Biology subjects

Mikhaleva, E. A.

Publications and source records attributed to Mikhaleva, E. A..

5 recordsLinked to original sources

bioRxiv2025

Piwi and piRNAs repress transcription of aberrant rRNA genes containing retrotransposon fragments

The genomes of eukaryotes comprise clusters of repeated rRNA genes, including defective copies that are silenced by poorly understood mechanisms. In Drosophila melanogaster, many 28S rDNA genes contain insertions of R1 or R2 retrotransposons. R2 elements can only transcribe as part of the pre-rRNA and then excise by the R2 ribozyme. Some rRNA genes carry truncated insertions, creating defective rRNA from which the R2 sequence cannot be excised. Here, we report that in Drosophila ovaries, the nuclear protein Piwi loaded with PIWI-interacting RNA (piRNA) is required to repress transcription of rDNA units with extensively truncated R2 insertions (R2short). Without Piwi, R2short-rDNA generates stable aberrant 28S rRNA containing [~]200 nt of R2 sequence. These rRNAs are excluded from cytoplasmic ribosomes and instead accumulate within the nucleoli of germ cells, where they may disrupt nucleolar homeostasis. Overall, our results show the involvement of the piRNA pathway in quality control of ribosomal transcription.

molecular biology↗

bioRxiv2023

Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or with NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin. Author summaryHeterochromatin in interphase nucleus is localized mostly at the nuclear periphery. However, the forces maintaining its peripheral localization are not well understood. Nuclear envelope consists of two lipid bilayer membranes separated by perinuclear space. The inner nuclear membrane is lined by the nuclear lamina, and both membranes are pierced by nuclear pore complexes composed of nucleoporins. Nuclear envelope can serve as a scaffold to which heterochromatin is attached. In the present study, we identified nucleoporin Elys as one of the key players maintaining peripheral localization of heterochromatin during interphase. Elys binds to multiple genomic sites located within heterochromatin and thus links it to nuclear pore complexes. However, the nucleoplasmic fraction of Elys binds to active genes and enhancers, resulting in decompactization of their chromatin.

genomics↗

bioRxiv2022

A study of the expression of germline-specific paralogs of the ubiquitously expressed NAC complex revealed their association with centrosomes

Protein homeostasis involves the ubiquitously expressed heterodimeric protein NAC (ribosome associated nascent polypeptide complex), consisting of - and {beta}-subunits. We previously found in Drosophila melanogaster the presence of germline-specific paralogous genes for NAC subunits (gNACs): unique for the -subunit and several highly homologous amplified genes for the {beta}-subunit, indistinguishable by the antibodies used, while they were detected as different phosphorylated isoforms in 2D electrophoresis with immunostaining. The distinct increase in gNAC expression in growing spermatocytes compared with their predecessors, gonioblasts, is accompanied by a clear presence of gNAC in the cytoplasm of dividing meiotic cells and spermatids. In oogenesis, gNAC expression is significantly lower than in the testis, but gNAC accumulation is found at the posterior pole of the mature oocyte, known as the germplasm region responsible for the germ cell formation in the offspring. gNAC-associated ribosomes from mature oocytes are enriched in mRNA sets encoding known germplasm and centrosome proteins. gNAC is also detected in a pericentriolar component of centrosomes: in syncytial dividing nuclei in the early embryos, in primordial germ cells and spermatocytes, including meiotic divisions stage. CRISPR/Cas9-mediated deficiency of the gNAC-alpha subunit causes female infertility. We propose the role of the gNAC phosphoregulatory paralog system as a component of the germline proteostasis network, coordinated with the centrosome functions. Here, we also extended our results by identifying cross-links between ubiquitous and germline-specific NAC-{beta} paralogs, finding an additional case of functional cross-talk between heterodimeric ubNAC and gNAC -subunit paralogs, which may maintain the robustness of proteostasis and fly fecundity.

molecular biology↗

bioRxiv2021

Detection of the germline specific NAC protein paralog enriched by intrinsically disordered regions in Drosophila melanogaster

Nascent polypeptide associated complex (NAC) consisting of - and {beta}-subunits is an essential conserved ubiquitously expressed ribosome-associated protein in eukaryotes. NAC is considered as a chaperone and co-translational regulator of nascent protein sorting providing homeostasis of cellular proteins. Here we discovered the germinal cell specific NAC (gNAC) homologue, which differs from the ubiquitously expressed NAC by the presence of expanded intrinsically disordered regions (IDRs) at the N- and C-ends of the - and {beta}-subunits, respectively. We propose these evolutionary acquisition of long IDRs drive gNAC to endow both the specific conformational plasticity for binding client proteins and novel functions regulated by post-transcriptional modifications (PTM). At the same time, we demonstrated that the well-known lethal effect of the loss of ubiquitous NAC-{beta} is suppressed by ectopic expression of its germinal paralog indicating the absence of strict functional differences between the ubiquitous and germline NAC-{beta} subunit paralogs for protein homeostasis.

molecular biology↗

bioRxiv2020

Role of Udd protein and heterochromatin in transcriptional selection of individual rRNA genes in the Drosophila germline

Eukaryotic genomes contain hundreds of nearly identical rRNA genes, many of which are transcriptionally silent. However, the mechanisms of selective regulation of individual rDNA units remain poorly understood. In Drosophila melanogaster, rDNA repeats containing insertions of R1/R2 retrotransposons within the 28S rRNA sequence undergo inactivation. Here we found that rRNA genes with insertions are specifically enriched with H3K9me3 and HP1a repressive marks, but disruption of heterochromatin components only slightly affects their silencing. Intriguingly, the loss of Udd (Under-developed) protein interacting with Pol I transcription initiation complex, causes an upregulation of R2-inserted rDNA copies in germ cells by two orders of magnitude that is accompanied by the reduction of heterochromatin marks. Thus, for the first time we revealed a factor required for distinguishing between active and silent rDNA units to such a large extent. To clarify a relationship between the rDNA transcriptional status and heterochromatin establishment, we showed that inhibition of transcription by actinomycin D increases the level of H3K9me3 mark erasing the epigenetic differences between inserted and uninserted rRNA genes. Altogether, we suggest that Udd coupled with Pol I transcription initiation machinery defines activation or silencing of individual rDNA units, whereas their transcription level consequently dictates their chromatin state.

molecular biology↗