# Illuminating the Molecular Mechanisms of Replication and Transcription Coordination

> **NIH GM F31** · UNIVERSITY OF PENNSYLVANIA · 2026 · $49,538

## Abstract

Project Summary/Abstract
The goal of this proposal is to understand how replication and transcription are spatially and temporally
coordinated at molecular scales during embryonic development. A long-standing assertion is that RNA Pol II (Pol
II) is completely evicted from DNA during replication to avoid steric conflict between transcription and replication
machinery. This eviction hypothesis rests largely on in vitro or population and time-averaged genomics or
biochemical experiments. These either may not recapitulate endogenous contexts or are unable to capture the
interactions kinetics of Pol II’s association with chromatin with adequate temporal resolution (of seconds to
minutes). In fact, recent in vivo experiments suggest that Pol II is not completely evicted from chromatin but
remains in proximity (~40nm) to promoters and gene bodies during replication. This relationship is facilitated by
Pol II interacting with PCNA, a sliding clamp protein associated with actively replicating domains in the nucleus
that grow and disappear as replication completes. These contradictory findings call into question the molecular
mechanisms that govern the coordination of transcription and replication machinery. I propose to use advanced
live microscopy and single molecule tracking to directly measure the interaction kinetics of transcription and
replication proteins in real time in developing Drosophila embryos. This work will provide molecular scale insights
on the coordination of replication and transcription in an in vivo context.
Our lab has established high resolution light-sheet microscopy which enables tracking of single protein
molecules within the nuclei of live Drosophila embryos. Single molecule tracking reveals how individual proteins
move within the nucleus and the kinetics of protein-protein and protein-chromatin interactions. Using these
approaches along with perturbations to replication and transcription, I will investigate the chromatin binding
kinetics of Pol 

## Key facts

- **NIH application ID:** 11263604
- **Project number:** 5F31GM157882-02
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Alexandria  Adigun
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** GM
- **Fiscal year:** 2026
- **Award amount:** $49,538
- **Award type:** 5
- **Project period:** 2025-02-01T00:00:00 → 2028-01-31T00:00:00

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11263604

## Citation

> US National Institutes of Health, RePORTER application 11263604, Illuminating the Molecular Mechanisms of Replication and Transcription Coordination (5F31GM157882-02). Retrieved via AI Analytics 2026-07-20 from https://api.ai-analytics.org/grant/nih/11263604. Licensed CC0.

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