M. Touchon, L. M. Bobay, and E. P. Rocha, The chromosomal accommodation and domestication of mobile genetic elements, Curr. Opin. Microbiol, vol.22, pp.22-29, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01122287

J. G. Lawrence and H. Ochman, Molecular archaeology of the Escherichia coli genome, Proc. Natl. Acad. Sci. U.S.A, vol.95, pp.9413-9417, 1998.

P. H. Oliveira, M. Touchon, J. Cury, and E. P. Rocha, The chromosomal organization of horizontal gene transfer in bacteria, Nat. Commun, vol.8, p.841, 2017.

H. Ochman, J. G. Lawrence, and E. A. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, pp.299-304, 2000.

M. J. Lercher and C. Pál, Integration of horizontally transferred genes into regulatory interaction networks takes many million years, Mol. Biol. Evol, vol.25, pp.559-567, 2008.

C. Park and J. Zhang, High expression hampers horizontal gene transfer, Genome Biol. Evol, vol.4, pp.523-532, 2012.

S. Lucchini, G. Rowley, M. D. Goldberg, D. Hurd, M. Harrison et al., H-NS mediates the silencing of laterally acquired genes in bacteria, PLoS Pathog, vol.2, p.81, 2006.

W. W. Navarre, M. Mcclelland, S. J. Libby, and F. C. Fang, Silencing of xenogeneic DNA by H-NS facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA, Gene. Dev, vol.21, pp.1456-1471, 2007.

C. Kahramanoglou, A. S. Seshasayee, A. I. Prieto, D. Ibberson, S. Schmidt et al., Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli, Nucleic Acids Res, vol.39, pp.2073-2091, 2011.

C. J. Dorman, H-NS, the genome sentinel, Nat. Rev. Microbiol, vol.5, pp.157-161, 2007.

K. Singh, J. N. Milstein, and W. W. Navarre, Xenogeneic silencing and its impact on bacterial genomes, Annu. Rev. Microbiol, vol.70, pp.199-213, 2016.

S. Kimura, T. P. Hubbard, B. M. Davis, and M. K. Waldor, The nucleoid binding protein H-NS biases genome-wide transposon insertion landscapes, mBio, vol.7, pp.1-6, 2016.

R. Sorek, Y. Zhu, C. J. Creevey, M. P. Francino, P. Bork et al., Genome-wide experimental determination of barriers to horizontal gene transfer, Science, vol.318, pp.1449-1452, 2007.

R. T. Dame, M. C. Noom, and G. J. Wuite, Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation, Nature, vol.444, pp.387-390, 2006.

Y. Liu, H. Chen, L. J. Kenney, and J. Yan, A divalent switch drives H-NS/DNA-binding conformations between stiffening and bridging modes, Gene. Dev, vol.24, pp.339-344, 2010.

E. Brambilla and B. Sclavi, Gene regulation by H-NS as a function of growth conditions depends on chromosomal position in Escherichia coli, vol.3, pp.605-614, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01230479

R. Srinivasan, V. F. Scolari, M. Cosentino-lagomarsino, and A. S. Seshasayee, The genome-scale interplay amongst xenogene silencing, stress response and chromosome architecture in Escherichia coli, Nucleic Acids Res, vol.43, pp.295-308, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01278030

S. S. Singh, N. Singh, R. P. Bonocora, D. M. Fitzgerald, J. T. Wade et al., Widespread suppression of intragenic transcription initiation by H-NS, Gene. Dev, vol.28, pp.214-219, 2014.

J. A. Bryant, L. E. Sellars, S. J. Busby, and D. J. Lee, Chromosome position effects on gene expression in Escherichia coli K-12, Nucleic Acids Res, vol.42, pp.11383-11392, 2014.

C. J. Dorman, Nucleoid-associated proteins and bacterial physiology, Adv. Appl. Microbiol, vol.67, pp.47-64, 2009.

O. Espéli and F. Boccard, Organization of the Escherichia coli chromosome into macrodomains and its possible functional implications, J Struct. Biol, vol.156, pp.304-310, 2006.

E. Esnault, M. Valens, O. Espéli, and F. Boccard, Chromosome structuring limits genome plasticity in Escherichia coli, PLoS Genet, vol.3, p.226, 2007.

M. Zarei, B. Sclavi, and M. Cosentino-lagomarsino, Gene silencing and large-scale domain structure of the E. coli genome, Mol. Biosyst, vol.9, pp.758-767, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01528422

R. T. Dame, O. J. Kalmykowa, and D. C. Grainger, Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria, PLoS Genet, vol.7, p.1002123, 2011.

C. J. Dorman, Genome architecture and global gene regulation in bacteria: making progress towards a unified model?, Nat. Rev. Microbiol, vol.11, pp.349-355, 2013.

M. Touchon, C. Hoede, O. Tenaillon, V. Barbe, S. Baeriswyl et al., Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths, PLoS Genet, vol.5, p.1000344, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00390293

I. Junier, O. Martin, and F. Képès, Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization, PLoS Comput. Biol, vol.6, p.1000678, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00484355

A. Dilthey and M. J. Lercher, Horizontally transferred genes cluster spatially and metabolically, Biol. Direct, vol.10, p.72, 2015.

