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Sofi S, Coverley D. CIZ1 in Xist seeded assemblies at the inactive X chromosome. Front Cell Dev Biol 2023; 11:1296600. [PMID: 38155839 PMCID: PMC10753822 DOI: 10.3389/fcell.2023.1296600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/04/2023] [Indexed: 12/30/2023] Open
Abstract
There is growing evidence that X-chromosome inactivation is driven by phase-separated supramolecular assemblies. However, among the many proteins recruited to the inactive X chromosome by Xist long non-coding RNA, so far only a minority (CIZ1, CELF1, SPEN, TDP-43, MATR3, PTBP1, PCGF5) have been shown to form Xist-seeded protein assemblies, and of these most have not been analyzed in detail. With focus on CIZ1, here we describe 1) the contribution of intrinsically disordered regions in RNA-dependent protein assembly formation at the inactive X chromosome, and 2) enrichment, distribution, and function of proteins within Xist-seeded assemblies.
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Affiliation(s)
- Sajad Sofi
- Department of Biology, University of York, York, United Kingdom
| | - Dawn Coverley
- Department of Biology, University of York, York, United Kingdom
- York Biomedical Research Institute, University of York, York, United Kingdom
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2
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Dobbs OG, Wilson RHC, Newling K, Ainscough JFX, Coverley D. Epigenetic instability caused by absence of CIZ1 drives transformation during quiescence cycles. BMC Biol 2023; 21:175. [PMID: 37580709 PMCID: PMC10426085 DOI: 10.1186/s12915-023-01671-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Cip1-interacting zinc finger protein 1 (CIZ1) forms RNA-dependent protein assemblies that stabilise epigenetic state, notable at the inactive X chromosome in females. CIZ1 has been linked with a range of human cancers and in mice genetic deletion of CIZ1 manifests as hyperproliferative lymphoid lineages in females. This suggests that its role in maintenance of epigenetic stability is linked with disease. RESULTS Here, we show that male and female CIZ1-null primary murine fibroblasts have reduced H4K20me1 and that this compromises nuclear condensation on entry to quiescence. Global transcriptional repression remains intact in condensation-deficient CIZ1-null cells; however, a subset of genes linked with chromatin condensation and homology-directed DNA repair are perturbed. Failure to condense is phenotypically mimicked by manipulation of the H4K20me1 methyltransferase, SET8, in WT cells and partially reverted in CIZ1-null cells upon re-expression of CIZ1. Crucially, during exit from quiescence, nuclear decondensation remains active, so that repeated entry and exit cycles give rise to expanded nuclei susceptible to mechanical stress, DNA damage checkpoint activation, and downstream emergence of transformed proliferative colonies. CONCLUSIONS Our results demonstrate a role for CIZ1 in chromatin condensation on entry to quiescence and explore the consequences of this defect in CIZ1-null cells. Together, the data show that CIZ1's protection of the epigenome guards against genome instability during quiescence cycles. This identifies loss of CIZ1 as a potentially devastating vulnerability in cells that undergo cycles of quiescence entry and exit.
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Affiliation(s)
- Olivia G Dobbs
- Department of Biology, University of York, York, YO10 5DD, UK.
- York Biomedical Research Institute, University of York, York, UK.
