RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse

In mouse brain cDNA libraries generated from small RNA molecules we have id entified a total of 201 different expressed RNA sequences potentially encod ing novel small non-messenger RNA species (snmRNAs), Based on sequence and structural motifs, 113 of these RNAs can be assigned to the C/D box or H/AC A box subclass of small nucleolar RNAs (snoRNAs), known as guide RNAs for r RNA, While 30 RNAs represent mouse homologues of previously identified huma n CCD or H/ACA snoRNAs, 83 correspond to entirely novel snoRNAs, Among thes e, for the first time, we identified four C/D box snoRNAs and four H/ACA bo x snoRNAs predicted to direct modifications within U2, U4 or U6 small nucle ar RNAs (snRNAs), Furthermore, 25 snoRNAs from either class lacked antisens e elements for rRNAs or snRNAs, Therefore, additional snoRNA targets have t o be considered, Surprisingly, six C/D box snoRNAs and one H/ACA box snoRNA were expressed exclusively in brain. Of the 88 RNAs not belonging to eithe r snoRNA subclass, at least 26 are probably derived from truncated heteroge neous nuclear RNAs (hnRNAs) or mRNAs, Short interspersed repetitive element s (SINEs) are located on five RNA sequences and may represent rare examples of transcribed SINEs, The remaining RNA species could not as yet be assign ed either to any snmRNA class or to a part of a larger hnRNA/mRNA, It is li kely that at least some of the latter will represent novel, unclassified sn mRNAs.