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Kletzien OA, Wuttke DS, Batey RT. The RNA-Binding Domain of hnRNP U Extends beyond the RGG/RG Motifs. Biochemistry 2024. [PMID: 38329035 DOI: 10.1021/acs.biochem.3c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG motif within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV cross-linking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing 11 of these identified cross-link sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG motif is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG motif with RNA-binding properties comparable to those of the canonical RGG/RG motif. These RGG/RG motifs serve redundant functions, with neither serving as the primary RBD. While in isolation, each RGG/RG motif has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling the binding of most of the designed RNA set with low to midnanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlight the perils of a reductionist approach to defining biochemical activities in this system and pave the way for a detailed investigation of its RNA-binding specificity.
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Affiliation(s)
- Otto A Kletzien
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
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2
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Kletzien OA, Wuttke DS, Batey RT. The RNA-binding domain of hnRNP U extends beyond the RGG/RG motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558674. [PMID: 37786719 PMCID: PMC10541603 DOI: 10.1101/2023.09.20.558674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG element within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV crosslinking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing eleven of these identified crosslink sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG element is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG element with RNA-binding properties comparable to the canonical RGG/RG element. These RGG/RG elements serve redundant functions, with neither serving as the primary RBD. While in isolation each RGG/RG element has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling binding of most of the designed RNA set with low to mid-nanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlights the perils of a reductionist approach to defining biochemical activities in this system and paves the way for a detailed investigation of its RNA-binding specificity.
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Affiliation(s)
- Otto A. Kletzien
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T. Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
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3
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A lifelong duty: how Xist maintains the inactive X chromosome. Curr Opin Genet Dev 2022; 75:101927. [PMID: 35717799 PMCID: PMC9472561 DOI: 10.1016/j.gde.2022.101927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/10/2022] [Accepted: 05/14/2022] [Indexed: 11/22/2022]
Abstract
Female eutherians transcriptionally silence one X chromosome to balance gene dosage between the sexes. X-chromosome inactivation (XCI) is initiated by the lncRNA Xist, which assembles many proteins within the inactive X chromosome (Xi) to trigger gene silencing and heterochromatin formation. It is well established that gene silencing on the Xi is maintained through repressive epigenetic processes, including histone deacetylation and DNA methylation. Recent studies revealed a new mechanism where RNA-binding proteins that interact directly with the RNA contribute to the maintenance of Xist localization and gene silencing. In addition, a surprising plasticity of the Xi was uncovered with many genes becoming upregulated upon experimental deletion of Xist. Intriguingly, immune cells normally lose Xist from the Xi, suggesting that thisXist dependence is utilized in vivo to dynamically regulate gene expression from the Xi. These new studies expose fundamental regulatory mechanisms for the chromatin association of RNAs, highlight the need for studying the maintenance of XCI and Xist localization in a gene- and cell-type-specific manner, and are likely to have clinical impact.
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Cao L, Luo Y, Guo X, Liu S, Li S, Li J, Zhang Z, Zhao Y, Zhang Q, Gao F, Ji X, Gao X, Li Y, You F. SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs. PLoS Pathog 2022; 18:e1010599. [PMID: 35658050 PMCID: PMC9200321 DOI: 10.1371/journal.ppat.1010599] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/15/2022] [Accepted: 05/17/2022] [Indexed: 12/19/2022] Open
Abstract
Regulation of chromatin structure and accessibility determines the transcription activities of genes, which endows the host with function-specific patterns of gene expression. Upon viral infection, the innate immune responses provide the first line of defense, allowing rapid production of variegated antiviral cytokines. Knowledge on how chromatin accessibility is regulated during host defense against viral infection remains limited. Our previous work found that the nuclear matrix protein SAFA surveilled viral RNA and regulated antiviral immune genes expression. However, how SAFA regulates the specific induction of antiviral immune genes remains unknown. Here, through integration of RNA-seq, ATAC-seq and ChIP-seq assays, we found that the depletion of SAFA specifically decreased the chromatin accessibility, activation and expression of virus induced genes. And mutation assays suggested that the RNA-binding ability of SAFA was essential for its function in regulating antiviral chromatin accessibility. RIP-seq results showed that SAFA exclusively bound with antiviral related RNAs following viral infection. Further, we combined the CRISPR-Cas13d mediated RNA knockdown system with ATAC-qPCR, and demonstrated that the binding between SAFA and according antiviral RNAs specifically mediated the openness of the corresponding chromatin and following robust transcription of antiviral genes. Moreover, knockdown of these associated RNAs dampened the accessibility of related genes in an extranuclear signaling pathway dependent manner. Interestingly, VSV infection cleaved SAFA protein at the C-terminus which deprived its RNA binding ability for immune evasion. Thus, our results demonstrated that SAFA and the interacting RNA products collaborated and remodeled chromatin accessibility to facilitate antiviral innate immune responses. Regulation of chromatin opening and gene expression underlies a key point during host defense against viral infection, which endows the host with timely and effective antiviral gene expression patterns. We previously reported that the nuclear matrix protein SAFA surveils viral RNA and regulates antiviral immune genes expression. However, how SAFA regulates the expression and what determines the specific induction of antiviral immune genes remains unclear. Here, we used a combination of high-throughput sequencing technologies and found that SAFA and the interacting RNA products collaborated and specifically remodeled chromatin accessibility to facilitate antiviral immune genes expression. We also found that VSV infection cleaved SAFA protein at the C-terminus and deprived its RNA binding ability for immune evasion. Our study provides new insights into the mechanism by which chromatin remodeling facilitates the induction of antiviral immune genes.
