rRNA modification in the nucleus and cytosol

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Homo sapiens
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Human ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Hernandez-Verdun et al. 2010, Boschi-Muller and Motorin 2013). The modified residues occur in regions of the rRNAs that are located in functionally important parts of the ribosome, notably in the A and P peptidyl transfer sites, the polypeptide exit tunnel, and intersubunit contacts (Polikanov et al. 2015, reviewed in Decatur and Fournier 2002, Chow et al. 2007, Sharma and Lafontaine 2015). The two most common modifications are pseudouridines and 2'-O-methylribonucleotides. Formation of pseudouridine from encoded uridine is catalyzed by box H/ACA small nucleolar ribonucleoprotein (snoRNP) complexes (reviewed in Hamma and Ferre-D'Amare 2010, Watkins and Bohnsack 2011, Ge and Yu 2013, Kierzek et al. 2014, Yu and Meier 2014) and methylation of the hydroxyl group of the 2' carbon is catalyzed by box C/D snoRNPs (Kiss-Laszlo et al. 1996, Lapinaite et al. 2013, reviewed in Watkins and Bohnsack 2011). The snoRNP complexes contain common sets of protein subunits and unique snoRNAs that guide each complex to its target nucleotide of the rRNA by base-pairing between the snoRNA and the rRNA (reviewed in Henras et al. 2004, Watkins and Bohnsack 2011). Other modifications of rRNA include 5-methylcytidine (reviewed in Squires and Preiss 2010), 1-methylpseudouridine, 7-methylguanosine, 6-dimethyladenosine, and 4-acetylcytidine (reviewed in Sharma and Lafontaine 2015). In yeast most modifications are introduced co-transcriptionally (Kos and Tollervey 2010, reviewed in Turowski and Tollervey 2015), however the order of modification events and pre-rRNA cleavage events is not well characterized.
Literature References
PubMed ID Title Journal Year
12114023 rRNA modifications and ribosome function

Fournier, MJ, Decatur, WA

Trends Biochem. Sci. 2002
24369424 The contribution of pseudouridine to stabilities and structure of RNAs

Kierzek, R, Gdaniec, Z, Turner, DH, Kierzek, E, Lisowiec, J, Malgowska, M

Nucleic Acids Res. 2014
25176256 Cotranscriptional events in eukaryotic ribosome synthesis

Turowski, TW, Tollervey, D

Wiley Interdiscip Rev RNA 2015
3418702 Locations of methyl groups in 28 S rRNA of Xenopus laevis and man. Clustering in the conserved core of molecule

Maden, BE

J. Mol. Biol. 1988
26410597 'View From A Bridge': A New Perspective on Eukaryotic rRNA Base Modification

Sharma, S, Lafontaine, DL

Trends Biochem. Sci. 2015
8674114 Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs

Henry, Y, Kiss, T, Caizergues-Ferrer, M, Bachellerie, JP, Kiss-László, Z

Cell 1996
23391857 RNA pseudouridylation: new insights into an old modification

Yu, YT, Ge, J

Trends Biochem. Sci. 2013
24121435 The structure of the box C/D enzyme reveals regulation of RNA methylation

Rakwalska-Bange, M, Simon, B, Gabel, F, Lapinaite, A, Carlomagno, T, Skjaerven, L

Nature 2013
22122054 Function and detection of 5-methylcytosine in eukaryotic RNA

Squires, JE, Preiss, T

Epigenomics 2010
412496 Methylated nucleotide sequences in HeLa-cell ribosomal ribonucleic acid. Correlation between the results from 'fingerprinting' hydrolysates obtained by digestion with T1 ribonuclease and with T1 plus pancreatic ribonuclease

Maden, BE, Khan, MS

Biochem. J. 1977
9211966 Eukaryotic ribosomal RNA: the recent excitement in the nucleotide modification problem

Maden, BE, Hughes, JM

Chromosoma 1997
25590339 RNA-guided isomerization of uridine to pseudouridine--pseudouridylation

Meier, UT, Yu, YT

RNA Biol 2014
24490730 Chemistry enters nucleic acids biology: enzymatic mechanisms of RNA modification

Motorin, Y, Boschi-Muller, S

Biochemistry Mosc. 2013
19917616 The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification

Ferré-D'Amaré, AR, Hamma, T

J. Biol. Chem. 2010
22065625 The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA

Watkins, NJ, Bohnsack, MT

Wiley Interdiscip Rev RNA 2012
17894445 Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications

Mahto, SK, Chow, CS, Lamichhane, TN

ACS Chem. Biol. 2007
15193314 RNA structure and function in C/D and H/ACA s(no)RNPs

Dez, C, Henry, Y, Henras, AK

Curr. Opin. Struct. Biol. 2004
25775268 Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

Steitz, TA, Polikanov, YS, Söll, D, Melnikov, SV

Nat. Struct. Mol. Biol. 2015
20347423 Yeast pre-rRNA processing and modification occur cotranscriptionally

Tollervey, D, Kos, M

Mol. Cell 2010
21956940 The nucleolus: structure/function relationship in RNA metabolism

Hernandez-Verdun, D, Thiry, M, Roussel, P, Sirri, V, Lafontaine, DL

Wiley Interdiscip Rev RNA 2010
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