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PMID:12837249

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Citation

Peng, WT, Robinson, MD, Mnaimneh, S, Krogan, NJ, Cagney, G, Morris, Q, Davierwala, AP, Grigull, J, Yang, X, Zhang, W, Mitsakakis, N, Ryan, OW, Datta, N, Jojic, V, Pal, C, Canadien, V, Richards, D, Beattie, B, Wu, LF, Altschuler, SJ, Roweis, S, Frey, BJ, Emili, A, Greenblatt, JF and Hughes, TR (2003) A panoramic view of yeast noncoding RNA processing. Cell 113:919-33

Abstract

Predictive analysis using publicly available yeast functional genomics and proteomics data suggests that many more proteins may be involved in biogenesis of ribonucleoproteins than are currently known. Using a microarray that monitors abundance and processing of noncoding RNAs, we analyzed 468 yeast strains carrying mutations in protein-coding genes, most of which have not previously been associated with RNA or RNP synthesis. Many strains mutated in uncharacterized genes displayed aberrant noncoding RNA profiles. Ten factors involved in noncoding RNA biogenesis were verified by further experimentation, including a protein required for 20S pre-rRNA processing (Tsr2p), a protein associated with the nuclear exosome (Lrp1p), and a factor required for box C/D snoRNA accumulation (Bcd1p). These data present a global view of yeast noncoding RNA processing and confirm that many currently uncharacterized yeast proteins are involved in biogenesis of noncoding RNA.

Links

PubMed

Keywords

Cells, Cultured; Fungal Proteins/genetics; Fungal Proteins/isolation & purification; Gene Expression Regulation, Fungal/genetics; Genome, Fungal; Mutation/genetics; Oligonucleotide Array Sequence Analysis; Phenotype; RNA Precursors/biosynthesis; RNA Precursors/genetics; RNA, Small Nucleolar/biosynthesis; RNA, Small Nucleolar/genetics; RNA, Transfer/biosynthesis; RNA, Transfer/genetics; RNA, Untranslated/biosynthesis; RNA, Untranslated/genetics; Ribonucleoproteins/biosynthesis; Yeasts/genetics; Yeasts/metabolism

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

YEAST:MRT4

involved_in

GO:0006364: rRNA processing

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:BCD1

involved_in

GO:0016074: sno(s)RNA metabolic process

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:BCD1

enables

GO:0003676: nucleic acid binding

ECO:0000303: author statement without traceable support used in manual assertion

F

Seeded From UniProt

complete

YEAST:LRP1

enables

GO:0044877: protein-containing complex binding

ECO:0000314: direct assay evidence used in manual assertion

F

Seeded From UniProt

complete

YEAST:RS26A

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:Q06672

F

Seeded From UniProt

complete

YEAST:UTP22

involved_in

GO:0006364: rRNA processing

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:PESC

involved_in

GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:NOP19

involved_in

GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:RRP17

involved_in

GO:0006364: rRNA processing

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:TSR2

involved_in

GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:TSR2

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P39938

F

Seeded From UniProt

complete

YEAST:GRC3

involved_in

GO:0006364: rRNA processing

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:MDN1

involved_in

GO:0006364: rRNA processing

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:KAD6

involved_in

GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:SAS10

involved_in

GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:FYV7

involved_in

GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:RRP36

involved_in

GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:EFG1P

involved_in

GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:PP12

involved_in

GO:0006364: rRNA processing

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete


See also

References

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