Combined Study of Gene Expression and Chromosome Three-Dimensional Structure in Escherichia coli During Growth Process

Badrinarayanan A, Le TB, Laub MT (2015) Bacterial chromosome organization and segregation. Annu Rev Cell Dev Biol 31:171–199. https://doi.org/10.1146/annurev-cellbio-100814-125211

Article  CAS  PubMed  PubMed Central  Google Scholar 

Krogh TJ, Møller-Jensen J, Kaleta C (2018) Impact of chromosomal architecture on the function and evolution of bacterial genomes. Front Microbiol 9:2019. https://doi.org/10.3389/fmicb.2018.02019

Article  PubMed  PubMed Central  Google Scholar 

Le TB, Imakaev MV, Mirny LA, Laub MT (2013) High-resolution mapping of the spatial organization of a bacterial chromosome. Science 342(6159):731–734. https://doi.org/10.1126/science.1242059

Article  CAS  PubMed  PubMed Central  Google Scholar 

Trussart M, Yus E, Martinez S, Baù D, Tahara YO, Pengo T, Widjaja M, Kretschmer S, Swoger J, Djordjevic S, Turnbull L, Whitchurch C, Miyata M, Marti-Renom MA, Lluch-Senar M, Serrano L (2017) Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae. Nat Commun 8:14665. https://doi.org/10.1038/ncomms14665

Article  PubMed  PubMed Central  Google Scholar 

Marbouty M, Le Gall A, Cattoni DI, Cournac A, Koh A, Fiche JB, Mozziconacci J, Murray H, Koszul R, Nollmann M (2015) Condensin- and replication-mediated bacterial chromosome folding and origin condensation revealed by Hi-C and super-resolution imaging. Mol Cell 59(4):588–602. https://doi.org/10.1016/j.molcel.2015.07.020

Article  CAS  PubMed  Google Scholar 

Wang X, Le TB, Lajoie BR, Dekker J, Laub MT, Rudner DZ (2015) Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis. Genes Dev 29(15):1661–1675. https://doi.org/10.1101/gad.265876.115

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cagliero C, Grand RS, Jones MB, Jin DJ, O’Sullivan JM (2013) Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription. Nucleic Acids Res 41(12):6058–6071. https://doi.org/10.1093/nar/gkt325

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lioy VS, Cournac A, Marbouty M, Duigou S, Mozziconacci J, Espéli O, Boccard F, Koszul R (2018) Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins. Cell 172(4):771-783.e718. https://doi.org/10.1016/j.cell.2017.12.027

Article  CAS  PubMed  Google Scholar 

Browning DF, Grainger DC, Busby SJ (2010) Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Curr Opin Microbiol 13(6):773–780. https://doi.org/10.1016/j.mib.2010.09.013

Article  CAS  PubMed  Google Scholar 

Dame RT, Rashid FM, Grainger DC (2020) Chromosome organization in bacteria: mechanistic insights into genome structure and function. Nat Rev Genet 21(4):227–242. https://doi.org/10.1038/s41576-019-0185-4

Article  CAS  PubMed  Google Scholar 

Guo F, Adhya S (2007) Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling. Proc Natl Acad Sci USA 104(11):4309–4314. https://doi.org/10.1073/pnas.0611686104

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nolivos S, Sherratt D (2014) The bacterial chromosome: architecture and action of bacterial SMC and SMC-like complexes. FEMS Microbiol Rev 38(3):380–392. https://doi.org/10.1111/1574-6976.12045

Article  CAS  PubMed  Google Scholar 

Espéli O, Borne R, Dupaigne P, Thiel A, Gigant E, Mercier R, Boccard F (2012) A MatP-divisome interaction coordinates chromosome segregation with cell division in E. coli. Embo J 31(14):3198–3211. https://doi.org/10.1038/emboj.2012.128

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dillon SC, Dorman CJ (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8(3):185–195. https://doi.org/10.1038/nrmicro2261

Article  CAS  PubMed  Google Scholar 

Le TB, Laub MT (2016) Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries. Embo J 35(14):1582–1595. https://doi.org/10.15252/embj.201593561

Article  CAS  PubMed  PubMed Central  Google Scholar 

Valens M, Penaud S, Rossignol M, Cornet F, Boccard F (2004) Macrodomain organization of the Escherichia coli chromosome. Embo J 23(21):4330–4341. https://doi.org/10.1038/sj.emboj.7600434

Article  CAS  PubMed  PubMed Central  Google Scholar 

Durfee T, Hansen AM, Zhi H, Blattner FR, Jin DJ (2008) Transcription profiling of the stringent response in Escherichia coli. J Bacteriol 190(3):1084–1096. https://doi.org/10.1128/jb.01092-07

Article  CAS  PubMed  Google Scholar 

Traxler MF, Summers SM, Nguyen HT, Zacharia VM, Hightower GA, Smith JT, Conway T (2008) The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli. Mol Microbiol 68(5):1128–1148. https://doi.org/10.1111/j.1365-2958.2008.06229.x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jin DJ, Cabrera JE (2006) Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli. J Struct Biol 156(2):284–291. https://doi.org/10.1016/j.jsb.2006.07.005

Article  CAS  PubMed  Google Scholar 

Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079. https://doi.org/10.1093/bioinformatics/btp352

Article  CAS  PubMed  PubMed Central  Google Scholar 

Anders S, Pyl PT, Huber W (2015) HTSeq–a python framework to work with high-throughput sequencing data. Bioinformatics 31(2):166–169. https://doi.org/10.1093/bioinformatics/btu638

Article  CAS  PubMed  Google Scholar 

Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8(8):1494–1512. https://doi.org/10.1038/nprot.2013.084

Article  CAS  PubMed  Google Scholar 

Yu G, Wang LG, Han Y, He QY (2012) ClusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16(5):284–287. https://doi.org/10.1089/omi.2011.0118

Article  CAS  PubMed  PubMed Central  Google Scholar 

Karp PD, Ong WK, Paley S, Billington R, Caspi R, Fulcher C, Kothari A, Krummenacker M, Latendresse M, Midford PE, Subhraveti P, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Collado-Vides J, Keseler IM, Paulsen I (2018) The EcoCyc database. EcoSal Plus. https://doi.org/10.1128/ecosalplus.ESP-0006-2018

Article  PubMed  PubMed Central  Google Scholar 

Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA (2012) Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9(10):999–1003. https://doi.org/10.1038/nmeth.2148

Article  CAS  PubMed  PubMed Central  Google Scholar 

Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E (2015) HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16:259. https://doi.org/10.1186/s13059-015-0831-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yaffe E, Tanay A (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43(11):1059–1065. https://doi.org/10.1038/ng.947

Article  CAS  PubMed  Google Scholar 

Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J (2012) Normalization of a chromosomal contact map. BMC Genomics 13:436. https://doi.org/10.1186/1471-2164-13-436

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485(7398):376–380. https://doi.org/10.1038/nature11082

Article  CAS  PubMed  PubMed Central  Google Scholar 

留言 (0)

沒有登入
gif