Accessing the inaccessible: Y Chromosome and heterochromatin in genomes of great apes
Open Access
- Author:
- Cechova, Monika
- Graduate Program:
- Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- December 13, 2019
- Committee Members:
- Kateryna Dmytrivna Makova, Dissertation Advisor/Co-Advisor
Stephen Wade Schaeffer, Committee Chair/Co-Chair
Francesca Chiaromonte, Committee Member
Paul Medvedev, Outside Member
Raquel Assis, Committee Member
Stephen Wade Schaeffer, Program Head/Chair - Keywords:
- Y chromosome
heterochromatin
great apes
satellite
Nanopore
PacBio
sex chromosomes
chromatin
mutation - Abstract:
- This dissertation focuses on the inaccessible regions of our genome, and the genome of great apes. The prime example of such region is Y chromosome; chromosome that is seminal for spermatogenesis and male fertility yet remains underexplored due to its repetitive structure and long, heterochromatic stretches. While these regions are currently elusive, the technological advancement, such as the advent of the long read technology and the appropriate tools, opens up the possibility to answer some of the long standing questions in the field, such as the intra- and inter- species variability of Y-chromosome genes, satellite arrays, and their consequences for the health and disease. We discuss rapid repeat evolution of satellite arrays in great apes, as revealed from long PacBio and Nanopore reads. Furthermore, we introduce new approaches for the assemblies of gorilla, bonobo, and orangutan Y chromosome and perform the first comparative analysis of Y chromosomes of great apes. We especially focus on palindromes (large inverted repeats on the Y chromosome) and show, for the first time, that they form strong chromatin interactions not only within themselves, but also with other palindromes. We propose that this mechanism facilitates gene conversion to preserve the sequence identity of palindrome arms, as well as non-allelic homologous recombination (NAHR) that results in the change of copy number of ampliconic genes. Further, we found that the genus Pan, including chimpanzee and bonobo, experienced accelerated substitution rates. This observation is consistent with high levels of sperm competition in Pan.