RNA Binding by Histone Methyltransferases Set1 and Set2.

Area of Science:

• Molecular Biology
• Epigenetics
• Yeast Genetics

Background:

• Histone methylation at H3K4 and H3K36 marks actively transcribed genes.
• Saccharomyces cerevisiae Set1 and Set2 catalyze H3K4 and H3K36 methylation, respectively.
• RNA polymerase II (RNAPII) is the enzyme responsible for transcribing genes.

Purpose of the Study:

• To investigate the in vivo interaction of Set1 and Set2 methyltransferases with RNA.
• To determine the functional consequences of RNA binding by Set1 on its chromatin association and catalytic activity.

Main Methods:

• UV cross-linking to capture in vivo RNA-protein interactions.
• High-throughput sequencing to identify bound RNAs.
• Analysis of chromatin occupancy and histone methylation levels.

Main Results:

• Both Set1 and Set2 were UV cross-linked to RNA in vivo.
• Set1 preferentially bound near transcription start sites, while Set2 associated with pre-mRNAs.
• Set1 binding to RNA, particularly SET1 mRNA and noncoding RNAs, was linked to gene silencing.
• Set1 lacking RRM2 showed reduced RNA binding, chromatin occupancy, and altered H3K4 methylation patterns.

Conclusions:

• RNA binding is a significant feature of Set1 and Set2 function in Saccharomyces cerevisiae.
• RNA interaction contributes to Set1's recruitment to chromatin and its role in H3K4 methylation.
• These findings reveal a novel layer of epigenetic regulation involving direct RNA interaction with histone-modifying enzymes.