Biology subjects

Mironov, A.

Publications and source records attributed to Mironov, A..

At least 19 recordsLinked to original sources

bioRxiv2026

PAIP1 couples mRNA export to cytoplasmic mRNP remodeling and poly(A) homeostasis

Messenger ribonucleoproteins (mRNPs) acquire distinct protein compositions as they move from the nucleus to the cytoplasm, yet how this transition is coordinated and how inefficient remodeling affects downstream mRNA metabolism remains poorly understood. Here, we identify PAIP1 as a metazoan cofactor of the mRNA export ATPase DDX19. By binding a conserved N-terminal motif in DDX19, PAIP1 is recruited to the nuclear pore, where it promotes exchange of the nuclear poly(A)-binding protein PABPN1 for cytoplasmic PABPC1, thereby coupling mRNA export to cytoplasmic mRNP maturation. PAIP1 depletion alters cytoplasmic mRNP composition, mRNA stability and poly(A)-tail homeostasis. In Drosophila embryos, where poly(A)-tail regulation of maternal mRNAs directs early development, maternal PAIP1 depletion shortens poly(A)-tails, delays zygotic genome activation, and causes severe developmental defects. Our findings identify an export-coupled mRNP maturation pathway linking PABP exchange to downstream mRNA metabolism.

molecular biology↗

bioRxiv2026

TORC1 spatial segregation and hysteresis are regulated by the small GTPase Arf1

TORC1 is a central regulator of growth, integrating inputs from kinases and signaling proteins. How TORC1 activity is regulated, is still not completely understood. The small GTPase Arf1 has been implicated in TORC1 regulation, but the underlying mechanism remains elusive. Here, we show that Arf1 controls TORC1 in an allele-specific manner under nutrient and heat stress in yeast. Unexpectedly, both the hyperactive mutant arf1-11 and the loss-of-function mutant arf1-18 reduce TORC1 activity, while other loss-of-function alleles did not. We reveal two distinct functions of Arf1: first, it ensures Golgi-to-vacuole/lysosome transport for the functional maintenance of these organelles; second, it regulates TORC1 activity at the ER-Golgi-vacuole interface. Hyperactive Arf1-11 drives sequestration of Kog1 and Tor1 into cytoplasmic foci, to which Arf1-11 can be equally recruited. Importantly, Arf1 also promotes TORC1 re-activation during stress recovery - so-called hysteresis. Our data reveal an unexpected dual function for Arf1 as a negative and a positive regulator of TORC1 activity in a context-dependent manner. TeaserThe small GPTase Arf1 acts as a dual switch for the key cellular growth regulator TORC1 by increasing or decreasing TORC1 activity depending on nutritional status and stress.

cell biology↗

bioRxiv2026

Ribosome profiling reveals extensive translational alterations in steatohepatitis-associated hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one the most lethal cancer types. While infections with hepatitis B or hepatitis C viruses remain the primary risk factors for HCC development worldwide, metabolic disease-associated steatohepatitis has become the fastest growing etiology of HCC, particularly in the West. Our study characterizes, for the first time, the remodeling of the translation landscape in steatohepatitis-associated HCC using ribosome profiling and mass spectrometry techniques. In striking contrast with the transcriptional alterations, which do not show strong dependence on associated co-morbidity, translational alterations are broader in the steatohepatitis compared to the viral background. These alterations affect hundreds of genes, whose products are often involved in subcellular protein localization. By quantifying the relationship between the ribosome occupancy of upstream or downstream open reading frames (uORFs or dORFs) and coding regions (CDSs), we provide evidence of uORFs attenuating the translation efficiency of CDSs in HCC. We also identify numerous novel translated regions, including from RNAs currently annotated as non-coding, some yielding peptides that can be reproducibly identified in mass spectrometry datasets. Our study thus provides novel molecular data on HCC with a focus on the steatohepatitis etiology, reveals unexpectedly extensive translational control in this co-morbidity, and gives multiple hints and candidate targets for follow-up experiments.

