Academic Journal
Bridge RNAs direct modular and programmable recombination of target and donor DNA.
| Τίτλος: | Bridge RNAs direct modular and programmable recombination of target and donor DNA. |
|---|---|
| Συγγραφείς: | Durrant MG; Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA., Perry NT; Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.; University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA., Pai JJ; Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA., Jangid AR; Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA., Athukoralage JS; Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA., Hiraizumi M; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan., McSpedon JP; Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA., Pawluk A; Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA., Nishimasu H; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.; Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.; Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto 600-8411, Japan.; Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan., Konermann S; Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA.; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA., Hsu PD; Arc Institute, 3181 Porter Drive, Palo Alto, CA 94304, USA.; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA. |
| Πηγή: | BioRxiv : the preprint server for biology [bioRxiv] 2024 Jan 26. Date of Electronic Publication: 2024 Jan 26. |
| Τύπος έκδοσης: | Preprint; Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| Περίληψη: | Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions, or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes involved in fundamental DNA repair processes such as homologous recombination or in the transposition of foreign genetic material by viruses and mobile genetic elements (MGEs). We report that IS110 insertion sequences, a family of minimal and autonomous MGEs, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables DNA insertion into genomic target sites as well as programmable DNA excision and inversion. The IS110 bridge system expands the diversity of nucleic acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design. |
| Σχόλια: | Update in: Nature. 2024 Jun;630(8018):984-993. doi: 10.1038/s41586-024-07552-4.. (PMID: 38926615) |
| References: | Biochemistry. 2023 Dec 19;62(24):3493-3499. (PMID: 36049184) Bioinformatics. 2017 Nov 15;33(22):3645-3647. (PMID: 29036507) J Bacteriol. 1997 Apr;179(7):2382-8. (PMID: 9079926) Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jan;87(1):012707. (PMID: 23410359) Nature. 2019 Dec;576(7785):149-157. (PMID: 31634902) Nature. 2017 Nov 23;551(7681):464-471. (PMID: 29160308) Nat Biotechnol. 2023 Sep 21;:. (PMID: 37735266) J Bacteriol. 1999 Aug;181(16):4937-48. (PMID: 10438765) Cell. 2018 Apr 19;173(3):665-676.e14. (PMID: 29551272) Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168) BMC Bioinformatics. 2011 Jan 04;12:3. (PMID: 21205310) Mol Cell. 2004 Jul 23;15(2):185-97. (PMID: 15260970) PLoS One. 2017 Oct 26;12(10):e0185056. (PMID: 29073143) Nature. 2016 May 19;533(7603):420-4. (PMID: 27096365) Nature. 2021 Nov;599(7886):692-696. (PMID: 34619744) Nature. 1983 Apr 14;302(5909):575-81. (PMID: 6300689) Nucleic Acids Res. 2018 May 4;46(8):4152-4163. (PMID: 29635476) Virology. 1995 Aug 20;211(2):397-407. (PMID: 7645244) Nucleic Acids Res. 2002 Jul 15;30(14):3059-66. (PMID: 12136088) Nat Biotechnol. 2017 Nov;35(11):1026-1028. (PMID: 29035372) Mol Genet Genomics. 2001 Aug;265(6):1004-10. (PMID: 11523772) Nat Rev Genet. 2010 Sep;11(9):636-46. (PMID: 20717154) Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37. (PMID: 21593126) J Bacteriol. 2003 Aug;185(16):4891-900. (PMID: 12897009) Cell. 2008 Jan 25;132(2):208-20. (PMID: 18243097) J Bacteriol. 2003 Nov;185(21):6371-84. (PMID: 14563872) Nat Biotechnol. 2020 Jul;38(7):824-844. (PMID: 32572269) Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1901-6. (PMID: 17264213) Curr Protoc Bioinformatics. 2020 Mar;69(1):e96. (PMID: 32162851) BMC Genomics. 2006 Mar 24;7:62. (PMID: 16563168) Nucleic Acids Res. 2020 Jan 10;48(1):472-485. (PMID: 31745551) Nucleic Acids Res. 2021 Sep 20;49(16):9211-9228. (PMID: 34379788) Mol Microbiol. 2001 Feb;39(3):641-51. (PMID: 11169105) Nature. 1998 Feb 19;391(6669):806-11. (PMID: 9486653) Science. 2021 Oct;374(6563):57-65. (PMID: 34591643) Bioinformatics. 2022 Jan 12;38(3):710-719. (PMID: 34694364) Bioinformatics. 2014 Nov 1;30(21):3128-30. (PMID: 25064567) Mol Biol Evol. 2020 May 1;37(5):1530-1534. (PMID: 32011700) Cold Spring Harb Symp Quant Biol. 1951;16:13-47. (PMID: 14942727) Microbiol Spectr. 2015 Apr;3(2):MDNA3-0030-2014. (PMID: 26104715) Science. 1989 Jun 16;244(4910):1288-92. (PMID: 2660260) Cell. 2014 Jun 5;157(6):1262-1278. (PMID: 24906146) Science. 2012 Aug 17;337(6096):816-21. (PMID: 22745249) BMC Bioinformatics. 2010 Mar 08;11:119. (PMID: 20211023) Cell Host Microbe. 2020 Nov 11;28(5):767. (PMID: 33181077) J Bacteriol. 2009 Oct;191(20):6408-14. (PMID: 19684137) Science. 2013 Feb 15;339(6121):819-23. (PMID: 23287718) Mol Microbiol. 1993 Jun;8(6):1017-24. (PMID: 7689686) Proc Natl Acad Sci U S A. 1982 Jun;79(11):3398-402. (PMID: 6954485) Bioinformatics. 2014 Jul 15;30(14):2068-9. (PMID: 24642063) Bioinformatics. 2013 Nov 15;29(22):2933-5. (PMID: 24008419) Biotechniques. 2006 Apr;40(4):460, 462, 464. (PMID: 16629393) Nucleic Acids Res. 2006 Jan 1;34(Database issue):D32-6. (PMID: 16381877) Nat Biotechnol. 2001 Nov;19(11):1047-52. (PMID: 11689850) Bioinformatics. 2019 Jul 15;35(14):i295-i304. (PMID: 31510672) |
| Grant Information: | T32 GM139780 United States GM NIGMS NIH HHS |
| Entry Date(s): | Date Created: 20240208 Latest Revision: 20260426 |
| Update Code: | 20260426 |
| PubMed Central ID: | PMC10849738 |
| DOI: | 10.1101/2024.01.24.577089 |
| PMID: | 38328150 |
| Βάση Δεδομένων: | MEDLINE |
| ISSN: | 2692-8205 |
|---|---|
| DOI: | 10.1101/2024.01.24.577089 |