Fish-Ing for Enhancers in the Heart

Identification and regulation of a novel leptin receptor-linked enhancer during zebrafish ventricle regeneration

AIMS

Vertebrates vary greatly in their abilities to regenerate injured hearts. Zebrafish possess a remarkable capacity for cardiac regeneration, making them an excellent model for regeneration research. Recent studies have reported the activation and underlying regulatory mechanisms of leptin b (lepb) and the leptin b-linked enhancer (LEN) in injured hearts. However, the regenerative response activity of the leptin receptor (lepr) and its regulatory mechanisms still warrant further exploration.

MATERIALS AND METHODS

We identified a novel lepr-linked enhancer (leprEnh) and generated a stable transgenic zebrafish line for validation. We also employed a genetic ventricle ablation system to elucidate the mechanisms governing its activation. Immunofluorescence, in situ hybridization and confocal imaging of larvae treated with various inhibitors during ventricle regeneration were performed.

KEY FINDINGS

Our results revealed that both lepr expression and leprEnh-directed EGFP fluorescence were weakly expressed in the ventricle during early heart development but displayed a sharp increase after ventricle ablation. Strong injury response activity was also observed in the atrium. Furthermore, the regeneration-responsive activity was attenuated by hemodynamic force alteration and was modulated by Notch, ErbB2 and BMP signaling pathways.

SIGNIFICANCE

Our study sheds light on the regulation of lepr and leprEnh during heart regeneration and provide a basis for screening for novel therapeutic targets for myocardial infarction.

The combinatorial binding syntax of transcription factors in forebrain-specific enhancers

Tissue-specific gene regulation in mammals involves the coordinated binding of multiple transcription factors (TFs). Using the forebrain as a model, we investigated the syntax of TF occupancy to determine tissue-specific enhancer regions. We analyzed forebrain-exclusive enhancers from the VISTA Enhancer Browser and a curated set of 23 TFs relevant to forebrain development and disease. Our findings revealed multiple distinct patterns of combinatorial TF binding, with the HES5-FOXP2-GATA3 triad being the most frequent in forebrain-specific enhancers. This syntactic structure was detected in 2614 enhancers from a genome-wide catalog of 25,000 predicted human forebrain enhancers. Notably, this catalog represents a computationally predicted dataset, distinct from the in vivo validated set of enhancers obtained from the VISTA Enhancer Browser. The shortlisted 2614 enhancers were further analyzed using genome-wide epigenetic data and evaluated for evolutionary conservation and disease relevance. Our findings highlight the value of these 2614 enhancers in forebrain-specific gene regulation and provide a framework for discovering tissue-specific enhancers, enhancing the understanding of enhancer function.

Troponin C gene mutations on cardiac muscle cell and skeletal Regulation: A comprehensive review

BACKGROUND

The troponin complex plays a crucial role in regulating skeletal and cardiac contraction. Congenital myopathies can occur due to several mutations in genes that encode skeletal troponin. Moreover, there is limited information regarding the composition of skeletal troponin. This review specifically examines a comprehensive review of the TNNC gene mutations on cardiac and skeletal regulations.

MAIN BODY

Troponin C (TNNC) has been linked to a newly discovered inherited muscle disorder. Genetic variations in genes that encode skeletal troponin can impair the function of sarcomeres. Various treatment approaches have been employed to mitigate the impact of variations, including the use of troponin activators, the injection of wild-type protein via AAV gene therapy, and myosin modification to enhance muscle contraction. The processes responsible for the pathophysiological implications of the variations in genes that encode skeletal troponin are not fully understood.

CONCLUSION

This comprehensive review will contribute to the understanding of the relationship between human cardiomyopathy and TNNC mutations and will guide the development of therapy approaches.

