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Published on: June 8, 2018
DDX54 regulates transcriptome dynamics during DNA damage response
Miha Milek1, Koshi Imami1, Neelanjan Mukherjee1
1Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany.
Abstract:
The cellular response to genotoxic stress is mediated by a well-characterized network of DNA surveillance pathways. The contribution of post-transcriptional gene regulatory networks to the DNA damage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts upon exposure of human breast carcinoma cells to ionizing radiation (IR). Interestingly, more than 260 proteins, including many nucleolar proteins, showed increased binding to poly(A)+ RNA in IR-exposed cells. The functional analysis of DDX54, a candidate genotoxic stress responsive RNA helicase, revealed that this protein is an immediate-to-early DDR regulator required for the splicing efficacy of its target IR-induced pre-mRNAs. Upon IR exposure, DDX54 acts by increased interaction with a well-defined class of pre-mRNAs that harbor introns with weak acceptor splice sites, as well as by protein-protein contacts within components of U2 snRNP and spliceosomal B complex, resulting in lower intron retention and higher processing rates of its target transcripts. Because DDX54 promotes survival after exposure to IR, its expression and/or mutation rate may impact DDR-related pathologies. Our work indicates the relevance of many uncharacterized RBPs potentially involved in the DDR.
Insights
This study reveals that RNA-binding proteins (RBPs) play a crucial role in the DNA damage response (DDR). Specifically, the RNA helicase DDX54 enhances the splicing of pre-mRNAs, promoting cell survival after genotoxic stress.
Area of Science:
- Molecular Biology
- Cellular Biology
- Genetics
Background:
- The DNA damage response (DDR) is critical for maintaining genomic stability.
- Post-transcriptional gene regulation's role in the DDR is not well understood.
- RNA-binding proteins (RBPs) are key regulators of gene expression.
Purpose of the Study:
- To identify RBPs that interact with polyadenylated transcripts upon genotoxic stress.
- To investigate the function of the RNA helicase DDX54 in the DDR.
- To understand how DDX54 influences pre-mRNA splicing during DNA damage.
Main Methods:
- Systematic identification of RBPs binding to poly(A)+ RNA in human breast carcinoma cells exposed to ionizing radiation (IR).
- Functional analysis of DDX54, including its interactions and role in splicing.
- Assessment of DDX54's impact on cell survival after IR exposure.
Main Results:
- Over 260 proteins, including nucleolar proteins, increased their binding to poly(A)+ RNA after IR.
- DDX54 was identified as an immediate-to-early DDR regulator.
- DDX54 enhances splicing of IR-induced pre-mRNAs with weak acceptor splice sites, reducing intron retention and increasing processing rates.
- DDX54 promotes cell survival following IR exposure.
Conclusions:
- RBPs, particularly DDX54, are significant regulators of the DDR.
- DDX54's function in splicing is essential for efficient DNA damage repair and cell survival.
- Uncharacterized RBPs may represent novel targets for understanding and treating DDR-related pathologies.
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