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Abstract
The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid-liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric heterochromatin domains. In this review, we will describe our understanding of heterochromatin organization and LLPS. In addition, we will highlight the increasing importance of multivalent weak homo- and heteromolecular interactions in LLPS-mediated heterochromatin compartmentalization in the complex environment inside living cells.
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Affiliation(s)
- Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - Hector Romero
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Faculty of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany,CONTACT M. Cristina Cardoso Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287Darmstadt, Germany
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2
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Sidhwani P, Straight AF. Epigenetic inheritance and boundary maintenance at human centromeres. Curr Opin Struct Biol 2023; 82:102694. [PMID: 37657353 PMCID: PMC10530090 DOI: 10.1016/j.sbi.2023.102694] [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: 02/27/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/03/2023]
Abstract
Centromeres are chromosomal regions that provide the foundation for microtubule attachment during chromosome segregation. Centromeres are epigenetically defined by nucleosomes containing the histone H3 variant centromere protein A (CENP-A) and, in many organisms, are surrounded by transcriptionally repressed pericentromeric chromatin marked by trimethylation of histone H3 lysine 9 (H3K9me3). Pericentromeric regions facilitate sister chromatid cohesion during mitosis, thereby supporting centromere function. Heterochromatin has a known propensity to spread into adjacent euchromatic domains unless it is properly bounded. Heterochromatin spreading into the centromere can disrupt kinetochore function, perturbing chromosome segregation and genome stability. In the fission yeast Schizosaccharomyces pombe, tRNA genes provide barriers to heterochromatin spread at the centromere, the absence of which results in abnormal meiotic chromosome segregation. How heterochromatin-centromere boundaries are established in humans is not understood. We propose models for stable epigenetic inheritance of centromeric domains in humans and discuss advances that will enable the discovery of novel regulators of this process.
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Affiliation(s)
- Pragya Sidhwani
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States. https://twitter.com/@pra_sidh
| | - Aaron F Straight
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States.
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3
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Zhou J, Lei X, Shafiq S, Zhang W, Li Q, Li K, Zhu J, Dong Z, He XJ, Sun Q. DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis. SCIENCE ADVANCES 2023; 9:eadg2699. [PMID: 37566662 PMCID: PMC10421056 DOI: 10.1126/sciadv.adg2699] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/13/2023] [Indexed: 08/13/2023]
Abstract
Programmed constitutive heterochromatin silencing is essential for eukaryotic genome regulation, yet the initial step of this process is ambiguous. A large proportion of R-loops (RNA:DNA hybrids) had been unexpectedly identified within Arabidopsis pericentromeric heterochromatin with unknown functions. Through a genome-wide R-loop profiling screen, we find that DDM1 (decrease in DNA methylation 1) is the primary restrictor of pericentromeric R-loops via its RNA:DNA helicase activity. Low levels of pericentromeric R-loops resolved by DDM1 cotranscriptionally can facilitate constitutive heterochromatin silencing. Furthermore, we demonstrate that DDM1 physically excludes histone H2A variant H2A.Z and promotes H2A.W deposition for faithful heterochromatin initiation soon after R-loop clearance. The dual functions of DDM1 in R-loop resolution and H2A.Z eviction are essential for sperm nuclei structure maintenance in mature pollen. Our work unravels the cotranscriptional R-loop resolution coupled with accurate H2A variants deposition is the primary step of constitutive heterochromatin silencing in Arabidopsis, which might be conserved across eukaryotes.
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Affiliation(s)
- Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xue Lei
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Sarfraz Shafiq
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Weifeng Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qin Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Jiafu Zhu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xin-jian He
- National Institute of Biological Sciences, Beijing, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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4
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Han JDJ. LncRNAs: the missing link to senescence nuclear architecture. Trends Biochem Sci 2023; 48:618-628. [PMID: 37069045 DOI: 10.1016/j.tibs.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023]
Abstract
During cellular senescence and organismal aging, cells display various molecular and morphological changes. Although many aging-related long noncoding RNAs (lncRNAs) are highly associated with senescence-associated secretory phenotype, the roles of lncRNAs in senescence-associated nuclear architecture and morphological changes are just starting to emerge. Here I review lncRNAs associated with nuclear structure establishment and maintenance, their aging-related changes, and then focus on the pervasive, yet underappreciated, role of RNA double-strand DNA triplexes for lncRNAs to recognize targeted genomic regions, making lncRNAs the nexus between DNA and proteins to regulate nuclear structural changes. Finally, I discuss the future of deciphering direct links of lncRNA changes to various nuclear morphology changes assisted by artificial intelligence and genetic perturbations.
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Affiliation(s)
- Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China; International Center for Aging and Cancer (ICAC), The First Affiliated Hospital, Hainan Medical University, Haikou, China.
