Hypersensitive Sites In Chromatin Research Articles

Cyclic AMP-induced Chromatin Changes Support the NFATc-mediated Recruitment of GATA-3 to the Interleukin 5 Promoter

Elevated intracellular cyclic AMP levels, which suppress the proliferation of naive T cells and type 1 T helper (Th1) cells are a property of T helper 2 (Th2) cells and regulatory T cells. While cyclic AMP signals interfere with the IL-2 promoter induction, they support the induction of Th2-type genes, in particular of il-5 gene. We show here that cyclic AMP signals support the generation of three inducible DNase I hypersensitive chromatin sites over the il-5 locus, including its promoter region. In addition, cyclic AMP signals enhance histone H3 acetylation at the IL-5 promoter and the concerted binding of GATA-3 and NFATc to the promoter. This is facilitated by direct protein-protein interactions involving the C-terminal Zn(2+)-finger of GATA-3 and the C-terminal region of the NFATc1 DNA binding domain. Because inhibition of NFATc binding to the IL-5 promoter in vivo also affects the binding of GATA-3, one may conclude that upon induction of Th2 effector cells NFATc recruits GATA-3 to Th2-type genes. These data demonstrate the functional importance of cyclic AMP signals for the interplay between GATA-3 and NFATc factors in the transcriptional control of lymphokine expression in Th2 effector cells.

PipTools: A Computational Toolkit to Annotate and Analyze Pairwise Comparisons of Genomic Sequences

Sequence conservation between species is useful both for locating coding regions of genes and for identifying functional noncoding segments. Hence interspecies alignment of genomic sequences is an important computational technique. However, its utility is limited without extensive annotation. We describe a suite of software tools, PipTools, and related programs that facilitate the annotation of genes and putative regulatory elements in pairwise alignments. The alignment server PipMaker uses the output of these tools to display detailed information needed to interpret alignments. These programs are provided in a portable format for use on common desktop computers and both the toolkit and the PipMaker server can be found at our Web site ( http://bio.cse.psu.edu/). We illustrate the utility of the toolkit using annotation of a pairwise comparison of the mouse MHC class II and class III regions with orthologous human sequences and subsequently identify conserved, noncoding sequences that are DNase I hypersensitive sites in chromatin of mouse cells.

Embryonic inheritance of the chromatin organisation of the imprinted H19 domain in mouse spermatozoa

Insulin-like growth factor 2 ( Igf 2) and H19 genes are oppositely imprinted and as such have been most extensively studied imprinted genes both genetically and at the molecular level. Imprints of the H19 gene, being established during spermatogenesis, are epigenetically transmitted to the somatic cells of the embryo. Current hypotheses attempting to explain the allele-specific silence of the H19 gene include DNA methylation and chromatin condensation. In order to understand the molecular basis of H19 epigenesis, it is crucial to identify the markings in the chromatin organising the imprinted domain in spermatozoa. Using Micrococcal nuclease (MNase), DNase I and Methidiumpropyl-EDTA. iron II (MPE·Fe(II)) as chromatin probes, we demonstrate that in mouse epididymal spermatozoa, at least 4 kb DNA upstream of the H19 ‘cap’ site, containing the imprinted and differentially methylated domain (DMD), is heterochromatic. The cleavage sites in this domain (−2 to −4 kb) exhibit ~425 bp periodicity. This structure is maintained in the paternal allele of normal embryos and is disrupted at −2.2, −2.65 and at −3.5 kb in embryos maternally disomic for the distal end of chromosome 7 (MatDp 7). The hypersensitive sites in chromatin precisely register the MPE·Fe(II) cleavage sites in chromosomal DNA. Therefore, the DNA sequences in the imprinted domain constrain the chromatin structure in a way similar to that of 1.688 g/cm 3 Drosophila satellite chromatin. In addition, we find that condensation of the paternal allele correlates with methylation-dependent alteration in the structure of DNA sequences in DMD. These results suggest that CpG-methylation induces localised changes in DNA conformation and these facilitate consequent remodelling of chromatin thereby allowing the paternal and maternal H19 alleles to be distinguished.

Analysis of DNaseI hypersensitive sites in chromatin by cleavage in permeabilized cells.

Analysis of DNaseI hypersensitive sites in chromatin by cleavage in permeabilized cells.

