{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T03:13:03Z","timestamp":1791861183628,"version":"4.3.4"},"reference-count":71,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2017,3,8]],"date-time":"2017-03-08T00:00:00Z","timestamp":1488931200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2017,3,8]],"date-time":"2017-03-08T00:00:00Z","timestamp":1488931200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the\n                    <jats:italic>Mycoplasma pneumoniae<\/jats:italic>\n                    chromosome at a 10\u2009kb resolution. We find a defined structure, with a global symmetry between two arms that connect opposite poles, one bearing the chromosomal Ori and the other the midpoint. Analysis of local structures at a 3\u2009kb resolution indicates that the chromosome is organized into domains ranging from 15 to 33\u2009kb. We provide evidence that genes within the same domain tend to be co-regulated, suggesting that chromosome organization influences transcriptional regulation, and that supercoiling regulates local organization. This study extends the current understanding of bacterial genome organization and demonstrates that a defined chromosomal structure is a universal feature of living systems.\n                  <\/jats:p>","DOI":"10.1038\/ncomms14665","type":"journal-article","created":{"date-parts":[[2017,3,8]],"date-time":"2017-03-08T05:08:45Z","timestamp":1488949725000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":123,"title":["Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae"],"prefix":"10.1038","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7258-7272","authenticated-orcid":false,"given":"Marie","family":"Trussart","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5992-9186","authenticated-orcid":false,"given":"Eva","family":"Yus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sira","family":"Martinez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Davide","family":"Ba\u00f9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuhei O.","family":"Tahara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9632-918X","authenticated-orcid":false,"given":"Thomas","family":"Pengo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Widjaja","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Kretschmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jim","family":"Swoger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Djordjevic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9255-9033","authenticated-orcid":false,"given":"Lynne","family":"Turnbull","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2296-3791","authenticated-orcid":false,"given":"Cynthia","family":"Whitchurch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7478-7390","authenticated-orcid":false,"given":"Makoto","family":"Miyata","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0151-4279","authenticated-orcid":false,"given":"Marc A.","family":"Marti-Renom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Lluch-Senar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu\u00eds","family":"Serrano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,3,8]]},"reference":[{"key":"BFncomms14665_CR1","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1038\/35066075","volume":"2","author":"T Cremer","year":"2001","unstructured":"Cremer, T. & Cremer, C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292\u2013301 (2001).","journal-title":"Nat. Rev. Genet."},{"key":"BFncomms14665_CR2","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/j.cell.2007.01.028","volume":"128","author":"T Misteli","year":"2007","unstructured":"Misteli, T. Beyond the sequence: cellular organization of genome function. Cell 128, 787\u2013800 (2007).","journal-title":"Cell"},{"key":"BFncomms14665_CR3","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1038\/nrmicro3007","volume":"11","author":"CJ Dorman","year":"2013","unstructured":"Dorman, C. J. Genome architecture and global gene regulation in bacteria: making progress towards a unified model? Nat. Rev. Microbiol. 11, 349\u2013355 (2013).","journal-title":"Nat. Rev. Microbiol."