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5
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Örkenby L, Skog S, Ekman H, Gozzo A, Kugelberg U, Ramesh R, Magadi S, Zambanini G, Nordin A, Cantú C, Nätt D, Öst A. Stress-sensitive dynamics of miRNAs and Elba1 in Drosophila embryogenesis. Mol Syst Biol 2023; 19:e11148. [PMID: 36938679 PMCID: PMC10167479 DOI: 10.15252/msb.202211148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 03/21/2023] Open
Abstract
Early-life stress can result in life-long effects that impact adult health and disease risk, but little is known about how such programming is established and maintained. Here, we show that such epigenetic memories can be initiated in the Drosophila embryo before the major wave of zygotic transcription, and higher-order chromatin structures are established. An early short heat shock results in elevated levels of maternal miRNA and reduced levels of a subgroup of zygotic genes in stage 5 embryos. Using a Dicer-1 mutant, we show that the stress-induced decrease in one of these genes, the insulator-binding factor Elba1, is dependent on functional miRNA biogenesis. Reduction in Elba1 correlates with the upregulation of early developmental genes and promotes a sustained weakening of heterochromatin in the adult fly as indicated by an increased expression of the PEV wm4h reporter. We propose that maternal miRNAs, retained in response to an early embryonic heat shock, shape the subsequent de novo heterochromatin establishment that occurs during early development via direct or indirect regulation of some of the earliest expressed genes, including Elba1.
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Affiliation(s)
- Lovisa Örkenby
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Signe Skog
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Helen Ekman
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Alessandro Gozzo
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Unn Kugelberg
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Rashmi Ramesh
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Srivathsa Magadi
- Division of Neurobiology (NEURO), Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Division of Molecular Medicine and Virology (MMV), Linköping University, Linköping, Sweden
| | - Anna Nordin
- Division of Molecular Medicine and Virology (MMV), Linköping University, Linköping, Sweden
| | - Claudio Cantú
- Division of Molecular Medicine and Virology (MMV), Linköping University, Linköping, Sweden
| | - Daniel Nätt
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anita Öst
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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Zhang X, Jiang Q, Li J, Zhang S, Cao Y, Xia X, Cai D, Tan J, Chen J, Han JDJ. KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA-DNA triplexes and HP1 binding. Nat Cell Biol 2022; 24:1617-1629. [PMID: 36266489 DOI: 10.1038/s41556-022-01008-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 09/07/2022] [Indexed: 01/18/2023]
Abstract
Transposon (de)repression and heterochromatin reorganization are dynamically regulated during cell fate determination and are hallmarks of cellular senescence. However, whether they are sequence specifically regulated remains unknown. Here we uncover that the KCNQ1OT1 lncRNA, by sequence-specific Hoogsteen base pairing with double-stranded genomic DNA via its repeat-rich region and binding to the heterochromatin protein HP1α, guides, induces and maintains epigenetic silencing at specific repetitive DNA elements. Repressing KCNQ1OT1 or deleting its repeat-rich region reduces DNA methylation and H3K9me3 on KCNQ1OT1-targeted transposons. Engineering a fusion KCNQ1OT1 with an ectopically targeting guiding triplex sequence induces de novo DNA methylation at the target site. Phenotypically, repressing KCNQ1OT1 induces senescence-associated heterochromatin foci, transposon activation and retrotransposition as well as cellular senescence, demonstrating an essential role of KCNQ1OT1 to safeguard against genome instability and senescence.
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Affiliation(s)
- Xiaoli Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Quanlong Jiang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiyang Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shiqiang Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian Xia
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Donghong Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Tan
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China.
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Nuclear matrix associated RNAs in posterior silk glands show developmental dynamics in Bombyx mori in 5th instar larvae. BMC Res Notes 2022; 15:68. [PMID: 35183251 PMCID: PMC8858543 DOI: 10.1186/s13104-022-05951-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 02/03/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES The nuclear matrix maintains and regulates chromatin structure. RNA is an integral component of the nuclear matrix and is essential to its structural maintenance. Bombyx mori is a major economic contributor in the sericulture industry and produces fibroin-the most important silk protein in its posterior silk glands during 5th instar larval stage. The present study investigates the composition of nuclear matrix RNA prepared from the posterior silk glands of Bombyx mori during fifth instar larval stage where maximum silk production occurs. The datasets from which the analysis is carried out are part of data note titled "Nuclear matrix associated RNA datasets of posterior silk glands of Bombyx mori during 5th instar larval development". RESULTS The results showed significant enrichment of nuclear matrix RNA from day 1, to day 5 and day 7. Nuclear RNA showed increased abundance from day 1 to day 5 and day 7. Nuclear matrix RNA exhibited repetitive RNA sequences, of which UGUCC and GCUGGU were the most abundant. Genes involved in metabolic pathways showed significant enrichment correlating with silk production. These results emphasize the role of dynamic, repetitive DNA transcripts in chromatin architecture and further reveal the close association between the nuclear matrix and gene expression.
