Clin Res Cardiol (2023). https://doi.org/10.1007/s00392-023-02180-w

Identification and functional epigenetic modulation of regulatory elements in cardiac myocytes

P. Laurette1, C. Cao1, M. Schwaderer2, N. Díaz i Pedrosa1, R. Bednarz1, L. Weiss3, F. Rezende3, D. P. Ramanujam4, S. Engelhardt4, R. Gilsbach1

1Innere Medizin VIII, Institut für Experimentelle Kardiologie, Universitätsklinikum Heidelberg, Heidelberg; 2Institut für experimentelle und klinische Pharmakologie und Toxikologie, Albert- Ludwigs-Universität Freiburg, Freiburg im Breisgau; 3Institut für Kardiovaskuläre Physiologie, Universitätsklinikum Frankfurt, Frankfurt am Main; 4Institut für Pharmakologie und Toxikologie, Technische Universität München (TUM), München;

Epigenome studies in cardiac myocytes revealed dynamic establishment of active regulatory sites during development and disease (Gilsbach et al., Nat. commun. 2018). The aim of this project was to identify target promoters of distal regulatory sites associated with Gata4 in cardiac cells and examine their functional consequences. Extensive mapping of the murine cardiomyocyte epigenome (HL1 cells) and annotation of regulatory elements revealed that Gata4 binding is highly enriched on strong enhancers. We combined pooled CRISPR interference of these enhancers with single-cell transcriptome sequencing to dissect the activity of hundreds of these elements simultaneously. Integration of this data with Hi-ChIP confirmed that a large set of these enhancers display spatial and functional communication with their associated target genes. Among those, we identified a strong Gata4-bound enhancer on chr18, which physically interacts with the 320kb distant promoter of Gata6, a key cardiac transcription factor implicated in pathological cardiac hypertrophy. CRISPRi mediated perturbation of this enhancer induced a reduction in Gata6 expression, protein levels and genome-wide binding as well as more than 600 genes significantly associated with cardiovascular developmental and stress processes in vitro and in models of cardiac disease. In conclusion, this study mapped enhancer-promoter interactions in cardiac myocytes and showed that functional (epi)genetic-modulation of distal regulatory elements allows steering of key gene expression programs. Furthermore it underlines the importance of lineage-specific cis-regulatory elements at the crossroads of cardiac transcription factor networks in the regulation of the cardiac myocytes transcriptome and the prospect of connecting thousands of DNA variants and genetic risk factors with biological mechanisms of associated diseases.

https://dgk.org/kongress_programme/jt2023/aP1369.html