High-resolution mapping of S1- and DNase I-hypersensitive sites in chromatin.

A new and easy technique for accurately mapping DNase I- and S1 nuclease-hypersensitive sites is described. The technique is a modification of primer extension and S1 nuclease methods conventionally used to map RNA ends.

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Native genomic blotting: high-resolution mapping of DNase I-hypersensitive sites and protein-DNA interactions.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.85.1.16 ◽

1988 ◽

Vol 85 (1) ◽

pp. 16-20 ◽

Cited By ~ 13

Author(s):

U. Pauli ◽

S. Chrysogelos ◽

J. Stein ◽

G. Stein

Keyword(s):

High Resolution ◽

Dnase I ◽

Dna Interactions ◽

Dnase I Hypersensitive Sites ◽

High Resolution Mapping ◽

Protein Dna Interactions ◽

Hypersensitive Sites ◽

Resolution Mapping

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Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Plant Methods ◽

10.1186/s13007-015-0087-1 ◽

2015 ◽

Vol 11 (1) ◽

Cited By ~ 15

Author(s):

Jason S. Cumbie ◽

Sergei A. Filichkin ◽

Molly Megraw

Keyword(s):

Arabidopsis Thaliana ◽

High Resolution ◽

Dnase I ◽

Dnase I Hypersensitive Sites ◽

High Resolution Mapping ◽

Hypersensitive Sites ◽

Resolution Mapping

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High-Resolution Mapping of In vivo Genomic Transcription Factor Binding Sites Using In situ DNase I Footprinting and ChIP-seq

DNA Research ◽

10.1093/dnares/dst013 ◽

2013 ◽

Vol 20 (4) ◽

pp. 325-338 ◽

Cited By ~ 12

Author(s):

O. Chumsakul ◽

K. Nakamura ◽

T. Kurata ◽

T. Sakamoto ◽

J. L. Hobman ◽

...

Keyword(s):

Transcription Factor ◽

High Resolution ◽

Binding Sites ◽

Transcription Factor Binding Sites ◽

Dnase I ◽

High Resolution Mapping ◽

Dnase I Footprinting ◽

Resolution Mapping

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DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays

Nature Methods ◽

10.1038/nmeth888 ◽

2006 ◽

Vol 3 (7) ◽

pp. 503-509 ◽

Cited By ~ 145

Author(s):

Gregory E Crawford ◽

Sean Davis ◽

Peter C Scacheri ◽

Gabriel Renaud ◽

Mohamad J Halawi ◽

...

Keyword(s):

High Resolution ◽

Dnase I ◽

Resolution Method ◽

Dnase I Hypersensitive Sites ◽

Hypersensitive Sites ◽

High Resolution Method

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High-resolution mapping of DNase I-hypersensitive sites of Drosophila heat shock genes in Drosophila melanogaster and Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.4.9.1853 ◽

1984 ◽

Vol 4 (9) ◽

pp. 1853-1863 ◽

Cited By ~ 36

Author(s):

N Costlow ◽

J T Lis

Keyword(s):

Saccharomyces Cerevisiae ◽

Drosophila Melanogaster ◽

Heat Shock ◽

High Resolution ◽

Consensus Sequence ◽

Dnase I ◽

Heat Shock Genes ◽

Base Pairs ◽

Dnase I Hypersensitive Sites ◽

Hypersensitive Sites

High-resolution analysis of the chromatin structure of the promoter regions of five Drosophila heat shock genes showed a similar location for the hypersensitive sequences relative to the start of transcription. For each of the five genes examined--those coding for hsp27, hsp26, hsp23, hsp70, and hsp83--the DNase I-hypersensitive sites in Drosophila melanogaster nuclei mapped to two regions upstream of the coding region. These sites occurred on the average, 115 and 17 base pairs upstream from the start of transcription of the five heat shock genes examined. This latter site corresponded to sequences at or near the TATA consensus sequence. Sites even further upstream of the hsp27, hsp26, and hsp83 genes were also evident. Additionally, for the two genes examined--hsp70 and hsp83--the DNase I-hypersensitive sites were preserved, at least within this level of resolution (+/- 10 base pairs), when the Drosophila genes were integrated into the Saccharomyces cerevisiae genome. This result indicates that the signals responsible for generating these hypersensitive sites are inherent in the DNA sequences and, in this case, are not highly species specific.

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High-resolution mapping of DNase I-hypersensitive sites of Drosophila heat shock genes in Drosophila melanogaster and Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.4.9.1853-1863.1984 ◽

1984 ◽

Vol 4 (9) ◽

pp. 1853-1863

Author(s):

N Costlow ◽

J T Lis

Keyword(s):

Saccharomyces Cerevisiae ◽

Drosophila Melanogaster ◽

Heat Shock ◽

High Resolution ◽

Consensus Sequence ◽

Dnase I ◽

Heat Shock Genes ◽

Base Pairs ◽

Dnase I Hypersensitive Sites ◽

Hypersensitive Sites

High-resolution analysis of the chromatin structure of the promoter regions of five Drosophila heat shock genes showed a similar location for the hypersensitive sequences relative to the start of transcription. For each of the five genes examined--those coding for hsp27, hsp26, hsp23, hsp70, and hsp83--the DNase I-hypersensitive sites in Drosophila melanogaster nuclei mapped to two regions upstream of the coding region. These sites occurred on the average, 115 and 17 base pairs upstream from the start of transcription of the five heat shock genes examined. This latter site corresponded to sequences at or near the TATA consensus sequence. Sites even further upstream of the hsp27, hsp26, and hsp83 genes were also evident. Additionally, for the two genes examined--hsp70 and hsp83--the DNase I-hypersensitive sites were preserved, at least within this level of resolution (+/- 10 base pairs), when the Drosophila genes were integrated into the Saccharomyces cerevisiae genome. This result indicates that the signals responsible for generating these hypersensitive sites are inherent in the DNA sequences and, in this case, are not highly species specific.

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