title: SOX4-mediated repression of specific tRNAs inhibits proliferation of human glioblastoma cells

city: DALLAS

first: jianjing

last: Yang

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Genomic targeted genes of SOX4 in U251 cell line

overall_design: SOX4 (1 input dataset, 3 immunoprecipitation datasets)

last: Smith

first: Jianjing

first: Chun-Li

last: Zhang


title: Derivation of trophoblast stem cells from naïve human pluripotent stem cells [ATAC-seq]

status: Public on Feb 13 2020

city: Saint Louis

first: Bo

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

country: USA

institute: Washington University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Naïve human pluripotent stem cells (hPSCs) provide a unique experimental platform of cell fate decisions during pre-implantation development, but their lineage potential remains incompletely characterized. As naïve hPSCs share transcriptional and epigenomic signatures with trophoblast cells, it has been proposed that the naïve state may have enhanced predisposition for differentiation along this extraembryonic lineage. Here we examined the trophoblast potential of isogenic naïve and primed hPSCs. We found that naïve hPSCs can directly give rise to human trophoblast stem cells (hTSCs) and undergo further differentiation into both extravillous and syncytiotrophoblast. In contrast, primed hPSCs do not support hTSC derivation, but give rise to non-self-renewing cytotrophoblasts in response to BMP4. Global transcriptome and chromatin accessibility analyses indicate that hTSCs derived from naïve hPSCs acquire features of pre-implantation trophectoderm. The derivation of hTSCs from naïve hPSCs will enable elucidation of early mechanisms that govern normal human trophoblast development and associated pathologies.

overall_design:
ATAC-seq of one cell type (human trophoblast stem cells).
The samples are human trophoblast stem cells derived from the blastocyst (BT5) or naive hPSCs (H9 and AN).  hTSCs were cultured as previously described (Okae et al., 2018). Briefly, a 6-well plate was coated with 5 μg/mL Collagen IV (Corning, 354233) at 37°C overnight. Cells were cultured in 2mL TS medium [DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X (Gibco, 51500), 1.5 mg/ml L-ascorbic acid (Wako, 013-12061), 50 ng/ml EGF (Rockland, 009-001-C26), 2 mM CHIR99021 (Stemgent, 04-0004), 0.5 mM A83-01 (BioVision, 1725), 1 mM SB431542 (BioVision, 1674), 0.8 mM VPA (Tocris, 2815), and 5 mM Y-27632] and in 5% CO2 and 20% O2. Media was changed every 2 days,and cells were passaged using TrypLE Express every 3 days at a ratio of 1:4.

first: Thorold

last: Theunissen

first: Chen

last: Dong

first: Paul

last: Gontarz

first: Ting

last: Wang

first: Xiaoyun

last: Xing


title: Lung metastasis of breast cancer

status: Public on Feb 17 2020

city: Heidelberg

first: Maren

last: Pein

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Junior Research Group Metastatic Niches

country: Germany

institute: German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Histone H3K27 demethylases regulate human Th17 cell maturation and effector functions by impacting on metabolism [III]

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: T helper (Th) cells are CD4+ effector T cells that play an instrumental role in immunity by shaping the inflammatory cytokine environment in a variety of physiological and pathological situations, including autoimmune conditions such as ankylosing spondylitis. Here we identify KDM6A/KDM6B histone H3K27 demethylases by inhibitor and knockdown approaches as central regulators of human Th1, Th2 and Th17 subsets and establish a direct link between KDM6A/KDM6B in regulating Th17 cell metabolism. In mature Th17 cells demethylase inhibition leads to suppression of IL-17 cytokine levels and reduced proliferation through a pronounced ATF4 driven metabolic stress response in T cells derived from PBMC fractions of healthy donors and patients with ankylosing spondylitis. Metabolomic analyses reveal that Th17 T-cell differentiation is associated with an increase in glycolytic metabolism, pentosephosphate pathway activity and protein glycosylation intermediates. GSK-J4 treatment was shown to be overtly impactful on the cellular biochemistry of Th17 differentiated T-cells, with prominent effects on differentiation-related changes in glucose utilization, anabolic processes, and a remarkable change in amino acid and TCA cycle metabolism. During differentiation from naïve Th precursors to mature Th17 populations, demethylase inhibition with the prototypic inhibitor GSK-J4 leads to increases of repressive H3K27me3 chromatin marks, thereby down-regulating the required TH17 key transcription factor RORC and effectively suppressing metabolic reprogramming from a naïve T cell ground state to a differentiated subset. These data are consistent with an opposing effect of GSK-J4 on Th17 T-cell differentiation pathways directly related to proliferation and effector cytokine profiles.

overall_design: Examination of open chromatin in Th17 cells. Cells were differentiated in Th17 polarising cytokines for 7 days then incubated with DMSO or GSK-J4 compounds for 24 hours.

middle: P


title: Histone H3K27 demethylases regulate human Th17 cell maturation and effector functions by impacting on metabolism


title: Runx1 negatively regulates inflammatory cytokine production by neutrophils in response to Toll-like receptor signaling

city: San Francisco

first: Qin

last: Zhu

state: CA

address: 600 Minnesota Street

institute: UCSF

type: Expression profiling by high throughput sequencing


title: Histone H3K27 demethylases regulate human Th17 cell maturation and effector functions by impacting on metabolism [II]

overall_design: Examination of H3K27me3 histone modifications in Th17 cells.


title: Derivation of trophoblast stem cells from naïve human pluripotent stem cells


title: Transcriptomic profiling of MDA-MD-231 and MDA-MB-231-LM1 cells isolated from mouse lungs at micrometastatic stage

summary: Cancer-associated fibroblasts promote the development of many primary malignancies, but their function in metastatic progression is poorly understood. Here, we demonstrate that colonization of the lungs by metastatic breast cancer cells induces an inflammatory phenotype in lung fibroblasts. CXCL9 and CXCL10 are induced in an NFκB-dependent manner in metastasis-associated fibroblasts in response IL-1α and IL-1β secreted by disseminated breast cancer cells. We find that the chemokine receptor CXCR3, that binds CXCL9/10, is expressed in a small subset of breast cancer cells that exhibits greater tumor-initiating ability when co-transplanted with fibroblasts. CXCR3-expressing cancer cells maintain JNK signaling that drives IL-1A/B expression, and thus rendering this subpopulation efficient in both inducing CXCL9/10 in lung fibroblasts and responding to the chemokines. Importantly, disruption of the CXCL9/10-CXCR3 axis significantly reduces metastatic colonization in xenograft and syngeneic mouse models suggesting an essential role of this paracrine crosstalk in metastatic progression and a potential therapeutic vulnerability for the treatment of metastatic breast cancer.

overall_design: For profiling of MDA-MB-231 (MDA) and MDA-MB-231-LM2 (MDA-LM2) breast cancer cells at a micrometastatic stage of lung colonization, NSG mice (6-8 weeks of age) were injected via the tail vein with MDA or highly metastatic MDA-LM2 breast cancer cells carrying a triple reporter expressing the genes herpes simplex virus thymidine kinase 1, green fluorescent proteins (GFP), and firefly luciferase, thus enabling bioluminescent imaging of lung metastatic progression. At week 1 post cancer cell injection (representing micrometastatic stage), lungs from mice with similar metastatic burden were harvested. Cancer cells were isolated from by fluorescence-activated cell sorting (FACS) based on GFP. Three biological replicates were analyzed.

first: M

first: T

last: Oskarsson


title: Transcriptomic profiling of CXCR3+/- SUM-159-LM1 breast cancer cells

overall_design: For profiling of CXCR3+ and CXCR3- breast cancer cells, SUM-159-LM1 (SUM-LM1) cells were seeded into ultra-low attachment cell culture flasks in Onco2 medium, consisting of HuMEC-medium (Invitrogen) supplemented 50 U/ml penicillin (Sigma-Aldrich), 50 μg/ml streptomycin (Sigma-Aldrich), 10 ng/ml basic fibroblast growth factor (bFGF, Invitrogen), 20 ng/ml EGF (Sigma-Aldrich), 5 μg/ml human insulin (Sigma-Aldrich) and 2 % vol/vol B27 (Life Technologies) at a density of 25,000 cells/ml (10 ml per flasks) and incubated at 37 °C for 1 week. Cells were pelleted and dissociated using StemPro Accutase (Life Technologies), counted and stained with 5 μg PE-conjugated anti-human CD183 (CXCR3) antibody (clone G025H7, BioLegend)  or PE-conjugated mouse IgG1, κ isotype control (BioLegend) per 1 Mio cells in 100 μl FACS buffer for 30 min on ice in the dark. CXCR3+ and CXCR3- cells were sorted into Arcturus PicoPure Extraction Buffer (ThermoFisher Scientific) on a  BD FACSAria1 machine. Three biological replicates were analyzed (3 independent sorts).


title: Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons [Bisulfite_Seq_discovery_cohort]

status: Public on Feb 12 2020

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

type: Methylation profiling by high throughput sequencing

summary:
	Background
Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in isolated prefrontal cortex neurons from control and PD brain hemispheres. DNA methylation is fine-mapped at enhancers and promoters, genome-wide, by targeted bisulfite sequencing in two independent sample cohorts.

Results
We find that neurons of the human prefrontal cortex exhibit hemispheric differences in DNA methylation. Hemispheric asymmetry in neuronal DNA methylation patterns is largely mediated by differential CpH methylation, and chromatin conformation analysis finds that it targets thousands of genes. With aging, there is a loss of hemispheric asymmetry in neuronal epigenomes, such that hemispheres epigenetically converge in late life. In neurons of PD patients, hemispheric asymmetry in DNA methylation is greater than in controls and involves many PD risk genes. Epigenetic, transcriptomic, and proteomic differences between PD hemispheres correspond to the lateralization of PD symptoms, with abnormalities being most prevalent in the hemisphere matched to side of symptom predominance. Hemispheric asymmetry and symptom lateralization in PD is linked to genes affecting neurodevelopment, immune activation, and synaptic transmission. PD patients with a long disease course have greater hemispheric asymmetry in neuronal epigenomes than those with a short disease course.

