Modern origin of numerous alternatively spliced human introns from tandem arrays

Abstract

Despite the widespread occurrence of spliceosomal introns in the genomes of higher eukaryotes, their origin remains controversial. One model proposes that the duplication of small genomic portions could have provided the boundaries for new introns. If this mechanism has occurred recently, the 5 and 3 boundaries of each resulting intron should display distinctive sequence similarity. Here, we report that the human genome contains an excess of introns with perfect matching sequences at boundaries. One-third of these introns interrupt the protein-coding sequences of known genes. Introns with the best-matching boundaries are invariably found in tandem arrays of direct repeats. Sequence analysis of the arrays indicates that many intron-breeding repeats have disseminated in several genes at different times during human evolution. A comparison with orthologous regions in mouse and chimpanzee suggests a young age for the human introns with the most-similar boundaries. Finally, we show that these human introns are alternatively spliced with exceptionally high frequency. Our study indicates that genomic duplication has been an important mode of intron gain in mammals. The alternative splicing of transcripts containing these intron-breeding repeats may provide the plasticity required for the rapid evolution of new human proteins.evolution ͉ polymorphism ͉ repeats ͉ splicing T he origin of spliceosomal introns and their dissemination in higher eukaryotes are controversial issues. Different mechanisms have been proposed to explain how introns have arisen at different times during eukaryotic evolution (1). Ancestral spliceosomal introns may have evolved from organellar type II introns (2). In a manner similar to type II introns, the transposition of a spliceosomal intron through its reverse splicing into an intronless gene has been proposed as an ancient dissemination mechanism (3). Many spliceosomal introns in higher eukaryotes are considered to be relatively recent (4-6), but there is very little direct evidence for the mechanisms by which they arose. Intron insertion by transposition of a p-SINE1 element has occurred in the rice catalase A gene (7). Likewise, transposon insertion supports the creation of a new intron in the Sh2 gene of maize (8). Reverse splicing and the genomic insertion of transposons have been proposed to explain recent intron gains in nematodes (5, 9). Intron transfer among paralogues is consistent with the distribution of introns in the globin genes of Chironomus (10). The tandem genomic duplication of a portion of coding sequences with an AGGT cryptic splice site was initially proposed by Rogers (11) as a mechanism to produce the boundaries of a new intron. Although this model was rejected almost immediately based on the lack of similarity at the boundaries of introns that were examined, this mechanism was revived 10 years later to explain the origin of introns in several fish genes (12).A new intron can also arise when a known boundary is spliced to a novel junction created by point mutations, as is...

Ubiquitous internal gene duplication and intron creation in eukaryotes

“…The fitted parameters are shown in Table 2. matching sequences at 5Ј and 3Ј exon-intron boundaries (20), in support of this model. However, it is still under debate as to whether such introns are authentic or their sequences are actually absent in cDNA (but present in mRNA) resulted from template switching during the reverse transcription in the preparation of cDNA/EST libraries (see also refs.…”

“…However, these hypotheses either have few examples to support them or have not been tested, and to date, the mechanisms of intron creation remain puzzling and controversial (20)(21)(22).…”

Alternative splicing: A missing piece in the puzzle of intron gain

“…No case of gain was reported in a mapping of annotated intron-exon boundaries of either 17,242 human or 16,068 mouse genes in alignments of human, mouse, rat, and dog genomic sequences (17) (this result appears to be at variance with that obtained by ref. 25, which reported many novel introns in humans, although the new intron-containing genes are either unannotated or in copy-number variant regions). D. melanogaster (subgenus Sophophora) is inferred to have gained Ϸ0.45 introns/gene/By during the Ϸ40 My elapsed since it split from the Drosophila subgenus (18).…”

Dual-specificity splice sites function alternatively as 5′ and 3′ splice sites

“…Recently, introns with significant sequence similarities at their 5Ј and 3Ј splice sites were described in ref. 25. It was proposed that sequences bearing cryptic splice sites can be duplicated to serve as the termini of a new intron.…”