Redesigning chromosomes for optimized Hi-C assay provides insights on loop formation and homologs pairing during meiosis

In all chromosome conformation capture based experiments the accuracy with which contacts are detected varies considerably because of the uneven distribution of restriction sites along genomes. In addition, repeated sequences as well as homologous, large identical regions remain invisible to the assay because of the ambiguities they introduce during the alignment of the sequencing reads along the genome. As a result, the investigation of homologs during meiosis prophase through 3C studies has been limited. Here, we redesigned and reassembled in yeast a 145kb region with regularly spaced restriction sites for various enzymes. Thanks to this Syn-3C design, we enhanced the signal to noise ratio and improved the visibility of the entire region. We also improved our understanding of Hi-C data and definition of resolution. The redesigned sequence is now distinguishable from its native homologous counterpart in an isogenic diploid strain. As a proof of principle, we track the establishment of homolog pairing during meiotic prophase in a synchronized population. This provides new insights on the individualization and pairing of homologs, as well as on their internal restructuration into arrays of loops during meiosis prophase. Overall, we show the interest of redesigned genomic regions to explore complex biological questions otherwise difficult to address.

Formaldehyde cross-linking followed by segmentation of the genome by a restriction enzyme (RE) are the first steps of the experimental protocol. The basic unit of "C" experiments therefore consists of restriction fragments (RFs) that are subsequently religated and captured to identify long range contacts. The best resolution that can be obtained is directly imposed by the positions of the RE sites along the genome. Both 6-cutter and 4-cutter REs have been used (Marie-Nelly et al, 2014;Sexton et al, 2012;Rao et al, 2014;Le et al, 2013), the latter with the expectation that the resolution increases with the number of sites. However, this approach suffers from two major caveats. First, restriction sites (RSs) are not regularly spaced along genomes. The distribution of RFs lengths follows a geometric distribution, with important variations along the genome that depend on the local GC content and the specific sequence recognized by the RE. Given that the likelihood for a RF to be crosslinked by formaldehyde during the first step in the procedure depends on its length (Cournac et al, 2012), the probability to detect a given fragment in any 3C experiment will in turn be strongly affected by this parameter (Fig 1A). Normalization procedures have been developed in order to correct the signal (Cournac et al, 2012;Imakaev et al, 2012) but these methods involve filtering out fragments with unusually low or high signal and aggregating the contact data over several consecutive fragments in longer bins of fixed genomic length, at the expense of actual resolution (Lajoie et al, 2015). Overall, the definition of Hi-C resolution has remained empiric, because of the lack of a control sequence where RF biases would be alleviated. The second limitation reflects the fact that repetitive sequences cannot be tracked because the sequencing reads obtained from a Hi-C experiment cannot be mapped unambiguously along the genome, alleviating the possibility to track homologous chromosomes in isogenic backgrounds.
One consequence of these limitations has been the absence of in-depth studies of meiotic prophase through Hi-C approach. Meiosis is the cell division where a diploid cell gives rise to four haploid gametes through two rounds of chromosome segregation with no replication in-between them. The prophase of the first division, where the homologous paternal and maternal chromosomes segregate, comprises a series of regulated events involving the recognition and pairing of homologs all along their length. Homologs, to become physically connected, must meet each other's in space, which implies a dynamic reorganization of the overall genome and disentanglement between paired DNA molecules (Zickler & Kleckner, 2016).
During the meiotic program shared by budding yeast and mammals (i.e. the succession of events mediated by evolutionary conserved molecular complexes), pairing occurs early on during the leptotene stage. This process can be accompanied and/or facilitated by dynamic movements of chromosomes, and lead to telomere clustering at the zygotene stage (bouquet stage; (Zickler & Kleckner, 2016) or other forms of movements mediated by chromosome ends directed by cytoskeletal components through direct association across the nuclear envelop (Koszul & Kleckner, 2009). These events have mostly been described using imaging techniques, or, when it comes to the analysis of the underlying molecular events, through site-specific assays. Dekker and coworkers pioneered the analysis of meiosis in the original chromosome conformation capture study (Dekker et al, 2002). Using restriction polymorphism to distinguish the maternal and paternal versions of a locus along chromosome III, they notably showed that 3C was able to capture homolog pairing, as well as centromere declustering. However, the higher-order organization surrounding the recombining locus remained unexplored. Similarly, the influence on homolog pairing of the vigorous movements mediated by chromosome ends remain unexplored using Hi-C (Koszul & Kleckner, 2009).
In order to investigate the behavior of two homologous chromosomes sharing the same nuclear space, we designed and assembled a dedicated "synthetic" genomic region (Koszul, 2016), also aimed at increasing the resolution of 3C-based experiments. As a proof of concept of this strategy, we describe here a redesigned ~150kb region (called synIV-3C) of Saccharomyces cerevisiae yeast chromosome 4. We then investigated its behavior during the first stages of meiotic prophase.

