Reading between the genes
LOOK WHO’S BOSS
By Bruce Goldman
Illustration by Greg Mably
GENES RULE. BUT THEY’RE NOT QUITE THE DICTATORS SOME HAVE CLAIMED AND OTHERS HAVE FEARED.
In the past decade or two, researchers have learned that genes themselves are governed by a benign bureaucracy of regulatory loops that curb some genes while stimulating others. Now they have discovered a new class of molecules that may play a major role in that regulation, from determining what cells want to be when they grow up to keeping them on task once they do.
This means that tailoring medicine to suit an individual requires looking beyond the genes. Or more precisely, looking between the genes, because that’s where the newest of new players originate. These molecules, long linear strands called lincRNA, are the latest surprise to arise from the vast spaces along chromosomes that separate one gene from another — spaces once considered so bereft of purpose they were disparaged as “junk DNA.”
And while some pioneering physicians have begun incorporating patients’ genetic information into their treatment plans, they can’t yet factor in molecules like lincRNAs that regulate those genes. At this early stage of discovery, they wouldn’t know what to test for. But with evidence building that at least a couple of lincRNAs have been implicated in cancer, it’s realistic to expect that testing people for these gene-regulating molecules will become part of medical practice. Knowing the genes alone will take us only so far along the road to personalized medicine.
RNA IN HUMBLER DAYS
LIKE ROYALTY ON A THRONE, GENES NEVER LEAVE THE NUCLEUS, WHICH LIES JUST ABOUT SMACK-DAB in the cell’s center. Yet the molecules that make up the working class of the cell, the proteins, are stitched together in the cell’s watery outer provinces, or cytoplasm. The genome delivers its edicts to the cytoplasm via messengers made of RNA, a substance seen previously as a passive “wax impression” of DNA, but looking more like an Olympic gymnast every day.
Until recently, RNA’s main claim to fame was largely as a bit player in the extravaganza that is gene activation. When the DNA double helix is inactive, its two strands are zipped up and spooled around specialized packaging proteins called histones. “Reading” a gene’s instructions requires unzipping the two strands at the site of the gene.
Somewhere around the beginning of life many billions of years ago, cells evolved bulky molecular machines (each of them an assembly including numerous large proteins) that can do this very well. These transcription machines can unpack and unpeel the DNA temporarily from its associated histone husk. They can part its two strands at key points. They can then hover above a strand near the start of a gene, barrel down the exposed DNA and crank out copies of its protein-coding instructions. The copies are made of RNA, which is chemically similar to DNA — they’re both chains of constituent chemical links called nucleotides — but RNA is more travel-ready and short-lived.
Fresh “messenger RNA” molecules float out of the nucleus into the cell’s far reaches. There in the cytoplasm they are fed into still other gigantic molecular machines, called ribosomes, their strings of nucleotides read as consecutive three-nucleotide chunks, and the proteins they specify produced according to a code whereby each three-letter RNA “word” indicates which of some 20 different chemical building blocks should next be spliced onto a growing protein molecule.
But not all genes in all cells get copied all the time. Different kinds of cells, and the same cells at different stages of their lives, are different because they make different proteins. Otherwise, we’d all be blobs of undifferentiated tissue. Just how do these differences in protein production come about?
The hulking transcription machines in the nucleus that zip and unzip DNA are exactly the same from one cell to the next. So are the ribosomes in the cytoplasm that decipher the genetic code to manufacture proteins. So those giant complexes can’t determine all by themselves which genes get read within a given cell at a given time.
Still other huge protein complexes sporting Jurassic Park–ish names such as Trithorax and Polycomb affix or remove small chemical tags to the DNA or histones in the vicinity of genes. The tags serve as long-lasting “read” or “skip” signals to the gene-reading machinery. But those lumbering juggernauts, Trithorax and Polycomb, are exactly the same in every cell, too. So who tells them where along the genome to slap those “read” and “skip” tags? Who guides them to the appropriate spots in the first place?
Cue the music. Enter lincRNA molecules, discovered by two researchers who looked where no one else was looking and found what no one else had thought would be there.
EUREKA MOMENT
A CELL CAN’T MAKE A PROTEIN WITHOUT MAKING RNA FIRST. THUS, A QUICK-AND-DIRTY WAY to see which genes in a cell or tissue are in active use as protein templates is to use a gene-expression chip: a microarray pioneered by Stanford School of Medicine biochemistry professor Pat Brown, PhD, and biochemistry and genetics professor Ronald Davis, PhD, in the mid-1990s. This device represents the amounts of RNA made from each gene on the chip as a separate pixel displayed on a computer screen — the more RNA made from that gene, the brighter the pixel — making it easy to analyze aggregate patterns of gene expression: that is, which ones are actively getting read, and which just sitting there, at any given time.
In 1999, shortly after the Human Genome Project pulled out its first plum from the genomic pudding — the full sequencing of chromosome 22 — Michael Snyder, PhD, at that time a Yale University geneticist, used the newly published sequence data to design a high-resolution gene-expression chip he called a tiling array. It combed the entirety of chromosome 22 for small snippets of RNA emanating not just from its known or likely protein-coding portions (“genes,” that is), but from anywhere along its entire length. Snyder’s custom-built tiling array would, in principle, allow the detection of RNA molecules made not only where you’d expect to find them being made — at, near or overlapping all the places where a protein-coding sequence had already been identified — but from anyplace along chromosome 22, including vast mysterious stretches between one gene and the next.
This was ambitious and, some thought, a waste of time and money. As the Human Genome Project unfolded, it began to look as though not much more than 1 percent of the genome consisted of recipes for viable proteins. The other 99 percent appeared to have no function, save for small sections near genes that served as landing strips and homing beacons for the molecular machines that read or mark up DNA. One high-profile Harvard biologist referred to the overwhelmingly large non-coding stretches as “junk DNA.” The name stuck.
“Many of us never really believed that,” says Snyder, who last year moved to Stanford to become professor and chair of the medical school’s genetics department.
Snyder told one of his graduate students, John Rinn, to take a close look at chromosome 22. Applying Snyder’s tiling array to the just-sequenced chromosome, Rinn found that RNA was getting made at all kinds of sites along the DNA that bore no resemblance to protein-coding genes. Some of these RNA molecules were very small, consisting of tens of nucleotides. But lots of them were thousands of nucleotides long, as lengthy as those that do code for a protein. These RNA molecules weren’t doing that, as could be determined by their nonsensical sequences — for example, they tended to contain too many three-nucleotide signals that, in effect, stop the protein-making machinery in its tracks. Yet they featured many of the same “gene-like” elements (for instance, regulatory nucleotide sequences that invite gene-reading machinery to have a sit) that protein-coding RNA molecules did.
“There were as many genes making RNA but not proteins as there were protein-coding genes,” Rinn recalls. “It was a Eureka moment.”
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Read more here/Leia mais aqui: Stanford Medicine
