# How histone modifications influence transcriptional bursting in a developing embryo

> **NIH NIH F32** · UNIVERSITY OF PENNSYLVANIA · 2020 · $67,446

## Abstract

Abstract
The goal of this proposal is to link histone post-translational modifications (HPTMs) to transcription rates and
bursting frequencies. In all eukaryotes studied, transcription at individual gene loci exhibits random oscillations
between active and inactive states, a phenomenon known as transcription bursting. Cell fate specification in
embryos is driven by genes whose bursting characteristics determine synchrony and robustness during
development, but the molecular interactions which generate the bursting frequencies observed in development
are unknown. To understand how transcription controls development, it is necessary to uncover the molecular
determinants that control the duration of bursts and the rates at which bursts occur in vivo. Eukaryotic
transcription is characterized by the enrichment of HPTMs at enhancers and promoters. Despite the strong
correlation between HPTMs and gene activity, it is unclear how HPTMs determine transcription rates and set
bursting frequencies. Moreover, HPTMs occur in many combinations at promoters and enhancers, generating
in theory many possible promoter states. Here, I will determine whether HPTMs confer multiple transcriptional
states during development and whether those states determine specific rates of transcription bursting. The
most powerful methods currently available to measure transcription rates are single mRNA FISH and live
nascent site imaging. To quantitatively describe state transitions using these assays, I will implement a
mathematical model of transcription states. The “two-state” model has been widely used to quantitatively
describe burst duration and frequency in terms of the average rates of switching between the active and
inactive states. However, it is untested whether the simple two-state approach can accurately describe the
transcription of a gene undergoing complex regulation during development, such as the gap gene hunchback.
Here I will determine whether the two-state model is sufficient to describe bursting frequencies of endogenous
hunchback. I will insert RNA loops into the endogenous hunchback locus to create an endogenous reporter. I
will use single mRNA FISH and live-imaging of the endogenous hunchback reporter to measure transcriptional
bursting kinetics. I will then determine how HPTMs affect the kinetics of hunchback transcription. I will
maternally knockdown an array of histone methyltransferases, acetyltransferases, demethylases, and
deacetylates and measure their effects on the transcriptional bursting of hunchback. For each HPTM
knockdown, I will determine which mathematical model best describes the single mRNA FISH and live-imaging
data. Together, these experiments will determine how changes in specific histone marks change hunchback
bursting kinetics and promoter state.

## Key facts

- **NIH application ID:** 9964499
- **Project number:** 5F32GM133162-02
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Joseph M Zinski
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $67,446
- **Award type:** 5
- **Project period:** 2019-06-01 → 2022-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9964499

## Citation

> US National Institutes of Health, RePORTER application 9964499, How histone modifications influence transcriptional bursting in a developing embryo (5F32GM133162-02). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/9964499. Licensed CC0.

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