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Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

ABSTRACT: Short nascent strands purification coupled to next-generation sequencing allowed us to identify replication origins on human genome in an extensive way, by mapping replication origins in 4 different cell types, IMR-90 fibroblasts, hESC H9 cells, iPSC Th Cl-4 cells and HeLa cells. We demonstrated the existence of a cell type-specific reprogrammable signature of the cell identity revealed by specific efficiencies of conserved origin positions and not by the selection of cell-type specific subsets of origins.

ORGANISM(S): Homo sapiens

PROVIDER: GSE37757 | GEO | 2012/07/01

SECONDARY ACCESSION(S): PRJNA163241

REPOSITORIES: GEO

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Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

Project description:Short nascent strands purification coupled to next-generation sequencing allowed us to identify replication origins on human genome in an extensive way, by mapping replication origins in 4 different cell types, IMR-90 fibroblasts, hESC H9 cells, iPSC Th Cl-4 cells and HeLa cells. We demonstrated the existence of a cell type-specific reprogrammable signature of the cell identity revealed by specific efficiencies of conserved origin positions and not by the selection of cell-type specific subsets of origins. 4 different cell types were analyzed. For each cell types, 2 different biological replicates of short nascent strands at replication origins were purified. Each SNS sample was sequencing at least one time.

2012-07-01 | E-GEOD-37757 | biostudies-arrayexpress

Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates

Project description:Replication of vertebrate genomes is tightly regulated to ensure accurate duplication, but our understanding of the interplay between genetic and epigenetic factors in this regulation remains incomplete. Here, we investigated the involvement of three elements enriched at gene promoters and replication origins: guanine-rich motifs potentially forming G-quadruplexes (pG4s), nucleosome-free regions (NFRs), and the histone variant H2A.Z, in the firing of origins of replication in vertebrates. We show that two pG4s on the same DNA strand (dimeric pG4s) are sufficient to induce assembly of an efficient minimal replication origin without inducing transcription. Dimeric pG4s in replication origins trigger formation of an NFR next to precisely positioned nucleosomes enriched in H2A.Z on this minimal origin and genome-wide. Thus, our data suggest a crucial role for dimeric pG4s in the organization and duplication of vertebrate genomes. It supports the hypothesis that a nucleosome close to an NFR is a shared signal for the formation of replication origins in eukaryotes.

2023-07-19 | GSE231492 | GEO

Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates

Project description:Dimeric G-quadruplex motifs-induced NFRs determine strong replication origins in vertebrates

| PRJNA966151 | ENA

RNASeq samples of OSKM reprogrammable MEFs treated with various compounds

Project description:RNASeq samples of OSKM reprogrammable MEFs treated with various compounds

| PRJNA971892 | ENA

Triple transgenic reprogrammable mouse model reveals no evidence of epigenetic memory in reprogrammed cells/induced pluripotent stem cells

Project description:Virtually any nucleated somatic cell can be reprogrammed to an induced pluripotent stem cell (iPSC). The process of reprogramming involves epigenetic remodelling to turn on pluripotency-associated genes and turn off lineage-specific genes. Some evidence shows that iPSC retain epigenetic marks of their cell of origin and this “epigenetic memory” influences differentiation potential, with a preference towards their cell of origin. Here, we reprogrammed proximal tubule cells (PTC) and tail tip fibroblasts (TTF), from a reprogrammable mouse, to iPSC and differentiated the iPSC to renal progenitors to understand if epigenetic memory plays a role in renal differentiation. The reprogrammable mouse model allowed us to eliminate the variability due to different cell donors and transfection of the reprogramming factors. We showed that early passage PTC iPSC and TTF iPSC expressed low levels of renal progenitor genes and high levels of pluripotency-associated genes, and the transcriptional levels of these genes were not significantly different between PTC iPSC and TTF iPSC. In agreement with this, we used ChIP-seq to demonstrate that the H3K4me3, H3K27 and H3K36me3 profiles of PTC iPSC and TTF iPSC were not different from each other for kidney developmental genes and pluripotency-associated genes. DNA methylation also demonstrated no difference between PTC iPSC and TTF iPSC. However, when the iPSC were differentiated to renal progenitors, the progenitors derived from PTC iPSC expressed higher levels of some renal progenitor genes compared to progenitors derived from TTF iPSC. This demonstrates that although PTC iPSC and TTF iPSC are epigenetically identical, there are still differences in their response and sensitivity to differentiation cues and this ultimately influences their differentiation propensity.

