Non-coding RNAs: functional molecules or a quality control error?
Fabricio Costa, 1Molecular Neurogenetics Unit, Massachusetts General Hospital and Harvard Medical School, Building 149, 13th street, Boston USA
17 August 2005
The article published by Babak et al. (1) used a microarray analysis and bioinformatic tools in order to search for new functional non-coding RNAs (ncRNAs) in mammalian transcriptomes. They analyzed intergenic and intronic regions that are conserved between humans, rat and mice. Using this approach, they were able to identify 55 highly expressed ncRNAs and, eight of these candidates, were confirmed by Northern Blotting in mice. Five of these ncRNAs were also expressed in rat tissues but none of them were expressed in human tissues. Using just eight candidates, the authors suggested that the new ncRNAs examples that are accumulating in mammalian sequence databases must be viewed with scrutiny regarding their functionality. Furthermore, the authors suggested that many of these ncRNA examples must be generated by errors in the quality-control pathways that degrade unstable transcripts as recently described in yeast (2).
I will disagree with some of the conclusions taken by the authors regarding the functionality of the new ncRNAs examples that are accumulating in RNA databases. The authors suggested that most of the ncRNAs in mammalian transcriptomes might not be functional indicating that they are just “transcriptional noise” as was already published by others (3). First, the number of human tissues analyzed for the expression of these new ncRNA examples does not suffice. There are reports showing that most of the ncRNAs are expressed in a tissue specific manner (4,5) and maybe the authors did not use a tissue or a cell type in which these genes are expressed in higher levels in humans. Another important methodological issue is that Northern Blot is able to evaluate just transcripts with high copy number expressed by the cells. The authors should have used real-time PCR or even a semi-quantitative PCR to really confirm that they are not expressed in any level in human tissues. Moreover, the fact that they are expressed in low levels and with low copy number does not justify that they are not functional. There are examples of protein-coding genes in literature that are expressed in low copy numbers, however they are able to produce functional proteins.
Another important point that might be discussed is the fact that most of the ncRNAs are not conserved between species and that they may have species-specific functions. In this respect, an elegant theory in which ncRNAs might be the key to complexity was recently proposed (6,7). Furthermore, changes in expression levels of ncRNAs have been implicated with cancer and other complex diseases (for review see reference 8). Taken together, this information leads one to the belief that different cell types in human tissues may express a different subset of ncRNAs and that their deregulation may underlie or be a marker for human diseases. Finally, the use of bioinformatic programs to predict secondary structure is not the best way to select ncRNAs that are functional. There may be examples of ncRNAs that does not have a secondary structure and are functional transcripts of some sort.
In respect to the quality-control pathway that degrades unstable transcripts, I will agree that if this pathway is dysregulated in cancer cells, non-coding transcripts with no function might be observed. But what about ncRNAs with different functions that has been described in normal cells (for review see reference 8)? Are they generated by defects in the transcription quality control of the cells? I do not think so.
In conclusion, since the protein-coding gene number between distant eukaryotes (worms, flies, mouse and humans) is very close, ncRNAs could be the big difference in terms of function in eukaryotic cells. These RNAs could be the molecular improvement in higher eukaryotes, especially in humans. This could be a reason for the absence of conservation between humans and mice/rat ncRNAs. Several pieces of evidence indicate that human cells may have a different subset of ncRNAs when compared to other higher eukaryotes.
REFERENCES
1. Babak T, Blencowe BJ, Hughes TR. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics 2005, 6(1): 104
2. Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Regnault B, Devaux F, Namane A, Seraphin B, Libri D, Jacquier A. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly (A) polymerase. Cell 2005,121(5): 725-737.
3. Huttenhofer A, Schattner P, Polacek N. Non-coding RNAs: hope or hype? Trends Genet 2005, 21; 289-297.
4. Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, et al. Human embryonic stem cells express a unique set of microRNAs. Dev Biol 2004, 270; 488-498.
5. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. Identification of tissue-specific microRNAs from mouse. Curr Biol 2002, 12(9):735-739.
6. Mattick JS. RNA regulation: a new genetics? Nat Rev Genet. 2004, 5: 316-323.
7. Mattick JS. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2001, 1:986-991.
8. Costa FF. Non-coding RNAs: new players in eukaryotic biology. Gene (In press)
Non-coding RNAs: functional molecules or a quality control error?
