DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells

By Lingyun Song, Gregory E. Crawford. Cold Spring Harbor Protocols, 2010

621 citations recorded by the source corpus.

Identification of active gene regulatory elements is a key to understanding transcriptional control governing biological processes like cell-type specificity, differentiation, development, proliferation, and response to the environment. Mapping DNase I hypersensitive (HS) sites has historically been a valuable tool for identifying all different types of regulatory elements, including promoters, enhancers, silencers, insulators and locus control regions. This method utilizes DNase I to selectively digest nucleosome-depleted DNA (presumably by transcription factors), whereas DNA regions tightly wrapped in nucleosome and higher order structures are more resistant. The traditional low-throughput method for identifying DNase I HS sites uses Southern blots. Here, we describe the complete and improved protocol for DNase-seq, a high-throughput method that identifies DNase I HS sites across the whole genome by capturing DNase-digested fragments and sequencing them by high-throughput next generation sequencing. In a single experiment, DNase-seq can identify most active regulatory regions from potentially any cell type from any species with a sequenced genome.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/399312c4a78f9da0f6095e2cf0fb03b17111b56c

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Citations in the corpus

Mapping genome-wide transcription-factor binding sites using DAP-seq (2017, methodology): “One powerful way to overcome this limitation is to overlay tissue-specific chromatin accessibility information from methods such as DNase-seq, ATAC-seq, and MNase-seq on DAP-seq datasets 21–23 .”
Dual role of FoxA1 in androgen receptor binding to chromatin, androgen signalling and prostate cancer (2011, methodology): “Genome-wide mapping of DHS sites (Song and Crawford, 2010) was used to examine in LNCaP-1F5 cells whether FoxA1 depletion resulted in an open chromatin conformation that subsequently created new ARBs, or whether chromatin was already in an open conformation prior to FoxA1 depletion.”
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis (2018, methodology): “DNase-seq (14) and ATAC-seq (15) are technologies developed to comprehensively map most of the TF binding sites in a biological sample through the characterization of regions that are accessible to DNase I or Tn5 transposase enzymatic activity.”
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities (2018, background): “A variety of techniques map nucleosomes and open chromatin, which include deoxyribonuclease-sequencing (DNase-seq) [75] and assay for transposase-accessible chromatin (ATAC-seq) [63].”
DNaseI sensitivity QTLs are a major determinant of human expression variation (2012, methodology): “Methods Summary DNase-seq libraries were created as described previousl”
Ensembl regulation resources (2016, neutral): “For example, histone modifications and TF binding locations previously identified with chromatin immunoprecipitation followed by microarray hybridisation (ChIP-chip) (12) now generally employ high-throughput sequencing (ChIP-seq) (13, 14); DNA methylation is assayed with MeDIP (15) or bisul-phite se”