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Garrido-Ramos MA. The Genomics of Plant Satellite DNA. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:103-143. [PMID: 34386874 DOI: 10.1007/978-3-030-74889-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.
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Bitman-Lotan E, Orian A. Nuclear organization and regulation of the differentiated state. Cell Mol Life Sci 2021; 78:3141-3158. [PMID: 33507327 PMCID: PMC8038961 DOI: 10.1007/s00018-020-03731-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/22/2022]
Abstract
Regulation of the differentiated identity requires active and continued supervision. Inability to maintain the differentiated state is a hallmark of aging and aging-related disease. To maintain cellular identity, a network of nuclear regulators is devoted to silencing previous and non-relevant gene programs. This network involves transcription factors, epigenetic regulators, and the localization of silent genes to heterochromatin. Together, identity supervisors mold and maintain the unique nuclear environment of the differentiated cell. This review describes recent discoveries regarding mechanisms and regulators that supervise the differentiated identity and protect from de-differentiation, tumorigenesis, and attenuate forced somatic cell reprograming. The review focuses on mechanisms involved in H3K9me3-decorated heterochromatin and the importance of nuclear lamins in cell identity. We outline how the biophysical properties of these factors are involved in self-compartmentalization of heterochromatin and cell identity. Finally, we discuss the relevance of these regulators to aging and age-related disease.
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Affiliation(s)
- Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel.
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10
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Wu SK, Roberts JT, Balas MM, Johnson AM. RNA matchmaking in chromatin regulation. Biochem Soc Trans 2020; 48:2467-2481. [PMID: 33245317 PMCID: PMC7888525 DOI: 10.1042/bst20191225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 01/12/2023]
Abstract
Beyond being the product of gene expression, RNA can also influence the regulation of chromatin. The majority of the human genome has the capacity to be transcribed and the majority of the non-protein-coding transcripts made by RNA Polymerase II are enriched in the nucleus. Many chromatin regulators can bind to these ncRNAs in the nucleus; in some cases, there are clear examples of direct RNA-mediated chromatin regulation mechanisms stemming from these interactions, while others have yet to be determined. Recent studies have highlighted examples of chromatin regulation via RNA matchmaking, a term we use broadly here to describe intermolecular base-pairing interactions between one RNA molecule and an RNA or DNA match. This review provides examples of RNA matchmaking that regulates chromatin processes and summarizes the technical approaches used to capture these events.
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Affiliation(s)
- Stephen K. Wu
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
| | - Justin T. Roberts
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
| | - Maggie M. Balas
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
| | - Aaron M. Johnson
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17 Ave., Aurora, CO, United States
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Tian Y, Cui L, Lin C, Wang Y, Liu Z, Miao X. LncRNA CDKN2B-AS1 relieved inflammation of ulcerative colitis via sponging miR-16 and miR-195. Int Immunopharmacol 2020; 88:106970. [PMID: 33182065 DOI: 10.1016/j.intimp.2020.106970] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND This study was aimed to explore the differential expression of lncRNA CDKN2B-AS1-miR-195-5p/miR-16-5p axis in ulcerative colitis (UC) and its role in regulating UC pathogenesis. METHODS One hundred and eighty-seven UC patients and one hundred and fifty-two healthy volunteers were recruited, and their blood samples were collected. Inflammatory cytokines in serum were determined with ELISA, and lncRNA CDKN2B-AS1, miR-195-5p and miR-16-5p levels were detected with RT-PCR. Then pcDNA3.1-CDKN2B-AS1, si-CDKN2B-AS1, miR-195-5p mimic, miR-195-5p inhibitor, miR-16-5p mimic and miR-16-5p inhibitor were transfected into HT29 cells, and proliferation and apoptosis of the cells were assessed. Dual-luciferase reporter gene assay was implemented to identify the sponging relationship between lncRNA CDKN2B-AS1 and miR-195-5p/miR-16-5p. RESULTS CDKN2B-AS1 level was negatively correlated with levels of inflammatory cytokines, including TNF-α, IL-6 and sIL-2R, yet miR-16-5p and miR-195-5p levels were negatively correlated with the CDKN2B-AS1 level. The CDKN2B-AS1 combined with miR-16-5p and miR-195-5p also achieved an optimum efficacy in differentiating between light and medium UC, light and severe UC, as well as medium and heavy UC. Furthermore, pcDNA3.1-CDKN2B-AS1 depressed expressions of IFN-γ, IL-8, IL-1β and TNF-α in HT29 cells (P < 0.05), and strengthened proliferation of the cells (P < 0.05). CDKN2B-AS1 also sponged and regulated miR-16-5p and miR-195-5p in HT29 cells, and miR-16-5p and miR-195-5p could reverse the effect of CDKN2B-AS1 on inflammatory cytokine production, barrier function and apoptosis of HT29 cells (P < 0.05). CONCLUSION LncRNA CDKN2B-AS1 regulated inflammation of UC by sponging miR-195-5p and miR-16-5p, providing an alternative for diagnosis and treatment of UC.
