Induction of chromosome damage by ultraviolet light and caffeine: Correlation of cytogenetic evaluation and flow karyotype

Cremer, Christoph; Cremer, Thomas; Gray, Joe W.

doi:10.1002/cyto.990020504

Cited by 16 publications

(6 citation statements)

References 18 publications

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“…Chromosomes occupy their own territory in the cell nucleus (Cremer et al 1982;Bolzer et al 2005;Cremer and Cremer 2006) and adopt a preferential radial position within the nucleus, with large chromosomes found more often at the nuclear periphery and small chromosomes found more interiorly. The spatial separation of chromosomes in the nucleus is not absolute: Chromosomal intermingling takes place at the periphery of the territories (Branco and Pombo 2006).…”

Section: Microscopy Observations Into Mammalian Genome Organizationmentioning

confidence: 99%

A decade of 3C technologies: insights into nuclear organization

Wit

Laat²

2012

Genes Dev.

650

487

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Over the past 10 years, the development of chromosome conformation capture (3C) technology and the subsequent genomic variants thereof have enabled the analysis of nuclear organization at an unprecedented resolution and throughput. The technology relies on the original and, in hindsight, remarkably simple idea that digestion and religation of fixed chromatin in cells, followed by the quantification of ligation junctions, allows for the determination of DNA contact frequencies and insight into chromosome topology. Here we evaluate and compare the current 3C-based methods (including 4C [chromosome conformation capture-on-chip], 5C [chromosome conformation capture carbon copy], HiC, and ChIA-PET), summarize their contribution to our current understanding of genome structure, and discuss how shape influences genome function.For more than a century, researchers have been making inquiries into the organization of the nucleus, the largest and most easily discernable organelle in the eukaryotic cell. Early in the 20th Century, Cajal (1903) identified subnuclear structures that were later named Cajal bodies. Twenty-five years later, Heitz (1928) observed differentially staining chromatin in interphase nuclei of mosses and described it as heterochromatin and euchromatin. Interest in nuclear structure was further fueled by the realization that the nucleus contains genetic material in the form of DNA fibers. In humans, when unwound, the DNA measures ;2 m, ;200,000 times the diameter of an average mammalian cell nucleus. Packing DNA inside the nucleus therefore imposes tremendous organizational challenges. While already conceptually interesting, the shape of the genome becomes even more fascinating when one realizes that it also relates to genome functioning. Although we are still far from understanding this exact relationship, breakthrough technologies are now available for the systematic and detailed analysis of nuclear organization.Traditionally, nuclear organization is studied by microscopy, and thus it is appropriate to start by highlighting some important observations made under the microscope.However, the emphasis of this review is on novel genomics strategies that are based on chromosome conformation capture (3C) technology. Ten years ago, Dekker et al. (2002) developed 3C technology, a biochemical strategy to analyze contact frequencies between selected genomic sites in cell populations. Since then, various 3C-derived genomics methods have been developed. In comparison with microscopy, 3C-based methods enable more systematic DNA topology studies at a higher resolution: These technologies can put observations made on single genes in selected cells in the context of genomic behavior in cell populations. The generated DNA contact maps start teaching us the rules that dictate genome structure and functioning inside the cell. As we explain here, these rules are probabilistic, not deterministic, implying that they cannot predict the shape and functioning of the genome in individual cells. To investigate this, microscopy i...

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Section: Microscopy Observations Into Mammalian Genome Organizationmentioning

confidence: 99%

A decade of 3C technologies: insights into nuclear organization

Wit

Laat²

2012

Genes Dev.

650

487

View full text Add to dashboard Cite

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“…Hierarchical conformations formed by chromosomes play a pivotal role in the regulation of gene expression. Previous studies have uncovered that individual chromosomes occupy specific territories 1 – 3 , and gene transcription has been shown to be correlated with the gene’s nuclear position relative to the nuclear lamina and the bulk of the chromosome territories 4 , 5 . Recent studies using high-throughput chromosome conformation capture (Hi-C) have revealed that genomes are organized into topological associated domains (TADs) of several hundred kilo-bases to one mega-base in length, and chromatin regions in a TAD are more likely to interact with other regions within the same TAD than with regions outside of the TAD.…”

Section: Introductionmentioning

confidence: 99%

Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation

Liang

et al. 2018

Cell Death Dis

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Chromatin conformation plays a key role in regulating gene expression and controlling cell differentiation. However, the whole-genome chromatin conformation changes that occur during leukemia cell differentiation are poorly understood. Here, we characterized the changes in chromatin conformation, histone states, chromatin accessibility, and gene expression using an all-trans retinoic acid (ATRA)-induced HL-60 cell differentiation model. The results showed that the boundaries of topological associated domains (TADs) were stable during differentiation; however, the chromatin conformations within several specific TADs were obviously changed. By combining H3K4me3, H3K27ac, and Hi-C signals, we annotated the differential gene-regulatory chromatin interactions upon ATRA induction. The gains and losses of the gene-regulatory chromatin interactions are significantly correlated with gene expression and chromatin accessibility. Finally, we found that the loss of GATA2 expression and DNA binding are crucial for the differentiation process, and changes in the chromatin structure around the GATA2 regulate its expression upon ATRA induction. This study provided both statistical insights and experimental details regarding the relationship between chromatin conformation changes and transcription regulation during leukemia cell differentiation, and the results suggested that the chromatin conformation is a new type of potential drug target for cancer therapy.

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“…Esto permitió observar la disposición de los cromosomas en interfase ya que los reajustes cromosómicos deberían de hacerse solo entre los cromosomas o partes de cromosomas que están contiguos. (6,7).…”

Section: Microscopio De Fluorescenciaunclassified

Organization of chromatin in diseases, development, and evolution: Nucleome 4D Project

García-Sagredo¹

2020

an. ranm

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Resumen El conocimiento de la biología celular ha ido enriqueciéndose a medida que se iban descubriendo los componentes de la célula. En este trabajo se pretende describir los avances en el conocimiento de la arquitectura de la cromatina en el núcleo y como esta arquitectura es crucial en la regulación génica. El hecho de que los territorios cromosómicos no estén distribuidos al azar, que su disposición radial dentro del núcleo dependa de la densidad y función de los genes activos en un momento determinado y que los dominios de asociación topológica sean cruciales en la expresión de los genes, explica la implicación de la arquitectura de la cromatina en la aparición de algunas enfermedades y su repercusión tanto en el desarrollo de un organismo como en la evolución. Añadiendo la variable tiempo, el proyecto nucleoma 4D pretende analizar la organización tridimensional del núcleo en el espacio y el tiempo.

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Induction of chromosome damage by ultraviolet light and caffeine: Correlation of cytogenetic evaluation and flow karyotype

Cited by 16 publications

References 18 publications

A decade of 3C technologies: insights into nuclear organization

A decade of 3C technologies: insights into nuclear organization

Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation

Organization of chromatin in diseases, development, and evolution: Nucleome 4D Project

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