Reading Islam et al. (2011):

From each transcript, a single read is obtained, corresponding to a template-switching site located preferentially at the 59 end of the mRNA.

By reading this page I think that a template switching site is an additional set of nucleotides added at the 3' end of the newly synthesized cDNA, that serve to anchor a oligo-nucleotide used by the reverse transcriptase to synthesize the second cDNA strand. It is called template switching because reverse transcriptase switches strand upon reaching this set of nucleotides.

Is it correct?

  1. Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. genome.cshlp.org 21, 1160–1167 (2011).

1 Answer 1


From the page you cited:

During first-strand synthesis, upon reaching the 5’ end of the RNA template, the terminal transferase activity of the MMLV reverse transcriptase adds a few additional nucleotide

That usually are CCC (1st is almost always C and the other two most of the times), see: Zajac et al., 2013

These CCCs are used for priming the Template Switching Oligo (TSO), that has GGG and whatever you want to add to the sequence (for instance UMIs and adapters).

So, answering to your question the polimerase does not switch strands, it switches from mRNA as a template to TSO as template. Because of that is called template switching.

enter image description here

You can see it in the graph from the page you cited. In the template switching step polimerase switch from the mRNA to the TSO and continue with the synthesis of the first cDNA strand using TSO as template.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.