncover a mRNA looping mechanism of translation control and identify METTL3-eIF3h as a potential cancer therapeutic target.

overall_design: METTL3 expression was depleted in HeLa cells using lentivirus mediated shRNA knockdown. The METTL3 knockdown cells and the control cells were subjected to sucrose gradient ultracentifuge for the polysome profiling. The RNA samples isolated from the polysome fractions and subpolysome fractions were used for high throughput sequencing for the analysis of translation efficiency. For the analysis of mRNA stability, METTL3 knockdown cells and the control cells were treated with ActD for different time points then the RNA samples were isolated for high throughput sequencing and the subsequent calculation of mRNA halflife.

first: Qi

last: Gregory


title: Epigenetic profiling changes of early adulthood with perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure (Yucheng second generation) [methylation]

city: Taipei

first: Kang-Yi

last: Su

address: No.1, Jen-Ai Road

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

type: Methylation profiling by genome tiling array

summary:
Genome-wide DNA methylation profiling of peripheral blood mononuclear cells from 30 male offspring from the Yucheng (perinatal polychlorinated biphenyls and polychlorinated dibenzofurans exposure) cohort and 30 male offspring from the Yucheng' neighborhood referents with similar backgrounds.
The Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across appromixmately 480,000 CpGs.

overall_design: Genomic DNA was bisulfite-converted using the EZDNA Methylation-Gold Kod (Zyno Research) and analysed using the Infinium HumanMethylation450 BeadChip (Illumina) following manufacturer's instructions.

first: K

middle: Y

first: M

first: N

middle: W

last: Lww

first: B

last: Ho

first: C

middle: L

last: Cheng

first: Y

last: Chuang

first: S

last: Yu

last: Guo


title: Mapping of histone modifications in aged hematopoietic stem cells (HSCs)

status: Public on Sep 20 2018

city: Heidelberg

first: Daniel

middle: B.

last: Lipka

address: INF 280

department: Epigenomics and Cancer Risk Factors

country: Germany

institute: German Cancer Research Center

summary: The decline of hematopoietic stem cell (HSC) function upon aging contributes to senescent immune remodeling and to leukemia pathogenesis. Aged HSCs show epigenetic alterations affecting DNA methylation, histone modifications, and show a reduction in the polar distribution of histone 4 lysine 16 acetylation (H4K16ac). Here, we determined the deposition patterns of H4K16ac in young, aged and re-juvenated HSCs using ChIP-seq.

overall_design: Examination of histone modifications in young, aged and aged/re-juvenated HSCs

first: Christoph

last: Plass


title: Bcl11b defines pro-T identity by site-specific cofactor recruitment and by repressing Id2 and Zbtb16 [ChIP-seq]

city: Pasadena

first: Maile

last: Romero-Wolf

state: CA

address: 1200 E California Blvd

department: BBE

institute: California Institute of Technology

summary: Multipotent progenitors confirm their T-lineage identity at the DN2a to DN2b pro-T cell transition, when expression of the essential transcription factor Bcl11b begins. This study defines the molecular basis of direct and indirect actions of Bcl11b in acquisition of T cell identity. In vivo and in vitro stage-specific deletions identify functional regulation targets genome-wide for mechanistic analysis. Bcl11b can associate with multiple co-factors and its direct action is needed to recruit these to selective target sites. Sites of Bcl11b-dependent cofactor recruitment are enriched at functionally regulated targets, and deletion of individual cofactors can relieve repression of many Bcl11b-repressed genes. In parallel, Bcl11b indirectly regulates a subset of its target genes by a gene network circuit via Id2 and Zbtb16, which are directly repressed by Bcl11b and control distinct alternative programs.

overall_design:
H3K27Ac genome occupancy profiling in  Lin- BM derived WT DN3 cells and Lin- BM derived Bcl11bKO DN3 cells.
ChIP-seq; Ten million of BM-derived DN3 cells with 1% formaldehyde for 10 min.  The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco).  Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power.  Five μg per 10^7 cells of anti-H3K27Ac Abs (ab4729, Abcam) were hybridized to Dynabeads anti-Rabbit (Invitrogen) and added to the diluted chromatin complex.  They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg/ml proteinase K).  Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator.  ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (E6240, NEB) and sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.

first: Hiroyuki

last: Hosokawa

first: Mary

last: Yui

first: Jonas

last: Ungerbäck

first: Masaki

last: Matsumoto

first: Keiichi

middle: I

last: Nakayama

first: Tomoaki

last: Tanaka

first: Ellen

last: Rothenberg


title: UPA-Seq: Prediction of functional lncRNAs using the sensitivities to UV-crosslinking

city: Sapporo

first: Shinichi

last: Nakagawa

state: Hokkaido

address: Kita 12-jo Nishi 6-chome, Kita-ku

department: Faculty of Pharmaceutical Sciences

institute: Hokkaido University

type: Non-coding RNA profiling by high throughput sequencing

summary: Assuming that functional lncRNAs form larger ribonucleoprotein complex and thus are easily crosslinked to proteins upon UV-irradiation, we performed RNA-Seq analyses of RNAs recovered from the aqueous phase after the UV-irradiation and phenol chloroform extraction (UPA-Seq)

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of expression profiles of UV-irradiated and non-irradiated cells (HepG2, HEK293, Neuro2a, HippCulture).

first: Taiwa

last: Komatsu

first: Mari

last: Mito

first: Fujii

last: Koichi

first: Shintaro

last: Iwasaki


title: Bulk RNA-seq U2OS cells treated with small molecules

city: Cambridge

first: Ajamete

last: Kaykas

address: 22 Windsor St

institute: Novartis

summary: We report the transcriptional changes associated with treatment of U2OS osteosarcoma cell line with DMSO, AML108, AMN107, BGW675, JAA804, LEE837 and LHD510.

overall_design: U2OS cells were treated with 100nM, 1000nM and 10000nM of DMSO, AML108, AMN107, BGW675, JAA804, LEE837 and LHD510 for 12 hrs and subjected to RNA-seq.

first: Robert

last: Altshuler


title: Bcl11b defines pro-T identity by site-specific cofactor recruitment and by repressing Id2 and Zbtb16

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

overall_design: Refer to individual Series


title: Bcl11b defines pro-T identity by site-specific cofactor recruitment and by repressing Id2 and Zbtb16 [RNA-seq]

overall_design: RNA-seq; Total RNA was isolated from 300,000 cells using an RNAeasy MicroKit (Qiagen).  Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) from ~1 μg of total RNA following manufacturer’s instructions.  Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt.


title: Next Generation Sequencing Facilitates Quantitative Analysis of CD45 positive immune cell Transcriptomes in four treated groups after hydrodynamic transfections

city: SAN DIEGO

first: gaowei

last: wang

state: CALIFORNIA

address: 3393 Lebon DR, APT 202

institute: University of California San Diego

summary:
Purpose: The goals of this study are to compare the transcriptome profilings (RNA-seq) of CD45 positive immune cells in the control, polyIC, anti-PD-L1 and combination groups.
Methods: All the CD45 positive immune cells of the mouse liver in control, polyIC, anti-PD-L1 and combination groups at day 24 were isolated, after hydrodynamic trasfection of c-Myc and N-ras at day 0. Then the mRNA profiles were generated by sequencing, in triplicate, using  Illumina HiSeq 4000. RNA-seq generated raw data were aligned to the GRCm38 mouse reference genome using Star program (2.3.0). Gene differential expression analysis was performed using Cuffdiff to obtain the expression levels of genes in each sample.Gene Set Enrichment Analysis (GSEA) analysis was performed for pathway analysis online (software.broadinstitute.org/gsea).
Results: By comparing to the control group, the number of differentially expressed genes and the overlaps in other groups were listed by Venn diagram. There were a total of 1654 differentially expressed genes specifically in the combination group. Gene set enrichment analysis (GSEA) of these 1654 genes demonstrated that the immune cells in the combination groups were particularly associated with adaptive and innate immune system and the progresses of antigen processing and presentations. The key genes involved in interferon-g (IFg) signaling pathway and some key genes, as indicators of anti-tumor cytotoxic function, were listed by heatmap.
Conclusions: The RNA-seq data further confirmed that combination of polyIC and PD-L1 Ab dramatically enhanced the anti-tumor immunity in the liver, especially the adaptive immune response.

overall_design: The mRNA profiles of CD45 positive immune cells from mouse liver in control, polyIC, anti-PD-L1 and combination groups at day 24 after hydrodynamic trasfection of c-Myc and N-ras (day 0) were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Liang

last: Wen

first: Gen-sheng

last: Feng


title: Differential Effects of Partial and Complete Loss of TREM2 on Microglial Injury Response and Tauopathy [RNA-Seq]

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Late-onset Alzheimer’s disease is the most common form of dementia. A rare hemizygous variant in a microglial-expressed gene, Triggering Receptor Expressed on Myeloid Cells 2 (TREM2), significantly increases risk for late-onset Alzheimer’s disease. This variant is thought to cause loss of function, inducing TREM2 haploinsufficiency. The ramifications of TREM2 haploinsufficiency on microglial function and tau pathology are major gaps in the field. We find that in contrast to the protective effects of complete TREM2 deficiency, TREM2 haploinsufficiency exacerbates tau pathology, inflammation, and atrophy at a late stage of disease in a mouse model of tauopathy. The differential effects of partial and complete loss of TREM2 are important considerations for TREM2-targeted therapeutic strategies.

