The DNase I sensitive domain of the chicken Iysozyme gene spans 24 kb

Jantzen, Klaus; Fritton, Hans P.; Igo‐Kemenes, Tibor

doi:10.1093/nar/14.15.6085

Cited by 89 publications

(54 citation statements)

References 32 publications

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“…We assayed the relative enrichment of precipitated DNA sequences by a real-time PCR assay with SYBR Green (22) and a collection of different primers recognizing all lysozyme cis-regulatory elements and sequences between the elements and far upstream. The primer at Ϫ10.07 kb corresponds to a sequence that has previously been shown to lie at the boundary of generally DNase I-sensitive and -resistant chromatin (34) and is far away from any DNase I-hypersensitive site. To additionally control the efficiency of precipitation and to normalize signals for different experiments and different cell types, we performed real-time PCR assays with primers corresponding to the coding region of the ␤-actin gene.…”

Section: Resultsmentioning

confidence: 99%

Developmentally Regulated Recruitment of Transcription Factors and Chromatin Modification Activities to Chicken Lysozyme cis-Regulatory Elements In Vivo

Lefèvre

Melnik

Wilson

et al. 2003

Molecular and Cellular Biology

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Expression of the chicken lysozyme gene is upregulated during macrophage differentiation and reaches its highest level in bacterial lipopolysaccharide (LPS)-stimulated macrophages. This is accompanied by complex alterations in chromatin structure. We have previously shown that chromatin fine-structure alterations precede the onset of gene expression in macrophage precursor cells and mark the lysozyme chromatin domain for expression later in development. To further examine this phenomenon and to investigate the basis for the differentiation-dependent alterations of lysozyme chromatin, we studied the recruitment of transcription factors to the lysozyme locus in vivo at different stages of myeloid differentiation. Factor recruitment occurred in several steps. First, early-acting transcription factors such as NF1 and Fli-1 bound to a subset of enhancer elements and recruited CREB-binding protein. LPS stimulation led to an additional recruitment of C/EBP␤ and a significant change in enhancer and promoter structure. Transcription factor recruitment was accompanied by specific changes in histone modification within the lysozyme chromatin domain. Interestingly, we present evidence for a transient interaction of transcription factors with lysozyme chromatin in lysozymenonexpressing macrophage precursors, which was accompanied by a partial demethylation of CpG sites. This indicates that a partially accessible chromatin structure of lineage-specific genes is a hallmark of hematopoietic progenitor cells.

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Section: Resultsmentioning

confidence: 99%

Developmentally Regulated Recruitment of Transcription Factors and Chromatin Modification Activities to Chicken Lysozyme cis-Regulatory Elements In Vivo

Lefèvre

Melnik

Wilson

et al. 2003

Molecular and Cellular Biology

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“…Chromatin located in the transcribed genes has previously been reported as sensitive to DNase I digestion. [1][2][3][4][5] The finding that chromatin in the transcribed intron is resistant to DNase I digestion is therefore of considerable interest. Since targets other than 7 and 10 were not analyzed as introns, further examination is required to determine whether intron chromatin in active genes is resistant to DNase I.…”

Section: Discussionmentioning

confidence: 99%

“…The TCAM-1 protein is a testisspecific membrane protein with a single transmembrane region. 6) Examination of chromatin sensitivity to DNase I has been reported for single genes and associated flanking regions, [1][2][3]5) and on loci such as b-globin. 4) No such analyses have yet been performed on regions such as the rat Ig-b/GH locus, where several cell type-specific and ubiquitously-expressed genes are located in a compact region.…”

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confidence: 99%

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State of Chromatin Sensitivity to DNase I in the Rat Ig-.BETA./Growth Hormone Locus Determined by Real-Time PCR

Osano

Otsuka

Ono

2004

Biological & Pharmaceutical Bulletin

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Using Ig-b b and growth hormone producing cells with liver-derived cells for controls, sensitivity of chromatin to DNase I was measured by real-time PCR at eleven targets in rat Ig-b b/growth hormone locus where four cell type-specific genes and two ubiquitously expressed genes are present in a compact 88-kb region. Chromatin situated at the promoter of actively-transcribed gene and placed at cell type-specific DNase I hypersensitive sites with enhancer activity was sensitive to DNase I. In the case of inactive gene, chromatin located in these regions was resistant to DNase I. Unexpectedly, however, chromatin placed in the transcribed intron was resistant to DNase I in two genes. DNase I sensitive chromatin was shown not to distribute locus-widely but rather to localize at the promoter and the enhancer of actively-transcribed genes in this locus.

