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Identifying the Mechanisms of Intron Gain: Progress and Trends


Identifying the Mechanisms of Intron Gain: Progress and Trends

Paul Yenerall et al. Biol Direct.


Continued improvements in Next-Generation DNA/RNA sequencing coupled with advances in gene annotation have provided researchers access to a plethora of annotated genomes. Subsequent analyses of orthologous gene structures have identified numerous intron gain and loss events that have occurred both recently and in the very distant past. This research has afforded exceptional insight into the temporal and lineage-specific rates of intron gain and loss among various species throughout evolution. Numerous studies have also attempted to identify the molecular mechanisms of intron gain and loss. However, even after considerable effort, very little is known about these processes. In particular, the mechanism(s) of intron gain have proven exceptionally enigmatic and remain topics of considerable debate. Currently, there exists no definitive consensus as to what mechanism(s) may generate introns. Because many introns are known to affect gene expression, it is necessary to understand the molecular process(es) by which introns may be gained. Here we review the seven most commonly purported mechanisms of intron gain and, when possible, summarize molecular evidence for or against the occurrence of each of these mechanisms. Furthermore, we catalogue indirect evidence that supports the occurrence of each mechanism. Finally, because these proposed mechanisms fail to explain the mechanistic origin of many recently gained introns, we also look at trends that may aid researchers in identifying other potential mechanism(s) of intron gain.


Figure 1
Figure 1
The seven proposed mechanisms of intron gain and loss. Introns shown are shorter in length than necessary for splicing strictly for illustrative purposes. a) Intron Transposition with “partial” recombination. Other routes of intron transposition (discussed in text) by which concurrent intron gains/losses may occur can be also envisioned. b) Transposon Insertion. Imprecise intron gain may also be envisioned (discussed in text). c) Tandem Genomic Duplication using duplicated AGGT sequences for splice sites. The segment to be duplicated is flanked by brackets. The template for the duplicated nucleotides is highlighted in yellow; the duplicated nucleotides are highlighted in red and underlined. Imprecise intron gain may also frequently occur (discussed in text). d) Intron Gain during Double-Strand Break Repair. Protein names are from mammals. Short direct repeats created by gap filling are underlined. The possible pathways of non-homologous end joining (NHEJ) are from proposals in [45-48]. e) Insertion of a Group II Intron. f) Intron Transfer. g) Intronization. Strong consensus donor and acceptor sites (following a single point mutation) are highlighted in yellow. The place at which the hypothetical point mutation occurs is highlighted in red.

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    1. Rogozin IB, Carmel L, Csuros M, Koonin EV. Origin and evolution of spliceosomal introns. Biol Direct. 2012;7:11. doi: 10.1186/1745-6150-7-11. - DOI - PMC - PubMed
    1. Koonin EV. Intron-dominated genomes of early ancestors of eukaryotes. J Hered. 2009;100:618–623. doi: 10.1093/jhered/esp056. - DOI - PMC - PubMed
    1. Graveley BR. Alternative splicing: increasing diversity in the proteomic world. Trends Genet. 2001;17:100–107. doi: 10.1016/S0168-9525(00)02176-4. - DOI - PubMed
    1. Choi T, Huang M, Gorman C, Jaenisch R. A generic intron increases gene expression in transgenic mice. Mol Cell Biol. 1991;11:3070–3074. - PMC - PubMed
    1. Le HH, Nott A, Moore MJ. How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci. 2003;28:215–220. doi: 10.1016/S0968-0004(03)00052-5. - DOI - PubMed

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