Nuclear scaffold attachment sites in the human globin gene complexes

Role of nuclear architecture in the initiation of eukaryotic DNA replication

The eukaryotic genome is compacted in the cell nucleus, in a way that allows its faithful and ordered replication each cell cycle. Chromatin is organized into topologically constrained loops that are anchored to the nuclear matrix by specific attachment regions (SARs). Chromatin loops were proposed to correspond to replication units. In particular, it has been suggested that replication origins coincide with SARs. Critical examination of these hypotheses has long been hampered by the elusive nature of higher eukaryotic DNA replication origins and termini. In recent years, however, a number of loci have been mapped for both SARs and replication units, and studies on the nuclear localization of replicating DNA and replication proteins have begun. We review these data and argue that they question this model. We then try to delineate other aspects of chromosome compartmentalization and cell-cycle remodeling which might be responsible for the specification and activation of metazoan DNA replication origins.

Repair pattern in the beta-globin gene cluster of human fibroblasts after ultraviolet irradiation

We have developed a novel technique to determine repair of structurally different DNA lesions. It was used to address the question of whether DNA repair in the absence of transcription occurs in a uniformly random manner or with preferences for certain regions. Human fibroblasts were exposed to ultraviolet light (3-10 J/m2) and treated with 7.5 mM hydroxyurea to inhibit replicative DNA synthesis. During the first hours after irradiation cells were treated with 5-bromodeoxyuridine to label the regions undergoing repair, with the presumption that the regions that have been more efficiently repaired would incorporate more of the nucleoside. A 155-kb DNA sequence containing the entire human beta-globin domain was reconstructed using sequences deposited in the EMBL gene bank. Twelve uniformly long single-copy RNA probes spanning the beta-globin cluster were synthesised in vitro and immobilized on microtiter plates. They were hybridized with DNA from the irradiated cells. The amount of 5-bromodeoxyuridine, incorporated as a result of repair in the DNA fractions hybridized to the different RNA probes, was determined immunochemically using antibody to this nucleoside. By this technique we registered increased repair efficiency in the zone of the permanent scaffold attachment region at the 5'-end of the beta-globin domain during the first hours after ultraviolet irradiation. This result was confirmed and by the more conventional T4 endonuclease V technique detecting the removal of cyclobutane pyrimidine dimers.

The cleavage of nuclear DNA into high molecular weight DNA fragments occurs not only during apoptosis but also accompanies changes in functional activity of the nonapoptotic cells

In this paper we demonstrate that apoptosis in primary culture of murine thymocytes and in continuously growing human cells is associated with the progressive disintegration of nuclear DNA into high molecular weight (HMW)-DNA fragments of about 50-150 kb. We also show that the formation of similarly sized HMW-DNA fragments takes place in the same cells in the absence of apoptotic inducers. Unlike an apoptotic fragmentation of nuclear DNA, the formation of HMW-DNA fragments in nonapoptotic cells is rapidly induced, has no correlation with the cell death, and is not associated with the development of oligonucleosomal "ladder" or apoptotic changes in nuclear morphology. The disintegration of DNA into HMW-fragments is also observed in nuclei isolated from healthy, nonapoptosizing tissues of various eukaryotes. We show that the formation of HMW-DNA fragments in the absence of apoptotic inducers is strongly dependent on the ionic detergents, is responsive to the topoisomerase II-specific poison, teniposide, and is completely reversible under conditions that favor topoisomerase II-dependent rejoining reaction. Also, we demonstrate that the formation of HMW-DNA fragments in continuously growing cell lines caused either by serum deprivation or monolayer establishment is of a transient nature and rapidly reverses to the control level following serum addition or dilution of monolayer. The results suggest that the cleavage of nuclear DNA into HMW-DNA fragments is associated not only with apoptosis but also accompanies changes in functional activity of nonapoptotic cells.

An atypical homeodomain in SATB1 promotes specific recognition of the key structural element in a matrix attachment region

SATB1 is a cell type-specific nuclear matrix attachment region (MAR) DNA-binding protein, predominantly expressed in thymocytes. We identified an atypical homeodomain and two Cut-like repeats in SATB1, in addition to the known MAR-binding domain. The isolated MAR-binding domain recognizes a certain DNA sequence context within MARs that is highly potentiated for base unpairing. Unlike the MAR-binding domain, the homeodomain when isolated binds poorly and with low specificity to DNA. However, the combined action of the MAR-binding domain and the homeodomain allows SATB1 to specifically recognize the core unwinding element within the base-unpairing region. The core unwinding element is critical for MAR structure, since point mutations within this core abolish the unwinding propensity of the MAR. The contribution of the homeodomain is abolished by alanine substitutions of arginine 3 and arginine 5 in the N-terminal arm of the homeodomain. Site-directed mutagenesis of the core unwinding element in the 3' MAR of the immunoglobulin heavy chain gene enhancer revealed the sequence 5'-(C/A)TAATA-3' to be essential for the increase in affinity mediated by the homeodomain. SATB1 may regulate T-cell development and function at the level of higher order chromatin structure through the critical DNA structural elements within MARs.