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Affiliation(s)
- Yuanyuan Tian
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China
| | - Lujia Cui
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China
| | - Cheng Lin
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China
| | - Yuxuan Wang
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China
| | - Zhanju Liu
- Department of Pathology, Haikou Hospital of Traditional Chinese Medicine, Haikou City, Hainan Province 570216, China
| | - Xinpu Miao
- Department of Gastroenterology, Hainan General Hospital & Hainan Affiliated Hospital of Hainan Medical University, Haikou City, Hainan Province 570311, China.
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Gylling HM, Gonzalez-Aguilera C, Smith MA, Kaczorowski DC, Groth A, Lund AH. Repeat RNAs associate with replication forks and post-replicative DNA. RNA (NEW YORK, N.Y.) 2020; 26:1104-1117. [PMID: 32393525 PMCID: PMC7430672 DOI: 10.1261/rna.074757.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Noncoding RNA has a proven ability to direct and regulate chromatin modifications by acting as scaffolds between DNA and histone-modifying complexes. However, it is unknown if ncRNA plays any role in DNA replication and epigenome maintenance, including histone eviction and reinstallment of histone modifications after genome duplication. Isolation of nascent chromatin has identified a large number of RNA-binding proteins in addition to unknown components of the replication and epigenetic maintenance machinery. Here, we isolated and characterized long and short RNAs associated with nascent chromatin at active replication forks and track RNA composition during chromatin maturation across the cell cycle. Shortly after fork passage, GA-rich-, alpha- and TElomeric Repeat-containing RNAs (TERRA) are associated with replicated DNA. These repeat containing RNAs arise from loci undergoing replication, suggesting an interaction in cis. Post-replication during chromatin maturation, and even after mitosis in G1, the repeats remain enriched on DNA. This suggests that specific types of repeat RNAs are transcribed shortly after DNA replication and stably associate with their loci of origin throughout the cell cycle. The presented method and data enable studies of RNA interactions with replication forks and post-replicative chromatin and provide insights into how repeat RNAs and their engagement with chromatin are regulated with respect to DNA replication and across the cell cycle.
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Affiliation(s)
- Helene M Gylling
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark
| | | | - Martin A Smith
- Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
- St-Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst, New South Wales 2010, Australia
| | | | - Anja Groth
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark
- The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark
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14
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Corless S, Höcker S, Erhardt S. Centromeric RNA and Its Function at and Beyond Centromeric Chromatin. J Mol Biol 2020; 432:4257-4269. [DOI: 10.1016/j.jmb.2020.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/21/2022]
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15
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RNA-mediated regulation of chromatin structures. Genes Genomics 2020; 42:609-617. [PMID: 32297146 DOI: 10.1007/s13258-020-00929-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 03/27/2020] [Indexed: 12/26/2022]
Abstract
It is now evident that transcriptional gene regulation usually requires the re-organization of chromatin architecture. Increasing evidence suggested various kinds of RNAs are involved in this process. Especially the nascent RNAs retained at their site of transcription can serve as a scaffold for organizing transcriptionally either favorable or unfavorable chromatin structures. An emerging concept of phase separation explains how these chromatin structures can be maintained as physically discrete subcompartments within membrane-less nucleoplasm. Evidences that support the crucial role of nascent RNAs in the formation of phase-separated condensates are now rapidly growing.
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16
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LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay. Nat Cell Biol 2020; 22:579-590. [PMID: 32251399 PMCID: PMC7212045 DOI: 10.1038/s41556-020-0504-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/05/2020] [Indexed: 12/20/2022]
Abstract
In fission yeast and plants, RNA-processing and degradation contribute to
heterochromatin silencing, alongside conserved pathways of transcriptional
repression. It was unknown if similar pathways exist in metazoans. Here we
describe a pathway of silencing in C. elegans somatic cells, in
which the highly conserved RNA binding complex LSM2-8 contributes selectively to
the repression of heterochromatic reporters and endogenous genes bearing the
Polycomb mark, histone H3K27me3. It acts by degrading selected transcripts
through the XRN-2 exoribonuclease. Disruption of the LSM2-8 pathway leads to
mRNA stabilization. Unlike previously described pathways of heterochromatic RNA
degradation, LSM2-8-mediated RNA degradation does not require nor deposit H3K9
methylation. Rather, loss of this pathway coincides with a localized reduction
in H3K27me3 at lsm-8-sensitive loci. Thus, we have uncovered a
mechanism of RNA degradation that selectively contributes to the silencing of a
subset of H3K27me3-marked genes, revealing a previously unrecognized layer of
post-transcriptional control in metazoan heterochromatin.
