|DUKOWIC-SCHULZE, S - University Of Minnesota|
|SUNDARARAJAN, A - National Center For Genome Research|
|THIRUVARANGAN, R - National Center For Genome Resources|
|PAWLOWSKI, W.P. - Cornell University - New York|
|MUDGE, J - National Center For Genome Resources|
|CHEN, C - University Of Minnesota|
Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2016
Publication Date: 6/2/2016
Citation: Dukowic-Schulze, S., Sundararajan, A., Thiruvarangan, R., Kianian, S., Pawlowski, W., Mudge, J., Chen, C. 2016. Novel meiotic miRNAs and indications for a role of phasiRNAs in meiosis. Frontiers in Plant Science. 7:762. doi: 10.3389/fpls.2016.00762.
Interpretive Summary: Meiosis is a critical process in generating genetic variation in all sexually reproducing organisms and evolution of all species. The exact mechanism by which homologous chromosomes pair, recombine and exchange genetic material is a topic of much investigation. IN here we isolated meiotic cells from maize and sequenced the transcripts to investigate certain molecular changes during zygotene, an early stage of meiosis during which steps of meiotic recombination and synapsis of paired homologous chromosomes. We discovered two novel micro-RNA from meiocytes their putative target genes. Furthermore, we detected abundant phased, secondry, small RNA (PhasiRNA) of 21 nt and 24 nt length. Data indicates elevated DNA methylation at phasiRNA loci, suggesting a possible role in cis DNA methylation. 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 play a role in chromosome pairing and recombination.
Technical 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 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, and identified putative target genes. Furthermore, we detected abundant phasiRNAs of 21 nt and 24 nt length. PhasiRNAs are phased small RNAs which occur in 21 nt 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.