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Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5' end processing and tRNA splicing.

Hiley SL, Babak T, Hughes TR - Nucleic Acids Res. (2005)

Bottom Line: We also monitored the accumulation of improperly processed flank sequences of pre-RNAs in strains depleted for known RNA nucleases, including RNase III, Dbr1p, Xrn1p, Rat1p and components of the exosome and RNase P complexes.Among the hundreds of aberrant RNA processing events detected, two novel substrates of Rnt1p (the RUF1 and RUF3 snoRNAs) were identified.We also identified a relationship between tRNA 5' end processing and tRNA splicing, processes that were previously thought to be independent.

View Article: PubMed Central - PubMed

Affiliation: Banting and Best Department of Medical Research, University of Toronto 112 College Street, Toronto, ON M5G 1L6, Canada.

ABSTRACT
We used a microarray containing probes that tile all known yeast noncoding RNAs (ncRNAs) to investigate RNA biogenesis on a global scale. The microarray verified a general loss of Box C/D snoRNAs in the TetO7-BCD1 mutant, which had previously been shown for only a handful of snoRNAs. We also monitored the accumulation of improperly processed flank sequences of pre-RNAs in strains depleted for known RNA nucleases, including RNase III, Dbr1p, Xrn1p, Rat1p and components of the exosome and RNase P complexes. Among the hundreds of aberrant RNA processing events detected, two novel substrates of Rnt1p (the RUF1 and RUF3 snoRNAs) were identified. We also identified a relationship between tRNA 5' end processing and tRNA splicing, processes that were previously thought to be independent. This analysis demonstrates the applicability of microarray technology to the study of global analysis of ncRNA synthesis and provides an extensive directory of processing events mediated by yeast ncRNA processing enzymes.

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Related in: MedlinePlus

Detecting known RNA processing events by microarray. Oligonucleotides corresponding to processed regions showing at least a 4-fold increase at least one of the mutant strains were subjected to hierarchical agglomerative clustering. Probes corresponding to accumulated sequences are colored red, according to the scale shown. The identities of the probes are shown in the black and white panel on the right. A fully labeled numerical version of this figure is available in the Supplementary Material.
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fig2: Detecting known RNA processing events by microarray. Oligonucleotides corresponding to processed regions showing at least a 4-fold increase at least one of the mutant strains were subjected to hierarchical agglomerative clustering. Probes corresponding to accumulated sequences are colored red, according to the scale shown. The identities of the probes are shown in the black and white panel on the right. A fully labeled numerical version of this figure is available in the Supplementary Material.

Mentions: Microarray oligonucleotide sequences and microarray data are found at . Spreadsheets containing the data displayed in Figure 2 are also available on the website.


Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5' end processing and tRNA splicing.

Hiley SL, Babak T, Hughes TR - Nucleic Acids Res. (2005)

Detecting known RNA processing events by microarray. Oligonucleotides corresponding to processed regions showing at least a 4-fold increase at least one of the mutant strains were subjected to hierarchical agglomerative clustering. Probes corresponding to accumulated sequences are colored red, according to the scale shown. The identities of the probes are shown in the black and white panel on the right. A fully labeled numerical version of this figure is available in the Supplementary Material.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1140755&req=5

fig2: Detecting known RNA processing events by microarray. Oligonucleotides corresponding to processed regions showing at least a 4-fold increase at least one of the mutant strains were subjected to hierarchical agglomerative clustering. Probes corresponding to accumulated sequences are colored red, according to the scale shown. The identities of the probes are shown in the black and white panel on the right. A fully labeled numerical version of this figure is available in the Supplementary Material.
Mentions: Microarray oligonucleotide sequences and microarray data are found at . Spreadsheets containing the data displayed in Figure 2 are also available on the website.

Bottom Line: We also monitored the accumulation of improperly processed flank sequences of pre-RNAs in strains depleted for known RNA nucleases, including RNase III, Dbr1p, Xrn1p, Rat1p and components of the exosome and RNase P complexes.Among the hundreds of aberrant RNA processing events detected, two novel substrates of Rnt1p (the RUF1 and RUF3 snoRNAs) were identified.We also identified a relationship between tRNA 5' end processing and tRNA splicing, processes that were previously thought to be independent.

View Article: PubMed Central - PubMed

Affiliation: Banting and Best Department of Medical Research, University of Toronto 112 College Street, Toronto, ON M5G 1L6, Canada.

ABSTRACT
We used a microarray containing probes that tile all known yeast noncoding RNAs (ncRNAs) to investigate RNA biogenesis on a global scale. The microarray verified a general loss of Box C/D snoRNAs in the TetO7-BCD1 mutant, which had previously been shown for only a handful of snoRNAs. We also monitored the accumulation of improperly processed flank sequences of pre-RNAs in strains depleted for known RNA nucleases, including RNase III, Dbr1p, Xrn1p, Rat1p and components of the exosome and RNase P complexes. Among the hundreds of aberrant RNA processing events detected, two novel substrates of Rnt1p (the RUF1 and RUF3 snoRNAs) were identified. We also identified a relationship between tRNA 5' end processing and tRNA splicing, processes that were previously thought to be independent. This analysis demonstrates the applicability of microarray technology to the study of global analysis of ncRNA synthesis and provides an extensive directory of processing events mediated by yeast ncRNA processing enzymes.

Show MeSH
Related in: MedlinePlus