1
|
Vieira AA, Almada-Correia I, Inácio J, Costa-Reis P, da Rocha ST. Female-bias in systemic lupus erythematosus: How much is the X chromosome to blame? Biol Sex Differ 2024; 15:76. [PMID: 39375734 PMCID: PMC11460073 DOI: 10.1186/s13293-024-00650-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 08/30/2024] [Indexed: 10/09/2024] Open
Abstract
Systemic lupus erythematosus (SLE or lupus) is an immune-mediated disease associated with substantial medical burden. Notably, lupus exhibits a striking female bias, with women having significantly higher susceptibility compared to men, up to 14-fold higher in some ethnicities. Supernumerary X chromosome syndromes, like Klinefelter (XXY) and Triple X syndrome (XXX), also present higher SLE prevalence, whereas Turner syndrome (XO) displays lower prevalence. Taken together, SLE prevalence in different X chromosome dosage sceneries denotes a relationship between the number of X chromosomes and the risk of developing lupus. The dosage of X-linked genes, many of which play roles in the immune system, is compensated between males and females through the inactivation of one of the two X chromosomes in female cells. X-chromosome inactivation (XCI) initiates early in development with a random selection of which X chromosome to inactivate, a choice that is then epigenetically maintained in the daughter cells. This process is regulated by the X-Inactive-Specific Transcript (XIST), encoding for a long non-coding RNA, exclusively expressed from the inactive X chromosome (Xi). XIST interacts with various RNA binding proteins and chromatin modifiers to form a ribonucleoprotein (RNP) complex responsible for the transcriptional silencing and heterochromatinization of the Xi. This ensures stable silencing of most genes on the X chromosome, with only a few genes able to escape this process. Recent findings suggest that the molecular components involved in XCI, or their dysregulation, contribute to the pathogenesis of lupus. Indeed, nonrandom XCI, elevated gene escape from XCI, and the autoimmune potential of the XIST RNP complex have been suggested to contribute to auto-immune diseases, such as lupus. This review examines these current hypotheses concerning how this dosage compensation mechanism might impact the development of lupus, shedding light on potential mechanisms underlying the pathogenesis of the disease.
Collapse
Affiliation(s)
- Adriana A Vieira
- Rheumatology Research Unit, Instituto de Medicina Molecular João Lobo Antunes, Lisbon, Portugal
| | - Inês Almada-Correia
- Rheumatology Research Unit, Instituto de Medicina Molecular João Lobo Antunes, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Inácio
- Rheumatology Research Unit, Instituto de Medicina Molecular João Lobo Antunes, Lisbon, Portugal
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Patrícia Costa-Reis
- Rheumatology Research Unit, Instituto de Medicina Molecular João Lobo Antunes, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Pediatric Rheumatology Unit, Pediatrics Department, Hospital de Santa Maria, Lisbon, Portugal
| | - S T da Rocha
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
| |
Collapse
|
2
|
Dror I, Tan T, Plath K. A critical role for X-chromosome architecture in mammalian X-chromosome dosage compensation. Curr Opin Genet Dev 2024; 87:102235. [PMID: 39053028 DOI: 10.1016/j.gde.2024.102235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
To regulate gene expression, the macromolecular components of the mammalian interphase nucleus are spatially organized into a myriad of functional compartments. Over the past decade, increasingly sophisticated genomics, microscopy, and functional approaches have probed this organization in unprecedented detail. These investigations have linked chromatin-associated noncoding RNAs to specific nuclear compartments and uncovered mechanisms by which these RNAs establish such domains. In this review, we focus on the long non-coding RNA Xist and summarize new evidence demonstrating the significance of chromatin reconfiguration in creating the inactive X-chromosome compartment. Differences in chromatin compaction correlate with distinct levels of gene repression on the X-chromosome, potentially explaining how human XIST can induce chromosome-wide dampening and silencing of gene expression at different stages of human development.
Collapse
Affiliation(s)
- Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tiao Tan
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, Jonsson Comprehensive Cancer Center, Brain Research Institute, Graduate Program in the Biosciences, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
3
|
Condemi L, Mocavini I, Aranda S, Di Croce L. Polycomb function in early mouse development. Cell Death Differ 2024:10.1038/s41418-024-01340-3. [PMID: 38997437 DOI: 10.1038/s41418-024-01340-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
Epigenetic factors are crucial for ensuring proper chromatin dynamics during the initial stages of embryo development. Among these factors, the Polycomb group (PcG) of proteins plays a key role in establishing correct transcriptional programmes during mouse embryogenesis. PcG proteins are classified into two complexes: Polycomb repressive complex 1 (PRC1) and PRC2. Both complexes decorate histone proteins with distinct post-translational modifications (PTMs) that are predictive of a silent transcriptional chromatin state. In recent years, a critical adaptation of the classical techniques to analyse chromatin profiles and to study biochemical interactions at low-input resolution has allowed us to deeply explore PcG molecular mechanisms in the very early stages of mouse embryo development- from fertilisation to gastrulation, and from zygotic genome activation (ZGA) to specific lineages differentiation. These advancements provide a foundation for a deeper understanding of the fundamental role Polycomb complexes play in early development and have elucidated the mechanistic dynamics of PRC1 and PRC2. In this review, we discuss the functions and molecular mechanisms of both PRC1 and PRC2 during early mouse embryo development, integrating new studies with existing knowledge. Furthermore, we highlight the molecular functionality of Polycomb complexes from ZGA through gastrulation, with a particular focus on non-canonical imprinted and bivalent genes, and Hox cluster regulation.
Collapse
Affiliation(s)
- Livia Condemi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ivano Mocavini
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- ICREA, Pg. Lluis Companys 23, 08010, Barcelona, Spain.
| |
Collapse
|
4
|
Alfeghaly C, Castel G, Cazottes E, Moscatelli M, Moinard E, Casanova M, Boni J, Mahadik K, Lammers J, Freour T, Chauviere L, Piqueras C, Boers R, Boers J, Gribnau J, David L, Ouimette JF, Rougeulle C. XIST dampens X chromosome activity in a SPEN-dependent manner during early human development. Nat Struct Mol Biol 2024:10.1038/s41594-024-01325-3. [PMID: 38834912 DOI: 10.1038/s41594-024-01325-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/25/2024] [Indexed: 06/06/2024]
Abstract
XIST (X-inactive specific transcript) long noncoding RNA (lncRNA) is responsible for X chromosome inactivation (XCI) in placental mammals, yet it accumulates on both X chromosomes in human female preimplantation embryos without triggering X chromosome silencing. The XACT (X-active coating transcript) lncRNA coaccumulates with XIST on active X chromosomes and may antagonize XIST function. Here, we used human embryonic stem cells in a naive state of pluripotency to assess the function of XIST and XACT in shaping the X chromosome chromatin and transcriptional landscapes during preimplantation development. We show that XIST triggers the deposition of polycomb-mediated repressive histone modifications and dampens the transcription of most X-linked genes in a SPEN-dependent manner, while XACT deficiency does not significantly affect XIST activity or X-linked gene expression. Our study demonstrates that XIST is functional before XCI, confirms the existence of a transient process of X chromosome dosage compensation and reveals that XCI and dampening rely on the same set of factors.
Collapse
Affiliation(s)
- Charbel Alfeghaly
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Gaël Castel
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Emmanuel Cazottes
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | | | - Eva Moinard
- Center for Research in Transplantation and Translational Immunology (CR2TI), CHU Nantes, Inserm, Nantes Université, Nantes, France
| | - Miguel Casanova
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Juliette Boni
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Kasturi Mahadik
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Jenna Lammers
- Service de Biologie de la Reproduction, CHU Nantes, Nantes Université, Nantes, France
| | - Thomas Freour
- Service de Biologie de la Reproduction, CHU Nantes, Nantes Université, Nantes, France
| | - Louis Chauviere
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Carla Piqueras
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France
| | - Ruben Boers
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Joachim Boers
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Laurent David
- Center for Research in Transplantation and Translational Immunology (CR2TI), CHU Nantes, Inserm, Nantes Université, Nantes, France
- BioCore, CNRS, CHU Nantes, Inserm, Nantes Université, Nantes, France
| | | | - Claire Rougeulle
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, Paris, France.
| |
Collapse
|
5
|
Martitz A, Schulz EG. Spatial orchestration of the genome: topological reorganisation during X-chromosome inactivation. Curr Opin Genet Dev 2024; 86:102198. [PMID: 38663040 DOI: 10.1016/j.gde.2024.102198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 06/11/2024]
Abstract
Genomes are organised through hierarchical structures, ranging from local kilobase-scale cis-regulatory contacts to large chromosome territories. Most notably, (sub)-compartments partition chromosomes according to transcriptional activity, while topologically associating domains (TADs) define cis-regulatory landscapes. The inactive X chromosome in mammals has provided unique insights into the regulation and function of the three-dimensional (3D) genome. Concurrent with silencing of the majority of genes and major alterations of its chromatin state, the X chromosome undergoes profound spatial rearrangements at multiple scales. These include the emergence of megadomains, alterations of the compartment structure and loss of the majority of TADs. Moreover, the Xist locus, which orchestrates X-chromosome inactivation, has provided key insights into regulation and function of regulatory domains. This review provides an overview of recent insights into the control of these structural rearrangements and contextualises them within a broader understanding of 3D genome organisation.
