Transient alterations of the chromatin structure of sea urchin early histone genes during embryogenesis

Down-regulation of Early Sea Urchin Histone H2A Gene Relies on cis Regulative Sequences Located in the 5′ and 3′ Regions and Including the Enhancer Blocker sns

The tandem repeated sea urchin alpha-histone genes are developmentally regulated by gene-specific promoter elements. Coordinate transcription of the five genes begins after meiotic maturation of the oocyte, continues through cleavage, and reaches its maximum at morula stage, after which these genes are shut off and maintained in a silenced state for the life cycle of the animal. Although cis regulative sequences affecting the timing and the level of expression of these genes have been characterized, much less is known about the mechanism of their repression. Here we report the results of a functional analysis that allowed the identification of the sequence elements needed for the silencing of the alpha-H2A gene at gastrula stage. We found that important negative regulative sequences are located in the 462 bp sns 5 fragment located in the 3' region. Remarkably, sns 5 contains the sns enhancer blocking element and the most 3' H2A codons. In addition, we made the striking observation that inhibition of the anti-enhancer activity of sns, by titration of the binding proteins in microinjected embryos, also affected the capability of sns 5 to down-regulate transgene expression at gastrula stage. A further sequence element essential for repression of the H2A gene was identified upstream of the enhancer, in the 5' region, and contains four GAGA repeats. Altogether these findings suggest that down-regulation of the alpha-H2A gene occurs by the functional interaction of the 5' and 3' cis sequence elements. These results demonstrate the involvement of a genomic insulator in the silencing of gene expression.

Developmentally-regulated interaction of a transcription factor complex containing CDP/cut with the early histone H3 gene promoter of the sea urchin Tetrapygus niger is associated with changes in chromatin structure and gene expression

During sea urchin embryogenesis the early histone genes are temporally expressed to accommodate the high demand for histone proteins during DNA replication at early cleavage stages of development. The early histone genes are transcriptionally active from the 16-cell stage, reaching a peak in expression at the 128-cell stage that gradually decreases until expression is completely inhibited at the late blastula stage. We are studying the gene regulatory mechanisms that control early histone gene expression in sea urchins to understand the interrelationships between chromatin remodeling and transcriptional activation during development. Here, we have investigated chromatin organization and transcription factor interactions by analyzing nuclease hypersensitivity and protein binding in the promoter region of the early histone H3 gene from the sea urchin Tetrapygus niger. We have found a DNase I hypersensitive domain centered at -90 in the early histone H3 gene promoter which is only detected in embryos at the 128-cell stage expressing high levels of early histone H3 mRNA. This hypersensitive site (-110 to -70) encompasses two regulatory elements (TnH3NFH3.1 and TnH3CCAAT). The -94 to -77 region of the histone H3 promoter is recognized by a transcription factor complex in nuclear extracts from 128-cell embryos. Methylation interference analysis and competition studies demonstrated a specific interaction at the CCAAT sequence. Using specific antibodies we find that the homeodomain transcription factor CDP/cut is the DNA-binding component of the complex interacting with the early histone H3 gene promoter in T. niger. Our results provide further evidence for the functional role of CDP/cut in developmental regulation of histone gene expression in phylogenetically diverse eukaryotic species.

Chromatin structure and analysis of mechanisms of activators and repressors

Some transcriptional repressors appear to organize chromatin structure as at least part of their mechanism. Some transcriptional activators appear to alter or remodel chromatin structure as at least part of their mechanism. Understanding transcriptional regulation thus requires methods for investigation of the chromatin structure of specific genes in different states of functional activity. This paper reviews chemical and enzymatic approaches to determination of chromatin structure, the methods used for analysis of the results, and criteria for interpretation of the data to infer chromatin structures.

Psoralen crosslinking of active and inactive sea urchin histone and rRNA genes

Chromatin structure is highly correlated with the transcriptional activity of specific genes. For example, it has been found that the regularity of nucleosome spacing is compromised when genes are transcribed. The rRNA genes from fungi, plants, and animals give distinctly bimodal distributions of psoralen crosslinking, which has led to the suggestion that these genes might be largely devoid of nucleosomes when transcriptionally active. We investigated the chromatin structure of the multicopy rRNA and histone genes during sea urchin early embryogenesis. The rRNA genes, which are weakly expressed, give a unimodal distribution of weak psoralen crosslinking, in contrast to the situation in all other organisms studied. The early histone genes were more accessible to psoralen crosslinking when active than inactive. The pattern of crosslinking suggests that these polII genes have a homogeneous structure and are still highly protected by nucleosomes when in the active conformation, unlike the situation in polI genes.

