In the May 16, 2006, issue of the Proceedings of the National Academy of Sciences, researchers from the University of Massachusetts reported new findings about how genes on the X chromosome are silenced.

The PNAS paper comes as the detailed sequencing and biological annotation of chromosome 1 is announced in today's issue of Nature.

Both the paper and press release accompanying the Nature paper understandably focus on the genes contained on chromosome 1. But as the PNAS paper demonstrated, dismissing the nongenic parts of the genome as "junk DNA" or "gene deserts" likely means hobbling one's ability to understand how gene expression really works.

If gene expression of the X chromosome were left to its own devices, females would end up with twice as much X-coded protein as males.

Cells need to prevent that bounty because "the balance of gene expression is very important to keeping cells viable," PNAS paper senior author Jeanne Lawrence told BioWorld Today. For example, in Down's syndrome, the affected individuals "have all the genes they need, but the balance is wrong." In females, one copy of the X chromosome is condensed into a so-called Barr body, its genes inactivated.

The twist, though, is that not the entire inactive X chromosome is shut down. "There are certain genes that persistently escape inactivation," Lawrence said - mainly those, intuitively enough, that also are found on the Y chromosome, preserving the protein equality of the sexes.

X chromosome silencing is done by XIST (pronounced "exist") RNA, a large molecule that more or less covers one chromosome and prevents its genes from being expressed. What Lawrence and her group showed in the PNAS paper is that the silencing is somehow done through effects on noncoding, repetitive DNA.

The scientists investigated 15 genes, eight of which are usually inactivated on the X chromosome. They expected to see one of two possible scenarios: either the active genes would be located outside of the Barr body and the inactive ones inside, or both active and inactive genes would be inside the Barr body.

Instead, what they saw was that "of the 15 genes we looked at, none of them were in the Barr body," Lawrence said. Instead, all of the genes were positioned on the outer border of the Barr body, leading to the next question: If it's not the genes, then what is in the Barr body?

What Lawrence and colleagues found inside the Barr body was primarily repetitive DNA known as Cot-1 DNA, and centromeric DNA. The authors concluded that "the core of the X chromosome essentially excludes genes and is composed primarily of noncoding repeat-rich DNA."

Lawrence said that while it is possible that there could be "fine structural differences" in the packaging of genes that are silenced and those that are not, she believes that other possibilities are more likely.

"XIST seems to be operating by affecting the structure of the chromosome," she said.

Lawrence said that during genomic analysis, including the Nature paper, DNA sequence repeats such as Cot-1 DNA still are routinely screened out, under the assumption that they are not relevant to understanding gene expression. Her work shows that "it's important to keep an open mind about what might be useful," she said. "It's not just genes being silenced."

Indeed, repeat DNA initially had a hard time getting enough respect - and resources - to just get sequenced by the Human Genome Project. Lawrence, who is a professor of cell biology at the University of Massachusetts Medical School, herself completed a three-year stint as member of the National Advisory Council for Human Genome Research; the council advises the Department of Health and Human Services and the National Institutes of Health on genomic research, training and programs related to the human genome initiative.

During Lawrence's tenure, there still was discussion about whether to truly sequence the whole genome, or just those parts of the sequence deemed to be functionally relevant; sequencing throughput capabilities were comparatively paltry when the human genome project began, which made sequencing all 3 billion plus base pairs of the human genome a daunting proposition. "So some people wanted to sequence just the cDNA," Lawrence said.

The cDNA (complementary DNA) is made from messenger RNA in the lab; so a strategy based on sequencing the cDNA would have yielded only those parts of the genome sequence that coded for proteins.

But other members of the advisory committee, who thought that the noncoding sequences probably also held "some good stuff," ultimately won out. And they were right: Noncoding DNAs have since become a major area of basic, as well as clinical, investigation.

In 2002, Science magazine's "Breakthrough of the Year" was small RNAs - RNAs that, despite never making it to the protein stage, fulfill increasingly appreciated roles within cells. In fact, Lawrence said, "a chromosome that's active is continually producing RNA from the bulk of the chromosome" - in previous studies, one-half to two-thirds of all transcription - "that might not be coding for anything."

Ultimately, such noncoding RNAs could prove useful in clinical settings, as well. Nagesh Mahanthappa, senior director of business development and strategy at Cambridge, Mass.-based Alnylam Pharmaceuticals Inc., told BioWorld Today that misregulation of how noncoding microRNAs are expressed, for example, is "increasingly being correlated with various disease states," including cancer and infectious diseases such as hepatitis C.

Scientists at Alnylam, along with co-authors at New York City's Rockefeller University and New York University, published data in Nature last November showing that chemically engineered oligonucleotides, which they termed "antagomirs," can silence endogenous miRNAs in mice; one antagomir down-regulated cholesterol biosynthesis and reduced plasma cholesterol levels.

Though the approach is too novel to have made it into the clinic, Mahanthappa predicted that "noncoding RNAs are going to be a fascinating class of targets."