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

Plant Methods ◽  
2015 ◽  
Vol 11 (1) ◽  
Author(s):  
Jason S. Cumbie ◽  
Sergei A. Filichkin ◽  
Molly Megraw
1985 ◽  
Vol 5 (6) ◽  
pp. 1538-1539 ◽  
Author(s):  
H Weintraub

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.


1985 ◽  
Vol 5 (6) ◽  
pp. 1538-1539
Author(s):  
H Weintraub

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.


2006 ◽  
Vol 3 (7) ◽  
pp. 503-509 ◽  
Author(s):  
Gregory E Crawford ◽  
Sean Davis ◽  
Peter C Scacheri ◽  
Gabriel Renaud ◽  
Mohamad J Halawi ◽  
...  

1984 ◽  
Vol 4 (9) ◽  
pp. 1853-1863 ◽  
Author(s):  
N Costlow ◽  
J T Lis

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.


1984 ◽  
Vol 4 (9) ◽  
pp. 1853-1863
Author(s):  
N Costlow ◽  
J T Lis

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.


Genetics ◽  
1996 ◽  
Vol 143 (4) ◽  
pp. 1861-1861

Abstract In the paper by Sin-Chieu Liu, Stanley P. Kowalski, Tien-Hung Lan, Kenneth A. Feldmann and Andrew H. Paterson (Genetics  142:  247–258; January, 1996) entitled “Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model,” several errors should be corrected. On page 248, right column, the last line should read “distribute as a χ12 distribution …” On page 249, left column, first paragraph, line 6 should be read “… in which R = r, …” On page 249, left column, the second line from the bottom should read “… R  0 = r.” On page 253, right colum, the fourth line from the bottom should read “(t  R>0.4)…” On page 253, the first line of the Figure 6 legend should read “Relationship between r (adjusted …” On page 258, the first text sentence should begin “The 1mj(dmjdr)2 term for each genotype class …,” the second text sentence should begin “The mean amount of information (ir) is the sum of the 1mj(dmjdr)2 term from each genotype class,” and the last text sentence should read “Because a = (1 − 2r) and b = (1 − r)1, …”


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