Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.
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 approximately 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.
Luo
Yuping
Y
College of Life Sciences, Nanchang University Nanchang 330047, People's Republic of China.
Li
Siguang
S
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D051379:Mice; D008969:Molecular Sequence Data; D010802:Phylogeny; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D014714:Vertebrates / Q000235:genetics
D020537:RNA, Small Nucleolar