Conclusions
Hemispheric differences in epigenetic gene regulation are prevalent in neurons and may affect the progression and symptoms of PD.

overall_design: To determine whether DNA methylation could contribute to hemisphere differences in neuronal function in the healthy brain and PD, we comprehensively fine-mapped DNA methylation at enhancers and promoters, genome-wide, in neurons isolated from the left and right prefrontal cortex of PD patients and controls (105 individuals: 48 healthy controls (brain hemisphere left: 25; right: 23) and 57 PD patients (brain hemisphere left: 23; right: 34)). We first isolated neuronal nuclei using an established antibody (NeuN+) and flow cytometry-based approach. We then fine-mapped DNA methylation at enhancer elements using a targeted bisulfite sequencing strategy, known as bisulfite padlock probe sequencing.

first: Elizabeth

last: Ensink

first: Sean

last: Lang

first: Lee

last: Marshall

first: Meghan

last: Schilthuis

first: Jared

last: Lamp

first: Irving

last: Vega

first: Viviane

last: Labrie


title: TF ChIP-seq from HEK293 (ENCSR146NLL)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
eGFP-REPIN1 ChIP-seq on human HEK293 cells.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing

status: Public on Feb 21 2020

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Shine-Dalgarno (SD) motifs are thought to play an important role in translational initiation in bacteria. Paradoxically, ribosome profiling studies in E. coli show no correlation between the strength of the SD in an mRNA and how efficiently it is translated. Performing profiling on ribosomes with altered anti-Shine-Dalgarno sequences, we reveal a genome-wide correlation between SD strength and ribosome occupancy that was previously masked by other contributing factors. Using the antibiotic retapamulin to trap initiation complexes at start codons, we find that the mutant ribosomes select start sites correctly, arguing that start sites are hard-wired for initiation through the action of other mRNA features. We show that A-rich sequences upstream of start codons promote initiation. Taken together, our genome-wide study reveals that SD motifs are not necessary for the ribosome to select where initiation occurs, though they do affect how efficiently initiation occurs at sites whose other features support initiation.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Ribosome profiling of purified MS2-tagged ribosomes with anti-Shine Dalgarno mutations from E. coli MG1655


title: Identification of osteolineage cell-derived extracellular vesicle cargo implicated in hematopoietic support

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Osteolineage cell-derived extracellular vesicles (EVs) play a regulatory role in hematopoiesis and have been shown to promote the ex vivo expansion of human hematopoietic stem and progenitor cells (HSPCs). Here, we demonstrate that EVs from different human osteolineage sources do not have the same HSPC expansion promoting potential. Comparison of stimulatory and non-stimulatory osteolineage EVs by next-generation sequencing and mass spectrometry analyses revealed distinct microRNA (miRNA) and protein signatures identifying EV-derived candidate regulators of ex vivo HSPC expansion. Accordingly, the treatment of umbilical cord blood-derived CD34+ HSPCs with stimulatory EVs altered HSPC transcriptome, including genes with known roles in cell proliferation. An integrative bioinformatics approach, which connects the HSPC gene expression data with the candidate cargo in stimulatory EVs, delineated the potentially targeted biological functions and pathways during hematopoietic cell expansion and development. In conclusion, our study gives novel insights into the complex biological role of EVs in osteolineage cell-HSPC crosstalk and promotes the utility of EVs and their cargo as therapeutic agents in regenerative medicine.

overall_design: Examination of the effect of extracellular vesicles on hematopoietic stem cells

first: Amel

last: Dudakovic

first: Andre

last: van Wijnen


title: Derivation of trophoblast stem cells from naïve human pluripotent stem cells [RNA-seq]

first: Bo

last: Zhang

overall_design: Bulk RNA-seq of seven cell types

first: Thorold

last: Theunissen

first: Chen

last: Dong

first: Paul

last: Gontarz


title: Characterization of rat ILCs reveals ILC2  as the dominant intestinal subset

city: Nantes

first: Ahmed

last: Abidi

state: Loire Atlantique

address: CHU Nantes - Hôtel Dieu 30 Bd Jean Monnet

country: France

institute: INSERM

summary: Innate lymphoid cells (ILCs) are tissue-resident lymphocytes that lack antigen-specific receptors and exhibit innate effector functions such as cytokine production that play an important role in immediate responses to pathogens especially at mucosal sites. Mouse and human ILC subsets have been extensively characterized in various tissues and in blood. In this study, we present the first characterization of ILCs and ILC subsets in rat gut and secondary lymphoid organs. ScRNAseq and flow cytometric data shows that phenotype and function of rat ILC subsets are conserved similar to human and mouse ILCs. However, contrary to human and mouse, our study unexpectedly revealed that ILC2 and not ILC3 was by far the dominant ILC subset in the rat intestinal lamina propria. ILC2 predominance in the gut was independent of rat strain, sex or housing facility. In contrast, ILC3 were the main ILC subset in mesenteric lymph nodes and Peyer patches, in which strain-dependent differences in ILC frequencies were also observed. In conclusion, our study demonstrates that in spite of highly conserved phenotype and function between mice, rat and humans, the distribution of ILC subsets in the intestinal mucosa is species-dependent, likely in response to both genetic and environmental factors.

overall_design: Single ILCs were sorted by flow cytometry for single cell RNAseq library preparation using Chromium Single Cell 3’ v3 Reagent Kit (10x Genomics)

first: Laurent

last: Thomas

first: Bériou

last: Gaëlle

first: Bouchet-Delbos

last: Laurence

first: Fourgeux

last: Cynthia

first: Louvet

last: Cédric

first: Triki-Marrakchi

last: Raja

first: Poschmann

last: Jeremie

first: Josien

last: Régis

first: Martin

last: Jérôme


title: Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons

first: Peipei

last: Li

summary:
Background
Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in isolated prefrontal cortex neurons from control and PD brain hemispheres. DNA methylation is fine-mapped at enhancers and promoters, genome-wide, by targeted bisulfite sequencing in two independent sample cohorts.

Results
We find that neurons of the human prefrontal cortex exhibit hemispheric differences in DNA methylation. Hemispheric asymmetry in neuronal DNA methylation patterns is largely mediated by differential CpH methylation, and chromatin conformation analysis finds that it targets thousands of genes. With aging, there is a loss of hemispheric asymmetry in neuronal epigenomes, such that hemispheres epigenetically converge in late life. In neurons of PD patients, hemispheric asymmetry in DNA methylation is greater than in controls and involves many PD risk genes. Epigenetic, transcriptomic, and proteomic differences between PD hemispheres correspond to the lateralization of PD symptoms, with abnormalities being most prevalent in the hemisphere matched to side of symptom predominance. Hemispheric asymmetry and symptom lateralization in PD is linked to genes affecting neurodevelopment, immune activation, and synaptic transmission. PD patients with a long disease course have greater hemispheric asymmetry in neuronal epigenomes than those with a short disease course.

Conclusions
Hemispheric differences in epigenetic gene regulation are prevalent in neurons and may affect the progression and symptoms of PD.


title: Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons [RNA-seq]

overall_design: In order to determine whether epigenetic divergence across hemispheres is relevant to hemispheric asymmetry in transcriptional patterns, we used RNA-sequencing to perform a transcriptional analysis in the prefrontal cortex of hemisphere of PD with known side of symptom predominance (n=36 individuals: 13 matched PD hemisphere, 11 unmatched PD hemisphere and controls n=12)

first: Elizabeth

last: Ensink

first: Sean

last: Lang

first: Lee

last: Marshall

first: Meghan

last: Schilthuis

first: Jared

last: Lamp

first: Irving

last: Vega

first: Viviane

last: Labrie


title: Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons [Bisulfite_Seq_replication_cohort]

overall_design: To determine whether DNA methylation could contribute to hemisphere differences in neuronal function in the healthy brain and PD, we comprehensively fine-mapped DNA methylation at enhancers and promoters, genome-wide, in neurons isolated from the left and right prefrontal cortex of PD patients and controls (57 individuals: 31 healthy controls (30 individuals with both left and right brain hemispheres, 1 with only left) and 26 PD patients (24 patients with both left and right brain hemispheres, 1 with only left, 1 with only right)). We first isolated neuronal nuclei using an established antibody (NeuN+) and flow cytometry-based approach. We then fine-mapped DNA methylation at enhancer elements using a targeted bisulfite sequencing strategy, known as bisulfite padlock probe sequencing.


title: Histone H3K27 demethylases regulate human Th17 cell maturation and effector functions by impacting on metabolism [I]

first: Adam

last: Cribbs


title: Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment

status: Public on Feb 11 2020

city: New York

first: Jennifer

last: Chan

state: New York

address: 1470 Madison Ave, Hess 9-201

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

type: Non-coding RNA profiling by high throughput sequencing

summary: We report reproductive tract extracellular vesicles (EVs) transmit information regarding stress in the paternal environment to sperm, ultimately altering fetal development. Using intracytoplasmic sperm injection, we found that sperm incubated with EVs collected from stress-treated epididymal epithelial cells produced offspring with altered neurodevelopment and adult stress reactivity. Proteomic and transcriptomic assessment of these EVs showed dramatic changes in protein and miRNA content long after stress treatment had ended.

overall_design: Examination of 1) impact of chronic stress on mouse sperm microRNA content over time (1 vs 12 weeks post-stress), 2) impact of corticostrone on secreted EV microRNA content from DC2 cells over time (1, 4, 8 days post-treatment), 3) impact of intracytoplasmic sperm injection with sperm incubated with control or corticosterone-treated EVs on mouse E12.5 brain and 4) E12.5 placentas, 5) impact of perceived stress dynamic on human sperm over 6 months

middle: C

first: Christopher

last: Morgan

first: Yasmine

middle: M

last: Cisse

first: Tracy

middle: L

last: Bale


title: Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells

city: Philadelphia

first: Naomi

last: Goldman

state: PA

address: 324 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania


title: ChIP-seq from sigmoid colon (ENCSR338PIQ)

first: ENCODE

last: DCC

summary:
POLR2A ChIP-seq on human sigmoid colon

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Increase in innate lymphoid cells during acute ST-segment elevated myocardial infarction and its clinical relevance

status: Public on Feb 23 2020

city: CHANGCHUN

first: mingyou

last: zhang

state: JILIN

address: 519 dongminzhu

country: China

institute: employer

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to compare ILC1s gene expression in ST segmment elevation myocardial infarction  patient compared with healthy control.

Results: Using an optimized data analysis workflow, More than 70 million clean reads were obtained from each sample group after elimination of low-quality reads. A total of 4204 DEGs were found up-regulated and 4712 DEGs down-regulated on comparison of ILC1s from STEMI patients and controls.

