DavidMcC wrote:... I now have my old course notes (mainly printed by the lecturers) in front of me.
Section 4.1 Regulation at the structural level. Active genes: - unfolding of chromatin during transcription
Electron micrograph of active genes.
During transcription, the compact chromatin opens up and long loops of DNA being transcribed is visible.

(And, yes, I admit that I used the wrong word previously, OK? Obviously, I have not included the micrograph.)

Chromatin AT active genes unfolds during transcription - this doesn't involve heterochromatin which consists of non-genic silent DNA making up the DNA component, so regardless of how you spin it, your contention that junk DNA exists so it can form chromatin that prevents abnormal gene expression is indeed, as I called it, piffle.

Also - your notes may be having it slightly arse backwards - there has to be a chromatin state that is transcription-permissive that is established concurrently or before transcription can take place. By and large we know what these changes are - histone hyperacetylation that is mediated by the KAT family of enzymes, demethylation mediated by the JMJD and KDM family of enzymes and methylation usually mediated by SET-domain methyltransferases at H3k4. You don't necessarily get chromatin relaxation at sites of active transcription as much as you get active transcription following transcription factor binding to active genes that are marked by the relevant histone marks.

GenesForLife wrote:

DavidMcC wrote:... I now have my old course notes (mainly printed by the lecturers) in front of me.
Section 4.1 Regulation at the structural level. Active genes: - unfolding of chromatin during transcription
Electron micrograph of active genes.
During transcription, the compact chromatin opens up and long loops of DNA being transcribed is visible.

(And, yes, I admit that I used the wrong word previously, OK? Obviously, I have not included the micrograph.)

Chromatin AT active genes unfolds during transcription -this doesn't involve heterochromatin which consists of non-genic silent DNA making up the DNA component, so regardless of how you spin it, your contention that junk DNA exists so it can form chromatin that prevents abnormal gene expression is indeed, as I called it, piffle.

Ha! You are the one spinning what I said, there. When did I ever say that junk DNA exists so that it can form chromatin that prevents abnormal gene expression. That would be b*ll*cks, indeed. What happens in evolution (which you apparently don't understand as well as you think), is that life adapts to what's there, and so a build up of inactive DNA in early eukaryotes probably enabled cell specialization and thus multicellular organisms. Also, of course it only opens up where it is required for expression. To do otherwise would be self-defeating!

I have noted that your overly aggressive style.

Also - your notes may be having it slightly arse backwards - there has to be a chromatin state that is transcription-permissive that is established concurrently or before transcription can take place.

The notes I quoted were not my own, they were printed for me by the employer. Also, it is hard to envision the gene to untwist if the local chromatin is still twisted.

DavidMcC wrote:... I also think you have the wrong idea about the evolutionary aspect of the above. It does not imply that "all junk DNA is chromatin, or that it evolved for a purpose", as you bizarrely inferred.

My gripe is still with your insinuation that chromatin that encompasses junk DNA stops the aberrant expression of genic DNA by wrapping round it. As I maintain - piffle.

Yep. The issue is not that DNA wrapping around nucleosomes into chromatin isn't protecting the DNA, the issue is that you don't need large swathes of neutrally evolving transposable elements to prevent accidental transcription. Simply increasing the size of the transcription factor binding site would mean you could make it much less likely for two such sites to be similar in sequence, which means you would avoid a lot more nonspecific binding resulting in accidental transcripts.

And again, the significant variations in genome size even between very closely related species is evidence against this kind of "protective junk" hypothesis.

And as I quote -

"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."

I find it amusing that you can't see how

[1] Given the premise that chromatin context is involved in repressing aberrant gene expression, which is indubitably true given the literature and

[2] Given your assertion that junk DNA contains of sequences that comprise the chromatin that wraps round actual genes

that junk DNA represses transcription of genes/prevents aberrant transcription thereof by wrapping round it as part of chromatin (as opposed to genic and non-genic DNA both having their own local chromatin - therefore rendering heterochromatin persona non-grata in the regulation of expression of genic DNA) is an inference your piffle inevitably leads to.

