N.Wells
Posts: 1836
Joined: Oct. 2005
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Larry Moran just posted a detailed discussion of the Blencowe paper. You should read it in its entirety, Gary: it does not support your earlier challenges.
Here are some highlights, from http://sandwalk.blogspot.com/2016....ml#more :
| Quote | | The authors looked at RNA-RNA interactions (hybrid formation) by mapping different RNA molecules that bound to each other. The idea is to map as many of these interactions as possible in order to get a handle on which of the RNAs have a significant biological function. The presence of an interaction does not prove that the RNA molecule(s) have a function since there are many cases where spurious transcripts could be complementary to an existing RNA. Only one of the RNAs might have a function or maybe neither has a function. However, it's one way of detecting possible functional RNAs. |
| Quote | A large fraction of the interactions involve associations between well-known functional RNA classes such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), spliceosomal RNAs (snRNAs), snoRNAs, and messenger RNAs (mRNAs). These interactions don't make a significant contribution to our understanding of which genes in the genome are functional since even if every interaction proved there was a function it would still only amount to a very tiny amount of the genome.
The authors did detect a few interactions involving long noncoding RNAs (lincRNAs) but this was only a small percentage of the total. There are thousands of lincRNAs but currently there are only about 200 that have known functions and not all of these are even human. ..... If all of those RNAs were functional they would occupy about 1% of the genome so this has has very little to do with whether 90% of our genome is junk. |
| Quote | | This paper does not make any significant contribution to our understanding of pervasive transcription and whether most of the transcripts are functional (hint: they aren't). It does not make a contribution to the debate over junk DNA since most of the RNAs that were detected were already in the functional category or strongly suspected of being functional. The authors make no claims about junk DNA in the paper because the paper is not about junk DNA. |
| Quote | | ........ The press release grossly distorts the actual content of the paper in order to sensationalize the results and promote the Donnelly Centre. ........ The press release makes it sound as though we are just learning about the existence of noncoding RNAs. |
| Quote | | It's true that we would like to know how many of the RNAs are functional but it's not true that we are completely clueless. There's plenty of evidence supporting the idea that only 10% of our genome is functional. It's very likely that the vast majority of transcripts are spurious and nonfunctional. |
| Quote | | ..... My colleagues Alex Pallazzo and his student Eliza Lee have addressed the issue of noncoding RNAs. They conclude that the default hypothesis has to be that most are nonfunctional unless there's solid evidence of function. Right now it looks like this evidence won't be found so most of these RNAs are spurious, they are junk RNA. |
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