Effects of Chromatin Structure Modifiers on the trans-Acting Heterochromatin Position Effect in Drosophila melanogaster.

The heterochromatin position effect is manifested in the inactivation of euchromatin genes transferred to heterochromatin. In chromosomal rearrangements, genes located near the new eu-heterochromatin boundary in the rearrangement (cis-inactivation) and, in rare cases, genes of a region of the normal chromosome homologous to the region of the eu-heterochromatin boundary of the chromosome with the rearrangement (trans-inactivation) are subject to inactivation. The In(2)A4 inversion is able to trans-inactivate the UAS-eGFP reporter gene located on the normal chromosome. We knockdown a number of chromatin proteins using temperature-controlled RNA interference and investigated the effect of knockdown on trans-inactivation of the reporter. We found suppression of trans-inactivation by knockdowns of Su(var)2-HP2, a protein that binds to the key heterochromatin protein HP1a, SAYP, a subunit of the chromatin remodelling complex, and Eggless histone methyltransferase (SETDB1), which introduces a H3K9me3 histone mark, recognized by the HP1a protein. The method of studying the effects of gene knockdown on heterochromatin position effects presented in this work is of independent methodological interest.

High Level of Gene Transcription at the Embryonic Stage Leads to the Suppression of Heterochromatic Trans-Inactivation in Drosophila melanogaster Adults.

In some cases, gene transfer from euchromatin to constitutive heterochromatin as a result of chromosomal rearrangement is accompanied by epigenetic inactivation of this gene (cis-inactivation). In the case of trans-inactivation, transgenes in the normal chromosome are repressed by the cis-inactivation-causing rearranged homologous chromosome. Trans-inactivation is a result of the somatic pairing of homologs and the transfer of the normal chromosomal segment to the heterochromatic compartment of the nucleus. Previously, we have shown that the degree of trans-inactivation of the UAS-eGFP reporter gene in adult flies depends on its transcription level that can be regulated by temperature using the GAL4 transcription activator and its temperature-sensitive inhibitor GAL80ts. In this paper, we investigated the epigenetic inheritance of the active/repressed state of the trans-inactivated reporter gene at different expression levels by measuring eGFP fluorescence in the individual cells of Malpighian tubules in adult flies. High expression levels at the embryonic stage protected the eGFP gene from trans-inactivation in adult flies. The activated state was inherited over the entire period of development and differentiation, while the activating effect of GAL4 was turned off.

[Participation of the piRNA pathway in recruiting a component of RNA polymerase I transcription initiation complex to germline cell nucleoli].

Proteins of the Piwi family and short Piwi-interacting RNAs (piRNAs) ensure the protection of the genome from transposable elements. We have previously shown that nuclear Piwi protein tends to concentrate in the nucleoli of the cells of Drosophila melanogaster ovaries. It could be hypothesized that the function of Piwi in the nucleolus is associated with the repression of R1 and R2 retrotransposons inserted into the rDNA cluster. Here, we show that Piwi participates in recruiting Udd protein to nucleoli. Udd is a component of the conserved Selectivity Factor I-like (SL1-like) complex, which is required for transcription initiation by RNA polymerase I. We found that Udd localization depends on Piwi in germline cells, but not in somatic cells of the ovaries. In contrast, knockdowns of the SL1-like components (Udd or TAF1b) do not disrupt Piwi localization. We also observed that the absence of Udd or TAF1b in germline cells, as well as the impairment of Piwi nuclear localization lead to the accumulation of late stage egg chambers in the ovaries, which could be explained by reduced rRNA transcription. These results allow us to propose for the first time a role for Piwi in the nucleolus that is not directly associated with transposable element repression.

[Nascent Polypeptide-Associated Complex as Tissue-Specific Cofactor during Germinal Cell Differentiation in Drosophila Testes].

During the process of spermatogenesis, the proliferation of spermatogonia (stem cell descendants) is replaced by their differentiation in growing spermatocytes responsible for the preparation to meiosis, which is accompanied by a cardinal change in transcriptional programs. We have demonstrated that, in drosophila, this process is accompanied by a splash of the expression of ß-subunit of nascent polypeptide-associated complex (NAC) associated by ribosomes. Nascent polypeptide-associated complex is known as a chaperone involved in co-translational protein folding. This is the first case of the detection of tissue-specific co-translational NAC cofactor in multicellular eukaryotes. It is proposed that spermatocyte specific NAC is involved in the modulation of the expression of the proteins that provide the functioning of subsequent stages of spermatogenesis.

Induction of Transposon Silencing in the Drosophila Germline.

In this review we consider the role of the piRNA system in transposable element silencing in the Drosophila melanogaster germline. We focus on new data that demonstrate the mechanisms of initiation of piRNA biogenesis in ovarian germinal cells and the role of Piwi protein in this process, including our own results.

