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Li YR, Ling LB, Chao A, Fugmann SD, Yang SY. Transient chromatin decompaction at the start of D. melanogaster male embryonic germline development. Life Sci Alliance 2024; 7:e202302401. [PMID: 38991729 PMCID: PMC11239976 DOI: 10.26508/lsa.202302401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
Embryonic germ cells develop rapidly to establish the foundation for future developmental trajectories, and in this process, they make critical lineage choices including the configuration of their unique identity and a decision on sex. Here, we use single-cell genomics patterns for the entire embryonic germline in Drosophila melanogaster along with the somatic gonadal precursors after embryonic gonad coalescence to investigate molecular mechanisms involved in the setting up and regulation of the germline program. Profiling of the early germline chromatin landscape revealed sex- and stage-specific features. In the male germline immediately after zygotic activation, the chromatin structure underwent a brief remodeling phase during which nucleosome density was lower and deconcentrated from promoter regions. These findings echoed enrichment analysis results of our genomics data in which top candidates were factors with the ability to mediate large-scale chromatin reorganization. Together, they point to the importance of chromatin regulation in the early germline and raise the possibility of a conserved epigenetic reprogramming-like process required for proper initiation of germline development.
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Affiliation(s)
- Yi-Ru Li
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Li Bin Ling
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Angel Chao
- https://ror.org/02dnn6q67 Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sebastian D Fugmann
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/00d80zx46 Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/02dnn6q67 Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shu Yuan Yang
- https://ror.org/00d80zx46 Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/00d80zx46 Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- https://ror.org/02dnn6q67 Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
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2
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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; 52:6906-6927. [PMID: 38742642 PMCID: PMC11229355 DOI: 10.1093/nar/gkae394] [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: 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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3
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Sokolov V, Kyrchanova O, Klimenko N, Fedotova A, Ibragimov A, Maksimenko O, Georgiev P. New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity. Nucleic Acids Res 2024; 52:6886-6905. [PMID: 38769058 PMCID: PMC11229372 DOI: 10.1093/nar/gkae393] [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: 09/08/2023] [Revised: 04/20/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024] Open
Abstract
In Drosophila, a group of zinc finger architectural proteins recruits the CP190 protein to the chromatin, an interaction that is essential for the functional activity of promoters and insulators. In this study, we describe a new architectural C2H2 protein called Madf and Zinc-Finger Protein 1 (Mzfp1) that interacts with CP190. Mzfp1 has an unusual structure that includes six C2H2 domains organized in a C-terminal cluster and two tandem MADF domains. Mzfp1 predominantly binds to housekeeping gene promoters located in both euchromatin and heterochromatin genome regions. In vivo mutagenesis studies showed that Mzfp1 is an essential protein, and both MADF domains and the CP190 interaction region are required for its functional activity. The C2H2 cluster is sufficient for the specific binding of Mzfp1 to regulatory elements, while the second MADF domain is required for Mzfp1 recruitment to heterochromatin. Mzfp1 binds to the proximal part of the Fub boundary that separates regulatory domains of the Ubx and abd-A genes in the Bithorax complex. Mzfp1 participates in Fub functions in cooperation with the architectural proteins Pita and Su(Hw). Thus, Mzfp1 is a new architectural C2H2 protein involved in the organization of active promoters and insulators in Drosophila.
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Affiliation(s)
- Vladimir Sokolov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna Fedotova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Airat Ibragimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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4
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Bonchuk AN, Georgiev PG. C2H2 proteins: Evolutionary aspects of domain architecture and diversification. Bioessays 2024:e2400052. [PMID: 38873893 DOI: 10.1002/bies.202400052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2-type zinc finger domains that specifically bind to DNA. Few well-studied C2H2 proteins, however, demonstrate their key role in the control of gene expression and chromosome architecture. Here we review the features of the domain architecture of C2H2 proteins and the likely origin of C2H2 zinc fingers. A comprehensive investigation of proteomes for the presence of proteins with multiple clustered C2H2 domains has revealed a key difference between groups of organisms. Unlike plants, transcription factors in metazoans contain clusters of C2H2 domains typically separated by a linker with the TGEKP consensus sequence. The average size of C2H2 clusters varies substantially, even between genomes of higher metazoans, and with a tendency to increase in combination with SCAN, and especially KRAB domains, reflecting the increasing complexity of gene regulatory networks.
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Affiliation(s)
- Artem N Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel G Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
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5
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Bhattacharya M, Lyda SF, Lei EP. Chromatin insulator mechanisms ensure accurate gene expression by controlling overall 3D genome organization. Curr Opin Genet Dev 2024; 87:102208. [PMID: 38810546 DOI: 10.1016/j.gde.2024.102208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Chromatin insulators are DNA-protein complexes that promote specificity of enhancer-promoter interactions and maintain distinct transcriptional states through control of 3D genome organization. In this review, we highlight recent work visualizing how mammalian CCCTC-binding factor acts as a boundary to dynamic DNA loop extrusion mediated by cohesin. We also discuss new studies in both mammals and Drosophila that elucidate biological redundancy of chromatin insulator function and interplay with transcription with respect to topologically associating domain formation. Finally, we present novel concepts in spatiotemporal regulation of chromatin insulator function during differentiation and development and possible consequences of disrupted insulator activity on cellular proliferation.
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Affiliation(s)
- Mallika Bhattacharya
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Savanna F Lyda
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, USA; Biological Sciences Graduate Program, University of Maryland, College Park, USA
| | - Elissa P Lei
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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6
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Vorobyeva NE, Krasnov AN, Erokhin M, Chetverina D, Mazina M. Su(Hw) interacts with Combgap to establish long-range chromatin contacts. Epigenetics Chromatin 2024; 17:17. [PMID: 38773468 PMCID: PMC11106861 DOI: 10.1186/s13072-024-00541-x] [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: 01/29/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) insulator-binding protein to genome topology remains unclear. RESULTS In this study, we provide evidence for the existence of long-range interactions between chromatin bound Su(Hw) and Combgap, which was first characterised as Polycomb response elements binding protein. Loss of Su(Hw) binding to chromatin results in the disappearance of Su(Hw)-Combgap long-range interactions and in a decrease in spatial self-interactions among a subset of Su(Hw)-bound genome sites. Our findings suggest that Su(Hw)-Combgap long-range interactions are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators' binding. CONCLUSIONS This study demonstrates that Su(Hw) insulator binding protein can form long-range interactions with Combgap, Polycomb response elements binding protein, and that these interactions are associated with active chromatin factors rather than with Polycomb dependent repression.