The SpHE gene is downregulated in sea urchin late blastulae despite persistence of multiple positive factors sufficient to activate its promoter

Previous studies of the regulatory region of the SpHE (hatching enzyme) gene of the sea urchin Strongylocentrotus purpuratus (Wei, Z., Angerer, L.M., Gagnon, M.L. and Angerer, R.C. (1995) Characterization of the SpHE promoter that are spatially regulated along the animal-vegetal axis of the sea urchin embryo. Dev. Biol. 171, 195-211) have shown that approximately 330 bp is necessary and sufficient to promote high level expression in embryos of transgenes that reproduce the spatially asymmetric pattern of endogenous gene activity along the maternally determined animal-vegetal embryonic axis. Furthermore, SpHE regulatory elements appear to be redundant since several different combinations are sufficient to elicit strong promoter activity and many subsets function like the endogenous gene only in non-vegetal cells of the blastula (Wei, Z., Angerer, L.M. and Angerer, R.C. (1997) Multiple positive cis-elements regulate the asymmetric expression of the SpHE gene along the sea urchin embryo animal-vegetal axis. Dev. Biol., 187, 71-88). Here we demonstrate by in vivo footprinting that many cis elements on the endogenous promoter are occupied when the gene is active in early blastulae, but the binding of corresponding trans factors is significantly reduced when the gene becomes inactive in late blastulae. In addition, downregulation of the promoter is accompanied by a transition from a non-nucleosomal to a nucleosome-like chromatin structure. Surprisingly, in vitro DNase I footprints of the 300 bp promoter using nuclear protein extracts from early and late blastulae are not detectably different and neither this sequence, nor a longer one extending to -1255, reproduces the loss of endogenous SpHE transcriptional activity after very early blastula stage. These observations imply that temporal repression of SpHE transcription involves a decrease in accessibility of the promoter to activators that are nevertheless present in nuclei and capable of activating transgene promoters. Temporal, but not spatial, downregulation is therefore likely to be regulated by negative activities functioning outside the -1255 promoter region which may serve as direct repressors or mediate an inactive chromatin structure.

Turnover of histone acetyl groups during sea urchin early development is not required for histone, heat shock and actin gene transcription

Histone acetylation is an extremely complex, reversible and specific process. In order to evaluate the importance of this modification for gene expression during sea urchin development, acetyl group turnover of histone lysine residues was blocked by sodium butyrate. The continuous presence of 15 Mm sodium butyrate in the incubation medium from the onset of development blocked gastrulation and resulted in chromatin containing hyperacetylated histone molecules in amounts usually not found in nature. At the mesenchyme blastula stage, the expression of the early histone genes was shut off and the expression of the late genes was switched on both in control and sodium butyrate-treated embryos. Investigation of the early histone gene chromatin structure in butyrate-treated embryos revealed a random distribution of nucleosomes when the genes were transcriptionally active as compared to regular nucleosomal packaging when genes were inactive. These changes in chromatin structure during development mimicked the chromatin structural transition of the early histone genes in control embryos. In addition, the ability of heat shock genes to be induced at elevated temperature and repressed at normal temperature was unaffected in butyrate treatment of embryos. Finally, the developmental profiles of the cytoskeletal CyIIIa actin gene expression in control and butyrate-treated embryos were very similar. The data presented suggest that turnover of histone acetyl groups and the overall level of histone acetylation are not determining factors in the up and down regulation of a number of genes during early development of sea urchin.

Embryonic regulation of histone ubiquitination in the sea urchin

We have used quantitative 2-D protein electrophoresis and immunoprecipitation to study the patterns of histone ubiquitination at 10 h and 36 h of embryonic development in Strongylocentrotus purpuratus. Variants csH2A, alpha H2A, beta H2A, gamma H2A, delta HA, H2AF./Z, alpha H2B, beta H2B, and gamma H2B showed up to sevenfold differences in level of monoubiquitination between variants, and individual variants showed up to sixfold changes during development. At 36 h of embryogenesis, the late variants were less ubiquitinated than the early variants, although the overall level of ubiquitination was appreciably greater than at 10 h. Antiubiquitin antibodies were used to precipitate formaldehyde-fixed chromatin fragments in order to estimate the degree of ubiquitination of the early histone genes. The 5' regulatory region of the active H3 gene appeared to be at least twice as ubiquitinated as the adjacent upstream spacer. However, the absolute level of ubiquitination of the early histone gene repeat seemed to be independent of transcriptional activity. These results show that variant-specific ubiquitination of histones is a part of the developmental program in sea urchin embryos, but is not clearly correlated with transcriptional activity of the early histone genes, except perhaps in the regulatory regions.