L. M. Bobay and H. Ochman, The evolution of bacterial genome architecture, Front. Genet, vol.8, p.72, 2017.

P. P. Dennis, M. Ehrenberg, and H. Bremer, Control of rRNA synthesis in Escherichia coli: a systems biology approach. Microbiol, Mol. Biol. R.: MMBR, vol.68, pp.639-668, 2004.

V. F. Scolari, M. Zarei, M. Osella, and M. Cosentino-lagomarsino, NuST: analysis of the interplay between nucleoid organization and gene expression, Bioinformatics, vol.28, pp.1643-1644, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01528444

S. Cooper and C. E. Helmstetter, Chromosome replication and the division cycle of Escherichia coli B/r, J. Mol. Biol, vol.31, pp.519-540, 1968.

A. Travers and G. Muskhelishvili, DNA supercoiling -a global transcriptional regulator for enterobacterial growth?, Nat. Rev. Microbiol, vol.3, pp.157-169, 2005.

B. Lang, N. Blot, E. Bouffartigues, M. Buckle, M. Geertz et al., High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes, Nucleic Acids Res, vol.35, pp.6330-6337, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00215991

M. Berger, A. Farcas, M. Geertz, P. Zhelyazkova, K. Brix et al., Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU, EMBO Rep, vol.11, pp.59-64, 2010.

V. S. Lioy, A. Cournac, M. Marbouty, S. Duigou, J. Mozziconacci et al., Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins, Cell, vol.172, pp.771-783, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02180787

N. Blot, R. Mavathur, M. Geertz, A. Travers, and G. Muskhelishvili, Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome, EMBO Rep, vol.7, pp.710-715, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00529439

S. Garcia-vallve, E. Guzman, M. A. Montero, and A. Romeu, HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes, Nucleic Acids Res, vol.31, pp.187-189, 2003.

D. F. Browning, D. C. Grainger, and S. J. Busby, Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression, Curr. Opin. Microbiol, vol.13, pp.773-780, 2010.

D. C. Grainger, M. D. Goldberg, D. J. Lee, and S. J. Busby, Selective repression by Fis and H-NS at the Escherichia coli dps promoter, Mol. Microbiol, vol.68, pp.1366-1377, 2008.

B. Green, C. Bouchier, C. Fairhead, N. L. Craig, and B. P. Cormack, Insertion site preference of Mu, Tn5, and Tn7 transposons, Mobile DNA, vol.3, p.3, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-00675691

D. C. Grainger, D. Hurd, M. Harrison, J. Holdstock, and S. J. Busby, Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome, Proc. Natl. Acad. Sci. U.S.A, vol.102, pp.17693-17698, 2005.

A. Zaslaver, S. Kaplan, A. Bren, A. Jinich, A. Mayo et al., Invariant distribution of promoter activities in Escherichia coli, PLoS Comput. Biol, vol.5, p.1000545, 2009.

Q. Zhang, E. Brambilla, R. Li, H. Shi, M. Cosentino-lagomarsino et al., A decrease in transcription capacity limits growth rate upon translation inhibition, 2019.

Y. Taniguchi, P. J. Choi, G. W. Li, H. Chen, M. Babu et al., Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells, Science, vol.329, pp.533-538, 2010.

M. Touchon and E. P. Rocha, Causes of insertion sequences abundance in prokaryotic genomes, Mol. Biol. Evol, vol.24, pp.969-981, 2007.

C. J. Dorman, Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription, Biochem. Soc. Trans, vol.41, pp.542-547, 2013.

Z. A. Ouafa, S. Reverchon, T. Lautier, G. Muskhelishvili, and W. Nasser, The nucleoid-associated proteins H-NS and FIS modulate the DNA supercoiling response of the pel genes, the major virulence factors in the plant pathogen bacterium Dickeya dadantii, Nucleic Acids Res, vol.40, pp.4306-4319, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01997059

A. Lal, A. Dhar, A. Trostel, F. Kouzine, A. S. Seshasayee et al., Genome scale patterns of supercoiling in a bacterial chromosome, Nat. Commun, vol.7, p.11055, 2016.

K. S. Jeong, J. Ahn, and A. B. Khodursky, Spatial patterns of transcriptional activity in the chromosome of Escherichia coli, 2004.

, Genome Biol, vol.5, p.86

P. Sobetzko, A. Travers, and G. Muskhelishvili, Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle, Proc. Natl. Acad. Sci. U.S.A, vol.109, pp.42-50, 2012.

P. S. Swain, M. B. Elowitz, and E. D. Siggia, Intrinsic and extrinsic contributions to stochasticity in gene expression, Proc. Natl. Acad. Sci. U.S.A, vol.99, pp.12795-12800, 2002.

S. Klumpp and T. Hwa, Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination, Proc. Natl. Acad. Sci. U.S.A, vol.105, pp.18159-18164, 2008.

K. E. Shearwin, B. P. Callen, and J. B. Egan, Transcriptional interference-a crash course, Trends Genet.: TIG, vol.21, pp.339-345, 2005.

G. Z. Wang, M. J. Lercher, and L. D. Hurst, Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise, Genome Biol. Evol, vol.3, pp.320-331, 2011.