Transcripts from both strands of a satellite DNA occur on lampbrush chromosome loops of the newt Notophthalmus

In situ hybridization at the electron microscope level: hybrid detection by autoradiography and colloidal gold

In situ hybridization has become a standard method for localizing DNA or RNA sequences in cytological preparations. We developed two methods to extend this technique to the transmission electron microscope level using mouse satellite DNA hybridization to whole mount metaphase chromosomes as the test system. The first method devised is a direct extension of standard light microscope level using mouse satellite DNA hybridization to whole mount metaphase chromosomes as the test system. The first method devised is a direct extension of standard light microscope in situ hybridization. Radioactively labeled complementary RNA (cRNA) is hybridized to metaphase chromosomes deposited on electron microscope grids and fixed in 70 percent ethanol vapor; hybridixation site are detected by autoradiography. Specific and intense labeling of chromosomal centromeric regions is observed even after relatively short exposure times. Inerphase nuclei present in some of the metaphase chromosome preparations also show defined paatterms of satellite DNA labeling which suggests that satellite-containing regions are associate with each other during interphase. The sensitivity of this method is estimated to at least as good as that at the light microscope level while the resolution is improved at least threefold. The second method, which circumvents the use of autoradiogrphic detection, uses biotin-labeled polynucleotide probes. After hybridization of these probes, either DNA or RNA, to fixed chromosomes on grids, hybrids are detected via reaction is improved at least threefold. The second method, which circumvents the use of autoradiographic detection, uses biotin-labeled polynucleotide probes. After hybridization of these probes, either DNA or RNA, to fixed chromosomes on grids, hybrids are detected via reaction with an antibody against biotin and secondary antibody adsorbed to the surface of over centromeric heterochromatin and along the associated peripheral fibers. Labeling is on average ten times that of background binding. This method is rapid and possesses the potential to allow precise ultrastructual localization of DNA sequences in chromosomes and chromatin.

Bioassay for components regulating eukaryotic gene expression: a chromosomal factor involved in the generation of histone mRNA 3' termini

We have adapted the oocyte injection procedure for the detection of regulatory components involved in the transcription of a eukaryotic mRNA gene. Injection of the histone gene repeat h22 DNA of Psammechinus miliaris into the Xenopus oocyte nucleus results in correct initiation of the histone mRNAs, but readthrough by RNA polymerase occurs at the 3' end of the H3 histone gene (Hentschel, C. C., Probst, E. & Birnstiel, M. L. (1980) Nature (London) 288, 100-102). Coinjection into the oocyte of a chromosomal salt wash fraction derived from sea urchin embryos results in the generation of authentic 3' termini of the histone H3 mRNA. We have partially purified the protein component by column chromatography and density gradient centrifugation. The regulatory factor binds to heparin columns and, hence, has the properties anticipated of an RNA- or DNA-binding protein. The sedimentation coefficient of the active component was determined to be about 12 S, suggesting a molecular weight of 200,000-250,000.

Structure of 1.71 lb gm/cm(3) bovine satellite DNA: evolutionary relationship to satellite I

The Eco RI fragments from the 2600 bp repeating unit of 1.711b gm/Cm(3) bovine satellite DNA were cloned in pBR322. The structure of the repeat unit was determined and compared to bovine satellite I DNA (rho CsCl = 1.715 gm/cm(3)). All of the DNA in the 1402 bp repeat of satellite I is represented in the sequence of the 2600 bp 1.711b gm/cm(3) repeat. The difference between the two repeats is due to a 1200 bp piece of DNA (INS) residing in the middle of the 1.711b gm/cm(3) repeat. The INS is AT-rich and has some repetitive components; it bears only limited similarity to the structure of eukaryotic transposable elements. We propose that the 1.711b gm/cm(3) satellite DNA arose via the amplification of a 1.715 gm/cm(3) satellite repeat altered by a 1200 bp insertion of DNA.

Identification of cloned Y chromosomal DNA sequences from a lampbrush loop of Drosophila hydei

By recombinant DNA techniques, a Y chromosomal sequence of Drosophila hydei was isolated. This DNA sequence of 8.93-kilobase length is a member of a family of repetitive sequences located in the short arm of the Y chromosome. Tissue-specific transcripts complementary to the cloned sequence were found in testes RNA. In situ hybridization demonstrated that such transcripts are present in the lampbrush loop pair "nooses" in primary spermatocyte nuclei--a loop pair that is associated with the only fertility gene in the short arm of the Y chromosome.

Transcription of complementary repeat sequences in amphibian oocytes

Repeat sequences are transcribed in the germinal vesicles of amphibian oocytes. In the hnRNA population both complements of the repeats are found and can be readily detected because they form intermolecular duplex structures. The structure and formation of duplex regions have been studied in the hnRNA of Xenopus laevis, Triturus cristatus, Amphiuma means and Necturus maculosus, a series of amphibians of increasing genome size (C-value). In T. cristatus, the duplex structures are mostly 600-1200 bp in length, whereas in X. laevis they are shorter and in N. maculosus they tend to be longer. Although the proportion of RNA sequence capable of rapidly forming duplex structures is different in different organisms, this property bears no relationship to C-value. However the sequence complexity of complementary repeats, as estimated from the rate of duplex formation, does show an increasing trend with C-value. The complementary repeats found in oocyte hnRNA are transcribed from families of DNA sequence that are each represented in the genome by thousands of copies. The extent of cross-species hybridization is low, indicating that the repeat sequences transcribed in different amphibian genera are not the same. In situ hybridization experiments indicate that the repeat sequences are spread throughout the genome. The evolution and possible function of complementary repeats are considered.

