4REGTPERC4REGTPsERCOur mission is to understand the molecular basis of genetic predisposition 0101-amxorP2-PAMU02-0101-02-tsddegreMRestingStimulated11PTGER4TTC33PTGER4sc-ATAC(scale=45UMI)sc-end5(scale=1000+UMI)ProximaltCREPRKAA1to human disease by functional annotation of disease-associated vari-ants and interrogation of their functions by functional genomics. Expression of genes specifying cell-types and states is primarily controlled by the activities of their cognate cis-regulatory elements (CREs), mostly promoters and enhancers, which are highly enriched in trait-associated variants. Therefore, understanding the cell-type/state-specific activities of CREs and their target gene expression not only helps to decipher the principles of gene regulation, but also the cell-type/state-specific contexts of genetic predisposition. Profiling of CREs in single cells allows us to gain a high resolution understanding of these principles. We demonstrated that single-cell RNA-5’end-sequencing (sc-5end-seq) methods can detect transcribed CREs (tCREs), enabling the quantification of promoter and enhancer activities in single cells. We found that sc-5end-seq with either random or oligo(dT) priming could detect enhancer RNAs at a surprisingly similar sensitivity. To identify genuine tCREs, we implemented a workflow that effectively eliminates false positives from sc-5end-seq data. Comparing tCRE to accessible CRE (aCRE, based on chromatin accessibility) in stimulated im-mune cells, we found that while both tCREs and aCREs recovered the cell-type specific CREs and stimulation-induced transcription factor activities, tCREs are more accurate in linking enhancers to promoters, more sensitive in detection of alternative promoters and more enriched in disease heritability. Our data high-lights an extra dimension of sc-5end data for studying gene regulation.Recent Major PublicationsDucoli L, Agrawal S, Sibler E, Kouno T, Tacconi C, Hon CC, Berger SD, Müllhaupt D, He Y, Kim J, D’Addio M, Dieterich LC, Carninci P, De Hoon MJL, Shin JW, Detmar M. LETR1 is a lymphatic endothelial-specific lncRNA that governs cell proliferation and migration through KLF4 and SEMA3C. Nature Communications 12, 925 (2021)Hon CC and Carninci P. Expanded ENCODE delivers in-valuable genomic encyclopedia. Nature 583, 685-686 (2020)Van der Wijst MGP, De Vries DH, Groot HE, Trynka G, Hon CC, Bonder MJ, Stegle O, Nawijn MC, Idaghdour Y, Van der Harst P, Ye CJ, Powell J, Theis FJ, Mahfouz A, Heinig M, Franke L. Single-cell eQTLGen Consortium: a personal-ized understanding of disease. eLife 9;9:e52155 (2020)Invited presentationsHon CC. “Building a better map to navigate through the genetic landscape of diseases” 84th Annual Scientific Meeting of the Japanese Circulation Society (Online) August 2020Crohn'sdiseaseSNP(r2>=0.5,scale=1)CoactivityamongtCREs(Ciceroscore>=0.2,scale=1)tCREsGenemodels(Entrez)sc-ATAC(scale=45UMI)sc-end5-dT(scale=3662UMI)sc-ATAC(scale=43UMI)sc-end5(scale=50+UMI)DistaltCREsDistaltCREsofPTGER4Genemodels(Entrez)chr5:40349192-40804356(455.2kb)Figure: Detection of tCRE activity in single cells at a Crohn’s disease risk locusa) Genetic association signal, sc-5end signal and chromatin accessibility at the Prosta-glandin E2 receptor 4 (PTERG4) locus. The PTERG4 locus is located in proximity to the linkage disequilibrium (LD) blocks associated with Crohn’s disease. We found a cluster of distal tCREs within these LD blocks that overlap with multiple disease-associated variants and are linked by co-activity (yellow arcs) to the proximal PTERG4 tCRE. PTGER4locusProximaltCREofPTGER4Genemodels(Entrez)1.5kbab01200tlifotlaifo000b) Expression of proximal and distal PTERG4 tCREs in single cells of resting and stimu-lated peripheral blood mononuclear cells. The expression of both proximal and distal PTERG4 tCREs is enriched in NK cells and T-cells and is activated upon stimulation, in keeping with the known pivotal roles of T-cells in autoimmune disorders.Resting10tCREexpression>=3Stimulated20UMAP-11020%cellsexpressed502575T-cell:CD4:naiveT-cell:CD4:memoryT-cell:CD8:naiveT-cell:CD8:cytotoxicNKcellB-cellDendriticcellMonocyte:CD14Monocyte:CD16T-cell:CD4:naiveT-cell:CD4:memoryT-cell:CD8:naiveT-cell:CD8:cytotoxicNKcellB-cellDendriticcellMonocyte:CD14Monocyte:CD16Laboratory for Genome Information AnalysisTeam Leader: Chung-Chau Hon
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