Purification of an oligo(dG).oligo(dC)-binding sea urchin nuclear protein, suGF1: a family of G-string factors involved in gene regulation during development

Contiguous deoxyguanosine residues (G strings) have been implicated in regulation of gene expression in several organisms via the binding of G-string factors. Regulation of expression of the chicken adult beta-globin gene may involve the interplay between binding of an erythrocyte-specific G-string factor, BGP1, and the stability of a positioned nucleosome (C. D. Lewis, S. P. Clark, G. Felsenfeld, and H. Gould, Genes Dev. 2:863-873, 1988). We have purified a 59.5-kDa nuclear protein (suGF1) from sea urchin embryos by DNA affinity chromatography. suGF1 has high binding affinity and specificity for oligo(dG).oligo(dC). The identity of the purified protein was confirmed by renaturation of sequence-specific DNA-binding activity from a sodium dodecyl sulfate-polyacrylamide gel slice and by Southwestern (DNA-protein) blotting. suGF1 binds in vitro to a G11 string present in the H1-H4 intergenic region of a sea urchin early histone gene battery. This suGF1 DNA recognition site occurs within a homopurine-homopyrimidine stretch previously shown to be incorporated into a positioned nucleosome core in vitro. DNase I footprinting shows that suGF1 protects the same base pairs on the promoter of the chicken beta A-globin gene as does BGP1. We show that a G-string cis-regulatory element of a sea urchin cell lineage-specific gene LpS1 (M. Xiang, S.-Y. Lu, M. Musso, G. Karsenty, and W. H. Klein, Development 113:1345-1355, 1991) also represents a high-affinity recognition site for suGF1. suGF1 may be a member of a family of G-string factors involved in the regulation of expression of unrelated genes during development of a number of different organisms.

Purification of an oligo(dG).oligo(dC)-binding sea urchin nuclear protein, suGF1: a family of G-string factors involved in gene regulation during development

Contiguous deoxyguanosine residues (G strings) have been implicated in regulation of gene expression in several organisms via the binding of G-string factors. Regulation of expression of the chicken adult beta-globin gene may involve the interplay between binding of an erythrocyte-specific G-string factor, BGP1, and the stability of a positioned nucleosome (C. D. Lewis, S. P. Clark, G. Felsenfeld, and H. Gould, Genes Dev. 2:863-873, 1988). We have purified a 59.5-kDa nuclear protein (suGF1) from sea urchin embryos by DNA affinity chromatography. suGF1 has high binding affinity and specificity for oligo(dG).oligo(dC). The identity of the purified protein was confirmed by renaturation of sequence-specific DNA-binding activity from a sodium dodecyl sulfate-polyacrylamide gel slice and by Southwestern (DNA-protein) blotting. suGF1 binds in vitro to a G11 string present in the H1-H4 intergenic region of a sea urchin early histone gene battery. This suGF1 DNA recognition site occurs within a homopurine-homopyrimidine stretch previously shown to be incorporated into a positioned nucleosome core in vitro. DNase I footprinting shows that suGF1 protects the same base pairs on the promoter of the chicken beta A-globin gene as does BGP1. We show that a G-string cis-regulatory element of a sea urchin cell lineage-specific gene LpS1 (M. Xiang, S.-Y. Lu, M. Musso, G. Karsenty, and W. H. Klein, Development 113:1345-1355, 1991) also represents a high-affinity recognition site for suGF1. suGF1 may be a member of a family of G-string factors involved in the regulation of expression of unrelated genes during development of a number of different organisms.

