Sudemycin E influences alternative splicing and changes chromatin modifications

Paolo Convertini,Gustavo Palacios,Chandraiah Lagisetti,Stefan Stamm,Pierre De La Grange,Yvonne N Fondufe-Mittendorf,Thomas R Webb,Philip M Potter,Manli Shen,Craig Horbinski

doi:10.1093/nar/gku151

Abstract

Sudemycin E is an analog of the pre-messenger RNA splicing modulator FR901464 and its derivative spliceostatin A. Sudemycin E causes the death of cancer cells through an unknown mechanism. We found that similar to spliceostatin A, sudemycin E binds to the U2 small nuclear ribonucleoprotein (snRNP) component SF3B1. Native chromatin immunoprecipitations showed that U2 snRNPs physically interact with nucleosomes. Sudemycin E induces a dissociation of the U2 snRNPs and decreases their interaction with nucleosomes. To determine the effect on gene expression, we performed genome-wide array analysis. Sudemycin E first causes a rapid change in alternative pre-messenger RNA splicing, which is later followed by changes in overall gene expression and arrest in the G2 phase of the cell cycle. The changes in alternative exon usage correlate with a loss of the H3K36me3 modification in chromatin encoding these exons. We propose that sudemycin E interferes with the ability of U2 snRNP to maintain an H3K36me3 modification in actively transcribed genes. Thus, in addition to the reversible changes in alternative splicing, sudemycin E causes changes in chromatin modifications that result in chromatin condensation, which is a likely contributing factor to cancer cell death.

Highlights

Almost all human polymerase II transcripts undergo alternative pre-messenger RNA splicing, which increases the number of proteins that can be encoded in the genome
Sudemycin E binds to SF3B1 and is toxic for some cancer cells
Sudemycin E (Figure 1A, left) is chemically related to spliceostatin A, a methylated derivative of FR901464, which is a natural product that binds to the U2 component SF3B1 and modulates splicing [19]

Summary

Introduction

Almost all human polymerase II transcripts undergo alternative pre-messenger RNA (pre-mRNA) splicing, which increases the number of proteins that can be encoded in the genome. U1 snRNP binds to the 50 splice site, followed by binding of splicing factor 1 to the branch point, which increases U2AF binding to the 30 splice site, stabilizing the entry of U2 snRNP and the release of splicing factor 1. In this spliceosomal A complex, the branch point adenosine is recognized by the U2 snRNP through an interaction between the U2 component SF3B1/(SAP155) and U2AF [2]. The U2 snRNP undergoes structural changes during the splicing reaction and releases its SF3 complex after the first catalytic splicing step [4]

Methods

Results

Conclusion