| | - Rosemary H C Wilson
- Department of Biology, University of York, York, YO10 5DD, UK
- Exact Sciences Innovation, The Sherard Building, Oxford Science Park, Edmund Halley Rd, Oxford, OX4 4DQ, UK
| | - Katherine Newling
- Department of Biology, University of York, York, YO10 5DD, UK
- Genomics and Bioinformatics Laboratory, Bioscience Technology Facility, University of York, York, YO10 5DD, UK
| | | | - Dawn Coverley
- Department of Biology, University of York, York, YO10 5DD, UK
- York Biomedical Research Institute, University of York, York, UK
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Sofi S, Williamson L, Turvey GL, Scoynes C, Hirst C, Godwin J, Brockdorff N, Ainscough J, Coverley D. Prion-like domains drive CIZ1 assembly formation at the inactive X chromosome. J Biophys Biochem Cytol 2022; 221:213067. [PMID: 35289833 PMCID: PMC8927971 DOI: 10.1083/jcb.202103185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/11/2021] [Accepted: 12/10/2021] [Indexed: 12/30/2022] Open
Abstract
CIZ1 forms large assemblies at the inactive X chromosome (Xi) in female fibroblasts in an Xist lncRNA-dependent manner and is required for accurate maintenance of polycomb targets genome-wide. Here we address requirements for assembly formation and show that CIZ1 undergoes two direct interactions with Xist, via independent N- and C-terminal domains. Interaction with Xist, assembly at Xi, and complexity of self-assemblies formed in vitro are modulated by two alternatively spliced glutamine-rich prion-like domains (PLD1 and 2). PLD2 is dispensable for accumulation at existing CIZ1-Xi assemblies in wild-type cells but is required in CIZ1-null cells where targeting, assembly, and enrichment for H3K27me3 and H2AK119ub occur de novo. In contrast, PLD1 is required for both de novo assembly and accumulation at preexisting assemblies and, in vitro, drives formation of a stable fibrillar network. Together they impart affinity for RNA and a complex relationship with repeat E of Xist. These data show that alternative splicing of two PLDs modulates CIZ1's ability to build large RNA-protein assemblies.
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Affiliation(s)
- Sajad Sofi
- Department of Biology, University of York, York, UK.,York Biomedical Research Institute, University of York, York, UK
| | - Louisa Williamson
- Department of Biology, University of York, York, UK.,York Biomedical Research Institute, University of York, York, UK
| | - Gabrielle L Turvey
- Department of Biology, University of York, York, UK.,York Biomedical Research Institute, University of York, York, UK
| | - Charlotte Scoynes
- Department of Biology, University of York, York, UK.,College of Science and Engineering, University of Edinburgh, Edinburgh, UK
| | - Claire Hirst
- Department of Biology, University of York, York, UK
| | - Jonathan Godwin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Justin Ainscough
- Department of Biology, University of York, York, UK.,York Biomedical Research Institute, University of York, York, UK
| | - Dawn Coverley
- Department of Biology, University of York, York, UK.,York Biomedical Research Institute, University of York, York, UK
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Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Nat Commun 2020; 11:6053. [PMID: 33247132 PMCID: PMC7695720 DOI: 10.1038/s41467-020-19879-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Firre encodes a lncRNA involved in nuclear organization. Here, we show that Firre RNA expressed from the active X chromosome maintains histone H3K27me3 enrichment on the inactive X chromosome (Xi) in somatic cells. This trans-acting effect involves SUZ12, reflecting interactions between Firre RNA and components of the Polycomb repressive complexes. Without Firre RNA, H3K27me3 decreases on the Xi and the Xi-perinucleolar location is disrupted, possibly due to decreased CTCF binding on the Xi. We also observe widespread gene dysregulation, but not on the Xi. These effects are measurably rescued by ectopic expression of mouse or human Firre/FIRRE transgenes, supporting conserved trans-acting roles. We also find that the compact 3D structure of the Xi partly depends on the Firre locus and its RNA. In common lymphoid progenitors and T-cells Firre exerts a cis-acting effect on maintenance of H3K27me3 in a 26 Mb region around the locus, demonstrating cell type-specific trans- and cis-acting roles of this lncRNA.
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Sun G, Ding XA, Argaw Y, Guo X, Montell DJ. Akt1 and dCIZ1 promote cell survival from apoptotic caspase activation during regeneration and oncogenic overgrowth. Nat Commun 2020; 11:5726. [PMID: 33184261 PMCID: PMC7664998 DOI: 10.1038/s41467-020-19068-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2020] [Indexed: 01/07/2023] Open
Abstract
Apoptosis is an ancient and evolutionarily conserved cell suicide program. During apoptosis, executioner caspase enzyme activation has been considered a point of no return. However, emerging evidence suggests that some cells can survive caspase activation following exposure to apoptosis-inducing stresses, raising questions as to the physiological significance and underlying molecular mechanisms of this unexpected phenomenon. Here, we show that, following severe tissue injury, Drosophila wing disc cells that survive executioner caspase activation contribute to tissue regeneration. Through RNAi screening, we identify akt1 and a previously uncharacterized Drosophila gene CG8108, which is homologous to the human gene CIZ1, as essential for survival from the executioner caspase activation. We also show that cells expressing activated oncogenes experience apoptotic caspase activation, and that Akt1 and dCIZ1 are required for their survival and overgrowth. Thus, survival following executioner caspase activation is a normal tissue repair mechanism usurped to promote oncogene-driven overgrowth.
