tag:blogger.com,1999:blog-37148773.post2060326070070455775..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Functional RNAs?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger20125tag:blogger.com,1999:blog-37148773.post-64877829787229919422015-01-18T18:02:10.957-05:002015-01-18T18:02:10.957-05:00Georgi
I am still unclear on one point:
I unde...Georgi<br /><br />I am still unclear on one point: <br /><br />I understand that Helix-turn-helix, Zinc fingers & Leucine zippers are part and parcel of the eukaryote TFBS story. If so, Transcription factors are dimers; if so, then in fact it is incorrect to claim that <br /><br /><i>A typical transcription factor binding site is about 6 bp ...</i><br /><br />That would be true only for the monomer and not the functional dimer.<br /><br />Of course, you raise another excellent point! Eukaryote enhancers bind a minimum of 3 Activator proteins (if I am not mistaken) and up to 8 Activator Proteins in enhancers for many genes.<br /><br />This ups the ante considerably when considering the notion of fortuitous junk transcription.<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82221812066523660492015-01-18T17:03:05.360-05:002015-01-18T17:03:05.360-05:00I am not familiar with the HACSN1 case, but those ...I am not familiar with the HACSN1 case, but those changes clearly have to be not in a single TFBS but multiple ones. That's what an enhancer is - multiple TFBSs. And it pretty much has to be. <br /><br />Because while it is OK to point out how many random TFBS matches exist in a genome when discussing TF binding, what is less often noted is that the vast majority of those are not detectably occupied. So if there is occupancy detected by ChIP-seq, that's something you do want to pay attention to. It does not mean that it is functional, but you need to take it seriously - clearing the chromatin barrier is a significant achievement on its own that forces one to take note of it. Unfortunately we still don't have a good answer to the question why some sites are bound and others are not. The usual explanations are pioneer factors and combinatorial occupancy, but the pioneer factors do not open all matches to their motifs either and the combinatorial occupancy concept is still quite fuzzy when it comes to the specifics.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13659281871270879752015-01-18T16:52:26.788-05:002015-01-18T16:52:26.788-05:00Hi Georgi – thank you for your patient assistance
...Hi Georgi – thank you for your patient assistance<br /><br />I thought that Helix-turn-helix, Zinc fingers & Leucine zippers – all resulted by mixing and matching of protein subunits into different heterodimers or homodimers.<br /><br />By definition that meant that while one subunit would interact with the first 6 bps, the other subunit necessarily had to interact with another upstream/downstream 6 bps that did not necessarily need to be palindromic with the first unless we were discussing homodimers.<br /><br />We are still speaking of sequence identity of 12 AND NOT 6 bps.<br /><br />I remain intrigued by those 13 nucleotide changes in an 81 nucleotide stretch in just ONE enhancer HACSN1 (are enhancer activator protein binding sites different perhaps?) representing quite an anomalous mutation rate that could not be attributed to drift. <br /><br />My understanding was that HACSN1 was first discovered by comparing Human/Chimp genome variation and focusing on areas of unusual high variability indicating putative high selection for mutation in short regions of DNA (in the case of HACSN1, a region of DNA spanning 81 bp).<br /><br />What am I missing here?Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61062403773654315562015-01-18T06:45:46.540-05:002015-01-18T06:45:46.540-05:00LexA is a bacterial TF
