Transcription factor DREF regulates expression of the microRNA gene bantam in Drosophila melanogaster.

The bantam gene encodes a vital microRNA and has a complex expression pattern in various tissues at different stages of Drosophila development. This microRNA is involved in the control of normal development of the ocular and wing imaginal discs, the central nervous system, and also in maintaining the undifferentiated state of stem cells in the ovaries of adult females. At the cellular level, bantam stimulates cell proliferation and prevents apoptosis. The bantam gene is a target of several conserved signaling cascades, in particular, Hippo. At the moment, at least ten proteins are known to directly regulate the expression of this gene in different tissues of Drosophila. In this study, we found that the bantam regulatory region contains motifs characteristic of binding sites for DREF, a transcription factor that regulates the expression of Hippo cascade genes. Using transgenic lines containing a full-length bantam lethality-rescuing deletion fragment and a fragment with a disrupted DREF binding site, we show that these motifs are functionally significant because their disruption at the bantam locus reduces expression levels in the larvae and ovaries of homozygous flies, which correlates with reduced vitality and fertility. The effect of DREF binding to the promoter region of the bantam gene on its expression level suggests an additional level of complexity in the regulation of expression of this microRNA. A decrease in the number of eggs laid and a shortening of the reproductive period in females when the DREF binding site in the regulatory region of the bantam gene is disrupted suggests that, through bantam, DREF is also involved in the regulation of Drosophila oogenesis.

Different Protein Groups Involved in Transcription Regulation in Development and Housekeeping Genes in Drosophila.

Antibodies to histone modifications and an insulator protein involved in the processes of transcription initiation and elongation are mapped in Drosophila polytene chromosomes. The CHRIZ protein (chromatin insulator) and H3K36me3 histone modification (RNA elongation) are detected only in the localization of housekeeping genes (interbands and gray bands of polytene chromosomes) and never in the regions of developmental genes (black bands and large puffs arising from them). Antibodies to H3S10P histone modification, which is associated with the initial elongation of the RNA strand during transcription, are found exclusively in small puffs, but not in housekeeping gene localization sites or large ecdysone-induced puffs, where housekeeping genes are localized. Antibodies to H4R3me2 histone modification (a co-repressor of the ecdysone receptor) are detected only in large ecdysone-induced puffs.

[MicroRNA Expression Profiling of Diffuse Large B-Cell Lymphoma].

Non-Hodgkin lymphoma (NHL) is a heterogeneous group of cancers that differ in pathogenesis and prognosis. The main methods of treating NHL include chemotherapy, immunochemotherapy, and radiation therapy. However, a significant proportion of these tumors are chemoresistant or rapidly recur after a short chemotherapy-induced remission. In this regard, the search for alternative cytoreductive therapeutic methods is relevant. Aberrant expression of microRNA (miRNA) is one of the mechanisms responsible for the emergence and progression of malignant lymphoid neoplasms. We analyzed the profile of miRNA expression in the biopsy material from lymph nodes affected by diffuse large B-cell lymphoma (DLBCL). The key material of the study was histological preparations of lymph nodes obtained by excisional diagnostic biopsy and treated using conventional histomorphological formalin fixation methods. The study group consisted of patients with DLBCL (n = 52); the control group consisted of patients with reactive lymphadenopathy (RL) (n = 40). It was shown that the miR-150 expression level in DLBCL was reduced by more than 12 times (p = 3.6 x 10^(-15)) compared with RL. Bioinformatics analysis revealed the involvement of miR-150 in the regulation of hematopoiesis and lymphopoiesis. The data we obtained allow us to consider miR-150 as a promising therapeutic target with great potential in clinical practice.

Otu and Rif1 Double Mutant Enables Analysis of Satellite DNA in Polytene Chromosomes of Ovarian Germ Cells in Drosophila melanogaster.

Polytene chromosomes in Drosophila serve as a classical model for cytogenetic studies. However, heterochromatic regions of chromosomes are typically under-replicated, hindering their analysis. Mutations in the Rif1 gene lead to additional replication of heterochromatic sequences, including satellite DNA, in salivary gland cells. Here, we investigated the impact of the Rif1 mutation on heterochromatin in polytene chromosomes formed in ovarian germ cells due to the otu gene mutation. By the analysis of otu11; Rif11 double mutants, we found that, in the presence of the Rif1 mutation, ovarian cells undergo additional polytenization of pericentromeric regions. This includes the formation of large chromatin blocks composed of satellite DNA. Thus, the effects of the Rif1 mutation are similar in salivary gland and germ cells. The otu11; Rif11 system opens new possibilities for studying factors associated with heterochromatin during oogenesis.

MicroRNAs in the Myelodysplastic Syndrome.