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Affiliation(s)
- Lili Cao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Yujie Luo
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Xuefei Guo
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Shengde Liu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Siji Li
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Junhong Li
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zeming Zhang
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Yingchi Zhao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Qiao Zhang
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Feng Gao
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of life science, Shandong University, Qingdao, China
| | - Yunfei Li
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- * E-mail: (YL); (FY)
| | - Fuping You
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- * E-mail: (YL); (FY)
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Gene regulation in time and space during X-chromosome inactivation. Nat Rev Mol Cell Biol 2022; 23:231-249. [PMID: 35013589 DOI: 10.1038/s41580-021-00438-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation (XCI) is the epigenetic mechanism that ensures X-linked dosage compensation between cells of females (XX karyotype) and males (XY). XCI is essential for female embryos to survive through development and requires the accurate spatiotemporal regulation of many different factors to achieve remarkable chromosome-wide gene silencing. As a result of XCI, the active and inactive X chromosomes are functionally and structurally different, with the inactive X chromosome undergoing a major conformational reorganization within the nucleus. In this Review, we discuss the multiple layers of genetic and epigenetic regulation that underlie initiation of XCI during development and then maintain it throughout life, in light of the most recent findings in this rapidly advancing field. We discuss exciting new insights into the regulation of X inactive-specific transcript (XIST), the trigger and master regulator of XCI, and into the mechanisms and dynamics that underlie the silencing of nearly all X-linked genes. Finally, given the increasing interest in understanding the impact of chromosome organization on gene regulation, we provide an overview of the factors that are thought to reshape the 3D structure of the inactive X chromosome and of the relevance of such structural changes for XCI establishment and maintenance.
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Raposo AC, Casanova M, Gendrel AV, da Rocha ST. The tandem repeat modules of Xist lncRNA: a swiss army knife for the control of X-chromosome inactivation. Biochem Soc Trans 2021; 49:2549-2560. [PMID: 34882219 PMCID: PMC8786293 DOI: 10.1042/bst20210253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 12/16/2022]
Abstract
X-inactive-specific transcript (Xist) is a long non-coding RNA (lncRNA) essential for X-chromosome inactivation (XCI) in female placental mammals. Thirty years after its discovery, it is still puzzling how this lncRNA triggers major structural and transcriptional changes leading to the stable silencing of an entire chromosome. Recently, a series of studies in mouse cells have uncovered domains of functional specialization within Xist mapping to conserved tandem repeat regions, known as Repeats A-to-F. These functional domains interact with various RNA binding proteins (RBPs) and fold into distinct RNA structures to execute specific tasks in a synergistic and coordinated manner during the inactivation process. This modular organization of Xist is mostly conserved in humans, but recent data point towards differences regarding functional specialization of the tandem repeats between the two species. In this review, we summarize the recent progress on understanding the role of Xist repetitive blocks and their involvement in the molecular mechanisms underlying XCI. We also discuss these findings in the light of the similarities and differences between mouse and human Xist.
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Affiliation(s)
- Ana Cláudia Raposo
- Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Casanova
- Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Simão Teixeira da Rocha
- Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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Kolpa HJ, Creamer KM, Hall LL, Lawrence JB. SAF-A mutants disrupt chromatin structure through dominant negative effects on RNAs associated with chromatin. Mamm Genome 2021; 33:366-381. [PMID: 34859278 PMCID: PMC9114059 DOI: 10.1007/s00335-021-09935-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022]
Abstract
Here we provide a brief review of relevant background before presenting results of our investigation into the interplay between scaffold attachment factor A (SAF-A), chromatin-associated RNAs, and DNA condensation. SAF-A, also termed heterogenous nuclear protein U (hnRNP U), is a ubiquitous nuclear scaffold protein that was implicated in XIST RNA localization to the inactive X-chromosome (Xi) but also reported to maintain open DNA packaging in euchromatin. Here we use several means to perturb SAF-A and examine potential impacts on the broad association of RNAs on euchromatin, and on chromatin compaction. SAF-A has an N-terminal DNA binding domain and C-terminal RNA binding domain, and a prominent model has been that the protein provides a single-molecule bridge between XIST RNA and chromatin. Here analysis of the impact of SAF-A on broad RNA-chromatin interactions indicate greater biological complexity. We focus on SAF-A's role with repeat-rich C0T-1 hnRNA (repeat-rich heterogeneous nuclear RNA), shown recently to comprise mostly intronic sequences of pre-mRNAs and diverse long non-coding RNAs (lncRNAs). Our results show that SAF-A mutants cause dramatic changes to cytological chromatin condensation through dominant negative effects on C0T-1 RNA's association with euchromatin, and likely other nuclear scaffold factors. In contrast, depletion of SAF-A by RNA interference (RNAi) had no discernible impact on C0T-1 RNA, nor did it cause similarly marked chromatin changes as did three different SAF-A mutations. Overall results support the concept that repeat-rich, chromatin-associated RNAs interact with multiple RNA binding proteins (RBPs) in a complex dynamic meshwork that is integral to larger-scale chromatin architecture and collectively influences cytological-scale DNA condensation.
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Affiliation(s)
- Heather J Kolpa
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.,Ashfield MedComms, Lyndhurst, NJ, 07071, USA
| | - Kevin M Creamer
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.,Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Lisa L Hall
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA. .,Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.
| | - Jeanne B Lawrence
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, 01655, USA. .,Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.
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Trigiante G, Blanes Ruiz N, Cerase A. Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression. Front Cell Dev Biol 2021; 9:735527. [PMID: 34722514 PMCID: PMC8552494 DOI: 10.3389/fcell.2021.735527] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic repeats have been intensely studied as regulatory elements controlling gene transcription, splicing and genome architecture. Our understanding of the role of the repetitive RNA such as the RNA coming from genomic repeats, or repetitive sequences embedded in mRNA/lncRNAs, in nuclear and cellular functions is instead still limited. In this review we discuss evidence supporting the multifaceted roles of repetitive RNA and RNA binding proteins in nuclear organization, gene regulation, and in the formation of dynamic membrane-less aggregates. We hope that our review will further stimulate research in the consolidating field of repetitive RNA biology.