Conclusion: The dynamic number and gene expression changes in the subtype ILC1s indicate the role of ILCs in STEMI.

overall_design: Methods: ILC1s mRNA profiles of STEMI patients and those of control were generated by deep sequencing, using Hiseq Xten . The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

first: Mingyou

last: Zhang

first: Jing


title: Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [CRISPR guide-seq]

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

institute: The Broad Institute

summary: Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we used seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in three disease-relevant immune cell types, based on a set of features related to regulatory potential. Trait/disease-associated variants were enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity. Of the 15 trait/disease-associated haplotypes at TNFAIP3, 9 had at least one variant meeting one or both of these criteria, with 3 of these haplotypes having a single prioritized variant. 5 of the 9 prioritized variants were further supported by genetic fine-mapping in our and other studies. Our work provides evidence for the efficacy and limitations of strategies for prioritizing disease- and trait-associated genetic variants.

overall_design: 2-4 replicates per experiment. CRISPRa targeted each of 2501 variants with an average of 5 guides per variant and CRISPRi targeted open chromatin of U937, Jurkat, and BJAB cell lines with an average of 30 guides per element. CRISPRa had 770 nontargeting guides CRIPSRi had 6282 nontargeting guides, both of which served as negative controls for each respective experiment. TNFAIP3 expression was measured using RNA Prime-flow with probes targeted to the TNFAIP3 transcript

first: John

last: Ray


title: Direct Phosphorylation and Stabilization of MYC by Aurora B Kinase Promote T Cell Leukemogenesis

city: Wuhan

first: jue

last: jiang

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province

department: Medical Research Institute

institute: Wuhan University

summary: The significance of MYC deregulation has been well-documented in T-cell acute lymphoblastic leukemia (T-ALL). MYC acts as an oncogenic driver in T-ALL and particularly in maintaining leukemia-initiating cell activity. Protein interactome analysis identified Aurora B kinase (AURKB) as a specific MYC binding partner and depletion of AURKB reduced the steady-state levels of MYC. Mechanistic studies demonstrated that AURKB directly phosphorylated MYC and promoted MYC protein stability, and conversely AURKB deficiency elicited rapid MYC degradation. We thus predicted that abrogation of AURKB would affect global MYC transcriptional program. To assess the transcriptional change in response to AURKB knockdown, RNA-Seq was performed using AURKB or control-depleted CUTLL1 cells.

overall_design: CUTLL1 cells were infected with lentiviruses expressing shRNA targeting AURKB or control and cultured for 48 h. Total RNAs from three biological replicates were extracted for sequencing analysis.

first: Jue

last: Jiang

first: Jingchao

last: Wang

first: Ming

last: Yue

first: Hudan

last: Liu


title: Cell lineage-specific transcriptome analysis for interpreting cell fate specification of proembryos

status: Public on Feb 10 2020

first: Peng

last: Zhao

address: Luojia Hill

department: College of Life Sciences

summary: The goal of present study is to construct lineage-specific transcriptome to investigate transcriptional changes in the process of apical and basal cell lineage specification. We provide a valuable lineage- specific transcriptome resource to elucidate differential transcription activity underlying progressive divergence of apical and basal cell lineages of early proembryos at genome-wide scale.

overall_design: To investigate spatial and temporary gene expression profile during the process of apical and basal cell lineage specification, proembryos at 1-cell and 32-cell embryo stages were first manually micro-dissected. Then, the apical and basal cell lineages were separated and collected for RNA-seq, respectively. To minimize the variance in the transcriptome and ensure the reliability, three independent biological replicates were performed for each cell type.

first: Mengxiang

last: Sun


title: Assessing the ability of various genomic features to prioritize causal non-coding variants associated with diseases and traits [ATAC-seq]

overall_design: profiling of cell lines (unstimulated and stimulated) using ATAC-seq


title: TF ChIP-seq from HEK293 (ENCSR443MVV)

summary:
eGFP-PRDM4 ChIP-seq on human HEK293 cells.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptomics of FGF6-stimulated mouse brown preadipocytes

status: Public on Feb 07 2020

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Uncoupling protein-1 (UCP1) plays a central role in energy dissipation in brown adipose tissue (BAT).  Using high-throughput library screening of secreted peptides, we identified two fibroblast growth factors (FGF), FGF6 and FGF9, as novel and potent inducers of UCP1 expression in adipocytes and preadipocytes.  Here we show the transcriptome of FGF6-stimulated mouse brown preadipocytes.

overall_design: Immortalized murine brown preadipocytes were treated with vehicle or FGF6 for 4, 8, and 24 hours. Total RNA was isolated using Direct-zol™ RNA miniprep Kits (Zymo Research, Irvine, CA). High-throughput sequencing was performed using a HiSeq 4000 instrument (Illumina) at BGI Americas.

first: Farnaz

last: Shamsi

first: Yu-Hua

last: Tseng


title: TF ChIP-seq from HEK293 (ENCSR185QFX)

summary:
eGFP-ZNF549 ChIP-seq on human HEK293 cells.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Rheumatoid arthritis patients, both newly diagnosed and methotrexate treated, show more DNA methylation differences in CD4+ memory than in CD4+ naïve T cells

city: Oslo

first: Kari

last: Guderud

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

summary: Differences in DNA methylation have been reported in B and T lymphocyte populations, including CD4+ T cells, isolated from rheumatoid arthritis (RA) patients when compared to healthy controls. CD4+ T cells are a heterogeneous cell type with subpopulations displaying distinct DNA methylation patterns. In this study, we investigated DNA methylation using reduced representation bisulfite sequencing in two CD4+ T cell populations (CD4+ memory and naïve cells) in three groups: newly diagnosed, disease modifying antirheumatic drugs (DMARD) naïve RA patients (N=11), methotrexate (MTX) treated RA patients (N=18), and healthy controls (N=9) matched for age, gender and smoking status. Analyses of these data revealed significantly more differentially methylated positions (DMPs) in CD4+ memory than in CD4+ naïve T cells (904 vs 19 DMPs) in RA patients compared to controls. The majority of DMPs (72%) identified in newly diagnosed and DMARD naïve RA patients with active disease showed increased DNA methylation (39 DMPs), whereas most DMPs (80%) identified in the MTX treated RA patients in remission displayed decreased DNA methylation (694 DMPs). Interestingly, we also found that about one third of the 101 known RA risk loci overlapped (+/- 500 kb) with the DMPs. Notably, introns of the UBASH3A gene harbour both the lead RA risk SNP and two DMPs in CD4+ memory T cells. Our results suggest that RA associated DNA methylation differences vary between the two T cell subsets, but are also influenced by RA characteristics such as disease activity, disease duration and/or MTX treatment.

overall_design: Two cohorts of Rheumatoid Arthritis patiens and controls.

first: Benedicte

middle: A

last: Lie


title: RNA-seq analysis on mTECs from Fezf2KO, AireKO and Chd4cKO mice

city: bunkyo

first: Yoshihiko

last: Tomofuji

state: Tokyo

address: hongo 7-3-1

department: Immunology

country: Japan

institute: University of Tokyo

summary: To gain insights into the difference in transcriptional programs regulated by Fezf2, Aire and Chd4, we performed RNA sequencing (RNA-seq) of mTECs from Fezf2-deficient, Aire-deficient and Chd4-deficient mice.

overall_design: RNA-seq analysis on mTECs from Fezf2KO, AireKO, WT, Chd4cKO and Chd4control mice in triplicates.

first: Akash

last: Taguchi

first: Hiroyuki

last: Takaba


title: SCA17 knock-in mice brain transcriptomes

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: To identify brain region specific proteins that contribute to brain region specific neurodegeneration, RNA sequencing was performed using cerebellum, striatum and prefrontal cortex tissues from 3-month-old SCA17 knock-in (KI) mice and wild-type (WT) littermates. We find 245 cerebellar specifically dysregulated genes (110 up-regulated genes and 145 down-regulated genes), 133 striatum specifically dysregulated genes (45 up-regulated genes and 88 down-regulated genes) and 17 prefrontal cortex specifically dysregulated genes (4 up-regulated genes and 13 down-regulated genes). Combined with other evidences, we demonstrate that cerebellum-enriched protein INPP5A contributes to selective neuropathology in mouse model of Spinocerebellar ataxias type 17

overall_design: To compare RNA level of cerebellum, striatum and prefrontal cortex from 3-month old WT and KI mice of SCA-17 by RNA sequencing, each group consists three mice.

first: Qiong

first: Yongcheng

first: Shihua

last: Li

first: Xiaojiang


title: Dissecting the early steps of MLL induced leukaemogenic transformation using a new mouse model of AML

city: Shanghai

first: Xiaonan

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

summary: Leukaemogenic mutations commonly disrupt cellular differentiation and/or enhance proliferation, thus perturbing the regulatory programs that control self-renewal and differentiation of stem and progenitor cells. Translocations involving the Mll1 (Kmt2a) gene generate powerful oncogenic fusion proteins, predominantly affecting infant and paediatric AML and ALL patients. The early stages of leukaemogenic transformation are typically inaccessible from human patients and conventional mouse models. Here, we took advantage of cells conditionally blocked at the multipotent haematopoietic progenitor stage to develop a new MLL-r model capturing the early cellular and molecular consequences of MLL-ENL expression based on a clear clonal relationship between the parental and leukaemic cells. Through a combination of scRNA-seq, ATAC-seq and genome-scale CRISPR-Cas9 screening, we identified pathways and genes likely to drive the early phases of leukaemogenesis. Finally, we demonstrated the broad utility of using matched parental and transformed cells for small molecule inhibitor studies by validating both known and new potential therapeutic targets.

