LOCALIZATION OF MOBILE P-ELEMENT INSERTIONS IN DOMAINS OF ACTIVE AND REPRESSED CHROMATIN IN DROSOPHILA MELANOGASTER’S GENOME

Classic polythene chromosomes from dipteran insects are extensively used as a model for interphase chromosomes. The peculiar morphology of polythene chromosomes is formed by the alternating densely packed chromatin of bands and less compact interbands. In recent years numerous data have been obtained on the precise localization of different proteins on the molecular map in the interphase chromosomes. A special algorithm has been developed based on the interband specific protein composition. This algorithm allows us to detect the positions of bands and interbands in the whole Drosophila’s genome. The goal of our investigation is to analyse of P-elements distribution in localized bands and interbands. We have found that P-elements distribution is not random in Drosophila’s genome. Insertions of P-elements predominantly take place in regions of genome predicted by algorithm as interbands. The density of P-element insertions in compacted bands is notably lower.

[Chromomeric organization of interphase chromosomes in Drosophila melanogaster]

As a result of treatment of bioinformatic data on the genome localization of structural proteins, histone modifications, DNase-hypersensitive regions, replication origins (taken from modENCODE) and their cytological localization to polytene chromosome structures, it is shown here that two types of interphase chromosomes -polytene chromosomes from salivary glands and from mitotically dividing cells cultures - demonstrate identical pictures of interband/band, i. e. the same localization and length on physical map and the same sets of proteins. In the interbands of both chromosome types we find the proteins that control initiation of transcription (RNA-polymerase II, transcription factors), replication (ORC2) as well as proteins modifying nucleosome structure (WDS, NURF) and proteins of insulators (BEAF). The nucleosome density and H1 histone concentration in the interbands are depleted; localization of DNase-hypersensitive regions corresponds strictly to the interbands. So, we conclude that both polytene and cell line interphase chromosomes are arranged according to general principle and polytene chromosomes represent precise model of interphase chromosomes. The interbands play a critical role in the initiation of transcription and replication. The interbands of interphase chromosomes are the sites of 5' parts of genes, while the 3' gene ends are located in the adjacent bands. The constancy of interbands decondensation results in the conclusion that the "interbands" genes are constantly active, i. e. they contain "house-keeping" genes. The large late replicating bands contain genes that do not have direct contact to the adjoining interbands are usually polygenic and contain tissue-specific genes.

[Intercalary heterochromatin in the genome of Drosophila]

The modern concept of intercalary heterochromatin as polytene chromosome regions exhibiting a number of specific characteristics is formulated. DNA constituting these regions is replicated late in the S period; therefore, some strands of polytene chromosomes are underrepresented; i.e., they are underreplicated. Late-replicating regions account for about 7% of the genome; genes are located there in clusters of as many as 40. In general, the gene density in the clusters is substantially lower than in the main part of the genome. Late-replicating regions have an inactivating capacity: genes incorporated into these regions as parts of transposons are inactivated with a higher probability. These regions contain a specific protein SUUR affecting the rate of replication completion.

[Contribution of the SuUR gene to the organization of epigenetically repressed regions of Drosophila melanogaster chromosomes]

A significant portion of a eukaryotic genome is silent (epigenetically repressed). In Drosophila melanogaster, this portion includes mainly regions of pericentric and intercalary heterochromatin and euchromatin regions subject to position-effect variegation. Detailed study of the organization of intercalary heterochromatin regions of Drosophila melanogaster polytene chromosomes started from the discovery of the SuUR gene (Suppressor of UnderReplication). The ability of the SuUR mutation to suppress underreplication in intercalary heterochromatin regions was used for molecular tagging of these regions. We showed that underreplicated intercalary heterochromatin regions contained silent unique genes and retained the features of late replication and transcriptionally inactive chromatin state in various cell types. Over 50% of these regions contain unique genes clustered on the base of coordinated expression. The origin of clusters and putative mechanisms of their gene expression are discussed. Data on the SuUR gene, its expression, and effect on polytene chromosome structure and replication are summarized.

[Dynamics of chromatin position within the interphase nucleus]

In this article we attempt to analyze the relationship between the processes, which occur in the nucleus, and the dynamics of chromatin, as well as to classify the changes in the position of chromatin in the cell nucleus during the lifetime of the cell. The proposed concept integrates possible types of chromatin movement within the nucleus.

[Microcloning and characteristics of DNA from regions of the centromeric heterochromatin of Drosophila melanogaster polytene chromosomes]

A method of microcloning, which involves microsurgical excision of chromosome fragments, DNA amplification by means of a polymerase chain reaction (PCR), and ligation of amplified products with plasmids, was employed in studying Drosophila polytene chromosomes for the first time. Clones of the DNA library thus obtained contained inserts varying in size from 0.1 to 0.5 kb. DNA sequencing of five clones of the library showed that pericentromeric heterochromatin contained the 17.6 and 297 retrotransposons, the ninja retrotransposon characteristic of D. simulans, and two Drosophila repetitive elements, a8 and a12, the function of which remains unknown.

