Genes Can Answer to More than One Master

May 5, 2000— Like discovering acar that has more than oneengine under the hood, cellbiologists are learning to theirsurprise that alternate molecularmachines can drive the basicprocess of transcription thatorchestrates the expression ofgenes. The core transcription machineryof RNA polymerase copies theinformation found in DNA genesonto messenger RNA moleculesthat then govern the productionof proteins. Although the reason for multipletranscriptional controls remainsmysterious, researchers speculatethat the mechanism might allowthe same gene to be used fordifferent purposes in different cells. Now, Howard Hughes Medical Institute (HHMI)researchers have taken an important step inunderstanding this phenomenon by pinpointing the firstgene in the fruit fly Drosophil melanogaster that is atarget of an alternate control molecule, called TRF1.They believe that the discovery opens the way for aricher understanding of how gene expression isregulated. In an article in the May 5, 2000, issue of the journalScience, HHMI investigator Robert Tjian and graduatestudent Michael C. Holmes report that the Drosophilagene tudor contains tandem promoter segments, one ofwhich responds to TRF1. "The discovery of TRF has been intriguing because forperhaps the last fifteen years we thought that thebasal transcriptional machinery of the cell wasessentially invariant," said Tjian, who is at theUniversity of California, Berkeley. "We thought that onlyone set of "general" proteins was involved, and that allthe regulation was directed by enhancer-bindingproteins that were specific to a particular genesequence. "It was like using the same engine over and over again,but just putting different gearing systems into it. Butthen we discovered that there were multiple engines." The scientists had found evidence that TRF1 isapparently one of several alternate transcriptionalcontrol molecules—called recognition factors—that canreplace the most prevalent control element, calledTATA-binding protein, or TBP. "While past studies had proven that TRF1 was involvedin transcription, the big question was why was itparticularly exciting just finding another TBP-likemolecule," said Tjian. "But then research revealed,surprisingly, that this molecule was not evenlydistributed in every cell. Some cell types, particularlythose in the central nervous system, expressed highlevels of this protein and others had either very lowlevels or none at all." To attempt to pinpoint a particular TRF1-responsivegene from among the 12,000 known Drosophila genes,the researchers first launched an "aerialreconnaissance" of Drosophila chromosomes. Using atechnique called polytene chromosome staining, theycreated an antibody that specifically targeted andattached to TRF1. They then bathed the giant salivarychromosomes from Drosophila in the antibody. Since theantibody also included a staining molecule, they couldhome in on potential TRF1-targeted genes by scanningthe fly genome for regions that were preferentiallystained. "We found that only about forty or fifty bands on thefly chromosomes lit up," said Tjian. "This told us thatour hypothesis that TRF1 was specialized for certaingenes was on the right track." To find the TRF1-responsive genes, the scientiststreated preparations of fly chromosomes with chemicalsthat formed bonds between TRF and the DNA. Theythen chopped up the chromosomes into small piecesand identified those pieces that had attached to theTRF1-specific antibodies. Using the pieces of chromosomes as clues, they wereable to work their way up to identifying whole genes.Screening those genes revealed that the Drosophilagene tudor is a potential target gene that can beactivated by TRF1. To validate the responsiveness oftudor to TRF1, the scientists cloned the promoter regionof tudor and tested whether it responded to TRF1 invitro. "The result of this test was more interesting than Ianticipated," said Tjian. "We thought that these geneswould either have a TBP-responding promoter or aTRF-responding promoter. But tudor had both—tandempromoters. I think this is perhaps the most unexpectedpiece of data in the paper." According to Tjian, the discovery of tandem promotersrepresents the opening of a new terrain for theexploration of transcription control. "Right now, trying to explain these tandem promoters istotal speculation," he emphasized. "However, if you lookat the genome of the fly, it's about 12,000 genes. Incontrast, the roundworm, C. elegans, has about 18,000genes. Now, the fly is at least as complex, if not morecomplex than the worm, and one way to achieve thathigher complexity with fewer genes is to make the samegene-coding capacity more versatile. One way thisversatility could evolve is by simply having moreelaborate control mechanisms over a smaller number ofgenes." Thus, said Tjian, the same gene might begoverned by alternate control schemes in differentcells. Tjian and his colleagues plan to look for other genesthat have multiple controls and to explore further thisnewfound diversity of gene control. "The take-home lesson from these studies is that we'renow appreciating more than ever before that the basicworkhorse transcriptional apparatus is much moreelaborate and probably more specific to organisms andtissues than we imagined," he said. Robert Tjian: http://www.hhmi.org/science/genetics/tjian.htm Text from: http://www.hhmi.org/news/tjian.html