Chera Alexandra, Stancu-Cretu Mircea, Zabet Nicolae Radu, Bucur Octavian
Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.
Carol Davila Nephrology Clinical Hospital, Bucharest, Romania.
Epigenetics Chromatin. 2024 Dec 30;17(1):39. doi: 10.1186/s13072-024-00558-2.
DNA methylation is an essential epigenetic mechanism for regulation of gene expression, through which many physiological (X-chromosome inactivation, genetic imprinting, chromatin structure and miRNA regulation, genome defense, silencing of transposable elements) and pathological processes (cancer and repetitive sequences-associated diseases) are regulated. Nanopore sequencing has emerged as a novel technique that can analyze long strands of DNA (long-read sequencing) without chemically treating the DNA. Interestingly, nanopore sequencing can also extract epigenetic status of the nucleotides (including both 5-Methylcytosine and 5-hydroxyMethylcytosine), and a large variety of bioinformatic tools have been developed for improving its detection properties. Out of all genomic regions, long read sequencing provides advantages in studying repetitive elements, which are difficult to characterize through other sequencing methods. Transposable elements are repetitive regions of the genome that are silenced and usually display high levels of DNA methylation. Their demethylation and activation have been observed in many cancers. Due to their repetitive nature, it is challenging to accurately estimate DNA methylation levels within transposable elements using short sequencing technologies. The advantage to sequence native DNA (without PCR amplification biases or harsh bisulfite treatment) and long and ultra long reads coupled with epigenetic states of the DNA allows to accurately estimate DNA methylation levels in transposable elements. This is a big step forward for epigenomic studies, and unsolved questions regarding gene expression and transposable elements silencing through DNA methylation can now be answered.
DNA甲基化是一种用于调控基因表达的重要表观遗传机制，通过该机制可调控许多生理过程（X染色体失活、基因印记、染色质结构和微小RNA调控、基因组防御、转座元件沉默）和病理过程（癌症及与重复序列相关的疾病）。纳米孔测序已成为一种新技术，它无需对DNA进行化学处理就能分析长链DNA（长读长测序）。有趣的是，纳米孔测序还能提取核苷酸的表观遗传状态（包括5-甲基胞嘧啶和5-羟甲基胞嘧啶），并且已经开发出了各种各样的生物信息学工具来改善其检测特性。在所有基因组区域中，长读长测序在研究重复元件方面具有优势，而通过其他测序方法很难对这些重复元件进行表征。转座元件是基因组中的重复区域，它们处于沉默状态，通常呈现高水平的DNA甲基化。在许多癌症中都观察到了它们的去甲基化和激活。由于其重复性质，使用短测序技术准确估计转座元件内的DNA甲基化水平具有挑战性。对天然DNA进行测序（无PCR扩增偏差或苛刻的亚硫酸氢盐处理）以及长读长和超长读长结合DNA的表观遗传状态，能够准确估计转座元件中的DNA甲基化水平。这是表观基因组学研究向前迈出的一大步，现在可以回答有关通过DNA甲基化实现基因表达和转座元件沉默的未解决问题。