Dynamics of interaction of RNA polymerase II with nucleosomes. II. During read-through and elongation

The sulfhydryl-specific fluorescence probe 1,5-IAEDANS (5-(2-((iodoacetyl)amino)ethyl)amino-naphthalene-1-sulfonic acid) was attached to the single cysteine of H3, and reconstituted fluorescent mononucleosomes were used as the template for in vitro transcription by the yeast RNA polymerase II (pol II). DNase I digestion analysis revealed that transcription of nucleosomes by pol II resulted in an overall loosening of the structure. Monitoring the transcription event by steady-state fluorescence analysis showed that nucleosomes only partially open during transcription. This opening is transient in nature, and nucleosomes close back as soon as the pol II falls off the template. Thus, using the technique of fluorescence spectroscopy, partial opening of nucleosome structure could be differentiated from complete dissociation into free DNA and histone octamer, a distinction that may not be possible by techniques like gel electrophoresis. Time-resolved fluorescence emission spectroscopy suggested that during read-through of the template by the pol II, histone octamers do not fall off the DNA. Only minor conformational changes within the histone octamer take place to accommodate the transcribing polymerase.

An octamer element is required for the expression of the alpha H2B histone gene during the early development of the sea urchin

Early (alpha) histone genes are one of several histone gene families in the sea urchin genome. They are expressed at high levels in blastula-stage embryos and are inactivated by the early gastrula stage. By microinjecting mutant early H2B genes into sea urchin zygotes and monitoring their transcriptional activity in blastula- and gastrula-stage embryos, we sought to identify the cis-regulatory elements responsible for this dramatic change in early H2B gene activity. We found that deletion of DNA 5' of -71 and 3' of +591 did not affect the timing or magnitude of early H2B gene expression. Neither was early H2B gene expression affected by the replacement of sequences downstream of -36 with the corresponding region of the L1 late H2B gene, expressed after the peak transcription of the early H2B gene. Further deletion of early H2B promoter sequences from -71 to -56, removing a conserved octamer element, resulted in near-complete inactivation of the early H2B gene in both blastula- and gastrula-stage embryos. Also inactivating early H2B gene expression were an internal deletion of the octamer element and a base substitution mutation that altered its sequence. This base substitution mutation also caused a parallel reduction in the ability of the octamer element to bind a factor present in nuclear extracts of sea urchin blastulae. These data strongly suggest that the proper expression of the early H2B gene in cleavage- and blastula-stage embryos depends on the octamer element and a factor with which it interacts.

Nucleosome spacing is compressed in active chromatin domains of chick erythroid cells

We have cleaved the chromatin of embryonic and adult chicken erythroid cells using a novel nuclease that is capable of resolving clearly the nucleosomes of active chromatin. We found that in active chromatin, nucleosomes are spaced up to 40 base pairs closer together than in inactive chromatin. This was true for both "housekeeping" and "luxury" genes and was observed whether the digestion was carried out on isolated nuclei in vitro or by activating the endogenous nuclease in vivo. The close spacing extended several kilobases into flanking chromatin, indicating that this is a domain property of active chromatin, not just a characteristic of regions disrupted by transcription. A simple interpretation of our results is that the nucleosomes of active chromatin are mobile in vivo and, not being constrained by linker histones, freely move closer together.

Nucleoprotein hybridization: a method for isolating active and inactive genes as chromatin

The developmentally regulated sea urchin early histone gene repeat (SUEHGR) from Strongylocentrotus purpuratus was isolated as chromatin by nucleoprotein hybridization. This technique is a novel method to isolate specific sequences as chromatin. Because the purification scheme is based only on the gene sequence and is independent of other physical properties such as protein composition and transcriptional activity, we were able to isolate the same gene in different functional states. Gene size chromatin fragments were solubilized by restriction endonuclease digestion of cell nuclei. Using T7 gene 6 exonuclease, the 3'termini of the fragments were exposed and then hybridized in solution to a biotinylated oligonucleotide complementary to one end of the SUEHGR fragment. The hybrids were bound to an Avidin D matrix. DTT cleavage of the biotin linker yielded a chromatin fraction greater than 700 fold enriched in SUEHGR. Overall yields were between 2% and 15%. The purity of the isolated material was independently measured to be greater than 80%. The homogeneous native structure of the inactive genes was preserved as shown by electron microscopy and micrococcal nuclease digestion of the purified SUEHGR. Minor heterogeneity was observed for the purified active genes by micrococcal nuclease digestion but the main features of the active chromatin were preserved during isolation. This isolation offers the first opportunity to study the structure of an RNA polymerase II gene at different stages of the cell cycle and development.

