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. 2016 May 10;9:18.
doi: 10.1186/s13072-016-0067-3. eCollection 2016.

Distinct Epigenetic Features of Differentiation-Regulated Replication Origins

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Free PMC article

Distinct Epigenetic Features of Differentiation-Regulated Replication Origins

Owen K Smith et al. Epigenetics Chromatin. .
Free PMC article

Abstract

Background: Eukaryotic genome duplication starts at discrete sequences (replication origins) that coordinate cell cycle progression, ensure genomic stability and modulate gene expression. Origins share some sequence features, but their activity also responds to changes in transcription and cellular differentiation status.

Results: To identify chromatin states and histone modifications that locally mark replication origins, we profiled origin distributions in eight human cell lines representing embryonic and differentiated cell types. Consistent with a role of chromatin structure in determining origin activity, we found that cancer and non-cancer cells of similar lineages exhibited highly similar replication origin distributions. Surprisingly, our study revealed that DNase hypersensitivity, which often correlates with early replication at large-scale chromatin domains, did not emerge as a strong local determinant of origin activity. Instead, we found that two distinct sets of chromatin modifications exhibited strong local associations with two discrete groups of replication origins. The first origin group consisted of about 40,000 regions that actively initiated replication in all cell types and preferentially colocalized with unmethylated CpGs and with the euchromatin markers, H3K4me3 and H3K9Ac. The second group included origins that were consistently active in cells of a single type or lineage and preferentially colocalized with the heterochromatin marker, H3K9me3. Shared origins replicated throughout the S-phase of the cell cycle, whereas cell-type-specific origins preferentially replicated during late S-phase.

Conclusions: These observations are in line with the hypothesis that differentiation-associated changes in chromatin and gene expression affect the activation of specific replication origins.

Keywords: Cell cycle; Cellular differentiation; Chromatin; CpG islands; H3K4me3; H3K9Ac; H3K9me3; Histone modification; Origin of replication; Proliferation.