},{"key":"BFncomms14665_CR4","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1016\/j.bbagrm.2011.12.007","volume":"1819","author":"L Baranello","year":"2012","unstructured":"Baranello, L., Levens, D., Gupta, A. & Kouzine, F. The importance of being supercoiled: how DNA mechanics regulate dynamic processes. Biochim. Biophys. Acta 1819, 632\u2013638 (2012).","journal-title":"Biochim. Biophys. Acta"},{"key":"BFncomms14665_CR5","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1038\/nrmicro2261","volume":"8","author":"SC Dillon","year":"2010","unstructured":"Dillon, S. C. & Dorman, C. J. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat. Rev. Microbiol. 8, 185\u2013195 (2010).","journal-title":"Nat. Rev. Microbiol."},{"key":"BFncomms14665_CR6","doi-asserted-by":"publisher","first-page":"1435","DOI":"10.1046\/j.1365-2958.1998.01025.x","volume":"29","author":"P Staczek","year":"1998","unstructured":"Staczek, P. & Higgins, N. P. Gyrase and Topo IV modulate chromosome domain size in vivo. Mol. Microbiol. 29, 1435\u20131448 (1998).","journal-title":"Mol. Microbiol."},{"key":"BFncomms14665_CR7","doi-asserted-by":"publisher","first-page":"1766","DOI":"10.1101\/gad.1207504","volume":"18","author":"L Postow","year":"2004","unstructured":"Postow, L., Hardy, C. D., Arsuaga, J. & Cozzarelli, N. R. Topological domain structure of the Escherichia coli chromosome. Genes Dev. 18, 1766\u20131779 (2004).","journal-title":"Genes Dev."},{"key":"BFncomms14665_CR8","doi-asserted-by":"publisher","first-page":"3023","DOI":"10.1016\/j.febslet.2015.04.012","volume":"589","author":"M Lakadamyali","year":"2015","unstructured":"Lakadamyali, M. & Cosma, M. P. Advanced microscopy methods for visualizing chromatin structure. FEBS Lett. 589, 3023\u20133030 (2015).","journal-title":"FEBS Lett."},{"key":"BFncomms14665_CR9","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1038\/nmeth929","volume":"3","author":"MJ Rust","year":"2006","unstructured":"Rust, M. J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Method 3, 793\u2013796 (2006).","journal-title":"Nat. Method"},{"key":"BFncomms14665_CR10","doi-asserted-by":"publisher","first-page":"1642","DOI":"10.1126\/science.1127344","volume":"313","author":"E Betzig","year":"2006","unstructured":"Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642\u20131645 (2006).","journal-title":"Science"},{"key":"BFncomms14665_CR11","doi-asserted-by":"publisher","first-page":"4258","DOI":"10.1529\/biophysj.106.091116","volume":"91","author":"ST Hess","year":"2006","unstructured":"Hess, S. T., Girirajan, T. P. K. & Mason, M. D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys. J. 91, 4258\u20134272 (2006).","journal-title":"Biophys. J."},{"key":"BFncomms14665_CR12","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1038\/nmeth.1257","volume":"5","author":"J F\u00f6lling","year":"2008","unstructured":"F\u00f6lling, J. et al. Fluorescence nanoscopy by ground-state depletion and single-molecule return. Nat. Methods 5, 943\u2013945 (2008).","journal-title":"Nat. Methods"},{"key":"BFncomms14665_CR13","doi-asserted-by":"publisher","first-page":"1306","DOI":"10.1126\/science.1067799","volume":"295","author":"J Dekker","year":"2002","unstructured":"Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306\u20131311 (2002).","journal-title":"Science"},{"key":"BFncomms14665_CR14","doi-asserted-by":"publisher","first-page":"1445","DOI":"10.1126\/science.1204697","volume":"333","author":"W Wang","year":"2011","unstructured":"Wang, W., Li, G.-W., Chen, C., Xie, X. S. & Zhuang, X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 333, 1445\u20131449 (2011).","journal-title":"Science"},{"key":"BFncomms14665_CR15","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1126\/science.1181369","volume":"326","author":"E Lieberman-Aiden","year":"2009","unstructured":"Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289\u2013293 (2009).","journal-title":"Science"},{"key":"BFncomms14665_CR16","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/s10577-010-9167-2","volume":"19","author":"D Ba\u00f9","year":"2011","unstructured":"Ba\u00f9, D. & Marti-Renom, M. Structure determination of genomic domains by satisfaction of spatial restraints. Chromosome Res. 19, 25\u201335 (2011).","journal-title":"Chromosome Res."