overall_design: RNA was isolated from cortical brain tissue from 8- to 9-month-old TREM2+/+, P301S+ TREM2+/+, P301S+ TREM2+/- and P301S+ TREM2-/- mice using the Rneasy mini kit.

first: Faten

last: Sayed

first: Maria

last: Telpoukhovskaia

first: Lay

last: Kodama

first: Yaqiao

last: Li

first: Yungui

last: Zhou

first: David

last: Le

first: Axel

last: Hauduc

first: Connor

last: Ludwig

first: Fuying

last: Gao

first: Claire

last: Clelland

first: Lihong

last: Zhan

first: Yonatan

last: Cooper

first: Dimitrios

last: Davalos

first: Katerina

last: Akassoglou

first: Li

last: Gan


title: Single cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid  during virologically suppressed HIV

city: New Haven

first: Shelli

last: Farhadian

state: CT

address: 135 College St

institute: Yale University School of Medicine

summary: Using single cell RNA sequencing (scRNA-seq) on cerebrospinal fluid (CSF) and blood from adults with HIV, we identified a rare (<5% of cells) subset of myeloid cells that are found only in CSF and that present a gene expression signature that overlaps significantly with neurodegenerative disease associated microglia

overall_design: examination of CSF and blood for human study volunteers, prepared via SeqWell

first: Sameet

last: Mehta


title: Influenza virus replication intensity and round of infection dictates the cellular response in vivo

city: MINNEAPOLIS

first: Ryan

last: Langlois

state: MN

institute: University of Minnesota

summary: Influenza A virus has a broad cellular tropism in the respiratory tract. Infected epithelial cells sense the infection and initiate an antiviral response. To define the antiviral response at the earliest stages of infection we used two different single cycle replication reporter viruses. These tools demonstrated heterogeneity in virus replication levels in vivo. Transcriptional profiling demonstrated tiers of interferon stimulated gene responses that were dependent on the magnitude of virus replication. Uninfected cells and cells with blunted replication expressed a distinct and potentially protective ISG signature. Finally, we used these single cycle reporter viruses to determine the antiviral landscape during virus spread, which unveiled disparate protection mediated by IFN. Together these results highlight the complexity of virus-host interactions within the infected lung and suggest that magnitude and round of replication tune the antiviral response.

overall_design: Mice were infected with 10^5 pfu of the indicated virus. Lungs from infefected C57BL/6 were taken at 24 hours post infection. Single cell suspensions were sorted for live CD45-CD31- and the indicated virus-driven fluorophore. Cells were FACS sorted directly into cell lysis buffer for RNA extraction. cDNA libraries were prepared using the SMARTer Universal Low Input RNA Kit (Takara Bio). SAmples were then profiled by illumina sequencing

first: Louisa

last: Sjaastad

first: Elizabeth

last: Fay

first: Jessica

middle: K

last: Fiege

first: Marissa

middle: G

last: Macchietto

first: Ian

last: Stone

first: Matthew

last: Markman

first: Steven

last: Shen


title: Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila

city: Chapel Hill

first: Robert

last: Duronio

address: CB #3280, Coker Hall

institute: University of North Carolina at Chapel Hill

summary: We replaced the endogenous histones of Drosophila melanogaster with either histones containing an H3K9R mutation or histones containing an H4K16R mutation to interrogate established genome-wide correlations between chromatin state, transcription, and DNA replication timing. We performed total RNA-seq in H4K16R males and females to investigate the role of H4K16 in dosage compensation of the male X chromosome. We found that H4K16 directly promotes hyper-expression of the male X chromosome in Drosophila. To generate replication timing profiles, we performed Repli-seq in HWT males and females, H4K16R males and females, and H3K9R females. We found that H3K9 promotes late replication of the pericentromeric heterochromatin and H4K16 promotes early replication of the male X chromosome.

overall_design: Experiments were performed on endogenous histone mutants rescued with a wild type (HWT), H4K16R mutant, or H3K9R mutant transgenic arrays. RNA-seq experiments were carried out in triplicate and Repli-seq experiments were carried out in duplicate. RNA-seq and Repli-seq were performed in wing imaginal discs from 3rd instar Drosophila larvae. S phase and G1 phase samples for Repli-seq were obtained using FACS on nuclei isolated from wing imaginal discs and replication timing values were calculated as S/G1 ratio.

first: Robin

last: Armstrong


title: In vivo analysis of spinal cord astrocyte and non-astrocyte gene expression after traumatic spinal cord injury, with or without  intraspinal treatment with hydrogel depot containing FGF+EGF

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: Comparison of genomic data from astrocytes and non-astrocyte cells from mice with or without FGF+EGF after SCI.  We conducted genome-wide RNA sequencing of (i) immunoprecipitated astrocyte-specific ribosome-associated RNA (ramRNA) and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells, from spinal cord tissue of mice recieving i) SCI alone, ii) SCI+hydrogel depot containing FGF+EGF,  or iii) SCI+empty hydrogel depot.

overall_design: Young adult mGFAP-Cre-RiboTag mice underwent severe crush SCI at thoracic level 10. Hydrogel depots were injected two days post-injury. At 14 days following SCI, the central 3mm of the SCI lesion was extracted, homogenized and (i) astrocyte-specific ribosome-associated RNA (ramRNA) precipitated via a hemagglutinin (HA) tag targeted to astrocytes, and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells in the same tissue samples.

first: Mark

last: Anderson

first: Timothy

last: O’Shea

first: Joshua

last: Burda

first: Yan

last: Ao

first: Sabry

last: Barlatey

first: Alexander

last: Bernstein

first: Jae

middle: H

last: Kim

first: Nicholas

middle: D

last: James

first: Alexandra

last: Rogers

first: Brian

last: Kato

first: Aexander

last: Wollenberg

first: Giovanni

last: Coppola

first: Chen

last: Wang

last: Deming

first: Zhigang

last: He

first: Gregoire

last: Courtine

first: Michael

last: Sofroniew


title: Subtype-specific regulatory network rewiring in acute myeloid leukemia [Hi-C]

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: Acute myeloid leukemia is a heterogeneous disease which is subdivided into different categories defined by disease-causing mutations in transcription factors, epigenetic regulators and signalling molecules. How different mutant regulators establish AML-specific transcriptional networks is unclear. Here we performed a comprehensive analysis of mutation-specific sets of cis-regulatory elements driving gene expression in AML blast cells from a carefully selected group of patients with alterations in genes encoding transcription factors (RUNX1, CEBPA) and signalling molecules (FTL3-ITD, RAS, NPM1). We show that each mutant regulator establishes a specific transcriptional and signalling network unrelated to normal cells driving the expression of unique sets of genes required for AML survival.

overall_design: promoter capture HiC expreiments have been used to study the chromatin landscape of AML with different mutations

first: Maria

middle: R

last: Imperato

first: Daniel

last: Coleman

first: Anetta

last: Ptasinska

first: Anna

last: Pickin

first: Sandeep

last: Potluri

first: Pierre

last: Cauchy

first: Paulynn

middle: S

last: Chin

first: Rosaria

last: Roffo

first: Liam

middle: N

last: Gilding

first: Sally

first: Andrew

last: Beggs

first: Justin

last: Loke

first: Sam

last: Clokie

first: H

last: Delwel

first: Manoj

last: Raghavan

last: Griffiths

first: Stephen

last: Richards

first: Peter

last: Cockerill

first: Constanze

last: Bonifer


title: Targeting the CALR Interactome in Myeloproliferative Neoplasms

status: Public on Sep 19 2018

city: New York

first: Richard

last: Koche

state: NY

address: 417 East 68th St

department: Center for Epigenetic research

institute: Memorial Sloan Kettering Cancer Center

summary: Mutations in the endoplasmic reticulum (ER) chaperone calreticulin (CALR) are common in myeloproliferative neoplasm (MPN) patients, activate the thrombopoietin receptor (MPL), and mediate constitutive JAK/STAT signaling.  The mechanisms by which CALR mutations cause myeloid transformation are incompletely defined.  We employed mass spectrometry proteomics to identify novel CALR-mutant interacting proteins.  Mutant CALR caused mislocalization of binding partners and increased recruitment of FLI1, ERP57 and CALR to the MPL promoter to enhance transcription. CALR 52 mutant was also found to increase genome-wide recruitment of Fli1 to the chromatin. Overall, these results show that type 1 CALR mutant modulates Fli1 cellular localization and recruitment.

