Impact of Interactions between Su(Hw)-Dependent Insulators on the Transvection Effect in Drosophila melanogaster.

Transvection is a phenomenon of interallelic communication in which enhancers can activate a specific promoter located on a homologous chromosome. Insulators play a significant role in ensuring functional interactions between enhancers and promoters. In the presented work, we created a model where two or three copies of the insulator are located next to enhancers and promoters localized on homologous chromosomes. Using the Su(Hw) insulator as a model, we showed that the functional interaction between a pair of insulators promotes enhancer-promoter trans-interactions. The interaction between the three insulators, on the contrary, can lead to the formation of chromatin loops that sterically hinder the full enhancer-promoter interaction. The results of the work suggest the participation of insulators in the regulation of homologous chromosome pairing and in communication between distant genomic loci.

CRISPR/Cas9 Essential Gene Editing in Drosophila.

Since the addition of the CRISPR/Cas9 technology to the genetic engineering toolbox, the problems of low efficiency and off-target effects hamper its widespread use in all fields of life sciences. Furthermore, essential gene knockout usually results in failure and it is often not obvious whether the gene of interest is an essential one. Here, we report on a new strategy to improve the CRISPR/Cas9 genome editing, which is based on the idea that editing efficiency is tightly linked to how essential the gene to be modified is. The more essential the gene, the less the efficiency of the editing and the larger the number of off-targets, due to the survivorship bias. Considering this, we generated deletions of three essential genes in Drosophila: trf2, top2, and mep-1, using fly strains with previous target gene overexpression ("pre-rescued" genetic background).

Study of the in Vivo Functional Role of Mutations in the BTB Domain of the CP190 Protein of Drosophila melanogaster.

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.

Study of the Association of Ouib and Nom with Heterochromatin in Drosophila melanogaster.

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.

Study of the Role of Long Noncoding roX RNA in Maintaining of the Dosage Compensation Complex in Drosophila melanogaster.

The proteins MSL1, MSL2, MSL3, MLE, and MOF and noncoding RNAs roX1 and roX2 form the Drosophila dosage compensation complex (DCC), which specifically binds to the X chromosome of males. It is known that noncoding RNA roX are primary component of the DCC in the process of assembly and spreading of the complex among the X chromosome of males. However, the role of this RNA in maintaining the structure of the already assembled complex remains unclear. In this work, we have shown that the full-assembled dosage compensation complex dissociates rather weakly when treated with RNases: the MLE helicase is effectively released from the complex, and the remaining protein components (MSL1, MSL2, and MSL3) undergo partial disassembly and continue to be part of subcomplexes. The results confirm the importance of the noncoding roX2 RNA not only in the processes of initiation of DCC assembly but also at the stage of maintaining the structure of the already assembled complex.

Recruitment to Chromatin of (GA)n-Associated Factors GAF and Psq in the Transgenic Model System Depends on the Presence of Architectural Protein Binding Sites.

Polycomb group (PcG) repressors and Trithorax group (TrxG) activators of transcription are essential for the proper development and maintenance of gene expression profiles in multicellular organisms. In Drosophila, PcG/TrxG proteins interact with DNA elements called PRE (Polycomb response elements). We have previously shown that the repressive activity of inactive PRE in transgenes can be induced by architectural protein-binding sites. It was shown that the induction of repression is associated with the recruitment of PcG/TrxG proteins, including the DNA-binding factors Pho and Combgap. In the present study, we tested the association of the two other PRE DNA-binding factors, GAF and Psq, with bxdPRE in the presence and absence of sites for architectural proteins. As a result, it was shown that both factors can be efficiently recruited to the bxdPRE only in the presence of adjacent binding sites for architectural proteins Su(Hw), CTCF, or Pita.

The Variable CTCF Site from Drosophila melanogaster Ubx Gene is Redundant and Has no Insulator Activity.

