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Transcription kinetics in environmental interactions – University of Copenhagen

Transcription kinetics in environmental interactions

Sessile organisms are great models to study environmental interactions, because retreat as a one-fits-all solution for diverse challenges is not an option. Instead these organisms respond to environmental changes by rapidly adjusting transcription genome-wide. Differences in non-coding transcription are part of these profoundly altered transcriptomes in response to environmental change. This fact has helped to map long non-coding RNA in human, yeast and Arabidopsis.

The dynamics of the environmentally plastic expression changes suggest that these responses are underpinned by core mechanisms controlling Pol II transcription. Stress-specific Transcription factors are important for Pol II to initiate transcription, but are only part of the story. Important control Pol II transcription occurs through effects on elongation and termination.

How control of Pol II elongation and termination takes part in plant environmental responses is an important open question. The speed Pol II varies during transcription, and a variety of factors associate with Pol II to modulate the speed and efficiency of Pol II elongation. Often these factors ensure smooth passage of Pol II through nucleosome-packaged DNA by remodeling the chromatin during transcription. The alignment of key plant developmental decisions (e.g. germination time and flowering time) relies on chromatin factors modulating Pol II transcription efficiency.

Termination of Pol II transcription depends on the speed of transcription, “fast” Pol II mutants can cause termination defects, and “slow” Pol II mutants may lead to premature termination (4). We are interested in mechanisms that affect the speed of Pol II elongation as part of plant environmental responses. So far, the transcription speed can only be studied indirectly in plants. We have generated Arabidopsis Pol II mutants with different speeds of transcription (fast or slow) to determine the role of Pol II transcription kinetics in plant environmental interactions. 

(4) Hazelbaker DZ, Marquardt S, Wlotzka W, Buratowski S. “Kinetic competition between RNA Polymerase II and Sen1-dependent transcription termination”. Mol Cell. 2013 Jan 10;49(1):55-66.

SpeedFigure: Plants respond to environmental changes are associated with differences in Pol II transcription. Transcriptional responses occur rapidly and throughout large fractions of the genome (including non-coding sequences). We are characterizing the environmental responses of Arabidopsis mutants with altered Pol II speed.