Chromosome Territories

Cremer, Thomas; Cremer, Marion

doi:10.1101/cshperspect.a003889

Cited by 981 publications

(892 citation statements)

References 120 publications

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“…FISH chromosome painting using preserved nuclei of wild-type spermatocytes revealed that chromosome 8 homologs occupy spatially limited territories during meiotic prophase, as previously reported in human spermatogonia ( Fig. 1C; Scherthan et al 1996), which is similar to the chromosome territories observed in interphase somatic cells (Cremer and Cremer 2010). Although most homologs are separated from each other during premeiotic S phase, some homologs start to locate in close proximity to one another (juxtaposed) at the early leptotene stage (Fig.…”

Section: Homolog Pairing Initiates In Early Leptotenementioning

confidence: 49%

Meiosis-specific cohesin mediates homolog recognition in mouse spermatocytes

Ishiguro¹,

et al. 2014

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During meiosis, homologous chromosome (homolog) pairing is promoted by several layers of regulation that include dynamic chromosome movement and meiotic recombination. However, the way in which homologs recognize each other remains a fundamental issue in chromosome biology. Here, we show that homolog recognition or association initiates upon entry into meiotic prophase before axis assembly and double-strand break (DSB) formation. This homolog association develops into tight pairing only during or after axis formation. Intriguingly, the ability to recognize homologs is retained in Sun1 knockout spermatocytes, in which telomere-directed chromosome movement is abolished, and this is the case even in Spo11 knockout spermatocytes, in which DSB-dependent DNA homology search is absent. Disruption of meiosis-specific cohesin RAD21L precludes the initial association of homologs as well as the subsequent pairing in spermatocytes. These findings suggest the intriguing possibility that homolog recognition is achieved primarily by searching for homology in the chromosome architecture as defined by meiosis-specific cohesin rather than in the DNA sequence itself.

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Section: Homolog Pairing Initiates In Early Leptotenementioning

confidence: 49%

Meiosis-specific cohesin mediates homolog recognition in mouse spermatocytes

Ishiguro¹,

et al. 2014

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“…Among these technologies are chromosome conformation capture (3C) (1) and its several iterations, such as Hi-C (2), which are applied to populations of nuclei to identify chromosomal regions that are in close proximity to each other (3,4). Another technology is fluorescence in situ hybridization (FISH), wherein nucleic acids are targeted by fluorescently labeled probes and then visualized via microscopy; this technology is an extension of methods that once used radioactive probes and autoradiography but have since been adapted to use nonradioactive labels (5)(6)(7)(8)(9)(10)(11). FISH is a single-cell assay, making it especially powerful for the detection of rare events that might otherwise be lost in mixed or asynchronous populations of cells.…”

mentioning

confidence: 99%

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

Beliveau

Joyce

Apostolopoulos

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

398

472

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A host of observations demonstrating the relationship between nuclear architecture and processes such as gene expression have led to a number of new technologies for interrogating chromosome positioning. Whereas some of these technologies reconstruct intermolecular interactions, others have enhanced our ability to visualize chromosomes in situ. Here, we describe an oligonucleotide-and PCR-based strategy for fluorescence in situ hybridization (FISH) and a bioinformatic platform that enables this technology to be extended to any organism whose genome has been sequenced. The oligonucleotide probes are renewable, highly efficient, and able to robustly label chromosomes in cell culture, fixed tissues, and metaphase spreads. Our method gives researchers precise control over the sequences they target and allows for single and multicolor imaging of regions ranging from tens of kilobases to megabases with the same basic protocol. We anticipate this technology will lead to an enhanced ability to visualize interphase and metaphase chromosomes.T he role of chromosome positioning in gene regulation and chromosome stability is fueling a growing interest in technologies that reveal the in situ organization of the genome. Among these technologies are chromosome conformation capture (3C) (1) and its several iterations, such as Hi-C (2), which are applied to populations of nuclei to identify chromosomal regions that are in close proximity to each other (3, 4). Another technology is fluorescence in situ hybridization (FISH), wherein nucleic acids are targeted by fluorescently labeled probes and then visualized via microscopy; this technology is an extension of methods that once used radioactive probes and autoradiography but have since been adapted to use nonradioactive labels (5-11). FISH is a single-cell assay, making it especially powerful for the detection of rare events that might otherwise be lost in mixed or asynchronous populations of cells. In addition, because FISH is applied to fixed cells, it can reveal the positioning of chromosomes relative to nuclear, cytoplasmic, and even tissue structures. FISH can also be used to visualize RNA, permitting the simultaneous assessment of gene expression, chromosome position, and protein localization.FISH probes are typically derived from cloned genomic regions or flow-sorted chromosomes, which are labeled directly via nick translation or PCR in the presence of fluorophore-conjugated nucleotides or labeled indirectly with nucleotide-conjugated haptens, such as biotin and digoxigenin, and then visualized with secondary detection reagents. Probe DNA is often fragmented into ∼150-to 250-bp pieces to facilitate its penetration into fixed cells (12) and, as many genomic clones contain repetitive sequences that occur abundantly in the genome, hybridization is typically performed in the presence of unlabeled repetitive DNA (13). Another limitation to clone-based probes is that the genomic regions that can be visualized with them are restricted by the availability of clones and the size of ...

