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Human-specific insertions and deletions inferred from mammalian genome sequences
Feng-Chi Chen1, Chueng-Jong Chen, Wen-Hsiung Li
1Division of Biostatistics and Bioinformatics, National Health Research Institute, Miaoli County 350, Taiwan.
Genome Research
|November 11, 2006
Summary
Small insertions and deletions (indels) significantly impact human and chimpanzee genome divergence. Most indels in human genes are eliminated, but those that remain may contribute to unique human traits.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Insertions and deletions (indels) are proposed to drive human-chimpanzee genome divergence more than nucleotide changes.
- Previous studies focused on large indels, leaving small indels (<100 bp) under-investigated.
Purpose of the Study:
- To systematically analyze small indels between human and chimpanzee genomes.
- To investigate the impact and functional consequences of human-specific small indels.
Main Methods:
- Inferred human-specific small indels using multiple mammalian genome alignments to overcome chimpanzee genome draft inaccuracies.
- Analyzed the distribution and functional enrichment of genes affected by these indels.
Main Results:
- >840,000 small indels were identified, affecting over 7000 human genes.
- Indels constitute only 0.21% sequence change in human genes, compared to 1.40% in pseudogenes, indicating selection against indels in genic regions.
- Genes with indel-affected exons are enriched in regulatory functions and depleted in catalytic/transporter activities.
Conclusions:
- Most small indels in genic regions are likely eliminated by natural selection.
- Human-specific indels may contribute to unique human traits by altering RNA and protein functions, particularly in regulatory pathways.
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