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Affiliation(s)
- Gongping Sun
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA.
| | - Xun Austin Ding
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA
| | - Yewubdar Argaw
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA
| | - Xiaoran Guo
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA
| | - Denise J Montell
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, CA, 93106, USA.
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Identification of DHX9 as a cell cycle regulated nucleolar recruitment factor for CIZ1. Sci Rep 2020; 10:18103. [PMID: 33093612 PMCID: PMC7582970 DOI: 10.1038/s41598-020-75160-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/12/2020] [Indexed: 11/15/2022] Open
Abstract
CIP1-interacting zinc finger protein 1 (CIZ1) is a nuclear matrix associated protein that facilitates a number of nuclear functions including initiation of DNA replication, epigenetic maintenance and associates with the inactive X-chromosome. Here, to gain more insight into the protein networks that underpin this diverse functionality, molecular panning and mass spectrometry are used to identify protein interaction partners of CIZ1, and CIZ1 replication domain (CIZ1-RD). STRING analysis of CIZ1 interaction partners identified 2 functional clusters: ribosomal subunits and nucleolar proteins including the DEAD box helicases, DHX9, DDX5 and DDX17. DHX9 shares common functions with CIZ1, including interaction with XIST long-non-coding RNA, epigenetic maintenance and regulation of DNA replication. Functional characterisation of the CIZ1-DHX9 complex showed that CIZ1-DHX9 interact in vitro and dynamically colocalise within the nucleolus from early to mid S-phase. CIZ1-DHX9 nucleolar colocalisation is dependent upon RNA polymerase I activity and is abolished by depletion of DHX9. In addition, depletion of DHX9 reduced cell cycle progression from G1 to S-phase in mouse fibroblasts. The data suggest that DHX9-CIZ1 are required for efficient cell cycle progression at the G1/S transition and that nucleolar recruitment is integral to their mechanism of action.
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Sprague D, Waters SA, Kirk JM, Wang JR, Samollow PB, Waters PD, Calabrese JM. Nonlinear sequence similarity between the Xist and Rsx long noncoding RNAs suggests shared functions of tandem repeat domains. RNA (NEW YORK, N.Y.) 2019; 25:1004-1019. [PMID: 31097619 PMCID: PMC6633197 DOI: 10.1261/rna.069815.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/14/2019] [Indexed: 05/30/2023]
Abstract
The marsupial inactive X chromosome expresses a long noncoding RNA (lncRNA) called Rsx that has been proposed to be the functional analog of eutherian Xist Despite the possibility that Xist and Rsx encode related functions, the two lncRNAs harbor no linear sequence similarity. However, both lncRNAs harbor domains of tandemly repeated sequence. In Xist, these repeat domains are known to be critical for function. Using k-mer based comparison, we show that the repeat domains of Xist and Rsx unexpectedly partition into two major clusters that each harbor substantial levels of nonlinear sequence similarity. Xist Repeats B, C, and D were most similar to each other and to Rsx Repeat 1, whereas Xist Repeats A and E were most similar to each other and to Rsx Repeats 2, 3, and 4. Similarities at the level of k-mers corresponded to domain-specific enrichment of protein-binding motifs. Within individual domains, protein-binding motifs were often enriched to extreme levels. Our data support the hypothesis that Xist and Rsx encode similar functions through different spatial arrangements of functionally analogous protein-binding domains. We propose that the two clusters of repeat domains in Xist and Rsx function in part to cooperatively recruit PRC1 and PRC2 to chromatin. The physical manner in which these domains engage with protein cofactors may be just as critical to the function of the domains as the protein cofactors themselves. The general approaches we outline in this report should prove useful in the study of any set of RNAs.
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Affiliation(s)
- Daniel Sprague
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Shafagh A Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales 2052, Australia
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jessime M Kirk
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jeremy R Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Paul B Samollow
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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