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“…These novel bioimaging methods have been employed to study the complex chromatin organization, which span several orders of magnitude to save genetic information on the mix of DNA and proteins, and to verify that organizational units, for example, domains with similar size as TADs, do exist in 3D genome [112]. However, it is challenging to employ SR microscopy to study the relationship between 3D genome organization and the regulation of gene transcription.…”

Section: Resultsmentioning

confidence: 99%

Developing bioimaging and quantitative methods to study 3D genome

et al. 2016

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The recent advances in chromosome configuration capture (3C)-based series molecular methods and optical superresolution (SR) techniques offer powerful tools to investigate three dimensional (3D) genomic structure in prokaryotic and eukaryotic cell nucleus. In this review, we focus on the progress during the last decade in this exciting field. Here we at first introduce briefly genome organization at chromosome, domain and sub-domain level, respectively; then we provide a short introduction to various super-resolution microscopy techniques which can be employed to detect genome 3D structure. We also reviewed the progress of quantitative and visualization tools to evaluate and visualize chromatin interactions in 3D genome derived from Hi-C data. We end up with the discussion that imaging methods and 3C-based molecular methods are not mutually exclusive ----actually they are complemental to each other and can be combined together to study 3D genome organization.Keywords: 3D Genome; quantitative methods; bioimaging; super resolution INTRODUCTIONIn eukaryotic nucleus, the organization of chromatin is very complex. Highly condensed chromatin and huge numbers of components, such as transcription factors, chromatin proteins and RNA-processing factors, cram together in a very small volume. Essential nuclear processes such as transcription, replication, and repair occur at spatially defined locations in the nucleus. Accumulating evidence suggests that the expression of many genes is correlated with their positions in cell nucleus, and the spatial organization of chromatins has played essential role in regulating transcriptional activity [1]. How these could be done is one of the greatest challenges in molecular biology. 1 DNA helix is hierarchically packaged into chromatin in an elegant way, and eventually form a chromosome in the eukaryotic nucleus over several levels of higher-order structures [1], indicating that a range of microscopy techniques with spatial and temporal scales that cover several orders of magnitude are necessary to understand the organization principles at different levels in a chromosome. For example, the structure of nucleosomes, the fundamental organization unit of chromatin, has been elucidated by X-ray crystals at nanometer scale [2]. The structure of "beads-on-a-string" fiber, which has a diameter of 11-nm and is the very first level of chromatin organization, is also well-understood through Electron Microscope [33]. However, substructure at the scale of 10-200 nm is poorly understood, especially in live cells, partly due to the requirement of biological system that the dynamics, process and function in biology need to be measured with high spatial (approximately nanometer) and temporal (approximately microsecond to millisecond) † These authors contributed equally to this work.

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Chromosome Territories

Cited by 981 publications

References 120 publications

Meiosis-specific cohesin mediates homolog recognition in mouse spermatocytes

Meiosis-specific cohesin mediates homolog recognition in mouse spermatocytes

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

Developing bioimaging and quantitative methods to study 3D genome

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