Nucleic Acids Research Advance Access published online on December 14, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl1086
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Genomics |
Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs
College of Life Sciences, Nanchang University Nanchang 330047, People's Republic of China
*To whom correspondence should be addressed. Tel: +86 791 8304099; Fax: +86 791 8302703; Email: siguangli{at}163.com
Received August 21, 2006. Revised November 20, 2006. Accepted November 21, 2006.
The family of box H/ACA snoRNA is an abundant class of non-protein-coding RNAs, which play important roles in the post-transcriptional modification of rRNAs and snRNAs. Here we report the characterization in the human genome of 202 sequences derived from box H/ACA snoRNAs. Most of them were retrogenes formed using the L1 integration machinery. About 96% of the box H/ACA RNA-related sequences are found in corresponding locations on the chimpanzee and human chromosomes, while the mouse shares 
50% of these human sequences, suggesting that some of the H/ACA RNA-related sequences in primate occurred after the rodent/primate divergence. Of the H/ACA RNA-related sequences, 49% are found in intronic regions of protein-coding genes and 64 H/ACA-related sequences can be folded to the typical secondary structure of the box H/ACA snoRNA family, while 30 of them were recognized as functional homologs of their corresponding box H/ACA snoRNAs previously reported. Of the 64 sequences with the typical secondary structure of the box H/ACA RNA family, 11 were found in EST databases and 5 among which were shown to be expressed in more than one human tissue. Notably, U107f is nested in an intron of a protein gene coding for nudix-type motif 13, but expressed from the opposite strand, and the searching of EST databases revealed it can be expressed in liver and spleen, even in melanotic melanoma.
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