overall_design:
We repor tFli1 increased nuclear localization and chromatin recruitement in CALR mutated cells
Examination of Fl1 ChIP-seq in MPL-WT-BA/F3 cells expressing EV, WT, DEL or INS CALR constructs

first: Jesper

last: Maag

first: Jane

last: Park

first: Elodie

last: Pronier


title: Subtype-specific regulatory network rewiring in acute myeloid leukemia

first: Salam

last: Assi


title: Subtype-specific regulatory network rewiring in acute myeloid leukemia [RNA-seq]

overall_design: RNA-seq expreiments have been used to study the chromatin landscape of AML with different mutations

first: Maria

last: Imperato

first: Daniel

last: Coleman

first: Anetta

last: Ptasinska

first: Anna

last: Pickin

first: Sandeep

last: Potluri

first: Pierre

last: Cauchy

first: Paulynn

last: Chin

last: James

middle: C

first: Michael


title: Robust single-cell DNA methylome profiling with snmC-seq2

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications of the method have been impeded by the modest quality of sequencing libraries. Here we report snmC-seq2, which provides improved read mapping, reduced artificial reads, enhanced throughput, and increased library complexity compared to snmC-seq. snmC-seq2 is an efficient strategy suited for large scale single-cell epigenomic studies.

overall_design: Single-cell DNA methylome profiling with snmC-seq2

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Jingtian

last: Zhou

first: Justin

middle: P

last: Sandoval

first: Laurie

last: Kurihara

first: Jacinta

last: Lucero

first: Rosa

last: Castanon

last: Nery

first: António

last: Pinto-Duarte

first: Brian

last: Bui

first: Conor

last: Fitzpatrick

first: Carolyn

last: O'Connor

first: Seth

last: Ruga

first: Marc

middle: E

last: Van Eden

first: David

last: Davis

first: Deborah

last: Mash

first: M

middle: M

last: Behrens


title: A genomic ruler to assess oncogenic transition between breast tumor and stroma

city: Laurel

first: Amanda

last: Ernlund

address: 11100 Johns Hopkins Rd

department: REDD

institute: Johns Hopkins APL

summary: Genome-wide gene expression changes were determined in histopathologically normal breast tissue in 33 women undergoing mastectomy for stage II and III primary invasive ductal carcinoma at serial distances in three dimensions from the tumor. Gene expression was determined by genome-wide mRNA analysis and subjected to metagene mRNA characterization

overall_design: 108 samples taken from patients at tumor, 5mm, 10mm, 15mm, 20mm from tumor were subjected to microarray analysis using HG-U133 Plus 2 affymetrix arrays


title: Subtype-specific regulatory network rewiring in acute myeloid leukemia [DNase-Hypersensitivity]

first: Salam

last: Assi

overall_design: DNAse1-seq expreiments have been used to study the chromatin landscape of AML with different mutations

middle: A

first: Maria

last: Imperato

first: Daniel

middle: J

last: Coleman

first: Anetta

last: Ptasinska

first: Anna

last: Pickin

first: Sandeep

last: Potluri

first: Pierre

last: Cauchy

first: Paulynn

last: Chin

first: Rosaria

last: Roffo

first: Liam

last: Gilding

first: Sally

last: James

first: Andrew

last: Beggs

last: Loke

first: Sam

last: Clokie

first: H

last: Delwel

first: Manoj

last: Raghavan

first: Michael

last: Griffiths

first: Stephen

last: Richards

first: Peter

last: Cockerill

first: Constanze

last: Bonifer


title: Transcriptional profiles in the chicken ductus arteriosus during hatching

city: Tokyo

first: Toru

last: Akaike

address: 3-25-8 Nishi-Shimbashi, Minato-ku

department: Cell Physiology

institute: The Jikei University

summary:
The ductus arteriosus constricts after birth or hatching and eventually closes to terminate embryonic circulation. Chicken embryos have two long ductus arteriosus. Then the pulmonary artery-sided and descending aorta-sided ductus arteriosus have distinct functional characteristics, such as oxygen responsiveness.
We used microarrays to elucidate the difference between the pulmonary artery-sided and descending aorta-sided ductus arteriosus in their transcriptional profiles.

overall_design: Chicken tissues of the right-sided ductus arteriosus and the aorta were selected at the internal pipping (IP) stage for RNA extraction and hybridization on Affymetrix microarrays. We then divided each long ductus arteriosus into two parts: the pulmonary artery-sided and descending aorta-sided ductus arteriosus.

first: Susumu

last: Minamisawa

first: Satoko

last: Sinjo

first: Eriko

last: Ohmori


title: ATAC-sequencing of innate lymphoid cells that were sorted from mouse skin

city: Bethesda

first: Tetsuro

last: Kobayashi

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm12N256

institute: NIAMS/NIH

summary:
Purpose: Regulome analysis of skin innate lymphoid cells
Methods: Innate lymphoid cells were sorted from epidermis, dermis and subcutis of adult B6 mice, respectively and subjected to transposition reaction and library preparation.
Results: 20,869 accessible regulatory elements were detected
Conclusions: This study reveals regulome landscape of skin innate lymphoid cells

overall_design: Regulome profiles of skin innate lymphoid cells were generated by ATAC-seq in duplicate

first: Keisuke

last: Nagao


title: RNA-sequencing of innate lymphoid cells that were sorted from mouse skin

summary:
Purpose: Transcriptomic analysis of skin innate lymphoid cells
Methods: Innate lymphoid cells were sorted from epidermis, dermis and subcutis of adult B6 mice, respectively and subjected to RNA isolation and library preparation.
Results: 3,078 differentially expressed genes (fold change>2 and p-value<0.05) were detected
Conclusions: This study reveals transcriptome landscape of skin innate lymphoid cells

overall_design: Transcriptome profiles of skin innate lymphoid cells were generated by RNA-seq in tripricate


title: Differential Expression of IL-2 Defines CD4 T cells fated for Follicular Helper and Non-follicular Helper Development (ATAC-Seq)

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

summary: IL-2 production defines precursors fated to become T Follicular Helper cells

overall_design: Sorted naïve IL-2.eGFP CD4 T cells were activated in vitro. Nuclei were  isolated from naïve CD4 T cells or CD69+ IL-2.eGFP+ and CD69+ IL-2.eGFP– cells 18-24 hours after activation.

first: D

last: DiToro

first: S

last: Witte

last: Pham

first: M

first: R

last: Hatton

first: C

last: Weaver


title: Differential Expression of IL-2 Defines CD4 T cells fated for Follicular Helper and Non-follicular Helper Development

overall_design: Refer to individual Series


title: The genomic landscape of microRNA-target interactions in human cells

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Sejong University

summary: MicroRNAs play important roles in physiology and pathology by repressing target gene expression, but it remains challenging to identify targets and regulatory networks on a global scale. MicroRNAs often pair with targets complementary to nucleotide 2 to 7, but such complementarity is not always found within targets. Here we show global views of microRNA-target interactions with unparalleled resolution and confidence by conducting a series of UV-crosslinking and immunoprecipitation experiments for AGO2. Our data indicate that direct interactions are mainly guided by seed complementarity. However, we find that different microRNAs recognize atypical sites with varying tolerance to mismatches. Pathway enrichment analyses reveal that many target genes encoding constituents of the same pathways such as Hippo and Wnt, yet unexpectedly, both positive and negative components are targeted by identical and/or different microRNAs from a same polycistronic cluster. The prevalence of incoherent feedforward loops epitomizes the complexity of microRNA-target networks and the pitfalls of reductionistic inference of miRNA functions. Our results illuminate target sites of miRNAs and regulatory networks that facilitate a deeper understanding of miRNA functions.

overall_design: CLIP-seq of endogenous AGO2 by using anti-AGO2-antibody (Proteintech) and IgG controls, sequencing of microRNAs associated with AGO2


title: Differential Expression of IL-2 Defines CD4 T cells fated for Follicular Helper and Non-follicular Helper Development (RNA-Seq)

overall_design: Sorted naïve IL-2.eGFP CD4 T cells were activvated in vitro or in vivo. Total RNA was isolated from CD69+ IL-2.eGFP+ and CD69+ IL-2.eGFP– CD4 T cells 18-24 hours after activation.


title: Lung adenocarcinoma UNC0638 gene expression

status: Public on Sep 18 2018

city: Boston

first: Samuel

last: Rowbotham

address: 300 Longwood Avenue

department: Stem Cell Hem/Onc

institute: Boston Children's Hospital

summary: Experiment was to determine the effects of G9a inhibition using chemical inhibitor UNC0638 on murine lung adenocarcinoma cell lines

overall_design: 4 indpendent samples from two different cell lines, CK1750 and TnM2 were grown with either UNC0638 or vehicle control for 4 days. Cells were then harvested and RNA purified and sequenced.

first: Carla

middle: F

last: Kim


title: Progressing enhancer landscape during mammary differentiation controls gene regulation [RNA-seq]

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary: The mammary luminal lineage relies on the common cytokine-sensing transcription factor STAT5 to establish super-enhancers during pregnancy and activate mammary genes required for the nutrition of the offspring. Exploiting progressive differentiation during lactation, we investigated how hormonal cues shape an evolving enhancer landscape and impact the biology of mammary cells. Employing ChIP-seq, we uncover a changing transcription factor occupancy at mammary enhancers. Using mouse genetics, we demonstrate changing biological properties of enhancers as lactation progresses, with individual enhancers gaining strength and an abolished need for the Wap seed enhancer. We further investigated whether permissive chromatin facilitates cell-specific transcription factor binding. Wap enhancers translocated into the widely expressed neighboring Ramp3 gene retained their mammary-specificity and failed to activate the receptive Ramp3 gene in non-mammary tissues. Our studies unveil a previously unrecognized progressive enhancer landscape, in which structurally equivalent components serve unique and differentiation-specific functions. While enhancer redundancy has been suggested and demonstrated for many genes, components of the cytokine-responsive mammary tripartite Wap super-enhancer display a remarkable specificity.