2022-11-21 | GSE195511 | GEO

RNASeq samples of OSKM reprogrammable MEFs treated with or without vitamin B12

Project description:RNASeq samples of OSKM reprogrammable MEFs treated with or without vitamin B12

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Single-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control

Project description:The chromatin at origins of replication is thought to influence DNA replication initiation in eukaryotic genomes. However, it remains unclear how the chromatin composition controls the firing of early-efficient (EE) or late-inefficient (LI) origins. Here, we used site-specific recombination and single-locus chromatin isolation to purify EE and LI replication origins in Saccharomyces cerevisiae . Using mass spectrometry, we define the histone modification landscape and identify the protein composition of native chromatin regions surrounding the EE and LI replication start sites. In addition to the known origin interactors, we find novel origin-associated factors, such as the kinetochore-associated Ask1/DASH complex. Strikingly, we show that Ask1 regulates the replication timing control of specific origins in yeast. Thus, our unbiased approach identifies functionally-relevant proteomes at single-copy loci and would be widely applicable to provide an in-depth quantitative characterization of histone modification and protein interaction networks of chromatin at any genomic locus of interest.

2023-02-16 | PXD032930 | Pride

Phosphorylated SIRT1 associates with replication origins to prevent excess replication initiation and preserve genomic stability

Project description:Chromatin structure affects DNA replication patterns, but the role of specific chromatin modifiers in regulating the replication process is yet unclear. We report that phosphorylation of the human SIRT1 deacetylase on Threonine 530 (T530-pSIRT1) modulates DNA synthesis. T530-pSIRT1 associates with replication origins and inhibits replication from a group of ÒdormantÓ potential replication origins, which initiate replication only when cells are subject to replication stress. Although both active and dormant origins bind T530-pSIRT1, active origins are distinguished from dormant origins by their unique association with an open chromatin mark, histone H3 methylated on lysine 4. SIRT1 phosphorylation also facilitates leading and lagging strand coordination. SIRT1 T530 phosphorylation is essential to prevent DNA breakage upon replication stress and cells harboring SIRT1 that cannot be phosphorylated exhibit a high prevalence of extrachromosomal elements, hallmarks of perturbed replication. These observations suggest that SIRT1 phosphorylation modulates the distribution of replication initiation events to insure genomic stability.

2017-06-02 | GSE94403 | GEO

Homo sapiens

Project description:Allele-Specific Analysis of DNA Replication Origins in Mammalian Cells

| PRJNA262831 | ENA

Single-copy locus isolation identifies distinct proteomes of early- and late-firing DNA replication origin chromatin

Project description:The chromatin at origins of replication is the template for DNA replication initiation in eukaryotic genomes. However, whether the chromatin composition instructs individual origins to fire early-efficiently (EE) or late-inefficiently (LI) remains to be investigated. Here, we used site-specific recombination and a single-locus chromatin isolation approach to purify selected EE and LI replication origins from chromosome III of Saccharomyces cerevisiae. Using mass spectrometry, we define the histone modification landscape and identify the protein composition of defined ~1kb native chromatin regions surrounding the EE and LI replication start sites. We confirm expected origin interactors but also find unexpected interactions, such as the Ask1 subunit of the kinetochore-associated DASH complex. Strikingly, we show that Ask1 is a critical factor in the replication timing control of specific origins in yeast. These results highlight that our unbiased approach can specifically identify the functionally-relevant proteome at a single-copy locus of interest and provide a detailed view of histone modification and protein interaction networks on replication origin chromatin. The current dataset contains proteomic data used for the histone PTM analysis.

2023-05-10 | PXD031984 | Pride

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