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Affiliation(s)
| | | | - Andrea Cerase
- Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, United Kingdom
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Fukuda A, Hazelbaker DZ, Motosugi N, Hao J, Limone F, Beccard A, Mazzucato P, Messana A, Okada C, San Juan IG, Qian M, Umezawa A, Akutsu H, Barrett LE, Eggan K. De novo DNA methyltransferases DNMT3A and DNMT3B are essential for XIST silencing for erosion of dosage compensation in pluripotent stem cells. Stem Cell Reports 2021; 16:2138-2148. [PMID: 34416176 PMCID: PMC8452533 DOI: 10.1016/j.stemcr.2021.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 12/31/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) have proven to be valuable tools for both drug discovery and the development of cell-based therapies. However, the long non-coding RNA XIST, which is essential for the establishment and maintenance of X chromosome inactivation, is repressed during culture, thereby causing erosion of dosage compensation in female hPSCs. Here, we report that the de novo DNA methyltransferases DNMT3A/3B are necessary for XIST repression in female hPSCs. We found that the deletion of both genes, but not the individual genes, inhibited XIST silencing, maintained the heterochromatin mark of H3K27me3, and did not cause global overdosage in X-linked genes. Meanwhile, DNMT3A/3B deletion after XIST repression failed to restore X chromosome inactivation. Our findings revealed that de novo DNA methyltransferases are primary factors responsible for initiating erosion of dosage compensation in female hPSCs, and XIST silencing is stably maintained in a de novo DNA-methylation-independent manner.
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Affiliation(s)
- Atsushi Fukuda
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan; The Institute of Medical Science, Tokai University, Kanagawa, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, Japan; Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan.
| | - Dane Z Hazelbaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nami Motosugi
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Jin Hao
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Francesco Limone
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amanda Beccard
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrizia Mazzucato
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Angelica Messana
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chisa Okada
- Support Center for Medical Research and Education, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Irune Guerra San Juan
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Menglu Qian
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Lindy E Barrett
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kevin Eggan
- The Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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10
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Wang W, Min L, Qiu X, Wu X, Liu C, Ma J, Zhang D, Zhu L. Biological Function of Long Non-coding RNA (LncRNA) Xist. Front Cell Dev Biol 2021; 9:645647. [PMID: 34178980 PMCID: PMC8222981 DOI: 10.3389/fcell.2021.645647] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression in a variety of ways at epigenetic, chromatin remodeling, transcriptional, and translational levels. Accumulating evidence suggests that lncRNA X-inactive specific transcript (lncRNA Xist) serves as an important regulator of cell growth and development. Despites its original roles in X-chromosome dosage compensation, lncRNA Xist also participates in the development of tumor and other human diseases by functioning as a competing endogenous RNA (ceRNA). In this review, we comprehensively summarized recent progress in understanding the cellular functions of lncRNA Xist in mammalian cells and discussed current knowledge regarding the ceRNA network of lncRNA Xist in various diseases. Long non-coding RNAs (lncRNAs) are transcripts that are more than 200 nt in length and without an apparent protein-coding capacity (Furlan and Rougeulle, 2016; Maduro et al., 2016). These RNAs are believed to be transcribed by the approximately 98-99% non-coding regions of the human genome (Derrien et al., 2012; Fu, 2014; Montalbano et al., 2017; Slack and Chinnaiyan, 2019), as well as a large variety of genomic regions, such as exonic, tronic, and intergenic regions. Hence, lncRNAs are also divided into eight categories: Intergenic lncRNAs, Intronic lncRNAs, Enhancer lncRNAs, Promoter lncRNAs, Natural antisense/sense lncRNAs, Small nucleolar RNA-ended lncRNAs (sno-lncRNAs), Bidirectional lncRNAs, and non-poly(A) lncRNAs (Ma et al., 2013; Devaux et al., 2015; St Laurent et al., 2015; Chen, 2016; Quinn and Chang, 2016; Richard and Eichhorn, 2018; Connerty et al., 2020). A range of evidence has suggested that lncRNAs function as key regulators in crucial cellular functions, including proliferation, differentiation, apoptosis, migration, and invasion, by regulating the expression level of target genes via epigenomic, transcriptional, or post-transcriptional approaches (Cao et al., 2018). Moreover, lncRNAs detected in body fluids were also believed to serve as potential biomarkers for the diagnosis, prognosis, and monitoring of disease progression, and act as novel and potential drug targets for therapeutic exploitation in human disease (Jiang W. et al., 2018; Zhou et al., 2019a). Long non-coding RNA X-inactive specific transcript (lncRNA Xist) are a set of 15,000-20,000 nt sequences localized in the X chromosome inactivation center (XIC) of chromosome Xq13.2 (Brown et al., 1992; Debrand et al., 1998; Kay, 1998; Lee et al., 2013; da Rocha and Heard, 2017; Yang Z. et al., 2018; Brockdorff, 2019). Previous studies have indicated that lncRNA Xist regulate X chromosome inactivation (XCI), resulting in the inheritable silencing of one of the X-chromosomes during female cell development. Also, it serves a vital regulatory function in the whole spectrum of human disease (notably cancer) and can be used as a novel diagnostic and prognostic biomarker and as a potential therapeutic target for human disease in the clinic (Liu et al., 2018b; Deng et al., 2019; Dinescu et al., 2019; Mutzel and Schulz, 2020; Patrat et al., 2020; Wang et al., 2020a). In particular, lncRNA Xist have been demonstrated to be involved in the development of multiple types of tumors including brain tumor, Leukemia, lung cancer, breast cancer, and liver cancer, with the prominent examples outlined in Table 1. It was also believed that lncRNA Xist (Chaligne and Heard, 2014; Yang Z. et al., 2018) contributed to other diseases, such as pulmonary fibrosis, inflammation, neuropathic pain, cardiomyocyte hypertrophy, and osteoarthritis chondrocytes, and more specific details can be found in Table 2. This review summarizes the current knowledge on the regulatory mechanisms of lncRNA Xist on both chromosome dosage compensation and pathogenesis (especially cancer) processes, with a focus on the regulatory network of lncRNA Xist in human disease.
