Signatures of domain shuffling in the human genome

Henrik Kaessmann, Sebastian Zöllner, Anton Nekrutenko, Wen Hsiung Li

Research output: Contribution to journalArticle

73 Citations (Scopus)

Abstract

To elucidate the role of exon shuffling in shaping the complexity of the human genome/proteome, we have systematically analyzed intron phase distributions in the coding sequence of human protein domains. We found that introns at the boundaries of domains show high excess of symmetrical phase combinations (i.e., 0-0, 1-1, and 2-2), whereas nonboundary introns show no excess symmetry. This suggests that exon shuffling has primarily involved rearrangement of structural and functional domains as a whole. Furthermore, we found that domains flanked by phase I introns have dramatically expanded in the human genome due to domain shuffling and that 1-1 symmetrical domains and domain families are nonrandomly distributed with respect to their age. The predominance and extracellular location of 1-1 symmetrical domains among domains specific to metazoans suggests that they are associated with the rise of multicellularity. On the other hand, 0-0 symmetrical domains tend to be over-represented among ancient protein domains that are shared between the eukaryotic and prokaryotic kingdoms, which is compatible with the suggestion of primordial domain shuffling in the progenote. To see whether the human data reflect general genomic patterns of metazoans, similar analyses were done for the nematode Caenorhabditis elegans. Although the C. elegans data generally concur with the human patterns, we identified fewer intron-bounded domains in this organism, consistent with the lower complexity of C. elegans genes.

Original languageEnglish (US)
Pages (from-to)1642-1650
Number of pages9
JournalGenome research
Volume12
Issue number11
DOIs
StatePublished - Nov 1 2002

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Human Genome
Introns
Caenorhabditis elegans
Exons
Proteome
Genes
Protein Domains

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Kaessmann, Henrik ; Zöllner, Sebastian ; Nekrutenko, Anton ; Li, Wen Hsiung. / Signatures of domain shuffling in the human genome. In: Genome research. 2002 ; Vol. 12, No. 11. pp. 1642-1650.
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Kaessmann, H, Zöllner, S, Nekrutenko, A & Li, WH 2002, 'Signatures of domain shuffling in the human genome', Genome research, vol. 12, no. 11, pp. 1642-1650. https://doi.org/10.1101/gr.520702

Signatures of domain shuffling in the human genome. / Kaessmann, Henrik; Zöllner, Sebastian; Nekrutenko, Anton; Li, Wen Hsiung.

In: Genome research, Vol. 12, No. 11, 01.11.2002, p. 1642-1650.

Research output: Contribution to journalArticle

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