Design and assembly of the Syn-3C region
Designer chromosome synIV-3C closely resembles the native chromosome with respect to genetic elements (see Material and Methods), but was "designed" to yield high resolution and high visibility in 3C experiments by providing nearly equally spaced restriction sites. The RSs of four different enzymes were removed from the native sequence with point mutations and subsequently reintroduced within the sequence at regularly spaced positions (400bp, 1,500bp, 2,000bp and 6,000bp for DpnII, XbaI, HindIII and NdeI, respectively; Fig 1B and Fig S2; Table 1). Fig 1C, the DpnII and HindIII RFs sizes in the redesigned synIV-3C region are normally distributed when compared to the skewed, native genome-wide distributions. Besides providing a way to increase the resolution of the 3C experiment, the design can also be used to focus on specific contacts, for instance between promoters and terminators (Fig S2). When possible, coding sequences were targeted preferentially and modified using synonymous mutations (Fig S1). We identified a 150kb window on chromosome 4 for which the uniformity of RFs lengths was maximized while the number of potentially deleterious base changes was minimized (the final choice for the region can also take into account sequence annotation and be guided by specific interests of the end-user). From this design, DNA building blocks were purchased and assembled in yeast BY (S288C) and SK1 background strains as described (Annaluru et al, 2014;Muller et al, 2012) (Material and Methods). Sequencing confirmed that 144kb within the targeted region were replaced by the redesigned sequence and that 100% of the mutations were introduced at the correct positions corresponding to a total of ~2% divergence with the reference genomes (3,229 bp out of 150,000). Analysis of the growth profile did not reveal significant negative effects of the modifications introduced in the SynIV-3C region compared to the isogenic parental strains (Fig S3).

Cis-contact pattern of the SynIV-3C region
To assess for the quality improvement of Hi-C data in the Syn-3C region, Hi-C experiments were performed in parallel on BY strain carrying the synIV-3C redesigned chromosome as well as on the native parental strain using DpnII and HindIII (Material and Methods). The raw DpnII contact map of chromosome 4 exhibited a remarkably "smooth" pattern within the redesigned region compared to the native flanking regions (Fig 1D). The read coverage over the region also exhibits a dramatic and compelling change, with a more homogeneous and regular distribution in the synthetic regions for both enzymes compared to a heterogeneous distribution in the native sequence ( Fig. 2A, B). Interestingly, careful examination of this distribution indicates that besides its own length, the capture frequency of a given fragment is also influenced by the length of its neighbors, resulting in a bias. To quantify the improvement in the SynIV-3C region we compared the signal with the signal over the same region obtained in the WT strain using the same number of aligned read pairs and identical bins of various sizes (Fig. 2C, D). At the smallest resolution tested (600bp for DpnII and 2,400bp for HindIII) the WT contact map exhibited numerous blind regions with no detectable contacts (empty bins), in sharp contrast with its synthetic counterpart (Fig. 2C, D). When fragments were aggregated in bins of increasing sizes (hence, resulting in a loss of resolution) these blind regions gradually disappear, although the heterogeneity of the data remains consistently higher in the WT compare to synIV-3C strain, as shown by the increased span of the color-scales of the WT maps.
In order to further quantify this heterogeneity, we computed the cumulative distributions of the number of contacts between bins separated by a given genomic distance s (bp) in the synIV-3C region and in its native counterpart for DpnII and HindIII (Figs 2C and 2D, respectively). The redesigned region systematically exhibited more homogeneous contacts counts and narrower distributions than the WT region, both at short (s = 2 x bins sizes; Figs 2C and D middle panels) and longer distances (Material and Methods and Fig. S5, S6). Some of the bins in the native region remain almost invisible to the assay as a result of the heterogeneity in RF distribution (blue squares on Figs 2C and D middle panels). We computed the coefficient of variation CV (i.e. standard deviation /mean) of these distributions for multiple values of s. We use this value as an indication of the signal to noise ratio (Figs 2C and D right panels).
Interestingly, we found that even for large bins, the CV is significantly and consistently smaller in the synthetic region, again indicating improved resolution. These results also clearly illustrate the advantage of using a frequent cutter (DpnII vs. HindIII) restriction enzyme with respect to resolution since the distribution of contact counts between bins remains much more spread with HindIII than with DpnII, even for native sequences (Fig 2B).

