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When egg and sperm combine, the new embryo bustles with activity. Its cells multiply so rapidly they largely ignore their DNA, other than to copy it and to read just a few essential genes. The embryonic cells mainly rely on molecular instructions placed in the egg by its mother in the form of RNA. Then, during the so-called midblastula transition, cells start transcribing massive amounts of their own DNA.
Earlier in her career, Associate Investigator Julia Zeitlinger, PhD, discovered that sometimes the transcription machinery, or RNA polymerase II, pauses at the beginning of a gene as if taking a lunch break. More often than not, pausing occurred at genes important for development. When she and her team used fruit fly embryos to test whether pausing may help get these molecular construction workers on-site before a big work order becomes due during the midblastula transition, they were in for a surprise.
Before the midblastula transition, RNA polymerase II appeared to rarely pause as it transcribed roughly one hundred early genes. And no construction crews were sitting idle on inactive genes in preparation for the midblastula transition. Pausing only became widespread during the midblastula transition itself. “What we found was not what we expected at all,” Zeitlinger says. “Instead of preparing for a huge workload, the construction crews were busy completing rush jobs.”
When the researchers computationally compared the regulatory elements at the beginning of each of the genes or promoters where pausing occurred with those where it didn’t, a pattern emerged. They found that three different types of promoters correlated with the construction crew’s pausing behavior.
“The most important result is that promoters are different,” Zeitlinger says. “The general paradigm for a long time has been a promoter is a promoter. But really what we see is that they have different functions.”
The study was published in the August 2013 issue of eLife Sciences.