Loss of heterozygosity on the long arm of human chromosome 7 in sporadic renal cell carcinomas

Cytogenetic and molecular analysis of DNA sequences with highly polymorphic microsatellite markers have implicated allele loss in several chromosomal regions including 3p, 6p, 6q, 8p, 9p, 9q, 11p and 14q in the pathogenesis of sporadic renal cell carcinomas (RCCs). Deletions involving the long arm of chromosome 7 have not been described in RCCs although they have been seen in several other tumor types. However, there have been no detailed analysis of loss of heterozygosity (LOH) of 7q sequences in sporadic RCCs. We therefore studied LOH for DNA sequences on 7q with 10 highly polymorphic markers in 92 matched normal/tumor samples representing sporadic RCCs including papillary, nonpapillary, and oncocytomas in order to determine whether allelic loss could be detected in a tumor type with no visible 7q rearrangements at the cytogenetic level. We found chromosome 7q allele loss in 59 of 92 cases (64%) involving one, two, or more microsatellite markers. The most common allele loss included loci D7S522 (24%) and D7S649 (30%) at 7q31.1-31.2, a region that contains one of the common fragile sites, FRA7G. By comparative multiplex PCR analysis, we detected a homozygous deletion of one marker in the 7q 31.1-31.2 region in one tumor, RC21. These results support the idea that a tumor suppressor gene in 7q31 is involved in the pathogenesis of sporadic renal cell carcinomas.

Mutations in the arginine-rich protein gene (ARP) in pancreatic cancer

The ARP gene encodes a highly conserved arginine-rich protein from chromosomal band 3p21.1. At the cytogenetic level this region is frequently deleted in a variety of different solid tumors, although not in pancreatic cancer. We have reported the presence of a specific mutation (ATG50-->AGG) or deletion of codon 50 of the ARP gene in different tumor types (Shridhar et al., 1996, 1996a). In the present study, we have observed mutations involving codon 50 in 11 of 37 pancreatic tumors. The frequency of codon 50 mutation is roughly the same in pancreatic tumors as in the other types of tumors previously examined. In addition, we have detected mutations at codon 51 in multiple PCR subclones in two other pancreatic tumors. Mutations in the ARP gene are thus commonly observed in pancreatic cancer, as well as many other cancers.

Frequent breakpoints in the region surrounding FRA3B in sporadic renal cell carcinomas

The constitutive fragile site at chromosomal band 3p14.2, FRA3B, is the most active common fragile site in the human genome. We have localized aphidicolin-induced breakpoints to two distinct clusters, separated by 200 Kb, in FRA3B (Paradee et al., 1996). Sequence analysis of these regions identified two polymorphic microsatellite markers immediately adjacent to each of these breakpoint clusters. In this report we have used these two new microsatellites and 14 additional 3p microsatellites to analyse chromosome 3p breakage and loss in 94 sporadic RCC samples, including nonpapillary, papillary and oncocytomas. We have found heterozygous loss of 3p14 sequences in >60% of the RCC samples, including both clear cell and papillary renal cell carcinomas. We have found frequent breakage in the region immediately surrounding FRA3B, demonstrating that FRA3B does play a role in chromosome breakage and loss in RCC. In contrast to other reports, >50% of the papillary tumors also showed LOH of 3p markers. We also observed microsatellite instability (MIN) with most of the tested markers in seven of eight oncocytomas and one of 69 clear cell carcinomas. The MIN in some oncocytomas was of the RER+ (replication error) type I phenotype. None of the five 3p14.2 markers detected any homozygous deletions in tumor samples, but 69/94 (73%) of the tumors had LOH for the region, which includes the recently identified FHIT gene.

Mutations in the arginine-rich protein gene, in lung, breast, and prostate cancers, and in squamous cell carcinoma of the head and neck

Arginine-rich protein (ARP) is a highly conserved gene that maps to human chromosomal band 3p21.1. This gene contains an imperfect trinucleotide repeat which encodes a string of arginines. We previously detected a specific mutation (ATG50-->AGG) within this region of the gene in 10 of 21 sporadic renal cell carcinomas. Here, we report the detection of the same mutation in 5 of 21 squamous cell carcinomas of the head and neck, 1 of 2 small cell lung cancer cell lines, 6 of 18 non-small cell lung carcinomas, 9 of 22 breast tumors, and 5 of 13 prostate tumors. This mutation was seen in several early stage tumors and may thus be an early event in tumorigenesis. We also detected a mutation at codon 53 of this gene in both primary and metastatic tumors from one patient. Other nucleotide changes were observed in a few PCR subclones, but their frequency was the same in both tumor and control samples, suggesting that many of these changes were PCR or subcloning artifacts rather than mutations in the tumor cells themselves.