Statistical analysis of Hi-C contact data
The sequencing step of a Hi-C library corresponds to the random sampling of all ligation events generated during the experiment. The outcome of this draw, for a given genomic distance s ± Δs between pairs of loci, is expected to follow a Poisson distribution if we suppose that each pair of loci has a strictly equal probability p to be drawn. For real data, this cannot be the case since other factors (such as for instance the restriction fragment size, or the average 3D folding of chromatin) can influence this probability. When the number of events becomes large enough though, the differences between the re-ligation probabilities of different loci will start to kick in and the distribution of contacts should switch to a Gaussian behavior, assuming that these probabilities follow a Gaussian distribution. The standard deviations (σ) of those two distributions (Poisson and Gaussian) scale either as the square root of the mean (μ) or as the mean, respectively. We took advantage of the fact that the overall contact number μ decreases with increasing genomic distances (s) to check whether these relations between μ and σ holds for real data (Fig. 3A).
To start our analysis with the highest contact numbers we aggregated the results from 12 Hi-C experiments performed in G1 or early S phase (from Lazar-Stefanita et al., 2017). In the following, we focused our analysis on the Syn3C region. For five different distances ( Fig. 3A; 1,400 ± 350 bp in red; 4,900 ± 350 bp in green; 9,100 ± 350 bp in purple; 1,330 ± 350 bp in cyan and 17,500 ± 350 bp in yellow), the five contact distributions computed from each restriction fragments pairs were re-scaled by their mean and superposed on the same plot ( Fig. 3A, inset).
The collapse of these re-scaled distributions clearly indicates a Gaussian behavior (i.e., the mean scales as the standard deviation). We next explored the relation between μ and s over a wider range of values. We used data for increasing values of s, corresponding to lower μ, as well as data aggregated over multiple experiments and data from capture experiments, corresponding to higher values of μ (Fig. 3B). When plotting the values of s for different μ, we found that both in the native and in the Syn-3C sequence context there is a crossover from the Poisson to the Gaussian distribution (indicated by the red and blue lines, respectively) and that the standard deviation for the Syn3C experiment in lower than in the WT counterpart for all the values of μ, as expected from the analysis done in Fig. 2. Interestingly, the two transition points can tell us about the importance of the bias of having uneven restriction fragments compared to other biases and/or biologically relevant variations. In the WT case, as soon as each pair of fragments receive one read, the distribution of counts switches to Gaussian, indicating that each pair has already been sampled unevenly. In the case of the Syn3C construct, where this bias is absent, one needs to aggregates 10 reads per fragment pairs to start to see variations among fragment pair re-ligation frequencies and switch to the Gaussian behavior. This highlights the strong effect of fragments length biases and justifies the use of large bins which will encompass many fragments as well as normalization procedures in all Hi-C experiments. For any genomic distance s, the value of μ can arbitrarily be increased by increasing the bin size, or resolution.
The existence of the transition between Poisson and Gaussian behaviors thus enables us to propose a rigorous way to determine the resolution of a Hi-C experiment by choosing a bin size which exactly corresponds to the transition point. It is worth underlying that according to this analysis the resolution of a Hi-C experiment can only be defined for a given genomic distance s.

Analysis of genome organization during meiosis prophase
The SynIV-3C chromosome was designed and assembled with the aim to investigate the interplay between homologous chromosomes during a variety of DNA related metabolic processes, including the mitotic and meiotic cell cycle. A diploid SK1 strain carrying the SynIV-3C region on one homolog, its native counterpart on the other homolog, but isogenic for the rest of the genome, was processed into a synchronized meiotic culture (Material and Methods). The synchrony of meiotic progression was assessed by monitoring meiotic replication by FACS analysis and the two meiotic divisions by DAPI staining. Cells that have passed through anaphase I or anaphase II contain two or four DAPI-stained bodies, respectively. After 6h in sporulation medium, ~40% of the cells display two or more DAPI bodies. By 8h, 70% of the cells are passed anaphase II, showing that most cells have completed meiosis synchronously ( Fig. 4B) (Hunter & Kleckner, 2001;Koszul et al, 2008). Hi-C contact maps were generated for cells sampled at 0, 3 and 4h from the synchronized culture, corresponding to WT mitotic, early zygotene and early pachytene cells (when a fraction of the population has passed anaphase I), respectively (Fig. 4C).
The differences between mitotic and early pachytene (4h) cells were determined by computing the log-ratio between the contact maps (bin: 5 kb;

Declustering of centromeres
A loss of inter-centromeric contacts was readily apparent during zygotene and pachytene compared to the pre-replication stage (green arrowheads; Fig. 4C, D, F). No significant enrichment in contacts between telomeres was observed (purple arrowheads; Fig. 4C, D, F). This result reflects the rapid declustering of centromeres that accompanies entry into meiotic prophase also observed through microscopy and 3C (Dekker et al, 2002;Trelles-Sticken et al, 1999). On the other hand, the absence of inter-telomeric contacts doesn't immediately support the transient and small increase in telomere clustering described at this stage and corresponding to the bouquet stage ( (Zickler & Kleckner, 1999;Trelles-Sticken et al, 1999). One possibility is that the subtelomeric sequences of the SK1 strain remain incomplete or incorrectly assembled and therefore escape monitoring using Hi-C. Alternatively, the transient increase in clustering is very rapid, or occurs a bit earlier, and was missed during this experiment. More experiments are therefore necessary to fully assess whether or not budding yeast meiotic program really present a "bouquet" stage.
In addition to the loss of discrete centromeric contacts, the ratio map also revealed the abolition of the "polymer brush" effect, which insulates centromeres and their flanking chromosomal regions from the rest of the chromosome arms (green arrows on the magnification of chromosome XV, Fig. 4D). As a result, the centromeric regions become almost indistinguishable from the rest of chromosome arms, and chromosomes appear as relatively individualized, homogenous entities. Once declustered, centromeres regions are more likely to contact other portions of the genome, resulting in the increased trans contact signal made by these regions with other chromosomes and visible on the ratio map (Fig. 4D). The transformation of chromosomes into well-individualized entities could be strikingly recapitulated by the 3D representation of the 2D maps ( Fig. 4E) (Lesne et al, 2014).

