title: Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome.
abstract: The chromodomain is 40-50 amino acids in length and is conserved in a wide range of chromatic and regulatory proteins involved in chromatin remodeling. Chromodomain-containing proteins can be classified into families based on their broader characteristics, in particular the presence of other types of domains, and which correlate with different subclasses of the chromodomains themselves. Hidden Markov model (HMM)-generated profiles of different subclasses of chromodomains were used here to identify sequences encoding chromodomain-containing proteins in the mouse transcriptome and genome. A total of 36 different loci encoding proteins containing chromodomains, including 17 novel loci, were identified. Six of these loci (including three apparent pseudogenes, a novel HP1 ortholog, and two novel Msl-3 transcription factor-like proteins) are not present in the human genome, whereas the human genome contains four loci (two CDY orthologs and two apparent CDY pseudogenes) that are not present in mouse. A number of these loci exhibit alternative splicing to produce different isoforms, including 43 novel variants, some of which lack the chromodomain. The likely functions of these proteins are discussed in relation to the known functions of other chromodomain-containing proteins within the same family.
authors.affiliation: ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St.Lucia, Queensland 4072, Australia.
authors.forename: Khairina
authors.initials: K
authors.lastname: Tajul-Arifin
authors.forename: Rohan
authors.initials: R
authors.lastname: Teasdale
authors.forename: Timothy
authors.initials: T
authors.lastname: Ravasi
authors.forename: David A
authors.initials: DA
authors.lastname: Hume
authors.forename: John S
authors.initials: JS
authors.lastname: Mattick
mesh_terms: D000123:Acetyltransferases / Q000737:chemistry / Q000235:genetics; D000818:Animals; D017487:Ankyrins / Q000737:chemistry / Q000235:genetics; D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics; D000090266:Chromobox Protein Homolog 5; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods / Q000706:statistics & numerical data; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D004265:DNA Helicases / Q000737:chemistry / Q000235:genetics; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic / Q000706:statistics & numerical data; D029721:Drosophila Proteins; D004746:Enoyl-CoA Hydratase / Q000737:chemistry / Q000235:genetics; D051548:Histone Acetyltransferases; D000076983:Histone Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; D006801:Humans; D008390:Markov Chains; D008780:Methyltransferases / Q000737:chemistry / Q000235:genetics; D051379:Mice; D009687:Nuclear Proteins / Q000737:chemistry / Q000235:genetics; D063146:Polycomb-Group Proteins; D011496:Protein Methyltransferases; D017434:Protein Structure, Tertiary / Q000235:genetics; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D020543:Proteome / Q000737:chemistry / Q000235:genetics; D012097:Repressor Proteins / Q000737:chemistry / Q000235:genetics; D056465:Retinoblastoma-Binding Protein 1; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D017487:Ankyrins; C533431:Arid4a protein, mouse; D002352:Carrier Proteins; D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D009687:Nuclear Proteins; D063146:Polycomb-Group Proteins; D011506:Proteins; D020543:Proteome; D012097:Repressor Proteins; D056465:Retinoblastoma-Binding Protein 1; C084011:SMARCA2 protein, human; D029701:Saccharomyces cerevisiae Proteins; C499503:Smarca2 protein, mouse; D014157:Transcription Factors; D000090266:Chromobox Protein Homolog 5; C093904:msl-3 protein, Drosophila; D000076983:Histone Methyltransferases; D008780:Methyltransferases; D011496:Protein Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; D000123:Acetyltransferases; D051548:Histone Acetyltransferases; C084108:SMARCA4 protein, human; C513194:Smarca4 protein, mouse; D004265:DNA Helicases; D004746:Enoyl-CoA Hydratase