Collapse
Affiliation(s)
- Alexandra Martitz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Edda G Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| |
Collapse
|
6
|
McIntyre KL, Waters SA, Zhong L, Hart-Smith G, Raftery M, Chew ZA, Patel HR, Graves JAM, Waters PD. Identification of the RSX interactome in a marsupial shows functional coherence with the Xist interactome during X inactivation. Genome Biol 2024; 25:134. [PMID: 38783307 PMCID: PMC11112854 DOI: 10.1186/s13059-024-03280-0] [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: 11/02/2023] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
The marsupial specific RSX lncRNA is the functional analogue of the eutherian specific XIST, which coordinates X chromosome inactivation. We characterized the RSX interactome in a marsupial representative (the opossum Monodelphis domestica), identifying 135 proteins, of which 54 had orthologues in the XIST interactome. Both interactomes were enriched for biological pathways related to RNA processing, regulation of translation, and epigenetic transcriptional silencing. This represents a remarkable example showcasing the functional coherence of independently evolved lncRNAs in distantly related mammalian lineages.
Collapse
Affiliation(s)
- Kim L McIntyre
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Shafagh A Waters
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Gene Hart-Smith
- Australian Proteome Analysis Facility, Macquarie University, Macquarie Park, NSW, Australia
| | - Mark Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Zahra A Chew
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, 2601, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT, 2601, Australia
| | | | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
| |
Collapse
|
7
|
Alammari F, Al-Hujaily EM, Alshareeda A, Albarakati N, Al-Sowayan BS. Hidden regulators: the emerging roles of lncRNAs in brain development and disease. Front Neurosci 2024; 18:1392688. [PMID: 38841098 PMCID: PMC11150811 DOI: 10.3389/fnins.2024.1392688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as critical players in brain development and disease. These non-coding transcripts, which once considered as "transcriptional junk," are now known for their regulatory roles in gene expression. In brain development, lncRNAs participate in many processes, including neurogenesis, neuronal differentiation, and synaptogenesis. They employ their effect through a wide variety of transcriptional and post-transcriptional regulatory mechanisms through interactions with chromatin modifiers, transcription factors, and other regulatory molecules. Dysregulation of lncRNAs has been associated with certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders. Altered expression and function of specific lncRNAs have been implicated with disrupted neuronal connectivity, impaired synaptic plasticity, and aberrant gene expression pattern, highlighting the functional importance of this subclass of brain-enriched RNAs. Moreover, lncRNAs have been identified as potential biomarkers and therapeutic targets for neurological diseases. Here, we give a comprehensive review of the existing knowledge of lncRNAs. Our aim is to provide a better understanding of the diversity of lncRNA structure and functions in brain development and disease. This holds promise for unravelling the complexity of neurodevelopmental and neurodegenerative disorders, paving the way for the development of novel biomarkers and therapeutic targets for improved diagnosis and treatment.
Collapse
Affiliation(s)
- Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ensaf M. Al-Hujaily
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Saudi Biobank Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Jeddah, Saudi Arabia
| | - Batla S. Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| |
Collapse
|
8
|
Matiz-Ceron L, Okuno M, Itoh T, Yoshida I, Mizushima S, Toyoda A, Jogahara T, Kuroiwa A. Loss of One X and the Y Chromosome Changes the Configuration of the X Inactivation Center in the Genus Tokudaia. Cytogenet Genome Res 2024; 164:23-32. [PMID: 38754392 DOI: 10.1159/000539294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
INTRODUCTION X chromosome inactivation (XCI) is an essential mechanism for dosage compensation between females and males in mammals. In females, XCI is controlled by a complex, conserved locus termed the X inactivation center (Xic), in which the lncRNA Xist is the key regulator. However, little is known about the Xic in species with unusual sex chromosomes. The genus Tokudaia includes three rodent species endemic to Japan. Tokudaia osimensis and Tokudaia tokunoshimensis lost the Y chromosome (XO/XO), while Tokudaia muenninki (TMU) acquired a neo-X region by fusion of the X chromosome and an autosome (XX/XY). We compared the gene location and structure in the Xic among Tokudaia species. METHODS Gene structure of nine genes in Xic was predicted, and the gene location and genome sequences of Xic were compared between mouse and Tokudaia species. The expression level of the gene was confirmed by transcripts per million calculation using RNA-seq data. RESULTS Compared to mouse, the Xic gene order and location were conserved in Tokudaia species. However, remarkable structure changes were observed in lncRNA genes, Xist and Tsix, in the XO/XO species. In Xist, important functional repeats, B-, C-, D-, and E-repeats, were partially or completely lost due to deletions in these species. RNA-seq data showed that female-specific expression patterns of Xist and Tsix were confirmed in TMU, however, not in the XO/XO species. Additionally, three deletions and one inversion were confirmed in the intergenic region between Jpx and Ftx in the XO/XO species. CONCLUSION Our findings indicate that even if the Xist and Tsix lncRNAs are expressed, they are incapable of producing a successful and lasting XCI in the XO/XO species. We hypothesized that the significant structure change in the intergenic region of Jpx-Ftx resulted in the inability to perform the XCI, and, as a result, a lack of Xist expression. Our results collectively suggest that structural changes in the Xic occurred in the ancestral lineage of XO/XO species, likely due to the loss of one X chromosome and the Y chromosome as a consequence of the degradation of the XCI system.
Collapse
Affiliation(s)
- Luisa Matiz-Ceron
- Reproductive and Developmental Science, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ikuya Yoshida
- Reproductive and Developmental Science, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Shusei Mizushima
- Reproductive and Developmental Science, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takamichi Jogahara
- Faculty of Law, Economics and Management, Okinawa University, Naha, Okinawa, Japan
| | - Asato Kuroiwa
- Reproductive and Developmental Science, Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| |
Collapse
|
9
|
Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol 2024; 25:396-415. [PMID: 38242953 PMCID: PMC11045326 DOI: 10.1038/s41580-023-00694-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets.
Collapse
Affiliation(s)
- Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
| |
Collapse
|
10
|
Liang M, Zhang L, Lai L, Li Z. Unraveling the role of Xist in X chromosome inactivation: insights from rabbit model and deletion analysis of exons and repeat A. Cell Mol Life Sci 2024; 81:156. [PMID: 38551746 PMCID: PMC10980640 DOI: 10.1007/s00018-024-05151-0] [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: 10/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 04/01/2024]
Abstract
X chromosome inactivation (XCI) is a process that equalizes the expression of X-linked genes between males and females. It relies on Xist, continuously expressed in somatic cells during XCI maintenance. However, how Xist impacts XCI maintenance and its functional motifs remain unclear. In this study, we conducted a comprehensive analysis of Xist, using rabbits as an ideal non-primate model. Homozygous knockout of exon 1, exon 6, and repeat A in female rabbits resulted in embryonic lethality. However, X∆ReAX females, with intact X chromosome expressing Xist, showed no abnormalities. Interestingly, there were no significant differences between females with homozygous knockout of exons 2-5 and wild-type rabbits, suggesting that exons 2, 3, 4, and 5 are less important for XCI. These findings provide evolutionary insights into Xist function.
Collapse
Affiliation(s)
- Mingming Liang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Lichao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100039, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
| |
Collapse
|
11
|
Malcore RM, Kalantry S. A Comparative Analysis of Mouse Imprinted and Random X-Chromosome Inactivation. EPIGENOMES 2024; 8:8. [PMID: 38390899 PMCID: PMC10885068 DOI: 10.3390/epigenomes8010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
The mammalian sexes are distinguished by the X and Y chromosomes. Whereas males harbor one X and one Y chromosome, females harbor two X chromosomes. To equalize X-linked gene expression between the sexes, therian mammals have evolved X-chromosome inactivation as a dosage compensation mechanism. During X-inactivation, most genes on one of the two X chromosomes in females are transcriptionally silenced, thus equalizing X-linked gene expression between the sexes. Two forms of X-inactivation characterize eutherian mammals, imprinted and random. Imprinted X-inactivation is defined by the exclusive inactivation of the paternal X chromosome in all cells, whereas random X-inactivation results in the silencing of genes on either the paternal or maternal X chromosome in individual cells. Both forms of X-inactivation have been studied intensively in the mouse model system, which undergoes both imprinted and random X-inactivation early in embryonic development. Stable imprinted and random X-inactivation requires the induction of the Xist long non-coding RNA. Following its induction, Xist RNA recruits proteins and complexes that silence genes on the inactive-X. In this review, we present a current understanding of the mechanisms of Xist RNA induction, and, separately, the establishment and maintenance of gene silencing on the inactive-X by Xist RNA during imprinted and random X-inactivation.
