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Cancer-associated SF3B1 mutation K700E causes widespread changes in U2/branchpoint recognition without altering
Andrey Damianov1, Chia-Ho Lin1, Jian Zhang2
1Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA.
Abstract:
Myelodysplastic syndromes and other cancers are often associated with mutations in the U2 snRNP protein SF3B1. Common SF3B1 mutations, including K700E, disrupt SF3B1 interaction with the protein SUGP1 and induce aberrant activation of cryptic 3' splice sites (ss), presumably resulting from aberrant U2/branch site (BS) recognition by the mutant spliceosome. Here, we apply the new method of U2 IP-seq to profile BS binding across the transcriptome of K562 leukemia cells carrying the SF3B1 K700E mutation. For cryptic 3' ss activated by K700E, we identify their associated BSs and show that they are indeed shifted from the WT sites. Unexpectedly, we also identify thousands of additional changes in BS binding in the mutant cells that do not alter 3' ss choice. These new BS are usually very close to the natural sites, occur upstream or downstream, and either exhibit stronger base-pairing potential with U2 snRNA or are adjacent to stronger polypyrimidine tracts than the WT sites. The widespread imprecision in BS recognition induced by K700E with limited changes in 3' ss selection supports a positive role for SUGP1 in early BS choice and expands the physiological consequences of this oncogenic mutation.
Insights
SF3B1 mutations, common in cancers, disrupt spliceosome function. This study reveals how the K700E mutation causes widespread imprecise branch site recognition, impacting splicing regulation.
Area of Science:
- Molecular Biology
- Genetics
- Cancer Biology
Background:
- Mutations in SF3B1, a U2 snRNP protein, are linked to myelodysplastic syndromes and other cancers.
- The K700E mutation in SF3B1 disrupts interactions with SUGP1, leading to aberrant splice site activation.
Purpose of the Study:
- To investigate the impact of the SF3B1 K700E mutation on branch site (BS) recognition using U2 IP-seq.
- To understand how this mutation affects spliceosome function and gene expression in leukemia cells.
Main Methods:
- Application of U2 IP-seq to profile branch site binding across the transcriptome.
- Analysis of K562 leukemia cells carrying the SF3B1 K700E mutation.
Main Results:
- Identified shifted branch sites associated with cryptic 3' splice sites activated by the K700E mutation.
- Discovered thousands of additional changes in branch site binding, often near natural sites, without altering 3' splice site choice.
- Observed that new branch sites exhibit stronger U2 snRNA base-pairing potential or are near stronger polypyrimidine tracts.
Conclusions:
- The SF3B1 K700E mutation induces widespread imprecision in branch site recognition.
- Limited changes in 3' splice site selection suggest a positive role for SUGP1 in early branch site choice.
- These findings expand the understanding of the physiological consequences of this oncogenic SF3B1 mutation.
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