# Genome wide identification and functional analysis of chromatin regulatory RNAs

> **NIH NIH R01** · STANFORD UNIVERSITY · 2020 · $618,576

## Abstract

In addition to the transcription of protein coding genes in the genome, a large amount of
transcription encodes RNA molecules that do not generate mRNA. These noncoding RNAs play
important roles in the cell that include regulating dosage compensation, controlling genomic
imprinting and regulating transcription. However, human cells transcribe thousands of
noncoding RNAs and we have only ascribed functions to a small number. One of the main
challenges to understanding the functions of noncoding RNAs is that technologies to rapidly
identify and characterize noncoding RNAs are lacking. In this proposal, we develop a novel
method that makes it possible to identify, in any cell type, all of the noncoding RNAs that
interact with chromosomes and at the same time map the sites where those RNAs bind
chromatin. Our approach involves directly linking noncoding RNAs to the underlying DNA by
generating a covalent chimera between a chromosome bound RNA and DNA. Using next
generation sequencing, we can identify the RNAs in the cell that are likely to regulate
chromosome structure or function and define their sites of action on the chromosome. In our
first Aim we use Drosophila cells to develop this approach, taking advantage of the fact that
established chromosomal RNAs, roX1 and roX2, are known to coat the X chromosome to
accomplish dosage compensation in the fly. We then broaden this approach in Aim 2 and
identify the RNAs that bind chromatin throughout the human genome and develop a new
analytical infrastructure to classify and functionally assign these RNAs. In Aim 3 develop
perturbation experiments to test the functions of noncoding RNAs and RNA motifs for their
impact on local chromosome accessibility, histone modification state and transcriptional output.
We apply a system to redirect noncoding RNAs to new genomic regions to test their functional
impact on chromosomes and to regulate different genomic regions through RNA dependent
control. By defining the landscape of chromatin associated RNAs in humans and the sites that
they regulate in the cell our proposal how these RNAs function as well as the impacts of defects
in RNA dependent control that result in cellular dysfunction.

## Key facts

- **NIH application ID:** 9833532
- **Project number:** 5R01HG009909-03
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** William James Greenleaf
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $618,576
- **Award type:** 5
- **Project period:** 2017-12-01 → 2021-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9833532

## Citation

> US National Institutes of Health, RePORTER application 9833532, Genome wide identification and functional analysis of chromatin regulatory RNAs (5R01HG009909-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9833532. Licensed CC0.

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