Collapse
Affiliation(s)
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48105, USA
| |
Collapse
|
12
|
Fayyaz F, Eshkiki ZS, Karamzadeh AR, Moradi Z, Kaviani F, Namazi A, Karimi R, Tabaeian SP, Mansouri F, Akbari A. Relationship between long non-coding RNAs and Hippo signaling pathway in gastrointestinal cancers; molecular mechanisms and clinical significance. Heliyon 2024; 10:e23826. [PMID: 38226210 PMCID: PMC10788524 DOI: 10.1016/j.heliyon.2023.e23826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/17/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) play a significant biological role in the regulation of various cellular processes such as cell proliferation, differentiation, apoptosis and migration. In various malignancies, lncRNAs interplay with some main cancer-associated signaling pathways, including the Hippo signaling pathway to regulate the various cellular processes. It has been revealed that the cross-talking between lncRNAs and Hippo signaling pathway involves in gastrointestinal (GI) cancers development and progression. Considering the clinical significance of these lncRNAs, they have also been introduced as potential biomarkers in diagnostic, prognostic and therapeutic strategies in GI cancers. Herein, we review the mechanisms of lncRNA-mediated regulation of Hippo signaling pathway and focus on the corresponding molecular mechanisms and clinical significance of these non-coding RNAs in GI cancers.
Collapse
Affiliation(s)
- Farimah Fayyaz
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Shokati Eshkiki
- Alimentary Tract Research Center, Clinical Sciences Research Institute, Imam Khomeini Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Amir Reza Karamzadeh
- Occupational Medicine Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Genetic, Faculty of Sciences, Qom Branch, Islamic Azad University, Qom, Iran
| | - Zahra Moradi
- Department of Genetic, Faculty of Sciences, Qom Branch, Islamic Azad University, Qom, Iran
- Young Researchers and Elite Club, Qom Branch, Islamic Azad University, Qom, Iran
| | - Faezeh Kaviani
- Department of Genetic, Faculty of Sciences, Qom Branch, Islamic Azad University, Qom, Iran
| | - Abolfazl Namazi
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Internal Medicine, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Roya Karimi
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Seidamir Pasha Tabaeian
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Internal Medicine, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Mansouri
- Department of Genetic, Faculty of Sciences, Qom Branch, Islamic Azad University, Qom, Iran
| | - Abolfazl Akbari
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
13
|
Keniry A, Blewitt ME. Chromatin-mediated silencing on the inactive X chromosome. Development 2023; 150:dev201742. [PMID: 37991053 DOI: 10.1242/dev.201742] [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] [Indexed: 11/23/2023]
Abstract
In mammals, the second X chromosome in females is silenced to enable dosage compensation between XX females and XY males. This essential process involves the formation of a dense chromatin state on the inactive X (Xi) chromosome. There is a wealth of information about the hallmarks of Xi chromatin and the contribution each makes to silencing, leaving the tantalising possibility of learning from this knowledge to potentially remove silencing to treat X-linked diseases in females. Here, we discuss the role of each chromatin feature in the establishment and maintenance of the silent state, which is of crucial relevance for such a goal.
Collapse
Affiliation(s)
- Andrew Keniry
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- Epigenetics and Development Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
14
|
Kaufmann C, Wutz A. IndiSPENsable for X Chromosome Inactivation and Gene Silencing. EPIGENOMES 2023; 7:28. [PMID: 37987303 PMCID: PMC10660550 DOI: 10.3390/epigenomes7040028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
For about 30 years, SPEN has been the subject of research in many different fields due to its variety of functions and its conservation throughout a wide spectrum of species, like worms, arthropods, and vertebrates. To date, 216 orthologues have been documented. SPEN had been studied for its role in gene regulation in the context of cell signaling, including the NOTCH or nuclear hormone receptor signaling pathways. More recently, SPEN has been identified as a major regulator of initiation of chromosome-wide gene silencing during X chromosome inactivation (XCI) in mammals, where its function remains to be fully understood. Dependent on the biological context, SPEN functions via mechanisms which include different domains. While some domains of SPEN are highly conserved in sequence and secondary structure, species-to-species differences exist that might lead to mechanistic differences. Initiation of XCI appears to be different between humans and mice, which raises additional questions about the extent of generalization of SPEN's function in XCI. In this review, we dissect the mechanism of SPEN in XCI. We discuss its subregions and domains, focusing on its role as a major regulator. We further highlight species-related research, specifically of mouse and human SPEN, with the aim to reveal and clarify potential species-to-species differences in SPEN's function.
Collapse
Affiliation(s)
| | - Anton Wutz
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology ETH Hönggerberg, 8093 Zurich, Switzerland;
| |
Collapse
|
15
|
Cherney RE, Eberhard QE, Giri G, Mills CA, Porrello A, Zhang Z, White D, Trotman JB, Herring LE, Dominguez D, Calabrese JM. SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells. RNA (NEW YORK, N.Y.) 2023; 29:1535-1556. [PMID: 37468167 PMCID: PMC10578485 DOI: 10.1261/rna.079569.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/23/2023] [Indexed: 07/21/2023]
Abstract
Scaffold attachment factor B (SAFB) is a conserved RNA-binding protein that is essential for early mammalian development. However, the functions of SAFB in mouse embryonic stem cells (ESCs) have not been characterized. Using RNA immunoprecipitation followed by RNA-seq (RIP-seq), we examined the RNAs associated with SAFB in wild-type and SAFB/SAFB2 double-knockout ESCs. SAFB predominantly associated with introns of protein-coding genes through purine-rich motifs. The transcript most enriched in SAFB association was the lncRNA Malat1, which also contains a purine-rich region in its 5' end. Knockout of SAFB/SAFB2 led to differential expression of approximately 1000 genes associated with multiple biological processes, including apoptosis, cell division, and cell migration. Knockout of SAFB/SAFB2 also led to splicing changes in a set of genes that were largely distinct from those that exhibited changes in expression level. The spliced and nascent transcripts of many genes whose expression levels were positively regulated by SAFB also associated with high levels of SAFB, implying that SAFB binding promotes their expression. Reintroduction of SAFB into double-knockout cells restored gene expression toward wild-type levels, an effect again observable at the level of spliced and nascent transcripts. Proteomics analysis revealed a significant enrichment of nuclear speckle-associated and RS domain-containing proteins among SAFB interactors. Neither Xist nor Polycomb functions were dramatically altered in SAFB/2 knockout ESCs. Our findings suggest that among other potential functions in ESCs, SAFB promotes the expression of certain genes through its ability to bind nascent RNA.
Collapse
Affiliation(s)
- Rachel E Cherney
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, 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 Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Quinn E Eberhard
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, 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
| | - Gilbert Giri
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, 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
| | - Christine A Mills
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Proteomics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Alessandro Porrello
- RNA Discovery Center, 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
| | - Zhiyue Zhang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - David White
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jackson B Trotman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, 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
| | - Laura E Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Proteomics Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, 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
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- RNA Discovery Center, 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
| |
Collapse
|
16
|
Lin J, Zhang J, Ma L, Fang H, Ma R, Groneck C, Filippova GN, Deng X, Ma W, Disteche CM, Berletch JB. KDM6A facilitates Xist upregulation at the onset of X inactivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553617. [PMID: 37645756 PMCID: PMC10462084 DOI: 10.1101/2023.08.16.553617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
X chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions. One of these genes is the highly conserved gene Kdm6a , which encodes a histone demethylase that removes methyl groups at H3K27 to facilitate gene expression. Here, we investigate the role of KDM6A in the regulation of Xist . We observed impaired upregulation of Xist during early stages of differentiation in hybrid mouse ES cells following CRISPR/Cas9 knockout of Kdm6a . This is associated with reduced Xist RNA coating of the Xi, suggesting diminished XCI potency. Indeed, Kdm6a knockout results in aberrant overexpression of genes from the Xi after differentiation. KDM6A binds to the Xist promoter and knockout cells show an increase in H3K27me3 at Xist . These results indicate that KDM6A plays a role in the initiation of XCI through histone demethylase-dependent activation of Xist during early differentiation.
Collapse
|
17
|
Valledor M, Byron M, Dumas B, Carone DM, Hall LL, Lawrence JB. Early chromosome condensation by XIST builds A-repeat RNA density that facilitates gene silencing. Cell Rep 2023; 42:112686. [PMID: 37384527 PMCID: PMC10461597 DOI: 10.1016/j.celrep.2023.112686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 10/31/2022] [Accepted: 06/08/2023] [Indexed: 07/01/2023] Open
Abstract
XIST RNA triggers chromosome-wide gene silencing and condenses an active chromosome into a Barr body. Here, we use inducible human XIST to examine early steps in the process, showing that XIST modifies cytoarchitecture before widespread gene silencing. In just 2-4 h, barely visible transcripts populate the large "sparse zone" surrounding the smaller "dense zone"; importantly, density zones exhibit different chromatin impacts. Sparse transcripts immediately trigger immunofluorescence for H2AK119ub and CIZ1, a matrix protein. H3K27me3 appears hours later in the dense zone, which enlarges with chromosome condensation. Genes examined are silenced after compaction of the RNA/DNA territory. Insights into this come from the findings that the A-repeat alone can silence genes and rapidly, but only where dense RNA supports sustained histone deacetylation. We propose that sparse XIST RNA quickly impacts architectural elements to condense the largely non-coding chromosome, coalescing RNA density that facilitates an unstable, A-repeat-dependent step required for gene silencing.