systems biology↗

bioRxiv2025

Sequence-based models for RNA-Protein interactions imputation might be insufficient for novel signal prediction in eCLIP data

Predicting specific RNA-protein interactions remains a challenging task: despite the existence of numerous methods, a unified approach has yet to emerge. Additional difficulties emerge from the properties of in vivo IP experiments and their systematic biases, such as the overrepresentation of highly expressed RNAs. Here, we present the PLERIO machine learning framework, which utilizes eCLIP data for a single protein to reconstruct the full spectrum of its potential interactions with the cellular transcriptome (i.e., both highly expressed and lowly expressed RNAs). In an effort to extrapolate our methodology to a multi-protein paradigm for de novo prediction of RNA-protein interactions on proteins lacking available eCLIP data, we extended our approach to 220 cellular proteins. We then demonstrate that this approach might not be well tailored to the limitations of current in vivo immunoprecipitation data and may only be meaningful for in vitro experiments such as RNAcompete.

bioinformatics↗

bioRxiv2025

Human pluripotent stem cell model of multiple epiphyseal dysplasia with MATN3 mutation identifies altered Matrix organisation and upregulation of the cholesterol biosynthesis pathway

Multiple epiphyseal dysplasia (MED), caused by mutations in MATN3, is a chondrodysplasia affecting the cartilage growth plate and is characterised by delayed epiphyseal ossification, short stature, and early onset osteoarthritis. Here we generated an in vitro human pluripotent stem cell (hPSC) model of cartilage growth-plate development to identify pathogenic mechanisms underlying MED. hPSCs were differentiated to chondrocytes via a mesenchymal intermediate, followed by TGF{beta}3+BMP2 induced chondrogenic pellet culture. MATN3-mutant hPSCs were generated by reprogramming MED patient PBMCs or by CRISPR-Cas9 gene editing to introduce a MATN3 mutation in a hESC line. RNAseq was used to assess chondrogenesis and identify MED pathogenic mechanisms. Transmission electron microscopy (TEM) was used to assess extracellular matrix assembly. The resultant hPSC-derived cartilage pellets displayed a typical cartilage morphology and strongly expressed cartilage matrix markers, e.g., collagen II and matrilin-3. Matrilin-3 protein was detected within both the matrix and cells of heterozygous mutant hPSC-cartilage pellets. RNAseq of mutant hPSC-cartilage pellets revealed significant enrichment for ECM organisation and cholesterol biosynthesis pathway genes as well as sightly increased expression of some unfolded protein response (UPR) marker genes. MATN3 mutant hPSC-derived cartilage pellets displayed abnormal matrix assembly, distended ER, accumulation of lipid droplets, and increased cholesterol content. Our model revealed mutant matrilin-3 induces cholesterol biosynthesis pathway upregulation and abnormal matrix assembly during MED pathogenesis. This study provides new insights into the molecular mechanisms underlying MED and highlights potential therapeutic targets.

cell biology↗

bioRxiv2025

COMPARATIVE ANALYSIS OF THE RNA-CHROMATIN INTERACTOME DATA

Two types of experiments are used to study RNA-chromatin interactions: a search for the interactome of individual RNAs (< > or OTA) and a genome-wide search for contacts of all RNAs (< > or ATA). The article presents a comparative analysis of these data. The concept of < > is introduced, which shows the overrepresentation of contacts in ATA data compared to the expected value obtained from RNA sequencing data. It is shown that the use of this characteristic allows one to select RNAs that interact with chromatin more specifically. The consistency of the replicas is studied, and data from experiments of different types are compared. As a result of the analysis, estimates of the completeness and specificity of the contacts found are obtained.

bioinformatics↗

bioRxiv2025

Regulation of mRNA polyadenylation governs mammalian body plan formation in gastruloids