},{"key":"BFncomms14665_CR17","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1016\/j.molcel.2011.09.010","volume":"44","author":"MA Umbarger","year":"2011","unstructured":"Umbarger, M. A. et al. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol. Cell 44, 252\u2013264 (2011).","journal-title":"Mol. Cell"},{"key":"BFncomms14665_CR18","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1126\/science.1242059","volume":"342","author":"TBK Le","year":"2013","unstructured":"Le, T. B. K., Imakaev, M. V., Mirny, L. A. & Laub, M. T. High-resolution mapping of the spatial organization of a bacterial chromosome. Science (New York, N.Y.) 342, 731\u2013734 (2013).","journal-title":"Science (New York, N.Y.)"},{"key":"BFncomms14665_CR19","doi-asserted-by":"publisher","first-page":"2151","DOI":"10.1101\/gad.241422.114","volume":"28","author":"F Le Dily","year":"2014","unstructured":"Le Dily, F. et al. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes Dev. 28, 2151\u20132162 (2014).","journal-title":"Genes Dev."},{"key":"BFncomms14665_CR20","doi-asserted-by":"publisher","first-page":"6058","DOI":"10.1093\/nar\/gkt325","volume":"41","author":"C Cagliero","year":"2013","unstructured":"Cagliero, C., Grand, R. S., Jones, M. B., Jin, D. J. & O\u2019Sullivan, J. M. Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription. Nucleic Acids Res. 41, 6058\u20136071 (2013).","journal-title":"Nucleic Acids Res."},{"key":"BFncomms14665_CR21","doi-asserted-by":"publisher","first-page":"e03318","DOI":"10.7554\/eLife.03318","volume":"3","author":"M Marbouty","year":"2014","unstructured":"Marbouty, M. et al. Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. eLife 3, e03318 (2014).","journal-title":"eLife"},{"key":"BFncomms14665_CR22","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1016\/j.molcel.2015.07.020","volume":"59","author":"M Marbouty","year":"2015","unstructured":"Marbouty, M. et al. Condensin- and replication-mediated bacterial chromosome folding and origin condensation revealed by hi-c and super-resolution imaging. Mol. Cell 59, 588\u2013602 (2015).","journal-title":"Mol. Cell"},{"key":"BFncomms14665_CR23","doi-asserted-by":"publisher","first-page":"1661","DOI":"10.1101\/gad.265876.115","volume":"29","author":"X Wang","year":"2015","unstructured":"Wang, X. et al. Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis. Genes Dev. 29, 1661\u20131675 (2015).","journal-title":"Genes Dev."},{"key":"BFncomms14665_CR24","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature11082","volume":"485","author":"JR Dixon","year":"2012","unstructured":"Dixon, J. R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376\u2013380 (2012).","journal-title":"Nature"},{"key":"BFncomms14665_CR25","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/nature11049","volume":"485","author":"EP Nora","year":"2012","unstructured":"Nora, E. P. et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 381\u2013385 (2012).","journal-title":"Nature"},{"key":"BFncomms14665_CR26","doi-asserted-by":"publisher","first-page":"1418","DOI":"10.1111\/j.1365-2958.2008.06239.x","volume":"68","author":"O Espeli","year":"2008","unstructured":"Espeli, O., Mercier, R. & Boccard, F. DNA dynamics vary according to macrodomain topography in the E. coli chromosome. Mol. Microbiol. 68, 1418\u20131427 (2008).","journal-title":"Mol. Microbiol."},{"key":"BFncomms14665_CR27","doi-asserted-by":"publisher","first-page":"1838","DOI":"10.1093\/nar\/28.8.1838","volume":"28","author":"E Perez-Rueda","year":"2000","unstructured":"Perez-Rueda, E. & Collado-Vides, J. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28, 1838\u20131847 (2000).","journal-title":"Nucleic Acids Res."},{"key":"BFncomms14665_CR28","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/S0065-2911(02)46002-X","volume":"46","author":"JD Helmann","year":"2002","unstructured":"Helmann, J. D. The extracytoplasmic function (ECF) sigma factors. Adv. Microb. Physiol. 46, 47\u2013110 (2002).","journal-title":"Adv. Microb. Physiol."