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Global reorganization of replication domains during embryonic stem cell differentiation.

Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Schübeler D, Gilbert DM - PLoS Biol. (2008)

Bottom Line: Replication-timing changes were coordinated with transcription changes for weak promoters more than strong promoters, and were accompanied by rearrangements in subnuclear position.We conclude that replication profiles are cell-type specific, and changes in these profiles reveal chromosome segments that undergo large changes in organization during differentiation.Moreover, smaller replication domains and a higher density of timing transition regions that interrupt isochore replication timing define a novel characteristic of the pluripotent state.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America.

ABSTRACT
DNA replication in mammals is regulated via the coordinate firing of clusters of replicons that duplicate megabase-sized chromosome segments at specific times during S-phase. Cytogenetic studies show that these "replicon clusters" coalesce as subchromosomal units that persist through multiple cell generations, but the molecular boundaries of such units have remained elusive. Moreover, the extent to which changes in replication timing occur during differentiation and their relationship to transcription changes has not been rigorously investigated. We have constructed high-resolution replication-timing profiles in mouse embryonic stem cells (mESCs) before and after differentiation to neural precursor cells. We demonstrate that chromosomes can be segmented into multimegabase domains of coordinate replication, which we call "replication domains," separated by transition regions whose replication kinetics are consistent with large originless segments. The molecular boundaries of replication domains are remarkably well conserved between distantly related ESC lines and induced pluripotent stem cells. Unexpectedly, ESC differentiation was accompanied by the consolidation of smaller differentially replicating domains into larger coordinately replicated units whose replication time was more aligned to isochore GC content and the density of LINE-1 transposable elements, but not gene density. Replication-timing changes were coordinated with transcription changes for weak promoters more than strong promoters, and were accompanied by rearrangements in subnuclear position. We conclude that replication profiles are cell-type specific, and changes in these profiles reveal chromosome segments that undergo large changes in organization during differentiation. Moreover, smaller replication domains and a higher density of timing transition regions that interrupt isochore replication timing define a novel characteristic of the pluripotent state.

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Relationship between Replication Timing and Histone Modifications(A and B) Correlation between replication timing and H3K4me3 of RefSeq gene promoters. The graphical format is the same as in Figure 5C and 5D, except that the heights of bins represent the percentages of H3K4me3-positive genes within each bin. Logistic regression (inner line) and 95% confidence intervals (outer lines) reveal a clear correlation in both ESCs (A) and NPCs (B) (p < 2 × 10−16 by the Likelihood Ratio test). H3K4me3 data were based on Mikkelsen et al [51].(C) Relationship between replication timing and histone modifications at the level of replication domains. Densities of different histone modifications (total intensity/domain size) based on a ChIP-Seq study [51] were calculated for all replication domains in a given state (ESC or NPC) and Pearson R2 values between replication timing and different histone modification densities were obtained.(D) Comparison of replication timing and different histone modifications in four exemplary 5-Mb genomic regions in ESCs and NPCs.(E) Box plots showing the distribution of replication-timing changes of “bivalently” modified genes (i.e., K4K27) in ESCs that change to four different modification state (K4K27, K27, K4, or none) in NPCs. Genes that remained “bivalent” showed a distribution similar to the three other classes. The p-values were obtained from a two-tailed t-test for comparison of two unpaired groups.
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pbio-0060245-g006: Relationship between Replication Timing and Histone Modifications(A and B) Correlation between replication timing and H3K4me3 of RefSeq gene promoters. The graphical format is the same as in Figure 5C and 5D, except that the heights of bins represent the percentages of H3K4me3-positive genes within each bin. Logistic regression (inner line) and 95% confidence intervals (outer lines) reveal a clear correlation in both ESCs (A) and NPCs (B) (p < 2 × 10−16 by the Likelihood Ratio test). H3K4me3 data were based on Mikkelsen et al [51].(C) Relationship between replication timing and histone modifications at the level of replication domains. Densities of different histone modifications (total intensity/domain size) based on a ChIP-Seq study [51] were calculated for all replication domains in a given state (ESC or NPC) and Pearson R2 values between replication timing and different histone modification densities were obtained.(D) Comparison of replication timing and different histone modifications in four exemplary 5-Mb genomic regions in ESCs and NPCs.(E) Box plots showing the distribution of replication-timing changes of “bivalently” modified genes (i.e., K4K27) in ESCs that change to four different modification state (K4K27, K27, K4, or none) in NPCs. Genes that remained “bivalent” showed a distribution similar to the three other classes. The p-values were obtained from a two-tailed t-test for comparison of two unpaired groups.