[The role of Piwi nuclear localization in the differentiation and proliferation of germline stem cells].

The Piwi protein and its orthologs are considered as the key components of the piRNA machinery implicated in transcriptional silencing of transposons. Неre, we show that nuclear localization of the Piwi protein is required not only for transposon repression, but also for proper differentiation of germline stem cells (GSCs). piwi^(Nt) mutation that causes loss of nuclear Piwi and its retention in the cytoplasm leads to the accumulation of undifferentiated GSC-like cells. The analysis of piwi^(Nt) mutation in combination with a bam gene mutation blocking GSC differentiation shows that the loss of nuclear Piwi decreases GSC proliferation rate. This is accompanied by the accumulation of DNA double-strand breaks in GSCs that may be caused by transposition events. Here, for the first time a set of transposons repressed by Piwi in GSCs and surrounding niche cells has been identified. The present study together with our previous data show that nuclear and cytoplasmic Piwi can regulate different stages of the functioning of germinal cells: cytoplasmic Piwi is sufficient to maintain GSCs, while nuclear Piwi localization is necessary for their proper proliferation and differentiation.

[Functions of piRNAs and the Piwi Protein in Drosophila].

Short (25-35 nucleotides) regulatory piPHK, along with RNA-binding proteins of the Piwi family, constitute an evolutionarily conserved system that functions mainly in eukaryotic gonads. The system can be regarded as a variant of the mechanism of RNA interference, which is based on the recognition of target RNA as a result of complementary interactions with piRNA. The variants of this regulatory system function in the germline cells, including stem cells and somatic cells of the niche, ensuring maintenance of the germline stem cells and their differentiation. One of the most important functions (but not the only one) of this system is the repression of transposons, which guarantees genome stability in germline cells. This review focuses on the works of the authors of the review in the context of outstanding international achievements in a rapidly evolving re- search area, the biology of piRNA and the function of the Piwi protein.

[PIWI protein as a nucleolus visitor in Drosophila melanogaster].

The evolutionarily conserved nuclear Piwi protein of Drosophila melanogaster is a representative of the Argonaute small RNA binding protein family. Guided by small piRNAs, Piwi functions in transposon silencing in somatic and germ cells of the gonad. We found that in ovarian somatic and germ cells, as well as in the established ovarian somatic cell line, Piwi is concentrated predominantly in the nucleolus--the main nuclear compartment, participating not only in rRNA synthesis, but also in various cell stress responses. We demonstrated the colocalization of Piwi with nucleolar marker proteins--fibrillarin and Nopp140. A mutation preventing Piwi transport to the nucleus and disturbing transposon silencing (piwi(Nt)) leads to 6-8-fold upregulation of rRNA genes expression, as evaluated by the level of transcripts of transposon insertions in 28S rRNA genes. RNase treatment of live cultured ovarian somatic cells depletes Piwi from the nucleolus. The same effect is observed upon inhibiting RNA polymerase I which transcribes rRNA, but not RNA polymerase II. In contrast, upon heat shock Piwi is concentrated in the nucleolus and is depleted from the nucleoplasm. These results implicate Piwi in RNA polymerase activity modulation and stress response in the nucleolus. We discuss possible noncanonical Piwi functions along with its canonical role in transposon silencing by piRNAs.

[Multifunctional protein complex NAC (nascent polypeptide associated complex].

The functions of the evolutionary conservative complex NAC (Nascent polypepetide Associated Complex) and its subunits are discussed. The heterodimeric NAC protein contains alpha- and beta-subunits and is found to be reversibly bounded to the ribosome in all eukaryotes, from yeast to humans. NAC contacts the nascent polypeptide and protects it from proteolysis. NAC participates in polypeptide chain folding and modulates protein secretion and transmembrane protein formation. Mutations and deletions of genes, encoding NAC subunits are lethal in early development of multicellular eukaryotes. NAC is involved in the ribosome biogenesis. The beta-subunit interacts with caspase-3 and may be involved in the regulation of the apoptotic pathway. The variants of NAC proteins can be considered as chaperone complexes, involved in the response of the cell and the organism to stress factors, as well as regulators of apoptosis. The genes encoding beta-subunits are rapidly evolved, their duplications cause the formation of tissue specific beta-subunit variants with a different number of putative caspase cleavage sites. The homodimer of alpha-subunits is shown to be the RNA/DNA binding protein and acts as a transcriptional cofactor. The diversity in the functioning of NAC is a prime example of a protein that performs a variety of biological functions (moonlighting protein).

Regulatory small RNAs.

Recent years have been marked by a burst of studies on the role of various RNAs in the regulation of gene expression. These regulatory effects act on the level of both chromatin in the nuclei and the cytoplasm during translation. The review papers of this issue are mainly dedicated to different types of small RNAs of 20-30 nucleotides. The small RNAs control diverse cellular functions including genome protection against transpositions of mobile elements of the genome.

