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Journal articles

The 3D organization of chromatin colors in mammalian nuclei

Abstract : While many computational methods have been proposed for 3D chromosome reconstruction from chromosomal contact maps, these methods are rarely used for the interpretation of such experimental data, in particular Hi-C data. We posit that this is due to the lack of an easy-to-use implementation of the proposed algorithms, as well as to the important computational cost of most methods. We here give a detailed implementation of the fast ShRec3D algorithm. We provide a tutorial that will enable the reader to reconstruct 3D consensus structures for human chromosomes and to decorate these structures with chromatin epigenetic states. We use this methodology to show that the bivalent chromatin, including Polycomb-rich domains, is spatially segregated and located in between the active and the quiescent chromatin compartments.
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Contributor : Annick Lesne Connect in order to contact the contributor
Submitted on : Wednesday, March 17, 2021 - 8:32:18 PM
Last modification on : Tuesday, June 14, 2022 - 3:43:58 AM
Long-term archiving on: : Monday, June 21, 2021 - 8:47:33 AM


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Leopold Carron, Jean-Baptiste Morlot, Annick Lesne, Julien Mozziconacci. The 3D organization of chromatin colors in mammalian nuclei. Methods in Molecular Biology, Humana Press/Springer Imprint, 2022, 2301, pp. 317-336. ⟨10.1007/978-1-0716-1390-0_17⟩. ⟨hal-03172656⟩



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