tag:blogger.com,1999:blog-37148773.post5726608749066555024..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Junk RNA or Imaginary RNA?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger17125tag:blogger.com,1999:blog-37148773.post-23925623350278942442010-05-22T14:50:51.775-04:002010-05-22T14:50:51.775-04:00I'll sign.
Stephen Anstey
Student, Memorial U...I'll sign.<br /><br />Stephen Anstey<br />Student, Memorial University<br />St. John's, NLAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32613601139189706692010-05-21T14:42:12.788-04:002010-05-21T14:42:12.788-04:00Junk RNA probably arose very earlyJunk RNA probably arose very earlyGeorgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9819802300605779562010-05-21T14:37:52.237-04:002010-05-21T14:37:52.237-04:00So RNA, then proteins, then DNA. Does this mean th...So RNA, then proteins, then DNA. Does this mean the first RNA was junk RNA and that protein coding RNA evolved from junk RNA?jbwnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6632532209207269892010-05-21T13:32:55.704-04:002010-05-21T13:32:55.704-04:00Most likely proteins, if RNA was firstMost likely proteins, if RNA was firstGeorgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62686007806576877222010-05-21T13:31:31.393-04:002010-05-21T13:31:31.393-04:00Thanks for the answer. Another question. Which evo...Thanks for the answer. Another question. Which evolved first, DNA or proteins?jbwnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-73955712177794643742010-05-21T13:23:41.826-04:002010-05-21T13:23:41.826-04:00jbw:
Are the parts of the DNA that are not transcr...jbw:<br /><i>Are the parts of the DNA that are not transcribed capable of being transcribed? Is there some defect in the sequence or are they not transcribed because of the machinery of transcription?</i><br /><br />Any part of DNA has *some* potential to be transcribed. With some low probability, various transcription factors can bind to any piece of DNA and lead to the formation of what is called "transcription initiation complex". Once this happens, there will be some RNA made. Most will be very short but some will look "normal". This is what Larry refers to as "transcription noise". <br /><br /><i>If the sequence is OK, do they code for proteins?</i> <br /><br />Some low percentage may even have sequence that's enough to encode a polypeptide (i.e., ATG followed by >50 in-frame codons before hitting TAA/TAG). Majority of those will code for "garbage" proteins that won't fold into anything functional.DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81628743397887681482010-05-21T11:36:48.916-04:002010-05-21T11:36:48.916-04:00Reading the article raised the following question ...Reading the article raised the following question in my mind:<br /><br />Are the parts of the DNA that are not transcribed capable of being transcribed? Is there some defect in the sequence or are they not transcribed because of the machinery of transcription?<br /><br />If the sequence is OK, do they code for proteins?jbwnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-50002115973733003182010-05-21T10:45:02.906-04:002010-05-21T10:45:02.906-04:00Dunbar says,
What amuses me is that Dr. Blencowe ...Dunbar says,<br /><br /><i>What amuses me is that Dr. Blencowe is an author on the paper you're praising right now, whereas not two weeks ago you expressed scepticism about his paper on the "splicing code".</i><br /><br />It amuses me too. Blencowe seems to have never met a splicing alternative that he doesn't believe and yet here he is on a paper that questions the significance of most low level transcripts.<br /><br />Go figure. <br /><br />I note that his contribution on the van Bakel paper is minor and he is not listed as one of the people who actually wrote the paper.<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21910767555058699882010-05-20T23:32:00.365-04:002010-05-20T23:32:00.365-04:00It's good to finally see results that make sen...It's good to finally see results that make sense in the context of what is already known. "The crazier it sounds the better" attitude of Nature's editors really is a powerful force.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64488234554008308702010-05-20T23:17:02.946-04:002010-05-20T23:17:02.946-04:00What amuses me is that Dr. Blencowe is an author o...What amuses me is that Dr. Blencowe is an author on the paper you're praising right now, whereas not two weeks ago you expressed scepticism about his paper on the "splicing code".