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17
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Taglini F, Chapman E, van Nues R, Theron E, Bayne EH. Mkt1 is required for RNAi-mediated silencing and establishment of heterochromatin in fission yeast. Nucleic Acids Res 2020; 48:1239-1253. [PMID: 31822915 PMCID: PMC7026591 DOI: 10.1093/nar/gkz1157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/12/2019] [Accepted: 11/28/2019] [Indexed: 01/04/2023] Open
Abstract
Constitutive domains of repressive heterochromatin are maintained within the fission yeast genome through self-reinforcing mechanisms involving histone methylation and small RNAs. Non-coding RNAs generated from heterochromatic regions are processed into small RNAs by the RNA interference pathway, and are subject to silencing through both transcriptional and post-transcriptional mechanisms. While the pathways involved in maintenance of the repressive heterochromatin state are reasonably well understood, less is known about the requirements for its establishment. Here, we describe a novel role for the post-transcriptional regulatory factor Mkt1 in establishment of heterochromatin at pericentromeres in fission yeast. Loss of Mkt1 does not affect maintenance of existing heterochromatin, but does affect its recovery following depletion, as well as de novo establishment of heterochromatin on a mini-chromosome. Pathway dissection revealed that Mkt1 is required for RNAi-mediated post-transcriptional silencing, downstream of small RNA production. Mkt1 physically associates with pericentromeric transcripts, and is additionally required for maintenance of silencing and heterochromatin at centromeres when transcriptional silencing is impaired. Our findings provide new insight into the mechanism of RNAi-mediated post-transcriptional silencing in fission yeast, and unveil an important role for post-transcriptional silencing in establishment of heterochromatin that is dispensable when full transcriptional silencing is imposed.
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Affiliation(s)
- Francesca Taglini
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Elliott Chapman
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rob van Nues
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Emmanuelle Theron
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Elizabeth H Bayne
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
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18
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Chen JY, Lim DH, Fu XD. Mechanistic Dissection of RNA-Binding Proteins in Regulated Gene Expression at Chromatin Levels. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:55-66. [PMID: 31900328 PMCID: PMC7332398 DOI: 10.1101/sqb.2019.84.039222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Eukaryotic genomes are known to prevalently transcribe diverse classes of RNAs, virtually all of which, including nascent RNAs from protein-coding genes, are now recognized to have regulatory functions in gene expression, suggesting that RNAs are both the products and the regulators of gene expression. Their functions must enlist specific RNA-binding proteins (RBPs) to execute their regulatory activities, and recent evidence suggests that nearly all biochemically defined chromatin regions in the human genome, whether defined for gene activation or silencing, have the involvement of specific RBPs. Interestingly, the boundary between RNA- and DNA-binding proteins is also melting, as many DNA-binding proteins traditionally studied in the context of transcription are able to bind RNAs, some of which may simultaneously bind both DNA and RNA to facilitate network interactions in three-dimensional (3D) genome. In this review, we focus on RBPs that function at chromatin levels, with particular emphasis on their mechanisms of action in regulated gene expression, which is intended to facilitate future functional and mechanistic dissection of chromatin-associated RBPs.
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Affiliation(s)
- Jia-Yu Chen
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Do-Hwan Lim
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, California 92093, USA
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19
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Erenpreisa J, Giuliani A. Resolution of Complex Issues in Genome Regulation and Cancer Requires Non-Linear and Network-Based Thermodynamics. Int J Mol Sci 2019; 21:E240. [PMID: 31905791 PMCID: PMC6981914 DOI: 10.3390/ijms21010240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/22/2019] [Accepted: 12/27/2019] [Indexed: 02/06/2023] Open
Abstract
The apparent lack of success in curing cancer that was evidenced in the last four decades of molecular medicine indicates the need for a global re-thinking both its nature and the biological approaches that we are taking in its solution. The reductionist, one gene/one protein method that has served us well until now, and that still dominates in biomedicine, requires complementation with a more systemic/holistic approach, to address the huge problem of cross-talk between more than 20,000 protein-coding genes, about 100,000 protein types, and the multiple layers of biological organization. In this perspective, the relationship between the chromatin network organization and gene expression regulation plays a fundamental role. The elucidation of such a relationship requires a non-linear thermodynamics approach to these biological systems. This change of perspective is a necessary step for developing successful 'tumour-reversion' therapeutic strategies.
