Epigenomics and transcriptomics profiles of developing zebrafish heart cells.

IF 6.9 2区综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES

Scientific Data Pub Date : 2025-10-07 DOI:10.1038/s41597-025-05895-9

Gulrez Chahal, Michael P Eichenlaub, Markus Tondl, Michał Pawlak, Monika Mohenska, Lin Grimm, Lauren Bottrell, Mark Drvodelic, Sara Alaei, Jeannette Hallab, Lisa N Waylen, Jose M Polo, Cédric Blanpain, Nathan Palpant, Fernando J Rossello, Minna-Liisa Änkö, Peter D Currie, Benjamin M Hogan, Cecilia Winata, Ekaterina Salimova, Hieu T Nim, Mirana Ramialison

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引用次数: 0

Abstract

cis-Regulatory elements (cREs) are essential for the spatio-temporal control of gene expression during development and disease. However, cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell-types, predominantly cardiomyocytes. Therefore, cardiomyocyte-specific modelling is required to understand the cis-regulation of the developing heart. Zebrafish are an ideal model to study heart development, as they share several physiological features with the human heart during cardiogenesis. Here, we present a comprehensive cardiomyocyte-specific repertoire of cREs isolated from zebrafish larvae. This data combines in vivo transcriptomics and epigenetic profiling, providing insights into cREs and their associated genes involved in heart development. We further perform transgenic reporter assays for the identified cREs associated with popdc2 and bmp10 genes, validating these genomic regions as cardiac regulatory elements. We share this comprehensive, reproducible cardiomyocyte-specific cREs resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects.

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发育中的斑马鱼心脏细胞的表观基因组学和转录组学分析。

顺式调控元件（cREs）在发育和疾病过程中对基因表达的时空调控至关重要。然而，cRE活性高度依赖于细胞和组织类型。发育中的心脏由几种细胞类型组成，主要是心肌细胞。因此，需要心肌细胞特异性建模来了解发育中的心脏的顺式调节。斑马鱼是研究心脏发育的理想模型，因为它们在心脏发生过程中具有与人类心脏相同的一些生理特征。在这里，我们提出了从斑马鱼幼虫中分离的全面的心肌细胞特异性cre库。这些数据结合了体内转录组学和表观遗传分析，为cre及其参与心脏发育的相关基因提供了见解。我们进一步对鉴定出的与popdc2和bmp10基因相关的cre进行了转基因报告基因检测，验证了这些基因组区域是心脏调控元件。我们分享这个全面的、可重复的心肌细胞特异性cre资源，作为一个可查询的网络工具，以了解心脏发育和先天性心脏缺陷出现的表观遗传和转录组机制。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Scientific Data Social Sciences-Education

CiteScore

11.20

自引率

4.10%

发文量

689

审稿时长

16 weeks

期刊介绍： Scientific Data is an open-access journal focused on data, publishing descriptions of research datasets and articles on data sharing across natural sciences, medicine, engineering, and social sciences. Its goal is to enhance the sharing and reuse of scientific data, encourage broader data sharing, and acknowledge those who share their data. The journal primarily publishes Data Descriptors, which offer detailed descriptions of research datasets, including data collection methods and technical analyses validating data quality. These descriptors aim to facilitate data reuse rather than testing hypotheses or presenting new interpretations, methods, or in-depth analyses.