overall_design: Single cell RNA sequencing of parental and MLLENL transformed Hoxb8 cells cultured in Flt3L/IL3/GM-CSF

first: Silvia

last: Basilico

first: Alison

last: Kennedy

first: Konstantinos

last: Tzelepis

first: George

last: Giotopoulos

first: Sarah

middle: J

last: Kinston

first: Pedro

last: Quiros

first: Kim

last: Wong

first: David

last: Adams

first: Larissa

middle: S

last: Carnevalli

first: Brian J

last: Huntly

last: Vassiliou

first: Fernando

last: Calero-Nieto

first: Berthold

last: Gottgens


title: New host-directed therapeutics for the treatment of Clostridioides difficile infection

city: Galveston

first: Sara

last: Dann

address: 301 University Blvd

institute: University of Texas Medical Branch

summary: Frequent and excessive use of antibiotics prime patients to Clostridioides difficile infection (CDI) that leads to fatal pseudomembranous colitis, with limited treatment options.  In earlier reports, we used a drug repurposing strategy and identified amoxapine (an antidepressant), doxapram (a breathing stimulant), and trifluoperazine (an antipsychotic), which provided significant protection to mice against lethal infections with several pathogens, including C. difficile. However, the mechanisms of action of these drugs were not known.  Here we provide evidence that all three drugs offered protection against experimental CDI by reducing bacterial burden and toxin levels, although the drugs were neither bacteriostatic nor bactericidal in nature and had minimal impact on the composition of the microbiota.  Drug-mediated protection was dependent on the presence of the microbiota, implicating its role in evoking host defenses that promoted protective immunity. By utilizing RNA-seq, we identified that each drug increased expression of several innate immune response-related genes, including those involved in the recruitment of neutrophils, production of interleukin (IL)-33, and the IL-22 signaling pathway. The RNA-seq data on selected genes were confirmed by qRT-PCR and protein assays. Focusing on amoxapine, which had the best anti-CDI outcome, we demonstrated that neutralization of IL-33 or depletion of neutrophils resulted in loss of drug efficacy. Overall, our lead drugs promote disease alleviation and survival in the murine model through activation of IL-33 and by clearing the pathogen through host defense mechanisms that critically include an early influx of neutrophils.

overall_design: Thirty hours post-infection with Clostridioides difficile spores, cecal tissue was harvested for total RNA isolation and subjected to RNAseq analysis. Data represent RNA pooled from 5 mice/group.

first: Jourdan

last: Andersson

first: Cristi

last: Galindo

first: Ashok

last: Chopra


title: DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state [RNA-seq]

status: Public on Feb 06 2020

first: Jianlong

last: Wang

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Mouse embryonic stem cells (ESCs) sporadically express preimplantation two-cell-stage (2C) transcripts, including MERVL endogenous retrovirus and Zscan4 cluster genes. Such 2C-like cells (2CLCs) can contribute to both embryonic and extraembryonic tissues when reintroduced into early embryos. We examined global nucleosome occupancy and gene expression in 2CLCs and identified miR-344 as the noncoding molecule that positively controls 2CLC potency. We found that activation of endogenous MERVL or miR-344-2 alone is sufficient to induce 2CLCs with induction of 2C genes and an expanded potency. Mechanistically, miR-344 is activated by the 2C-state driver DUX and post-transcriptionally represses ZMYM2 and LSD1, which recruit the HDAC corepressor to MERVL LTR for transcriptional repression. Consistently, zygotic depletion of Zmym2 compromises the totipotency-to-pluripotency transition during early development. Our studies establish the novel DUX->miR-344--|Zmym2/Lsd1 axis that controls MERVL for expanded stem cell potency.

overall_design: RNA sequencing analysis was performed in WT, Zmym2KO, miR344-activated, and MERVL-activated ESCs, and embryos with miR-344 mimics or siZmym2 injection.

first: Xin

last: Huang


title: RNAseq analysis of taxol and palbociclib combination in pancreatic cancer

city: Madrid

first: Elena

last: Piñeiro-Yáñez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

summary: RNAseq from pancreatic cancer cell lines treated with DMSO, taxol, palbociclib or the combination at short-term time-points.

overall_design: Three pancreatic cancer cell lines were treated with DMSO, taxol, palbociclib and their sequential combination (T->P). Samples were collected at 24, 36, 48 and 72 hours of treatment and processed for RNA sequencing.

first: Beatriz

last: Salvador

first: Mónica

last: Álvarez-Fernández

first: Aicha

last: El Bakkali

first: María

last: del Camino Menéndez

first: Elisabet

last: Zapatero-Solana

last: López-Casas

first: Tomas

last: Di Domenico

first: Todd

last: VanArsdale

last: Shields

first: Manuel

last: Hidalgo

first: Marcos

last: Malumbres


title: Real-time quantitative PCR miRNA analysis of human hepatocytes

city: Salt

first: Jessica

last: Latorre

address: C/ Dr Castany s/n

institute: IDIBGI

summary:
Primary human hepatocytes were treated with compounds modulating steatosis: palmitic acid, compound C and metformin
qPCR miRNA expression profiling. Hepatocytes were treated as indicated in the summary. Equal amount total RNA was pooled prior to miRNA expression analysis

overall_design: Treatments (palmitate, compound C and metformin) were compared versus their respective controls (BSA, DMSO and PBS, respectively)


title: DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state [ZMYM2 ChIP-seq]

overall_design: Genome binding/occupancy profiling of Zmym2 was performed in ESCs by ChIP sequencing.


title: DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state [ATAC-seq]

overall_design: ATAC sequencing was performed in DR+/+ and DR-/- ESCs.


title: Modelling of pancreatic cancer biology: transcriptomic signature for 3D PDX-derived organoids and primary cell line organoid development

status: Public on Feb 05 2020

city: Swords

first: Shannon

last: Nelson

state: Dublin

address: Glasnevin

department: NICB

country: Ireland

institute: DCU

summary: With a five-year survival rate of 9%, pancreatic ductal adenocarcinoma (PDAC) the deadliest of all cancers. The rapid mortality makes PDAC difficult to research, and inspires a resolve to create reliable, tractable cellular models for preclinical cancer research. PDAC organoids are increasing used to model PDAC as they maintain the differentiation status, molecular and genomic signatures of the original tumour. In this paper, we present novel methodologies and experimental approaches to develop PDAC organoids from PDX tumours, and the simultaneous development of matched primary cell lines. Moreover, we also identify a method of recapitulating primary cell line cultures to organoids (CLOs). We highlight the usefulness of CLOs as PDAC organoid models, as they maintain similar transcriptomic signatures as their matched patient-derived organoids and PDXs. These models provide a manageable, expandable in vitro resource for downstream applications such as high throughput screening, functional genomics, and tumour microenvironment studies.

overall_design: Three biological repliates were analysed for each of the five conditions (two cell lines; two matched cell line organoid (CLO); one matched organoid) and one biological replicate for PDX sample

first: Chenxi

last: Zhang

first: Sandra

last: Roche

first: Fiona

last: O'Neill

first: Niall

last: Swan

first: Yonglun

last: Luo

first: AnneMarie

last: Larkin

first: John

last: Crown

first: Naomi

last: Walsh


title: Transcriptional responses of Dictyostelium discoideum exposed to different classes of bacteria

status: Public on Feb 08 2020

city: Lausanne

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: Dictyostelium discoideum amoebae feed by ingesting bacteria, then killing them in phagosomes. Ingestion and killing of different bacteria have been shown to rely on largely different molecular mechanisms. One would thus expect that D. discoideum adapts its ingestion and killing machinery when encountering different bacteria. In this study, we investigated by RNA sequencing if and how D. discoideum amoebae respond to the presence of different bacteria by modifying their gene expression patterns. Each bacterial species analyzed induced a specific modification of the transcriptome. Bacteria such as Bacillus subtilis, Klebsiella pneumoniae, or Mycobacterium marinum induced a specific and different transcriptional response, while Micrococcus luteus did not trigger a significant gene regulation. Although folate has been proposed to be one of the key molecules secreted by bacteria and recognized by hunting amoebae, it elicited a very specific and restricted transcriptional signature, distinct from that triggered by any bacteria analyzed here. Our results indicate that D. discoideum amoebae respond in a highly specific, almost non-overlapping manner to different species of bacteria. We additionally identify specific sets of genes that can be used as reporters of the response of D. discoideum to different bacteria.

overall_design: After co-incubation for 4h between bacteria and wild-type D. discoideum cells, the uningested bacteria were removed by centrifugation at 1000 g for 2 min, RNA was extracted from cells using the directzol RNA extraction kit (Zymo research) following the manufacturer’s instructions for total RNA isolation. To remove contaminating genomic DNA, samples were treated with 0.25U of DNase I (Zymo) per 1 μg of RNA for 15 min at 25°C. RNA was quantified using Qubit 4.0 (Invitrogen) and its quality was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies). The total RNA preparation was used as a template for cDNA synthesis and NGS library construction using the Ovation Universal System (NuGEN Technologies, San Carlos, California, USA). 100 ng of total DNAse I-treated RNA was used for first- and second-strand cDNA synthesis following the manufacturer’s protocol. In order to obtain a comparable library size, a double bead cut strategy was applied using the 10X genomics protocol. cDNA was recovered using magnetic beads with two ethanol washing steps, followed by enzymatic end repair of the fragments. Barcoded adapters were ligated to each sample before strand selection. Ribosomal RNAs were targeted for depletion by the addition of custom-designed oligonucleotides specific for D. discoideum (5S, 18S and 28S). To amplify the libraries, 18 cycles of PCR were performed. The quality of the libraries was monitored by TapeStation (Agilent, High Sensitivity D1000 ScreenTape, # 5067–5584). Samples were pooled in approximately equimolar amounts and analyzed in 50 bp single read flow cells (Illumina, # 15022187; Hiseq 4000). The numbers of replicates for each conditions are indicated below.

first: Otmane

last: Lamrabet

first: Astrid

last: Melotti

first: Frédéric

first: Nabil

last: Hanna

first: Jackie

last: Perrin

first: Jahn

last: Nitschke

first: Marco

last: Pagni

first: Hubert

last: Hulbi

first: Thierry

last: Soldati

first: Pierre

last: Cosson


title: Chromatin accessibility promotes hematopoietic and leukemia stem cell activity [ATAC-seq]

first: Andrew

last: Lane

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: In this project, we studied how the nucleosome binding protein HMGN1 affects myeloid differentiation and hematopoietic and leukemia stem cell activity.

overall_design: ATAC-seq in primary hematopoietic cells from wild-type or HMGN1 overexpressing transgenic mice assessed at 2 timepoints of myeloid differentiation.

first: Lucia

last: Cabal-Hierro


title: Smarcad1 coordinates innate immunity-linked gene expression in the intestinal epithelium[organoids RNA-seq]

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Smarcad1 is one of the most conserved chromatin remodelling factors, from yeast to human, with suggested functions in gene silencing, heterochromatin maintenance and genome stability. However, its role in tissue function is poorly understood. As this factor is highly expressed in the stem- and proliferative zone in the intestinal epithelium, we explored the role of this factor in this tissue. Intestine tissue-specific deletion of Smarcad1 resulted in notable changes in gene expression in the small intestine, colon and organoids from small intestine. Strikingly, we found an increase of expression of several genes linked to innate immunity and a dramatic increase of a Bglap3 coding for an osteocalcin isoform, a protein normally expressed in osteoblasts.

