scholarly journals In Vivo Analysis of DNase I Hypersensitive Sites in the Human CFTR Gene

1999 ◽  
Vol 5 (4) ◽  
pp. 211-223 ◽  
Author(s):  
Danielle S. Moulin ◽  
Ania L. Manson ◽  
Hugh N. Nuthall ◽  
David J. Smith ◽  
Clare Huxley ◽  
...  
Keyword(s):  
Dnase I ◽  
Cftr Gene ◽  
Dnase I Hypersensitive Sites ◽  
Hypersensitive Sites ◽  
In Vivo Analysis

Lineage-Specific Transcriptional Regulation of GATA1 Is Dependent on Lineage-Specific Utilisation of Multiple Cis-Elements and Haematopoietic Transcription Factors.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1610-1610
Author(s):  
Paresh Vyas ◽  
Boris Guyot ◽  
Veronica Valverde-Garduno ◽  
Eduardo Anguita ◽  
Isla Hamlett ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dnase I ◽  
Red Cells ◽  
Erythroid Cells ◽  
Cis Elements ◽  
Dnase I Hypersensitive Sites ◽  
Hypersensitive Sites ◽  
Transcription Factor Occupancy

Abstract Normal differentiation of red cells, platelets and eosinophils from a myeloid progenitor requires expression of the transcription factor GATA1. Moreover, GATA1 expression level influences lineage output; higher levels promote erythromegakaryocytic differentiation and lower levels eosinophil maturation. Conversely, repression of GATA1 expression is required for monocyte/neutrophil development. GATA1 expression is principally controlled transcriptionally. Thus, dissecting the molecular basis of transcriptional control of GATA1 expression will be one important facet in understanding how myeloid lineages are specified. To address this question we sought to identify all DNA sequences important for GATA1 expression. Previous analysis identified 3 murine (m)Gata1 cis-elements (an upstream enhancer, mHS-3.5, a haematopoietic IE promoter and elements in a GATA1 intron, mHS+3.5) conserved in sequence between human(h) and mouse. These studies also suggested additional unidentified elements were required for erythroid and eosinophil GATA1 expression. We compared sequence, mapped DNase I hypersensitive sites (HS) and determined histone H3/H4 acetylation over ~120 kb flanking the hGATA1 locus and corresponding region in mouse to pinpoint cis-elements. Remarkably, despite lying in a ~10 MB conserved syntenic segment, the chromatin structures of both GATA1 loci are strikingly different. Two previously unidentified haematopoietic cis-elements, one in each species (mHS-25 and hHS+14), are not conserved in position and sequence and have enhancer activity in erythroid cells. Chromatin immunoprecipitation studies show both mHS-25 and hHS+14 are bound in vivo in red cells by the transcription factors GATA1, SCL, LMO2, Ldb1. These findings suggest that some cis-elements regulating human and mouse GATA1 genes differ. Further analysis of in vivo transcription factor occupancy at GATA1 cis-elements in primary mouse eosinophils and red cells, megakaryocytic cells (L8057) and control fibroblasts show lineage- and cis-element-specific patterns of regulator binding (see table below). In red cells and megakaryocytes, GATA1, SCL, LMO2 and Ldb1 bind at two regulatory elements (mhHS-25 and mHS-3.5). Interestingly, the megakaryocyte transcriptional regulator Fli1 factor binds to mHS+3.5 specifically in megakaryocytes. In eosinophils, a different pattern of DNase I HS and transcription factor binding is seen. GATA1, PU.1 and C/EBPe (all regulate eosinophil gene expression) bind IE promoter and/or mHS+3.5. Collectively, these results suggest lineage-specific GATA1 expession is dependent on combinations of cis-elements and haematopoietic trans-acting factors that are unique for each lineage. DNase I Hypersensitive sites and transcription factor occupancy at mGATA1 cis-elements. mHS-26/-25* mHS-3.5 mIE mHS+3.5 m: mouse, h: human, *: HS identified in this study, TF: transcription factor Primary erythroid cells HS present, GATA1, SCL, LMO2, Ldb1 HS present, GATA1, SCL, LMO2, Ldb1 HS present, GATA1 HS present, GATA1 Megakaryocytic cells HS present, GATA1, SCL, LMO2, Ldb1 HS present, GATA1, SCL, LMO2, Ldb1 HS present, GATA1 HS present, GATA1 and Fli1 Primary eosinophils HS absent HS present, No TF detected HS present, GATA1 and C/EBPε HS present, GATA1, C/EBP ε and PU.1 Fibroblasts HS absent HS absent HS absent HS absent

scholarly journals Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene

2002 ◽  
Vol 269 (2) ◽  
pp. 553-559 ◽  
Author(s):  
Marios Phylactides ◽  
Rebecca Rowntree ◽  
Hugh Nuthall ◽  
David Ussery ◽  
Ann Wheeler ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Dnase I ◽  
Cftr Gene ◽  
Dnase I Hypersensitive Sites ◽  
Hypersensitive Sites

scholarly journals Analysis of DNase-I-hypersensitive sites at the 3′ end of the cystic fibrosis transmembrane conductance regulator gene (CFTR)