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Affiliation(s)
- Jekaterina Erenpreisa
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Alessandro Giuliani
- Environmental and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy;
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20
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Shen BA, Landick R. Transcription of Bacterial Chromatin. J Mol Biol 2019; 431:4040-4066. [PMID: 31153903 PMCID: PMC7248592 DOI: 10.1016/j.jmb.2019.05.041] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Decades of research have probed the interplay between chromatin (genomic DNA associated with proteins and RNAs) and transcription by RNA polymerase (RNAP) in all domains of life. In bacteria, chromatin is compacted into a membrane-free region known as the nucleoid that changes shape and composition depending on the bacterial state. Transcription plays a key role in both shaping the nucleoid and organizing it into domains. At the same time, chromatin impacts transcription by at least five distinct mechanisms: (i) occlusion of RNAP binding; (ii) roadblocking RNAP progression; (iii) constraining DNA topology; (iv) RNA-mediated interactions; and (v) macromolecular demixing and heterogeneity, which may generate phase-separated condensates. These mechanisms are not mutually exclusive and, in combination, mediate gene regulation. Here, we review the current understanding of these mechanisms with a focus on gene silencing by H-NS, transcription coordination by HU, and potential phase separation by Dps. The myriad questions about transcription of bacterial chromatin are increasingly answerable due to methodological advances, enabling a needed paradigm shift in the field of bacterial transcription to focus on regulation of genes in their native state. We can anticipate answers that will define how bacterial chromatin helps coordinate and dynamically regulate gene expression in changing environments.
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Affiliation(s)
- Beth A Shen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States.
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21
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Abstract
Mammalian genomes are extensively transcribed, which produces a large number of both coding and non-coding transcripts. Various RNAs are physically associated with chromatin, through being either retained in cis at their site of transcription or recruited in trans to other genomic regions. Driven by recent technological innovations for detecting chromatin-associated RNAs, diverse roles are being revealed for these RNAs and associated RNA-binding proteins (RBPs) in gene regulation and genome function. Such functions include locus-specific roles in gene activation and silencing, as well as emerging roles in higher-order genome organization, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions.
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Affiliation(s)
- Xiao Li
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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22
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Pillon MC, Lo YH, Stanley RE. IT'S 2 for the price of 1: Multifaceted ITS2 processing machines in RNA and DNA maintenance. DNA Repair (Amst) 2019; 81:102653. [PMID: 31324529 PMCID: PMC6764878 DOI: 10.1016/j.dnarep.2019.102653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cells utilize sophisticated RNA processing machines to ensure the quality of RNA. Many RNA processing machines have been further implicated in regulating the DNA damage response signifying a strong link between RNA processing and genome maintenance. One of the most intricate and highly regulated RNA processing pathways is the processing of the precursor ribosomal RNA (pre-rRNA), which is paramount for the production of ribosomes. Removal of the Internal Transcribed Spacer 2 (ITS2), located between the 5.8S and 25S rRNA, is one of the most complex steps of ribosome assembly. Processing of the ITS2 is initiated by the newly discovered endoribonuclease Las1, which cleaves at the C2 site within the ITS2, generating products that are further processed by the polynucleotide kinase Grc3, the 5'→3' exonuclease Rat1, and the 3'→5' RNA exosome complex. In addition to their defined roles in ITS2 processing, these critical cellular machines participate in other stages of ribosome assembly, turnover of numerous cellular RNAs, and genome maintenance. Here we summarize recent work defining the molecular mechanisms of ITS2 processing by these essential RNA processing machines and highlight their emerging roles in transcription termination, heterochromatin function, telomere maintenance, and DNA repair.
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Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Yu-Hua Lo
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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23
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Jang SM, Kauzlaric A, Quivy JP, Pontis J, Rauwel B, Coluccio A, Offner S, Duc J, Turelli P, Almouzni G, Trono D. KAP1 facilitates reinstatement of heterochromatin after DNA replication. Nucleic Acids Res 2019; 46:8788-8802. [PMID: 29955894 PMCID: PMC6158507 DOI: 10.1093/nar/gky580] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/25/2018] [Indexed: 12/30/2022] Open
Abstract
During cell division, maintenance of chromatin features from the parental genome requires their proper establishment on its newly synthetized copy. The loss of epigenetic marks within heterochromatin, typically enriched in repetitive elements, endangers genome stability and permits chromosomal rearrangements via recombination. However, how histone modifications associated with heterochromatin are maintained across mitosis remains poorly understood. KAP1 is known to act as a scaffold for a repressor complex that mediates local heterochromatin formation, and was previously demonstrated to play an important role during DNA repair. Accordingly, we investigated a putative role for this protein in the replication of heterochromatic regions. We first found that KAP1 associates with several DNA replication factors including PCNA, MCM3 and MCM6. We then observed that these interactions are promoted by KAP1 phosphorylation on serine 473 during S phase. Finally, we could demonstrate that KAP1 forms a complex with PCNA and the histone-lysine methyltransferase Suv39h1 to reinstate heterochromatin after DNA replication.