The myeloperoxidase gene proximal enhancer directs hematopoietic-specific expression in transgenic mice

The myeloperoxidase (MPO) gene is expressed specifically in immature myeloid cells. The MPO gene includes a promoter proximal enhancer which is coincident with DNaseI hypersensitive chromatin sites and is specifically active in myeloid cell lines. We developed transgenic murine lines in which 1.3 kb of murine MPO proximal 5′ flanking region DNA was linked to a TATAA homology and RNA initiation site derived from the HSV-TK promoter and to a luciferase reporter (MPOTKLUC). In each of six founder lines, high-level luciferase activity was evident in marrow, thymus and spleen. Modest- to high-level luciferase expression was also evident in brain and in the heart in several of the lines, and luciferase activity was at or near background levels in lung, liver, kidney, stomach, colon, bladder, skeletal muscle, skin and small intestine in all of the MPOTKLUC transgenic mice. Within marrow cells, luciferase activity was evident in myeloid (GR-1+), B lymphoid (B220+) and T-lymphoid (CD4+) cells. Additional regulatory regions, thus, may be required to further restrict MPO gene expression to immature myeloid cells.

The developmental activation of the chicken lysozyme locus in transgenic mice requires the interaction of a subset of enhancer elements with the promoter.

The complete chicken lysozyme locus is expressed in a position independent fashion in macrophages of transgenic mice and forms the identical chromatin structure as observed with the endogenous gene in chicken cells. Individual lysozyme cis -regulatory elements reorganize their chromatin structure at different developmental stages. Accordingly, their activities are developmentally regulated, indicating a differential role of these elements in locus activation. We have shown previously that a subset of enhancer elements and the promoter are sufficient to activate transcription of the chicken lysozyme gene at the correct developmental stage. Here, we analyzed to which grade the developmentally controlled chromatin reorganizing capacity of cis -regulatory elements in the 5'-region of the chicken lysozyme locus is dependent on promoter elements, and we examined whether the lysozyme locus carries a dominant chromatin reorganizing element. To this end we generated transgenic mouse lines carrying constructs with a deletion of the lysozyme promoter. Expression of the transgene in macrophages is abolished, however, the chromatin reorganizing ability of the cis -regulatory elements is differentially impaired. Some cis -elements require the interaction with the promoter to stabilize transcription factor complexes detectable as DNase I hypersensitive sites in chromatin, whereas other elements reorganize their chromatin structure autonomously.

Identification of cis-acting elements as DNase I hypersensitive sites in lysozyme gene chromatin

DNase I hypersensitive sites in chromatin of eukaryotic cells mark the positions of multifactorial cis-acting elements. Mapping DH sites by indirect end labeling is a convenient procedure used for identifying regulatory elements within extensive regions of chromatin and for gaining information about their functional specificity as well as their fine structure.

Dynamic Changes in the Chromatin of the Chicken Lysozyme Gene Domain During Differentiation of Multipotent Progenitors to Macrophages

The chicken lysozyme locus is regulated in oviduct and macrophages by a complex set of well-characterized cis-regulatory DNA elements. We determined the DNase I hypersensitive chromatin site pattern of the chromatin of the lysozyme locus in retrovirally transformed cell lines representing different stages of myelomonocytic cell differentiation. In the transformed multipotent progenitor stage and in erythroblasts, only a DNase I hypersensitive chromatin site at a silencer element located -2.4 kb upstream of the transcriptional start site is present. At the myeloblast stage DNase I hypersensitive chromatin sites are formed both at the distal enhancer located at -6.1 kb and at the promoter. Later in differentiation, at the monocytic stage, a second DNase I hypersensitive chromatin site appears at the medial enhancer located at -2.7 kb. Parallel with DNase I hypersensitive chromatin site formation at the medial enhancer, the DNase I hypersensitive chromatin site at the silencer element disappears. These chromatin rearrangements correlate with the mRNA expression of the gene that is undetectable in multipotent progenitors and maximal in a lipopolysaccharide-stimulated monocyte cell line. Our results show that the chromatin structure and the transcriptional activity of the gene are tightly coupled during commitment and maturation of the myelomonocytic lineage.

Dynamic chromatin: The regulatory domain organization of eukaryotic gene loci

It is hypothesized that nuclear DNA is organized in topologically constrained loop domains defining basic units of higher order chromatin structure. Our studies are performed in order to investigate the functional relevance of this structural subdivision of eukaryotic chromatin for the control of gene expression. We used the chicken lysozyme gene locus as a model to examine the relation between chromatin structure and gene function. Several structural features of the lysozyme locus are known: the extension of the region of general DNAasel sensitivity of the active gene, the location of DNA-sequences with high affinity for the nuclear matrix in vitro, and the position of DNAasel hypersensitive chromatin sites (DHSs). The pattern of DHSs changes depending on the transcriptional status of the gene. Functional studies demonstrated that DHSs mark the position of cis-acting regulatory elements. Additionally, we discovered a novel cis-activity of the border regions of the DNAasel sensitive domain (A-elements). By eliminating the position effect on gene expression usually observed when genes are randomly integrated into the genome after transfection, A-elements possibly serve as punctuation marks for a regulatory chromatin domain. Experiments using transgenic mice confirmed that the complete structurally defined lysozyme gene domain behaves as an independent regulatory unit, expressing the gene in a tissue specific and position independent manner. These expression features were lost in transgenic mice carrying a construct, in which the A-elements as well as an upstream enhancer region were deleted, indicating the lack of a locus activation function on this construct. Experiments are designed in order to uncover possible hierarchical relationships between the different cis-acting regulatory elements for stepwise gene activation during cell differentiation. We are aiming at the definition of the basic structural and functional requirements for position independent and high level gene expression. The result of these experiments will have important consequences for random gene transfer with predictable and reproducible expression of transgenes.

