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Transcription bridges gap between enhancer and promoter

06 Apr 2020

Enhancers are crucial for regulating gene expression. Transcription of an active enhancer allows it to make physical contact with its target gene promoter, a new study shows.

Genetic information encoded in DNA is the fundamental basis for all biological species. Which genes are translated into products – proteins and RNA – and when this occurs are tightly regulated steps. Enhancers are central for this regulation: Through a cascade of factors, enhancers influence whether and to what degree a gene is “transcribed” by RNA polymerase. However, how enhancers regulate transcription is not fully known. Rushad Pavri and his lab at the Research Institute of Molecular Pathology provide a new level of detailed insight into one mode by which enhancers regulate genes. They report their findings in the journal Nature Genetics.

To the biologists’ surprise, ten years ago, enhancers themselves were shown to be transcribed. However, little is known about how and whether this transcription and/or the resulting enhancer RNA (eRNA) contribute to an enhancer’s function – a question on which Johanna Fitz, at the time a PhD student in Pavri’s group and first author of the new publication, and her colleagues wanted to shed light.

Without transcription, an active enhancer doesn’t engage with its target promoter

To do so, the researchers removed Spt5, a factor required by RNA polymerase II, in activated B cells. This reduces RNA polymerase II activity. Pavri and his group focused on a locus important for B cell function, called the immunoglobulin heavy chain locus (Igh), which encodes the heavy chains of antibodies. Igh has a super-enhancer, called the 3’ regulatory region (3’RR), that is essential for its expression.

In Spt5-depleted cells, transcription of both the 3’RR and Igh genes is decreased. But apart from transcription, the researchers found that all analysed aspects of 3’RR activation appear normal: the 3’RR has accessible and acetylated chromatin, and it is bound by transcription factors and coactivators. Nevertheless, the enhancer can’t physically engage with its target promoter.

Transcription may make enhancer more mobile

Pavri and his lab hypothesised that Spt5 depletion reduces 3’RR transcription, which inhibits the interaction between the 3’RR and the promoter. To test their hypothesis, they restored transcription of two of four enhancers in the 3’RR. This partially rescues transcription of the target Igh gene. Using short-acting pharmacological inhibitors of transcription, the researchers found that Spt5-mediated 3’RR transcription is likely necessary to initiate a new interaction with the promoter, but not to maintain an interaction.

Taken together, Pavri and his team show that Spt5-dependent transcription at the 3’RR enables the active enhancer to physically engage with target genes. Combining their mechanistic insights with a recent imaging study, Pavri and his team propose that transcription drives the 3’RR’s mobility: being more mobile allows the enhancer to interact with its target promoter(s). With their work, the researchers provide an unprecedented level of insight into this mode of gene regulation, which the team’s genome-wide analysis of enhancer-promoter interactions suggests is also at work at some other loci.

Original Publication:
Johanna Fitz, Tobias Neumann, Monika Steininger, Eva-Maria Wiedemann, Adriana Cantoran Garcia, Alexander Athanasiadis, Ursula E. Schoeberl and Rushad Pavri. “Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction”. Nature Genetics, 6 April 2020.