Replication timing properties of the human HPRT locus on active, inactive and reactivated X chromosomes

X chromosome inactivation is associated with a highly asynchronous pattern of DNA replication at most X-linked loci in females. We studied the human HPRT locus, which is subject to X inactivation and expressed from only the active homolog, with the goal of comparing replication properties between the active and inactive homologs in this region using a fluorescence in situ hybridization approach. We found that in normal female lymphoblasts this locus is replicated in a highly asynchronous manner across a broad, discrete 500-600 kb zone with earliest replication appearing at the gene coding sequence. This general timing profile is maintained in normal male lymphoblasts, as well as in hamster x human hybrid cells containing the active human X chromosome. However, the inactive human X chromosome in the hamster cell background does not appear to function in a fully equivalent manner to the normal inactive X chromosome in female cells. Furthermore, reactivation of the inactive human X chromosome in a hamster x human hybrid system by 5-azacytidine treatment and HAT selection restores early replication at the HPRT gene itself, but does not change the overall domain behavior.

Matrix-attachment regions in the mouse chromosome 7F imprinted domain

We have mapped the matrix-attachment regions (MARs) in 200 kilobases of the mouse Chromosome (Chr) 7F imprinted domain. MARs are genetic elements known to have effects in cis on methylation at nonimprinted loci. The imprinting of the Igf2 and Ins2 genes is dependent on the transcription of the downstream H19 gene. The transcription of H19 is dependent in turn on its methylation status. The cis-acting regulators of methylation at this site are not known. As MARs are potential regulators not only of methylation but also other elements of genomic imprinting, we mapped the MARs within the 200 kilobases around H19. This report describes the mapping of four MARs from this region.

The heat shock cognate 80 gene of tomato is flanked by matrix attachment regions

Matrix attachment regions (MARs) are thought to participate in the organization and segregation of independent chromosomal loop domains. Although there are several reports on the action of MARs in the context of heterologous genes, information is more limited on the role of MARs associated with plant genes. Transgenic studies suggest that the upstream, intron and downstream regions of the developmentally regulated heat shock cognate 80 gene (HSC80) of tomato participate in chromatin organization. In this study, we tested the in vitro affinity of the HSC80 gene to chromosomal scaffolds prepared from shoot apices of tomato. We found that a 1.5 kb upstream region and a 1.4 kb downstream region, but not the intron region, are MARs. These MARs interact with tomato and pea scaffolds and bind regardless of the expression status of HSC80 in the tissue from which the nuclei were isolated. Comparison to two known yeast MARs, ARS1 and CENIII, showed that the HSC80 5'MAR binds more avidly to tomato scaffolds than ARS1, while no binding of CENIII was observed. Competition binding between the two HSC80 MARs indicated that the 5'MAR can outcompete the 3'MAR and not vice versa. Last, we observed that the interaction of the 3'MAR with the scaffold could result in an electrophoretic mobility shift resistant to SDS, protease, and phenol treatment. In conclusion, MARs whose binding properties can be clearly differentiated are closely flanking the HSC80 gene. The discovery of MARs in regions which have a distinct function in HSC80 transgenes but not in transient expression assays, is consistent with a chromosomal scaffold role in HSC80 gene regulation.

Functional interrelationships between nuclear structure and transcriptional control: contributions to regulation of cell cycle- and tissue-specific gene expression

Multiple levels of nuclear structure contribute to functional interrelationships with transcriptional control in vivo. The linear organization of gene regulatory sequences is necessary but insufficient to accommodate the requirements for physiological responsiveness to homeostatic, developmental, and tissue-related signals. Chromatin structure, nucleosome organization, and gene-nuclear matrix interactions provide a basis for rendering sequences accessible to transcription factors supporting integration of activities at independent promoter elements of cell cycle- and tissue-specific genes. A model is presented for remodeling of nuclear organization to accommodate developmental transcriptional control.

Scaffold attachment regions in centromere-associated DNA

Due to indications that kinetochore proteins are an integral part of the protein scaffold component of the chromosome (Earnshaw et al. 1984), we chose to map the distribution of scaffold attachment regions (SARs) at centromeres. Using the SAR mapping assay of Mirkovitch et al., Southern blots were prepared and probed with 32P-labeled fragments from the human 1.9 kb centromeric alpha-satellite repeat unit of chromosome 1 or the 1.7 kb centromeric alpha-satellite repeat unit of chromosome 16. Our results demonstrated the presence of one SAR site per 1.9 kb repeat unit in chromosome 1, and every 1.7 kb repeat unit in chromosome 16, separated by regions of small DNA loops over the length of the alpha-satellite regions. We also identified several in vitro vertebrate topoisomerase II and cenP-B consensus sequences throughout the chromosome 1 alpha-satellite region using computer and base ratio analysis, to address the question as to why some alpha-satellite regions are SAR related and others are not. To provide in situ indications of SAR localization in the human genome, SAR DNA and non-SAR DNA were prepared following lithium 3,5-di-iodosalicylate extraction. Sequences protected from DNAse I digestion by SAR proteins, as compared with unprotected DNA that was digested by the enzyme, was labeled with biotin-UTP, hybridized to chromosomal DNA in situ, and then detected with fluorescein-avidin-DCS. Both SAR and non-SAR DNA selectively labeled virtually all centromeric regions of the human metaphase karyotype. Chromosomal arms were less strongly bound by SAR DNA, with a pattern that followed the chromosomal axis. In the more condensed chromosomes an R-banding pattern was evident. In general, labeling patterns produced by both SAR and non-SAR fractions were similar, as expected from the indications that SAR DNAs are heterogenous in sequence and do not form a specific class of sequences. We conclude that centromeric regions of several, possibly all, human metaphase chromosomes are also regions where the chromosomal axis contains loops, smaller in size than in the arms and where attachment sites are concentrated. This clustering of SARs may be responsible in part for the tight chromatin packing associated with the primary constriction of the centromeric region.