overall_design: Total RNA-seq was done for mammary tissues at day one and ten of lactation.

first: Hye

last: Lee


title: Transcriptome of E17 wild-type and Myh10L458R/L458R mutant lungs

status: Public on Sep 17 2018

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Transcriptomic analysis between E17 wild-type and Myh10L458R/L458R mutant lungs (left lobes)

overall_design: Lung mRNA profiles of E17 wild-type and Myh10L458R/L458R mutant lungs were generated by deep sequencing.

first: Hyun-Taek

last: Guenther

first: Didier

last: Stainier


title: Physical basis for long-distance communication along meiotic chromosomes (ChIP-seq)

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

summary: Viable gamete formation requires segregation of homologous chromosomes connected, in most species, by crossovers.  DNA double-strand break (DSB) formation and the resulting crossovers are regulated at multiple levels to prevent overabundance along chromosomes.  Meiotic cells coordinate these events between distant sites, but the physical basis of long-distance chromosomal communication has been unknown.  We show that DSB hotspots up to ~200 kb (~35 cM) apart form clusters via hotspot-binding proteins Rec25 and Rec27 in fission yeast.  Clustering coincides with hotspot competition and interference over similar distances.  Without Tel1 (ATM tumor-suppressor homolog), DSB and crossover interference become negative, reflecting coordinated action along a chromosome.  These results indicate that DSB hotspots within a limited chromosomal region and bound by their protein determinants form a clustered structure that, via Tel1, allows only one DSB per region.  Such a “roulette” process among clusters explains the observed pattern of crossover interference in fission yeast.  Key structural and regulatory components of clusters are phylogenetically conserved, suggesting conservation of this vital regulation.  Based on these observations, we discuss variations on a model in which clustering and competition between DSB sites leads to DSB interference and in turn produces crossover interference.

overall_design: Eight total samples split between two sequencing runs.  These eight samples consist of four pairs of immunoprecipitations.  Each pair is the immunopreciptated DNA being ligated before or after crosslinkeds were removed.

first: Randy

middle: W

last: Hyppa

first: Gareth

last: Cromie

first: Gerald

last: Smith


title: Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation

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


title: Physical basis for long-distance communication along meiotic chromosomes

type: Genome binding/occupancy profiling by array


title: Differential Gene expression in the mouse mammary tumors of  PyMT-Malat1 wild-type (WT), PyMT-Malat1 knockout (KO) and PyMT-Malat1 knockout with Malat1 transgene expression (TG)

city: Houston

first: Jongchan

address: 6565 MD Anderson Blvd

institute: UT MD Anderson

summary: Previously, lncRNA Malat1 knockout mice were generated by insertional inactivation. By crossing this line to MMTV-PyMT mammary tumor mouse model, we produced PyMT;Malat1 wild-type (WT) and PyMT;Malat1 knockout (KO). Furthermore, we generated Malat1 transgenic mice by targeting ROSA26 locus and bred them to PyMT;Malat1 knockout mice to produce Malat1-rescued PyMT;Malat1 knockout;Malat1 transgenic animals (TG). Using mammary tumors from the three groups of animals, we performed RNA-Seq analysis to identify differentially up-regulated genes in KO tumors to find novel target genes of YAP-TEAD pathway.

overall_design: mRNA profiles of biological duplicate mammary tumors from PyMT;Malat1 wild-type (WT), PyMT;Malat1 knockout (KO) and PyMT;Malat1 knockout;Malat1 transgenic animals (TG) using RNA-Seq

first: Yumeng

last: Wang

first: Han

last: Liang

first: Li

last: Ma


title: The APT complex is involved in non-coding RNA transcription and is distinct from CPF [ChIP-seq]

city: Goettingen

first: Michael

last: Lidschreiber

address: Am Fassberg 11

institute: Max-Planck-Institute for Multidisciplinary Scienes

summary: The 3′-ends of eukaryotic pre-mRNAs are processed in the nucleus by a large multiprotein complex, the cleavage and polyadenylation factor (CPF). CPF cleaves RNA, adds a poly(A) tail and signals transcription termination. CPF harbors four enzymatic activities essential for these processes but how these are coordinated remains poorly understood. Several subunits of the CPF including two protein phosphatases are also found in a related complex, the ‘associated with Pta1’ (APT) complex, but the relationship between CPF and APT is unclear. Here, we show that the APT complex is physically distinct from CPF. The 21 kDa Syc1 protein is associated only with APT, and not with CPF, and is therefore the defining subunit of APT. Using ChIP-seq, PAR-CLIP and RNA-seq, we show that Syc1 has functions separable from those of CPF. Syc1 plays a role in sn/snoRNA production whereas CPF processes the 3ʹ-ends of protein-coding pre-mRNAs. These results define distinct protein machineries for synthesis of mature eukaryotic protein-coding and non-coding RNAs.

overall_design: In this study, we used photoactivatable ribonucleoside-enhanced crosslinking and immuno-precipitation (PAR-CLIP) and ChIP-seq to map direct protein-RNA interactions and protein-DNA interactions, respectively, in vivo. We applied these methods to subunits of the CPF and APT complexes of the yeast Saccharomyces cerevisiae. Both ChIP and PAR-CLIP occupancy profiles suggested that the APT defining subunit Syc1 is preferentially associated with sn/snoRNA genes and transcripts. Thus, we also investigated RNA synthesis in vivo using metabolic labeling with 4-thiouracil, followed by sequencing of the newly synthesized, labeled RNA (4tU-seq) and compared syc1 knock-out cells to wild-type.

first: Ashley

last: Easter

first: Sofia

last: Battaglia

first: Carlo

last: Baejen

first: Kerstin

last: Maier

first: Patrick

last: Cramer

first: Lori

last: Passmore


title: The APT complex is involved in non-coding RNA transcription and is distinct from CPF [PAR-CLIP]


title: ATAC-sequencing and RNA-sequencing of innate lymphoid cells that were sorted from mouse skin

first: Tetsuro

last: Kobayashi


title: The APT complex is involved in non-coding RNA transcription and is distinct from CPF [RNA-seq]


title: Transcriptional profiling in Kenyon cells reveals dynamic regulation of learning and memory genes after acquisition of long-term courtship memory

city: Halifax

first: Spencer

middle: Gordon

last: Jones

state: NS

address: 5850 College St

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

summary:
Purpose: The formation and recall of long term memory (LTM) requires neuron activity induced gene expression. Transcriptome analysis has been used to identify genes that have altered expression after memory acquisition, however, we still have an incomplete picture of the transcriptional changes that are required for LTM formation. The complex spatial and temporal dynamics of memory formation creates significant challenges in defining memory-relevant gene expression changes. The mushroom body (MB) is a signaling hub in the insect brain that integrates sensory information to form memories. Our study looks to further elucidate the transcriptional mechanisms underlying LTM by profiling gene expression changes in nuclei of the MB during a time course of LTM formation.
Methods: We isolated and sequenced fly RNA from biologically paired whole head (WH) and mushroom body (MB) nuclei. MB nuclei were isolated using INTACT (isolation of nuclei tagged in a specific cell type). LTM was induced using a seven-hour courtship conditioning protocol. Fly heads were collected one hour and 24-hours after this period of sexual rejection. Samples of naive, socially isolated males were also collected at the same age and time-of-day for comparison.
Results and conclusions: We identified more transcriptional changes 1 hour after memory acquisition (WH = 322, MB = 305) than at 24 hours (WH = 20, MB = 24). WH samples showed downregulation of developmental genes and upregulation of sensory response genes. In contrast, MB samples showed vastly different gene expression changes affecting biological processes that are specifically related to LTM.  MB-downregulated genes were highly enriched for metabolic function, consistent with the MB-specific energy influx that occurs during LTM formation. MB-upregulated genes were highly enriched for known learning and memory processes, including calcium mediated neurotransmitter release and cAMP signalling. The neuron activity inducible genes hr38 and sr were also specifically induced in the MB. These results highlight the importance of sampling time and cell type in capturing biologically relevant transcriptional changes involved in learning and memory. Our data suggests that MB cells transiently upregulate known memory related pathways after memory acquisition, and provides a critical frame of reference for further investigation into the role MB-specific gene regulation in memory.

overall_design: Nuclear RNA profiles with >10 million genic reads were generated for both whole head samples (five naïve, three 1h-AR, four 24h-AR) and mushroom body samples (four naïve, four 1h-AR, four 24h-AR).