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Affiliation(s)
- Nadezhda E Vorobyeva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alexey N Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Marina Mazina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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7
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Fogarty EA, Buchert EM, Ma Y, Nicely AB, Buttitta LA. Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592773. [PMID: 38766255 PMCID: PMC11100713 DOI: 10.1101/2024.05.06.592773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The mechanisms that maintain a non-cycling status in postmitotic tissues are not well understood. Many cell cycle genes have promoters and enhancers that remain accessible even when cells are terminally differentiated and in a non-cycling state, suggesting their repression must be maintained long term. In contrast, enhancer decommissioning has been observed for rate-limiting cell cycle genes in the Drosophila wing, a tissue where the cells die soon after eclosion, but it has been unclear if this also occurs in other contexts of terminal differentiation. In this study, we show that enhancer decommissioning also occurs at specific, rate-limiting cell cycle genes in the long-lived tissues of the Drosophila eye and brain, and we propose this loss of chromatin accessibility may help maintain a robust postmitotic state. We examined the decommissioned enhancers at specific rate-limiting cell cycle genes and show that they encode dynamic temporal and spatial expression patterns that include shared, as well as tissue-specific elements, resulting in broad gene expression with developmentally controlled temporal regulation. We extend our analysis to cell cycle gene expression and chromatin accessibility in the mammalian retina using a published dataset, and find that the principles of cell cycle gene regulation identified in terminally differentiating Drosophila tissues are conserved in the differentiating mammalian retina. We propose a robust, non-cycling status is maintained in long-lived postmitotic tissues through a combination of stable repression at most cell cycle gens, alongside enhancer decommissioning at specific rate-limiting cell cycle genes.
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Affiliation(s)
- Elizabeth A. Fogarty
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Elli M. Buchert
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Yiqin Ma
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Ava B. Nicely
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
| | - Laura A. Buttitta
- Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109
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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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9
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Kamalyan S, Kyrchanova O, Klimenko N, Babosha V, Vasileva Y, Belova E, Fursenko D, Maksimenko O, Georgiev P. The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality. Epigenetics Chromatin 2024; 17:9. [PMID: 38561749 PMCID: PMC10983669 DOI: 10.1186/s13072-024-00534-w] [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: 08/29/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND CTCF is highly likely to be the ancestor of proteins that contain large clusters of C2H2 zinc finger domains, and its conservation is observed across most bilaterian organisms. In mammals, CTCF is the primary architectural protein involved in organizing chromosome topology and mediating enhancer-promoter interactions over long distances. In Drosophila, CTCF (dCTCF) cooperates with other architectural proteins to establish long-range interactions and chromatin boundaries. CTCFs of various organisms contain an unstructured N-terminal dimerization domain (DD) and clusters comprising eleven zinc-finger domains of the C2H2 type. The Drosophila (dCTCF) and human (hCTCF) CTCFs share sequence homology in only five C2H2 domains that specifically bind to a conserved 15 bp motif. RESULTS Previously, we demonstrated that CTCFs from different organisms carry unstructured N-terminal dimerization domains (DDs) that lack sequence homology. Here we used the CTCFattP(mCh) platform to introduce desired changes in the Drosophila CTCF gene and generated a series of transgenic lines expressing dCTCF with different variants of the N-terminal domain. Our findings revealed that the functionality of dCTCF is significantly affected by the deletion of the N-terminal DD. Additionally, we observed a strong impact on the binding of the dCTCF mutant to chromatin upon deletion of the DD. However, chromatin binding was restored in transgenic flies expressing a chimeric CTCF protein with the DD of hCTCF. Although the chimeric protein exhibited lower expression levels than those of the dCTCF variants, it efficiently bound to chromatin similarly to the wild type (wt) protein. CONCLUSIONS Our findings suggest that one of the evolutionarily conserved functions of the unstructured N-terminal dimerization domain is to recruit dCTCF to its genomic sites in vivo.
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Affiliation(s)
- Sofia Kamalyan
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Valentin Babosha
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Yulia Vasileva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Dariya Fursenko
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, 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 St, Moscow, 119334, Russia.
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia.
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10
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Guntur AR, Smith JE, Brahmandam A, DeBauche P, Cronmiller C, Lundell MJ. ZFH-2 is required for Drosophila ovarian follicle development and is expressed at the band/interband boundaries of polytene chromosomes. Dev Biol 2023; 504:1-11. [PMID: 37666353 DOI: 10.1016/j.ydbio.2023.09.001] [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: 04/06/2023] [Revised: 08/29/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
The transcription factor ZFH-2 has well-documented roles in Drosophila neurogenesis and other developmental processes. Here we provide the first evidence that ZFH-2 has a role in oogenesis. We demonstrate that ZFH-2 is expressed in the wild-type ovary and that a loss of zfh-2 function produces a mutant ovary phenotype where egg chambers are reduced in number and fused. We also show that a loss of zfh-2 function can suppress a daughterless loss-of-function ovary phenotype suggesting a possible genetic relationship between these two genes in the ovary. We also show that ZFH-2 is located at the boundary between bands and interbands on polytene chromosomes and that at a subset of these sites ZFH-2 colocalizes with the insulator/promoter cofactor CP190.
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Affiliation(s)
- Ananya R Guntur
- Department of Biology, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - John E Smith
- Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA, 22904, USA
| | - Archana Brahmandam
- Department of Biology, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Phillip DeBauche
- Department of Biology, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Claire Cronmiller
- Department of Biology, University of Virginia, P.O. Box 400328, Charlottesville, VA, 22904, USA
| | - Martha J Lundell
- Department of Biology, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA.
