photograph by Emily Shur

The Silencer: MicroRNA

Tiny RNAs help plants thrive by stifling other RNAs. Where in the cell they do their work and how they avoid destruction is becoming clearer.

An unusual Arabidopsis plant with dark, curly leaves and clusters of tinier-than-normal flowers seeded Xuemei Chen’s interest in small strands of RNA that do big things. Only 20 to 24 nucleotides long, microRNAs make an outsized difference in how plants develop, says Chen, an HHMI–Gordon and Betty Moore Foundation investigator at the University of California, Riverside.

“MicroRNAs are really short, and they don’t encode any protein,” explains Chen as she prepares a cup of herbal tea for a visitor. “Instead, they regulate the fate of messenger RNAs.” MicroRNAs find and turn off specific messenger RNAs (mRNAs) to fine-tune gene expression.

MicroRNAs were considered an “oddity” when first discovered in worms in the 1990s, says Chen. Hers was one of three laboratories to determine, in 2002, that plants have them too. Her strange-looking Arabidopsis had a mutation in a gene, HEN1, which, it turned out, the plant needed to produce all microRNAs. Chen’s postdoc, Wonkeun Park, showed that the HEN1 mutants had lower levels of microRNAs than normal plants.

“When he showed me [the data] I thought, wow, hallelujah,” recalls Chen. The HEN1 mutants were malformed because many genes, missing their corresponding microRNAs, were out of whack. Researchers were surprised that such teeny bits of RNA, which they hadn’t even known existed in plants, were so crucial to the organism’s shape.

I hope the entire
RNA silencing field
will pay attention to
the membrane connection.

Xuemei Chen

Chen spent the next decade studying how microRNAs are made, and she recently turned her attention to their degradation and where in the cell they do their work. After its synthesis in the nucleus, the precursor microRNA matures as enzymes cut out unneeded parts. The first trimming steps take place in the nucleus; then the microRNA exits to the cell’s main compartment (the cytoplasm) and gets its finishing touches, including the addition of small chemical tags attached by enzymes like HEN1. Ready to go, the finished microRNA teams up with a group of proteins to find its target mRNA, which it identifies by a nucleotide sequence that matches its own. The microRNA and its protein partners quash production of the protein encoded by the mRNA, either by blocking translation or by destroying the mRNA.

Sometimes a plant wants to get rid of a microRNA so it can keep the corresponding mRNAs around. The fate of the microRNA comes down to two of those little chemical tags: the methyl group added by HEN1 and another tag called uridine. An enzyme called HESO1 decorates the microRNA with a chain of uridines, according to a paper Chen’s team published in Current Biology in 2012. Each tag is a sign to the cell: the methyl says, “Keep me,” and the uridines say, “Destroy me.”

For a while, Chen was puzzled as to why microRNAs needed a “Keep me” methyl group; wasn’t the absence of a “Destroy me” uridine tag sufficient? She reported the reason in the April 29, 2014, issue of the Proceedings of the National Academy of Sciences. HESO1 could, potentially, add the same “Destroy me” signal to the mRNAs, which sit right next to the microRNAs in the protein complex. The only way HESO1 can tell the difference between mRNAs and microRNAs is the methyl group. The methyl is the microRNA’s protective gear: it prevents HESO1 from adding uridines, thereby warding off the microRNA’s destruction.

Chen’s also been looking at where in the cell microRNAs do their mRNA silencing. Scientists presumed that microRNAs blocked mRNAs floating free within the cell’s watery cytoplasm, but few had actually checked. So Chen and her colleagues used fluorescent proteins to label some of the proteins that participate in mRNA silencing. Under their microscopes, they saw the fluorescent green and yellow signals in the cell’s endoplasmic reticulum—a series of membrane tubules involved in protein synthesis. That does not necessarily rule out RNA silencing in the cell interior, Chen reported in Cell in 2013; it just shows that the endoplasmic reticulum is one site where it definitely happens.

This finding has important ramifications, Chen says. Because researchers assumed that RNA silencing took place outside organelles, they have often done their experiments in test tubes with no membranes present. That could be a mistake, Chen says, since it doesn’t match the natural environment of RNA silencing. “I hope the entire RNA silencing field will pay attention to the membrane connection,” she says.

Chen plans to learn as much as she can about these controlling bits of RNA. Because microRNAs are important in animals as well as plants, Chen’s work could have far-reaching implications. Scientists already know that microRNAs participate in some human diseases, such as cancer.

“At the molecular level, people are not that different from Arabidopsis,” Chen says.