Altered Enhancer and Promoter Usage Leads to Differential Gene Expression in the Normal and Failed Human Heart

Abstract

Background: The failing heart is characterized by changes in gene expression. However, the regulatory regions of the genome that drive these gene expression changes have not been well defined in human hearts. Methods: To define genome-wide enhancer and promoter use in heart failure, cap analysis of gene expression sequencing was applied to 3 healthy and 4 failed human hearts to identify promoter and enhancer regions used in left ventricles. Healthy hearts were derived from donors unused for transplantation and failed hearts were obtained as discarded tissue after transplantation. Results: Cap analysis of gene expression sequencing identified a combined potential for ≈23 000 promoters and ≈5000 enhancers active in human left ventricles. Of these, 17 000 promoters and 1800 enhancers had additional support for their regulatory function. Comparing promoter usage between healthy and failed hearts highlighted promoter shifts which altered aminoterminal protein sequences. Enhancer usage between healthy and failed hearts identified a majority of differentially used heart failure enhancers were intronic and primarily localized within the first intron, revealing this position as a common feature associated with tissue-specific gene expression changes in the heart. Conclusions: This data set defines the dynamic genomic regulatory landscape underlying heart failure and serves as an important resource for understanding genetic contributions to cardiac dysfunction. Additionally, regulatory changes contributing to heart failure are attractive therapeutic targets for controlling ventricular remodeling and clinical progression.

An atlas of transcribed human cardiac promoters and enhancers reveals an important role of regulatory elements in heart failure

“…Deeper sequencing allowed the identi cation of regulatory elements with low expression levels involved in cell maintenance and embryogenesis. We con rmed the presence of over 17,000 promoters, and due to deeper sequencing and larger sample size, we detected an order of magnitude more enhancers, ~14,000 current state of knowledge in this eld 12 . We developed a robust classi cation pipeline and identi ed over 3,000 novel regulatory regions not present in the FANTOM5 database and not described in other studies.…”

“…Comparing healthy to failing hearts, annotation of the top differentially expressed clusters revealed enrichment in embryonic processes enrichment suggesting a shift in gene expression due to re-expression of developmental genes in heart failure 12 , which are generally silent in the adult heart. To further understand the shift of regulatory elements in heart failure, we compared healthy to ischemic and non-ischemic cardiomyopathy samples.…”

“…Libraries appeared saturated at the level of 1-2 million reads. Despite the saturation, deeper sequencing may still uncover the activity of low expressed genes and pseudogenes, including snRNA related to RNA transport and mRNA splicing 12 .…”

Alternative Transcription Start Site Usage and Functional Implications in Pathogenic Fungi

“…In mammals, usage of alternative splicing (aSpl),) alternative TSSs (aTSSs), and alternative Poly(A) sites (aPAS) is prominent [ 25 , 26 , 27 , 28 , 29 ]. These processes are developmentally regulated [ 30 ], and defects in these processes are associated with a number of genetic diseases, such as thalassemia, retinitis pigmentosa, heart failure, and various types of cancer [ 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. Interestingly, quantitative analysis of TSS usage suggested that aTSS and aPAS usage represents a major source of transcript isoform diversity in human tissues [ 39 ].…”

Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy

“…7 To identify the potential CREs in human failing hearts, cap analysis of gene expression sequencing was performed in 3 healthy and 4 failed human left ventricles to map the initiation sites of both capped coding and noncoding RNAs. 8 That study identified the transcribing promoters and the first intronic enhancer in failed ventricles but most distal enhancers (eg, intergenic enhancers) in heart failure were not explored. By performing chromatin immunoprecipitation sequencing (ChIP-seq) for H3K27ac (acetylation of lysine 27 on histone H3; an active enhancer and promoter mark 9 ) in nonfailing and end-stage failing human heart tissues, a recent study identified specific enhancers and promoters implicated for established molecular pathways in heart failure.…”