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11
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Pekina YV, Babosha VA, Georgiev PG, Fedotova AA. Study of the Association of Ouib and Nom with Heterochromatin in Drosophila melanogaster. DOKL BIOCHEM BIOPHYS 2023; 513:S26-S29. [PMID: 38472665 DOI: 10.1134/s1607672924700741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 03/14/2024]
Abstract
In Drosophila, a large group of actively transcribed genes is located in pericentromeric heterochromatin. It is assumed that heterochromatic proteins recruit transcription factors to gene promoters. Two proteins, Ouib and Nom, were previously shown to bind to the promoters of the heterochromatic genes nvd and spok. Interestingly, Ouib and Nom are paralogs of the M1BP protein, which binds to the promoters of euchromatic genes. We have shown that, like M1BP, the Quib and Nom proteins bind to CP190, which is involved in the recruitment of transcription complexes to promoters. Unlike heterochromatic proteins, Ouib and Nom do not interact with the major heterochromatic protein HP1a and bind to euchromatic promoters on polytene chromosomes from the larval salivary glands. The results suggest a new mechanism for the recruitment of transcription factors into the heterochromatic compartment of the nucleus.
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Affiliation(s)
- Y V Pekina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - V A Babosha
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | - P G Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - A A Fedotova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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12
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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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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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14
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Hodkinson LJ, Smith C, Comstra HS, Ajani BA, Albanese EH, Arsalan K, Daisson AP, Forrest KB, Fox EH, Guerette MR, Khan S, Koenig MP, Lam S, Lewandowski AS, Mahoney LJ, Manai N, Miglay J, Miller BA, Milloway O, Ngo N, Ngo VD, Oey NF, Punjani TA, SiMa H, Zeng H, Schmidt CA, Rieder LE. A bioinformatics screen reveals hox and chromatin remodeling factors at the Drosophila histone locus. BMC Genom Data 2023; 24:54. [PMID: 37735352 PMCID: PMC10515271 DOI: 10.1186/s12863-023-01147-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/07/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. RESULTS To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets of 27 unique factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax (Ubx), Abdominal-A (Abd-A), and Abdominal-B (Abd-B), suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other factors that target the histone gene array: JIL-1, hormone-like receptor 78 (Hr78), the long isoform of female sterile homeotic (1) (fs(1)h) as well as the general transcription factors TBP associated factor 1 (TAF-1), Transcription Factor IIB (TFIIB), and Transcription Factor IIF (TFIIF). CONCLUSIONS Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.
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Affiliation(s)
- Lauren J Hodkinson
- Genetics and Molecular Biology graduate program, Emory University, Atlanta, GA, 30322, USA
| | - Connor Smith
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - H Skye Comstra
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Bukola A Ajani
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Eric H Albanese
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Kawsar Arsalan
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Alvaro Perez Daisson
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Katherine B Forrest
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Elijah H Fox
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Matthew R Guerette
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Samia Khan
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Madeleine P Koenig
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Shivani Lam
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Ava S Lewandowski
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Lauren J Mahoney
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Nasserallah Manai
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - JonCarlo Miglay
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Blake A Miller
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Olivia Milloway
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Nhi Ngo
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Vu D Ngo
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Nicole F Oey
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Tanya A Punjani
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - HaoMin SiMa
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Hollis Zeng
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Casey A Schmidt
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA.
| | - Leila E Rieder
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA.
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15
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Chimata AV, Darnell H, Raj A, Kango-Singh M, Singh A. Transcriptional pausing factor M1BP regulates cellular homeostasis by suppressing autophagy and apoptosis in Drosophila eye. AUTOPHAGY REPORTS 2023; 2:2252307. [PMID: 37746026 PMCID: PMC10512699 DOI: 10.1080/27694127.2023.2252307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/26/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023]
Abstract
During organogenesis cellular homeostasis plays a crucial role in patterning and growth. The role of promoter proximal pausing of RNA polymerase II, which regulates transcription of several developmental genes by GAGA factor or Motif 1 Binding Protein (M1BP), has not been fully understood in cellular homeostasis. Earlier, we reported that M1BP, a functional homolog of ZKSCAN3, regulates wingless and caspase-dependent cell death (apoptosis) in the Drosophila eye. Further, blocking apoptosis does not fully rescue the M1BPRNAi phenotype of reduced eye. Therefore, we looked for other possible mechanism(s). In a forward genetic screen, members of the Jun-amino-terminal-(NH2)-Kinase (JNK) pathway were identified. Downregulation of M1BP ectopically induces JNK, a pro-death pathway known to activate both apoptosis and caspase-independent (autophagy) cell death. Activation of JNK pathway components can enhance M1BPRNAi phenotype and vice-versa. Downregulation of M1BP ectopically induced JNK signaling, which leads to apoptosis and autophagy. Apoptosis and autophagy are regulated independently by their genetic circuitry. Here, we found that blocking either apoptosis or autophagy alone rescues the reduced eye phenotype of M1BP downregulation; whereas, blocking both apoptosis and autophagy together significantly rescues the M1BP reduced eye phenotype to near wild-type in nearly 85% progeny. This data suggests that the cellular homeostasis response demonstrated by two independent cell death mechanisms, apoptosis and autophagy, can be regulated by a common transcriptional pausing mechanism orchestrated by M1BP. Since these fundamental processes are conserved in higher organisms, this novel functional link between M1BP and regulation of both apoptosis and autophagy can be extrapolated to humans.