overall_design: Comparisons between wild type mice and Vil-Cre mediated KO of Smarcad1 in the intestinal epithelium. C57BL/6 background. RNA-seq performed on small intestine-derived organoids as biological triplicates.

first: Claudia

last: Stellato

first: Renan

last: Correra

first: Juri

last: Kazakevych

last: Vinolo

first: Patrick

last: Varga-Weisz


title: Smarcad1 coordinates innate immunity-linked gene expression in the intestinal epithelium[SI RNA-seq]

summary: Smarcad1 is one of the most conserved chromatin remodelling factors, from yeast to human, with suggested functions in gene silencing, heterochromatin maintenance and genome stability. However, its role in tissue function is poorly understood. As this factor is highly expressed in the stem- and proliferative zone in the intestinal epithelium, we explored the role of this factor in this tissue. Intestine tissue-specific deletion of Smarcad1 resulted in notable changes in gene expression in the small intestine, colon and organoids from small intestine.  Strikingly, we found an increase of expression of several genes linked to innate immunity and a dramatic increase of a Bglap3 coding for an osteocalcin isoform, a protein normally expressed in osteoblasts. Our study demonstrates that an innate immunity response can be coordinated by a chromatin remodelling factor

overall_design: Comparisons between wild type mice and Vil-Cre mediated KO of Smarcad1 in the small intestinal epithelium. C57BL/6 background. RNA-seq  performed in 4 replicates on whole small intestinal tissue.

first: Claire

last: Fraser


title: Chromatin accessibility promotes hematopoietic and leukemia stem cell activity [ChIP-seq]

overall_design: ChIP-seq for H2K27ac and H3K27me (and total H3 for normalization) in control (WT) or HMGN1 overexpressing (OE) mouse myeloid cells that were immortalized with HoxB8.

first: Peter

last: van Galen


title: Smarcad1 coordinates innate immunity-linked gene expression in the intestinal epithelium [ATAC-seq]

summary: How intestinal epithelial cells interact with the host immune system and the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is one of the most conserved chromatin remodelling factors, from yeast to human, with suggested functions in gene silencing, heterochromatin maintenance and genome stability. However, its role in tissue function is poorly understood. As this factor is highly expressed in the stem- and proliferative zone in the intestinal epithelium, we explored the role of this factor in this tissue. Specific deletion of Smarcad1 in the intestinal epithelium led to colitis resistance in the dextran sodium sulphate colitis model. Intestine tissue-specific deletion of Smarcad1 resulted in notable changes in gene expression in the small intestine and colon. Absence of Smarcad1 led to changes in chromatin accessibility and significant changes in histone H3K9me3 but not H3K9me2 over many sites, including many genes that are differentially regulated upon Smarcad1 deletion. Our study demonstrates that an innate immunity response can be coordinated by a chromatin remodelling factor.

overall_design: Comparisons between wild type mice and Vil-Cre mediated KO of Smarcad1 in the intestinal epithelium. C57BL/6 background. ATAC-seq performed in triplicates on whole crypt epithelium of the small intestine.


title: Smarcad1 coordinates innate immunity-linked gene expression in the intestinal epithelium [16S Amplicon-seq]

summary: Smarcad1 is one of the most conserved chromatin remodelling factors, from yeast to human, with suggested functions in gene silencing, heterochromatin maintenance and genome stability. However, its role in tissue function is poorly understood. As this factor is highly expressed in the stem- and proliferative zone in the intestinal epithelium, we explored the role of this factor in this tissue. Specific deletion of Smarcad1 in the intestinal epithelium led to colitis resistance in the dextran sodium sulphate colitis model. We identified candidate members of the gut microbiome that elicit an epithelial Smarcad1-dependent colitis response.

overall_design: Compared genotypes: wild type mice and Vil-Cre mediated KO of Smarcad1 in the small intestinal epithelium. C57BL/6 background. Enriched microbiota by bedding transfer from another SPF-facility. 16S Amplicon-Seq performed on donor microbiota (triplicates) and WT/KO microbiota before and after enrichment (10 replicates per cohort), 43 samples total.


title: The role of histone H3K27 acetylation for enhancer activity in embryonic stem cells

status: Public on Feb 09 2020

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

summary: By substituting lysine 27 in histone variant H3.3 to arginine in mouse embryonic stem cells, we measured H3K27ac/H3K4me1/H3K4me3 and other acetylation modifications in H3.3K27R mutant cells, together with RNA-seq and ATAC-seq to measure the transcription activity and chromatin accessibility, respectively.

overall_design: WT mouse ESC served as controls , and two H3.3K27R mutant lines (Mut18 and Mut43) were sequenced. Two independent biological replicates were measured for ChIP-seq / RNA-seq /ATAC-seq experiments, and input data were shared among histone ChIP experiments for each cell line.

first: Tiantian

first: Qiang

last: Dong

first: Jun

last: Xiong

first: Bing

last: Zhu


title: Chromatin Folding Domains Disruptions by Somatic Genomic Rearrangements in Human Cancers

city: Houston

first: Kadir

middle: Caner

last: Akdemir

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Genomic material within the nucleus is folded into successive layers in order to package and organize the long string of linear DNA. This hierarchical level of folding is closely associated with transcriptional regulation and DNA replication. Genes within the same folding domain demonstrate similar expression and histone-modification profiles1. Therefore, boundaries separating different domains have important roles in reinforcing the stability of these domain-wide features. Indeed, domain boundary disruptions in human genetic disorders2,3 or human cancers lead to misregulation of certain genes4,5, due to de novo enhancer exposure to promoters. However, the frequency of boundary disruptions in human cancers, and whether there are recurrently affected boundaries in specific cancer types, remains unclear. Here, to understand effects and distributions of somatic structural variations (SVs) across TADs, we utilized 288,457 high-confidence somatic structural variations from 2658 high-coverage whole genome sequencing datasets across various cancer types. We comprehensively profiled structural variations effects on the domain boundaries and the regulation of genes in human cancers. Notably, most of the TAD disruptions do not result in appreciable changes in nearby gene expression where more than 2-fold expression change was observed in only 14% of regions with the boundary deletions. In addition, we demonstrated that SV types affect TADs differently, specifically, complex rearrangements drastically change chromatin folding maps in the cancer genomes.

overall_design: Profiling chromatin conformation dynamics in four cancer cell lines.

first: Jesse

last: Dixon


title: Smarcad1 coordinates innate immunity-linked gene expression in the intestinal epithelium [Cocr RNA-seq]

summary: Smarcad1 is one of the most conserved chromatin remodelling factors, from yeast to human, with suggested functions in gene silencing, heterochromatin maintenance and genome stability. However, its role in tissue function is poorly understood. As this factor is highly expressed in the stem- and proliferative zone in the intestinal epithelium, we explored the role of this factor in this tissue. Intestine tissue-specific deletion of Smarcad1 resulted in notable changes in gene expression in the small intestine, colon and organoids from small intestine.

overall_design: Comparisons between wild type mice and Vil-Cre mediated KO of Smarcad1 in the intestinal epithelium. C57BL/6 background. RNA-seq  performed in triplicates on colon epithelial cells (CO) isolated as whole crypts.

first: Anke

last: Liebert


title: DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state

city: New York

first: Jianlong

last: Wang

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

overall_design: Refer to individual Series


title: Genome-wide maps of chromatin state in Fezf2 or Chd4 KO mTECs

first: Yoshihiko

last: Tomofuji

summary: To integrate the epigenomic landscapes of chromatin accessibility regulated by Chd4 and Fezf2, we performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis of mTECs from wild type (WT), Chd4 cKO and Fezf2 cKO mTECs.

overall_design: ATAC-seq in mTECs from 3 types of mice.

first: Akashi

last: Taguchi

first: Hiroyuki

last: Takaba


title: Smarcad1 coordinates innate immunity-linked gene expression in the intestinal epithelium [wCO RNA-seq]

first: Felix

last: Krueger

summary: Smarcad1 is one of the most conserved chromatin remodelling factors, from yeast to human, with suggested functions in gene silencing, heterochromatin maintenance and genome stability. However, its role in tissue function is poorly understood. As this factor is highly expressed in the stem- and proliferative zone in the intestinal epithelium, we explored the role of this factor in this tissue. Specific deletion of Smarcad1 in the intestinal epithelium led to colitis resistance in the dextran sodium sulphate colitis model. Intestine tissue-specific deletion of Smarcad1 resulted in notable changes in gene expression in the small intestine, colon and organoids from small intestine. Strikingly, we found an increase of expression of several genes linked to innate immunity. Our study demonstrates that an innate immunity response can be coordinated by a chromatin remodelling factor. It highlights the role of intestinal epithelial cells in the colitis response and we identified candidate members of the gut microbiome that elicit an epithelial Smarcad1-dependent colitis response.

overall_design: Compared genotypes: wild type mice and Vil-Cre mediated KO of Smarcad1 in the small intestinal epithelium. C57BL/6 background. Enriched microbiota by bedding transfer from another SPF-facility. RNA-seq  performed on whole small intestinal tissue. Triplicates for untreated control samples,  5 replicates for DSS-induced colitis samples. 16 samples total.


title: Expression data from fibroblasts with knock-down of Brg1 and Brm

status: Public on Feb 04 2020

city: Nice

first: Dominic

last: van Essen

address: 28 Avenue Valombrose

institute: Institute for Research on Cancer & Aging, Nice (IRCAN)

summary: We used microarrays to asses gene expression in 3T3 fibroblasts, after knock-down of Brg1 and Brm using stable shRNA interference.  Cells were treated with 5ng/ml mouse TNF-alpha to stimulate inducible gene activation.

overall_design: 3T3 fibroblasts were transduced with retroviral vectors encoding an shRNA targeting Brg1 and Brm.  Subconfluent cultures of cells were treated for 1hr  with TNF-alpha before RNA extraction.

