# Developing a robust method for analyzing transcription factor mediated chromatin interactions

> **NIH NIH R21** · UNIVERSITY OF SOUTHERN CALIFORNIA · 2023 · $248,125

## Abstract

Developing a robust method for analyzing transcription factor mediated chromatin interactions
Transcription factors (TFs) mediate the interactions between distal regulatory elements and gene promoters
to control specific gene expression; disruption of this process by mutations in the protein coding regions or
the non-coding DNA binding sites of TFs could lead to dysregulation of transcription and human diseases. An
increasing number of genomics tools (such as Hi-C) have been developed for mapping long range chromatin
interactions. What is missing in these DNA-centric approaches are TFs and their cofactors, although
bioinformatics approaches have been developed to infer the roles of TFs in chromatin interactions. Current
technologies (such as HiChIP) for mapping protein-mediated chromatin interactions have worked well with
high abundance proteins but not for most TFs. This is largely due to the high variability and low efficiency of
antibodies used in the immunoprecipitation of chromatin complexes associated with the TF of interest. The
introduction of in situ biotinylated TFs has greatly improved the sensitivity and reproducibility of ChIP-seq
(a.k.a biochip-seq), but this strategy cannot be extended to the mapping of TF-mediated chromatin
interactions. This is because all Hi-C based mapping techniques, including HiChIP, use biotinylated
nucleotide to label the ligation junction to enrich contact signals. Consequently, streptavidin binding would
pull down all chromatin contacts indiscriminately. To overcome this problem, the proposed studies aim to
develop a new method for mapping TF-mediated chromatin interaction by adapting the HiChIP protocol to
biotinylated TFs (referred to as bioHiChIP) (Aim 1) and test the application of bioHiChIP in mapping
chromatin interactions mediated by biotinylated FOXP3 (Aim 2). The bioHiChIP is designed to be a simple
and easy-to-operate protocol for robust mapping of protein-mediated chromatin interactions. It will serve as a
powerful tool for the broad research community to take advantage of the increasing research resources of
transgenic model organisms with biotinylated TFs to study the detailed mechanisms of transcription
regulation in physiological functions and pathological diseases.

## Key facts

- **NIH application ID:** 10667811
- **Project number:** 1R21HG012627-01A1
- **Recipient organization:** UNIVERSITY OF SOUTHERN CALIFORNIA
- **Principal Investigator:** LIN CHEN
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $248,125
- **Award type:** 1
- **Project period:** 2023-05-01 → 2025-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10667811

## Citation

> US National Institutes of Health, RePORTER application 10667811, Developing a robust method for analyzing transcription factor mediated chromatin interactions (1R21HG012627-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10667811. Licensed CC0.

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