DNA topoisomerase II inhibitors enhance random integration of transfected vectors into human chromosomes

To study the involvement of DNA topoisomerase (topo) II on nonhomologous (illegitimate) recombination, we examined the effect of topo II inhibitors on random integration of exogenous vectors into human chromosomes. We transfected human cell lines PA1, HeLa and EJ-1 with linearized plasmid pSV2neo by electroporation, treated with topo II inhibitors and determined the frequency of Geneticin-resistant (G418r) colonies. We found that three topo II inhibitors, etoposide (VP-16), ICRF-193 and amsacrine (m-AMSA), greatly enhanced the frequency of G418r colonies. These effects were maximally expressed by as little as 12 hrs treatment with the drugs. Similar enhancements were found with different vectors (closed-circular and linear), different cell types, or by different transfection methods (calcium precipitation and lipofection). In contrast, the inhibitor treatments did not affect the transient expression of chloramphenicol acetyltransferase and beta-galactosidase activity following transfection with pSV2CAT and pCH110, respectively. Southern blot analysis revealed that the integration pattern of transfected pSV2neo into PA1 chromosomes was random and not characteristic for each inhibitor. These results suggest that topo II inhibitors directly act at a nonhomologous recombination reaction, promoting the integration process of transfected vectors into human chromosomes. We discuss the enhancement mechanism with a special emphasis on DNA strand breaks induced by the inhibitors.

Nuclear matrix interactions within the sperm genome

Analysis of the haploid-expressed human PRM1 --> PRM2 --> TNP2 genic domain has revealed two regions of attachment to the sperm nuclear matrix. These sperm nuclear matrix attachment regions delimit the DNase I-sensitive domain of this haploid-expressed locus. The domain is intermediately associated with but not attached to the nuclear matrix. DNase I-sensitive genes within the mature sperm nucleus, such as protamine 1, protamine 2, transition protein 2, alpha-globin, and beta-actin, display this intermediate affinity for the sperm nuclear matrix. This may denote their role in templating the male genome prior to fertilization, thus ensuring the formation of a viable male pronucleus during early embryonic development.

The architectural organization of nuclear metabolism

Nucleic acid metabolism is structurally organized in the nucleus. DNA replication and transcription have been localized to particular nuclear domains. Additional domains have been identified by their morphology or by their composition; for example, by their high concentration of factors involved in RNA splicing. The domain organization of the nucleus is maintained by the nuclear matrix, a nonchromatin nuclear scaffolding that holds most nuclear RNA and organizes chromatin into loops. The nuclear matrix is built on a network of highly branched core filaments that have an average diameter of 10 nm. Many of the intermediates and the regulatory and catalytic factors of nucleic acid metabolism are retained in nuclear matrix preparations, suggesting that nucleic acid synthesis and processing are structure-bound processes in cells. Tissue-specific and malignancy-induced variations in nuclear structure and metabolism may result from altered matrix architecture and composition.

Contributions of nuclear architecture to transcriptional control

Three parameters of nuclear structure contribute to transcriptional control. The linear representation of promoter elements provides competency for physiological responsiveness within the contexts of development as well as cycle- and phenotype-dependent regulation. Chromatin structure and nucleosome organization reduce distances between independent regulatory elements providing a basis for integrating components of transcriptional control. The nuclear matrix supports gene expression by imposing physical constraints on chromatin related to three-dimensional genomic organization. In addition, the nuclear matrix facilitates gene localization as well as the concentration and targeting of transcription factors. Several lines of evidence are presented that are consistent with involvement of multiple levels of nuclear architecture in cell growth and tissue-specific gene expression during differentiation. Growth factor and steroid hormone responsive modifications in chromatin structure, nucleosome organization, and the nuclear matrix that influence transcription of the cell cycle-regulated histone gene and the bone tissue-specific osteocalcin gene during progressive expression of the osteoblast phenotype are considered.

Scaffold/matrix-attached regions: structural properties creating transcriptionally active loci

The expression characteristics of the human interferon-beta gene, as part of a long stretch of genomic DNA, led to the discovery of the putative domain bordering elements. The chromatin structure of these elements and their surroundings was determined during the process of gene activation and correlated with their postulated functions. It is shown that these "scaffold-attached regions" (S/MAR elements) have some characteristics in common with and others distinct from enhancers with which they cooperate in various ways. Our model of S/MAR function will focus on their properties of mediating topological changes within the respective domain.

Chromatin domains and prediction of MAR sequences

Polynuceosomes are constrained into loops or domains and are insulated from the effects of chromatin structure and torsional strain from flanking domains by the cross-complexation of matrix-attached regions (MARs) and matrix proteins. MARs or SARs have an average size of 500 bp, are spaced about every 30 kb, and are control elements maintaining independent realms of gene activity. A fraction of MARs may cohabit with core origin replication (ORIs) and another fraction might cohabit with transcriptional enhancers. DNA replication, transcription, repair, splicing, and recombination seem to take place on the nuclear matrix. Classical AT-rich MARs have been proposed to anchor the core enhancers and core origins complexed with low abundancy transcription factors to the nuclear matrix via the cooperative binding to MARs of abundant classical matrix proteins (topoisomerase II, histone H1, lamins, SP120, ARBP, SATB1); this creates a unique nuclear microenvironment rich in regulatory proteins able to sustain transcription, replication, repair, and recombination. Theoretical searches and experimental data strongly support a model of activation of MARs and ORIs by transcription factors. A set of 21 characteristics are deduced or proposed for MAR/ORI sequences including their enrichment in inverted repeats, AT tracts, DNA unwinding elements, replication initiator protein sites, homooligonucleotide repeats (i.e., AAA, TTT, CCC), curved DNA, DNase I-hypersensitive sites, nucleosome-free stretches, polypurine stretches, and motifs with a potential for left-handed and triplex structures. We are establishing Banks of ORI and MAR sequences and have undertaken a large project of sequencing a large number of MARs in an effort to determine classes of DNA sequences in these regulatory elements and to understand their role at the origins of replication and transcriptional enhancers.

