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Murthy S, Dey U, Olymon K, Abbas E, Yella VR, Kumar A. Discerning the Role of DNA Sequence, Shape, and Flexibility in Recognition by Drosophila Transcription Factors. ACS Chem Biol 2024; 19:1533-1543. [PMID: 38902964 DOI: 10.1021/acschembio.4c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The precise spatial and temporal orchestration of gene expression is crucial for the ontogeny of an organism and is mainly governed by transcription factors (TFs). The mechanism of recognition of cognate sites amid millions of base pairs in the genome by TFs is still incompletely understood. In this study, we focus on DNA sequence composition, shape, and flexibility preferences of 28 quintessential TFs from Drosophila melanogaster that are critical to development and body patterning mechanisms. Our study finds that TFs exhibit distinct predilections for DNA shape, flexibility, and sequence compositions in the proximity of transcription factor binding sites (TFBSs). Notably, certain zinc finger proteins prefer GC-rich areas with less negative propeller twist, while homeodomains mainly seek AT-rich regions with a more negative propeller twist at their sites. Intriguingly, while numerous cofactors share similar binding site preferences and bind closer to each other in the genome, some cofactors that have different preferences bind farther apart. These findings shed light on TF DNA recognition and provide novel insights into possible cofactor binding and transcriptional regulation mechanisms.
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Affiliation(s)
- Smrithi Murthy
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Kaushika Olymon
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Eshan Abbas
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
| | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur 520002, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784028, India
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2
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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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3
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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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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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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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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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8
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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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9
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Krasnov AN, Evdokimova AA, Mazina MY, Erokhin M, Chetverina D, Vorobyeva NE. Coregulators Reside within Drosophila Ecdysone-Inducible Loci before and after Ecdysone Treatment. Int J Mol Sci 2023; 24:11844. [PMID: 37511602 PMCID: PMC10380596 DOI: 10.3390/ijms241411844] [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: 06/09/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Ecdysone signaling in Drosophila remains a popular model for investigating the mechanisms of steroid action in eukaryotes. The ecdysone receptor EcR can effectively bind ecdysone-response elements with or without the presence of a hormone. For years, EcR enhancers were thought to respond to ecdysone via recruiting coactivator complexes, which replace corepressors and stimulate transcription. However, the exact mechanism of transcription activation by ecdysone remains unclear. Here, we present experimental data on 11 various coregulators at ecdysone-responsive loci of Drosophila S2 cells. We describe the regulatory elements where coregulators reside within these loci and assess changes in their binding levels following 20-hydroxyecdysone treatment. In the current study, we detected the presence of some coregulators at the TSSs (active and inactive) and boundaries marked with CP190 rather than enhancers of the ecdysone-responsive loci where EcR binds. We observed minor changes in the coregulators' binding level. Most were present at inducible loci before and after 20-hydroxyecdysone treatment. Our findings suggest that: (1) coregulators can activate a particular TSS operating from some distal region (which could be an enhancer, boundary regulatory region, or inactive TSS); (2) coregulators are not recruited after 20-hydroxyecdysone treatment to the responsive loci; rather, their functional activity changes (shown as an increase in H3K27 acetylation marks generated by CBP/p300/Nejire acetyltransferase). Taken together, our findings imply that the 20-hydroxyecdysone signal enhances the functional activity of coregulators rather than promoting their binding to regulatory regions during the ecdysone response.
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Affiliation(s)
- Aleksey N Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | | | - Marina Yu Mazina
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Nadezhda E Vorobyeva
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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10
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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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11
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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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12
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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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13
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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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14
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The GCN5: its biological functions and therapeutic potentials. Clin Sci (Lond) 2021; 135:231-257. [PMID: 33443284 DOI: 10.1042/cs20200986] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022]
Abstract
General control non-depressible 5 (GCN5) or lysine acetyltransferase 2A (KAT2A) is one of the most highly studied histone acetyltransferases. It acts as both histone acetyltransferase (HAT) and lysine acetyltransferase (KAT). As an HAT it plays a pivotal role in the epigenetic landscape and chromatin modification. Besides, GCN5 regulates a wide range of biological events such as gene regulation, cellular proliferation, metabolism and inflammation. Imbalance in the GCN5 activity has been reported in many disorders such as cancer, metabolic disorders, autoimmune disorders and neurological disorders. Therefore, unravelling the role of GCN5 in different diseases progression is a prerequisite for both understanding and developing novel therapeutic agents of these diseases. In this review, we have discussed the structural features, the biological function of GCN5 and the mechanical link with the diseases associated with its imbalance. Moreover, the present GCN5 modulators and their limitations will be presented in a medicinal chemistry perspective.
