Studies on the intranuclear distribution and properties of mouse satellite DNA

The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues

Pericentric heterochromatin (PCH) forms spatio-temporarily distinct compartments and affects chromosome organization and stability. Albeit some of its components are known, an elucidation of its proteome and how it differs between tissues in vivo is lacking. Here, we find that PCH compartments are dynamically organized in a tissue-specific manner, possibly reflecting compositional differences. As the mouse brain and liver exhibit very different PCH architecture, we isolated native PCH fractions from these tissues, analyzed their protein compositions using quantitative mass spectrometry, and compared them to identify common and tissue-specific PCH proteins. In addition to heterochromatin-enriched proteins, the PCH proteome includes RNA/transcription and membrane-related proteins, which showed lower abundance than PCH-enriched proteins. Thus, we applied a cut-off of PCH-unspecific candidates based on their abundance and validated PCH-enriched proteins. Amongst the hits, MeCP2 was classified into brain PCH-enriched proteins, while linker histone H1 was not. We found that H1 and MeCP2 compete to bind to PCH and regulate PCH organization in opposite ways. Altogether, our workflow of unbiased PCH isolation, quantitative mass spectrometry, and validation-based analysis allowed the identification of proteins that are common and tissue-specifically enriched at PCH. Further investigation of selected hits revealed their opposing role in heterochromatin higher-order architecture in vivo.

Relative position of constitutive heterochromatin and of nucleolar structures during mouse spermiogenesis

In this study, the selective fluorochrome staining of constitutive heterochromatin and a specific ultrastructural silver-staining of nucleolar material (i.e., the nucleolus organizing regions) were undertaken to be used as indicators for the chromosomal arrangement during mouse spermiogenesis. Since in mice all somatic chromosomes are telocentric and the constitutive heterochromatin and nucleolar organizing regions are closely associated to the centromeres, this combination of techniques provided for the first time ultrastructural evidence 1) for the dispersion of the constitutive heterochromatic chromocentre and a centrifugal migration to the postacrosomal portion of the nuclear envelope where constitutive heterochromatin seems to mediate the assembling of microtubules in the so-called manchette. As elongation continues, the constitutive heterochromatin migrates back into central position and forms the "focous of earlier condensing chromatin", which initiates further chromatin condensation. 2) The fate of the nucleolus during spermiogenesis could also be further clarified: The nucleolus is first associated with the chromocentre, but starts to disintegrate during elongation phase. However, argyrophilic remnants are still visible in the centre of the nucleus, pointing to an ongoing transcriptional activity. When they final disappear, they leave behind "nuclear vacuoles" in the dense chromatin mass of the mature sperm nucleus.

Liver chromatin fractions in Mus and Akodon. The concept of constitutive heterochromatin

The liver chromatin from Mus musculus and Akodon molinae was separated in 8 fractions by differential centrifugation. Like fractions from both species showed approximately similar contents of DNA, equivalent ratios of histone to non-histone proteins, corresponding template activities and equal amounts of positive C-banded material. On the other hand, heavy chromatin fractions of Mus were highly enriched in satellite DNA whereas no satellite DNA was found in Akodon chromatin. Heavy chromatin fractions isolated by differential sedimentation have been usually homologued with the constitutive heterochromatin. The properties of the constitutive chromatin are discussed and the validity of the foregoing concept is challenged. It is proposed to define the constitutive heterochromatin as those chromatin regions comprising highly repeated DNA sequences clustered in restricted areas of chromosomes and not transcribed (satellite DNA).

Highly repetitive component alpha and related alphoid DNAs in man and monkeys

The genomes of Old-World, New-World, and prosimian primates contain members of a large class of highly repetitive DNAs that are related to one another and to component alpha DNA of the African green monkey by their sequence homologies and restriction site periodicities. The members of this class of highly repetitive DNAs are termed the alphoid DNAs, after the prototypical member, component alpha of the African green monkey which was the first such DNA to be identified (Maio, 1971) and sequenced (Rosenberg et al., 1978). The alphoid DNAs appear to be uniquely primate sequences.--From the restriction enzyme cleavage patterns and Southern blot hybridizations under different stringency conditions, the alphoid DNAs comprise multiple sequence families exhibiting varying degrees of homology to component alpha DNA. They also share common elements in their restriction site periodicities (172 . n base-pairs), in the long-range organization of their repeating units, and in their banding behavior in CsCl and Cs2SO4 bouyant density gradients, in which they band within the bulk DNA as cryptic repetitive components.--In the three species from the Family Cercopithecidae examined, the alphoid DNAs represent the most abundant, tandemly repetitive sequence components, comprising about 24% of the African green monkey genome and 8 to 10% of the Rhesus monkey and baboon genomes. In restriction digests, the bulk of the alphoid DNAs among the Cercopithecidae appeared quantitatively reduced to a simple series of arithmetic segments based on a 172 base-pair (bp) repeat. In contrast with these simple restriction patterns, complex patterns were observed when human alphoid DNAs were cleaved with restriction enzymes. Detailed analysis revealed that the human genome contains multiple alphoid sequence families which differ from one another both in their repeat sequence organization and in their degree of homology to the African green monkey component alpha DNA.--The finding of alphoid sequences in other Old-World primate families, in a New-World monkey, and in a prosimian primate attests to the antiquity of these sequences in primate evolution and to the sequence conservatism of a large class of mammalian highly repetitive DNA. In addition, the relative conservatism exhibited by these sequences may distinguish the alphoid DNAs from more recently evolved highly repetitive components and satellite DNAs which have a more restricted taxonomical distribution.

