1
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Zhou H, Huang Y, Jia C, Pang Y, Liu L, Xu Y, Jin P, Qian J, Ma F. NF-κB factors cooperate with Su(Hw)/E4F1 to balance Drosophila/human immune responses via modulating dynamic expression of miR-210. Nucleic Acids Res 2024:gkae394. [PMID: 38742642 DOI: 10.1093/nar/gkae394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
MicroRNAs (miRNAs) play crucial regulatory roles in controlling immune responses, but their dynamic expression mechanisms are poorly understood. Here, we firstly confirm that the conserved miRNA miR-210 negatively regulates innate immune responses of Drosophila and human via targeting Toll and TLR6, respectively. Secondly, our findings demonstrate that the expression of miR-210 is dynamically regulated by NF-κB factor Dorsal in immune response of Drosophila Toll pathway. Thirdly, we find that Dorsal-mediated transcriptional inhibition of miR-210 is dependent on the transcriptional repressor Su(Hw). Mechanistically, Dorsal interacts with Su(Hw) to modulate cooperatively the dynamic expression of miR-210 in a time- and dose-dependent manner, thereby controlling the strength of Drosophila Toll immune response and maintaining immune homeostasis. Fourthly, we reveal a similar mechanism in human cells, where NF-κB/RelA cooperates with E4F1 to regulate the dynamic expression of hsa-miR-210 in the TLR immune response. Overall, our study reveals a conservative regulatory mechanism that maintains animal innate immune homeostasis and provides new insights into the dynamic regulation of miRNA expression in immune response.
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Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
- Institute of Laboratory Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, 210002 Nanjing, Jiangsu, China
| | - Yu Huang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Chaolong Jia
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Yujia Pang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
- Institute of Laboratory Medicine, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, 210002 Nanjing, Jiangsu, China
| | - Li Liu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Yina Xu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Jinjun Qian
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 210023 Nanjing, Jiangsu, China
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
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2
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Melnikova L, Molodina V, Georgiev P, Golovnin A. Development of a New Model System to Study Long-Distance Interactions Supported by Architectural Proteins. Int J Mol Sci 2024; 25:4617. [PMID: 38731837 PMCID: PMC11083095 DOI: 10.3390/ijms25094617] [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: 03/19/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
Chromatin architecture is critical for the temporal and tissue-specific activation of genes that determine eukaryotic development. The functional interaction between enhancers and promoters is controlled by insulators and tethering elements that support specific long-distance interactions. However, the mechanisms of the formation and maintenance of long-range interactions between genome regulatory elements remain poorly understood, primarily due to the lack of convenient model systems. Drosophila became the first model organism in which architectural proteins that determine the activity of insulators were described. In Drosophila, one of the best-studied DNA-binding architectural proteins, Su(Hw), forms a complex with Mod(mdg4)-67.2 and CP190 proteins. Using a combination of CRISPR/Cas9 genome editing and attP-dependent integration technologies, we created a model system in which the promoters and enhancers of two reporter genes are separated by 28 kb. In this case, enhancers effectively stimulate reporter gene promoters in cis and trans only in the presence of artificial Su(Hw) binding sites (SBS), in both constructs. The expression of the mutant Su(Hw) protein, which cannot interact with CP190, and the mutation inactivating Mod(mdg4)-67.2, lead to the complete loss or significant weakening of enhancer-promoter interactions, respectively. The results indicate that the new model system effectively identifies the role of individual subunits of architectural protein complexes in forming and maintaining specific long-distance interactions in the D. melanogaster model.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia;
| | - Varvara Molodina
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia;
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia;
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia;
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3
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Melnikova LS, Molodina VV, Georgiev PG, Golovnin AK. Role of Mod(mdg4)-67.2 Protein in Interactions between Su(Hw)-Dependent Complexes and Their Recruitment to Chromatin. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:626-636. [PMID: 38831500 DOI: 10.1134/s0006297924040035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 06/05/2024]
Abstract
Su(Hw) belongs to the class of proteins that organize chromosome architecture, determine promoter activity, and participate in formation of the boundaries/insulators between the regulatory domains. This protein contains a cluster of 12 zinc fingers of the C2H2 type, some of which are responsible for binding to the consensus site. The Su(Hw) protein forms complex with the Mod(mdg4)-67.2 and the CP190 proteins, where the last one binds to all known Drosophila insulators. To further study functioning of the Su(Hw)-dependent complexes, we used the previously described su(Hw)E8 mutation with inactive seventh zinc finger, which produces mutant protein that cannot bind to the consensus site. The present work shows that the Su(Hw)E8 protein continues to directly interact with the CP190 and Mod(mdg4)-67.2 proteins. Through interaction with Mod(mdg4)-67.2, the Su(Hw)E8 protein can be recruited into the Su(Hw)-dependent complexes formed on chromatin and enhance their insulator activity. Our results demonstrate that the Su(Hw) dependent complexes without bound DNA can be recruited to the Su(Hw) binding sites through the specific protein-protein interactions that are stabilized by Mod(mdg4)-67.2.
