XL-DNase-seq
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ABSTRACT:
PROVIDER: PRJEB23174 | ENA |
REPOSITORIES: ENA
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Project description:XL-DNase-seq: improved footprinting of dynamic transcription factors
| PRJEB22841 | ENA
Project description:DNase I footprinting is an established assay for identifying transcription factor (TF)-DNA interactions with single base pair resolution. High throughput DNase-seq assays have recently been used to detect in vivo DNase footprints across the genome. A number of computational approaches have been developed to accurately identify DNase-seq footprints and these methods have been used as a predictor of TF-DNA interactions by itself or in combination with other epigenetic features. However, recent studies have pointed to a substantial cleavage bias of DNase and its impact on footprinting, casting doubts on its predictive performance. To assess the potential for using DNaseI to identify individual binding sites, we performed DNase-seq experiments on deproteinized naked genomic DNA isolated from two different cell types and determined sequence cleavage bias associated with the DNase-seq protocol. This allowed us to build cleavage bias corrected footprint models specific to individual transcription factors. The predictive performance of these DNase-seq-based binding site models demonstrated that predicted footprints corresponded to high confidence TF-DNA interactions. To quantify the DNase I sequence-dependent cleavage bias, we performed DNase-seq experiments using deproteinized DNA from K562 and MCF7 cell lines.
2014-09-04 | E-GEOD-61105 | biostudies-arrayexpress
Project description: Not available
| S-EPMC6547507 | biostudies-literature
Project description:DNase I footprinting is an established assay for identifying transcription factor (TF)-DNA interactions with single base pair resolution. High throughput DNase-seq assays have recently been used to detect in vivo DNase footprints across the genome. A number of computational approaches have been developed to accurately identify DNase-seq footprints and these methods have been used as a predictor of TF-DNA interactions by itself or in combination with other epigenetic features. However, recent studies have pointed to a substantial cleavage bias of DNase and its impact on footprinting, casting doubts on its predictive performance. To assess the potential for using DNaseI to identify individual binding sites, we performed DNase-seq experiments on deproteinized naked genomic DNA isolated from two different cell types and determined sequence cleavage bias associated with the DNase-seq protocol. This allowed us to build cleavage bias corrected footprint models specific to individual transcription factors. The predictive performance of these DNase-seq-based binding site models demonstrated that predicted footprints corresponded to high confidence TF-DNA interactions.
2014-09-04 | GSE61105 | GEO
Project description:DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBS) in regulatory regions via footprinting. Recent studies have demonstrated the sequence bias of DNase I and its adverse effects on footprinting efficiency. However, footprinting and the impact of sequence bias have not been extensively studied for ATAC-seq. Here, we undertake a systematic comparison of the two methods and show that a modification to the ATAC-seq protocol increases its yield and its agreement with DNase-seq data from the same cell line. We demonstrate that the two methods have distinct sequence biases and correct for these protocol-specific biases when performing footprinting. Despite differences in footprint shapes, the locations of the inferred footprints in ATAC-seq and DNase-seq are largely concordant. However, the protocol-specific sequence biases in conjunction with the sequence content of TFBSs impacts the discrimination of footprint from background, which leads to one method outperforming the other for some TFs. Finally, we address the depth required for reproducible identification of open chromatin regions and TF footprints.
