Answers.Body: <p>On most coding genes (with the exception of replication dependent histone genes), <em>Transcripts</em> (as opposed to transcrip<strong>tion</strong>) are terminated by cleavage polyadenylation sites, where the growing transcript is cleaved by a protein complex and the poly-A tail. However, PolII continues to transcribe until it is terminated by torpedo termination (see <a href="https://en.wikipedia.org/wiki/Terminator_(genetics)#In_eukaryotes" rel="noreferrer">here</a>). Normally this extra RNA after the polyA site is degraded by Xrn2, but if you capture any particular snapshot of the RNA in the cell at any one time there will be a small amount that corresponds to this run on transcription. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-11T11:14:08.433Z
Answers.Text: Thanks for your help, Ian! The situation you mentioned seems could only occur downstream of the gene. Is that correct?
Answers.UserDisplayName: l0110
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-12T09:23:01.243Z
Answers.Text: Yes, this should only happen downstream of a gene.
Answers.UserDisplayName: Ian Sudbery
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-11T10:22:47.427Z
Answers.LastActivityDate: 2018-06-11T10:22:47.427Z
Answers.UserDisplayName: Ian Sudbery
Answers.Body: <p>The general idea behind a run-on fragment is that it's background noise. This derives from an open area of the genome that's next to an area that's actually being transcribed. Thus, all of the machinery for transcription is already present, so if the region adopts a bit more of an open conformation then that machinery can sporadically bind and start transcribing. You can get those either up- or down-stream of genes. A lot of things like this are just background transcriptional noise.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-11T11:03:49.483Z
Answers.Text: Thanks, Devon!!! Is there a paper, for example, a review or research paper related to this topic that I can read more (and cite in the future)?
Answers.UserDisplayName: l0110
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-11T11:05:38.417Z
Answers.Text: Not that I know of, though perhaps @IanSudbery knows of one.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-11T06:59:32.270Z
Answers.LastActivityDate: 2018-06-11T06:59:32.270Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I used <a href="http://ccb.jhu.edu/software/stringtie/gffcompare.shtml" rel="nofollow noreferrer">gffcompare</a> recently to compare a newly assembled transcriptome and a published transcriptome. The class code "p" transcripts are "possible polymerase run on".</p>
  
  <p><img src="https://ccb.jhu.edu/software/stringtie/gffcompare_codes_2col.gif" alt="Image"></p>
  
  <p>What does that mean? I tried very hard but still cannot find the answer.</p>
  
Tags: <transcriptome>
Title: What is "Possible polymerase run-on fragment"?
ThreadText: # What is "Possible polymerase run-on fragment"?
  
  (Asked by: username_0 on 2018-06-10)
  
  I used [gffcompare](http://ccb.jhu.edu/software/stringtie/gffcompare.shtml) recently to compare a newly assembled transcriptome and a published transcriptome. The class code "p" transcripts are "possible polymerase run on".
  
  ![Image](https://ccb.jhu.edu/software/stringtie/gffcompare_codes_2col.gif)
  
  What does that mean? I tried very hard but still cannot find the answer.
  
  **Tags:** transcriptome
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2018-06-11. Score: 5 | Accepted answer
  
  The general idea behind a run-on fragment is that it's background noise. This derives from an open area of the genome that's next to an area that's actually being transcribed. Thus, all of the machinery for transcription is already present, so if the region adopts a bit more of an open conformation then that machinery can sporadically bind and start transcribing. You can get those either up- or down-stream of genes. A lot of things like this are just background transcriptional noise.
  
  > **Comments:**
  > **username_0**: Thanks, username_2!!! Is there a paper, for example, a review or research paper related to this topic that I can read more (and cite in the future)?  
  > **username_2**: Not that I know of, though perhaps @username_1 knows of one.  
  
  ---
  
  ### Answer by username_1 on 2018-06-11. Score: 6
  
  On most coding genes (with the exception of replication dependent histone genes), *Transcripts* (as opposed to transcrip**tion**) are terminated by cleavage polyadenylation sites, where the growing transcript is cleaved by a protein complex and the poly-A tail. However, PolII continues to transcribe until it is terminated by torpedo termination (see [here](https://en.wikipedia.org/wiki/Terminator_(genetics)#In_eukaryotes)). Normally this extra RNA after the polyA site is degraded by Xrn2, but if you capture any particular snapshot of the RNA in the cell at any one time there will be a small amount that corresponds to this run on transcription.
  
  > **Comments:**
  > **username_0**: Thanks for your help, Ian! The situation you mentioned seems could only occur downstream of the gene. Is that correct?  
  > **username_1**: Yes, this should only happen downstream of a gene.  
  
  ---
  
  