Transcription mediated insulation and interference direct gene cluster expression switches

Area of Science:

• Molecular Biology
• Yeast Genetics
• Gene Regulation

Background:

• Tandemly arranged genes in yeast exhibit differential expression during the metabolic cycle and with varying carbon sources, suggesting bi-modal gene expression switches.
• The precise mechanisms controlling these bi-modal gene expression switches remain largely unelucidated.

Purpose of the Study:

• To investigate the role of transcription in controlling bi-modal gene expression switches in yeast.
• To elucidate how the HMS2 gene and its transcription states coordinate gene regulation in neighboring loci.

Main Methods:

• Native elongating transcript analysis (NET-seq) was employed to study transcription dynamics.
• Genetic engineering of the HMS2 gene was performed to explore alternative transcription unit (TU) formations.

Main Results:

• Transcription is integral to bi-modal switches, enabling reciprocal expression within gene clusters.
• The HMS2 gene dynamically switches between sense- and antisense-dominant transcription states, regulating adjacent gene expression.
• Engineered HMS2 revealed diverse mono-, di-, and tri-cistronic TUs, with promoters/terminators excluded by transcriptional interference and antisense TUs providing insulation.

Conclusions:

• The balance between transcriptional insulation and interference at gene clusters is crucial for facilitating gene expression switches.
• These regulatory mechanisms allow yeast to adapt gene expression in response to intracellular and extracellular environmental changes.