In partial fulfillment of the requirements for the degree of

Doctor of Philosophy in Bioinformatics

(School of Biological Sciences)

Dan Sun

Will defend her thesis:

Genetic and epigenetic analyses of avian sex chromosomes and sex chromosome-like autosomes

Monday, June 10th, 2019

11:00 AM

Engineered Biosystems Building, Children's Healthcare of Atlanta Seminar Room (EBB 1005)

Thesis Advisor:

Dr. Soojin Yi

School of Biological Sciences

Georgia Institute of Technology

Committee members:

Dr. King Jordan

School of Biological Sciences

Georgia Institute of Technology

Dr. Joseph Lachance

School of Biological Sciences

Georgia Institute of Technology

Dr. Gregory Gibson

School of Biological Sciences

Georgia Institute of Technology

Dr. Donna Maney

Department of Psychology

Emory University

Abstract:

Sex chromosomes have originated multiple times throughout eukaryotes. In species with the XY sex-determination system, dosage compensation is often efficient, and its epigenetic basis has been well studied. However, the extent of epigenetic differentiation between males and females in female-heterogametic systems (ZW), which generally lack complete compensation, is poorly understood. In the first study, I examined the genome-wide DNA methylation landscapes between sexes in birds. Despite highly similar methylation patterns between males and females, extremely localized methylation differentiation on the Z chromosome is employed to solve dose problems for genes potentially essential to females, at least twice in the evolutionary history of the fowl lineage. The second and third studies focus on a pair of autosomes (2 and 2m) in the white-throated sparrow that resemble sex chromosomes. In this species, two plumage morphs that mate almost exclusively with each other exhibit striking behavioral differences: within the same sex, birds of the white-striped morph (2/2m) display more territorial aggression and less nestling provision than birds of the tan-striped morph (2/2). In the second study, I characterized the extent of nucleotide and gene expression divergence between the two chromosomes as well as the degree of genetic degeneration of the non-recombining 2m chromosome. I found that similar to the evolutionary path taken by sex chromosomes across many taxa, dosage compensation evolved to re-balance gene expression between morphs in this autosomal system. In the third study, by utilizing newly sequenced DNA methylation data of 20 sparrows from the two plumage morphs, I showed that DNA methylation is involved in gene expression divergence but not dosage compensation in the 2 and 2m system. In addition, I discussed how age and sex effects interweave with morph effects to shape the methylation landscape in this species. Taken together, my dissertation work offers new insights into the epigenetic regulation of gene expression in avian sex chromosomes and sex chromosome-like autosomes.