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Drosophila Melanogaster Marat Sabirov1,2†, Olga Kyrchanova1,2†, Galina V Sabirov et al. Epigenetics & Chromatin (2021) 14:16 https://doi.org/10.1186/s13072-021-00391-x Epigenetics & Chromatin RESEARCH Open Access Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster Marat Sabirov1,2†, Olga Kyrchanova1,2†, Galina V. Pokholkova3†, Artem Bonchuk1,2†, Natalia Klimenko2, Elena Belova1,2, Igor F. Zhimulev3, Oksana Maksimenko2* and Pavel Georgiev1* Abstract Background: Pita is required for Drosophila development and binds specifcally to a long motif in active promoters and insulators. Pita belongs to the Drosophila family of zinc-fnger 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 pro- teins 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 regula- tory elements are composed of combinations of binding sites that interact with several architectural proteins with similar functions. Keywords: Chromatin insulator, Bithorax, Abd-B, BTB domain, Domain boundary, Open chromatin Introduction *Correspondence: [email protected]; [email protected] Te development of modern approaches for the study †Marat Sabirov, Olga Kyrchanova, GalinaV. Pokholkova, and Artem Bonchuk contributed equally to this work of genome architecture, including chromosome confor- 1 Department of the Control of Genetic Processes, Institute of Gene mation capture methods, coupled to high-throughput Biology, Russian Academy of Sciences, 3 4/5 Vavilov St., Moscow 119334, sequencing (Hi-C) and high-resolution microscopy Russia 2 Center for Precision Genome Editing and Genetic Technologies techniques has revealed the hierarchical organization of for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, genome [1, 2]. Chromosomes are composed of discrete 34/5 Vavilov St., Moscow 119334, Russia sub-megabase domains, called topologically associated Full list of author information is available at the end of the article © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/. The Creative Commons Public Domain Dedication waiver (http:// creat iveco mmons. org/ publi cdoma in/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Sabirov et al. Epigenetics & Chromatin (2021) 14:16 Page 2 of 16 domains (TADs) [3–5]. In genomes, regulatory elements, iab domains [30–37]. Pita binds to Fab-7 and Mcp and including enhancers, promoters, insulators, and silenc- is required for their boundary activities [19, 20, 38]. Five ers, actively interact with each other, which determines Pita binding sites can replace the Fab-7 boundary in the correct and stable level of gene expression [6, 7]. Te blocking the cross-talk of the iab-6 and iab-7 regulatory boundaries between TADs delineate specifc genomic domains [19]. regions, and more efective interactions between regula- Previously, Pita was found to interact with CP190 [25], tory elements occur within these regions than between which is also known to bind several other C2H2 architec- diferent regions [8]. According to the generally accepted tural proteins, including dCTCF and Suppressor of hairy model, the cohesin complex, which is retained at CTCF wing [Su(Hw)] [18, 25, 39–42]. protein binding sites, plays a primary role in the forma- Here, we studied the interaction mechanisms between tion of chromatin loops in mammals [9]. Auxiliary roles Pita and CP190. Two domains that interact with the BTB in the organization of specifc interactions between domain of CP190 were mapped in Pita. Te recruitment enhancers and promoters have been assigned to the of CP190 is required for the chromatin opening and insu- proteins LBD1, yin yang 1 (YY1), and ZF143 [10–13]. lator functions of Pita. However, mutant fies that express Because the LBD1 protein is the only one of these pro- Pita lacking the CP190 interaction region display normal teins to contain a well-described homodimerization viability and wild-type (wt) phenotype, demonstrating domain [14], how specifc interactions between enhanc- that these activities are not essential for Pita functions ers and promoters occurs remains unclear. in vivo. In Drosophila, we suggested the existence of a large family of architectural proteins, which typically contain Results N-terminal homodimerization domains and arrays of Mapping regions within the Pita protein that interact the zinc-fnger Cys2-His2 (C2H2) domains [15–22]. Te with the BTB domain of CP190 specifc interactions that occur between the N-terminal To understand the interaction mechanism between the domains of architectural proteins can support selective architectural protein Pita and the BTB domain of CP190, distance interactions between regulatory elements. Pita we attempted to precisely map the interaction regions in belongs to a large family of architectural proteins that Pita. Previously, we found that the BTB domain of CP190 feature zinc fnger-associated domains (ZADs) at the interacted with the 95–302 aa region of Pita, which was N-terminus [21, 23]. Investigations of three architectural mapped between the ZAD and the C2H2 cluster [25]. We proteins, Pita, Zw5, and ZIPIC, showed that the ZAD used bacteria to express overlapping glutathione S-trans- domains form only homodimers and support specifc ferase (GST)-fusion peptides that covered the 95–302 aa distance interactions between sites bound by the same region of Pita. Te borders of the deletion derivatives architectural protein [17]. Te 683 aa Pita protein con- were set according to conserved blocks of amino acids tains an N-terminal ZAD domain (17–93 aa) and a cen- in Pita protein from various Drosophila species. Te tral cluster, consisting of 10 C2H2 zinc-fnger domains obtained GST-peptides were tested for interactions with (286–562 aa) [24, 25]. Pita is an essential Drosophila pro- the CP190 BTB domain, fused with 6×His, in a pull- tein, and the strong hypomorph pita mutants die during down assay (Fig. 1a). Tis process allowed us to map the larval stage [24, 26]. two binding regions between 95–165 aa and 220–232 aa Pita binds to a large 15-bp consensus site that is fre- (Fig. 1b, c). Interestingly, the deletion of 220–232 aa, quently found in gene promoters and intergenic regula- which was defned as a 13 aa core, resulted in the com- tory elements, including boundary/insulator elements plete loss of interaction between the 95–302 fragment in the Bithorax complex (Bx-C) [19, 25]. Te Bithorax and BTB in a pull-down assay, even though this protein complex (BX-C) contains three homeotic genes, Ultra- fragment still contained the second binding region. Te bithorax (Ubx), abdominal-A (abd-A), and Abdominal-B 13 aa core was predicted to be unstructured, but it con- (Abd-B), which are responsible for specifying the par- tains several conserved hydrophobic residues (Fig. 1d). asegments (PS5 to PS13) that comprise the posterior Taken together, these results showed that the BTB two-thirds of the fy segments [27–29]. Te expression of domain interacts with the 95–165 aa region and the 13 aa each homeotic gene in the appropriate parasegment-spe- core, whose sequences have no obvious homology. Te cifc pattern is controlled by independent cis-regulatory 95–165 aa region appeared to stabilize the interaction domains that are separated by boundaries. For example, between the BTB domain and the 13 aa core. the regulatory domains iab-5, iab-6, and iab-7, deter- To better understand the functional signifcance of mine the expression of Abd-B in the abdominal segments the interaction between Pita and CP190, we deleted the A5, A6, and A7, respectively. Te Mcp, Fab-6, Fab-7, and 13 aa core that is necessary for Pita to bind with CP190 Fab-8 boundaries ensure the autonomous function of in vivo (PitaΔCP1). Te Pitawt and PitaΔCP1 proteins were Sabirov et al. Epigenetics & Chromatin (2021) 14:16 Page 3 of 16 Fig.
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