PS - Your comment about my overly aggressive style does not parse correctly. You have noted that my overly aggressive style what?

DavidMcC wrote:Look, I didn't invent this stuff - it was part of my "Basic Bio" course by my employer, which was active in the field of biotechnology (involving DNA amplification on electronic chips).
So, you two don't accept that portions of a chromosome untwist ("fluff up") during gene expression, to allow enzymes to access the gene?

Of course that is accepted, this is common knowledge. This is not what has been in contention here.

DavidMcC wrote:The theory was that multicellular animals exploit the extra protection of genes from enzymes, which are large molecules, except during expression.

You don't need large swathes of neutrally evolving DNA to get the protective effect of chromatin packaging. Simply making genes wrap into the chromatin complex will ensure that protection. The primary protection against accidental transcription is transcription factor binding site size. They're usually about 10 bases long, which can be shown probabilistically to be more than enough to ensure any two loci are extremely unlikely to evolve the exact same binding site.

DavidMcC wrote:

Rumraket wrote: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.

That was not my argument. I was taught that a major difference between prokaryotes and eukaryotes involved the latter having to keep most genes in any one cell completely silent all of the time, otherwise the wrong proteins and RNAs might be made in that cell, which could be fatal. That was part of the rationale given.

And as explained, chromatin packaging and transcription factor binding specificity itself ensures that, junk DNA or not. Again, look at the genome size variation! It would seem strange to imagine one species of fish needing 670 times as much protective junk than another. Or that between two virtually identical onions, one would maintain a genome five times greater than the other for that purpose.

No, it's simply junk being generated at higher rate than purifying selection can get rid of it. What you're doing is engaging in an ad-hoc adaptationist rationalization to explain the existence of large swathes of neutrally evolving DNA.

There isn't a process that goes round deleting DNA randomly - as Rumraket says says - you could have accumulation of vast amounts of neutrally evolving junk just because there isn't a way to get rid of it, and it isn't deleterious.

GenesForLife wrote:And as I quote -

"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."

I find it amusing that you can't see how

[1] Given the premise that chromatin context is involved in repressing aberrant gene expression, which is indubitably true given the literature and

[2] Given your assertion that junk DNA contains of sequences that comprise the chromatin that wraps round actual genes

that junk DNA represses transcription of genes/prevents aberrant transcription thereof by wrapping round it as part of chromatin (as opposed to genic and non-genic DNA both having their own local chromatin - therefore rendering heterochromatin persona non-grata in the regulation of expression of genic DNA) is an inference your piffle inevitably leads to.

Only in your mind.

PS - Your comment about my overly aggressive style does not parse correctly. You have noted that my overly aggressive style what?

OK, the word, "that" was left in by mistake. Your mention of it suggests that your main motivation here is to find ammunition with which to go on the attack. It does not bode well for the thread. You seem to be a hackenslash clone.

GfL, as this is your thread, it is up to you what you want to make it about. However, making it about finding ammunition to use against me is not a very commendable direction to send it in.

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

There, there's you saying that junk DNA (which only exists in heterochromatin) makes up the chromatin packaging that wraps round genes (which it doesn't, as I've already explained) , and go on to claim that this "has the important function of preventing accidental gene expression"; which shows the insinuation in my penultimate post is simply not constrained to my own mind.

To quote your words, you said that junk DNA makes up chromatin that wraps round genes, and serves to prevent accidental gene expression.

" You seem to be a hackenslash clone."

Clone would be taking it a bit too far, even if contempt for ill-conceived rubbish is a trait we share.