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Affiliation(s)
- Larisa S Melnikova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Varvara V Molodina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Pavel G Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Anton K Golovnin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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4
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Melnikova L, Golovnin A. Multiple Roles of dXNP and dADD1- Drosophila Orthologs of ATRX Chromatin Remodeler. Int J Mol Sci 2023; 24:16486. [PMID: 38003676 PMCID: PMC10671109 DOI: 10.3390/ijms242216486] [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: 10/09/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The Drosophila melanogaster dADD1 and dXNP proteins are orthologues of the ADD and SNF2 domains of the vertebrate ATRX (Alpha-Thalassemia with mental Retardation X-related) protein. ATRX plays a role in general molecular processes, such as regulating chromatin status and gene expression, while dADD1 and dXNP have similar functions in the Drosophila genome. Both ATRX and dADD1/dXNP interact with various protein partners and participate in various regulatory complexes. Disruption of ATRX expression in humans leads to the development of α-thalassemia and cancer, especially glioma. However, the mechanisms that allow ATRX to regulate various cellular processes are poorly understood. Studying the functioning of dADD1/dXNP in the Drosophila model may contribute to understanding the mechanisms underlying the multifunctional action of ATRX and its connection with various cellular processes. This review provides a brief overview of the currently available information in mammals and Drosophila regarding the roles of ATRX, dXNP, and dADD1. It discusses possible mechanisms of action of complexes involving these proteins.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
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5
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Golovnin A, Melnikova L, Babosha V, Pokholkova GV, Slovohotov I, Umnova A, Maksimenko O, Zhimulev IF, Georgiev P. The N-Terminal Part of Drosophila CP190 Is a Platform for Interaction with Multiple Architectural Proteins. Int J Mol Sci 2023; 24:15917. [PMID: 37958900 PMCID: PMC10648081 DOI: 10.3390/ijms242115917] [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: 10/04/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
CP190 is a co-factor in many Drosophila architectural proteins, being involved in the formation of active promoters and insulators. CP190 contains the N-terminal BTB/POZ (Broad-Complex, Tramtrack and Bric a brac/POxvirus and Zinc finger) domain and adjacent conserved regions involved in protein interactions. Here, we examined the functional roles of these domains of CP190 in vivo. The best-characterized architectural proteins with insulator functions, Pita, Su(Hw), and dCTCF, interacted predominantly with the BTB domain of CP190. Due to the difficulty of mutating the BTB domain, we obtained a transgenic line expressing a chimeric CP190 with the BTB domain of the human protein Kaiso. Another group of architectural proteins, M1BP, Opbp, and ZIPIC, interacted with one or both of the highly conserved regions in the N-terminal part of CP190. Transgenic lines of D. melanogaster expressing CP190 mutants with a deletion of each of these domains were obtained. The results showed that these mutant proteins only partially compensated for the functions of CP190, weakly binding to selective chromatin sites. Further analysis confirmed the essential role of these domains in recruitment to regulatory regions associated with architectural proteins. We also found that the N-terminal of CP190 was sufficient for recruiting Z4 and Chromator proteins and successfully achieving chromatin opening. Taken together, our results and the results of previous studies showed that the N-terminal region of CP190 is a platform for simultaneous interaction with various DNA-binding architectural proteins and transcription complexes.
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Affiliation(s)
- Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Valentin Babosha
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Galina V. Pokholkova
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, Novosibirsk 630090, Russia (I.F.Z.)
| | - Ivan Slovohotov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Anastasia Umnova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Igor F. Zhimulev
- Laboratory of Molecular Cytogenetics, Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, Novosibirsk 630090, Russia (I.F.Z.)
