Non-coding transcript variants of protein-coding genes – what are they good for?

Abstract

The total number of protein-coding genes in the human genome is not significantly higher than those in much simpler eukaryotes, despite a general increase in genome size proportionate to the organismal complexity. The large non-coding transcriptome and extensive differential splicing, are increasingly being accepted as the factors contributing to the complex mammalian physiology and architecture. Recent studies reveal additional layers of functional complexity: some long non-coding RNAs have been re-defined as micropeptide or microprotein encoding transcripts, and in turn some protein-coding RNAs are bifunctional and display also non-coding functions. Moreover, several protein-coding genes express long non-coding RNA splice-forms and generate circular RNAs in addition to their canonical mRNA transcripts, revoking the strict definition of a gene as coding or non-coding. In this mini review, we discuss the current understanding of these hybrid genes and their possible roles and relevance.

Translation and functional roles of circular RNAs in human cancer

“…It has been indicated that circRNA can serve as prognostic biomarkers because of their stable characteristics [32]. Moreover, several works have demonstrated hidden peptides encoded by circRNAs, which will largely broaden our understanding on the cellular physiology functions [33][34][35]. circRNAs have been considered as 'non-coding' elements, and the circRNA translation will provide a new perspective and new horizon for cancer treatment and diagnosis.…”

Extensive In Silico Analysis of ATL1 Gene: Discovered Five Mutations that may Cause Hereditary Spastic Paraplegia Type 3A

“…The Variant Effect Predictor annotates mutations using an extensive array of reference data from previously detected mutations, evidence based results, and estimation of biophysical consequences of mutations; and that is what makes VEP an accurate webbased tool. [42] VEP described regulatory consequences for several mutations, including 15 mutations within a coding region, 15 mutations within a non-coding region, 2 mutations within upstream gene, 9 mutations within downstream gene, 1 mutation within non-coding transcript exon, and 2 mutations within 5 prime UTR variant; briefly, mutations within a coding region affect the protein function, while mutations within noncoding regions can significantly affect disease and could be contribute in the phenotypic feature and RNA-binding proteins (RBPs); [52,53] while mutations in the upstream, downstream, 5′-, and 3′-UTRs might affect transcription or translation process. [54] The consequences are shown in (Table 6) while (Figure 2) demonstrates the summary pie charts and statistics.…”

Identification of Six novel missense single nucleotide polymorphisms in the MAOA gene predisposing to aggressive behavior. Bioinformatics study

“…The Variant Effect Predictor annotates mutations using an extensive array of reference data from previously detected mutations, evidence based results, and estimation of biophysical consequences of mutations; and that is what makes VEP an accurate web based tool.. (39) VEP described regulatory consequences for several mutations, including 10 mutations within coding region, 5 mutations within a non-coding region. briefly, mutations within coding region affect the protein function, while mutations within non-coding regions can significantly affect disease and could contribute in the phenotypic feature and RNA-binding proteins (RBPs);(40, 41) while mutations in the upstream, downstream, 5⍰-, and 3⍰-UTRs might affect transcription or translation process. (42) The consequences are shown in Table(5).…”