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. 2019 Oct 3;10:4486. doi: 10.1038/s41467-019-12211-8

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — Highly structured homolog pairing resembles features of cis-organization. a Haplotype-resolved Hi-C map of F1 hybrid embryos. Arrows, trans-homolog diagonals. b–d Homologs juxtaposed in a b railroad track fashion, c a loose, laissez-faire mode, or d a highly disordered structure. e Homolog pairing may encompass a range of structures defined by precision, proximity, and continuity. f Rabl positioning of chromosomes. The g zoomed-in maps of chromosomal arms (color coded boxes in a; L, left; R, right) and h respective contact frequencies as a function of genomic distance (see Methods). i trans-homolog, j cis maternal, and k cis paternal maps of matching regions on chr3L. l Ratio of cis Pat/cis Mat Hi-C maps indicates the cis contact patterns of two homologs are highly consistent. m The ratio of trans-homolog/average cis maps suggests that pairing resembles cis contacts, albeit with lower interactions in some regions (dark blue). n Homolog pairing displays highly structured trans-domains (black) and trans-boundaries (gray), reflecting cis-organization of homologs