Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing

Nat Protoc. 2015 May;10(5):645-59. doi: 10.1038/nprot.2015.039. Epub 2015 Apr 2.


The heterogeneity of DNA methylation within a population of cells necessitates DNA methylome profiling at single-cell resolution. Recently, we developed a single-cell reduced-representation bisulfite sequencing (scRRBS) technique in which we modified the original RRBS method by integrating all the experimental steps before PCR amplification into a single-tube reaction. These modifications enable scRRBS to provide digitized methylation information on ∼1 million CpG sites within an individual diploid mouse or human cell at single-base resolution. Compared with the single-cell bisulfite sequencing (scBS) technique, scRRBS covers fewer CpG sites, but it provides better coverage for CpG islands (CGIs), which are likely to be the most informative elements for DNA methylation. The entire procedure takes ∼3 weeks, and it requires strong molecular biology skills.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CpG Islands*
  • DNA Methylation*
  • Female
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Male
  • Mammals / genetics*
  • Mice
  • Polymerase Chain Reaction / instrumentation
  • Polymerase Chain Reaction / methods
  • Quality Control
  • Single-Cell Analysis / methods*
  • Sulfites


  • Sulfites
  • hydrogen sulfite