CHH DNA methylation increases at 24-PHAS loci depend on 24-nt phased small interfering RNAs in maize meiotic anthers

New Phytol. 2021 Mar;229(5):2984-2997. doi: 10.1111/nph.17060. Epub 2020 Dec 12.


Plant phased small interfering RNAs (phasiRNAs) contribute to robust male fertility; however, specific functions remain undefined. In maize (Zea mays), male sterile23 (ms23), necessary for both 24-nt phasiRNA precursor (24-PHAS) loci and Dicer-like5 (Dcl5) expression, and dcl5-1 mutants unable to slice PHAS transcripts lack nearly all 24-nt phasiRNAs. Based on sequence capture bisulfite-sequencing, we find that CHH DNA methylation of most 24-PHAS loci is increased in meiotic anthers of control plants but not in the ms23 and dcl5 mutants. Because dcl5-1 anthers express PHAS precursors, we conclude that the 24-nt phasiRNAs, rather than just activation of PHAS transcription, are required for targeting increased CHH methylation at these loci. Although PHAS precursors are processed into multiple 24-nt phasiRNA products, there is substantial differential product accumulation. Abundant 24-nt phasiRNA positions corresponded to high CHH methylation within individual loci, reinforcing the conclusion that 24-nt phasiRNAs contribute to increased CHH methylation in cis.

Keywords: Dcl5; Ms23; DNA methylation; Zea mays (maize); phasiRNA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • DNA Methylation / genetics
  • Gene Expression Regulation, Plant*
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • RNA, Plant
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism
  • Zea mays* / genetics
  • Zea mays* / metabolism


  • Plant Proteins
  • RNA, Plant
  • RNA, Small Interfering