Exploration of cis-regulatory diversity underlying phenotypic innovation - Project Summary
The falling costs of DNA sequencing has resulted in a proliferation of genome-wide association studies (GWAS)
seeking to identify causal variants associated with disease and other important phenotypes. However, a striking
93% of phenotype-associated variants fall within non-coding regions, often several hundreds of kilobases away
from the nearest gene. Recent studies have demonstrated that such variants are enriched within cis-regulatory
elements (CREs) and can affect transcriptional outcomes. CREs are composed of clusters of 4-30 bp DNA motifs
recognized by sequence-specific transcription factors (TFs) that cooperatively establish patterns of transcription
in a development and cell type-specific manner. However, it remains unclear how genetic variants within CREs
mechanistically perturb patterns of transcription and contribute towards phenotypic diversity at the scale of
individual cells, tissues and whole organisms. The aim of this proposal is to determine the molecular relationships
among genetic variants, CREs, and gene transcription across diverse cell types and genetic backgrounds, and
their concerted effects on cellular and organismal phenotypes.
Zea mays (maize) is characterized by extensive intraspecies phenotypic and genetic variation comparable
to the levels observed among primates. The genetic framework of this proposal, the 282 maize diversity panel,
was specifically constructed from geographically dispersed individuals to represent the full spectrum of extant
variation within the species. The rate of linkage-disequilibrium decay in the 282 maize diversity panel is 10-40X
that of human and mouse genomes, affording significantly smaller population sizes with equivalent resolution.
The rationale for this study is that the abundance of genetic variation, genomic resources, reduced population
size requirements and recent expansion of reference-quality genomes (~35) present an ideal model to
investigate the mechanistic basis of phenotypic diversity stemming from regulatory variation. The proposed
research is innovative in that cutting edge genomic approaches, including scATAC-seq and snRNA-seq, will be
utilized in parallel with microscopy-based imaging across 200 maize genotypes to test the central hypothesis
that CRE variation underlies distinct spatiotemporal patterns of gene transcription that collectively manifest in
phenotypic diversity at cellular and organismal levels. Realization of the proposed aims will usher a new
understanding of the determinants of cell type-specificity and the phenotypic consequences of evolving gene
regulatory landscapes. Successful completion the proposed work will lay the foundation for future interrogation
of the mechanistic role of genetic variants towards human disease, relevant to the missions of the NIH.
This application was specifically designed to enhance the applicants career development through associated
training activities in mentorship, grant writing, and scientific communication. Accomplishment of the career
training plan will facilitate the successful transition of the applicant from a post-doctoral position to a faculty
position at a research-intensive institution.
