Eukaryotic DNA is wrapped around nucleosomes to be packaged into a cell’s nucleus. Nucleosomes are made up of a combination of canonical histones (H2A, H2B, H3, and H4) and histone variants. Histone variants are evolutionarily derived from their canonical counterparts and can replace canonical histones to perform specialized chromatin functions. Given their crucial and widespread functions, mutations of histone genes are correlated with poor prognosis in cancers. Histones and their variants are typically evolutionarily conserved in sequence and function. Therefore, lineage-specific differences in histone repertoires present unique opportunities to understand their functional consequences on genomic organization and biological processes. Here, we study two such changes in the H2A repertoires of budding yeast and fruit flies. Most eukaryotes including humans have an H2A repertoire of canonical H2A and two variants– H2A.X important for DNA damage response (DDR) and H2A.Z essential for gene regulation. However, in yeast, H2A.X entirely replaced H2A, and in flies, H2A.X and H2A.Z are fused into a single variant H2Av. We take two approaches to discover the adaptive advantages of these changes. First, we are studying the evolutionary origins and diversification of H2A repertoires in yeast. We find that many basally branching fungi have a canonical H2A, suggesting that only some yeast have lost canonical H2A. Second, we are recreating the fly and human H2A repertoire in S. cerevisiae. We find that while yeast with a fly-like H2A repertoire have a DDR, it is dramatically reduced compared to wild-type yeast. This raises the intriguing possibility that a fly-like repertoire might lead to a trade-off of compromised DDR in fly genomes. We are now analyzing how DDR-dependent processes like meiosis are altered in fly-like yeast. By leveraging the power of evolution and yeast genetics our work will reveal the biological consequences of unexpected histone innovation.

Alphaviruses are arthropod-borne viruses that are responsible for febrile illness, chronic arthralgias, and premature deaths worldwide. Yet, there are no existing vaccines or therapeutics for the treatment of alphaviral diseases. Despite the limited size and coding capacity of alphavirus RNA genomes, most alphaviruses can adapt to multiple, evolutionarily divergent vertebrate and insect host species. As such, alphavirus RNA genomes and proteins carry host-specific adaptive features to compensate for the differences between hosts, such as body temperature (28°C in insects vs. 37°C in vertebrates) and methods of host immune response. Previous experiments have shown that continuous passaging of the dual-host alphavirus Sindbis virus (SINV) in Adedes albopictus (C6/36) cells results in a gain of fitness in said cells and a loss of fitness in human embryonic kidney (HEK293T) cells, resulting in a mosquito-adapted SINV (SINV^M). Using a modified long-read sequencing method (MrHAMER), we identified an assortment of fixed mutations that were serially acquired over the course of mosquito cell adaptation. Interestingly, multiple synonymous mutations were mapped to the 5' end of the SINV RNA genome, which is known to adopt functionally important RNA structures necessary for virus replication and genome packaging. Additionally, non-synonymous mutations were acquired within the viral structural genes. In this study, I aimed to understand the functional consequences of these two classes of SINV^M mutations with regards to viral fitness in insect and vertebrate cells. Furthermore, I assessed if the phenotype of these mutants were influenced by host body temperature by incubating the infected HEK293T and Vero cells at both 28°C and 37°C. We envision that studying these mutations will allow us to better understand the selective pressures influencing alphavirus evolution and potentially identify host-specific viral determinants of infection. Ultimately, this knowledge will allow us to identify ways to intervene at different stages of the alphaviral transmission cycle.

Most eukaryotes use histones to package the genome. However, many animals package their sperm genomes using specialized DNA-binding proteins called protamines, which package DNA in sperm more tightly to fit inside the sperm head. Based on the transcriptional silencing role of protamines, we hypothesize that protamines can suppress meiotic drivers, which kill other sperm to bias their own transmission. Previously, we found that one protamine gene, Mst77F, is required to suppress meiotic drivers on the Y-chromosome in Drosophila melanogaster. Since drive is generally deleterious for the transmission of autosomal alleles (due to lower male fertility for example) theory predicts that multiple suppressors of drive will arise in populations; Mst77F may represent just one such suppressor. We hypothesized that multiple natural variants in distinct genetic loci interact with and impact meiotic drive in Drosophila melanogaster. To identify these natural variants, I crossed wildtype flies to knock out flies and generate hemizygous Mst77F flies carrying genetic backgrounds from four different populations. I measured the fertility and drive strength by crossing a single hemizygous male from each cross to five wild type females. In all cases, I found that the sex ratio was skewed to favor male offspring, indicating they all carry X-linked targets. However, I did not identify any dominant genetic variation associated with the drive strength, indicating Mst77F might be the major suppressor of this drive. I am conducting reciprocal crosses to determine whether Y chromosomes from different populations carry the same strength of drive. In the future, I will extend my analyses to other genetic backgrounds. My study contributes to a better understanding of the pervasive effects of meiotic drive in natural populations and unexpected functions of protamines.