Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana

Abstract

BackgroundIn the past few decades, non-coding RNAs (ncRNAs) have emerged as important regulators of gene expression in eukaryotes. Most studies of ncRNAs in plants have focused on the identification of silencing microRNAs (miRNAs) and small interfering RNAs (siRNAs). Another important family of ncRNAs that has been well characterized in plants is the small nucleolar RNAs (snoRNAs) and the related small Cajal body-specific RNAs (scaRNAs). Both target chemical modifications of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). In plants, the snoRNA genes are organized in clusters, transcribed by RNA Pol II from a common promoter and subsequently processed into mature molecules. The promoter regions of snoRNA polycistronic genes in plants are highly enriched in two conserved cis-regulatory elements (CREs), Telo-box and Site II, which coordinate the expression of snoRNAs and ribosomal protein coding genes throughout the cell cycle.ResultsIn order to identify novel ncRNA genes, we have used the snoRNA Telo-box/Site II motifs combination as a functional promoter indicator to screen the Arabidopsis genome. The predictions generated by this process were tested by detailed exploration of available RNA-Seq and expression data sets and experimental validation. As a result, we have identified several snoRNAs, scaRNAs and 'orphan' snoRNAs. We also show evidence for 16 novel ncRNAs that lack similarity to any reported RNA family. Finally, we have identified two dicistronic genes encoding precursors that are processed to mature snoRNA and miRNA molecules. We discuss the evolutionary consequences of this result in the context of a tight link between snoRNAs and miRNAs in eukaryotes.ConclusionsWe present an alternative computational approach for non-coding RNA detection. Instead of depending on sequence or structure similarity in the whole genome screenings, we have explored the properties of promoter regions of well-characterized ncRNAs. Interestingly, besides expected ncRNAs predictions we were also able to recover single precursor arrangement for snoRNA-miRNA. Accompanied by analyses performed on rice sequences, we conclude that such arrangement might have interesting functional and evolutionary consequences and discuss this result in the context of a tight link between snoRNAs and miRNAs in eukaryotes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2221-x) contains supplementary material, which is available to authorized users.

Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis

“…Site II motifs have been shown to be present in promoters of some, but not all, snoRNA genes. They also have been shown to be present in ribosomal genes (28)(29)(30). To examine the relation between this cis element and the expression of HID2 in planta, we constructed pHID2 WT :GUS and pHID2 mut :GUS and (Fig.…”

Los RNAs pequeños nucleolares y su participación en el cáncer

“…Hasta la fecha se conoce muy poco acerca de la organización de los promotores de los genes que son transcritos de manera autónoma y que codifican para snoRNAs. En las levaduras, estos promotores están formados por octámeros y motivos CCAAT, cajas TATA y Homol D, y elementos ricos en A/T, en donde se unen factores de transcripción tales como Rap1 (RA-P1A, miembro de la familia de oncogenes RAS), Abf1p (musculina) y Tbf1; estas regiones son transcritas por la RNA polimerasa II [29][30][31] . Se sabe que la caja Homol D es crítica para la transcripción del snoRNA U3, mientras que la caja TATA tiene una gran influencia sobre la eficiencia de la transcripción, pero no es esencial 30 .…”

“…En las levaduras, estos promotores están formados por octámeros y motivos CCAAT, cajas TATA y Homol D, y elementos ricos en A/T, en donde se unen factores de transcripción tales como Rap1 (RA-P1A, miembro de la familia de oncogenes RAS), Abf1p (musculina) y Tbf1; estas regiones son transcritas por la RNA polimerasa II [29][30][31] . Se sabe que la caja Homol D es crítica para la transcripción del snoRNA U3, mientras que la caja TATA tiene una gran influencia sobre la eficiencia de la transcripción, pero no es esencial 30 . Además de estos motivos, hay otros localizados río arriba del U3 que también son capaces de dirigir la transcripción de su promotor 29 , lo cual denota la complejidad que tiene la transcripción de los snoRNAs.…”

When small RNAs become smaller: non - canonical functions of snoRNAs and their derivatives

“…Interestingly, using an alternative computational approach for non-coding RNA detection based on the properties of promoter regions of well-characterized ncRNAs, in 2015 Qu et al were able to detect two dicistronic genes encoding precursors that are processed into mature snoRNA and miRNA molecules in Arabidopsis thaliana (Qu et al, 2015). Both, the snoRNAs and the miRNA transcribed from the two identified dicistronic snoRNA-miRNA775 and sno-miRNA779 genes have a common precursor and they use two distinct maturation pathways that preserve the integrity of both ncRNAs.…”