Multifunctionality of PIWI proteins in control of germline stem cell fate.

PIWI proteins interacting with specific type of small RNAs (piRNAs) repress transposable elements in animals. Besides, they have been shown to participate in various cellular processes: in the regulation of heterochromatin formation including telomere structures, in the control of translation and the cell cycle, and in DNA rearrangements. PIWI proteins were first identified by their roles in the self-renewal of germline stem cells. PIWI protein functions are not limited to gonadogenesis, but the role in determining the fate of stem cells is their specific feature conserved throughout the evolution of animals. Molecular mechanisms underlying these processes are far from being understood. This review focuses on the role of PIWI proteins in the control of maintenance and proliferation of germinal stem cells and its relation to the known function of PIWI in transposon repression.

Heterochromatin formation and transcription in relation to trans-inactivation of genes and their spatial organization in the nucleus.

The role of transcription in heterochromatin formation in the nuclei of eukaryotes, originally shown for the pericentromeric heterochromatin assembly in fission yeasts, has now become an accepted paradigm extended to multicellular eukaryotes. It has been shown that small RNAs involved in the RNA interference system in its broadest sense can play an important role in this multi-step process - they are recognized by complementary interactions with the newly formed nuclear transcripts and recruit protein complexes to the local genomic sites for heterochromatinization. The role of transcription as a trigger of this process at the sites of genomic repeats will be considered in this review using various examples of heterochromatin formation, with an emphasis on discussion of its role in trans-chromosomal interactions causing gene inactivation.

[Correlation on a cellular level of gene transcriptional silencing and heterochromatin compartment dragging in case of PEV-producing eu-heterochromatin rearrangement in Drosophila melanogaster].

Eu-heterochromatic rearrangements transfer genes into the heterochromatin and cause their variegated inactivation (PEV). Genes affected by PEV often demonstrate association with heterochromatic nuclear compartment (a distinct area composed of heterochromatin sequences like satellite DNA and enriched in specific chromatin proteins e.g. HP1). Here, we investigate the nuclear localization and the expression levels of the genes subjected to PEV caused by chromosome inversion, In(2)A4. We demonstrate that the degree of PEV-caused gene inactivation depends on a developmental stage, and the maximum of repression corresponds to the gene expression activation period. In the case of In(2)A4 rearrangement we detect the dragging of affected euchromatic region into heterochromatic nuclear compartment and the increase in HP1 occupancy in this region. We developed a protocol of simultaneous RNA-DNA-protein staining to demonstrate firstly in a single cell a strong correlation between transcriptional activity of affected gene and its distance from chromosome 2 satellite DNA.

Mapping of cis-regulatory sites in the promoter of testis-specific stellate genes of Drosophila melanogaster.

Tandem Stellate genes organized into two clusters in heterochromatin and euchromatin of the X-chromosome are part of the Ste-Su(Ste) genetic system required for maintenance of male fertility and reproduction of Drosophila melanogaster. Stellate genes encode a regulatory subunit of protein kinase CK2 and are the main targets of germline-specific piRNA-silencing; their derepression leads to appearance of protein crystals in spermatocytes, meiotic disturbances, and male sterility. A short promoter region of 134 bp appears to be sufficient for testis-specific transcription of Stellate, and it contains three closely located cis-regulatory elements called E-boxes. By using reporter analysis, we confirmed a strong functionality of the E-boxes in the Stellate promoter for in vivo transcription. Using selective mutagenesis, we have shown that the presence of the central E-box 2 is preferable to maintain a high-level testis-specific transcription of the reporter gene under the Stellate promoter. The Stellate promoter provides transcription even in heterochromatin, and corresponding mRNAs are translated with the generation of full-size protein products in case of disturbances in the piRNA-silencing process. We have also shown for the first time that the activity of the Stellate promoter is determined by chromatin context of the X-chromosome in male germinal cells, and it increases at about twofold when relocating in autosomes.

[The interplay of transposon silencing genes in the Drosophila melanogaster germline].