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“…In myeloid cells the gene is up-regulated during the differentiation of multipotent myeloid progenitor cells to mature granulocytes and macrophages (5,6). The structural dimensions of the chicken lysozyme locus are defined by an increased general DNase I sensitivity of chromatin over an array of 24 kb around the transcribed region (7). All DHS and thus also all cis-regulatory elements are confined within this chromatin domain (5,6,8,9).…”

Section: The Complete Chicken Lysozyme Locus Comprises the Regulatorymentioning

confidence: 99%

The Chicken Lysozyme Locus as a Paradigm for the Complex Developmental Regulation of Eukaryotic Gene Loci

Bonifer

Jägle²,

Huber

1997

Journal of Biological Chemistry

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Gene loci of higher organisms have complex structural features. In some cases their coding regions occupy many, even hundreds, of kilobases of DNA. Additionally, the sequences that contain the information for the correct spatial and temporal regulation of a particular gene locus during development often exceed the extensions of the coding region by severalfold.The question of what type of information is encoded in these vast amounts of DNA has puzzled researchers from the beginning.It is now clear that eukaryotic genes are regulated by a number of different cis-regulatory elements distributed over large distances. A convenient way to assay the number and the distribution of cis-regulatory elements has been the mapping of DHS 1 in chromatin. Such local chromatin perturbations are in most cases caused by the binding of transcription factors to their cognate DNA sequences. The pattern of DHS can undergo dramatic developmental changes, indicating a change in the activity of cis-regulatory elements. In addition, the analysis of protein-DNA interactions at a single-nucleotide resolution level in vivo has demonstrated that, depending on the developmental stage, different combinations of transcription factors can occupy the same cis-regulatory element (1, 2). These experiments indicate that the transcriptional activation of a gene locus is achieved by the cooperation of several different cisregulatory elements, which, in turn, assemble transcription factors in a sequential, developmentally controlled fashion. However, the assembly of active transcription factor complexes on natural genes does not occur on naked DNA but in a chromatin context, where nucleosome-DNA interactions have to be counteracted. Hence, the activation of a gene locus requires at least the following steps: the perturbation of chromatin structure by the binding of transcription factors on cis-regulatory elements, the developmentally controlled reorganization of transcription factor complexes, the assembly of the basal transcription machinery and its interaction with upstream regulatory elements, the onset of mRNA synthesis, and, in many cases, the maintenance of an active transcriptional state during multiple rounds of DNA synthesis.How can the molecular basis of locus activation be experimentally studied? While the basal activities of individual cisregulatory elements of particular gene loci can be analyzed by transient and stable transfection experiments, the molecular mechanism of activation of a gene locus from the transcriptionally silent state can only be studied in a developing system, preferentially in transgenic animals. The ideal model locus should be small, thus facilitating the manipulation of individual cis-regulatory elements within the context of an entire genomic locus, and it should be extensively characterized on the molecular level. In addition, to dissect the role of different cis-regulatory elements in the developmental control of gene locus activation, it should be possible to follow cell differentiation experimentally, thus enab...

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The DNase I sensitive domain of the chicken Iysozyme gene spans 24 kb

Cited by 89 publications

References 32 publications

Developmentally Regulated Recruitment of Transcription Factors and Chromatin Modification Activities to Chicken Lysozyme cis-Regulatory Elements In Vivo

Developmentally Regulated Recruitment of Transcription Factors and Chromatin Modification Activities to Chicken Lysozyme cis-Regulatory Elements In Vivo

State of Chromatin Sensitivity to DNase I in the Rat Ig-.BETA./Growth Hormone Locus Determined by Real-Time PCR

The Chicken Lysozyme Locus as a Paradigm for the Complex Developmental Regulation of Eukaryotic Gene Loci

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