first: Kevin

last: Nixon

first: Jamie

last: Kramer


title: Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

summary: Vascular smooth muscle cells (VSMCs) show pronounced heterogeneity across and within vascular beds, with direct implications for their function in injury response and atherosclerosis. Here we combine single-cell transcriptomics with lineage tracing to examine VSMC heterogeneity in healthy mouse vessels. The transcriptional profiles of single VSMCs consistently reflect their region-specific developmental history and show heterogeneous expression of vascular disease-associated genes involved in inflammation, adhesion and migration. We detect a rare population of VSMC-lineage cells that express the multipotent progenitor marker Sca1, progressively downregulate contractile VSMC genes and upregulate genes associated with VSMC response to inflammation and growth factors. We find that Sca1 upregulation is a hallmark of VSMCs undergoing phenotypic switching in vitro and in vivo, and reveal an equivalent population of Sca1-positive VSMC-lineage cells in atherosclerotic plaques. Together, our analyses identify disease-relevant transcriptional signatures in VSMC-lineage cells in healthy blood vessels, with implications for disease susceptibility, diagnosis and prevention.

overall_design: This entry contains data from the following analyses: (1) Bulk RNA-seq of mouse VSMCs isolated from aortic arch (AA) and descending thoracic aorta (DT) regions in triplicates. (2)  Pooled RNA-seq of mouse Sca1- VSMCs and Sca1- or Sca1+ adventitial cells in triplicates. (3) Single-cell RNA-seq of VSMCs from the AA and DT regions (143 cells). (4) VSMC lineage label positive and negative cells isolated from the medial layer of mouse aorta, which expressed or did not express the Sca1 protein (155 cells). (5) 10X single-cell RNA-seq analysis of: lineage positive plaque cells isolated from mice following 14 or 18 weeks of high fat diet feeding, cells isolated from the whole aorta and lineage positive VSMCs from the medial layer.

first: Mikhail

last: Spivakov

first: Helle

last: Jørgensen

first: Lina

last: Dobnikar

first: Annabel

middle: L

last: Taylor

first: Joel

last: Chappell

first: Jennifer

last: Harman


title: Gene expression profiling of HSCs treated with Eltrombopag

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Department of Cell Biology

institute: Albert Einstein College of Medicine


title: The APT complex is involved in non-coding RNA transcription and is distinct from CPF

first: Michael

last: Lidschreiber


title: Expression data of human bone-marrow mesenchymal stem cells treated with ApoA-I for different time-points during osteogenesis

status: Public on Sep 15 2018

city: Taipei

first: Yu-Chuan

last: Liu

address: 128 Academia Road, Section 2, Nankang

department: Genomic Research Center

institute: Academia Sinica

summary:
Human mesenchymal stem cells are differentiated into osteoblasts in the presence or absence of ApoA-I treatment, the global gene profiles of MSCs with different time-points are compared. Day 0 is primary human MSCs without induction was used the baseline for comparision.
We used microarrays to investigate the global gene expression profiles in hBM-MSCs with ApoA-I treatment for 1, 3, 5 days during osteogenesis

overall_design: We treated mesenchymal stem cells with or without ApoA-I for 1, 3, 5 days during osteogenesis.  MSCs without  induction on day 0 served as control group.

first: Shang-Chih

last: Yang


title: Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

summary: We molecularly characterized thousands of liver endothelial cells and immune cells using scRNAseq. We next sequenced pairs of hepatocytes and attached endothelial cells, and used the hepatocyte genes to infer the liver lobule coordinates of these pairs, thus obtaining the global zonation patterns of endothelial genes.

overall_design: mRNA profiles from single cells and paired-cells extracted from mouse liver were sequenced in several batches in an Illumina NextSeq.

first: Shalev

last: Itzkovitz

first: Ido

last: Amit

last: Bahar Halpern

first: Rom

last: Shenhav

first: Hassan

last: Massalha

first: Beata

last: Toth

first: Adi

last: Egozi

first: Chiarra

last: Medgalia

first: Andreas

last: Moor

first: Eyal

last: David

first: Efi

last: Massasa

first: Amir

last: Giladi

first: Ziv

last: Porat


title: Regulation of myeloid function by LC3-associated phagocytosis promotes tumor immune tolerance

city: Memphis

first: Doug

last: Green

state: Tn

address: 262 Danny Thomas Pl

department: Immunology

institute: St. Jude Children's Research Hospital

summary: Targeting autophagy in cancer cells and in the tumor microenvironment are current goals of cancer therapy. However, components of canonical autophagy play roles in other biological processes, adding complexity to this goal. One such alternative function of autophagy proteins is LC3-associated phagocytosis (LAP), which functions in phagosome maturation and subsequent signaling events. Here we show that impairment of LAP in the myeloid compartment, rather than canonical autophagy, induces control of tumor growth by tumor-associated macrophages (TAM) upon phagocytosis of dying tumor cells. Single cell RNAseq analysis revealed that defects in LAP induce pro-inflammatory gene expression and trigger STING-mediated type I interferon responses in TAM. We found that the anti-tumor effects of LAP impairment require tumor-infiltrating T cells, dependent upon the STING and the type I interferon response. Therefore, autophagy proteins in the myeloid cells of the tumor microenvironment contribute to immune suppression of T lymphocytes by effecting LAP.

overall_design: Rubcn+/- and Rubcn-/- tumor-infiltrating myeloid cells were isolated from Lewis lung carcinoma subcutaneous grafts

first: Robert

last: Carter

first: Larissa

last: Cunha


title: Gene expression profiling of human HSCs treated with Eltrombopag

first: Britta

last: Will

summary: Eltrombopag, a small molecule thrombopoietin receptor (TPO-R) agonist and potent intracellular iron chelator, has shown remarkable efficacy to stimulate sustained multilineage hematopoiesis in patients with bone marrow failure syndromes, suggesting an effect at the most immature hematopoietic stem and multipotent progenitor level. While the functional and molecular effects of Eltrombopag on megakaryopoiesis have been carefully studied in the recent past, insights into its mechanistic impact on the earliest stages of hematopoiesis have been limited. Additionally, previous studies also revealed molecular pathway of Eltrombopag apart from stimulation of TPO signaling, detail characterization remains to be addressed. In this study, we investigated the effects of Eltrombopag, in comparison with TPO, on highly-purified primary hematopoietic stem cells (HSCs) from healthy human donors. The binding of Eltrombopag to TPO-R is species-specific to human and primate cells. we also utilized HSCs isolated mouse as separation-of-function models to directly assess the molecular effect of Eltrombopag on HSCs independent of TPOR stimulation.

overall_design: Bone marrow was enriched for mononuclear cells by density gradient centrifugation using Ficoll-Paque Plus (GE Healthcare, Pittsburgh, PA). Mononuclear cells were further enriched for CD34+ cells by immunomagnetic cell separation techniques (Miltenyi Biotec, Auburn, CA). Then hematopoietic stem cells (Lineage−CD34+CD38−CD49f+) were purified from CD34+ enriched cells by multiparameter-high speed fluorescence-activated cell sorting (FACS) on either FACS Aria II (Becton Dickinson, Franklin Lakes, NJ) or MoFlo Astrios (Beckman Coulter, Indianapolis, IN)

first: Yun-Ruei

last: Kao

first: Ulrich

last: Steidl


title: Progressing enhancer landscape during mammary differentiation controls gene regulation [ChIP-seq]

first: Michaela

last: Willi

overall_design: ChIP-seq for STAT5A, GR, RNA Pol II, MED1 and H3K27ac in the mammary tissues of wild type, △E1, △E3, △E1a/3, △E1a/2/3, E12-R3 and E2-R3 mutant mice at day one and ten of lactation. ChIP-seq for STAT3, GR and H3K27ac in the kidney tissues of wild type and E12-R3 mutant mice.

first: Hye

middle: K

last: Lee


title: RNA Seq analysis following 1X or 3X Male Courtship Suppression training in Drosophila

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: To obtain a comprehensive view of genes contributing to long-term memory we performed mRNA sequencing from single Drosophila heads following behavioral training that produces long-lasting memory.

overall_design: Virgin males exposed to unreceptive females for one or three two-hour sessions separated by 30 minutes were collected one hour after training for comparison to mock trained flies, with six replicates for each condition, for RNA-Seq analysis of the fly heads with an Illumina HiSeq 2500.

