Epigenomic and Transcriptomic Dynamics During Human Heart Organogenesis

Abstract

Rationale: There is growing evidence that common variants and rare sequence alterations in regulatory sequences can result in birth defects or predisposition to disease. Congenital heart defects (CHDs) are the most common birth defect and have a clear genetic component, yet only a third of cases can be attributed to structural variation in the genome or a mutation in a gene. The remaining unknown cases could be caused by alterations in regulatory sequences. Objective: Identify regulatory sequences and gene expression networks that are active during organogenesis of the human heart. Determine if these sites and networks are enriched for disease relevant genes and associated genetic variation. Methods and Results: We characterized chromatin state and gene expression dynamics during human heart organogenesis. We profiled seven histone modifications in embryonic hearts from each of nine distinct Carnegie stages (CS13-14, CS16-21, and CS23), annotated chromatin states, and compared these maps to over 100 human tissues and cell types. We also generated RNA-seq data, performed differential expression, and constructed weighted gene co-expression networks. We identified 177,412 heart enhancers, 12,395 had not been previously annotated as strong enhancers. We identified 92% of all functionally validated heart positive enhancers (n=281, 7.5x enrichment, p<2.2x10 -16 ). Integration of these data demonstrated novel heart enhancers are enriched near genes expressed more strongly in cardiac tissue and are enriched for variants associated with electrocardiogram measures and atrial fibrillation. Our gene expression network analysis identified gene modules strongly enriched for heart related functions, regulatory control by heart specific enhancers, and putative disease genes. Conclusions: Well-connected "hub" genes with heart-specific expression targeted by embryonic heart-specific enhancers are likely disease candidates. Our functional annotations will allow for better interpretation of whole genome sequencing data in the large number of patients affected by CHDs.

Mending a broken heart: In vitro, in vivo and in silico models of congenital heart disease

“…Genetic variants at such non-coding regulatory sequences might influence the presentation of complex disorders by influencing chromatin accessibility, histone modifications, and downstream consequences of chromatin remodeling and gene expression (Table 3). Cardiac epigenomic maps have been generated for human and rodent hearts (Preissl et al, 2015;VanOudenhove et al, 2020), but only little is known about how specific histone modifications contribute to individual CHD phenotypes. Our understanding of epigenetic enhancer-promoter regulation of cardiogenesis has recently advanced with the development of genome-wide association studies (GWAS) and chromatin quantitative trait loci (chQTL; Box 1) analyses, elucidated by the epigenetic profiling of specific tissues, and by chromosome conformation capture (3C) and its derivatives (4C, Hi-C and HiChIP) that profile the spatial interaction of loci within and between chromosomes.…”

Heart Enhancers: Development and Disease Control at a Distance

“…(More putative variants were identified other than these five representative ones) Kapoor et al, 2019 This mode of gene regulation can recruit transcriptional machinery from cell-lineage genes in a process known as cofactor squelching (Schmidt et al, 2015(Schmidt et al, , 2016. Indeed a detailed knowledge of acute and chronic inflammatory enhancer biology during heart development and disease is essential and integrating this information with emerging compendiums of heart epigenomic data (such as Vanoudenhove et al, 2020) will be valuable. Integrating enhancer information into the functional annotation of non-coding variants is no doubt a powerful approach; however, it should be noted that disrupting enhancer activities is not the only mechanism underlying the pathological consequences of non-coding variants.…”

“…To study cardiac enhancer dynamics across multiple stages of in vitro cardiac differentiation or in vivo development, several studies from individual labs as well as consortiums, have utilized robust genome-wide assays that do not rely on mapping specific transcription factors, namely ChIP-seq for histone modifications ( Paige et al, 2012 ; Wamstad et al, 2012 ; Nord et al, 2013 ; Vanoudenhove et al, 2020 ), and DNase-seq and ATAC-seq for chromatin accessibility ( Bertero et al, 2019 ; Gorkin et al, 2020 ; Meuleman et al, 2020 ). These studies revealed highly dynamic chromatin states accompanying cardiac differentiation and development.…”

“…Since the heart is the first organ formed in embryogenesis, the embryonic stage that is required to capture the initial phase of cardiogenesis is especially early in development, and is likely during early gastrulation ( Scott, 2012 ; Devine et al, 2014 ; Lescroart et al, 2014 ). Though heart enhancers have been extensively characterized across many developmental stages in various species [such as Nord et al (2013) and Vanoudenhove et al (2020) and many others in Tables 3 – 5 ], there is a paucity of datasets that characterize enhancers active at the initial stage of vertebrate heart development, such as the transition from mesoderm progenitors to cardiac lineages. The majority of in vivo studies in vertebrates used relatively mature cardiac samples, including embryonic hearts with defined chamber structures (e.g., E10.5 and onward in mice) or postnatal heart tissues ( Tables 3 – 5 ).…”

“…This mode of gene regulation can recruit transcriptional machinery from cell-lineage genes in a process known as cofactor squelching ( Schmidt et al, 2015 , 2016 ). Indeed a detailed knowledge of acute and chronic inflammatory enhancer biology during heart development and disease is essential and integrating this information with emerging compendiums of heart epigenomic data (such as Vanoudenhove et al, 2020 ) will be valuable.…”