At The Scientist: “Junk RNA” is top science news in 2019

_{Denyse O'Leary

January 2, 2020

'Junk DNA', Genetics, Intelligent Design}

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A “completely unknown biology,” says a researcher. The paper on “glycoRNAs, or noncoding RNA strung with complex sugars called glycans” is still in preprint:

“There really is no framework in biology as we know it today that would explain how RNA and glycans could ever be in the same place at the same time, much less be connected to each other,” senior author Carolyn Bertozzi, a chemical biologist at Stanford University, told The Scientist in October.
Kerry Grens, “The Science News that Shaped 2019—“A completely unknown biology” ” at The Scientist

Remember when all that non-coding stuff was a vast library of junk that was evidence for Darwinian evolution?

Comments

Silver Asiatic @16: "I wonder when one side will eventually concede. Or will they hold out to the bitter end?" No, they won't concede. They will hold out to the bitter end. It's the nature of the human nature. We must humbly admit that we can't change it. C'est la vie, mon ami! :)OLV_{January 2, 2020
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Silver Asiatic and Martin_r: Have you ever been in a long flight and have seen the stuffs attached to the back of the seat in front of you? One is used to place the food trays they serve for breakfast, lunch or dinner. Another -at the eyes level- is used to display information. Now, let's assume we don't know what that stuff is for. We could get rid of all that stuff and test the plane to see if it flies. After confirming that the plane flies just fine without all that removed stuff, the airline starts to notice an increasing loss of passengers to other airlines that still have that "junk" attached to the back of the seats in long flights. That's a surprisingly unexpected result, isn't it? :) Another way to look at this is by playing loud rock music to a crab dancing on a table. As we remove the crab legs one at a time we notice that the crab starts missing the rhythm and slows down considerably. After removing the last leg the crab stops dancing completely. Conclusion: the crab got completely deaf, hence its legs are associated with the hearing system. :) Testing functionality is not a joke. It's a serious task that must be done carefully and with open mind.OLV_{January 2, 2020
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OLV
Let’s see what we get in 2021.
Thanks, yes. As above, the "debate", keeps "advancing". I wonder when one side will eventually concede. Or will they hold out to the bitter end?Silver Asiatic_{January 2, 2020
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Silver Asiatic @12: "It certainly must be astonishing for people who believe the lies they tell themselves" Exactly! Good point. Thanks.OLV_{January 2, 2020
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Taken together, our analyses provide further evidence of the potential functionality of 69% of the FANTOM CAT lncRNAs (n = 19,175 of 27,919), advancing the current scientific debate on the functional relevance of pervasive transcription from mammalian genomes.
There's a debate? Interesting. This finding "advances the debate". I think that means, "one side keeps losing".Silver Asiatic_{January 2, 2020
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Silver Asiatic, The information posted @9 & @11 is mostly a follow-up to what you posted @5. Note the progression 2015-2017-2019. Let's see what we get in 2021. :)OLV_{January 2, 2020
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Thanks, OLV.
it is astonishing that there are still new cell types to be found.
It certainly must be astonishing for people who believe the lies they tell themselves.
The discovery challenges the basic dogma of how these cells function—another reminder there is still so much unknown even in our own blood.
Another reminder that the basic dogma is wrong and that the evolutionary high-priests should be held in contempt. It's not only that so much is unknown, but that explanations on what is already observed are false and must be rejected.Silver Asiatic_{January 2, 2020
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An atlas of human long non-coding RNAs with accurate 5? ends (2017)
we identify 19,175 potentially functional lncRNAs in the human genome.

this study systematically elucidates the diversity of lncRNAs and summarizes the functional relevance of nearly 20,000 lncRNAs as an online resource, which can be further used in prioritizing lncRNA candidates for functional studies.

These observations support the notion that selectively more constrained lncRNAs are more likely to be functional, although it does not exclude the potential functionality of lncRNAs with weaker selective constraints. Taken together, our analyses provide further evidence of the potential functionality of 69% of the FANTOM CAT lncRNAs (n = 19,175 of 27,919), advancing the current scientific debate on the functional relevance of pervasive transcription from mammalian genomes. To what extent the remaining 31% represents spurious transcription initiation by RNA polymerase II is still an open question. Although most of the lncRNAs detected here are likely to originate from genuine TSSs (Supplementary Note 6), additional studies are needed to completely understand their biogenesis and assess their functionality. To this end, we have summarized their expression patterns, genomic features, conservation and intersection with genetic data into a comprehensive resource (http://fantom.gsc.riken.jp/cat/). This encompasses a web application to retrieve gene-, trait- and cell-type-based information and ZENBU43 views for visualizing genomic data. We anticipate wide applications of this resource in prioritizing lncRNA candidates for further elucidation of their functions, which is continuing in the sixth iteration of FANTOM (http://fantom.gsc.riken.jp/6/).
OLV_{January 2, 2020
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I assumed that Bob O'H was trying to say something, but that was my mistake.Silver Asiatic_{January 2, 2020
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Silver Asiatic, Thanks for the link you posted @5: Non-coding RNA: what is functional and what is junk? (2015)
It is clear that the human genome contains a large number of functional ncRNAs. Indeed it is likely that the list of biologically validated ncRNAs, as listed in the LncRNA Database (Quek et al., 2014), will continue to grow. As others have pointed out, even if 10% of current lncRNAs prove to be functional, this would represent a wealth of new biology. However, given our current understanding of biochemistry and evolution, it is likely that most of the RNAs generated from the low levels of pervasive transcription, and likely a substantial number of currently annotated “lncRNAs,” are non-functional.
An atlas of human long non-coding RNAs with accurate 5? ends (2017) From this OP: "Junk" DNA? The Science News that Shaped 2019
With all the extensive investigations scientists have conducted of the human immune system over the past century, it is astonishing that there are still new cell types to be found. scientists also reported that humans’ natural killer cells, thought to form the innate immune response, can also keep memories of past encounters with offending antigens, much like the adaptive immune response does. The discovery challenges the basic dogma of how these cells function—another reminder there is still so much unknown even in our own blood.
OLV_{January 2, 2020
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From this OP: “A completely unknown biology” huh? Glycans May Bind to RNA?
Although still in preprint form, results published this fall introduced a new aspect to cell biology: glycoRNAs, or noncoding RNA strung with complex sugars called glycans. Glycans are normally sequestered in the endoplasmic reticulum and Golgi bodies, away from RNA in the cytoplasm and nucleus. “There really is no framework in biology as we know it today that would explain how RNA and glycans could ever be in the same place at the same time, much less be connected to each other,” senior author Carolyn Bertozzi, a chemical biologist at Stanford University, told The Scientist in October. “Whatever it is, it’s a completely unknown biology.” Expect to see more insight into this mysterious new cellular entity—its function, its structure, and its prevalence.
Mammalian Y RNAs are modified at discrete guanosine residues with N-glycans
these findings suggest the existence of a ubiquitous interface of RNA biology and glycobiology suggesting an expanded role for glycosylation beyond canonical lipid and protein scaffolds.

