Modified Nucleotides within RNAs in S. cerevisiae
These tables list positions of nucleotide modifications, both pseudouridylation and ribose 2'-O-methylation, within ribosomal RNAs (5S rRNA, 5.8S rRNA, 18S rRNA, and 25S rRNA) and snRNAs (U1 snRNA, U2 snRNA, and U5 snRNA). Many of these modifications are performed by small nucleolar ribonucleic acid complexes (snoRNPs) where a specific snoRNA guides the position of modification; in these cases, only the snoRNA is listed, though the proteins of the snoRNP complex are required to catalyze the modification. For a list of all snoRNAs, see the table of snoRNAs in S. cerevisiae. Other modifications are directed and catalyzed by a protein enzyme without snoRNA guidance. Within the sequence context column, the modified nucleotide is shown in red.
Many thanks to Wayne Decatur and Dorota Piekna-Przybylska for providing the coordinates of the modification sites within the 18S and 25S rRNAs with respect to the genome of S. cerevisiae. Note that older papers have used alternate coordinate systems; links to tables providing the correspondance between old and current coordinates are provided within these two tables. For more detailed information about the snoRNAs, see the SGD Locus Summaries for each or the snoRNA database at UMass Amherst.
| Modified Position within the 5S rRNA compiled June 2008 | |||
| Position | Modification Type | Sequence Context of Modification | Gene Associated with Modification |
| 501 | pseudouridylation | AACUGUAGUUA | PUS7 |
| References | |||
| 1. Decatur WA and Schnare MN, et al. (2008) Different mechanisms for Pseudouridine formation in yeast 5S and 5.8S rRNAs. Mol Cell Biol 28(10):3089-100 SGD Paper | PubMed | |||
| Modified Position within the 5.8S rRNA compiled June 2008 | |||
| Position | Modification Type | Sequence Context of Modification | Gene Associated with Modification |
| 731 | pseudouridylation | GUGAAUUGCAG | snR43 |
| References | |||
| 1. Decatur WA and Schnare MN, et al. (2008) Different mechanisms for Pseudouridine formation in yeast 5S and 5.8S rRNAs. Mol Cell Biol 28(10):3089-100 SGD Paper | PubMed | |||
| Modified Position within the 18S rRNA compiled June 2007 see alternate numbering systems for the 18S ribose methylations see alternate numbering systems for the 18S pseudouridylations | |||
| Position | Modification Type | Sequence Context of Modification | Gene Associated with Modification |
| 28 | ribose 2'-O-methylation (on A) | GUCAUAUGCUU | snR74 |
| 100 | ribose 2'-O-methylation (on A) | GGCUCAUUAAA | snR51 |
| 106 | pseudouridylation | UUAAAUCAGUU | snR44 |
| 120 | pseudouridylation | GUUUAUUUGAU | snR49 |
| 211 | pseudouridylation | AUUUAUUAGAU | snR49 |
| 302 | pseudouridylation | UCAAAUUUCUG | snR49 |
| 414 | ribose 2'-O-methylation (on C) | CACAUCCAAGG | snR128 |
| 420 | ribose 2'-O-methylation (on A) | CAAGGAAGGCA | snR52 |
| 436 | ribose 2'-O-methylation (on A) | CGCGCAAAUUA | snR87 |
| 466 | pseudouridylation | GGUAGUGACAA | snR189 |
| 541 | ribose 2'-O-methylation (on A) | CGAGGAACAAU | snR41 |
| 578 | ribose 2'-O-methylation (on U) | CGCGGUAAUUC | snR77 |
| 619 | ribose 2'-O-methylation (on A) | CAGUUAAAAAG | snR47 |
| 632 | pseudouridylation | CGUAGUUGAAC | snR161 |
| 759 | pseudouridylation | AAAAUUAGAGU | snR80 |
| 766 | pseudouridylation | GAGUGUUCAAA | snR161 |
| 796 | ribose 2'-O-methylation (on A) | AUAUUAGCAUG | snR53 |
| 974 | ribose 2'-O-methylation (on A) | CAAGAACGAAA | snR54 |
| 999 | pseudouridylation | GAUGAUCAGAU | snR31 |
| 1007 | ribose 2'-O-methylation (on C) | GAUACCGUCGU | snR79 |
