Human Genome Replication Proceeds through Four Chromatin States

Julienne, Hannah; Zoufir, Azédine; Audit, Benjamin; Arnéodo, A.

doi:10.1371/journal.pcbi.1003233

Cited by 57 publications

(102 citation statements)

References 132 publications

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“…For example, the repressive mark H3K27me3 has been reported to associate with early to mid replication and with early and mid origins (Chandra et al, 2012;Julienne et al, 2013;Picard et al, 2014), as well as with late replication (Thurman et al, 2007). In our data, peaks of H3K27me3 appear to follow two different patterns.…”

Section: Replication Timing In Relation To Chromatin Packagingmentioning

confidence: 43%

“…We found a similar association of early replication and active modifications in maize. Many active modifications (e.g., H3K4me2/3, H3K36me3, and H3ac) are typically found in the same regions of the genome (Roudier et al, 2011;Julienne et al, 2013) and are usually more indicative of gene expression than replication time . By selecting H3K4me3 and H3K56ac, we have likely captured a reasonable consensus of the open regions containing active histone marks within the cell types in the maize root tip.…”

Section: Replication Timing In Relation To Chromatin Packagingmentioning

confidence: 99%

“…There is less consensus on the association of late replication with repressive chromatin modifications (e.g., H3K27me3, H3K9me2/3, and H3K20me3) (e.g., Lee et al, 2010;Julienne et al, 2013;Rhind and Gilbert, 2013) and observed associations vary among cell types (Hiratani et al, 2008;Ryba et al, 2010;Rhind and Gilbert, 2013). For example, the repressive mark H3K27me3 has been reported to associate with early to mid replication and with early and mid origins (Chandra et al, 2012;Julienne et al, 2013;Picard et al, 2014), as well as with late replication (Thurman et al, 2007).…”

Section: Replication Timing In Relation To Chromatin Packagingmentioning

confidence: 99%

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Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear

Song²,

Zynda³

et al. 2017

Plant Cell

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All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ;32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.

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Section: Replication Timing In Relation To Chromatin Packagingmentioning

confidence: 43%

Section: Replication Timing In Relation To Chromatin Packagingmentioning

confidence: 99%

Section: Replication Timing In Relation To Chromatin Packagingmentioning

confidence: 99%

See 1 more Smart Citation

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear

Song²,

Zynda³

et al. 2017

Plant Cell

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“…When further investigating the spatial distribution of the P1, P2, P3 and P4 promoters along human chromosomes, our study reveals a remarkable gene organization in relation with the MRT. In 50% of the human genome that are covered by megabase-sized replication U-domains Julienne et al 2013), a significant enrichment of highly expressed P1 genes is observed in a closed neighbourhood of the early C1 initiation zones that border these domains. P2 promoters are mainly found in the mid-S C2 environment at finite distance (∼200-300 kb) from U-domain borders.…”

Section: Conclusion/perspectivesmentioning

confidence: 99%

“…In the third section, we perform a combinatorial analysis of chromatin marks in K562 and we describe the epigenetic content of the four prevalent chromatin states at gene promoters. In the fourth section, we study the coherence between promoter activity, as characterized by their 'small-scale' chromatin state, and the 'large-scale' chromatin environment (namely the C1, C2, C3 and C4 chromatin states found in Julienne et al (2013)). In this comparative analysis we emphasize the expected as well as the unexpected importance of gene density on the observed relationship between these two scales characterizing transcription and replication data respectively.…”

Section: Introductionmentioning

confidence: 99%

Epigenetic regulation of the human genome: coherence between promoter activity and large-scale chromatin environment

