Chance and Necessity: Emerging Introns in Intronless Retrogenes

Abstract

Retrogenes are duplicated genes generated via retroposition, which were conventionally believed to contain no introns. However, emerging data showed that a significant number of retrogenes do have introns. Thus, these genes represent an attractive system to study how new genes evolve exon–intron structure. Comparison between parental genes and retrogenes revealed that retrogenes mainly evolve chimeric structures by fusing with local host genes or recruiting pre‐existing intergenic sequences. Additionally, retrogenes could gain introns by inheriting introns of parental genes or by transforming parental exonic sequences. The functional necessity on intron gain in retrogenes remains largely elusive although limited data suggest that newborn introns play regulatory roles, enable exon shuffling and alternative splicing. Accumulation of population genomic data may help to understand which evolutionary force shapes the fixation of introns in both retrogenes and de novo originated genes given the same intron birth process acts on both type of new genes.

Key Concepts:

  • Retrogenes evolve new exon–intron structures mainly by chimerism in both plants and animals.

  • Retrogenes could directly inherit introns from their parental genes.

  • Retrogenes could gain introns by intronization mechanism.

  • Intron insertion is rare in retrogenes.

  • Introns in retrogenes may have three functions: exon shuffling, alternative splicing and expression regulation.

Keywords: retroposition; chimerism; inheritance of parental intron; intronization; alternative splicing

Figure 1.

How chimerism occurs. The top and bottom part indicate parental gene and retrogene, respectively. Thicker boxes represent coding exons, while thinner boxes represent UTRs. ‘H’‐like tags represent introns. The retroposed regions are marked in purple, while other regions are marked in blue (genic) or orange (intergenic region). The sequence correspondence between parental and retrogene is marked with dotted lines. Semi‐rectangle lines with arrows indicate the direction of transcription. (a) The retrogene jingwei was fused with the neighbouring gene yande. The other region of yande, including nine exons and nine introns is degenerated. (b) The retrogene was inserted into the intron between UTR and coding exon, and fused with 5′ UTR later. (c) The noncoding gene sphinx recruits two exons and one intron from the 5′ flanking intergenic region.

Figure 2.

How intron inheritance occurs. The figure convention follows Figure . In case of preproinsulin I (a) and LOC_Os05g39720.1 (b) one intron appeared to be inherited from the corresponding parental gene, respectively. For LOC_Os05g39720.1, this retrocopy was also fused with the flanking region to form a chimeric gene.

Figure 3.

How intronization occurs. The figure convention follows Figure except that the newly evolved intronic regions are shown in yellow. (a) The retrogene AT1G15040 (Arabidopsis) gained an intron after point mutations from ‘AC’ to ‘GT’, acting as the splicing donor site. (b) In retrogene HSP90AA4P (human), three new introns were generated by intronization. There is no mutation at the splice sites in the two introns near the 5′ terminus, whereas one transition from ‘A’ to ‘G’ (indicated in red) at the splice sites occurred in the intron near the 3′ terminus.

Figure 4.

Models on why retrogene needs to evolve introns. (a) The insertion of a retrocopy to the intronic region of a gene (or recruiting the nearby sequences) will result in an exon shuffling event. (b) The occurrence of new splice sites or the activation of previously cryptic sites will generate two or more possible splice variants. (c) The coding potential will be disrupted by a PTC mutation in a long exonic region unless the PTC site is spliced out by a new intron. (d) Retrogene intron can recruit remote promoters and other regulatory elements, leading to regulation of its expression.

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Tan, Shengjun, Zhu, Zhenglin, Zhu, Tao, Te, Rigen, and Zhang, Yong E(Aug 2014) Chance and Necessity: Emerging Introns in Intronless Retrogenes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0022886]