Biology subjects

Eliseeva, I. A.

Publications and source records attributed to Eliseeva, I. A..

5 recordsLinked to original sources

bioRxiv2026

New insight into the RNA-chaperon activity of nucleobindin 1

Nucleobindin 1 (NUCB1) is a multifunctional conserved protein located in Golgi luminal, nucleus, extracellular and cytosolic pools. NUCB1 is multidomain protein comprised of a signal peptide, a DNA-binding domain, a leucine zipper and Ca2+ -binding domain. The multiple domains and localization of NUCB1 potentiates its interactions with various partners, such as DNA, Gi3 protein, cyclooxygenase 2, LRP10 and RNA suggests its importance in the regulation of many cellular events. We revealed that NUCB1 contains three RNA-binding regions and able to interact with two RNA fragments. It was suggested possible variants of the participation of NUCB1 in the interaction of the two partially complementary RNAs. The RNA-binding properties of the NUCB1 were also confirmed in vivo experiments.

molecular biology↗

bioRxiv2026

A Joint Promoterome-Proteome Atlas Highlights the Molecular Diversity of Human Skeletal Muscles

More than 600 distinct skeletal muscles constitute up to 40% of the total mass of the human body. Human skeletal muscles differ in anatomical position, morphology, origin, and function, but the diversity of their molecular phenotypes, the gene expression and protein abundance profiles, remains poorly explored. Here, we report the large-scale CAGE-Seq promoterome profiling of 75 human skeletal muscles, complemented by 22 matched proteomes obtained with mass spectrometry. We identified 37001 transcribed regulatory elements and 1804 protein groups encompassing 1895 proteins, 80% of which demonstrated non-uniform expression across different muscles. The skeletal muscles of the eye, tongue, and diaphragm had the most distinctive molecular phenotypes, while the overall diversity was driven by hundreds of transcription factors with tissue-specific activity. By analyzing the allelic imbalance of CAGE-Seq reads, we discovered 6653 allele-specific single-nucleotide variants often coinciding with muscle-related GWAS SNPs, including muscle volume. Finally, we provide an interactive online atlas of transcriptomic and proteomic molecular phenotypes, facilitating further studies of gene regulation and heritable pathologies of skeletal muscles.

genomics↗

bioRxiv2025

Transcript-wide m6A methylation defines the efficiency of the cap-independent translation initiation

N6-methyladenosine (m6A) role in translation control and, particularly, in cap-independent initiation has attracted major attention. A common approach is to study the impact of m6A depending on its particular location in the transcripts, but the global impact of m6A along mRNAs remains unclear. Here, we combined ribosome profiling under conditions of mTOR inhibition and m6A mapping to identify distinct subsets of mRNAs that differ in their sensitivity to the suppression of cap-dependent initiation. The sensitivity was strongly correlated with the total m6A methylation of the transcripts. Further, we demonstrated that upon decreased mTOR activity, m6A methylation facilitated the enhanced association of mRNAs with components of the eIF4F complex. Thus, the efficiency of cap-independent translation initiation is primarily defined not by precise localization but by the total level of m6A methylation, and m6A has a compensatory role in maintaining translation when the canonical cap-dependent pathway is impaired. All in all, our findings underscore the significance of contemplating global m6A methylation status as a pivotal element in translational control, particularly under stress or signaling perturbations. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/690160v2_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@e18178org.highwire.dtl.DTLVardef@fb0346org.highwire.dtl.DTLVardef@19406eaorg.highwire.dtl.DTLVardef@1520821_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Inferring binding specificities of human transcription factors with the wisdom of crowds

DNA motif discovery and, particularly, computational modeling of transcription factor binding motifs, has been a mecca of algorithmic bioinformatics for several decades. Here, we report the results of the largest open community challenge in Inferring BInding Specificities (IBIS), where participants all over the world were invited to construct binding specificity models from multi-assay experimental data for poorly studied human transcription factors. The submissions were rigorously tested against a rich held-out dataset. Benchmarking demonstrated a consistent advantage of properly designed deep learning models over traditional positional weight matrices and other machine learning methods. Yet, the positional weight matrices displayed a surprisingly strong performance out of the box, being only slightly behind the best deep learning models. A post-challenge assessment of a selection of other deep learning methods further solidified this finding. IBIS highlights the power of benchmarking in finding adequate DNA motif representations, emphasizes the pros and cons of various machine learning methods applied to DNA motif modeling, and establishes a rich dataset, benchmarking protocols, and computational framework for a fair cross-platform evaluation of future models of transcription factor binding motifs in DNA sequences. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/688692v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1c6677corg.highwire.dtl.DTLVardef@b4124aorg.highwire.dtl.DTLVardef@1ce2b1org.highwire.dtl.DTLVardef@66e917_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2020

Enhanced C/EBPs binding to C>T mismatches facilitates fixation of CpG mutations

Knowledge of mechanisms responsible for mutagenesis of adult stem cells is crucial to track genomic alterations that may affect cell renovation and provoke malignant cell transformation. Mutations in regulatory regions are widely studied nowadays, though mostly in cancer. In this study, we decomposed the mutation signature of adult stem cells, mapped the corresponding mutations into transcription factor binding regions, and assessed mutation frequency in sequence motif occurrences. We found binding sites of C/EBP transcription factors strongly enriched with [C>T]G mutations within the core CG dinucleotide related to deamination of the methylated cytosine. This effect was also exhibited in related cancer samples. Structural modeling predicted enhanced CEBPB binding to the consensus sequence with the [C>T]G mismatch, which was then confirmed in the direct experiment. We propose that it is the enhanced binding of C/EBPs that shields C>T transitions from DNA repair and leads to selective accumulation of the [C>T]G mutations within binding sites.

genomics↗