How many lncRNAs are functional?

There's solid evidence that 90% of your genome is junk. Most of it is transcribed at some time but the transcripts are transient and usually confined to the nucleus. They are junk RNA [Functional RNAs?]. This is the view held by many experts but you wouldn't know that from reading the scientific literature and the popular press. The opposition to junk DNA gets much more attention in both venues.

There are prominent voices expressing the view that most of the genome is devoted to producing functional RNAs required for regulating gene expression [John Mattick still claims that most lncRNAs are functional]. Most of these RNAs are long noncoding RNAs known as lncRNAs. Although most of them fail all reasonable criteria for function there are still those who maintain that tens of thousands of them are functional [How many lncRNAs are functional: can sequence comparisons tell us the answer?].

There are very few serious reviews that address the controversy over function (but see Palazzo and Lee, 2015 ... the figure is from their paper). That's why I want to highlight a review that's just been published in Cell. It's a review that recognizes the controversy over function and points to the possibility that most putative lncRNAs may be junk (Kopp and Mendell, 2018). I'm going to quote directly from the introduction and the conclusion to show you how scientific reviews are supposed to be written.

There is a broad range of estimates for the number of lncRNA genes in mammals, ranging from less than 20,000 to over 100,000 in humans. Nevertheless, the function and biological relevance of the vast majority of lncRNAs remain enigmatic. Given that transcriptional regulatory elements, such as enhancers and promoters, are now known to initiate transcription bi-directionally, it is likely that many lncRNAs—if not the majority—actually represent RNAs that initiate at enhancers or promoters but do not perform sequence-specific functions. This conclusion is further suggested by the fact that many lncRNAs are localized to the nucleus with low expression levels and little primary sequence conservation. Recent reports of local gene regulation by lncRNA loci reinforce this notion and suggest that in many cases, the act of transcription or DNA elements within the lncRNA locus are more likely to be the source of regulatory activity than the actual lncRNA itself. Given these observations, it is clear that the mere existence or production of an RNA does not automatically imply its functionality. Indeed, we must assume until proven otherwise that of the tens of thousands of annotated lncRNAs, those that function independently of the DNA sequence from which they are transcribed represent a small minority. Nevertheless, even if a small percentage of lncRNAs are functional, they would still constitute a major gene class with hundreds or possibly thousands of members.

The best available data shows that less than 500 putative lncRNAs have a well-defined function. When I'm calculating the amount of functional DNA in the human genome I usually assume 5,000 genes for noncoding RNAs—most of them are not lncRNAs. I still think that's a good estimate.

The act of transcription around promoter regions may play a role in regulation. In such cases, the sequence of the transcript may be irrelevant but the transcribed region of the genome has a function. There aren't very many proven examples of this type of function. In most cases it looks like the transcripts are just due to sloppy initiation. Kopp and Mendell make an important point in the introduction when they say that the mere existence of a transcript does not mean it has a function. This point is usually ignored in the scientific literature.

The authors reinforce this view in their conclusions. They emphasize a point that most scientists find awkward; namely, that the default assumption must be lack of function (junk RNA) and the burden of proof is on those who propose that most lncRNAs have a function. When we detect a transcript, the most we can say for certain is that there's a transcription initiation site nearby. It may or may not be important.

Over the last decade, the study of lncRNAs has stimulated vigorous debate over the question of whether noncoding RNAs represent “transcriptional noise” or truly functional biomolecules. Clearly, there is no unifying answer—meaningful understanding of lncRNA function (or lack thereof) can only be achieved from detailed study on a case-by-case basis. Importantly, our evolving understanding of the prevalence of genomic elements that produce noncoding transcripts, such as enhancers, has mandated that we approach the experimental evaluation of a lncRNA locus with an agnostic view regarding whether the produced RNA is functional. As Occam’s razor dictates, the simplest hypothesis, in this case that the production of a lncRNA most likely marks the presence of a regulatory DNA element, is often the correct one.

I'm pleased to see that more and more scientists are recognizing the very real controversies over junk DNA and the role of pervasive transcription. Unfortunately, it still takes a bit of courage to stand up to the dominant (but incorrect) paradigm promoted by the ENCODE publicity campaign over the past decade.

---

Kopp, F., and Mendell, J.T. (2018) Functional Classification and Experimental Dissection of Long Noncoding RNAs. Cell, 172:393-407. [doi: 10.1016/j.cell.2018.01.011]

Palazzo, A.F., and Lee, E.S. (2015) Non-coding RNA: what is functional and what is junk? Frontiers in Genetics, 6. [doi: 10.3389/fgene.2015.00002]