A gene from human chromosomal band 3p21.1 encodes a highly conserved arginine-rich protein and is mutated in renal cell carcinomas

We have identified a gene, called ARP for Arginine-rich protein, in human chromosomal band 3p21. It is approximately 600 Kb telomeric to the ACY1 locus (Miller et al., 1989) and encodes a previously unidentified 234 amino acid long, highly basic protein. This gene is highly conserved at the DNA and RNA level. It is found in all species including hamster, rat, mouse, bovine and yeast. We have detected a point mutation (ATG50 to AGG) or deletion of ATG50 in 10 of 21 sporadic renal cell carcinomas. The mutable region is in an imperfect trinucleotide repeat in the coding region which is non-polymorphic among 50 normal individuals examined. The point mutation (ATG50 to AGG) or deletion of codon 50 removes a methionine and increases the stretch of arginines encoded by the AGG repeats in the ARP gene.

Isolation of two contigs of overlapping cosmids derived from human chromosomal band 3p21.1 and identification of 5 new 3p21.1 genes

Consistent loss of DNA sequences from several regions on the short arm of human chromosome 3 has suggested that multiple tumor suppressor genes reside on chromosome 3p in various types of cancer cells. We have focused our efforts on an analysis of chromosomal band 3p21.1 since aminoacylase-1 (ACY1), which is localized to this band, has been shown to have lower levels of expression in several small cell and non-small cell lung cancer cell lines. Starting with two cosmids within 3p21.1, D3S92 and D3S93, we have isolated two separate contigs of overlapping cosmids within 3p21.1, by screening a library of 5700 chromosome 3-specific cosmid clones. Detailed restriction maps for these two contigs show that they contain multiple clusters of rare cutting restriction endonuclease sites. One contig extends for 100 kb and encompassed both ACY1 and D3S92, and the other extends about 80 kb around the D3S93 locus. Many different restriction fragments derived from these two contigs were found to be evolutionarily conserved and hybridized to distinct message transcripts. These fragments were used to identify homologous cDNAs from an adenogastric cDNA library, and several of these cDNAs were partially sequenced. We have identified five new genes from these two contigs and there is evidence to suggest that several additional genes reside within these cosmid contigs. The genes identified from 3p21.1 were then hybridized to DNA, isolated from a series of lung cancer cell lines and matched normal and tumor DNA from lung cancer patients. No alterations were detected with any of these probes, both at the DNA or RNA levels. A similar analysis with DNA fragments derived from these two genomic regions also failed to detect any alterations.

Seven genes on the short arm of human chromosome 3 map to two regions on Macropus eugenii (tammar wallaby) chromosome 2

Seven genes were mapped by in situ hybridization to metaphase chromosomes of the marsupial species Macropus eugenii, using a series of human-derived cloned probes (six cosmids and one cDNA). The genes were located in two widely separated clusters on the long arm of M. eugenii chromosome 2, in contrast to their location in a single cluster on the distal half of the short arm of human chromosome 3. Multiple rearrangements had to be involved in the evolutionary divergence of these chromosome segments from the unknown arrangement in the common ancestor.

Lamin A/C gene and a related sequence map to human chromosomes 1q12.1-q23 and 10

Lamins A and C are products of alternate splicing of one transcript from a single gene. We have isolated a partial cDNA, cE1-2, whose 800-bp sequence is 99% identical to the 3' untranslated region of the lamin A/C gene. We report here the mapping of this gene and a closely related sequence to human chromosomes 1 and 10, more specifically, to 1q12.1-q23. The localization of cE1-2 hybridizing sequences to two different chromosomes suggests that one of these loci represents an as yet unknown member of the lamin gene family, either a pseudogene or an expressed gene.

