Definition of 5‘ and 3‘ structural boundaries of the chromatin domain containing the ovalbumin multigene family

Expression in transgenic mice of two genes of different tissue specificity integrated into a single chromosomal site

Transgenic mice were used to study the expression of pairs of genes with distinctly different tissue specificities, covalently linked and integrated into the same chromosomal site. A transgenic strain carrying, in close proximity and in the same orientation, the rat fast skeletal muscle myosin light-chain 2 (MLC2) gene and the mouse rearranged immunoglobulin kappa light-chain gene expressed the immunoglobulin gene specifically in the lymphoid tissues, whereas rat MLC2 transcripts were found in skeletal muscle but not in the spleen or the other tissues that were tested. In another transgenic strain, carrying the rat MLC2 gene and a modified rat skeletal muscle actin gene (actin-globin chimeric gene), transcripts of the rat MLC2 gene were detected in skeletal muscle only, whereas the actin-globin transcripts were detected in skeletal muscle as well as in the heart. Moreover, the expression of the chimeric gene was also developmentally regulated. Expression was higher in cardiac muscle than in the skeletal muscle of neonatal mice, whereas expression was higher in skeletal muscle in adult mice. This pattern is consistent with the regulation of the expression of the endogenous skeletal muscle actin gene. Thus, in those transgenic strains that expressed both genes, each gene retained its tissue specificity, in spite of their close proximity. These results indicate a high degree of autonomy of the control elements included in the cloned genomic DNA fragment and demonstrate that a single chromosomal site can be permissive for the proper expression of two genes with different tissue specificities.

Overlapping transcription units in the transient receptor potential locus of Drosophila melanogaster

We report the identification in Drosophila melanogaster of two mRNA transcripts that are derived from the transient receptor potential locus by transcription in opposite directions. The two transcripts overlap; one transcript has, as part of its 5'-untranslated sequence, the reverse complement of 442 bp of the 3' terminus of the transcript derived from the opposite DNA strand. Conceptual translation of the corresponding cDNA sequences predicted for one of the transcripts a polypeptide whose C terminus shares sequence and structural similarity with the cell-wall-binding domain of protein A from Staphylococcus aureus; for the transcript derived from the opposite DNA strand, a polypeptide of 264 amino acids was predicted, which showed no significant sequence homology with any known protein. The two transcripts have different tissue specificities: one is expressed predominantly in the eye and the other is in the body. These findings may have implications in the relationship between the organization of overlapping genes on opposite DNA strands and regulation of gene expression by antisense RNA.

Nuclease sensitivity of alpha-fetoprotein, metallothionein-1, and immunoglobulin gene sequences in mouse during development

The production of alpha-fetoprotein (AFP) and metallothionein-1 (MT-1) in mouse tissues follows a well-defined developmental pattern. The genes for these proteins are highly transcribed in embryo liver but transcribed at a very low rate in adult liver and in brain at all stages of development. A dot hybridization procedure was defined for quantitative screening for AFP, MT-1, immunoglobulin, and satellite DNA sequences to determine the relative degree of micrococcal nuclease sensitivity of these DNA sequences in fetal, newborn, and adult liver and brain, and the visceral yolk sac of the embryo. It was found that, for the DNA sequences assayed, three distinct chromatin conformations exist. DNA that does not code for protein (satellite DNA) was highly resistant to nuclease cleavage. DNA that codes for protein, but is not available for transcription (unrearranged immunoglobulin (C mu) genes in brain, liver, and yolk sac) was fourfold more sensitive to cleavage than were satellite DNA sequences. A further sevenfold increase in nuclease sensitivity was detected in genes actively being transcribed (MT-1 and AFP genes in embryo liver). Quiescent MT-1 and AFP genes were intermediate in nuclease-sensitivity between active genes and unrearranged C mu genes. These data indicate that MT-1 and AFP genes are permanently established in a nuclease-sensitive chromatin conformation early in liver development, and that conformation is maintained regardless of the degree of transcription of the genes. A second, reversible change in chromatin structure occurs in step with changes in the degree of developmentally regulated expression of AFP and MT-1 genes.

