Patterns of Transposable Element Distribution Around Chromatin Ligation Points Revealed by Micro-C Data Analysis

Alexandr V. Vikhorev, Michael M. Rempel, Oksana O. Polesskaya, Ivan V. Savelev, Max V. Myakishev-Rempel
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Abstract

Transposable elements (TEs) constitute a significant portion of eukaryotic genomes, yet their role in chromatin organization remains poorly understood. This study investigates the distribution patterns of TEs around chromatin ligation points (LPs) identified through Micro-C experiments in human cells. We analyzed the density of various TE families within a 100kb window centered on LPs, focusing on major families such as Alu and LINE-1 (L1) elements. Our findings reveal distinct, non-random distribution patterns that differ between TE families and exhibit consistent strand-specific biases. These patterns were reproducible across two independent datasets and showed marked differences from random genomic distributions. Notably, we observed family-specific variations in TE density near LPs, with some families showing depletion at LPs followed by periodic fluctuations in density. The consistency of these patterns across TE families and their orientation relative to chromosome arms suggest a fundamental relationship between TEs and higher-order chromatin structure. Our results provide new insights into the potential role of TEs in genome organization and challenge the notion of TEs as passive genomic components. This study lays the groundwork for future investigations into the functional implications of TE distribution in chromatin architecture and gene regulation.
通过 Micro-C 数据分析揭示染色质连接点周围转座元件的分布模式
可转座元件(Transposable elements,TEs)在真核基因组中占很大比例,但它们在染色质组织中的作用却鲜为人知。本研究调查了通过人类细胞中的Micro-C实验确定的染色质连接点(LPs)周围TEs的分布模式。我们分析了以 LPs 为中心的 100kb 窗口内各种 TE 家族的密度,重点分析了 Alu 和 LINE-1 (L1) 元件等主要家族。我们的发现揭示了不同 TE 族之间不同的、非随机的分布模式,并表现出一致的链特异性偏倚。这些模式在两个独立的数据集上都可以重现,并显示出与随机基因组分布的明显差异。值得注意的是,我们观察到了LPs附近TE密度的家族特异性变化,一些家族在LPs处显示出耗竭,随后密度出现周期性波动。这些模式在TE家族间的一致性以及它们相对于染色体臂的取向表明,TE与高阶染色质结构之间存在基本关系。我们的研究结果为TEs在基因组组织中的潜在作用提供了新的见解,并对TEs作为被动基因组元件的概念提出了挑战。这项研究为今后研究TE在染色质结构和基因调控中的分布的功能含义奠定了基础。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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