first: Kausik

last: Si

first: Raquel

last: Azpeleta

first: Jason

last: Gill

first: Jianping

last: Wu

first: Ryan

last: Welte


title: Animal model of acute-on-chronic alcoholic liver injury [DDC study]

status: Public on Sep 14 2018

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

institute: TEXAS A&M UNIVERSITY

summary:
Background and aims: Liver is a major target organ for alcohol-induced disease and the spectrum of pathological states elicited by alcohol in liver comprises steatosis, alcoholic steatohepatitis, progressive fibrosis and cirrhosis, conditions that may progress to hepatocellular carcinoma. Many experimental animal models of alcoholic steatohepatitis exist that vary in duration, mode of alcohol administration and the degree and types of liver injury produced. While most of these models, regardless whether alcohol is administered through liquid diet or intragastrically, produce steatohepatitis and mild fibrosis, it is widely acknowledged that these models fail to fully recapitulate key characteristics of severe forms of alcoholic liver disease, such as alcoholic hepatitis. Recent studies attempted to combine alcohol and fibrosis and achieved promising results in mouse models that achieve some of the key features of alcoholic liver disease accompanied by exacerbated fibrosis and acute renal injury. This study combined a chronic cholestatic liver fibrosis model induced by 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) with a mouse model of intragastric alcohol feeding.
Methods: Adult male C57BL6/J mice were treated with 3,5-diethoxycarbonyl-1,4-dihydrocolidine (DDC) containing diet (0.05% w/w) to induce chronic liver fibrosis. Following DDC-induced fibrogenesis, ethyl alcohol (EtOH) (up to 27 g/ kg/day, up to 28 days) was administered continuously to mice via a gastric feeding tube (Tsukamoto-Frenchmodel of alcoholic liver disease).
Results: Exposure to DDC or EtOH alone resulted in liver fibrosis or steatosis, respectively. Combined treatment with DDC and EtOH lead to an additive effect on liver injury, as evident by the development of hepatic inflammation, steatosis, and pericellular fibrosis, and by increased serum transaminase levels, compared to mice treated with either agent alone. Liver transcriptomic changes specific to combined treatment group included pathways involved in the cell cycle and DNA damage. Analyses of feces from these mice revealed alcohol-associated changes to the bile acid profile and gut microbiome.
Conclusions: Mice treated with DDC and EtOH displayed several key characteristics of human alcoholic hepatitis, including pericellular fibrosis, increased hepatic bacterial load with dysbiosis, reduced capacity of the microbiome to synthesize secondary bile acids.

overall_design: Animal model of acute-on-chronic alcoholic hepatitis

first: Shinji

last: Furuya

first: Hisataka

last: Fukushima


title: mRNA expression analysis of human lung cancer cell line CUTO-3 and colorectal cancer cell line KM12-luc treated with TRK inhibitor CH7057288

city: Kamakura

first: Hiroshi

last: Tanaka

state: Kanagawa

address: 200 Kajiwara

institute: Chugai Pharmaceutical Co., Ltd.

summary: CUTO-3 and KM12-luc cell lines were treated with DMSO or 1 uM CH7057288 for 4 and 24 hours. Cellular RNA was extracted, processed to generate an mRNA library, and sequenced from both ends of the library using HiSeq 2500 Sequencing System. RSEM software was used to align reads against RefSeq transcripts and calculate expression values (FPKM) for each gene.

overall_design:
mRNA expression analysis of two cell lines treated with TRK inhibitor was performed by RANA-seq
Raw data has not been submitted due to patient privacy laws in Japan.


title: Transcriptome-wide analysis of TRIM21-mediated changes in gene expression after challenge with virus and antibody

first: Leo

last: James

state: Cambridgeshire

address: Francis Crick Avenue

department: PNAC

summary: We report that TRIM21 plays a crucial role in mediating antibody interference of adenovirus gene delivery and simultaneously initiates a transcriptional programme of immune genes.

overall_design: Transcriptional changes in the liver of WT and TRIM21 KO animals 4h after injection with PBS (control samples), Ad5, Ad5 + rh9C12-WT or Ad5+rh9C12-H433A. 4 replicates per condition; 32 samples in total.

first: Maria

last: Bottermann

first: Laurens

last: van Tienen


title: Antimicrobial peptides modulate long-term memory

overall_design: Refer to individual Series


title: Transcriptome profiling of light-induced gene expression in the suprachiasmatic nucleus of T7 and T24 cycle-housed mice

first: Samer

last: Hattar

address: 35 Convent Drive, Bldg 35A

institute: National Institute of Mental Health

summary: To investigate changes in SCN photic responsiveness after exposure to an ultradian light cycle (T7 cycle; alternating 3.5-hour periods of light and darkness), we performed RNA-sequencing on isolated SCN samples obtained from T24 and T7 light cycle-housed mice that received a light pulse during their active phases. Our results indicate that the SCN becomes refractory to light induction of immediate-early gene expression after exposure to the T7 light cycle.

overall_design: Gene expression profiling in n=3 (T24) and n=4 (T7) biological replicates of SCN tissue (3 individual SCN samples pooled per biological replicate) harvested from T24 or T7 cycle-housed mice after exposure to a light pulse during their active phase.

first: Michael

middle: B

last: Thomsen

first: Diego

last: Fernandez


title: Identification of human gene expression induced by 4MU-xyloside treatment

city: Ako

first: Hiderou

last: Yoshida

state: Hyogo

address: Kamigori, Koto 3-2-1

department: Life Science

institute: University of Hyogo

summary: The Golgi stress response is a homeostatic mechanism that augments the functional capacity of the Golgi apparatus when Golgi function becomes insufficient (Golgi stress). Three response pathways of the Golgi stress response have been identified in mammalian cells, the TFE3, HSP47 and CREB3 pathways, which augment the capacity of specific Golgi functions such as N-glycosylation, anti-apoptotic activity and pro-apoptotic activity, respectively. On the contrary, glycosylation of proteoglycans (PGs) is another important function of the Golgi, although the response pathway upregulating expression of glycosylation enzymes for PGs in response to Golgi stress remains unknown. Here, we found that expression of glycosylation enzymes for PGs was induced upon insufficiency of PG glycosylation capacity in the Golgi (PG-Golgi stress), and that transcriptional induction of genes encoding glycosylation enzymes for PGs was independent of the known Golgi stress response pathways and ER stress response. Promoter analyses of genes encoding these glycosylation enzymes revealed the novel enhancer element PGSE, which regulates their transcriptional induction upon PG-Golgi stress. From these observations, the response pathway we discovered is a novel Golgi stress response pathway, which we have named the PG pathway.

overall_design: Three control samples (DMSO-treated) and three 4MU-xyloside-treated samples

first: Mai

last: Taniguchi

first: Kanae

last: Sasaki


title: Trancriptional profile of WT and Notch2 cDC2s after immunization with SRBC

city: Saint Louis

first: Carlos

middle: Gustavo

last: Briseno

state: Missouri

address: 660 S Euclid

institute: Washington University School of Medicine

summary: To determine any expresssion changes in cDC2s from WT and CD11c-Cre Notch2f/f mice immunized with sheep red blood cells

overall_design: cDC2s were sorted from spleens of WT or CD11c-Cre Notch2f/f mice that were left untreated or after 24 hours of being treated with sheep red blood cells i.p.

middle: G

first: Kenneth

last: Murphy


title: Antiretroviral therapy potentiates high-fat diet induced obesity and glucose intolerance

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

summary:
Background Breakthroughs in HIV treatment, especially antiretroviral therapy (ART), have massively reduced mortality. However, ART-treated individuals display elevated rates of obesity, diabetes, and cardiovascular disease, collectively known as metabolic syndrome. These co-morbidities represent a considerable threat to long-term survival and quality of life. Previous studies have shown that high-fat feeding induces persistent low-grade systemic and adipose tissue inflammation contributing to insulin resistance and metabolic dysregulation via adipose-infiltrating macrophages.
Methods and Results Studies herein test the hypothesis that ART potentiates the inflammatory effects of a high-fat diet (HFD). C57Bl/6J mice on a HFD or standard chow containing ART or vehicle, were subjected to functional metabolic testing, RNA-sequencing of epididymal white adipose tissue (eWAT), and array-based kinomic analysis of eWAT-infiltrating macrophages. ART-treated mice on a HFD displayed fat mass accumulation, impaired glucose tolerance, and potentiated insulin resistance. Gene set enrichment and kinomic array analyses revealed a pro-inflammatory transcriptional signature depicting granulocyte migration and activation.
Conclusions The current study reveals a HFD-ART interaction that increases inflammatory transcriptional pathways in eWAT consistent with macrophage infiltration, resulting in impaired glucose metabolism, energy balance, and metabolic dysfunction.

overall_design: RNA sequencing analysis of mice given high-fat diet or standard chow diet with/without Atripla (Efavirenz, Emtricidabine, and Tenofovir disoproxil fumarate) for 80 days

first: Kirk

last: Habegger

first: Hubert

last: Tse

first: Adam

middle: R

last: Wende


title: Screening of lncRNAs involved in cancer cell evasion of extrinsic and intrinsic apoptotic pathways

status: Public on Sep 13 2018

city: Birmingham Gardens

first: YUANYUAN

last: ZHANG

state: NSW

address: UNIVERSITY DRIVE, University Dr

country: Australia

institute: The University of Newcastle

summary: We generated ME4405 TRAIL-selected (TRAIL.S) and ME4405 UMI-77-selected (UMI-77.S) cell sub-lines that were resistant to TRAIL and the Mcl-1 inhibitor UMI-77, respectively, after long-term exposure to drug treatment. By performing RNA-sequencing analysis, we found that 37 upregulated lncRNAs in common between TRAIL.S and UMI-77.S cells, suggesting these lncRNAs may function in both extrinsic and intrinsic apoptotic pathways.

overall_design: Examination of functional lncRNA(s) responsible for cancer cells evading apoptosis.