},{"key":"BFncomms14665_CR29","doi-asserted-by":"publisher","first-page":"572","DOI":"10.1016\/S1369-5274(98)80091-X","volume":"1","author":"R Herrmann","year":"1998","unstructured":"Herrmann, R. & Reiner, B. Mycoplasma pneumoniae and Mycoplasma genitalium: a comparison of two closely related bacterial species. Curr. Opin. Microbiol. 1, 572\u2013579 (1998).","journal-title":"Curr. Opin. Microbiol."},{"key":"BFncomms14665_CR30","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1111\/j.1365-2958.2011.07560.x","volume":"80","author":"AD Cameron","year":"2011","unstructured":"Cameron, A. D., Stoebel, D. M. & Dorman, C. J. DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica. Mol. Microbiol. 80, 85\u2013101 (2011).","journal-title":"Mol. Microbiol."},{"key":"BFncomms14665_CR31","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1111\/j.1365-2958.2011.07717.x","volume":"81","author":"W Zhang","year":"2011","unstructured":"Zhang, W. & Baseman, J. B. Transcriptional regulation of MG_149, an osmoinducible lipoprotein gene from Mycoplasma genitalium. Mol. Microbiol. 81, 327\u2013339 (2011).","journal-title":"Mol. Microbiol."},{"key":"BFncomms14665_CR32","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1128\/MMBR.62.4.1094-1156.1998","volume":"62","author":"S Razin","year":"1998","unstructured":"Razin, S., Yogev, D. & Naot, Y. Molecular biology and pathogenicity of mycoplasmas. Microbiol. Mol. Biol. Rev. 62, 1094\u20131156 (1998).","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"BFncomms14665_CR33","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1128\/CMR.17.4.697-728.2004","volume":"17","author":"KB Waites","year":"2004","unstructured":"Waites, K. B. & Talkington, D. F. Mycoplasma pneumoniae and its role as a human pathogen. Clin. Microbiol. Rev. 17, 697\u2013728 table of contents (2004).","journal-title":"Clin. Microbiol. Rev."},{"key":"BFncomms14665_CR34","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1128\/JB.183.5.1621-1630.2001","volume":"183","author":"S Seto","year":"2001","unstructured":"Seto, S., Layh-Schmitt, G., Kenri, T. & Miyata, M. Visualization of the attachment organelle and cytadherence proteins of Mycoplasma pneumoniae by immunofluorescence microscopy. J. Bacteriol. 183, 1621\u20131630 (2001).","journal-title":"J. Bacteriol."},{"key":"BFncomms14665_CR35","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1111\/j.1365-2958.2007.05586.x","volume":"63","author":"KW Mouw","year":"2007","unstructured":"Mouw, K. W. & Rice, P. A. Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb. Mol. Microbiol. 63, 1319\u20131330 (2007).","journal-title":"Mol. Microbiol."},{"key":"BFncomms14665_CR36","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1186\/1471-2180-8-167","volume":"8","author":"M Sluijter","year":"2008","unstructured":"Sluijter, M., Hoogenboezem, T., Hartwig, N. G. & Vink, C. The Mycoplasma pneumoniae MPN229 gene encodes a protein that selectively binds single-stranded DNA and stimulates recombinase A-mediated DNA strand exchange. BMC Microbiol. 8, 167 (2008).","journal-title":"BMC Microbiol."},{"key":"BFncomms14665_CR37","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1002\/prot.21340","volume":"67","author":"D Das","year":"2007","unstructured":"Das, D. et al. Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae. Proteins 67, 776\u2013782 (2007).","journal-title":"Proteins"},{"key":"BFncomms14665_CR38","doi-asserted-by":"publisher","first-page":"4923","DOI":"10.1093\/nar\/gkv422","volume":"43","author":"S Torres-Puig","year":"2015","unstructured":"Torres-Puig, S., Broto, A., Querol, E., Pinol, J. & Pich, O. Q. A novel sigma factor reveals a unique regulon controlling cell-specific recombination in Mycoplasma genitalium. Nucleic Acids Res. 43, 4923\u20134936 (2015).","journal-title":"Nucleic Acids Res."