Temporal gene regulation by p53 is associated with the rotational setting of its binding motifs in nucleosomes
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ABSTRACT:
PROVIDER: PRJNA660785 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12566302.fastq.gz | Fastqsanger.gz | |||
| SRR12566303.fastq.gz | Fastqsanger.gz | |||
| SRR12566304.fastq.gz | Fastqsanger.gz | |||
| SRR12566305.fastq.gz | Fastqsanger.gz | |||
| SRR12566306.fastq.gz | Fastqsanger.gz |
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Project description:HCT116 cells treated with 5-FU along with DMSO and non-treatment controls using time-course RNA-seq were used to investigate target genes regulated by p53 at the different timepoints.
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Project description:Proper nucleosome positioning is essential for gene regulation and genomic integrity. The need for nucleosomes to be assembled throughout the genome has to be balanced with known intrinsic sequence preferences of nucleosomes. Current models posit that chromatin regulators override the intrinsic preferences to establish the nucleosome landscapes observed in vivo. Here, in contrast, we find that chromatin regulators take advantage of both the preference of the nucleosomes for A/T dinucleotides to face inward and G/C outward every 10 bp relative to the histone surface and the existing dinucleotide frequencies of the genome to move nucleosomes in discrete 10 bp steps. We find that the rotational settings of nucleosomes are identical in vivo and in vitro in yeast. Remodelers and transcription elongation change the preference among the alternative translational positions 10 bp apart that a given rotational setting allows. Our results support a model where strong rotational settings introduce a 10 bp ratchet for nucleosome mobilization, leading to quantized shifts in nucleosome positions in yeast and mouse cells.
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Project description:Plant and animal centromeres comprise megabases of highly repeated satellite sequences, yet centromere function can be specified epigenetically on single-copy DNA by the presence of nucleosomes containing a centromere-specific variant of histone H3 (cenH3). We determined the positions of cenH3 nucleosomes in rice (Oryza sativa), which has centromeres composed of both the 155-bp CentO repeat and single-copy non-CentO sequences. We find that cenH3 nucleosomes protect 90-100 bp of DNA from micrococcal nuclease digestion, sufficient for only a single wrap of DNA around the cenH3 nucleosome core. cenH3 nucleosomes are translationally phased with 155-bp periodicity on CentO repeats, but not on non-CentO sequences. CentO repeats have a ~10-bp periodicity in WW dinucleotides and in micrococcal nuclease cleavage, providing evidence for rotational phasing of cenH3 nucleosomes on CentO, and suggesting that satellites evolve for translational and rotational stabilization of centromeric nucleosomes. Examination of measured size of rice centromere nucleosome
2013-11-06 | E-GEOD-50755 | biostudies-arrayexpress
Project description:Plant and animal centromeres comprise megabases of highly repeated satellite sequences, yet centromere function can be specified epigenetically on single-copy DNA by the presence of nucleosomes containing a centromere-specific variant of histone H3 (cenH3). We determined the positions of cenH3 nucleosomes in rice (Oryza sativa), which has centromeres composed of both the 155-bp CentO repeat and single-copy non-CentO sequences. We find that cenH3 nucleosomes protect 90-100 bp of DNA from micrococcal nuclease digestion, sufficient for only a single wrap of DNA around the cenH3 nucleosome core. cenH3 nucleosomes are translationally phased with 155-bp periodicity on CentO repeats, but not on non-CentO sequences. CentO repeats have a ~10-bp periodicity in WW dinucleotides and in micrococcal nuclease cleavage, providing evidence for rotational phasing of cenH3 nucleosomes on CentO, and suggesting that satellites evolve for translational and rotational stabilization of centromeric nucleosomes.
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Project description:The precise mechanisms governing sequence-dependent positioning of nucleosomes on DNA remain unknown in detail. Existing algorithms, taking into account the sequence-dependent deformability of DNA and its interactions with the histone globular domains, predict rotational setting of only 65% of human nucleosomes mapped in vivo. To uncover novel factors responsible for the nucleosome positioning, we analyzed potential involvement of the histone N-tails in this process. To this aim, we reconstituted the H2A/H4 N-tailless nucleosomes on human BRCA1 DNA (~100 kb) and compared their positions and sequences with those of the wild-type nucleosomes. In the case of H2A tailless nucleosomes, the AT content of DNA sequences is changed locally at superhelical location (SHL) ±4, while maintaining the same rotational setting as their wild-type counterparts. Conversely, the H4 tailless nucleosomes display widespread changes of the AT content near SHL ±1 and SHL ±2, where the H4 N-tails interact with DNA. Furthermore, a substantial number of H4 tailless nucleosomes exhibit rotational setting opposite to that of the wild-type nucleosomes. Thus, our findings strongly suggest that the histone N-tails are operative in selection of nucleosome positions, which may have wide-ranging implications for epigenetic modulation of chromatin states.
