Co-option of the lineage-specificLAVAretrotransposon in the gibbon genome

Abstract

Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis. We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.

Comparative Analyses of Gibbon Centromeres Reveal Dynamic Genus-Specific Shifts in Repeat Composition

“…2 C ). These observations, together with our previous findings using whole-genome shotgun sequences ( Okhovat et al 2020) , indicate that the LAVA element is overall more prevalent in the HLE genome compared with other genera, and that LAVA is distinctly enriched in HLE centromeric regions demarcated by CENP-A and CENP-B DNA binding.…”

“…ChIP-seq was carried out on gibbon lymphoblastoid cell lines (LCLs) established previously ( Carbone et al 2014 ; Lazar et al 2018 ; Okhovat et al 2020) and for this study, from four different gibbons species: Nomascus leucogenys (NLE), Hoolock leuconedys (HLE), Hylobates moloch (HMO), and Symphalangus syndactylus (SSY), each representing one of the four extant gibbon genera (supplementary table S1, Supplementary Material online). Alignments of CENP-A, CENP-B, and CENP-C protein sequences between human and gibbons indicates high likelihood of cross-reactivity of human-specific antibodies with gibbon (95% identity across CENP-A with only 1 amino acid difference in the peptide used to generate the antibody, 98% identity across CENP-B, and 100% across CENP-C proteins).…”

“…2 A ), we examined whether centromere proteins preferentially bind specific repeat components within the LAVA sequence. Meta-summit analyses, previously optimized for LAVA ( Fernandes et al 2020 ; Okhovat et al 2020) , were completed for CENP ChIP-seq data sets across all four gibbon genera, since even non-HLE libraries showed >2-fold enrichment of LAVA elements in CENP libraries relative to input ( fig. 3 B ; supplementary fig.…”

“…We used an approach originally described by Fernandes et al (2020) and adapted for the LAVA element in Okhovat et al (2020) to identify putative CENP bindings sites in the consensus LAVA sequence. Briefly, we used Bowtie2 ( Langmead and Salzberg 2012) with the –very-sensitive settings to align the trimmed reads from each input and CENP ChIP-seq library to the gibbon reference genome (Nleu3.0).…”

Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae

“…The analysis of TE heterozygosity in the giraffe populations reveals a similar pattern to that from the SNP analysis by [ 18 ], except regarding the northern giraffes. The arithmetic mean coverage of our genome data set is 19X, which was shown to be optimal to reliably call both TE insertions and genotypes [ 25 , 54 ]. By analyzing the heterozygosity of older TE insertions at deeper nodes in the phylogeny, we find that the clade-specific heterozygosity patterns have already originated in the MRCA to the species.…”