Inferring causal relationships among histone modifications in exon skipping event

IF 4.2 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Methods Pub Date : 2024-11-09 DOI:10.1016/j.ymeth.2024.11.008

Pengmian Feng , Yuanfang Tian , Wei Chen

引用次数: 0

Abstract

Alternative splicing is a crucial process of gene expression. Over 90% multi-exonic genes in human genome undergo alternative splicing. Although the splicing code has been proposed, it still couldn’t satisfactorily explain the tissue-specific alternative splicing. Results of co-transcriptional RNA processing analysis demonstrated that, except for trans- and cis-acting elements, histone modifications also play a role in alternative splicing. In the present work, we analyzed the associations among 27 kinds of histone modifications in H1 human embryonic stem cell. In order to illustrate the casual relationships between histone modification and alternative splicing, we built the Bayesian network and validated its robustness by using cross validation test. In addition to the combinatorial patterns, distinct histone modification patterns were also observed in the alternative spliced exons and surrounding intron regions, indicating that histone modifications could substantially mark alternative splicing.

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推断外显子缺失事件中组蛋白修饰的因果关系

替代剪接是基因表达的关键过程。人类基因组中 90% 以上的多外显子基因都会发生替代剪接。虽然有人提出了剪接密码，但仍无法令人满意地解释组织特异性的替代剪接。共转录 RNA 处理分析结果表明，除了反式和顺式作用元件外，组蛋白修饰也在替代剪接中发挥作用。在本研究中，我们分析了 H1 人类胚胎干细胞中 27 种组蛋白修饰之间的关联。为了说明组蛋白修饰与替代剪接之间的偶然关系，我们建立了贝叶斯网络，并通过交叉验证测试验证了其稳健性。除了组合模式外，在替代剪接的外显子和周围的内含子区域也观察到了不同的组蛋白修饰模式，这表明组蛋白修饰可以在很大程度上标记替代剪接。

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

Methods 生物-生化研究方法

CiteScore

9.80

自引率

2.10%

发文量

222

审稿时长

11.3 weeks

期刊介绍： Methods focuses on rapidly developing techniques in the experimental biological and medical sciences. Each topical issue, organized by a guest editor who is an expert in the area covered, consists solely of invited quality articles by specialist authors, many of them reviews. Issues are devoted to specific technical approaches with emphasis on clear detailed descriptions of protocols that allow them to be reproduced easily. The background information provided enables researchers to understand the principles underlying the methods; other helpful sections include comparisons of alternative methods giving the advantages and disadvantages of particular methods, guidance on avoiding potential pitfalls, and suggestions for troubleshooting.