A chicken transferrin gene in transgenic mice escapes X-chromosome inactivation

Mammalian X-chromosome inactivation involves a coordinate shutting down of physically linked genes. Several proposed models require the presence of specific sequences near genes to permit the spread of inactivation into these regions. If such models are correct, one might predict that heterologous genes transferred onto the X chromosome might lack the appropriate signal sequences and therefore escape inactivation. To determine whether a foreign gene inserted into the X chromosome is subject to inactivation, transgenic mice harboring 11 copies of the complete, 17-kilobase chicken transferrin gene on the X chromosome were used. Male mice hemizygous for this insert were bred with females bearing Searle's translocation, an X-chromosome rearrangement that is always active in heterozygous females (the unrearranged X chromosome is inactive). Female offspring bearing the Searle's translocation and the chicken transferrin gene had the same amount of chicken transferrin messenger RNA in liver as did transgenic male mice or transgenic female mice lacking the Searle's chromosome. This result shows that the inserted gene is not subject to X-chromosome inactivation and suggests that the inactivation process cannot spread over 187 kilobases of DNA in the absence of specific signal sequences required for inactivation.

Simian virus 40 associates with nuclear superstructures at early times of infection

The association of infecting simian virus 40 with insoluble nuclear structures was assayed by disrupting infected nuclei and assaying insoluble fractions for virus. Three methods were used which lyse nuclei but maintain the insolubility of residual nuclear structures: sonication, high-salt-Triton-EDTA extraction, and low-salt-lithium diiodosalicylate extraction. After each type of nuclear extraction, infecting simian virus 40 remained associated with the residual nuclear structures. This association depended strictly on natural viral infections and on the use of buffers containing moderate amounts of salt and Mg2+ for the isolation of infected nuclei. These viral interactions exhibited behavior similar to host cell DNA interactions studied by analogous assays. Both viral DNA and coat proteins were found associated with the host cell nuclear superstructure. We concluding that at early times after infection the viral templates mimic the state of the host cell chromatin by attaching to the cellular nuclear matrix.

Polite DNA: functional density and functional compatibility in genomes

Certain as yet poorly defined functions of DNA appear to involve collectively domain-sized sequences. It is proposed that most sequence segments within a domain may be either functionally superfluous or instrumental, depending on how many related sequences are present in the domain. When redundant and functionally dispensable, such DNA segments presumably still have to conform to compositional or sequence-motif patterns that characterize the domain. In its relations with neighboring sequences, such DNA is required to be "polite." Polite DNA is DNA that, without being crucially involved in function, is subject to constraints of conformity and, through its base composition, respects a function for which it is not required. This concept is developed by contrasting the distribution of specific and general functions over DNA with this distribution as found in proteins and by distinguishing functional compatibility from pivotal functionality. The sequence constraints to which heterochromatin as well as, apparently, long interspersed repetitive sequences are known to be subject seem to imply that DNA, even when it does not carry out a pivotal function, is indeed, at the very least, required to be polite.

Reduced stability of RNA coding for yolk polypeptide 3 in Drosophila melanogaster ovary

In Drosophila three yolk polypeptides (YP1, YP2 and YP3) are synthesized at two sites in the adult female: in the fat body tissue, from which they are transported via the haemolymph to the ovary, and in the ovarian follicle cells which surround the developing oocytes. All three yolk polypeptides are synthesized at equal levels in the fat body. In this paper we show that the steady-state level of YP3 RNA is significantly reduced in the ovary in comparison with the fat body, and that none of the yolk protein genes is amplified either in the fat body or the follicle cells. In order to determine the basis of the reduced level of YP3 RNA in the ovary, which could result from a lower rate of transcription or through a decreased stability of the RNA, we have devised an in vivo method of determining relative rates of gene transcription. In both the fat body and the ovary all three yolk proteins are transcribed at similar rates. Thus we infer that YP3 RNA is destabilised in the ovary, accounting for the reduction in its steady-state level.