Collapse
Affiliation(s)
- Melvys Valledor
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Meg Byron
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Brett Dumas
- Department of Medicine, Boston University Medical Center, Boston, MA 02118, USA
| | - Dawn M Carone
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA
| | - Lisa L Hall
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
| |
Collapse
|
18
|
Braceros AK, Schertzer MD, Omer A, Trotman JB, Davis ES, Dowen JM, Phanstiel DH, Aiden EL, Calabrese JM. Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn. Cell Rep 2023; 42:112803. [PMID: 37436897 PMCID: PMC10441531 DOI: 10.1016/j.celrep.2023.112803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/10/2023] [Accepted: 06/26/2023] [Indexed: 07/14/2023] Open
Abstract
During mouse embryogenesis, expression of the long non-coding RNA (lncRNA) Airn leads to gene repression and recruitment of Polycomb repressive complexes (PRCs) to varying extents over a 15-Mb domain. The mechanisms remain unclear. Using high-resolution approaches, we show in mouse trophoblast stem cells that Airn expression induces long-range changes to chromatin architecture that coincide with PRC-directed modifications and center around CpG island promoters that contact the Airn locus even in the absence of Airn expression. Intensity of contact between the Airn lncRNA and chromatin correlated with underlying intensity of PRC recruitment and PRC-directed modifications. Deletion of CpG islands that contact the Airn locus altered long-distance repression and PRC activity in a manner that correlated with changes in chromatin architecture. Our data imply that the extent to which Airn expression recruits PRCs to chromatin is controlled by DNA regulatory elements that modulate proximity of the Airn lncRNA product to its target DNA.
Collapse
Affiliation(s)
- Aki K Braceros
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Megan D Schertzer
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Arina Omer
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jackson B Trotman
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jill M Dowen
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Douglas H Phanstiel
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA; Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
| |
Collapse
|
19
|
Singh A, Rappolee DA, Ruden DM. Epigenetic Reprogramming in Mice and Humans: From Fertilization to Primordial Germ Cell Development. Cells 2023; 12:1874. [PMID: 37508536 PMCID: PMC10377882 DOI: 10.3390/cells12141874] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
In this review, advances in the understanding of epigenetic reprogramming from fertilization to the development of primordial germline cells in a mouse and human embryo are discussed. To gain insights into the molecular underpinnings of various diseases, it is essential to comprehend the intricate interplay between genetic, epigenetic, and environmental factors during cellular reprogramming and embryonic differentiation. An increasing range of diseases, including cancer and developmental disorders, have been linked to alterations in DNA methylation and histone modifications. Global epigenetic reprogramming occurs in mammals at two stages: post-fertilization and during the development of primordial germ cells (PGC). Epigenetic reprogramming after fertilization involves rapid demethylation of the paternal genome mediated through active and passive DNA demethylation, and gradual demethylation in the maternal genome through passive DNA demethylation. The de novo DNA methyltransferase enzymes, Dnmt3a and Dnmt3b, restore DNA methylation beginning from the blastocyst stage until the formation of the gastrula, and DNA maintenance methyltransferase, Dnmt1, maintains methylation in the somatic cells. The PGC undergo a second round of global demethylation after allocation during the formative pluripotent stage before gastrulation, where the imprints and the methylation marks on the transposable elements known as retrotransposons, including long interspersed nuclear elements (LINE-1) and intracisternal A-particle (IAP) elements are demethylated as well. Finally, DNA methylation is restored in the PGC at the implantation stage including sex-specific imprints corresponding to the sex of the embryo. This review introduces a novel perspective by uncovering how toxicants and stress stimuli impact the critical period of allocation during formative pluripotency, potentially influencing both the quantity and quality of PGCs. Furthermore, the comprehensive comparison of epigenetic events between mice and humans breaks new ground, empowering researchers to make informed decisions regarding the suitability of mouse models for their experiments.
Collapse
Affiliation(s)
- Aditi Singh
- CS Mott Center, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, USA; (A.S.); (D.A.R.)
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48202, USA
| | - Daniel A. Rappolee
- CS Mott Center, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, USA; (A.S.); (D.A.R.)
- Reproductive Stress Measurement, Mechanisms and Management, Corp., 135 Lake Shore Rd., Grosse Pointe Farms, MI 48236, USA
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA
- Department of Physiology, Wayne State University, Detroit, MI 48202, USA
| | - Douglas M. Ruden
- CS Mott Center, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, USA; (A.S.); (D.A.R.)
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48202, USA
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA
| |
Collapse
|
20
|
Cherney RE, Mills CA, Herring LE, Braceros AK, Calabrese JM. A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB. Biol Open 2023; 12:bio059955. [PMID: 37283223 PMCID: PMC10259849 DOI: 10.1242/bio.059955] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
The Polycomb Repressive Complex 2 (PRC2) is a conserved enzyme that tri-methylates Lysine 27 on Histone 3 (H3K27me3) to promote gene silencing. PRC2 is remarkably responsive to the expression of certain long noncoding RNAs (lncRNAs). In the most notable example, PRC2 is recruited to the X-chromosome shortly after expression of the lncRNA Xist begins during X-chromosome inactivation. However, the mechanisms by which lncRNAs recruit PRC2 to chromatin are not yet clear. We report that a broadly used rabbit monoclonal antibody raised against human EZH2, a catalytic subunit of PRC2, cross-reacts with an RNA-binding protein called Scaffold Attachment Factor B (SAFB) in mouse embryonic stem cells (ESCs) under buffer conditions that are commonly used for chromatin immunoprecipitation (ChIP). Knockout of EZH2 in ESCs demonstrated that the antibody is specific for EZH2 by western blot (no cross-reactivity). Likewise, comparison to previously published datasets confirmed that the antibody recovers PRC2-bound sites by ChIP-Seq. However, RNA-IP from formaldehyde-crosslinked ESCs using ChIP wash conditions recovers distinct peaks of RNA association that co-localize with peaks of SAFB and whose enrichment disappears upon knockout of SAFB but not EZH2. IP and mass spectrometry-based proteomics in wild-type and EZH2 knockout ESCs confirm that the EZH2 antibody recovers SAFB in an EZH2-independent manner. Our data highlight the importance of orthogonal assays when studying interactions between chromatin-modifying enzymes and RNA.
Collapse
Affiliation(s)
- Rachel E. Cherney
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- RNA Discovery Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - Christine A. Mills
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Proteomics Core Facility, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - Laura E. Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Proteomics Core Facility, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - Aki K. Braceros
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- RNA Discovery Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Curriculum in Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| | - J. Mauro Calabrese
- Department of Pharmacology, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- RNA Discovery Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA.
| |
Collapse
|
21
|
Ma Y, Zhu Y, Shang L, Qiu Y, Shen N, Wang J, Adam T, Wei W, Song Q, Li J, Wicha MS, Luo M. LncRNA XIST regulates breast cancer stem cells by activating proinflammatory IL-6/STAT3 signaling. Oncogene 2023; 42:1419-1437. [PMID: 36922677 PMCID: PMC10154203 DOI: 10.1038/s41388-023-02652-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/19/2023] [Accepted: 02/24/2023] [Indexed: 03/17/2023]
Abstract
Aberrant expression of XIST, a long noncoding RNA (lncRNA) initiating X chromosome inactivation (XCI) in early embryogenesis, is a common feature of breast cancer (BC). However, the roles of post-XCI XIST in breast carcinogenesis remain elusive. Here we identify XIST as a key regulator of breast cancer stem cells (CSCs), which exhibit aldehyde dehydrogenase positive (ALDH+) epithelial- (E) and CD24loCD44hi mesenchymal-like (M) phenotypes. XIST is variably expressed across the spectrum of BC subtypes, and doxycycline (DOX)-inducible knockdown (KD) of XIST markedly inhibits spheroid/colony forming capacity, tumor growth and tumor-initiating potential. This phenotype is attributed to impaired E-CSC in luminal and E- and M-CSC activities in triple-negative (TN) BC. Gene expression profiling unveils that XIST KD most significantly affects cytokine-cytokine receptor interactions, leading to markedly suppressed expression of proinflammatory cytokines IL-6 and IL-8 in ALDH- bulk BC cells. Exogenous IL-6, but not IL-8, rescues the reduced sphere-forming capacity and proportion of ALDH+ E-CSCs in luminal and TN BC upon XIST KD. XIST functions as a nuclear sponge for microRNA let-7a-2-3p to activate IL-6 production from ALDH- bulk BC cells, which acts in a paracrine fashion on ALDH+ E-CSCs that display elevated cell surface IL-6 receptor (IL6R) expression. This promotes CSC self-renewal via STAT3 activation and expression of key CSC factors including c-MYC, KLF4 and SOX9. Together, this study supports a novel role of XIST by derepressing let-7 controlled paracrine IL-6 proinflammatory signaling to promote CSC self-renewal.
