tag:blogger.com,1999:blog-37148773.post5513042850524230801..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The Dark Matter RisesLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger23125tag:blogger.com,1999:blog-37148773.post-31049572387644109792013-08-23T06:53:51.382-04:002013-08-23T06:53:51.382-04:00A key question in the field is whether the transcr...<i>A key question in the field is whether the transcripts resulting from pervasive transcription of intergenic regions are functional or the result of noisy transcription. The lincRNAs we describe are specifically regulated and contain conserved sequence, attributes inconsistent with transcriptional noise.</i><br /><br />http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003569<br /><br />I thought you might be interested.<br /><br />Cheers.The Social Pathologisthttps://www.blogger.com/profile/12927698533626086780noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1390508454689626092013-08-02T08:14:00.428-04:002013-08-02T08:14:00.428-04:00I still maintain that in order to *show* that “the...I still maintain that in order to *show* that “the cis-regulatory potential of TF-bound DNA is determined largely by highly local sequence features and not by genomic context” you need to place these elements at various sites in the genome. Maybe we are disagreeing about the meanings of the term *show* vs. *suggest*, which I think would have been more appropriate.<br /><br />Nevertheless, I would guess that you and your colleagues have investigated the local sequence features of the TFs *bound* and *unbound* DNA elements in the genome. What do the results show?<br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36823816998235437942013-08-01T19:08:31.486-04:002013-08-01T19:08:31.486-04:00That's right, because in the paper we compare ...That's right, because in the paper we compare the function of TF bound DNA to unbound motifs. It's not that complicated.Anonymoushttps://www.blogger.com/profile/00474549004146223010noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19910962331730780942013-08-01T17:09:20.416-04:002013-08-01T17:09:20.416-04:00Your conclusion (see quote form your Abstract in m...Your conclusion (see quote form your Abstract in my previous comment) refers to the cis-regulatory potential of <b>*TF-bound DNA*</b>, not the cis-regulatory potential of <b> “putative transcription factor binding sites that are *unbound* in the genome”</b> as you state in your reply. Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60415310721737006232013-08-01T16:16:54.019-04:002013-08-01T16:16:54.019-04:00Well William Jennings Bryan at the Scopes Trial sa...Well William Jennings Bryan at the Scopes Trial said humans are not mammals. How dare you devalue human life by calling my children vertebrates?Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85540603382649690582013-08-01T13:52:33.393-04:002013-08-01T13:52:33.393-04:00The plasmid is the point - the sequences were remo...The plasmid is the point - the sequences were removed from their genomic context and placed into a permissive plasmid context. <br /><br />The prediction made by most of my colleagues was that putative transcription factor binding sites that are unbound in the genome (i.e., non-functional), would prove to be highly functional in the plasmid context. Turns out that's not true. Non-functional sites in the genome behaved like randomly generated DNA on the plasmid.Anonymoushttps://www.blogger.com/profile/00474549004146223010noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13981024918259059622013-08-01T11:41:22.826-04:002013-08-01T11:41:22.826-04:00The study reported by White et al. PNAS paper (htt...The study reported by White et al. PNAS paper (http://www.ncbi.nlm.nih.gov/pubmed/23818646) is interesting and valuable. However, there is a big problem with the main conclusion of the study:<br /><br /><i>“Our results show that the cis-regulatory potential of TF-bound DNA is determined largely by highly local sequence features and not by genomic context.</i><br /><br />Although that might be indeed the case, their results *do not* show that “the cis-regulatory potential of TF-bound DNA is determined largely by highly local sequence features and not by genomic context”, simply because their sequences were assayed in *plasmid* not in *genomic* context.<br /><br />I think that drawing such a misleading conclusion, when the authors were well aware of the limitation of their study, is similar to the drawing of conclusion of the ENCODE study, which, ironically, White et al. have set to evaluate. <br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28286155191177834682013-08-01T11:05:42.413-04:002013-08-01T11:05:42.413-04:00Holy crap you're right! Apparently according t...Holy crap you're right! Apparently according to Mattick, humans and other vertebrates are not chordates. It's a phylogenetic revolution! That figure is completely IDiotic, which makes one wonder about the mind that created it.Chris Caprettehttps://www.blogger.com/profile/14145872954644056603noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-44706636137688675772013-08-01T11:01:20.573-04:002013-08-01T11:01:20.573-04:00Yep, you beat me to it. It would be nice to slap a...Yep, you beat me to it. It would be nice to slap a couple of onion species on that graph.Chris Caprettehttps://www.blogger.com/profile/14145872954644056603noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29649314945443492492013-08-01T10:05:59.504-04:002013-08-01T10:05:59.504-04:00This figure is the original DAP:
