# Regulation of Chromosomal DNA Replication Dynamics in S cerevisiae

> **NIH NIH R01** · UNIVERSITY OF SOUTHERN CALIFORNIA · 2020 · $469,303

## Abstract

PROJECT SUMMARY
The extremely long DNA molecules that comprise eukaryotic genomes are wrapped, folded, and looped to
compact and organize the DNA for its essential activities, including gene expression, DNA replication, and
DNA repair. Exactly how the spatial architecture of chromosomes regulates DNA processes is still poorly
understood, and relatively few involved factors have been identified. DNA replication origins are subject to
epigenetic regulation of their activity resulting in differential replication timings and origin efficiencies during S
phase. This level of control over replication origins helps ensure an appropriate level of origin activity for
genome stability, however, the molecular mechanism(s) responsible for this regulation have remained obscure.
We discovered the budding yeast Fox proteins, Forkhead 1 (Fkh1) and Forkhead 2 (Fkh2) as key regulators of
replication origin initiation timing, required for most early origin firing across the yeast genome. Fkh1 and/or
Fkh2 (Fkh1/2) bind to specific sequences at some origins (called Fkh-activated origins). Recent studies
indicate that a key function of Fkh1/2 is to recruit Dbf4-dependent kinase (DDK), which is required for
replication origin initiation. This project is geared toward fully understanding the cell cycle-regulated binding of
Fkh1/2 with origins and Fkh1/2 interactions with DDK. We have identified a potential dimerization motif in
Fkh1/2 that is required for its function in origin regulation but not in other functions like transcriptional regulation.
We will determine the function of this motif in origin regulation. Fkh1 establishes the origin-timing program in
G1 phase and this correlates with re-localization of Fkh1-activated origins from the late-replicating nuclear
periphery to an early-replicating interior environment of the nucleus. The exact significance of these
movements is unclear but likely represent the assembly of origin clusters that will transform into replication
factories. Therefore, this system provides a novel and powerful opportunity to elucidate fundamental
mechanisms of chromosomal dynamics, which is a major goal of this proposal. We will use genetic
approaches to eliminate function of candidate regulator proteins to dissect the molecular events associated
with origin dynamics and replication initiation. We will also develop new tools for better analysis of protein-
DNA interactions. Finally, we will perform experiments to strip away epigenetic layers of origin regulation to
reveal the underlying sequence-based determinants of origin firing. We will determine the impact on genome
stability of these layers of regulation. These studies have strong potential to reveal novel molecular events at
the DNA level governing the dynamics of chromosomes and their essential genetic elements, such as
replication origins.

## Key facts

- **NIH application ID:** 9991856
- **Project number:** 5R01GM065494-15
- **Recipient organization:** UNIVERSITY OF SOUTHERN CALIFORNIA
- **Principal Investigator:** OSCAR M APARICIO
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $469,303
- **Award type:** 5
- **Project period:** 2003-02-01 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9991856

## Citation

> US National Institutes of Health, RePORTER application 9991856, Regulation of Chromosomal DNA Replication Dynamics in S cerevisiae (5R01GM065494-15). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9991856. Licensed CC0.

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