Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex.

Adam M Jenkins,Robert M Waterhouse,Marc At Muskavitch

doi:10.1186/s12864-015-1507-3

Abstract

BackgroundLong non-coding RNAs (lncRNAs) have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential, and many of them constitute scaffolds for ribonucleoprotein complexes with critical roles in epigenetic regulation. Various lncRNAs have been implicated in the modulation of chromatin structure, transcriptional and post-transcriptional gene regulation, and regulation of genomic stability in mammals, Caenorhabditis elegans, and Drosophila melanogaster. The purpose of this study is to identify the lncRNA landscape in the malaria vector An. gambiae and assess the evolutionary conservation of lncRNAs and their secondary structures across the Anopheles genus.ResultsUsing deep RNA sequencing of multiple Anopheles gambiae life stages, we have identified 2,949 lncRNAs and more than 300 previously unannotated putative protein-coding genes. The lncRNAs exhibit differential expression profiles across life stages and adult genders. We find that across the genus Anopheles, lncRNAs display much lower sequence conservation than protein-coding genes. Additionally, we find that lncRNA secondary structure is highly conserved within the Gambiae complex, but diverges rapidly across the rest of the genus Anopheles.ConclusionsThis study offers one of the first lncRNA secondary structure analyses in vector insects. Our description of lncRNAs in An. gambiae offers the most comprehensive genome-wide insights to date into lncRNAs in this vector mosquito, and defines a set of potential targets for the development of vector-based interventions that may further curb the human malaria burden in disease-endemic countries.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1507-3) contains supplementary material, which is available to authorized users.

Highlights

Long non-coding RNAs have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential, and many of them constitute scaffolds for ribonucleoprotein complexes with critical roles in epigenetic regulation
Alignment and validation of RNA sequencing (RNAseq) data sets Our transcriptome analysis for each life stage was supported by two RNAseq data sets: one “high read depth (HRD)” set with more than 140 million reads/stage that was used for subsequent Long non-coding RNAs (lncRNAs) discovery, and one “low read depth (LRD)” set that contained approximately 30 million reads/stage that constituted biological replicates for the validation of our High read depth (HRD) data sets
Evolutionary conservation of lncRNA sequences and secondary structures In light of recent studies of the evolutionary conservation, and the lack thereof, among lncRNAs in tetrapods [33,35], we examined the conservation of An. gambiae lncRNAs across the Anopheles genus

Summary

Introduction

Long non-coding RNAs (lncRNAs) have been defined as mRNA-like transcripts longer than 200 nucleotides that lack significant protein-coding potential, and many of them constitute scaffolds for ribonucleoprotein complexes with critical roles in epigenetic regulation. Large-scale functional genomic projects such as ENCODE and modENCODE, as well as high-throughput genomic screens, have revealed the presence of extensive sets of lncRNAs in humans (approximately 9,300), as well as in model organisms (e.g., approximately 900 in nematodes and 1,100 in fruit flies) [19,20,21,22,23,24,25,26,27] The functions of these lncRNAs, remain largely unknown, with a few exceptions that include lncRNAs with defined roles in embryogenesis, development, dosage compensation and sleep behavior [27,28,29,30,31,32]. It has been proposed that lncRNAs could be used as targets to regulate gene expression and development, as an alternative to the standard model of using small molecule drugs as antagonists of mRNA-encoded proteins [36] This premise may be extended to controlling vector-transmitted infectious diseases by identifying and perturbing non-coding RNA (ncRNA) targets in vector insects [37]

Objectives

Methods

Results

Conclusion