Dartmouth Medical School geneticists discover new role for antisense RNA

Dartmouth Medical School geneticists studying the biological clock have opened yet another window into the role of an unusual form of RNA known as antisense that blocks the messages of protein-encoding genes.

They found that antisense RNA appears to regulate core timing genes in the circadaian clock that drives the 24-hour light-dark cycle of Neurospora, a model organism better known as bread mold.

The results are reported in the February 27 Nature by Drs. Jennifer Loros and Jay C. Dunlap, both DMS professors, and Susan K. Crosthwaite, formerly a postdoctoral fellow at DMS, and Cas Kramer, both of the University of Manchester, England.

Messenger RNA, which has a single-stranded sequence of nucleotides, is called “sense” because it can be decoded to produce a gene product (a protein). Like DNA, this mRNA can form duplexes with a second strand of RNA whose base sequence is complementary to the first strand. The second strand is called the antisense strand because its nucleotide sequence is the complement of “sense” message. When mRNA forms a duplex with a complementary antisense RNA sequence, the message translation is turned off so the sense strand can no longer be decoded to yield a protein product.

As scientists identify more antisense RNAs, they are beginning to realize these might affect a wide variety of processes. The recent findings, write the authors, “provide an unexpected link between antisense RNA and circadian timing.”

Studying the development of spores in the bread mold Neurospora, Dunlap and Loros have teased apart the molecular gears that form the basis of most living clocks. Light and dark cycles reset the clocks, they found, the way turning the hands of a clock does. The clock mechanism, a biological oscillator, keeps time through the delicately balanced interplay of the Neurospora clock genes and proteins in a complex of feedback loops.

“We found a long RNA antisense transcript that arises from the frequency gene, known to encode factors important for the operation of the circadian clock in Neurospora,” says Dunlap. “The sense transcript encodes proteins that are involved in the feedback loop that is the oscillator in the clock. The antisense transcript runs in the opposite direction, and apparently does not encode a protein, so its actual role is unknown at present. It may simply bock translation, or it may destabilize the sense message. Antisense transcripts are already known, but usually they are quite small, on the order of 20 to 25 bases. This one is quite large, nearly 5,000 bases.”

In normal bread mold strains living in the dark, levels of antisense frequency transcripts cycle with respect to the amount of sense frequency transcripts, and they are inducible by light, the researchers determined. However, in strains mutated to abolish induction of antisense frequency RNA by light, the internal clock time was delayed, and resetting of the clock by light was altered.

If similar environmental factors regulate both sense and antisense transcripts, the authors suggest, a role for antisense frequency RNA might be to confer the ability to keep accurate time by limiting the clock response to extremes in the environment. Likewise other antisense RNAs might be involved in maintaining internal stability in other organisms.