},{"key":"BFncomms14665_CR39","doi-asserted-by":"publisher","first-page":"1268","DOI":"10.1126\/science.1176951","volume":"326","author":"M Guell","year":"2009","unstructured":"Guell, M. et al. Transcriptome complexity in a genome-reduced bacterium. Science 326, 1268\u20131271 (2009).","journal-title":"Science"},{"key":"BFncomms14665_CR40","doi-asserted-by":"publisher","first-page":"1263","DOI":"10.1126\/science.1177263","volume":"326","author":"E Yus","year":"2009","unstructured":"Yus, E. et al. Impact of genome reduction on bacterial metabolism and its regulation. Science 326, 1263\u20131268 (2009).","journal-title":"Science"},{"key":"BFncomms14665_CR41","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1038\/msb.2011.38","volume":"7","author":"T Maier","year":"2011","unstructured":"Maier, T. et al. Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol. Syst. Biol. 7, 511 (2011).","journal-title":"Mol. Syst. Biol."},{"key":"BFncomms14665_CR42","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/msb.2013.6","volume":"9","author":"JA Wodke","year":"2013","unstructured":"Wodke, J. A. et al. Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. Mol. Syst. Biol. 9, 653 (2013).","journal-title":"Mol. Syst. Biol."},{"key":"BFncomms14665_CR43","doi-asserted-by":"publisher","first-page":"e1003191","DOI":"10.1371\/journal.pgen.1003191","volume":"9","author":"M Lluch-Senar","year":"2013","unstructured":"Lluch-Senar, M. et al. Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet. 9, e1003191 (2013).","journal-title":"PLoS Genet."},{"key":"BFncomms14665_CR44","doi-asserted-by":"publisher","first-page":"780","DOI":"10.15252\/msb.20145558","volume":"11","author":"M Lluch-Senar","year":"2015","unstructured":"Lluch-Senar, M. et al. Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol. Syst. Biol. 11, 780 (2015).","journal-title":"Mol. Syst. Biol."},{"key":"BFncomms14665_CR45","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1038\/nmeth.2148","volume":"9","author":"M Imakaev","year":"2012","unstructured":"Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Method 9, 999\u20131003 (2012).","journal-title":"Nat. Method"},{"key":"BFncomms14665_CR46","doi-asserted-by":"publisher","first-page":"628","DOI":"10.1093\/nar\/24.4.628","volume":"24","author":"H Hilbert","year":"1996","unstructured":"Hilbert, H., Himmelreich, R., Plagens, H. & Herrmann, R. Sequence analysis of 56 kb from the genome of the bacterium Mycoplasma pneumoniae comprising the dnaA region, the atp operon and a cluster of ribosomal protein genes. Nucleic Acids Res 24, 628\u2013639 (1996).","journal-title":"Nucleic Acids Res"},{"key":"BFncomms14665_CR47","doi-asserted-by":"publisher","first-page":"3465","DOI":"10.1093\/nar\/gkv221","volume":"43","author":"M Trussart","year":"2015","unstructured":"Trussart, M. et al. Assessing the limits of restraint-based 3D modeling of genomes and genomic domains. Nucleic Acids Res. 43, 3465\u20133477 (2015).","journal-title":"Nucleic Acids Res."},{"key":"BFncomms14665_CR48","doi-asserted-by":"crossref","unstructured":"Serra, F., Ba\u00f9, D., Filion, G. & Marti-Renom, M. A. Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling. Preprint at:. bioRxiv (2016).","DOI":"10.1101\/036764"},{"key":"BFncomms14665_CR49","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1093\/jmicro\/dfr044","volume":"60","author":"JE Heuser","year":"2011","unstructured":"Heuser, J. E. The origins and evolution of freeze-etch electron microscopy. J. Electron Microsc. (Tokyo) 60, S3\u2013S29 (2011).","journal-title":"J. Electron Microsc. (Tokyo)"},{"key":"BFncomms14665_CR50","doi-asserted-by":"publisher","first-page":"4957","DOI":"10.1529\/biophysj.107.120345","volume":"94","author":"MG Gustafsson","year":"2008","unstructured":"Gustafsson, M. G. et al. Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys. J. 94, 4957\u20134970 (2008).","journal-title":"Biophys. J."},{"key":"BFncomms14665_CR51","doi-asserted-by":"publisher","first-page":"1082","DOI":"10.1128\/JB.185.3.1082-1091.2003","volume":"185","author":"S Seto","year":"2003","unstructured":"Seto, S. & Miyata, M. Attachment organelle formation represented by localization of cytadherence proteins and formation of the electron-dense core in wild-type and mutant strains of Mycoplasma pneumoniae. J. Bacteriol. 185, 1082\u20131091 (2003).","journal-title":"J. Bacteriol."