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

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.

Download Full-text

The chromatin structure of Saccharomyces cerevisiae autonomously replicating sequences changes during the cell division cycle

Molecular and Cellular Biology ◽

10.1128/mcb.11.10.5301-5311.1991 ◽

1991 ◽

Vol 11 (10) ◽

pp. 5301-5311

Author(s):

J A Brown ◽

S G Holmes ◽

M M Smith

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Division ◽

Chromatin Structure ◽

Dnase I ◽

S Phase ◽

Cell Division Cycle ◽

Characteristic Change ◽

The Core ◽

Dnase I Hypersensitive Sites ◽

Hypersensitive Sites

The chromatin structures of two well-characterized autonomously replicating sequence (ARS) elements were examined at their chromosomal sites during the cell division cycle in Saccharomyces cerevisiae. The H4 ARS is located near one of the duplicate nonallelic histone H4 genes, while ARS1 is present near the TRP1 gene. Cells blocked in G1 either by alpha-factor arrest or by nitrogen starvation had two DNase I-hypersensitive sites of about equal intensity in the ARS element. This pattern of DNase I-hypersensitive sites was altered in synchronous cultures allowed to proceed into S phase. In addition to a general increase in DNase I sensitivity around the core consensus sequence, the DNase I-hypersensitive site closest to the core consensus became more nuclease sensitive than the distal site. This change in chromatin structure was restricted to the ARS region and depended on replication since cdc7 cells blocked near the time of replication initiation did not undergo the transition. Subsequent release of arrested cdc7 cells restored entry into S phase and was accompanied by the characteristic change in ARS chromatin structure.

Download Full-text

Correlation between patterns of DNase I-hypersensitive sites and upstream promoter activity of the human epsilon-globin gene at different stages of erythroid development

Molecular and Cellular Biology ◽

10.1128/mcb.10.3.1199-1208.1990 ◽

1990 ◽

Vol 10 (3) ◽

pp. 1199-1208

Author(s):

P Bushel ◽

K Rego ◽

L Mendelsohn ◽

M Allan

Keyword(s):

Globin Gene ◽

K562 Cells ◽

Dnase I ◽

Base Pairs ◽

Dnase I Hypersensitive Sites ◽

Hypersensitive Sites ◽

Hel Cells ◽

Globin Synthesis ◽

Erythroleukemic Cell ◽

Erythroid Development

DNA 5' to the human epsilon-globin gene exhibits unique patterns of DNase I-hypersensitive sites (DHS) in three human erythroleukemic cell lines which represent the embryonic (K562), fetal (HEL), and adult (KMOE) stages of erythroid development. We have mapped 10 epsilon-globin DHS in K562 cells, in which the epsilon-globin gene is maximally active. Major sites are located -11.7, -10.5, -6.5, -2.2 kilobase pairs (kbp) and -200 base pairs (bp) upstream of the gene and directly over the major cap site. Minor sites are located -5.5, -4.5, and -1.48 kbp and -900 bp upstream of the cap site. In HEL cells, in which the epsilon-globin gene is expressed at extremely low levels, the -11.7-, -10.5-, -5.5-, -4.5-, and -2.2-kbp DHS are no longer detectable; the -200-bp site is approximately 300-fold less sensitive to DNase I; and the -1.48-kbp, -900-bp, and major cap site DHS are 3- to 4-fold less sensitive. Only the DHS located -6.5 kbp relative to the major cap site is detectable at all three stages of erythroid development, including KMOE cells in which epsilon-globin synthesis is undetectable. We suggest that this site may be implicated in maintaining the entire beta-globin cluster in an active chromatin conformation. The five DHS downstream of the -6.5-kbp element possess associated promoters. Thus two distinct types of DHS exist--promoter positive and promoter negative. In HEL cells, all the upstream promoters are inactivated, although the -1.48-kbp and -900- and -200-bp DHS are still present. This suggests that the maintenance of DHS and regulation of their associated promoters occur by independent mechanisms. The inactivation of the upstream promoters in HEL cells while the major cap site remains active represents a unique pattern of expression and suggests that HEL cells possess regulatory factors which specifically down regulate the epsilon-globin upstream promoters.

