Effect of active loop extrusion on the two-contact correlations in the interphase chromosome
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arXiv
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| Autores principales: | , |
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| Formato: | Preprint |
| Publicado: |
2024
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| _version_ | 1866910401861517312 |
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| author | Starkov, Dmitry Belan, Sergey |
| author_facet | Starkov, Dmitry Belan, Sergey |
| contents | The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance between them. However, these datasets do not tell us anything about the joint statistics of simultaneous contacts between genomic loci in individual cells. This kind of statistical information can be extracted using the single-cell Hi-C method, which is capable of detecting a large fraction of simultaneous contacts within a single cell, as well as through modern methods of fluorescent labeling and super-resolution imaging. Motivated by the prospect of the imminent availability of relevant experimental data, in this work we theoretically model the joint statistics of pairs of contacts located along a line perpendicular to the main diagonal of the single-cell contact map. The analysis is performed within the framework of an ideal polymer model with quenched disorder of random loops, which, as previous studies have shown, allows to take into account the influence of the loop extrusion process on the conformational properties of interphase chromatin. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2404_04853 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Effect of active loop extrusion on the two-contact correlations in the interphase chromosome Starkov, Dmitry Belan, Sergey Statistical Mechanics Biological Physics The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance between them. However, these datasets do not tell us anything about the joint statistics of simultaneous contacts between genomic loci in individual cells. This kind of statistical information can be extracted using the single-cell Hi-C method, which is capable of detecting a large fraction of simultaneous contacts within a single cell, as well as through modern methods of fluorescent labeling and super-resolution imaging. Motivated by the prospect of the imminent availability of relevant experimental data, in this work we theoretically model the joint statistics of pairs of contacts located along a line perpendicular to the main diagonal of the single-cell contact map. The analysis is performed within the framework of an ideal polymer model with quenched disorder of random loops, which, as previous studies have shown, allows to take into account the influence of the loop extrusion process on the conformational properties of interphase chromatin. |
| title | Effect of active loop extrusion on the two-contact correlations in the interphase chromosome |
| topic | Statistical Mechanics Biological Physics |
| url | https://arxiv.org/abs/2404.04853 |