Gene within a gene: nested Drosophila genes encode unrelated proteins on opposite DNA strands

A pupal cuticle protein gene has been found within an intron of a Drosophila gene that encodes three purine pathway enzymatic activities. The intronic gene is encoded on the DNA strand opposite the purine pathway gene and is itself interrupted by an intron. Whereas the purine pathway gene is active throughout development, the intronic cuticle protein gene is expressed primarily over a 3 hr period in the abdominal epidermal cells of prepupae that secrete the pupal cuticle. Therefore, a housekeeping gene and a developmentally regulated gene function in a nested arrangement.

Structure of transcriptionally active chromatin

Transcriptionally active or potentially active genes can be distinguished by several criteria from inactive sequences. Active genes show both an increased general sensitivity to endonucleases like DNase I or micrococcal nuclease and the presence of nuclease hypersensitive sites. Frequently, the nuclease hypersensitive sites are present just upstream of the transcription initiation site covering sequences that are crucial for the promoter function. Viral or cellular transcription enhancer elements are also associated with DNase I hypersensitive sites. At least for the SV40 enhancer, it was shown by electronmicroscopic studies that the DNase I hypersensitive DNA segment is excluded from nucleosomes. It is highly plausible that the binding of regulatory proteins to enhancer or promoter sequences is responsible for the exclusion of these DNA segments from nucleosomes and for the formation of nuclease hypersensitive sites. We speculate that the binding of such proteins may switch on a change in the conformation and/or the protein composition of a chromatin segment or domain containing one to several genes. Biochemical analysis of fractionated nucleosome particles or of active and inactive chromatin fractions have revealed differences in the composition as well as in the degree of modification of histones in these two subfractions of the chromosome. However, until present it is impossible to define unambiguously what are the crucial structural elements that distinguish between particles present on active and inactive chromatin.

DNase I and nuclease S1 sensitivity of the rabbit beta 1 globin gene in nuclei and in supercoiled plasmids

We have examined the nuclease sensitivity of the 5' flanking region of the rabbit beta 1 globin gene in bone marrow nuclei and in supercoiled plasmids. A DNase I hypersensitive site was found about 100 base-pairs 5' to the cap site in bone marrow nuclei. S1 nuclease can introduce a specific double-strand cut in the DNA in the same region. The presence of the nuclease-hypersensitive region correlates with the active transcription of gene beta 1 in bone marrow. Treatment with nuclease S1 of a supercoiled plasmid containing 1400 base-pairs of 5' flanking sequences as well as part of the beta 1 gene reveals a major double-strand cut 400 base-pairs 5' to the cap site. This cut maps within a stretch of repeating dinucleotides (C-T)12 and does not correspond to the in vivo site. Introduction of an RsaI fragment containing the nuclease S1-hypersensitive site into plasmid pBR322 shows that this fragment alone is sufficient to generate the hypersensitive site. Deletion of that RsaI fragment from the beta 1 plasmid reveals another site 1300 base-pairs upstream. Further deletion of this secondary site uncovers numerous other sites, none of which corresponds to the site in nuclei. Chromatin reconstitution with plasmids carrying the 5' flanking region of beta 1 and histones is capable of suppressing the in vitro nuclease-S1-hypersensitive site at --400 but is incapable of generating the in vivo site at --100. Fine analysis at the nucleotide level of the early events in the digestion with nuclease S1 shows that the enzyme attacks preferentially the sequence (G-A)12 on the message complementary strand. The region of DNA containing the supercoil-dependent S1 site adopts at least three different conformations that can be resolved electrophoretically. These different conformations are detected in linear restriction fragments and may represent non-B DNA or unusual B-form DNA.

Determinants of heat shock-induced chromosome puffing

Modified Drosophila heat shock genes were introduced into the germ line by P element transformation. The genes were altered such that several factors could be tested for their influence upon chromosome puffing. Deletion of promoter sequences upstream of position -73 of an hsp70-IacZ hybrid gene was sufficient to abolish puffing. Analysis of progressive 5' deletions defines a 16 bp interval that contains sequences required for both heat-induced puffing and gene expression. An internal deletion of the hsp70-IacZ gene that reduces the transcript size from 9 kb to 0.8 kb results in a dramatic reduction in puff size. The chromosomal insertion sites of 26 variant hsp70 or hsp26 genes fail to influence puffing greatly with one marked exception. This transformant possesses an insert that fails to puff and exhibits a tissue-restricted pattern of expression. These results indicate that variation in either promoter strength or transcript length have profound effects on puffing.

