Posted: May 18, 2014 8:31 pm
by Rumraket
DavidMcC wrote:
Rumraket wrote:Relatedly:
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004351
The Case for Junk DNA
Alexander F. Palazzo , T. Ryan Gregory

Overview

With the advent of deep sequencing technologies and the ability to analyze whole genome sequences and transcriptomes, there has been a growing interest in exploring putative functions of the very large fraction of the genome that is commonly referred to as “junk DNA.” Whereas this is an issue of considerable importance in genome biology, there is an unfortunate tendency for researchers and science writers to proclaim the demise of junk DNA on a regular basis without properly addressing some of the fundamental issues that first led to the rise of the concept. In this review, we provide an overview of the major arguments that have been presented in support of the notion that a large portion of most eukaryotic genomes lacks an organism-level function. Some of these are based on observations or basic genetic principles that are decades old, whereas others stem from new knowledge regarding molecular processes such as transcription and gene regulation.


The junk-DNA concept IS NOT AN ARGUMENT FROM IGNORANCE.

Indeed, not!
AFAIK, the main category of "junk DNA" refers to sequences that make up the chromatin "packaging" that wraps round the actual genes most of the time.

No, the main category of junk is deactivated transposable elements. Retro transposons. Mostly this is mutated reverse transcriptase genes that have selfishly inserted themselves all over the genome many many times. At a rate that is higher than random deletion events could have got rid of it. That's the largest fraction of the junk, but not the only junk.

DavidMcC wrote:This has the important function of helping to prevent "accidental" gene expression.

No, it might inadvertently have that effect. But that effect is evidentially not strong enough to confer a selective advantage to the extend that we can reliably expect promotion of such "protective junk" or whatever you might want to call it. Evidence for absense of this postulated selective contraint is found in the huge variations of genome size even within very closely related species. Case in point - The Onion test.

Another line of evidence that seems to contradict your postulate here is the almost total absense of such "protective junk" from most single-celled organisms.

DavidMcC wrote: Genes can only be expressed after the chromatin around them has "fluffed up".

Well, you mean genes can only be expressed into RNA transcripts when the double helix has been unwound and helicase has "unzipped" the double strand. Pervasive transcription (also sometimes called transcriptional noise or noisy transcription) at low levels is an observed fact.
Otherwise functional transcription factors will simply occasionally randomly attach to neutrally evolving sequence and produce a transcript (as shown both through in vitro experiments with transcription factors binding to random stretches of DNA, and through measured expression levels in vivo).
Exactly because the reckognition-site is most often not totally identical to the "intended" target site, the binding affinity is lower and the expression level will consequently be extremely low.

DavidMcC wrote:This should be seen as funtional DNA, even though it is not active in terms of translating into any RNA

You mean transcribed, not translated. Also, it IS active in terms of being transcribed into RNA. That's basically the result of the whole ENCODE project. But again, as would be expected for simple biochemical reasons, neutrally evolving DNA will occasionally mutate into stretches of DNA with some sequence similarity to known enhancer and promoter regions. Consequently, we would simply expect occasional low-affinity binding of transcription factors to this randomly mutating DNA. This is what we observe, almost the entire genome is transcribed, but the vast majority is expressed at an extremely low level. When we say low level, we are talking expression levels below a single RNA transcript pr. cell. That is absurdly low. The implication here should be pretty obvious. That is very a very high probability just the result of a "noisy transcription".

DavidMcC wrote:because it could easily be fatal to a multicellular organism if any particular cell expresses any inappropriate genes at a significant level.

Yes, at a significant level. Which would require sequences with very high sequence similarity to known enhancer/promoter regions.

DavidMcC wrote:Thus, "junk DNA" is a misnomer in any case, and should have been abandoned long ago, perhaps in favour of something like "permanently silent DNA", or whatever.

David, maybe you should actually read the publication?

It's obvious there are many mechanisms at work that eventually result in the creation of unneeded and nonfunctional DNA sequence that doesn't have enough of a selective constraint operating on it to kill off carriers. A simple and famous example is the vitamin C pseudogene, GULOP. Do you really want to maintain the GULOP gene is being kept around to protect other genes? There are thousands of pseudogenes. Many of the retro transposons are a form of pseudogenes in themselves, being that they consist of deactivated reverse transcriptase genes that either initially originated in ancient viral infections, or emerged from mutated telomerase enzymes. Junk is simply a manifest fact.

We don't have to engage in this kind of ad-hoc, adaptationist rationalization. A lot of evolution is neutral and random, not everything has a selective purpose or advantage. We don't have to postulate that it does to explain it's existence or to understand it's origin and evolutionary history.