Origins of replication and the nuclear matrix: the DHFR domain as a paradigm

The eukaryotic genome appears to be organized in a loopwise fashion by periodic attachment to the nuclear matrix. The proposal that a chromatin loop corresponds to a functional domain has stirred interest in the properties of the DNA sequences at the bases of these loops, the matrix-attached regions (MARs). Evidence has been presented suggesting that certain MARs act as boundary elements isolating domains from their chromosomal context. MARs have also been found in the vicinity of promoters and enhancers and they could act by displacing these cis-regulatory elements into the proper nuclear subcompartment. Attachment to the matrix might also play a role in DNA replication. A large body of evidence indicates that replication occurs on the nuclear matrix. This implies that any DNA sequence will be attached to the matrix at a certain time during the cell cycle. This transient mode of attachment contrasts with the proposed permanent attachment of origins of DNA replication with the nuclear matrix. While some data exist that support this suggestion, the current lack of understanding of the mammalian replication origin precludes definitive conclusions regarding the role of MARs in the initiation process.

Nuclear domains and the nuclear matrix

This overview describes the spatial distribution of several enzymatic machineries and functions in the interphase nucleus. Three general observations can be made. First, many components of the different nuclear machineries are distributed in the nucleus in a characteristic way for each component. They are often found concentrated in specific domains. Second, nuclear machineries for the synthesis and processing of RNA and DNA are associated with an insoluble nuclear structure, called nuclear matrix. Evidently, handling of DNA and RNA is done by immobilized enzyme systems. Finally, the nucleus seems to be divided in two major compartments. One is occupied by compact chromosomes, the other compartment is the space between the chromosomes. In the latter, transcription takes place at the surface of chromosomal domains and it houses the splicing machinery. The relevance of nuclear organization for efficient gene expression is discussed.

The nuclear matrix and the regulation of chromatin organization and function

Nuclear DNA is organized into loop domains, with the base of the loop being bound to the nuclear matrix. Loops with transcriptionally active and/or potentially active genes have a DNase I-sensitive chromatin structure, while repressed chromatin loops have a condensed configuration that is essentially invisible to the transcription machinery. Core histone acetylation and torsional stress appear to be responsible for the generation and/or maintenance of the open potentially active chromatin loops. The transcriptionally active region of the loop makes several dynamic attachments with the nuclear matrix and is associated with core histones that are dynamically acetylated. Histone acetyltransferase and deacetylase, which catalyze this rapid acetylation and deacetylation, are bound to the nuclear matrix. Several transcription factors are components of the nuclear matrix. Histone acetyltransferase, deacetylase, and transcription factors may contribute to the dynamic attachment of the active chromatin domains with the nuclear matrix at sites of ongoing transcription.

The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein family

B lymphocyte-restricted transcription of immunoglobulin heavy-chain (IgH) genes is specified by elements within the variable region (VH) promoter and the intronic enhancer (E mu). The gene encoding a protein that binds a VH promoter proximal site necessary for induced mu-heavy-chain transcription has been cloned. This B-cell specific protein, termed Bright (B cell regulator of IgH transcription), is found in both soluble and matrix insoluble nuclear fractions. Bright binds the minor groove of a restricted ATC sequence that is sufficient for nuclear matrix association. This sequence motif is present in previously described matrix-associating regions (MARs) proximal to the promoter and flanking E mu. Bright can activate E mu-driven transcription by binding these sites, but only when they occur in their natural context and in cell lines permissive for E mu activity. To bind DNA, Bright requires a novel tetramerization domain and a previously undescribed domain that shares identity with several proteins, including SWI1, a component of the SWI/SNF complex.

Nuclear factor binding sites in human beta globin IVS2

The second intron of the human beta globin gene (beta IVS2) has been previously identified as a region required for proper expression of beta globin. To further characterize this region, we have footprinted the entire beta IVS2 and have analyzed regions of interest by electrophoretic mobility shift assay. Through these studies we have identified four utilized binding sites for the erythroid regulatory factor GATA-1, two sites bound by general transcription factor Oct-1, two sites bound by the nuclear matrix attachment DNA binding protein special A-T-rich binding protein 1, and a site bound by a potential homeobox protein. Additionally, we have found several factors displaying temporal or tissue specificity by electrophoretic mobility shift assay, which may be potentially involved in the regulation of beta globin expression. These proteins are not supershifted by antibodies to factors important in erythroid regulation such as GATA-1, NFE-2, or YY1, or by antibodies against more general transcription factors.

A novel matrix attachment region DNA binding motif identified using a random phage peptide library

SATB1 is a nuclear matrix attachment DNA (MAR)-binding protein which is predominantly expressed in thymocytes. This protein binds to the minor groove specifically recognizing an unusual DNA context exhibited by a specific MAR region with strong base-unpairing propensity. A phage library displaying nonamer random peptides without any built-in structure was used to identify a MAR binding motif of SATB1. One predominant cyclic peptide C1 of CRQNWGLEGC selected by a MAR-affinity column showed 50% identity with a segment in SATB1 (amino acids 355-363). Replacement of the C1 similarity segment in SATB1 by a random amino acid sequence or its truncation resulted in more than 80% reduction in MAR binding. In contrast, replacement of the same SATB1 segment with the C1 peptide restored full MAR binding activity and specificity as the wild-type protein. Single amino acid mutation of the conserved Arg or Glu residue to Ala greatly reduced MAR binding. Taken together our data show that a nine amino acid sequence in SATB1 represents a key MAR binding motif. Phage display may provide a general tool for rapid identification of DNA binding peptide motifs.

Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1

We provide evidence for the location of matrix attachment sites along a contiguous region of 280 kb on maize chromosome 1. We define nine potential loops that vary in length from 6 kb to > 75 kb. The distribution of the different classes of DNA within this continuum with respect to the predicted structural loops reveals an interesting correlation: the long stretches of mixed classes of highly repetitive DNAs are often segregated into topologically sequestered units, whereas low-copy-number DNAs (including the alcohol dehydrogenase1 [adh1] gene) are positioned in separate loops. Contrary to expectations, several classes of highly repeated elements with representatives in this region were found to be transcribed, and some of these exhibited tissue-specific patterns of expression.

Progressive maturation of chromatin structure regulates HSP70.1 gene expression in the preimplantation mouse embryo

In the widely studied model organisms, Drosophila and Xenopus, early embryogenesis involves an extended series of nuclear divisions prior to activation of the zygotic genome. The mammalian embryo differs in that the early cleavage phase is already characterized by regulated cell cycles with specific zygotic gene expression. In the mouse, where major activation of the zygotic genome occurs at the 2-cell stage, the HSP70.1 gene is among the earliest genes to be expressed. We investigated the developmentally regulated expression of this gene during the preimplantation period, using a luciferase transgene, with or without flanking scaffold attachment regions (SARs). Cleavage stage-specific modifications in expression profiles were examined in terms of histone H4 acetylation status, topoisomerase II activity, and the localisation of HMG-I/Y, a nuclear protein with known affinity for the AT-tracts of SARs. We demonstrate that HSP70.1-associated transcription factors are not limiting, and that instead, there is a progressive maturation of chromatin structure that is directly involved in HSP70.1 regulation during early mouse development.

A haploid expressed gene cluster exists as a single chromatin domain in human sperm

Mammalian spermiogenesis is marked by the initial disruption of the nuclear-histone-DNA complex by the transition proteins for ultimate replacement with protamines. The genes for three of these low molecular weight basic nuclear proteins exist as a single linear array of PRM1, PRM2, and TNP2 on human chromosome 16p13.2. To begin to address the mechanism governing their transcriptional potentiation, a region of approximately 40 kilo-bases of the human genome encompassing these genes was introduced into the germ line of mice. Fluorescence in situ hybridization and Southern analysis showed that this segment of the human genome integrated into independent chromosomal sites while maintaining its fidelity. Transcript analysis demonstrated that the expression of the endogenous mouse protamine Prm1 and Prm2 genes as well as the mouse transition protein Tnp2 gene were expressed along with their human transgene counterparts. The pattern of expression of these transgenic human genes within this multigenic cluster faithfully represented that observed in vivo. In addition, all members of this transgenic gene cluster were expressed in proportions similar to those in human testis. Copy number-dependent and position-independent expression of the transgenic construct demonstrated that the corresponding biological locus was contained within this segment of the human genome. Furthermore, DNase I sensitivity established that in sperm the human PRM1-->PRM2-->TNP2 genic domain was contained as an approximately 28.5-kilobase contiguous segment bounded by an array of nuclear matrix associated topoisomerase II consensus sites. This is the first description of a multigenic male gamete-specific domain as a fundamental gene regulatory unit. A model of haploid-specific gene determination is presented.

Mutations in a putative global transcriptional regulator cause X-linked mental retardation with alpha-thalassemia (ATR-X syndrome)

The ATR-X syndrome is an X-linked disorder comprising severe psychomotor retardation, characteristic facial features, genital abnormalities, and alpha-thalassemia. We have shown that ATR-X results from diverse mutations of XH2, a member of a subgroup of the helicase superfamily that includes proteins involved in a wide range of cellular functions, including DNA recombination and repair (RAD16, RAD54, and ERCC6) and regulation of transcription (SW12/SNF2, MOT1, and brahma). The complex ATR-X phenotype suggests that XH2, when mutated, down-regulates expression of several genes, including the alpha-globin genes, indicating that it could be a global transcriptional regulator. In addition to its role in the ATR-X syndrome, XH2 may be a good candidate for other forms of X-linked mental retardation mapping to Xq13.

The role of scaffold attachment regions in the structural and functional organization of plant chromatin

Studies on nuclear scaffolds and scaffold attachment regions (SARs) have recently been extended to different plant species and indicate that SARs are involved in the structural and functional organization of the plant genome, as is the case for other eukaryotes. One type of SAR seems to delimit structural chromatin loops and may also border functional units of gene expression and DNA replication. Another group of SARs map close to regulatory elements and may be directly involved in gene expression. In this overview, we summarize the structural and functional properties of plant SARs in comparison with those of SARs from animals and yeast.

