Cytoplasmic localization of human repetitive DNA revealed by in situ hybridization

Plasma membrane associated transcription of cytoplasmic DNA

Cytoplasmic membrane-associated DNA (cmDNA) is a species of DNA that attaches to the plasma membrane and has physical and chemical properties that differ from those of bulk chromosomal and mitochondrial DNAs. Here, we used deep sequencing to analyze cmDNA and showed that satellite DNAs consisting of both of simple (CCATT)(N) repeats from the pericentromere regions of the chromosomes and 171-bp α-satellite repeat sequences from centromeres were highly enriched. Importantly, we found there is a special cytoplasmic membrane-associated transcription system in which DNA-dependent RNA polymerase II, which colocalizes with template cmDNA at the plasma membrane, can transcribe the membrane-associated 171-bp α-satellite repeat sequences into RNA. Analysis of phosphorylation patterns indicated that the RNA polymerase II in the plasma membrane is in a different chemical state from its nuclear counterpart.

Epigenetics and cancer

Both genetics and epigenetics regulate gene expression in cancer. Regulation by genetics involves a change in the DNA sequence, whereas epigenetic regulation involves alteration in chromatin structure and methylation of the promoter region. During the initiation, development, and progression of cancer, a number of genes undergo epigenetic changes. Some of these changes can be used as biomarkers for early detection of cancer as well as to follow treatment. A panel of epigenetic biomarkers is preferred to a single biomarker in clinical assays. Changes in gene expression due to epigenetic regulation can be reversed by chemicals, and this approach opens up a novel approach in cancer prevention and treatment.

Induced detachment of acentric chromatin from mitotic chromosomes leads to their cytoplasmic localization at G(1) and the micronucleation by lamin reorganization at S phase

Acentric and atelomeric double minute chromatin found in human cancer cells are eliminated from cells by selective incorporation into the micronuclei. We showed previously that most of the micronuclei were formed at S phase and mediated by the nuclear bud-shaped structures that selectively entrap double minutes. In this paper, we have examined the behavior of double minutes in relation to the nuclear lamin protein in cell cycle-synchronized human COLO 320DM tumor cells. At the G(1) phase, we observed that a portion of double minutes was localized at the cytoplasm and showed no association with lamin. The frequency of this localization was increased by hydroxyurea, an inducer of micronuclei, if treated at the preceding S phase. The acentric double minutes were normally segregated to daughter cells by attaching to the mitotic chromosomes, and the hydroxyurea-treatment induced their detachment, possibly through the introduction of the double strand break. When the cells entered S phase, our data suggested that the lamin protein accumulated around the cytoplasmic double minutes at the proximity of the nucleus leading to the formation of the nuclear bud-shaped structure and the initiation of DNA replication. This association of cytoplasmic double minutes with lamin coincided with the large-scale rearrangement of the intranuclear lamin protein. The implication of these findings as well as their application to a broad spectrum of other acentric, atelomeric and autonomously replicating molecules are discussed.

DNA-mediated transport of the intermediate filament protein vimentin into the nucleus of cultured cells

