RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II

Isabel X Wang; Leighton J Core; Hojoong Kwak; Lauren Brady; Alan Bruzel; Lee McDaniel; Allison L Richards; Ming Wu; Christopher Grunseich; John T Lis; Vivian G Cheung

doi:10.1016/j.celrep.2014.01.037

RNA-DNA differences are generated in human cells within seconds after RNA exits polymerase II

Cell Rep. 2014 Mar 13;6(5):906-15. doi: 10.1016/j.celrep.2014.01.037. Epub 2014 Feb 20.

Authors

Isabel X Wang¹, Leighton J Core², Hojoong Kwak³, Lauren Brady⁴, Alan Bruzel⁵, Lee McDaniel⁶, Allison L Richards⁷, Ming Wu⁸, Christopher Grunseich⁹, John T Lis¹⁰, Vivian G Cheung¹¹

Affiliations

¹ Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
² Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
³ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
⁴ Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA.
⁵ Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
⁶ Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.
⁷ Human Genetics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA.
⁸ Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
⁹ Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
¹⁰ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA. Electronic address: johnlis@cornell.edu.
¹¹ Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Departments of Pediatrics and Genetics, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: vgcheung@umich.edu.

Abstract

RNA sequences are expected to be identical to their corresponding DNA sequences. Here, we found all 12 types of RNA-DNA sequence differences (RDDs) in nascent RNA. Our results show that RDDs begin to occur in RNA chains ~55 nt from the RNA polymerase II (Pol II) active site. These RDDs occur so soon after transcription that they are incompatible with known deaminase-mediated RNA-editing mechanisms. Moreover, the 55 nt delay in appearance indicates that they do not arise during RNA synthesis by Pol II or as a direct consequence of modified base incorporation. Preliminary data suggest that RDD and R-loop formations may be coupled. These findings identify sequence substitution as an early step in cotranscriptional RNA processing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Catalytic Domain
Cell Culture Techniques
DNA / genetics
DNA / metabolism*
Gene Expression
Humans
RNA / genetics
RNA / metabolism*
RNA Polymerase II / metabolism*
Transcription, Genetic

Substances

RNA
DNA
RNA Polymerase II

Abstract

Publication types

MeSH terms

Substances

Grants and funding