scM&T-Seq

scM&T-Seq

scM&T-Seq allows parallel analysis of both epigenetic and gene expression patterns from single cells using Smart-seq2 and scBS-seq. scM&T-Seq is built upon G&T-seq, but instead of using MDA for DNA sequencing, it uses scBS-Seq to determine DNA methylation patterns.

Single cells are isolated and individually lysed. The mRNAs are captured with streptavidin-coupled mRNA capture primers to separate them physically from the DNA strands. Smart-seq2 uses RT with template switching and tagmentation to generate cDNA libraries from the mRNA. DNA libraries are prepared via scBS-seq, which involves bisulfite conversion of DNA strands to identify methylated cytosines. Both libraries are ready for sequencing.

Pros:

• Investigates links between epigenetic and transcriptional heterogeneity in single cells
• Because DNA and RNA are physically separated and amplified independently, there is no need to mask coding sequences during analysis

Cons:

• Smart-seq2 is not strand-specific and applicable to only poly(A)+ RNA
• Does not distinguish between 5mC and 5hmC

• scM&T-Seq: Angermueller C., Clark S. J., Lee H. J., Macaulay I. C., Teng M. J., et al. (2016) Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nat Methods 13: 229-232

1. Clark S. J., Lee H. J., Smallwood S. A., Kelsey G. and Reik W. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity. Genome Biol. 2016;17:72
2. Wen L. and Tang F. Single-cell sequencing in stem cell biology. Genome Biol. 2016;17:71

1. Hu Y., Huang K., An Q., et al. Simultaneous profiling of transcriptome and DNA methylome from a single cell. Genome Biol. 2016;17:88