# Mapping of Novel Candidate Functional Elements with Bru-Seq Technology

> **NIH NIH UM1** · UNIVERSITY OF MICHIGAN AT ANN ARBOR · 2020 · $466,080

## Abstract

ABSTRACT
The ENCODE project has provided a tremendous resource for scientists with a treasure trove of data from a
large set of different cell types describing RNA expression (RNA-seq), epigenetic signatures (ChIP-seq),
chromatin structure (DNase-seq, ATAC-seq, Hi-C, ChIA-PET) and binding patterns of specific proteins to
both DNA and RNA (ChIP-seq, CLIP-seq, RIP-seq). We have recently developed a set of techniques that
are based on the specific labeling of nascent RNA with bromouridine (Bru) followed by lysis, capturing of the
Bru-labeled RNA using specific antibodies and deep sequencing. Bru-seq captures the nascent RNA
transcriptome, a signature of ongoing transcription in the genome where the relative rates of transcription of
all genes can be obtained. In BruChase-seq, cells are labeled with Bru and then chased in uridine for
different periods of time to allow for the determination of the relative stability of all transcripts are assessed.
Finally, BruUV-seq allows for the capturing of RNA species that normally are rapidly turned over by the
RNA exosome and can be used to map active enhancer elements producing eRNA genome-wide. In this
UM1 grant application we are proposing to use these three Bru-seq techniques to obtain critical novel
information on the nascent RNA transcriptome, RNA stabilome and active enhancome that will complement
and enrich existing ENCODE data. We are proposing to focus our mapping efforts on two specific Aims:
Aim 1: Obtain nascent RNA transcriptome, RNA stabilome and active enhancome data for human and
mouse ENCODE cell lines. Aim 2: Obtain dynamic signatures of nascent transcription, RNA stability and
activity of enhancer elements genome-wide following cellular exposure to environmental perturbations. The
mapping efforts proposed in this UM1 grant application are seeking to identify novel candidate regulatory
elements genome-wide that will complement and extend existing ENCODE data. Furthermore, dynamic
studies will be initiated to assess the activities of regulatory elements during selected cell transitions and
specific cellular responses.
GOALS:
The main goal of this proposal is to generate comprehensive novel data sets using our newly developed
Bru-seq analysis platform that will complement and extend existing ENCODE data. The emphasis will be on
mapping candidate functional elements in the human genome.

## Key facts

- **NIH application ID:** 9853027
- **Project number:** 5UM1HG009382-04
- **Recipient organization:** UNIVERSITY OF MICHIGAN AT ANN ARBOR
- **Principal Investigator:** Mats Ljungman
- **Activity code:** UM1 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $466,080
- **Award type:** 5
- **Project period:** 2017-02-01 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9853027

## Citation

> US National Institutes of Health, RePORTER application 9853027, Mapping of Novel Candidate Functional Elements with Bru-Seq Technology (5UM1HG009382-04). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/9853027. Licensed CC0.

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