Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA924005 | ENA |
REPOSITORIES: ENA
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Project description:Long-range single-molecule mapping of chromatin accessibility in eukaryotes
| PRJNA527027 | ENA
Project description:Active regulatory elements in eukaryotes are typically characterized by an open, nucleosome-depleted chromatin structure; mapping areas of open chromatin has accordingly emerged as a widely used tool in the arsenal of modern functional genomics. However, existing approaches for profiling chromatin accessibility are limited by their reliance on DNA fragmentation and short read sequencing, which leaves them unable to provide information about the state of chromatin on larger scales or reveal coordination between the chromatin state of individual distal regulatory elements. To address these limitations, we have developed a method for profiling accessibility of individual chromatin fibers at multi-kilobase length scale (SMAC-seq, or Single-Molecule long-read Acessible Chromatin mapping sequencing assay), enabling the simultaneous, high-resolution, single-molecule assessment of the chromatin state of distal genomic elements. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases (CpG and GpC 5-methylcytosine (5mC) and N6-methyladenosine (m6A) enzymes) and the ability of long-read single-molecule nanopore sequencing to directly read out the methylation state of individual DNA bases. Applying SMAC-seq to the budding yeast Saccharomyces cerevisiae, we demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule protection footprints of nucleosomes and transcription factors, and quantify the correlation between the chromatin states of distal genomic elements
2019-12-01 | GSE128290 | GEO
Project description:The cohesin complex is central to chromatin looping, but mechanisms by which these long-range chromatin interactions are formed and persist remain unclear. We demonstrate that interactions between a transcription factor and the cohesin loader NIPBL regulate enhancer-promoter looping and promote long-range gene regulation. Using mass-spectrometry, genome mapping, and single-molecule tracking methods, we demonstrate that NIPBL and cohesin regulate the dynamics and function of the glucocorticoid receptor (GR). Moreover, glucocorticoid treatment stabilizes NIPBL and cohesin interactions by promoting loop extrusion and chromatin looping. Patient-derived acute myeloid leukemia cells harboring cohesin mutations exhibit a reduced response to glucocorticoids (GCs), suggesting that the GR-NIPBL-cohesin interaction is defective in these patients, and they may be poor candidates for GC treatment.
2021-06-01 | GSE162617 | GEO
Project description:We report the application of single-molecule-based DNA sequencing technology for high-throughput profiling of long-range chromatin interactions in Sox2-deleted and wild type NSC, by improved ChIA-PET procedure (in situ ChIA-PET) with antiRNApolII antibodies. By obtaining sequences from chromatin immunoprecipitated DNA, we generated genome-wide maps of inter-molecular ligated DNA representing long-range interactions in chromatin.
2019-03-07 | GSE90557 | GEO
Project description:Polycomb group (PcG) proteins bind and regulate hundreds of genes. Previous evidence has suggested that long-range chromatin interactions may contribute to the regulation of PcG target genes. Here, we adapted the Chromosome Conformation Capture on Chip (4C) assay to systematically map chromosomal interactions in Drosophila melanogaster larval brain tissue. Our results demonstrate that PcG target genes interact extensively with each other in nuclear space. These interactions are highly specific for PcG target genes, because non-target genes with either low or high expression show distinct interactions. Notably, interactions are mostly limited to genes on the same chromosome arm, and we demonstrate that a topological rather than a sequence-based mechanism is responsible for this constraint. Our results demonstrate that many interactions among PcG target genes exist, and that these interactions are guided by overall chromosome architecture. We applied Chromosome Conformation Capture on Chip (4C) to map long-range chromatin interactions among PcDs on a genome-wide scale. Moreover, we implemented a modification of the 4C protocol in which the 4C PCR products are further amplified in a linear fashion using a T7 RNA amplification procedure. Finally, we fluorescently labeled the amplified products with dye and hybridized them to a specially designed microarray, which covers approximately 92% of the non-repetitive fly genome. In this way, we could identify all fragments that are in close contact with a chosen locus with limited material from a single fly tissue (i.e. larval brain).
2011-05-09 | E-GEOD-23166 | biostudies-arrayexpress
Project description:We present a long-read, single-molecule mapping technology that generates hybrid genetic/epigenetic profiles of native chromosomal DNA. The genome-wide distribution of 5-hmC in human peripheral blood cells correlates well with 5-hmC DNA immunoprecipitation (hMeDIP) sequencing. However, the long single-molecule read-length of 100 kbp-1 Mbp produces 5-hmC profiles across variable genomic regions that failed to show up in the sequencing data. In addition, optical 5-hmC mapping shows a strong correlation between the 5-hmC density in gene bodies and the corresponding level of gene expression.
2018-06-08 | GSE115454 | GEO
Project description:Mapping of Long-Range Chromatin Interactions using Proximity Ligation Assisted ChIP-seq
| PRJNA340368 | ENA
Project description:N6-methyladenine (6mA) is a natural DNA modification and functions primarily in restriction-modification (R-M) systems in prokaryotes. Recent studies uncovered the existence and revealed the genome-wide distribution of 6mA in eukaryotes. Specifically, it was reported that 6mA was mainly enriched in mammalian mitochondrial DNA (mtDNA) and could regulate mitochondrial activity. we achieved the genome-wide mapping of 6mA in E. coli genome and mammalian mtDNA at single-nucleotide resolution.
2022-01-26 | GSE194212 | GEO
Project description:In dinoflagellates, the most unique and divergent nuclear organization among the known diversity of eukaryotes has evolved. The list of highly unusual features of dinoflagellate nuclei and genomes is long -- permanently condensed liquid crystalline chromosomes, in which histones are not the main packaging component, genes organized as very long unidirectional gene arrays, general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. Most of these fascinating properties were originally identified in the 1970s and 1980s but have received very little attention in recent decades using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, and also often coincides with the boundaries between gene arrays. It is generally anti-correlated with chromatin accessibility, the levels of which are lower in those regions. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.
2023-10-19 | GSE241969 | GEO