},{"key":"BFncomms14665_CR52","doi-asserted-by":"publisher","first-page":"14136","DOI":"10.1073\/pnas.0804982105","volume":"105","author":"IA Berlatzky","year":"2008","unstructured":"Berlatzky, I. A., Rouvinski, A. & Ben-Yehuda, S. Spatial organization of a replicating bacterial chromosome. Proc. Natl Acad Sci. USA 105, 14136\u201314140 (2008).","journal-title":"Proc. Natl Acad Sci. USA"},{"key":"BFncomms14665_CR53","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1016\/j.cels.2016.04.015","volume":"2","author":"I Junier","year":"2016","unstructured":"Junier, I., Unal, E. B., Yus, E., Llor\u00e9ns-Rico, V. & Serrano, L. Insights into the mechanisms of basal coordination of transcription using a genome-reduced bacterium. Cell Syst. 2, 391\u2013401 (2016).","journal-title":"Cell Syst."},{"key":"BFncomms14665_CR54","doi-asserted-by":"publisher","first-page":"4474","DOI":"10.1073\/pnas.73.12.4474","volume":"73","author":"M Gellert","year":"1976","unstructured":"Gellert, M., O'Dea, M. H., Itoh, T. & Tomizawa, J. Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase. Proc. Natl Acad. Sci. USA 73, 4474\u20134478 (1976).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFncomms14665_CR55","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1159\/000094058","volume":"11","author":"MF Balish","year":"2006","unstructured":"Balish, M. F. & Krause, D. C. Mycoplasmas: a distinct cytoskeleton for wall-less bacteria. J. Mol. Microbiol. Biotechnol. 11, 244\u2013255 (2006).","journal-title":"J. Mol. Microbiol. Biotechnol."},{"key":"BFncomms14665_CR56","doi-asserted-by":"publisher","first-page":"16478","DOI":"10.1073\/pnas.0608051103","volume":"103","author":"BM Hasselbring","year":"2006","unstructured":"Hasselbring, B. M., Jordan, J. L., Krause, R. W. & Krause, D. C. Terminal organelle development in the cell wall-less bacterium Mycoplasma pneumoniae. Proc. Natl Acad. Sci. USA 103, 16478\u201316483 (2006).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFncomms14665_CR57","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1128\/jb.112.3.1375-1379.1972","volume":"112","author":"DC Quinlan","year":"1972","unstructured":"Quinlan, D. C. & Maniloff, J. Membrane association of the deoxyribonucleic acid growing-point region in Mycoplasma gallisepticum. J. Bacteriol. 112, 1375\u20131379 (1972).","journal-title":"J. Bacteriol."},{"key":"BFncomms14665_CR58","doi-asserted-by":"publisher","first-page":"1326","DOI":"10.1128\/JB.185.4.1326-1337.2003","volume":"185","author":"PS Lee","year":"2003","unstructured":"Lee, P. S., Lin, D. C., Moriya, S. & Grossman, A. D. Effects of the chromosome partitioning protein Spo0J (ParB) on oriC positioning and replication initiation in Bacillus subtilis. J. Bacteriol. 185, 1326\u20131337 (2003).","journal-title":"J. Bacteriol."},{"key":"BFncomms14665_CR59","doi-asserted-by":"publisher","first-page":"15435","DOI":"10.1073\/pnas.0807448105","volume":"105","author":"E Toro","year":"2008","unstructured":"Toro, E., Hong, S. H., McAdams, H. H. & Shapiro, L. Caulobacter requires a dedicated mechanism to initiate chromosome segregation. Proc. Natl Acad. Sci. USA 105, 15435\u201315440 (2008).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFncomms14665_CR60","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1111\/j.1365-2958.2006.05346.x","volume":"62","author":"HJ Nielsen","year":"2006","unstructured":"Nielsen, H. J., Ottesen, J. R., Youngren, B., Austin, S. J. & Hansen, F. G. The Escherichia coli chromosome is organized with the left and right chromosome arms in separate cell halves. Mol. Microbiol. 62, 331\u2013338 (2006).","journal-title":"Mol. Microbiol."},{"key":"BFncomms14665_CR61","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.1111\/j.1365-2958.2010.07394.x","volume":"78","author":"BM Booker","year":"2010","unstructured":"Booker, B. M., Deng, S. & Higgins, N. P. DNA topology of highly transcribed operons in Salmonella enterica serovar Typhimurium. Mol. Microbiol. 78, 1348\u20131364 (2010).","journal-title":"Mol. Microbiol."},{"key":"BFncomms14665_CR62","doi-asserted-by":"publisher","first-page":"950","DOI":"10.1016\/j.cell.2014.03.025","volume":"157","author":"L Giorgetti","year":"2014","unstructured":"Giorgetti, L. et al. