What is Biological Dark Matter? скачать в хорошем качестве

What is Biological Dark Matter?

Science Spotlight 1 In this spotlight, Dr. Williamson covers biological dark matter. He defines what biological dark matter is and goes through the various categories: microbial dark matter, dark DNA, dark RNA, dark proteins, dark viruses, and other dark molecules. References Rinke, C., Schwientek, P., Sczyrba, A. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013). https://doi.org/10.1038/nature12352 Hug, L., Baker, B., Anantharaman, K. et al. A new view of the tree of life. Nat Microbiol 1, 16048 (2016). https://doi.org/10.1038/nmicrobiol.20... Parks, D.H., Rinke, C., Chuvochina, M. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2, 1533–1542 (2017). https://doi.org/10.1038/s41564-017-00... Escudeiro P, Henry CS, Dias RPM. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. Curr Res Microb Sci. 2022 Aug 7;3:100159. doi: 10.1016/j.crmicr.2022.100159. PMID: 36561390; PMCID: PMC9764257. Yuguo Zha, Hui Chong, Pengshuo Yang, Kang Ning, Microbial Dark Matter: from Discovery to Applications, Genomics, Proteomics & Bioinformatics, Volume 20, Issue 5, 2022, Pages 867-881, ISSN 1672-0229, https://doi.org/10.1016/j.gpb.2022.02.... Wang Y, Gallagher LA, Andrade PA, Liu A, Humphreys IR, Turkarslan S, Cutler KJ, Arrieta-Ortiz ML, Li Y, Radey MC, McLean JS, Cong Q, Baker D, Baliga NS, Peterson SB, Mougous JD. Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle. Cell. 2023 Oct 26;186(22):4803-4817.e13. doi: 10.1016/j.cell.2023.08.017. Epub 2023 Sep 7. PMID: 37683634; PMCID: PMC10633639. Liu, Y., Makarova, K.S., Huang, WC. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). https://doi.org/10.1038/s41586-021-03... Palazzo AF, Gregory TR (2014) The Case for Junk DNA. PLoS Genet 10(5): e1004351. https://doi.org/10.1371/journal.pgen.... Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet. 2023 May 16;14:1150212. doi: 10.3389/fgene.2023.1150212. PMID: 37260773; PMCID: PMC10228655. DeepMind’s new AlphaGenome AI tackles the ‘dark matter’ in our DNA, https://www.nature.com/articles/d4158... Kapranov P, St Laurent G. Dark Matter RNA: Existence, Function, and Controversy. Front Genet. 2012 Apr 23;3:60. doi: 10.3389/fgene.2012.00060. PMID: 22536205; PMCID: PMC3332219. Chen LL, Kim VN. Small and long non-coding RNAs: Past, present, and future. Cell. 2024 Nov 14;187(23):6451-6485. doi: 10.1016/j.cell.2024.10.024. PMID: 39547208. ‘The entire protein universe’: AI predicts shape of nearly every known protein, https://www.nature.com/articles/d4158... ‘Dark proteins’ hiding in our cells could hold clues to cancer and other diseases, https://www.nature.com/articles/d4158... Ross JL. The Dark Matter of Biology. Biophys J. 2016 Sep 6;111(5):909-16. doi: 10.1016/j.bpj.2016.07.037. PMID: 27602719; PMCID: PMC5018137. Deutsch EW, Kok LW, Mudge JM, Ruiz-Orera J, Fierro-Monti I, et al. High-quality peptide evidence for annotating non-canonical open reading frames as human proteins. bioRxiv [Preprint]. 2024 Sep 9:2024.09.09.612016. doi: 10.1101/2024.09.09.612016. PMID: 39314370; PMCID: PMC11419116. Azam S, Yang F, Wu X. Finding functional microproteins. Trends Genet. 2025 Feb;41(2):107-118. doi: 10.1016/j.tig.2024.12.001. Epub 2025 Jan 2. PMID: 39753408; PMCID: PMC11794006. Filée J, Tétart F, Suttle CA, Krisch HM. Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12471-6. doi: 10.1073/pnas.0503404102. Epub 2005 Aug 22. PMID: 16116082; PMCID: PMC1194919. Santiago-Rodriguez TM, Hollister EB. Unraveling the viral dark matter through viral metagenomics. Front Immunol. 2022 Sep 16;13:1005107. doi: 10.3389/fimmu.2022.1005107. PMID: 36189246; PMCID: PMC9523745. Zheludev IN, Edgar RC, Lopez-Galiano MJ, de la Peña M, Babaian A, Bhatt AS, Fire AZ. Viroid-like colonists of human microbiomes. Cell. 2024 Nov 14;187(23):6521-6536.e18. doi: 10.1016/j.cell.2024.09.033. Epub 2024 Oct 30. PMID: 39481381; PMCID: PMC11949080. Mallapaty S. AI scans RNA 'dark matter' and uncovers 70,000 new viruses. Nature. 2024 Oct;634(8035):765-766. doi: 10.1038/d41586-024-03320-6. PMID: 39394343. Minch B, Moniruzzaman M. Expansion of the genomic and functional diversity of global ocean giant viruses. Npj Viruses. 2025 Apr 21;3(1):32. doi: 10.1038/s44298-025-00122-z. PMID: 40295861; PMCID: PMC12012013. Monge ME, Dodds JN, Baker ES, Edison AS, Fernández FM. Challenges in Identifying the Dark Molecules of Life. Annu Rev Anal Chem (Palo Alto Calif). 2019 Jun 12;12(1):177-199. doi: 10.1146/annurev-anchem-061318-114959. Epub 2019 Mar 18. PMID: 30883183; PMCID: PMC6716371.