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Hidden modes of DNA binding by human nuclear receptors

Author

Listed:
  • Devesh Bhimsaria

    (Indian Institute of Technology Roorkee)

  • José A. Rodríguez-Martínez

    (University of Puerto Rico Río Piedras)

  • Jacqui L. Mendez-Johnson

    (Promega Corporation)

  • Debostuti Ghoshdastidar

    (Indian Institute of Science)

  • Ashwin Varadarajan

    (University of Wisconsin–Madison)

  • Manju Bansal

    (Indian Institute of Science)

  • Danette L. Daniels

    (Promega Corporation
    Foghorn Therapeutics)

  • Parameswaran Ramanathan

    (University of Wisconsin–Madison)

  • Aseem Z. Ansari

    (St. Jude Children’s Research Hospital)

Abstract

Human nuclear receptors (NRs) are a superfamily of ligand-responsive transcription factors that have central roles in cellular function. Their malfunction is linked to numerous diseases, and the ability to modulate their activity with synthetic ligands has yielded 16% of all FDA-approved drugs. NRs regulate distinct gene networks, however they often function from genomic sites that lack known binding motifs. Here, to annotate genomic binding sites of known and unexamined NRs more accurately, we use high-throughput SELEX to comprehensively map DNA binding site preferences of all full-length human NRs, in complex with their ligands. Furthermore, to identify non-obvious binding sites buried in DNA–protein interactomes, we develop MinSeq Find, a search algorithm based on the MinTerm concept from electrical engineering and digital systems design. The resulting MinTerm sequence set (MinSeqs) reveal a constellation of binding sites that more effectively annotate NR-binding profiles in cells. MinSeqs also unmask binding sites created or disrupted by 52,106 single-nucleotide polymorphisms associated with human diseases. By implicating druggable NRs as hidden drivers of multiple human diseases, our results not only reveal new biological roles of NRs, but they also provide a resource for drug-repurposing and precision medicine.

Suggested Citation

  • Devesh Bhimsaria & José A. Rodríguez-Martínez & Jacqui L. Mendez-Johnson & Debostuti Ghoshdastidar & Ashwin Varadarajan & Manju Bansal & Danette L. Daniels & Parameswaran Ramanathan & Aseem Z. Ansari, 2023. "Hidden modes of DNA binding by human nuclear receptors," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39577-0
    DOI: 10.1038/s41467-023-39577-0
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    References listed on IDEAS

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    1. Jinsen Li & Tsu-Pei Chiu & Remo Rohs, 2024. "Predicting DNA structure using a deep learning method," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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