Changes in the nuclear polyamine content of chick erythrocytes during embryonic development

The polyamine content of the circulating erythrocyte population in the embryonic chick was studied during its development. Total cellular polyamine content fell dramatically between 5 and 7 days of development, paralleling the decrease in metabolic activity exhibited by these cells. Nuclei were isolated from the erythrocytes by a non-aqueous technique, which not only eliminated the polyamine loss that occurred with aqueous isolation, but also prevented redistribution of the polyamines from the cytoplasm. Nuclear spermidine and spermine contents decreased markedly between 5 and 6 days of development from 31 to 10 pmol/microgram of DNA and from 33 to 18 pmol/microgram of DNA respectively. Thereafter the spermine content remained constant, but the spermidine content continued to decline. Good correlations between spermidine and RNA contents were observed in both cells and nuclei, and similarly between spermine and RNA contents in cells, but no such correlation was observed between spermine and RNA in nuclei.

Heterogeneity of DNA methylation in murine L5178Y lymphoblasts

Comparison of the extent of methylation in mouse DNA fragments rendered MgCl2 soluble after mild DNase II digestion of nuclei, with different reassociation rate and nucleoli-bound, revealed the existence of 3 regions of the genome particularly 5-methylcytosine-rich: the sequences considered to be related to the transcriptionally active chromatin with the highest content of this base and fast reassociating, as well as nucleolar DNA with somewhat lower proportion of the methylated cytosines.

Behaviour of sex chromosome associated satellite DNAs in somatic and germ cells in snakes

Sex chromosome associated satellite DNAs is isolated from the snakes Elaphe radiata (sat III) (Singh et al., 1976) and Bungarus fasciatus (Elapidae) (minor satellite) are evolutionarily conserved throughout the suborder Ophidia. An autosome limited satellite DNA (B. fasciatus major satellite) is not similarly conserved. Both types of satellites have been studied by in situ hybridisation in various somatic tissues and germ cells where it has been observed that the W sex chromosome remains condensed in interphase nuclei. In growing oocytes however, the W chromosome satellite rich heterochromatin decondenses completely whilst the autosomal satellite rich regions remain condensed. Later, the cycle is reversed and the W chromosome condenses whilst the autosomal satellite regions decondense. In a primitive snake (Eryx johni johni) where the sex chromosomes are not differentiated and where there is no satellite DNA specific to them, these phenomena are absent. - The differential behaviour of autosomal and sex chromosome associated satellite DNAs is discussed in the light of gene regulation.

Bleomycin: effect on satellite DNA in mouse fibroblasts

The effect of Bleomycin on the semiconservative replication of mouse nuclear DNA has been studied. When asynchronously dividing mouse fibroblasts (L-cells) were grown in the presence of 5-bromodeoxyuridine (25 mg/l medium) for 18 h, three hybrid DNA bands with densities of 1.722, 1.752, and 1.761 kg/l appeared after caesium chloride density gradient centrifugation of nuclear DNA. In cells exposed to Bleomycin (100 mg/l) however, replication of satellite DNA is more strongly inhibited than is the replication of the main band DNA; preferentially the thymidinerich hybrid duplex at 1.761 kg/l could no longer be detected.

The rejoining of DNA double-strand breaks and a model for the formation of chromosomal rearrangements

The recombination type of process, which has been proposed by Resnick to explain the rejoining of radiation-induced DNA double-strand breaks, is combined with the molecular theory of radiation action to provide a description of the formation of chromosomal rearrangments. It is shown that the majority of chromosomal aberration types found at the first mitosis after radiation can be explained on the basis of one radiation-induced DNA double-strand break in the backbone of the unineme chromatid, followed by the enzymatically controlled recombinational process for the rejoining of the double-strand break. The recombinogenic process for the repair of DNA double-strand breaks relies on the close association between the broken DNA double helix and homologous DNA. The homologous nature of repeated DNA base pair sequences is used, in this model, to explain the occurrence of chromosomal exchanges between non-homologous chromosomes. The important role which repetitive DNA plays in the formation of chromosomal rearrangements and in the distribution of 'break-points' found in radiation experiments is discussed.

Factors influencing the yield of satellite DNA in extractions from Drosophila virilis and Drosophila melanogaster adults and embryos

The application of different DNA extraction methods to identical batches of Drosophila virilis and Drosophila melanogaster flies or embryos has revealed that the ionic strength of a homogenization medium is of critical importance if chloroform extractions are performed. The low yield of satellite DNA after homogenization in low salt buffers is less severe if EDTA is included in the buffer. Phenol extraction procedures result in no such differential behavior of satellite and main band DNA, but under certain circumstances a particular satellite fraction of Drosophila virilis DNA may be lost.

