Variability in organization and expression of multi-copy genes on human sex chromosomes

The human genome has two sex chromosomes—the Y, harboring genes critical for male fertility, and the X, carrying genes important for reproduction, cognition, and immunity. Because of their high repetitive element content and haploid nature in males, the X and the Y have been completely sequenced and assembled by the Telomere-to-Telomere (T2T) Consortium only recently. The repetitive organization of the Y is critical for its survival without interchromosomal recombination. Indeed, the Y does not recombine with the other chromosomes over most of its length, except for the short pseudoautosomal regions where it recombines with the X. The repeats on the Y—tandem repeats and palindromes (inverted repeats) in particular—enable intrachromosomal recombination and facilitate gene conversion, restoring sequences of multi-copy gene families. We have recently discovered that the X also has many gene-rich palindromes, which also likely undergo gene conversion. Yet, we currently lack information on variation in the organization and expression of sex chromosome genes located in repetitive structures across multiple humans. Our overarching goal is to decipher the molecular processes governing structural changes of sex chromosomes leading to phenotypic consequences. As an essential step towards fulfilling this goal, here we will focus on the following Specific Aims. In Aim 1, we will study variation in prevalence, structure, and gene content of palindromes and tandem repeats on the human X and Y chromosomes. We will investigate which palindromes and tandem repeats are conserved in terms of presence/absence, structure, and gene content across hundreds of nearly T2T human genome assemblies generated by the Human Pangenome Reference Consortium (HPRC). In Aim 2, we will evaluate potential natural selection acting on expression levels of multi-copy genes on the X and the Y. Most Y genes, and many X genes, are expressed in testis. Thus, we will examine variation in their expression levels across hundreds of testis transcriptome datasets generated by the Genotype-Tissue Expression (GTEx) project. Using these data, we will test for selection acting to maintain optimal expression for sex chromosome genes. Overall, our project will make an essential contribution to uncovering variation in organization, copy number, and expression of sex chromosome genes. Our results evaluating such variation in healthy humans will serve as a baseline for inquiries into disease conditions. Our thorough investigation of variation of multi-copy genes on sex chromosomes will significantly contribute to our understanding of human reproductive disorders, including male infertility. Our project requires access to large-scale data sets and computational resources enabled by the ANVIL platform. Project Number: 1R03HG014804-01 | Fiscal Year: 2026 | NIH Institute/Center: National Human Genome Research Institute (NHGRI) | Principal Investigator: KATERYNA MAKOVA | Institution: PENNSYLVANIA STATE UNIVERSITY, THE, UNIVERSITY PARK, PA | Award Amount: $393,250 | Activity Code: R03 | Study Section: Special Emphasis Panel[ZRG1 BBBT-U (56)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11284358