Genome architecture in definitive erythroid cells at base-pair resolution
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ABSTRACT:
PROVIDER: PRJNA641874 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:By using a novel chromatin conformation capture (3C) method (Micro Capture-C (MCC)), which allows physical contacts to be determined at base-pair resolution. We demonstrate interactions between different classes of regulatory elements in unprecedented detail.
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Project description:By using a novel chromatin conformation capture (3C) method (Micro Capture-C (MCC)), which allows physical contacts to be determined at base-pair resolution. We demonstrate interactions between different classes of regulatory elements in unprecedented detail. T119_S12-S17 and E14_S10-S14 contains data of viewpoint from enhancers that are active in both ES and erythroid cells. NIPBL, CTCF and Rad21 CHIP libraries were prepared and analyzed as previously reported in Hanssen LLP. et al., 2017.
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Project description:We have combined standard micrococcal (MNase) digestion of nuclei with a modified protocol for construction paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a cell population, suggesting dynamic behavior. By varying the time of MNase digestion, we have been able to observe changes that reflect differential sensitivity of particles, including eviction of nucleosomes. Our protocol and mapping method provide a general strategy for characterizing full epigenomes. We used micrococcal nuclease mapping, chromatin immunoprecipitation and paired-end sequencing to determine the structure of yeast centromeres at single base-pair resolution.
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Project description:We have combined standard micrococcal (MNase) digestion of nuclei with a modified protocol for construction paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a cell population, suggesting dynamic behavior. By varying the time of MNase digestion, we have been able to observe changes that reflect differential sensitivity of particles, including eviction of nucleosomes. Our protocol and mapping method provide a general strategy for characterizing full epigenomes.
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Project description:The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function, yet existing methods for mapping nucleosomes do not provide the necessary single base pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centers based on chemical modification of engineered histones. The resulting map locates nucleosome center positions genome-wide in unprecedented detail and accuracy. It reveals novel aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing, and the higher order structure of the chromatin fiber itself.
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Project description:The immunodeficiency, centromere instability and facial anomalies (ICF) syndrome is associated with mutation of the DNA methyl-transferase DNMT3B, resulting in a reduction of enzyme activity. Aberrant expression of immune system genes and hypomethylation of pericentromeric regions accompanied by chromosomal instability were determined as alterations driving the disease phenotype. However, so far only technologies capable of analyzing single loci were applied to determine epigenetic alterations in ICF patients. In the current study, we performed whole-genome bisulphite sequencing to assess alteration in DNA methylation at base-pair resolution.
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Project description:The exact positions of nucleosomes along genomic DNA can influence many aspects of chromosome function, yet existing methods for mapping nucleosomes do not provide the necessary single base pair accuracy to determine these positions. Here we develop and apply a new approach for direct mapping of nucleosome centers based on chemical modification of engineered histones. The resulting map locates nucleosome center positions genome-wide in unprecedented detail and accuracy. It reveals novel aspects of the in vivo nucleosome organization that are linked to transcription factor binding, RNA polymerase pausing, and the higher order structure of the chromatin fiber itself. 6 samples were analyzed with high throughout parallel sequencing. All samples were created using the same chemical mapping protocol except with varying reaction times. The different reaction times did not make any significant difference in the nucleosome maps so all the data, for the 6 samples, were combined into one data set for the paper and are all considered replicates. The 6 samples are as follows: 1. 20 minute reaction time (single-end sequencing) 2. 20 minute reaction time (single-end sequencing) 3. 1 minute reaction time (single-end sequencing) 4. 1.5 minute reaction time (single-end sequencing) 5. 20 minute reaction time (paired-end sequencing) 6. 1.5 minute reaction time (paired-end sequencing)
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