Characterizing ZC3H18, a Multi-domain Protein at the Interface of RNA Production and Destruction Decisions
Kinga Winczura,
Manfred Schmid,
Claudia Iasillo,
Kelly R. Molloy,
Lea Mørch Harder,
Jens S. Andersen,
John LaCava,
Torben Heick Jensen
Affiliations
Kinga Winczura
Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark; Laboratory of Cellular and Structural Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
Manfred Schmid
Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
Claudia Iasillo
Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
Kelly R. Molloy
Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
Lea Mørch Harder
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
Jens S. Andersen
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
John LaCava
Laboratory of Cellular and Structural Biology, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
Torben Heick Jensen
Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark; Corresponding author
Summary: Nuclear RNA metabolism is influenced by protein complexes connecting to both RNA-productive and -destructive pathways. The ZC3H18 protein binds the cap-binding complex (CBC), universally present on capped RNAs, while also associating with the nuclear exosome targeting (NEXT) complex, linking to RNA decay. To dissect ZC3H18 function, we conducted interaction screening and mutagenesis of the protein, which revealed a phosphorylation-dependent isoform. Surprisingly, the modified region of ZC3H18 associates with core histone proteins. Further examination of ZC3H18 function, by genome-wide analyses, demonstrated its impact on transcription of a subset of protein-coding genes. This activity requires the CBC-interacting domain of the protein, with some genes being also dependent on the NEXT- and/or histone-interacting domains. Our data shed light on the domain requirements of a protein positioned centrally in nuclear RNA metabolism, and they suggest that post-translational modification may modulate its function. : The ZC3H18 protein is involved in RNA decay mediated by the CBC-NEXT complex. Winczura et al. identify a phosphorylation-dependent interaction of ZC3H18 with histones, and they find separate CBCA-, NEXT-, and histone-binding domains. They suggest a role for ZC3H18 in mRNA biogenesis, which for some genes is independent of its role in RNA decay. Keywords: ZC3H18, NEXT, CBC, RNA exosome, histones, transcription, RNA decay