Nuclear Enzymes, Fragile Sites, and Cancer

The finding of a large number of recurrent fragile sites on human chromosomes provides suggestive evidence for the origin of recurrent chromosomal rearrangements that are a common feature in most neoplasias. These fragile sites can be induced by a wide variety of mutagens and carcinogens that are known to act through different molecular mechanisms. They correlate with two-thirds of the recurrent cancer chromosomal breakpoints known thus far and with the location of most mapped oncogenes and growth factors. Because we have now found that a large number of fragile sites can also be induced by agents such as DNase I and benzo[a]pyrene diol-epoxide (BPDE), which are known to induce hypersensitive chromatin sites, it is possible that a class of fragile sites represents regulatory regions of active genes. We have also introduced restriction enzymes into cultured lymphocytes and found that fragile sites are expressed in a pattern similar to that produced by DNase I and BPDE. Because fragile sites have a higher expression with advancing age, cigarette smoking, and deficiency of folic acid and B12 vitamins, they may represent active genomic sites that are vulnerable to physiological and environmental disturbance.

14] Analysis of hypersensitive sites in chromatin

This chapter focuses on the analysis of hypersensitive sites in chromatin. Although the precise cause and effect of the phenomenon of nuclease hypersensitivity in chromatin remains to be fully elucidated, the identification of nuclease hypersensitive sites in cellular chromatin is useful as a marker of nonnucleosomal organization that could also reflect an underlying sequence-specific protein-DNA interaction. The sequence of experiments can serve as a general strategy for surveying the chromatin organization of a eukaryotic gene or region of special interest, with the intention of further analyzing those regions in which the break in nucleosomal arrangement is reflected by a change in nuclease sensitivity. Such an in vivo analysis is an important study of gene regulation as it provides information on the protein-DNA interactions that are actually occurring in the cell nucleus. This chapter concludes with describing the various properties of restriction endonuclease protection and limitations of the ExoIII protection techniques.

Nuclease hypersensitive sites in chromatin.

Nuclease hypersensitive sites in chromatin.

DNase I-hypersensitive sites in the chromatin structure of the lysozyme gene in steroid hormone target and non-target cells.

The pattern of DNase I-hypersensitive sites in the chromatin domain of the lysozyme gene was investigated in several organs and cell-types of the chicken. In the cluster of hypersensitive chromatin sites framing the gene, different classes of sites could be discerned: A subset was common to essentially all cells examined except for erythrocytes. Thus several highly nuclease susceptible structures exist around the gene even in its repressed state. Beside the promoter region a second site 6.1 kb upstream of the transcriptional start site of the gene strictly correlates with the transcriptionally active or potentially active state of the gene in both, oviduct cells and macrophages. A final class of sites is specific for the particular lysozyme expressing tissue and the presence of its members distinguish whether the gene is steroid regulated or in a steroid independent active mode.

DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation

Helical-twist, roll and torsion-angle variations calculated by the Calladine (1982)-Dickerson (1983) rules were scanned along several nucleotide sequences for which DNAase I cleavage data are available. It has been shown that for short synthetic oligomers DNAase I cuts preferentially at positions of high helical twist (Dickerson & Drew, 1981; Lomonossoff et al., 1981). Our calculations indicate that DNAase I sensitive and hypersensitive sites in chromatin are correlated with regions of successive, large, helical-twist angle variations from regular B-DNA. In many cases these regions exhibit large variations in base-pair roll and backbone torsion angles as well. It has been suggested that DNAase I cuts in the vicinity of cruciforms. However, it was recently demonstrated by Courey & Wang (1983) and Gellert et al. (1983) that such cruciform formation in a negatively supercoiled DNA is kinetically forbidden under physiological conditions. We thus propose that clustering of large twist-angle (and/or roll and backbone torsion angle) variations may be among the conformational features recognized by the enzyme. Specific cuts can then preferentially occur at base-pair steps with high helical twists.