Identification and Characterization of LINE and SINE Retrotransposons in the African Hedgehog (Atelerix albiventris, Erinaceidae) and Their Association with 3D Genome Organization and Gene Expression
Mengyuan Zhu, Jianxuan Zhou, Nannan Chen, Jianing Xu, Haipeng Wang, Libo Jiang, Fengtang Yang
TL;DR
This study explores how LINE and SINE retrotransposons are distributed in the African hedgehog genome and how they might influence gene expression and spine development.
Contribution
The study characterizes LINE and SINE retrotransposons in the African hedgehog and links them to genome organization and gene regulation.
Findings
SINEs are found in GC-rich, highly methylated regions, while LINEs are in AT-rich, hypomethylated regions.
SINEs are associated with euchromatin, and LINEs with heterochromatin.
Some TEs are linked to genes involved in epidermal and skeletal development.
Abstract
Background: The African hedgehog (Atelerix albiventris) exhibits specialized skin differentiation leading to spine formation, yet its regulatory mechanisms remain unclear. Transposable elements (TEs), particularly LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements), are known to influence genome organization and gene regulation. Objectives: Given the high proportion of SINEs in the hedgehog genome, this study aims to characterize the distribution, evolutionary dynamics, and potential regulatory roles of LINEs and SINEs, focusing on their associations with chromatin architecture, DNA methylation, and gene expression. Methods: We analyzed LINE and SINE distribution using HiFi sequencing and classified TE families through phylogenetic reconstruction. Hi-C data were used to explore TE interactions with chromatin architecture, while whole-genome 5mCpG…
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Taxonomy
TopicsChromosomal and Genetic Variations · Genomics and Chromatin Dynamics · Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities