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

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

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

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

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

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


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


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

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