Nucleosomal arrangement affects single-molecule transcription dynamics.

Area of Science:

• Molecular Biology
• Biophysics
• Genetics

Background:

• Gene expression in eukaryotes is regulated by chromatin organization.
• The precise mechanisms by which chromatin affects the transcription dynamics of individual RNA polymerases remain unclear.

Purpose of the Study:

• To investigate how chromatin structure, specifically nucleosomes, influences the transcription dynamics of single yeast RNA polymerase II (Pol II) molecules.
• To quantify the ability of Pol II to navigate nucleosomal DNA and predict its passage probability.

Main Methods:

• Utilized dual trap optical tweezers to monitor single yeast RNA polymerase II (Pol II) molecules transcribing a DNA template containing two nucleosomes.
• Analyzed changes in transcription speed and pausing behavior to determine a drift coefficient (χ).

Main Results:

• Developed a drift coefficient (χ) to characterize the enzyme's recovery from nucleosomal backtracks, predicting passage probability.
• Observed that the presence and arrangement of a second nucleosome significantly alter Pol II transcription dynamics.
• Found that Pol II passage is enhanced when the second nucleosome is rotationally oriented away from the first.

Conclusions:

• Chromatin arrangement, including nucleosome spacing and rotational orientation, critically affects RNA polymerase II transcription dynamics.
• The study provides a biophysical basis for understanding how chromatin modulates gene expression at the single-molecule level.