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15
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Kyrchanova O, Klimenko N, Postika N, Bonchuk A, Zolotarev N, Maksimenko O, Georgiev P. Drosophila architectural protein CTCF is not essential for fly survival and is able to function independently of CP190. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194733. [PMID: 34311130 DOI: 10.1016/j.bbagrm.2021.194733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022]
Abstract
CTCF is the most likely ancestor of proteins that contain large clusters of C2H2 zinc finger domains (C2H2) and is conserved among most bilateral organisms. In mammals, CTCF functions as the main architectural protein involved in the organization of topology-associated domains (TADs). In vertebrates and Drosophila, CTCF is involved in the regulation of homeotic genes. Previously, it was found that null mutations in the dCTCF gene died as pharate adults, which failed to eclose from their pupal case, or shortly after hatching of adults. Here, we obtained several new null dCTCF mutations and found that the complete inactivation of dCTCF appears is limited mainly to phenotypic manifestations of the Abd-B gene and fertility of adult flies. Many modifiers that are not associated with an independent phenotypic manifestation can significantly enhance the expressivity of the null dCTCF mutations, indicating that other architectural proteins are able to functionally compensate for dCTCF inactivation in Drosophila. We also mapped the 715-735 aa region of dCTCF as being essential for the interaction with the BTB (Broad-Complex, Tramtrack, and Bric a brac) and microtubule-targeting (M) domains of the CP190 protein, which binds to many architectural proteins. However, the mutational analysis showed that the interaction with CP190 was not important for the functional activity of dCTCF in vivo.
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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
| | - 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
| | - Nikolay Postika
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Artem Bonchuk
- 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
| | - Nikolay Zolotarev
- 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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16
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Sabirov M, Kyrchanova O, Pokholkova GV, Bonchuk A, Klimenko N, Belova E, Zhimulev IF, Maksimenko O, Georgiev P. Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster. Epigenetics Chromatin 2021; 14:16. [PMID: 33752739 PMCID: PMC7983404 DOI: 10.1186/s13072-021-00391-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Background Pita is required for Drosophila development and binds specifically to a long motif in active promoters and insulators. Pita belongs to the Drosophila family of zinc-finger architectural proteins, which also includes Su(Hw) and the conserved among higher eukaryotes CTCF. The architectural proteins maintain the active state of regulatory elements and the long-distance interactions between them. In particular, Pita is involved in the formation of several boundaries between regulatory domains that controlled the expression of three hox genes in the Bithorax complex (BX-C). The CP190 protein is recruited to chromatin through interaction with the architectural proteins. Results Using in vitro pull-down analysis, we precisely mapped two unstructured regions of Pita that interact with the BTB domain of CP190. Then we constructed transgenic lines expressing the Pita protein of the wild-type and mutant variants lacking CP190-interacting regions. We have demonstrated that CP190-interacting region of the Pita can maintain nucleosome-free open chromatin and is critical for Pita-mediated enhancer blocking activity in BX-C. At the same time, interaction with CP190 is not required for the in vivo function of the mutant Pita protein, which binds to the same regions of the genome as the wild-type protein. Unexpectedly, we found that CP190 was still associated with the most of genome regions bound by the mutant Pita protein, which suggested that other architectural proteins were continuing to recruit CP190 to these regions. Conclusions The results directly demonstrate role of CP190 in insulation and support a model in which the regulatory elements are composed of combinations of binding sites that interact with several architectural proteins with similar functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00391-x.
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Affiliation(s)
- Marat Sabirov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 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
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 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
| | - Galina V Pokholkova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences (IMCB RAS), Novosibirsk, Russia
| | - Artem Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 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
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 3 4/5 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
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences (IMCB RAS), Novosibirsk, 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, 3 4/5 Vavilov St., Moscow, 119334, Russia.
