Biology subjects

Vorobyeva, N. E.

Publications and source records attributed to Vorobyeva, N. E..

4 recordsLinked to original sources

bioRxiv2025

NOVEL PRINCIPLES OF MOLECULAR GENETIC MAPPING OF THE INTERPHASE GENOME OF Drosophila melanogaster

Genome and chromosome maps have played a great role in the development of molecular genetics and biology. Gene activation, expression, and inactivation directly depend on the chromosomal (protein, nucleosomal) environment of the gene and formation of specific protein complexes on various gene structures. Polytene chromosomes are the only object in which interphase chromosomes can be analyzed, but the known Drosophila genome maps provide only an abstract view of gene distribution on a physical map, and there is no connection between these genes and the structures of interphase polytene chromosomes. A combination of bioinformatic methods was applied in this study; the data on interphase distribution of chromatin, H3K36me3 histone modifications, and the insulator protein Chriz, as well as the ChIP-seq, FAIRE-seq, and FISH methods, were used to investigate the genome-wide localization of key marker proteins. Having combined these mapping techniques for the small region 1AF of the X chromosome, we developed a novel method for analyzing the mutual arrangement of developmental and housekeeping genes, their promoters, and various types of proteins in the interphase genome and chromosome structures: compacted black bands, interbands, and gray bands, as well as sites of localization of exons and introns of housekeeping genes. Mapping was based on three consecutive stages: the 4 state Hidden Markov Model (hereinafter referred to as 4HMM) and data distribution for H3K36me3 and Chriz from the cells in which polytene chromosomes had been formed were used to localize interbands; FISH probes were then prepared from interband DNA, and blocks of developmental and housekeeping genes in interphase chromosome structures were mapped. The elaborated mapping methods can be further used to build similar maps for the entire interphase genome of Drosophila. Comparison of the map of bands and interbands in the region 1AF revealed full matching of the boundaries of black bands (developmental genes) and TADs. Within the regions where the housekeeping genes are located (the groups of interbands and gray bands), the TADs is formed on the basis of a gene cluster (the interband-gray band complex).

genomics↗

bioRxiv2025

Pcbp1 orchestrates amino acid metabolism burst during the naive-to-primed pluripotency transition

Embryo implantation is accompanied by the naive-to-primed pluripotency transition in epiblast cells, making them receptive to external differentiation signals. In addition to this developmental program switch, implantation suggests that an anabolic boost is required for this process, as the embryo-uterine connection begins supplying the requisite nutrients. In this study, we show that the DNA-binding protein Pcbp1 plays a key role in intensifying amino acid metabolism during the priming of pluripotent stem cells. Knockout of the Pcbp1 gene leads to embryo growth arrest a few days after implantation. By modeling the naive-to-primed pluripotency transition in vitro, we observe reduced proliferation and induction of apoptosis in cells deficient for Pcbp1. Using multi-omics approaches, we uncover a crucial role for Pcbp1 in driving a transcriptional burst of numerous genes involved in the import and the de novo synthesis of essential and conditionally essential amino acids. Pcbp1 deficiency is consequently associated with a slowdown in protein biosynthesis, explaining the early lethal phenotype of knockout embryos. Our findings thus uncover the molecular mechanisms underlying anabolic changes during the naive-to-primed pluripotency transition and highlight the essential role of Pcbp1 in this process, also pointing to its functions in highly proliferative cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/658314v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1e17b48org.highwire.dtl.DTLVardef@64e940org.highwire.dtl.DTLVardef@10d6b00org.highwire.dtl.DTLVardef@1ec0d23_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2024

Unraveling transposable element-mediated regulatory landscape in diverse human immune cells

Transposable elements (TEs) are key contributors to genetic novelty. Despite increasing evidence of their importance, their roles in shaping the regulatory landscape of diverse immune cell populations remain largely unclear. Using single-cell multiome data from human peripheral blood mononuclear cells, we annotated the cell-specific cis-regulatory elements for major immune cell populations and identified a highly cell-specific signature of the overrepresented TE families. Focusing on monocytes that bear fast-evolving transcriptomes, we found that high proportions of their enhancers are TE-derived and bound by multiple pioneer transcription factors. Among them, we confirmed that the core myeloid regulator SPI1 can bind and regulate hundreds of TE-derived enhancers, which further affect the expression of adjacent immune genes. Additionally, interspecies comparison reveals that non-conserved monocyte enhancers are frequently generated by lineage-specific TE insertions, and correlate with the evolved gene expression between human and mouse. Overall, our study supports the importance of TEs in shaping the regulatory landscape of diverse immune cell populations.

genomics↗

bioRxiv2023

CDK8/19 Inhibition Attenuates G1 Arrest Induced by BCR-ABL Antagonists and Accelerates Death of Chronic Myelogenous Leukemia Cells

Imatinib mesylate (IM) and other BCR-ABL tyrosine kinase inhibitors (BCR-ABLi) are the mainstay of chronic myelogenous leukemia (CML) treatment. However, activation of circumventing signaling pathways and quiescence may limit BCR-ABLi efficacy. CDK8/19 Mediator kinases have been implicated in the emergence of non-genetic drug resistance. Dissecting the effects of pharmacological CDK8/19 inhibition on CML survival in response to BCR-ABLi, we found that a selective, non-toxic CDK8/19 inhibitor (CDK8/19i) Senexin B (SenB) and other CDK8/19i sensitized K562 cells to different BCR-ABLi via attenuation of cell cycle arrest. In particular, SenB prevented IM-induced upregulation of genes that negatively regulate cell cycle progression. SenB also antagonized IM-activated p27Kip1 elevation thereby diminishing the population of G1-arrested cells. After transient G1 arrest, cells treated with IM+SenB re-entered the S phase, where they were halted and underwent replicative stress. Consequently, the combination of IM and SenB intensified apoptotic cell death, measured by activation of caspase 9 and 3, subsequent cleavage of poly(ADPriboso)polymerase 1, positive Annexin V staining and increase of subG1 fraction. In contrast, IM-treated BCR-ABL-positive KU812 CML cells, which did not induce p27Kip1, readily died regardless of SenB treatment. Thus, CDK8/19i prevent the quiescence-mediated escape from BCR-ABLi-induced apoptosis, suggesting a strategy for avoiding the CML relapse.

cancer biology↗