Chromosome folding
The ratio contact maps also display a strong increase in intra-chromosomal contacts at early-pachytene compared to mitotic cells, as reflected by a red and large diagonal that clearly appears when magnifying individual chromosomes (inset on Fig. 4D). The folding can also be assessed by computing the contact probability p as a function of genomic distance of all chromosome arms (Naumova et al, 2013;Lieberman-Aiden et al, 2009;Lazar-Stefanita et al, 2017). The p(s) curves were computed for two premeiotic replicates (0h), three mitotic G1 replicates (Lazar-Stefanita et al., 2017), zygotene (3h) and early-pachytene (4h) chromosomes.
The two later curves display sharp differences compared to premeiotic and G1 mitotic cells.
First, contacts frequencies increase between loci positioned 20 to 50 kb apart, with a peak around 50 kb (Fig 4G). Then, contacts sharply decrease, suggesting a general stiffening of the polymer associated with the loss of distant loci to contact each other's. This pattern suggests that chromosomes fold during meiotic prophase into a structure that favor contacts under a certain distance, while disfavoring local and long range interactions, and points at the formation of chromatin loops.

Visualization of meiotic loops using Hi-C
After or during meiotic replication, the two sister chromatids of each homolog becomes organized as arrays of ~20 kb loops tethered to a protein structural axis composed ( Fig. 3A) (Zickler & Kleckner, 2016;Blat et al, 2002;Zickler & Kleckner, 1999). The meiosis-specific cohesion subunit Rec8 is one of the component present along these axis (Klein et al, 1999). Rec8 is distributed into discrete domains corresponding to meiotic loops bases, and contributes to the establishment of cohesion between sister chromatids. These loops provide a highly-organized chromosome architecture context for the formation and resolution of meiotic DNA doublestrand breaks generated during leptotene (Padmore et al, 1991;Blat et al, 2002;Kim et al, 2010;Sommermeyer et al, 2013;Acquaviva et al, 2013). It was proposed that the expansion state of the chromatin within the loops modulates the degree of compaction and stiffness of the chromosomes at the different stages of prophase (Kleckner et al, 2004; see also Koszul et al, 2008). The impact of loop formation on chromosomes had never been addressed through Hi-C, and we took advantage of this pilot study to have a glimpse on these processes.
First, we investigated whether Rec8-mediated loops were visible on the Hi-C contact maps of zygotene and early-pachytene cells by displaying the Rec8 binding regions along chromosome axis. Both at 3 and 4h, the short range intra-chromosomal contacts displayed a heterogeneous signal, with triangular shapes domains reminiscent of the topological domains observed along the mitotic chromosomes of other species appearing along chromosomes ( Fig.   5A) (Dixon et al, 2012;Sexton et al, 2012;Nora et al, 2012). The boundaries between these domains correlate with Rec8 enriched regions (Ito et al, 2014;Glynn et al, 2004), suggesting that this signal may correspond to chromatid loops bridged at their bases to the chromosomal axis.
To further test whether these domains are indeed meiotic loops, we compared the aggregated intrachromosomal contacts made by Rec8-binding sites to random positions in mitotic (0 h) and early-pachytene cells (4h). The ratio between the cumulated contact maps made by 100kb windows (5 kb bins) centered on Rec8 binding sites and random maps display no significant enrichment in mitotic conditions (Fig. 5B, left column). At 4h into meiotic prophase, the same analysis display a strikingly different pattern, with the Rec8 bound sites now clearly delimiting two distinct domains (Fig. 5B, right column). In addition, these sites now display enriched contacts with DNA regions positioned on average 20 to 25 kb upstream and downstream the chromosome. This contact pattern is typical of loops bridging distant loci in cis (Rao et al, 2014;Lazar-Stefanita et al, 2017), and altogether these results demonstrate that Rec8 is positioned at the basis of chromatin loops during meiotic prophase. Therefore, Hi-C detects loop formation during meiotic prophase. The difference between zygotene and early-pachytene stages was not readily apparent from this work, although changes in chromosomes stiffness have been reported and proposed at these stages (Koszul et al, 2008;Kleckner et al, 2004). One possibility is that at 4h the amount of cells with fully complete synaptonemal complex axis (pachytene cells) remains limited. Another option is that the signal within the loops is so strong that variations over long distances between zygotene and pachytene remain negligible when assessed by Hi-C. More work on synchronous cultures of wild type and mutant cells should answer these questions and provide new insights on these mechanisms.

