Alternative Splicing and Evolutionary Change

Alternative splicing (AS) of eukaryotic genes is an important regulatory process by which a gene can produce multiple mRNAs and proteins under different cell conditions. For instance, splice variation may be developmental stage- or tissue-specific, or may differ between disease versus normal states. Most importantly, AS can produce a large variety of proteins from a relatively small number of genes, and thus could potentially explain how increasingly complex organisms emerged during evolution.

With the recent availability of genome sequences and alignments from a variety of eukaryotic species, it has become possible to analyze the relationship between alternative splicing and evolutionary change. Our data set consists of three classes of alternative splicing events in the human genome: constitutive (nonAlt), alternative major-form (AltD) and alternative minor-form (AltI) (Modrek and Lee 2003; Figure 1). Using a comparative genomics analysis across multiple species, we were able to characterize and subsequently determine distinguishing evolutionary profiles for the three exon categories based on: i) evolutionary exon dynamics (proportion of recent and old exons) within each set; ii) intronic sequence conservation, and iii) exonic sequence divergence.

Figure 1. Categories of splicing events: constitutive, alternative minor-form and alternative major-form exons.

Results

• Most constitutive (nonAlt) exons (74%) and major-form (AltD) exons (80%) are conserved across all taxa, suggesting that they were ancestral or had been created early on in the evolution of vertebrates. In contrast, a vast majority (85%) of minor-form exons (AltI) appear to have been inserted recently in the human lineage, following the chicken split.
• Intronic sequences surrounding AltI exons are more frequently conserved than for the other two categories, and may harbor intronic regulatory signals to promote the exon's inclusion.
• The third codon position is the least conserved (based on the proportions of matches/transitions/transversions) in AltI exons and the most conserved in AltD exons. This suggests that while AltI exons are evolving rapidly, AltD exons are under negative selective pressure, possibly to maintain critical splicing regulatory elements.

To find out more about our ongoing work, or to download data, please see the references below.

Methods

Annotation. Alternative splicing events in the human genomes were determined from cDNA-to-genome alignments of mRNA (RefSeq, MGC) and EST (dbEST) sequences produced with our ESTmapper/sim4 alignment software. Alignments were grouped into gene models using our gene annotation pipeline AIR, and constitutive/alternative exons were determined within each gene.

Exon classification. Constitutive and alternative (skipped) exons were determined based on the presence/absence in isoforms of the gene. The classification into the major-form and minor-form exon categories --i.e. exons occurring in the major-form and the minor-form transcripts of the gene, respectively-- was estimated from the relative abundance of the exon in cDNA evidence (Figure 1). A small number of alternative skipped exons did not fall into the two categories.

Evolutionary analyses. 'Multiz' whole-genome multiple alignments were downloaded from the UCSC Genome Browser and used to determine the presence of human annotated exons in each of the other species (at >50% coverage), and to extract patterns of sequence conservation and point mutation in the other genomes. The present/absent profile for each exon was then used to determine its likely time of creation within the species phylogeny.

References:

[1] Florea, L. and X. Zhao (2005) --- "Sequence conservation and variation in alternative splicing in relation to evolutionary change", 24th Summer Symposium in Molecular Biology - Comparative and Functional Genomics, Penn State University, University Park, PA. [Poster, Data]
[2] Guven, E. and L. Florea (2007) --- "Sequence signatures of exon dynamics in the evolution of alternative splicing", Cold Spring Harbor Meeting - The Biology of Genomes, Abstracts, 129.
[3] Florea, L. (2008) --- "Alternative splicing in the human genome and its evolutionary consequences", In Encyclopedia of Life Sciences: Handbook of Human Molecular Evolution, D.N. Cooper & H. Kehrer-Sawatzki Eds., John Wiley & Sons Ltd., Chichester, UK, in press.
 

NOTE: The original data set in [1] was generated for the human genome assembly version HG17. We recommend that you download the most recent version, built for HG18.