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

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.