CRL3ARMC5 ubiquitin ligase and Integrator phosphatase form parallel mechanisms to control early stages of RNA Pol II transcription

Roberta Cacioppo; Alexander Gillis; Iván Shlamovitz; Andrew Zeller; Daniela Castiblanco; Alastair Crisp; Benjamin Haworth; Angela Arabiotorre; Pegah Abyaneh; Yu Bao; Julian E Sale; Scott Berry; Ana Tufegdžić Vidaković

doi:10.1016/j.molcel.2024.11.024

CRL3^ARMC5 ubiquitin ligase and Integrator phosphatase form parallel mechanisms to control early stages of RNA Pol II transcription

Mol Cell. 2024 Dec 19;84(24):4808-4823.e13. doi: 10.1016/j.molcel.2024.11.024. Epub 2024 Dec 11.

Affiliations

¹ Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
² EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia; UNSW RNA Institute, University of New South Wales, Sydney, NSW, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia.
³ EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia; UNSW RNA Institute, University of New South Wales, Sydney, NSW, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia. Electronic address: [email protected].
⁴ Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. Electronic address: [email protected].

PMID: 39667934
DOI: 10.1016/j.molcel.2024.11.024

Abstract

Control of RNA polymerase II (RNA Pol II) through ubiquitylation is essential for the DNA-damage response. Here, we reveal a distinct ubiquitylation pathway in human cells, mediated by CRL3^ARMC5, that targets excessive and defective RNA Pol II molecules at the initial stages of the transcription cycle. Upon ARMC5 loss, RNA Pol II accumulates in the free pool and in the promoter-proximal zone but is not permitted into elongation. We identify Integrator subunit 8 (INTS8) as a gatekeeper preventing the release of excess RNA Pol II molecules into gene bodies. Combined loss of ARMC5 and INTS8 has detrimental effects on cell growth and results in the uncontrolled release of excessive RNA Pol II complexes into early elongation, many of which are transcriptionally incompetent and fail to reach the ends of genes. These findings uncover CRL3^ARMC5 and Integrator as two distinct pathways acting in parallel to monitor the quantity and quality of transcription complexes before they are licensed into elongation.

Keywords: ARMC5; CUL3; INTS8; Integrator; RNA polymerase II; elongation; pausing; promoter-proximal; transcription; ubiquitin.

MeSH terms

Cell Proliferation
HEK293 Cells
HeLa Cells
Humans
Phosphoprotein Phosphatases / genetics
Phosphoprotein Phosphatases / metabolism
Promoter Regions, Genetic
RNA Polymerase II* / genetics
RNA Polymerase II* / metabolism
Transcription Elongation, Genetic
Transcription, Genetic*
Ubiquitin-Protein Ligases* / genetics
Ubiquitin-Protein Ligases* / metabolism
Ubiquitination*

Substances

RNA Polymerase II
Ubiquitin-Protein Ligases
Phosphoprotein Phosphatases