There is a difference betw...LexA is a bacterial TF<br /><br />There is a difference between prokaryotic and eukaryotic TFs - the prokaryotic ones have longer motifs. For which there are good evolutionary reasons. <br /><br />The 6bp comments referred to the eukaryotic ones. There are of course plenty of eukaryotic examples with longer motifs - CTCF, NRSF, etc. But most are indeed short, 6 to 8pGeorgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67282435540035269172015-01-18T06:31:07.207-05:002015-01-18T06:31:07.207-05:00re: A typical transcription factor binding site ...re: <i> A typical transcription factor binding site is about 6 bp.</i><br /><br />Uhmm... actually I was under the impression that the consensus sequence for typical transcriptional binding sites were larger than restriction sites.<br /><br />for example:<br /><br />http://upload.wikimedia.org/wikipedia/commons/thumb/8/85/LexA_gram_positive_bacteria_sequence_logo.png/500px-LexA_gram_positive_bacteria_sequence_logo.png<br /><br />Yes the consensus logo for the LexA-binding motif has six crucial nucleotides. But these are mirrored by a complementary palindromic 6 base sequence further downstream.<br /><br />Classical footprint analyses in olden days before bioinformatics indicated a greater surface area of protein-DNA contact.<br /><br />Meanwhile I am reminded of crucial differences between Chimpanzees and Humans that were obviously subject to significant selection pressures<br /><br />Those 13 nucleotide changes in an 81 nucleotide stretch in just ONE enhancer HACSN1 ( what I thought typical for transcription factor binding sites) represents quite an anomalous mutation rate that could not be attributed to drift.<br /><br />http://sandwalk.blogspot.com/2015/01/evolutionary-biochemistry-and.html?showComment=1420901851573#c5429010300897190288<br /><br />OK, I have gotten off the topic of lnRNA, but I just wanted to clarify whether or not "<i>a typical transcription factor binding site is about 6 bp</i>.<br /><br />Again, thanks to everybody for their patience and indulgence.Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18387618298072976752015-01-17T20:53:38.575-05:002015-01-17T20:53:38.575-05:00Georgi. I'm afraid that this too looks like we...Georgi. I'm afraid that this too looks like weaseling to me and, I suspect again, to other readers. I also suspect that everyone would be interested in your answers to the questions, and the fact that people keep asking them should suggest to you that they think you haven't answered them. Now if you don't care that people think you're being a weasel, no problem.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16436191837345993052015-01-17T17:56:15.026-05:002015-01-17T17:56:15.026-05:00My posts in this very same thread provide more tha...My posts in this very same thread provide more than sufficient information to answer your questions.<br /><br />Then there are things like Google Scholar that will give you even more information.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45761974909973623812015-01-17T17:42:09.038-05:002015-01-17T17:42:09.038-05:00@Georgi,
Before engaging in discussions about ENC...@Georgi,<br /><br />Before engaging in discussions about ENCODE and related projects, it would make sense that you address some of the issues raised in previous posts (<a href="http://sandwalk.blogspot.com/2014/10/nature-criticizes-science-hyperbole-and.html#comment-form" rel="nofollow"> http://sandwalk.blogspot.com/2014/10/nature-criticizes-science-hyperbole-and.html#comment-form</a>):<br /><br />Laurence A. Moran; Friday, October 31, 2014 9:36:00 AM:<br /><br /><i>“Georgi, there are 30 authors on the PNAS paper from last April. How many of them do you think are prepared to stand by everything that's in that paper and how many will claim that the paper may not represent their views because they never approved the draft that was sent to PNAS?”</i><br /><br />Georgi Marinov; Friday, October 31, 2014 2:49:00 PM:<br /><br /><i>I have said enough over the many threads on these subjects here for my position to be clear to anyone who has read my posts.</i><br /><br />John Harshman; Friday, October 31, 2014 3:25:00 PM:<br /><br /><i>No, that's the problem. Your position isn't clear. When you say the main Nature paper was "technically correct", that sounds to everyone like a way of avoiding the controversy by pedantic legalism. Larry's trying to pin you down here, and you keep squirming. Or that's how it looks to me and, I suspect, to other readers. An unequivocal statement would be nice.</i><br /><br />I also raised the following issues that you to did not address:<br /><br /><i>(1) Is there anything wrong with ENCODE’s flagship paper in Nature? If the answer is yes, please let us know what’s wrong with it.<br /><br />(2). Is there anything wrong with the presentation of ENCODE findings by Ewan Birney and other ENCODE leaders to science writers and media? If the answer is yes, please let us know what’s wrong with it</i><br />Claudiu Bandeahttps://www.blogger.com/profile/00561965985406236525noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65862108485499335672015-01-17T16:36:31.807-05:002015-01-17T16:36:31.807-05:00We've been through this so many times. Why do ...We've been through this so many times. Why do we have to do it again?Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12399960622029492242015-01-17T16:02:49.131-05:002015-01-17T16:02:49.131-05:00A typical transcription factor binding site is abo...<i>A typical transcription factor binding site is about 6 bp.</i><br /><br />Irrelevant. So is a typical restriction site. The argument to make is that selection against spurious transcription (or spurious suppression) is so weak that it makes no difference.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29906181777559761112015-01-17T12:03:35.380-05:002015-01-17T12:03:35.380-05:00Laurence A. Moran: “Most *knowledgeable* biochemis...Laurence A. Moran: <i>“Most *knowledgeable* biochemists are aware of the fact that transcription factors and RNA polymerase can bind at many sites in the genome that have nothing to do with transcription of a normal gene”</i><br /><br />I think you underestimate the understanding and knowledge of the scientists working on genomics and gene expression. Similar to the ENCODE scientists, which represent some of the finest academic institutions in the world, I think all leading scientists working on lncRNAs are highly knowledgeable.<br /> <br />However, in order to be competitive and at the top of their field, many of them choose to misrepresent the current knowledge in order to promote their studies and results. Ultimately, these shrewd scientists are themselves ‘victims’ of the current science enterprise, which is based on a deficient peer review system (see my note in PubMed Commons entitled: “Multiple knockout mouse models reveal that some lincRNAs might be required for life and brain development” at: <a href="http://www.ncbi.nlm.nih.gov/pubmed/24381249" rel="nofollow"> http://www.ncbi.nlm.nih.gov/pubmed/24381249</a>)<br /><br />You might also want to see a note entitled “Everlasting confusion on ‘functional DNA’ and ‘junk DNA’” addressing the ENCODE project (<a href="http://www.ncbi.nlm.nih.gov/pubmed/23479647" rel="nofollow">http://www.ncbi.nlm.nih.gov/pubmed/23479647</a>). Here is an excerpt from this note:<br /><br /><i>“After all, the ENCODE ‘function fiasco’ was not the result of misunderstanding the concept of biological function, nor was it due to scientific incompetence as suggested by others (2). On the contrary, because it conflicted with some of the project’s objectives and with its significance, there was a concerted effort not to bring this concept forward (3); indeed, as clearly shown in a recent ENCODE publication (4), at least some ENCODE members seem well aware of the scientific rationale and criteria for addressing putative biological functions for genomic DNA….<br /><br />References<br /><br />(2) Graur D et al., 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol., 5:578-90. Graur D, 2013.<br /><br />(3) Bandea CI. 2014. Closing the gap between ‘words’ and ‘facts’ in evaluating genome biology and the ENCODE project. PubMed Commons (National Library of Medicine; Bethesda, MD). Comment on: Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA., 110:5294-300.<br /> <br />(4) Kellis M. et al., 2014. Defining functional DNA elements in the human genome. Proc Natl Acad Sci USA., 111:6131-8. Kellis M, 2014.”</i><br />Claudiu Bandeahttps://www.blogger.com/profile/00561965985406236525noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55842348568194077692015-01-16T20:42:13.622-05:002015-01-16T20:42:13.622-05:00Georgi Marinov: I'd say there is selection as ...Georgi Marinov: I'd say there is selection as long as s isn't zero, but it is ineffective if |4Ns| is much less than 1, as then selection is overwhelmed by drift.<br /><br />Mikkel: No, if |4Ns| is quite small, drift overwhelms selection, and by about 10-20 N generations drift has finished fixing or losing the allele. Waiting longer won't help. It is only if we have a deterministic model, with an infinite population, that waiting long enough causes selection to have an effect. In effect in that idealized case N is infinity of |4Ns| is too.