The RNA Polymerase II Factor RPAP1 Is Critical for Mediator-Driven Transcription and Cell Identity

Cian J Lynch; Raquel Bernad; Isabel Calvo; Sandrina Nóbrega-Pereira; Sergio Ruiz; Nuria Ibarz; Ana Martinez-Val; Osvaldo Graña-Castro; Gonzalo Gómez-López; Eduardo Andrés-León; Vladimir Espinosa Angarica; Antonio Del Sol; Sagrario Ortega; Oscar Fernandez-Capetillo; Enrique Rojo; Javier Munoz; Manuel Serrano

doi:10.1016/j.celrep.2017.12.062

The RNA Polymerase II Factor RPAP1 Is Critical for Mediator-Driven Transcription and Cell Identity

Cell Rep. 2018 Jan 9;22(2):396-410. doi: 10.1016/j.celrep.2017.12.062.

Authors

Cian J Lynch¹, Raquel Bernad¹, Isabel Calvo², Sandrina Nóbrega-Pereira³, Sergio Ruiz⁴, Nuria Ibarz⁵, Ana Martinez-Val⁵, Osvaldo Graña-Castro⁶, Gonzalo Gómez-López⁶, Eduardo Andrés-León⁷, Vladimir Espinosa Angarica⁸, Antonio Del Sol⁹, Sagrario Ortega¹⁰, Oscar Fernandez-Capetillo¹¹, Enrique Rojo¹², Javier Munoz⁵, Manuel Serrano¹³

Affiliations

¹ Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Cellular Plasticity and Disease Group, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.
² Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
³ Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal.
⁴ Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
⁵ ProteoRed-ISCIII Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
⁶ Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
⁷ Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Bioinformatics Unit, Institute of Parasitology and Biomedicine Lopez-Neyra, Granada 18016, Spain.
⁸ Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; Cancer Science Institute, National University of Singapore, Singapore 117599, Singapore.
⁹ Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg.
¹⁰ Transgenic Mouse Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
¹¹ Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 171 21, Sweden.
¹² Department of Plant Molecular Genetics, National Center of Biotechnology (CNB-CSIC), Madrid 280049, Spain.
¹³ Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Cellular Plasticity and Disease Group, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain. Electronic address: [email protected].

Abstract

The RNA polymerase II-associated protein 1 (RPAP1) is conserved across metazoa and required for stem cell differentiation in plants; however, very little is known about its mechanism of action or its role in mammalian cells. Here, we report that RPAP1 is essential for the expression of cell identity genes and for cell viability. Depletion of RPAP1 triggers cell de-differentiation, facilitates reprogramming toward pluripotency, and impairs differentiation. Mechanistically, we show that RPAP1 is essential for the interaction between RNA polymerase II (RNA Pol II) and Mediator, as well as for the recruitment of important regulators, such as the Mediator-specific RNA Pol II factor Gdown1 and the C-terminal domain (CTD) phosphatase RPAP2. In agreement, depletion of RPAP1 diminishes the loading of total and Ser5-phosphorylated RNA Pol II on many genes, with super-enhancer-driven genes among the most significantly downregulated. We conclude that Mediator/RPAP1/RNA Pol II is an ancient module, conserved from plants to mammals, critical for establishing and maintaining cell identity.

Keywords: Mediator; RNA polymerase II; cell identity; differentiation; enhancer; interactome; transcription.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
RNA Polymerase II / genetics*
Transcription, Genetic / genetics*

Substances

RNA Polymerase II