Template-switching artifacts resemble alternative polyadenylation

Zsolt Balázs, Dóra Tombácz, Zsolt Csabai, Norbert Moldován, Michael Snyder, Zsolt Boldogkoi

Research output: Contribution to journalArticle

Abstract

Background: Alternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative polyadenylation are generally disregarded, while alternative polyadenylation artifacts are attributed to internal priming. Results: Here, we analyzed both long-read cDNA sequencing and direct RNA sequencing data of two organisms, generated by different sequencing platforms. We developed a filtering algorithm which takes into consideration that template-switching can be a source of artifactual polyadenylation when filtering out spurious polyadenylation sites. The algorithm outperformed the conventional internal priming filters based on comparison to direct RNA sequencing data. We also showed that the polyadenylation artifacts arise in cDNA sequencing at consecutive stretches of as few as three adenines. There was no substantial difference between the lengths of poly(A) tails at the artifactual and the true transcriptional end sites even though it is expected that internal priming artifacts have shorter poly(A) tails than genuine polyadenylated reads. Conclusions: Our findings suggest that template switching plays an important role in the generation of spurious polyadenylation and support the need for more rigorous filtering of artifactual polyadenylation sites in cDNA data, or that alternative polyadenylation should be annotated using native RNA sequencing.

Original languageEnglish
Article number824
JournalBMC genomics
Volume20
Issue number1
DOIs
Publication statusPublished - Nov 8 2019

Fingerprint

Polyadenylation
Artifacts
RNA Sequence Analysis
Complementary DNA
Messenger RNA
Adenine

Keywords

  • cDNA sequencing
  • Direct RNA sequencing
  • Internal priming
  • Long-read sequencing
  • Polyadenylation
  • RNA sequencing
  • Template switching

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Balázs, Z., Tombácz, D., Csabai, Z., Moldován, N., Snyder, M., & Boldogkoi, Z. (2019). Template-switching artifacts resemble alternative polyadenylation. BMC genomics, 20(1), [824]. https://doi.org/10.1186/s12864-019-6199-7

Template-switching artifacts resemble alternative polyadenylation. / Balázs, Zsolt; Tombácz, Dóra; Csabai, Zsolt; Moldován, Norbert; Snyder, Michael; Boldogkoi, Zsolt.

In: BMC genomics, Vol. 20, No. 1, 824, 08.11.2019.

Research output: Contribution to journalArticle

Balázs, Z, Tombácz, D, Csabai, Z, Moldován, N, Snyder, M & Boldogkoi, Z 2019, 'Template-switching artifacts resemble alternative polyadenylation', BMC genomics, vol. 20, no. 1, 824. https://doi.org/10.1186/s12864-019-6199-7
Balázs, Zsolt ; Tombácz, Dóra ; Csabai, Zsolt ; Moldován, Norbert ; Snyder, Michael ; Boldogkoi, Zsolt. / Template-switching artifacts resemble alternative polyadenylation. In: BMC genomics. 2019 ; Vol. 20, No. 1.
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