The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

Umbarger, Mark A.; Toro, Esteban; Wright, Matthew A.; Porreca, Gregory J.; Baù, Davide; Hong, Sun-Hae; Fero, M.J.; Zhu, Lihua Julie; Martí‐Renom, Marc A.; McAdams, Harley H.; Shapiro, Lucy; Dekker, Job; Church, George M.

doi:10.1016/j.molcel.2011.09.010

Cited by 259 publications

(303 citation statements)

References 64 publications

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“…The next steps differ from method to method, and ultimately conclude with the sequencing and mapping of DNA fragments to their original positions on the chromosomes [10][11][12][13] . Specifically, such whole-genome contact maps have recently been published, including those of Homo sapiens (HS) 11 , Saccharomyces cerevisiae (SC) 12 , Schizosaccharomyces pombe (SP) 13 , Caulobacter crescentus 14 , Drosophila melanogaster 15 , Mus musculus (MM) 16 , Arabidopsis thaliana (AT) 17 and Plasmodium falciparum 18 .…”

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confidence: 99%

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

2014

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It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of threedimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.

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confidence: 99%

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

2014

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“…The unbiased nature of the 5C readout and the greater coverage area also enables tandem studies of complex relationship between 3D organization, epigenome, and transcriptome. 5C has been used to study human mitotic chromosomes and the 3D architecture of the Caulobacter crescentus genome (Naumova et al 2013;Umbarger et al 2011). It has also been used to study the organization of Hox clusters in human and mouse systems (Rousseau et al 2014a;Wang et al 2011).…”

Section: The Birth and The Maturation Of 3cmentioning

confidence: 99%

Chromosome conformation capture technologies and their impact in understanding genome function

2016

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It has been more than a decade since the first chromosome conformation capture (3C) assay was described. The assay was originally devised to measure the frequency with which two genomic loci interact within the three-dimensional (3D) nuclear space. Over time, this method has evolved both qualitatively and quantitatively, from detection of pairwise interaction of two unique loci to generating maps for the global chromatin interactome. Combined with the analysis of the epigenetic chromatin context, these advances led to the unmasking of general genome folding principles. The evolution of 3C-based methods has been supported first by the revolution in ChIP and then by sequencingbased approaches, methods that were primarily tools to study the unidimensional genome. The gradual improvement of 3C-based methods illustrates how the field adapted to the need to gradually address more subtle questions, beginning with enquiries of reductionist nature to reach more holistic perspectives, as the technology advanced, in a process that is greatly improving our knowledge on genome behavior and regulation. Here, we describe the evolution of 3C and other 3C-based methods for the analysis of chromatin interactions, along with a brief summary of their contribution in uncovering the significance of the threedimensional world within the nucleus. We also discuss their inherent limitations and caveats in order to provide a critical view of the power and the limits of this technology.

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“…Umbarger and colleagues used a high throughput chromosome conformation capture assay (called, 5C) to quantify thousands of interloci interaction frequencies (Umbarger et al 2011). These frequencies were then used to infer the average three-dimensional distances between each locus.…”

Section: Organization Of the Bacterial Chromosomementioning

confidence: 99%

Spatio-Temporal Organization of Replication in Bacteria and Eukaryotes (Nucleoids and Nuclei)

Jackson

Wang²,

Rudner³

2012

Cold Spring Harbor Perspectives in Biology

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Here we discuss the spatio-temporal organization of replication in eubacteria and eukaryotes. Although there are significant differences in how replication is organized in cells that contain nuclei from those that do not, you will see that organization of replication in all organisms is principally dictated by the structured arrangement of the chromosome. We will begin with how replication is organized in eubacteria with particular emphasis on three well studied model organisms. We will then discuss spatial and temporal organization of replication in eukaryotes highlighting the similarities and differences between these two domains of life.

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The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

Cited by 259 publications

References 64 publications

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

Chromosome conformation capture technologies and their impact in understanding genome function

Spatio-Temporal Organization of Replication in Bacteria and Eukaryotes (Nucleoids and Nuclei)

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