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Espejo-Serrano C, Aitken C, Tan BF, May DG, Chrisopulos RJ, Roux KJ, Demmers JA, Mackintosh SG, Gribnau J, Bustos F, Gontan C, Findlay GM. Chromatin targeting of the RNF12/RLIM E3 ubiquitin ligase controls transcriptional responses. Life Sci Alliance 2024; 7:e202302282. [PMID: 38199845 PMCID: PMC10781586 DOI: 10.26508/lsa.202302282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Protein ubiquitylation regulates key biological processes including transcription. This is exemplified by the E3 ubiquitin ligase RNF12/RLIM, which controls developmental gene expression by ubiquitylating the REX1 transcription factor and is mutated in an X-linked intellectual disability disorder. However, the precise mechanisms by which ubiquitylation drives specific transcriptional responses are not known. Here, we show that RNF12 is recruited to specific genomic locations via a consensus sequence motif, which enables co-localisation with REX1 substrate at gene promoters. Surprisingly, RNF12 chromatin recruitment is achieved via a non-catalytic basic region and comprises a previously unappreciated N-terminal autoinhibitory mechanism. Furthermore, RNF12 chromatin targeting is critical for REX1 ubiquitylation and downstream RNF12-dependent gene regulation. Our results demonstrate a key role for chromatin in regulation of the RNF12-REX1 axis and provide insight into mechanisms by which protein ubiquitylation enables programming of gene expression.
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Affiliation(s)
- Carmen Espejo-Serrano
- https://ror.org/01zg1tt02 MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Catriona Aitken
- https://ror.org/01zg1tt02 MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Beatrice F Tan
- https://ror.org/018906e22 Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Danielle G May
- https://ror.org/00sfn8y78 Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
| | - Rachel J Chrisopulos
- https://ror.org/00sfn8y78 Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
| | - Kyle J Roux
- https://ror.org/00sfn8y78 Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | - Jeroen Aa Demmers
- https://ror.org/018906e22 Proteomics Center and Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Joost Gribnau
- https://ror.org/018906e22 Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francisco Bustos
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
- https://ror.org/00sfn8y78 Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | - Cristina Gontan
- https://ror.org/018906e22 Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Greg M Findlay
- https://ror.org/01zg1tt02 MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
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2
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Bustos F, Mathur S, Espejo-Serrano C, Toth R, Hastie CJ, Virdee S, Findlay GM. Activity-based probe profiling of RNF12 E3 ubiquitin ligase function in Tonne-Kalscheuer syndrome. Life Sci Alliance 2022; 5:e202101248. [PMID: 35764390 PMCID: PMC9240097 DOI: 10.26508/lsa.202101248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Ubiquitylation enzymes are involved in all aspects of eukaryotic biology and are frequently disrupted in disease. One example is the E3 ubiquitin ligase RNF12/RLIM, which is mutated in the developmental disorder Tønne-Kalscheuer syndrome (TOKAS). RNF12 TOKAS variants largely disrupt catalytic E3 ubiquitin ligase activity, which presents a pressing need to develop approaches to assess the impact of variants on RNF12 activity in patients. Here, we use photocrosslinking activity-based probes (photoABPs) to monitor RNF12 RING E3 ubiquitin ligase activity in normal and pathogenic contexts. We demonstrate that photoABPs undergo UV-induced labelling of RNF12 that is consistent with its RING E3 ligase activity. Furthermore, photoABPs robustly report the impact of RNF12 TOKAS variants on E3 activity, including variants within the RING domain and distal non-RING regulatory elements. Finally, we show that this technology can be rapidly deployed in human pluripotent stem cells. In summary, photoABPs are versatile tools that can directly identify disruptions to RING E3 ubiquitin ligase activity in human disease, thereby providing new insight into pathogenic mechanisms.
