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

Transposable elements constitute a significant portion of eukaryotic genomes, yet their role in chromatin organization remains poorly understood.

This study aimed to computationally investigate the density patterns of transposons around chromatin contact points identified from public Micro-C chromatin conformation data from human cell culture. The density peak patterns of various transposable families and subfamilies were studied within a 100kb window centered on contact points. The analysis was focused on the most abundant transposons, such as Alu and LINE-1.

The computational analysis revealed highly pronounced, non-random density patterns of transposons around the chromatin contact points. The patterns were produced by aligning all ligation points and plotting the average density around them. The patterns were strikingly different between transposable element families and substantially different between the members of the families. The patterns were found to be reproducible across independent studies and biological replicates. Among major families and subfamilies, no members were found to have reproducible density patterns around the contact points. Randomly generated coordinates produced less pronounced patterns, which were not correlated between replicates as expected for the negative control.

Some families showed enrichment, and others demonstrated depletion at contact points, while 100Kb window-wide patterns remained correlated between biological replicates. The patterns were asymmetric relative to the chromosomal orientation. Additionally, the patterns were oriented relative to the transposon sequence direction.