Summary Chromosomes in proliferating metazoan cells undergo dramatic structural metamorphoses every cell cycle, alternating between highly condensed mitotic structures facilitating chromosome segregation, and decondensed interphase structures accommodating transcription, gene silencing and DNA replication. Here we use single-cell Hi-C to study chromosome conformations in thousands of individual cells, and discover a continuum of cis-interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological associated domains (TADs), contact insulation and long-range loops, all defined by bulk Hi-C maps, are governed by distinct cell-cycle dynamics. In particular, DNA replication correlates with build-up of compartments and reduction in TAD insulation, while loops are generally stable from G1 through S and G2. Whole-genome 3D structural models reveal a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data thereby allow for re-interpretation of chromosome conformation maps through the prism of the cell cycle.

During meiosis, homologous chromosomes pair at close proximity to form the synaptonemal complex (SC). This association is mediated by transverse filament proteins that hold the axes of homologous chromosomes together along their entire length. Transverse filament proteins are highly aggregative and can form an aberrant aggregate called the polycomplex that is unassociated with chromosomes. Here, we show that the Ecm11-Gmc2 complex is a novel SC component, functioning to facilitate assembly of the yeast transverse filament protein, Zip1. Ecm11 and Gmc2 initially localize to the synapsis initiation sites, then throughout the synapsed regions of paired homologous chromosomes. The absence of either Ecm11 or Gmc2 substantially compromises the chromosomal assembly of Zip1 as well as polycomplex formation, indicating that the complex is required for extensive Zip1 polymerization. We also show that Ecm11 is SUMOylated in a Gmc2-dependent manner. Remarkably, in the unSUMOylatable ecm11 mutant, assembly of chromosomal Zip1 remained compromised while polycomplex formation became frequent. We propose that the Ecm11-Gmc2 complex facilitates the assembly of Zip1 and that SUMOylation of Ecm11 is critical for ensuring chromosomal assembly of Zip1, thus suppressing polycomplex formation.

Paternal and maternal epigenomes undergo marked changes after fertilization 1 . Recent epigenomic studies have revealed the unusual chromatin landscapes that are present in oocytes, sperm and early preimplantation embryos, including atypical patterns of histone modifications [2][3][4] and differences in chromosome organization and accessibility, both in gametes [5][6][7][8] and after fertilization 5,8-10 . However, these studies have led to very different conclusions: the global absence of local topological-associated domains (TADs) in gametes and their appearance in the embryo 8,9 versus the pre-existence of TADs and loops in the zygote 5,11 . The questions of whether parental structures can be inherited in the newly formed embryo and how these structures might relate to allelespecific gene regulation remain open. Here we map genomic interactions for each parental genome (including the X chromosome), using an optimized single-cell highthroughput chromosome conformation capture (HiC) protocol 12,13 , during preimplantation in the mouse. We integrate chromosome organization with allelic expression states and chromatin marks, and reveal that higher-order chromatin structure after fertilization coincides with an allele-specific enrichment of methylation of histone H3 at lysine 27. These early parental-specific domains correlate with gene repression and participate in parentally biased gene expression-including in recently described, transiently imprinted loci 14 . We also find TADs that arise in a non-parentalspecific manner during a second wave of genome assembly. These de novo domains are associated with active chromatin. Finally, we obtain insights into the relationship between TADs and gene expression by investigating structural changes to the paternal X chromosome before and during X chromosome inactivation in preimplantation female embryos 15 . We find that TADs are lost as genes become silenced on the paternal X chromosome but linger in regions that escape X chromosome inactivation. These findings demonstrate the complex dynamics of three-dimensional genome organization and gene expression during early development.We performed allele-specific single-cell HiC, modified from previous studies 12,13 , on single blastomeres (at the 1-, 2-, 4-, 8-and 64-cell stages, as well as oocytes) from highly polymorphic F 1 hybrid embryos that were obtained by crossing female Mus musculus domesticus (C57Bl/6J) with male Mus musculus castaneus CAST/EiJ) (Fig. 1 a, b). After excluding cells with poor data quality (Methods, Extended Data Fig. 1a), we used the relative coverage of the two X chromosomes to investigate sex-specific differences beyond autosomes (Extended Data Fig. 1b). Finally, we used cell cycle phasing 13 to remove cells in the pre-M and M phases, in which chromosomes lose their organization into compartments and/or domains 13,16 (Extended Data Fig. 1c-e). Looking first at the total contacts (that is, not split between alleles), we detected the formation of TAD-like domains, with clear boundaries that appear...