Answers.Body: <p>From the page <a href="https://www.idtdna.com/pages/education/decoded/article/use-of-template-switching-oligos-(ts-oligos-tsos)-for-efficient-cdna-library-construction" rel="nofollow noreferrer">you cited</a>:</p>
  
  <blockquote>
    <p>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</p>
  </blockquote>
  
  <p>That usually are CCC (1st is almost always C and the other two most of the times), see: <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085270" rel="nofollow noreferrer">Zajac et al., 2013</a></p>
  
  <p>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). </p>
  
  <p>So, answering to your question the <strong>polimerase does not switch strands</strong>, it <strong>switches from mRNA as a template to TSO as template</strong>. Because of that is called template switching.</p>
  
  <p><a href="https://i.sstatic.net/w1D7z.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/w1D7z.jpg" alt="enter image description here"></a></p>
  
  <p>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. </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-04-10T12:17:02.027Z
Answers.LastActivityDate: 2018-04-10T13:13:58.147Z
Answers.LastEditDate: 2018-04-10T13:13:58.147Z
Answers.UserDisplayName: jxx_fa
Body: <p>Reading Islam et al. (2011):</p>
  
  <blockquote>
    <p>From each transcript, a single read is obtained, corresponding to a template-switching site located preferentially at the 59 end of the mRNA.</p>
  </blockquote>
  
  <p>By reading <a href="https://www.idtdna.com/pages/education/decoded/article/use-of-template-switching-oligos-(ts-oligos-tsos)-for-efficient-cdna-library-construction" rel="noreferrer">this page</a> 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. </p>
  
  <p>Is it correct?</p>
  
  <ol>
  <li>Islam, S. et al. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129258/" rel="noreferrer">Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq</a>. genome.cshlp.org
  21, 1160–1167 (2011).</li>
  </ol>
  
Tags: <scrnaseq>
Title: What's a template switching site?
ThreadText: # What's a template switching site?
  
  (Asked by: username_0 on 2018-04-06)
  
  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](https://www.idtdna.com/pages/education/decoded/article/use-of-template-switching-oligos-(ts-oligos-tsos)-for-efficient-cdna-library-construction) 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](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129258/). genome.cshlp.org
     21, 1160–1167 (2011).
  
  **Tags:** scrnaseq
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-04-10. Score: 5 | Accepted answer
  
  From the page [you cited](https://www.idtdna.com/pages/education/decoded/article/use-of-template-switching-oligos-(ts-oligos-tsos)-for-efficient-cdna-library-construction):
  
  > 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](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085270)
  
  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](https://i.sstatic.net/w1D7z.jpg)](https://i.sstatic.net/w1D7z.jpg)
  
  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.
  
  
  ---
  
  