Abstract
Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3′ untranslated region (UTR), 5′ UTR, CDS-binding). These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved and how sRNAs integrate with complex regulatory networks.
Highlights
Small RNAs are important regulators for multiple cellular functions and they are ubiquitous in all domains of life. sRNAs, called non-coding RNAs, are RNAs that do not function as mRNAs, ribosomal RNAs, or transfer RNAs in the cell. sRNAs in bacteria and eukarya play essential roles in transcriptional regulation, chromosome replication, RNA processing and modification, mRNA stability and translation and even protein degradation and translocation [1,2,3]
While Ago homologs have been found in archaeal genomes, there is no evidence for eukaryotic-like RNA interference in these organisms [16]
Microarray and 454-pyrosequencing technologies provided a mean to validate these predicted sRNAs and further identified novel sRNAs by the hundreds. It is the unprecedented discovery of more than 2900 sRNAs in H. volcanii by two recent high-throughput sequencing (HTS) studies—which is quite remarkable considering that the genome of this organism encodes for just over 4000 proteins [4,14]—that has permanently altered our view of the archaeal transcriptome
Summary
Small RNAs (sRNAs) are important regulators for multiple cellular functions and they are ubiquitous in all domains of life. sRNAs, called non-coding RNAs (ncRNAs), are RNAs that do not function as mRNAs, ribosomal RNAs, or transfer RNAs in the cell. sRNAs in bacteria and eukarya play essential roles in transcriptional regulation, chromosome replication, RNA processing and modification, mRNA stability and translation and even protein degradation and translocation [1,2,3]. SRNAs in bacteria and eukarya play essential roles in transcriptional regulation, chromosome replication, RNA processing and modification, mRNA stability and translation and even protein degradation and translocation [1,2,3]. SRNAs are typically 50 to 300 nt in length and act by targeting mRNA stability, translation, or by binding to proteins [18]. Trans-encoded sRNAs are encoded at genomic location distinct from their target mRNAs, such as intergenic regions and act via limited base pairing [19] (Figure 1B). Reported regulatory roles of archaeal sRNAs the CDS and overlapping multiple mRNAs. An example of an intergenic sRNA secondary structure is shown in (B) [5].
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