Nuclear architecture supports integration of physiological regulatory signals for transcription of cell growth and tissue-specific genes during osteoblast differentiation

During the past several years it has become increasingly evident that the three-dimensional organization of the nucleus plays a critical role in transcriptional control. The principal theme of this prospect will be the contribution of nuclear structure to the regulation of gene expression as functionally related to development and maintenance of the osteoblast phenotype during establishment of bone tissue-like organization. The contributions of nuclear structure as it regulates and is regulated by the progressive developmental expression of cell growth and bone cell related genes will be examined. We will consider signalling mechanisms that integrate the complex and interdependent responsiveness to physiological mediators of osteoblast proliferation and differentiation. The focus will be on the involvement of the nuclear matrix, chromatin structure, and nucleosome organization in transcriptional control of cell growth and bone cell related genes. Findings are presented which are consistent with involvement of nuclear structure in gene regulatory mechanisms which support osteoblast differentiation by addressing four principal questions: 1) Does the representation of nuclear matrix proteins reflect the developmental stage-specific requirements for modifications in transcription during osteoblast differentiation? 2) Are developmental stage-specific transcription factors components of nuclear matrix proteins? 3) Can the nuclear matrix facilitate interrelationships between physiological regulatory signals that control transcription and the integration of activities of multiple promoter regulatory elements? 4) Are alterations in gene expression and cell phenotypic properties in transformed osteoblasts and osteosarcoma cells reflected by modifications in nuclear matrix proteins? There is a striking representation of nuclear matrix proteins unique to cells, tissues as well as developmental stages of differentiation, and tissue organization. Together with selective association of regulatory molecules with the nuclear matrix in a growth and differentiation-specific manner, there is a potential for application of nuclear matrix proteins in tumor diagnosis, assessment of tumor progression, and prognosis of therapies where properties of the transformed state of cells is modified. It is realistic to consider the utilization of nuclear matrix proteins for targeting regions of cell nuclei and specific genomic domains on the basis of developmental phenotypic properties or tissue pathology.

A 5' beta-globin matrix-attachment region and the polyoma enhancer together confer position-independent transcription

Insertions of reporter constructs into the genome of higher eukaryotes typically lead to variegated gene expression due to position effects at the sites of integration. The 20-kb human beta-globin (beta Glb) locus control region (LCR) has been found to dampen these position effects when included in an expression vector. Several studies have indicated that much of the activity of the beta Glb-LCR resides in hypersensitive site II, which contains a strong enhancer. In this study, we have focused on the matrix-attachment region (MAR) at the 5' boundary of the beta Glb-LCR. We find that the beta Glb-MAR, by itself, has little effect on transcription of a reporter gene in stable transformants. However, when the beta Glb-MAR is linked in cis with the polyoma virus enhancer, the MAR-enhancer construct confers high levels of copy-dependent transcription that is independent of the chromosomal site of integration. These results suggest that the beta Glb-MAR may work synergistically with particular enhancer elements to dampen chromosomal position effects and ensure high-level expression.

Binding specificity of a nuclear scaffold: supercoiled, single-stranded, and scaffold-attached-region DNA

Scaffold-attached-region (SAR) elements of DNA enhance transcriptional rates, and this has been correlated with their ability to undergo separation into single strands (ssDNA) under conditions of negative superhelicity (Bode et al., 1992). The competition studies presented here suggest that the SAR-scaffold interaction is based, in part, on the recognition of single strands, while about one-half of SAR sites are inaccessible to ssDNA. Conversely, since there are 20,000 SAR sites but more than 60,000 sites for ssDNA per nuclear equivalent, not all ssDNA sites are open for SARs. In addition, a completely separate set of binding centers recognizing and enzymatically converting DNA of superhelical density below -0.04 can be titrated. These findings reflect multiple binding specificities for scaffold preparations that are routinely used for screening scaffold-attached regions.

The immunoglobulin mu enhancer core establishes local factor access in nuclear chromatin independent of transcriptional stimulation

Factor access in chromatin has been proposed to be facilitated by transcriptional enhancers. With the aim of uncoupling factor access from transcriptional stimulation by protein-protein contacts, we analyzed the potential of enhancer fragments to confer accessibility upon a linked promoter for prokaryotic T7 RNA polymerase. Access to the T7 promoter in pre-B cells from transgenic mice was examined by transcribing chromatin of isolated nuclei with T7 RNA polymerase. A 95-bp immunoglobulin mu enhancer core element was necessary and sufficient to confer accessibility upon the T7 promoter independent of its chromosomal position. This enhancer-dependent factor access could be uncoupled from an active transcriptional state of the transgene and was not accompanied by the formation of pronounced DNase I hypersensitive sites. Additional mu enhancer sequences comprising previously identified matrix attachment regions and a cryptic promoter were required to induce DNase I hypersensitivity. Together, these data provide evidence that the 95-bp mu enhancer core can establish localized factor access in nuclear chromatin independent of detectable transcription by endogenous polymerases and suggest that multiple steps are involved in the alteration of chromatin structure.

SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin

An experimental assay was developed to search for proteins capable of antagonizing histone H1-mediated general repression of transcription. T7 RNA polymerase templates containing an upstream scaffold-associated region (SAR) were highly selectively repressed by H1 relative to non-SAR control templates. This is due to the nucleation of H1 assembly into flanking DNA brought about by the numerous A-tracts (AT-rich sequences containing short homopolymeric runs of dA.dT base pairs) of the SAR. Partial, selective titration of these A-tracts by the high mobility group (HMG) protein HMG-I/Y led to the complete derepression of transcription from the SAR template by inducing the redistribution of H1 on to non-SAR templates. SARs are associated with many highly transcribed regulated genes where they may serve to facilitate the HMG-I/Y-mediated displacement of histone H1 in chromatin. Indeed, HMG-I/Y was found to be strongly enriched in the H1-depleted subfraction which can be isolated from chromatin.