| 1126 | ribose 2'-O-methylation (on G) | CGCAAGGCUGA | snR41 |
| 1181 | pseudouridylation | GCGGCUUAAUU | snR85 |
| 1187 | pseudouridylation | UAAUUUGACUC | snR36 |
| 1191 | pseudouridylation Note that subsequent additional modifications generate m1acp3-psi. |
UUGACUCAACA | snR35 |
| 1269 | ribose 2'-O-methylation (on U) | GGUGGUGGUGC | snR55 |
| 1271 | ribose 2'-O-methylation (on G) | UGGUGGUGCAU | snR40 |
| 1290 | pseudouridylation | UUAGUUGGUGG | snR83 |
| 1415 | pseudouridylation | AAGUUUGAGGC | snR83 |
| 1428 | ribose 2'-O-methylation (on G) | UAACAGGUCUG | snR56 |
| 1572 | ribose 2'-O-methylation (on G) | UCAACGAGGAA | nR57 |
| 1639 | ribose 2'-O-methylation (on C) | CACCGCCCGUC | snR70 |
| References | |||
| 1. All information in this table courtesy of Wayne Decatur and Dorota Piekna-Przybylska; also see the table of snoRNAs or the locus summary and literature guide pages for each specific gene to view references. | |||
| 2. Piekna-Przybylska D, et al. (2007) New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 13(3):305-12 SGD Paper | PubMed | |||
| Modified Position within the 25S rRNA compiled June 2007 see alternate numbering systems for the 25S ribose methylations see alternate numbering systems for the 25S pseudouridylations | |||
| Position | Modification Type | Sequence Context of Modification | Gene Associated with Modification |
| 649 | ribose 2'-O-methylation (on A) | GAAACACGGAC | snR18 |
| 650 | ribose 2'-O-methylation (on C) | AAACACGGACC | snR18 |
| 663 | ribose 2'-O-methylation (on C) | GGAGUCUAACG | snR58 |
| 776 | pseudouridylation | AUGGAUUUGAG | snR80 |
| 805 | ribose 2'-O-methylation (on G) | GACCCGAAAGA | snR39B |
| 807 | ribose 2'-O-methylation (on A) | CCCGAAAGAUG | snR39 snR59 |
| 817 | ribose 2'-O-methylation (on A) | GGUGAACUAUG | snR60 |
| 867 | ribose 2'-O-methylation (on G) | UCGUAGCGGUU | snR50 |
| 876 | ribose 2'-O-methylation (on A) | UUCUGACGUGC | snR72 |
| 898 | ribose 2'-O-methylation (on U) | CGAAUUUGGGU | snR40 |
| 908 | ribose 2'-O-methylation (on G) | UAUAGGGGCGA | snR60 |
| 960 | pseudouridylation | UUCCCUCAGGA | snR8 |
| 966 | pseudouridylation | CAGGAUAGCAG | snR43 |
| 986 | pseudouridylation | UCAGUUUUAUG | snR8 |
| 990 | pseudouridylation | UUUUAUGAGGU | snR49 |
| 1004 | pseudouridylation | GCGAAUGAUUA | snR5 |
| 1042 | pseudouridylation | CCUAUUCUCAA | snR33 |
| 1052 | pseudouridylation | AACUUUAAAUA | snR81 |
| 1056 | pseudouridylation | UUAAAUAUGUA | snR44 |
| 1110 | pseudouridylation | AGCUUUUAGUG | snR82 |
| 1124 | pseudouridylation | CAUUUUUGGUA | snR5 |
| 1133 | ribose 2'-O-methylation (on A) | UAAGCAGAACU | snR61 |
| 1437 | ribose 2'-O-methylation (on C) | CAGAUCUUGGU | snR24 |
| 1449 | ribose 2'-O-methylation (on C) | GUAGUAGCAAA | snR24 |
| 1450 | ribose 2'-O-methylation (on C) | UAGUAGCAAAU | snR24 |
| 1888 | ribose 2'-O-methylation (on U) | AAUAAUGUAGA | snR62 |
| 2129 | pseudouridylation | GAAUCUGACUG | snR3 |
| 2133 | pseudouridylation | CUGACUGUCUA | snR3 |
| 2191 | pseudouridylation | UGAUUUCUGCC | snR32 |
| 2197 | ribose 2'-O-methylation (on C) | CUGCCCAGUGC | snR76 |
| 2220 | ribose 2'-O-methylation (on A) | AGUGAAGAAAU | snR47 |
| 2256 | ribose 2'-O-methylation (on A) | GAGUAACUAUG | snR63 |
| 2258 | pseudouridylation | GUAACUAUGAC | snR191 |
| 2260 | pseudouridylation | AACUAUGACUC | snR191 |
| 2264 | pseudouridylation | AUGACUCUCUU | snR3 |
| 2266 | pseudouridylation | GACUCUCUUAA | snR84 |
| 2314 | pseudouridylation | AUGAAUGGAUU | snR86 |
| 2340 | pseudouridylation | GUCCCUAUCUA | snR9 |
| 2349 | pseudouridylation | UACUAUCUAGC | snR82 |
