Alternative Mechanisms for DNA Engagement by BET Bromodomain-Containing Proteins

Prakriti Kalra, Huda Zahid, Alex Ayoub, Yali Dou, William C.K. Pomerantz

Research output: Contribution to journalArticlepeer-review


Epigenetic reader domains regulate chromatin structure and modulate gene expression through the recognition of post-translational modifications on histones. Recently, reader domains have also been found to harbor double-stranded (ds) DNA-binding activity, which is as functionally critical as histone association. Here, we explore the dsDNA recognition of the N-terminal bromodomain of the bromodomain and extra-terminal (BET) protein, BRD4. Using protein-observed 19F NMR, 1H-15N HSQC NMR, electrophoretic mobility shift assays (EMSA), and competitive-inhibition assays, we establish the binding surface of dsDNA and find it to be largely overlapping with the acetylated histone (KAc)-binding site. Rather than engaging in electrostatic contacts, we find dsDNA to interact competitively within the KAc-binding pocket. These interactions are distinct from the highly homologous BET bromodomain, BRDT. Nine additional bromodomains have also been characterized for interacting with dsDNA, including tandem BET bromodomains. Together, these studies help establish a binding model for dsDNA interactions with BRD4 bromodomains and elucidate the chromatin-recognition mechanisms of the BRD4 protein for regulating gene expression.

Original languageEnglish (US)
Pages (from-to)1260-1272
Number of pages13
Issue number13
StatePublished - Jul 5 2022

Bibliographical note

Funding Information:
This work was funded by the NIH MIRA award, R35 GM140837-01 (W.C.K.P) and R01 CA250329 (Y.D.), and a University of Minnesota doctoral dissertation fellowship (H.Z.)

Publisher Copyright:
© 2022 American Chemical Society. All rights reserved.

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural


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