The framework in which glycobiology is presently understood excludes RNA as a substrate for N-glycosylation. Our discovery of glycoRNA suggest this is an incomplete view and points to a new axis of RNA glycobiology, including unprecedented enzymology, trafficking, and cell biology.

For the first time, scientists have found that complex sugars called glycans may bind to some RNA molecules,

The findings could substantially alter the current perception of RNA’s function.

“There really is no framework in biology as we know it today that would explain how RNA and glycans could ever be in the same place at the same time, much less be connected to each other,” senior author Carolyn Bertozzi, a chemical biologist at Stanford University, tells The Scientist.

a surprising finding that the researchers had never seen before.

“It was a really weird discovery. At first we were skeptical. . . We tried to shoot it down in every way that we could think of, and it just kept holding up,” says Bertozzi.

The researchers don’t yet know how the RNA and the sugars are bound

“Whatever it is, it’s a completely unknown biology,” says Bertozzi.

“This paper, if verified, would certainly open up an entirely new direction of research investigating gene expression, gene regulation, quality control of transcription, and RNA turnover,”

“I was surprised and excited to see it. It’s an unexpected and thought-provoking observation,” says Torsten Krude at the University of Cambridge

“If the results are consistent and verified by others, and if it holds the test of time and scrutiny, it would be an exciting new aspect to RNA biology.”
OLV_{January 2, 2020
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Martin_r @4: Excellent insightful commentary! Thanks!OLV_{January 2, 2020
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Silver Asiatic - read what PaV wrote carefully.Bob O'H_{January 2, 2020
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Bob O'H
Of course they would be. It would show they were utterly clueless about basic biochemistry.
From a paper
Non-coding RNA: what is functional and what is junk? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306305/ Importantly, we advocate that in the absence of any such data, the appropriate null hypothesis is that the RNA in question is junk.
Dr. Palazzo has received several awards and is an editorial board member of the journal PLoS One. It's good to know that he's clueless about biochemistry. It must certainly be true of everyone else he is connected to. We might be tempted to pay attention to something they said.Silver Asiatic_{January 2, 2020
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this post mentioned so called 'glycans'.... honestly, how many of you heard of glycans and the glycome ? from NewScientist: "Move over, DNA. Life's other code is more subtle and far more powerful "Our cells use a sugary language to identify and interact with each other. "It turns out that every type of cell in our bodies has a unique sugar coating. "And whenever anything interacts with a cell, it must recognise that sugar code and use the appropriate secret handshake." "use the appropriate secret handshake." ???? "use the appropriate secret handshake." ???? in other words, to use a PASSWORD ... i am only a stupid mechanical engineer, but are biologists - natural science graduates - really suggesting, that cells use PASSWORDS ??? first DNA code, now this ? and all that happened by random unguided natural process ? It seems that biologists really believe in miracles ... Someone should call the doctor... Full article is here: https://www.newscientist.com/article/mg24132230-300-move-over-dna-lifes-other-code-is-more-subtle-and-far-more-powerful/martin_r_{January 2, 2020
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Biologists are too embarassed to call “non-coding RNA” what once it was called, “Junk DNA.”
Of course they would be. It would show they were utterly clueless about basic biochemistry.Bob O'H_{January 2, 2020
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Bob O'H: Here's the start of the little blurb on this discovery:
Although still in preprint form, results published this fall introduced a new aspect to cell biology: glycoRNAs, or noncoding RNA strung with complex sugars called glycans.
Biologists are too embarassed to call "non-coding RNA" what once it was called, "Junk DNA." But everyone around here remembers the argument. We remember the ENCODE project. We remember all the protestations. And we remember how wrong biologists were.PaV_{January 2, 2020
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Junk RNA? The Scientist doesn't mention junk in either the article linked to, or the original report.Bob O'H_{January 2, 2020
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