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Genes for intermediate filament proteins and the draft sequence of the human genome

novel keratin genes and a surprisingly high number of pseudogenes related to keratin genes 8 and 18

¹ Institute of Genetics, Division of Molecular Genetics and Bonner Forum Biomedizin, University of Bonn, 53117 Bonn, Germany
² Max-Planck-Institute for Biophysical Chemistry, Department of Biochemistry, 37070 Goettingen, Germany
^* Authors for correspondence (e-mail: t.magin{at}uni-bonn.de ; m.hesse{at}uni-bonn.de ; r.longo{at}gwdg.de )

View larger version (28K): [in a new window]   Fig. 1. Classification and chromosomal localization of intermediate filament genes and pseudogenes. The table lists intermediate filament genes, pseudogenes and gene fragments identified in the draft of the human genome. Keratin genes 8 and 18, which gave rise to 62 and 35 processed pseudogenes, respectively, are marked with a red bar. Potential novel keratin genes/gene fragments in the type I and II clusters are indicated by an asterisk. Chromosomal localization of pseudogenes is indicated by numbers in brackets. Pseudogenes related to hair keratin genes are denoted by ; indicates type I keratin genes recently identified (Bawden et al., 2001). These are most closely related to K10. We propose to name them according to the Moll nomenclature as indicated in the text (Moll et al., 1982). The expression pattern of the newly identified keratin genes remains to be determined.

View larger version (15K): [in a new window]   Fig. 2. Chromosomal localization of keratin 8 (A) and 18 pseudogenes (B). Chromosomes numbers are marked in blue. Integration sites per chromosome are marked in red. Coloured bars along chromosomes indicate the integration sites. The extent of sequence identity to K8 and 18 is indicated by red (alignment score >200), blue (alignment score 80-200) and green (alignment score 50-80) bars.

View larger version (66K): [in a new window]   Fig. 3. Comparison of type II keratins identified in this study. An alignment of the type II keratin sequences is given in the single letter code (residue numbers on top) with gaps introduced to maximize the amino acid alignment (dashes). Ends of the -helical subdomains of the rod (1A, 1B, 2A and 2B) are indicated by solid arrowheads. For comparison, sequences of human keratins 1 and 5, the closest relatives, are co-aligned. For K6i, a different C-terminal sequence has been determined (M. Rogers, personal communication). Starting from position 443, it reads MSGEFPSPVS ISIISSTSGG SVYGFRPSMV SGGYVANS SNCISGVCSV RGGEGRSRGS ANDYKDTLGK GSSLSAPSKK TSR*. Asterisk indicates termination codon.

View larger version (15K): [in a new window]   Fig. 4. Phylogenetic relationship of the human type I and II keratins. The phylogenetic tree shown was generated following the alignment of human type I (A) and type II keratins (B). Multiple sequence alignments were performed using the CLUSTAL program. Evolutionary tree construction was prepared using the CLUSTREE program. For the alignment, sequences published in the human genome draft were used (International Human Genome Sequencing Consortium, 2001).