The establishment of the body plan during gastrulation represents a hallmark of animal life. It emerges from the interplay of gene-regulatory programs and positional cues, yet how these signals are integrated post-transcriptionally remains largely unexplored. Here, we combine the scalability of mouse gastruloids with a single-cell CRISPR screening platform to functionally dissect germ layer specification at single-cell transcriptomic resolution. Focusing on post-transcriptional regulation, we systematically map drivers of mesodermal and endodermal fate and identify the deadenylase Cnot8. Loss of Cnot8 leads to widespread poly(A) tail elongation and transcript stabilization, shifting mesoderm differentiation toward ectopic notochord fate, thereby profoundly impacting axial patterning. Collectively, our findings identify mRNA deadenylation as a fundamental mechanism linking cellular identity with morphogenetic signaling during mammalian body plan formation.

developmental biology↗

bioRxiv2025

Unveiling the genetic basis of the low pH response in the acidophilic yeast Maudiozyma bulderi as a potential host for biorefinery

Non-conventional yeasts represent a great genetic and phenotypic diversity with potential for industrial strain development in the bio-production of green chemicals. In recent years, mass genome sequencing of non-conventional yeasts has opened avenues to improved understanding of transcriptional networks and phenotypic plasticity and gene function, including the discovery of novel genes. Here, we investigated the expressional and morphological changes at low-pH in three strains of the acidophilic yeast Maudiozyma bulderi (previously Kazachstania bulderi and Saccharomyces bulderi): CBS 8638, CBS 8639 and NRRL Y-27205. The comparison of the transcriptome of cells growing in a bioreactor at pH=5.5 vs pH= 2.5, primarily showed dysregulation of genes involved in cell wall integrity, with NRRL Y-27205 the least acidophilic strain, showing the largest transcriptional response when compared to the other two strains. We identified four uncharacterised genes, unique to M. bulderi, and predicted function as transporters, upregulated at low pH. Microscopy studies showed that M. bulderi cell wall is not damaged in acidic environment, and the membrane lipid composition remains stable at low pH, unlike S. cerevisiae. Overall, our data on transcriptional variability in M. bulderi highlights genes and cellular pathways involved in the acidophilic adaptation of this species and can aid further strain development.

genomics↗

bioRxiv2025

Multiplexed proximity labelling proteomics identifies a non-canonical Bcl-2 family interactome associated with apoptotic priming

Bcl-2 family proteins govern the intrinsic apoptotic pathway by regulating mitochondrial outer membrane permeabilisation (MOMP), releasing apoptogenic factors into the cytosol. How close a cell is to MOMP, termed mitochondrial priming, is determined by the interactions between different Bcl-2 proteins at the outer mitochondrial membrane (OMM). However, Bcl-2 proteins can also drive diverse processes that do not result in cell death, such as incomplete MOMP, sublethal caspase activation, pro-inflammatory signalling and regulation of cellular metabolism. To understand the wider Bcl-2 family interactome and how it might be involved in these processes, we undertook an unbiased proteomic BioID screen, using both pro- and anti-apoptotic Bcl-2 family members as bait proteins. We found that most high-confidence potential interactions in non-apoptotic cells were outside the canonical Bcl-2 family interactome. Analysis of how this interactome changed in response to either BH3-mimetics or full-length BH3-only proteins revealed dynamic changes at multiple organelles and membrane contact sites in response to altered mitochondrial priming. These findings underscore the complex and varied interactions of the Bcl-2 family proteins, expanding their scope and function beyond the frequently studies intra-family interactions.

cell biology↗

bioRxiv2024

Interplay between material properties and cellular effects drives distinct pattern of interaction of graphene oxide with cancer and non-cancer cells

