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非编码 886 (/), 表观遗传的奇异鸟-对未来研究的启示。

Non-coding 886 (/), the epigenetic odd duck - implications for future studies.

机构信息

Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.

Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.

出版信息

Epigenetics. 2024 Dec;19(1):2332819. doi: 10.1080/15592294.2024.2332819. Epub 2024 Mar 25.

Abstract

Non-coding 886 (, ) 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 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 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 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 , discuss how the characteristics of 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 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.

摘要

非编码 886(,)是唯一具有人类多态性印记的基因,其甲基化状态不受遗传决定。关于该基因的甲基化模式的建立、稳定性和后果,以及从该基因座转录的 RNA 的性质和功能的现有文献是相互矛盾的。例如,该基因座的甲基化状态被报道在整个生命过程中和体组织中是稳定的,但也易受环境影响。产生的 RNA 的性质已经被多次重新定义,在癌症发生过程中,这些 RNA 被报道具有相互矛盾的作用。此外,由于 基因座的双峰甲基化模式,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。在此,我们旨在总结关于 的现有文献,讨论为什么该基因的特征会导致相互矛盾的结果,并重新解释、重新分析以及在可能的情况下复制当前文献中呈现的结果。我们还介绍了关于 甲基化模式的分布如何与人群的地理起源相关的新发现,并描述了多种人类肿瘤中的甲基化变化。通过这个特殊的遗传基因座和 RNA 的例子,我们旨在强调在 DNA 甲基化和非编码 RNA 分析中存在的问题,并为未来的分析提出应该考虑的建议。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/216e/10965113/15c802d3047c/KEPI_A_2332819_F0001_OC.jpg

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