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Affiliation(s)
| | | | | | | | | | | | - Dongyi Zhang
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, China
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11
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Song Z, Lin J, Li Z, Huang C. The nuclear functions of long noncoding RNAs come into focus. Noncoding RNA Res 2021; 6:70-79. [PMID: 33898883 PMCID: PMC8053782 DOI: 10.1016/j.ncrna.2021.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), defined as untranslated and tightly-regulated transcripts with a length exceeding 200 nt, are common outputs of the eukaryotic genome. It is becoming increasingly apparent that many lncRNAs likely serve as important regulators in a variety of biological processes. In particular, some of them accumulate in the nucleus and function in diverse nuclear events, including chromatin remodeling, transcriptional regulation, RNA processing, DNA damage repair, etc. Here, we unite recent progresses on the functions of nuclear lncRNAs and provide insights into the future research directions of this field.
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Affiliation(s)
- Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Corresponding author. School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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12
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Xie W, Zhu H, Zhao M, Wang L, Li S, Zhao C, Zhou Y, Zhu B, Jiang X, Liu W, Ren C. Crucial roles of different RNA-binding hnRNP proteins in Stem Cells. Int J Biol Sci 2021; 17:807-817. [PMID: 33767590 PMCID: PMC7975692 DOI: 10.7150/ijbs.55120] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/07/2021] [Indexed: 11/05/2022] Open
Abstract
The self-renewal, pluripotency and differentiation of stem cells are regulated by various genetic and epigenetic factors. As a kind of RNA binding protein (RBP), the heterogeneous nuclear ribonucleoproteins (hnRNPs) can act as "RNA scaffold" and recruit mRNA, lncRNA, microRNA and circRNA to affect mRNA splicing and processing, regulate gene transcription and post-transcriptional translation, change genome structure, and ultimately play crucial roles in the biological processes of cells. Recent researches have demonstrated that hnRNPs are irreplaceable for self-renewal and differentiation of stem cells. hnRNPs function in stem cells by multiple mechanisms, which include regulating mRNA stability, inducing alternative splicing of mRNA, epigenetically regulate gene expression, and maintaining telomerase activity and telomere length. The functions and the underlying mechanisms of hnRNPs in stem cells deserve further investigation.
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Affiliation(s)
- Wen Xie
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Hecheng Zhu
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,Changsha Kexin Cancer Hospital, Changsha, Hunan 410205, China
| | - Ming Zhao
- Changsha Kexin Cancer Hospital, Changsha, Hunan 410205, China
| | - Lei Wang
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Shasha Li
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Cong Zhao
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Yao Zhou
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Bin Zhu
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Xingjun Jiang
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Weidong Liu
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Caiping Ren
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
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13
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Lu Z, Guo JK, Wei Y, Dou DR, Zarnegar B, Ma Q, Li R, Zhao Y, Liu F, Choudhry H, Khavari PA, Chang HY. Structural modularity of the XIST ribonucleoprotein complex. Nat Commun 2020; 11:6163. [PMID: 33268787 PMCID: PMC7710737 DOI: 10.1038/s41467-020-20040-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs are thought to regulate gene expression by organizing protein complexes through unclear mechanisms. XIST controls the inactivation of an entire X chromosome in female placental mammals. Here we develop and integrate several orthogonal structure-interaction methods to demonstrate that XIST RNA-protein complex folds into an evolutionarily conserved modular architecture. Chimeric RNAs and clustered protein binding in fRIP and eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains that interact with distinct sets of effector proteins. CRISPR-Cas9-mediated permutation of the Xist A-repeat location shows that A-repeat serves as a nucleation center for multiple Xist-associated proteins and m6A modification. Thus modular architecture plays an essential role, in addition to sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and suggests a general strategy for mechanistic studies of large ribonucleoprotein assemblies.
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Affiliation(s)
- Zhipeng Lu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA, 90089, USA.
| | - Jimmy K Guo
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Diana R Dou
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Brian Zarnegar
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Qing Ma
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Synthetic Biology Department, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, PR China
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Fan Liu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Hani Choudhry
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, 22252, Saudi Arabia
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA.