Collapse
Affiliation(s)
- Yuxi Ma
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yongyou Zhu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Li Shang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, 48109, USA
| | - Yan Qiu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Na Shen
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jonathan Wang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Tiffany Adam
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Wei Wei
- Department of Breast and Thyroid Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Qingxuan Song
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jun Li
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Max S Wicha
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, 48109, USA.
| | - Ming Luo
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, 48109, USA.
- Department of Breast and Thyroid Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
| |
Collapse
|
22
|
Cherney RE, Mills CA, Herring LE, Braceros AK, Calabrese JM. A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535391. [PMID: 37066147 PMCID: PMC10103960 DOI: 10.1101/2023.04.03.535391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The Polycomb Repressive Complex 2 (PRC2) is a conserved enzyme that tri-methylates Lysine 27 on Histone 3 (H3K27me3) to promote gene silencing. PRC2 is remarkably responsive to the expression of certain long noncoding RNAs (lncRNAs). In the most notable example, PRC2 is recruited to the X-chromosome shortly after expression of the lncRNA Xist begins during X-chromosome inactivation. However, the mechanisms by which lncRNAs recruit PRC2 to chromatin are not yet clear. We report that a broadly used rabbit monoclonal antibody raised against human EZH2, a catalytic subunit of PRC2, cross-reacts with an RNA-binding protein called Scaffold Attachment Factor B (SAFB) in mouse embryonic stem cells (ESCs) under buffer conditions that are commonly used for chromatin immunoprecipitation (ChIP). Knockout of EZH2 in ESCs demonstrated that the antibody is specific for EZH2 by western blot (no cross-reactivity). Likewise, comparison to previously published datasets confirmed that the antibody recovers PRC2-bound sites by ChIP-Seq. However, RNA-IP from formaldehyde-crosslinked ESCs using ChIP wash conditions recovers distinct peaks of RNA association that co-localize with peaks of SAFB and whose enrichment disappears upon knockout of SAFB but not EZH2. IP and mass spectrometry-based proteomics in wild-type and EZH2 knockout ESCs confirm that the EZH2 antibody recovers SAFB in an EZH2-independent manner. Our data highlight the importance of orthogonal assays when studying interactions between chromatin-modifying enzymes and RNA.
Collapse
|
23
|
Nepita I, Piazza S, Ruglioni M, Cristiani S, Bosurgi E, Salvadori T, Vicidomini G, Diaspro A, Castello M, Cerase A, Bianchini P, Storti B, Bizzarri R. On the Advent of Super-Resolution Microscopy in the Realm of Polycomb Proteins. BIOLOGY 2023; 12:374. [PMID: 36979066 PMCID: PMC10044799 DOI: 10.3390/biology12030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023]
Abstract
The genomes of metazoans are organized at multiple spatial scales, ranging from the double helix of DNA to whole chromosomes. The intermediate genomic scale of kilobases to megabases, which corresponds to the 50-300 nm spatial scale, is particularly interesting, as the 3D arrangement of chromatin is implicated in multiple regulatory mechanisms. In this context, polycomb group (PcG) proteins stand as major epigenetic modulators of chromatin function, acting prevalently as repressors of gene transcription by combining chemical modifications of target histones with physical crosslinking of distal genomic regions and phase separation. The recent development of super-resolution microscopy (SRM) has strongly contributed to improving our comprehension of several aspects of nano-/mesoscale (10-200 nm) chromatin domains. Here, we review the current state-of-the-art SRM applied to PcG proteins, showing that the application of SRM to PcG activity and organization is still quite limited and mainly focused on the 3D assembly of PcG-controlled genomic loci. In this context, SRM approaches have mostly been applied to multilabel fluorescence in situ hybridization (FISH). However, SRM data have complemented the maps obtained from chromosome capture experiments and have opened a new window to observe how 3D chromatin topology is modulated by PcGs.
Collapse
Affiliation(s)
- Irene Nepita
- Nanoscopy, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
| | - Simonluca Piazza
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
- R&D Department, Genoa Instruments s.r.l., Via E. Melen 83, 16152 Genova, Italy
| | - Martina Ruglioni
- Department of Surgical, Medical and Molecular Pathology, and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy
| | - Sofia Cristiani
- Department of Surgical, Medical and Molecular Pathology, and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy
| | - Emanuele Bosurgi
- Department of Surgical, Medical and Molecular Pathology, and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy
| | - Tiziano Salvadori
- Department of Surgical, Medical and Molecular Pathology, and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
| | - Alberto Diaspro
- Nanoscopy, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
- DIFILAB, Dipartimento di Fisica, Università degli Studi di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Marco Castello
- Nanoscopy, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
- R&D Department, Genoa Instruments s.r.l., Via E. Melen 83, 16152 Genova, Italy
| | - Andrea Cerase
- Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, Strada Statale dell’Abetone Brennero 4, 56123 Pisa, Italy
| | - Paolo Bianchini
- Nanoscopy, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
- DIFILAB, Dipartimento di Fisica, Università degli Studi di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Barbara Storti
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Ranieri Bizzarri
- Nanoscopy, Istituto Italiano di Tecnologia, Via E. Melen 83, 16152 Genova, Italy
- Department of Surgical, Medical and Molecular Pathology, and Critical Care Medicine, University of Pisa, Via Roma 65, 56126 Pisa, Italy
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127 Pisa, Italy
| |
Collapse
|
24
|
Henry S, Kokity L, Pirity MK. Polycomb protein RYBP activates transcription factor Plagl1 during in vitro cardiac differentiation of mouse embryonic stem cells. Open Biol 2023; 13:220305. [PMID: 36751888 PMCID: PMC9905990 DOI: 10.1098/rsob.220305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
RING1 and YY1 binding protein (RYBP) is primarily known to function as a repressor being a core component of the non-canonical polycomb repressive complexes 1 (ncPRC1s). However, several ncPRC1-independent functions of RYBP have also been described. We previously reported that RYBP is essential for mouse embryonic development and that Rybp null mutant embryonic stem cells cannot form contractile cardiomyocytes (CMCs) in vitro. We also showed that PLAGL1, a cardiac transcription factor, which is often mutated in congenital heart diseases (CHDs), is not expressed in Rybp-null mutant CMCs. However, the underlying mechanism of how RYBP regulates Plagl1 expression was not revealed. Here, we demonstrate that RYBP cooperated with NKX2-5 to transcriptionally activate the P1 and P3 promoters of the Plagl1 gene and that this activation is ncPRC1-independent. We also show that two non-coding RNAs residing in the Plagl1 locus can also regulate the Plagl1 promoters. Finally, PLAGL1 was able to activate Tnnt2, a gene important for contractility of CMCs in transfected HEK293 cells. Our study shows that the activation of Plagl1 by RYBP is important for sarcomere development and contractility, and suggests that RYBP, via its regulatory functions, may contribute to the development of CHDs.
Collapse
Affiliation(s)
- Surya Henry
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Lilla Kokity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Melinda Katalin Pirity
- Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, 6726 Szeged, Hungary
| |
Collapse
|
25
|
Gruhn WH, Tang WW, Dietmann S, Alves-Lopes JP, Penfold CA, Wong FC, Ramakrishna NB, Surani MA. Epigenetic resetting in the human germ line entails histone modification remodeling. SCIENCE ADVANCES 2023; 9:eade1257. [PMID: 36652508 PMCID: PMC9848478 DOI: 10.1126/sciadv.ade1257] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Epigenetic resetting in the mammalian germ line entails acute DNA demethylation, which lays the foundation for gametogenesis, totipotency, and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genes and transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCs exhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signatures at most genes and TEs and the acquisition of a neutral or paused epigenetic state without transcriptional activation. Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such as evolutionarily young TEs and some developmental genes, which require H3K9me3 and H3K27me3, respectively, for efficient transcriptional repression. Accordingly, transcriptional repression in hPGCs presents an exemplary balanced system relying on local maintenance of heterochromatic features and a lack of inductive cues.
Collapse
Affiliation(s)
- Wolfram H. Gruhn
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Walfred W.C. Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Sabine Dietmann
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - João P. Alves-Lopes
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- NORDFERTIL Research Lab Stockholm, Childhood Cancer Research Unit, J9:30, Department of Women’s and Children’s Health, Karolinska Institutet and Karolinska University Hospital, Visionsgatan 4, 17164, Solna, Stockholm, Sweden
| | - Christopher A. Penfold
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Frederick C. K. Wong
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Navin B. Ramakrishna
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore 138672, Singapore
| | - M. Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| |
Collapse
|
26
|
Evolving understandings for the roles of non-coding RNAs in autoimmunity and autoimmune disease. J Autoimmun 2022:102948. [DOI: 10.1016/j.jaut.2022.102948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
|
27
|
Scholl A, De S. Epigenetic Regulation by Polycomb Complexes from Drosophila to Human and Its Relation to Communicable Disease Pathogenesis. Int J Mol Sci 2022; 23:ijms232012285. [PMID: 36293135 PMCID: PMC9603650 DOI: 10.3390/ijms232012285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 12/05/2022] Open
Abstract
Although all cells in the human body are made of the same DNA, these cells undergo differentiation and behave differently during development, through integration of external and internal stimuli via 'specific mechanisms.' Epigenetics is one such mechanism that comprises DNA/RNA, histone modifications, and non-coding RNAs that regulate transcription without changing the genetic code. The discovery of the first Polycomb mutant phenotype in Drosophila started the study of epigenetics more than 80 years ago. Since then, a considerable number of Polycomb Group (PcG) genes in Drosophila have been discovered to be preserved in mammals, including humans. PcG proteins exert their influence through gene repression by acting in complexes, modifying histones, and compacting the chromatin within the nucleus. In this article, we discuss how our knowledge of the PcG repression mechanism in Drosophila translates to human communicable disease research.
