The latest review by my colleagues here in the biochemistry department at the University of Toronto (Toronto, Canada), concludes that only a small fraction of these putative lncRNAs have a function (Palazzo and Lee, 2015). They point out that in the absence of evidence for function, the null hypothesis is that these RNAs are junk and the genes don't exist. That's not the view that annotators at Ensembl take.
The central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs (lncRNAs) have attracted much attention due to their large number and biological significance. Many lncRNAs have been identified as mapping to regulatory elements including gene promoters and enhancers, ultraconserved regions and intergenic regions of protein-coding genes. Yet, the biological function and molecular mechanisms of lncRNA in human diseases in general and cancer in particular remain largely unknown. Data from the literature suggest that lncRNA, often via interaction with proteins, functions in specific genomic loci or use their own transcription loci for regulatory activity. In this review, we summarize recent findings supporting the importance of DNA loci in lncRNA function and the underlying molecular mechanisms via cis or trans regulation, and discuss their implications in cancer. In addition, we use the 8q24 genomic locus, a region containing interactive SNPs, DNA regulatory elements and lncRNAs, as an example to illustrate how single nucleotide polymorphism (SNP) located within lncRNAs may be functionally associated with the individual’s susceptibility to cancer.This is getting to be a familiar refrain. I understand how modern scientists might be confused about the difference between the Watson and the Crick versions of the Central Dogma [see The Central Dogma of Molecular Biology]. Many textbooks perpetuate the myth that Crick's sequence hypothesis is actually the Central Dogma. That's bad enough but lots of researchers seem to think that their false view of the Central Dogma goes even further. They think it means that the ONLY kind of genes in your genome are those that produce mRNA and protein.
I don't understand how such a ridiculous notion could arise but it must be a common misconception, otherwise why would these authors think that non-coding RNAs are a challenge to the Central Dogma? And why would the reviewers and editors think this was okay?
I'm pretty sure that I've interpreted their meaning correctly. Here's the opening sentences of the introduction to their paper ...
The Encyclopedia of DNA Elements (ENCODE) project has revealed that at least 75% of the human genome is transcribed into RNAs, while protein-coding genes comprise only 3% of the human genome. Because of a long-held protein-centered bias, many of the genomic regions that are transcribed into non-coding RNAs (ncRNAs) had been viewed as ‘junk’ in the genome, and the associated transcription had been regarded as transcriptional ‘noise’ lacking biological meaning.They think that the Central Dogma is a "protein-centered bias." They think the Central Dogma rules out genes that specify noncoding RNAs. (Like tRNA and ribosomal RNA?)
Later on they say ....
The protein-centered dogma had viewed genomic regions not coding for proteins as ‘junk’ DNA. We now understand that many lncRNAs are transcribed from ‘junk’ regions, and even those encompassing transposons, pseudogenes and simple repeats represent important functional regulators with biological relevance.It's simply not true that scientists in the past viewed all noncoding DNA as junk, at least not knowledgeable scientists [What's in Your Genome?]. Furthermore, no knowledgeable scientists ever interpreted the Central Dogma of Molecular Biology to mean that the only functional genes in a genome were those that encoded proteins.
Apparently Lee, Vincent, Picler, Fodde, Berindan-Neagoe, Slack, and Calin knew scientists who DID believe such nonsense. Maybe they even believed it themselves.
Judging by the frequency with with such statements appear in the scientific literature, I can only assume that this belief is widespread among biochemists and molecular biologists. How in the world did this happen? How many Sandwalk readers were taught that the Central Dogma rules out all genes for noncoding RNAs? Did you have such a protein-centered bias about the role of genes? Who were your teachers?
Didn't anyone teach you who won the Nobel Prize in 1989? Didn't you learn about snRNAs? What did you think RNA polymerases I and III were doing in the cell?
Ling, H., Vincent, K., Pichler, M., Fodde, R., Berindan-Neagoe, I., Slack, F.J., and Calin, G.A. (2015) Junk DNA and the long non-coding RNA twist in cancer genetics. Oncogene (published online January 26, 2015) [PDF]
Palazzo, A.F. and Lee, E.S. (2015) Non-coding RNA: what is functional and what is junk? Frontiers in genetics 6: 2 (published online January 26, 2015 [Abstract]