Received: 7 August 2018 | Accepted: 14 September 2018 DOI: 10.1002/jcb.27843 RESEARCH ARTICLE Interactome analysis of the human Cap‐specific mRNA (nucleoside‐2′‐O‐)‐methyltransferase 1 (hMTr1) protein Fernando Moreira Simabuco 1,2 | Isadora Carolina Betim Pavan 2 | Nathalie Fortes Pestana 2,4 | Paulo Costa Carvalho 3 | Fernanda Luisa Basei 3 | Daniela Campos Granato 1 | Adriana Franco Paes Leme 1 | Nilson Ivo Tonin Zanchin 3 1 Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas SP, Brazil 2 Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas, Limeira SP, Brazil 3 Instituto Carlos Chagas, Fundação Oswaldo Cruz—FIOCRUZ, Curitiba, Brazil 4 Centro Universitário da Fundação Hermínio Ometto‐FHO, Araras SP, Brazil Correspondence Fernando Moreira Simabuco, Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas, R. Pedro Zaccaria, 1300, Limeira SP, CEP 13484‐350, Brazil. E‐mail: simabuco@gmail.com Funding information Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), Grant/ Award Number: 2012/13558‐7; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Grant/Award Number: 447553/2014‐3; PAPES/ Fundação Oswaldo Cruz (FIOCRUZ); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Abstract In a previous study, we have shown that the gene promoter of a protein termed KIAA0082 is regulated by interferon and that this protein interacts with the RNA polymerase II. It has been subsequently shown that KIAA0082 is the human cap‐ specific messenger RNA (mRNA) (nucleoside‐2′‐O‐)‐methyltransferase 1 (hMTr1), which catalyzes methylation of the 2′‐O‐ribose of the first nucleotide of capped mRNAs. Pre‐mRNAs are cotranscriptionally processed, requiring coordinate interactions or dissociations of hundreds of proteins. hMTr1 potentially binds to the 5′‐end of the whole cellular pre‐mRNA pool. Besides, it contains a WW protein interaction domain and thus is expected to be associated with several proteins. In this current study, we determined the composition of complexes isolated by hMTr1 immunoprecipitation from HEK293 cellular extracts. Consistently, a large set of proteins that function in pre‐mRNA maturation was identified, including splicing factors, spliceosome‐associated proteins, RNA helicases, heterogeneous nuclear ribonucleoproteins (HNRNPs), RNA‐binding proteins and proteins involved in mRNA 5′‐ and 3′‐end processing, forming an extensive interaction network. In total, 137 proteins were identified in two independent experiments, and some of them were validated by immunoblotting and immunofluorescence. Besides, we further characterized the nature of several hMTr1 interactions, showing that some are RNA dependent, including PARP1, ILF2, XRCC6, eIF2α, and NCL, and others are RNA independent, including FXR1, NPM1, PPM1B, and PRMT5. The data presented here are consistent with the important role played by hMTr1 in pre‐mRNA synthesis. KEYWORDS human cap‐specific messenger RNA (mRNA) (nucleoside‐2′‐O‐)‐methyltransferase 1 (hMTr1)/ ISG95/CMTR1, interactome, pre‐mRNA processing, pre‐mRNA ribonucleoprotein complexes, pre‐mRNA splicing 1 | INTRODUCTION The human cap‐specific messenger RNA (mRNA) (nucleo- side‐2′‐O‐)‐methyltransferase 1 (hMTr1) was initially known as the uncharacterized protein KIAA0082 and drew attention years ago in gene expression studies showing that it was upregulated in chimpanzees and cell lines infected with hepatitis C virus, 1-3 in HeLa cells infected with vaccinia J Cell Biochem. 2018;1-15. wileyonlinelibrary.com/journal/jcb © 2018 Wiley Periodicals, Inc. | 1