A research group at the Stowers Institute for Medical Research says it has put to rest the notion that a gene promoter is only a promoter. They report, in the current issue of eLife Sciences, that promoters actually have a range of different functions.

The team, led by associate investigator Julia Zeitlinger, Ph.D., demonstrated that in Drosophila melanogaster, genes active in the first two hours of a fertilized egg are read quickly due to instructions from a promoter. Within each promoter region, different combinations of short control elements or “boxes” form a code that instructs RNA polymerases where and when to start transcribing. Researchers long thought that once an RNA polymerase appears at the “worksite” it would quickly finish the job.

As a postdoctoral fellow at MIT, Dr. Zeitlinger unexpectedly discovered that sometimes RNA polymerase II pauses at the beginning of a gene.

“We were wondering whether pausing was being used for preparing global gene activation during the midblastula transition,” says Kai Chen, Ph.D., a former graduate student in Dr. Zeitlinger’s lab and the study’s first author. “We expected to see widespread pausing before that transition.”

Working with D. melanogaster, Dr. Chen used a method called ChIP-seq, which can locate RNA polymerase II molecules on any gene. Paused polymerases would show up only at the beginning of genes. Working polymerases, on the other hand, would be found throughout the gene body.

The results took the Stowers team by surprise. Before the midblastula transition, RNA Polymerase II appeared to rarely pause as it transcribed roughly 100 early genes. Pausing only became widespread only during the midblastula transition itself.

“What we found was not what we expected at all,” explains Dr. Zeitlinger. The polymerase has to come to the promoter and immediately transcribe because there’s so little time to do the job. That’s one way of making transcription faster.”

When Dr. Chen and colleagues computationally compared the DNA sequences of promoters where pausing occurred with those where it didn’t, a pattern emerged. They found that three different types of promoters correlated with pausing behavior.

The genes that RNA Polymerase II reads before the midblastula transition were often preceded by a promoter that inhibited any pausing. These promoters contain what’s known as a TATA-box, named for its conserved arrangement of nucleotides, most commonly TATAA.

As cell division slows down during the midblastula transition, cells have the luxury of pausing, perhaps to fine-tune when transcription begins, according to Dr. Zeitlinger.

These midblastula genes were regulated by promoters that contain a variety of specific promoter elements associated with paused RNA polymerase, including GAGA, Downstream Promoter Element (DPE), Motif Two Element (MTF), and Pause Button (PB).

The team also found a third type of promoter, which contained both the TATA-box and the pausing sequences. At these genes, RNA polymerase II does not pause initially but begins to pause during the midblastula transition.

“My lab is interested in understanding how development or even diseases are encoded in the genome,” Zeitlinger says. “If we understand transcription, then we can predict a lot of what genomes encode, in terms of disease or differences between individuals.”

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