Complexes of Piwi proteins and Piwi-interacting RNAs (piRNAs) carry out the repression of transposable elements in animal gonads. The Piwi protein clade is represented in D. melanogaster by three members: Piwi, Aub and Ago3. Piwi protein functions in the nuclei of somatic and germinal ovarian cells, whereas Aub and Ago3 are cytoplasmic proteins of germinal cells. Aub and Ago3 interact with each other in the perinuclear nuage organelle to perform piRNA amplification via the ping-pong mechanism. Previously, derepression of several transposable elements as a result of mutations in the piRNA silencing system was shown. Here we quantify the increase in expression level of an enlarged number of retrotransposons due to the mutations in the piwi gene, nuage components coding aub, mael and spn-E genes and the RNA helicase armi gene mutation that impairs Piwi nuclear localization, but not the ping-pong cycle. We reveal that piwi, armi, aub, spn-E and mael genes participate together in the repression of several transposons (HMS-Beagle, Gate and HeT-A), whereas silencing of land G elements requires the same genes except piwi. We suggest that Armi has other functions besides the localizing of Piwi protein in the nuclei. Our data suggest also a role of cytoplasmic Aub, Spn-E and Mael nuage proteins in Piwi-mediated repression of Gate and HMS-Beagle transposons in the germline nuclei. As a whole, our results corroborate the idea that genome stabilization in the germline is realized by different silencing strategies specific for different transposable elements. At the same time, our data suggest the existence of yet unknown mechanisms of interplay between nuclear and cytoplasmic components of the piRNA machinery in the germline.

[Molecular variability of testes-specific betaNACtes genes in Drosophila melanogaster genome].

Family of betaNACtes genes in the Drosophila melanogaster genome is a model to investigate the mechanisms of molecular evolution of recently evolved genes. The betaNACtes genes encode proteins, homologous to beta subunit of nascent polypeptide-associated complex (NAC), are expressed in testes and localized on the X chromosome as two two-gene clusters and one separate copy. We collected population polymorphism data for betaNACtes genes using several wild-type stocks of D. melanogaster and compared betaNACtes paralogs with each other. We have shown heterogeneous pattern of betaNACtes genes polymorphism: genes in 3' region of two-gene clusters are low polymorphic, whereas separate betaNACtesl gene is most variable. 5'betaNACtes copies in two-gene tandems are practically identical, whereas 3'betaNACtes copies are highly diverged. Thus, we propose local gene conversion providing selective homogenization of 5'genes. Comparison of betaNACtes paralogs has shown that majority of amino acid differences are in N-terminal part of proteins, containing betaNAC domain. McDonald-Kreitman test of betaNACtes paralog divergence shows the involvement of positive selection in the course of betaNACtes gene family evolution.

[Heterochromatic DNA repeats in Drosophila and unusual gene silencing in yeast cells].

The 1.25-kb heterochromatic Stellate repeats of Drosophila melanogaster are capable of stably persisting in transgenic constructs and silencing the white reporter gene (mosaic position effect variegation). This system reveals an unusual form of silencing, which is insensitive to known modifiers of position effect variegation. The unusual form of silencing was studied with yeast Saccharomyces cerevisiae, a simple eukaryotic model. To be transferred into yeast cells, the D. melanogaster Stellate repeats were cloned in the pYAC4 centromeric vector (CEN4, URA3, TRP1, HIS3). The HIS3 and/or URA3 genes could be inactive in plasmids consisting of pYAC4 and the Stellate insert in yeast cells. Deletion of D. melanogaster DNA from the plasmid was found to activate the URA3 and HIS3 genes. It was assumed that the genes were repressed rather than damaged in the presence of the Stellate repeats and that a new form of gene silencing was revealed in S. cerevisiae.

Small RNAs and cancerogenesis.

Disturbances of microRNA generation and functioning as inhibitors of gene expression at the translational level are considered as specific and diagnostic features of cancer. This review also highlights the role of short interfering RNA (siRNA) in modified epigenomic chromatin structure, which may cause cancer transformation. Future directions of cancer epigenomics are considered in the light of the involvement of siRNA in epigenomic modification of chromatin.

[Role of short RNAs in regulating the expression of genes and mobile elements in germ cells].

Two main types of short RNAs, 21 to 25 nucleotides long, are involved in the negative regulation of gene expression in eukaryotes: microRNAs and small interfering RNAs (siRNAs) of the RNA interference system. MicroRNAs predominantly suppress the translation of mRNA targets, while siRNAs not only prevent mRNA translation and/or lead to mRNA degradation, but are also involved in the regulation of gene expression at the transcriptional level. In germ cells translational regulation of gene expression plays a significant role and its mechanism has been extensively studied in oogenesis of Drosophila@. The role of heterochromatization and chromatin compaction, which can repress the expression of mobile elements and other repeated elements of the genome, was studied to a lesser extent. Activation and transposition of mobile elements accompanied by mutations and chromosome rearrangements are especially dangerous in germline cells. It has been proposed that a specialized class of short RNAs, repeat associated siRNAs (rasiRNAs), can be involved in repression of the expression of mobile elements in Drosophila germ cells. Here we describe the findings on subcellular ribonucleoprotein structures characteristic of germ cells: perinuclear and polar granules containing proteins of the RNA interference and microRNA maturation system. Also, we present our own results revealing the role of genes of the RNA interference system in mobile element silencing in Drosophila.