G. A. Benders, V. N. Noskov, E. A. Denisova, C. Lartigue, D. G. Gibson et al., Cloning whole bacterial genomes in yeast, Nucleic Acids Res, vol.38, pp.2558-2569, 2010.
DOI : 10.1007/978-1-61779-564-0_13

URL : http://europepmc.org/articles/pmc2860123?pdf=render

Y. Blat, R. U. Protacio, N. Hunter, and N. Kleckner, Physical and functional interactions among basic chromosome organizational features govern early steps of meiotic chiasma formation, Cell, vol.111, pp.791-802, 2002.
DOI : 10.1016/s0092-8674(02)01167-4

URL : https://doi.org/10.1016/s0092-8674(02)01167-4

J. D. Boeke, G. Church, A. Hessel, N. J. Kelley, A. Arkin et al., The genome project-write, Science, vol.353, pp.126-127, 2016.
DOI : 10.1126/science.aaf6850

S. M. Burgess, N. Kleckner, and B. M. Weiner, Somatic pairing of homologs in budding yeast: existence and modulation, Genes Dev, vol.13, pp.1627-1641, 1999.

A. Cournac, H. Marie-nelly, M. Marbouty, R. Koszul, and J. Mozziconacci, Normalization of a chromosomal contact map, BMC Genom, vol.13, p.436, 2012.
DOI : 10.1186/1471-2164-13-436

URL : https://hal.archives-ouvertes.fr/pasteur-00769663

J. Dekker, K. Rippe, M. Dekker, and N. Kleckner, Capturing chromosome conformation, Science, vol.295, pp.1306-1311, 2002.
DOI : 10.1126/science.1067799

J. Dekker and L. Mirny, The 3D genome as moderator of chromosomal communication, Cell, vol.164, pp.1110-1121, 2016.

Z. Duan, M. Andronescu, K. Schutz, S. Mcllwain, Y. J. Kim et al., A three-dimensional model of the yeast genome, Nature, vol.465, pp.363-367, 2010.

J. S. Dymond, S. M. Richardson, C. E. Coombes, T. Babatz, H. Müller et al., Synthetic chromosome arms function in yeast and generate phenotypic diversity by design, Nature, vol.477, pp.471-476, 2011.
DOI : 10.1038/nature10403

URL : http://europepmc.org/articles/pmc3774833?pdf=render

J. H. Gibcus, K. Samejima, A. Goloborodko, I. Samejima, N. Naumova et al., A pathway for mitotic chromosome formation, Science, vol.359, p.6135, 2018.
DOI : 10.1126/science.aao6135

URL : https://science.sciencemag.org/content/sci/359/6376/eaao6135.full.pdf

E. F. Glynn, P. C. Megee, H. Yu, C. Mistrot, E. Unal et al., Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae, PLoS Biol, vol.2, p.259, 2004.

A. Goloborodko, M. V. Imakaev, J. F. Marko, and L. Mirny, Compaction and segregation of sister chromatids via active loop extrusion, Elife, vol.5, p.14864, 2016.
DOI : 10.7554/elife.14864

URL : https://doi.org/10.7554/elife.14864

K. A. Henderson and S. Keeney, Tying synaptonemal complex initiation to the formation and programmed repair of DNA double-strand breaks, Proc Natl Acad Sci, vol.101, pp.4519-4524, 2004.

T. Hsieh, A. Weiner, B. Lajoie, J. Dekker, N. Friedman et al., Mapping nucleosome resolution chromosome folding in yeast by micro-C, Cell, vol.162, pp.108-119, 2015.
DOI : 10.1016/j.cell.2015.05.048

URL : https://doi.org/10.1016/j.cell.2015.05.048

T. Hsieh, G. Fudenberg, A. Goloborodko, and O. J. Rando, Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome, Nat Methods, vol.13, pp.1009-1011, 2016.

J. R. Hughes, N. Roberts, S. Mcgowan, D. Hay, E. Giannoulatou et al., Analysis of hundreds of cisregulatory landscapes at high resolution in a single, high-throughput experiment, Nat Genet, vol.46, pp.205-212, 2014.

N. Hunter and N. Kleckner, The single-end invasion: an asymmetric intermediate at the double-strand break to double-holliday junction transition of meiotic recombination, Cell, vol.106, pp.59-70, 2001.

M. Imakaev, G. Fudenberg, R. P. Mccord, N. Naumova, A. Goloborodko et al., Iterative correction of Hi-C data reveals hallmarks of chromosome organization, Nat Methods, vol.9, pp.999-1003, 2012.