CTCF is the most thoroughly studied chromatin architectural protein and it is found in both Drosophila and mammals. CTCF preferentially binds to promoters and insulators and is thought to facilitate formation of chromatin loops. In a subset of sites, CTCF binding depends on the epigenetic status of the surrounding chromatin. One such variable CTCF site (vCTCF) was found in the intron of the Ubx gene, in close proximity to the BRE and abx enhancers. CTCF binds to the variable site in tissues where Ubx gene is active, suggesting that the vCTCF site plays a role in facilitating contacts between the Ubx promoter and its enhancers. Using CRISPR/Cas9 and attP/attB site-specific integration methods, we investigated the functional role of vCTCF and showed that it is not required for normal Drosophila development. Furthermore, a 2161-bp fragment containing vCTCF does not function as an effective insulator when substituted for the Fab-7 boundary in the Bithorax complex. Our results suggest that vCTCF function is redundant in the regulation of Ubx.

Fragments of the Fab-3 and Fab-4 Boundaries of the Drosophila melanogaster Bithorax Complex That Include CTCF Sites Are not Effective Insulators.

The segment-specific regulatory domains of the Bithorax complex (BX-C), which consists of three homeotic genes Ubx, abd-A and Abd-B, are separated by boundaries that function as insulators. Most of the boundaries contain binding sites for the architectural protein CTCF, which is conserved for higher eukaryotes. As was shown previously, the CTCF sites determine the insulator activity of the boundaries of the Abd-B regulatory region. In this study, it was shown that fragments of the Fab-3 and Fab-4 boundaries of the abd-A regulatory region, containing CTCF binding sites, are not effective insulators.

The NCoR Co-repressor Interacts with the Kaiso Transcription Factor through a Mechanism Different from That of BCL6 Interaction.

The vertebrate transcription factor Kaiso binds specifically to methylated DNA sequences using C2H2-type zinc fingers. In addition to C2H2-domains, the BTB/POZ domain, which forms homodimers, is located at the N-terminus of Kaiso. Kaiso, like several other well-studied BTB/POZ proteins, including BCL6, interacts with the NCoR (nuclear co-repressor) protein, which determines the landing of transcriptional repressive complexes on chromatin. Using the yeast two-hybrid system, we have shown that the N-terminal domain of NCoR interacts with the C-terminal zinc fingers of Kaiso, and not with its BTB/POZ domain, as previously assumed. The results obtained demonstrate that NCoR interacts with various transcription factor domains, which can increase the efficiency of attracting NCoR-dependent repressor complexes to regulatory regions of the genome.

The Piragua Gene Is not Essential for Drosophila Development.

Proteins with clusters of C2H2 zinc finger domains (C2H2-proteins) constitute the most abundant class of transcription factors in higher eukaryotes. N-terminal ZAD (zinc finger-associated domain) dimerization domain has been identified in a large group of C2H2-proteins mostly in insects. The piragua gene encodes one of these proteins, Fu2. We have generated CRISPR/Cas9-mediated deletion of the piragua gene that has no phenotype. We have used φC31-mediated attP/attB recombination to generate a transgenic line expressing Fu2 protein fused with HA epitope. This line will be useful for analysis of DNA binding profile and functions of Fu2 protein.

Sfmbt Co-purifies with Hangover and SWI/SNF-Remodelers in Drosophila melanogaster.

Polycomb group (PcG) proteins are chromatin-associated factors involved in the repression of gene transcription. In the present study, we characterized the interactome of the Sfmbt factor at the embryonic stage of development. For this, the Sfmbt protein complex was affinity purified from the nuclear extract, followed by highly specific peptide sequencing (IP/LC-MS). As a result, a number of previously uncharacterized Sfmbt interactions were discovered. In particular, Sfmbt top-interacting proteins include the DNA-binding protein Hangover and components of the SWI/SNF family of chromatin remodelers.

Mutations of Phosphorylation Sites in MSL1 Protein Do Not Affect Dosage Compensation in Drosophila melanogaster.

Proteins MSL1 and MSL2 form the core of the Drosophila dosage compensation complex, which specifically binds to the X chromosome of males. Phosphorylation of certain amino acid residues was previously shown to regulate MSL1 activity. In the present work, transgenic lines of Drosophila expressing mutant variants of the MSL1 protein were obtained, in which amino acids undergoing phosphorylation were replaced. As a result, it was shown that inactivation of phosphorylation sites does not affect the efficiency of specific binding of the dosage compensation complex to the X chromosome of males and its functional activity.

Study of the N-Terminal Domain Homodimerization in Human Proteins with Zinc Finger Clusters.