http://www.genom...This figure is the original DAP:<br /><br />http://www.genomicron.evolverzone.com/2007/09/dogs-ass-plots-daps/<br />T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-19088925274287621832013-08-01T06:28:27.176-04:002013-08-01T06:28:27.176-04:00Some range bars would be nice. Presumably that'...Some range bars would be nice. Presumably that's what the sloping bar top represents. Fungi/Plants barely overlap in total genome size range, and as a composite group cover 4 orders of magnitude, yet their noncoding proportion remains a healthy 65-75%-ish throughout? http://en.wikipedia.org/wiki/File:Genome_Sizes.pngAllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60658710277092705262013-08-01T04:29:08.355-04:002013-08-01T04:29:08.355-04:00Even if those 5 points were all true, most DNA cou...Even if those 5 points were all true, most DNA could be non-functional, in any sensible sense of 'functional'. Peterhttps://www.blogger.com/profile/10384316385523253372noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38847691806977278062013-08-01T02:47:19.607-04:002013-08-01T02:47:19.607-04:00Obviously ants and giant squid have so much in com...Obviously ants and giant squid have so much in common. I'm sure there's virtually no range in the amount of ncDNA they have. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14192241215491026422013-08-01T01:35:34.600-04:002013-08-01T01:35:34.600-04:00Yes, you're right, the 100% limit is important...Yes, you're right, the 100% limit is important there. It is a plot of percentage of the genome not coding for proteins. So if you have N bases noncoding and C bases coding it is plotting N/(N+C).<br /><br />A more intuitive measure of amount of noncoding DNA would be N/C. That is the one which would be much higher in (say) lungfish that in humans. Plotted the way Mattick plots it, humans and lungfish and up both very close to 100%.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80103512175202879072013-08-01T00:45:08.948-04:002013-08-01T00:45:08.948-04:00It can't go higher than 100% :P
In any case, ...It can't go higher than 100% :P<br /><br />In any case, it's still wildly misleading, this "Plants/fungi" bar should show a much greater range, still going above the human one and almost all the way to the bottom. <br /><br />That figure really is unbelievably stupid. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51404274388156532842013-07-31T23:38:26.985-04:002013-07-31T23:38:26.985-04:00Mike White's team has published a relatively n...Mike White's team has published a relatively new paper that might be relevant to the discussion about the definition of function in the genomic context: <a href="http://thefinchandpea.com/2013/07/17/using-a-null-hypothesis-to-find-function-in-the-genome/" rel="nofollow">Finding function in the genome with a null hypothesis</a><br /><br />He also addressed some of Mattick's points in the most recent HUGO paper:<br /><a href="http://thefinchandpea.com/2013/07/31/10654/" rel="nofollow">Having your cake and eating it: more arguments over human genome function</a> unhttps://www.blogger.com/profile/02527051725365759129noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82270314492846965322013-07-31T23:27:09.973-04:002013-07-31T23:27:09.973-04:00Chordatocentrism rears its ugly head once again.Chordatocentrism rears its ugly head once again.Matt Ghttps://www.blogger.com/profile/07745943486966305844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32400126148383915222013-07-31T21:42:06.046-04:002013-07-31T21:42:06.046-04:00Well what the hell is the point of separating vert...Well what the hell is the point of separating vertebrates from chordates, or lumping all invertebrates together?<br /><br />Imagine lumping together the mantis shrimp and platyhelminthes! It's insane.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13884476484533808322013-07-31T20:31:37.680-04:002013-07-31T20:31:37.680-04:00Separating humans from vertebrates in the figure? ...Separating humans from vertebrates in the figure? What is the justification for that?Matt Ghttps://www.blogger.com/profile/07745943486966305844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88970728626511177772013-07-31T18:49:51.766-04:002013-07-31T18:49:51.766-04:001. False: We've known about regulatory RNAs fo...1. False: We've known about regulatory RNAs for over 35 years. <br /><br />2. False implication: There's no evidence that the regions that are transcribed are genes by any reasonable definition of "genes."<br /><br />3. True<br /><br />4. True: Several examples of regulatory RNAs are known.<br /><br />5. False. <br /><br />Two out of five is not good.<br /><br />Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69614021147943210532013-07-31T18:38:44.522-04:002013-07-31T18:38:44.522-04:00I think Mattick is one of the best writers in the ...I think Mattick is one of the best writers in the field of biology; the language is exquisite and the composition sophisticated. Moreover, his writings are usually consistent with the data. Take for example the abstract of the "The dark matter rises: the expanding world of regulatory RNAs" article. Here is my true/false evaluation:<br /><br />#1. The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms.<br /><br />True or false: True<br /> <br />#2. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non–protein coding genes that express small and long ncRNAs (non-coding RNAs).<br /><br />True or false: True<br /><br />#3. Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression.<br /> <br />True or false: True<br /><br />#4. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases.<br /><br />True or false: True<br /><br />#5. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.<br /><br />True or false: True<br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25128606548238019532013-07-31T18:38:25.242-04:002013-07-31T18:38:25.242-04:00Good idea. It would have also been nice to put, at...Good idea. It would have also been nice to put, at the immediate right of the human bar, the largest mammalian genome size (so far): 8.40pg for <i>Tympanoctomys barrerae</i>, the red viscacha rat. While it isn't the pinnacle of all creation, it's clearly almost three times as complex as <i>H. sapiens</i>.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52635922070571162013-07-31T18:22:02.442-04:002013-07-31T18:22:02.442-04:00In Mattick's figure, I think you cut off the r...In Mattick's figure, I think you cut off the right-hand part of it: the part showing the even-higher bars for the onion, the congo eel, and the lungfish.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.com