<br /><br />Speaking of big biology papers, there's this one, doi:10.1126/science.1176495, which I haven't read yet but looks really neatAlexhttps://www.blogger.com/profile/02590604089043425452noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67926663116645459902010-05-20T14:45:28.316-04:002010-05-20T14:45:28.316-04:00Also, remember that ENCODE is being done genome-wi...Also, remember that ENCODE is being done genome-wide right now so there will be more on the subject in the near future. Here is some of the data that has been publicly released and you may want to take a look at:<br /><br />http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=160136038&c=chrX&g=wgEncodeCshlShortRnaSeq<br /><br />http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=160136038&c=chrX&g=wgEncodeRikenCageGeorgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7278213993039529822010-05-20T14:41:10.716-04:002010-05-20T14:41:10.716-04:00Such rare transcripts are much more compatible wit...<i>Such rare transcripts are much more compatible with accident than design, don't you think?</i><br /><br />Where have I mentioned anything about design? And I didn't say that they are extremely rarely transcribed, there is a difference between RNA levels and transcriptional activity. Things may be getting transcribed, because for some reason the process of transcription itself is important or for no reason at all, and then degraded very quickly.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-47293710431246155912010-05-20T14:30:42.961-04:002010-05-20T14:30:42.961-04:00to Sean Eddy,
You were the "academic" e...to Sean Eddy,<br /><br />You were the "academic" editor for this paper. I know you have an interest in the topic so what's your take on the earlier literature? <br /><br />Papers were being published without any attempt to account for possible artifacts and without any attempt to mention that accidental transcription was a serious possibility. How did those papers get by reviewers and editors?<br /><br />Why did real scientific papers become indistinguishable from press releases?<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22038684165640023522010-05-20T14:24:40.059-04:002010-05-20T14:24:40.059-04:00Georgi Marinov says,
Just to correct one thing: 3...Georgi Marinov says,<br /><br /><i>Just to correct one thing: 30bp of sequence is what people were getting in 2008, now it's 75-100bp and you can sequence both ends of the fragment.</i><br /><br />I'm aware of the optimistic claims in the latest papers. However, in this paper the authors were concerned about the stringency of their data so they restricted their hits to the first 25-28 bases allowing for one mismatch. <br /><br />I agree with the rest of your comment. What this paper claims is that any remaining intergenic RNA must be confined to the occasional transcript every few cell generations. Such rare transcripts are much more compatible with accident than design, don't you think?<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38466306939878296092010-05-20T12:17:08.210-04:002010-05-20T12:17:08.210-04:00I don't see how it does that.I don't see how it does that.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61120370418764686012010-05-20T12:05:20.195-04:002010-05-20T12:05:20.195-04:00Georgi, Figure 1A and 1B in the paper already addr...Georgi, Figure 1A and 1B in the paper already address your point. The authors show strong evidence that RNAseq is far more sensitive than tiled arrays.Sean Eddyhttps://www.blogger.com/profile/15551555799454926533noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68252494722001082702010-05-20T11:55:50.605-04:002010-05-20T11:55:50.605-04:00Just to correct one thing: 30bp of sequence is wha...Just to correct one thing: 30bp of sequence is what people were getting in 2008, now it's 75-100bp and you can sequence both ends of the fragment. The paper in question uses 2x50bp reads, however they only sequenced 23M reads per sample on average. Which is significant (and outdated too, the new HiSeq/SOLID4 instruments get 100M reads in a single lane so massive improvements in read numbers are are coming soon), as I will explain in a second.<br /><br />One of the fundamental differences between tiling arrays and RNA-Seq is that RNA-Seq is a digital measurement, while arrays are an analog one. So with arrays there is the possibility of compressing the dynamic range of the assay and seeing a lot more of the truly rare stuff that you would have to sequence billions of RNA-Seq reads to get to. Which will happen in the not so distant future, but we don't have now, and the paper in question certainly hasn't done either. <br /><br />While I am no fan of the "The whole genome is transcribed, let's celebrate" spin of the data, the paper in question by no means puts and end to the discussion. The genome may very well be transcribed at relatively low levels, with those transcripts being degraded very quickly so that they become very hard to detect. Which does not mean that those transcripts have any function, or that even the process of transcription itself is important (we know it is for some types of heterochromatin assembly processes, for example), which is a more likely possibility, but still not supported by sufficient evidence.Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.com