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Cell cycle analysis of histone marks and 4C in human Fucci ESCs

ABSTRACT: Using the Fucci cell cycle indicator system in hESCs, we evaluated the patterns of bivalent histone marks and enhancer histone marks during the cell cycle by ChIP-seq. We further evaluated how the chromatin architecture changed during the cell cycle. We found that bivalent domains are cell cycle regulated, and H3K4me3 specifically peaks during the late G1 stage of the cell cycle. H3K27me3, however, is largely unchanged during the cell cycle. Cell cycle-regulated bivalent domains interact with enhancers and form cell cycle regulated chromatin interactions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE61176 | GEO | 2015/06/23

SECONDARY ACCESSION(S): PRJNA260404

REPOSITORIES: GEO

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Cell cycle analysis of histone marks and 4C in human Fucci ESCs

Project description:Using the Fucci cell cycle indicator system in hESCs, we evaluated the patterns of bivalent histone marks and enhancer histone marks during the cell cycle by ChIP-seq. We further evaluated how the chromatin architecture changed during the cell cycle. We found that bivalent domains are cell cycle regulated, and H3K4me3 specifically peaks during the late G1 stage of the cell cycle. H3K27me3, however, is largely unchanged during the cell cycle. Cell cycle-regulated bivalent domains interact with enhancers and form cell cycle regulated chromatin interactions. FACS-isolated cell cycle fractions (DN, early G1; KO2, late G1; AzL, S-phase; and AzH, G2/M) from Fucci hESCs were subject to ChIP-seq for H3K4me3, H3K27me3, H3K27ac and H3K4me1, and used for sequencing along with input controls for each of the 4 cell cycle fractions (20 samples total), using Illumina platform, or 4C-seq for each cell cycle fraction using viewpoints neighboring the GATA6 or SOX17 promoters.

2015-06-23 | E-GEOD-61176 | biostudies-arrayexpress

HCT 116 cells expressing Fucci (fluorescent ubiquitination-based cell cycle indicator); G1 phase vs. S/G2/M phase

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Unique cell cycle-dependent variations in the pluripotent epigenetic landscape define novel cohorts of temporal expressed bivalent genes during hESCs differentiation

Project description:By mapping the genomic enrichmentsÂ of H3K4me3 and H3K27me3 modifications in pure populations of hESCs during the G2, mitotic and G1 phases of the cell cycle, we characterize cell cycle-dependent variations in the epigenetic landscape of bivalent genes, altering the current view of mitotic inheritance in pluripotent cells. We identified novel classes of bivalent domains that are highly enriched with H3K4me3 during mitosis, depleted during G1 only, and ubiquitously bivalent. These bivalent domains are associated with specific genes and expression patterns during differentiation. These cell cycle-dependent epigenetic profiles are unique to hESCs and are not observed following initiation of phenotype commitment. Our results establish a new dimension in cell cycle-dependent chromatin regulation that advances understanding of contributions the pluripotent epigenetic landscape to hESC identity. Study of two histone modifications, H3K4me3 and H3K27me3, during three cell cycle phases in two cell types. Study of gene expression from these two cell types in asynchronous cells.

2015-12-23 | E-GEOD-55502 | biostudies-arrayexpress

Unique cell cycle-dependent variations in the pluripotent epigenetic landscape define novel cohorts of temporal expressed bivalent genes during hESCs differentiation

Project description:By mapping the genomic enrichments of H3K4me3 and H3K27me3 modifications in pure populations of hESCs during the G2, mitotic and G1 phases of the cell cycle, we characterize cell cycle-dependent variations in the epigenetic landscape of bivalent genes, altering the current view of mitotic inheritance in pluripotent cells. We identified novel classes of bivalent domains that are highly enriched with H3K4me3 during mitosis, depleted during G1 only, and ubiquitously bivalent. These bivalent domains are associated with specific genes and expression patterns during differentiation. These cell cycle-dependent epigenetic profiles are unique to hESCs and are not observed following initiation of phenotype commitment. Our results establish a new dimension in cell cycle-dependent chromatin regulation that advances understanding of contributions the pluripotent epigenetic landscape to hESC identity.

2015-12-23 | GSE55502 | GEO

HCT 116 cells expressing Fucci (fluorescent ubiquitination-based cell cycle indicator); G1 phase vs. S/G2/M phase

2014-01-09 | E-GEOD-34940 | biostudies-arrayexpress

Gene expression profiling by array of human non-transformed RPE-FUCCI (Fluorescent Ubiquitination-based Cell Cycle Indicator) cells

Project description:Progression through the cell cycle is driven by cyclin dependent kinases that control gene expression, orchestration of the mitotic spindle and cell division. Here we used a Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) and performed transcriptomic analysis of human non-transformed cells. Cell sorting allowed efficient isolation of G1, S and G2 cells from asynchronously growing cell cultures. Altogether, we identified 701 differentially expressed genes in G1 and G2 cells.

2021-04-06 | E-MTAB-9626 | biostudies-arrayexpress

Homo sapiens

Project description:Cell cycle analysis of histone marks and 4C in human Fucci ESCs

| PRJNA260404 | ENA

Cell cycle positioning drives heterogeneity within the pluripotent stem cell compartment

Project description:Heterogeneity in pluripotent cells marks a metastable state where cells may drift between native and lineage-primed populations. While the role for these heterogeneities are unclear, they may reflect the dynamic equilibriums of signaling networks and have a direct effect on differentiation potentialities. Here, we report the role of the cell cycle in establishing heterogeneity of human pluripotent stem cells. By utilizing the FUCCI cell cycle indicator system coupled to fluorescent activated cell sorting (FACS), we have uncovered that the cell cycle drives heterogeneity at the epigenetic, transcriptional and post-transcriptional levels. Our data show widespread dynamics in 5-hydroxymethylcytosine (5hmC) during the cell cycle. Furthermore, transcript profiling by RNA-sequencing identified >500 genes that were cell cycle-regulated, of which the largest cohort of genes were transcriptional regulators. In sum, we demonstrate the role of the cell cycle in coordinating cellular transitions between metastable states in pluripotent stem cells. mRNA sequencing of the cell cycle phases; early & late G1, S and G2/S from human ES cells in triplicate.

2013-12-19 | E-GEOD-53481 | biostudies-arrayexpress

Cell cycle positioning drives heterogeneity within the pluripotent stem cell compartment

2013-12-19 | GSE53481 | GEO

Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline

Project description:The male germline transcriptome changes dramatically during the mitosis-to-meiosis transition to activate late spermatogenesis genes and to transiently suppress genes commonly expressed in somatic lineages and spermatogenesis progenitor cells, termed somatic/progenitor genes. These changes reflect epigenetic regulation. Induction of late spermatogenesis genes during spermatogenesis is facilitated by poised chromatin established in the stem cell phases of spermatogonia, whereas silencing of somatic/progenitor genes during meiosis and postmeiosis is associated with formation of bivalent domains which also allows the recovery of the somatic/progenitor program after fertilization. Importantly, during spermatogenesis mechanisms of epigenetic regulation on sex chromosomes are different from autosomes: X-linked somatic/progenitor genes are suppressed by meiotic sex chromosome inactivation without deposition of H3K27me3. Our results suggest that bivalent H3K27me3 and H3K4me2/3 domains are not limited to developmental promoters (which maintain bivalent domains that are silent throughout the reproductive cycle), but also underlie reversible silencing of somatic/progenitor genes during the mitosis-to-meiosis transition in late spermatogenesis. 29 samples analyzed by ChIP-Seq

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