DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues
Abstract Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous s...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-04-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-47396-0 |
| _version_ | 1797209249879687168 |
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| author | Kian Hong Kock Patrick K. Kimes Stephen S. Gisselbrecht Sachi Inukai Sabrina K. Phanor James T. Anderson Gayatri Ramakrishnan Colin H. Lipper Dongyuan Song Jesse V. Kurland Julia M. Rogers Raehoon Jeong Stephen C. Blacklow Rafael A. Irizarry Martha L. Bulyk |
| author_facet | Kian Hong Kock Patrick K. Kimes Stephen S. Gisselbrecht Sachi Inukai Sabrina K. Phanor James T. Anderson Gayatri Ramakrishnan Colin H. Lipper Dongyuan Song Jesse V. Kurland Julia M. Rogers Raehoon Jeong Stephen C. Blacklow Rafael A. Irizarry Martha L. Bulyk |
| author_sort | Kian Hong Kock |
| collection | DOAJ |
| description | Abstract Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies. |
| first_indexed | 2024-04-24T09:51:42Z |
| format | Article |
| id | doaj.art-fb03d33422b540199802faeaf082a440 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-24T09:51:42Z |
| publishDate | 2024-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-fb03d33422b540199802faeaf082a4402024-04-14T11:21:34ZengNature PortfolioNature Communications2041-17232024-04-0115111910.1038/s41467-024-47396-0DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residuesKian Hong Kock0Patrick K. Kimes1Stephen S. Gisselbrecht2Sachi Inukai3Sabrina K. Phanor4James T. Anderson5Gayatri Ramakrishnan6Colin H. Lipper7Dongyuan Song8Jesse V. Kurland9Julia M. Rogers10Raehoon Jeong11Stephen C. Blacklow12Rafael A. Irizarry13Martha L. Bulyk14Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolDepartment of Biostatistics and Computational Biology, Dana-Farber Cancer InstituteDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical SchoolDepartment of Biostatistics, Harvard T.H. Chan School of Public HealthDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolProgram in Biological and Biomedical Sciences, Harvard UniversityDepartment of Data Science, Dana-Farber Cancer InstituteDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical SchoolAbstract Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.https://doi.org/10.1038/s41467-024-47396-0 |
| spellingShingle | Kian Hong Kock Patrick K. Kimes Stephen S. Gisselbrecht Sachi Inukai Sabrina K. Phanor James T. Anderson Gayatri Ramakrishnan Colin H. Lipper Dongyuan Song Jesse V. Kurland Julia M. Rogers Raehoon Jeong Stephen C. Blacklow Rafael A. Irizarry Martha L. Bulyk DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues Nature Communications |
| title | DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues |
| title_full | DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues |
| title_fullStr | DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues |
| title_full_unstemmed | DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues |
| title_short | DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues |
| title_sort | dna binding analysis of rare variants in homeodomains reveals homeodomain specificity determining residues |
| url | https://doi.org/10.1038/s41467-024-47396-0 |
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