Evolution of vault RNAs.
Vault RNAs (vtRNAs) are small, about 100 nt long, polymerase III transcripts contained in the vault particles of eukaryotic cells. Presumably due to their enigmatic function, they have received little attention compared with most other noncoding RNA (ncRNA) families. Their poor sequence conservation makes homology search a complex and tedious task even within vertebrates. Here we report on a systematic and comprehensive analysis of this rapidly evolving class of ncRNAs in deuterostomes, providing a comprehensive collection of computationally predicted vtRNA genes. We find that all previously described vtRNAs are located at a conserved genomic locus linked to the protocadherin gene cluster, an association that is conserved throughout gnathostomes. Lineage-specific expansions to small vtRNA gene clusters are frequently observed in this region. A second vtRNA locus is syntenically conserved across eutherian mammals. The vtRNAs at the two eutherian loci exhibit substantial differences in their promoter structures, explaining their differential expression patterns in several human cancer cell lines. In teleosts, expression of several paralogous vtRNA genes, most but not all located at the syntenically conserved protocadherin locus, was verified by reverse transcriptase-polymerase chain reaction.
Stadler
Peter F
PF
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
Chen
Julian J-L
JJ
Hackermüller
Jörg
J
Hoffmann
Steve
S
Horn
Friedemann
F
Khaitovich
Phillip
P
Kretzschmar
Antje K
AK
Mosig
Axel
A
Prohaska
Sonja J
SJ
Qi
Xiaodong
X
Schutt
Katharina
K
Ullmann
Kerstin
K
D000818:Animals; D001483:Base Sequence; D045744:Cell Line, Tumor; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D020394:Vault Ribonucleoprotein Particles / Q000235:genetics* / Q000378:metabolism
D012333:RNA, Messenger; D020394:Vault Ribonucleoprotein Particles; D012313:RNA