PS - I don't need to make it about finding ammunition to use against you; all I'm saying is that said piffle is piffle, regardless of who comes up with it. I'd be very tempted to highlight the fact that the only person who is personalising things is you, by talking about things like posting styles and personalities, while all I've been doing is showing the rubbish you've asserted to be rubbish. The irony of that, I hope, isn't lost on you.

Rumraket wrote:

DavidMcC wrote:Look, I didn't invent this stuff - it was part of my "Basic Bio" course by my employer, which was active in the field of biotechnology (involving DNA amplification on electronic chips).
So, you two don't accept that portions of a chromosome untwist ("fluff up") during gene expression, to allow enzymes to access the gene?

Of course that is accepted, this is common knowledge. This is not what has been in contention here.

Perhaps you should tell that to GfL, because he rejected it from me, claiming that it was only the "genic DNA" itself that was fluffing up.

DavidMcC wrote:The theory was that multicellular animals exploit the extra protection of genes from enzymes, which are large molecules, except during expression.

You don't need large swathes of neutrally evolving DNA to get the protective effect of chromatin packaging. Simply making genes wrap into the chromatin complex will ensure that protection.

OK, I'll take your word for that. At least you're keeping the thread rational.

The primary protection against accidental transcription is transcription factor binding site size. They're usually about 10 bases long, which can be shown probabilistically to be more than enough to ensure any two loci are extremely unlikely to evolve the exact same binding site.

DavidMcC wrote:

Rumraket wrote: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.

That was not my argument. I was taught that a major difference between prokaryotes and eukaryotes involved the latter having to keep most genes in any one cell completely silent all of the time, otherwise the wrong proteins and RNAs might be made in that cell, which could be fatal. That was part of the rationale given.

And as explained, chromatin packaging and transcription factor binding specificity itself ensures that, junk DNA or not. Again, look at the genome size variation! It would seem strange to imagine one species of fish needing 670 times as much protective junk than another. Or that between two virtually identical onions, one would maintain a genome five times greater than the other for that purpose.

No, it's simply junk being generated at higher rate than purifying selection can get rid of it. What you're doing is engaging in an ad-hoc adaptationist rationalization to explain the existence of large swathes of neutrally evolving DNA.

OK. I guess that there is very little selection against a very large genome, because it is only an issue during mitosis and meiosis, which is only occasional.

DavidMcC wrote:

Rumraket wrote:

DavidMcC wrote:Look, I didn't invent this stuff - it was part of my "Basic Bio" course by my employer, which was active in the field of biotechnology (involving DNA amplification on electronic chips).
So, you two don't accept that portions of a chromosome untwist ("fluff up") during gene expression, to allow enzymes to access the gene?

Of course that is accepted, this is common knowledge. This is not what has been in contention here.

Perhaps you should tell that to GfL, because he rejected it from me, claiming that it was only the "genic DNA" itself that was fluffing up.

I said

Chromatin AT active genes unfolds during transcription

Chromatin at active genes, which is genic DNA + histones, I didn't say genic DNA fluffs up. Keep digging.

One question for Rumraket: This may not be known, but which genetic mechanisms that allowed cell specialization might have been available to the earliest multicellular animals? (If they did not have the modern panoply of mechanisms for preventing accidental gene expression, then maybe it would have been necessary for them to use only non-genic DNA for suppressing accidental gene expression.)

DavidMcC wrote:One question for Rumraket: This may not be known, but which genetic mechanisms that allowed cell specialization might have been available to the earliest multicellular animals? (If they did not have the modern panoply of mechanisms for preventing accidental gene expression, then maybe it would have been necessary for them to use only non-genic DNA for suppressing accidental gene expression.)

The existence of chromatin precedes multicellular life; archaebacteria have histones http://www.ncbi.nlm.nih.gov/pubmed/23240084. Histones that comprise the chromatin at genic DNA are sufficient to regulate gene expression - you wouldn't need non-genic DNA to do this.