first: Yuanyuan

last: Zhang

first: Xu

middle: D


title: Tet2 orchestrates dynamics of hydroxy-methylation and chromatin state during cell reprogramming [ATAC-seq]

city: Paris

first: samuel

last: Collombet

address: 46 rue d'Ulm

department: Biology

country: France

institute: Ecole Normale Superieure

summary: Studies of DNA hydroxy-methylation and chromatin state dynamics during highly-efficient somatic cell reprogramming

overall_design: Chromatin accessibility profiling of MEF reprogramming to (induced) pluripotent stem cells using ATACseq

first: Jose

last: Sardina

first: Samuel

first: Antonio

last: Gomez

first: Thomas

last: Graf


title: PP2A is essential for Th17 differentiaiton

city: Hangzhou

first: Xuexiao

last: Jin

address: 866 Yuhangtang Road

country: China

institute: Zhejiang University

summary: Phosphatase PP2A expression level is positively correlated to the clinical severity of systemic lupus erythematosus (SLE) and IL17A cytokine overproduction, indicating a potential role of PP2A in controlling TH17 differentiation and inflammation. By generating a mouse strain with the ablation of the catalytic subunit α of PP2A in peripheral mature T cells (PP2A cKO), we provide evidence here that PP2A complex is essential in TH17 differentiation. Hence, PP2A cKO mice exhibited a selective reduction of TH17 cell numbers and an attenuated disease severity in an experimental autoimmune encephalomyelitis (EAE) model. Importantly, PP2A deficiency ablated c-terminal phosphorylation of SMAD2 whereas increased c-terminal phosphorylation of SMAD3. Through direct binding to and regulating the activity of RORγt, the phosphorylational changes of these R-SMADs subsequently reduced Il17a transcription. Finally, PP2A inhibitors recapitulated the phenotype of PP2A cKO mice, i.e., inhibiting TH17 differentiation and protecting mice from EAE. Together, the current study proves that phosphatase PP2A is essential for TH17 differentiation, and inhibition of PP2A could be a possible therapeutic approach for the controlling of TH17-driven autoimmune diseases.

overall_design: mRNA profiles of in vitro polarized PP2A WT and PP2A cKO Th17 cells were generated by deep sequencing, in two biological replicates, using  Illumina NovaSeq 6000

first: Qin

last: Xu


title: Tet2 orchestrates dynamics of hydroxy-methylation and chromatin state during cell reprogramming [hMeDIP-seq]

overall_design: hydroxy-methylation profiling of MEF reprogramming to (induced) pluripotent stem cells using hMedIP-seq


title: Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation [ChIP-seq]

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

summary: Self-renewal of embryonic stem cells (ESCs) cultured in serum-LIF is incomplete with some cells initiating differentiation. While this is reflected in heterogeneous expression of naive pluripotency transcription factors (TFs), the link between TF heterogeneity and differentiation is not fully understood. Here we purify ESCs with distinct TF expression levels from serum-LIF cultures to uncover early events during commitment from naïve pluripotency. ESCs carrying fluorescent Nanog and Esrrb reporters show Esrrb downregulation only in NANOGlow cells.  Independent Esrrb reporter lines demonstrate that ESRRBnegative ESCs cannot effectively self-renew. Upon ESRRB loss, pre-implantation pluripotency gene expression collapses. ChIP-Seq identifies different regulatory element classes that bind both OCT4 and NANOG in ESRRBhigh cells. Class I elements lose NANOG and OCT4 binding in ESRRBnegative ESCs and associate with genes expressed preferentially in naïve ESCs. In contrast, class II elements retain OCT4 but not NANOG binding in ESRRBnegative cells and associate with more broadly expressed genes. Therefore, mechanistic differences in TF function act cumulatively to restrict potency during exit from naïve pluripotency.

overall_design: ChIP-seq for Oct4 and Nanog in ESCs sorted by Esrrb level (high, medium, negative), 6 datasets total

first: Nicola

last: Festuccia

first: Andrea

last: Corsinotti

first: Alessia

last: Gagliardi

first: Douglas

last: Colby

first: Simon

last: Tomlinson

first: Ian

last: Chambers


title: Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation.

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


title: Transcriptome of liver tissue in 2 week old and E17.5 Stabilin-1 knock-out mice

city: Turku

first: Kati

last: Elima

address: Tykistökatu 6

department: MediCity

country: Finland

institute: University of Turku

summary: Stabilin-1/CLEVER-1 is a multidomain protein present in lymphatic and vascular endothelial cells and in M2 immunosuppressive macrophages. Stabilin-1 functions in scavenging, endocytosis and leukocyte adhesion to and transmigration through the endothelial cells.

overall_design: The transcriptome of liver tissue in 2wk old and E17.5 Stab1 knock-out mice was compared to that of corresponding wild type mice


title: SWI/SNF component ARID1A restrains pancreatic neoplasia formation

status: Public on Sep 12 2018

city: Dallas

first: Sam

last: Wang

address: 5323 Harry Hines Blvd.

department: Surgery

institute: UT Southwestern Medical Center


title: SWI/SNF component ARID1A restrains pancreatic neoplasia formation [RNA-seq]

summary: ARID1A restrains the formation of PanIN, pancreas ductal adenocarcinoma, and intraductal mucinous neoplasms

overall_design: We generated pancreas specific Arid1a knockout mice (Ptf1a-Cre; Arid1a f/f).  Mice without Cre were used as controls.  N=4 for each group. Mice were 6-8 week old and were of mixed background. They were littermate controls.

first: Hao

last: Zhu


title: Epigenetic and transcriptional profiling of triple negative breast cancer

city: Nashville

last: Perreault

state: TN

address: 746 Robinson Research Building

institute: Vanderbilt University

summary: The human HCC1806 cell line is frequently used as a preclinical model for triple negative breast cancer (TNBC). Given that dysregulated epigenetic mechanisms are involved in cancer pathogenesis, emerging therapeutic strategies target chromatin regulators, such as histone deacetylases. A comprehensive understanding of the epigenome and transcription profiling in HCC1806 provides the framework for evaluating efficacy and molecular mechanisms of epigenetic therapies. Thus, to study the interplay of transcription and chromatin in the HCC1806 preclinical model, we performed nascent transcription profiling using Precision Run-On coupled to sequencing (PRO-seq). Additionally, we mapped the genome-wide locations for RNA polymerase II (Pol II), CTCF, the histone variant H2A.Z, and 7 histone modifications using ChIP-exo. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq with near base pair precision mapping of protein-DNA interactions. In this Data Descriptor, we present detailed information on experimental design, data generation, quality control analysis, and data validation. We discuss how these data lay the foundation for future analysis to understand the relationship between the nascent transcription and chromatin.

overall_design: We performed nascent transcription profiling using Precision Run-On coupled to sequencing (PRO-seq). Additionally, we mapped the genome-wide locations for RNA polymerase II (Pol II), CTCF, the histone variant H2A.Z, and 7 histone modifications using ChIP-exo. ChIP-exonuclease (ChIP-exo) is a refined version of ChIP-seq with near base pair precision mapping of protein-DNA interactions.

first: Danielle

last: Walheim

first: Bryan

last: Venters


title: Effect of CFIm25 knock-out on RNA polymerase II transcription

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

summary: ChIP-seq of RNA polyerase II and Input in 293 and 293 CFIm25 KO to investigate the effect on pol II of knocking-down by Crispr/Cas9 CFIm25. ChIP-seq was performed after DMSO and DRB treatment (30 minutes, 100 µM)

overall_design: Examination by ChIP-seq of the effect of CFIm25 KO on RNA polymerase II

first: Jessica

last: Hardy

first: Shona

last: Murphy

first: Chris

last: Norbury


title: Defective mitochondrial cardiolipin remodeling dampens HIF-1a expression in hypoxia

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary: Mitochondria fulfill vital metabolic functions and act as crucial cellular signaling hubs integrating their metabolic status into the cellular context. Here, we show that defective cardiolipin-remodeling, upon loss of the cardiolipin acyl transferase Tafazzin, mutes HIF-1a signaling in hypoxia. Tafazzin-deficiency does not affect posttranslational HIF-1a regulation but rather HIF-1a gene-expression, a dysfunction recapitulated in iPSCs-derived cardiomyocytes from Barth Syndrome patients with Tafazzin-deficiency. RNAseq analyses confirmed drastically altered signaling in Tafazzin mutant cells. In hypoxia, Tafazzin-deficient cells display reduced production of reactive oxygen species (ROS) perturbing NF-kB activation and concomitantly HIF-1a gene-expression. In agreement, Tafazzin-deficient mice hearts display reduced HIF-1a levels and undergo maladaptive hypertrophy with heart failure in response to pressure overload challenge. We conclude that defective mitochondrial cardiolipin-remodeling dampens HIF-1a signaling through inactivation of a non-canonical signaling pathway: Lack of NF-kB activation through reduced mitochondrial ROS production diminishes HIF-1a transcription.

overall_design: Cells lacking tafazzin were subjected to hypoxia and compared to the ones at normoxia or isogenic WT cells either at hypoxia or nomoxia

first: Arpita

last: Chowdhury

first: Peter

last: Rehling


title: Transcriptome differences between primary brown adipocytes of wildtype and UCP1-KO mice

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

summary: We analyzed coding transcript abundance in fully differentiated, primary brown adipocytes from murine, interscapular brown adipose tissue of wildtype and UCP1-KO mice.

overall_design: We prepared primary cells from the stromal-vascular fraction of murine interscapular brown fat and differentiated these in vitro into brown adipocytes. Three independent cultures each were generated from wildtype 129SvEvS1 mice and UCP1-KO mice on the same strain background. We sequenced total RNA and determined transcript abundance.

