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Comparative analysis of lincRNA in insect species - PubMed

  • ️Sun Jan 01 2017

Comparative Study

Comparative analysis of lincRNA in insect species

Alberto Lopez-Ezquerra et al. BMC Evol Biol. 2017.

Abstract

Background: The ever increasing availability of genomes makes it possible to investigate and compare not only the genomic complements of genes and proteins, but also of RNAs. One class of RNAs, the long noncoding RNAs (lncRNAs) and, in particular, their subclass of long intergenic noncoding RNAs (lincRNAs) have recently gained much attention because of their roles in regulation of important biological processes such as immune response or cell differentiation and as possible evolutionary precursors for protein coding genes. lincRNAs seem to be poorly conserved at the sequence level but at least some lincRNAs have conserved structural elements and syntenic genomic positions. Previous studies showed that transposable elements are a main contribution to the evolution of lincRNAs in mammals. In contrast, plant lincRNA emergence and evolution has been linked with local duplication events. However, little is known about their evolutionary dynamics in general and in insect genomes in particular.

Results: Here we compared lincRNAs between seven insect genomes and investigated possible evolutionary changes and functional roles. We find very low sequence conservation between different species and that similarities within a species are mostly due to their association with transposable elements (TE) and simple repeats. Furthermore, we find that TEs are less frequent in lincRNA exons than in their introns, indicating that TEs may have been removed by selection. When we analysed the predicted thermodynamic stabilities of lincRNAs we found that they are more stable than their randomized controls which might indicate some selection pressure to maintain certain structural elements. We list several of the most stable lincRNAs which could serve as prime candidates for future functional studies. We also discuss the possibility of de novo protein coding genes emerging from lincRNAs. This is because lincRNAs with high GC content and potentially with longer open reading frames (ORF) are candidate loci where de novo gene emergence might occur.

Conclusion: The processes responsible for the emergence and diversification of lincRNAs in insects remain unclear. Both duplication and transposable elements may be important for the creation of new lincRNAs in insects.

Keywords: Evolution; RNA secondary structure; Transcriptomics; lincRNA.

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Figures

Fig. 1
Fig. 1

GC content and TE content of lincRNAs. a GC content of lincRNAs, lincRNA introns and coding sequences. LincRNAs have an intermediate GC content: higher than introns but lower than coding sequences. b Percentage of repeats of lincRNAs. LincRNAs have also an intermediate level of repeats. More repeats than coding sequences but less than introns. c Conserved lincRNAs have less TE. In contrast lincRNAs with signals of conservation in their ORF or paralogs have more TEs

Fig. 2
Fig. 2

Secondary structure analysis of lincRNAs. a Distribution of Z-scores with folding strength (FS). Both are highly correlated (rho=0.46, p-value 2.2e16) which indicates that strongly folded sequences also tend to be more stable than their shuffled controls. b Distribution of Z-scores obtained from MFE of lincRNAs compared to shuffled sequences. A negative correlation (rho=-0.22, p-value 2.2e16) indicates than thermodynamically stable sequences (i.e longer because MFE scales with length) have higher Z-scores although several short sequences outliers with very strong Z-scores are present. c Comparison of Z-scores for FS obtained between lincRNAs and 10000 CDS from the seven species. CDS shows significantly bigger FS than lincRNAs. d Comparison of Z-scores for MFE calculations obtained between lincRNAs and 1O000 CDS from the seven species. Z-scores are significantly higher for lincRNAs

Fig. 3
Fig. 3

Conservation analysis of lincRNAs in the seven studied species. Comparison of lincRNAs exons was performed using BLAST with the native lincRNAs, with the sequences of the lincRNAS with masked repeats and with the longest ORF of all the lincRNAs. A low sequence conservation was observed for lincRNAs in insects. Five hundred ninety three lincRNAs were observed conserved in their nucleotide sequence both with masking and without masking repeats. Furthermore 43 lincRNAs showed signals of conservation in their ORFs and 68 showed indication of conservation only without masking repeats

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