Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon

Area of Science:

• Genomics
• Evolutionary Biology
• Epigenetics

Background:

• Great apes exhibit karyotype stability with minimal large-scale rearrangements.
• Gibbons, in contrast, show high rates of chromosomal rearrangements linked to rapid centromere evolution.

Purpose of the Study:

• To characterize the fully assembled centromeres in the eastern hoolock gibbon (Hoolock leuconedys, HLE).
• To investigate the genomic and epigenetic features driving gibbon centromere evolution and chromosomal instability.

Main Methods:

• Whole-genome sequencing and assembly.
• Centromeric DNA characterization.
• Epigenetic analysis (CpG methylation).
• Replication timing analysis.
• Comparative genomic analysis.

Main Results:

• HLE centromeres contain diverse transposable elements (TEs), differing from canonical alpha-satellites in other apes.
• A CpG methylation centromere dip region was identified, conserved despite the absence of satellite arrays.
• Atypical centromeric features, including protein-coding genes and mismatched replication timing, were uncovered.
• Duplications and deletions specific to HLE centromeres were identified, distinguishing them from other gibbons.
• Differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at breakpoints were observed.

Conclusions:

• Gibbon centromere evolution is shaped by a unique combination of genomic features, including diverse TEs and epigenetic modifications.
• These attributes contribute to chromosome instability and rapid karyotype evolution in gibbons.
• The findings provide insights into the mechanisms driving primate chromosomal evolution.