# Site-Specific Photochemistry on Epigenetic Readers for Interactome Profiling

> **NIH NIH R01** · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · 2020 · $296,486

## Abstract

Abstract. Lysine acetylation in proteins contributes significantly to cellular differentiation and
development. At the molecular level, effector modules called bromodomains recognize
acetylated lysine to facilitate downstream signaling through binding of macromolecular
complexes to specific genomic loci. Despite their fundamental role in biology and disease, an
unbiased cataloguing of acetylated interacting partners of a specific bromodomain is lacking
possibly due to the weak, highly dynamic and context-dependent nature of such interactions.
However, such molecular information is essential in delineating precise mechanism by which
bromodomains partake in the intricate process of transcriptional regulation in biology and
disease. The current proposal outlines a unique strategy termed `Interaction-Based Protein and
Promoter Profiling' (IBPP) by introducing a photo-crosslinkable amino acid into the hydrophobic
cage of bromodomains to capture transiently interacting partners followed by their proteomic
and genomic characterizations. We will apply IBPP to BET bromodomains (BRD2, BRD3, BRD4
and BRDT) to identify their interacting partners from intact cells. Subsequent biochemical
validation and functional studies of the newly identified interactome will lead to improved
mechanistic understanding of acetylation and bromodomain-mediated gene regulation in normal
cells as well as in human malignancies. Salient points of our approach include the ability to
identify weak and transient binding partners (because of crosslinking) with high temporal control
(because of light as the perturbing agent) of closely related members of BET family (via protein
engineering with unnatural mutagenesis) in cell-type specific manner. Since crosslinking occurs
in the deeply embedded `aromatic cage' in bromodomains, selectivity in identifying authentic
interacting partners is expected to be much higher compared to chromatin immunoprecipitation
(ChIP) that relies on formaldehyde-based non-selective crosslinking method. Successful
implication of IBPP will be invaluable in providing both molecular as well as system level
understanding of the dynamic functions of more than sixty bromodomain-containing human
proteins.

## Key facts

- **NIH application ID:** 9898385
- **Project number:** 5R01GM123234-04
- **Recipient organization:** UNIVERSITY OF PITTSBURGH AT PITTSBURGH
- **Principal Investigator:** Kabirul Islam
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $296,486
- **Award type:** 5
- **Project period:** 2017-04-01 → 2022-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9898385

## Citation

> US National Institutes of Health, RePORTER application 9898385, Site-Specific Photochemistry on Epigenetic Readers for Interactome Profiling (5R01GM123234-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9898385. Licensed CC0.

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