Effects of epigenetic silencing of transposable elements on local recombination rate
Authors: Yuheng Huang; Grace Yuh Chwen Lee
Affiliation: UC-Irvine
Keywords: a. genome evolution; e. heterochromatin
A wide range of taxa shows a negative association between transposable elements (TEs) density and meiotic recombination rates across genomes. Such association is commonly thought to be caused by reduced efficacy of selection against TEs in regions of low recombination or direct modification of recombination rates by TEs. Much of the research on TE evolution has focused on the selection explanation, leaving the latter possibility is largely unexplored. One possible mechanism by which TEs impact local recombination rates is through the modifications of chromatin environments. To reduce the selfish replication of TEs, hosts have evolved mechanisms to epigenetically silence them through the enrichment of heterochromatic marks at TEs. And it has been demonstrated that the enrichment of heterochromatic marks suppresses recombination initiation. Indeed, across the genomes, the heterochromatin environment is positively correlated with TE density and negatively correlated with recombination rates among different taxa. Therefore, we hypothesize that the TE-mediated heterochromatin enrichment can suppress the local recombination rate. To test the hypothesis, we aim to identify the associations between the distribution of recombination and epigenetically silenced TEs in three inbred strains with distinct TE insertion profiles. To measure recombination rate at a fine scale, we developed a novel approach that uses long-read sequencing to identify recombinant haplotypes in pooled individuals. We collected F1 offspring from two crosses and backcrossed them to the shared paternal line. For each cross, we collected more than 6000 F2 offspring and sequenced them with PacBio in a pool, aiming to identify crossover events using the long reads. This approach mitigates the need of sequencing individual flies in the traditional approach for constructing recombination maps. To benchmark this approach, we also sequenced 192 F2 flies individually with Illumina short-reads as well as in a single pool using PacBio long-reads to assess the sensitivity and specificity of our proposed new approach. We will then measure the enrichment of a repressive heterochromatic mark (H3K9me3) around the TEs and test their associations with recombination rates.