# The effect of nucleosomes on the earliest stages of RNA polymerase II transcription

> **NIH NIH R01** · CLEVELAND CLINIC LERNER COM-CWRU · 2024 · $373,119

## Abstract

Project summary- Much of the control of gene expression is exerted at two points: assembly of the RNA
polymerase II (Pol II) preinitiation complex at promoters and the successful advance of Pol II into productive
elongation. Pol II promoters are accompanied by an immediately downstream (+1) nucleosome typically
located just beyond the likely boundary of the promoter. It is often speculated that promoter activity is
controlled by this distinctive local chromatin architecture, which includes histone modifications and histone
variants specific to promoter-proximal nucleosomes. However, the roles that adjacent nucleosomes play in the
assembly of the transcription complex remain poorly understood. After transcription initiates Pol II complexes
elongate very slowly, eventually encountering the +1 nucleosome while associating with positive and negative
factors. Most of these complexes terminate while a minority advance into effective elongation and traverse the
nucleosome. The extent to which complexes achieve full elongation competence is a major determinant of
overall promoter strength, but it is not known how the +1 nucleosome barrier modulates the crucial competition
between maturation into productive elongation and termination. Our overall aim is to biochemically dissect
Pol II initiation and early elongation to understand the mechanistic basis for distinct outcomes for Pol
II complexes within the local chromatin context. We are approaching these questions using a nuclear
extract based in vitro transcription system in which transcription complex assembly and early elongation are
challenged by a +1 nucleosome positioned at a series of precise downstream locations. These nucleosomes
can include the histone modifications and histone variants typically found near promoters. Our current results
already provide important and novel insights into both the negative and positive effects of +1 nucleosomes on
transcription complex assembly. These effects depend significantly on promoter class (presence or absence
of the TATA element) and on promoter-enriched histone modifications whose function is currently unknown. In
the studies proposed here, we will substantially extend the present findings to uncover the mechanistic basis
for the control of Pol II transcription complex assembly by the +1 nucleosome. We have also found with
extract-based transcription that both the advance into productive elongation and termination can be studied in
single reactions. This will allow us for the first time to uncover the mechanisms and factors that competitively
drive both relevant fates for Pol II immediately following initiation from a promoter in the context of an
appropriately located and modified +1 nucleosome.

## Key facts

- **NIH application ID:** 10975301
- **Project number:** 2R01GM121428-05
- **Recipient organization:** CLEVELAND CLINIC LERNER COM-CWRU
- **Principal Investigator:** Donal Luse
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $373,119
- **Award type:** 2
- **Project period:** 2018-09-01 → 2028-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10975301

## Citation

> US National Institutes of Health, RePORTER application 10975301, The effect of nucleosomes on the earliest stages of RNA polymerase II transcription (2R01GM121428-05). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10975301. Licensed CC0.

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