The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1.

João Paulo Pereira De Almeida,Felipe Ten- Caten,Tie Koide,José Vicente Gomes-Filho,Alan P R Lorenzetti,Ricardo Z N Vêncio

doi:10.3390/genes10040280

Abstract

Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3′ ends of these transcripts. We analyzed the resulting asRNAs according to the size, location, function of genes on the opposite strand, expression levels and conservation. We show that at least 21% of the genes contain asRNAs in H. salinarum. Most of these asRNAs are expressed at low levels. They are located antisense to genes related to distinctive characteristics of H. salinarum, such as bacteriorhodopsin, gas vesicles, transposases and other important biological processes such as translation. We provide evidence to support asRNAs in type II toxin–antitoxin systems in archaea. We also analyzed public Ribosome profiling (Ribo-seq) data and found that ~10% of the asRNAs are ribosome-associated non-coding RNAs (rancRNAs), with asRNAs from transposases overrepresented. Using a comparative transcriptomics approach, we found that ~19% of the asRNAs annotated in H. salinarum belong to genes with an ortholog in Haloferax volcanii, in which an aTSS could be identified with positional equivalence. This shows that most asRNAs are not conserved between these halophilic archaea.

Highlights

Antisense RNAs are non-coding RNAs transcribed from the opposite strand of a given gene
We identified the primary transcription start sites (TSS) for asRNAs in H. salinarum NRC-1 by reanalyzing dRNA-seq data sampled at three time points over growth [38]
The first step was to reanalyze dRNA-seq data, where RNAs with triphosphorylated 50 ends were enriched by treatment with terminator exonuclease and compared to untreated samples

Summary

Introduction

Antisense RNAs (asRNAs) are non-coding RNAs (ncRNAs) transcribed from the opposite strand of a given gene. AsRNAs can be assumed to be cis-acting as they are complementary to the messenger RNA (mRNA) of the gene from which they derive. This does not restrict asRNA action to the gene on the opposite strand, they can act in trans [1]. AsRNAs can act as regulators at different stages of gene expression [2] They can modulate the stability and lifespan of RNAs by either occluding degradation sites or forming double-stranded complexes (dsRNAs) that are targets for RNases [3]. They may directly influence translation, inhibiting this process by occluding ribosome binding sites or promoting conformational alterations that might increase or decrease the frequency of translation of its target [2,4,5]

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Results

Conclusion