The Importance of Non-coding RNAs

What Are Non-Coding RNAs?

What was once considered “junk” may end up being the most important part of our genome. Non-coding RNA (ncRNA) is RNA that is transcribed from DNA but diverts from the “central dogma” because it does not code for proteins. NcRNAs are ubiquitous in eukaryotes: while 90 percent of eukaryotic genomes are transcribed, only 1-2 percent are translated into proteins.

NcRNA plays a core role in the study of epigenetics and appears to be heavily involved in modulation of other RNA activity, as well as post-translational modifications of proteins influencing their function. This article will show the known roles of ncRNA in regulating transcription and demonstrate how next-generation sequencing (NGS) techniques have the potential to discover new forms and functions of this fundamental part of the epigenome.

History of nc-RNA

The first non-coding RNA was discovered in the 1980s, the result of experiments that showed that E. coli micF was a gene that had its own promoter and encoded for a small ncRNA that inhibited translation in response to environmental stresses, geneticist Nicholas Delihas of Stony Brook University wrote in a 2015 paper.¹ Similar molecules were not discovered in eukaryotic cells for another five years. Only recently has the discovery of more ncRNAs and realization that they make up 60 percent of all RNAs has underscored the fundamental importance of these molecules in regulation of gene expression.²

Today, non-coding RNA is a flourishing (some say exploding) research area. But while our understanding of these molecules has improved dramatically, we still do not understand exactly how they molecularly ally with certain protein structures, nor do we have a sense of how many different types of non-coding RNAs exist. Even the subtypes of ncRNA (explained further below) do not have populations that are fully identified.

These RNAs represent, as Australian geneticist John Mattick wrote in 2006, “a hidden layer of internal signals that control various levels of gene expression in physiology and development, including chromatin architecture/epigenetic memory, transcription, RNA splicing, editing, translation and turnover.”³ The RNAs may likely play a part in development, metabolism, nervous system function and intelligence, and of course, disease.⁴

Currently Known ncRNAs

There are a wide variety of ncRNAs that have been discovered, which take on an equally broad range of regulatory functions:

• miRNA — Also known as microRNAs, these 20-24 nucleotide single stranded molecules form RNA induced silencing complexes (RISC), which have proteins like Dicer that interact with mRNAs. MicroRNAs pair with complementary sequences on target mRNA transcripts, silencing the gene expression of the target.
• siRNA—Small interfering RNAs started out as long double-stranded RNA that Dicer processes into 20-24 nucleotide RNA strips that regulate gene silencing when in contact with a RISC. siRNA controls post-transcription silencing using RNA interference (RNAi), interfering with expression of a complementary sequence.
• piwiRNA—Also called “piRNA,” these interact with the piwi family of proteins, and are involved in chromatin regulation and transposon activity in germline and somatic cells. piRNA can be antisense to expressed transposons and cleave those transposons in complexes that contain piwi proteins, which generates more piRNAs. The resulting chain reactions then boost transposon silencing.
• lncRNA—long, non-coding RNAs are greater than 200 nucleotides, and make up most of all non-coding RNA. lncRNAs can be spliced, adenylated and otherwise modified after transcription. Some lncRNAs are involved in modifying expression on histones. These RNAs control epigenetic gene silencing and can affect tumor development by regulating genes involved in metastasis and cancer cell angiogenesis.
• scRNA, snRNA, snoRNA—short for small cytoplasmic RNA, small nuclear RNA and small nucleolar RNA, these molecules guide chemical modifications of ribosomal RNA, transfer RNA and other small nuclear RNAs.
• Other non-coding RNAs have been discovered recently, and their roles are not yet clear. These include enhancer RNAs that have about 800 nucleotides and may act to activate transcription, and promoter associated RNAs, which are themselves weakly expressed but associated with highly expressed genes.

NGS and Other Revealing Techniques

Several techniques, including PCR and ChIP, have been used to identify and characterize non-coding RNAs. NGS, while first criticized by some because of its original cost and labor requirements, is now emerging as a valuable—and increasingly cost-effective—tool for discovering more non-coding RNAs and determining their exact RNA sequence (and therefore, function).

NGS has made the following advances happen:

• In two years, nearly 10,000 new sequences have been added to the miRbase Registry
• Non-coding RNAs in complex transcriptomes have been profiled
• Strand-specific sequencing and analysis of sense and anti-sense noncoding RNA has been done
• Allele-specific expression is becoming better understood
• Minute changes and tweaks in RNA sequences have been linked to noncoding RNA expression changes and cellular effects

The variety of ncRNAs are still being discovered, and their roles in cellular physiology have yet to be fully understood. But their days of being disregarded as “junk” are long over, as modern next-generation sequencing and other techniques accelerate our knowledge of these important cellular components.

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References

1. Delihas, N. (2015). World J Biol Chem. 2015 Nov 26; 6(4): 272–280.
2. Ibid.
3. Mattick, J., Makunin, I.V. (2006). Human Molecular Genetics, Volume 15, Issue suppl_1, 15 April 2006, Pages R17–R29.
4. Ibid.