State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
Genet Sel Evol. 2022 Jul 27;54(1):54. doi: 10.1186/s12711-022-00745-3.
The porcine repetitive element 1 (PRE1) is the most abundant short interspersed nuclear element (SINE) in the Sus scrofa genome and it has been suggested that some PRE1 can have regulatory functions. The million copies of PRE1 in the porcine genome have accumulated abundant CpG dinucleotides and unique structural variations, such as direct repeats and patterns of sequence degeneration. The aims of this study were to analyse these structural variations to trace the origin and evolutionary pattern of PRE1 and to investigate potential methylation-related functions of PRE1 based on methylation patterns of PRE1 CpG dinucleotides in different tissues.
We investigated the evolutionary trajectory of PRE1 and found that PRE1 originated from the ancestral CHRS-S1 family through three main successive partial duplications. We found that the partial duplications and deletions of PRE1 were likely due to RNA splicing events during retrotransposition. Functionally, correlation analysis showed that the methylation levels of 103 and 261 proximal PRE1 were, respectively, negatively and positively correlated with the expression levels of neighboring genes (Spearman correlation, P < 0.01). Further epigenomic analysis revealed that, in the testis, demethylation of proximal PRE1 in the HORMAD1 and HACD3 genes had tissue-specific enhancer and promoter functions, while in the muscle, methylation of proximal PRE1 repeats in the TCEA3 gene had an enhancer function.
The characteristic sequences of PRE1 reflect unique patterns of origin and evolution and provide a structural basis for diverse regulatory functions.
猪重复元件 1（PRE1）是猪基因组中最丰富的短散布核元件（SINE），有人认为某些 PRE1 可能具有调节功能。猪基因组中的百万个 PRE1 积累了丰富的 CpG 二核苷酸和独特的结构变异，如直接重复和序列退化模式。本研究旨在分析这些结构变异，以追踪 PRE1 的起源和进化模式，并基于 PRE1 CpG 二核苷酸在不同组织中的甲基化模式研究 PRE1 潜在的甲基化相关功能。
我们研究了 PRE1 的进化轨迹，发现 PRE1 起源于祖先 CHRS-S1 家族，通过三次主要的连续部分重复。我们发现 PRE1 的部分重复和缺失可能是由于逆转座过程中的 RNA 剪接事件引起的。功能相关性分析表明，103 个和 261 个近端 PRE1 的甲基化水平分别与邻近基因的表达水平呈负相关和正相关（Spearman 相关性，P<0.01）。进一步的表观基因组学分析表明，在睾丸中，HORMAD1 和 HACD3 基因中近端 PRE1 的去甲基化具有组织特异性增强子和启动子功能，而在肌肉中，TCEA3 基因中近端 PRE1 重复的甲基化具有增强子功能。
PRE1 的特征序列反映了独特的起源和进化模式，为其多样化的调节功能提供了结构基础。
