Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

Cagliero, Cédric; Grand, Ralph S.; Jones, MaryPat; Jin, Ding Jun; O’Sullivan, Justin M.

doi:10.1093/nar/gkt325

Cited by 121 publications

(150 citation statements)

References 76 publications

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“…Since the majority of the DNA in 3C libraries does not contain any 3C ligation junctions, this approach yielded a small number of usable reads that was nonetheless sufficient to identify contact networks in the small S. cerevisiae genome. GCC has since been used to map the spatial organization of the Escherichia coli nucleoid (119). Another group developed a 4C-inspired approach, which involved the ligation of biotinylated adaptors to mark ligation junctions (120).…”

Section: Inferring Genome Organizationmentioning

confidence: 99%

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

Fraser

Williamson

Bickmore

et al. 2015

Microbiol Mol Biol Rev

203

174

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SUMMARY In humans, nearly two meters of genomic material must be folded to fit inside each micrometer-scale cell nucleus while remaining accessible for gene transcription, DNA replication, and DNA repair. This fact highlights the need for mechanisms governing genome organization during any activity and to maintain the physical organization of chromosomes at all times. Insight into the functions and three-dimensional structures of genomes comes mostly from the application of visual techniques such as fluorescence in situ hybridization (FISH) and molecular approaches including chromosome conformation capture (3C) technologies. Recent developments in both types of approaches now offer the possibility of exploring the folded state of an entire genome and maybe even the identification of how complex molecular machines govern its shape. In this review, we present key methodologies used to study genome organization and discuss what they reveal about chromosome conformation as it relates to transcription regulation across genomic scales in mammals.

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Section: Inferring Genome Organizationmentioning

confidence: 99%

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

Fraser

Williamson

Bickmore

et al. 2015

Microbiol Mol Biol Rev

203

174

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“…Interactions between bacterial rRNA operons have not been detected by chromosome capture approaches that use cross-linking and next-generation sequencing to identify interactions between DNA sequences in growing cells (e.g., Cagliero et al 2013;Dekker et al 2013;Le et al 2013;M Laub, pers. comm.…”

Section: Other Modelsmentioning

confidence: 99%

Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus

et al. 2016

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The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome organization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180°on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity. Colocalization of the rRNA operons required the rrn P1 promoter region but not the rrn P2 promoter or the rRNA structural genes and occurred with and without active transcription. Non-rRNA operon pairs did not colocalize, and the magnitude of their physical separation generally correlated with that of their genetic separation. Our results show that E. coli bacterial chromosome folding in three dimensions is not dictated entirely by genetic position but rather includes functionally related, genetically distant loci that come into close proximity, with rRNA operons forming a structure reminiscent of the eukaryotic nucleolus.

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“…These nucleoids are highly complex, and the underlying organizational mechanisms appear to be remarkably similar to that of eukaryotic cells (3,9). The nucleoid occupies the central part of the bacterial cell (8), and its shape is dependent on a variety of factors, such as environmental conditions or genetic mutations (7,(10)(11)(12)(13). For example, significant nucleoid compaction occurs after exposure of Escherichia coli to UV light, due to a global reorganization in response to DNA damage and the activation of the SOS response (12,13).…”

mentioning

confidence: 99%

“…The SeqA protein can also be claimed to belong to the group of NAPs due to its ability to organize newly replicated DNA (10,(38)(39)(40)(41)(42). Additionally, it has been implicated as an important factor in the correct folding of the chromosome (43)(44)(45).…”

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confidence: 99%

Lack of the H-NS Protein Results in Extended and Aberrantly Positioned DNA during Chromosome Replication and Segregation in Escherichia coli

2016

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The architectural protein H-NS binds nonspecifically to hundreds of sites throughout the chromosome and can multimerize to stiffen segments of DNA as well as to form DNA-protein-DNA bridges. H-NS has been suggested to contribute to the orderly folding of the Escherichia coli chromosome in the highly compacted nucleoid. In this study, we investigated the positioning and dynamics of the origins, the replisomes, and the SeqA structures trailing the replication forks in cells lacking the H-NS protein.In H-NS mutant cells, foci of SeqA, replisomes, and origins were irregularly positioned in the cell. Further analysis showed that the average distance between the SeqA structures and the replisome was increased by ϳ100 nm compared to that in wild-type cells, whereas the colocalization of SeqA-bound sister DNA behind replication forks was not affected. This result may suggest that H-NS contributes to the folding of DNA along adjacent segments. H-NS mutant cells were found to be incapable of adopting the distinct and condensed nucleoid structures characteristic of E. coli cells growing rapidly in rich medium. It appears as if H-NS mutant cells adopt a "slow-growth" type of chromosome organization under nutrient-rich conditions, which leads to a decreased cellular DNA content. IMPORTANCE It is not fully understood how and to what extent nucleoid-associated proteins contribute to chromosome folding and organization during replication and segregation in Escherichia coli. In this work, we find in vivo indications that cells lacking the nucleoid-associated protein H-NS have a lower degree of DNA condensation than wild-type cells. Our work suggests that H-NS is in-volved in condensing the DNA along adjacent segments on the chromosome and is not likely to tether newly replicated strands of sister DNA. We also find indications that H-NS is required for rapid growth with high DNA content and for the formation of a highly condensed nucleoid structure under such conditions. A cross all domains of life, it is crucial that genomes are structurally organized in a way that compacts DNA to fit inside the confined space of a cell and at the same time allows for interaction with key proteins performing replication, transcription, recombination, and repair (1-7). Unlike eukaryotic cells, bacterial cells do not possess an envelope-enclosed organelle for storage and handling of genomic DNA. The DNA is instead organized into compact bodies called nucleoids (3)(4)(5)8). These nucleoids are highly complex, and the underlying organizational mechanisms appear to be remarkably similar to that of eukaryotic cells (3, 9). The nucleoid occupies the central part of the bacterial cell (8), and its shape is dependent on a variety of factors, such as environmental conditions or genetic mutations (7, 10-13). For example, significant nucleoid compaction occurs after exposure of Escherichia coli to UV light, due to a global reorganization in response to DNA damage and the activation of the SOS response (12, 13).Certain types of proteins, called nucle...

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Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

Cited by 121 publications

References 76 publications

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

Colocalization of distant chromosomal loci in space in E. coli: a bacterial nucleolus

Lack of the H-NS Protein Results in Extended and Aberrantly Positioned DNA during Chromosome Replication and Segregation in Escherichia coli

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