A number of characteristic properties of intermediate filament (IF) proteins, such as nucleic acid-binding activity, affinity for histones and structural relatedness to transcription factors and nuclear matrix proteins, in conjunction with the tight association of IFs with the nucleus, suggest that these proteins might also fulfill nuclear functions in addition to their structure-organizing and -stabilizing activities in the cytoplasm. Yet, cytoplasmic IF proteins do not possess nuclear localization signals. In a search for carriers capable of transporting the IF protein vimentin into the nucleus, complexes of FITC-vimentin with various DNAs were microinjected into the cytoplasm of cultured cells and the intracellular distribution of the protein was followed by confocal laser scanning microscopy. The single-stranded oligodeoxyribonucleotides oligo(dG)25, oligo[d(GT)12G] and oligo[d(G3T2A)4G] proved to be excellent nuclear carriers for vimentin. However, in fibroblasts, fluorescence-labeled vimentin taken up by the nuclei remained undetectable with affinity-purified, polyclonal anti-vimentin antibody, whereas it was readily identifiable in the nuclei of microinjected epithelial cells in this way. Moreover, when FITC-vimentin was preinjected into fibroblasts and allowed to assemble into the endogenous vimentin filament system, it was still transferred into the nucleus by post-injected oligo(dG)25, although to a lesser extent. Superhelical circular DNAs, like pBR322, SV40 and mitochondrial DNA, were also characterized by considerable capacities for nuclear vimentin transport; these transport potentials were totally destroyed by relaxation or linearization of the DNA molecules. Nevertheless, certain linear double-stranded DNA molecules with a high affinity for vimentin IFs, such as repetitive telomere and centromere or mobile long interspersed repeat (LINE) DNA, could carry FITC-vimentin into the nucleus. This was also true for a 375 bp extrachromosomal linear DNA fragment which occurs in the cytoplasm of mouse tumor cells and which is capable of immortalizing human lymphocytes. On the basis of these results, it appears very likely that cellular and viral products of reverse transcription as well as other extrachromosomal DNAs, which are circular, superhelical and apparently shuttling between the cytoplasm and the nucleus (eccDNA), are constantly loaded with vimentin in vimentin-positive cells. Since such DNAs are considered as markers of genomic instability, it is conceivable that vimentin directly participates as an architectural, chromatin-modifying protein in recombinatorial processes set off by these DNAs in the nucleus.

Induction of complete segregation of cellular DNA and non-encapsidated viral genomes in herpes simplex virus type 1 infected HeLa cells as revealed by in situ hybridization

The intranuclear distribution of human Alu elements and herpes simplex virus type 1 (HSV-1) genomes was examined in HeLa cells by post-embedding in situ hybridization using in parallel appropriate biotinylated DNA probes. The bound probes were detected by direct immunogold labeling. In non-infected cells, human Alu elements detected by BLUR 8 were randomly scattered over the masses and strands of chromatin throughout the nucleus. The marked asynchrony of the HSV-1 cycle in individual HeLa cells of 17 h infected cultures allowed us to study the respective distributions of cell and viral DNA during the course of the infectious cycle. Labeling of human Alu elements revealed that cellular DNA had become confined to the border of infected nuclei without extension of cellular DNA fibers into the newly formed electron-translucent regions that occupied the centers of the infected nuclei. Labeling of HSV-1 DNA detected by a viral DNA probe revealed that non-encapsidated viral genomes were present exclusively within this centrally located viral region whereas encapsidated HSV-1 genomes, which were more widely distributed in the infected cell, were seen within the marginated host chromatin as well as the central viral region. Therefore, HSV-1 infection induces a regrouping of human Alu elements, that is, of host chromatin at the nuclear border. Non-encapsidated HSV-1 genomes and cellular DNA do not co-localize. Instead, they always constitute two adjacent compartments without spatial interrelationships.

Isolation and characterization of a novel cDNA which identifies both neural-specific and ubiquitously expressed GS alpha mRNAs

Heterotrimeric G proteins consisting of alpha, beta, and gamma subunits couple sensory, hormone, and neurotransmitter receptors to intracellular and transmembrane effectors. Several splicing variants of the GS (the G protein that stimulates adenylyl cyclase) alpha subunit (GS alpha) have been described. Some of these couple receptors to stimulation of adenylyl cyclase and Ca2+ channels, whereas others encode truncated proteins whose functions are not currently defined. We describe a 1321N1 human astrocytoma cDNA clone for a novel GS alpha isoform isolated from astrocytoma cells (G(astro)) that is identical to GS alpha-1 with the exception of a novel 5' sequence extending into the previously described exon 1 of GS alpha, a single base change, and an alternative polyadenylation site. Analysis by northern blotting and reverse transcription/PCR confirms the presence of an mRNA corresponding to this cDNA in astrocytoma cells. Additional northern analysis indicates that G(astro) recognizes two novel GS alpha mRNAs in the rat: a 2.0-kb mRNA expressed only in neural and neuroendocrine tissues and a 1.8-kb mRNA that is ubiquitously expressed. Functional analysis of G(astro) is complicated by the apparent insertion of alphoid satellite DNA into the transcription unit. The resulting cDNA encodes a truncated protein that may be translated from the methionine in exon 2 as previously described.