Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure

Trends in Genetics

Volumn 31, Issue 3, 2015, Pages 157-163

  Coleman, Annette W ^a  

^a BROWN UNIVERSITY   (United States)

Author keywords

Internal transcribed spacer; Nuclear ribosome synthesis; RNA secondary structure; RRNA processing

Indexed keywords

INTERNAL TRANSCRIBED SPACER; NUCLEAR RNA; RIBOSOME RNA; RIBOSOMAL SPACER DNA; RNA PRECURSOR;

CISTRON; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REVIEW; RIBOSOME; RNA CLEAVAGE; RNA PROCESSING; RNA STRUCTURE; RNA TRANSCRIPTION; ANIMAL; CHEMISTRY; CONFORMATION; EVOLUTION; GENE EXPRESSION; GENETICS; HUMAN; METABOLISM; MOUSE; NUCLEOTIDE SEQUENCE; PLANT; RAT; YEAST;

EUKARYOTA; MUS; RATTUS;

ANIMALS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; DNA, RIBOSOMAL SPACER; GENE EXPRESSION; HUMANS; MICE; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLANTS; RATS; RNA PRECURSORS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, RIBOSOMAL; YEASTS;

EID: 84923609079     PISSN: 01689525     EISSN: 13624555     Source Type: Journal    
DOI: 10.1016/j.tig.2015.01.002     Document Type: Review

References (47)