Collapse
|
28
|
Hernández-Romero IA, Valdes VJ. De Novo Polycomb Recruitment and Repressive Domain Formation. EPIGENOMES 2022; 6:25. [PMID: 35997371 PMCID: PMC9397058 DOI: 10.3390/epigenomes6030025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
Every cell of an organism shares the same genome; even so, each cellular lineage owns a different transcriptome and proteome. The Polycomb group proteins (PcG) are essential regulators of gene repression patterning during development and homeostasis. However, it is unknown how the repressive complexes, PRC1 and PRC2, identify their targets and elicit new Polycomb domains during cell differentiation. Classical recruitment models consider the pre-existence of repressive histone marks; still, de novo target binding overcomes the absence of both H3K27me3 and H2AK119ub. The CpG islands (CGIs), non-core proteins, and RNA molecules are involved in Polycomb recruitment. Nonetheless, it is unclear how de novo targets are identified depending on the physiological context and developmental stage and which are the leading players stabilizing Polycomb complexes at domain nucleation sites. Here, we examine the features of de novo sites and the accessory elements bridging its recruitment and discuss the first steps of Polycomb domain formation and transcriptional regulation, comprehended by the experimental reconstruction of the repressive domains through time-resolved genomic analyses in mammals.
Collapse
Affiliation(s)
| | - Victor Julian Valdes
- Department of Cell Biology and Development, Institute of Cellular Physiology (IFC), National Autonomous University of Mexico (UNAM), Mexico City 04510, Mexico
| |
Collapse
|
29
|
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.
Collapse
|
30
|
Xist-mediated silencing requires additive functions of SPEN and Polycomb together with differentiation-dependent recruitment of SmcHD1. Cell Rep 2022; 39:110830. [PMID: 35584662 DOI: 10.1016/j.celrep.2022.110830] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/17/2022] [Accepted: 04/26/2022] [Indexed: 11/20/2022] Open
Abstract
X chromosome inactivation (XCI) is mediated by the non-coding RNA Xist, which directs chromatin modification and gene silencing in cis. The RNA binding protein SPEN and associated corepressors have a central role in Xist-mediated gene silencing. Other silencing factors, notably the Polycomb system, have been reported to function downstream of SPEN. In recent work, we found that SPEN has an additional role in correct localization of Xist RNA in cis, indicating that its contribution to chromatin-mediated gene silencing needs to be reappraised. Making use of a SPEN separation-of-function mutation, we show that SPEN and Polycomb pathways, in fact, function in parallel to establish gene silencing. We also find that differentiation-dependent recruitment of the chromosomal protein SmcHD1 is required for silencing many X-linked genes. Our results provide important insights into the mechanism of X inactivation and the coordination of chromatin-based gene regulation with cellular differentiation and development.
Collapse
|
31
|
Dossin F, Heard E. The Molecular and Nuclear Dynamics of X-Chromosome Inactivation. Cold Spring Harb Perspect Biol 2022; 14:a040196. [PMID: 34312245 PMCID: PMC9121902 DOI: 10.1101/cshperspect.a040196] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In female eutherian mammals, dosage compensation of X-linked gene expression is achieved during development through transcriptional silencing of one of the two X chromosomes. Following X chromosome inactivation (XCI), the inactive X chromosome remains faithfully silenced throughout somatic cell divisions. XCI is dependent on Xist, a long noncoding RNA that coats and silences the X chromosome from which it is transcribed. Xist coating triggers a cascade of chromosome-wide changes occurring at the levels of transcription, chromatin composition, chromosome structure, and spatial organization within the nucleus. XCI has emerged as a paradigm for the study of such crucial nuclear processes and the dissection of their functional interplay. In the past decade, the advent of tools to characterize and perturb these processes have provided an unprecedented understanding into their roles during XCI. The mechanisms orchestrating the initiation of XCI as well as its maintenance are thus being unraveled, although many questions still remain. Here, we introduce key aspects of the XCI process and review the recent discoveries about its molecular basis.
Collapse
Affiliation(s)
- François Dossin
- European Molecular Biology Laboratory, Director's Unit, 69117 Heidelberg, Germany
| | - Edith Heard
- European Molecular Biology Laboratory, Director's Unit, 69117 Heidelberg, Germany
| |
Collapse
|
32
|
Wang W, Qiao S, Li G, Cheng J, Yang C, Zhong C, Stovall DB, Shi J, Teng C, Li D, Sui G. A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters. Nucleic Acids Res 2022; 50:4917-4937. [PMID: 35390165 PMCID: PMC9122595 DOI: 10.1093/nar/gkac233] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/19/2022] [Accepted: 04/05/2022] [Indexed: 12/28/2022] Open
Abstract
As an oncogenic transcription factor, Yin Yang 1 (YY1) regulates enhancer and promoter connection. However, gaps still exist in understanding how YY1 coordinates coactivators and chromatin enhancer elements to assemble enhancers and super-enhancers. Here, we demonstrate that a histidine cluster in YY1’s transactivation domain is essential for its formation of phase separation condensates, which can be extended to additional proteins. The histidine cluster is also required for YY1-promoted cell proliferation, migration, clonogenicity and tumor growth. YY1-rich nuclear puncta contain coactivators EP300, BRD4, MED1 and active RNA polymerase II, and colocalize with histone markers of gene activation, but not that of repression. Furthermore, YY1 binds to the consensus motifs in the FOXM1 promoter to activate its expression. Wild-type YY1, but not its phase separation defective mutant, connects multiple enhancer elements and the FOXM1 promoter to form an enhancer cluster. Consistently, fluorescent in situ hybridization (FISH) assays reveal the colocalization of YY1 puncta with both the FOXM1 gene locus and its nascent RNA transcript. Overall, this study demonstrates that YY1 activates target gene expression through forming liquid-liquid phase separation condensates to compartmentalize both coactivators and enhancer elements, and the histidine cluster of YY1 plays a determinant role in this regulatory mechanism.
Collapse
Affiliation(s)
- Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Shiyao Qiao
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jiahui Cheng
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Cuicui Yang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chen Zhong
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Daniel B Stovall
- College of Arts and Sciences, Winthrop University, Rock Hill, SC 29733, USA
| | - Jinming Shi
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chunbo Teng
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| |
Collapse
|
33
|
Li J, Ming Z, Yang L, Wang T, Liu G, Ma Q. Long noncoding RNA XIST: Mechanisms for X chromosome inactivation, roles in sex-biased diseases, and therapeutic opportunities. Genes Dis 2022; 9:1478-1492. [PMID: 36157489 PMCID: PMC9485286 DOI: 10.1016/j.gendis.2022.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022] Open
Abstract
Sexual dimorphism has been reported in various human diseases including autoimmune diseases, neurological diseases, pulmonary arterial hypertension, and some types of cancers, although the underlying mechanisms remain poorly understood. The long noncoding RNA (lncRNA) X-inactive specific transcript (XIST) is involved in X chromosome inactivation (XCI) in female placental mammals, a process that ensures the balanced expression dosage of X-linked genes between sexes. XIST is abnormally expressed in many sex-biased diseases. In addition, escape from XIST-mediated XCI and skewed XCI also contribute to sex-biased diseases. Therefore, its expression or modification can be regarded as a biomarker for the diagnosis and prognosis of many sex-biased diseases. Genetic manipulation of XIST expression can inhibit the progression of some of these diseases in animal models, and therefore XIST has been proposed as a potential therapeutic target. In this manuscript, we summarize the current knowledge about the mechanisms for XIST-mediated XCI and the roles of XIST in sex-biased diseases, and discuss potential therapeutic strategies targeting XIST.
Collapse
|
34
|
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: 97] [Impact Index Per Article: 48.5] [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.
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
X-chromosome reactivation: a concise review. Biochem Soc Trans 2021; 49:2797-2805. [PMID: 34821360 DOI: 10.1042/bst20210777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Mammalian females (XX) silence transcription on one of the two X chromosomes to compensate the expression dosage with males (XY). This process - named X-chromosome inactivation - entails a variety of epigenetic modifications that act synergistically to maintain silencing and make it heritable through cell divisions. Genes along the inactive X chromosome are, indeed, refractory to reactivation. Nonetheless, X-chromosome reactivation can occur alongside with epigenome reprogramming or by perturbing multiple silencing pathways. Here we review the events associated with X-chromosome reactivation during in vivo and in vitro reprogramming and highlight recent efforts in inducing Xi reactivation by molecular perturbations. This provides us with a first understanding of the mechanisms underlying X-chromosome reactivation, which could be tackled for therapeutic purposes.
