GEO DataSets

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The H3-H4 modification landscape is restored by parental histone recycling and post-replication modification of new histone H3-H4. How DNA replication impact on histone H2A-H2B is unknown. Here, we track H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30173 GPL30172 GPL19057

54 Samples

Download data: BED, BW

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and need to be restored faithfully to maintain appropriate gene expression, including post-translational modifications (PTMs) of newly deposited histones. Whether histones H2A-H2B are accurately recycled during DNA replication and the behaviour of their associated marks during and post replication is unknown. Here we comprehensively map key modifications on H2A-H2B including H2A.Z during DNA replication. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

22 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL30173 GPL19057 GPL30172

366 Samples

Download data: BW, TXT

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The H3-H4 modification landscape is restored by parental histone recycling and post-replication modification of new histone H3-H4. How DNA replication impact on histone H2A-H2B is unknown. Here, we track H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

134 Samples

Download data: BED, TXT

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The H3-H4 modification landscape is restored by parental histone recycling and post-replication modification of new histone H3-H4. How DNA replication impact on histone H2A-H2B is unknown. Here, we track H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30173 GPL30172 GPL19057

156 Samples

Download data: BW

(Submitter supplied) Chromatin organisation is disrupted genome wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naïve histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is copied during DNA replication or the epigenomeis perturbed. Here we develop Chromatin Occupancy after Replication, ChOR-seq, a technology that combines chromatin immunopreciptation of histone marks and purification of newly replicated DNA by streptavidin pull-down followed by next generation sequencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

22 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL20301

57 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Chromatin organisation is disrupted genome wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naïve histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is copied during DNA replication or the epigenomeis perturbed. Here we develop Chromatin Occupancy after Replication, ChOR-seq, a technology that combines chromatin immunopreciptation of histone marks and purification of newly replicated DNA by streptavidin pull down followed by next generation sequencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

11 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Chromatin organisation is disrupted genome wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naïve histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is copied during DNA replication or the epigenomeis perturbed. Here we develop Chromatin Occupancy after Replication, ChOR-seq, a technology that combines chromatin immunopreciptation of histone marks and purification of newly replicated DNA by streptavidin pull-down followed by next generation sequencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. more...

Organism:

Toxoplasma gondii RH

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24058

23 Samples

Download data: BED, BROADPEAK, BW, NARROWPEAK

(Submitter supplied) Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. more...

Organism:

Toxoplasma gondii RH; Toxoplasma gondii ME49

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL15564 GPL15563

10 Samples

Download data: GFF, PAIR, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL19132 GPL21306 GPL25244

154 Samples

Download data

(Submitter supplied) Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onwards. Lack of new histone synthesis and parental histone recycling leads to more accessible chromatin and reduced nucleosome occupancy. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL25244

18 Samples

Download data: BW

(Submitter supplied) Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onwards. Lack of new histone synthesis and parental histone recycling leads to more accessible chromatin and reduced nucleosome occupancy. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

81 Samples

Download data: BED, BW

(Submitter supplied) Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onwards. Lack of new histone synthesis and parental histone recycling leads to more accessible chromatin and reduced nucleosome occupancy. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

8 Samples

Download data: BW

(Submitter supplied) Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onwards. Lack of new histone synthesis and parental histone recycling leads to more accessible chromatin and reduced nucleosome occupancy. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21306

24 Samples

Download data: BW

(Submitter supplied) Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onwards. Lack of new histone synthesis and parental histone recycling leads to more accessible chromatin and reduced nucleosome occupancy. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

23 Samples

Download data: TXT

(Submitter supplied) Histone variants are key components of the epigenetic code and evolved to perform specific functions in transcriptional regulation, DNA repair, chromosome segregation and other fundamental processes. H2B.Z is a rare, apicomplexan-specific variant of histone H2B. Here we show that in Plasmodium falciparum H2B.Z localises to euchromatic intergenic regions throughout intraerythrocytic development and together with H2A.Z forms a double-variant nucleosomes subtype. more...

Organism:

Plasmodium falciparum 3D7

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15857

6 Samples

Download data: GFF

(Submitter supplied) Faithful transfer of parental histones to newly replicated daughter DNA strands is critical for inheritance of epigenetic states. Although replication proteins that facilitate parental histone transfer have been identified, how intact histone H3-H4 tetramers travel relatively large distances from the front to the back of the replication fork remains unknown. Here, we use AlphaFold-Multimer structural predictions combined with biochemical and genetic approaches to identify the Mrc1/CLASPIN subunit of the replisome as a histone chaperone. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL20584

8 Samples

Download data: BW

(Submitter supplied) DNA replication is a tightly regulated process that ensures the precise duplication of the genome during cell cycle. Licensing and activation of eukaryotic replication origins are controlled primarily by chromatin. However, the chromatin features involved and the regulatory mechanism remain largely unknown. In this study, we found that H2A.Z binds Suv420H1 directly to promote H4K20me2 deposition on nucleosome both in vitro and in vivo. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL11154

63 Samples

Download data: BED, BW, TXT