Understanding how graphene oxide (GO) interacts with cells is crucial for its safe and efficient biomedical applications. Despite extensive research, a systematic investigation using a panel of cell lines, thoroughly characterized label-free nanomaterials, and complementary analytical techniques is lacking. Here, we examined the uptake of thin GO sheets with distinct lateral dimensions in 13 cell lines: 8 cancer (HeLa, A549, PC3, DU-145, LNCaP, SW-480, SH-SY5Y, U87-MG) and 5 non-cancer (BEAS-2B, NIH/3T3, PNT-2, HaCaT, 293T), using confocal microscopy, transmission electron microscopy, and flow cytometry. Our results reveal a striking difference in GO uptake: non-cancer cells internalized GO efficiently, while in cancer cells, GO predominantly interacted with the plasma membrane, showing minimal to no internalization. Comparison to other nanomaterials (polystyrene beads and graphene flakes) confirmed that cancer cells internalize materials similarly to non-cancer cells, indicating GO-specific interactions. We identified that GO thickness plays a pivotal role in this differential uptake. Additionally, GO disrupted the actin cytoskeleton, impairing migration in cancer but not in non-cancer cells. We propose that thin GO sheets act as a cue upon interaction with the plasma membrane of cancer cell lines, subsequently inducing actin filaments disruption leading to impaired endocytosis, migration activity, and reduced capacity of cancer cells towards GO uptake.

cell biology↗

bioRxiv2024

Pentose Phosphate Pathway Protects E. coli from Antibiotic Lethality

Disruption of both branches of the canonical pentose phosphate pathway (PPP) in E. coli by combined inactivation of the zwf and talAB genes provokes the restoration of the ancient anabolic variant of PPP (aPPP). In the aPPP, pentose-5-phosphates are synthesized unidirectionally from fructose-6-phosphate and glyceraldehyde-3-phosphate by transketolase B, aldolase A, and phosphatase GlpX, converting sedoheptulose-1,7-bisphosphate to sedoheptulose-7-phosphate. Unexpectedly, the double zwf talAB mutant exhibits decreased survival after treatment by diverse classes of antibiotics with little effect on the minimal inhibitory concentration. Simultaneously, we found that killing effect of antimicrobials on the zwf talAB mutant could be reversed by the inactivation of either purR or deoB genes, both responsible for ribose-5-phosphate content in the mutant strain. Enhanced biosynthesis of the cell wall component ADP-heptose from sedoheptulose-7-phosphate also suppressed killing effect of antibiotics on the zwf talAB mutant. Furthermore, the inactivation of the Entner-Doudoroff pathway ({Delta}edd) or shifting the metabolic equilibrium by the addition of exogenous phosphogluconate reverts aPPP to glycolysis, preventing the accumulation of excess pentose phosphates and the occurrence of the futile cycle in zwf talAB cells, thus desensitizing them to antibiotics. Our findings show that ribose-5-phosphate metabolism plays a crucial role in bacterial tolerance to a wide range of bactericidal antibiotics. We propose that targeting PPP could be a promising strategy for developing new therapeutic agents aimed at potentiating clinically significant antimicrobials. IMPORTANCERecent studies have revealed the crucial role of bacterial cells metabolic status in its susceptibility to the lethal action of antibacterial drugs. However, there is still no clear understanding of which key metabolic nodes are optimal targets to improve the effectiveness of bacterial infection treatment. Our study establishes that the disruption of the canonical pentose phosphate pathway induces one-way anabolic synthesis of pentose phosphates (aPPP) in E. coli cells, significantly increasing the killing efficiency of various antibiotics. It is also demonstrated that the activation of ribose-5-phosphate utilization processes restores bacterial tolerance to antibiotics. We consider the synthesis of ribose-5-phosphate to be one of the determining factors of bacterial cell stress resistance. Understanding bacterial metabolic pathways, particularly the aPPPs role in antibiotic sensitivity, offers insights for developing novel adjuvant therapeutic strategies to enhance antibiotic potency.