Chromatin structure of the developmentally regulated early histone genes of the sea urchin Strongylocentrotus purpuratus

Chromatin organization of the early histone gene repeat was studied at the early embryonic stages of the sea urchin S. purpuratus. Micrococcal nuclease digestion showed a highly irregular packaging of the whole repeat at the period of transcriptional activity, which was progressively replaced by more regular nucleosomal arrays upon developmentally programmed inactivation. No evidence for unique positioning of the nucleosomes was found. Regions upstream of each of the genes were hypersensitive to DNAase I digestion in the active state. These regions contained one (H2A and H2B), or two (H3 and H4) well-defined DNAase I cutting sites, or two poorly-defined sites (H1). They mapped within DNA sequences shown previously to be required for proper expression of the genes. Hypersensitivity continued in the hatching blastula, which have a conventional nucleosomal structure and a much reduced transcriptional activity. Hypersensitivity of these regions during morula and early blastula was not dependent on the torsional strain in chromatin, as it was not influenced by extensive gamma ray-induced nicking of the DNA in nuclei. By late blastula no hypersensitive regions were present.

Active beta-globin gene transcription occurs in methylated, DNase I-resistant chromatin of nonerythroid chicken cells

We report active, inappropriate transcription of the chicken beta A-globin gene in normal fibroblasts, cultured MSB cells, and brain. We were unable to detect ovalbumin gene transcription in these same tissues. Most of the globin gene transcripts were found to be truncated near the beginning of the gene, suggesting the existence of a premature termination process that is preferentially active under conditions of inappropriate transcription. The inappropriately transcribed beta A-globin gene chromatin remained DNase I resistant and highly methylated. Thus, the DNase I-sensitive conformation of erythrocyte beta A chromatin was correlated not with beta A transcription per se but with beta A expression. Although both transcribed and nontranscribed genes within the globin domain exhibited the same DNase I sensitivity in erythrocyte nuclei, a housekeeping gene active in erythrocytes exhibited a different level of DNase I sensitivity. However, this gene exhibited the same level of DNase I sensitivity in both erythrocytes and a cultured cell line. These observations are consistent with the proposal (G. Blobel, Proc. Natl. Acad. Sci. USA 82:8527-8529, 1985) that the DNase I sensitivity of a gene may reflect properties of chromatin related to cotranscriptional and posttranscriptional aspects of mRNA production rather than to transcription per se.

Active beta-globin gene transcription occurs in methylated, DNase I-resistant chromatin of nonerythroid chicken cells

We report active, inappropriate transcription of the chicken beta A-globin gene in normal fibroblasts, cultured MSB cells, and brain. We were unable to detect ovalbumin gene transcription in these same tissues. Most of the globin gene transcripts were found to be truncated near the beginning of the gene, suggesting the existence of a premature termination process that is preferentially active under conditions of inappropriate transcription. The inappropriately transcribed beta A-globin gene chromatin remained DNase I resistant and highly methylated. Thus, the DNase I-sensitive conformation of erythrocyte beta A chromatin was correlated not with beta A transcription per se but with beta A expression. Although both transcribed and nontranscribed genes within the globin domain exhibited the same DNase I sensitivity in erythrocyte nuclei, a housekeeping gene active in erythrocytes exhibited a different level of DNase I sensitivity. However, this gene exhibited the same level of DNase I sensitivity in both erythrocytes and a cultured cell line. These observations are consistent with the proposal (G. Blobel, Proc. Natl. Acad. Sci. USA 82:8527-8529, 1985) that the DNase I sensitivity of a gene may reflect properties of chromatin related to cotranscriptional and posttranscriptional aspects of mRNA production rather than to transcription per se.

Cis-acting elements of the sea urchin histone H2A modulator bind transcriptional factors

Functional tests, performed by microinjection into Xenopus laevis oocytes, show that a DNA fragment containing the modulator of the early histone H2A gene of Paracentrotus lividus enhances transcription of a reporter gene when located, in the physiological orientation, upstream of the tk basal promoter. Gel retardation and DNase I footprinting assays further reveal that the H2A modulator contains at least two binding sites [upstream sequence elements 1 and 2 (USE 1 and USE 2)] for nuclear factors extracted from sea urchin embryos, which actively transcribe the early histone gene set. Interestingly, USE 1 is highly homologous to a cis-acting element previously identified in the H2A modulator of Psammechinus miliaris [Grosschedl, R., Mächler, M., Rohrer, U. & Birnstiel, M. L. (1983) Nucleic Acids Res. 11, 8123-8136]. Finally, a cloned oligonucleotide containing the USE 1 sequence competes efficiently in Xenopus oocytes with the H2A modulator to prevent enhancement of transcription of the reporter gene. From these results, we conclude that USE 1 and perhaps USE 2 in the H2A modulator are upstream transcriptional elements that are recognized by trans-acting factors common to Xenopus and sea urchin.