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Project description:The tumor suppressor protein p53 is a DNA-binding transcription factor (TF) that, once activated, coordinates the expression of thousands of target genes. Increased p53 binding to gene promoters occurs shortly after p53 activation. Intriguingly, gene transcription exhibits differential kinetics with some genes being induced early (early genes) and others being induced late (late genes). To understand pre-binding factors contributing to the temporal gene regulation by p53, we performed time-course RNA sequencing experiments in human colon cancer cell line HCT116 treated with fluorouracil to identify early and late genes. Published p53 ChIP fragments co-localized with the early or late genes were used to uncover p53 binding sites (BS). We demonstrate that the BS associated with early genes are clustered around gene starts with decreased nucleosome occupancy. DNA analysis shows that these BS are likely exposed on nucleosomal surface if wrapped into nucleosomes, thereby facilitating stable interactions with and fast induction by p53. By contrast, p53 BS associated with late genes are distributed uniformly across the genes with increased nucleosome occupancy. Predicted rotational settings of these BS show limited accessibility. We therefore propose a hypothetical model in which the BS are fully, partially or not accessible to p53 in the nucleosomal context. The partial accessibility of the BS allows subunits of a p53 tetramer to bind, but the resulting p53-DNA complex may not be stable enough to recruit cofactors, which leads to delayed induction. Our work highlights the importance of DNA conformations of p53 BS in gene expression dynamics.
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Project description:We used wheat as rotational crop to assess the influence of continuous cropping on microbiome in Pinellia ternata rhizosphere and the remediation of rotational cropping to the impacted microbiota. Illumina high-throughput sequencing technology was utilized for this method to explore the rhizosphere microbial structure and diversity based on continuous and rotational cropping.
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Project description:Cisplatin and carboplatin are used successfully to treat various types of cancer. The drugs target the nucleosomes of cancer cells and form intrastrand DNA cross-links that are located in the major groove. We constructed two site-specifically modified nucleosomes containing defined intrastrand cis-{Pt(NH3)2}(2+) 1,3-d(GpTpG) cross-links. Histones from HeLa-S3 cancer cells were transferred onto synthetic DNA duplexes having nucleosome positioning sequences. The structures of these complexes were investigated by hydroxyl radical footprinting. Employing nucleosome positioning sequences allowed us to quantify the structural deviation induced by the cisplatin adduct. Our experiments demonstrate that a platinum cross-link locally overrides the rotational setting predefined in the nucleosome positioning sequence such that the lesion faces toward the histone core. Identical results were obtained for two DNA duplexes in which the sites of platination differed by approximately half a helical turn. Additionally, we determined that cisplatin unwinds nucleosomal DNA globally by approximately 24 degree. The intrastrand cis-{Pt(NH3)2}(2+) 1,3-d(GpTpG) cross-links are located in an area of the nucleosome that contains locally overwound DNA in undamaged reference nucleosomes. Because most nucleosome positions in vivo are defined by the intrinsic DNA sequence, the ability of cisplatin to influence the structure of these positioned nucleosomes may be of physiological relevance.
| S-EPMC2501106 | biostudies-literature
Project description:We constructed two site-specifically modified nucleosomes containing an intrastrand cis-{Pt(NH3)2}2+ 1,3-d(GpTpG) cross-link, similar to one formed by the anticancer drugs carboplatin and cisplatin on DNA, and investigated their structures by hydroxyl radical footprinting and exonuclease III digestion. Hydroxyl radical footprinting demonstrated that the presence of the platinum cross-link selects out a specific rotational setting of DNA on the histone octamer core in each of two reconstituted nucleosomes in which the platinum positions differ by half a DNA helical turn. The {Pt(NH3)2}2+ cross-link is situated in a structurally similar location, with the undamaged strand projecting outward, forcing the DNA to adopt opposite rotational settings in its wrapping around the histone octamer in the two nucleosomes. Enzymatic digestion by exonuclease III of the nucleosome substrates revealed that the platinum cross-link affects the translational positioning of the DNA, forcing it into an asymmetric arrangement with respect to the core histone proteins. We suggest that these phasing phenomena may be central to the recognition and processing of platinum-DNA adducts in cancer cells treated with these drugs and possibly may be common to other DNA damaging events.
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Project description:soil from rotational shifting cultivation Raw sequence reads
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