Molecular and cytogenetical characterization of the 10A1-2 band and adjoining region in the Drosophila melanogaster polytene X chromosome

Some 300 kb of DNA from the 9F12-10A7 X chromosome region (seven bands) uncovered by Df(1)vL3 were cloned and 31 break points of chromosome rearrangements within the region were mapped. Positions of 12 genes found earlier in genetic saturation experiments, transcripts and P element-induced mutations were located on the physical map using either chromosome rearrangements or Southern blot hybridizations. Data on the position of the break points, genes and polytene chromosome bands allow the following conclusions to be made. (1) The size of the bands in the region varies between 4 kb (10A6 and 7) and 183-195 kb (10A1-2). The compaction ratio of DNA in bands varies from 8-36 (10A6 + 7) to 151-161 (10A1-2). Therefore, fine and thick bands appear to have different kinds of DNP packaging. (2) The bands differ in genetic content. Fine bands contain from one to three genes. In contrast, the 10A1-2 band contains three genes and at least six transcribed DNA fragments. (3) Comparison of genetic and physical maps shows that in this region 0.01 centiMorgan corresponds to 3.3 kb of DNA.

Localization of genes ecs, dor and swi in eight Drosophila species

A cluster of genes corresponding to the early ecdysone stimulated puff 2B of the Drosophila melanogaster X chromosome has been localized using in situ hybridization in eight Drosophila species. Genes ecs, dor and swi from this cluster have been mapped in D. funebris, D. virilis, D. hydei, D. repleta, D. mercatorum and D. paranaensis to the telomeric region of the X chromosome, in D. kanekoi to the distal region, and in D. pseudoobscura, to the proximal region of the X chromosome. It is assumed that organization of this cluster in these species is conserved. In D. hydei, multiple hybridization sites of certain DNA probes from this region were found.

Gene-directed mutagenesis in bacteriophage T7 provided by polyalkylating RNAs complementary to selected DNA sites

Bacteriophage T7 early transcripts were used as carriers of alkylating groups to affect complementary T7 DNA sites for inducing mutations in preselected genes. A heterofunctional polyalkylating agent N,N,N'-tri-(beta-chloroethyl)-N'-(p-formylphenyl)propylene diamine-1,3 was attached to 3-5% of the transcript nucleotides. The controlled alkylating groups carried on RNA were activated after RNA . DNA hybridization. The modified transcripts were shown to hybridize only with the complementary H strand and to form covalently bound R loops in the appropriate T7 sites. The T7 DNA molecules locally alkylated by the modified transcripts of gene 1.3 coding for T7 ligase were packaged into T7 proteins and used to infect Escherichia coli B. As judged by plating efficiency and the ligase-deficient E. coli BL2 strain, 4 of 140 plaques obtained after infection contained mutants defective in gene 1.3 in amounts of 0.7-1.5%. The T7 DNA locally alkylated by the modified transcripts of gene 0.3 and 1.1 were used for the transfection of E. coli C1757. Analysis of 24 plaques produced by transfection indicated that 3 contained mutants defective in gene 0.3 in amounts of 2-10%. The mutants had also a second unidentified mutation. Complementation analysis data suggest that the second mutation is due to a defect in gene 1.1. The results obtained demonstrate the efficiency of the approach developed for gene-directed mutagenesis.

[Production of directed mutations in T7 phage by transfecting Escherichia coli using locally alkylated T7 DNA]

Modified polyribonucleotides carrying a number of alkylating groups were used for alkylation of complementary sites of DNA to induce gene-directed mutations. Polyfunctional alkylating mustard, N,N,N'-tri-(beta-chloroethyl)-N'-(p-formylphenyl)-propylene diamine-1,3, moieties were attached to T7 phage early transcripts. The transcripts modified to 4-5% were hybridized with T7 DNA to form R-loops, and RNA molecules were covalently bound to the complementary DNA sites as a result of the activation of RNA carried alkylating groups. T7 DNA molecules alkylated by modified RNAs transcribed from 0.3 and 1.1 T7 phage genes were used for transfection of Escherichia coli. In the progeny of phages generated by the transfection of 24 negative colonies, 3 contained double amber mutants in amounts of 2-10%. Complementation tests permitted to assign all mutations to the same complementation group. Recombination analysis established that one of the mutations concerns gene 0.3. The results of complementation studies indicate that the second mutation, with high probability, concerns gene 1.1.

[Selective modification of T7 DNA at the region of early genes by early RNA carrying multiple alkylating groups]

A method of selective modification of certain regions of the genome which may become useful for inactivation of certain genes or for directed mutagenesis is proposed. For this purpose RNA products of certain genes carrying alkylating groupings randomly distributed along the polymer were used. The RNA modified to an extent of 4--5 alkylating residues per 100 nucleotides retains the ability to specific formation of DNA--RNA hybrid complexes. The alkylating molecule is N,N,N'-tri-(beta-chlorethyl), N'-(p-formylphenyl)propylene diamine-1,3. The aliphatic alkylating functions serve for attachment to RNA. The aromatic alkylating function inactivated by the formyl grouping at the para-position of the benzene ring is used for modification of DNA after hybrid formation by reduction of formyl grouping with sodium borohydride. The covalently binding of modified RNA is exhibited to occur in only the case of T7 DNA H-chain, the one complementary to the RNA derivative. L-chain does not hybridize, nor does it undergo alkylation by the RNA product thus indicating high selectivity of alkylation within the hybrid complex.