N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding

Katherine I Zhou; Marc Parisien; Qing Dai; Nian Liu; Luda Diatchenko; Joseph R Sachleben; Tao Pan

doi:10.1016/j.jmb.2015.08.021

N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding

J Mol Biol. 2016 Feb 27;428(5 Pt A):822-833. doi: 10.1016/j.jmb.2015.08.021. Epub 2015 Sep 4.

Authors

Katherine I Zhou¹, Marc Parisien², Qing Dai³, Nian Liu³, Luda Diatchenko², Joseph R Sachleben⁴, Tao Pan⁵

Affiliations

¹ Medical Scientist Training Program, The University of Chicago, Chicago, IL 60637, USA.
² The Alan Edwards Centre for Research on Pain, McGill University, Montréal, QC, Canada H3A 0G4.
³ Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.
⁴ Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA.
⁵ Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Institute of Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA. Electronic address: taopan@uchicago.edu.

Abstract

N(6)-Methyladenosine (m(6)A) is a reversible and abundant internal modification of messenger RNA (mRNA) and long noncoding RNA (lncRNA) with roles in RNA processing, transport, and stability. Although m(6)A does not preclude Watson-Crick base pairing, the N(6)-methyl group alters the stability of RNA secondary structure. Since changes in RNA structure can affect diverse cellular processes, the influence of m(6)A on mRNA and lncRNA structure has the potential to be an important mechanism for m(6)A function in the cell. Indeed, an m(6)A site in the lncRNA metastasis associated lung adenocarcinoma transcript 1 (MALAT1) was recently shown to induce a local change in structure that increases the accessibility of a U5-tract for recognition and binding by heterogeneous nuclear ribonucleoprotein C (HNRNPC). This m(6)A-dependent regulation of protein binding through a change in RNA structure, termed "m(6)A-switch", affects transcriptome-wide mRNA abundance and alternative splicing. To further characterize this first example of an m(6)A-switch in a cellular RNA, we used nuclear magnetic resonance and Förster resonance energy transfer to demonstrate the effect of m(6)A on a 32-nucleotide RNA hairpin derived from the m(6)A-switch in MALAT1. The observed imino proton nuclear magnetic resonance resonances and Förster resonance energy transfer efficiencies suggest that m(6)A selectively destabilizes the portion of the hairpin stem where the U5-tract is located, increasing the solvent accessibility of the neighboring bases while maintaining the overall hairpin structure. The m(6)A-modified hairpin has a predisposed conformation that resembles the hairpin conformation in the RNA-HNRNPC complex more closely than the unmodified hairpin. The m(6)A-induced structural changes in the MALAT1 hairpin can serve as a model for a large family of m(6)A-switches that mediate the influence of m(6)A on cellular processes.

Keywords: FRET; MALAT1 lncRNA; N(6)-methyladenosine (m(6)A); NMR; RNA structural modeling.

Publication types

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

MeSH terms

Adenosine / analogs & derivatives*
Adenosine / chemistry
Alternative Splicing
Humans
Models, Molecular
Nucleic Acid Conformation*
Protein Binding*
RNA, Long Noncoding / chemistry*
RNA, Messenger / chemistry*

Substances

MALAT1 long non-coding RNA, human
RNA, Long Noncoding
RNA, Messenger
N-methyladenosine
Adenosine

Abstract

Publication types

MeSH terms

Substances

Grants and funding