RRBS-Seq/scRRBS

RRBS-Seq/scRRBS

Reduced-representation bisulfite sequencing (RRBS-Seq ) or single-cell reduced-representation bisulfite sequencing (scRRBS ) is a protocol that uses one or multiple restriction enzymes on the genomic DNA to produce sequence-specific fragmentation. The fragmented genomic DNA is then treated with bisulfite and sequenced. This is the method of choice to study specific regions of interest. It is particularly effective where methylation is high, such as in promoters and repeat regions. 

Pros:

• Genome-wide coverage of CpGs in islands at single-base resolution
• Areas dense in CpG methylation are covered

Cons:

• Restriction enzymes cut at specific sites, providing biased sequence selection
• Method measures 10-15% of all CpGs in genome
• Cannot distinguish between 5mC and 5hmC
• Does not cover non-CpG areas, genome-wide CpGs, and CpGs in areas without the enzyme restriction site

Methods Links:

• RRBS: Meissner A., Gnirke A., Bell G. W., Ramsahoye B., Lander E. S., et al. (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33: 5868-5877
• scRRBS: Guo H., Zhu P., Guo F., Li X., Wu X., et al. (2015) Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing. Nat Protoc 10: 645-659

1. Guo H., Zhu P., Guo F., Li X., Wu X., et al. (2015) Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing. Nat Protoc 10: 645-659
2. Hannon E., Chand A. N., Evans M. D., Wong C. C. Y., Grubb M. S., et al. A role for CaV1 and calcineurin signalling to depolarization-induced changes in neuronal DNA methylation. Neuroepigenetics  
3. Lin X., Stenvang J., Rasmussen M. H., Zhu S., Jensen N. F., et al. (2015) The potential role of Alu Y in the development of resistance to SN38 (Irinotecan) or oxaliplatin in colorectal cancer. BMC Genomics 16: 404
4. Lee E.-J., Rath P., Liu J., Ryu D., Pei L., et al. Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells. Journal of Genetics and Genomics  
5. Yang Y., Sebra R., Pullman B. S., Qiao W., Peter I., et al. (2015) Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC Genomics 16: 350
6. Zhang G., Esteve P. O., Chin H. G., Terragni J., Dai N., et al. (2015) Small RNA-mediated DNA (cytosine-5) methyltransferase 1 inhibition leads to aberrant DNA methylation. Nucleic Acids Res 43: 6112-6124