Nature of DNA sequences at the attachment regions of genes to the nuclear matrix

Matrix-attached regions (MARs) have been demonstrated to nest origins of replication and transcriptional enhancers. A set of 13 rules is proposed aimed at facilitating the classification of a DNA sequence as a matrix attachment region.(ABSTRACT TRUNCATED AT 250 WORDS)

Homeodomain protein binding sites, inverted repeats, and nuclear matrix attachment regions along the human beta-globin gene complex

beta-Globin genes in primates arose during evolution by duplication of an ancestral gene, and their order of arrangement along the DNA is related to their timing of expression during development. We believe that nuclear matrix anchorage sites (MARs) along the beta-globin gene complex considered to be mass binding sites for transcription protein factors, some of which are developmental stage specific and others ubiquitous, play a decisive role in cell memory by determining the developmental stage-specific expression of the genes. The AT-rich class of MARs appears to possess a significant number of ATTA and ATTTA motifs known to be mass binding sites for homeodomain proteins that determine body formation in development. MARs also appear to harbor origins of replication, to be enriched in inverted repeats (dyad symmetry motifs) and were proposed to include the DNase I hypersensitive sites of a particular gene determined at the chromatin level. This study is an attempt to finely identify MARs at the nucleotide level along the beta-globin gene complex. Searches of a contiguous stretch of about 73.3 kb of human sequences comprising and surrounding the epsilon, gamma G-, gamma A-, delta-, and beta-globin genes of the human beta-globin gene complex for homeotic protein binding sites as well as for inverted repeats has shown that these elements are clustered nonrandomly at particular sites within the beta-globin gene complex. These sites are presumed to be the AT-rich class of MARs of the beta-globin gene complex. The inverted repeats which are characteristic of origins of replication and some promoter/enhancer regions and the homeotic protein sites seem to include the DNase I hypersensitive sites of the gene complex. Indeed, dyad symmetry sequences are present close to the four DNase I HS sites in the locus control region (LCR) of the gene complex as well as in the 5' flanking regions and the large introns of the delta- and beta-globin genes. A search of the putative MAR regions of the gene complex suggests that, in addition to their enrichment in ATTA motifs, palindromes, and DNase I hypersensitive sites, these regions may comprise TG-rich motifs and potential Z-DNA as well as polypurine and polypyrimidine blocks. From the positions of palindromes and clusters of homeodomain protein sites along the complex we propose that an extended origin of replication able to initiate at several sites is present in the LCR and two others surrounding the delta- and beta-globin genes.(ABSTRACT TRUNCATED AT 400 WORDS)

Multitude of inverted repeats characterizes a class of anchorage sites of chromatin loops to the nuclear matrix

In order to understand the nature of DNA sequences that organize chromatin into domains or loops, we have cloned the nuclear matrix DNA (1.7% of the total DNA) from human myelogenous leukemia cells in culture. Nuclear matrix is formed by interactions between specific stretches of DNA of about 0.1 to 5.0 kb with protein transcription factors, nuclear enzymes, and structural proteins. Nuclear matrix is believed to be the exclusive nuclear microenvironment in which initiation of DNA replication, transcription, and repair take place. The matrix attachment regions (MARs) of DNA have transcriptional enhancer activity, harbor the origins of replication of the human genome, and define the borders between neighboring chromatin loops. In this study we report the sequence of the human MAR fragment 19.2 of a size of 542 bp. Hum. MAR 19.2 is composed of TG-, CA-, CT-, and GA-rich blocks and shows 8 perfect and imperfect inverted repeats. Thus, we have identified a novel class of MARs with sequence characteristics divergent from the AT-rich class of MARs. The inverted repeats of the 19.2 sequence might be stabilized into their cruciform configuration by torsional strain and by specific transcription/replication protein factors. This MAR might function in the initiation of replication of the flanking chromatin domain and in the regulation of the transcriptional activity of the gene(s) that reside in this domain.

alpha-Thalassaemia

The large number of naturally occurring mutants of this well-characterized locus provides an excellent opportunity for elucidating the relationship between its structure and function. Comparisons of what has been learned about the alpha-globin locus with complementary observations on the beta-globin locus, provide a strategy for understanding the co-ordinate regulation of eukaryotic gene expression. From a practical point of view it is important to remember that millions of individuals throughout the world are carriers of alpha-thalassaemia and every year many thousands of pregnancies are at risk of producing children with the severe alpha-thalassaemia syndromes. The data summarized here provide the basis for accurately predicting the genotype in such cases and thus enabling appropriate prenatal testing. However, because this is a genetic disease that predominantly affects individuals from countries with limited health resources, simpler and cheaper methods of screening and diagnosis will have to be developed before this information has a significant impact on the attendant morbidity and mortality (see Chapter 9, this volume).

Pulsed-field gel electrophoresis analysis of higher-order chromatin structures of Zea mays. Highly methylated DNA in the 50 kb chromatin structure

We have investigated the presence of higher-order chromatin structures in different maize tissues. Taking advantage of the pulsed-field gel electrophoresis technique to analyse large DNA fragments from intact nuclei and cells, we have determined the size distribution of the high-molecular-weight DNA fragments obtained from chromatin degradation by endogenous nucleases in isolated nuclei. Chromatin digestion leads to the appearance of stable DNA fragments of about 50 kb in all the tissues examined, suggesting the folding of DNA in higher-order chromatin domain structures. It has been reported that such chromatin domains are formed by loops of the 30 nm fibers anchored to the nuclear matrix by a complex set of proteins, including DNA topoisomerase II. Treatment of maize protoplasts with the calcium ionophore A23187 and the antitumour drug VM-26, which specifically inhibit the religation of the cleaved DNA in the topoisomerase II reaction, also produces the 50 kb structure. Analysis of the DNA contained in the 50 kb chromatin structure shows a higher degree of methylation than in bulk maize chromosomal DNA. The role of methylated DNA in the chromatin folding is discussed.