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17
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Melnikova L, Molodina V, Erokhin M, Georgiev P, Golovnin A. HIPP1 stabilizes the interaction between CP190 and Su(Hw) in the Drosophila insulator complex. Sci Rep 2019; 9:19102. [PMID: 31836797 PMCID: PMC6911044 DOI: 10.1038/s41598-019-55617-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/29/2019] [Indexed: 12/14/2022] Open
Abstract
Suppressor of Hairy-wing [Su(Hw)] is one of the best characterized architectural proteins in Drosophila and recruits the CP190 and Mod(mdg4)-67.2 proteins to chromatin, where they form a well-known insulator complex. Recently, HP1 and insulator partner protein 1 (HIPP1), a homolog of the human co-repressor Chromodomain Y-Like (CDYL), was identified as a new partner for Su(Hw). Here, we performed a detailed analysis of the domains involved in the HIPP1 interactions with Su(Hw)-dependent complexes. HIPP1 was found to directly interact with the Su(Hw) C-terminal region (aa 720–892) and with CP190, but not with Mod(mdg4)-67.2. We have generated Hipp1 null mutants (HippΔ1) and found that the loss of Hipp1 does not affect the enhancer-blocking or repression activities of the Su(Hw)-dependent complex. However, the simultaneous inactivation of both HIPP1 and Mod(mdg4)-67.2 proteins resulted in reduced CP190 binding with Su(Hw) sites and significantly altered gypsy insulator activity. Taken together, these results suggested that the HIPP1 protein stabilized the interaction between CP190 and the Su(Hw)-dependent complex.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Varvara Molodina
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Maksim Erokhin
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334, Moscow, Russia.
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18
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The Role of Insulation in Patterning Gene Expression. Genes (Basel) 2019; 10:genes10100767. [PMID: 31569427 PMCID: PMC6827083 DOI: 10.3390/genes10100767] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022] Open
Abstract
Development is orchestrated by regulatory elements that turn genes ON or OFF in precise spatial and temporal patterns. Many safety mechanisms prevent inappropriate action of a regulatory element on the wrong gene promoter. In flies and mammals, dedicated DNA elements (insulators) recruit protein factors (insulator binding proteins, or IBPs) to shield promoters from regulatory elements. In mammals, a single IBP called CCCTC-binding factor (CTCF) is known, whereas genetic and biochemical analyses in Drosophila have identified a larger repertoire of IBPs. How insulators function at the molecular level is not fully understood, but it is currently thought that they fold chromosomes into conformations that affect regulatory element-promoter communication. Here, we review the discovery of insulators and describe their properties. We discuss recent genetic studies in flies and mice to address the question: Is gene insulation important for animal development? Comparing and contrasting observations in these two species reveal that they have different requirements for insulation, but that insulation is a conserved and critical gene regulation strategy.
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19
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The same domain of Su(Hw) is required for enhancer blocking and direct promoter repression. Sci Rep 2019; 9:5314. [PMID: 30926937 PMCID: PMC6441048 DOI: 10.1038/s41598-019-41761-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/14/2019] [Indexed: 12/22/2022] Open
Abstract
Suppressor of Hairy-wing [Su(Hw)] is a DNA-binding architectural protein that participates in the organization of insulators and repression of promoters in Drosophila. This protein contains acidic regions at both ends and a central cluster of 12 zinc finger domains, some of which are involved in the specific recognition of the binding site. One of the well-described in vivo function of Su(Hw) is the repression of transcription of neuronal genes in oocytes. Here, we have found that the same Su(Hw) C-terminal region (aa 720–892) is required for insulation as well as for promoter repression. The best characterized partners of Su(Hw), CP190 and Mod(mdg4)-67.2, are not involved in the repression of neuronal genes. Taken together, these results suggest that an unknown protein or protein complex binds to the C-terminal region of Su(Hw) and is responsible for the direct repression activity of Su(Hw).