Homolog-homolog contacts using the SynIV-3C and native regions
To characterize more specifically the inter-homolog contacts between the synthetic and native chromosome IV regions an enrichment step for this region was performed using a Capture-C strategy (Hughes et al, 2014). This led to a ~20 fold increase in reads from the SynIV-3C region and its native counterpart that were used to generate the contact map at 0, 3 and 4 hours ( Fig. 5C right panels; see Supplementary methods for controls). To monitor whether changes in contacts between the two homolog regions may result from their similar distance to the centromere, the contact pattern of two heterologous 150kb regions positioned at equal distances from the centromeres on arms of approximately similar sizes (XVR and XIIIR) were generated (Fig. 5C, left panels). These heterologous regions became more insulated from each other's as cell enter meiotic prophase, reflecting the individualization of chromosomes and loss of Rabl organization (see also Fig. 4D). On the other hand, the SynIV-3C and native homologous regions, which are clearly distinguishable from each other's thanks to the SNP introduced in the synthetic design, display a contact frequency that increases over time, from 1.4% of reads before replication to 6.2% in early pachytene.
The two homologs do not appear to be closely and/or strongly juxtaposed, as shown by the weak diagonal that appears over time in zygotene and early pachytene cells. This observation strongly suggests that the synaptonemal complex plays a role not only in the maintenance of homolog structure by bridging chromosomal axis, but also in insulated the two homologs from each other's. To overcome this barrier, meiotic DNA double-strand breaks are indeed relocalized to the SC, where inter-homolog contact is promoted and eventually recombination can proceed (Sommermeyer et al, 2013;Acquaviva et al, 2013). Because the SynIV-3C and native regions differ on average by 2%, we wondered whether this polymorphism could affect their folding and/or meiotic recombination processes. The computation of the p(s) for each of the two homologous region at the three timepoints reveal a similar trend than the one observed for the whole genome (Fig. 5D), showing that the design does not affect chromatin folding. To verify whether this design impairs meiotic recombination, we performed a restriction assay taking advantage of the restriction polymorphism introduced between the two regions (Fig. 5E). Crossing over were detected at the meiotic DSB hotspot tested within the region, suggesting that meiotic recombination can proceed in this genetic environment (Fig. 5E).
More analyses remain to be performed to verify that this is the case over the entire region.
Eventually, the synthetic design could be adapted to alleviate this concern, for instance by removing polymorphisms within 2 kb of DSB hotspots of interests. Nevertheless, this experiment shows that the present approach allows to track recombination events concomitantly to the higher-order architecture of the chromosomes.

Conclusion
The yeast genome presents a relatively homogeneous GC content and a few repeated sequences. The gain in resolution achieved by redesigning RS along the genome should therefore be even higher in organisms with more heterogeneous genomic content and will enable unbiased tracking of entire regions that are otherwise inaccessible to the experiment.
One could envision, for instance, assembling the redesigned chromosome in yeast (Benders et al, 2010), before replacing its native counterpart in the organisms of interest (such as a bacteria, or eventually on mammalian cells). Other advantages of the approach include the modularity of the assembly step (Supplementary Note 2), that allows the introduction of building blocks carrying genetic elements of interest within the redesigned region. For instance, one could introduce highly expressed promoters in the middle of "gene desert" areas, to investigate the effect of gene expression on the local chromatin structure. One can also "shuffle" some of these building blocks, to look at the influence of specific DNA binding proteins on the contact networks. This specific 3C-friendly design is the first time, to our knowledge, where a large (>100kb) region of chromosome is specifically redesigned and assembled for the purpose of improving an assay so that we can now address more precisely and accurately specific questions related to the biology of the cell. It paves the way to more studies exploiting the power of synthetic biology to boost, refine, and maybe reshape traditional molecular biology approaches through orthogonal ones.
Here, we take advantage of the design to track for the first time using Hi-C the large structural changes that affect chromosomes during meiosis prophase. We showed that Hi-C clearly points at the formation of loops, whose bases overlap with binding sites of the meioticspecific cohesion subunit Rec8. The redesigned region now also allows to distinguish, to a large extent, the two homologs. Preliminary results suggest that the loops along each homolog are not closely juxtaposed in space, and that the synaptonemal complex constitutes a barrier inbetween. This observation further supports the mechanical necessity to generate bridges between homologs for recombination to proceed.

Strains
The SynIV-3C region was assembled in the s288C and SK1 genetic backgrounds by transformation of BY4742 and ORT4602 (Sollier et al, 2004) to generate strains RSG_Y181 and RSG_Y189, respectively (see above). The SK1 diploid heterozygous for the SynIV-3C region (RSG_Y190) was obtained by crossing RSG_Y189 and ORT4601 (Sollier et al, 2004). Genotypes are provided in Table 2.

