Fernanda M Bosada1, Jia Liu2,3, Antoine A F de Vries2,3, Vincent M Christoffels1, Antoinette F van Ouwerkerk1, Juan Zhang2,3, Karel van Duijvenboden1, Mark Chaffin4, Nathan R Tucker4,5, Daniel Pijnappels2,3, Patrick T Ellinor4,5, Phil Barnett1. 1. From the Department of Medical Biology, Amsterdam University Medical Centers, Academic Medical Center, the Netherlands (A.F.v.O., F.M.B., K.v.D., P.B., V.M.C.). 2. Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, the Netherlands (J.L., J.Z., D.P., A.A.F.d.V.). 3. Netherlands Heart Institute, Holland Heart House, Utrecht (J.L., J.Z., D.P., A.A.F.d.V.). 4. Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA (M.C., N.R.T., P.T.E.). 5. Cardiovascular Research Center, Massachusetts General Hospital, Boston (N.R.T., P.T.E.).
Abstract
RATIONALE: Genome-wide association studies have identified a large number of common variants (single-nucleotide polymorphisms) associated with atrial fibrillation (AF). These variants are located mainly in noncoding regions of the genome and likely include variants that modulate the function of transcriptional regulatory elements (REs) such as enhancers. However, the actual REs modulated by variants and the target genes of such REs remain to be identified. Thus, the biological mechanisms by which genetic variation promotes AF has thus far remained largely unexplored. OBJECTIVE: To identify REs in genome-wide association study loci that are influenced by AF-associated variants. METHODS AND RESULTS: We screened 2.45 Mbp of human genomic DNA containing 12 strongly AF-associated loci for RE activity using self-transcribing active regulatory region sequencing and a recently generated monoclonal line of conditionally immortalized rat atrial myocytes. We identified 444 potential REs, 55 of which contain AF-associated variants (P<10-8). Subsequently, using an adaptation of the self-transcribing active regulatory region sequencing approach, we identified 24 variant REs with allele-specific regulatory activity. By mining available chromatin conformation data, the possible target genes of these REs were mapped. To define the physiological function and target genes of such REs, we deleted the orthologue of an RE containing noncoding variants in the Hcn4 (potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4) locus of the mouse genome. Mice heterozygous for the RE deletion showed bradycardia, sinus node dysfunction, and selective loss of Hcn4 expression. CONCLUSIONS: We have identified REs at multiple genetic loci for AF and found that loss of an RE at the HCN4 locus results in sinus node dysfunction and reduced gene expression. Our approach can be broadly applied to facilitate the identification of human disease-relevant REs and target genes at cardiovascular genome-wide association studies loci.
RATIONALE: Genome-wide association studies have identified a large number of common variants (single-nucleotide polymorphisms) associated with atrial fibrillation (AF). These variants are located mainly in noncoding regions of the genome and likely include variants that modulate the function of transcriptional regulatory elements (REs) such as enhancers. However, the actual REs modulated by variants and the target genes of such REs remain to be identified. Thus, the biological mechanisms by which genetic variation promotes AF has thus far remained largely unexplored. OBJECTIVE: To identify REs in genome-wide association study loci that are influenced by AF-associated variants. METHODS AND RESULTS: We screened 2.45 Mbp of human genomic DNA containing 12 strongly AF-associated loci for RE activity using self-transcribing active regulatory region sequencing and a recently generated monoclonal line of conditionally immortalized rat atrial myocytes. We identified 444 potential REs, 55 of which contain AF-associated variants (P<10-8). Subsequently, using an adaptation of the self-transcribing active regulatory region sequencing approach, we identified 24 variant REs with allele-specific regulatory activity. By mining available chromatin conformation data, the possible target genes of these REs were mapped. To define the physiological function and target genes of such REs, we deleted the orthologue of an RE containing noncoding variants in the Hcn4 (potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4) locus of the mouse genome. Mice heterozygous for the RE deletion showed bradycardia, sinus node dysfunction, and selective loss of Hcn4 expression. CONCLUSIONS: We have identified REs at multiple genetic loci for AF and found that loss of an RE at the HCN4 locus results in sinus node dysfunction and reduced gene expression. Our approach can be broadly applied to facilitate the identification of human disease-relevant REs and target genes at cardiovascular genome-wide association studies loci.
Authors: Jeffrey D Steimle; Francisco J Grisanti Canozo; Minjun Park; Zachary A Kadow; Md Abul Hassan Samee; James F Martin Journal: JCI Insight Date: 2022-06-08
Authors: Ravi Mandla; Hongmei Ruan; Giselle Galang; Catherine Jung; Tanvi Sinha; Nicole R Stone; Roland S Wu; Brandon J Mannion; Prasanna K R Allu; Kevin Chang; Ashwin Rammohan; Marie B Shi; Len A Pennacchio; Brian L Black; Vasanth Vedantham Journal: Circ Res Date: 2020-10-12 Impact factor: 17.367
Authors: Chukwuemeka G Anene-Nzelu; Mick C J Lee; Wilson L W Tan; Albert Dashi; Roger S Y Foo Journal: Nat Rev Cardiol Date: 2021-08-11 Impact factor: 32.419
Authors: Jasmeet S Reyat; Winnie Chua; Victor R Cardoso; Anika Witten; Peter M Kastner; S Nashitha Kabir; Moritz F Sinner; Robin Wesselink; Andrew P Holmes; Davor Pavlovic; Monika Stoll; Stefan Kääb; Georgios V Gkoutos; Joris R de Groot; Paulus Kirchhof; Larissa Fabritz Journal: JCI Insight Date: 2020-08-20