2005
DOI: 10.1101/gr.4074106
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Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

Abstract: A major goal in genomics is to understand how genes are regulated in different tissues, stages of development, diseases, and species. Mapping DNase I hypersensitive (HS) sites within nuclear chromatin is a powerful and well-established method of identifying many different types of regulatory elements, but in the past it has been limited to analysis of single loci. We have recently described a protocol to generate a genome-wide library of DNase HS sites. Here, we report high-throughput analysis, using massively… Show more

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Cited by 436 publications
(351 citation statements)
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“…3). The region including DNAm sites cg02346997, cg21777015 and cg22322184 as well as SNPs rs34861192 and rs3219175 overlaps with a region characterised by DNase I hypersensitivity [34] and a high level of histone modification (H3K4m1/2/3, H3K27ac), which are indicators of a potential regulatory region. Binding sites for the transcription factors c-Rel, CCAAT/enhancer binding protein α (C/EBPα), activating transcription factor 2 (ATF2) and activator protein (AP1) have been identified within a 619 bp region upstream of the translation start site of RETN [35].…”
Section: Discussionmentioning
confidence: 99%
“…3). The region including DNAm sites cg02346997, cg21777015 and cg22322184 as well as SNPs rs34861192 and rs3219175 overlaps with a region characterised by DNase I hypersensitivity [34] and a high level of histone modification (H3K4m1/2/3, H3K27ac), which are indicators of a potential regulatory region. Binding sites for the transcription factors c-Rel, CCAAT/enhancer binding protein α (C/EBPα), activating transcription factor 2 (ATF2) and activator protein (AP1) have been identified within a 619 bp region upstream of the translation start site of RETN [35].…”
Section: Discussionmentioning
confidence: 99%
“…The peaks of nascent promoter RNAs flank a region that consistently exhibits low nucleosome density. 27,[32][33][34][35] Each RNAPII complex on DNA occupies approximately 50 nt and the space between the two RNAPII peaks seen at promoters is approximately 300 nts. This is essentially the same size as the NFR.…”
Section: Divergent Transcription In Yeastmentioning
confidence: 99%
“…Thomas J. Vasicek, Medtronic, Inc Thomas Vasicek gave an overview of applications in genome analysis using Massively Parallel Signal Sequencing (MPSS), which is a method for evaluating genome structure [Jongeneel et al, 2005] or gene expression by counting mRNA molecules present in a sample [Crawford et al, 2006]. Individual mRNAs are identified by sequencing 17-20 nucleotides at a unique site in each mRNA.…”
Section: Comprehensive Genome Structure and Transcriptome Analysis Fomentioning
confidence: 99%