This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Tajul-Arifin, K. Articles by Mattick, J. S. Search for Related Content PubMed PubMed Citation Articles by Tajul-Arifin, K. Articles by Mattick, J. S. Social Bookmarking                   What's this?

Letter

Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome

¹ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St.Lucia, Queensland 4072, Australia ²School of Molecular and Microbial Sciences, University of Queensland, St.Lucia, Queensland 4072, Australia ³Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan ⁴Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan

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.

⁵ Takahiro Arakawa, Piero Carninci, Jun Kawai, and Yoshihide Hayashizaki.

⁶ Corresponding author.
EMAIL j.mattick{at}imb.uq.edu.au; FAX 61-7-3365-8813.

[Supplemental material is available online at www.genome.org.]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				E. Ritou, M. Bai, and S. D. Georgatos Variant-specific patterns and humoral regulation of HP1 proteins in human cells and tissues J. Cell Sci., October 1, 2007; 120(19): 3425 - 3435. [Abstract] [Full Text] [PDF]

				A. Flaus, D. M. A. Martin, G. J. Barton, and T. Owen-Hughes Identification of multiple distinct Snf2 subfamilies with conserved structural motifs Nucleic Acids Res., May 31, 2006; 34(10): 2887 - 2905. [Abstract] [Full Text] [PDF]

				E. Bernstein, E. M. Duncan, O. Masui, J. Gil, E. Heard, and C. D. Allis Mouse polycomb proteins bind differentially to methylated histone h3 and RNA and are enriched in facultative heterochromatin. Mol. Cell. Biol., April 1, 2006; 26(7): 2560 - 2569. [Abstract] [Full Text] [PDF]

				J. S. Mattick and I. V. Makunin Small regulatory RNAs in mammals Hum. Mol. Genet., April 15, 2005; 14(suppl_1): R121 - R132. [Abstract] [Full Text] [PDF]