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Affiliation(s)
| | - Hannah Darnell
- Department of Biology, University of Dayton, Dayton, OH, USA
| | - Akanksha Raj
- Department of Biology, University of Dayton, Dayton, OH, USA
| | - Madhuri Kango-Singh
- Department of Biology, University of Dayton, Dayton, OH, USA
- Premedical Program, University of Dayton, Dayton, OH, USA
- Integrative Science and Engineering (ISE), University of Dayton, Dayton, OH, USA
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, USA
- Premedical Program, University of Dayton, Dayton, OH, USA
- Center for Tissue Regeneration & Engineering (TREND), University of Dayton, Dayton, OH, USA
- Integrative Science and Engineering (ISE), University of Dayton, Dayton, OH, USA
- Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA
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16
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Kyrchanova O, Ibragimov A, Postika N, Georgiev P, Schedl P. Boundary bypass activity in the abdominal-B region of the Drosophila bithorax complex is position dependent and regulated. Open Biol 2023; 13:230035. [PMID: 37582404 PMCID: PMC10427195 DOI: 10.1098/rsob.230035] [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: 02/07/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
Expression of Abdominal-B (Abd-B) in abdominal segments A5-A8 is controlled by four regulatory domains, iab-5-iab-8. Each domain has an initiator element (which sets the activity state), elements that maintain this state and tissue-specific enhancers. To ensure their functional autonomy, each domain is bracketed by boundary elements (Mcp, Fab-7, Fab-7 and Fab-8). In addition to blocking crosstalk between adjacent regulatory domains, the Fab boundaries must also have bypass activity so the relevant regulatory domains can 'jump over' intervening boundaries and activate the Abd-B promoter. In the studies reported here we have investigated the parameters governing bypass activity. We find that the bypass elements in the Fab-7 and Fab-8 boundaries must be located in the regulatory domain that is responsible for driving Abd-B expression. We suggest that bypass activity may also be subject to regulation.
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Affiliation(s)
- Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Airat Ibragimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Nikolay Postika
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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17
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Wang R, Xu Q, Wang C, Tian K, Wang H, Ji X. Multiomic analysis of cohesin reveals that ZBTB transcription factors contribute to chromatin interactions. Nucleic Acids Res 2023; 51:6784-6805. [PMID: 37264934 PMCID: PMC10359638 DOI: 10.1093/nar/gkad401] [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: 12/15/2022] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the cohesin in chromatin and identified transcription factors, RNA-binding proteins and chromatin regulators associated with cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with cohesin that warrant further investigation.
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Affiliation(s)
- Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qiqin Xu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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18
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Kyrchanova O, Ibragimov A, Postika N, Georgiev P, Schedl P. Boundary Bypass Activity in the Abdominal-B Region of the Drosophila Bithorax Complex is Position Dependent and Regulated. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543971. [PMID: 37333165 PMCID: PMC10274778 DOI: 10.1101/2023.06.06.543971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Expression of Abdominal-B ( Abd-B ) in abdominal segments A5 - A8 is controlled by four regulatory domains, iab-5 - iab-8 . Each domain has an initiator element (which sets the activity state), elements that maintain this state and tissue-specific enhancers. To ensure their functional autonomy, each domain is bracketed by boundary elements ( Mcp , Fab-7 , Fab-7 and Fab-8 ). In addition to blocking crosstalk between adjacent regulatory domains, the Fab boundaries must also have bypass activity so the relevant regulatory domains can "jump over" intervening boundaries and activate the Abd-B promoter. In the studies reported here we have investigated the parameters governing bypass activity. We find that the bypass elements in the Fab-7 and Fab-8 boundaries must be located in the regulatory domain that is responsible for driving Abd-B expression. We suggest that bypass activity may also be subject to regulation. Summary Statement Boundaries separating Abd-B regulatory domains block crosstalk between domains and mediate their interactions with Abd-B . The latter function is location but not orientation dependent.
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Affiliation(s)
- Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Airat Ibragimov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Nikolay Postika
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
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19
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Poliacikova G, Barthez M, Rival T, Aouane A, Luis NM, Richard F, Daian F, Brouilly N, Schnorrer F, Maurel-Zaffran C, Graba Y, Saurin AJ. M1BP is an essential transcriptional activator of oxidative metabolism during Drosophila development. Nat Commun 2023; 14:3187. [PMID: 37268614 DOI: 10.1038/s41467-023-38986-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 05/23/2023] [Indexed: 06/04/2023] Open
Abstract
Oxidative metabolism is the predominant energy source for aerobic muscle contraction in adult animals. How the cellular and molecular components that support aerobic muscle physiology are put in place during development through their transcriptional regulation is not well understood. Using the Drosophila flight muscle model, we show that the formation of mitochondria cristae harbouring the respiratory chain is concomitant with a large-scale transcriptional upregulation of genes linked with oxidative phosphorylation (OXPHOS) during specific stages of flight muscle development. We further demonstrate using high-resolution imaging, transcriptomic and biochemical analyses that Motif-1-binding protein (M1BP) transcriptionally regulates the expression of genes encoding critical components for OXPHOS complex assembly and integrity. In the absence of M1BP function, the quantity of assembled mitochondrial respiratory complexes is reduced and OXPHOS proteins aggregate in the mitochondrial matrix, triggering a strong protein quality control response. This results in isolation of the aggregate from the rest of the matrix by multiple layers of the inner mitochondrial membrane, representing a previously undocumented mitochondrial stress response mechanism. Together, this study provides mechanistic insight into the transcriptional regulation of oxidative metabolism during Drosophila development and identifies M1BP as a critical player in this process.
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Affiliation(s)
- Gabriela Poliacikova
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Marine Barthez
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Thomas Rival
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Aïcha Aouane
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Nuno Miguel Luis
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Fabrice Richard
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Fabrice Daian
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Nicolas Brouilly
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Frank Schnorrer
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Corinne Maurel-Zaffran
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Yacine Graba
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France
| | - Andrew J Saurin
- Aix-Marseille Univ, CNRS, Developmental Biology Institute of Marseille (IBDM), UMR 7288, Case 907, Turing Center for Living Systems, Parc Scientifique de Luminy, 13288, Marseille Cedex 09, France.
