J Cancer 2015; 6(6):555-567. doi:10.7150/jca.11997

Review

Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers

Zhiyu Peng1✉, Chengfu Yuan2, Lucas Zellmer2, Siqi Liu3✉, Ningzhi Xu4✉, D. Joshua Liao2✉

1. Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, P. R. China
2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
3. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P. R. China
4. Laboratory of Cell and Molecular Biology, Cancer Institute, Chinese Academy of Medical Science, Beijing 100021, P. R. China

Abstract

Recent RNA-sequencing technology and associated bioinformatics have led to identification of tens of thousands of putative human chimeric RNAs, i.e. RNAs containing sequences from two different genes, most of which are derived from neighboring genes on the same chromosome. In this essay, we redefine “two neighboring genes” as those producing individual transcripts, and point out two known mechanisms for chimeric RNA formation, i.e. transcription from a fusion gene or trans-splicing of two RNAs. By our definition, most putative RNA chimeras derived from canonically-defined neighboring genes may either be technical artifacts or be cis-splicing products of 5'- or 3'-extended RNA of either partner that is redefined herein as an unannotated gene, whereas trans-splicing events are rare in human cells. Therefore, most authentic chimeric RNAs result from fusion genes, about 1,000 of which have been identified hitherto. We propose a hypothesis of “consecutive reverse transcriptions (RTs)”, i.e. another RT reaction following the previous one, for how most spurious chimeric RNAs, especially those containing a short homologous sequence, may be generated during RT, especially in RNA-sequencing wherein RNAs are fragmented. We also point out that RNA samples contain numerous RNA and DNA shreds that can serve as endogenous random primers for RT and ensuing polymerase chain reactions (PCR), creating artifacts in RT-PCR.

Keywords: artifacts, chimeric RNAs, endogenous random primers

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How to cite this article:
Peng Z, Yuan C, Zellmer L, Liu S, Xu N, Liao DJ. Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers. J Cancer 2015; 6(6):555-567. doi:10.7150/jca.11997. Available from http://www.jcancer.org/v06p0555.htm