Studying the cis-regulatory changes that have shaped human evolution

Introduction

While the phenotypes that set us apart from our closest extinct and extant relatives have been largely demarcated, we are still far from understanding the genetics of human adaptation, and how these changes affect our current anatomy, physiology, and health. Most human adaptations have likely occurred in regulatory regions, particularly in cis-regulatory elements, such as promoters and enhancers. However, our ability to study cis-regulatory evolution is limited due to the complexity of identifying cis-regulatory changes and linking them to phenotypes.

Proposed Approach

We believe these limitations can now be tackled by merging several cutting-edge approaches, primarily hybrid cells and massively parallel reporter assays (MPRAs), augmented by developing sorely needed new ones.

Aim 1

In Aim 1, we will generate human-ape hybrid cells and use them to identify the gamut of cis-regulatory expression changes separating humans from other apes.

Aim 2

In Aim 2, we will perform MPRAs to map the function of each of the variants that distinguish modern humans, Neanderthals, Denisovans, and apes.

Aim 3

In Aim 3, we will develop methMPRA, a novel method to map the role of DNA methylation in shaping gene expression.

Aim 4

In Aim 4, we will synergize these data to study human evolution at the sequence, methylation, expression, and phenotypic level.

Project Outcomes

The proposed project will:

1. Generate comprehensive resources, including the first catalogs of the sequence and methylation changes that shaped human gene regulation.
2. Develop a novel method to characterize en masse the cis-effects of methylation on expression.
3. Develop novel platforms (human-ape hybrid cells) to map human cis-regulation.
4. Identify genetic changes underlying human traits.

Together, this will pave the way to understanding the role of gene regulation in human evolution.