Design principles of Syn-3C chromosomes.
We aimed at modifying the native sequence of a budding yeast chromosome according to our design principles while introducing as little modifications as possible. Because we were planning on re-assembling only a 150kb window within the genome, we scanned through the overall sequence using a scoring quality function to look for the candidate regions qualifying as the ideal target, i.e. where our principles would introduce a minimal number of mutations. The starting material was the S. cerevisiae SK1 strain genome sequence and annotations (Liti et al, 2009) and a list of 9 restriction enzymes (EcoRI, HindIII, NdeI, PstI, SacI, SacII, SalI, XbaI, XhoI and DpnII). RE were selected based on their low cost and restriction efficiency. A genome index file was then computed, that contained the following information for each base pair:  Whether it consists of a "forbidden mutation" site, defined by us as follow: i) start and stop codons of known ORFs, ii) regulatory transcription pre-initiation complexes binding regions identified through ChIP-Seq exo, encompassing TATA-box binding sites (Rhee & Pugh, 2012), iii) the consensus sequence of Autonomous Replicating Sequences (ARS), i.e. the core sequence within S. cerevisiae replication origins (list of ARS obtained from oridb (Siow et al, 2012), iv) intron borders, v) centromeres, vi) tRNA.
 Whether the position belongs to a restriction site.
 If it belongs to an intergenic or coding region, and in the latter case, the codon it belongs to and its position.
Sliding windows of 150 kb moving with 10kb steps were then generated over the entire genome.
In parallel, we defined the restriction pattern we wanted to generate:  Regularly spaced intervals for 400, 1,500, 2,000 and 6,000 bp  Gene promoter/terminator (substitutions within a coding sequence strongly preferred) For each window, we computed all possible changes to apply to the genome so that all combinations of five out of the eight chosen 6-cutter enzymes were repositioned to generate all Overall, we selected the 10 "best" windows located at least at 150 kb from either a centromere or a telomere. The quality score was weighted by the presence of "forbidden positions" within the window, for instance when a start codon overlaps a restriction site to be deleted. Finally, a manual curation, aiming at fixing potential conflicts (such as 2 RSs overlapping the same bases, or accidental re-creation of a RS of one enzyme when processing a second one), followed, and was performed on the genome windows presenting the best quality scores.
We chose the final window based also on our research interests, i.e. containing at least two early replicating replication origins (Siow et al, 2012;Raghuraman et al, 2001), and several hotspots of meiotic DNA double-strand breaks (Pan et al, 2011). We also attempted to avoid too many retrotransposable elements or other DNA repeats. The final window was positioned on chromosome IV::700,000-850,000, with restriction patterns as follow: DnpII ↔ 400 bp window; XbaI ↔ 1,500 bp window; HindIII ↔ 2,000 bp window; NdeI ↔ 6,000 bp window; HhaI ↔ promoter/terminator (see summary on Fig EV2). 1037 mutations were present in the sequence, the vast majority corresponding to the modifications necessary to reorganize DpnII RS (Table 1).
Other modifications were introduced into the sequence. First, PCRTags similar to those used in the Sc2.0 design (Annaluru et al, 2014;Dymond et al, 2011) specific to either the native or synthetic sequence were also introduced within the window. Performing PCR using these primers allow testing for the presence and absence of the synthetic and native sequence, respectively. PCRTags were manually curated to adapt them to the restriction design, and overall 59 PCR tags out of 154 needed to be modified accordingly.
Overall, a total of 3,229 bp were modified (~2% of the 150,000 bp window). 743 codons were modified, but no change in the sequences of the corresponding proteins were introduced.
Although we took great care in the design of the sequence and algorithm, our ongoing experiments nevertheless suggest this design is perfectible and could be simplified. First, windows of 400 and 1,000 bp are probably sufficient to assay the structure at a reasonable resolution. Also, SNPs have to be introduced in repeats or low complexity DNA to facilitate mapping of the reads. Finally, a possibility to find the best frame for each interval/pattern is to start with the positions of RS overlapping forbidden sites as seed.

Assembly of the redesigned chromosome.
The redesigned sequence was split into 52 fragments of ~3,000 bp (i.e., blocks), with 200 bp overlaps between them. In addition sequences corresponding either to the auxotrophic marker genes URA3 or LEU2 were added to blocks 20, 37, 52 (URA3) and blocks 11, 28, 47 (LEU2), followed by 200 bp sequences of the WT neighboring chromosomal region. The replacement of the native sequence of strain BY4742 with the redesigned blocks was performed through a succession of six transformations, up to 11 blocks at a time (Muller et al, 2012).
After each transformation, independent colonies were sampled and PCRs performed at the PCR tags positions to identify the transformants that have replaced all of the native sequence with the redesigned one (Fig. EV3). Upon the last transformation, the selected transformant genome was sequenced and the region 707, 556-852,114 (144,558 bp) was found to be replaced by the synthetic blocks.

Growth rate analysis
Growth assays were performed to see if the transformants exhibited changes in fitness. Little to no growth defect could be identified when blocks 1 to 47 replaced the native sequence. The final transformation with blocks 48 till 52 led repeatedly to the recovery of transformants exhibiting a slow-growth, petite phenotype (Slonimski, 1949), reflecting a block in the aerobic respiratory chain pathway and a decrease in ATP. Since the region concerned by the 6 th transformation only involved a few kb, we decided to keep the first 145 kb already successfully reassembled and discard this last step. However, crossing this petite strain with a WT strain gave diploids without growth defects. Sporulation of these diploids gave offsprings with growth rates also similar to WT, suggesting stable complementation of mitochondrial genomes.

Pre-growth and sporulation of yeast
Pre-growth and sporulation of the RSG_Y190 strain was carried out as described (Oh et al, 2009).

RNA Isolation from Yeast for RNA Sequencing
Three independent RNA-seq libraries were generated for BY4742, SK1 and Syn3C strains. For each library, a single colony was grown in a 2 mL YPD culture overnight at 30°C. The next morning, 10 mL cultures in YPD were started from 10 6 cells/mL until they reached 2.10 7 cell/mL. The cells were pelleted by spinning at 5000 rpm at 4°C for 5 min. The pellet was resuspended in 0.5 mL of Tris-HCl (10 mM, pH 7,5) and transferred to a microfuge tube. The cells were pelleted again by spinning briefly and discarding the supernatant. The cells were resuspended in 400 µL RNA TES buffer (10 mM Tris-HCl, pH 7.5 10 mM EDTA 0.5% SDS). 400 µL of acid phenol/chloroform was then added to the cells and vortexed for 1 min, and heated at 65°C for 30 minutes, briefly vortexing some time to time. The cells were placed on ice for 5 min band centrifuge at 13000 rpm at 4°C for 5 min. The aqueous layer (~400 µL) was then transferred into another microfuge tube; an equal amount of phenol/chloroform acid was added a second time, mixed well and centrifuged at 13000 rpm at 4°C for 5 min. The RNA (~400 µL) was precipitated by adding 40 µL of sodium acetate (3 M) and 1,1 mL of absolute ethanol and incubating the tube at −80˚C for a least 30 min. The RNA was pelleted by centrifuging at 13000 rpm at 4˚C for 20 min. The RNA pellet was then washed with 500 µL of 70% ethanol, air-dried and then resuspended in 50 µL of water. 15 µg were treated with 2U of DNase TURBO (Invitrogen) and cleaned up by phenol extraction and ethanol precipitation before being prepared for sequencing.