microbiology↗

bioRxiv2024

HiMoRNA and RNA-Chrom integration: Chromatin-Associated LncRNAs in Genome-Wide Epigenetic Regulation

Long non-coding RNAs (lncRNAs) significantly contribute to genome structure and regulation. Many lncRNAs are known to interact with chromatin and in this way to affect gene expression patterns through epigenetic regulation. Still, experimental protocols for lncRNA-chromatin interactions do not provide any insight into the mechanisms of lncRNA-based genome-wide regulation. Here we present an integration of HiMoRNA - a resource containing correlated lncRNA-epigenetic changes in specific genomic locations genome-wide, - and RNA-Chrom, a resource featuring uniformly processed experimental data on RNA-chromatin interactions. Our integration approach allows generating interpretable and experimentally supported hypotheses on the mechanisms of lncRNA epigenetic regulation of gene expression. For this integration we have tailored the interface of HiMoRNA such that for many lncRNAs experimentally detected RNA-chromatin contacts are available from RNA-Chrom for browsing, analysis and downloading. HiMoRNA peaks supported by RNA-Chrom contacts can be explained by external experimental data. We believe that the integration of HiMoRNA and RNA-Chrom is a convenient and valuable approach that can provide experimental and mechanistic insights and greatly facilitate functional annotation of lncRNAs.

bioinformatics↗

bioRxiv2023

Pauperization of Emerin from nuclear envelope drives prostate cancer cell migration and invasiveness

Micronuclei (MN) can arise from many causes, including the breakage of aberrant cytokinetic chromatin bridge. The frequent observation of MN in tumors raises the specter that they might not merely be passive elements but could instead play active roles in tumor progression. Here, we test the hypothesis that the presence of micronuclei could induce specific phenotypic and functional changes to the cell and lead to increased cancer invasive potential. With a variety of imaging and molecular methods in vitro and in clinical samples from prostate cancer (PCa) patients, we show that chromosome bridge resolution can lead to EMD accumulation and formation of EMD-rich MN. Such structure is negative for Lamin A/C and positive for LBR and Sec6{beta}. It can cause EMD pauperization from NE affecting migratory and invasive properties of a cell and can be translated to PCa patients poor prognosis.

cancer biology↗

bioRxiv2023

Comparative analysis of the RNA-chromatin interactions data. Completeness and accuracy

Non-coding RNAs play an essential role in a wide variety of biological processes. We have previously developed RNA-Chrom, an analytical database containing uniformly processed RNA-chromatin interactions data. Here, we analyzed the consistency of these data with each other and performed a comparative analysis of human and mouse datasets from "all-to-all" experiments (interactome of all possible RNAs in a cell) and "one-to-all" experiments (individual RNA interactome). We analyzed the dependence of RNA cis-contacts density as a function of distance to the RNA source gene and found that in all experiments, density of cis-contacts decreases with distance. We tested whether the most contacting RNAs of one "all-to-all" experiment ("RNA-leaders") are the same for the other "all-to-all" experiments. Our analysis shows that "all-to-all" experiments are not complete and require substantially deeper sequencing, and conclusions can only be drawn for highly contacting RNAs. We noted that for "all-to-all" experiments, sequencing depth and the type of cell treatment give a significant impact on the contact map, while the cell line does not have as much of an impact.

bioinformatics↗

bioRxiv2023

CCAR1 promotes DNA repair via an unanticipated role in alternative splicing

DNA repair is directly performed by hundreds of core factors and indirectly regulated by thousands of others. We massively expanded a CRISPR inhibition and Cas9-editing screening system to discover factors indirectly modulating homology directed repair (HDR) in the context of [~]18000 individual gene knockdowns. We focused on CCAR1, a poorly understood gene that we found reduced both HDR and interstrand crosslink repair, phenocopying the loss of the Fanconi Anemia pathway. CCAR1 loss abrogated FANCA protein without substantial reduction in the level of its mRNA or that of other FA genes. We instead found that CCAR1 prevents inclusion of a poison exon in FANCA. Transcriptomic analysis revealed that the CCAR1 splicing modulatory activity is not limited to FANCA, and it instead regulates widespread changes in alternative splicing that would damage coding sequences in mouse and human cells. CCAR1 therefore has an unanticipated function as a splicing fidelity factor.

