Dependence of enhancer-mediated transcription of the immunoglobulin mu gene on nuclear matrix attachment regions

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.

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.

Aberrant regulation of the IgH 3' enhancer by c-myc in plasmacytoma cells

The identification of enhancers at the 3' end of the IgH locus has prompted a re-evaluation of the regulation of Ig gene expression. Moreover, these elements may provide a possible explanation as to how the c-myc oncogene becomes dysregulated upon translocation into the IgH locus with the IgH intragenic enhancer on the reciprocal chromosome. These 3' enhancers have also been shown to redirect promoter utilization on c-myc reporter gene constructs in transient transfection experiments. This region of the locus also contains the B cell specific IgH 3' enhancer. This temporally regulated enhancer has been implicated in the mechanisms that control class switch recombination. Here we demonstrate that overexpression of the c-myc protein in mouse plasmacytoma cells (MPC-11) and HeLa cells can transcriptionally upregulate a reporter gene construct driven by a subregion (domain C) of the IgH 3' enhancer. Domain C contains a functional dual symmetry E-box motif, CACGTG. The DNA binding experiments demonstrate that USF was the major factor interacting with this motif. Based on these observations, we speculate that the c-myc protein may upregulate expression of translocated c-myc in mouse plasmacytomas possibly via an USF-binding E-box motif in the IgH 3' enhancer.

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.

Mutually exclusive interaction of a novel matrix attachment region binding protein and the NF-muNR enhancer repressor. Implications for regulation of immunoglobulin heavy chain expression

The immunoglobulin heavy chain (IgH) intronic enhancer stimulates transcription from functional promoters in B lymphocytes but not other cell types. The observation that binding sites for the nuclear factor-mu negative regulator (NF-muNR) enhancer repressor overlap nuclear matrix attachment regions (MARs) in this enhancer has lead to the hypothesis that the cell type specificity of the enhancer might be controlled by regulating nuclear matrix attachment (Scheuermann, R. H., and Chen, U. (1989) Genes & Dev. 3, 1255-1266). To understand the role of MARs in IgH enhancer regulation, we have identified a novel MAR-binding protein, MAR-BP1, from soluble nuclear matrix preparations based on its ability to bind to the MARs associated with the IgH enhancer. Purified MAR-BP1 migrates as a 33-kDa protein, and it can be found in nuclear matrix preparations from a number of different types of lymphoid cell lines. Although specific binding sites have been difficult to localize by chemical or enzymatic footprinting procedures, NF-muNR binding sites are critical for efficient MAR-BP1 binding. Indeed, binding of the IgH enhancer to either intact nuclear matrix preparations or to MAR-BP1 is mutually exclusive to NF-muNR binding. These results are consistent with a model for cell-type specific regulation in which binding of the NF-muNR repressor to the IgH enhancer prevents nuclear matrix attachment in inappropriate cells by interfering with MAR-BP1/enhancer interaction.

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.

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.

Repression of the immunoglobulin heavy chain 3' enhancer by helix-loop-helix protein Id3 via a functionally important E47/E12 binding site: implications for developmental control of enhancer function

The activity of the immunoglobulin 3' enhancer is restricted to the late stages of B lymphoid development. Here we further examine the molecular basis for the temporally restricted activity of the B-lymphoid IgH 3' enhancer. We demonstrate that a binding site (E5 site) for the E47 and/or E12 proteins is functionally important for enhancer activity. The multimerized E5 site acts as a B cell-specific enhancer and, when assayed in COS cells, can be transactivated by E47/E12 proteins. This transactivation in COS cells, as well as the activity of the full length 3' enhancer in plasma cells, can be repressed by overexpression of the dominant negative nuclear regulator Id3. When examining the tissue distribution of Id3 in murine cell lines, we find that Id3 is expressed throughout the pre-B and B cell stages, but is down-regulated at the plasma cell stage. Thus, Id3 may contribute to the temporal regulation of the IgH 3' enhancer.

Position-independent expression of whey acidic protein transgenes

The expression of a 3-kilobase genomic rat whey acidic protein (WAP) clone (-949/+2020) in transgenic mice has been demonstrated previously to be copy number-dependent and independent of the site of integration (Dale, T., Krnacik, M. J., Schmidhauser, C., Yang, C. Q.-L., Bissell, M. J., and Rosen, J. M. (1992) Mol. Cell. Biol. 12, 905-914). The present study demonstrated that position-independent expression of the rat WAP -949/+2020 transgene was dependent on transgene spacing. Position-independent expression also was inhibited by an internal replacement of 49 base pair within the conserved GC-rich 3'-untranslated region (3'-UTR) with an identically sized nonspecific DNA sequence. Using electrophoretic mobility shift assays, nuclear factors isolated from mouse and human cells were shown to associate specifically with the rWAP 3'-UTR DNA, but not with the 3'-UTR containing the internal replacement or specific point mutations. Since a single copy of the 3'-UTR inserted 5' of the promoter could not rescue the 3'-UTR deletion, the 3'-UTR element does not appear to be functioning as either a classic enhancer or insulator element. However, the level of expression of rWAP transgenes was correlated with transgene association with the chromosomal scaffold in vivo.

DNA-binding and chromatin localization properties of CHD1

CHD1 is a novel DNA-binding protein that contains both a chromatin organization modifier (chromo) domain and a helicase/ATPase domain. We show here that CHD1 preferentially binds to relatively long A.T tracts in double-stranded DNA via minor-groove interactions. Several CHD1-binding sites were found in a well-characterized nuclear-matrix attachment region, which is located adjacent to the intronic enhancer of the kappa immunoglobulin gene. The DNA-binding activity of CHD1 was localized to a 229-amino-acid segment in the C-terminal portion of the protein, which contains sequence motifs that have previously been implicated in the minor-groove binding of other proteins. We also demonstrate that CHD1 is a constituent of bulk chromatin and that it can be extracted from nuclei with 0.6 M NaCl or with 2 mM EDTA after mild digestion with micrococcal nuclease. In contrast to another chromo-domain protein, HP1, CHD1 is not preferentially located in condensed centromeric heterochromatin, even though centromeric DNA is highly enriched in (A+T)-rich tracts. Most interestingly, CHD1 is released into the cytoplasm when cells enter mitosis and is reincorporated into chromatin during telophase-cytokinesis. These observations lend credence to the idea that CHD1, like other proteins with chromo or helicase/ATPase domains, plays an important role in the determination of chromatin architecture.

SARs stimulate but do not confer position independent gene expression

Two minimal scaffold-associated regions (SARs) from Drosophila were tested in stably transformed cells for their effects on the expression of reporter genes. The expression of genes bounded by two SARs is consistently stimulated by about 20- to 40-fold, if the average of a pool of cell transformants is analyzed. However, analysis of individual, stable cell transformants demonstrates that flanking SAR elements do not confer position-independent expression on the reporter gene and that the extent of position-dependent variegation is similarly large with or without the flanking SAR elements. The SAR stimulation of expression is observed in stable but not in transiently transfected cell lines. The Drosophila scs and scs' boundary elements, which do not bind to the nuclear matrix in vitro, are only about one-tenth as active as SARs in stimulating expression in stable transformants. Interestingly, the SAR stimulatory effect can be blocked by a fragment containing CpG islands (approximately 70% GC), if positioned between the SAR and the enhancer. In contrast, when inserted in the same position, control fragments, such as the scs/scs' elements, do not interfere with SAR function.