Nucleic Acids Research Advance Access originally published online on September 13, 2007
Nucleic Acids Research 2007 35(18):6249-6258; doi:10.1093/nar/gkm668
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Nucleic Acids Research, 2007, Vol. 35, No. 18 6249-6258
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution
Department of Biochemistry and Molecular Biology, New Jersey Medical School, UMDNJ, 185 South Orange Ave., P. O. Box 1709, Newark, NJ 07101-1709, USA
*To whom correspondence should be addressed. Tel: 973 972 4411; Fax: 973 972 5594; Email: mathews{at}umdnj.edu
Received June 27, 2007. Revised August 13, 2007. Accepted August 13, 2007.
Nuclear factor 90 (NF90) is a double-stranded RNA-binding protein implicated in multiple cellular functions, but with few identified RNA partners. Using in vivo cross-linking followed by immunoprecipitation, we discovered a family of small NF90-associated RNAs (snaR). These highly structured non-coding RNAs of 
117 nucleotides are expressed in immortalized human cell lines of diverse lineages. In human tissues, they are abundant in testis, with minor distribution in brain, placenta and some other organs. Two snaR subsets were isolated from human 293 cells, and additional species were found by bioinformatic analysis. Their genes often occur in multiple copies arranged in two inverted regions of tandem repeats on chromosome 19. snaR-A is transcribed by RNA polymerase III from an intragenic promoter, turns over rapidly, and shares sequence identity with Alu RNA and two potential piRNAs. It interacts with NF90's double-stranded RNA-binding motifs. snaR orthologs are present in chimpanzee but not other mammals, and include genes located in the promoter of two chorionic gonadotropin hormone genes. snaRs appear to have undergone accelerated evolution and differential expansion in the great apes.
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