Distinct structural bases for sequencespecific DNA binding by mammalian BEN domain proteins

Luqian Zheng, Jingjing Liu, Lijie Niu, Mohammad Kamran, Ally W.H. Yang, Arttu Jolma, Qi Dai, Timothy R. Hughes, Dinshaw J. Patel, Long Zhang, Supriya G. Prasanth, Yang Yu, Aiming Ren, Eric C. Lai

Research output: Contribution to journalArticlepeer-review


The BEN domain is a recently recognized DNA binding module that is present in diverse metazoans and certain viruses. Several BEN domain factors are known as transcriptional repressors, but, overall, relatively little is known of howBEN factors identify their targets in humans. In particular, X-ray structures of BEN domain:DNA complexes are only known for Drosophila factors bearing a single BEN domain, which lack direct vertebrate orthologs. Here, we characterize several mammalian BEN domain (BD) factors, including from twoNACCfamily BTB-BEN proteins and from BEND3, which has four BDs. In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. Weconducted detailed functional, genomic, and structural studies of BEND3. We show that BD4 is a major determinant for in vivo association and repression of endogenous BEND3 targets. We obtained a high-resolution structure of BEND3-BD4 bound to its preferred binding site, which reveals how BEND3 identifies cognateDNAtargets and shows differences with one of its non-DNA-binding BEN domains (BD1). Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins. Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins.

Original languageEnglish (US)
Pages (from-to)225-240
Number of pages16
JournalGenes and Development
Issue number3-4
StatePublished - Feb 1 2022


  • DNA binding activity
  • Gene regulation
  • Protein-DNA structure
  • Transcription factor

ASJC Scopus subject areas

  • Genetics
  • Developmental Biology


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