first: Simona

last: Saccani


title: Chromatin accessibility promotes hematopoietic and leukemia stem cell activity [RNA-seq]

first: Andrew

last: Lane

summary: In this project, we studied how the nucleosome binding protein HMGN1 affects myeloid differentiation and hematopoietic and leukemia stem cell activity

overall_design: RNA-seq in primary hematopoietic cells from wild-type or HMGN1 overexpressing transgenic mice assessed at 3 timepoints of myeloid differentiation

first: Lucia

last: Cabal-Hierro


title: Role of engrailed 2 (EN2) in esophageal squamous cell carcinoma

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

summary: A number of homeobox genes have been found to be implicated in the development of various cancers. Here, we investigated the role of engrailed 2 (EN2), a member of the homeobox gene superfamily, in esophageal squamous cell carcinoma

overall_design: RNA profiling was performed using gene expression microarray. A lentivirus system was used to establish a stable cell line expressing exogenous EN2. The malignant phenotype was analyzed by means of proliferation, clonogenicity, wound-healing, and invasion assays. The CRISPR/Cas9 system was adopted to deplete the endogenous EN2. The ShRNA-mediated method was used to knock down the expression of SPARC. Separately, the structure–function relationship was determined by the site-directed mutagenesis method.

first: Yong

last: Cao

first: Xiaoyan

first: Li

last: Tang

first: Yan

last: Li

first: Xueqing

last: Song

first: Xu

last: Liu

first: Mingying

first: Feng

last: Chen

first: Haisu

last: Wan


title: Promoter nucleosome positioning in dendritic cells (DCs) and fibroblasts


title: DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state [LSD1 ChIP-seq]

first: Jianlong

last: Wang

summary: Mouse embryonic stem cells (ESCs) sporadically express preimplantation two-cell-stage (2C) transcripts, including MERVL endogenous retrovirus and Zscan4 cluster genes. Such 2C-like cells (2CLCs) can contribute to both embryonic and extraembryonic tissues when reintroduced into early embryos. We examined global nucleosome occupancy and gene expression in 2CLCs and identified miR-344 as the noncoding molecule that positively controls 2CLC potency. We found that activation of endogenous MERVL or miR-344-2 alone is sufficient to induce 2CLCs with induction of 2C genes and an expanded potency. Mechanistically, miR-344 is activated by the 2C-state driver DUX and post-transcriptionally represses ZMYM2 and LSD1, which recruit the HDAC corepressor to MERVL LTR for transcriptional repression. Consistently, zygotic depletion of Zmym2 compromises the totipotency-to-pluripotency transition during early development. Our studies establish the novel DUXmiR-344--|Zmym2/LsdSD1 axis that controls MERVL for expanded stem cell potency.

overall_design: Genome binding/occupancy profiling of Zmym2 was performed in ESCs by ChIP sequencing.

first: Xin

last: Huang


title: Smarcad1 coordinates innate immunity-linked gene expression in the intestinal epithelium [ChIP-seq]

city: Cambridge

first: Felix

overall_design: Comparisons between wild type mice and Vil-Cre mediated KO of Smarcad1 in the intestinal epithelium. C57BL/6 background. H3K9me2/3 ChIP-seq performed in triplicates on whole crypt epithelium of the small intestine.

first: Marianna

last: Portovedo

first: Juri

last: Kazakevych

first: Marco

last: Vinolo

first: Patrick

last: Varga-Weisz


title: Pyridoxine induces glutathione synthesis via PKM2-mediated Nrf2 transactivation and confers neuroprotection

city: Nanjing

first: Yao

last: Wei

state: Jiangsu

address: 138 Xianlin Road

institute: Nanjing University of Chinese medicine

summary: Oxidative stress is a major pathogenic mechanism in Parkinson’s disease (PD). As an important cellular antioxidant, glutathione (GSH) balances the production and incorporation of free radicals to protect neurons from oxidative damage. Unfortunately, the GSH level is greatly decreased in the brains of PD patients. Hence, clarifying the molecular mechanism of GSH deficiency may help deepen our knowledge of PD pathogenesis. Here we report that the astrocytic dopamine D2 receptor (DRD2) regulates GSH synthesis via PKM2-mediated Nrf2 transactivation. Besides, we find that pyridoxine can dimerize PKM2 to promote GSH biosynthesis. Further experiments show that pyridoxine supplementation increases the resistance of nigral dopaminergic neurons to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced neurotoxicity in wild-type mice as well as in astrocytic Drd2 conditional knockout mice. Given that dopamine agonist treatment in PD is limited by their intolerable side effects and diminished effectiveness over time, we anticipate dimerizing PKM2 to be a new strategy for PD treatment.

overall_design: RNA sequencing in astrocytes from mice before or after quinpirole administration, in triplicate.

first: Gang

last: Hu


title: CBX4 role in U2OS/MTX300

city: Guang Zhou

state: State...

address: Dongfengdong road 651

institute: Sun Yat-sen University Cancer Center

summary: In our study, we found that CBX4 was critical to osteosarcoma metastasis.CBX4, also known as polycomb 2 (Pc2), belongs to the CBX protein family, including CBX2, 4, 6, 7, and 8, which has been shown to participate in the polycomb repressive complex 1 (PRC1) and characterized as a transcriptional repressor. To identify the downstream target genes of CBX4 in osteosarcoma, we conducted the RNA-seq analysis of CBX4 overexpression or knockdown in osteosarcoma cell line U2OS/MTX300.

overall_design: U2OS/MTX300 cells overexpressing CBX4 are compared to Vector, and shCBX4 are compared to shControl

first: Tiebang

last: Kang


title: Chromatin accessibility promotes hematopoietic and leukemia stem cell activity

city: Boston

first: Andrew

last: Lane


title: Meta-analysis of honey bee neurogenomic response to deformed wing virus (drone)

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

summary: This dataset represents RNA-Seq data that was later found to have widespread contamination with Deformed Wing virus (DWV). It has been incorporated in a meta-analysis of DWV's impact on brain gene expression

overall_design: Post-hoc analysis of DWV contamination in healthy-appearing drone honey bees.

first: Amy

last: Cash Ahmed


title: Meta-analysis of honey bee neurogenomic response to deformed wing virus (worker)

overall_design: Post-hoc analysis of DWV contamination in healthy-appearing worker honey bees.


title: Regulation of Stomatal Development by Stomatal Lineage miRNAs

status: Public on Feb 03 2020

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

summary: Stomata in the plant epidermis play a vital role in growth and survival by controlling gas exchange and immunity to pathogens.  A genetic frame of key transcriptional factors and cellular communication has been established, by which plants modulate stomatal cell fate and patterning.  miRNAs contribute to functional and developmental plasticity in multicellular organisms.  However, it remains very elusive as to whether miRNAs pitch in stomatal development.  Here, we reveal dynamic miRNA expression profiles from stomatal lineage cells in a development stage-specific manner and show that stomatal lineage miRNAs positively and negatively regulate stomatal formation and pattern to avoid clustered and paired stomata.  Target prediction of stomatal lineage miRNAs suggests potential cellular processes involved in stomatal development.  Furthermore, dysregulation of stomatal lineage miRNAs and their target mRNAs disclose unexpected genetic pathways modulating stomatal development.  Our study demonstrates that miRNAs constitute an additional layer in the complex regulatory mechanism of stomatal development.

overall_design: miRNA profiling from AGO1-associated small RNAs in stomatal lineage cells in arabisopsis

first: Jiali

last: Zhu

first: Seulbee

last: Lee

first: Jae

middle: H

first: Daehee

last: Hwang

first: June

last: Kwak

first: Yun

last: Kim


title: Smarcad1 coordinates innate immunity-linked gene expression in the intestinal epithelium [sorted cells RNA-seq]

first: Felix

last: Krueger

summary: Smarcad1 is one of the most conserved chromatin remodelling factors, from yeast to human, with suggested functions in gene silencing, heterochromatin maintenance and genome stability. However, its role in tissue function is poorly understood. As this factor is highly expressed in the stem- and proliferative zone in the intestinal epithelium, we explored the role of this factor in this tissue. Intestine tissue-specific deletion of Smarcad1 resulted in notable changes in gene expression in the small intestine, colon and organoids from small intestine. Strikingly, we found an increase of expression of several genes linked to innate immunity and a dramatic increase of a Bglap3 coding for an osteocalcin isoform, a protein normally expressed in osteoblasts.

overall_design: Comparisons between wild type mice and Vil-Cre mediated KO of Smarcad1 in the intestinal epithelium. C57BL/6 background. RNA-seq  performed in triplicates on flow-sorted intestinal stem cell (ISC), transit amplifying cells (TA), adult enterocytes (AE) and colon epithelial cells (CO).

first: Anke

last: Liebert


title: Anaphase-promoting complex-dependent control of cell identity

city: Berkeley

first: Eugene

last: Oh

address: 330 Li Ka Shing

institute: UC Berkeley

summary: Tissue development and homeostasis rely on the proliferation of progenitor cells, whose identities are established by tightly controlled gene expression networks. However, mRNA synthesis is inhibited during mitosis, and the transcriptional programs that define a cell type must be restarted upon entry into each new cell cycle; how this is accomplished is poorly understood. Here, we identified a ubiquitin-dependent mechanism that integrates gene expression with cell division to preserve cell identity. We found that WDR5 and TBP, which bind active promoters during interphase, recruit the E3 ligase anaphase-promoting complex (APC/C) to specific transcription start sites during mitosis. This allows the APC/C to locally decorate histones with K11/K48-linked ubiquitin chains, which destabilizes nucleosomes and ensures continued gene expression in the next cell cycle. Mitotic exit and transcription re-initiation are therefore controlled by the same essential regulator, the APC/C, which provides a robust mechanism to maintain cell identity through cell division.

overall_design: RNA-seq analysis in asynchronous or mitotically synchronized human embryonic stem cells (H1). MNase/ChIP-seq of K11 linked ubiquitin chains (lab reagent), WDR5 (Diagenode, C15410027), TBP (Cell Signaling, 44059), histone H2B (Cell Signaling, 12364) and histone H3 (Abcam, 1791) in human embryonic stem cells (H1).

first: Michael

last: Rape


title: TIP5 primes prostate luminal cells for the oncogenic transformation mediated by PTEN-loss

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

institute: University of Zurich

summary: Prostate cancer (PCa) is the second leading cause of cancer death in men. Its clinical and molecular heterogeneity and the lack of in vitro models outline the complexity of PCa in the clinical and research settings. We established an in vitro mouse PCa model based on organoid technology that takes into account the cell of origin and the order of events. Primary PCa with deletion of the tumor suppressor gene PTEN (PTEN-del) can be modeled through Pten-downregulation in mouse organoids. We used this system to elucidate the contribution of TIP5 in PCa initiation, a chromatin regulator that is implicated in aggressive PCa. High TIP5 expression correlates with primary PTEN-del PCa and this combination strongly associates with reduced PSA recurrence-free survival. TIP5 is critical for the initiation of PCa of luminal origin mediated by Pten loss whereas it is dispensable once Pten-loss mediated transformation is established. Cross-species analyses revealed a PTEN gene signature that identified a group of aggressive primary PCa characterized by PTEN-deletion, high-TIP5 expression, and a TIP5-regulated gene expression profile. The results highlight the modelling of PCa with organoids as a powerful tool to elucidate the role of genetic alterations found in recent studies in their time order and cell of origin, thereby providing further optimization for tumour stratification to improve the clinical management of PCa.

