Introns Evolution in Duplicated Human Genes

Abstract

The material covered herein touches on the recent understanding of the fate of introns in human duplicated genes. A structural genomics framework has been provided to account for the functional asymmetry of sister copies after the duplication event(s). Structural shift between duplicated copies are very remarkable. Indeed, translocation/transposition of newly born copies to other chromosomal areas are accompanied not only by aminoacid substitutions but also by dramatic changes in introns size, composition and splicing patterns, as well as the emergence of intronic CpG‐island and other regulatory DNA elements.

As an evolutionary working hypothesis, for the short‐term evolution (within mammalian orders), interchromosomal translocations may be followed by accelerated evolution (relaxed constraints) and consequently alteration in expression patterns of the displaced copy, with major changes in introns constitution. For the long term, namely at the compositional transition that characterises fish/amphibian and mammalian regional genome patterns (isochores), the translocated copies (gene copies of the gene‐dense ‘ancestral genome core’) underwent a strong guanine+cytosine (GC) enrichment to become the genes of the actual ‘genome core’ (actual open chromatin). Introns from these copies, in concert with their genomic surrounding, had accumulated major structural changes and their host genes acquired different functions and/or regulations.

Key Concepts:

  • Noncoding DNA; open chromatin; negative selection; recombination hot spots.

  • Noncoding DNA: DNA sequences that do not encode for protein sequences and was therefore sometimes referred to as ‘junk DNA’, but for which there is now ample evidence for functionality (e.g. micro RNAs, ribozymes and long ncRNA).

  • Open chromatin: It forms euchromatin, which contains regions harbouring promoters, enhancers and actively transcribed genes.

  • Recombination hot spots: Regions of the chromosome that have frequent recombination events.

  • Negative selection: Selection acting to eliminate emerging deleterious mutations that reduces carriers fitness. It is also called purifying selection.

Keywords: chromatin; translocation; duplication; alternative splicing; CpG islands; transposons

Figure 1.

A scheme of the general evolutionary pathway of ancient gene duplications. Duplication of the ancestral copy followed by (trans)location of one of the two sister copies to the ancestral open chromatin regions (dark grey) and subsequent major compositional shift. The GC‐richest copy (black box) became preferentially associated with CpG‐islands (not in scale), its introns shortened and partially lost its Alus (open cicles) and LINEs transposons (open tiangles). Changes in splicing patterns are not indicated. Vertical lines between exons and introns indicate the degree of differential GC levels. Reproduced with permission from Jabbari et al..

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Jabbari, Kamel(Jan 2013) Introns Evolution in Duplicated Human Genes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020784.pub2]