DavidMcC wrote:One question for Rumraket: This may not be known, but which genetic mechanisms that allowed cell specialization might have been available to the earliest multicellular animals? (If they did not have the modern panoply of mechanisms for preventing accidental gene expression, then maybe it would have been necessary for them to use only non-genic DNA for suppressing accidental gene expression.)

First off it's important to note that accidental gene expression still happens, but at very low levels. The primary protection against accidental transcription is for the binding site to have a unique sequence not found anywhere else in the genome (goes for both single celled and multicellular organisms). With a large genome with many transcription sites (whether that be protein coding or RNA genes), you obviously need a certain minimum activation site length (a stretch of sequence usually 10 bases long) to ensure that no two sequences are identical. This way, a transcription factor (usually a protein) can reckognize a single specific sequence only.

That means the protein will only attach to the DNA and initiate transcription in places where it "fits" with the specific matching DNA sequence. It's a structural thing of course, a certain stretch of DNA will have a certain 3 dimensional structure, and the protein has a structure that fits only this sequence of DNA bases.

But the problem is that the junk DNA is randomly mutating without constraint. That means eventually some stretch of junk will simply end up being somewhat similar to one of those binding sites. They're usually not totally identical, which is why the protein will only attach to the DNA weakly/for a short time and stick around for a single or a few transcripts before letting go again (think brownian motion and molecules bumping into the transcription factor, making it let go again). Sometimes of course, the junk site will be similar enough to the "intended" binding site that the protein sticks around longer and produces many transcripts, and as you correctly noted earlier this can potentially cause problems if that transcript turns out to interfere with normal cellular processes.

On the other hand, such accidental transcripts can also turn out to have useful functions, so this is how many ORFan genes originate, as GFL's op post explains. Because selection can then retain such a site and keep mutations that increases the efficiency of the transcription factor, making it bind tighter and thus keep transcription turned on.

Short answer: the first organisms would simply have used target site size to prevent accidental transcription(or at least, to keep the expression levels so low they're unlikely to cause havoc).

Chromatin packaging is not so much a protection against accidental transcription, as it's for protection against accidental damage to the DNA and to decrease it's volume.

Rumraket wrote:

DavidMcC wrote:One question for Rumraket: This may not be known, but which genetic mechanisms that allowed cell specialization might have been available to the earliest multicellular animals? (If they did not have the modern panoply of mechanisms for preventing accidental gene expression, then maybe it would have been necessary for them to use only non-genic DNA for suppressing accidental gene expression.)

First off it's important to note that accidental gene expression still happens, but at very low levels. The primary protection against accidental transcription is for the binding site to have a unique sequence not found anywhere else in the genome (goes for both single celled and multicellular organisms). With a large genome with many transcription sites (whether that be protein coding or RNA genes), you obviously need a certain minimum activation site length (a stretch of sequence usually 10 bases long) to ensure that no two sequences are identical. This way, a transcription factor (usually a protein) can reckognize a single specific sequence only.

That means the protein will only attach to the DNA and initiate transcription in places where it "fits" with the specific matching DNA sequence. It's a structural thing of course, a certain stretch of DNA will have a certain 3 dimensional structure, and the protein has a structure that fits only this sequence of DNA bases.

But the problem is that the junk DNA is randomly mutating without constraint. That means eventually some stretch of junk will simply end up being somewhat similar to one of those binding sites. They're usually not totally identical, which is why the protein will only attach to the DNA weakly/for a short time and stick around for a single or a few transcripts before letting go again (think brownian motion and molecules bumping into the transcription factor, making it let go again). Sometimes of course, the junk site will be similar enough to the "intended" binding site that the protein sticks around longer and produces many transcripts, and as you correctly noted earlier this can potentially cause problems if that transcript turns out to interfere with normal cellular processes.

On the other hand, such accidental transcripts can also turn out to have useful functions, so this is how many ORFan genes originate, as GFL's op post explains. Because selection can then retain such a site and keep mutations that increases the efficiency of the transcription factor, making it bind tighter and thus keep transcription turned on.