Molecular biology of the sea urchin embryo

Research on the early development of the sea urchin offers new insights into the process of embryogenesis. Maternal messenger RNA stored in the unfertilized egg supports most of the protein synthesis in the early embryo, but the structure of maternal transcripts suggests that additional functions are also possible. The overall developmental patterns of transcription and protein synthesis are known, and current measurements describe the expression of specific genes, including the histone genes, the ribosomal genes, and the actin genes. Possible mechanisms of developmental commitment are explored for regions of the early embryo that give rise to specified cell lineages, such as the micromere-mesenchyme cell lineage.

Properties of active nucleosomes as revealed by HMG 14 and 17 chromatography

Nucleosomes from actively transcribed genes (active nucleosomes) contain nonhistone proteins HMG 14 and 17 and are preferentially sensitive to digestion by DNAse I. Active nucleosomes isolated by chromatography on an HMG 14 and 17 glass bead affinity column were analyzed with respect to overall structure, accessory nonhistone components and modifications to the DNA and histones. The experiments lead to the following conclusions: the DNA in the active nucleosome is undermethylated compared to bulk DNA; topoisomerase I is a non-stoichiometric component of the active nucleosome fraction; the level of histone acetylation is enriched in active nucleosomes, but the extent of enrichment cannot account for HMG binding; and the two histone H3 molecules in the active nucleosome can dimerize more readily and are, therefore, probably closer together than those in the bulk of the nucleosomes. Additionally it is shown that HMG 14 and 17 prefer to bind to single- vs. double-stranded nucleic acids. The role of HMG 14 and 17 in producing a highly DNAse I sensitive structure and correspondingly helping to facilitate transcription is discussed in terms of these properties.

The Croonian Lecture, 1981. Lampbrush chromosomes

Lampbrush chromosomes were first observed nearly 100 years ago, and this lecture attempts a historical survey of what has been learnt from their study, particularly that over the past 30 years. There have been many controversies concerning the structure and functional significance of lampbrush chromosomes, and although their general structural layout has now, after several misconceptions, been firmly established their functional significance remains controversial. Research on lampbrush chromosomes played a significant part in establishing that chromatids in the germ lines of eukaryotic organisms are unineme in regard to DNA, and thereby exposed the C-value paradox. It also helped to establish that a DNA duplex is continuous throughout the length of a chromatid, but that the DNA/histone complex is at intervals reflected back on itself to form lateral loops. This organization, at one time thought to be a special feature of lampbrush chromosomes, now appears to be widespread in chromosomes undergoing compaction. However, despite attempts to determine the sequence organization of those portions of the DNA that are transcribed by lampbrush chromosomes, the function of these transcripts remains an open question, and the C-value paradox is still unresolved.

A new era in mammalian gene mapping: somatic cell genetics and recombinant DNA methodologies

Mammalian gene mapping techniques are now sufficiently advanced to contribute significantly to prenatal diagnosis and to human molecular genetics. Restriction fragment mapping can be used to place polymorphic genetic markers at random sites within the genome, and these sites used to assign genes responsible for disease conditions to a chromosomal region. Somatic cell genetic techniques can then be applied to saturate that region with additional restriction fragment markers, some of which will be closely linked to the disease gene. Closely linked restriction fragment markers, especially flanking pairs of markers, can act as predictors for the transmission of defective genes to offspring. A series of tightly linked flanking restriction markers might in addition contribute to the eventual isolation and cloning of the disease gene itself.

Histone genes are located at the sphere loci of newt lampbrush chromosomes

In situ hybridization experiments on mitotic and lampbrush chromosomes show that histone genes and an associated 222 bp repeated sequence, satellite 1, are located at or near the sphere loci of chromosomes 2 and 6 of the newt Notophthalmus viridescens. During the lampbrush chromosome stage, transcripts of the histone genes and of satellite 1 occur on loops associated with the spheres. Histones genes are located at sites on the mitotic chromosomes of Triturus cristatus and T. alpestris which are consistent with the known positions of spheres on their lampbrush chromosomes.

Histone gene clusters of the newt notophthalmus are separated by long tracts of satellite DNA

The genomic organization of the histone genes of the newt Notophthalmus viridescens is described. Genes for the five proteins are clustered on a 9.0 kb segment of cloned DNA which is part of a homogeneous family of sequences containing 600--800 members per haploid genome. The 9.0 kb histone gene clusters are not adjacent in the genome, but are separated from neighboring clusters by up to 50 kb or more of cluster spacer sequences; some or all of these spacer sequences are members of a predominantly centromeric satellite DNA with a 2235 bp repeating unit.