Torsional stress promotes the DNAase I sensitivity of active genes

Active genes are known to have an altered chromatin structure that is preferentially sensitive to digestion with DNAase I. We find that when chicken red blood cells are incubated in media containing the topoisomerase II inhibitor novobiocin, the preferential DNAase I sensitivity of the active beta-globin genes is reversed in vivo with as little as 20 min of drug treatment. Control experiments suggest that inhibition of a topoisomerase II is responsible for this alteration in active gene conformation. Reversal of DNAase I sensitivity can also be induced in vitro by partial cleavage of the nuclear DNA with staphylococcal nuclease. We propose that the altered structure around active genes is maintained by continuous DNA supercoiling and that in the absence of this superhelical tension active chromatin reverts to a less DNAase I-sensitive ground state.

Reversible and persistent changes in chromatin structure accompany activation of a glucocorticoid-dependent enhancer element

A derivative of mouse mammary tumor virus (MTV) DNA, LTL, was constructed in vitro and introduced into the genome of mouse L cells. Transcription of LTL was stimulated by dexamethasone, a glucocorticoid hormone. Two features of LTL chromatin structure are altered upon hormone treatment. First, "moderate" DNAase I sensitivity of the entire LTL element increases following addition of dexamethasone; this alteration persists after hormone withdrawal, when LTL transcription is shut off. Second, a discrete DNAase I-hypersensitive region is induced with a time course that closely parallels the rate of increasing transcription from the MTV promoter; this structure disappears upon hormone removal. The induced hypersensitive region coincides with a segment of the MTV long terminal repeat sequence that specifically binds purified glucocorticoid receptor in vitro and functions as a hormone-dependent enhancer element in vivo. We suggest that specific glucocorticoid receptor-DNA interactions may alter the configuration of DNA or chromatin in the vicinity of the binding sites, thereby creating an active transcriptional enhancer.

Replication timing of genes and middle repetitive sequences

DNA replication in mammals is temporally bimodal. "Housekeeping" genes, which are active in all cells, replicate during the first half of the S phase of cell growth. Tissue-specific genes replicate early in those cells in which they are potentially expressed, and they usually replicate late in tissues in which they are not expressed. Replication during the first half of the S phase is, therefore, a necessary but not sufficient condition for gene transcription. A change in the replication timing of a tissue-specific gene appears to reflect the commitment of that gene to transcriptional competence or to quiescence during ontogeny. Most families of middle repetitive sequences replicate either early or late. These data are consistent with a model in which two functionally distinct genomes coexist in the nucleus.

Chromatin assembly in Xenopus oocytes: in vivo studies

We have followed the time course of chromatin assembly, DNA supercoiling, and transcription on a Xenopus 5S RNA gene clone injected into germinal vesicles of Xenopus oocytes. During the first 2 hr after DNA injection, there is a gradual enhancement in transcription that correlates with the increase in superhelical density of the DNA template; on the other hand, nucleosome assembly is already completed by 10-30 min after DNA injection. To probe further the DNA structure in the assembled minichromosomes, we injected enzymes and chemicals into the germinal vesicle. DNAase I and topoisomerase I injections reveal that the circular DNA has been assembled into two discrete and equally abundant types of chromatin: one type, which we call "dynamic" chromatin, is torsionally strained and is thus fully relaxed by those two enzymes. The other type, which we call "static" chromatin, still yields supercoiled DNA molecules after deproteinization. The dynamic chromatin is also relaxed by injection of novobiocin, and simultaneously, 5S RNA transcription is turned off. The results of our in vivo experiments suggest that the dynamic chromatin is the one that is transcriptionally active. We discuss the biological relevance of these findings.

