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Clerkin, A. B.

Publications and source records attributed to Clerkin, A. B..

2 recordsLinked to original sources
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

Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model

The three-dimensional structure of chromatin has emerged as an important feature of eukaryotic gene regulation. Recent technological advances in DNA sequencing-based assays have revealed locus- and chromatin state-specific structural patterns at the length scale of a few nucleosomes ([~]1 kb). However, interpreting these data sets remains challenging. Radiation-induced correlated cleavage of chromatin (RICC-seq) is one such chromatin structure assay that maps DNA-DNA-contacts at base pair resolution by sequencing single-stranded DNA fragments released from irradiated cells. Here, we develop a flexible modeling and simulation framework to enable the interpretation of RICC-seq data in terms of oligonucleosome structure ensembles. Nucleosomes are modeled as rigid bodies with excluded volume and adjustable DNA wrapping, connected by linker DNA modeled as a worm-like chain. We validate the models parameters against cryo-electron microscopy and sedimentation data. Our results show that RICC-seq is sensitive to nucleosome spacing, nucleosomal DNA wrapping, and the strength of inter-nucleosome interactions. We show that nucleosome repeat lengths consistent with orthogonal assays can be extracted from experimental RICC-seq data using a 1D convolutional neural net trained on RICC-seq signal predicted from simulated ensembles. We thus provide a suite of analysis tools that add quantitative structural interpretability to RICC-seq experiments.

genomics↗