overall_design: Transcriptomic analysis of Tip5 depeltion in basal and luminal mouse prostate epithelial cells. Transcriptomic analysis of gene expression in mouse prostate organoids upon Pten downregulation and Tip5 depletion in different cellular context and time order.

first: Karolina

last: Pietrzak

first: Rostyslav

last: Kuzyakiv

first: Ronald

last: Simon

first: Marco

last: Bolis

first: Dominik

last: Bär

first: Jean-Philippe

last: Theurillat

first: Guido

last: Sauter


title: Decode-seq: a practical approach to improve differential gene expression analysis

status: Public on Feb 02 2020

first: Qiang

last: Tu

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: It is often the case that inadequate numbers of biological replicates are utilized in differential gene expression analysis. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling a large number of replicates simultaneously. This approach significantly improved the performance of differential gene expression analysis. Using this approach in medaka fish (Oryzias latipes), we discovered novel genes with sexually dimorphic expression, and genes necessary for germ cell development. We appeal that the common practice of using three replicates in differential gene expression analysis should be abandoned.

sample_organism:
Oryzias latipes
Homo sapiens
Mus musculus

overall_design:
Each library contains 20 to 60 barcoded samples, total 12 libraries and 360 barcoded samples.

DE1-1, DE1-2, and DE1-3 contain replicates of mix4.5 (human RNA with 4.5% mouse RNA), mix1.5 (1.5% mouse RNA) and mix0.9 (0.9% mouse RNA), 100ng input RNA per sample;

DE2-2, DE2-3, DE2-4, and DE2-5 contain replicates of F (medaka female gonadal RNA), M (medaka male gonadal RNA) and D (DMY mutant male medaka RNA).

DE3-3 and DE3-4 contain replicates of the same mixes as DE1, 10ng and 1ng input RNA per sample respectively;

DE8-6, DE8-12-1 and DE8-12-2 contain replicates of mix5 (human RNA with 5% mouse RNA) and mix1 (1% mouse RNA), 100ng input RNA per sample;

All libraries were constructed using the Decode-seq protocol we developed except DE8-6, which was constructed using the previous published BRB-seq protocol

first: Yingshu

last: Li


title: Gene expression profiling of IRBIT mutant flies

status: Public on Feb 01 2020

city: Bethesda

first: Alexei

last: Arnaoutov

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

institute: NICHD

summary: In order to understand the biological role of Drosophila IRBIT, we generated null mutant fruitflies.  We performed Illumina platform-based RNA-Seq analysis to investigate transcriptional consequences of the mutation using fly midguts as well as whole animals.

overall_design: We performed gene expression profiling on wildtype and IRBIT mutant flies.  We prepared RNA-Seq libraries from midguts and whole flies.  Flies were reared to be 1 day, 7 days, 40 days, or 50 days old.  Males and females separately prepared under different treatments: normal, deoxyadenosine, deoxyguanosine, hydroxyurea.  We also culture flies in two different conditions of normal versus axenic conditions.  Experiments were triplicated for RNA-Seq except for 50 day-old samples.  We generated, stranded, single-end RNA-Seq libraries to have 50 or 76 read-lengths.

first: H

last: Lee

first: A

first: M

last: Serpe

first: B

last: Oliver

last: Dasso


title: Comparative transcriptomic analysis  of a wood decomposing fungus in various atmospheres

city: Helsinki

first: Hans

last: Mattila

address: Viikinkaari 9

department: Microbiology department

country: Finland

institute: University of Helsinki

summary:
AIM: By adopting comparative transcriptomic approach, we investigated the gene expression of wood decomposing Basidiomycota fungus Phlebia radiata. Our aim was to reveal how hypoxia and lignocellulose structure affect primary metabolism and the expression of wood decomposition related genes.
RESULTS: Hypoxia was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides by the fungus. Our results manifest how oxygen depletion affects not only over 200 genes of fungal primary metabolism but also plays central role in regulation of secreted CAZyme (carbohydrate-active enzyme) encoding genes. Based on these findings, we present a hypoxia-response mechanism in wood-decaying fungi divergent from the regulation described for Ascomycota fermenting yeasts and animal-pathogenic species of Basidiomycota.

overall_design: Three biological replicates were analyzed with RNA-Seq.

first: Mari

last: Mäkinen

first: Jaana

last: Kuuskeri

first: Taina

last: Lundell


title: Activation of mosquito immunity blocks the development of transmission-stage filarial nematodes

city: Philadelphia

first: Michael

last: Povelones

address: 3800 Spruce St.

department: Pathobiology

institute: University of Pennsylvania School of Veterinary Medicine

summary: Mosquito-borne helminth infections are responsible for a significant worldwide disease burden in both humans and animals. Accordingly, development of novel strategies to reduce disease transmission by targeting these pathogens in the vector are of paramount importance. We found that a strain of Aedes aegypti that is refractory to infection by Dirofilaria immitis, the agent of canine heartworm disease, mounts a stronger immune response during infection than does a susceptible strain. Moreover, activation of the Toll immune signaling pathway in the susceptible strain arrests larval development of the parasite, thereby decreasing the number of transmissionstage larvae. Notably, this strategy also blocks transmission stage Brugia malayi, an agent of human lymphatic filariasis. Our data show that mosquito immunity can play a pivotal role in restricting filarial nematode development and suggest that genetically engineering mosquitoes with enhanced immunity will help reduce disease transmission.

sample_organism:
Dirofilaria immitis
Aedes aegypti

platform_organism:
Dirofilaria immitis
Aedes aegypti

overall_design:
Total RNA-sequencing.
Ae. aegypti (S): susceptible strain referred to as 'Blackeye'
Ae. aegypti (R): refractory strain referred to as 'Liverpool'.

first: Elizabeth

middle: B

last: Edgerton

first: Corbett

middle: T

last: Berry


title: Next generation sequencing for the prenatal (30--90 day) testosterone (T) treatment and its effect on  gene expression in fetal day 90 (D90) and adult year 2 (Y2) ovaries.

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

department: Animal Science

institute: Michigan State University

summary: A direct correlation between changes in epigenetic marks and gene expression in adult ovaries from prenatally- T-treated sheep establishes epigenetic changes as one of the underlying causes for  differential expression of genes in PCOS ovary.

overall_design: Using DESeq2 R package, differentially expressed genes (DEGs) were identified between control (n = 3) and T- treatment (n = 3) for fetal D90 and control (n = 3) and T (n = 4) for adult Y2, respectively

first: Niharika

last: Sinha

first: Sambit

last: Roy


title: ChipSeq of GS-TRa1 is Gad2CrexThraGS striatum

status: Public on Jan 31 2020

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

institute: ENSL

summary: Whole striatum Chipseq from mice expressing a tagged TRalpha1 in GABAergic neurons only

overall_design: Comparison between input and IP fraction

first: S

last: Richard

first: F


title: Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain [ChIPseq]

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

summary: Breast cancer metastasis is the leading cause of breast cancer-related mortalities in women. Differential gene expression programs enriched in the primary tumor is able to distinguish patients that experience relapse to different organs. Epigenomic changes often underlie transcriptomic differences and give rise to stable phenotypes. However, the epigenomic differences present in organotropic metastasis remains underexplored. Here we profile the active chromatin landscape of the claudin-low cell line MDA-MB-231 and its metastatic subpopulations that preferentially grow in the brain (BrM2), and lung (LM2). We find that metastatic cells harbor increased promoter and enhancer activation. Using ATAC-seq, we also define transcription factors that are enriched in an organotropic manner. Chromatin accessibility of metastatic cells correlates with shorter progression-free survival and is enriched in patients who have more aggressive subtypes of breast cancer.

overall_design: RNAseq, ChIPseq (H3K4me3, H3K27ac) and ATACseq of MDA-MB-231 Par, LM2, and BrM2 cell lines

first: Wesley

last: Cai

first: Don

middle: X

last: Nguyen


title: RNA-seq mouse donor T-cells after day of BMT

city: Ann Arbor

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: RNAs isolated from mouse T cells were processed for sequencing. Naive T cells were wer isoalted from either from WT or Wapl deficiency T cells. The tranfered T cells (either WT or Wapl deficient) were isolated on day 7 after allogeinic or syngeneic BMT. The main purposes of these experiment are to seeking the impact of Wapl KO on gene expression in T cells either in naive status or after BMT.

overall_design: Independent biologic triplicate naïve or donor T-cells (WT and Wapl KO) were harvested for RNA-seq from a pool of 2-4 mouse. Donor T cells were isolated from recipients 7 days after allogeneic or syngeneic HSCT and naive T cells were isolated from biologic triplicate healthy non-transplanted control animals.

first: Pavan

last: Reddy

first: Yaping

last: Sun

first: Daniel

last: Peltier


title: Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain [ATACseq]


title: mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence [RNA-seq]

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

institute: Seoul National University

summary: Quiescence is a cellular state in which cells undergo reversible cell cycle arrest in response to environmental challenges or lack of stimuli. When favorable conditions are engaged, the cells exit quiescence and start to proliferate. For example, quiescent stem cells and oocytes are activated by differentiation signals and fertilization, respectively. The regulation of quiescent state is also crucial for lymphocytes, such as T cells. Inappropriate activation of T cells often leads to autoimmune diseases and thus, the balance between quiescent and activated T cells must be preserved. Despite its importance, however, how T cells maintain the ‘quiescent state’ and exit from it remain largely unknown. Here, we identify BTG1 and BTG2 (BTG1/2) as factors responsible for T cell quiescence. Knockout of Btg1/2 in T cells resulted in a reduced threshold to T cell activation, increased proliferation and a concomitant reduction of the frequency of naive T cells. Loss of BTG1/2 rendered naive T cells to become spontaneously activated even without TCR stimuli. Interestingly, we found a global increase in mRNA abundance in naive T cells that lack BTG1/2. In addition, depletion of BTG1/2 led to an increase in mRNA half-life and poly(A) tail length. Thus, BTG1/2 promotes deadenylation and degradation of mRNA in naive T cells. Our study demonstrates a key mechanism underlying T cell quiescence, and suggests low mRNA abundance as a key feature for maintaining quiescent T cells.