Short answer: the first organisms would simply have used target site size to prevent accidental transcription(or at least, to keep the expression levels so low they're unlikely to cause havoc).

Chromatin packaging is not so much a protection against accidental transcription, as it's for protection against accidental damage to the DNA and to decrease it's volume.

Yup, and you don't need non-genic chromatin to serve that protective function either; genes have their own histones that they are associated with.

Rumraket wrote:

DavidMcC wrote:One question for Rumraket: This may not be known, but which genetic mechanisms that allowed cell specialization might have been available to the earliest multicellular animals? (If they did not have the modern panoply of mechanisms for preventing accidental gene expression, then maybe it would have been necessary for them to use only non-genic DNA for suppressing accidental gene expression.)

First off it's important to note that accidental gene expression still happens, but at very low levels.

This is an argument for saying that the many other mechanisms for suppressing aren't quite sufficient after all!

The primary protection against accidental transcription is for the binding site to have a unique sequence not found anywhere else in the genome (goes for both single celled and multicellular organisms). With a large genome with many transcription sites (whether that be protein coding or RNA genes), you obviously need a certain minimum activation site length (a stretch of sequence usually 10 bases long) to ensure that no two sequences are identical. This way, a transcription factor (usually a protein) can reckognize a single specific sequence only.

That means the protein will only attach to the DNA and initiate transcription in places where it "fits" with the specific matching DNA sequence. It's a structural thing of course, a certain stretch of DNA will have a certain 3 dimensional structure, and the protein has a structure that fits only this sequence of DNA bases.

But the problem is that the junk DNA is randomly mutating without constraint. That means eventually some stretch of junk will simply end up being somewhat similar to one of those binding sites. They're usually not totally identical, which is why the protein will only attach to the DNA weakly/for a short time and stick around for a single or a few transcripts before letting go again (think brownian motion and molecules bumping into the transcription factor, making it let go again). Sometimes of course, the junk site will be similar enough to the "intended" binding site that the protein sticks around longer and produces many transcripts, and as you correctly noted earlier this can potentially cause problems if that transcript turns out to interfere with normal cellular processes.

On the other hand, such accidental transcripts can also turn out to have useful functions, so this is how many ORFan genes originate, as GFL's op post explains. ...

A. I thought I had just admitted that I was wrong about the importance of chromatin in suppressing random gene expression.
B. GFL 's point about novel genes coming out of accidental transcripts misses the point that these are nevertheless bad for the organism in the short term. NS may be good for the long term survival of the species, but the price is paid by the dead individuals!

Chromatin packaging is not so much a protection against accidental transcription, as it's for protection against accidental damage to the DNA and to decrease it's volume.

OK, that's something I didn't know. Thanks.

DavidMcC wrote:

Rumraket wrote:

DavidMcC wrote:One question for Rumraket: This may not be known, but which genetic mechanisms that allowed cell specialization might have been available to the earliest multicellular animals? (If they did not have the modern panoply of mechanisms for preventing accidental gene expression, then maybe it would have been necessary for them to use only non-genic DNA for suppressing accidental gene expression.)

First off it's important to note that accidental gene expression still happens, but at very low levels.

This is an argument for saying that the many other mechanisms for suppressing aren't quite sufficient after all!

Sufficient for what - completely removing noisy transcription? Then sure, extant mechanisms aren't sufficient for that. But natural selection isn't concerned with perfection, only sufficient to ensure a viable organism. If a byproduct of the transcription system is low level noisy transcription, but this doesn't normally (or sufficiently) influence normal organismal function in a negative way, then there's not enough of a selective pressure to get rid of it.

