Abstract
BackgroundWe previously have studied the insertion and deletion polymorphism by sequencing no more than one hundred introns in a mixed human population and found that the minimal introns tended to maintain length at an optimal size. Here we analyzed re-sequenced 179 individual genomes (from African, European, and Asian populations) from the data released by the 1000 Genome Project to study the size dynamics of minimal introns.Principal FindingsWe not only confirmed that minimal introns in human populations are selected but also found two major effects in minimal intron evolution: (i) Size-effect: minimal introns longer than an optimal size (87 nt) tend to have a higher ratio of deletion to insertion than those that are shorter than the optimal size; (ii) GC-effect: minimal introns with lower GC content tend to be more frequently deleted than those with higher GC content. The GC-effect results in a higher GC content in minimal introns than their flanking exons as opposed to larger introns (≥125 nt) that always have a lower GC content than that of their flanking exons. We also observed that the two effects are distinguishable but not completely separable within and between populations.ConclusionsWe validated the unique mutation dynamics of minimal introns in keeping their near-optimal size and GC content, and our observations suggest potentially important functions of human minimal introns in transcript processing and gene regulation.
Highlights
Intron is an important and necessary subassembly of eukaryotic genes and plays precise and complicated roles especially in the case of mRNA processing and alternative splicing [1,2,3,4]
We discovered an effect that the length of minimal introns tended to be maintained at an optimal size based on resequencing 93 representative minimal introns and 12 indels in an average of 45.7 random samples from a world-wide human population [13]
When plotted the derived allele frequency (DAF) of the indel data, we found that all curves showed a uni-modal distribution, slightly skewed toward left (Figure 1A)
Summary
Intron is an important and necessary subassembly of eukaryotic genes and plays precise and complicated roles especially in the case of mRNA processing and alternative splicing [1,2,3,4]. We discovered an effect that the length of minimal introns tended to be maintained at an optimal size based on resequencing 93 representative minimal introns and 12 indels in an average of 45.7 random samples from a world-wide human population [13]. We further analyzed human minimal introns and minimal intron-containing genes (MIGs), and showed many their unique features, including non-random distribution among human chromosomes, tendency to reside near the 39 end of transcripts, and higher expression level than other genes [14]. We previously have studied the insertion and deletion polymorphism by sequencing no more than one hundred introns in a mixed human population and found that the minimal introns tended to maintain length at an optimal size. We analyzed re-sequenced 179 individual genomes (from African, European, and Asian populations) from the data released by the 1000 Genome Project to study the size dynamics of minimal introns
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