RNA-Seq Analysis of synIII
Single-end non-strand-specific RNA-seq of the Syn3C and BY4742 were performed using Illumina Nextseq and standard TruSeq preparations kits, after depletion of ribosomal RNA. Reads were mapped using Bowtie2 to the reference S. cerevisiae BY4742 and Syn3C genome. For each gene, reads were counted if mapping quality was lower than 30 and analyzed for differential expression using DESeq2, with standard parameters.

Hi-C experiments
S. cerevisiae G1 daughter cells of the redesigned strain were recovered from an exponentially growing population through an elutriation procedure . Hi-C libraries were generated as described (Lazar-Stefanita et al, 2017;Dekker et al, 2002). G1 daughter cells were cross-linked for 20 minutes with fresh formaldehyde (3% final concentration). To generate the libraries with different restriction enzymes, aliquots of 3 x 10 9 cells were resuspended in 10 ml sorbitol 1M and incubated 30 minutes with DTT 5mM and Zymolyase 100T (CFinal=1 mg/ml) to digest the cell wall. Spheroplasts were then washed first with 5 ml of sorbitol 1M, then with 5 ml of 1X restriction buffer (depending on the restriction enzyme used). The spheroplasts were then resuspended either in 3.5 ml of the corresponding restriction buffer (NEB). For each aliquot/experiment, the cells were then split into three tubes (V=500µL) and incubated in SDS (3%) for 20 minutes at 65°C.
Crosslinked DNA was digested at 37°C overnight with 15 units of the appropriate restriction enzyme (NEB, DpnII, HindIII or NdeI). The digestion mix was then centrifuged for 20 minutes at 18000 g and the supernatant discarded. The pellets were then resuspended and pooled into 400 µL of cold water. Depending on the sequence of the restriction site overhangs, the extremities of the fragments were repaired in the presence of either 14-dCTP biotin or 14-dATP biotin (Invitrogen). Biotinylated DNA molecules were then incubated 4 hours at 16°C in presence of 250 U of T4 DNA ligase (Thermo Scientific, 12.5 ml final volume). DNA purification was achieved through an overnight incubation at 65°C in presence of 250µg/ml proteinase K in 6.2mM EDTA followed by precipitation step in presence of RNAse.

Processing of the reads and contact maps generations
The raw data from each 3C experiment was processed as follow: first, PCR duplicates were collapsed using the 6 Ns present on each of the custom-made adapter and trimmed. Reads were then aligned using Bowtie 2 in its most sensitive mode against S. cerevisiae reference genome (native genome) or against the S. cerevisiae reference adapted for the Syn-3C region on chromosome 4 (SynIV-3C genome). An iterative alignment procedure was used: for each read the length of the sequence mapped increases gradually from 20 bp until the mapping became unambiguous (mapping quality > 30). Paired reads were aligned independently and each mapped read was assigned to a restriction fragment. Religation events has been filtered out through the information about the orientation of the sequences as described in (Cournac et al, 2012). The distribution of the reads along the synthetic region and its native counterpart is represented in Fig 2. Contact matrices were built for the wild type and the mutant by binning the aligned reads into units of single restriction fragments. DpnII and HindIII contact maps for the SynIV-3C region and its native counterpart were randomly resampled in order to present the same number of contacts. The raw contact maps were then subsequently binned into units (i.e. bins) of 600, 1,200, 2,400, 4,800 and 9,600 base pairs. Contacts maps were generated using the levelplot function of the R lattice package. Matrices for the synthetic region were subsequently obtained by extracting the diagonal blocks for bins falling in the 719,756bp to 849,206bp interval. Outliers has been removed from the matrices if the number of the contacts surpassed by 20 times the top 5‰ threshold of the number of contacts between restriction fragment pairs.

Statistical analysis
The CV is defined as the ratio between the standard deviation and the mean of the contact histograms at fixed distance s; to take into account the finite-size effect, we discarded bins at the edge of the contact matrix in order to keep the statistics (number of bins) for different values of s constant, up to s < 15,000 bp in DpnII and s < 70,000 bp in HindIII datasets. To show that the improvement is specific to the new restriction pattern and is unlikely to be find spontaneously within the genome, we compared the SynIV-3C results with seven regions of similar size along chromosome 4 (460,856-590,306 bp; 590,306-719,756 bp; 849,206-978,656 bp; 978,656-1,108,106 bp;1,108,106-1,237,556 bp;1,2375,56-1,367,006 bp; 1,367,006-1,496,456 bp). The quality improvement was assessed by computing the logarithm of the ratio of the CVs of the SynIV-3C and native region (Fig EV5).

