Limits...
Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe.

Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SI - Nature (2014)

Bottom Line: We show that heterochromatin mediates chromatin fibre compaction at centromeres and promotes prominent inter-arm interactions within centromere-proximal regions, providing structural constraints crucial for proper genome organization.Loss of heterochromatin relaxes constraints on chromosomes, causing an increase in intra- and inter-chromosomal interactions.Together, our analyses uncover fundamental genome folding principles that drive higher-order chromosome organization crucial for coordinating nuclear functions.

View Article: PubMed Central - PubMed

Affiliation: 1] Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA [2].

ABSTRACT
Eukaryotic genomes are folded into three-dimensional structures, such as self-associating topological domains, the borders of which are enriched in cohesin and CCCTC-binding factor (CTCF) required for long-range interactions. How local chromatin interactions govern higher-order folding of chromatin fibres and the function of cohesin in this process remain poorly understood. Here we perform genome-wide chromatin conformation capture (Hi-C) analysis to explore the high-resolution organization of the Schizosaccharomyces pombe genome, which despite its small size exhibits fundamental features found in other eukaryotes. Our analyses of wild-type and mutant strains reveal key elements of chromosome architecture and genome organization. On chromosome arms, small regions of chromatin locally interact to form 'globules'. This feature requires a function of cohesin distinct from its role in sister chromatid cohesion. Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structures and global chromosome territories. By contrast, heterochromatin, which loads cohesin at specific sites including pericentromeric and subtelomeric domains, is dispensable for globule formation but nevertheless affects genome organization. We show that heterochromatin mediates chromatin fibre compaction at centromeres and promotes prominent inter-arm interactions within centromere-proximal regions, providing structural constraints crucial for proper genome organization. Loss of heterochromatin relaxes constraints on chromosomes, causing an increase in intra- and inter-chromosomal interactions. Together, our analyses uncover fundamental genome folding principles that drive higher-order chromosome organization crucial for coordinating nuclear functions.

Show MeSH

Related in: MedlinePlus

Cohesin is required for globule formationa, Hi-C heatmap at 10kb resolution for rad21-K1. b, 4C-like profiles showing the average contact probabilities of centromeres and telomeres WT, wild type. c, Distribution of intra-arm, inter-arm and inter-chromosomal contact frequencies. d, Hi-C heatmaps of a segment of chromosome 2 overlaid with blue lines corresponding to cohesin (Psc3) peaks from the 10kb binned profile (top); Hi-C directional preference profile (below). To compare results from different experiments, color scales were chosen such that the maximum value corresponds to the ninety-ninth percentile of intra-arm contact frequencies. The boundaries detected in rad21-K1 may result from random fluctuations in directionality due to experimental limitations, or remaining cooperative factors required for boundary establishment. e, Relative contact probability around a cohesin peak as a function of insulation distance averaged over all cohesin peaks (insulation plot). Depletion of contact probability (blue stripe) is not observed in rad21-K1.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4465753&req=5

Figure 2: Cohesin is required for globule formationa, Hi-C heatmap at 10kb resolution for rad21-K1. b, 4C-like profiles showing the average contact probabilities of centromeres and telomeres WT, wild type. c, Distribution of intra-arm, inter-arm and inter-chromosomal contact frequencies. d, Hi-C heatmaps of a segment of chromosome 2 overlaid with blue lines corresponding to cohesin (Psc3) peaks from the 10kb binned profile (top); Hi-C directional preference profile (below). To compare results from different experiments, color scales were chosen such that the maximum value corresponds to the ninety-ninth percentile of intra-arm contact frequencies. The boundaries detected in rad21-K1 may result from random fluctuations in directionality due to experimental limitations, or remaining cooperative factors required for boundary establishment. e, Relative contact probability around a cohesin peak as a function of insulation distance averaged over all cohesin peaks (insulation plot). Depletion of contact probability (blue stripe) is not observed in rad21-K1.

Mentions: Cohesin affects chromatin architecture in budding yeast19,20 and in other eukaryotes5-7,21,22, but its exact role is unclear. Cohesin enrichment at the 3’end of convergent genes (see below)23, which correlate with globule boundaries, led us to investigate its role in globule formation. Hi-C analysis of rad21-K1, which contains a partial loss of function mutation in a cohesin subunit24, revealed a loss of globules and greater intermingling of chromosomes (Fig. 2a). Centromeres and telomeres were less refractory to interaction with chromosomal arms (Fig. 2b). Moreover, we observed greater intra-chromosomal inter-arm (1.6-fold increase) and inter-chromosomal contact frequencies (2.5-fold increase) compared to wild type (Fig. 2c). Contact probability decay as a function of genomic distance was quite different for rad21-K1. The inflection at 100kb was absent and contact probability decayed more slowly afterwards (Extended Data Fig. 3), indicating loss of locally compacted globules. Globule boundaries corresponded to sites of cohesin enrichment in wild type, but did not correspond to these positions in rad21-K1 (Fig. 2d), suggesting a functional link between cohesin binding and organization of the chromatin fiber.


Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe.

Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SI - Nature (2014)

Cohesin is required for globule formationa, Hi-C heatmap at 10kb resolution for rad21-K1. b, 4C-like profiles showing the average contact probabilities of centromeres and telomeres WT, wild type. c, Distribution of intra-arm, inter-arm and inter-chromosomal contact frequencies. d, Hi-C heatmaps of a segment of chromosome 2 overlaid with blue lines corresponding to cohesin (Psc3) peaks from the 10kb binned profile (top); Hi-C directional preference profile (below). To compare results from different experiments, color scales were chosen such that the maximum value corresponds to the ninety-ninth percentile of intra-arm contact frequencies. The boundaries detected in rad21-K1 may result from random fluctuations in directionality due to experimental limitations, or remaining cooperative factors required for boundary establishment. e, Relative contact probability around a cohesin peak as a function of insulation distance averaged over all cohesin peaks (insulation plot). Depletion of contact probability (blue stripe) is not observed in rad21-K1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4465753&req=5

Figure 2: Cohesin is required for globule formationa, Hi-C heatmap at 10kb resolution for rad21-K1. b, 4C-like profiles showing the average contact probabilities of centromeres and telomeres WT, wild type. c, Distribution of intra-arm, inter-arm and inter-chromosomal contact frequencies. d, Hi-C heatmaps of a segment of chromosome 2 overlaid with blue lines corresponding to cohesin (Psc3) peaks from the 10kb binned profile (top); Hi-C directional preference profile (below). To compare results from different experiments, color scales were chosen such that the maximum value corresponds to the ninety-ninth percentile of intra-arm contact frequencies. The boundaries detected in rad21-K1 may result from random fluctuations in directionality due to experimental limitations, or remaining cooperative factors required for boundary establishment. e, Relative contact probability around a cohesin peak as a function of insulation distance averaged over all cohesin peaks (insulation plot). Depletion of contact probability (blue stripe) is not observed in rad21-K1.
Mentions: Cohesin affects chromatin architecture in budding yeast19,20 and in other eukaryotes5-7,21,22, but its exact role is unclear. Cohesin enrichment at the 3’end of convergent genes (see below)23, which correlate with globule boundaries, led us to investigate its role in globule formation. Hi-C analysis of rad21-K1, which contains a partial loss of function mutation in a cohesin subunit24, revealed a loss of globules and greater intermingling of chromosomes (Fig. 2a). Centromeres and telomeres were less refractory to interaction with chromosomal arms (Fig. 2b). Moreover, we observed greater intra-chromosomal inter-arm (1.6-fold increase) and inter-chromosomal contact frequencies (2.5-fold increase) compared to wild type (Fig. 2c). Contact probability decay as a function of genomic distance was quite different for rad21-K1. The inflection at 100kb was absent and contact probability decayed more slowly afterwards (Extended Data Fig. 3), indicating loss of locally compacted globules. Globule boundaries corresponded to sites of cohesin enrichment in wild type, but did not correspond to these positions in rad21-K1 (Fig. 2d), suggesting a functional link between cohesin binding and organization of the chromatin fiber.

Bottom Line: We show that heterochromatin mediates chromatin fibre compaction at centromeres and promotes prominent inter-arm interactions within centromere-proximal regions, providing structural constraints crucial for proper genome organization.Loss of heterochromatin relaxes constraints on chromosomes, causing an increase in intra- and inter-chromosomal interactions.Together, our analyses uncover fundamental genome folding principles that drive higher-order chromosome organization crucial for coordinating nuclear functions.

View Article: PubMed Central - PubMed

Affiliation: 1] Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA [2].

ABSTRACT
Eukaryotic genomes are folded into three-dimensional structures, such as self-associating topological domains, the borders of which are enriched in cohesin and CCCTC-binding factor (CTCF) required for long-range interactions. How local chromatin interactions govern higher-order folding of chromatin fibres and the function of cohesin in this process remain poorly understood. Here we perform genome-wide chromatin conformation capture (Hi-C) analysis to explore the high-resolution organization of the Schizosaccharomyces pombe genome, which despite its small size exhibits fundamental features found in other eukaryotes. Our analyses of wild-type and mutant strains reveal key elements of chromosome architecture and genome organization. On chromosome arms, small regions of chromatin locally interact to form 'globules'. This feature requires a function of cohesin distinct from its role in sister chromatid cohesion. Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structures and global chromosome territories. By contrast, heterochromatin, which loads cohesin at specific sites including pericentromeric and subtelomeric domains, is dispensable for globule formation but nevertheless affects genome organization. We show that heterochromatin mediates chromatin fibre compaction at centromeres and promotes prominent inter-arm interactions within centromere-proximal regions, providing structural constraints crucial for proper genome organization. Loss of heterochromatin relaxes constraints on chromosomes, causing an increase in intra- and inter-chromosomal interactions. Together, our analyses uncover fundamental genome folding principles that drive higher-order chromosome organization crucial for coordinating nuclear functions.

Show MeSH
Related in: MedlinePlus