5-base sequencing
5-base sequencing refers to the detection of five nucleotide bases in DNA, including the four standard bases (adenine, guanine, cytosine, and thymine) and a modified base, 5-methylcytosine (5mC), an important epigenetic marker.[1] In a typical DNA sequencing experiment, the epigenetic modification is lost during PCR amplification step and only the base forms of nucleotides are recognized.[2] In a 5-base sequencing based experiment, the information about methylation of cytosines is preserved through chemical or enzymatic modification allowing inference of methylation status during bioinformatics analysis.[3] More recently, nanopore or single-molecule realtime sequencing have enabled direct detection of methylated cytosines without any conversion of the DNA.[4][5]
See also
[edit]References
[edit]- ^ López, V.; Fernández, A. F.; Fraga, M. F. (August 2017). "The role of 5-hydroxymethylcytosine in development, aging and age-related diseases". Ageing Research Reviews. 37: 28–38. doi:10.1016/j.arr.2017.05.002. ISSN 1872-9649. PMID 28499883.
- ^ "What is the 6-base genome? | biomodal". 2024-03-27. Retrieved 2025-07-31.
- ^ Lister, Ryan; Ecker, Joseph R. (June 2009). "Finding the fifth base: genome-wide sequencing of cytosine methylation". Genome Research. 19 (6): 959–966. doi:10.1101/gr.083451.108. ISSN 1088-9051. PMC 3807530. PMID 19273618.
- ^ Angeloni, Allegra; Ferguson, James; Bogdanovic, Ozren (2022). "Nanopore Sequencing and Data Analysis for Base-Resolution Genome-Wide 5-Methylcytosine Profiling". Methods in Molecular Biology (Clifton, N.J.). 2458: 75–94. doi:10.1007/978-1-0716-2140-0_5. ISSN 1940-6029. PMID 35103963.
- ^ Tse, O. Y. Olivia; Jiang, Peiyong; Cheng, Suk Hang; Peng, Wenlei; Shang, Huimin; Wong, John; Chan, Stephen L.; Poon, Liona C. Y.; Leung, Tak Y.; Chan, K. C. Allen; Chiu, Rossa W. K.; Lo, Y. M. Dennis (2021-02-02). "Genome-wide detection of cytosine methylation by single molecule real-time sequencing". Proceedings of the National Academy of Sciences. 118 (5): e2019768118. doi:10.1073/pnas.2019768118. PMC 7865158. PMID 33495335.