非编码 886(nc886/vtRNA2-1),表观遗传学的怪鸭--对未来研究的启示。

IF 2.9 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Epigenetics Pub Date : 2024-12-01 Epub Date: 2024-03-25 DOI:10.1080/15592294.2024.2332819
Emma Raitoharju, Sonja Rajić, Saara Marttila
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引用次数: 0

摘要

非编码 886(nc886,vtRNA2-1)是人类唯一的多态印记基因,其甲基化状态不是由遗传决定的。有关甲基化模式的建立、稳定性和后果,以及从该基因座转录的 nc886 RNA 的性质和功能的现有文献相互矛盾。例如,据报道,该基因座的甲基化状态在整个生命过程和不同的体细胞组织中都是稳定的,但也容易受到环境的影响。产生的 nc886 RNA 的性质已被多次重新定义,据报道,这些 RNA 在致癌过程中的作用相互矛盾。此外,由于 nc886 位点的双峰甲基化模式,传统的全基因组甲基化分析可能会导致假阳性结果,尤其是在较小的数据集中。在此,我们旨在总结有关 nc886 的现有文献,讨论 nc886 的特征如何导致相互矛盾的结果,并重新解释、分析和尽可能复制现有文献中的结果。我们还介绍了关于 nc886 甲基化模式的分布如何与人口的地理来源相关联的新发现,并描述了多种人类肿瘤中的甲基化变化。通过这个特殊基因位点和 RNA 的例子,我们旨在强调 DNA 甲基化和非编码 RNA 分析中的一般问题,并就未来分析中应考虑的因素提出我们的建议。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Non-coding 886 (nc886/vtRNA2-1), the epigenetic odd duck - implications for future studies.

Non-coding 886 (nc886, vtRNA2-1) is the only human polymorphically imprinted gene, in which the methylation status is not determined by genetics. Existing literature regarding the establishment, stability and consequences of the methylation pattern, as well as the nature and function of the nc886 RNAs transcribed from the locus, are contradictory. For example, the methylation status of the locus has been reported to be stable through life and across somatic tissues, but also susceptible to environmental effects. The nature of the produced nc886 RNA(s) has been redefined multiple times, and in carcinogenesis, these RNAs have been reported to have conflicting roles. In addition, due to the bimodal methylation pattern of the nc886 locus, traditional genome-wide methylation analyses can lead to false-positive results, especially in smaller datasets. Herein, we aim to summarize the existing literature regarding nc886, discuss how the characteristics of nc886 give rise to contradictory results, as well as to reinterpret, reanalyse and, where possible, replicate the results presented in the current literature. We also introduce novel findings on how the distribution of the nc886 methylation pattern is associated with the geographical origins of the population and describe the methylation changes in a large variety of human tumours. Through the example of this one peculiar genetic locus and RNA, we aim to highlight issues in the analysis of DNA methylation and non-coding RNAs in general and offer our suggestions for what should be taken into consideration in future analyses.

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来源期刊
Epigenetics
Epigenetics 生物-生化与分子生物学
CiteScore
6.80
自引率
2.70%
发文量
82
审稿时长
3-8 weeks
期刊介绍: Epigenetics publishes peer-reviewed original research and review articles that provide an unprecedented forum where epigenetic mechanisms and their role in diverse biological processes can be revealed, shared, and discussed. Epigenetics research studies heritable changes in gene expression caused by mechanisms others than the modification of the DNA sequence. Epigenetics therefore plays critical roles in a variety of biological systems, diseases, and disciplines. Topics of interest include (but are not limited to): DNA methylation Nucleosome positioning and modification Gene silencing Imprinting Nuclear reprogramming Chromatin remodeling Non-coding RNA Non-histone chromosomal elements Dosage compensation Nuclear organization Epigenetic therapy and diagnostics Nutrition and environmental epigenetics Cancer epigenetics Neuroepigenetics
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