Southern blot analysis of crossing over formation at the CCT6 hotspot
The CCT6 locus was chosen because it is the strongest Spo11-induced DSB hotspot in the synthetic region (Pan et al, 2011). Cells were harvested and DNA was extracted as described (Oh et al, 2009), except that no crosslinking step was performed. The DNA was digested with NdeI and XbaI (New England Biolabs), migrated on a 1% UltraPure Agarose (Invitrogen) 1X TAE for 15 hours at 70 V, and capillary transferred onto a Hybond-XL membrane (GE Healthcare) following the manufacturer instructions. Southern blot hybridization was performed at 65°C in Church buffer (1% BSA, 0.25 M Na2HPO4 pH 7.3, 7% SDS, 1 mM EDTA) with a 1,104 bp-long radiolabeled probe corresponding to the rightmost region common to both the native and SynIV-3C restriction fragments (obtained from SK1 genomic DNA with primers 5'-TGGTGAAGAACTCAGGATTC-3' and 5'-CAGTTACAATGAAGTCCAGG-3') and radiolabeled phage lambda DNA (molecular ladder). Radiolabeling was performed with P 32 -dCTP with the High Prime labeling kit (Roche) following the manufacturer instructions. The membrane was washed,

Figure 3. Relation between standard deviation and mean for each pair of fragments located at similar genomic distances s ± Δs
A The mean number of contact of restriction fragments (big symbols) at a fixed range of distances (s +/-350bp, see text) decreases as a power law (red line) with exponent -0.6. Small circles represent the contact number of individual pairs of restriction fragments. Inset: Distributions of contact numbers re-scaled by their means B The relation between the variance and the mean of these distributions undergoes a transition from Poisson to Gaussian. WT and Syn3C data were obtained by aggregating data-sets respectively from  and (Lazar-Stefanita et al, 2017). Capture-C data are from this study. The red line corresponds to the theoretical Poisson behavior, whereas the blue line corresponds to the theoretical Gaussian behavior fitting the CV from data.

A
Schematic representation of the structural changes affecting homologs during meiotic prophase. Sister chromatids organize as arrays of loops along each homolog axis (green lines) after replication. At leptotene, DNA double-strand breaks (DSBs) occur. During zygotene, homologs come together partially and the syneptonemal complex (SC, grey) originates at DSBs and centromeres. At pachytene, homologs are fully synapsed and undergo vigorous motion (purple arrows).

B
Meiotic progression, as measured by completion of MI and MII divisions.
C Contacts maps of synchronized populations of cells after 0 (bottom left) and 4 (top right) hours in sporulation medium. The 16 yeast chromosomes are displayed atop the maps. Purple arrowheads: inter-telomere contacts. Green arrowheads: inter-centromeric contacts.
D Log-ratio of the two contact maps from (C). The blue to red color scale reflects the enrichment in contacts in one population with respect to the other (log2). The inset on the bottom left displays the magnification of chromosome XV. The green arrows point at the contacts made at t=4h by the centromere with the left and right arms.

E
Boxplots representing the variation in number of normalized contacts for centromeres (left) and telomeres (right) between 0, 3 and 4h in sporulation media. Variations between t=0h replicates, 3h and 0h, and 4h and 0h, were computed. The relative Wilcoxon test supports a decrease in centromere contacts at t=3 and 4h compared to t=0h.

F
Average intra-chromosomal contact frequency p between two loci with respect to their genomic distance s along the chromosome (log-log scale; p(s)) during mitotic G1 (brown curve; three replicates from Lazar-Stefanita et al., 2017), meiotic t=0h (black curve; two replicates), 3h (red curve) and 4h (blue curve).

A
Magnification of chromosomes V and VI contact maps during meiotic time course at t=0, 3 and 4 hours (bin size: 5kb). The blue rectangles point at bins enriched in Rec8 protein. Green triangles: centromere position.

B
Top panels: aggregated intrachromosomal contacts made by 100kb windows (5 kb bins) centered on Rec8 enriched bins (top right) or randomly chosen (bottom left). Middle panels: ratio between the cumulated contact maps of the above panel. Blue color shows a depletion of contacts in the random maps, whereas the red signal points at an enrichment in contacts in the maps centered on Rec8 enriched bins. Purple arrowheads point at looping signal between the center of the window (corresponding to the Rec8 enriched bin) and flanking regions. Bottom panel: schematic representation of the disposition of the chromatin at the corresponding timepoints.

C
Normalized frequency of contacts as a function of genomic distance within the SynIV-3C and its WT counterpart for t=0, 3, and 4h.

D
Contacts between the SynIV-3C region and its native homolog (left panels) and between two windows of similar sizes positions at an equal distance (d) to the centromere but belonging to two other chromosomes (right panels). The percentages on each column reflects different measurements. For the inter-homolog panels, they represent the number of pairs of reads bridging homologs (trans contacts) divided by the total number of pairs aligning within the regions. On the other hand, for inter-heterologs, the percentage represents the amount of pairs of reads bridging the two distinct regions, divided by the total number of pairs aligning within the distinct regions. This illustrates the gradual chromosomal individualization.

E
Crossing over between the SynIV-3C region and the native counterpart. Top: schematic representation of how the redesigned restriction pattern allows characterization of CO events using a probe (black line p) at a DSB hotspot (Material and Methods). Middle: meiotic recombination of cells progressing into meiosis and analyzed using restriction pattern similar to (Hunter & Kleckner, 2001