Abstract
Small RNAs (sRNAs) are ~20 to 24 nucleotide single-stranded RNAs that play crucial roles in regulation of gene expression. In plants, sRNAs are classified into microRNAs (miRNAs), repeat-associated siRNAs (ra-siRNAs), phased siRNAs (pha-siRNAs), cis and trans natural antisense transcript siRNAs (cis- and trans-nat siRNAs). Pima (Gossypium barbadense L.) is one of the most economically important fiber crops, producing the best and longest spinnable fiber. Although some miRNAs are profiled in Pima, little is known about siRNAs, the largest subclass of plant sRNAs. In order to profile these gene regulators in Pima, a comprehensive analysis of sRNAs was conducted by mining publicly available sRNA data, leading to identification of 678 miRNAs, 3,559,126 ra-siRNAs, 627 pha-siRNAs, 136,600 cis-nat siRNAs and 79,994 trans-nat siRNAs. The 678 miRNAs, belonging to 98 conserved and 402 lineage-specific families, were produced from 2,138 precursors, of which 297 arose from introns, exons, or intron/UTR-exon junctions of protein-coding genes. Ra-siRNAs were produced from various repeat loci, while most (97%) were yielded from retrotransposons, especially LTRs (long terminal repeats). The genes encoding auxin-signaling-related proteins, NBS-LRRs and transcription factors were major sources of pha-siRNAs, while two conserved TAS3 homologs were found as well. Most cis-NATs in Pima overlapped in enclosed and convergent orientations, while a few hybridized in divergent and coincided orientations. Most cis- and trans-nat siRNAs were produced from overlapping regions. Additionally, characteristics of length and the 5’-first nucleotide of each sRNA class were analyzed as well. Results in this study created a valuable molecular resource that would facilitate studies on mechanism of controlling gene expression.
Highlights
Small RNAs are short, single-stranded RNAs that silence gene expression transcriptionally or post-transcriptionally [1,2,3], which is known as RNA-induced silencing. sRNAs are produced from longer, double stranded RNA precursors by DICER-LIKE proteinsPLOS ONE | DOI:10.1371/journal.pone.0116826 February 13, 2015sRNAs in Pima (DCLs) in plants [4]
SRNAs are classified into microRNAs and small interfering RNAs, according to their origin and biogenesis [10]. miRNAs are processed from hairpinshaped RNA precursors that are transcribed by RNA polymerase II [11]
Most miRNAs are derived from non-coding genes, whose transcripts are further processed by DCLs with presence of the zinc finger protein SERRATE [12], HYPONASTIC LEAVES1 [13,14], the G-patch domain protein TOUGH [15] and hnRNP-like protein [16]
Summary
Small RNAs (sRNAs) are short, single-stranded RNAs that silence gene expression transcriptionally or post-transcriptionally [1,2,3], which is known as RNA-induced silencing. sRNAs are produced from longer, double stranded RNA (dsRNA) precursors by DICER-LIKE proteinsPLOS ONE | DOI:10.1371/journal.pone.0116826 February 13, 2015sRNAs in Pima (DCLs) in plants [4]. Many miRNAs target transcription factors, such as SQUAMOSA Promoter Binding Protein-Like, MYB and HD-ZIP [22,23], which are crucial for plant growth, development and stress response [21,24,25], but the so-called long miRNAs (24-nt in length) function to direct DNA methylation [8]. TAS3 homologs are widely found in various plants, and their ta-siRNAs are shown to play crucial roles in regulation of plant developmental timing and stress response [36,37,38] Both cis- and trans-nat siRNAs are processed from natural antisense transcripts (NATs) by DCL proteins in plants [10,39] but differ by their origin. Nat-derived siRNAs are shown to regulate diverse physiological processes, such as fertilization and stress response to environmental cues [7,39,40,41,42]
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