Circadian structural transitions of chromatin

Introduction

Transcription factors (TFs) distinctly mark regions of the genome for expression and are the pillars of cell identity. Yet, even at the basic level of DNA recognition by TFs, we know very little about how this is achieved.

Background

In eukaryotes, all DNA-templated processes occur in chromatin; however, most studies elucidating the molecular mechanisms of transcription have been performed on histone-free DNA.

Project Objectives

In the proposed project, we will use TFs as centerpieces to understand how, in the circadian system, the interplay between transcriptional regulatory complexes and chromatin shapes the eukaryotic genome to control gene expression.

Methodology

Specifically, we will use biochemical approaches paired with functional genomics and cryo-EM (single particle and tomography) to investigate:

1. How histone identity affects TF-DNA engagement.
2. How TFs and histone modifications influence chromatin organization across biological scales, from nucleotide sequence to chromatin structure in situ.

Experimental Design

We will exploit circadian time in mammalian cells and the unicellular green algae, Chlamydomonas, to elucidate the dynamic gene regulation of a biological system under natural conditions.

Expected Outcomes

Using diverse model organisms will enable us to reveal common, conserved properties and processes. Ultimately, these studies will provide unique insight into the fundamental mechanisms of gene regulation while dissecting the molecular mechanisms of biological timekeeping.