Identification and Copy Number Variant Analysis of Enhancer Regions of Genes Causing Spinocerebellar Ataxia

Currently, routine diagnostics for spinocerebellar ataxia (SCA) look for polyQ repeat expansions and conventional variations affecting the proteins encoded by known SCA genes. However, ~40% of the patients still remain without a genetic diagnosis after routine tests. Increasing evidence suggests that variations in the enhancer regions of genes involved in neurodegenerative disorders can also cause disease. Since the enhancers of SCA genes are not yet known, it remains to be determined whether variations in these regions are a cause of SCA. In this pilot project, we aimed to identify the enhancers of the SCA genes ATXN1, ATXN3, TBP and ITPR1 in the human cerebellum using 4C-seq, publicly available datasets, reciprocal 4C-seq, and luciferase assays. We then screened these enhancers for copy number variants (CNVs) in a cohort of genetically undiagnosed SCA patients. We identified two active enhancers for each of the four SCA genes. CNV analysis did not reveal any CNVs in the enhancers of the four SCA genes in the genetically undiagnosed SCA patients. However, in one patient, we noted a CNV deletion with an unknown clinical significance near one of the ITPR1 enhancers. These results not only reveal elements involved in SCA gene regulation but can also lead to the discovery of novel SCA-causing genetic variants. As enhancer variations are being increasingly recognized as a cause of brain disorders, screening the enhancers of ATXN1, ATXN3, TBP and ITPR1 for variations other than CNVs and identifying and screening enhancers of other SCA genes might elucidate the genetic cause in undiagnosed patients.

Exposure to tris (1,3-dichloro-2-propyl) phosphate affects the embryonic cardiac development of Oryzias melastigma

Tris (1,3-dichloro-2-propyl) phosphate (TDCPP) is a growing concern and may be a potential risk to marine environmental health due to its widespread usage and distribution. However, the toxic effects of TDCPP on cardiac development in marine fish have not been reported. In this study, Oryzias melastigma embryos were exposed to TDCPP at doses of 0, 0.04, 0.4, 4 and 40 μg/L from early embryogenesis to 10 days postfertilization (dpf). Then, the heart rate and sinus venosus-bulbus arteriosus (SV-BA) distance of the exposed embryos were measured at 5, 6, 8 and 10 dpf. Furthermore, alterations in the mRNA levels of the genes encoding cyclooxygenase-2 (COX-2), bone morphogenetic protein 4 (BMP4), fibroblast growth factor 8 (FGF8), and GATA-binding protein 4 (GATA4) were evaluated at 5, 6, 8 and 10 dpf. We found that the heart rate significantly increased in all TDCPP exposure groups at 10 dpf. The SV-BA distance significantly decreased in all TDCPP exposure groups at all developmental stages (except for the 0.4 μg/L group at 5 dpf and the 4 μg/L group at 10 dpf). The mRNA expression of COX-2 was downregulated at 5 dpf, BMP4 was downregulated at 5 and 6 dpf, FGF8 was downregulated at 5, 6 and 8 dpf, GATA4 was downregulated at 8 dpf, and GATA4 was upregulated at 10 dpf. These results indicate that the changes in heart rate and SV-BA distance might be accompanied by disturbances in the four genes involved in cardiac development. Our findings will help to illustrate the possible cardiac toxic effects of marine fish exposed to TDCPP.

Identification of ancestral gnathostome Gli3 enhancers with activity in mammals

Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15-21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. These results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.

Advances in Cardiac Development and Regeneration Using Zebrafish as a Model System for High-Throughput Research

Heart disease is the leading cause of death in the United States and worldwide. Understanding the molecular mechanisms of cardiac development and regeneration will improve diagnostic and therapeutic interventions against heart disease. In this direction, zebrafish is an excellent model because several processes of zebrafish heart development are largely conserved in humans, and zebrafish has several advantages as a model organism. Zebrafish transcriptomic profiles undergo alterations during different stages of cardiac development and regeneration which are revealed by RNA-sequencing. ChIP-sequencing has detected genome-wide occupancy of histone post-translational modifications that epigenetically regulate gene expression and identified a locus with enhancer-like characteristics. ATAC-sequencing has identified active enhancers in cardiac progenitor cells during early developmental stages which overlap with occupancy of histone modifications of active transcription as determined by ChIP-sequencing. CRISPR-mediated editing of the zebrafish genome shows how chromatin modifiers and DNA-binding proteins regulate heart development, in association with crucial signaling pathways. Hence, more studies in this direction are essential to improve human health because they answer fundamental questions on cardiac development and regeneration, their differences, and why zebrafish hearts regenerate upon injury, unlike humans. This review focuses on some of the latest studies using state-of-the-art technology enabled by the elegant yet simple zebrafish.