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
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6
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Melnikova L, Molodina V, Babosha V, Kostyuchenko M, Georgiev P, Golovnin A. The MADF-BESS Protein CP60 Is Recruited to Insulators via CP190 and Has Redundant Functions in Drosophila. Int J Mol Sci 2023; 24:15029. [PMID: 37834476 PMCID: PMC10573801 DOI: 10.3390/ijms241915029] [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: 08/25/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Drosophila CP190 and CP60 are transcription factors that are associated with centrosomes during mitosis. CP190 is an essential transcription factor and preferentially binds to housekeeping gene promoters and insulators through interactions with architectural proteins, including Su(Hw) and dCTCF. CP60 belongs to a family of transcription factors that contain the N-terminal MADF domain and the C-terminal BESS domain, which is characterized by the ability to homodimerize. In this study, we show that the conserved CP60 region adjacent to MADF is responsible for interacting with CP190. In contrast to the well-characterized MADF-BESS transcriptional activator Adf-1, CP60 is recruited to most chromatin sites through its interaction with CP190, and the MADF domain is likely involved in protein-protein interactions but not in DNA binding. The deletion of the Map60 gene showed that CP60 is not an essential protein, despite the strong and ubiquitous expression of CP60 at all stages of Drosophila development. Although CP60 is a stable component of the Su(Hw) insulator complex, the inactivation of CP60 does not affect the enhancer-blocking activity of the Su(Hw)-dependent gypsy insulator. Overall, our results indicate that CP60 has an important but redundant function in transcriptional regulation as a partner of the CP190 protein.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia; (L.M.)
| | - Varvara Molodina
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia; (L.M.)
| | - Valentin Babosha
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia (P.G.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Margarita Kostyuchenko
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia; (L.M.)
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia (P.G.)
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia; (L.M.)
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7
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Siouda M, Dujardin AD, Dekeyzer B, Schaeffer L, Mulligan P. Chromodomain on Y-like 2 (CDYL2) implicated in mitosis and genome stability regulation via interaction with CHAMP1 and POGZ. Cell Mol Life Sci 2023; 80:47. [PMID: 36658409 PMCID: PMC11072993 DOI: 10.1007/s00018-022-04659-7] [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: 06/16/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 01/21/2023]
Abstract
Histone H3 trimethylation on lysine 9 (H3K9me3) is a defining feature of mammalian pericentromeres, loss of which results in genome instability. Here we show that CDYL2 is recruited to pericentromeres in an H3K9me3-dependent manner and is required for faithful mitosis and genome stability. CDYL2 RNAi in MCF-7 breast cancer cells and Hela cervical cancer cells inhibited their growth, induced apoptosis, and provoked both nuclear and mitotic aberrations. Mass spectrometry analysis of CDYL2-interacting proteins identified the neurodevelopmental disease-linked mitotic regulators CHAMP1 and POGZ, which are associated with a central non-conserved region of CDYL2. RNAi rescue assays identified both the CDYL2 chromodomain and the CHAMP1-POGZ interacting region as required and, together, sufficient for CDYL2 regulation of mitosis and genome stability. CDYL2 RNAi caused loss of CHAMP1 localization at pericentromeres. We propose that CDYL2 functions as an adaptor protein that connects pericentromeric H3K9me3 with CHAMP1 and POGZ to ensure mitotic fidelity and genome stability.
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Affiliation(s)
- Maha Siouda
- Centre Léon Bérard, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Audrey D Dujardin
- Centre Léon Bérard, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Blanche Dekeyzer
- Centre Léon Bérard, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France
| | - Laurent Schaeffer
- Faculté de Médecine, Physiopathology and Genetics of Neurons and Muscles Division, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Université de Lyon, INSERM U1217, CNRS, UMR5310, 3ème étage, Aile B, 8 Avenue Rockefeller, 69008, Lyon, France
- Centre de Biotechnologie Cellulaire, CBC Biotec, CHU de Lyon - HCL Groupement Est, 59 Bvd Pinel, 69677, Cedex Bron, France
| | - Peter Mulligan
- Centre Léon Bérard, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Lyon, France.
