Long noncoding RNAs in the model species Brachypodium distachyon

Abstract

Eukaryotic genomes are pervasively transcribed and only a small portion of the transcribed sequences belongs to protein coding genes. High-throughput sequencing technology contributed to consolidate this perspective, allowing the identification of numerous noncoding RNAs with key roles in biological processes. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nt with limited phylogenetic conservation, expressed at low levels and characterized by tissue/organ specific expression profiles. Although a large set of lncRNAs has been identified, the functional roles of lncRNAs are only beginning to be recognized and the molecular mechanism of lncRNA-mediated gene regulation remains largely unexplored, particularly in plants where their annotation and characterization are still incomplete. Using public and proprietary poly-(A)+ RNA-seq data as well as a collection of full length ESTs from several organs, developmental stages and stress conditions in three Brachypodium distachyon inbred lines, we describe the identification and the main features of thousands lncRNAs. Here we provide a genome-wide characterization of lncRNAs, highlighting their intraspecies conservation and describing their expression patterns among several organs/tissues and stress conditions. This work represents a fundamental resource to deepen our knowledge on long noncoding RNAs in C3 cereals, allowing the Brachypodium community to exploit these results in future research programs.

Long non-coding RNAs in wild wheat progenitors

“…1). In agreement with the main characteristics described in the literature of plant lncRNAs (Liu et al 2012;Shuai et al 2014;Wang et al 2014;Zhang et al 2014;Chen et al 2015;Zhu et al 2015;De Quattro et al 2017), our data suggest that wild wheat lncRNAs are mostly mono-exonic (77% in T. urartu and 80 % in Ae. tauschii) or harbor fewer exons than protein coding genes.…”

“…INDUCED BY PHOSPHATE STARVATION, involved in the phosphate uptake, interacts with miR-399 through a partial complementarity, thus preventing the cleavage of PHOSPHATE 2, the miR-399 target, which, in turn, negatively affects phosphate shoot content and its remobilization (Franco-Zorrilla et al 2007). Despite these well-defined examples, the systematic characterization of lncRNA loci is still in its infancy, although in the past few years a number of rigorous genomewide mapping lncRNA studies based on extensive RNA-sequencing have been published for various plant species, such as Arabidopsis thaliana (Liu et al 2012;Wang et al 2014), Brachypodium distachyon (De Quattro et al 2017), rice Wang et al 2016) (Shuai et al 2014;Chen et al 2015;Tian et al 2016) and tomato (Zhu et al 2015).…”

The regulatory landscape of early maize inflorescence development

“…To investigate whether intergenic HS chromatin signatures were associated with expression of lncRNAs, we used a pipeline described by De Quattro et al (2017) [48] to annotate lncRNAs expressed in maize inflorescence primordia by re-analyzing RNA-seq data from a developmental series of tassel and ear primordia stages [30]. We identified 2,679 high-confidence lncRNAs derived from 2,520 unique loci ( Figure 5a; Additional File 1: Figures S11 and S12; Additional File 11: Dataset S10; Additional File 12:…”

“…There is also experimental evidence for the contribution of TEs in the evolution of lncRNAs; for example, TE-derived sequences conferring regulatory activities [61]. In maize and other grasses, retroelements were found to be most associated with lncRNAs [48,62,63]. Coincidently, 36% of the inflorescence-expressed lincRNAs originated from an annotated TE, largely Copia and Gypsy classes (Additional File 1: Figure S15).…”

“…High-confidence lncRNAs were annotated according to De Quattro et al [48,122]. Non-redundant transcripts assembled from the RNA-seq data were scanned using published criteria for defining lncRNA transcripts [50,123]: we filtered out sequences that i) were less than 200 bp, ii) were open reading frame encoding proteins with more than 100 amino acids, iii) were known functional protein domains deposited in the database Pfam v30 [124] (BLASTX cutoff E-value ≤ 1.0E -3), iv) had the potential to encode functional proteins based on the program CPC [125], and/or v) had homology with maize structural RNA domains deposited in the database Rfam v12 [126] (BLASTN cutoff E-value 1.0E ≤ -10).…”