Abstract
For many decades, the major function of mRNA was thought to be to provide protein-coding information embedded in the genome. The advent of high-throughput sequencing has led to the discovery of pervasive transcription of eukaryotic genomes and opened the world of RNA-mediated gene regulation. Many regulatory RNAs have been found to be incapable of protein coding and are hence termed as non-coding RNAs (ncRNAs). However, studies in recent years have shown that several previously annotated non-coding RNAs have the potential to encode proteins, and conversely, some coding RNAs have regulatory functions independent of the protein they encode. Such bi-functional RNAs, with both protein coding and non-coding functions, which we term as ‘cncRNAs’, have emerged as new players in cellular systems. Here, we describe the functions of some cncRNAs identified from bacteria to humans. Because the functions of many RNAs across genomes remains unclear, we propose that RNAs be classified as coding, non-coding or both only after careful analysis of their functions.
Highlights
The ‘one gene one enzyme’ hypothesis proposed by Beadle and Tatum in 1941 [1] and the elucidation of the double helical structure of DNA in 1953 [2] led Crick to propose of the central dogma of molecular biology placing RNA at the center of the directional information flow from genes to their protein products [3]
The discovery of cis-regulatory elements in DNA controlling gene expression by virtue of their interaction with cognate transcription factors captured the imagination and interest of scientists, and for many years, the regulatory roles of RNA were largely ignored. This protein-centric view of gene regulation was challenged by the discovery of small regulatory RNAs and gene silencing by RNA interference (RNAi) [9,10,11]
A large number of ncRNAs lacking canonical open reading frame (ORF) are transcribed by polymerase II, spliced, capped and polyadenylated just like messenger RNAs (mRNAs) [145,146]
Summary
The ‘one gene one enzyme’ hypothesis proposed by Beadle and Tatum in 1941 [1] and the elucidation of the double helical structure of DNA in 1953 [2] led Crick to propose of the central dogma of molecular biology placing RNA at the center of the directional information flow from genes to their protein products [3]. The discovery of cis-regulatory elements in DNA controlling gene expression by virtue of their interaction with cognate transcription factors captured the imagination and interest of scientists, and for many years, the regulatory roles of RNA were largely ignored. This protein-centric view of gene regulation was challenged by the discovery of small regulatory RNAs (e.g., miRNAs) and gene silencing by RNA interference (RNAi) [9,10,11].
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