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 the 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] In October 2025, Illumina announced a proprietary 5-base sequencing solution using an engineered DNA for 5mC detection on top of standard bases.[6]

The approach can further be extended to detect 5hmC modification, known as 6-base genome or sequencing.[2]

See also

References

  1. ^ 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. hdl:10651/44229. ISSN 1872-9649. PMID 28499883.
  2. ^ a b "What is the 6-base genome? | biomodal". 2024-03-27. Retrieved 2025-07-31.
  3. ^ 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.
  4. ^ Angeloni, Allegra; Ferguson, James; Bogdanovic, Ozren (2022). "Nanopore Sequencing and Data Analysis for Base-Resolution Genome-Wide 5-Methylcytosine Profiling". Chromatin. Methods in Molecular Biology (Clifton, N.J.). Vol. 2458. pp. 75–94. doi:10.1007/978-1-0716-2140-0_5. ISBN 978-1-0716-2139-4. ISSN 1940-6029. PMID 35103963.
  5. ^ 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. Bibcode:2021PNAS..11819768T. doi:10.1073/pnas.2019768118. PMC 7865158. PMID 33495335.
  6. ^ "Illumina fuels multiomic discovery with launch of 5-base solution, unlocking simultaneous genomic and epigenomic insights". www.illumina.com. Retrieved 2025-10-31.
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