Figures

Fig. 1
Fig. 1
A recurrent group of shared replication origins in normal and cancer cells. The numbers of shared replication origins among a normal and b cancer cells. For each cell line, the overall number of origin peaks is plotted in the top column followed by the number of origins in that cell line that were also present in the other cells indicated (sequential intersections; for details, see “Methods” section and Table 1 and Additional file 1: S2a–c). For example, in panel a, top group, EB represents the number of origin peaks present in the EB sample; EB + ES depicts the number of origin peaks present in the EB sample that were also present in the ES sample; EB + ES + AS depicts the number of origin peaks present in the EB sample that were also present in the ES and the AS samples, etc. The last column for each cell line group shows the number of origins remaining following sequential intersections with a all four normal cell lines or b all four cancer cell lines. Normal cell lines were AS (AS_IPS), PWS (PWS_IPS), ES (H1ES) and EB. Cancer cell lines were K562 (K), MCF7 (M), HCT116 (H) and U2OS (U)
Fig. 2
Fig. 2
CpG islands (CGIs) are significantly enriched among shared replication origins. Distribution of a all replication origins in the indicated cells and b origins associated with CpG islands (CGI origins). Origins were stratified as shared and cell type specific (for a definition of shared and cell-type-specific origins, see the text and legend to Table 1) or partially shared (origins initiating replication in some cells, but not others). Distributions are displayed in 100 % stacked column charts
Fig. 3
Fig. 3
Example ColoWeb output: comparison of the distribution of K562 replication origins to K562 histone modification H3K4me3. The x axis represents distance from the center of a replication origins or b randomized regions. Each scatterplot contains 100 rows. Each row contains data for 50 randomly selected regions [origin-containing regions in (a) and randomized fragments of the same GC content in (b)], divided across 100 bases bins. The grayscale corresponds to the extent of H3K4 trimethylation in each bin. c, d Graphs summarizing the colocalized peaks for the analyses represented in (a, b), respectively. The green horizontal lines for the mean and high/low oscillation values (40th and 60th percentiles, respectively) are shown on the histogram. The shaded area, covering the region under the peak and above the upper variance level [48], corresponds to the above mean integral (AMI) used in colocalization studies. For more examples of scatterplots, see Additional file 1: Fig. S3
Fig. 4
Fig. 4
Association of replication origins with chromatin features. Representative ColoWeb alignments of chromatin features with replication origins from several cancer and non-cancer cell lines. Only cell lines that were extensively characterized for chromatin modifications in the literature (ES, MCF7 and K562, with EB origins analyzed vs. K562 modifications) were included in this analysis. AMI values corresponding to the histograms are shown in Additional file 1: Table S4 and scatterplots are shown in Additional file 1: Fig. S3
Fig. 5
Fig. 5
Replication origins clustered by preferential association with chromatin features. A heat map showing clustered standardized mean-centered AMI values (for examples, see Fig. 4, Additional file 1: Fig. S3 and Additional file 1: Table S4) representing the extent of preferential association between origins and chromatin markers. For each chromatin modification, AMI values measure the extent of association with replication origins exceeding the general association of the same modification with flanking regions. The map, clustered by both cell line and chromatin feature, is color coded, with deep red representing higher mean-centered AMI values and deep blue representing lower values (origins from the cancer cell lines U2OS and HCT116 cells were not included in this clustered analysis due to the scarcity of available chromatin data). Replication origins associated strongly with unmethylated CpGs and H3K4me3 and, to a lesser extent, with H3K9 acetylation
Fig. 6
Fig. 6
Shared and cell-type-specific replication origins clustered by association with chromatin features. Alignment of origins with chromatin modifications was performed using ColoWeb [48] as exemplified in Fig. 4. Heat maps representing the extent of preferential association of origins with distinct chromatin modifications were clustered by chromatin modifications and cell lines. The extent of association between origins and each modification is color coded, with deeper red color representing higher mean-centered AMI values and blue representing lower values. Shared and cell-type-specific replication origins clustered separately and displayed distinct associations with chromatin modifications
Fig. 7
Fig. 7
Association of subsets of EB replication origins with annotated genomic domains. Subsets of EB replication origins (all origins, shared origins and cell-type-specific origins) were stratified based on replication timing and investigated for their association with K562 genomic domains using SAGA analysis [56]. For each subgroup, the extent of enrichment for a particular domain is indicated on the scale of color bar. Repressive domains include constitutive heterochromatin (CON), facultative heterochromatin (FAC) and quiescent domains (QUI). Active domains include broad expression domains (BRD) and specific expression domains (SPC). The groups designated “early,” “late” and “middle” represent all origins stratified by replication time (during S-phase). The “none” group corresponds to all non-origin positions
Fig. 8
Fig. 8
Timing of replication initiation in shared and cell-type-specific origins. Groups of a EB shared, b EB cell-type-specific, c K562 shared and d K562 cell-type-specific replication origins were stratified according to replication time. Replicating quintiles were created from BED files based on TimEX replication timing data for the EB cells [51] and Repli-seq for the K562 cell line [62]. The frequency of replication initiation in the first, third and fifth quintiles was plotted for genomic regions flanking replication origins. The histogram x axis extends 5-kb upstream and 5-kb downstream from the center of shared or cell-type-specific replication origins. The y axis represents the number of peaks shared among the indicated samples. Data are summarized in the histogram (e). Bar graph depicting the percent of shared (left) and cell-type-specific (right) origins found in each replication timing period. Shared replication origins exhibited a slight preference for early replication, whereas cell-type-specific replication origins were enriched in late timing stages
Fig. 9
Fig. 9
Summary of chromatin modifications associated with shared and cell-type-specific replication origins. Shared origins associated most strongly with unmethylated CpG islands, H3K4me3 and H3K9Ac, while cell-type-specific origins associated mostly with methylated CpG islands and H3K9me3, and preferentially replicated late

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References

    1. Masai H, Matsumoto S, You Z, Yoshizawa-Sugata N, Oda M. Eukaryotic chromosome DNA replication: where, when, and how? Annu Rev Biochem. 2010;79:89–130. doi: 10.1146/annurev.biochem.052308.103205. - DOI - PubMed
    1. Cayrou C, Coulombe P, Mechali M. Programming DNA replication origins and chromosome organization. Chromosome Res. 2010;18(1):137–145. doi: 10.1007/s10577-009-9105-3. - DOI - PubMed
    1. Aladjem MI. Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nat Rev Genet. 2007;8(8):588–600. doi: 10.1038/nrg2143. - DOI - PubMed
    1. Fu H, Wang L, Lin CM, Singhania S, Bouhassira EE, Aladjem MI. Preventing gene silencing with human replicators. Nat Biotechnol. 2006;24(5):572–576. doi: 10.1038/nbt1202. - DOI - PubMed
    1. O’Malley J, Skylaki S, Iwabuchi KA, Chantzoura E, Ruetz T, Johnsson A, Tomlinson SR, Linnarsson S, Kaji K. High-resolution analysis with novel cell-surface markers identifies routes to iPS cells. Nature. 2013;499(7456):88–91. doi: 10.1038/nature12243. - DOI - PMC - PubMed

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