Long noncoding RNAs in the model species Brachypodium distachyon

Concetta De Quattro,Mario Enrico Pè,Edoardo Bertolini

doi:10.1038/s41598-017-11206-z

Concetta De Quattro, Mario Enrico Pè + Show 1 more

Open Access

https://doi.org/10.1038/s41598-017-11206-z

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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.

Highlights

Eukaryotic genomes are pervasively transcribed and only a small portion of the transcribed sequences belongs to protein coding genes
Even if the main feature of Long noncoding RNAs (lncRNAs) is the lack of evident open reading frames (ORFs), a large fraction of lncRNAs has been shown to be associated with ribosomes in ribosome profiling experiments, showing the potentiality to code for small functional peptides[17]
A newly discovered class of endogenous noncoding RNAs, termed circular RNAs, has been described in animal and plant species, adding to the transcriptome complexity[19]. Depending on their genomic origin, lncRNAs are classified in long intergenic ncRNAs or long genic ncRNAs, which are further subgrouped in exonic ncRNAs, intronic ncRNAs and natural antisense transcripts (NATs), transcribed from the complementary DNA strand of the associated coding genes[20, 21]

Summary

Introduction

Eukaryotic genomes are pervasively transcribed and only a small portion of the transcribed sequences belongs to protein coding genes. Depending on their genomic origin, lncRNAs are classified in long intergenic ncRNAs (lincRNAs) or long genic ncRNAs, which are further subgrouped in exonic ncRNAs, intronic ncRNAs (incRNAs) and natural antisense transcripts (NATs), transcribed from the complementary DNA strand of the associated coding genes[20, 21]. Because of their mRNA-like features, lincRNAs are the most abundant class of eukaryotic lncRNAs found in poly(A)+ RNA-seq data[22]

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