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. 2018 Jul 24;46(18):9367–9383. doi: 10.1093/nar/gky633

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© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 4. — 3D chromatin structure features of forests and prairies at domain level. (A, D, G, I) The proportions of intra-domain contact and inter-domain contact of the same and different type in prairie for (A) different cells in mouse early embryonic development, (D) different differentiation stages of four mouse cell types, (G) different human samples, and (I) growing and senescent cells. (B, E, H) The segregation ratio between inter-domain contacts of the same type and different type for (B) different cells in mouse embryonic development, (E) different differentiation stages of four mouse cell types, and (H) different human samples. (C, F, I, J) Contact probability and modelled chromatin 3D structures of different cells in (C) mouse early embryonic development, (F) mouse differentiation, (I) cell senescence, and (J) different human samples. The F–F, F–P, and P–P contact probability were calculated as a function of genomic distance s, and the modelled 3D chromatin structures were constructed following previous paper (7). Forests (red) and prairies (blue) are mapped onto the modelled structures. (C) At the early developmental stage of mouse (e.g. PN3), the F–F, F–P and P–P contact probability are of similar values. As early embryo development proceeds, the F–P lowers noticeably, whereas that of P–P remains largely unchanged. Forests become more segregated in space. (F) In pluripotent cells for mouse, long-range P–P is in general lower than that of forests, but the difference between them significantly decreases and long-range contacts for both forests and prairies increase as cells differentiate. (J) For differentiated human somatic tissues such as cortex and left ventricle, the F–F and P–P are of similar genome distance dependences, with that of F–P having lower values than both of them. Different cell types exhibit distinctly different 3D structures, with cortex being the least compact. In proliferating cells (e.g., liver) and IMR90 cell line, the P–P is higher than that of F–F, and their forests and prairies are more spatially segregated. (I) The P–P curve of senescent cells is also above that of growing cells, while that of F–P is almost the same. The structure of senescent cells appears to segregate into several large domains, different from the global segregation of cell lines.

Inline graphic — 3D chromatin structure features of forests and prairies at domain level. (A, D, G, I) The proportions of intra-domain contact and inter-domain contact of the same and different type in prairie for (A) different cells in mouse early embryonic development, (D) different differentiation stages of four mouse cell types, (G) different human samples, and (I) growing and senescent cells. (B, E, H) The segregation ratio between inter-domain contacts of the same type and different type for (B) different cells in mouse embryonic development, (E) different differentiation stages of four mouse cell types, and (H) different human samples. (C, F, I, J) Contact probability and modelled chromatin 3D structures of different cells in (C) mouse early embryonic development, (F) mouse differentiation, (I) cell senescence, and (J) different human samples. The F–F, F–P, and P–P contact probability were calculated as a function of genomic distance s, and the modelled 3D chromatin structures were constructed following previous paper (7). Forests (red) and prairies (blue) are mapped onto the modelled structures. (C) At the early developmental stage of mouse (e.g. PN3), the F–F, F–P and P–P contact probability are of similar values. As early embryo development proceeds, the F–P lowers noticeably, whereas that of P–P remains largely unchanged. Forests become more segregated in space. (F) In pluripotent cells for mouse, long-range P–P is in general lower than that of forests, but the difference between them significantly decreases and long-range contacts for both forests and prairies increase as cells differentiate. (J) For differentiated human somatic tissues such as cortex and left ventricle, the F–F and P–P are of similar genome distance dependences, with that of F–P having lower values than both of them. Different cell types exhibit distinctly different 3D structures, with cortex being the least compact. In proliferating cells (e.g., liver) and IMR90 cell line, the P–P is higher than that of F–F, and their forests and prairies are more spatially segregated. (I) The P–P curve of senescent cells is also above that of growing cells, while that of F–P is almost the same. The structure of senescent cells appears to segregate into several large domains, different from the global segregation of cell lines.