文章标题：Integrated transcriptomics and epigenomics reveal chamber-specific and species-specific characteristics of human and mouse hearts
获取地址：https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001229
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PLoS Biol 2021 May 18;19(5):e3001229. doi: 10.1371/journal.pbio.3001229. eCollection 2021 May.
参考测序中国公众号的报道：https://mp.weixin.qq.com/s/_7h2M8XaqSqxY-PvCJiLKQ

Abstract

DNA methylation, chromatin accessibility, and gene expression represent different levels information in biological process, but a comprehensive multiomics analysis of the mammalian heart is lacking. Here, we applied nucleosome occupancy and methylome sequencing(NOMe-seq), which detected DNA methylation and chromatin accessibility simultaneously, as well as RNA-seq, for multiomics analysis of the 4 chambers of adult and fetal human hearts, and adult mouse hearts.
Our results showed conserved region-specific patterns in the mammalian heart at transcriptome and DNA methylation level. Adult and fetal human hearts showed distinct features in DNA methylome, chromatin accessibility, and transcriptome. Novel long noncoding RNAs were identified in the human heart, and the gene expression profiles of major cardiovascular diseases associated genes were displayed. Furthermore, cross-species comparisons revealed human-specific and mouse-specific differentially expressed genes between the atria and ventricles. We also reported the relationship among multiomics and found there was a bell-shaped relationship between gene-body methylation and expression in the human heart. In general, our study provided comprehensive spatiotemporal and evolutionary insights into the regulation of gene expression in the heart.
【DNA甲基化、染色质可及性和基因表达代表了生物过程中不同水平的信息，但目前缺乏对哺乳动物心脏的全面的多组学分析。在这里，我们应用核小体占用和甲基组测序，同时检测DNA甲基化和染色质可及性，以及RNA-seq，对成人、胎儿心脏和成年小鼠心脏的4个心室进行多组学分析。
我们的研究结果显示了哺乳动物心脏在转录组和DNA甲基化水平上的保守区域特异性模式。成人和胎儿心脏在DNA甲基组、染色质可及性和转录组方面表现出明显的特征。在人类心脏中发现了新的长链非编码rna，并显示了主要心血管疾病相关基因的表达谱。此外，跨物种比较揭示了人类特异性和小鼠特异性心房和心室之间的差异表达基因。我们还报道了多组学之间的关系，并发现基因体甲基化与人类心脏表达之间存在钟形关系。总之，我们的研究为心脏基因表达调控提供了全面的时空和进化视角。】
测序技术：NOMe-seq and RNA-seq

Methods

Data Availability

The authors confirm that all data underlying the findings are fully available without restriction. The raw NOMe-seq and RNA-seq data of human have been deposited in Genome Sequence Archive (GSA) for Human under the accession code HRA000365. The raw NOMe-seq and RNA-seq data of mouse have been deposited in GSA under CRA003798. The processed NOMe-seq data of human have been deposited in OMix (https://bigd.big.ac.cn/omix/) under the ID OMIX247, and the processed RNA-seq data of human and BAM files of 176 novel lncRNAs have been deposited in OMix under OMIX243. The processed NOMe-seq and RNA-seq data of mouse have been deposited in OMix under OMIX245 and OMIX242, respectively. All data mentioned above can be accessed in GSA under BioProject ID PRJCA003611.