Biology subjects

Banecki, K.

Publications and source records attributed to Banecki, K..

6 recordsLinked to original sources

bioRxiv2025

Chromatin as a Coevolutionary Graph: Modeling the Interplay of Replication with Chromatin Dynamics

Modeling DNA replication requires capturing the interplay of multiple biophysical processes and their effects on chromatin structure. We present RepliSage, a multi-scale framework that integrates three key factors: replication timing, loop extrusion, and compartmentalization. Replication forks act as moving barriers that reorganize chromatin during S phase by interfering with loop extrusion. Our approach combines: (1) fork propagation simulated from single-cell replication timing data, (2) Monte Carlo modeling of loop extrusion and epigenetic state transitions, and (3) 3D reconstruction using OpenMM, where loops are modeled as harmonic bonds and epigenetic states drive compartmental interactions. Chromatin is represented as a graph where both the links and the node states change over time. By adjusting model parameters across cell cycle phases, we reproduce known structural transitions and explore how replication stress alters genome organization. This is the first framework to dynamically integrate all three processes for simulating chromatin architecture during the cell cycle.

bioinformatics↗

bioRxiv2024

The challenge of chromatin model comparison and validation a project from the first international 4D Nucleome Hackathon

The computational modeling of chromatin structure is highly complex and challenging due to the hierarchical organization of chromatin, which reflects its diverse biophysical principles, as well as inherent dynamism, which underlies its complexity. The variety of methods for chromatin structure modeling, which are based on different approaches, assumptions and scales of modeling, suggests that there is a necessity for a comprehensive benchmark. This inspired us to conduct a project at the NIH-funded 4D Nucleome Hackathon on March 18-21, 2024 at The University of Washington in Seattle, USA. The hackathon provided an amazing opportunity to gather an international, multi-institutional and unbiased group of experts to discuss, understand and undertake the challenges of chromatin model comparison and validation. These challenges seem straightforward in theory, however in practice, they are challenging and ambiguous. To address them, we developed a bioinformatics workflow for chromatin model comparison and validation, in which we use distance matrices to represent chromatin models, and we calculate Spearman correlation coefficients between pairs of matrices to estimate correlations between models, as well as between models and experimental data. During the 4-day hackathon, we tested our workflow on several distinct software packages for chromatin structure modeling and we discovered several challenges that include: 1) different aspects of chromatin biophysics and scales complicate model comparisons, 2) expertise in biology, bioinformatics, and physics is necessary to conduct a comprehensive research on chromatin structure, 3) bioinformatic software, which is often developed in academic settings, is characterized by insufficient support and documentation. Therefore, our work constitutes a way to advance the modeling of the 3D organization of the human genome, while emphasizing the importance of establishing guidelines for software development and standardization.

genomics↗

bioRxiv2024

Multiscale Molecular Modelling of Chromatin with MultiMM: From Nucleosomes to the Whole Genome

MotivationWe present a user-friendly 3D chromatin simulation model based on OpenMM, addressing the challenges posed by existing models with use-specific implementations. Our approach employs a multi-scale energy minimization strategy, capturing chromatins hierarchical structure. Initiating with a Hilbert curve-based structure, users can input files specifying nucleosome positioning, loops, compartments, or subcompartments. ResultsThe model utilizes an energy minimization approach with a large choice of numerical integrators, providing the entire genomes structure within minutes. Output files include the generated structures for each chromosome, offering a versatile and accessible tool for chromatin simulation in bioinformatics studies. Furthermore, MultiMM is capable of producing nucleosomeresolution structures by making simplistic geometric assumptions about the structure and the density of nucleosomes on the DNA. Code availabilityOpen-source software and the manual are freely available on https://github.com/SFGLab/MultiMM.

bioinformatics↗

bioRxiv2024

Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes

Chromosome Conformation Capture (3C) methods, including Hi-C (a high-throughput variation of 3C), detect pairwise interactions between DNA regions, enabling the reconstruction of chromatin architecture in the nucleus. HiChIP is a modification of the Hi-C experiment, which includes a chromatin immunoprecipitation step (ChIP), allowing genome-wide identification of chromatin contacts mediated by a protein of interest. In mammalian cells, cohesin protein complex is one of the major players in the establishment of chromatin loops. We present an improved cohesin HiChIP experimental protocol. Using comprehensive bioinformatic analysis, we show that performing cohesin HiChIP with two cross-linking agents (formaldehyde [FA] and EGS) instead of the typically used FA alone, results in a substantially better signal-to-noise ratio, higher ChIP efficiency and improved detection of chromatin loops and architectural stripes. Additionally, we propose an automated pipeline called nf-HiChIP (https://github.com/SFGLab/hichip-nf-pipeline) for processing HiChIP samples starting from raw sequencing reads data and ending with a set of significant chromatin interactions (loops), which allows efficient and timely analysis of multiple samples in parallel, without the need of additional ChIP-seq experiments. Finally, using novel approaches for biophysical modelling and stripe calling we generate accurate loop extrusion polymer models for a region of interest and a detailed picture of architectural stripes, respectively.

genomics↗

bioRxiv2024

Tri-omic mapping revealed concerted dynamics of 3D epigenome and transcriptome in brain cells

Exploring the genomic basis of transcriptional programs has been a longstanding research focus. Here, we report a high-throughput single-cell tri-omic method to capture chromatin accessibility, interaction, and RNA simultaneously (ChAIR). After validating in cultured cells, we applied ChAIR to brain cells across mouse lifespan and delineated the concerted dynamics of 3D-epigenomic architecture and transcription during maturation and aging. Particularly, ultra-long chromatin megacontacts and promoter-associated 3D-epigenomic states are effective in defining cell identity and revealing spatially-resolved anatomic specificity. Importantly, we found that neurons in different brain regions and non-neuronal cells may undergo divergent genomic mechanisms during differentiation and aging. Our results demonstrated ChAIRs robustness of connecting chromatin folding architecture with cellular property and its potential applications to address complex questions in single-cell resolution and spatial specificity.

genomics↗

bioRxiv2019

LAX28 is required for assembly of the inner dynein arm l1 and tether/tether head complex in the Leishmania flagellum

Motile eukaryotic flagella beat through coordinated activity of dynein motor proteins yet the mechanisms of dynein coordination and regulation are incompletely understood. The inner dynein arm IDA f/I1 complex and the tether/tether head (T/TH) complex are thought to be key regulators but, unlike IDA f/I1, T/TH proteins show limited conservation across flagellates. Here we characterised T/TH-associated proteins in the protist Leishmania mexicana. Proteome analysis of{Delta} CFAP44 mutant axonemes showed that they lacked IDA f/I1 protein IC140 and a novel 28-kDA axonemal protein, LAX28. Sequence analysis identified similarities between LAX28 and the uncharacterised human sperm tail protein TEX47, sharing features with sensory BLUF-domain proteins. Leishmania lacking LAX28, CFAP44 or IC140 retained some motility albeit with reduced swimming speed and directionality and a propensity for flagellar curling. Expression of tagged proteins in different null mutant backgrounds showed that the axonemal localisation of LAX28 requires CFAP44 and IC140, and the axonemal localisations of CFAP44 and IC140 both depend on LAX28. These data demonstrate a role for LAX28 in motility and show mutual dependencies of IDA f/1I and T/TH-associated proteins for axonemal assembly in Leishmania.\n\nSummary StatementThe inner dynein arm f/l1 complex is required for coordinating flagellar motility. Here we show that LAX28 is needed for its function and localization in the flagellum of Leishmania mexicana.

cell biology↗