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14
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Lee HM, Kuijer MB, Ruiz Blanes N, Clark EP, Aita M, Galiano Arjona L, Kokot A, Sciaky N, Simon JM, Bhatnagar S, Philpot BD, Cerase A. A small-molecule screen reveals novel modulators of MeCP2 and X-chromosome inactivation maintenance. J Neurodev Disord 2020; 12:29. [PMID: 33172406 PMCID: PMC7657357 DOI: 10.1186/s11689-020-09332-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/22/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is a neurodevelopmental disorder caused by mutations in the X-linked methyl-CpG binding protein 2 (MeCP2) gene. While MeCP2 mutations are lethal in most males, females survive birth but show severe neurological defects. Because X-chromosome inactivation (XCI) is a random process, approximately 50% of the cells silence the wild-type (WT) copy of the MeCP2 gene. Thus, reactivating the silent WT copy of MeCP2 could provide therapeutic intervention for RTT. METHODS Toward this goal, we screened ~ 28,000 small-molecule compounds from several libraries using a MeCP2-luciferase reporter cell line and cortical neurons from a MeCP2-EGFP mouse model. We used gain/increase of luminescence or fluorescence as a readout of MeCP2 reactivation and tested the efficacy of these drugs under different drug regimens, conditions, and cellular contexts. RESULTS We identified inhibitors of the JAK/STAT pathway as XCI-reactivating agents, both by in vitro and ex vivo assays. In particular, we show that AG-490, a Janus Kinase 2 (JAK2) kinase inhibitor, and Jaki, a pan JAK/STAT inhibitor, are capable of reactivating MeCP2 from the inactive X chromosome, in different cellular contexts. CONCLUSIONS Our results suggest that inhibition of the JAK/STAT pathway is a new potential pathway to reinstate MeCP2 gene expression as an efficient RTT treatment.
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Affiliation(s)
- Hyeong-Min Lee
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Current Address: High-Throughput Bioscience Center, Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Bram Kuijer
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Ellen P Clark
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Megumi Aita
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Agnieszka Kokot
- Department of Biochemistry and Molecular Genetics, Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Noah Sciaky
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sanchita Bhatnagar
- Department of Biochemistry and Molecular Genetics, Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Benjamin D Philpot
- Department of Cell Biology & Physiology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Andrea Cerase
- Blizard Institute, Queen Mary University of London, London, UK.
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15
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Akkipeddi SMK, Velleca AJ, Carone DM. Probing the function of long noncoding RNAs in the nucleus. Chromosome Res 2020; 28:87-110. [PMID: 32026224 PMCID: PMC7131881 DOI: 10.1007/s10577-019-09625-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/20/2019] [Accepted: 12/29/2019] [Indexed: 12/26/2022]
Abstract
The nucleus is a highly organized and dynamic environment where regulation and coordination of processes such as gene expression and DNA replication are paramount. In recent years, noncoding RNAs have emerged as key participants in the regulation of nuclear processes. There are a multitude of functional roles for long noncoding RNA (lncRNA), mediated through their ability to act as molecular scaffolds bridging interactions with proteins, chromatin, and other RNA molecules within the nuclear environment. In this review, we discuss the diversity of techniques that have been developed to probe the function of nuclear lncRNAs, along with the ways in which those techniques have revealed insights into their mechanisms of action. Foundational observations into lncRNA function have been gleaned from molecular cytology-based, single-cell approaches to illuminate both the localization and abundance of lncRNAs in addition to their potential binding partners. Biochemical, extraction-based approaches have revealed the molecular contacts between lncRNAs and other molecules within the nuclear environment and how those interactions may contribute to nuclear organization and regulation. Using examples of well-studied nuclear lncRNAs, we demonstrate that the emerging functions of individual lncRNAs have been most clearly deduced from combined cytology and biochemical approaches tailored to study specific lncRNAs. As more functional nuclear lncRNAs continue to emerge, the development of additional technologies to study their interactions and mechanisms of action promise to continually expand our understanding of nuclear organization, chromosome architecture, genome regulation, and disease states.
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Affiliation(s)
| | - Anthony J Velleca
- Department of Molecular Phamacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dawn M Carone
- Department of Biology, Swarthmore College, Swarthmore, PA, USA.
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16
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Bansal P, Kondaveeti Y, Pinter SF. Forged by DXZ4, FIRRE, and ICCE: How Tandem Repeats Shape the Active and Inactive X Chromosome. Front Cell Dev Biol 2020; 7:328. [PMID: 32076600 PMCID: PMC6985041 DOI: 10.3389/fcell.2019.00328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Recent efforts in mapping spatial genome organization have revealed three evocative and conserved structural features of the inactive X in female mammals. First, the chromosomal conformation of the inactive X reveals a loss of topologically associated domains (TADs) present on the active X. Second, the macrosatellite DXZ4 emerges as a singular boundary that suppresses physical interactions between two large TAD-depleted "megadomains." Third, DXZ4 reaches across several megabases to form "superloops" with two other X-linked tandem repeats, FIRRE and ICCE, which also loop to each other. Although all three structural features are conserved across rodents and primates, deletion of mouse and human orthologs of DXZ4 and FIRRE from the inactive X have revealed limited impact on X chromosome inactivation (XCI) and escape in vitro. In contrast, loss of Xist or SMCHD1 have been shown to impair TAD erasure and gene silencing on the inactive X. In this perspective, we summarize these results in the context of new research describing disruption of X-linked tandem repeats in vivo, and discuss their possible molecular roles through the lens of evolutionary conservation and clinical genetics. As a null hypothesis, we consider whether the conservation of some structural features on the inactive X may reflect selection for X-linked tandem repeats on account of necessary cis- and trans-regulatory roles they may play on the active X, rather than the inactive X. Additional hypotheses invoking a role for X-linked tandem repeats on X reactivation, for example in the germline or totipotency, remain to be assessed in multiple developmental models spanning mammalian evolution.