Download Full-text

The Ly-6E.1 (Sca-1) gene requires a 3' chromatin-dependent region for high-level gamma-interferon-induced hematopoietic cell expression

Blood ◽

10.1182/blood.v87.7.2750.bloodjournal8772750 ◽

1996 ◽

Vol 87 (7) ◽

pp. 2750-2761 ◽

Cited By ~ 17

Author(s):

A Sinclair ◽

B Daly ◽

E Dzierzak

Keyword(s):

Consensus Sequence ◽

Hematopoietic Cells ◽

Regulatory Elements ◽

Dnase I ◽

Gamma Interferon ◽

Hematopoietic Cell ◽

Hematopoietic Stem ◽

Dnase I Hypersensitive Sites ◽

Hypersensitive Sites ◽

High Level

The Ly-6E.1/A.2 gene product recognized by the Sca-1 antibody has been found on murine hematopoietic stem cells and some hematopoietic precursors, T lymphocytes, and nonhematopoietic cell lineages, suggesting a complex array of gene regulatory elements. The ability to use the Ly6E.1/A.2 transcriptional regulatory elements to direct expression of heterologous genes will allow for the manipulation of these cells during development and in hematopoietic cell transplantations. To identify the elements necessary for high-level expression, we have made deletion constructs of Ly-6E.1 gene flanking regions containing DNase I hypersensitive sites, tested them for expression in hematopoietic cells, and have performed kinetic analyses to correlate the appearance of hypersensitive sites with gene transcription and protein expression. We show that a 3′ region containing two DNase I hypersensitive sites at +8.7 and +8.9 kb is required for high-level, gamma-interferon (gamma-IFN)-induced expression of the Ly-6E.1 gene and that a consensus sequence for a gamma-IFN-responsive element localizes to the +8.7 site. We also provide a description of allele- and cell-specific DNase I hypersensitive site patterns of the Ly-6E.1 and Ly-6A.2 genes. Taken together, these data indicate that while both 5′ and 3′ hypersensitive sites are rapidly induced with gamma-IFN, the 3′ most distal hypersensitive sites are involved in directing high levels of expression of Sca-1 in hematopoietic cells.

Download Full-text

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

Molecular and Cellular Biology ◽

10.1128/mcb.5.6.1538 ◽

1985 ◽

Vol 5 (6) ◽

pp. 1538-1539 ◽

Cited By ~ 16

Author(s):

H Weintraub

Keyword(s):

High Resolution ◽

Dnase I ◽

Primer Extension ◽

S1 Nuclease ◽

Dnase I Hypersensitive Sites ◽

High Resolution Mapping ◽

Hypersensitive Sites ◽

Resolution Mapping

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.

Download Full-text

Chromatin structure of a P-element-transduced hsp-28 gene in Drosophila melanogaster

Molecular and Cellular Biology ◽

10.1128/mcb.6.11.4126-4129.1986 ◽

1986 ◽

Vol 6 (11) ◽

pp. 4126-4129

Author(s):

J C Eissenberg ◽

S C Elgin

Keyword(s):

Gene Expression ◽

Drosophila Melanogaster ◽

Chromatin Structure ◽

Dnase I ◽

P Element ◽

Direct Selection ◽

Wild Type ◽

Dnase I Hypersensitive Sites ◽

Hypersensitive Sites ◽

Selection For

The Drosophila hsp-28 gene was heat inducible when transduced to novel chromosomal sites even when no direct selection for transduced gene expression was imposed. The pattern of DNase I-hypersensitive sites 5' to the wild type and transduced copy of hsp-28 was similar. In addition, DNase I-hypersensitive sites occurred within the P-element sequences flanking transduced loci.

Download Full-text

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

Download Full-text

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

Download Full-text

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

Download Full-text

The heat shock consensus sequence is not sufficient for hsp70 gene expression in Drosophila melanogaster.

Molecular and Cellular Biology ◽

10.1128/mcb.5.1.197 ◽

1985 ◽

Vol 5 (1) ◽

pp. 197-203 ◽

Cited By ~ 35

Author(s):

J Amin ◽

R Mestril ◽

R Lawson ◽

H Klapper ◽

R Voellmy

Keyword(s):

Drosophila Melanogaster ◽

Heat Shock ◽

Consensus Sequence ◽

Gene Promoter ◽

Cell Types ◽

Hsp70 Gene ◽

Base Pairs ◽

Hybrid Gene ◽

Induced Expression ◽

African Green Monkey Kidney

A hybrid gene in which the expression of an Escherichia coli beta-galactosidase gene was placed under the control of a Drosophila melanogaster 70,000-dalton heat shock protein (hsp70) gene promoter was constructed. Mutant derivatives of this hybrid gene which contained promoter sequences of different lengths were prepared, and their heat-induced expression was examined in D. melanogaster and COS-1 (African green monkey kidney) cells. Mutants with 5' nontranscribed sequences of at least 90 and up to 1,140 base pairs were expressed strongly in both cell types. Mutants with shorter 5' extensions (of at least 63 base pairs) were transcribed and translated efficiently in COS-1 but not at all in D. melanogaster cells. Thus, in contrast to the situation in COS-1 cells, the previously defined heat shock consensus sequence which is located between nucleotides 62 and 48 of the hsp70 gene 5' nontranscribed DNA segment is not sufficient for the expression of the D. melanogaster gene in homologous cells. A second consensus-like element 69 to 85 nucleotides upstream from the cap site is postulated to be also involved in the heat-induced expression of the hsp70 gene in D. melanogaster cells.

Download Full-text