Collapse
|
37
|
Markaki Y, Gan Chong J, Wang Y, Jacobson EC, Luong C, Tan SYX, Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, Mistry BA, Dror I, Dossin F, Schöneberg J, Heard E, Guttman M, Chou T, Plath K. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell 2021; 184:6174-6192.e32. [PMID: 34813726 PMCID: PMC8671326 DOI: 10.1016/j.cell.2021.10.022] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 07/29/2021] [Accepted: 10/11/2021] [Indexed: 02/08/2023]
Abstract
The lncRNA Xist forms ∼50 diffraction-limited foci to transcriptionally silence one X chromosome. How this small number of RNA foci and interacting proteins regulate a much larger number of X-linked genes is unknown. We show that Xist foci are locally confined, contain ∼2 RNA molecules, and nucleate supramolecular complexes (SMACs) that include many copies of the critical silencing protein SPEN. Aggregation and exchange of SMAC proteins generate local protein gradients that regulate broad, proximal chromatin regions. Partitioning of numerous SPEN molecules into SMACs is mediated by their intrinsically disordered regions and essential for transcriptional repression. Polycomb deposition via SMACs induces chromatin compaction and the increase in SMACs density around genes, which propagates silencing across the X chromosome. Our findings introduce a mechanism for functional nuclear compartmentalization whereby crowding of transcriptional and architectural regulators enables the silencing of many target genes by few RNA molecules.
Collapse
Affiliation(s)
- Yolanda Markaki
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Johnny Gan Chong
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yuying Wang
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elsie C Jacobson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christy Luong
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shawn Y X Tan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joanna W Jachowicz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Davide Maestrini
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Bhaven A Mistry
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Claremont McKenna College, Claremont, CA 91711, USA
| | - Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Francois Dossin
- European Molecular Biology Laboratory, Director's Unit, Heidelberg 69117, Germany
| | - Johannes Schöneberg
- Departments of Pharmacology & Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093, USA
| | - Edith Heard
- European Molecular Biology Laboratory, Director's Unit, Heidelberg 69117, Germany
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
38
|
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Edith Heard
- Director's Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Claire Rougeulle
- Department of Epigenetics and Cell Fate, Université de Paris, CNRS, F-75006 Paris, France
| |
Collapse
|
39
|
Bonitto K, Sarathy K, Atai K, Mitra M, Coller HA. Is There a Histone Code for Cellular Quiescence? Front Cell Dev Biol 2021; 9:739780. [PMID: 34778253 PMCID: PMC8586460 DOI: 10.3389/fcell.2021.739780] [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: 07/12/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022] Open
Abstract
Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.
Collapse
Affiliation(s)
- Kenya Bonitto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kirthana Sarathy
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kaiser Atai
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mithun Mitra
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
40
|
Trotman JB, Braceros KCA, Cherney RE, Murvin MM, Calabrese JM. The control of polycomb repressive complexes by long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1657. [PMID: 33861025 PMCID: PMC8500928 DOI: 10.1002/wrna.1657] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/12/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
The polycomb repressive complexes 1 and 2 (PRCs; PRC1 and PRC2) are conserved histone-modifying enzymes that often function cooperatively to repress gene expression. The PRCs are regulated by long noncoding RNAs (lncRNAs) in complex ways. On the one hand, specific lncRNAs cause the PRCs to engage with chromatin and repress gene expression over genomic regions that can span megabases. On the other hand, the PRCs bind RNA with seemingly little sequence specificity, and at least in the case of PRC2, direct RNA-binding has the effect of inhibiting the enzyme. Thus, some RNAs appear to promote PRC activity, while others may inhibit it. The reasons behind this apparent dichotomy are unclear. The most potent PRC-activating lncRNAs associate with chromatin and are predominantly unspliced or harbor unusually long exons. Emerging data imply that these lncRNAs promote PRC activity through internal RNA sequence elements that arise and disappear rapidly in evolutionary time. These sequence elements may function by interacting with common subsets of RNA-binding proteins that recruit or stabilize PRCs on chromatin. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Jackson B. Trotman
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Keean C. A. Braceros
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rachel E. Cherney
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - McKenzie M. Murvin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - J. Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
41
|
Irwin AB, Bahabry R, Lubin FD. A putative role for lncRNAs in epigenetic regulation of memory. Neurochem Int 2021; 150:105184. [PMID: 34530054 PMCID: PMC8552959 DOI: 10.1016/j.neuint.2021.105184] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
Abstract
The central dogma of molecular genetics is defined as encoded genetic information within DNA, transcribed into messenger RNA, which contain the instructions for protein synthesis, thus imparting cellular functionality and ultimately life. This molecular genetic theory has given birth to the field of neuroepigenetics, and it is now well established that epigenetic regulation of gene transcription is critical to the learning and memory process. In this review, we address a potential role for a relatively new player in the field of epigenetic crosstalk - long non-coding RNAs (lncRNAs). First, we briefly summarize epigenetic mechanisms in memory formation and examine what little is known about the emerging role of lncRNAs during this process. We then focus discussions on how lncRNAs interact with epigenetic mechanisms to control transcriptional programs under various conditions in the brain, and how this may be applied to regulation of gene expression necessary for memory formation. Next, we explore how epigenetic crosstalk in turn serves to regulate expression of various individual lncRNAs themselves. To highlight the importance of further exploring the role of lncRNA in epigenetic regulation of gene expression, we consider the significant relationship between lncRNA dysregulation and declining memory reserve with aging, Alzheimer's disease, and epilepsy, as well as the promise of novel therapeutic interventions. Finally, we conclude with a discussion of the critical questions that remain to be answered regarding a role for lncRNA in memory.
Collapse
Affiliation(s)
- Ashleigh B Irwin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rudhab Bahabry
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
| |
Collapse
|
42
|
Micheel J, Safrastyan A, Wollny D. Advances in Non-Coding RNA Sequencing. Noncoding RNA 2021; 7:70. [PMID: 34842804 PMCID: PMC8628893 DOI: 10.3390/ncrna7040070] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.
Collapse
Affiliation(s)
| | | | - Damian Wollny
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, 07743 Jena, Germany; (J.M.); (A.S.)
| |
Collapse
|
43
|
Sabol M, Calleja-Agius J, Di Fiore R, Suleiman S, Ozcan S, Ward MP, Ozretić P. (In)Distinctive Role of Long Non-Coding RNAs in Common and Rare Ovarian Cancers. Cancers (Basel) 2021; 13:cancers13205040. [PMID: 34680193 PMCID: PMC8534192 DOI: 10.3390/cancers13205040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 02/05/2023] Open
Abstract
Rare ovarian cancers (ROCs) are OCs with an annual incidence of fewer than 6 cases per 100,000 women. They affect women of all ages, but due to their low incidence and the potential clinical inexperience in management, there can be a delay in diagnosis, leading to a poor prognosis. The underlying causes for these tumors are varied, but generally, the tumors arise due to alterations in gene/protein expression in cellular processes that regulate normal proliferation and its checkpoints. Dysregulation of the cellular processes that lead to cancer includes gene mutations, epimutations, non-coding RNA (ncRNA) regulation, posttranscriptional and posttranslational modifications. Long non-coding RNA (lncRNA) are defined as transcribed RNA molecules, more than 200 nucleotides in length which are not translated into proteins. They regulate gene expression through several mechanisms and therefore add another level of complexity to the regulatory mechanisms affecting tumor development. Since few studies have been performed on ROCs, in this review we summarize the mechanisms of action of lncRNA in OC, with an emphasis on ROCs.
Collapse
Affiliation(s)
- Maja Sabol
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta; (J.C.-A.); (R.D.F.); (S.S.)
| | - Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta; (J.C.-A.); (R.D.F.); (S.S.)
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta; (J.C.-A.); (R.D.F.); (S.S.)
| | - Sureyya Ozcan
- Department of Chemistry, Middle East Technical University (METU), 06800 Ankara, Turkey;
- Cancer Systems Biology Laboratory (CanSyl), Middle East Technical University (METU), 06800 Ankara, Turkey
| | - Mark P. Ward
- Department of Histopathology, Trinity St James’s Cancer Institute, Emer Casey Molecular Pathology Laboratory, Trinity College Dublin and Coombe Women’s and Infants University Hospital, D08 RX0X Dublin, Ireland;
| | - Petar Ozretić
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
- Correspondence: ; Tel.: +385-(1)-4571292
| |
Collapse
|
44
|
Exploring chromatin structural roles of non-coding RNAs at imprinted domains. Biochem Soc Trans 2021; 49:1867-1879. [PMID: 34338292 PMCID: PMC8421051 DOI: 10.1042/bst20210758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/11/2022]
Abstract
Different classes of non-coding RNA (ncRNA) influence the organization of chromatin. Imprinted gene domains constitute a paradigm for exploring functional long ncRNAs (lncRNAs). Almost all express an lncRNA in a parent-of-origin dependent manner. The mono-allelic expression of these lncRNAs represses close by and distant protein-coding genes, through diverse mechanisms. Some control genes on other chromosomes as well. Interestingly, several imprinted chromosomal domains show a developmentally regulated, chromatin-based mechanism of imprinting with apparent similarities to X-chromosome inactivation. At these domains, the mono-allelic lncRNAs show a relatively stable, focal accumulation in cis. This facilitates the recruitment of Polycomb repressive complexes, lysine methyltranferases and other nuclear proteins — in part through direct RNA–protein interactions. Recent chromosome conformation capture and microscopy studies indicate that the focal aggregation of lncRNA and interacting proteins could play an architectural role as well, and correlates with close positioning of target genes. Higher-order chromatin structure is strongly influenced by CTCF/cohesin complexes, whose allelic association patterns and actions may be influenced by lncRNAs as well. Here, we review the gene-repressive roles of imprinted non-coding RNAs, particularly of lncRNAs, and discuss emerging links with chromatin architecture.