2018-11-23 | GSE108513 | GEO
Project description:We systematicaly evaluated two major factors, enzyme digestion level and fragment size, that would affect DNase-seq experiment. We found that while under- or over-digestion sigificantly decreases the DNase-seq signal, there is a broad range of suitable digestion level. In addition, we found fragment smaller than nucleosome size is optimal to identify transcription factor binding events. We tested digestion level of 5U, 25U, 50U, 75U, 100U and fragment size of 50-100bp, 100-200bp, 200-300bp
2013-11-25 | E-GEOD-51915 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE25344: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (Dnase-seq) GSE25416: High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Refer to individual Series
2010-11-18 | E-GEOD-25442 | biostudies-arrayexpress
Project description:Understanding the kinetics of circadian transcriptional regulation has recently advanced thanks to genome-wide dynamic mapping of RNA Polymerase II, chromatin marks such as histone 3 modifications, and several core clock regulatory factors. To obtain deeper mechanistic insights into the determinant of phase-specific transcription, we here extend previous analyses of the CycliX Consortium by integrating new genome-wide datasets enabling systematic identification of active regulatory regions in the mouse liver. DNase I hypersensitive sites (DHS)-mapping within nuclear chromatin is a powerful method to identify active regulatory elements in the genome. Experiments were performed throughout the diurnal cycle to obtain a temporal map of active regulatory elements. In addition, we quantified H3K27ac, which mark active regulatory regions, throughout the diurnal cycle and RNA Polymerase II using chromatin immunoprecipitation data analysis. DHS were validated as likely regulatory elements by footprinting analyses and overlaps with published ChIP-seq datasets. Analysis of the regions displaying diurnal patterns revealed promoter, transcription start site (TSS)-proximal and TSS-distal elements potentially involved in the regulation of rhythmic gene transcription. Peak phases of DNase I accessibility and H3K27ac levels correlated well with RNA Polymerase II loadings, and regulatory elements oscillated with phases close to those of nearest TSS, which prompted us to use these signals to infer regulatory relationships. Comparisons with results in a Bmal1 -/- genotype (KO) revealed comparable levels of diurnal transcription oscillations likely driven by nutrient and food-entrained rhythms. Using linear modeling, we inferred activities of transcription factors around the clock in WT and KO datasets to reveal that in absence of a functional core circadian clock, FOX transcription factors and glucocorticoid receptor appear to be the main drivers of phase-specific expression. This raises the interesting question of whether light-driven circadian entrainment from the central pacemaker in the SCN acts to counter effect food-related signals.
2016-12-31 | GSE60430 | GEO
Project description:Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many nuclear factors dissociate from mitotic chromosomes, the observation that certain nuclear factors and chromatin features remain associated with individual loci during mitosis originated the hypothesis that they could provide transcriptional memory through mitosis. To obtain the first genome-wide view of the dynamics of chromatin structure during mitosis, we compared the DNase sensitivity of interphase and mitotic chromatin at two stages of cellular maturation in a rapidly dividingmurine erythroblastmodel. Despite global chromosome condensation visible during mitosis at the microscopic level, the chromatin accessibility landscape is largely unaltered. However, mitotic chromatin accessibility is locally dynamic, with individual loci maintaining none, some, or all of their interphase accessibility. Mitotic reduction in accessibility occurs primarily within narrow, highly hypersensitive sites that frequently coincide with transcription factor binding sites, whereas broader domains of moderate accessibility tend to be more stable. In mitosis, proximal promoters generally maintain their accessibility, whereas distal regulatory elements preferentially lose accessibility. Promoters with the highest degree of accessibility preservation in mitosis tend to also be accessible across many murine tissues in interphase. Transcription factor GATA1 exerts site-specific changes in interphase accessibility that are most pronounced at distal regulatory elements, but does not visibly influence mitotic accessibility. We conclude that features of open chromatin are remarkably stable through mitosis and are modulated at the level of individual genes and regulatory elements. Dnase-Seq data is integrated with Chip-seq [GSE36589, GSE30142] and RNA-seq to examine epigentic changes in mitosis. We performed DNase-seq on two cell lines, G1E and G1E-ER4, both on an asynchronus population, and on a sample of cells in mitosis; each of the 4 experiments in triplicate.
2014-10-01 | E-GEOD-61885 | biostudies-arrayexpress
Project description:Structural analysis of chromosome folding in vivo has been revolutionized by Chromosome Conformation Capture (3C) and related methods, which use proximity ligation to identify chromosomal loci in physical contact. We recently described a variant 3C technique, Micro-C, in which chromatin is fragmented to mononucleosomes using micrococcal nuclease, enabling nucleosome-resolution folding maps of the genome. Here, we describe an improved Micro-C protocol using long crosslinkers, termed Micro-C XL, which exhibits greatly increased signal to noise, and provides further insight into the folding of the yeast genome. We also find that signal to noise is much improved in Micro-C XL libraries generated from relatively insoluble chromatin as opposed to soluble material, providing a simple method to physically enrich for bona-fide long-range interactions. Micro-C XL maps of the budding and fission yeast genomes reveal both short-range chromosome fiber features such as chromosomally-interacting domains (CIDs), as well as higher-order features such as clustering of centromeres and telomeres, thereby addressing the primary discrepancy between prior Micro-C data and reported 3C and Hi-C analyses. Interestingly, comparison of chromosome folding maps of S. cerevisiae and S. pombe revealed widespread qualitative similarities, yet quantitative differences, between these distantly-related species. Micro-C XL thus provides a single assay suitable for interrogation of chromosome folding at length scales from the nucleosome to the full genome.
2016-09-13 | GSE85220 | GEO