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20
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Fedotova AA, Georgiev PG, Bonchuk AN. Study of the in Vivo Functional Role of Mutations in the BTB Domain of the CP190 Protein of Drosophila melanogaster. DOKL BIOCHEM BIOPHYS 2023; 509:47-50. [PMID: 37340291 DOI: 10.1134/s1607672922600208] [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: 10/24/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 06/22/2023]
Abstract
The Drosophila transcription factor СР190 is one of the key proteins that determine the activity of housekeeping gene promoters and insulators. CP190 has an N-terminal BTB domain that allows for dimerization. Many of known Drosophila architectural proteins interact with the hydrophobic peptide-binding groove in the BTB domain, which is presumably a mechanisms for recruiting CP190 to regulatory elements. To study the role of the BTB domain in the interaction with architectural proteins, we obtained transgenic flies expressing CP190 variants with mutations in the peptide-binding groove, which disrupts their interaction with architectural proteins. As a result of the studies, it was found that mutations in the BTB domain do not affect binding of the CP190 protein to polytene chromosomes. Thus, our studies confirm the previously obtained data that CP190 is recruited to regulatory elements by several transcription factors interacting, in addition to BTB, with other CP190 domains.
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Affiliation(s)
- A A Fedotova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - P G Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - A N Bonchuk
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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21
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Cavalheiro GR, Girardot C, Viales RR, Pollex T, Cao TBN, Lacour P, Feng S, Rabinowitz A, Furlong EEM. CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles. SCIENCE ADVANCES 2023; 9:eade1085. [PMID: 36735786 PMCID: PMC9897672 DOI: 10.1126/sciadv.ade1085] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/03/2023] [Indexed: 05/31/2023]
Abstract
The boundaries of topologically associating domains (TADs) are delimited by insulators and/or active promoters; however, how they are initially established during embryogenesis remains unclear. Here, we examined this during the first hours of Drosophila embryogenesis. DNA-FISH confirms that intra-TAD pairwise proximity is established during zygotic genome activation (ZGA) but with extensive cell-to-cell heterogeneity. Most newly formed boundaries are occupied by combinations of CTCF, BEAF-32, and/or CP190. Depleting each insulator individually from chromatin revealed that TADs can still establish, although with lower insulation, with a subset of boundaries (~10%) being more dependent on specific insulators. Some weakened boundaries have aberrant gene expression due to unconstrained enhancer activity. However, the majority of misexpressed genes have no obvious direct relationship to changes in domain-boundary insulation. Deletion of an active promoter (thereby blocking transcription) at one boundary had a greater impact than deleting the insulator-bound region itself. This suggests that cross-talk between insulators and active promoters and/or transcription might reinforce domain boundary insulation during embryogenesis.
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Affiliation(s)
- Gabriel R. Cavalheiro
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Baden-Württemberg, Germany
- Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Baden-Württemberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Baden-Württemberg, Germany
| | - Rebecca R. Viales
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Baden-Württemberg, Germany
| | - Tim Pollex
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Baden-Württemberg, Germany
| | - T. B. Ngoc Cao
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Baden-Württemberg, Germany
| | - Perrine Lacour
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Baden-Württemberg, Germany
- École Normale Supérieure, 45 rue d’Ulm, 75005 Paris, France
| | - Songjie Feng
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Baden-Württemberg, Germany
| | - Adam Rabinowitz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Baden-Württemberg, Germany
| | - Eileen E. M. Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Baden-Württemberg, Germany
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22
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Hodkinson LJ, Smith C, Comstra HS, Albanese EH, Ajani BA, Arsalan K, Daisson AP, Forrest KB, Fox EH, Guerette MR, Khan S, Koenig MP, Lam S, Lewandowski AS, Mahoney LJ, Manai N, Miglay J, Miller BA, Milloway O, Ngo VD, Oey NF, Punjani TA, SiMa H, Zeng H, Schmidt CA, Rieder LE. A bioinformatics screen reveals Hox and chromatin remodeling factors at the Drosophila histone locus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.06.523008. [PMID: 36711759 PMCID: PMC9881919 DOI: 10.1101/2023.01.06.523008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets and 27 factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax, Abdominal-A and Abdominal-B, suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other transcription factors that target the histone gene array: JIL-1, Hr78, the long isoform of fs(1)h as well as the generalized transcription factors TAF-1, TFIIB, and TFIIF. Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.
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Affiliation(s)
- Lauren J Hodkinson
- Genetics and Molecular Biology graduate program, Emory University, Atlanta, GA 30322, USA
| | - Connor Smith
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - H Skye Comstra
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Eric H Albanese
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Bukola A Ajani
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Kawsar Arsalan
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | | | - Katherine B Forrest
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Elijah H Fox
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Matthew R Guerette
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Samia Khan
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Madeleine P Koenig
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Shivani Lam
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Ava S Lewandowski
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Lauren J Mahoney
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Nasserallah Manai
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - JonCarlo Miglay
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Blake A Miller
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Olivia Milloway
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Vu D Ngo
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Nicole F Oey
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Tanya A Punjani
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - HaoMin SiMa
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Hollis Zeng
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Casey A Schmidt
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Leila E Rieder
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
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23
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Li M, Kasan K, Saha Z, Yoon Y, Schmidt-Ott U. Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid. PLoS One 2023; 18:e0274716. [PMID: 36595500 PMCID: PMC9810180 DOI: 10.1371/journal.pone.0274716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023] Open
Abstract
The C2H2 zinc finger gene cucoid establishes anterior-posterior (AP) polarity in the early embryo of culicine mosquitoes. This gene is unrelated to genes that establish embryo polarity in other fly species (Diptera), such as the homeobox gene bicoid, which serves this function in the traditional model organism Drosophila melanogaster. The cucoid gene is a conserved single copy gene across lower dipterans but nothing is known about its function in other species, and its evolution in higher dipterans, including Drosophila, is unresolved. We found that cucoid is a member of the ZAD-containing C2H2 zinc finger (ZAD-ZNF) gene family and is orthologous to 27 of the 91 members of this family in D. melanogaster, including M1BP, ranshi, ouib, nom, zaf1, odj, Nnk, trem, Zif, and eighteen uncharacterized genes. Available knowledge of the functions of cucoid orthologs in Drosophila melanogaster suggest that the progenitor of this lineage specific expansion may have played a role in regulating chromatin. We also describe many aspects of the gene duplication history of cucoid in the brachyceran lineage of D. melanogaster, thereby providing a framework for predicting potential redundancies among these genes in D. melanogaster.
