[Joint locus of a/b-globin genes in Danio rerio is segregated into structural subdomains active at different stages of development].

In the domain model of eukaryotic genome organization, the functional unit of the genome, along with the relevant regulatory elements, is considered to be a gene or a gene family. In hot-blooded vertebrate animals, the domains of a- and b-globin genes are positioned at different chromosomes and are organized and regulated in different fashion. In cold-blooded animals, in particular in tropical fish Danio rerio, a- and b globin genes are located in a common gene cluster. However, the joint a/b-globin gene cluster is subdivided into two development stage-specific subdomains, the adult one and the embryonic-larval one. In an attempt to find out whether this functional segregation correlates with structural segregation of the domain we compared the DNase I sensitivity and profiles of histone modifications of adult and embryonic-larval segments of the domain in cultured D. rerio fibroblasts. We have demonstrated that, in these nonerythroid cells, adult and embryonic- larval subdomains possess different DNase I sensitivities and different profiles of H3K27me3, a histone modification introduced by PRC2 complex. These observations suggest that joint a/b globin gene domain of Danio rerio is segregated into two structural subdomain harboring adult and embryonic-larval globin genes.

[Patterns of the histone modifications across the chicken alpha-globin genes domain].

Using native chromatin immunoprecipitation (N-ChIP) followed by TaqMan RT-PCR quantitative analysis we have determined the profiles of histone acetylation and histone methylation within the alpha-globin gene domain before and after switching of embryonic globin genes expression. The results obtained do not support a supposition that the inactivation of the embryonic alpha-type globin gene pi in erythroid cells of the adult lineage is mediated via formation of an inactive chromatin domain. On the other hand we have demonstrated that suppression of the gene pi activity in erythroid cells of adult lineage correlates with the decrease of the histone acetylation level within the embryonic subdomain of the alpha-globin gene domain.

[Spatial organization of the chicken alpha-globin gene domain in cells of different].

We have developed a technique for mapping the sites of DNA attachment to the nuclear matrix by hybridization of nuclear matrix DNA with an oligonucleotide array. The latter was made by immobilization of 60-mer oligonucleotides distributed within the area under study with a 2 Kb step on nylon filter. Using this approach we have analyzed the mode of interaction of a 100 Kb fragment of chicken chromosome 16 including the alpha-globin gene domain with the nuclear matrix. The 40 Kb DNA loop including all alpha-globin genes was detected in erythroid cells. One of the borders of this loop colocalized with the previously mapped MAR element and CTCF-dependent enhancer-blocking element. Also, a long transcribed area was found to be preferentially associated with the nuclear matrix. The spatial organization of the area under study in lymphoid cells was drastically different from this observed in erythroid cells.

[Regulatory systems of genome domains with vague boundaries]. / Reguliatornye sistemy genomnykh domenov s razmytymi granitsami.

The specific features of genome domains lacking distinct boundaries are considered. These domains cannot be mapped by testing extended genome regions for nuclease sensitivity and thereby differ from structural domains determined at the level of DNA folding in chromatin. Yet they possess the properties of typical functional domains, containing a gene or several coordinated genes along with a complex of cis-regulatory elements, which control these genes. Domains with vague boundaries may be mapped with certain structural tests, e.g., by assessing histone acetylation or the distribution of tissue-specific DNase I-hypersensitive sites through extended genome regions. The mechanisms are described in detail that regulate the function of genes in domains with vague boundaries, including overlapping domains with genes differing in tissue specificity of expression.

[Genome domains and domain regulatory elements]. / Genomnye domeny i reguliatornye élementy domennogo urovnia.

Gene activity regulation at the level of genome domains is considered with special emphasis on locus control regions (LCR), which are thought to act as dominant regulatory elements providing for the active state of tissue-specific gene domains. Detailed analysis was made of experimental data on the organization and function of mammalian beta-globin gene LCR. On recent evidence, this LCR is necessary for high-level expression of the globin genes, but not for the active state of the domain. These data are compared with earlier findings suggesting a key role of LCR in the organization of active genome domains. The boundaries of functional genome domains are also considered.