Biology subjects

Lagunov, T.

Publications and source records attributed to Lagunov, T..

5 recordsLinked to original sources

bioRxiv2025

Zooming into rearranged genome: applying pipeline of cytological, genomic, and transcriptomic methods for structural variant interpretation

Recent advances in genomic technologies have greatly enhanced our understanding of genotype-phenotype relationships and improved diagnostic of genetic diseases. However, the dissection of complex structural variants remains challenging due to the limitations of current methods in resolving their breakpoint and interpreting phenotypes involving multiple disrupted genes. In this study, we demonstrate how an integrative approach--combining cytological, genomic, and transcriptomic methods--enables the detection, structural and functional characterization of a complex structural variants affecting the MBD5, USP34, and XPO1 genes. Our findings underscore the utility of the Exo-C, a modified chromosome conformation capture technique, in resolving complex rearrangements. We also report, for the first time, a composite neurodevelopmental phenotype resulting from the combined effects of MBD5-associated intellectual disability and 2p15p16.1 microdeletion syndromes.

genomics↗

bioRxiv2025

Effects of Extruder Dynamics and Noise on Simulated Chromatin Contact Probability Curves

Loop extrusion by SMC complexes is a key mechanism underlying chromatin folding during both interphase and mitosis. Despite this shared mechanism, computational models of loop extrusion often rely on fundamentally different assumptions: interphase models typically use dynamic extruders with finite lifetimes, whereas mitotic models employ static extruders placed according to loop size distributions. In this work, we investigate whether these modeling paradigms are interchangeable or yield intrinsically incompatible results. Using publicly available Hi-C data from mitotic chicken cells, we systematically compare dynamic and static loop extrusion models implemented in the Polychrom framework. We evaluate how key parameters such as the extruder lifetime, extrusion velocity, and spatial noise affect the simulated contact probability curves P(s) and loop size distributions. Our results reveal that while both model types can be tuned to approximate the general shape of P(s), they produce distinct internal structures and divergent relationships between loop size and contact decay. We also show that increased extruder lifetimes lead to excessive nested loop formation, which alters both loop statistics and P(s) derivatives. Introducing spatial exclusion constraints between extruders partially restores consistency with static models. These findings highlight that differences in extruder behavior and polymer noise levels can significantly impact chromatin model outcomes and must be carefully accounted for when interpreting or comparing simulation results across biological conditions. Author summaryChromatin organization plays a crucial role in gene regulation and cellular function, yet our understanding of its three-dimensional structure relies heavily on computational modeling and the interpretation of complex experimental data. In this study, we use coarse-grained modeling approaches to simulate chromatin folding and systematically investigate how different analysis metrics and data processing methods influence the conclusions drawn from such models. By comparing widely used metrics and exploring the effects of normalization and noise, we highlight potential pitfalls and biases that can arise in chromatin modeling studies. Our findings provide practical recommendations for researchers in the field, aiming to improve the robustness and reproducibility of computational analyses of chromatin architecture. This work will help guide future studies toward more reliable interpretations of chromatin structure and its biological implications.

genomics↗

bioRxiv2025

The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization

Lampbrush chromosomes are giant meiotic bivalents in growing oocyte nuclei that have served as a classic model system for studying chromatin organization and RNA synthesis for over a century. Despite their importance, the molecular mechanisms underlying lampbrush chromosomes formation and their distinctive chromomere-loop architecture have remained poorly understood. Moreover, the influence of hypertranscription on chromatin organization during oogenesis remains enigmatic. Here, we provide the first comprehensive genomic, cytological, and biophysical analysis of lampbrush chromosome organization by integrating single-cell Hi-C, RNA-seq, NOMe-seq, FISH mapping, and chromatin simulations. Single-nucleus Hi-C analysis revealed CTCF-independent contact domains with stable boundaries defined by transcription units in a convergent orientation. Contact domains identified through Hi-C analysis correspond to insulated chromomeres in lampbrush chromosomes. Small transcriptionally inactive contact domains surrounded by transcription units in the diverged orientation form "chromatin knots", which are often detached from the chromosome axis. Transcription loops frequently manifest as a "cross" pattern with reduced contacts within chromatin domains. Integrative analysis of the whole-genome data uncovers the mechanisms underlying lampbrush chromosome structure, revealing how hypertranscription modulates chromatin stiffness and repositions SMC complexes to establish the distinctive chromomere-loop organisation. Biophysical modeling through polymer simulation reproduces key features of lampbrush chromosomes, including transcription loop formation, chromomere compaction, and insulation patterns. These findings offer a unifying framework for understanding the remarkable chromatin architecture of lampbrush chromosomes and their transcription-dependent organization. Highlights- First integration of single-cell Hi-C, RNA-seq, NOMe-seq and microscopy methods uncovers molecular mechanisms underlying lampbrush chromosome architecture. - Hi-C reveals contact patterns corresponding to lampbrush chromomeres and transcription loops, validated through BAC-based FISH mapping. - Lampbrush chromosomes are segmented into contact domains formed via a CTCF-independent mechanism, with boundaries coinciding with convergently oriented gene pairs. - Hypertranscription shapes lampbrush chromosome through multiple mechanisms, increasing stiffness and decreasing compaction of transcribed units, generating outward pressure, pushing transcription loops away from the chromosome axis, and repositioning SMC complexes to form transcription-dependent domains with stable boundaries. - Hi-C and RNA-seq data analysis as well as polymer simulations demonstrate that cohesive cohesin functions as a transcription-anchored barrier essential for domain insulation in lampbrush chromosomes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=144 HEIGHT=200 SRC="FIGDIR/small/635017v4_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@5a425dorg.highwire.dtl.DTLVardef@1bb11e8org.highwire.dtl.DTLVardef@94a8aborg.highwire.dtl.DTLVardef@1cd9adb_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

A novel approach for simultaneous detection of structural and single-nucleotide variants based on a combination of chromosome conformation capture and exome sequencing

Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type--whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Through several case studies, we demonstrate how Exo-Cs multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.

genomics↗

bioRxiv2022

Comparison and critical assessment of single-cell Hi-C protocols

Advances in single-cell sequencing technologies make it possible to study the genome architecture in single cells. The rapid growth of the field has been fueled by the development of innovative single-cell Hi-C protocols. However, the protocols vary considerably in their efficiency, bias, scale and costs, and their relative advantages for different applications are unclear. Here, we compare the two most commonly used single-cell Hi-C protocols. We use long-read sequencing to analyze molecular products of the Hi-C assay and show that whole-genome amplification step results in increased number of artifacts, larger coverage biases, and increased amount of noise compared to PCR-based amplification. Our comparison provides guidance for researchers studying chromatin architecture in individual cells.

genomics↗