Comments on: Genes are only part of the story: ncRNA does stuff

By: Paul Nelson

Paul Nelson — Wed, 16 Jan 2008 16:03:28 +0000

The main reason I read articles with titles like this one is to see if there are any new functions discovered in the ncRNA (and ncDNA). I am sure many, many more will be discovered as time goes on, but one thing that strikes me – and never seems to be mentioned – is that our DNA – all of it, the coding parts (open reading frames), Ribosomal parts, parts that are trascribed into miRNAs, SNPs, etc – as well as all the so called “Junk” – are part of our genome – our chromsomes. This makes up the “whole body of the genome”, and this is necessary for Meiosis and Mitosis. And that is what keeps us alive, as individuals and as a species. By analogy, it’s like if you think everything except the plumbing, wiring, doors, windows, furniture and all the accoutrements like computers, TVs etc in your house are not “Junk” but everything else is. Try living in a house without bricks and mortar, or a roof. Or a floor. Or wooden framing. Might get a bit chilly in wintertime.

By: windy

windy — Wed, 16 Jan 2008 13:10:43 +0000

It may be that every single nucleotide that is not part of a codon that is ultimately transcribed and translated to an amino acid chained into a protein is absolutely without function. Then, the classical term "Junk DNA" fits.

You are free to argue that "Junk DNA" is a misnomer but this is really quite a strawman. The first sentence can't be true since we know that noncoding promoters and such things exist. There's nothing in the classical definition of junk DNA about every single noncoding nucleotide having to be non-functional!

By: Greg Laden

Greg Laden — Wed, 16 Jan 2008 12:24:56 +0000

apalazzo: That is because your comments are being censored!Only kidding. I’ve looked at this end and there is nothing there. You must be having a problem with your browser or something.

By: apalazzo

apalazzo — Wed, 16 Jan 2008 11:23:40 +0000

Larry,I had a whole paragraph under that sentence developing an idea. That paragraph vanished. I then retyped it and it vanished again … I won’t try a third time.

By: Larry Moran

Larry Moran — Wed, 16 Jan 2008 09:40:39 +0000

There’s a problem here and elsewhere. About 50-70% of the genome is continuously transcribed.The “problem” is that what you say is not correct. It has not been demonstrated that 50-70% of the (mammalian) genome is “continuously” transcribed in the sense that you imply.

By: apalazzo

apalazzo — Wed, 16 Jan 2008 07:50:28 +0000

(damn what happened to the rest of my comment?)the authors show that <1% of the genome is expressed as ncRNAs with an interesting pattern. There is no evidence here that "most of the genome is functional". Another peeve - there is no functional data in this paper. How do we know that these bits of RNAs are important? Perhaps the interesting patterns are just incidental to a patterns of transcriptional factors +lots of cryptic transcriptional start sites? Or perhaps it is just stable bits of transcripts that survive the various nuclear environments differently. If someone knocks one down and sees some phenotype then people will pay attention, as it stands these are only interesting observations.

By: apalazzo

apalazzo — Wed, 16 Jan 2008 07:38:26 +0000

There's a problem here and elsewhere. About 50-70% of the genome is continuously transcribed. Yet only 1-2% of it codes for proteins. So why? There may be some ncRNAs that may perform a specific task, and the authors here show that <1% of the ncRNA may be expressed in an interesting pattern. But it still looks like the rest doesn't do much. In contrast there is plenty of evidence out there that the act of transcription is important to remodel how the DNA is packed. And this paper does not provide any evidence that the genome contains "mostly functional" ncRNAs.

By: Sigmund

Sigmund — Wed, 16 Jan 2008 03:07:02 +0000

RPM, while it is clear that the majority of the human genome is non functional what we are dealing with is not defined islands of functional elements (coding, functional RNA and non-coding regulatory sequences) separated by seas of non functional DNA. What we are increasingly finding is large numbers of important regulatory elements scattered throughout the genome. Sequences that were once ‘junk’ can later acquire function through mutations of one kind or the other. While the whole question of ‘junk DNA’ is a semantic point for genomicists it is not that way for other biologists and the general public. They wont know enough about microRNAs, antisense genes, enhancers, repressors, insulator elements, matrix attachment regions – all of which are still being identified within DNA sequences that were not found to be protein encoding. What the public don’t understand is that genomicists have always assumed that such regulatory elements do exist within the non coding sequences – we just haven’t characterized them sufficiently yet. This is the reason why the discovery institute has started trumpeting functional elements found within previously described ‘junk DNA’ as some sort of success of their predictive abilities. The

By: Greg Laden

Greg Laden — Tue, 15 Jan 2008 21:24:52 +0000

Its funny how people are so touchy about Junk DNA. It’s not like I killed your puppy or something…It may be that every single nucleotide that is not part of a codon that is ultimately transcribed and translated to an amino acid chained into a protein is absolutely without function. Then, the classical term “Junk DNA” fits.I do regret saying “The “Junk DNA” story is largely a myth, as you probably already know. DNA does not have to code for one of the few tens of thousands of proteins or enzymes known for any given animal, for example, to have a function. We know that.” (even though it is utterly true if you include DNA that “codes for” things that are not proteins, control regions, and effects of genome size, and possibly other things such as suggested in this paper) then following that with “we actually don’t know a lot more than that, or more exactly, there is not a widely accepted dogma for the role of “non-coding DNA.” second. I should have made the second point use more words and the first point use fewer words, then reversed the order of the points. Then what i was saying would have been more obvious to people skimming the post…Jeesh… and I thought anthropologists were touchy…

By: RPM

RPM — Tue, 15 Jan 2008 20:26:09 +0000

The "Junk DNA" story is largely a myth, as you probably already know.No, I don't already know. The majority of the human genome is non-functional. Why not describe it as junk. Sure, a small fraction of the genome is functional (including protein coding genes, non-translated transcribed sequences, and transcriptional regulatory regions), but most of it can be best described as junk.