M. Ito, K. Kugou, J. A. Fawcett, S. Mura, S. Ikeda et al., Meiotic recombination cold spots in chromosomal cohesion sites, Genes Cells Devoted Mol Cell Mech, vol.19, pp.359-373, 2014.
DOI : 10.1111/gtc.12138

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1111/gtc.12138

K. P. Kim, B. M. Weiner, L. Zhang, A. Jordan, J. Dekker et al., Sister cohesion and structural axis components mediate homolog bias of meiotic recombination, Cell, vol.143, pp.924-937, 2010.
DOI : 10.1016/j.cell.2010.11.015

URL : https://doi.org/10.1016/j.cell.2010.11.015

N. Kleckner, D. Zickler, G. H. Jones, J. Dekker, R. Padmore et al., A mechanical basis for chromosome function, Proc Natl Acad Sci, vol.101, pp.12592-12597, 2004.
DOI : 10.1073/pnas.0402724101

URL : http://www.pnas.org/content/pnas/101/34/12592.full.pdf

F. Klein, P. Mahr, M. Galova, S. Buonomo, C. Michaelis et al., A central role for cohesins in sister chromatid cohesion, formation of axial elements, and recombination during yeast meiosis, Cell, vol.98, pp.91-103, 1999.

R. Koszul, K. P. Kim, M. Prentiss, N. Kleckner, and S. Kameoka, Meiotic chromosomes move by linkage to dynamic actin cables with transduction of force through the nuclear envelope, Cell, vol.133, pp.1188-1201, 2008.

R. Koszul and N. Kleckner, Dynamic chromosome movements during meiosis: a way to eliminate unwanted connections?, Trends Cell Biol, vol.19, pp.716-724, 2009.
DOI : 10.1016/j.tcb.2009.09.007

URL : http://europepmc.org/articles/pmc2787882?pdf=render

R. Koszul, Beyond the bounds of evolution: synthetic chromosomes, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01419924

, How and what for?, C R Biol, vol.339, pp.324-328

B. R. Lajoie, J. Dekker, and N. Kaplan, The Hitchhiker's guide to Hi-C analysis: practical guidelines, Methods, vol.72, pp.65-75, 2015.
DOI : 10.1016/j.ymeth.2014.10.031

URL : http://europepmc.org/articles/pmc4347522?pdf=render

I. Lam and S. Keeney, Mechanism and regulation of meiotic recombination initiation, Cold Spring Harb Perspect Biol, vol.7, p.16634, 2015.
DOI : 10.1101/cshperspect.a016634

URL : http://cshperspectives.cshlp.org/content/7/1/a016634.full.pdf

L. Lazar-stefanita, V. F. Scolari, G. Mercy, H. Muller, T. M. Guérin et al., Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle, EMBO J, vol.36, pp.2684-2697, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01596511

T. Le, M. V. Imakaev, L. A. Mirny, and M. T. Laub, High-resolution mapping of the spatial organization of a bacterial chromosome, Science, vol.342, pp.731-734, 2013.

A. Lesne, J. Riposo, P. Roger, A. Cournac, and J. Mozziconacci, 3D genome reconstruction from chromosomal contacts, Nat Methods, vol.11, pp.1141-1143, 2014.
DOI : 10.1038/nmeth.3104

Z. Liang, D. Zickler, P. M. Chang, F. S. Witz, G. Maeshima et al., Chromosomes progress to metaphase in multiple discrete steps via global compaction/expansion cycles, Cell, vol.161, pp.1124-1137, 2015.
DOI : 10.1016/j.cell.2015.04.030

URL : https://hal.archives-ouvertes.fr/hal-01199662

E. Lieberman-aiden, N. L. Van-berkum, L. Williams, M. Imakaev, T. Ragoczy et al., Comprehensive mapping of longrange interactions reveals folding principles of the human genome, Science, vol.326, pp.289-293, 2009.

