Evolutionary dynamics of deletions removing regulatory features in the human noncoding genome

Abstract

Genomic deletions provide a powerful loss-of-function model in noncoding regions to assess the role of purifying selection on human noncoding genetic variation. Regulatory element function is characterized by non-uniform tissue/cell-type activity, necessarily linking the study of fitness consequences from regulatory variants to their corresponding cellular activity. In this dissertation, I expound how I and my collaborators used a callset of deletions I generated from genomes of participants in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and deletions from the 1000 Genomes Project (1000GP) in order to examine whether purifying selection preserves noncoding sites of chromatin accessibility marked by DNase I hypersensitivity (DHS), histone modification (enhancer, transcribed, polycomb-repressed, heterochromatin), and topologically associated domain loops (TAD-loops). To examine this in a cellular activity-aware manner, I developed a statistical method, Pleiotropy Ratio Score (PlyRS), which calculates a correlation-adjusted count of "cellular pleiotropy" for each noncoding base-pair by analyzing shared regulatory annotations across tissues/cell-types. Comparing real deletion PlyRS values to simulations in a length-matched framework and using genomic covariates in analyses, we found that purifying selection acts to preserve both DHS and enhancer sites, as evident by both depletion of deletions overlapping these annotations and a shift in the allele frequency spectrum of overlapping deletions towards rare alleles. However, we did not find evidence of purifying selection for transcribed, polycomb-repressed, or heterochromatin sites. Additionally, we found evidence that purifying selection is acting on TAD-loop boundary integrity by preserving co-localized CTCF binding sites. Notably, at regions of DHS, enhancer, and CTCF within TAD-loop boundaries we found evidence that both sites of tissue/cell-type-specific activity and sites of cellularly pleiotropic activity are preserved by selection.