Development and validation of monoclonal antibodies against N6-methyladenosine for the detection of RNA modifications

PLoS One. 2019 Oct 2;14(10):e0223197. doi: 10.1371/journal.pone.0223197. eCollection 2019.

Abstract

RNA contains various chemical modifications, among which N6-methyladenosine (m6A) is the most prevalent modified nucleotide in eukaryotic mRNA. Emerging evidence suggests that m6A plays an important role in regulating a variety of cellular functions by controlling mRNA processing, translation and degradation. Because m6A is not detectable by standard chemical modification-based approaches, immunological methods, such as ELISA, immunoblotting, immunohistochemistry, m6A RNA immunoprecipitation sequencing and m6A individual-nucleotide resolution cross-linking and immunoprecipitation, have been employed to detect m6A in RNA. Although the most important factor determining the success of these methods is the integrity of highly specific antibodies against m6A, the development of m6A-specific monoclonal antibodies has been challenging. We developed anti-m6A monoclonal antibodies using our recently developed single cell-based monoclonal antibody production system. The binding of one selected antibody, #B1-3, to RNA oligoribonucleotide containing a single m6A had an equilibrium dissociation constant of 6.5 nM, and this antibody exhibited negligible binding to oligoribonucleotides containing a single N1-methyladenosine and unmodified adenosine. The binding was competed by the addition of increasing concentrations of N6-methyl-ATP but not N1-methyl-ATP or ATP. Furthermore, this mAb specifically crosslinked m6A-containing oligoribonucleotide by ultraviolet light, resulting in the induction of cDNA truncation at m6A position. These results show the feasibility of using the validated m6A monoclonal antibody for the specific detection of m6A in RNA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Adenosine / analogs & derivatives*
  • Adenosine / immunology
  • Animals
  • Antibodies, Monoclonal / biosynthesis*
  • Base Sequence
  • Guinea Pigs
  • Immunization
  • Oligoribonucleotides / immunology
  • Pseudouridine / metabolism
  • RNA / metabolism*
  • Rabbits
  • Reverse Transcription

Substances

  • Antibodies, Monoclonal
  • Oligoribonucleotides
  • Pseudouridine
  • RNA
  • N-methyladenosine
  • Adenosine

Grants and funding

This research was supported in part by grants from the Hokuriku Industrial Advancement Center (HIAC) (H27HIAC122) for Kurosawa, N., and the Basic Science and Platform Technology Program for Innovative Biological Medicine (15657579), and the Emerging/Re-emerging Infectious Diseases Project of Japan (16768665) from Japan Agency for Medical and Development (AMED) for Isobe, M., and MEXT: Regional Innovation Strategy Support Program for Matsuzawa, S., and Isobe, M. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Medical & Biological Laboratories Co., Ltd., provided support in the form of salaries for the author [SM], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of the author is articulated in the ‘author contributions’ section.