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Affiliation(s)
- Muzi Li
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Koray Kasan
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Zinnia Saha
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Yoseop Yoon
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
| | - Urs Schmidt-Ott
- Dept. of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, United States of America
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24
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Kyrchanova OV, Bylino OV, Georgiev PG. Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and Drosophila. Front Genet 2022; 13:1081088. [PMID: 36531247 PMCID: PMC9751008 DOI: 10.3389/fgene.2022.1081088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
The spatial organization of chromosomes is involved in regulating the majority of intranuclear processes in higher eukaryotes, including gene expression. Drosophila was used as a model to discover many transcription factors whose homologs play a key role in regulation of gene expression in mammals. According to modern views, a cohesin complex mostly determines the architecture of mammalian chromosomes by forming chromatin loops on anchors created by the CTCF DNA-binding architectural protein. The role of the cohesin complex in chromosome architecture is poorly understood in Drosophila, and CTCF is merely one of many Drosophila architectural proteins with a proven potential to organize specific long-range interactions between regulatory elements in the genome. The review compares the mechanisms responsible for long-range interactions and chromosome architecture between mammals and Drosophila.
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25
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Amankwaa B, Schoborg T, Labrador M. Drosophila insulator proteins exhibit in vivo liquid-liquid phase separation properties. Life Sci Alliance 2022; 5:5/12/e202201536. [PMID: 35853678 PMCID: PMC9297610 DOI: 10.26508/lsa.202201536] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022] Open
Abstract
Drosophila insulator proteins and the cohesin subunit Rad21 coalesce in vivo to form liquid-droplet condensates, suggesting that liquid–liquid phase separation mediates their function in 3D genome organization. Mounting evidence implicates liquid–liquid phase separation (LLPS), the condensation of biomolecules into liquid-like droplets in the formation and dissolution of membraneless intracellular organelles (MLOs). Cells use MLOs or condensates for various biological processes, including emergency signaling and spatiotemporal control over steady-state biochemical reactions and heterochromatin formation. Insulator proteins are architectural elements involved in establishing independent domains of transcriptional activity within eukaryotic genomes. In Drosophila, insulator proteins form nuclear foci known as insulator bodies in response to osmotic stress. However, the mechanism through which insulator proteins assemble into bodies is yet to be investigated. Here, we identify signatures of LLPS by insulator bodies, including high disorder tendency in insulator proteins, scaffold–client–dependent assembly, extensive fusion behavior, sphericity, and sensitivity to 1,6-hexanediol. We also show that the cohesin subunit Rad21 is a component of insulator bodies, adding to the known insulator protein constituents and γH2Av. Our data suggest a concerted role of cohesin and insulator proteins in insulator body formation and under physiological conditions. We propose a mechanism whereby these architectural proteins modulate 3D genome organization through LLPS.
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Affiliation(s)
- Bright Amankwaa
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, USA
| | - Todd Schoborg
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, USA
| | - Mariano Labrador
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN, USA
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26
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Takeuchi C, Yokoshi M, Kondo S, Shibuya A, Saito K, Fukaya T, Siomi H, Iwasaki Y. Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers. Nucleic Acids Res 2022; 50:11580-11599. [PMID: 36373634 PMCID: PMC9723646 DOI: 10.1093/nar/gkac1034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/17/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
Telomeres in Drosophila are composed of sequential non-LTR retrotransposons HeT-A, TART and TAHRE. Although they are repressed by the PIWI-piRNA pathway or heterochromatin in the germline, the regulation of these retrotransposons in somatic cells is poorly understood. In this study, we demonstrated that specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells. Among the variants, we found that the Mod(mdg4)-N variant represses HeT-A expression the most efficiently. Subtelomeric sequences bound by Mod(mdg4)-N block enhancer activity within subtelomeric TAS-R repeats. This enhancer-blocking activity is increased by the tandem association of Mod(mdg4)-N to repetitive subtelomeric sequences. In addition, the association of Mod(mdg4)-N couples with the recruitment of RNA polymerase II to the subtelomeres, which reinforces its enhancer-blocking function. Our findings provide novel insights into how telomeric retrotransposons are regulated by the specific variants of insulator proteins associated with subtelomeric sequences.
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Affiliation(s)
- Chikara Takeuchi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Moe Yokoshi
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Shu Kondo
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka 411-8540, Japan
| | - Aoi Shibuya
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kuniaki Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka 411-8540, Japan
| | - Takashi Fukaya
- Laboratory of Transcription Dynamics, Research Center for Biological Visualization, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | | | - Yuka W Iwasaki
- To whom correspondence should be addressed. Tel: +81 3 5363 3529; Fax: +81 3 5363 3266;
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27
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Romanov SE, Shloma VV, Koryakov DE, Belyakin SN, Laktionov PP. Insulator Protein CP190 Regulates Expression оf Spermatocyte Differentiation Genes in Drosophila melanogaster Male Germline. Mol Biol 2022. [DOI: 10.1134/s0026893323010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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28
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Torosin NS, Golla TR, Lawlor MA, Cao W, Ellison CE. Mode and Tempo of 3D Genome Evolution in Drosophila. Mol Biol Evol 2022; 39:6750036. [PMID: 36201625 PMCID: PMC9641997 DOI: 10.1093/molbev/msac216] [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] [Indexed: 01/09/2023] Open
Abstract
Topologically associating domains (TADs) are thought to play an important role in preventing gene misexpression by spatially constraining enhancer-promoter contacts. The deleterious nature of gene misexpression implies that TADs should, therefore, be conserved among related species. Several early studies comparing chromosome conformation between species reported high levels of TAD conservation; however, more recent studies have questioned these results. Furthermore, recent work suggests that TAD reorganization is not associated with extensive changes in gene expression. Here, we investigate the evolutionary conservation of TADs among 11 species of Drosophila. We use Hi-C data to identify TADs in each species and employ a comparative phylogenetic approach to derive empirical estimates of the rate of TAD evolution. Surprisingly, we find that TADs evolve rapidly. However, we also find that the rate of evolution depends on the chromatin state of the TAD, with TADs enriched for developmentally regulated chromatin evolving significantly slower than TADs enriched for broadly expressed, active chromatin. We also find that, after controlling for differences in chromatin state, highly conserved TADs do not exhibit higher levels of gene expression constraint. These results suggest that, in general, most TADs evolve rapidly and their divergence is not associated with widespread changes in gene expression. However, higher levels of evolutionary conservation and gene expression constraints in TADs enriched for developmentally regulated chromatin suggest that these TAD subtypes may be more important for regulating gene expression, likely due to the larger number of long-distance enhancer-promoter contacts associated with developmental genes.
