The gist of the article is that researchers have figured out new ways to probe the secondary structure of RNA [A cellular puzzle: The weird and wonderful architecture of RNA]. Here's the paragraph that annoys me ...
Scientists' view of RNA has transformed over the past few decades. Once, most RNAs were thought to be relatively uninteresting pieces of limp spaghetti that ferried information between the molecules that mattered, DNA and protein. Now, biologists know that RNAs serve many other essential functions: they help with protein synthesis, control gene activity and modify other RNAs. At least 85% of the human genome is transcribed into RNA, and there is vigorous debate about what, if anything, it does.I think there are better, more accurate, ways of explaining the history so I thought I'd give it a try.
Beginning in the 1950s, scientists recognized that RNA molecules served important roles in the cell. In addition to carrying information from DNA to proteins (messenger RNA, or mRNA), RNAs served as important components of the protein synthesis pathway. Adapter RNAs, now known as transfer RNAs (tRNAs), were predicted almost 60 years ago and ribosomal RNAs (rRNAs) were discovered a bit later.This article is published in Nature. I understand that many Nature readers are not familiar with biochemistry and molecular biology but that's no reason to dumb down the writing and misrepresent the history of the field.
By the late 1960s, it was apparent that these RNAs had a well defined secondary structure formed by base pairing between different parts of the molecule. By the end of the 1970s, a whole host of other RNAs had been discovered including those required for splicing, regulation, and various other functions inside the cell. All of these RNAs were understood to have well-defined secondary and tertiary three-dimensional structures.
A host of other small RNAs were identified in the 1990s. Many of them are involved in some aspects of control and regulation but it isn't clear which ones have defined functions and which ones might be "junk RNA" that arises from accidental transcription. It has been known for over 50 years that most of the human genome is transcribed at one time or another but most of these transcripts are rare. Many biochemists and molecular biologists believe that most of these RNAs are junk.
Naked RNAs cannot exist as linear molecules inside the cell. The thermodynamics of renaturation means that these RNAs will form secondary, double-stranded, regions whenever possible—and it will always be possible. This conclusion is based on experiments from over half-a-century ago. The work that's reported here looks at the formation of such structures in bulk cellular RNA that has been isolated from cells and at structures that might form in vivo. As expected, lots of naked RNAs have secondary structure but the structures inside the cell are different. Messenger RNAs, for example have less secondary structure while they are being translated. This analysis doesn't tell us very much about whether most of the small RNAs are functional or not since all RNAs will form double-stranded regions even if they are junk.
BTW, Elie Dolgin does a fine job of explaining why RNAs have 3D structure ...
The bulk of the RNA world is like unexplored, shifting sand. “We know next to nothing about the structure of most RNAs,” says Robert Spitale, a chemist at the University of California, Irvine. RNA molecules typically exist as a linear string of nucleotides — or bases — for only an instant after they are produced from their template DNA. They quickly fold back on themselves, and complementary nucleotides pair up. They then contort further into complex 3D configurations, interact with proteins and other RNAs and change shape to carry out different jobs.My main criticism is that he doesn't give much consideration to the idea that most of the RNAs could be nonfunctional and still have structure. I also don't think he describes the history as accurately as he should and he doesn't take into account the evidence that most of the RNAs have to be junk.
I don't know why there aren't more science journalists writing from the perspective that most of our genome is junk. Is it because the leading journals, like Nature, don't accept such articles, or is it because science journalists in general don't believe that most of our genome is junk?