The myelodysplastic syndrome (MDS) holds a special place among blood cancers, as it represents a whole spectrum of hematological disorders with impaired differentiation of hematopoietic precursors, bone marrow dysplasia, genetic instability and is noted for an increased risk of acute myeloid leukemia. Both genetic and epigenetic factors, including microRNAs (miRNAs), are involved in MDS development. MicroRNAs are short non-coding RNAs that are important regulators of normal hematopoiesis, and abnormal changes in their expression levels can contribute to hematological tumor development. To assess the prognosis of the disease, an international assessment system taking into account a karyotype, the number of blast cells, and the degree of deficiency of different blood cell types is used. However, the overall survival and effectiveness of the therapy offered are not always consistent with predictions. The search for new biomarkers, followed by their integration into the existing prognostic system, will allow for personalized treatment to be performed with more precision. Additionally, this paper explains how miRNA expression levels correlate with the prognosis of overall survival and response to the therapy offered.

Expression of micrornas in molecular genetic breast cancer subtypes.

BACKGROUND: It is shown that each type of human malignancies has a unique set of expressed miRNAs, and tumor-specific miRNAs in biological tissues of a patient are stable. The aim of this study was to determine the differences in the expression of miRNAs in tumor tissue of invasive breast carcinoma compared to normal tissue, as well as to analyze the variable expression of miRNAs in molecular genetic subtypes of breast cancer. METHODS: We determined differences in mRNA expression in 35 biopsies of tumor tissue of various molecular genetic subtypes of breast cancer and 35 biopsies of adjacent conventionally normal breast tissue by RT-PCR in real time. We assessed the expression levels of miRNA-21, 221, 222, 155, 205, 20a , 125b and 200a. RESULTS: A significant increase in the level of expression of the oncogenic miRNA-20a (p=0.000141) and miRNA-221 (p=0.037777) in the triple negative cancer in comparison with the luminal A and luminal B/HER2/neu-negative breast cancer subtypes was established. Assessment of significance of the results was conducted using ROC analysis. For miRNA-221 AUC value was 0.772, for miRNA-20a AUC value was 0.949. The obtained results suggest the possibility of using the levels of miRNA-21, 155, 205, 125b expression in tumor tissue to assess a malignant potential of a breast carcinoma. The levels of expression of oncogenic miRNA-221 and miRNA-20a are increased in TNBC compared with luminal A and luminal B/HER2/neu-negative breast cancer subtypes, supporting the characteristic of TNBC as the most aggressive subtype of breast cancer. MiRNA-20a is a marker of TNBC compared with luminal subtypes of breast cancer. MICRO ABSTRACT: To identify markers for breast cancer with triple-negative phenotype, we evaluated expression levels of siRNA-21, 221, 222, 155, 205, 20a, 125b, 200a and 146b in the tumor tissue of 35 patients by RT-PCR. AUC value equal to 0.949 in the ROC-analysis allows us to recommend the miRNA-20a as a marker of triple negative breast cancer to differentiate it from the luminal subtypes.

Architecture of Promoters of House-Keeping Genes in Polytene Chromosome Interbands of Drosophila melanogaster.

This is the first study to investigate the molecular-genetic organization of polytene chromosome interbands located on both molecular and cytological maps of Drosophila genome. The majority of the studied interbands contained one gene with a single transcription initiation site; the remaining interbands contained one gene with several alternative promoters, two or more unidirectional genes, and "head-to-head" arranged genes. In addition, intricately arranged interbands containing three or more genes in both unidirectional and bidirectional orientation were found. Insulator proteins, ORC, P-insertions, DNase I hypersensitive sites, and other open chromatin structures were situated in the promoter region of the genes located in the interbands. This area is critical for the formation of the interband, an open chromatin region in which gene transcription and replication are combined.

Gene dunce Localization in the Polytene Chromosome of Drosophila melanogaster Long Span Batch of Adjacent Chromosomal Structures.

The molecular and chromosomal localization of the dunce gene was studied. This gene (167.3 kb) consists almost entirely of introns, in which a cluster of seven short tissue-specific genes is located. On the basis of the results of FISH analysis of the gene fragments, we established that the dunce gene is located within nine chromosomal structures (four bands and five interbands), which contradicts the common idea that genes are located in only one structure (band or interband) or at the boundary of these structures. Our results are quite unexpected and original and greatly expand the current understanding of the genetic organization of interphase chromosomes.

New Haplotypes of the Mitochondrial Gene CytB in the Nesting Population of the Siberian Black Kite Milvus migrans lineatus Gray, 1831 in the Territory of the Republic of Tyva.

We analyzed a fragment of mitochondrial CytB locus obtained from young and adult black kites Milvus migrans lineatus from 19 nests in the Republic of Tyva, Russia. Three previously known (CytB-6, CytB-14, CytB-19) and three new haplotypes identified as CytB-6.1, CytB-6.2, and CytB-19.1 were detected. We described a set of substitutions specific to M. migrans lineatus but not to M. migrans migrans, the European subspecies of black kite.