G. Liti, D. M. Carter, A. M. Moses, J. Warringer, L. Parts et al., Population genomics of domestic and wild yeasts, Nature, vol.458, pp.337-341, 2009.
DOI : 10.1038/nature07743

URL : http://europepmc.org/articles/pmc2659681?pdf=render

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

W. Ma, F. Ay, C. Lee, G. Gulsoy, X. Deng et al., , 2015.

, Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes, Nat Methods, vol.12, pp.71-78

M. Marbouty, C. Ermont, B. Dujon, G. Richard, and R. Koszul, Purification of G1 daughter cells from different Saccharomycetes species through an optimized centrifugal elutriation procedure, Yeast, vol.31, pp.159-166, 2014.
DOI : 10.1002/yea.3005

URL : https://hal.archives-ouvertes.fr/pasteur-01420008

H. Marie-nelly, M. Marbouty, A. Cournac, G. Liti, G. Fischer et al., Filling annotation gaps in yeast genomes using genome-wide contact maps, Bioinformatics, vol.30, pp.2105-2113, 2014.
DOI : 10.1093/bioinformatics/btu162

URL : https://hal.archives-ouvertes.fr/pasteur-01488132

E. Martini, V. Borde, M. Legendre, S. Audic, B. Regnault et al., Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways, PLoS Genet, vol.7, p.1002305, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01258245

G. Mercy, J. Mozziconacci, V. F. Scolari, K. Yang, G. Zhao et al., 3D organization of synthetic and scrambled chromosomes, Science, vol.355, p.4597, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01523221

P. B. Møens and R. E. Pearlman, Chromatin organization at meiosis, BioEssays, vol.9, pp.151-153, 1988.

H. Muller, N. Annaluru, J. W. Schwerzmann, S. M. Richardson, J. S. Dymond et al., Assembling large DNA segments in yeast, Methods Mol Biol, vol.852, pp.133-150, 2012.

T. Nagano, Y. Lubling, T. J. Stevens, S. Schoenfelder, E. Yaffe et al., Single cell Hi-C reveals cell-to-cell variability in chromosome structure, Nature, vol.502, pp.59-64, 2013.

N. Naumova, M. Imakaev, G. Fudenberg, Y. Zhan, B. R. Lajoie et al., Organization of the mitotic chromosome, Science, vol.342, pp.948-953, 2013.

S. D. Oh, L. Jessop, J. P. Lao, T. Allers, M. Lichten et al., Stabilization and electrophoretic analysis of meiotic recombination intermediates in Saccharomyces cerevisiae, Methods Mol Biol, vol.557, pp.209-234, 2009.

P. Olivares-chauvet, Z. Mukamel, A. Lifshitz, O. Schwartzman, N. O. Elkayam et al., Capturing pairwise and multi-way chromosomal conformations using chromosomal walks, Nature, vol.540, pp.296-300, 2016.
DOI : 10.1038/nature20158

R. Padmore, L. Cao, and N. Kleckner, Temporal comparison of recombination and synaptonemal complex formation during meiosis in S. cerevisiae, Cell, vol.66, pp.1239-1256, 1991.

J. Pan, M. Sasaki, R. Kniewel, H. Murakami, H. G. Blitzblau et al., A hierarchical combination of factors shapes the genome-wide topography of yeast meiotic recombination initiation, Cell, vol.144, pp.719-731, 2011.

S. Panizza, M. A. Mendoza, M. Berlinger, L. Huang, A. Nicolas et al., Spo11-accessory proteins link double-strand break sites to the chromosome axis in early meiotic recombination, Cell, vol.146, pp.372-383, 2011.

A. Piazza, R. Koszul, and W. Heyer, Chapter two-a proximity ligationbased method for quantitative measurement of D-loop extension in S. cerevisiae, Methods in enzymology, Spies M, Malkova A (eds), pp.27-44, 2018.

M. K. Raghuraman, E. A. Winzeler, D. Collingwood, S. Hunt, L. Wodicka et al., Replication dynamics of the yeast genome, Science, vol.294, pp.115-121, 2001.

V. Ramani, D. A. Cusanovich, R. J. Hause, W. Ma, R. Qiu et al., Mapping 3D genome architecture through in situ DNase Hi-C, Nat Protoc, vol.11, pp.2104-2121, 2016.
DOI : 10.1038/nprot.2016.126

URL : http://europepmc.org/articles/pmc5547819?pdf=render

S. Rao, M. H. Huntley, N. C. Durand, E. K. Stamenova, I. D. Bochkov et al., A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, vol.159, pp.1665-1680, 2014.

H. S. Rhee and B. F. Pugh, Genome-wide structure and organization of eukaryotic pre-initiation complexes, Nature, vol.483, pp.295-301, 2012.

S. M. Richardson, L. A. Mitchell, G. Stracquadanio, K. Yang, J. S. Dymond et al., Design of a synthetic yeast genome, Science, vol.355, pp.1040-1044, 2017.