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35681510902535310652015-01-16T20:32:36.983-05:002015-01-16T20:32:36.983-05:00I have a bookmark on page 57 of the 109 page book ...I have a bookmark on page 57 of the 109 page book titled:<br />"Immunology and the Quest for an HIV Vaccine: A New Perspective" see:<br />http://www.amazon.com/Immunology-Quest-HIV-Vaccine-Perspective/dp/146850830X<br />because that's where I stopped about six months ago because it was so repetitive and uninformative.<br /><br />Anyway the authors claimed (repeatedly and without apparent evidence) that noncoding RNA elements were part of an unappreciated molecular immune system that operates entirely within individual cells. There thesis seemed to be that since much of the Junk was old fragments of retroviruses, disabling these transcribed segments gave their "molecular immune system" practice for the big day when they were confronted by real retrovirus elements.Anonymoushttps://www.blogger.com/profile/09434496437597399894noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5882296954452418372015-01-16T19:54:49.142-05:002015-01-16T19:54:49.142-05:00@Joe Felsenstein
"Whether natural selection w...@Joe Felsenstein<br /><i>"Whether natural selection will be effective is a function of whether 4Ns exceeds 1 in absolute value, where s is the selection coefficient."</i><br /><br />Isn't time also a factor here? I'm of the understanding that you and Simon have pointed out several times that even very small s values become important on geological timescales. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18670388132725155802015-01-16T17:31:05.404-05:002015-01-16T17:31:05.404-05:00Let's clarify the terminology a bit here. Let&...Let's clarify the terminology a bit here. Let's say we have s and it's negative. Are we only allowed to say that there is selection against the allele if |s| > 1/4N or we can also say that there is selection against it but it's overwhelmed by drift so in the end it does not do anything? This is a source of confusion (I personally tend to do the latter).Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84736894966641571442015-01-16T16:50:31.130-05:002015-01-16T16:50:31.130-05:00This is where I take the argument that I usually u...This is where I take the argument that I usually use against Larry and use it to agree with him. Whether natural selection will be effective is a function of whether 4Ns exceeds 1 in absolute value, where s is the selection coefficient. In these cases (selection favoring deletion or change of one of these useless transcription sites, for example, or selection to delete a short stretch of bases from our junk DNA) the selection coefficient s is most likely not big enough to be effective. Even though 1/(4N) may be small the value of s is most likely a lot smaller than that.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34116536971826888352015-01-16T14:33:25.523-05:002015-01-16T14:33:25.523-05:00A typical transcription factor binding site is abo...A typical transcription factor binding site is about 6 bp. There should be about one every 4000 bp in the human genome. That's 750,000 sites per haploid genome of 1.5 million in a typical diploid cell. It's hard to imagine how there could be significant selection against one of them such that eliminating one would confer a selective advantage. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19375782129329104292015-01-16T14:31:58.097-05:002015-01-16T14:31:58.097-05:00To the extent that they are harmful, there is.
Th...To the extent that they are harmful, there is.<br /><br />Then what happens is of course a matter of selection coefficients and population genetic environment...Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75343329996359513112015-01-16T13:47:09.491-05:002015-01-16T13:47:09.491-05:00'The Central Dogma: "Once information has...'The Central Dogma: "Once information has got into a protein it can't get out again". Information here means the sequence of the amino acid residues, or other sequences related to it.'<br />Crick (1956) http://profiles.nlm.nih.gov/SC/B/B/F/T/_/scbbft.pdfBjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27662655385420845482015-01-16T13:43:33.286-05:002015-01-16T13:43:33.286-05:00I do wonder if there's any selection against s...I do wonder if there's any selection against spurious (should we say "ectopic"?) transcription factor binding sites and other control sequences. Is there evidence of such selection in any organism? Have there been any studies? There is at least selection against restriction sites, which are a sort of control sequence.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.com