Mentions: We also examined the relationship between replication timing and other epigenetic marks that have been analyzed in mESCs and NPCs [51]. A clear correlation between early replication and both lysine 4 tri-methylation of histone H3 (H3K4me3) and H3K36me3 was observed, both at the level of individual genes (Figure 6A and 6B) and when the density of these marks was integrated within the boundaries of each replication domain (Figure 6C). Similar to transcription, a positive correlation was maintained during differentiation. This was expected due to the association of these chromatin marks with transcription [52]. However, there was a significant decrease in the positive correlation to these marks during differentiation (Figure 6C), as well as the overall number of H3K4me3 promoters (Figure 6A and 6B), which is consistent with the recent finding that there is more overall coding and noncoding transcription in ESCs versus NPCs [49]. In contrast, there was little or no relationship between late replication and the repressive marks H3K27me3, H3K9me3, or H4K20me3 in ESCs or NPCs (Figure 6C), which was also evident from visual inspection of representative genomic regions that exhibit changes in replication timing during differentiation (Figure 6D). In fact, a large fraction of genes that changed replication timing during differentiation did not contain H3K27me3 at their promoters in either ESCs or NPCs, which was also true for genes that remained late replicating in both differentiation states (Table S1). Moreover, the lack of correlation to replication timing was confirmed at the level of genes using independently derived H3K27me3 and H3K9me3 microarray data for more than 10,000 promoters in mouse ESCs and NPCs (H3K27me3: R2 = 0.004 [53] or 0.01 [54] in ESCs, 0.003 [54] in NPCs; H3K9me3: R2 = 0.007 [53] in ESCs; see Table S1). We conclude that replication timing correlates with annotated chromatin marks that reflect transcription, but not repression.


Global reorganization of replication domains during embryonic stem cell differentiation.

Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Schübeler D, Gilbert DM - PLoS Biol. (2008)

Relationship between Replication Timing and Histone Modifications(A and B) Correlation between replication timing and H3K4me3 of RefSeq gene promoters. The graphical format is the same as in Figure 5C and 5D, except that the heights of bins represent the percentages of H3K4me3-positive genes within each bin. Logistic regression (inner line) and 95% confidence intervals (outer lines) reveal a clear correlation in both ESCs (A) and NPCs (B) (p < 2 × 10−16 by the Likelihood Ratio test). H3K4me3 data were based on Mikkelsen et al [51].(C) Relationship between replication timing and histone modifications at the level of replication domains. Densities of different histone modifications (total intensity/domain size) based on a ChIP-Seq study [51] were calculated for all replication domains in a given state (ESC or NPC) and Pearson R2 values between replication timing and different histone modification densities were obtained.(D) Comparison of replication timing and different histone modifications in four exemplary 5-Mb genomic regions in ESCs and NPCs.(E) Box plots showing the distribution of replication-timing changes of “bivalently” modified genes (i.e., K4K27) in ESCs that change to four different modification state (K4K27, K27, K4, or none) in NPCs. Genes that remained “bivalent” showed a distribution similar to the three other classes. The p-values were obtained from a two-tailed t-test for comparison of two unpaired groups.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2561079&req=5