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Affiliation(s)
- Prakhar Bansal
- Department of Genetics and Genome Sciences, School of Medicine, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
| | - Yuvabharath Kondaveeti
- Department of Genetics and Genome Sciences, School of Medicine, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
| | - Stefan F. Pinter
- Department of Genetics and Genome Sciences, School of Medicine, UCONN Health, University of Connecticut, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
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17
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Jansz N, Nesterova T, Keniry A, Iminitoff M, Hickey PF, Pintacuda G, Masui O, Kobelke S, Geoghegan N, Breslin KA, Willson TA, Rogers K, Kay GF, Fox AH, Koseki H, Brockdorff N, Murphy JM, Blewitt ME. Smchd1 Targeting to the Inactive X Is Dependent on the Xist-HnrnpK-PRC1 Pathway. Cell Rep 2019; 25:1912-1923.e9. [PMID: 30428357 DOI: 10.1016/j.celrep.2018.10.044] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/06/2018] [Accepted: 10/11/2018] [Indexed: 01/08/2023] Open
Abstract
We and others have recently reported that the SMC protein Smchd1 is a regulator of chromosome conformation. Smchd1 is critical for the structure of the inactive X chromosome and at autosomal targets such as the Hox genes. However, it is unknown how Smchd1 is recruited to these sites. Here, we report that Smchd1 localizes to the inactive X via the Xist-HnrnpK-PRC1 (polycomb repressive complex 1) pathway. Contrary to previous reports, Smchd1 does not bind Xist or other RNA molecules with any specificity. Rather, the localization of Smchd1 to the inactive X is H2AK119ub dependent. Following perturbation of this interaction, Smchd1 is destabilized, which has consequences for gene silencing genome-wide. Our work adds Smchd1 to the PRC1 silencing pathway for X chromosome inactivation.
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Affiliation(s)
- Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tatyana Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Greta Pintacuda
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Osamu Masui
- Centre for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Simon Kobelke
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Niall Geoghegan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kelsey A Breslin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Tracy A Willson
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Kelly Rogers
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Graham F Kay
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Haruhiko Koseki
- Centre for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia; Department of Genetics, University of Melbourne, Melbourne, VIC 3010, Australia.
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18
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Abstract
The non-coding RNA Xist regulates the process of X chromosome inactivation, in which one of the two X chromosomes present in cells of early female mammalian embryos is selectively and coordinately shut down. Remarkably Xist RNA functions in cis, affecting only the chromosome from which it is transcribed. This feature is attributable to the unique propensity of Xist RNA to accumulate over the territory of the chromosome on which it is synthesized, contrasting with the majority of RNAs that are rapidly exported out of the cell nucleus. In this review I provide an overview of the progress that has been made towards understanding localized accumulation of Xist RNA, drawing attention to evidence that some other non-coding RNAs probably function in a highly analogous manner. I describe a simple model for localized accumulation of Xist RNA and discuss key unresolved questions that need to be addressed in future studies.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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19
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Abstract
In mammals, dosage compensation of sex chromosomal genes between females (XX) and males (XY) is achieved through X-chromosome inactivation (XCI). The X-linked X-inactive-specific transcript (Xist) long noncoding RNA is indispensable for XCI and initiates the process early during development by spreading in cis across the X chromosome from which it is transcribed. During XCI, Xist RNA triggers gene silencing, recruits a plethora of chromatin modifying factors, and drives a major structural reorganization of the X chromosome. Here, we review our knowledge of the multitude of epigenetic events orchestrated by Xist RNA to allow female mammals to survive through embryonic development by establishing and maintaining proper dosage compensation. In particular, we focus on recent studies characterizing the interaction partners of Xist RNA, and we discuss how they have affected the field by addressing long-standing controversies or by giving rise to new research perspectives that are currently being explored. This review is dedicated to the memory of Denise Barlow, pioneer of genomic imprinting and functional long noncoding RNAs (lncRNAs), whose work has revolutionized the epigenetics field and continues to inspire generations of scientists.
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20
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Balaton BP, Dixon-McDougall T, Peeters SB, Brown CJ. The eXceptional nature of the X chromosome. Hum Mol Genet 2019; 27:R242-R249. [PMID: 29701779 DOI: 10.1093/hmg/ddy148] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
Abstract
The X chromosome is unique in the genome. In this review we discuss recent advances in our understanding of the genetics and epigenetics of the X chromosome. The X chromosome shares limited conservation with its ancestral homologue the Y chromosome and the resulting difference in X-chromosome dosage between males and females is largely compensated for by X-chromosome inactivation. The process of inactivation is initiated by the long non-coding RNA X-inactive specific transcript (XIST) and achieved through interaction with multiple synergistic silencing pathways. Identification of Xist-interacting proteins has given insight into these processes yet the cascade of events from initiation to maintenance have still to be resolved. In particular, the initiation of inactivation in humans has been challenging to study as: it occurs very early in development; most human embryonic stem cell lines already have an inactive X; and the process seems to differ from mouse. Another difference between human and mouse X inactivation is the larger number of human genes that escape silencing. In humans over 20% of X-linked genes continue to be expressed from the otherwise inactive X chromosome. We are only beginning to understand how such escape occurs but there is growing recognition that escapees contribute to sexually dimorphic traits. The unique biology and epigenetics of the X chromosome have often led to its exclusion from disease studies, yet the X constitutes 5% of the genome and is an important contributor to disease, often in a sex-specific manner.
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Affiliation(s)
- Bradley P Balaton
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Thomas Dixon-McDougall
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Samantha B Peeters
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Carolyn J Brown
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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21
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Local Tandem Repeat Expansion in Xist RNA as a Model for the Functionalisation of ncRNA. Noncoding RNA 2018; 4:ncrna4040028. [PMID: 30347781 PMCID: PMC6316617 DOI: 10.3390/ncrna4040028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/08/2023] Open
Abstract
Xist, the master regulator of the X chromosome inactivation in mammals, is a 17 kb lncRNA that acts in cis to silence the majority of genes along the chromosome from which it is transcribed. The two key processes required for Xist RNA function, localisation in cis and recruitment of silencing factors, are genetically separable, at least in part. Recent studies have identified Xist RNA sequences and associated RNA-binding proteins (RBPs) that are important for these processes. Notably, several of the key Xist RNA elements correspond to local tandem repeats. In this review, I use examples to illustrate different modes whereby tandem repeat amplification has been exploited to allow orthodox RBPs to confer new functions for Xist-mediated chromosome inactivation. I further discuss the potential generality of tandem repeat expansion in the evolution of functional long non-coding RNAs (lncRNAs).