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Affiliation(s)
- Nicole S Torosin
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | - Tirupathi Rao Golla
- LifeCell, Kelambakkam Main Road, Keelakottaiyur, Chennai 600127, Tamil Nadu, India
| | - Matthew A Lawlor
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | - Weihuan Cao
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
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29
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Baumgartner L, Handler D, Platzer SW, Yu C, Duchek P, Brennecke J. The Drosophila ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters. eLife 2022; 11:80067. [PMID: 36193674 PMCID: PMC9531945 DOI: 10.7554/elife.80067] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/11/2022] [Indexed: 12/15/2022] Open
Abstract
RNA interference systems depend on the synthesis of small RNA precursors whose sequences define the target spectrum of these silencing pathways. The Drosophila Heterochromatin Protein 1 (HP1) variant Rhino permits transcription of PIWI-interacting RNA (piRNA) precursors within transposon-rich heterochromatic loci in germline cells. Current models propose that Rhino’s specific chromatin occupancy at piRNA source loci is determined by histone marks and maternally inherited piRNAs, but also imply the existence of other, undiscovered specificity cues. Here, we identify a member of the diverse family of zinc finger associated domain (ZAD)-C2H2 zinc finger proteins, Kipferl, as critical Rhino cofactor in ovaries. By binding to guanosine-rich DNA motifs and interacting with the Rhino chromodomain, Kipferl recruits Rhino to specific loci and stabilizes it on chromatin. In kipferl mutant flies, Rhino is lost from most of its target chromatin loci and instead accumulates on pericentromeric Satellite arrays, resulting in decreased levels of transposon targeting piRNAs and impaired fertility. Our findings reveal that DNA sequence, in addition to the H3K9me3 mark, determines the identity of piRNA source loci and provide insight into how Rhino might be caught in the crossfire of genetic conflicts. The genes within our DNA encode the essentials of our body plan and how each task in the body is achieved. However, our genome also contains many repetitive regions of DNA that do not encode functional genes. Some of these regions are genetic parasites known as transposons that try to multiply and spread around the DNA of their host. To prevent transposon DNA from interfering with the way the body operates, humans and other animals have evolved elaborate defense mechanisms to identify transposons and prevent them from multiplying. In one such mechanism, known as the piRNA pathway, the host makes small molecules known as piRNAs that have sequences complementary to those of transposons, and act as guides to silence the transposons. The instructions to make these piRNAs are stored in the form of transposon fragments in dedicated regions of host DNA called piRNA clusters. These clusters thereby act as genetic memory, allowing the host to recognize and silence specific transposons in other locations within the host’s genome. In fruit flies, a protein called Rhino binds to piRNA clusters that are densely packed to allow piRNAs to be made. However, it remained unclear how Rhino is able to identify and bind to piRNA clusters, but not to other similarly densely packed regions of DNA. Baumgartner et al. used a combination of genetic, genomic, and imaging approaches to study how Rhino finds its way in the fruit fly genome. They found that another protein called Kipferl interacts with Rhino and is required for Rhino to bind to nearly all piRNA clusters. Since Kipferl can by itself bind to the sequences that Rhino needs to find, the results suggest that Kipferl acts to recruit and initiate Rhino binding within densely packed piRNA clusters. Further experiments found that, in flies lacking Kipferl, Rhino binds to regions of DNA called Satellite repeats, hinting that these selfish sequences may compete for Rhino for their own benefit. The finding that Kipferl and Rhino work together to define the memory system of the piRNA pathway strongly advances our understanding of how a sequence-specific defense system based on small RNAs can be established.
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Affiliation(s)
- Lisa Baumgartner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Sebastian Wolfgang Platzer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Changwei Yu
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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30
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Bag I, Chen Y, D'Orazio K, Lopez P, Wenzel S, Takagi Y, Lei EP. Isha is a su(Hw) mRNA-binding protein required for gypsy insulator function. G3 (BETHESDA, MD.) 2022; 12:jkac152. [PMID: 35708663 PMCID: PMC9434307 DOI: 10.1093/g3journal/jkac152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Chromatin insulators are DNA-protein complexes localized throughout the genome capable of establishing independent transcriptional domains. It was previously reported that the Drosophila su(Hw) mRNA physically associates with the gypsy chromatin insulator protein complex within the nucleus and may serve a noncoding function to affect insulator activity. However, how this mRNA is recruited to the gypsy complex is not known. Here, we utilized RNA-affinity pulldown coupled with mass spectrometry to identify a novel RNA-binding protein, Isha (CG4266), that associates with su(Hw) mRNA in vitro and in vivo. Isha harbors a conserved RNA recognition motif and RNA Polymerase II C-terminal domain-interacting domain (CID). We found that Isha physically interacts with total and elongating Polymerase II and associates with chromatin at the 5' end of genes in an RNA-dependent manner. Furthermore, ChIP-seq analysis reveals Isha overlaps particularly with the core gypsy insulator component CP190 on chromatin. Depletion of Isha reduces enhancer-blocking and barrier activities of the gypsy insulator and disrupts the nuclear localization of insulator bodies. Our results reveal a novel factor Isha that promotes gypsy insulator activity that may act as a nuclear RNA-binding protein adapter for su(Hw) noncoding mRNA.
