Abstract
BackgroundVarious small RNA (sRNA) sizes and varieties have been identified, but their relationship as well as relationship with their origins and allocations have not been well understood or investigated.ResultsBy comparing sRNAs generated from two barley cultivars, Golden Promise (GP) and Pallas, we identified that the generation of different sizes and types of sRNAs in barley was locus-, chromosome- and/or cultivar-dependent. 20-nt sRNAs mainly comprising miRNAs and chloroplast-derived sRNAs were significantly over-expressed in Pallas vs. GP on chromosomes 3H and 6H. MiRNAs-enriched 21-nt sRNAs were significantly over-expressed in Pallas vs. GP only on chromosome 4H. On chromosome 5H this size of sRNAs was significantly under-expressed in Pallas, so were 22-nt sRNAs mainly comprising miRNAs and repeat-derived sRNAs. 24-nt sRNAs mostly derived from repeats were evenly distributed in all chromosomes and expressed similarly between GP and Pallas. Unlike other sizes of sRNAs, 24-nt sRNAs were little conserved in other plant species. Abundant sRNAs were mostly generated from 3’ terminal regions of chromosome 1H and 5’ terminal regions of chromosome 5H. Over-expressed miRNAs in GP vs. Pallas primarily function in stress responses and iron-binding.ConclusionsOur study indicates that 23−24-nt sRNAs may be linked to repressive chromatin modifications and function in genome stability while 20−21-nt sRNAs may be important for the cultivar specificity. This study provides a novel insight into the mechanism of sRNA expression and function in barley.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3023-5) contains supplementary material, which is available to authorized users.
Highlights
Various small RNA sizes and varieties have been identified, but their relationship as well as relationship with their origins and allocations have not been well understood or investigated
MiRNAs are single-stranded RNAs derived from hairpin precursors, which are processed from miRNA primary transcripts transcribed from genomic DNA, while Short interfering RNA (siRNA) are double-stranded RNAs derived from transposable elements (TEs), tandem repeats, convergent mRNA transcripts, natural sense-antisense pairs, duplexes involving pseudogene-derived antisense transcripts and the sense mRNAs from their cognate genes
They are generated by RNA-dependent RNA polymerase 2 (RDR2) and Dicer-like 3 (DCL3), which depends on the changes of transposon position and copy number during evolution [7]. 21-nt secondary siRNAs, including phased siRNAs or trans-acting siRNAs and nat-siRNAs that act in cis or in trans, are derived from dsRNA precursors and triggered by other small RNA (sRNA) together with DCL4 and RDR6 [7]
Summary
Various small RNA (sRNA) sizes and varieties have been identified, but their relationship as well as relationship with their origins and allocations have not been well understood or investigated. 23−24-nt (especially 24-nt) heterochromatic siRNAs are derived from intergenic and/or repetitive genomic regions and are a major class of endogenous siRNAs [7]. They are generated by RNA-dependent RNA polymerase 2 (RDR2) and Dicer-like 3 (DCL3), which depends on the changes of transposon position and copy number during evolution [7]. 21-nt secondary siRNAs, including phased siRNAs (phasiRNAs) or trans-acting siRNAs (ta-siRNAs) and nat-siRNAs that act in cis or in trans, are derived from dsRNA precursors and triggered by other sRNAs together with DCL4 and RDR6 [7]. Recent studies showed that secondary ta-siRNAs and cis-nat-siRNAs produced from overlapping proteincoding genes can be triggered by 22-nt miRNAs [8]. 23−24nt siRNAs are associated with AGO4 or AGO6 and promote DNA methylation in asymmetric CHH sites and H3K9 histone methylation at the target DNA loci to silence transposon activity for maintaining genome integrity [9]
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