# TF-chRDP: a method for simultaneously capturing transcription factor binding chromatin-associated RNA, DNA and protein

## TL;DR

This paper introduces a new method called TF-chRDP that captures DNA, RNA, and proteins bound to transcription factors in one experiment, improving the study of gene regulation.

## Contribution

TF-chRDP is a novel method that simultaneously captures RNA, DNA, and protein interactions with transcription factors in a single experiment.

## Key findings

- TF-chRDP successfully enriched DNA, RNA, and proteins associated with the transcription factor p53.
- The method demonstrated high specificity for capturing chromatin-associated biomolecules.
- TF-chRDP provides an efficient tool for studying transcription factor-bound RNA-DNA-protein complexes.

## Abstract

Transcription factors (TFs) play a crucial role in the regulation of gene expression and the structural organization of chromatin. They interact with proteins, RNA, and chromatin DNA to exert their functions. Therefore, an efficient and straightforward experimental approach that simultaneously captures the interactions of transcription factors with DNA, RNA, and proteins is essential for studying these regulatory proteins. In this study, we developed a novel method, TF-chRDP (Transcription Factor binding Chromatin-associated RNA, DNA, and Protein), which allows for the concurrent capture of these biomolecules in a single experiment. We enriched chromatin complexes using specific antibodies and divided the chromatin into three fractions: one for DNA library preparation to analyze the genomic binding sites of transcription factors, another for RNA library preparation to investigate the RNA associated with transcription factor binding, and the third for proteomic analysis to identify protein cofactors interacting with transcription factors. We applied this method to study the transcription factor p53 and its associated chromatin complexes. The results demonstrated high specificity in the enrichment of DNA, RNA and proteins. This method provides an efficient tool for simultaneously capturing chromatin-associated RNA, DNA and protein bound to specific TF, making it particularly useful for analyzing the role of protein-DNA-RNA complexes in transcriptional regulation.