Long noncoding RNAs (lncRNAs) are everywhere these days. In the past few months, major reviews have appeared in Science, Genetics, and Nature Structural & Molecular Biology. In April, Nature profiled the growing job prospects in lncRNA research, noting, “Enthusiasm for lncRNA has replaced much of the science community's scepticism” (1).
A decade ago, things looked very different. Although researchers were aware of a few biologically important long noncoding RNAs, such as Xist and H19, these were largely discounted as special cases. In fact, so ingrained was this opinion that John Mattick, an lncRNA pioneer then at the University of Queensland, was pretty much flying solo in 2001 when he proposed that regulatory RNAs, not proteins, “form the primary control architecture that underpins eukaryotic differentiation and development” (2).
“It seemed to me, and it still does, that people have missed the point,” says Mattick, who is now the Executive Director of the Garvan Institute of Medical Research in Sydney, Australia. “Most of the assumptions that we operate on in molecular biology derive from the initial assumption that most genetic information is transacted by proteins. And while that's largely true in bacteria, it's not true for humans.”
In bacteria, RNA largely exits in its most well-known, well-characterized forms: tRNA, rRNA, and mRNA. But according to Mattick, in humans and other higher eukaryotes, most RNAs orchestrate very specific epigenetic hierarchies that control gene expression in four dimensions. “They're actually the computational engine of multicellular development.”
And a very malleable, robust engine at that. A single segment of the genome may contain layer upon layer of control sequences, thanks to a combination of epigenetic signals, sense and antisense transcription, and alternative splicing. “Each locus, each region of the genome is unzipped—transcribed, that is—in wildly different patterns. It's just extraordinary how densely packed our genome is with information,” explains Mattick.
Today, the broader research community seems finally to have caught on, awarding more research dollars than ever before to efforts focused on characterizing key players within the RNA world.
Still, it's no surprise that the researchers who choose to pursue these curious molecular RNA creatures seem to consider themselves explorers within a strange new world—a world Harvard University geneticist John Rinn calls “Noncodarnia.”Through the wardrobe
Although Rinn (whose Twitter handle is @noncodarnia) has been pursing noncoding RNAs since graduate school, that's not what he wanted to do when he first enrolled at Yale. “I was certain to be a crystallographer,” he recalls. But during an “amazing rotation” through Michael Snyder's lab, he discovered microarrays and was hooked, studying the transcriptional output first of chromosome 22 and, eventually, the entire genome.
That output included noncoding RNAs, a topic Rinn wanted to pursue as a postdoc. Most potential advisors he approached, though, were unconvinced. Then he met dermatology researcher Howard Chang at Stanford University, who was just setting up his own lab and was willing to take on an unconventional project.
“A lot of people at the time didn't want a postdoc to study a lot of bogus hocus-pocus,” says Rinn. However, the gamble paid off. In 2007, Rinn and Chang discovered HOTAIR, an lncRNA from the human HOX locus that also binds the epigenetic regulator Polycomb Repressive Complex 2 (PRC2). Researchers had previously suspected that noncoding RNAs could play a role in epigenetics, but HOTAIR was the first RNA molecule shown to actually carry out such a function.
“RNA has always been the deviant molecule,” notes the 37-year-old Rinn. “It always will do something you think something couldn't do.”
RNA enzymes? Check. Telomere maintenance? Check. RNA interference? Check, again.
But unlike those other RNAs, lncRNAs don't have a single, defined function. “We're calling long noncoding RNAs a class, when actually the only definition is that they are longer than 200 bp,” says Ana Marques, a Research Fellow at the University of Oxford who uses evolutionary approaches to understand lncRNA function. As a consequence, working out the function of novel lncRNAs is very difficult.