17 August 2005
The article published by Babak et al. (1) used a microarray analysis and bioinformatic tools in order to search for new functional non-coding RNAs (ncRNAs) in mammalian transcriptomes. They analyzed intergenic and intronic regions that are conserved between humans, rat and mice. Using this approach, they were able to identify 55 highly expressed ncRNAs and, eight of these candidates, were confirmed by Northern Blotting in mice. Five of these ncRNAs were also expressed in rat tissues but none of them were expressed in human tissues. Using just eight candidates, the authors suggested that the new ncRNAs examples that are accumulating in mammalian sequence databases must be viewed with scrutiny regarding their functionality. Furthermore, the authors suggested that many of these ncRNA examples must be generated by errors in the quality-control pathways that degrade unstable transcripts as recently described in yeast (2).
I will disagree with some of the conclusions taken by the authors regarding the functionality of the new ncRNAs examples that are accumulating in RNA databases. The authors suggested that most of the ncRNAs in mammalian transcriptomes might not be functional indicating that they are just “transcriptional noise” as was already published by others (3). First, the number of human tissues analyzed for the expression of these new ncRNA examples does not suffice. There are reports showing that most of the ncRNAs are expressed in a tissue specific manner (4,5) and maybe the authors did not use a tissue or a cell type in which these genes are expressed in higher levels in humans. Another important methodological issue is that Northern Blot is able to evaluate just transcripts with high copy number expressed by the cells. The authors should have used real-time PCR or even a semi-quantitative PCR to really confirm that they are not expressed in any level in human tissues. Moreover, the fact that they are expressed in low levels and with low copy number does not justify that they are not functional. There are examples of protein-coding genes in literature that are expressed in low copy numbers, however they are able to produce functional proteins.
Another important point that might be discussed is the fact that most of the ncRNAs are not conserved between species and that they may have species-specific functions. In this respect, an elegant theory in which ncRNAs might be the key to complexity was recently proposed (6,7). Furthermore, changes in expression levels of ncRNAs have been implicated with cancer and other complex diseases (for review see reference 8). Taken together, this information leads one to the belief that different cell types in human tissues may express a different subset of ncRNAs and that their deregulation may underlie or be a marker for human diseases. Finally, the use of bioinformatic programs to predict secondary structure is not the best way to select ncRNAs that are functional. There may be examples of ncRNAs that does not have a secondary structure and are functional transcripts of some sort.
In respect to the quality-control pathway that degrades unstable transcripts, I will agree that if this pathway is dysregulated in cancer cells, non-coding transcripts with no function might be observed. But what about ncRNAs with different functions that has been described in normal cells (for review see reference 8)? Are they generated by defects in the transcription quality control of the cells? I do not think so.
In conclusion, since the protein-coding gene number between distant eukaryotes (worms, flies, mouse and humans) is very close, ncRNAs could be the big difference in terms of function in eukaryotic cells. These RNAs could be the molecular improvement in higher eukaryotes, especially in humans. This could be a reason for the absence of conservation between humans and mice/rat ncRNAs. Several pieces of evidence indicate that human cells may have a different subset of ncRNAs when compared to other higher eukaryotes.
REFERENCES
1. Babak T, Blencowe BJ, Hughes TR. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics 2005, 6(1): 104
2. Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Regnault B, Devaux F, Namane A, Seraphin B, Libri D, Jacquier A. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly (A) polymerase. Cell 2005,121(5): 725-737.
3. Huttenhofer A, Schattner P, Polacek N. Non-coding RNAs: hope or hype? Trends Genet 2005, 21; 289-297.
4. Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, et al. Human embryonic stem cells express a unique set of microRNAs. Dev Biol 2004, 270; 488-498.
5. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. Identification of tissue-specific microRNAs from mouse. Curr Biol 2002, 12(9):735-739.
6. Mattick JS. RNA regulation: a new genetics? Nat Rev Genet. 2004, 5: 316-323.
7. Mattick JS. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep 2001, 1:986-991.
8. Costa FF. Non-coding RNAs: new players in eukaryotic biology. Gene (In press)
Competing interests
None