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Affiliation(s)
- Francisco Bustos
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Sunil Mathur
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Carmen Espejo-Serrano
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Rachel Toth
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - C James Hastie
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Satpal Virdee
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Greg M Findlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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Wang F, Gervasi MG, Bošković A, Sun F, Rinaldi VD, Yu J, Wallingford MC, Tourzani DA, Mager J, Zhu LJ, Rando OJ, Visconti PE, Strittmatter L, Bach I. Deficient spermiogenesis in mice lacking Rlim. eLife 2021; 10:e63556. [PMID: 33620316 PMCID: PMC7935487 DOI: 10.7554/elife.63556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
The X-linked gene Rlim plays major roles in female mouse development and reproduction, where it is crucial for the maintenance of imprinted X chromosome inactivation in extraembryonic tissues of embryos. However, while females carrying a systemic Rlim knockout (KO) die around implantation, male Rlim KO mice appear healthy and are fertile. Here, we report an important role for Rlim in testis where it is highly expressed in post-meiotic round spermatids as well as in Sertoli cells. Systemic deletion of the Rlim gene results in lower numbers of mature sperm that contains excess cytoplasm, leading to decreased sperm motility and in vitro fertilization rates. Targeting the conditional Rlim cKO specifically to the spermatogenic cell lineage largely recapitulates this phenotype. These results reveal functions of Rlim in male reproduction specifically in round spermatids during spermiogenesis.
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Affiliation(s)
- Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Maria Gracia Gervasi
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Ana Bošković
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Fengyun Sun
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Vera D Rinaldi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Mary C Wallingford
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Darya A Tourzani
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Jesse Mager
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Pablo E Visconti
- Department of Veterinary & Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Lara Strittmatter
- Electron Microscopy Core, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical SchoolWorcesterUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
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Palmer EE, Carroll R, Shaw M, Kumar R, Minoche AE, Leffler M, Murray L, Macintosh R, Wright D, Troedson C, McKenzie F, Townshend S, Ward M, Nawaz U, Ravine A, Runke CK, Thorland EC, Hummel M, Foulds N, Pichon O, Isidor B, Le Caignec C, Demeer B, Andrieux J, Albarazi SH, Bye A, Sachdev R, Kirk EP, Cowley MJ, Field M, Gecz J. RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features. Am J Hum Genet 2020; 107:1157-1169. [PMID: 33159883 PMCID: PMC7820564 DOI: 10.1016/j.ajhg.2020.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Interpretation of the significance of maternally inherited X chromosome variants in males with neurocognitive phenotypes continues to present a challenge to clinical geneticists and diagnostic laboratories. Here we report 14 males from 9 families with duplications at the Xq13.2-q13.3 locus with a common facial phenotype, intellectual disability (ID), distinctive behavioral features, and a seizure disorder in two cases. All tested carrier mothers had normal intelligence. The duplication arose de novo in three mothers where grandparental testing was possible. In one family the duplication segregated with ID across three generations. RLIM is the only gene common to our duplications. However, flanking genes duplicated in some but not all the affected individuals included the brain-expressed genes NEXMIF, SLC16A2, and the long non-coding RNA gene FTX. The contribution of the RLIM-flanking genes to the phenotypes of individuals with different size duplications has not been fully resolved. Missense variants in RLIM have recently been identified to cause X-linked ID in males, with heterozygous females typically having normal intelligence and highly skewed X chromosome inactivation. We detected consistent and significant increase of RLIM mRNA and protein levels in cells derived from seven affected males from five families with the duplication. Subsequent analysis of MDM2, one of the targets of the RLIM E3 ligase activity, showed consistent downregulation in cells from the affected males. All the carrier mothers displayed normal RLIM mRNA levels and had highly skewed X chromosome inactivation. We propose that duplications at Xq13.2-13.3 including RLIM cause a recognizable but mild neurocognitive phenotype in hemizygous males.
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Affiliation(s)
- Elizabeth E Palmer
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia; School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia; Kinghorn Centre for Clinical Genomics, Garvan Institute, Darlinghurst, Sydney, NSW 2010, Australia.
