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Friday, January 31, 2020

lncRNA nonsense from Los Alamos

A group of scientists at the Los Alamos National Laboratory (Los Alamos, NM, USA) and their collaborators in Vienna (Austria) and Lethbridge (Alberta, Canada) have worked out the structure of Braveheart lncRNA from mice.
Kim, D.N., Thiel, B.C., Mrozowich, T., Hennelly, S.P., Hofacker, I.L., Patel, T.R., Sanbonmatsu, K.Y. (2020) Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution. Nat. Commun. 11:148 [doi: 10.1038/s41467-019-13942-4]
The authors point out in their paper that lncRNAs are difficult to work with and the 3D structures of only a small number have been characterized. There's nothing in the paper about the problems associated with determining the functions of lncRNAs and nothing about the number of lncRNAs except for this brief opening statement: "Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome ..."

Contrast the statements in the publication with the press release from Los Alamos National Laboratory [Scientists image heart RNA structure for the first time]. The press release contains hyperbolic statements that qualify as fake news (i.e. it is incorrect).
Before the human genome was sequenced in 2000, it was thought that it mostly contained instructions for proteins, the workhorse molecules of human cells.1 Scientists were shocked to discover that less than 10 percent of the genome encoded proteins.2 Ever since, the other 90 percent was deemed to be “junk DNA” or “dark matter.” Enter RNA, the molecular cousin of DNA. Scientists originally assumed the main purpose of RNA was simply to coordinate as a messenger for DNA in the synthesis of proteins.3 However, it has recently been shown that more than 90 percent of the genome encodes a new and mysterious class of RNAs, called long non-coding RNA molecules (lncRNA).4

These RNA molecules help to control the turning on and off of genes; their malfunction causes birth defects, autism and even cancer in some cases. They are also key to reprogramming adult stem cells. Even though the molecules make up 90 percent of the genome, scientists have almost no idea how they work,5 or even what they look like. In this study, one of the largest RNA-only 3-D studies, the new 3-D images sets the stage for future studies that will shed more light on how they control genes.
1. This is incorrect. No knowledgeable scientist ever thought that 50% of the genome consisted of DNA sequences that encoded proteins. The current reference sequence shows that genes make up about 30% of the genome but coding regions account for only about 1%. (Most of the genes consist of introns.)

2. Knowledgeable scientists were not shocked. The human genome sequence is mostly junk and that's exactly what they expected [False History and the Number of Genes 2010] [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].

3. This statement is misleading. By the year 2001, when the draft human genome sequence was published, knowledgeable scientists were well aware of a dozens of examples of noncoding RNAs.

4. This statement is false [How many lncRNAs are functional?].

5. This statement is misleading. Not only do scientist have no idea how they work they also have no idea whether the majority of presumed lncRNAs are even functional. Most of them are probably just junk RNA.

Note: I have sent links to this blog post to the senior authors of the paper and the author of the press release asking for comments.


João said...

OMG, that's pretty embarrassing. I hope thet hear to you and correct the mistakes.

Rosie Redfield said...

I'll add the Wikipedia page on 'Long noncoding RNAs' to my list of pages with serious overemphasis on 'functions' and general ignorance of evolutionary principles.