Scientists uncover new RNA processing mechanism and a new class of small RNAs

Nov 26 2008

A very small fraction of our genetic material - about 2% - performs the crucial task scientists once thought was the sole purpose of the genome: to serve as a blueprint for the production of proteins, the molecules that make cells work and sustain life.

This 2% of human DNA is converted into intermediary molecules called RNAs, which in turn carry instructions within cells for protein manufacture.

And what of the other 98% of the genome? It has been assumed by many to be genetic junk, a massive accumulation of "code" that evolution has rendered superfluous. Now, however, scientists are discovering that the vast bulk of the DNA in our genomes, while it does not "code" for the specific RNA molecules that serve as templates for protein synthesis, do nevertheless perform various kinds of work. But what types of work, involving what kinds of cellular mechanisms? Given its relative abundance, non-coding DNA and RNA present inviting targets for experimentation.

For years, a laboratory at Cold Spring Harbor Laboratory (CSHL) led by Professor David L. Spector, Ph.D., has studied events within the cell nucleus, where the genetic material is contained. In the November 26th issue of Cell , Spector and a team led by graduate student Jeremy Wilusz report their discovery of a previously unknown mechanism in the nucleus that processes non-coding RNA molecules.

Spector and colleagues discovered the mechanism while examining a non-coding RNA molecule called MALAT1. Resident in the cell nucleus, MALAT1 was observed to split into two parts, one long and one very short—the latter qualifying as a species of RNA that scientists call small RNAs. The small RNA segment was observed to migrate out of the nucleus into the cell's aqueous cytoplasm. The longer remnant of MALAT1 remained in the nucleus, accumulating in distinct zones called nuclear speckles.

Although it is not yet clear what these processed parts of the original MALAT1 molecule do, their disparate destinations in the cell suggest that they likely serve different functions. And that, Dr. Spector says, is intriguing in part because MALAT1 is known to be a good marker of cancer progression: it is found at abnormally high levels in the nuclei of cancer cells with a propensity to become metastatic.

The discovery of the cytoplasmic small RNA fragment of the non-coding MALAT1 molecule, which the CSHL team calls mascRNA, (MALAT1-associated small cytoplasmic RNA) is "just the tip of the iceberg of a whole new class of small RNAs," according to Spector.

This new kid on the small RNA block was found by Spector's lab to be present in most cell types, and is highly conserved, or retained by evolution across many species. In the growing menagerie of small RNA molecules, mascRNA is processed and assumes a physical shape much like that of transfer RNA, or tRNA, an RNA string that folds into a cloverleaf-shaped structure.

tRNA molecules are part of the construction crew that builds proteins; they carry amino acids--the building blocks of proteins-- to protein chains as they are being assembled. But the CSHL team's results suggest that mascRNA, which is smaller than most tRNAs, does not likely perform this function. Yet mascRNA's location in the cell's cytoplasm and its pathway of biogenesis does hint at a possible function. Spector suspects it may act as a "sponge" for proteins, preventing them from reaching their natural destinations within the cell. Another possibility is that mascRNA simply serves to alert the cell that the long non-coding RNA fragment that it originally split off from-- MALAT1--is "available" in the nucleus for other cellular duties.

Researchers now think that at least 40% of long, non-coding RNAs--a considerable chunk of RNA segments that float around the nucleus--may be processed to generate smaller RNA pieces such as mascRNA, and also other classes of RNA. While the hunt has begun for other tRNA-like small RNAs and their precursor RNAs like MALAT1, the new results from Spector's lab provide a first look at how these bits are produced.

In the case of coding RNAs, once their sequence has been "read" off a DNA template, a molecular complex snips off the tail end of this new piece and tacks on a signal at its end that protects the new molecule from degradation and marks it for export out of the nucleus. In non-coding MALAT1, however, the CSHL team found the protective signal was already embedded within the molecule, just ahead of the portion that later detached to form mascRNA. The molecular complex responsible for cleaving MALAT1 therefore knew precisely where to make its cut--right after the embedded signal--rather than at MALAT1's tail end. In this way, MALAT1 is effectively preconfigured to liberate the mascRNA fragment.

The mechanism that retains the long MALAT1 molecule within the nucleus while expelling the mascRNA fragment into the cytoplasm is still elusive. "The answer will come when we identify more and more RNAs that are built like the MALAT1 precursor and are processed to give rise to different types of RNAs," says Spector.

In the meantime, his lab's current work provides reason to believe that the community of non-coding RNAs has many more surprises to reveal. To the extent that its members can be shown to perform specific functions, it will seem increasingly inapt to consider non-coding RNAs the byproducts of "junk DNA."