Genome architecture in definitive erythroid cells at base-pair resolution
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE153256 | GEO | 2021/04/16
REPOSITORIES: GEO
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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:Genome architecture in definitive erythroid cells at base-pair resolution
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Project description:Enhancer looping governs gene regulatory circuitry but is challenging to detect. Here we present Tri-4C, an ultrafine mapping method for distal chromatin contacts using triple restriction enzyme (RE) digestion. Tri-4C identifies enhancer loops that are undetectable by current single RE- based methods and reveals quantitative loop strengths in enhancer interaction networks underlying dynamic gene control. This multi-RE approach may be applied to general 3C-derived methods for accurate detection of enhancer loops.
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Project description:Chromosome conformation capture (3C) provides an adaptable tool through which to study diverse biological questions. Currently, 3C techniques provide either low-resolution interaction profiles across the entire genome, e.g. HiC, or high-resolution interaction profiles at up to several hundred loci, e.g. NG Capture-C and 4C-seq. Generation of high-resolution, genome-wide interaction profiles can feasibly be achieved through efficiency improvements to current high-resolution methods. To this end we systematically tested and removed areas inefficiency in NG Capture-C to develop a new method Nuclear Capture-C, which provides a 300% increase in informative sequencing content. Using Nuclear Capture-C we target 8,026 erythroid promoters in triplicate, showing that this method can achieve high-resolution genome-wide 3C interaction profiles at scale.
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Project description:NG Capture-C provides high resolution chromatin conformation capture (3C) interaction maps. NG Capture-C was carried out in erythroid and hESC cells at the Hba, Hbb, Myc, and Slc25a37 locus to generate sequence libraries for analytical software testing.
2020-11-02 | GSE129378 | GEO
Project description:Here, we developed a novel chromosome conformation capture (3C) method for capturing the 3D spatial contacts of endogenous genomic loci without a need for crosslinking. This method, i3C, was applied to multiple loci in two different human primary (ENCODE) cell lines, HUVEC and IMR90, and in the absence or presence of a proinflammatory stimulus (TNFalpha). Coupled to high throughput sequencing on an Illumina HiSeq200 platform, i3C generated aprrox. 8 million single-end reads per experiment.
2016-12-10 | E-MTAB-4719 | biostudies-arrayexpress
Project description:Background: DNA in the nucleus of a living cell carries out its functions in the context of a complex, three-dimensional chromatin architecture. Several recently developed methods, each an extension of the chromatin conformation capture (3C) assay, have enabled the genome-wide profiling of chromatin contacts between pairs of loci in yeast, fruit fly, human and mouse. Especially in complex eukaryotes, data generated by these methods, coupled with other genome-wide datasets, demonstrated that non-random chromatin folding correlates strongly with cellular processes such as gene expression and DNA replication. Here we describe a novel assay to map genome-wide chromatin contacts, tethered multiple 3C (TM3C), that involves a simple protocol of restriction enzyme digestion and religation of fragments upon agarose gel beads followed by deep DNA paired-end sequencing. In addition to identifying contacts between pairs of loci, TM3C enables identification of contacts among more than two loci simultaneously. Results: We use TM3C to assay the genome architectures of two human cell lines: KBM7, a near-haploid chronic leukemia cell line, and NHEK, a normal diploid human epidermal keratinocyte cell line. We confirm that the contact frequency maps produced by TM3C exhibit features characteristic of existing genome architecture datasets, including the expected scaling of contact probabilities with genomic distance, as well as a low noise-to-signal ratio between inter- and intrachromosomal contacts. We also confirm that TM3C captures several known cell type-specific contacts, ploidy shifts and translocations, such as Ph+ formation in KBM7. Furthermore, we develop a two-phase mapping strategy that separately maps chimeric subsequences within a single read, allowing us to identify contacts involving three or four loci simultaneously, potentially corresponding to combinatorial regulation events. This mapping strategy also greatly increases the number of distinct binary contacts identified and, therefore, the coverage obtained for a fixed number of mapped reads. We confirm a subset of the triplet contacts involving the IGF2-H19 imprinting control region (ICR) using PCR analysis for KBM7 cells. Assaying the genome architecture of a near-haploid cell line allows us to create 3D models of a human cell line without averaging signal from two homologous copies of a chromosome. Our 3D models of KBM7 show clustering of small chromosomes with each other and large chromosomes with each other, consistent with previous studies of the genome architectures of other human cell lines. Conclusion: TM3C is a simple protocol for ascertaining genome architecture and can be used to identify simultaneous contacts among three or four loci. Application of TM3C to a near-haploid human cell line revealed large-scale features of chromosomal organization and complex chromatin loops that may play a role in regulating reciprocal expression of the IGF2 and H19 genes. Analysis of the spatial organization of two human cell lines (KBM7, a near-haploid chronic leukemia cell line, and NHEK, a normal diploid human epidermal keratinocyte cell line) using tethered multiple 3C (TM3C), a novel and simple protocol for ascertaining genome architecture which can be used to identify simultaneous contacts among three or four loci in addition to binary contacts that can be identified using traditional chromosome conformation capture coupled with next generation sequencing (Hi-C).
2015-04-29 | E-GEOD-60623 | biostudies-arrayexpress
Project description:Defining genome architecture 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)
2012-05-16 | E-GEOD-36063 | biostudies-arrayexpress