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Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells [DNase-Hypersensitivity]

ABSTRACT: Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100-1200 bp DNase I-double cleavage fragments (also called double-hit fragments). But next generation sequencing requires a DNA library containing DNA fragments of 100-500bp. Therefore, we have modified the double-hit method and use short DNA fragments to generate DNA libraries for next generation sequencing. We call this method Short DHS Assay (Short DNAse I Hypersensitive Site assay). The short segments are 100-300bp and can be directly cloned and used for high-throughput sequencing. We identified 83,897 DHSs in 2,343,479 tags across the human genome. Our results indicate that the DHSs identified by the Short DHS assay are consistent with those identified by longer fragments in previous studies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE38914 | GEO | 2015/06/19

SECONDARY ACCESSION(S): PRJNA169335

REPOSITORIES: GEO

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Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

Project description:DNase I hypersensitive sites (DHSs) provide important information on the presence of transcriptional regulatory elements and the state of chromatin in mammalian cells1, 2, 3. Conventional DNase sequencing (DNase-seq) for genome-wide DHSs profiling is limited by the requirement of millions of cells4, 5. Here we report an ultrasensitive strategy, called single-cell DNase sequencing (scDNase-seq) for detection of genome-wide DHSs in single cells. We show that DHS patterns at the single-cell level are highly reproducible among individual cells. Among different single cells, highly expressed gene promoters and enhancers associated with multiple active histone modifications display constitutive DHS whereas chromatin regions with fewer histone modifications exhibit high variation of DHS. Furthermore, the single-cell DHSs predict enhancers that regulate cell-specific gene expression programs and the cell-to-cell variations of DHS are predictive of gene expression. Finally, we apply scDNase-seq to pools of tumour cells and pools of normal cells, dissected from formalin-fixed paraffin-embedded tissue slides from patients with thyroid cancer, and detect thousands of tumour-specific DHSs. Many of these DHSs are associated with promoters and enhancers critically involved in cancer development. Analysis of the DHS sequences uncovers one mutation (chr18: 52417839G>C) in the tumour cells of a patient with follicular thyroid carcinoma, which affects the binding of the tumour suppressor protein p53 and correlates with decreased expression of its target gene TXNL1. In conclusion, scDNase-seq can reliably detect DHSs in single cells, greatly extending the range of applications of DHS analysis both for basic and for translational research, and may provide critical information for personalized medicine. Exploring the landscape of chromatin accessibility in single cells and clinical samples

2015-11-25 | E-GEOD-61844 | biostudies-arrayexpress

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

2015-11-25 | GSE61844 | GEO

Short tandem repeats are important contributors to silencer elements in T cells

Project description:Analysis of Dnase Hypersensitive Site (DHS) of P5424 mouse cell line using High-throughput reporter assay

2022-05-12 | GSE202547 | GEO

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

Project description:Upon fertilization, parental chromatin undergoes extensive reprogramming to generate the highly dynamic chromatin of the inner cell mass (ICM) cells from which an organism is derived. How the chromatin regulatory landscape is established during this process has remained a mystery due to the technical difficulties in chromatin analysis using limited cell numbers. Using a low-input DNase I sequencing (liDNase-seq) method, we generated DNase I-hypersensitive site (DHS) maps of mouse preimplantation embryos. We found that the DHSs are progressively established during development, with Oct4 contributing to a drastic gain of DHSs at the 8-cell stage. In addition, single nucleotide polymorphism analysis revealed that imprinted gene promoters harbor allele-specific DHSs before the onset of allelic gene expression. Furthermore, Nfya is required for 2-cell promoter DHS formation and zygotic genome activation. Thus, our study not only reveals chromatin regulatory landscapes, but also identifies key transcription factors important for DHS establishment in mammalian embryos.

2016-06-03 | GSE76642 | GEO

Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells [Illumina arrays]

Project description:We explored the relationship between the distribution of DNase I hypersensitive site(DHSs) and levels of gene expression. Expression values from 5 to 11 are raw log2 ratio-transformed data from gene expression arrays. We found that the distribution of DHSs in promoter region and CpG islands is positively correlated with gene expression levels and 3’UTR DHSs are negatively correlated with active expression of genes.