molecular biology↗

bioRxiv2023

Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding ofproteins with alpha helical domains

Increasingly many studies reveal how ribosome composition can be tuned to optimally translate the transcriptome of individual cell types. In this study, we investigated the expression pattern, structure within the ribosome and effect on protein synthesis of the ribosomal protein paralog 39L (RPL39L). With a novel mass spectrometric approach we have quantified the expression of RPL39L in human pluripotent cells, cancer cell lines and tissue samples, and in mouse germ cells. We generated RPL39L knock-out mouse embryonic stem cell (mESC) lines and demonstrated that RPL39L impacts the dynamics of translation, to support the pluripotency and differentiation, spontaneous and along the germ cell lineage. Most differences in protein abundance between WT and RPL39L KO lines were explained by widespread proteasomal activity. By CryoEM analysis of purified RPL39 and RPL39L-containing ribosomes we found that, unlike RPL39, RPL39L has two distinct conformations in the exposed segment of the nascent peptide exit tunnel, creating a distinct hydrophobic patch that has been predicted to support the efficient co-translational folding of alpha helices. Our study shows that ribosomal protein paralogs provide switchable modular components that can tune translation to the protein production needs of individual cell types.

molecular biology↗

bioRxiv2023

Heparan sulfates regulate axonal excitability and context generalization through Ca2+/calmodulin-dependent protein kinase II

Our previous studies demonstrated that enzymatic removal of highly sulfated heparan sulfates with heparinase 1 impaired axonal excitability and reduced expression of ankyrin G at the axon initial segments in the CA1 region of the hippocampus ex vivo, impaired context discrimination in vivo, and elevated Ca2+/calmodulin-dependent protein kinase II (CaMKII) activity in vitro. Here, we show that in vivo delivery of heparinase 1 in the CA1 region of the hippocampus elevated autophosphorylation of CaMKII 24 hours after injection in mice. Patch-clamp recording in CA1 neurons revealed no significant heparinase effects on the amplitude or frequency of miniature excitatory and inhibitory postsynaptic currents, while the threshold for action potential generation was increased and fewer spikes were generated in response to current injection. Delivery of heparinase on the next day after contextual fear conditioning induced context overgeneralization 24 hours after injection. Co-administration of heparinase with the CaMKII inhibitor (autocamtide-2-related inhibitory peptide) rescued neuronal excitability and expression of ankyrin G at the axon initial segment. It also restored context discrimination, suggesting a key role of CaMKII in neuronal signaling downstream of heparan sulfate proteoglycans and highlighting a link between impaired CA1 pyramidal cell excitability and context generalization during recall of contextual memories.

neuroscience↗

bioRxiv2022

RNA-Chrom: a manually-curated analytical database of RNA-chromatin interactome

Every year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organisation of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.), to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data can help to reach the system-level of studying non-coding RNAs. Here we present the RNA-Chrom manually-curated analytical database, which contains the coordinates of billions of contacts of thousands of human and mouse RNAs with chromatin. Through the user-friendly web interface (https://rnachrom2.bioinf.fbb.msu.ru/), two approaches to the analysis of the RNA-chromatin interactome were implemented. Firstly, to find out whether the RNA of interest to a user contacts with chromatin, and if so, with which genes or DNA loci? Secondly, to find out which RNAs are in contact with the DNA locus of interest to a user (and probably participate in its regulation), and if there are such, what is the nature of their interaction? For a more detailed study of contact maps and their comparison with other data, the web interface allows a user to view them in the UCSC Genome Browser.

bioinformatics↗