Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape

Area of Science:

• Molecular Biology
• Epigenetics
• Cancer Biology

Background:

• Transcription and pre-messenger RNA splicing are functionally coupled processes.
• The impact of cancer-associated mutations in splicing factors, like SF3B1, on transcription is not well understood.
• Understanding these disruptions is crucial for identifying novel therapeutic targets in cancer.

Purpose of the Study:

• To investigate how cancer-associated SF3B1 mutations affect RNA polymerase II (RNAPII) transcription.
• To elucidate the molecular mechanisms linking SF3B1 mutations to transcriptional and epigenetic alterations.
• To identify potential therapeutic strategies targeting the observed molecular defects.

Main Methods:

• Utilized isogenic cell lines, patient samples, and a mutant mouse model.
• Assessed RNAPII elongation rates and promoter-associated RNAPII density.
• Investigated pre-spliceosome assembly and protein-protein interactions.
• Performed an unbiased screen to identify epigenetic regulators.
• Analyzed chromatin accessibility and H3K4me3 marks.

Main Results:

• SF3B1 mutations significantly reduce RNAPII elongation rate and promoter density.
• Elongation defects stem from impaired pre-spliceosome assembly due to altered SF3B1 protein interactions.
• Reduced promoter-proximal RNAPII density leads to decreased chromatin accessibility and H3K4me3 marks.
• Epigenetic factors in the Sin3/HDAC/H3K4me pathway were identified that can reverse these changes.

Conclusions:

• Cancer-associated SF3B1 mutations disrupt the coordination of transcription and splicing, leading to significant transcriptional defects.
• Mutant SF3B1 states functionally mimic epigenetic disorders by altering the chromatin landscape.
• Targeting the Sin3/HDAC complex presents a promising therapeutic avenue for cancers with SF3B1 mutations.