2015-06-19 | GSE38913 | GEO

Genome-wide expression profiling analysis of a Hmgn2 and Hmgn1/2 double knock out mutant mouse model

Project description:DNase I hypersensitive sites (DHSs) are a hallmark of chromatin regions containing regulatory DNA such as enhancers and promoters; however, the factors affecting the establishment and maintenance of these sites are not fully understood. We now show that HMGN1 and HMGN2, nucleosome-binding proteins that are ubiquitously expressed in vertebrate cells, maintain the DHS landscape of mouse embryonic fibroblasts (MEFs) synergistically. Loss of one of these HMGN variants led to a compensatory increase of binding of remaining variant. Genome wide mapping of the DHSs in Hmgn1-/-, Hmgn2-/- and Hmgn1-/-n2-/- MEFs reveals that loss of both, but not a single HMGN variant, leads to significant remodeling of the DHS landscape, especially at enhancer regions marked by H3K4me1 and H3K27ac. Loss of HMGN variants affects the induced expression of stress responsive genes in MEFs, the transcription profiles of several mouse tissues, and leads to altered phenotypes that are not seen in mice lacking only one variant. We conclude that the compensatory binding of HMGN variants to chromatin maintains the DHS landscape and the transcription fidelity necessary to retain wild type phenotypes. Our studies provide insights into mechanisms that maintain regulatory sites in chromatin and into functional compensation among nucleosome binding architectural proteins.

2017-10-01 | GSE66442 | GEO

BRG1 contributes to the global chromatin accessibility revealed by its acute depletion

Project description:DNase I hypersensitivity (DHS) of chromatin indicates the presence of important regulatory elements of transcription such as enhancers and promoters and plays critical roles for their activities. However, the mechanisms that control the global DHS have not been fully understood. In this report, we show that acute depletion of BRG1 by the auxin-dependent degron system, the essential ATPase subunit of the mammalian chromatin remodeling SWI/SNF-like BAF complexes, severely compromised genome-wide DHSs of chromatin, while the traditional conditional deletion of the Brg1 gene using Cre/Flox system led to only very modest changes of DHSs. The global decrease of DHSs is associated with a genome-wide decrease of transcription. We demonstrate that the DHS change is related with changes in nucleosome positioning at promoters and enhancers. Our data suggest that acute depletion of proteins reveal target genes of BRG1 that are not detected by the traditional models.

2024-03-05 | GSE156569 | GEO

Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells [Illumina arrays]

2015-06-19 | E-GEOD-38913 | biostudies-arrayexpress

Genome-wide identification of regulatory elements in preSertoli cells based on DNaseI hypersensitivity

Project description:Identifying transcriptional networks active during development has been hindered by the slow pace at which regulatory elements are identified, and by the difficulty in purifying cells from developing tissues. We used DNaseI-seq to identify functional regulatory elements in purified fetal preSertoli cells and uncovered thousands of preSertoli-specific DNaseI hypersensitive sites (DHSs) that are likely to activate or repress genes required for Sertoli cell development and function. To demonstrate their functional significance, we validated the preSertoli-specific enhancer activity of a DHS located 50 kb upstream of the Wt1 gene. This genome-wide data will guide many future studies into gene-regulatory mechanisms that operate in the fetal gonad and may lead to the identification of non-coding mutations leading to DSDs. One biological replicate was analyzed for each of the seven mouse samples using DNase-seq.

2013-12-07 | E-GEOD-53076 | biostudies-arrayexpress

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

Project description:We mapped DNaseI hypersensitive sites (DHSs) and applied genomic footprinting to define in vivo transcription factor (TF) occupancy at nucleotide resolution across the A. thaliana genome in whole seedlings during heat- and light-response states. We find that trait-associated variation localizes within DHSs, and that extensive TF occupancy within protein-coding exons has shaped A. thaliana codon usage. Analysis of >700,000 TF footprints disclosed an extensive cis-regulatory lexicon, and enabled construction of large-scale TF cross-regulatory networks. Although the cis- and trans-regulatory repertoire is markedly distinct from mammals, the architecture of A. thaliana TF networks is strikingly similar to those of human. Analysis of the DHS landscape and TF network dynamics during heat shock and photomorphogenesis revealed thousands of conditionally-sensitive elements and enabled mapping of key regulatory circuits. Our results provide an extensive resource for understanding and enabling diverse aspects of A. thaliana biology. Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old dark-grown seedlings exposed to 0hr light, 30min light, 3hr light or 24hr LD conditions. Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old LD-grown seedlings treated with a brief sever heat shock or kept under control conditions. Replicates are included when available; controls and read-normalized samples (samples that were subsampled to the same read-depth) are also included here.

2013-12-15 | E-GEOD-53322 | biostudies-arrayexpress

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