- Faculté de Médecine, Physiopathology and Genetics of Neurons and Muscles Division, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Université de Lyon, INSERM U1217, CNRS, UMR5310, 3ème étage, Aile B, 8 Avenue Rockefeller, 69008, Lyon, France.
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8
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Simmons JR, An R, Amankwaa B, Zayac S, Kemp J, Labrador M. Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila. PLoS Genet 2022; 18:e1010396. [PMID: 36197938 PMCID: PMC9576066 DOI: 10.1371/journal.pgen.1010396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/17/2022] [Accepted: 08/24/2022] [Indexed: 11/27/2022] Open
Abstract
Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of Topologically Associating Domains (TADs). Here, we demonstrate an association between gypsy insulator proteins and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components su(Hw) and Cp190 results in a significant reduction in γH2Av levels in chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av, but not H2Av, is a component of insulator bodies, which are protein condensates that form during osmotic stress. Phosphatase activity is required for insulator body dissolution after stress recovery. Together, our results implicate the H2A variant with a novel mechanism of insulator function and boundary formation.
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Affiliation(s)
- James R. Simmons
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Ran An
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Bright Amankwaa
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Shannon Zayac
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Justin Kemp
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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9
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Chen S, Rosin LF, Pegoraro G, Moshkovich N, Murphy PJ, Yu G, Lei EP. NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization. Nucleic Acids Res 2022; 50:7906-7924. [PMID: 35819192 PMCID: PMC9371915 DOI: 10.1093/nar/gkac600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 11/14/2022] Open
Abstract
Chromatin insulators are DNA-protein complexes that can prevent the spread of repressive chromatin and block communication between enhancers and promoters to regulate gene expression. In Drosophila, the gypsy chromatin insulator complex consists of three core proteins: CP190, Su(Hw), and Mod(mdg4)67.2. These factors concentrate at nuclear foci termed insulator bodies, and changes in insulator body localization have been observed in mutants defective for insulator function. Here, we identified NURF301/E(bx), a nucleosome remodeling factor, as a novel regulator of gypsy insulator body localization through a high-throughput RNAi imaging screen. NURF301 promotes gypsy-dependent insulator barrier activity and physically interacts with gypsy insulator proteins. Using ChIP-seq, we found that NURF301 co-localizes with insulator proteins genome-wide, and NURF301 promotes chromatin association of Su(Hw) and CP190 at gypsy insulator binding sites. These effects correlate with NURF301-dependent nucleosome repositioning. At the same time, CP190 and Su(Hw) both facilitate recruitment of NURF301 to chromatin. Finally, Oligopaint FISH combined with immunofluorescence revealed that NURF301 promotes 3D contact between insulator bodies and gypsy insulator DNA binding sites, and NURF301 is required for proper nuclear positioning of gypsy binding sites. Our data provide new insights into how a nucleosome remodeling factor and insulator proteins cooperatively contribute to nuclear organization.
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Affiliation(s)
- Shue Chen
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Leah F Rosin
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nellie Moshkovich
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patrick J Murphy
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Guoyun Yu
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elissa P Lei
- Nuclear Organization and Gene Expression Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.,Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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10
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Stow EC, Simmons JR, An R, Schoborg TA, Davenport NM, Labrador M. A Drosophila insulator interacting protein suppresses enhancer-blocking function and modulates replication timing. Gene 2022; 819:146208. [PMID: 35092858 DOI: 10.1016/j.gene.2022.146208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/17/2021] [Accepted: 01/13/2022] [Indexed: 01/02/2023]
Abstract
Insulators play important roles in genome structure and function in eukaryotes. Interactions between a DNA binding insulator protein and its interacting partner proteins define the properties of each insulator site. The different roles of insulator protein partners in the Drosophila genome and how they confer functional specificity remain poorly understood. The Suppressor of Hairy wing [Su(Hw)] insulator is targeted to the nuclear lamina, preferentially localizes at euchromatin/heterochromatin boundaries, and is associated with the gypsy retrotransposon. Insulator activity relies on the ability of the Su(Hw) protein to bind the DNA at specific sites and interact with Mod(mdg4)67.2 and CP190 partner proteins. HP1 and insulator partner protein 1 (HIPP1) is a partner of Su(Hw), but how HIPP1 contributes to the function of Su(Hw) insulator complexes is unclear. Here, we demonstrate that HIPP1 colocalizes with the Su(Hw) insulator complex in polytene chromatin and in stress-induced insulator bodies. We find that the overexpression of either HIPP1 or Su(Hw) or mutation of the HIPP1 crotonase-like domain (CLD) causes defects in cell proliferation by limiting the progression of DNA replication. We also show that HIPP1 overexpression suppresses the Su(Hw) insulator enhancer-blocking function, while mutation of the HIPP1 CLD does not affect Su(Hw) enhancer blocking. These findings demonstrate a functional relationship between HIPP1 and the Su(Hw) insulator complex and suggest that the CLD, while not involved in enhancer blocking, influences cell cycle progression.