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Affiliation(s)
- Suk Min Jang
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Annamaria Kauzlaric
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Jean-Pierre Quivy
- Institut Curie, Centre de Recherche, Paris 75248, France.,Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France.,Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France.,Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France.,Sorbonne University, PSL, Paris 75005, France
| | - Julien Pontis
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Benjamin Rauwel
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Andrea Coluccio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris 75248, France.,Centre National de la Recherche Scientifique (CNRS), UMR3664, Paris 75248, France.,Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris 75248, France.,Université Pierre et Marie Curie (UPMC), UMR3664, Paris 75248, France.,Sorbonne University, PSL, Paris 75005, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
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24
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Rani R, Yaseen AM, Malwade A, Sevilimedu A. An RNA aptamer to HP1/Swi6 facilitates heterochromatin formation at an ectopic locus in S.pombe. RNA Biol 2019; 16:742-753. [PMID: 30794054 DOI: 10.1080/15476286.2019.1584026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
In the fission yeast Schizosaccharomyces pombe (S.pombe), heterochromatin domains are established and maintained by protein complexes that contain numerous RNA binding domains among their components. The fission yeast HP1 protein Swi6 is one such component and contains an unstructured RNA-binding hinge, which is important for the integrity and silencing of heterochromatin. In this study, we have used an RNA aptamer that likely binds to the Swi6 hinge with high affinity, as a tool to perturb the natural interactions mediated by this domain. When the hinge is blocked by the aptamer RNA, Swi6 appears to become less restricted to the pericentromeres and is enriched at specific euchromatic loci. This suggests a role for the Swi6 hinge, along with the chromoshadow domain (previously shown) in controlling the spread of heterochromatin in S.pombe. The study also highlights the potential of using a synthetic aptamer RNA as a tool to perturb nucleic acid - protein interaction in vivo with the objective of understanding the functional relevance of such an interaction.
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Affiliation(s)
- Rita Rani
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
| | - Abdul Mohd Yaseen
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
| | - Akshay Malwade
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
| | - Aarti Sevilimedu
- a Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS) , Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus , Telangana , India
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25
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Ruiz-Ruano FJ, Navarro-Domínguez B, Camacho JPM, Garrido-Ramos MA. Characterization of the satellitome in lower vascular plants: the case of the endangered fern Vandenboschia speciosa. ANNALS OF BOTANY 2019; 123:587-599. [PMID: 30357311 PMCID: PMC6417484 DOI: 10.1093/aob/mcy192] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Vandenboschia speciosa is a highly vulnerable fern species, with a large genome (10.5 Gb). Haploid gametophytes and diploid sporophytes are perennial, can reproduce vegetatively, and certain populations are composed only of independent gametophytes. These features make this fern a good model: (1) for high-throughput analysis of satellite DNA (satDNA) to investigate possible evolutionary trends in satDNA sequence features; (2) to determine the relative contribution of satDNA and other repetitive DNAs to its large genome; and (3) to analyse whether the reproduction mode or phase alternation between long-lasting haploid and diploid stages influences satDNA abundance or divergence. METHODS We analysed the repetitive fraction of the genome of this species in three different populations (one comprised only of independent gametophytes) using Illumina sequencing and bioinformatic analysis with RepeatExplorer and satMiner. KEY RESULTS The satellitome of V. speciosa is composed of 11 satDNA families, most of them showing a short repeat length and being A + T rich. Some satDNAs had complex repeats composed of sub-repeats, showing high similarity to shorter satDNAs. Three families had particular structural features and highly conserved motifs. SatDNA only amounts to approx. 0.4 % of its genome. Likewise, microsatellites do not represent more than 2 %, but transposable elements (TEs) represent approx. 50 % of the sporophytic genomes. We found high resemblance in satDNA abundance and divergence between both gametophyte and sporophyte samples from the same population and between populations. CONCLUSIONS (1) Longer (and older) satellites in V. speciosa have a higher A + T content and evolve from shorter ones and, in some cases, microsatellites were a source of new satDNAs; (2) the satellitome does not explain the huge genome size in this species while TEs are the major repetitive component of the V. speciosa genome and mostly contribute to its large genome; and (3) reproduction mode or phase alternation between gametophytes and sporophytes does not entail accumulation or divergence of satellites.