1999 ◽  
Vol 341 (3) ◽  
pp. 601-611 ◽  
Author(s):  
Hugh N. NUTHALL ◽  
Danielle S. MOULIN ◽  
Clare HUXLEY ◽  
Ann HARRIS
Keyword(s):  
Cystic Fibrosis ◽  
Regulatory Element ◽  
Dnase I ◽  
Cftr Gene ◽  
Transmembrane Conductance Regulator ◽  
Regulator Gene ◽  
Transmembrane Conductance ◽  
Dnase I Hypersensitive Sites ◽  
Hypersensitive Sites ◽  
Cystic Fibrosis Transmembrane

The cystic fibrosis transmembrane conductance regulator gene (CFTR) exhibits a complex pattern of expression that shows temporal and spatial regulation, although the control mechanisms are not fully known. We have mapped DNase-I-hypersensitive sites (DHSs) flanking the CFTR gene with the aim of identifying potential regulatory elements. We previously characterized DHSs at -79.5 and -20.9 kb with respect to the CFTR translational start site and a regulatory element in the first intron of the gene at 185+10 kb. We have now mapped five DHSs lying 3′ to the CFTR gene at 4574+5.4, +6.8, +7.0, +7.4 and +15.6 kb that show some degree of tissue specificity. The DHSs are seen in chromatin extracted from human primary epithelial cells and cell lines; the presence of the +15.6 kb site is tissue-specific in transgenic mice carrying a human CFTR yeast artificial chromosome. Further analysis of the 4574+15.6 kb DHS implicates the involvement of CCAAT-enhancer-binding protein (C/EBP), cAMP-response-element-binding protein (CREB)/activating transcription factor (ATF) and activator protein 1 (AP-1) family transcription factors at this regulatory element.

scholarly journals Chromatin Architecture near a Potential 3′ End of the Igh Locus Involves Modular Regulation of Histone Modifications during B-Cell Development and In Vivo Occupancy at CTCF Sites

2005 ◽  
Vol 25 (4) ◽  
pp. 1511-1525 ◽  
Author(s):  
Francine E. Garrett ◽  
Alexander V. Emelyanov ◽  
Manuel A. Sepulveda ◽  
Patrick Flanagan ◽  
Sabrina Volpi ◽  
...  
Keyword(s):  
B Cells ◽  
B Cell ◽  
Histone Modifications ◽  
Dnase I ◽  
B Cell Development ◽  
Open Chromatin ◽  
Developmentally Regulated ◽  
Dnase I Hypersensitive Sites ◽  
Hypersensitive Sites

ABSTRACT The murine Igh locus has a 3′ regulatory region (3′ RR) containing four enhancers (hs3A, hs1,2, hs3B, and hs4) at DNase I-hypersensitive sites. The 3′ RR exerts long-range effects on class switch recombination (CSR) to several isotypes through its control of germ line transcription. By measuring levels of acetylated histones H3 and H4 and of dimethylated H3 (K4) with chromatin immunoprecipitation assays, we found that early in B-cell development, chromatin encompassing the enhancers of the 3′ RR began to attain stepwise modifications typical of an open conformation. The hs4 enhancer was associated with active chromatin initially in pro- and pre-B cells and then together with hs3A, hs1,2, and hs3B in B and plasma cells. Histone modifications were similar in resting splenic B cells and in splenic B cells induced by lipopolysaccharide to undergo CSR. From the pro-B-cell stage onward, the ∼11-kb region immediately downstream of hs4 displayed H3 and H4 modifications indicative of open chromatin. This region contained newly identified DNase I-hypersensitive sites and several CTCF target sites, some of which were occupied in vivo in a developmentally regulated manner. The open chromatin environment of the extended 3′ RR in mature B cells was flanked by regions associated with dimethylated K9 of histone H3. Together, these data suggest that 3′ RR elements are located within a specific chromatin subdomain that contains CTCF binding sites and developmentally regulated modules.

The prediction of human DNase I hypersensitive sites based on DNA sequence information

2021 ◽  
Vol 209 ◽  
pp. 104223
Author(s):  
Wei Su ◽  
Fang Wang ◽  
Jiu-Xin Tan ◽  
Fu-Ying Dao ◽  
Hui Yang ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dnase I ◽  
Sequence Information ◽  
Dnase I Hypersensitive Sites ◽  
Hypersensitive Sites

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

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.

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