Developmental control of promoter-specific factors responsible for the embryonic activation and inactivation of the sea urchin early histone H3 gene

We have begun an investigation of the molecular basis for the temporal embryonic expression of the early histone H3 gene of the sea urchin Strongylocentrotus purpuratus. Cloned constructs exhibit the proper temporal regulation following microinjection into one-cell zygotes of the related sea urchin species, Lytechinus pictus. Deletion analysis of the upstream promoter region of the H3 gene revealed several regions that are involved in both positive and negative control. DNase I footprinting, mobility shift, and methylation interference experiments reveal multiple sequence-specific DNA-binding proteins that interact with at least five distinct regions within 200 bp upstream of the RNA initiation site. Extracts prepared from staged embryos revealed that the ability of the factors to bind their target sequences was regulated. Proteins bound at four different sites were detected only at stages when the H3 gene was active transcriptionally. In addition, three different forms of a CCAAT-binding protein also are regulated temporally. The activity of these protein(s), however, correlates inversely with the transcriptional activity of the gene. The TATA box and CCAAT sequences are all that is required for expression of low levels of H3 transcripts with the proper temporal pattern. This approach should be useful in understanding the mechanisms used to regulate temporal patterns of gene expression during early embryogenesis.

A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution

A model for eukaryotic chromatin organization is presented in which the basic structural and functional unit is the DNA domain. This simple model predicts that both chromosome replication and cell type-specific control of gene expression depend on a combination of stable and dynamic DNA-nuclear matrix interactions. The model suggests that in eukaryotes, DNA regulatory processes are controlled mainly by the intranuclear compartmentalization of the specific DNA sequences, and that control of gene expression involves multiple steps of specific DNA-nuclear matrix interactions. Predictions of the model are tested using available biochemical, molecular and cell biological data. In addition, the domain model is discussed as a simple molecular mechanism to explain cell differentiation in multi-cellular organisms and to explain the evolution of eukaryotic genomes consisting mainly of repetitive sequences and "junk" DNA.

Developmental regulation of micro-injected histone genes in sea urchin embryos

The developmental behavior of cloned histone genes of Psammechinus miliaris was studied by injection into eggs of two related sea urchin species followed by fertilization. All five early histone genes were faithfully expressed in early blastula embryos as shown by SP6 RNA mapping. A 5-10 times lower expression rate was estimated for the injected early H2A gene from its competition strength with the endogenous gene. Transcripts of this early H2A gene accumulated during the cleavage stages and decayed in late embryos in parallel with the endogenous early H2A mRNA. However, an introduced late H2B gene was incorrectly regulated, since its mRNA level did not increase from the blastula to the gastrula stage. The sperm H2B-1 gene, normally inactive in development, was 80 times less well expressed than the early H2A gene in transformed blastulae. A fusion gene with the early H2A promoter linked to the structural sperm H2B gene was, however, efficiently transcribed suggesting that all essential information for an early expression pattern is contained within the 5' region of the early H2A gene.

Expression of a collagen gene in mesenchyme lineages of the Strongylocentrotus purpuratus embryo

We have previously described cloning of an exon of a sea urchin collagen gene and shown that its expression is temporally regulated during embryogenesis, beginning during blastula formation. We have now localized the protein encoded by the gene and the sites of its mRNA synthesis in the developing embryo. Antibody to a synthetic peptide reacts with a 208,000 Mr protein that is digestible by collagenase. Fractionation of pluteus stage embryos demonstrates that the protein is localized primarily with cells that form the syncytium of primary mesenchyme that elaborates the larval endoskeleton; furthermore, immunofluorescence localizes the epitope to the periphery of the endoskeleton in situ. Transcripts of the gene accumulate only in mesenchyme cells, especially those of the primary mesenchyme lineage. Measurements of absolute transcript abundance show that collagen mRNA is present in blastula primary mesenchyme cells at 600-700 copies per cell and at about fourfold lower amounts in other mesenchyme cells.