| 2280 | ribose 2'-O-methylation (on A) | AGCCAAAUGCC | snR13 |
| 2281 | ribose 2'-O-methylation (on A) | GCCAAAUGCCU | snR13 |
| 2288 | ribose 2'-O-methylation (on G) | GCCUCGUCAUC | snR75 |
| 2337 | ribose 2'-O-methylation (on C) | ACUGUCCCUAU | snR64 |
| 2347 | ribose 2'-O-methylation (on U) | UCUACUAUCUA | snR65 |
| 2351 | pseudouridylation | CUAUCUAGCGA | snR82 |
| 2416 | pseudouridylation | UGAGCUUGACU | snR11 |
| 2417 | ribose 2'-O-methylation (on U) | GAGCUUGACUC | snR66 |
| 2421 | ribose 2'-O-methylation (on U) | UUGACUCUAGU | snR78 |
| 2619 | ribose 2'-O-methylation (on G) | GGCUGGGGCGG | snR67 |
| 2640 | ribose 2'-O-methylation (on A) | AAACGAUAACG | snR68 |
| 2724 | ribose 2'-O-methylation (on U) | UGAUUUUCAGU | snR67 |
| 2729 | ribose 2'-O-methylation (on U) | UUCAGUGUGAA | snR51 |
| 2735 | pseudouridylation | GUGAAUACAAA | snR189 |
| 2791 | ribose 2'-O-methylation (on G) | GGCUAGAGGUG | snR48 |
| 2793 | ribose 2'-O-methylation (on G) | CUAGAGGUGCC | snR48 |
| 2815 | ribose 2'-O-methylation (on G) | CACAGGGAUAA | nR38 |
| 2826 | pseudouridylation | CUGGCUUGUGG | snR34 |
| 2865 | pseudouridylation | UUUGAUUCUUC | snR46 |
| 2880 | pseudouridylation | UCGGCUCUUCC | snR34 |
| 2921 | ribose 2'-O-methylation (on U) | UGGAUUGUUCA | snR52 |
| 2922 | ribose 2'-O-methylation (on G) | GGAUUGUUCAC | SPB1 |
| 2923 | pseudouridylation | GAUUGUUCACC | snR10 |
| 2944 | pseudouridylation | GAACGUGAGCU | snR37 |
| 2946 | ribose 2'-O-methylation (on A) | ACGUGAGCUGG | snR71 |
| 2948 | ribose 2'-O-methylation (on C) | GUGAGCUGGGU | snR69 |
| 2959 | ribose 2'-O-methylation (on C) | UUAGACCGUCG | snR73 |
| 2975 | pseudouridylation | CAGGUUAGUUU | snR42 |
| References | |||
| 1. All information in this table courtesy of Wayne Decatur and Dorota Piekna-Przybylska; also see the table of snoRNAs or the locus summary and literature guide pages for each specific gene to view references. | |||
| 2. Piekna-Przybylska D, et al. (2007) New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 13(3):305-12 SGD Paper | PubMed | |||
| Modified Position within the U1 snRNA compiled June 2007 | |||
| Position | Modification Type | Sequence Context of Modification | Gene Associated with Modification |
| 51 | pseudouridylation | AUACUUACCU | not yet known |
| 61 | pseudouridylation | AUACUUACCUU | not yet known |
| References | |||
| 1. Massenet S, et al. (1999) Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol Cell Biol 19(3):2142-54 SGD Paper | PubMed | |||
| Modified Position within the U2 snRNA compiled June 2007 | |||
| Position | Modification Type | Sequence Context of Modification | Gene Associated with Modification |
| 351 | pseudouridylation | AAGUGUAGUAU | PUS7 |
| 421 | pseudouridylation | GUAUCUGUUCU | snR81 |
| 441 | pseudouridylation | UCUGUUCUUUU | PUS1 |
| References | |||
| 1. Massenet S, et al. (1999) Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol Cell Biol 19(3):2142-54 SGD Paper | PubMed | |||
| 2. Ma X, et al. (2003) Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism. EMBO J 22(8):1889-97 SGD Paper | PubMed | |||
| 3. Ma X, et al. (2005) Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism. EMBO J 24(13):2403-13 SGD Paper | PubMed | |||
| Modified Position within the U5 snRNA compiled June 2007 | |||
| Position | Modification Type | Sequence Context of Modification | Gene Associated with Modification |
| 991 | pseudouridylation | CCUUUUACCAG | not yet known |
| References | |||
| 1. Massenet S, et al. (1999) Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol Cell Biol 19(3):2142-54 SGD Paper | PubMed | |||