Border Structure of Intercalary Heterochromatin Bands of Drosophila melanogaster Polytene Chromosomes.

The precise genomic localization of the borders of 62 intercalary heterochromatin bands in Drosophila polytene chromosomes was determined. A new type of bands containing chromatin of different states was identified. This type is a combination of the gray band and the intercalary heterochromatin band, creating a genetic structure that with a light microscope is identified as a continuous band. The border structure of such bands includes the coding regions of genes with ubiquitous activity.

Genetic Organization of Open Chromatin Domains Situated in Polytene Chromosome Interbands in Drosophila.

New data on the organization of genes entirely located in the open domains for chromatin transcription and occupying only one chromosome structure (interband) were obtained. The characteristic features of these genes are the small size (on average, 1-2 kb), depletion of the replicative complex proteins in the regulatory region, and the presence of specific motifs for binding transcription factors, as compared to the genes occupying two structures (interband and gray band). The biological function of these genes is associated primarily with the processes of gene expression and RNA metabolism.

Drosophila polytene chromosome bands formed by gene introns.

Genetic organization of bands and interbands in polytene chromosomes has long remained a puzzle for geneticists. It has been recently demonstrated that interbands typically correspond to the 5'-ends of house-keeping genes, whereas adjacent loose bands tend to be composed of coding sequences of the genes. In the present work, we made one important step further and mapped two large introns of ubiquitously active genes on the polytene chromosome map. We show that alternative promoter regions of these genes map to interbands, whereas introns and coding sequences found between those promoters correspond to loose grey bands. Thus, a gene having its long intron "sandwiched" between to alternative promoters and a common coding sequence may occupy two interbands and one band in the context of polytene chromosomes. Loose, partially decompacted bands appear to host large introns.

Targeted mutagenesis of Drosophila RNaseZ gene by homologous recombination.

For the first time we used a homologous recombination method to obtain complete and precise deletion of Drosophila dRNaseZ gene. In the founder line of flies in which the RNaseZ sequence was replaced by attP site, the full-length sequence of the gene was reintegrated, and its functionality was shown. This approach will allow us to generate further gene mutations in different domains of dRNaseZ protein and discover a broad spectrum and uncover functions outside of tRNA processing.

CHARACTERISTIC OF THE CHROMATIN TYPE CORRESPONDING TO THIN «GREY¼ BANDS IN POLYTHENE CHROMOSOMES OF DROSOPHILA MELANOGASTER.

Recently, we developed a bioinformatic algorithm dividing drosophila genome into 4 types of chromatin which differ in protein composition. This allows us to propose a model of structural and functional organization of interphase chromosomes which postulates an existence of correlation between the chromatin types and morphological structures of polytene chromosomes. So, constantly and everywhere open chromatin type named «aquamarine¼ is characteristic of interbands, while the combinations of the other three types («lazurite¼, «malachite¼ and «ruby¼) form the bands. In this study, we characterized protein composition, genetic organization and morphological features of 39 «lazurite¼-chromatin regions in polytene chromosomes. We found out that «lazurite¼-chromatin usually form thin «grey¼ bands and more rarely ­ boundary portions of large bands. This type of chromatin contains coding parts and 3R-ends of genes and is enriched with proteins and histone modifications associated with active transcription at the stage of elongation. The expression patterns of these genes differ greatly depending on the type of chromatin in their 5R-regions.

A COMBINED METHOD FOR MAPPING POLYTHENE CHROMOSOMES ON THE EXAMPLE OF THE FOURTH MICROCHROMOSOME OF DROSOPHILA MELANOGASTER.

Genetic activity of interphase chromosomes is associated with their structural organization, but the mechanism of these relations is still unclear. Classic polythene chromosomes of dipteran insects are a convenient model for such investigations. Despite intensive study of polythene chromosomes of Drosophila melanogaster is carried out, an exact conformity of bands and interbands to the molecular map of the genome remains unknown in most cases. For addressing this issue, the genetic map and molecular characteristics of chromatin have been compared with the banding pattern of the fourth chromosome, which is the smallest chromosome in the D. melanogaster genome and is different in many ways from other chromosomes. This is a unique chromatin domain of D. melanogaster, which is characterized by specific proteins, including HP1, POF and EGG. Matching of cytological and physical maps of the fourth chromosome has been carried out by FISH. Genomic coordinates of bands and interbands have been determined. This result makes it possible to investigate the regulation of gene activity of the fourth chromosome in the context of molecular characteristics of cytological structures in which these genes are located.

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.

