Non-coding RNAs (ncRNA) are RNA molecules that function without being translated into a protein. One of the largest classes of ncRNA is known as snoRNA (small nucleolar RNA), thus named as they are localized within the nucleolus. The snoRNA class is divided into two major familes, the C/D and H/ACA. These snoRNA serve as guide RNAs for 2' O methylation and pseudouridylation of specific nucleotides, respectively. Both classes of snoRNAs indicate the site of modification by direct base pairing with the target RNA. The majority of these guide RNAs are responsible for the post-transcriptional modification of ribosomal RNAs (rRNA) and in some cases of snRNAs (small nuclear RNAs). These modifications are crucial for rRNA processing, stability and maturation.
The pseudouridylation guide snoRNAs in Trypansomes consist of a single-hairpin followed by an AGA-box[1]. The snoRNA’s pseudouridylation pocket consists of two short sequences that are complementary to the flanking rRNA sequence of the uridine to be converted. The uridine residue, which undergoes pseudouridylation, is found 14-16 bp upstream from the AGA-box. The pseudouridylation guide snoRNAs in most eukaryotes consist of two hairpins, a 5' hairpin followed by a single-stranded H-box (ANANNA, where N stands for any nucleotide) and a 3' hairpin followed by an ACA-box. Since the discovery of single stem H/ACA molecules in Trypanosomes, similar single hairpin RNAs have been discovered in Archea [2][3], and Euglena [4]. Single-stem and double-stem H/ACAs operate in a similar fashion.
| H/ACA ID | Target | Reference |
|---|---|---|
| TB3Cs2H1 | Ψ308-L5 | Myslyuk et al. 2008 [5] |
| TB3Cs2H2 | Ψ1658-L5 | Myslyuk et al. 2008 [5] |
| TB8Cs4H1 | Ψ358-L3 | Myslyuk et al. 2008 [5] |
| TB8Cs4H2 | Ψ141-L3 | Myslyuk et al. 2008[5] |
| TB9Cs6H1 | Ψ199-L5, Ψ29-5.8S | Myslyuk et al. 2008[5] |
| TB9Cs6H2 | Ψ1653-L5 | Myslyuk et al. 2008[5] |
| TB10Cs5H1 | Ψ1254-L3 | Myslyuk et al. 2008[5] |
| TB10Cs5H2 | Ψ131-S | Myslyuk et al. 2008[5] |
| TB10Cs5H3 | Ψ1276-S | Myslyuk et al. 2008[5] |
| TB11Cs5H1 | Ψ1710-S | Myslyuk et al. 2008[5] |
| TB11Cs5H2 | Ψ176-L3 | Myslyuk et al. 2008[5] |
| TB11Cs5H3 | Ψ1314-L3 | Myslyuk et al. 2008[5] |
| TB6Cs1H1 | Ψ380-L3 | Liang et al. 2005[6] |
| TB6Cs1H2 | Liang et al. 2005[6] | |
| TB6Cs1H3 | Ψ662-S | Liang et al. 2005[6] |
| TB6Cs1H4 | Ψ824-L5 | Liang et al. 2005[6] |
| TB6Cs2H1 | Ψ1001-SSU | Liang et al. 2005[6] |
| TB8Cs2H1 | Ψ1113-S | Liang et al. 2005[6] |
| TB8Cs3H1 | Ψ1423-S | Liang et al. 2005[6] |
| TB9Cs1H1 | Ψ1088-S,Ψ1272-L3 | Liang et al. 2005[6] |
| TB9Cs1H2 | Ψ1619-S | Liang et al. 2005[6] |
| TB9Cs1H3 | Ψ1250-L5 | Liang et al. 2005[6] |
| TB9Cs2H1 | Ψ617-L3 | Liang et al. 2005[6] |
| TB9Cs2H2 | Ψ1412-L5 | Liang et al. 2005[6] |
| TB9Cs3H1 | Ψ1208-L3 | Liang et al. 2005[6] |
| TB9Cs3H2 | Ψ1103-L5 | Liang et al. 2005[6] |
| TB9Cs4H1 | Ψ2123-S | Liang et al. 2005[6] |
| TB9Cs4H2 | Ψ1336-L3 | Liang et al. 2005[6] |
| TB9Cs4H3 | Liang et al. 2005[6] | |
| TB10Cs1H1 | Ψ659-L3 | Liang et al. 2005[6] |
| TB10Cs1H2 | Ψ901-L5 | Liang et al. 2005[6] |
| TB10Cs1H3 | Ψ40-S | Liang et al. 2005[6] |
| TB10Cs2H1 | Ψ1167-L3 | Liang et al. 2005[6] |
| TB10Cs2H2 | Ψ1173-L5 | Liang et al. 2005[6] |
| TB10Cs3H1 | Ψ263-S | Liang et al. 2005[6] |
| TB10Cs3H2 | Ψ397-L3 | Liang et al. 2005[6] |
| TB10Cs4H1 | Ψ2248-L5 | Liang et al. 2005[6] |
| TB10Cs4H2 | Ψ1186-S | Liang et al. 2005[6] |
| TB10Cs4H3 | Ψ1773-L5 | Liang et al. 2005[6] |
| TB10Cs4H4 | Ψ505-S | Liang et al. 2005[6] |
| TB11Cs2H1 | Ψ28 SL | Liang et al. 2005[6] |
| TB11Cs3H1 | Ψ1308-L3 | Liang et al. 2005[6] |
| TB11Cs3H2 | Ψ475-L3 | Liang et al. 2005[6] |
| TB11Cs4H1 | Ψ1357-L3 | Liang et al. 2005[6] |
| TB11Cs4H2 | Ψ566-L3 | Liang et al. 2005[6] |
| TB11Cs4H3 | Ψ61-S | Liang et al. 2005[6] |
References
edit- ^ Liang XH, Liu L, Michaeli S. Identification of the first trypanosome H/ACA RNA that guides pseudouridine formation on rRNA. J Biol Chem. 2001 Oct 26;276(43):40313-8. Epub 2001 Aug 1.
- ^ Tang TH, Bachellerie JP, Rozhdestvensky T, Bortolin ML, Huber H, Drungowski M, Elge T, Brosius J, Huttenhofer A. Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc Natl Acad Sci U S A. 2002 May 28;99(11):7536-41.
- ^ Rozhdestvensky TS, Tang TH, Tchirkova IV, Brosius J, Bachellerie JP, Huttenhofer A. Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res. 2003 Feb 1;31(3):869-77.
- ^ Russell AG, Schnare MN, Gray MW. Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis. RNA. 2004 Jul;10(7):1034-46.
- ^ a b c d e f g h i j k l Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S, Unger R. Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes. BMC Bioinformatics. 2008 Nov 5;9:471.
- ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa ab ac ad ae af ag ah Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S. A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification. RNA. 2005 May;11(5):619-45.