Julienne

Zoufir

Audit

et al. 2013

Frontiers in Life Science

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Increasing knowledge of chromatin structure in various cell types raises the challenge of deciphering the contribution of epigenetic modifications to the regulation of nuclear functions in mammals. In a recent study, we have analysed the genomewide distributions of thirteen epigenetic marks in the human cell line K562 at 100 kb resolution of Mean Replication Timing (MRT) data. Using classical clustering techniques, we have shown that the combinatorial complexity of these epigenetic data can be reduced to four predominant chromatin states that replicate at different periods of the S-phase. C1 is an early replicating transcriptionally active euchromatin state, C2 a mid-S repressive type of chromatin associated with Polycomb complexes, C3 a silent chromatin with lack of chromatin marks that replicates later than C2 but before C4, a HP1-associated heterochromatin state that replicates at the end of S-phase. These four chromatin states display remarkable similarities with those recently reported in fly, worm and plants at higher ∼ 1 kb resolution of gene expression data. Here, we extend our integrative analysis of epigenetic data in the K562 human cell line to this smaller scale by focusing on gene promoters (±3 kb around transcription start sites). We show that these promoters can similarly be classified into four main chromatin states: P1 regroups all the marks of transcriptionally active chromatin and corresponds to CpG rich promoters of highly expressed genes; P2 is notably associated with the histone modification H3K27me3 that is the mark of a polycomb repressed chromatin state; P3 corresponds to promoters that are not enriched for any available marks as the signature of a 'null' or 'black' silent heterochromatin state and P4 characterizes the few gene promoters that contain only the constitutive heterochromatin histone modification H3K9me3. When investigating the coherence between promoter activity (P1, P2, P3 or P4) and the large-scale chromatin environment (C1, C2, C3 or C4), we find that the higher the gene density in a considered 100 kb-window, the higher (resp. the lower) the probability of a P1 active promoter (resp. silent P2, P3 and P4 promoters) to be surrounded by an open euchromatin C1 (resp. facultative C2, black C3 or HP1-associated C4 heterochromatin) environment. From large to small scales, it is mainly C4 and to a lesser extent C3 heterochromatin environments both corresponding to gene poor regions, that strongly conditions promoters to belong to the inactive P3 and P4 classes. If C1 (resp. C2) environment surrounds a majority of corresponding active P1 (resp. P2) promoters, it also contains a non-negligible proportion of inactive P2 and P3 (resp. active P1 and inactive P3) promoters. When further investigating the large-scale organization of human genes with respect to 'master' replication origins that were shown to border megabase-sized U-shaped MRT domains, we reveal some significant enrichment of highly expressed P1 genes in a closed neighbourhood of these early initiation zones consistently...

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Genome Organisation and Chromosome Architecture from Interphase to Metaphase

Bernardi

2016

Encyclopedia of Life Sciences

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It is well established that vertebrate and other eukaryotic genomes are compositionally compartmentalised into long (≥200 Kb) sequences, the isochores, that are fairly homogeneous in their basic composition, and belong to a small number of families (five in the human genome). On the other hand, recent investigations in many laboratories have led to a new vision of interphase chromatin, which basically consists of large loops (average size ∼186 Kb in the case of the human genome) and anchors held together by ‘architectural’ proteins such as CTCF (the CCCTC‐binding factor) and cohesin. A very recent analysis has revealed correlations between isochores from different families and the architectural features of chromosomes through the cell cycle. This leads to a unifying view of the genome organisation and chromosome architecture. Key Concepts The long‐range compositional organisation of the genome of vertebrates and of other eukaryotes (i.e. the isochore organisation) is correlated with the chromosome architecture through the cell cycle. This leads to a unifying view of genome organisation and chromosome architecture. In spite of very extensive investigations over many years, the organization of the eukaryotic genome and the architecture of chromosomes from interphase to metaphase are two problems that are still open because of their complexity. A combination of a large‐scale compositional analysis of vertebrate genomes and of the recent results on the architecture of interphase chromatin led to a solution of those problems. The large‐scale compositional analysis revealed that vertebrate genomes consist of long (≥200 kilobases) fairly homogenous DNA segments, the isochores. Cross‐linking of contact regions of chromatin and sequencing (chromosome conformation captureand its variants) provided a picture of three‐dimensional interphase chromatin structure. The long‐range compositional organization of the genome of vertebrates and of other eukaryotes (i.e., the isochore organization) was shown to be correlated with the chromosome architecture through the cell cycle. The correlations between the isochore organization of the genome and the chromosome architecture through the cell cycle (especially the architecture of interphase chromatin structure) led to a unifying view of genome organization and chromosome architecture.

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Human Genome Replication Proceeds through Four Chromatin States

Cited by 57 publications

References 132 publications

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Epigenetic regulation of the human genome: coherence between promoter activity and large-scale chromatin environment

Genome Organisation and Chromosome Architecture from Interphase to Metaphase

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