Formation of stable chromatin structures on the histone H4 gene during differentiation in Tetrahymena thermophila

The relationship between chromatin structure and the transcriptional activity of the histone H4-I gene of Tetrahymena thermophila was explored. Indirect end-labeling studies demonstrated that major DNase I- and micrococcal nuclease-hypersensitive sites flank the active macronuclear genes but not the inactive micronuclear genes. Runon transcription experiments with isolated macronuclei indicated that histone gene transcription rates decreased when cells were starved. However, macronuclear nuclease-hypersensitive sites persisted upon starvation. Thus, one level of transcriptional control of the H4-I gene results in altered chromatin structure and is established during nuclear differentiation. The rate of transcription is also controlled, but not through hypersensitive site-associated structures.

Chromatin structure of the cytochrome P-450c gene changes following induction

The chromatin structure of cytochrome P-450c and P-450d genes, which in the liver are highly inducible by 3-methylcholanthrene, was studied in normal and carcinogen-treated rats by using a cDNA probe specific for P-450c and a genomic probe that recognizes both genes. Digestion with micrococcal nuclease revealed that the active genes are not present in the typical 200 base pair nucleosomal structure. Gene induction is associated with a rearrangement of the nuclear organization of the genes. By use of indirect end-label hybridization, three DNase I hypersensitive sites were mapped, one in the 5'-terminal region and two in the 3' region of the P-450c gene. Gene induction, by treatment with 3-methylcholanthrene, changes the location of the DNase I site present in the 5' region without affecting the sites present in the 3' region. Rat thymus chromatin does not contain these DNase I hypersensitive sites, suggesting that, in the liver, the chromatin structure is altered so as to allow tissue-specific expression of the P-450c gene. The chromatin structure of the highly inducible P-450c gene is compared to that of the P-450m gene, which is induced to a significantly smaller extent and is constitutively expressed.

Isolation and characterization of spicule proteins from Strongylocentrotus purpuratus

A simple method is described for the isolation of spicules from pluteus embryos of the sea urchin, Strongylocentrotus purpuratus. Radio-iodination of the demineralized matrix reveals six bands on SDS protein gels. Treatment with N-glycanase leads us to believe that some of these proteins are N-linked glycoproteins.

Site and stage specific action of endogenous nuclease and micrococcal nuclease on histone genes of sea urchin embryos

The early histone genes of sea urchin embryos are expressed exclusively during cleavage stages of embryogenesis. The chromatin containing these genes was examined by nuclease sensitivity. An endogenous nuclease active during cleavage, produces 1300-bp segments containing early histone genes. The cutting sites have been mapped; there are very sensitive sites close to the cap site for H1, H2A, H2B, and H4. Chromatin obtained from embryos of later stages, when the genes are not expressed, do not display this pattern of nuclease sensitivity. Micrococcal nuclease produces nucleosomes that contain histone genes when used with nuclei from later stages, but not with nuclei from cleavage stages.

Chromosomal organization of the herpes simplex virus genome during acute infection of the mouse central nervous system

After corneal inoculation, herpes simplex virus type 1 replicates in the mouse eye, trigeminal ganglia, and brainstem, producing first an acute and then a latent infection. Previous work from this laboratory focused on the structure of the viral DNA in this system. We have now examined the structure of the viral genome at the chromosome level by using micrococcal nuclease digestion. Studies with disaggregated cell preparations made from the brainstems of acutely infected mice show that the majority of the viral DNA is in a nonnucleosomal form; however, a nucleosomelike fraction was also consistently detected. A similar result was obtained for viral DNA in herpes simplex virus type 1-infected C1300 (clone NA) neuroblastoma cells (a neuronal cell line).

Formation of stable chromatin structures on the histone H4 gene during differentiation in Tetrahymena thermophila

The relationship between chromatin structure and the transcriptional activity of the histone H4-I gene of Tetrahymena thermophila was explored. Indirect end-labeling studies demonstrated that major DNase I- and micrococcal nuclease-hypersensitive sites flank the active macronuclear genes but not the inactive micronuclear genes. Runon transcription experiments with isolated macronuclei indicated that histone gene transcription rates decreased when cells were starved. However, macronuclear nuclease-hypersensitive sites persisted upon starvation. Thus, one level of transcriptional control of the H4-I gene results in altered chromatin structure and is established during nuclear differentiation. The rate of transcription is also controlled, but not through hypersensitive site-associated structures.