Percent satellite DNA as a function of tissue and age of mice

A selective loss of satellite DNA was found to occur to different extents as a function of tissue and age of mice using several common DNA extraction and purification procedures. This result emphasizes a serious problem that may be encountered in comparative studies of DNA structure and composition if selective loss of specific DNA sequences occurs. We have developed a DNA extraction and purification procedure that is simple and reliable and gives a high percent DNA yield, which substantially reduces the selective loss of heterochromatin DNA sequences. The method features a centrifugation step of a proteolytic digest of chromatin in 2.4 M CsCl. Percent DNA yield of 82-98% are routinely obtained with no apparent loss of satellite DNA sequences from different tissues or ages of mice. Utilizing this method, percent satellite DNA was found to remain essentially constant at 11 +/- 1% for spleen, kidney, and brain tissues obtained from mice of 10-780 days of age. However, for liver, percent satellite DNA remained at about 7-8% from 10 to 300 days of age and then increased to about 12-13% from 300 to 600 days of age. During this latter time interval (300-600 days), an increase of DNA per nucleus of about 3-fold occurred, due to the formation of tetra- and octaploid cell types. A steady loss in the total number of nuclei per gram of liver as a function of age was also found. These two opposing effects resulted in a nearly constant amount of DNA per gram and per organ for liver throughout the lifespan of the mouse.

Isopycnic centrifugation of sheared L-cell chromatin in metrizamide gradients

Isopycnic gradient centrifugation of L-929 cell chromatin in a 38% (W/V) metrizamide solution yields two distinct fractions. The fraction banding at a density of 1.24 gm/cm(2) (H chromatin) contains about 10% of the DNA present in the fraction banding at a density of 1.18 gm/cm(2) (L chromatin). Both fractions contain the same proportions of satellite to main band DNA's. Some differences can be seen in the DNA: protein ratios and types of proteins present in the H and L chromatin fractions.

Novel properties of satellite DNA from muskmelon

The purified dense satellite of muskmelon (Cucumis melo L.) represents 30% of the total DNA and forms a sharp, unimodal peak in both neutral and alkaline CsCl gradients. Spectrophotometric melting and DNA reassociation analyses revealed that one-third of the satellite is high melting and has a complexity of about 2.5 x 10(5) daltons, while the remaining two-thirds of the satellite melts 8 degrees lower and has a complexity of about 5 x 10(8) daltons. The thermal stability of reassociated satellite DNA indicates that the multiple copies of the two melting fractions are essentially identical. The sharp, unimodal peak in Cs(2)SO(4) becomes two distinct peaks when either silver or mercuric ions are included in the Cs(2)SO(4) gradient

A rapidly-banding component of animal DNA preparations that interferes with buoyant density studies

Rapidly-banding components of purified animal cell DNA's have been observed which have abnormal buoyant densities and show anomalous band profiles when centrifuged to equilibrium in cesium salts. These components interfere with the separation of animal DNA fractions and with the analysis of animal cell DNA's by buoyant density techniques. They can be detected by examining photographs of analytical buoyant-density ultracentrifugations before equilibrium has been reached. These rapidly-banding components are removed by phenol treatment.

Relatedness of mouse satellite deoxyribonucleic acid to deoxyribonucleic acid of various Mus species

Mouse (Mus musculus musculus) satellite DNA is able to reassociate with repeated DNA sequences of Mus caroli and Mus cervicolor, but low thermal stability of the products indicates significant differences between satellite and related DNAs of these two Mus species. There appear to be several satellite-related populations in M. caroli DNA, each of which forms hybrids of low thermal stability with repeated sequences of M. cervicolor DNA. DNAs from the subspecies Mus musculus molossinus and Mus musculus castaneus reassociate with mouse satellite to form hybrids of very high thermal stability, but the satellite content of M. m. musculus DNA is only about 60% that of M. m. musculus DNA. Reassociation of M. m. musculus nonrepeated DNA with M. m. molossinus DNA reveals no detectable differences between them; reassociation with M. caroli (or M. cervicolor) DNA yields a product whose melting temperature depression relative to homologous DNA is about 5 degrees .

Satellite DNA

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Intracellular iron-binding macromolecules in HeLa cells

The concentration of the iron-chelating agent, desferrioxamine (Desferal), that just inhibits iron entry into HeLa cells is also the concentration that inhibits DNA synthesis. As a first step in clarification of the mechanism whereby iron may partake in DNA synthesis, we have partially characterized several of the intracellular iron-binding sites. Most cytoplasmic iron appears to be bound to a polysaccharide containing glucose that sediments at about 32 S. Nucleolar iron is bound to a single protein, the mobility of which is independent of the concentration of sodium dodecyl sulfate in an acrylamide gel. In contrast the pattern and mobility of nuclear iron, other than nucleolar, is heterogeneous and markedly affected by the concentration of sodium dodecyl sulfate. The evidence suggests that nuclear iron is bound to protein through one or more intermediate(s).