Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays
Abstract CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harb...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-02-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-45728-8 |
| _version_ | 1797273902990229504 |
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| author | Fabian Blombach Michal Sýkora Jo Case Xu Feng Diana P. Baquero Thomas Fouqueau Duy Khanh Phung Declan Barker Mart Krupovic Qunxin She Finn Werner |
| author_facet | Fabian Blombach Michal Sýkora Jo Case Xu Feng Diana P. Baquero Thomas Fouqueau Duy Khanh Phung Declan Barker Mart Krupovic Qunxin She Finn Werner |
| author_sort | Fabian Blombach |
| collection | DOAJ |
| description | Abstract CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbour extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposons. Cbp1 recruits Cren7 forming together ‘chimeric’ chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third helix-turn-helix domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays. |
| first_indexed | 2024-03-07T14:50:46Z |
| format | Article |
| id | doaj.art-ae9128ebd98f4588bdf6f50de591a387 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-07T14:50:46Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-ae9128ebd98f4588bdf6f50de591a3872024-03-05T19:42:51ZengNature PortfolioNature Communications2041-17232024-02-0115111710.1038/s41467-024-45728-8Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arraysFabian Blombach0Michal Sýkora1Jo Case2Xu Feng3Diana P. Baquero4Thomas Fouqueau5Duy Khanh Phung6Declan Barker7Mart Krupovic8Qunxin She9Finn Werner10RNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College LondonRNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College LondonRNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College LondonCRISPR and Archaea Biology Research Center, Microbial Technology Institute, Shandong UniversityInstitut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology UnitRNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College LondonRNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College LondonRNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College LondonInstitut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology UnitCRISPR and Archaea Biology Research Center, Microbial Technology Institute, Shandong UniversityRNAP laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College LondonAbstract CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbour extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposons. Cbp1 recruits Cren7 forming together ‘chimeric’ chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third helix-turn-helix domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.https://doi.org/10.1038/s41467-024-45728-8 |
| spellingShingle | Fabian Blombach Michal Sýkora Jo Case Xu Feng Diana P. Baquero Thomas Fouqueau Duy Khanh Phung Declan Barker Mart Krupovic Qunxin She Finn Werner Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays Nature Communications |
| title | Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays |
| title_full | Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays |
| title_fullStr | Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays |
| title_full_unstemmed | Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays |
| title_short | Cbp1 and Cren7 form chromatin-like structures that ensure efficient transcription of long CRISPR arrays |
| title_sort | cbp1 and cren7 form chromatin like structures that ensure efficient transcription of long crispr arrays |
| url | https://doi.org/10.1038/s41467-024-45728-8 |
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