first: Yongguo

last: Li

first: Sabine

last: Schweizer

first: Martin

last: Klingenspor


title: SWI/SNF component ARID1A restrains pancreatic neoplasia formation [ChIP-seq]

overall_design: We used immortalized human pancreatic ductal epithelial cells (Ouyang, Am J Path 2000, purchased from ATCC) and used Crispr/Cas9 to generate Arid1a knockout cells. The cells that underwent editing but retained Arid1a expression on Western were used as control. These lines were derived from single cell clones. We performed Chip-Seq against H3K27ac, using input as control. We performed one replicate. Clone 71 was wild-type and clone 9 was knock out.


title: Seh1 Interacts with Olig2 and Brd7 to Promote Oligodendrocyte Differentiation and Myelination (ATAC_Seq)

city: xiamen

first: Liu

last: Zhixiong

state: Fujian

address: Xiangan Nanlu 4221-120

department: School of Life Sciences

institute: Xiamen University

summary: Nuclear pore complex components (Nups) are involved in neural development and alterations in Nup genes are linked to human neurological diseases. However, the physiological functions of specific Nups and the underlying mechanisms involved in these processes remain elusive. Here we show that tissue-specific depletion of nucleoporin Seh1 causes dramatic myelination defects in the Central Nervous System (CNS). Seh1-deficient Oligodendrocyte Progenitor Cells (OPCs) proliferate properly, but fail to differentiate into mature oligodendrocytes, which impairs myelin production and remyelination after demyelinating injury. Genome-wide analyses show that Seh1 regulates a core myelinogenic regulatory network and depletion of Seh1 alters open chromatin configurations at its target genes. Mechanistically, Seh1 regulates OPCs differentiation by assembling Olig2 and Brd7 into a transcription complex at nuclear pores. Together, our results reveal that Seh1 is required for oligodendrocyte differentiation and myelination by promoting assembly of an Olig2-dependent transcription complex and expose nucleoporins as key players in the CNS.

overall_design: ChIP was performed on rat oligodendrocyte progenitor cells and immature oligodendrocytes(T3 D1) using antibodies against seh1 or IgG. RNA-seq was performed on mouse control or Seh1cKO immature oligodendrocytes(T3 D2). Atac-seq was performed on mouse control or Seh1cKO oligodendrocyte progenitor cells and immature oligodendrocytes(T3 D1).

first: Liang

last: Zhang

first: Zhixiong

last: Liu


title: BCL6 confers KRAS-mutant NSCLCs resistance to BET inhibitors [ChIP-Seq]

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

summary: We report that BCL6 interacts with BRD3 and that BRD3 inhibition upregulates BCL6. By obtaining sequence from chromatin immunoprecipitated DNA of A549 cells, we generated genome-wide binding gene spectrums of BCL6 and BRD3. By locating -3000 to +200 bps around TSS, we find that BRD3 binds to the promoters of 2470 genes and that BCL6 binds to the promoters of 694 genes, with 82 genes shared by BRD3 and BCL6. Interestingly, BCL6 itself is one of these 82 shared genes, implying that BCL6 mediated self-repression may require the participation of BRD3. Other shared genes includes SGK2, IDH2, HOXB6, SIRT1, SOCS3 and ZFNs, demonstrating the widely involvement of BRD3 in the regulatory role of BCL6. To examine the dependency of BCL6 on BRD3, we also compared BCL6-binding spectrums with or without a BET inhibitor, OTX015. The ChIP-seq data with BCL6 antibody exhibited a diverse BCL-binding spectrum composed of 731 genes in OTX015 treatment, with only 117 genes overlapped with that of DMSO treatment. These data demonstrates that BET inhibition is sufficient to change BCL6-binding spectrum. This study provides a new insight of BCL6 regulatory roles in KRAS-mutant NSCLCs, where BRD3 is recruited by BCL6 and affect BCL6 binding preference as a cofactor.

overall_design: Examination of BCL6 and BRD3 binding spectrums in unstressed conditions. 2. Comparation of BCL6-binding genes with or without a BET inhibitor, OTX015 (1 μM for 6 hr), by ChIP-seq assay.

first: Jiawei

last: Guo

first: Bin

last: Zou


title: Cerulein induced acute pancreatitis in C57Bl/6J

city: Stockholm

first: Rainer

middle: Lothar

last: Heuchel

address: Karolinska Institutet, Novum, KFC, Plan 6A, PaCaRes Lab

department: Clinical Science, Intervention and Technology (CLINTEC)

country: Sweden

institute: Karolinska Institutet

summary:
There still is a lack of specific, early markers for acute pancreatitis.
We used the gene expression profiling Affimetrix mouse gene 1.0 ST arrays (Affymetrix , Inc. Santa Clara, CA), to cmpare the gene expression between control mice and mice with induced experimental acute pancreatitis, in order to identify new potential biomarkers of acute pancreatitis.

overall_design: Wildtype C57Bl6J mice were injected intraperitoneally with 9 hourly injections of 50 mg/kg caerulein (n = 6) in order to induce an experimental acute pancreatitis, or sodium chloride as control ( n = 4).

first: Hui

last: Gao


title: Hyaluronidase

city: La Jolla

first: tatsuya

last: dokoshi

address: 9500 gilman

institute: UCSD

summary: In this study we evaluated the role of hyaluronan (HA) in reactive adipogenesis, a local expansion of preadipocytes that provides host defense by release of antimicrobial peptides. We observed that HA accumulated during maturation of adipocytes in vitro and was associated with increased expression of preadipocyte factor 1 (Pref-1), Zinc finger protein 423 (Zfp423) and early B cell factor 1 (Ebf1). Although HA is normally abundant in the extracellular matrix, a further increase in HA staining occurred in mice at sites of reactive adipogenesis following injury of colon by dextran sodium sulfate or injury of skin from infection with S. aureus. HA also abundantly accumulated around adipocytes seen in the colon of patients with inflammatory bowel disease. This HA was necessary for adipocyte maturation since digestion of HA by administration of soluble hyaluronidase or transgenic expression of hyaluronidase 1 inhibited adipogenesis in vitro and in vivo. Furthermore, hyaluronidase also suppressed inflammation of both skin and colon and decreased antimicrobial peptide expression by developing preadipocytes. This resulted in increased bacterial transit across the epithelial barrier despite decreased tissue injury from inflammation. These observations suggest HA plays an important role in reactive adipogenesis and host defense after injury.

overall_design: Compare control vs PEGPH20 treatment group before colitis and after colitis.

first: Richard

last: Gallo


title: Barcoded DNA sequencing (BarSeq) samples from passaging of Caulobacter crescentus in medium containing cheesecloth

status: Public on Sep 11 2018

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: BarSeq experiment enriching for C. crescentus mutants that do not adhere to cheesecloth.

overall_design: C. crescentus caulo_47 barcoded transposon library was grown in peptone-yeast extract (PYE) medium with (Cheese) or without (PYE) cheesecloth for five passages (1-5). Each passaging experiment was performed in triplicate (A, B and C).

first: David

last: Hershey


title: The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation

city: Grand Rapids

first: Hong

last: Wen

address: 333 Bostwick Ave. N.E.

department: Center for Epigenetics

institute: Van Andel Research Institute

summary: Recognition of post-translational modifications on histones by epigenetic readers is a fundamental mechanism for the regulation of chromatin and transcription. Compared to the large number of readers that recognize histone methylation, only a few acetyllysine readers have been identified, including bromodomain, YEATS, and double plant homeodomain zinc finger (DPF). Here, we report the identification of a novel reader of histone H3, the ZZ-type zinc finger (ZZ) domain of ZZZ3, a subunit of the Ada-Two-A Containing (ATAC) histone acetyltransferase complex. The solution NMR structure of the ZZ in complex with the H3 peptide reveals a unique histone-binding mechanism involving caging of the N-terminal Alanine 1 of histone H3 in an acidic cavity of the ZZ domain. Importantly, acetylation on Lysine 4 of H3 (H3K4ac) enhances the binding, and in cells, ZZZ3 colocalizes with H3K4ac across the genome. The recognition of histone acetylation by ZZ is essential for chromatin occupancy of ZZZ3 and functions of the ATAC complex. Depletion of ZZZ3 or disruption of the ZZ-H3 interaction dampens ATAC dependent promoter histone H3K9 acetylation and the expression of ribosomal protein encoding genes. Overall, our study identifies the ZZ domain of ZZZ3 as a novel epigenetic reader that links the GCN5/ATAC complex to histone acetylation.

overall_design: ZZZ3, H3K4ac, and H3K4me3 ChIP-seq in H1299 cells and H3K9ac ChIP-seq in control and ZZZ3 KD H1299 cells; ZZZ3 ChIP-seq in control, ZZZ3 KD and KD cells ectopically expressing shRNA-resistant WT or indicated mutants; Flag ChIP-seq in vector and cells overexpressing WT or indicated mutants. mRNA-seq of control and ZZZ3 KD in H1299 cells.

first: Jie

last: Lyu

first: Wenyi

last: Mi

first: Xiaobing

last: Shi