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Affiliation(s)
- Emily C Stow
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - James R Simmons
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Ran An
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Todd A Schoborg
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Nastasya M Davenport
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996, USA.
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Magaña-Acosta M, Valadez-Graham V. Chromatin Remodelers in the 3D Nuclear Compartment. Front Genet 2020; 11:600615. [PMID: 33329746 PMCID: PMC7673392 DOI: 10.3389/fgene.2020.600615] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodeling complexes (CRCs) use ATP hydrolysis to maintain correct expression profiles, chromatin stability, and inherited epigenetic states. More than 20 CRCs have been described to date, which encompass four large families defined by their ATPase subunits. These complexes and their subunits are conserved from yeast to humans through evolution. Their activities depend on their catalytic subunits which through ATP hydrolysis provide the energy necessary to fulfill cellular functions such as gene transcription, DNA repair, and transposon silencing. These activities take place at the first levels of chromatin compaction, and CRCs have been recognized as essential elements of chromatin dynamics. Recent studies have demonstrated an important role for these complexes in the maintenance of higher order chromatin structure. In this review, we present an overview of the organization of the genome within the cell nucleus, the different levels of chromatin compaction, and importance of the architectural proteins, and discuss the role of CRCs and how their functions contribute to the dynamics of the 3D genome organization.
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Affiliation(s)
- Mauro Magaña-Acosta
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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12
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Melnikova LS, Georgiev PG, Golovnin AK. The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes. Acta Naturae 2020; 12:15-33. [PMID: 33456975 PMCID: PMC7800606 DOI: 10.32607/actanaturae.11144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
The mechanisms underlying long-range interactions between chromatin regions and the principles of chromosomal architecture formation are currently under extensive scrutiny. A special class of regulatory elements known as insulators is believed to be involved in the regulation of specific long-range interactions between enhancers and promoters. This review focuses on the insulators of Drosophila and mammals, and it also briefly characterizes the proteins responsible for their functional activity. It was initially believed that the main properties of insulators are blocking of enhancers and the formation of independent transcription domains. We present experimental data proving that the chromatin loops formed by insulators play only an auxiliary role in enhancer blocking. The review also discusses the mechanisms involved in the formation of topologically associating domains and their role in the formation of the chromosomal architecture and regulation of gene transcription.
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Affiliation(s)
- L. S. Melnikova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - P. G. Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - A. K. Golovnin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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13
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Meyer-Nava S, Nieto-Caballero VE, Zurita M, Valadez-Graham V. Insights into HP1a-Chromatin Interactions. Cells 2020; 9:E1866. [PMID: 32784937 PMCID: PMC7465937 DOI: 10.3390/cells9081866] [Citation(s) in RCA: 8] [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: 06/26/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
Understanding the packaging of DNA into chromatin has become a crucial aspect in the study of gene regulatory mechanisms. Heterochromatin establishment and maintenance dynamics have emerged as some of the main features involved in genome stability, cellular development, and diseases. The most extensively studied heterochromatin protein is HP1a. This protein has two main domains, namely the chromoshadow and the chromodomain, separated by a hinge region. Over the years, several works have taken on the task of identifying HP1a partners using different strategies. In this review, we focus on describing these interactions and the possible complexes and subcomplexes associated with this critical protein. Characterization of these complexes will help us to clearly understand the implications of the interactions of HP1a in heterochromatin maintenance, heterochromatin dynamics, and heterochromatin's direct relationship to gene regulation and chromatin organization.
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Affiliation(s)
| | | | | | - Viviana Valadez-Graham
- Instituto de Biotecnología, Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62210, Mexico; (S.M.-N.); (V.E.N.-C.); (M.Z.)
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