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Tuesday, February 06, 2018

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]


Gary Gaulin said...

Speaking of RNA's is this from neuroscience:


A temporary vessel

Tonegawa is confident that the very existence of physical links between neurons stores memories. But other researchers have their own notions.

Back in the 1950s, McConnell suspected that RNA, cellular material that can help carry out genetic instructions but can also carry information itself, might somehow store memories.

This unorthodox idea, that RNA is involved in memory storage, has at least one modern-day supporter in Glanzman, who plans to present preliminary data at a meeting in April that suggest injections of RNA can transfer memory between sea slugs.

Glanzman thinks that RNA is a temporary storage vessel for memories, though. The real engram, he suggests, is the folding pattern of DNA in cells’ nuclei. Changes to how tightly DNA is packed can govern how genes are deployed. Those changes, part of what’s known as the epigenetic code, can be made — and even transferred — by roving RNA molecules, Glanzman argues. He is quick to point out that his idea, memory transfer by RNA, is radical. “I don’t think you could find another card-carrying Ph.D. neuroscientist who believes that.”

Other researchers, including neurobiologist David Sweatt of Vanderbilt University in Nashville, also suspect that long-lasting epigenetic changes to DNA hold memories, an idea Sweatt has been pursuing for 20 years. Because epigenetic changes can be stable, “they possess the unique attribute necessary to contribute to the engram,” he says.

Gary Gaulin said...

Wow!!!!!!!! I'm loving this paper!

Long before the advent of single-cell RNA-Seq, highly-precise spatial organization of lncRNAs had been observed by in situ hybridization, which showed that the expression of many lncRNAs is restricted to individual brain regions, structures, or cell types (Figure IC) [15].

The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome

Full-Text PDF

Does anyone have any evidence that expression of many lncRNAs is not restricted to individual brain regions, structures, or cell types?

Gary Gaulin said...

Another treasure trove of information, this time from a company named Exiqon:

What are lncRNAs?

Gary Gaulin said...

Larry, the Tissue Specific results from "Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs" tops off a good answer to your question with exciting new evolutionary significant research that I have for decades been anxiously waiting for:

Consistent with previous studies [2, 14], the brain, testis, lung and skin tissues have more TS lncRNAs and TS protein coding genes, perhaps due to the presence of heterogeneous cell types in these tissues or from a need for more diverse lncRNA repertoires. Interestingly, the high number of TS lncRNA in testis has been discovered by several previous studies [9, 10, 13]. Both our study and Cabili et al. found that the testis tissue has the highest number of TS lncRNAs across the tissues considered, and 36.5% TS lincRNAs are also detected by Cabili et al., which is significant. Thus, testis-specific lincRNAs may define a new class of RNAs in this organ. These results might be because this organ may represent a breeding ground for new genes, and may be due to the particularly efficient activity of proto-promoters in testis cells [9, 15]. Many TS lncRNAs are also found in other tissues. For example, two TS lncRNAs of the pancreas tissue, CTD-2503O16.4 (ENSG00000249856) and LINC00511 (ENSG00000227036) have been uncovered to be high-confidence human islet-cell genes [16]. On the contrary, the number of TS lncRNAs is lower in the breast, muscle and adipose tissues, reflecting more specialized functions of these tissues. In addition, we found that the TS lncRNAs overlap with those identified by Cabili et al. based on the K-means clustering with the tissue specificity distance measure (Supplementary Table S3).

I expected this to be the molecular level intelligence brain that goes from one thought to the next through time, by reproducing/renewing itself each time via reproduction. Quick illustration again:

LncRNAs are in my opinion essentially RNA based components needed for self-assembly of networked brain circuits, for the part of us that's billions of years old. I expect the answer to just how smart the molecular level brain actually is will be even more amazing, but making a connectome for the entire innards of reproductive cells makes the (still years away) full connectome for the giant brain in our cranium seem easy.

Hopefully you can at least agree that with lncRNA research making visible progress towards finding a useful function it's necessary that they make as fast as possible progress towards wherever that goes, or else we're all stuck waiting longer than is necessary for them to get there.

Larry Moran said...


I’m reasonably tolerant of kooks as long as they only make the occasional comment on my blog. You are testing the limit of my tolerance.

This is your first warning.

Gary Gaulin said...

Well that's a creepy thing to say to the only person who responded to your question.

I was hoping you would address all the (looks OK to me) lncRNA research now being conducted, instead of throwing an insult.