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22
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Galupa R, Heard E. X-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation. Annu Rev Genet 2018; 52:535-566. [PMID: 30256677 DOI: 10.1146/annurev-genet-120116-024611] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In somatic nuclei of female therian mammals, the two X chromosomes display very different chromatin states: One X is typically euchromatic and transcriptionally active, and the other is mostly silent and forms a cytologically detectable heterochromatic structure termed the Barr body. These differences, which arise during female development as a result of X-chromosome inactivation (XCI), have been the focus of research for many decades. Initial approaches to define the structure of the inactive X chromosome (Xi) and its relationship to gene expression mainly involved microscopy-based approaches. More recently, with the advent of genomic techniques such as chromosome conformation capture, molecular details of the structure and expression of the Xi have been revealed. Here, we review our current knowledge of the 3D organization of the mammalian X-chromosome chromatin and discuss its relationship with gene activity in light of the initiation, spreading, and maintenance of XCI, as well as escape from gene silencing.
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Affiliation(s)
- Rafael Galupa
- Genetics and Developmental Biology Unit and Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris, France; .,Current affiliation: Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Edith Heard
- Genetics and Developmental Biology Unit and Mammalian Developmental Epigenetics Group, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, 75248 Paris, France; .,Collège de France, 75231 Paris, France
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23
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Lu Z, Carter AC, Chang HY. Mechanistic insights in X-chromosome inactivation. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0356. [PMID: 28947655 DOI: 10.1098/rstb.2016.0356] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2017] [Indexed: 11/12/2022] Open
Abstract
X-chromosome inactivation (XCI) is a critical epigenetic mechanism for balancing gene dosage between XY males and XX females in eutherian mammals. A long non-coding RNA (lncRNA), XIST, and its associated proteins orchestrate this multi-step process, resulting in the inheritable silencing of one of the two X-chromosomes in females. The XIST RNA is large and complex, exemplifying the unique challenges associated with the structural and functional analysis of lncRNAs. Recent technological advances in the analysis of macromolecular structure and interactions have enabled us to systematically dissect the XIST ribonucleoprotein complex, which is larger than the ribosome, and its place of action, the inactive X-chromosome. These studies shed light on key mechanisms of XCI, such as XIST coating of the X-chromosome, recruitment of DNA, RNA and histone modification enzymes, and compaction and compartmentalization of the inactive X. Here, we summarize recent studies on XCI, highlight the critical contributions of new technologies and propose a unifying model for XIST function in XCI where modular domains serve as the structural and functional units in both lncRNA-protein complexes and DNA-protein complexes in chromatin.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- Zhipeng Lu
- Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ava C Carter
- Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Dynamic Personal Regulomes, Stanford University, Stanford, CA 94305, USA
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24
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Abstract
Immunodetection of nuclear antigens is often complicated by epitope masking, so that proteins known to function in the nucleus are sometimes not easily detected at their sites of action. Moreover, protein populations that are detected before unmasking can be very different to those seen after removal of nucleic acids. This is particularly true for components of the nuclear matrix, including those known to function at the inactive X chromosome. Here we describe an unmasking protocol that reveals previously undetected proteins at the inactive X chromosome in mouse fibroblasts.
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Affiliation(s)
- Emma R Stewart
- Department of Biology, University of York, Wentworth Way, UK.
| | - Dawn Coverley
- Department of Biology, University of York, Wentworth Way, UK.
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25
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Pintacuda G, Young AN, Cerase A. Function by Structure: Spotlights on Xist Long Non-coding RNA. Front Mol Biosci 2017; 4:90. [PMID: 29302591 PMCID: PMC5742192 DOI: 10.3389/fmolb.2017.00090] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/05/2017] [Indexed: 12/29/2022] Open
Abstract
Recent experimental evidence indicates that lncRNAs can act as regulatory molecules in the context of development and disease. Xist, the master regulator of X chromosome inactivation, is a classic example of how lncRNAs can exert multi-layered and fine-tuned regulatory functions, by acting as a molecular scaffold for recruitment of distinct protein factors. In this review, we discuss the methodologies employed to define Xist RNA structures and the tight interplay between structural clues and functionality of lncRNAs. This model of modular function dictated by structure, can be also generalized to other lncRNAs, beyond the field of X chromosome inactivation, to explain common features of similarly folded RNAs.