Collapse
|
45
|
Policarpo R, Sierksma A, De Strooper B, d'Ydewalle C. From Junk to Function: LncRNAs in CNS Health and Disease. Front Mol Neurosci 2021; 14:714768. [PMID: 34349622 PMCID: PMC8327212 DOI: 10.3389/fnmol.2021.714768] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/25/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in RNA sequencing technologies helped to uncover the existence of tens of thousands of long non-coding RNAs (lncRNAs) that arise from the dark matter of the genome. These lncRNAs were originally thought to be transcriptional noise but an increasing number of studies demonstrate that these transcripts can modulate protein-coding gene expression by a wide variety of transcriptional and post-transcriptional mechanisms. The spatiotemporal regulation of lncRNA expression is particularly evident in the central nervous system, suggesting that they may directly contribute to specific brain processes, including neurogenesis and cellular homeostasis. Not surprisingly, lncRNAs are therefore gaining attention as putative novel therapeutic targets for disorders of the brain. In this review, we summarize the recent insights into the functions of lncRNAs in the brain, their role in neuronal maintenance, and their potential contribution to disease. We conclude this review by postulating how these RNA molecules can be targeted for the treatment of yet incurable neurological disorders.
Collapse
Affiliation(s)
- Rafaela Policarpo
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| | - Annerieke Sierksma
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center For Brain & Disease Research, Leuven, Belgium.,Laboratory for the Research of Neurodegenerative Diseases, Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium.,UK Dementia Research Institute, University College London, London, United Kingdom
| | - Constantin d'Ydewalle
- Neuroscience Discovery, Janssen Research & Development, Janssen Pharmaceutica N.V., Beerse, Belgium
| |
Collapse
|
46
|
Aliperti V, Skonieczna J, Cerase A. Long Non-Coding RNA (lncRNA) Roles in Cell Biology, Neurodevelopment and Neurological Disorders. Noncoding RNA 2021; 7:36. [PMID: 34204536 PMCID: PMC8293397 DOI: 10.3390/ncrna7020036] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Development is a complex process regulated both by genetic and epigenetic and environmental clues. Recently, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in several tissues including the brain. Altered expression of lncRNAs has been linked to several neurodegenerative, neurodevelopmental and mental disorders. The identification and characterization of lncRNAs that are deregulated or mutated in neurodevelopmental and mental health diseases are fundamental to understanding the complex transcriptional processes in brain function. Crucially, lncRNAs can be exploited as a novel target for treating neurological disorders. In our review, we first summarize the recent advances in our understanding of lncRNA functions in the context of cell biology and then discussing their association with selected neuronal development and neurological disorders.
Collapse
Affiliation(s)
- Vincenza Aliperti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Justyna Skonieczna
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
| | - Andrea Cerase
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
| |
Collapse
|
47
|
Colognori D, Sunwoo H, Wang D, Wang CY, Lee JT. Xist Repeat A contributes to early recruitment of Polycomb complexes during X-chromosome inactivation. Dev Cell 2021; 56:1236-1237. [PMID: 33945784 DOI: 10.1016/j.devcel.2021.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- David Colognori
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hongjae Sunwoo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Danni Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chen-Yu Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
48
|
Fursova NA, Turberfield AH, Blackledge NP, Findlater EL, Lastuvkova A, Huseyin MK, Dobrinić P, Klose RJ. BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome. Genes Dev 2021; 35:749-770. [PMID: 33888563 PMCID: PMC8091973 DOI: 10.1101/gad.347005.120] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/02/2021] [Indexed: 12/21/2022]
Abstract
Histone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A monoubiquitylation (H2AK119ub1), which is enriched at Polycomb-repressed gene promoters but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we found that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive genome-wide accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 preferentially counteracts Ser5 phosphorylation on the C-terminal domain of RNA polymerase II at gene regulatory elements and causes reductions in transcription and transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes, which leads to their derepression, providing a potential molecular rationale for why the BAP1 ortholog in Drosophila has been characterized as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification.
Collapse
Affiliation(s)
- Nadezda A Fursova
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anne H Turberfield
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Emma L Findlater
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Paula Dobrinić
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| |
Collapse
|
49
|
Wei G, Almeida M, Bowness JS, Nesterova TB, Brockdorff N. Xist Repeats B and C, but not Repeat A, mediate de novo recruitment of the Polycomb system in X chromosome inactivation. Dev Cell 2021; 56:1234-1235. [PMID: 33945783 DOI: 10.1016/j.devcel.2021.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Guifeng Wei
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mafalda Almeida
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joseph S Bowness
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Tatyana B Nesterova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
50
|
Tjalsma SJD, Hori M, Sato Y, Bousard A, Ohi A, Raposo AC, Roensch J, Le Saux A, Nogami J, Maehara K, Kujirai T, Handa T, Bagés‐Arnal S, Ohkawa Y, Kurumizaka H, da Rocha ST, Żylicz JJ, Kimura H, Heard E. H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing. EMBO Rep 2021; 22:e51989. [PMID: 33605056 PMCID: PMC7926250 DOI: 10.15252/embr.202051989] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/22/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
During X chromosome inactivation (XCI), in female placental mammals, gene silencing is initiated by the Xist long non-coding RNA. Xist accumulation at the X leads to enrichment of specific chromatin marks, including PRC2-dependent H3K27me3 and SETD8-dependent H4K20me1. However, the dynamics of this process in relation to Xist RNA accumulation remains unknown as is the involvement of H4K20me1 in initiating gene silencing. To follow XCI dynamics in living cells, we developed a genetically encoded, H3K27me3-specific intracellular antibody or H3K27me3-mintbody. By combining live-cell imaging of H3K27me3, H4K20me1, the X chromosome and Xist RNA, with ChIP-seq analysis we uncover concurrent accumulation of both marks during XCI, albeit with distinct genomic distributions. Furthermore, using a Xist B and C repeat mutant, which still shows gene silencing on the X but not H3K27me3 deposition, we also find a complete lack of H4K20me1 enrichment. This demonstrates that H4K20me1 is dispensable for the initiation of gene silencing, although it may have a role in the chromatin compaction that characterises facultative heterochromatin.
Collapse
Affiliation(s)
- Sjoerd J D Tjalsma
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
| | - Mayako Hori
- Graduate School of Bioscience and BiotechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Yuko Sato
- Graduate School of Bioscience and BiotechnologyTokyo Institute of TechnologyYokohamaJapan
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
| | - Aurelie Bousard
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
| | - Akito Ohi
- Graduate School of Bioscience and BiotechnologyTokyo Institute of TechnologyYokohamaJapan
| | - Ana Cláudia Raposo
- Faculdade de MedicinaInstituto de Medicina MolecularJoão Lobo AntunesUniversidade de LisboaLisboaPortugal
| | - Julia Roensch
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
| | - Agnes Le Saux
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
| | - Jumpei Nogami
- Division of TranscriptomicsMedical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Kazumitsu Maehara
- Division of TranscriptomicsMedical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Tomoya Kujirai
- Institute for Quantitative BiosciencesThe University of TokyoTokyoJapan
| | - Tetsuya Handa
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
| | - Sandra Bagés‐Arnal
- The Novo Nordisk Foundation Center for Stem Cell BiologyCopenhagenDenmark
| | - Yasuyuki Ohkawa
- Division of TranscriptomicsMedical Institute of BioregulationKyushu UniversityFukuokaJapan
| | | | - Simão Teixeira da Rocha
- Faculdade de MedicinaInstituto de Medicina MolecularJoão Lobo AntunesUniversidade de LisboaLisboaPortugal
| | - Jan J Żylicz
- Mammalian Developmental Epigenetics GroupInstitut CurieCNRS UMR3215, INSERM U934PSL UniversityParisFrance
- The Novo Nordisk Foundation Center for Stem Cell BiologyCopenhagenDenmark
- Department of PhysiologyDevelopment and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Hiroshi Kimura
- Graduate School of Bioscience and BiotechnologyTokyo Institute of TechnologyYokohamaJapan
- Cell Biology CenterInstitute of Innovative ResearchTokyo Institute of TechnologyYokohamaJapan
| | - Edith Heard
- EMBL HeidelbergHeidelbergGermany
- Collège de FranceParisFrance
| |
Collapse
|