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 Positions within the 5S rRNA

compiled June 2008

Position

Modification Type

Sequence Context of Modification

Gene Associated with Modification

50 (1) pseudouridylation AACUGUAGUUA PUS7 (1)
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 Papers Entry  Pubmed Entry

Modified Positions within the 5.8S rRNA

compiled June 2008

Position

Modification Type

Sequence Context of Modification

Gene Associated with Modification

73 (1) pseudouridylation GUGAAUUGCAG snR43 (1)
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 Papers Entry  Pubmed Entry

Modified Positions 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(s) 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 (U14)
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 snR57
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 Papers Entry  Pubmed Entry

Modified Positions 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 (U18)
650 ribose 2'-O-methylation (on C) AAACACGGACC snR18 (U18)
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 and 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 (U24)
1449 ribose 2'-O-methylation (on C) GUAGUAGCAAA snR24 (U24)
1450 ribose 2'-O-methylation (on C) UAGUAGCAAAU snR24 (U24)
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 snR38
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 Papers Entry  Pubmed Entry

Modified Positions within the U1 snRNA

compiled June 2007

Position

Modification Type

Sequence Context of Modification

Gene Associated with Modification

5 (1) pseudouridylation AUACUUACCU not yet known
6 (1) 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 Papers Entry  Pubmed Entry

Modified Positions within the U2 snRNA

compiled June 2007

Position

Modification Type

Sequence Context of Modification

Gene Associated with Modification

35 (1) pseudouridylation AAGUGUAGUAU PUS7 (2)
42 (1) pseudouridylation GUAUCUGUUCU snR81 (3)
44 (1) pseudouridylation UCUGUUCUUUU PUS1 (1)
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 Papers Entry  Pubmed Entry
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 Papers Entry  Pubmed Entry
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 Papers Entry  Pubmed Entry

Modified Positions within the U5 snRNA

compiled June 2007

Position

Modification Type

Sequence Context of Modification

Gene Associated with Modification

99 (1) 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 Papers Entry  Pubmed Entry