Abstract
Spliceosomal introns in higher eukaryotes are present in a high percentage of protein coding genes and represent a high proportion of transcribed nuclear DNA. In the last fifteen years, a growing mass of data concerning functional roles carried out by such intervening sequences elevated them from a selfish burden carried over by the nucleus to important active regulatory elements. Introns mediate complex gene regulation via alternative splicing; they may act in cis as expression enhancers through IME (intron-mediated enhancement of gene expression) and in trans as negative regulators through the generation of intronic microRNA. Furthermore, some introns also contain promoter sequences for alternative transcripts. Nevertheless, such regulatory roles do not require long conserved sequences, so that introns are relatively free to evolve faster than exons: this feature makes them important tools for evolutionary studies and provides the basis for the development of DNA molecular markers for polymorphisms detection. A survey of introns functions in the plant kingdom is presented.
Highlights
Thirty years have elapsed since the discovery of interrupted genes in Adenovirus2 mRNA, defined as “amazing rearrangements” [1]
Introns mediate complex gene regulation via alternative splicing; they may act in cis as expression enhancers through Intron Mediated Enhancement of gene expression (IME) and in trans as negative regulators through the generation of intronic microRNA
This results in the regulated production of huge amounts of transcripts of unknown functions (TUFs), that are devoid of any protein coding potential and derived from intragenic regions, pseudogenes or from gene noncoding strands
Summary
Thirty years have elapsed since the discovery of interrupted genes in Adenovirus mRNA, defined as “amazing rearrangements” [1]. Introns can be no more regarded as junk DNA, in the light of the increasing amount of data provided by genome sequencing projects and because of the discovery of regulatory functions that can be attributed to them If their presence has certainly contributed, early in eukaryotic evolution, to increase the number of protein structures through genome rearrangements and exon shuffling [5], introns still offer enormous plasticity to gene expression, through alternative splicing that greatly increases the cell transcriptional and translational output, a phenomenon whose dimension has been highlighted in recent years. Between 60 to 70% of the human genome has recently been estimated to be transcribed in one or both strands [13] To this regard, it has been proposed that introns and other ncRNAs, have evolved to constitute a network of controlling molecules that co-ordinately regulate gene expression through multiple interactions with other molecules such as DNA, RNA and proteins. Nowadays we are witnessing an epochal shift with regard to the genome fundamental unit: the previous proteo-centric view is being replaced by a more widely distributed and multifunctional model that is centred on transcripts [12]
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