Analysis of DNase I-hypersensitive sites in the chromatin of the chicken adenosine receptor 2B gene reveals multiple cell-type-specific cis-regulatory elements

Braas, Daniel; Kattmann, Dana; Miethe, Josef; Klempnauer, K H

doi:10.1016/s0378-1119(02)01155-1

Cited by 3 publications

(4 citation statements)

References 22 publications

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“…DHS were mapped according to the method described by Sippel et al (40), as described in detail by Braas et al (5). The mim-1 enhancer region was analyzed by digesting the genomic DNA isolated from DNase Itreated nuclei with HindIII and probing Southern blots with a 0.4-kb SacI/ HindIII DNA fragment from the mim-1 upstream region.…”

Section: Methodsmentioning

confidence: 99%

C/EBPβ Induces Chromatin Opening at a Cell-Type-Specific Enhancer

Plachetka

Chayka

Wilczek

et al. 2008

Molecular and Cellular Biology

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We have used the chicken mim-1 gene as a model to study the mechanisms by which transcription factors gain initial access to their target sites in compacted chromatin. The expression of mim-1 is restricted to the myelomonocytic lineage of the hematopoietic system where it is regulated synergistically by the Myb and CCAAT/enhancer binding protein (C/EBP) factors. Myb and C/EBP␤ cooperate at two distinct cis elements of mim-1, the promoter and a cell-type-specific enhancer, both of which are associated with DNase I hypersensitive sites in myelomonocytic cells but not in mim-1-nonexpressing cells. Previous work has shown that ectopic expression of Myb and C/EBP␤ activates the endogenous mim-1 gene in a nonhematopoietic cell type (fibroblasts), where the gene is normally completely silent. Here, we investigated the molecular details of this finding and show that the activation of mim-1 occurs by two independent mechanisms. In the absence of Myb, C/EBP␤ triggers the initial steps of chromatin opening at the mim-1 enhancer without inducing transcription of the gene. mim-1 transcription occurs only in the presence of Myb and is associated with chromatin opening at the promoter. Our work identifies a novel function for C/EBP␤ in the initial steps of a localized chromatin opening at a specific, physiologically relevant target region.The significant changes in gene expression that occur during processes such as differentiation, proliferation, and apoptosis are often controlled at the transcriptional level. In eukaryotic organisms, the transcriptional activation of genes occurs in the chromatin context. The basic unit of chromatin is the nucleosome, which consists of an octameric complex of the core histones H2A, H2B, H3, and H4 and 146 base pairs of DNA wrapped around the protein core and connected by linker DNA. Further folding of nucleosomes through the binding of histone H1 leads to compact higher-order structures in which the DNA is not easily accessible for transcription factors or the transcriptional machinery. Access by the transcription machinery to DNA is facilitated by various chromatin remodeling enzymes that cause localized changes of the chromatin structure. These remodeling complexes are themselves recruited by transcription factors to specific cis-acting sequences (for reviews see references 4, 23, 26, 41, 47, and 48). Although we have a rather detailed picture of the chromatin remodeling events that occur after transcription factors have associated with their binding sites, the mechanisms by which these proteins gain initial access to their binding sites in nucleosomally organized and tightly packed DNA are less well understood. Cirillo et al. (14) have used the term "pioneer factor" to describe a class of transcription factors that are capable of entering into silent chromatin and initiating chromatin opening.

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Section: Methodsmentioning

confidence: 99%

C/EBPβ Induces Chromatin Opening at a Cell-Type-Specific Enhancer

Plachetka

Chayka

Wilczek

et al. 2008

Molecular and Cellular Biology

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“…DHS were mapped according to Sippel et al (43) as described in detail by Braas et al (2). Genomic DNA isolated from DNase I-treated nuclei was digested with HindIII and analyzed by Southern blotting.…”

Section: Methodsmentioning

confidence: 99%

v-Myb Mediates Cooperation of a Cell-Specific Enhancer with the mim-1 Promoter

Chayka

Kintscher

Braas

et al. 2005

Molecular and Cellular Biology

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The oncogenic transcription factor v-Myb disrupts myelomonocytic differentiation and transforms myelomonocytic cells by deregulating the expression of specific target genes. One of these genes, the chicken mim-1 gene, is activated by Myb exclusively in myelomonocytic cells and, therefore, has been an interesting model system to study how Myb activates a target in a lineage-specific manner. Previous work has suggested that Myb activates mim-1 by cooperating with CCAAT box/enhancer binding protein beta (C/EBP␤) or other C/EBP transcription factors at the mim-1 promoter. We have now identified and characterized a powerful Mybdependent enhancer located 2 kb upstream of the mim-1 promoter. The enhancer is preferentially active in myelomonocytic cells, confers Myb responsiveness onto a heterologous promoter, and dramatically increases Myb responsiveness of the mim-1 promoter. Chromatin immunoprecipitation demonstrates that v-Myb and C/EBP␤ are bound to the enhancer in v-Myb-transformed cells; furthermore, cooperation of the enhancer with the mim-1 promoter is greatly stimulated by C/EBP␤ and p300. Taken together, our results show that the regulation of mim-1 expression by v-Myb is more complex than previously assumed and involves two distinct regions of the mim-1 gene. A major function of v-Myb (in addition to its role at the mim-1 promoter) apparently is to activate the mim-1 enhancer and, together with C/EBP␤ and p300, facilitate its cooperation with the promoter. Interestingly, our work also shows that the v-Myb protein encoded by avian myeloblastosis virus is defective in this function, suggesting an explanation for why primary avian myeloblastosis virus-transformed myeloblasts do not express the mim-1 gene.

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“…2001; Zaslaver et al . 2004) and in vivo TF binding techniques(Beer and Tavazoie 2004; Braas et al . 2003; Elemento and Tavazoie 2005; Pritsker et al .…”

Section: Introductionmentioning

confidence: 99%

“…In addition, recent advances in high throughput gene expression analysis technologies can provide large amounts of detailed expression data. These techniques include DNA microarray (Conway and Schoolnik 2003; Eisen et al 1998; Spellman et al 1998), SAGE (serial analysis of gene expression) (Angelastro et al 2000) and in vivo gene expression using promoter reporters (Anderson et al 1988; Bjarnason et al 2003; Blouin K. 1996; Kalir et al 2001; Setty et al 2003; Van Dyk et al 2001; Zaslaver et al 2004) and in vivo TF binding techniques (Beer and Tavazoie 2004; Braas et al 2003; Elemento and Tavazoie 2005; Pritsker et al 2004; Rosenfeld et al 2005) (Ui et al 1998).…”

Section: Introductionmentioning

confidence: 99%

The identification of functional motifs in temporal gene expression analysis

Song

Bjarnason

Surette

2005

Evol Bioinform Online

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The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR) and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur) binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

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Analysis of DNase I-hypersensitive sites in the chromatin of the chicken adenosine receptor 2B gene reveals multiple cell-type-specific cis-regulatory elements

Cited by 3 publications

References 22 publications

C/EBPβ Induces Chromatin Opening at a Cell-Type-Specific Enhancer

C/EBPβ Induces Chromatin Opening at a Cell-Type-Specific Enhancer

v-Myb Mediates Cooperation of a Cell-Specific Enhancer with the mim-1 Promoter

The identification of functional motifs in temporal gene expression analysis

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