pbio-0060245-g006: Relationship between Replication Timing and Histone Modifications(A and B) Correlation between replication timing and H3K4me3 of RefSeq gene promoters. The graphical format is the same as in Figure 5C and 5D, except that the heights of bins represent the percentages of H3K4me3-positive genes within each bin. Logistic regression (inner line) and 95% confidence intervals (outer lines) reveal a clear correlation in both ESCs (A) and NPCs (B) (p < 2 × 10−16 by the Likelihood Ratio test). H3K4me3 data were based on Mikkelsen et al [51].(C) Relationship between replication timing and histone modifications at the level of replication domains. Densities of different histone modifications (total intensity/domain size) based on a ChIP-Seq study [51] were calculated for all replication domains in a given state (ESC or NPC) and Pearson R2 values between replication timing and different histone modification densities were obtained.(D) Comparison of replication timing and different histone modifications in four exemplary 5-Mb genomic regions in ESCs and NPCs.(E) Box plots showing the distribution of replication-timing changes of “bivalently” modified genes (i.e., K4K27) in ESCs that change to four different modification state (K4K27, K27, K4, or none) in NPCs. Genes that remained “bivalent” showed a distribution similar to the three other classes. The p-values were obtained from a two-tailed t-test for comparison of two unpaired groups.
Mentions: We also examined the relationship between replication timing and other epigenetic marks that have been analyzed in mESCs and NPCs [51]. A clear correlation between early replication and both lysine 4 tri-methylation of histone H3 (H3K4me3) and H3K36me3 was observed, both at the level of individual genes (Figure 6A and 6B) and when the density of these marks was integrated within the boundaries of each replication domain (Figure 6C). Similar to transcription, a positive correlation was maintained during differentiation. This was expected due to the association of these chromatin marks with transcription [52]. However, there was a significant decrease in the positive correlation to these marks during differentiation (Figure 6C), as well as the overall number of H3K4me3 promoters (Figure 6A and 6B), which is consistent with the recent finding that there is more overall coding and noncoding transcription in ESCs versus NPCs [49]. In contrast, there was little or no relationship between late replication and the repressive marks H3K27me3, H3K9me3, or H4K20me3 in ESCs or NPCs (Figure 6C), which was also evident from visual inspection of representative genomic regions that exhibit changes in replication timing during differentiation (Figure 6D). In fact, a large fraction of genes that changed replication timing during differentiation did not contain H3K27me3 at their promoters in either ESCs or NPCs, which was also true for genes that remained late replicating in both differentiation states (Table S1). Moreover, the lack of correlation to replication timing was confirmed at the level of genes using independently derived H3K27me3 and H3K9me3 microarray data for more than 10,000 promoters in mouse ESCs and NPCs (H3K27me3: R2 = 0.004 [53] or 0.01 [54] in ESCs, 0.003 [54] in NPCs; H3K9me3: R2 = 0.007 [53] in ESCs; see Table S1). We conclude that replication timing correlates with annotated chromatin marks that reflect transcription, but not repression.

Bottom Line: Replication-timing changes were coordinated with transcription changes for weak promoters more than strong promoters, and were accompanied by rearrangements in subnuclear position.We conclude that replication profiles are cell-type specific, and changes in these profiles reveal chromosome segments that undergo large changes in organization during differentiation.Moreover, smaller replication domains and a higher density of timing transition regions that interrupt isochore replication timing define a novel characteristic of the pluripotent state.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America.

ABSTRACT
DNA replication in mammals is regulated via the coordinate firing of clusters of replicons that duplicate megabase-sized chromosome segments at specific times during S-phase. Cytogenetic studies show that these "replicon clusters" coalesce as subchromosomal units that persist through multiple cell generations, but the molecular boundaries of such units have remained elusive. Moreover, the extent to which changes in replication timing occur during differentiation and their relationship to transcription changes has not been rigorously investigated. We have constructed high-resolution replication-timing profiles in mouse embryonic stem cells (mESCs) before and after differentiation to neural precursor cells. We demonstrate that chromosomes can be segmented into multimegabase domains of coordinate replication, which we call "replication domains," separated by transition regions whose replication kinetics are consistent with large originless segments. The molecular boundaries of replication domains are remarkably well conserved between distantly related ESC lines and induced pluripotent stem cells. Unexpectedly, ESC differentiation was accompanied by the consolidation of smaller differentially replicating domains into larger coordinately replicated units whose replication time was more aligned to isochore GC content and the density of LINE-1 transposable elements, but not gene density. Replication-timing changes were coordinated with transcription changes for weak promoters more than strong promoters, and were accompanied by rearrangements in subnuclear position. We conclude that replication profiles are cell-type specific, and changes in these profiles reveal chromosome segments that undergo large changes in organization during differentiation. Moreover, smaller replication domains and a higher density of timing transition regions that interrupt isochore replication timing define a novel characteristic of the pluripotent state.

Show MeSH
Related in: MedlinePlus