# Eukaryotic RNA Processing and Chromatin Modification

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA LOS ANGELES · 2020 · $319,800

## Abstract

PROJECT SUMMARY
Although synthesis of RNA and its processing, including splicing, have historically been studied as
biochemically distinct reactions, these processes are, in fact, spatio-temporally coupled such that RNA splicing
takes place in the context of chromatin. This has lead to the prediction that specific chromatin marks may
influence splicing. Our preliminary analyses of both yeast and mammalian transcriptomes implicate histone
H3K36 methylation as a key player in splicing regulation in both systems. Here we leverage the power of yeast
genetics and molecular biology to gain fundamental mechanisms into the coordination of chromatin
modification and splicing, which we will further analyze in mammalian immune cells. The question of how
chromatin influences splicing is particularly prescient in light of the observation that splicing primarily occurs
while pre-mRNAs are associated with chromatin, suggesting that some factor(s) help retain pre-mRNAs to
chromatin and only release the mRNA once splicing is completed. We propose the conceptually innovative
idea that spliceosome disassembly is coupled to the state of the chromatin. Based upon preliminary data and
strong collaborations with UCLA colleagues with expertise in bioinformatics, immunology, and mammalian
alternative splicing, we have developed innovative tools to address the hypothesis that chromatin,
particularly histone H3K36 methylation (H3K36me), and Prp43’s interaction with it affect co-
transcriptional splicing
Aim 1. Determine the relationship between Set2 dependent H3K36me and RNA splicing in yeast
Aim 2. Determine how the yeast protein Prp43 affects co-transcriptional splicing outcomes
Preliminary yeast studies lead to a number of hypotheses that can be tested in HSC-derived macrophages, in
which the methyltransferase SETD2 or the factor that tethers mammalian Prp43, to the spliceosome has been
knocked out using CRISPR-Cas9. With this system we will:
Aim 3. Determine how histone H3 methylation and/or mammalian Prp43 (DHX15) interaction with
chromatin affects splicing outcomes and macrophage biology

## Key facts

- **NIH application ID:** 9880307
- **Project number:** 5R01GM085474-09
- **Recipient organization:** UNIVERSITY OF CALIFORNIA LOS ANGELES
- **Principal Investigator:** TRACY L JOHNSON
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $319,800
- **Award type:** 5
- **Project period:** 2010-04-01 → 2022-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9880307

## Citation

> US National Institutes of Health, RePORTER application 9880307, Eukaryotic RNA Processing and Chromatin Modification (5R01GM085474-09). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9880307. Licensed CC0.

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