1. French S.L., et al. In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol. Cell. Biol. 2003, 23:558-1568.
2. Osheim Y.N., et al. Pre-18S ribosomal RNA is structurally compacted into the SSU processome prior to being cleaved from the nascent transcript in Saccharomyces cerevisiae. Mol. Cell 2004, 16:943-964.
3. Tafforeau L., et al. The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of pre-rRNA processing factors. Mol. Cell 2013, 51:539-551.
4. Saez-Vasquez J., et al. Characterization of a crucifer plant pre-rRNA processing complex. Biochem. Soc. Trans. 2004, 32:578-580.
5. Elder J.F., Turner B.J. Concerted evolution of repetitive DNA sequences in eukaryotes. Q. Rev. Biol. 1995, 70:297-320.
6. Goldman W.E., et al. Mouse rDNA: sequences and evolutionary analysis of spacer and mature RNA regions. Mol. Cell. Biol. 1983, 3:1488-1500.
7. Gutell R.R., et al. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. Nucleic Acids Res. 1993, 21:3055-3074.
8. Tague B.W., Gerbi S.A. Processing of the large rRNA precursor: two proposed categories of RNA-RNA interactions in eukaryotes. J. Mol. Evol. 1984, 20:362-367.
9. Peyretaillade E., et al. Microsporidian Encephalitozoon cuniculi, a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core. Nucleic Acids Res. 1998, 26:3513-3520.
10. Coleman A.W. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res. 2007, 35:3322-3329.
11. Hausner G., Wang X. Unusual compact rDNA gene arrangements within some members of the Ascomycota: evidence for molecular co-evolution between ITS1 and ITS2. Genome 2005, 48:648-660.
12. Petrov A.S., et al. Evolution of the ribosome at atomic resolution. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:10251-10256.
13. Coleman A.W. Analysis of mammalian rDNA internal transcribed spacers. PLoS ONE 2013, 8:e79122.
14. Bernstein K.A., et al. The SSU processome is a ribosome assembly intermediate. Cell 2004, 3:1619-1626.
15. Dragon F., et al. Pre-18S ribosomal RNA is structurally compacted into the SSU processome prior to being cleaved from nascent transcripts in Saccharomyces cerevisiae. Mol. Cell 2004, 16:943-954.
16. Veldman G., et al. Some characteristics of processing sites in ribosomal precursor RNA of yeast. Nucleic Acids Res. 1980, 8:2907-2920.
17. Peculis B.A., Steitz J.A. Disruption of U8 nucleolar snRNA inhibits 5.8S and 28S rRNA processing in the Xenopus oocyte. Cell 1993, 73:1233-1245.
18. Geerlings T.H., et al. The final step in the formation of 25SrRNA in Saccharomyces cerevisiae is performed by 5'>3' exonucleases. RNA 2000, 6:1698-1703.
19. Mitchell P., et al. The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. Genes Dev. 1996, 10:502-513.
20. Lebaron S., et al. Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits. Nat. Struct. Mol. Biol. 2012, 19:744-753.
21. Granneman S., et al. A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease. EMBO J. 2011, 19:4006-4019.
22. Joseph N., et al. Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Res. 1999, 27:4533-4540.
23. Cote C.A., et al. Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast. RNA 2002, 8:786-797.
24. Van der Sande C.A., et al. Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA. J. Mol. Biol. 1992, 223:899-910.
25. Van Nues R.W., et al. Evolutionarily conserved structural elements are critical for processing of internal transcribed spacer 2 from Saccharomyces cerevisiae precursor ribosomal RNA. J. Mol. Biol. 1995, 250:24-36.
26. Yeh L-C.C., Lee J.C. Structural analysis of the internal transcribed spacer 2 of the precursor ribosomal RNA from Saccharomyces cerevisiae. J. Mol. Biol. 1990, 211:699-712.
27. Van Nues R.W., et al. Separate structural elements within internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26S rRNA. Nucleic Acids Res. 1994, 22:912-919.
28. 2 in the yeast pre-RNA. RNA 1996, 2:51-62.
29. Henry Y., et al. The 5' end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J. 1994, 13:2452-2463.
30. 3 is linked. RNA 1996, 2:63-73.
31. Zakrzewska-Placzek M., et al. Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA. Nucleic Acids Res. 2010, 38:4487-4502.
32. Hadjiolova K.V., et al. Mapping of the major early endonuclease cleavage site of the rat precursor to rRNA within the intertranscribed spacer sequence of rDNA. Biochem. Biophys. Acta 1984, 782:1952-2001.
33. Wang M., Pestov D.G. 5' End surveillance by Zrn2 acts as a shared mechanism for mammalian pre-RNA maturation and decay. Nucleic Acids Res. 2010, 38:1811-1822.
34. Sloan K.E., et al. Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human ribosomal RNA processing. J. Cell Biol. 2013, 200:577-588.
35. Preti M., et al. Gradual processing of the ITS1 from the nucleolus to the cytoplasm during synthesis of the human 18S RNA. Nucleic Acids Res. 2013, 41:4709-4723.
36. Idol R.A., et al. Cells depleted for RPS 19, a protein associated with Diamond Blackfan anemia, show defects in 18S ribosomal RNA synthesis and small ribosomal subunit production. Blood Cells Mol. Dis. 2007, 39:35-42.
37. Rouquette J., et al. Nuclear export and cytoplasmic processing of precursors to the 40S ribosomal subunits in mammalian cells. EMBO J. 2005, 24:2862-2872.
38. Millineux S-T., Lafontaine D.L.J. Mapping the cleavage sites on mammalian pre-RNAs: where do we stand?. Biochimie 2012, 94:1521-1532.
39. Carron C., et al. Analysis of two human pre-ribosomal factors, bystatin and hTsr1, highlights differences in evolution of ribosome biogenesis between yeast and mammals. Nucleic Acids Res. 2011, 39:280-291.
40. Schultz J., et al. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 2005, 11:361-364.
41. Schillewaert S., et al. The evolutionarily conserved protein LAS1 is required for pre-rRNA processing at both ends of ITS2. Mol. Cell. Biol. 2012, 32:430-444.
42. Good L., et al. The ribosomal-RNA-processing pathway in Schizosaccharomyces pombe. Eur. J. Biochem. 1997, 247:314-321.
43. Pendrak M.L., Roberts D. Ribosomal RNA processing in Candida albicans. RNA 2011, 17:2235-2248.
44. Michot B., et al. Evolutionarily conserved structural features in the ITS2 of mammalian pre-rRNAs and potential interactions with the snoRNA U8 detected by comparative analysis of new mouse sequences. Nucleic Acids Res. 1999, 27:2271-2282.
45. Reddy R., et al. The nucleotide sequence of 8S RNA bound to preribosomal RNA of Novikoff hepatoma. J. Biol. Chem. 1983, 258:584-589.
46. Bowman L.H., et al. Location of the initial cleavage sites in mouse pre-rRNA. Mol. Cell Biol. 1983, 3:1501-1510.
47. Hadjiolova K.V., et al. Processing of truncated mouse or human rRNA transcribed from ribosomal minigenes transfected into mouse cells. Mol. Cell. Biol. 1994, 14:4044-4056.