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Getting the genome in shape: the formation of loops, domains and compartments.

Bouwman BA, de Laat W - Genome Biol. (2015)

Bottom Line: The hierarchical levels of genome architecture exert transcriptional control by tuning the accessibility and proximity of genes and regulatory elements.Here, we review current insights into the trans-acting factors that enable the genome to flexibly adopt different functionally relevant conformations.

View Article: PubMed Central - PubMed

Affiliation: Hubrecht Institute - KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.

ABSTRACT
The hierarchical levels of genome architecture exert transcriptional control by tuning the accessibility and proximity of genes and regulatory elements. Here, we review current insights into the trans-acting factors that enable the genome to flexibly adopt different functionally relevant conformations.

No MeSH data available.


Cell-to-cell variability in genomic neighborhoods. The upper half shows a simplified overview of chromatin behavior during the cell cycle. Chromosome territory positioning differs between mother cell and daughter cells (but can be fairly similar between two daughter cells owing to symmetric spindle positioning). In the lower half, the zoom view schematically shows the high levels of variation between the genomic neighborhoods of a given topologically associating domain (TAD) of interest (indicated in blue) across the mother cell and the two daughter cells 1 and 2. TADs are represented by colored spheres
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Fig1: Cell-to-cell variability in genomic neighborhoods. The upper half shows a simplified overview of chromatin behavior during the cell cycle. Chromosome territory positioning differs between mother cell and daughter cells (but can be fairly similar between two daughter cells owing to symmetric spindle positioning). In the lower half, the zoom view schematically shows the high levels of variation between the genomic neighborhoods of a given topologically associating domain (TAD) of interest (indicated in blue) across the mother cell and the two daughter cells 1 and 2. TADs are represented by colored spheres

Mentions: To evaluate these issues, it is important to keep in mind how chromosome folding changes during cell division. Spatial genome organization is generally studied in non-synchronous cells, of which interphase cells make up the biggest proportion. In interphase nuclei, chromosomes are decondensed and organized hierarchically into the transcriptionally relevant structures described above. To prepare for cell division, chromosomes untangle and condense, while transcription ceases almost entirely. Mitotic chromosomes no longer show preferential higher-order contacts or compartmentalized TAD-based organization [46], and it is suggested that enhancer-promoter looping is absent as well [47–50]. Shortly after cell division, chromosomes decondense and reposition themselves in a stochastic manner (Fig. 1), implying that genome topology is not passed down to daughter cells in a precise way. Although individual genes are relatively mobile during early G1 phase, they become quickly constrained to a small nuclear subvolume, after which genome folding is relatively stable for the rest of interphase [51–53].Fig. 1


Getting the genome in shape: the formation of loops, domains and compartments.

Bouwman BA, de Laat W - Genome Biol. (2015)

Cell-to-cell variability in genomic neighborhoods. The upper half shows a simplified overview of chromatin behavior during the cell cycle. Chromosome territory positioning differs between mother cell and daughter cells (but can be fairly similar between two daughter cells owing to symmetric spindle positioning). In the lower half, the zoom view schematically shows the high levels of variation between the genomic neighborhoods of a given topologically associating domain (TAD) of interest (indicated in blue) across the mother cell and the two daughter cells 1 and 2. TADs are represented by colored spheres
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4536798&req=5

Fig1: Cell-to-cell variability in genomic neighborhoods. The upper half shows a simplified overview of chromatin behavior during the cell cycle. Chromosome territory positioning differs between mother cell and daughter cells (but can be fairly similar between two daughter cells owing to symmetric spindle positioning). In the lower half, the zoom view schematically shows the high levels of variation between the genomic neighborhoods of a given topologically associating domain (TAD) of interest (indicated in blue) across the mother cell and the two daughter cells 1 and 2. TADs are represented by colored spheres
Mentions: To evaluate these issues, it is important to keep in mind how chromosome folding changes during cell division. Spatial genome organization is generally studied in non-synchronous cells, of which interphase cells make up the biggest proportion. In interphase nuclei, chromosomes are decondensed and organized hierarchically into the transcriptionally relevant structures described above. To prepare for cell division, chromosomes untangle and condense, while transcription ceases almost entirely. Mitotic chromosomes no longer show preferential higher-order contacts or compartmentalized TAD-based organization [46], and it is suggested that enhancer-promoter looping is absent as well [47–50]. Shortly after cell division, chromosomes decondense and reposition themselves in a stochastic manner (Fig. 1), implying that genome topology is not passed down to daughter cells in a precise way. Although individual genes are relatively mobile during early G1 phase, they become quickly constrained to a small nuclear subvolume, after which genome folding is relatively stable for the rest of interphase [51–53].Fig. 1

Bottom Line: The hierarchical levels of genome architecture exert transcriptional control by tuning the accessibility and proximity of genes and regulatory elements.Here, we review current insights into the trans-acting factors that enable the genome to flexibly adopt different functionally relevant conformations.

View Article: PubMed Central - PubMed

Affiliation: Hubrecht Institute - KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.

ABSTRACT
The hierarchical levels of genome architecture exert transcriptional control by tuning the accessibility and proximity of genes and regulatory elements. Here, we review current insights into the trans-acting factors that enable the genome to flexibly adopt different functionally relevant conformations.

No MeSH data available.