Evolutionary, Structural and Functional Characterization of X-palindromic Regions and Their Associated Genes

Abstract

The mammalian sex chromosomes are enriched in large (>10kb), nearly identical (>99%) segmental duplications containing testis-expressed gene families. These genomic regions are highly variable in size, ranging from a single duplication present in a palindromic orientation (singleton palindrome) to vast duplications consisting of 10-100s copies present in both palindromic and tandem orientation (palindrome array, or ampliconic array). Both singleton palindromes and palindrome arrays harbor palindrome-associated testis-expressed gene families. In contrast to the majority of single copy sex-linked genes which are post-meiotically silenced, palindrome-associated gene families are expressed post-meiotically. Palindrome-associated gene families independently evolved, with only 30% shared between humans and mice. Furthermore, palindrome-associated gene families are rapidly evolving at the sequence level and can vary substantially in gene copy number, which are hallmarks of genes involved in fertility and speciation. These observations suggest that palindrome-associated genes have evolved mechanisms to evade the post-meiotic gene silencing which single copy X- and Y-linked genes are subject to and that palindrome-associated gene families play important post-meiotic roles in male fertility. In this thesis, I explore the evolutionary history, the importance of palindrome structure, and the functions of genes harbored within palindromes.

Using genetically engineered mouse models, I manipulated the structure and copy number of segmental duplications in two singleton palindromes (Mageb5 and 4930567H17Rik) and two palindrome arrays (Slx and Slxl1). My studies demonstrate the post-meiotic expression of palindrome-associated genes correlates with gene copy number and is not dependent on their palindromic orientation. The singleton palindrome gene families, Mageb5 and 4930567H17Rik, are not dosage sensitive as males with a single copy of either gene exhibit no defects in fertility or spermatogenesis as compared to wild-type males. My investigation of Slx and Slxl1 gene families reveal they are Mus-lineage specific, partially redundant, and essential for male fertility. The complete deletion of both Slx and Slxl1, results in post-meiotic spermatogenetic defects and male infertility. Additionally, alterations in Slxl1, but not Slx, gene copy number distorts the ratio of male to female offspring. This unequal transmission of X and Y chromosomes is indicative of meiotic drive, the non-Mendelian transmission of chromosomes. We hypothesize that Slxl1 competes with a related palindromic array associated gene family on the Y-chromosome, Sly, as alterations in the ratio of Slxl1 to Sly copy number impact the offspring sex ratio. We believe meiotic drive contributed to the massive amplification of Slxl1 and Sly on the mouse sex chromosomes. As selfish elements, duplications of Slxl1 and Sly enhanced not only their own transmission but the transmission of the entire X- or Y-chromosome, respectively, resulting in the massive co-amplification of Slxl1 and Sly.

In sum, my studies highlight the structural and functional diversity of palindrome-associated genes in the context of spermatogenesis. Furthermore, this work outlines an approach that can be used to study and characterize additional palindrome-associated gene biology within the Mus-lineage as well as other species.