IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events

Rina Fujiwara; Si-Nan Zhai; Dongming Liang; Aayushi P Shah; Matthew Tracey; Xu-Kai Ma; Christopher J Fields; María Saraí Mendoza-Figueroa; Michele C Meline; Deirdre C Tatomer; Li Yang; Jeremy E Wilusz

doi:10.1016/j.molcel.2023.10.035

IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events

Mol Cell. 2023 Dec 21;83(24):4445-4460.e7. doi: 10.1016/j.molcel.2023.10.035. Epub 2023 Nov 22.

Affiliations

¹ Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
² Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
³ Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
⁴ Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
⁵ Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: jeremy.wilusz@bcm.edu.

PMID: 37995689
PMCID: PMC10841813 (available on 2024-12-21)
DOI: 10.1016/j.molcel.2023.10.035

Abstract

The metazoan-specific Integrator complex catalyzes 3' end processing of small nuclear RNAs (snRNAs) and premature termination that attenuates the transcription of many protein-coding genes. Integrator has RNA endonuclease and protein phosphatase activities, but it remains unclear if both are required for complex function. Here, we show IntS6 (Integrator subunit 6) over-expression blocks Integrator function at a subset of Drosophila protein-coding genes, although having no effect on snRNAs or attenuation of other loci. Over-expressed IntS6 titrates protein phosphatase 2A (PP2A) subunits, thereby only affecting gene loci where phosphatase activity is necessary for Integrator function. IntS6 functions analogous to a PP2A regulatory B subunit as over-expression of canonical B subunits, which do not bind Integrator, is also sufficient to inhibit Integrator activity. These results show that the phosphatase module is critical at only a subset of Integrator-regulated genes and point to PP2A recruitment as a tunable step that modulates transcription termination efficiency.

Keywords: 3′ end processing; INTAC; Integrator complex; Integrator subunit 6; PP2A; RNA polymerase II; promoter-proximal termination; protein phosphatase 2A; snRNA; transcription.

MeSH terms

Animals
Drosophila Proteins* / metabolism
Drosophila melanogaster
RNA
RNA Polymerase II / genetics
RNA Polymerase II / metabolism
RNA, Small Nuclear / genetics
Transcription Factors / metabolism
Transcription Termination, Genetic*

Substances

RNA
RNA Polymerase II
RNA, Small Nuclear
Transcription Factors
Drosophila Proteins

Grants and funding

R35 GM119735/GM/NIGMS NIH HHS/United States