Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis

Stefanie Dukowic-Schulze,Changbin Chen,Thiruvarangan Ramaraj,Joann Mudge,Wojciech P Pawlowski,Anitha Sundararajan,Shahryar Kianian

doi:10.3389/fpls.2016.00762

Abstract

Small RNAs (sRNA) add additional layers to the regulation of gene expression, with siRNAs directing gene silencing at the DNA level by RdDM (RNA-directed DNA methylation), and micro RNAs (miRNAs) directing post-transcriptional regulation of specific target genes, mostly by mRNA cleavage. We used manually isolated male meiocytes from maize (Zea mays) to investigate sRNA and DNA methylation landscapes during zygotene, an early stage of meiosis during which steps of meiotic recombination and synapsis of paired homologous chromosomes take place. We discovered two novel miRNAs from meiocytes, zma-MIR11969 and zma-MIR11970, and identified putative target genes. Furthermore, we detected abundant phasiRNAs of 21 and 24 nt length. PhasiRNAs are phased small RNAs which occur in 21 or 24 nt intervals, at a few hundred loci, specifically in male reproductive tissues in grasses. So far, the function of phasiRNAs remained elusive. Data from isolated meiocytes now revealed elevated DNA methylation at phasiRNA loci, especially in the CHH context, suggesting a role for phasiRNAs in cis DNA methylation. In addition, we consider a role of these phasiRNAs in chromatin remodeling/dynamics during meiosis. However, this is not well supported yet and will need more additional data. Here, we only lay out the idea due to other relevant literature and our additional observation of a peculiar GC content pattern at phasiRNA loci. Chromatin remodeling is also indicated by the discovery that histone genes were enriched for sRNA of 22 nt length. Taken together, we gained clues that lead us to hypothesize sRNA-driven DNA methylation and possibly chromatin remodeling during male meiosis in the monocot maize which is in line with and extends previous knowledge.

Highlights

Examining gene expression provides important information to understand how processes in distinct cell types and stages during development are orchestrated
Small RNAs differ in their biogenesis and function, and originally there was a clear distinction between micro RNAs (miRNAs) which act in trans and small interfering RNA (siRNA) which act in cis (Figure 1A)
We previously reported the characterization of mRNA-seq data obtained from isolated maize meiocytes via polyA selection and Illumina sequencing (Dukowic-Schulze et al, 2014a), and have exploited this data further to examine the expression of genes in Small RNAs (sRNA) pathways

Summary

Introduction

Examining gene expression provides important information to understand how processes in distinct cell types and stages during development are orchestrated. MiRNAs have important roles in down-regulating gene expression especially in plant development (Jones-Rhoades and Bartel, 2004; Borges et al, 2011; reviewed in: Mallory and Vaucheret, 2006), while siRNAs are primarily targeting and silencing exogenous sequences like transposable elements (TEs), transgenes and viruses (reviewed in: Baulcombe, 2004). The tasiRNA loci are few in number (four TAS families in Arabidopsis; Chen et al, 2007) but have identified important target genes including Auxin Responsive Factors (ARFs, involved in growth and development), pentatricopeptide repeat proteins (PPRs, involved in RNA processing) and nucleotide-binding, leucine-rich repeat proteins (NB-LRRs, involved in disease defense; Allen et al, 2005; Adenot et al, 2006; Fahlgren et al, 2006; Howell et al, 2007; Zhai et al, 2011; Xia et al, 2013). The existence and abundance of phasiRNAs during male gametogenesis in plants points to a unique function for these sRNA species, but the function remained elusive so far

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Discussion

Conclusion