S. A. Schalbetter, A. Goloborodko, G. Fudenberg, J. Belton, C. Miles et al., SMC complexes differentially compact mitotic chromosomes according to genomic context, Nat Cell Biol, vol.19, pp.1071-1080, 2017.
DOI : 10.1038/ncb3594

URL : http://europepmc.org/articles/pmc5640152?pdf=render

A. Schwacha and N. Kleckner, Identification of joint molecules that form frequently between homologs but rarely between sister chromatids during yeast meiosis, Cell, vol.76, pp.51-63, 1994.

T. Sexton, E. Yaffe, E. Kenigsberg, F. Bantignies, B. Leblanc et al., Three-dimensional folding and functional organization principles of the Drosophila genome, Cell, vol.148, pp.458-472, 2012.

C. C. Siow, S. R. Nieduszynska, C. A. Müller, and C. A. Nieduszynski, OriDB, the DNA replication origin database updated and extended, Nucleic Acids Res, vol.40, pp.682-686, 2012.
DOI : 10.1093/nar/gkr1091

URL : https://academic.oup.com/nar/article-pdf/40/D1/D682/9478513/gkr1091.pdf

P. Slonimski, Action de l'acriflavine sur les levures IV. Mode d'utilisation du glucose par les mutants "petite colonie, Ann Inst Pasteur, vol.76, pp.510-530, 1949.

J. Sollier, W. Lin, C. Soustelle, K. Suhre, A. Nicolas et al., Set1 is required for meiotic S-phase onset, double-strand break formation and middle gene expression, EMBO J, vol.23, pp.1957-1967, 2004.
DOI : 10.1038/sj.emboj.7600204

URL : http://emboj.embopress.org/content/23/9/1957.full.pdf

V. Sommermeyer, C. Béneut, E. Chaplais, M. E. Serrentino, and V. Borde, Spp1, a member of the set1 complex, promotes meiotic DSB formation in promoters by tethering histone H3K4 methylation sites to chromosome axes, Mol Cell, vol.49, pp.43-54, 2013.

X. Sun, L. Huang, T. E. Markowitz, H. G. Blitzblau, D. Chen et al., Transcription dynamically patterns the meiotic chromosome-axis interface, Elife, vol.4, p.7424, 2015.
DOI : 10.7554/elife.07424

URL : https://doi.org/10.7554/elife.07424

E. Trelles-sticken, J. Loidl, and H. Scherthan, Bouquet formation in budding yeast: initiation of recombination is not required for meiotic telomere clustering, J Cell Sci, vol.112, pp.651-658, 1999.

H. Wong, H. Marie-nelly, S. Herbert, P. Carrivain, H. Blanc et al., A predictive computational model of the dynamic 3D interphase yeast nucleus, Curr Biol, vol.22, pp.1881-1890, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01420017

L. Xu, M. Ajimura, R. Padmore, C. Klein, and N. Kleckner, NDT80, a meiosisspecific gene required for exit from pachytene in Saccharomyces cerevisiae, 1995.

, Mol Cell Biol, vol.15, pp.6572-6581

E. Yaffe and A. Tanay, Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nat Genet, vol.43, pp.1059-1065, 2011.
DOI : 10.1038/ng.947

M. Yu and B. Ren, The three-dimensional organization of mammalian genomes, Annu Rev Cell Dev Biol, vol.33, pp.265-289, 2017.

J. Yue, J. Li, L. Aigrain, J. Hallin, K. Persson et al., Contrasting evolutionary genome dynamics between domesticated and wild yeasts, Nat Genet, vol.49, pp.913-924, 2017.
DOI : 10.1038/ng.3847

URL : https://hal.archives-ouvertes.fr/hal-01546021

D. Zickler and N. Kleckner, Meiotic chromosomes: integrating structure and function, Annu Rev Genet, vol.33, pp.603-754, 1999.
DOI : 10.1146/annurev.genet.33.1.603

D. Zickler and N. Kleckner, Recombination, pairing, and synapsis of homologs during meiosis, Cold Spring Harb Perspect Biol, vol.7, p.16626, 2015.
DOI : 10.1101/cshperspect.a016626

URL : https://hal.archives-ouvertes.fr/hal-01199651

D. Zickler and N. Kleckner, A few of our favorite things: pairing, the bouquet, crossover interference and evolution of meiosis, Semin Cell Dev Biol, vol.54, pp.135-148, 2016.

, License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

, Institut Pasteur Molecular Systems Biology, vol.14, pp.8293-2018