SHPRH regulates rRNA transcription by recognizing the histone code in an mTOR-dependent manner

Area of Science:

• Molecular Biology
• Epigenetics
• Gene Regulation

Background:

• DNA repair proteins often possess multifaceted cellular roles beyond their canonical functions.
• SHPRH (SNF2 histone tautomerase) is known to catalyze PCNA polyubiquitylation during DNA replication stress.
• Investigating non-canonical functions of DNA repair proteins can reveal novel regulatory mechanisms.

Purpose of the Study:

• To elucidate the additional functions of SHPRH beyond DNA repair.
• To investigate the role of SHPRH in ribosomal DNA (rDNA) transcription.
• To understand the molecular mechanisms underlying SHPRH's involvement in rRNA synthesis.

Main Methods:

• Localization studies of SHPRH at the rDNA promoter within nucleoli.
• Chromatin immunoprecipitation assays to assess SHPRH enrichment.
• Histone modification analysis, specifically trimethylation of H3K4.
• Co-immunoprecipitation to identify interacting protein partners, including RNA polymerase I complex components.
• Investigating the impact of cellular conditions (starvation) and pharmacological treatments (actinomycin D, rapamycin) on SHPRH localization.
• Depletion studies using siRNA targeting CHD4.

Main Results:

• SHPRH localizes to the ribosomal DNA (rDNA) promoter in the nucleoli, facilitating rRNA transcription.
• SHPRH recruitment to the rDNA promoter is mediated by its plant homeodomain (PHD) interacting with un-trimethylated H3K4.
• SHPRH enrichment at the rDNA promoter is sensitive to cell starvation, actinomycin D, rapamycin, and CHD4 depletion.
• SHPRH physically interacts with the RNA polymerase I complex, suggesting a direct role in transcription initiation.
• The observed effects are dependent on the mammalian target of rapamycin (mTOR) pathway.

Conclusions:

• SHPRH plays a significant role in regulating rRNA transcription, independent of its DNA repair function.
• SHPRH's interaction with histone H3, modulated by H3K4 methylation status, is crucial for its function at the rDNA promoter.
• The mammalian target of rapamycin (mTOR) pathway is essential for SHPRH-mediated rRNA transcription.
• These findings highlight a novel link between DNA repair proteins, epigenetic regulation, and ribosome biogenesis.