overall_design: Two replicates of naive CD4 T cells (TCRb+CD4+CD25-CD62LhiCD44low) from WT and DKO mice, respectively.

first: Soo-Seok

last: Hwang

first: Richard

last: Flavell


title: Transcriptome analysis of Drrp6 and Drrp6, sen1DNIM by RNAseq

city: Paris

first: Odil

last: Porrua Fuerte

address: 15 rue Helene Brion

institute: Institut Jacques Monod-CNRS

summary: Pervasive transcription is a widespread phenomenon leading to the production of a plethora of non-coding RNAs (ncRNAs) without apparent function. Pervasive transcription poses a risk that needs to be controlled to prevent the perturbation of gene expression. In yeast, the highly conserved helicase Sen1 restricts pervasive transcription by inducing termination of non-coding transcription. However, the mechanisms underlying the specific function of Sen1 at ncRNAs are poorly understood. Here we identify a motif in an intrinsically disordered region of Sen1 that mimics the phosphorylated carboxy terminal domain (CTD) of RNA polymerase II  and characterize structurally its recognition by the CTD-interacting domain of Nrd1, an RNA-binding protein that binds specific sequences in ncRNAs. In addition, we show that Sen1-dependent termination strictly requires the recognition of the Ser5-phosphorylated form of the CTD by the N-terminal domain of Sen1. Furthermore, we find that the N-terminal and the C-terminal domains of Sen1 can mediate intra-molecular interactions. Our results shed light onto the network of protein-protein interactions that control termination of non-coding transcription by Sen1.

overall_design: Examination of the transcriptome of yeast strains expressing either wild-type or a mutant variant of SEN1 acking a Nrd1-Interaction motif in a Drrp6 background

last: Porrua


title: mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence

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

overall_design: Refer to individual Series


title: Termination of non-coding transcription in yeast relies on both a CTD-interaction domain and a CTD-mimic in Sen1


title: A genome-wide survey of DNA methylation in OsNAR2.1 transgenic plants

city: Nanjing, Jiangshu Province

first: Xiaorong

last: Fan

state: Jiangshu

address: Tongwei Road 1

institute: Nanjing Agricultural University

summary: DNA methylation is an important mechanism of  plant epigenomes, involved in regulating gene expression under environment stress. Nitrogen (N) resource is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with the  flexible environmental N changes, transgenic technolgies have been applied to enhance the N use efficiency (NUE) in crops. Here, we use Whole Genome Bisulfite Sequencing  (WGBS) and Methylated DNA Immunoprecipitation Sequencing (MEDIP-seq) to study genome-wide methylation across transgenic plants with higher NUE, transgenic controls and their wild types.

overall_design: Compared with wuyujing 7 (the wild type), the majority of methylation was investigated by WGBS in T0 plants of regeneration from callus(CK), pOsNAR2.1-OsNAR2.1 transgenic high NUE plants (pOsNAR2.1-OsNAR2.1), and false positive plants without gene separated from pOsNAR2.1-OsNAR2.1 transgenic line (FP). We also performed Methylated DNA Immunoprecipitation Sequencing (MEDIP-seq) for  wild type of Oryza sativa L. ssp. Japonica cv. Nipponbare (NP),  T8 generation plant of knockdown plant of OsNAR2.1 by RNA interference (RNAi)  and T8 generation plant of over expression plant of OsNAR2.1 by pUbi-OsNAR2.1 transgenic (pUbi-OsNAR2.1).

first: Xiaoru

first: Jingguang

last: Chen

first: Yinna

last: Su

first: Yufeng

last: Wu

first: Juan

last: Wang

first: Yuchi

last: Gao

first: Guohua

last: Xu


title: Functional hypoxia drives neuroplasticity and neurogenesis via brain erythropoietin

status: Public on Jan 30 2020

city: Göttingen

first: Hannelore

last: Ehrenreich

address: Hermann Rein Straße 3

department: Clinical Neuroscience

institute: Max Planck Institute of Experimental Medicine

summary: Erythropoietin (EPO), named after its role in hematopoiesis, is also expressed in the mammalian brain. In clinical settings, recombinant EPO had revealed a remarkable improvement of cognitive functions, but the underlying mechanisms have remained obscure. Animal studies demonstrated, however, that neuronal EPO effects are independent of an elevated hematocrit. Here, we show with a novel line of reporter mice that cognitive challenge leads to local/endogenous hypoxia in hippocampal pyramidal neurons where it induces enhanced expression of both EPO and EPO receptor (EPOR). High-dose EPO administration, which amplifies auto/paracrine EPO/EPOR signaling, prompts the emergence of new CA1 neurons and enhanced dendritic spine densities. Single cell sequencing reveals rapid increase in newly differentiating neurons. Importantly, improved performance on complex running wheels after EPO treatment is imitated by exposure to mild exogenous/inspiratory hypoxia. All these effects depend on neuronal expression of the Epor gene. Taken together, this suggests a novel cellular model of neuroplasticity in which neuronal networks, challenged by cognitive tasks, drift into transient hypoxia which becomes a trigger of neuronal EPO/EPOR expression. This regulatory circle causes long-lasting neuroplastic adaptation, and as fundamental cellular mechanism, may be relevant for strategies aiming at cognitive improvement.

overall_design: 6 mice (3 Placebo, 3 EPO treated), sacrificed 6h after injection, CA1 isolated

first: Debia

last: Wakhloo

first: Franziska

last: Scharkowski

first: Yasmina

last: Curto

first: Umer

last: Butt

first: Vikas

last: Bansal

first: Agnes

last: Steixner-Kumar

first: Liane

last: Wuestefeld

first: Ashish

last: Rajput

first: Sahab

last: Arinrad

first: Matthias

last: Zillmann

first: Anna

last: Seelbach

first: Imam

last: Hassouna

first: Katharina

last: Schneider

first: Abdul

middle: Q

last: Ibrahim

first: Hauke

last: Werner

first: Henrik

last: Martens

first: Kamilla

last: Miskowiak

first: Sonja

last: Wojcik

first: Stefan

last: Bonn

last: Nacher

first: Klaus-Armin

last: Nave


title: Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics [ChIP-seq RNAPII]

city: Los Angeles

first: Kim

last: Ngo

state: CA

address: 611 Charles E Young Dr. East

department: MIMG

institute: University of California, Los Angeles

summary: NFkB RelA is the potent transcriptional activator of inflammatory response genes. We stringently defined a list of direct RelA target genes by integrating physical (ChIPseq) and functional (RNAseq in knockouts) datasets. We then dissected each gene’s regulatory strategy by testing RelA variants in a novel primary-cell genetic complementation assay.  All endogenous target genes required that RelA makes DNA-base-specific contacts, and none could be activated by the DNA binding domain alone. However, endogenous target genes differed widely in how they employ the two transactivation domains. Through model-aided analysis of the dynamic timecourse data we reveal gene-specific synergy and redundancy of TA1 and TA2. Given that post-translational modifications control TA1 activity and intrinsic affinity for coactivators determines TA2 activity, the differential TA logics suggests context-dependent vs. context-independent control of endogenous RelA-target genes. While some inflammatory initiators appear to require co-stimulatory TA1 activation, inflammatory resolvers are a part of the NFkB RelA core response.

overall_design: We performed ChIP-seq with antibody specific for RNA Polymerase II in primary wild-type MEFs treated with TNF.

first: Alexander

last: Hoffmann


title: Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics

summary: NFkB RelA is the potent transcriptional activator of inflammatory response genes. We stringently defined a list of direct RelA target genes by integrating physical (ChIPseq) and functional (RNAseq in knockouts) datasets. We then dissected each gene's regulatory strategy by testing RelA variants in a novel primary-cell genetic complementation assay.  All endogenous target genes required that RelA makes DNA-base-specific contacts, and none could be activated by the DNA binding domain alone. However, endogenous target genes differed widely in how they employ the two transactivation domains. Through model-aided analysis of the dynamic timecourse data we reveal gene-specific synergy and redundancy of TA1 and TA2. Given that post-translational modifications control TA1 activity and intrinsic affinity for coactivators determines TA2 activity, the differential TA logics suggests context-dependent vs. context-independent control of endogenous RelA-target genes. While some inflammatory initiators appear to require co-stimulatory TA1 activation, inflammatory resolvers are a part of the NFkB RelA core response.

overall_design: We performed ChIP-seq with antibody specific for NF-kappaB RelA subunit from retroviral complementation of RelA-deficient primary mouse embryonic fibroblasts with RelA (WT/mutants) stimulated with TNF


title: High-resolution transcriptome-wide maps of Sen1 RNA-binding by CRAC

first: Odil

last: Porrua Fuerte

overall_design: Analysis of the effect of several Sen1 mutations on Sen1 recruitment to RNAPII transcripts by CRAC

last: Porrua


title: Identification and validation of potential key long noncoding RNAs in sorafenib-resistant hepatocellular carcinoma cells

city: Nanning

first: Manya

last: Wu

address: No.22, Shuangyong Road

institute: Guangxi Medical University

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of lncRNAs expression profile in sorafenib resistant hepatocellular carcinoma cells. We identified 1240 differentially expressed lncRNAs with 576 up-regulated and 664 down-regulated (fold change > 2, P < 0.05) in sorafenib-resistant (HUH7-S) HCC cells (fold change > 2, P < 0.05) in sorafenib-resistant (HepG2-S) HCC cells, compared to parental sorafenib-sensitive (HUH7, HepG2) HCC cells by high-throughput sequencing. In addition, based on GO (Gene Ontology) term enrichment analysis, these differentially expressed lncRNAs are mainly related to binding and catalytic activity and biological regulation of metabolic processes in both the Huh7-S and HepG2-S cell lines compared to parental cell lines. Moreover, the differentially expressed genes analyzed by KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway were significantly related to tight junction. Among them, TCONS_00284048 and TCONS_00006019 expression were consistently up-regulated in resistant HCC cells, whereas both of them knock down increased the sensitivity of Huh7-S and HepG2-S cells to sorafenib.

overall_design: There were 12 samples in total. Examination of sorafenib-resistant and parental sorafenib-sensitive in 2 human hcc cell lines.

first: Xiaoling

last: Luo