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Affiliation(s)
- Indira Bag
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yang Chen
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karole D'Orazio
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prisma Lopez
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elissa P Lei
- Corresponding author: Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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31
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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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Chen Y, Chen S, Lei EP. DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma. Bioinformatics 2022; 38:4062-4069. [PMID: 35809062 PMCID: PMC9438959 DOI: 10.1093/bioinformatics/btac498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/20/2022] [Accepted: 07/08/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION ChIP-seq detects protein-DNA interactions within chromatin, such as that of chromatin structural components and transcription machinery. ChIP-seq profiles are often noisy and variable across replicates, posing a challenge to the development of effective algorithms to accurately detect differential peaks. Methods have recently been designed for this purpose but sometimes yield conflicting results that are inconsistent with the underlying biology. Most existing algorithms perform well on limited datasets. To improve differential analysis of ChIP-seq, we present a novel Differential analysis method for ChIP-seq based on Limma (DiffChIPL). RESULTS DiffChIPL is adaptive to asymmetrical or symmetrical data and can accurately report global differences. We used simulated and real datasets for transcription factors (TFs) and histone modification marks to validate and benchmark our algorithm. DiffChIPL shows superior performance in sensitivity and false positive rate in different simulations and control datasets. DiffChIPL also performs well on real ChIP-seq, CUT&RUN, CUT&Tag and ATAC-seq datasets. DiffChIPL is an accurate and robust method, exhibiting better performance in differential analysis for a variety of applications including TF binding, histone modifications and chromatin accessibility. AVAILABILITY AND IMPLEMENTATION https://github.com/yancychy/DiffChIPL. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yang Chen
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Shue Chen
- Nuclear Organization and Gene Expression Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, USA
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Kaushal A, Dorier J, Wang B, Mohana G, Taschner M, Cousin P, Waridel P, Iseli C, Semenova A, Restrepo S, Guex N, Aiden EL, Gambetta MC. Essential role of Cp190 in physical and regulatory boundary formation. SCIENCE ADVANCES 2022; 8:eabl8834. [PMID: 35559678 PMCID: PMC9106302 DOI: 10.1126/sciadv.abl8834] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 04/01/2022] [Indexed: 05/31/2023]
Abstract
Boundaries in animal genomes delimit contact domains with enhanced internal contact frequencies and have debated functions in limiting regulatory cross-talk between domains and guiding enhancers to target promoters. Most mammalian boundaries form by stalling of chromosomal loop-extruding cohesin by CTCF, but most Drosophila boundaries form CTCF independently. However, how CTCF-independent boundaries form and function remains largely unexplored. Here, we assess genome folding and developmental gene expression in fly embryos lacking the ubiquitous boundary-associated factor Cp190. We find that sequence-specific DNA binding proteins such as CTCF and Su(Hw) directly interact with and recruit Cp190 to form most promoter-distal boundaries. Cp190 is essential for early development and prevents regulatory cross-talk between specific gene loci that pattern the embryo. Cp190 was, in contrast, dispensable for long-range enhancer-promoter communication at tested loci. Cp190 is thus currently the major player in fly boundary formation and function, revealing that diverse mechanisms evolved to partition genomes into independent regulatory domains.
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Affiliation(s)
- Anjali Kaushal
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Julien Dorier
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland
| | - Bihan Wang
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Giriram Mohana
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Michael Taschner
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Pascal Cousin
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Patrice Waridel
- Protein Analysis Facility, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland
| | - Anastasiia Semenova
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Simon Restrepo
- arcoris bio AG, Lüssirainstrasse 52, 6300 Zug, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- National Institute of Genetics, 1111 Yaya, Mishima, Shizuoka 411-8540, Japan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 20120, China
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Bonchuk AN, Boyko KM, Nikolaeva AY, Burtseva AD, Popov VO, Georgiev PG. Structural insights into highly similar spatial organization of zinc-finger associated domains with a very low sequence similarity. Structure 2022; 30:1004-1015.e4. [DOI: 10.1016/j.str.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/28/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
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Mechanisms of CP190 Interaction with Architectural Proteins in Drosophila Melanogaster. Int J Mol Sci 2021; 22:ijms222212400. [PMID: 34830280 PMCID: PMC8618245 DOI: 10.3390/ijms222212400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 01/08/2023] Open
Abstract
Most of the known Drosophila architectural proteins interact with an important cofactor, CP190, that contains three domains (BTB, M, and D) that are involved in protein–protein interactions. The highly conserved N-terminal CP190 BTB domain forms a stable homodimer that interacts with unstructured regions in the three best-characterized architectural proteins: dCTCF, Su(Hw), and Pita. Here, we identified two new CP190 partners, CG4730 and CG31365, that interact with the BTB domain. The CP190 BTB resembles the previously characterized human BCL6 BTB domain, which uses its hydrophobic groove to specifically associate with unstructured regions of several transcriptional repressors. Using GST pull-down and yeast two-hybrid assays, we demonstrated that mutations in the hydrophobic groove strongly affect the affinity of CP190 BTB for the architectural proteins. In the yeast two-hybrid assay, we found that architectural proteins use various mechanisms to improve the efficiency of interaction with CP190. Pita and Su(Hw) have two unstructured regions that appear to simultaneously interact with hydrophobic grooves in the BTB dimer. In dCTCF and CG31365, two adjacent regions interact simultaneously with the hydrophobic groove of the BTB and the M domain of CP190. Finally, CG4730 interacts with the BTB, M, and D domains of CP190 simultaneously. These results suggest that architectural proteins use different mechanisms to increase the efficiency of interaction with CP190.
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Maslova A, Krasikova A. FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains. Front Cell Dev Biol 2021; 9:753097. [PMID: 34805161 PMCID: PMC8597843 DOI: 10.3389/fcell.2021.753097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.
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Affiliation(s)
| | - Alla Krasikova
- Laboratory of Nuclear Structure and Dynamics, Cytology and Histology Department, Saint Petersburg State University, Saint Petersburg, Russia
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