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20
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Melnikova L, Kostyuchenko M, Molodina V, Parshikov A, Georgiev P, Golovnin A. Multiple interactions are involved in a highly specific association of the Mod(mdg4)-67.2 isoform with the Su(Hw) sites in Drosophila. Open Biol 2018; 7:rsob.170150. [PMID: 29021216 PMCID: PMC5666082 DOI: 10.1098/rsob.170150] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/18/2017] [Indexed: 12/13/2022] Open
Abstract
The best-studied Drosophila insulator complex consists of two BTB-containing proteins, the Mod(mdg4)-67.2 isoform and CP190, which are recruited to the chromatin through interactions with the DNA-binding Su(Hw) protein. It was shown previously that Mod(mdg4)-67.2 is critical for the enhancer-blocking activity of the Su(Hw) insulators and it differs from more than 30 other Mod(mdg4) isoforms by the C-terminal domain required for a specific interaction with Su(Hw) only. The mechanism of the highly specific association between Mod(mdg4)-67.2 and Su(Hw) is not well understood. Therefore, we have performed a detailed analysis of domains involved in the interaction of Mod(mdg4)-67.2 with Su(Hw) and CP190. We found that the N-terminal region of Su(Hw) interacts with the glutamine-rich domain common to all the Mod(mdg4) isoforms. The unique C-terminal part of Mod(mdg4)-67.2 contains the Su(Hw)-interacting domain and the FLYWCH domain that facilitates a specific association between Mod(mdg4)-67.2 and the CP190/Su(Hw) complex. Finally, interaction between the BTB domain of Mod(mdg4)-67.2 and the M domain of CP190 has been demonstrated. By using transgenic lines expressing different protein variants, we have shown that all the newly identified interactions are to a greater or lesser extent redundant, which increases the reliability in the formation of the protein complexes.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Margarita Kostyuchenko
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Varvara Molodina
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Alexander Parshikov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
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21
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Zolotarev N, Maksimenko O, Kyrchanova O, Sokolinskaya E, Osadchiy I, Girardot C, Bonchuk A, Ciglar L, Furlong EEM, Georgiev P. Opbp is a new architectural/insulator protein required for ribosomal gene expression. Nucleic Acids Res 2017; 45:12285-12300. [PMID: 29036346 PMCID: PMC5716193 DOI: 10.1093/nar/gkx840] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/14/2017] [Indexed: 12/22/2022] Open
Abstract
A special class of poorly characterized architectural proteins is required for chromatin topology and enhancer–promoter interactions. Here, we identify Opbp as a new Drosophila architectural protein, interacting with CP190 both in vivo and in vitro. Opbp binds to a very restrictive set of genomic regions, through a rare sequence specific motif. These sites are co-bound by CP190 in vivo, and generally located at bidirectional promoters of ribosomal protein genes. We show that Opbp is essential for viability, and loss of opbp function, or destruction of its motif, leads to reduced ribosomal protein gene expression, indicating a functional role in promoter activation. As characteristic of architectural/insulator proteins, the Opbp motif is sufficient for distance-dependent reporter gene activation and enhancer-blocking activity, suggesting an Opbp-mediated enhancer–promoter interaction. Rather than having a constitutive role, Opbp represents a new type of architectural protein with a very restricted, yet essential, function in regulation of housekeeping gene expression.
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Affiliation(s)
- Nikolay Zolotarev
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., Moscow 119334, Russia
| | - Oksana Maksimenko
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., Moscow 119334, Russia
| | - Olga Kyrchanova
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., Moscow 119334, Russia
| | - Elena Sokolinskaya
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., Moscow 119334, Russia.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119234, Russia
| | - Igor Osadchiy
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., Moscow 119334, Russia
| | - Charles Girardot
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
| | - Artem Bonchuk
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., Moscow 119334, Russia
| | - Lucia Ciglar
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
| | - Pavel Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova St., Moscow 119334, Russia
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22
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Melnikova L, Kostyuchenko M, Molodina V, Parshikov A, Georgiev P, Golovnin A. Interactions between BTB domain of CP190 and two adjacent regions in Su(Hw) are required for the insulator complex formation. Chromosoma 2017; 127:59-71. [PMID: 28939920 DOI: 10.1007/s00412-017-0645-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/11/2017] [Accepted: 09/05/2017] [Indexed: 12/26/2022]
Abstract
The best-studied Drosophila insulator complex consists of two BTB-containing proteins, the Mod(mdg4)-67.2 isoform and CP190, which are recruited cooperatively to chromatin through interactions with the DNA-binding architectural protein Su(Hw). While Mod(mdg4)-67.2 interacts only with Su(Hw), CP190 interacts with many other architectural proteins. In spite of the fact that CP190 is critical for the activity of Su(Hw) insulators, interaction between these proteins has not been studied yet. Therefore, we have performed a detailed analysis of domains involved in the interaction between the Su(Hw) and CP190. The results show that the BTB domain of CP190 interacts with two adjacent regions at the N-terminus of Su(Hw). Deletion of either region in Su(Hw) only weakly affected recruiting of CP190 to the Su(Hw) sites in the presence of Mod(mdg4)-67.2. Deletion of both regions in Su(Hw) prevents its interaction with CP190. Using mutations in vivo, we found that interactions with Su(Hw) and Mod(mdg4)-67.2 are essential for recruiting of CP190 to the Su(Hw) genomic sites.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, Russia, 119334
| | - Margarita Kostyuchenko
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, Russia, 119334
| | - Varvara Molodina
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, Russia, 119334
| | - Alexander Parshikov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, Russia, 119334
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, Russia, 119334.
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, Russia, 119334.
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