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Affiliation(s)
- Greta Pintacuda
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Andrea Cerase
- European Molecular Biology Laboratory, Monterotondo, Italy
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26
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Creamer KM, Lawrence JB. XIST RNA: a window into the broader role of RNA in nuclear chromosome architecture. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160360. [PMID: 28947659 PMCID: PMC5627162 DOI: 10.1098/rstb.2016.0360] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2017] [Indexed: 12/31/2022] Open
Abstract
XIST RNA triggers the transformation of an active X chromosome into a condensed, inactive Barr body and therefore provides a unique window into transitions of higher-order chromosome architecture. Despite recent progress, how XIST RNA localizes and interacts with the X chromosome remains poorly understood. Genetic engineering of XIST into a trisomic autosome demonstrates remarkable capacity of XIST RNA to localize and comprehensively silence that autosome. Thus, XIST does not require X chromosome-specific sequences but operates on mechanisms available genome-wide. Prior results suggested XIST localization is controlled by attachment to the insoluble nuclear scaffold. Our recent work affirms that scaffold attachment factor A (SAF-A) is involved in anchoring XIST, but argues against the view that SAF-A provides a unimolecular bridge between RNA and the chromosome. Rather, we suggest that a complex meshwork of architectural proteins interact with XIST RNA. Parallel work studying the territory of actively transcribed chromosomes suggests that repeat-rich RNA 'coats' euchromatin and may impact chromosome architecture in a manner opposite of XIST A model is discussed whereby RNA may not just recruit histone modifications, but more directly impact higher-order chromatin condensation via interaction with architectural proteins of the nucleus.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
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Affiliation(s)
- K M Creamer
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - J B Lawrence
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
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27
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Repeat E anchors Xist RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1). Proc Natl Acad Sci U S A 2017; 114:10654-10659. [PMID: 28923964 DOI: 10.1073/pnas.1711206114] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
X chromosome inactivation is an epigenetic dosage compensation mechanism in female mammals driven by the long noncoding RNA, Xist. Although recent genomic and proteomic approaches have provided a more global view of Xist's function, how Xist RNA localizes to the inactive X chromosome (Xi) and spreads in cis remains unclear. Here, we report that the CDKN1-interacting zinc finger protein CIZ1 is critical for localization of Xist RNA to the Xi chromosome territory. Stochastic optical reconstruction microscopy (STORM) shows a tight association of CIZ1 with Xist RNA at the single-molecule level. CIZ1 interacts with a specific region within Xist exon 7-namely, the highly repetitive Repeat E motif. Using genetic analysis, we show that loss of CIZ1 or deletion of Repeat E in female cells phenocopies one another in causing Xist RNA to delocalize from the Xi and disperse into the nucleoplasm. Interestingly, this interaction is exquisitely sensitive to CIZ1 levels, as overexpression of CIZ1 likewise results in Xist delocalization. As a consequence, this delocalization is accompanied by a decrease in H3K27me3 on the Xi. Our data reveal that CIZ1 plays a major role in ensuring stable association of Xist RNA within the Xi territory.
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28
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Ridings-Figueroa R, Stewart ER, Nesterova TB, Coker H, Pintacuda G, Godwin J, Wilson R, Haslam A, Lilley F, Ruigrok R, Bageghni SA, Albadrani G, Mansfield W, Roulson JA, Brockdorff N, Ainscough JFX, Coverley D. The nuclear matrix protein CIZ1 facilitates localization of Xist RNA to the inactive X-chromosome territory. Genes Dev 2017; 31:876-888. [PMID: 28546514 PMCID: PMC5458755 DOI: 10.1101/gad.295907.117] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/20/2017] [Indexed: 12/20/2022]
Abstract
Here, Ridings-Figueroa et al. show that the nuclear matrix protein Cip1-interacting zinc finger protein 1 (CIZ1) is highly enriched on the inactive X chromosome (Xi) in mouse and human female cells and is retained by interaction with the RNA-dependent nuclear matrix. Their findings suggest that CIZ1 has an essential role in anchoring Xist to the nuclear matrix in specific somatic lineages. The nuclear matrix protein Cip1-interacting zinc finger protein 1 (CIZ1) promotes DNA replication in association with cyclins and has been linked to adult and pediatric cancers. Here we show that CIZ1 is highly enriched on the inactive X chromosome (Xi) in mouse and human female cells and is retained by interaction with the RNA-dependent nuclear matrix. CIZ1 is recruited to Xi in response to expression of X inactive-specific transcript (Xist) RNA during the earliest stages of X inactivation in embryonic stem cells and is dependent on the C-terminal nuclear matrix anchor domain of CIZ1 and the E repeats of Xist. CIZ1-null mice, although viable, display fully penetrant female-specific lymphoproliferative disorder. Interestingly, in mouse embryonic fibroblast cells derived from CIZ1-null embryos, Xist RNA localization is disrupted, being highly dispersed through the nucleoplasm rather than focal. Focal localization is reinstated following re-expression of CIZ1. Focal localization of Xist RNA is also disrupted in activated B and T cells isolated from CIZ1-null animals, suggesting a possible explanation for female-specific lymphoproliferative disorder. Together, these findings suggest that CIZ1 has an essential role in anchoring Xist to the nuclear matrix in specific somatic lineages.
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Affiliation(s)
| | - Emma R Stewart
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Tatyana B Nesterova
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Heather Coker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Greta Pintacuda
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jonathan Godwin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Rose Wilson
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Aidan Haslam
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Fred Lilley
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Renate Ruigrok
- Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sumia A Bageghni
- Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ghadeer Albadrani
- Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), University of Leeds, Leeds LS2 9JT, United Kingdom.,Princess Nourah Bint Abdulrahman University (PNU), Riyadh, Kingdom of Saudi Arabia
| | - William Mansfield
- Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, United Kingdom
| | - Jo-An Roulson
- Leeds Institute of Molecular Medicine (LIMM), University of Leeds, Leeds LS9 7TF, United Kingdom
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Justin F X Ainscough
- Department of Biology, University of York, York YO10 5DD, United Kingdom.,Leeds Institute of Cardiovascular and Metabolic Medicine (LICAMM), University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Dawn Coverley
- Department of Biology, University of York, York YO10 5DD, United Kingdom
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29
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Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation. Nat Struct Mol Biol 2017; 24:197-204. [DOI: 10.1038/nsmb.3370] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/05/2017] [Indexed: 02/07/2023]
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30
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Sakaguchi T, Hasegawa Y, Brockdorff N, Tsutsui K, Tsutsui K, Sado T, Nakagawa S. Control of Chromosomal Localization of Xist by hnRNP U Family Molecules. Dev Cell 2016; 39:11-12. [DOI: 10.1016/j.devcel.2016.09.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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