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Affiliation(s)
- F J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - B Navarro-Domínguez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - J P M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - M A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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26
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Kurup JT, Kidder BL. Identification of H4K20me3- and H3K4me3-associated RNAs using CARIP-Seq expands the transcriptional and epigenetic networks of embryonic stem cells. J Biol Chem 2018; 293:15120-15135. [PMID: 30115682 DOI: 10.1074/jbc.ra118.004974] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 11/06/2022] Open
Abstract
RNA has been shown to interact with various proteins to regulate chromatin dynamics and gene expression. However, it is unknown whether RNAs associate with epigenetic marks such as post-translational modifications of histones, including histone 4 lysine 20 trimethylation (H4K20me3) or trimethylated histone 3 lysine 4 (H3K4me3), to regulate chromatin and gene expression. Here, we used chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) to survey RNAs associated with H4K20me3- and H3K4me3-marked chromatin on a global scale in embryonic stem (ES) cells. We identified thousands of mRNAs and noncoding RNAs that associate with H4K20me3- and H3K4me3-marked chromatin. H4K20me3- and H3K4me3-interacting RNAs are involved in chromatin organization and modification and RNA processing, whereas H4K20me3-only RNAs are involved in cell motility and differentiation, and H3K4me3-only RNAs are involved in metabolic processes and RNA processing. Expression of H3K4me3-associated RNAs is enriched in ES cells, whereas expression of H4K20me3-associated RNAs is enriched in ES cells and differentiated cells. H4K20me3- and H3K4me3-interacting RNAs originate from genes that co-localize with features of active chromatin, including transcriptional machinery and active promoter regions, and the histone modification H3K36me3 in gene body regions. We also found that H4K20me3 and H3K4me3 are associated with distinct gene features including transcripts of greater length and exon number relative to unoccupied transcripts. H4K20me3- and H3K4me3-marked chromatin is also associated with processed RNAs (exon transcripts) relative to unspliced pre-mRNA and ncRNA transcripts. In summary, our results provide evidence that H4K20me3- and H3K4me3-associated RNAs represent a distinct subnetwork of the ES cell transcriptional repertoire.
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Affiliation(s)
- Jiji T Kurup
- From the Department of Oncology and.,the Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Benjamin L Kidder
- From the Department of Oncology and .,the Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan 48201
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27
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Larson AG, Narlikar GJ. The Role of Phase Separation in Heterochromatin Formation, Function, and Regulation. Biochemistry 2018; 57:2540-2548. [PMID: 29644850 PMCID: PMC9084486 DOI: 10.1021/acs.biochem.8b00401] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In eukaryotic cells, structures called heterochromatin play critical roles in nuclear processes ranging from gene repression to chromosome segregation. Biochemical and in vivo studies over the past several decades have implied that the diverse functions of heterochromatin rely on the ability of these structures to spread across large regions of the genome, to compact the underlying DNA, and to recruit different types of activities. Recent observations have suggested that heterochromatin may possess liquid droplet-like properties. Here, we discuss how these observations provide a new perspective on the mechanisms for the assembly, regulation, and functions of heterochromatin.
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Affiliation(s)
- Adam G. Larson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, United States
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, California 94158, United States
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158, United States
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28
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Garrido-Ramos MA. Satellite DNA: An Evolving Topic. Genes (Basel) 2017; 8:genes8090230. [PMID: 28926993 PMCID: PMC5615363 DOI: 10.3390/genes8090230] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Satellite DNA represents one of the most fascinating parts of the repetitive fraction of the eukaryotic genome. Since the discovery of highly repetitive tandem DNA in the 1960s, a lot of literature has extensively covered various topics related to the structure, organization, function, and evolution of such sequences. Today, with the advent of genomic tools, the study of satellite DNA has regained a great interest. Thus, Next-Generation Sequencing (NGS), together with high-throughput in silico analysis of the information contained in NGS reads, has revolutionized the analysis of the repetitive fraction of the eukaryotic genomes. The whole of the historical and current approaches to the topic gives us a broad view of the function and evolution of satellite DNA and its role in chromosomal evolution. Currently, we have extensive information on the molecular, chromosomal, biological, and population factors that affect the evolutionary fate of satellite DNA, knowledge that gives rise to a series of hypotheses that get on well with each other about the origin, spreading, and evolution of satellite DNA. In this paper, I review these hypotheses from a methodological, conceptual, and historical perspective and frame them in the context of chromosomal organization and evolution.
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Affiliation(s)
- Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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