Histone H1 distribution and epitope exposure within chromatin high-order structure
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA561782 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10029301_1.fastq.gz | Fastqsanger.gz | |||
| SRR10029301_2.fastq.gz | Fastqsanger.gz | |||
| SRR10029302_1.fastq.gz | Fastqsanger.gz | |||
| SRR10029302_2.fastq.gz | Fastqsanger.gz | |||
| SRR10029303_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
Project description:Within the cell nucleus, histone H1 is the most mobile histone. Yet, it is regarded as key to the establishment and stability of chromatin higher-order structure. The implication is that chromatin higher-order structure is dynamic, in part due to the mobility of H1. Defining the positions of H1 on chromatin in situ, therefore, represents a challenge. Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq) is traditionally the method for mapping histones onto DNA elements. But since sonication fragmentation precedes ChIP, there is a consequent loss of information about chromatin higher-order structure. A second formaldehyde fixation after antibody binding to intact in situ chromatin, but before sonication (xxChIP-seq), preserves this information and reveals which histone epitopes are inaccessible in situ. In this study, the distribution of two histone H1 variants H1.2 and H1.5 is defined and compared by both xChIP-seq and xxChIP-seq in undifferentiated HL-60/S4 cells, illustrating the influences of preserved chromatin higher-order structure. We have found that xChIP and xxChIP signals are anticorrelated. H1.2 versus H1.5-enrichments were particularly distinct near bound Pol II, SMC3 proteins, as well as domains marked by H3K4me1, H3K9ac, H3K27ac and H3K36me3. H1.5-enriched regions have an average nucleosome repeat length NRL=184 bp, as opposed to 190 bp for H1.2-enriched regions. We have also studied the distribution of H1 variants with respect to DNA methylation. Most changes of DNA methylation during differentiation appear within ~60bp from the nucleosome entry/exit and are preferably associated with H1.2-bound nucleosomes, whereas H1.5 histones are depleted from CpGs. Our results suggest that different physical packing of nucleosomes may exist in H1.2- versus H1.5-enriched areas, characterized by differential H1 epitope exposure as assessed by xChIP and xxChIP.
2020-06-14 | GSE136264 | GEO
Project description:At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles, are distributed differentially along the genome, or regulate specific promoters. By taking advantage of specific antibodies to H1 variants and HA-tagged recombinant H1 variants expressed in a breast cancer-derived cell line, we have investigated the distribution of the different somatic H1 variants (H1.2 to H1.5, H1.0 and H1X) in particular promoters and genome-wide.
2014-02-04 | GSE49334 | GEO
Project description:At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles, are distributed differentially along the genome, or regulate specific promoters. By taking advantage of specific antibodies to H1 variants and HA-tagged recombinant H1 variants expressed in a breast cancer-derived cell line, we have investigated the distribution of the different somatic H1 variants (H1.2 to H1.5, H1.0 and H1X) in particular promoters and genome-wide.
2014-02-04 | GSE49333 | GEO
Project description:At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles, are distributed differentially along the genome, or regulate specific promoters. By taking advantage of specific antibodies to H1 variants and HA-tagged recombinant H1 variants expressed in a breast cancer-derived cell line, we have investigated the distribution of the different somatic H1 variants (H1.2 to H1.5, H1.0 and H1X) in particular promoters and genome-wide. Genome-wide analysis of H1.0, H1.2, H1.4, H1X and H3
2014-02-04 | E-GEOD-49334 | biostudies-arrayexpress
Project description:At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the different variants have specific roles, are distributed differentially along the genome, or regulate specific promoters. By taking advantage of specific antibodies to H1 variants and HA-tagged recombinant H1 variants expressed in a breast cancer-derived cell line, we have investigated the distribution of the different somatic H1 variants (H1.2 to H1.5, H1.0 and H1X) in particular promoters and genome-wide. Analysis of H1 (H1.0, H1.2, H1.3, H1.4, H1.5 and H1X) and H3 abundance in promoter regions
2014-02-04 | E-GEOD-49333 | biostudies-arrayexpress
Project description:Most important characteristics of antibodies are that they typically strongly bind to specific epitopes, thereby expressing low dissociation constants (KDs) and high Gibbs free binding energies (delta Gs). In this study, we describe an off-line nano-electrospray mass spectrometry method, termed ITEM-TWO, which enables one to simultaneously identify epitopes and obtain characteristic gas phase dissociation constants of antibody - epitope interactions in a single experiment. To validate the method, we characterize the interaction between an antiHistag antibody and its epitope peptide obtained from a tryptic digest of a His-tag containing beta actin. In a mixture of solution 1 (tryptic digest of a His-tag containing recombinant human beta-actin protein in 30 mM ammonium bicarbonate) and solution 2 (antiHis-tag antibody in 200 mM ammonium acetate) the specific immune complexes form (molar ratio 2.2 : 1). Without any purification steps this mixture (solution 3) is then electrosprayed. With the aid of a quadrupole ion filter, the immune complex ions are separated from unbound peptide ions. Increasing the voltage difference (DeltaCV) in the subsequent collision cell results in collision induced dissociation (CID) by which the epitope peptide(s) is(are) released from the immune complex. The mass(es) of the complex-released peptide(s) is(are) then measured in a ToF analyzer by which the epitope is identified. A step-wise increase in DeltaCV allows the simultaneous determination of the intensities of (i) the surviving ionized immune complexes together with (ii) released epitope peptide ions plus (iii) the left behind antibody ions. From the ions´ normalized intensity ratios are deduced the apparent gas phase dissociation constants (KD#m0g) and the apparent dissociation energies over temperature values (delta G#m0g / T) of the gas phase dissociation processes.
2019-11-07 | PXD016024 | Pride
Project description:Caulobacter sp. H1 strain:H1 Genome sequencing
| PRJNA546640 | ENA
Project description:Lactobacillus sp. H1 strain:H1 Genome sequencing
| PRJNA874879 | ENA
Project description:We studied how H1 regulates higher-order chromatin architecture by performing Hi-C. In addition, we tested the effects of H1 domains on nucleosome organisation and DNA methylation by performing MNase-seq and Bisulfite-seq.
2024-02-15 | GSE176526 | GEO
Project description:Halomonas sp. H1 strain:H1 Genome sequencing and assembly
| PRJNA737521 | ENA