COMPREHENSIVE APPROACH TO MAPPING LATE-REPLICATING BANDS IN POLYTHENE CHROMOSOMES OF DROSOPHILA MELANOGASTER.

Heterogeneity of chromatin structure underlies the banding pattern of Drosophila polythene chromosomes. Recently, a four-color model of chromatin has been proposed, with one chromatin type, aquamarine, largely corresponding to interbands (Zhimulev et al., 2014). In this model, most of the previously mapped regions of intercalary heterochromatin are represented by the ruby chromatin type. In the present report, we used the distal part of the chromosome arm 2R to show that all dense late-replicating bands in this region invariably encompass ruby chromatin type. We propose a comprehensive approach that combines cytology mapping data of the FlyBase-annotated genes, novel tools for predicting cytogenetic features of chromosomes based on their prothein composition and data on the sequence of replication in polythene chromosome bands. This approach allows to establish accurately the correspondence between reference late-replicating bands visible on cytology maps and the molecular map.

[Microrna, evolution and cancer].

MicroRNAs are known as a posttranscriptional negative regulators of gene expression by binding to the 3'UTP of target mRNAs in cytoplasm. More than 1600 microRNAs expressed in human cells, are involved in the regulation of embryogenesis, differentiation, cell cycle, apoptosis, senescence, thus determining cell fate. Up to 60 % of protein coding genes are under their control. Various sets of microRNAs found in different human tissues under normal and pathological conditions, including cancer, suggest that miRNAs are involved in most cellular pathways. To date, there is no doubt that regulatory potential of the genome is largely determined by miRNAs. In our study, we performed a comparative phylogenetic analysis of the origin and evolution of the total set of 1048 miRNAs in the human genome and investigated the role of certain miRNAs in carcinogenesis of thyroid and mammary glands, as potential diagnostic and prognostic biomarkers of malignancy. Analysis of phylogenetic distribution of miRNAs in the human genome has shown four peaks of appearance of new miRNA genes in the evolution from Methazoa to H. sapiens. The highest amount of new miRNA genes appeared after divergence of H. s. from common ancestor with P. t. Expansion of transposable elements in genome was accompanied by the origin of new miRNA genes on the basis of their sequences. More than 14 % from 1600 miRNAs of human genome originated from mobile elements and still remain. Profiles of expression of 5 miRNAs, pertaining to oncomicroRNAs - miR-21, -221, -222, -155 and -205 - allow distinguishing ductal invasive carcinoma of mammary gland and thyroid papillary carcinoma. The data obtained suggest different ways and roles of participation of the same miRNAs in carcinogenesis of thyroid and mammary glands. So, these miRNAs and profiles of their expression might be used in the diagnosis and prognosis of cancer.

[Late-replicating regions in salivary gland polytene chromosomes of Drosophila melanogaster].

About 240 specific regions that are replicated at the very end of the S-phase have been identified in D. melanogaster polytene chromosomes. These regions have a repressive chromatine state, low gene density, long intergenic distances and are enriched in tissue specific genes. In polytene chromosomes, about a quarter of these regions have no enough time to complete replication. As a result, underreplication zones represented by fewer DNA copy number, appear. We studied 60 chromosome regions that demonstrated the most pronounced under-replication. By comparing the location of these regions on a molecular map with syntenic blocks found earlier for Drosophila species by von Grotthuss et al., 2010, we have shown that across the genus Drosophila, these regions tend to have conserved gene order. This forces us to assume the existence of evolutionary mechanisms aimed at maintaining the integrity of these regions.

[Cytophotometric determination of genome size in two species of Cyclops Lake Baikal (Crustacea: Copepoda: Cyclopoina) in ontogenetic development].

Genome size of Cyclops in cells at early stages of cleavage (up to the 5th division) and in somatic cells were estimated by a static digital Feulgen cytophotometry in order to study the quantitative changes in DNA content during chromatin diminution. Our realization of the cytophotometric method was approbeted on five different digital-imaging systems in blood cells of four vertebrate species. In all cases, we observed a direct correlation of the obtained and known from the literature data on the genome size and a high reproducibility, which allows to use these systems in future work. We also optimized the conditions for DNA hydrolysis of both blood smears, and for two species of Cyclops from the Moscow population, as 30 min in 5 N HCl at 24 degrees C. Here we first revealed chromatin diminution in two endemic Baikal species of Cyclopoida: Acanthocyclops incolotaenia and Diacyclops galbinus estimated the extent ofchromatin diminution in Diacyclops galbinus as 95.5-96.2 %. Cytometric analysis of the third species, Mesocyclops leuckarti, did not reveal obvious chromatin diminution. We also optimized the conditions for DNA hydrolysis of both blood smear preparations, and for two species of copepods from the Moscow population, as 30 min in 5N HCl at 24 degrees C.