| | - Renee Carroll
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Raman Kumar
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Andre E Minoche
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Lucinda Murray
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | | | - Dale Wright
- Discipline of Genomic Medicine and Discipline of Child & Adolescent Health, University of Sydney, Sydney, NSW 2010, Australia; Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Chris Troedson
- Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Fiona McKenzie
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6009, Australia; Genetic Services of Western Australia, Perth, WA 6008, Australia
| | | | - Michelle Ward
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Urwah Nawaz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Anja Ravine
- Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Pathwest Laboratory Medicine WA, Perth, WA 6008, Australia
| | - Cassandra K Runke
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Marybeth Hummel
- West Virginia University School of Medicine, Department of Pediatrics, Section of Medical Genetics Morgantown, WV 26506-9600, USA
| | - Nicola Foulds
- Wessex Clinical Genetics Services, Southampton SO16 5YA, UK
| | - Olivier Pichon
- Service de génétique médicale - Unité de Génétique Clinique, CHU de Nantes - Hôtel Dieu, Nantes 44093, France
| | - Bertrand Isidor
- Service de génétique médicale - Unité de Génétique Clinique, CHU de Nantes - Hôtel Dieu, Nantes 44093, France
| | - Cédric Le Caignec
- Service de génétique médicale, Institut fédératif de Biologie, CHU Hopital Purpan, Toulouse 31059, France
| | - Bénédicte Demeer
- Center for Human Genetics, CLAD Nord de France, CHU Amiens-Picardie, Amiens 80080, France; CHIMERE EA 7516, University Picardie Jules Verne, Amiens 80025, France
| | - Joris Andrieux
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille 59000, France
| | | | - Ann Bye
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Rani Sachdev
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Edwin P Kirk
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW 2033, Australia
| | - Mike Field
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
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7
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Wang F, Bach I. Rlim/Rnf12, Rex1, and X Chromosome Inactivation. Front Cell Dev Biol 2019; 7:258. [PMID: 31737626 PMCID: PMC6834644 DOI: 10.3389/fcell.2019.00258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/16/2019] [Indexed: 12/28/2022] Open
Abstract
RLIM/Rnf12 is an E3 ubiquitin ligase that has originally been identified as a transcriptional cofactor associated with LIM domain transcription factors. Indeed, this protein modulates transcriptional activities and multiprotein complexes recruited by several classes of transcription factors thereby enhancing or repressing transcription. Around 10 years ago, RLIM/Rnf12 has been identified as a major regulator for the process of X chromosome inactivation (XCI), the transcriptional silencing of one of the two X chromosomes in female mice and ESCs. However, the precise roles of RLIM during XCI have been controversial. Here, we discuss the cellular and developmental functions of RLIM as an E3 ubiquitin ligase and its roles during XCI in conjunction with its target protein Rex1.
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Affiliation(s)
- Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States
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8
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Wang X, Rusin A, Walkey CJ, Lin JJ, Johnson DL. The RNA polymerase III repressor MAF1 is regulated by ubiquitin-dependent proteasome degradation and modulates cancer drug resistance and apoptosis. J Biol Chem 2019; 294:19255-19268. [PMID: 31645432 DOI: 10.1074/jbc.ra119.008849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/01/2019] [Indexed: 01/03/2023] Open
Abstract
MAF1 homolog, negative regulator of RNA polymerase III (MAF1) is a key repressor of RNA polymerase (pol) III-dependent transcription and functions as a tumor suppressor. Its expression is frequently down-regulated in primary human hepatocellular carcinomas (HCCs). However, this reduction in MAF1 protein levels does not correlate with its transcript levels, indicating that MAF1 is regulated post-transcriptionally. Here, we demonstrate that MAF1 is a labile protein whose levels are regulated through the ubiquitin-dependent proteasome pathway. We found that MAF1 ubiquitination is enhanced upon mTOR complex 1 (TORC1)-mediated phosphorylation at Ser-75. Moreover, we observed that the E3 ubiquitin ligase cullin 2 (CUL2) critically regulates MAF1 ubiquitination and controls its stability and subsequent RNA pol III-dependent transcription. Analysis of the phenotypic consequences of modulating either CUL2 or MAF1 protein expression revealed changes in actin cytoskeleton reorganization and altered sensitivity to doxorubicin-induced apoptosis. Repression of RNA pol III-dependent transcription by chemical inhibition or knockdown of BRF1 RNA pol III transcription initiation factor subunit (BRF1) enhanced HCC cell sensitivity to doxorubicin, suggesting that MAF1 regulates doxorubicin resistance in HCC by controlling RNA pol III-dependent transcription. Together, our results identify the ubiquitin proteasome pathway and CUL2 as important regulators of MAF1 levels. They suggest that decreases in MAF1 protein underlie chemoresistance in HCC and perhaps other cancers and point to an important role for MAF1 and RNA pol III-mediated transcription in chemosensitivity and apoptosis.
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Affiliation(s)
- Xianlong Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Aleksandra Rusin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Christopher J Walkey
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | | | - Deborah L Johnson
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
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