CTCF belongs to a large family of transcription factors with clusters of C2H2-type zinc finger domains (C2H2 proteins) and is a main architectural protein in mammals. Human CTCF has a homodimerizing unstructured domain at the N-terminus which is involved in long-distance interactions. To test the presence of similar N-terminal domains in other human C2H2 proteins, a yeast two-hybrid system was used. In total, the ability of unstructured N-terminal domains to homodimerize was investigated for six human C2H2 proteins with an expression profile similar to CTCF. The data indicate the lack of the homodimerization ability of these domains. On the other hand, three C2H2 proteins containing the structured domain DUF3669 at the N-terminus demonstrated homo- and heterodimerization activity.

TTK Isoforms Interact with Two Regions of the Mep-1 Protein of Drosophila melanogaster.

The Drosophila TTK protein is involved in the processes of cell differentiation and is represented by two isoforms, TTK69 and TTK88, which have a common N-terminal BTB domain and different C-terminal sequences. Earlier, it was shown that TTK69 represses the activity of enhancers and promoters by recruiting a conserved among higher eukaryotes NURD complex to chromatin. The Mep-1 protein was found in the NURD-complex of Drosophila, and this protein can interact with the C-terminal region of TTK69. In the present study, using the yeast two-hybrid system, we mapped the interacting regions of the TTK and Mep-1 proteins. We identified regions in the unique C-terminal regions of TTK isoforms that can interact simultaneously with two regions of the Mep-1 protein. The results show that, despite the low homology of the C-terminal regions, the TTK isoform retains the ability to interact with two conserved regions of the Mep-1 protein, which suggests the functional significance of this interaction.

The BEAF-32 Protein Directly Interacts with Z4/putzig and Chriz/Chromator Proteins in Drosophila melanogaster.

In Drosophila, the BEAF-32, Z4/putzig, and Chriz/Chromator proteins colocalize in the interbands of polytene chromosomes. It was assumed that these proteins can form a complex that affects the structure of chromatin. However, the mechanism of the formation of such a complex has not been studied. We have proved for the first time that the BEAF-32, Z4/putzig, and Chriz/Chromator proteins interact directly with each other and localized the protein domains that provide multiple protein-protein interactions. Based on the data obtained, we developed a model of the mechanism of the formation the BEAF/Z4/Chriz complex and its recruitment to chromatin.

CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers.

In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.

Human CTCF Interacts with Drosophila CP190, but not with Kaiso.

Human CTCF (hCTCF) is a major architectural protein in mammals. In Drosophila, the CTCF homologue (dCTCF) interacts with the BTB domain of the CP190 protein, which is involved in the establishment of open chromatin and activity of insulators. Previously, it was shown that the BTB protein Kaiso interacts with hCTCF and regulates its activity. We have carried out a detailed study of the interaction between these proteins in the yeast two-hybrid assay. Surprisingly, Kaiso did not interact with hCTCF and its Drosophila homologue. On the other hand, CP190 interacted with the C-terminus of hCTCF. The results obtained demonstrate that the interaction between CTCF and CP190 proteins is highly conserved. It is likely that humans have other BTB proteins that perform the functions described for the Drosophila CP190.

The Chriz Protein Promotes the Recruitment of the Z4 Protein to the STAT-Dependent Promoters.

Proteins Z4/putzig and Chriz/Chromator are involved in the chromatin organization on the promoters of the majority of Drosophila genes. It was shown that the Chriz protein region from aa 273 to 503 is required for the interaction with the Z4 protein. Deletion of this sequence leads to derepression of a number of STAT-dependent genes and development of melanotic tumors in flies. The results of this study suggest that the Chriz protein promotes the recruitment of the Z4 protein to chromatin.

The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes.

The mechanisms underlying long-range interactions between chromatin regions and the principles of chromosomal architecture formation are currently under extensive scrutiny. A special class of regulatory elements known as insulators is believed to be involved in the regulation of specific long-range interactions between enhancers and promoters. This review focuses on the insulators of Drosophila and mammals, and it also briefly characterizes the proteins responsible for their functional activity. It was initially believed that the main properties of insulators are blocking of enhancers and the formation of independent transcription domains. We present experimental data proving that the chromatin loops formed by insulators play only an auxiliary role in enhancer blocking. The review also discusses the mechanisms involved in the formation of topologically associating domains and their role in the formation of the chromosomal architecture and regulation of gene transcription.