Chromosome Conformation Capture Carbon Copy Technology

Dostie, Josée; Ye, Zhan; Dekker, Job

doi:10.1002/0471142727.mb2114s80

Cited by 44 publications

(37 citation statements)

References 17 publications

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“…Classical molecular biology techniques could be used to test this interesting hypothesis. The development of new biochemical techniques to visualize the 3-D conformation of the eukaryotic genome, like capturing chromosome conformation (3C) (129,130,131) and circularized chromosome conformation capture (4C), carbon-copy chromosome conformation capture (5C), and high-throughput 3C (Hi-C), etc. (132,133,134), as well as the genetic approach based on site-specific recombination developed in reference 1, offers potential ways to validate the existence of such "long-range" interactions inside a bacterial genome.…”

Section: Discussionmentioning

confidence: 99%

DNA Looping in Prokaryotes: Experimental and Theoretical Approaches

Cournac

Plumbridge

2013

Journal of Bacteriology

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bTranscriptional regulation is at the heart of biological functions such as adaptation to a changing environment or to new carbon sources. One of the mechanisms which has been found to modulate transcription, either positively (activation) or negatively (repression), involves the formation of DNA loops. A DNA loop occurs when a protein or a complex of proteins simultaneously binds to two different sites on DNA with looping out of the intervening DNA. This simple mechanism is central to the regulation of several operons in the genome of the bacterium Escherichia coli, like the lac operon, one of the paradigms of genetic regulation. The aim of this review is to gather and discuss concepts and ideas from experimental biology and theoretical physics concerning DNA looping in genetic regulation. We first describe experimental techniques designed to show the formation of a DNA loop. We then present the benefits that can or could be derived from a mechanism involving DNA looping. Some of these are already experimentally proven, but others are theoretical predictions and merit experimental investigation. Then, we try to identify other genetic systems that could be regulated by a DNA looping mechanism in the genome of Escherichia coli. We found many operons that, according to our set of criteria, have a good chance to be regulated with a DNA loop. Finally, we discuss the proposition recently made by both biologists and physicists that this mechanism could also act at the genomic scale and play a crucial role in the spatial organization of genomes. Different levels of DNA organization exist within bacterial chromosomes. In the case of Escherichia coli, the genome has been shown to be organized, on the largest scale, in four individual macrodomains (Ter, Ori, Right, and Left) and two less-structured regions (1) that have a precise localization within the cell throughout the cell cycle and are associated with specific binding proteins (2). Large-scale DNA loops have been visualized by nucleoidspreading techniques and are thought to be stabilized by membrane and/or RNA components (3, 4). Then, at the scale of 10 kb, there are topological domains formed by supercoiled structures (5, 6) whose barriers are not placed stably at fixed sites but instead are randomly distributed (7). These intermediate loops can be stabilized with nucleoid-associated proteins like H-NS (8). Finally, there are smaller loops of a few hundred base pairs made by specific transcription factors that have a direct impact on transcription. Although loops of different sizes can have functional consequences for genomic organization and genetic regulation, it is the last category that we focus on in this review.A first hint that a transcription factor can bind simultaneously to two sites derived from the work of Kania and Müller-Hill in 1977 (9). However, the first experimental demonstration and clear proposal for the existence of a DNA loop affecting gene regulation was in 1984, by the team of Robert Schleif (10), working on the regulatory region of the ara...

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Section: Discussionmentioning

confidence: 99%

DNA Looping in Prokaryotes: Experimental and Theoretical Approaches

Cournac

Plumbridge

2013

Journal of Bacteriology

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“…Since 4C elucidates only interactions between a single restriction fragment and the rest of the genome, it cannot be used to predict the conformation of entire domains or chromosomes (90,91). The chromosome conformation capture carbon copy (5C) method, on the other hand, is suitable for this type of analysis, as it can detect up to millions of 3C ligation junctions between many restriction fragment pairs simultaneously (92)(93)(94)(95)(96)(97).…”

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

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204

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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“…Recent molecular studies based on three-dimensional genome-wide mapping of chromatin interactions (chromosome conformation capture, 3-5C) confirm the presence of CTs and interactions within and between them Dekker et al 2002;Lieberman-Aiden et al 2009;Dostie et al 2007;Zhao et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness

2012

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The spatial chromatin organisation and molecular interactions within and between chromatin domains and chromosome territories (CTs) are essential for fundamental processes such as replication, transcription and DNA repair via homologous recombination. To analyse the distribution and interaction of whole CTs, centromeres, (sub)telomeres and ~100-kb interstitial chromatin segments in endopolyploid nuclei, specific FISH probes from Arabidopsis thaliana were applied to 2-64C differentiated leaf nuclei. Whereas CTs occupy a distinct and defined volume of the nucleus and do not obviously intermingle with each other in 2-64C nuclei, ~100-kb sister chromatin segments within these CTs become more non-cohesive with increasing endopolyploidy. Centromeres, preferentially located at the nuclear periphery, may show ring- or half-moon like shapes in 2C and 4C nuclei. Sister centromeres tend to associate up to the 8C level. From 16C nuclei on, they become progressively separated. The higher the polyploidy level gets, the more separate chromatids are present. Due to sister chromatid separation in highly endopolyploid nuclei, the centromeric histone variant CENH3, the 180-bp centromeric repeats and pericentromeric heterochromatin form distinct subdomains at adjacent but not intermingling positions. The (sub)telomeres are frequently associated with each other and with the nucleolus and less often with centromeres. The extent of chromatid separation and of chromatin decondensation at subtelomeric chromatin segments varies between chromosome arms. A mainly random distribution and similar shapes of CTs even at higher ploidy levels indicate that in general no substantial CT reorganisation occurs during endopolyploidisation. Non-cohesive sister chromatid regions at chromosome arms and at the (peri)centromere are accompanied by a less dense chromatin conformation in highly endopolyploid nuclei. We discuss the possible function of this conformation in comparison to transcriptionally active regions at insect polytene chromosomes.

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Chromosome Conformation Capture Carbon Copy Technology

Cited by 44 publications

References 17 publications

DNA Looping in Prokaryotes: Experimental and Theoretical Approaches

DNA Looping in Prokaryotes: Experimental and Theoretical Approaches

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

Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness

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