Genome-wide analysis of leafbladeless1-regulated and phased small RNAs underscores the importance of the TAS3 ta-siRNA pathway to maize development

PLoS Genet. 2014 Dec 11;10(12):e1004826. doi: 10.1371/journal.pgen.1004826. eCollection 2014 Dec.

Abstract

Maize leafbladeless1 (lbl1) encodes a key component in the trans-acting short-interfering RNA (ta-siRNA) biogenesis pathway. Correlated with a great diversity in ta-siRNAs and the targets they regulate, the phenotypes conditioned by mutants perturbing this small RNA pathway vary extensively across species. Mutations in lbl1 result in severe developmental defects, giving rise to plants with radial, abaxialized leaves. To investigate the basis for this phenotype, we compared the small RNA content between wild-type and lbl1 seedling apices. We show that LBL1 affects the accumulation of small RNAs in all major classes, and reveal unexpected crosstalk between ta-siRNA biogenesis and other small RNA pathways regulating transposons. Interestingly, in contrast to data from other plant species, we found no evidence for the existence of phased siRNAs generated via the one-hit model. Our analysis identified nine TAS loci, all belonging to the conserved TAS3 family. Information from RNA deep sequencing and PARE analyses identified the tasiR-ARFs as the major functional ta-siRNAs in the maize vegetative apex where they regulate expression of AUXIN RESPONSE FACTOR3 (ARF3) homologs. Plants expressing a tasiR-ARF insensitive arf3a transgene recapitulate the phenotype of lbl1, providing direct evidence that deregulation of ARF3 transcription factors underlies the developmental defects of maize ta-siRNA biogenesis mutants. The phenotypes of Arabidopsis and Medicago ta-siRNA mutants, while strikingly different, likewise result from misexpression of the tasiR-ARF target ARF3. Our data indicate that diversity in TAS pathways and their targets cannot fully account for the phenotypic differences conditioned by ta-siRNA biogenesis mutants across plant species. Instead, we propose that divergence in the gene networks downstream of the ARF3 transcription factors or the spatiotemporal pattern during leaf development in which these proteins act constitute key factors underlying the distinct contributions of the ta-siRNA pathway to development in maize, Arabidopsis, and possibly other plant species as well.

Publication types

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

MeSH terms

  • Arabidopsis / genetics
  • Gene Expression Regulation, Plant*
  • Genetic Loci
  • Genotype
  • High-Throughput Nucleotide Sequencing
  • Indoleacetic Acids / metabolism
  • Mutation
  • Phenotype
  • Plant Development / genetics*
  • Plant Leaves
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism
  • RNA, Small Interfering / genetics*
  • RNA, Small Interfering / metabolism
  • Sequence Analysis, RNA
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transgenes
  • Zea mays / genetics*

Substances

  • Indoleacetic Acids
  • Plant Proteins
  • RNA, Small Interfering
  • Transcription Factors

Grants and funding

This work was supported with funding from Pioneer- DuPont and by a grant from the National Science Foundation (MCB-1159098) to MCPT and MH. Pioneer- DuPont generated the small RNA libraries. The funders had no role in study design, data analysis, decision to publish, or preparation of the manuscript.