DavidMcC wrote:

Rumraket wrote:The primary protection against accidental transcription is for the binding site to have a unique sequence not found anywhere else in the genome (goes for both single celled and multicellular organisms). With a large genome with many transcription sites (whether that be protein coding or RNA genes), you obviously need a certain minimum activation site length (a stretch of sequence usually 10 bases long) to ensure that no two sequences are identical. This way, a transcription factor (usually a protein) can reckognize a single specific sequence only.

That means the protein will only attach to the DNA and initiate transcription in places where it "fits" with the specific matching DNA sequence. It's a structural thing of course, a certain stretch of DNA will have a certain 3 dimensional structure, and the protein has a structure that fits only this sequence of DNA bases.

But the problem is that the junk DNA is randomly mutating without constraint. That means eventually some stretch of junk will simply end up being somewhat similar to one of those binding sites. They're usually not totally identical, which is why the protein will only attach to the DNA weakly/for a short time and stick around for a single or a few transcripts before letting go again (think brownian motion and molecules bumping into the transcription factor, making it let go again). Sometimes of course, the junk site will be similar enough to the "intended" binding site that the protein sticks around longer and produces many transcripts, and as you correctly noted earlier this can potentially cause problems if that transcript turns out to interfere with normal cellular processes.

On the other hand, such accidental transcripts can also turn out to have useful functions, so this is how many ORFan genes originate, as GFL's op post explains. ...

A. I thought I had just admitted that I was wrong about the importance of chromatin in suppressing random gene expression.

In so far as chromatin unpacking functions as a kind of expression control, it's subject to the same basic biophysical constraints as transcription from DNA to RNA. Think about it. As GFL points out, genes are associated with their own specific histones that unpack the chromatin in specific locations to allow transcription of those specific genes. How would the histones achieve this kind of selectivity and not just unbiasedly attach to any chromatin complex and start unpacking? It obviously has to reckognise a unique structural signature that is only associated with a specific piece of DNA sequence. So we're basically back to the same problem facing the actual transcription itself: A specific protein has to associate with a specific sequence in order to bind efficiently and initiate a process. That means the system would have the same basic vulnerability - if the junk regions are randomly mutating, sooner or later and simply through chance, an area will start to look similar to an area containing genes, which means you will have a potential for something like noisy histone activity.

DavidMcC wrote:B. GFL 's point about novel genes coming out of accidental transcripts misses the point that these are nevertheless bad for the organism in the short term.

Why? Some times they are, some times they aren't. They're evidently not bad enough for natural selection to have gotten entirely rid of the the process.

DavidMcC wrote:NS may be good for the long term survival of the species, but the price is paid by the dead individuals!

Sure, but how often does this happen really? We actually don't know. And if the carriers manage to reproduce before such kinds of accidental transcripts can lead to cancers or whatever, then the price of the individual has no effect on the long-term evolution of the species.

DavidMcC wrote:

Rumraket wrote:Chromatin packaging is not so much a protection against accidental transcription, as it's for protection against accidental damage to the DNA and to decrease it's volume.

OK, that's something I didn't know. Thanks.

You're welcome.

Rumraket wrote:...

DavidMcC wrote:NS may be good for the long term survival of the species, but the price is paid by the dead individuals!

Sure, but how often does this happen really? We actually don't know. And if the carriers manage to reproduce before such kinds of accidental transcripts can lead to cancers or whatever, then the price of the individual has no effect on the long-term evolution of the species.
...

It follows from the basic theory of NS, that the flip side of selection is either death of the unlucky individuals with bad genes and/or bad chromosomes or at least failure to breed as well as their peers. Obviously, it depends on the genes involved, but when the integrity of the chromosomes is involved, I imagine that an early death must be a strong possiblity.

I weant to come back about Rumraket's point about fish with large genomes. Firstly, I suspect that that is more due to genome and/or chromosome duplication than to massive quantities of extra, non-genic DNA just appearing, due to failure to suppress it. Secondly, the point that single-celled eukaryotes still exist says nothing about whether wrapped chromosomes help multicellularity, but more about the continued existence of an ecological niche for them.