The regulation of human globin gene expression

The haemopoietic system provides a well-characterized and accessible system for studying the mechanisms of developmental regulation and differentiation in higher eukaryotes. Our current understanding of the steps involved in the early stages of differentiation are poorly understood but a great deal is now known about the mechanisms by which globin expression is regulated in cells committed to the erythroid lineage. Many of the critical cis-acting sequences and some of the important trans-acting factors involved have been identified and current work is focusing on how these interact to produce high levels of tissue-specific and developmentally regulated expression of the human globin genes.

The regulation of human globin gene switching

This paper describes the mechanism of regulation of the human beta-globin on the basis of a number of natural mutations and experiments in transgenic mice. From these data we conclude that this multigene locus is regulated at a number of different levels involving specific interactions between the Locus Control Region (LCR) and the individual genes. Most important is the action of stage specific transcription factors acting on sequences immediately flanking the genes. In addition, specificity is obtained through specific interaction of the genes with the LCR and through competition of the genes for interaction with the LCR.

The elusive nuclear matrix

The structure of the interphase nucleus is a major area of current interest in cell biology. It is thought likely that the nucleus is organised around some form of structural matrix and that this matrix will play a role in processes as diverse as chromosome replication and the integration of gene expression. However, the structure of the matrix within the nucleus has remained elusive, largely because attempts to define it have been dogged by technical problems arising from the great complexity of this organelle. This situation is now being changed by the application of in situ analysis and of molecular genetic methodologies which are opening up this hitherto intractable field.

The association of the human epsilon-globin gene with the nuclear matrix: a reconsideration

The association of the human epsilon-globin gene with the nuclear matrix was studied in erythroid and non-erythroid cell lines. Using a high salt method to prepare histone depleted nuclei we studied the association of variety of fragments covering a 7.8 kb region which contains the human epsilon-globin gene. We furthermore studied the association of a set of DNA fragments covering the 13 kb human G gamma/A gamma-globin gene domain, the 16 kb psi beta/delta-globin gene domain and the 10 kb beta-globin gene domain with the nuclear matrix of K562 and Raji cells. The results show that all fragments studied are easily released from the nuclear matrix, indicating no specific association. Summarizing our results we could say that a region starting 5.7 kb 5' to the human epsilon-globin gene and ending 4 kb 3' to the human beta-globin gene seems to contain no attachment sites with the nuclear matrix of both erythroid and non-erythroid cells.

Binding of matrix attachment regions to lamin B1

Eukaryotic chromatin is organized into topologically constrained loops that are attached to the nuclear matrix. The regions of DNA that interact with the matrix are called matrix attachment regions (MARs). We studied the spatial distribution of MAR-binding sites in the nuclear matrix from rat liver cells, following a combined biochemical and ultrastructural approach. We found that MAR-binding sites are distributed equally over the internal fibrogranular network and the peripheral nuclear lamina. Internal and peripheral binding sites have similar binding characteristics: both sets of binding sites show specific and saturable binding of MARs from different organisms. By means of a DNA-binding protein blot assay and in vitro binding studies, we identified lamin B1 as a MAR-binding protein, which provides evidence for a specific interaction of DNA with the nuclear lamina.

Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin

Current models suggest that tissue-specific genes are arranged in discrete, independently controlled segments of chromatin referred to as regulatory domains. Transition from a closed to open chromatin structure may be an important step in the regulation of gene expression. To determine whether the human alpha-globin cluster, like the beta-globin cluster, lies within a discrete, erythroid-specific domain, we have examined the long-range genomic organization and chromatin structure around this region. The alpha genes lie adjacent to at least four widely expressed genes. The major alpha-globin regulatory element lies 40 kb away from the cluster within an intron of one of these genes. Therefore, unlike the beta cluster, cis-acting sequences controlling alpha gene expression are dispersed within a region of chromatin that is open in both erythroid and nonerythroid cells. This implies a difference in the hierarchical control of alpha- and beta-globin expression.

A transcription-dependent DNase I-hypersensitive site in a far upstream segment of the chicken alpha-globin gene domain coincides with a matrix attachment region

A site of hypersensitivity to DNase I has been found at the 5'-side of the chicken alpha-globin gene domain, ca. 8 Kbp upstream to the first gene. The presence of this site in different types of chicken cells correlates with the transcriptional status of the domain. A matrix attachment region (MAR) has also been found in the same subfragment, suggesting that it may be involved in the control of transcription of the chicken alpha-globin genes.

Characterization of a plant scaffold attachment region in a DNA fragment that normalizes transgene expression in tobacco

Using a low-salt extraction procedure, we isolated nuclear scaffolds from tobacco that bind specific plant DNA fragments in vitro. One of these fragments was characterized in more detail; this characterization showed that it contains sequences with structural properties analogous to animal scaffold attachment regions (SARs). We showed that scaffold attachment is evolutionarily conserved between plants and animals, although different SARs have different binding affinities. Furthermore, we demonstrated that flanking a chimeric transgene with the characterized SAR-containing fragment reduces significantly the variation in expression in series of transformants with an active insertion, whereas a SAR fragment from the human beta-globin locus does not. Moreover, the frequency distribution patterns of transgene activities showed that most of the transformants containing the plant SAR fragment had expression levels clustered around the mean. These data suggest that the particular plant DNA fragment can insulate the reporter gene from expression-influencing effects exerted from the host chromatin.