Computational identification of non-coding RNAs in Saccharomyces cerev
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《核酸研究医学期刊》
In our article we reported eight new noncoding RNA genes named RUF1 through RUF8 (‘RNA of Unknown Function’). Subsequent experiments have demonstrated that three of the RUF loci were the result of experimental errors, and that one of them is not a ncRNA but in fact a doubly-spliced mRNA.
We cannot verify the expression of RNAs from the RUF4, RUF6 and RUF7 loci. The Northern results shown in the paper are from single 5'-labeled oligonucleotide probes. These results continue to be reproducible, but other probes, including additional oligo probes and strand-specific riboprobes, fail to confirm the presence of these RNAs. We have concluded that the published positive Northern results must arise from cross hybridization artifacts. Additionally, RACE–PCR results that supported RUF4 and RUF7 transcription appear to be the result of genomic DNA contamination and fortuitous mispriming of the RACE–PCR reactions near the expected ends of these transcripts. With more extensively DNased RNA preparations that eliminate the signal from genomic PCR, the positive RACE–PCR signals from RUF4 and RUF7 cannot be reproduced.
RUF8 (candidate 71), which we called a ‘possible ncRNA’, is in fact a three exon transcript for a protein-coding gene, which was pointed out to us by Paul Cliften based on his comparative analyses of yeast . We failed to consider that yeast might have a three-exon gene. This locus is now annotated as the SUS1 gene .
The existence of transcripts for RUF1, RUF2, RUF3 and RUF5 has been reconfirmed by both Northerns and RACE–PCR. We have revised our annotations of the ends of these RNAs based on additional RACE–PCR sequencing.
Both GenBank and the Saccharomyces Genome Database have been updated to reflect these changes. RUF4, RUF6, RUF7 and RUF8 have been withdrawn, and the annotations for RUF1, RUF2, RUF3 and RUF5 have been updated.
We regret the errors in our work, and we apologize for any inconvenience that our erroneous conclusions have caused. A more detailed description of the revised results and conclusions is available at http://www.genetics.wustl.edu/eddy/publications/#McCutcheonEddy03.(John P. McCutcheon and Sean R. Eddy)
We cannot verify the expression of RNAs from the RUF4, RUF6 and RUF7 loci. The Northern results shown in the paper are from single 5'-labeled oligonucleotide probes. These results continue to be reproducible, but other probes, including additional oligo probes and strand-specific riboprobes, fail to confirm the presence of these RNAs. We have concluded that the published positive Northern results must arise from cross hybridization artifacts. Additionally, RACE–PCR results that supported RUF4 and RUF7 transcription appear to be the result of genomic DNA contamination and fortuitous mispriming of the RACE–PCR reactions near the expected ends of these transcripts. With more extensively DNased RNA preparations that eliminate the signal from genomic PCR, the positive RACE–PCR signals from RUF4 and RUF7 cannot be reproduced.
RUF8 (candidate 71), which we called a ‘possible ncRNA’, is in fact a three exon transcript for a protein-coding gene, which was pointed out to us by Paul Cliften based on his comparative analyses of yeast . We failed to consider that yeast might have a three-exon gene. This locus is now annotated as the SUS1 gene .
The existence of transcripts for RUF1, RUF2, RUF3 and RUF5 has been reconfirmed by both Northerns and RACE–PCR. We have revised our annotations of the ends of these RNAs based on additional RACE–PCR sequencing.
Both GenBank and the Saccharomyces Genome Database have been updated to reflect these changes. RUF4, RUF6, RUF7 and RUF8 have been withdrawn, and the annotations for RUF1, RUF2, RUF3 and RUF5 have been updated.
We regret the errors in our work, and we apologize for any inconvenience that our erroneous conclusions have caused. A more detailed description of the revised results and conclusions is available at http://www.genetics.wustl.edu/eddy/publications/#McCutcheonEddy03.(John P. McCutcheon and Sean R. Eddy)