DNA supercoiling modulates eukaryotic transcription in a gene-orientation dependent manner

Area of Science:

• Molecular Biology
• Genetics
• Epigenetics

Background:

• Transcription-induced torsional stress alters DNA supercoiling.
• Supercoiling can propagate and affect DNA-associated protein activity.
• Gene expression at one locus can influence nearby transcription events.

Purpose of the Study:

• Investigate the impact of DNA supercoiling on histone modifications and neighboring gene transcription.
• Determine the role of topoisomerases in regulating DNA supercoiling and transcription in C. elegans.

Main Methods:

• Acute depletion of topoisomerases I and II.
• Global Run-on sequencing (GRO-seq) for nascent transcription.
• Chromatin immunoprecipitation sequencing (ChIP-seq) for RNA Polymerase II occupancy.
• RNA sequencing (RNA-seq) for gene expression.
• Cut & Tag assay for histone modifications.

Main Results:

• Topoisomerase depletion caused genome-wide transcription changes with minimal histone modification alterations.
• C. elegans topoisomerase I is crucial for transcription elongation and partially redundant with topoisomerase II.
• Negative supercoiling promotes transcription of divergently oriented genes.
• Positive supercoiling suppresses transcription of convergently oriented genes.
• Topoisomerase depletion synchronized expression of divergent gene pairs but disrupted convergent gene expression.

Conclusions:

• DNA supercoiling, generated by transcription, influences neighboring gene transcription in an orientation-dependent manner.
• Negative supercoiling facilitates coordinated expression of divergent gene pairs.
• Excessive positive supercoiling inhibits transcription, disrupting convergent gene expression.