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell 157, 950\u2013963 (2014).","journal-title":"Cell"},{"key":"BFncomms14665_CR63","doi-asserted-by":"publisher","first-page":"aad6253","DOI":"10.1126\/science.aad6253","volume":"351","author":"CA Hutchison 3rd","year":"2016","unstructured":"Hutchison, C. A. 3rd et al. Design and synthesis of a minimal bacterial genome. Science 351, aad6253 (2016).","journal-title":"Science"},{"key":"BFncomms14665_CR64","doi-asserted-by":"publisher","first-page":"e01377","DOI":"10.1128\/mBio.01377-14","volume":"5","author":"C Raeside","year":"2014","unstructured":"Raeside, C. et al. Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. MBio 5, e01377\u201314 (2014).","journal-title":"MBio"},{"key":"BFncomms14665_CR65","doi-asserted-by":"publisher","first-page":"R913","DOI":"10.1016\/j.cub.2007.09.005","volume":"17","author":"MC Noom","year":"2007","unstructured":"Noom, M. C., Navarre, W. W., Oshima, T., Wuite, G. J. & Dame, R. T. H-NS promotes looped domain formation in the bacterial chromosome. Curr. Biol. 17, R913\u2013R914 (2007).","journal-title":"Curr. Biol."},{"key":"BFncomms14665_CR66","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"SB Needleman","year":"1970","unstructured":"Needleman, S. B. & Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443\u2013453 (1970).","journal-title":"J. Mol. Biol."},{"key":"BFncomms14665_CR67","doi-asserted-by":"publisher","first-page":"4382","DOI":"10.1128\/JB.186.13.4382-4386.2004","volume":"186","author":"M Miyata","year":"2004","unstructured":"Miyata, M. & Petersen, J. D. Spike structure at the interface between gliding mycoplasma mobile cells and glass surfaces visualized by rapid-freeze-and-fracture electron microscopy. J. Bacteriol. 186, 4382\u20134386 (2004).","journal-title":"J. Bacteriol."},{"key":"BFncomms14665_CR68","doi-asserted-by":"publisher","first-page":"e1001389","DOI":"10.1371\/journal.pbio.1001389","volume":"10","author":"MP Strauss","year":"2012","unstructured":"Strauss, M. P. et al. 3D-SIM super resolution microscopy reveals a bead-like arrangement for FtsZ and the division machinery: implications for triggering cytokinesis. PLoS Biol. 10, e1001389 (2012).","journal-title":"PLoS Biol."},{"key":"BFncomms14665_CR69","doi-asserted-by":"publisher","first-page":"797","DOI":"10.1093\/bioinformatics\/btu720","volume":"31","author":"T Pengo","year":"2015","unstructured":"Pengo, T., Holden, S. J. & Manley, S. PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy. Bioinformatics 31, 797\u2013798 (2015).","journal-title":"Bioinformatics"},{"key":"BFncomms14665_CR70","doi-asserted-by":"publisher","first-page":"2389","DOI":"10.1093\/bioinformatics\/btu202","volume":"30","author":"M Ovesny","year":"2014","unstructured":"Ovesny, M., Krizek, P., Borkovec, J., Svindrych, Z. & Hagen, G. M. ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. Bioinformatics 30, 2389\u20132390 (2014).","journal-title":"Bioinformatics"},{"key":"BFncomms14665_CR71","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.1016\/j.cell.2014.11.021","volume":"159","author":"SS Rao","year":"2014","unstructured":"Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665\u20131680 (2014).","journal-title":"Cell"}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/ncomms14665.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/ncomms14665","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/ncomms14665.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,22]],"date-time":"2022-12-22T18:59:58Z","timestamp":1671735598000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/ncomms14665"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3,8]]},"references-count":71,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,4,28]]}},"alternative-id":["BFncomms14665"],"URL":"https:\/\/doi.org\/10.1038\/ncomms14665","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.727380455.793567777","asserted-by":"object"},{"id-type":"doi","id":"10.3410\/f.727380455.793531552","asserted-by":"object"}]},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3,8]]},"assertion":[{"value":"4 November 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 January 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 March 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"14665"}}