Actively transcribed genes are associated with the nuclear matrix

In the chicken oviduct, it has been well documented that steroid hormones stimulate the transcription of specific genes such as the ovalbumin gene. In addition to the presence of specific hormone receptors in the tissue, gene expression seems to require that target genes exist in large DNase I sensitive chromosomal domains. This structure appears necessary but not sufficient for transcriptional activation. In search of still other levels of control, we have investigated the interactions of genes with the nuclear matrix, a structure which has been implicated in DNA synthesis, transcription and RNA processing. Here we have isolated nuclear matrix and used a nondegradative method to fractionate nuclear DNA based on its preferential association with the matrix. The preparation was digested with a restriction enzyme and both matrix-bound and released DNAs were recovered. We found that only actively expressed genes were associated with the matrix. Furthermore, within a 100-kilobase (kb) DNase I sensitive chromosomal domain, only the transcribed regions were associated with the matrix. This association was shown to be reversible when hormone was withdrawn. Our results suggest that the nuclear matrix is the site of nuclear transcription and may represent another potential level of control for regulation of gene expression in the eukaryotic cell.

A foreign beta-globin gene in transgenic mice: integration at abnormal chromosomal positions and expression in inappropriate tissues

We have investigated the chromosomal location, inheritance, and expression of a cloned rabbit beta-globin gene introduced into the mouse germ line by microinjection into mouse eggs. Experiments utilizing in situ hybridization to metaphase chromosomes show that the gene has integrated into one or two different chromosomal loci in each of five mouse lines analyzed. Each locus contains between three and forty copies of the foreign DNA sequence arranged in a tandem array, and the sequences at each locus are stably inherited as a single Mendelian marker. Neither globin mRNA nor polypeptides encoded by the rabbit beta-globin gene are detected in erythroid cells in the seven transgenic lines examined, indicating that the expression of the foreign gene is not correctly regulated. However, in two of the mouse lines, rabbit beta-globin transcripts are found at a low level in specific, although inappropriate, tissues: skeletal muscle in one line and testis in another line. These unusual patterns of beta-globin gene transcription are heritable traits in the two mouse lines and may result from the beta-globin gene's integration at abnormal chromosomal positions.

The seminal vesicle secretion IV gene: detection of S1 nuclease-sensitive sites in supercoiled plasmid pSVS 3.3

We have investigated the sites sensitive to the S1 nuclease which are presented in a supercoiled plasmid, pSVS 3.3. This plasmid contains the entire transcription unit plus 5'- and 3'-flanking regions of the rat seminal vesicle IV gene on a 3.3 kb Eco RI fragment (Harris et al., 1983). Using a cDNA probe of rat seminal vesicle secretion product IV (SVS IV) mRNA, we have demonstrated S1 nuclease-sensitive sites in the 5'-flanking and in the 3'-flanking regions of SVS IV gene. The site in the 5'flanking region has been mapped to approximately 117 bp upstream from the CAP site. This site at -117 bp can potentially form a cruciform structure as inferred from the presence of inverted repeats in this region (Lilley, 1981; Panayotatos and Wells, 1981). We have now shown such a structure most probably exists. The S1 nuclease-sensitive site in the 3'flanking region is present in an area of highly repeated sequence.

Characterization of Giemsa dark- and light-band DNA

Using synchronized cultures of V79-8 Chinese hamster lung fibroblasts, we either alternately labeled early- and late-replicating DNA, or substituted one of these with bromodeoxyuridine to separate them in CsCl density gradients or to identify the bromodeoxyuridine-containing chromosome bands by fluorescence microscopy. The Giemsa light R bands were shown to replicate in the first half of S phase, and the dark G bands were shown to replicate in the last half of S phase. S phase was bimodal, with a distinct pause in the rate of DNA synthesis that separated the period of R-band DNA synthesis from that of G-band DNA synthesis. G-band DNA was found to be 3.2% richer in AT than R-band DNA. Surprisingly, G- and R-band DNA appeared equally transcriptionally active in that alternate labels in chromatin were digested with the same kinetics by DNAase I, and in reassociation experiments, total poly(A)+ RNA drove nick-translated G- and R-band DNA probes similarly. G- and R-band DNA also reassociated with identical kinetics, demonstrating that they contain equal proportions of all kinetic-complexity classes of sequences.