Abstract
AATF is a central regulator of the cellular outcome upon p53 activation, a finding that has primarily been attributed to its function as a transcription factor. Recent data showed that AATF is essential for ribosome biogenesis and plays a role in rRNA maturation. AATF has been implicated to fulfil this role through direct interaction with rRNA and was identified in several RNA-interactome capture experiments. Here, we provide a first comprehensive analysis of the RNA bound by AATF using CLIP-sequencing. Interestingly, this approach shows predominant binding of the 45S pre-ribosomal RNA precursor molecules. Furthermore, AATF binds to mRNAs encoding for ribosome biogenesis factors as well as snoRNAs. These findings are complemented by an in-depth analysis of the protein interactome of AATF containing a large set of proteins known to play a role in rRNA maturation with an emphasis on the protein-RNA-complexes known to be required for the generation of the small ribosomal subunit (SSU). In line with this finding, the binding sites of AATF within the 45S rRNA precursor localize in close proximity to the SSU cleavage sites. Consequently, our multilayer analysis of the protein-RNA interactome of AATF reveals this protein to be an important hub for protein and RNA interactions involved in ribosome biogenesis.
Highlights
The apoptosis antagonizing transcription factor (AATF), known as Che-1, was originally identified as an RNA polymerase II interacting protein with anti-apoptotic capacities
In order to confirm this finding and to show it is not limited to our experiment we screened for the presence of AATF in published RNA interactome capture (RIC) datasets
In order to confirm its binding to RNA and to determine the identity of the RNA molecules bound to AATF, we analyzed enhanced crosslinking and immunoprecipitation data generated by the ENCODE consortium[30]
Summary
The apoptosis antagonizing transcription factor (AATF), known as Che-1, was originally identified as an RNA polymerase II interacting protein with anti-apoptotic capacities. It is important to note that AATF was recently identified by independent RNAi screens for factors involved in ribosomal subunit production and rRNA processing[15,16]. This connection is interesting due to two considerations. We confirmed AATF to be an RNA-binding protein and extended the analysis to a comprehensive characterization of its RNA-interactome using RNA-sequencing of its targets after crosslinking and immunoprecipitation (eCLIP-seq)
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