Methylation of the 5' flanking sequences of the ribosomal DNA in human cell lines and in a human-hamster hybrid cell line

In a human lymphoblastoid cell line (Z83) in which rDNA genes on chromosome 22 are amplified but transcribed at a low level, immunocytological studies with antibodies to 5 methylcytidine provided evidence for hypermethylation of the rDNA. The extent of methylation of the 5' flanking sequences of the ribosomal DNA was examined by comparing the size of restriction fragments obtained by digestion of genomic DNA with EcoRI and HpaII or EcoRI and MspI. Southern blots indicated hypermethylation of the 5' flanking sequences of many copies of rRNA genes in these cells, but not in a control lymphoblastoid cell line without rDNA amplification. Results obtained with a somatic hybrid human-hamster cell line, in which the rRNA genes on the single human chromosome 22 are inactive, showed that only a small fraction of the CCGG sites in the 5' flanking sequences of the transcriptionally silent rRNA genes in this hybrid were methylated. Since inactive rRNA genes can show such a minimal level of methylation, it is likely that the extreme hypermethylation of the amplified rRNA genes in Z83 occurred in association with their inactivation rather than following it.

Traditional and molecular cytogenetics

Traditional cytogenetic methods have relied on tissue culture techniques to generate adequate mitotic cells for the analysis of chromosome disorders for prenatal diagnosis. Chromosome banding techniques allow the evaluation of mitotic cells for structural and numerical aberrations and define the nature of any rearrangement. With the advent of fluorescent in situ hybridization methodology, which combines the molecular technologies of chromosome-specific probes and in situ molecular hybridization, it has become possible to analyze chromosomal numerical and structural aberrations from interphase cells. The use of molecular cytogenetic techniques should greatly increase the speed and diagnostic resolution of clinical specimens.

The human loci DNF15S2 and D3S94 have a high degree of sequence similarity to acyl-peptide hydrolase and are located at 3p21.3

The short arm of chromosome 3 undergoes genetic loss in most small-cell lung cancers and renal cell carcinomas. The most frequently deleted region includes the DNF15S2 locus (mapped to 3p21), suggesting that a putative recessive tumor-suppressor gene might be located nearby. A cosmid clone, cA476, contains the D3S94 locus and two HTF islands and detects a PstI RFLP. We have isolated cDNAs homologous to conserved fragments within cA476; and these cDNAs have 96% sequence similarity to a cDNA derived from the DNF15S2 locus. Sequence information from cDNAs derived from both the rat and pig acyl-peptide hydrolase (E.C.3.4.19.1) gene show that they have a high degree of sequence similarity to cDNAs derived from D3S94 and DNF15S2, suggesting that they are all the same locus. Cosmid cA476 (DNF15S2) has been mapped, by fluorescent in situ hybridization, to chromosome 3p21.3. D3S94 and DNF15S2 are quite distinct from aminoacylase 1 (ACY1), which has been physically linked to D3S2, D3S92, and D3S93, all localized within 3p21.1.

Isolation and characterization of a mouse subtelomeric sequence

A mouse subtelomeric sequence, ST1, was generated from genomic DNA of the mouse HR9 (129/Sv origin) cell line by the polymerase chain reaction (PCR) using a single telomeric primer. ST1 was cloned and characterized: it is composed of 670 bp of novel DNA sequence flanked on each end by inverted telomeric hexanucleotide repeats (TTAGGG)n. PCR amplification from BALB/c mouse DNA using this single primer gave the same major product. Southern analysis and PCR using internal ST1 primers confirmed that the ST1 sequence is present in mouse genomic DNA. In situ hybridization to metaphase chromosomes of SJL origin mapped ST1 to many, if not every, mouse telomere. PCR experiments using different combinations of the telomeric, minor satellite, and ST1 primers indicated that some ST1 copies are adjacent to minor satellite sequences, that telomeric and ST1 sequences are not generally interspersed with minor satellite sequences, and that ST1 and the minor satellite have a consistent and specific orientation relative to each other and to the telomere.

Isolation and comparative mapping of a human chromosome 20-specific alpha-satellite DNA clone

We have isolated and characterized a human genomic DNA clone (PZ20, locus D20Z2) that identifies, under high-stringency hybridization conditions, an alphoid DNA subset specific for chromosome 20. The specificity was determined using fluorescence in situ hybridization. Sequence analysis confirmed our previously reported data on the great similarity between the chromosome 20 and chromosome 2 alphoid subsets. Comparative mapping of pZ20 on chimpanzee and gorilla chromosomes, also performed under high-stringency conditions, indicates that the alphoid subset has ancestral sequences on chimpanzee chromosome 11 and gorilla chromosome 19. However, no hybridization was observed to chromosomes 21 in the great apes, the homolog of human chromosome 20.

Comparative mapping of a gorilla-derived alpha satellite DNA clone on great ape and human chromosomes

We have isolated an alpha satellite DNA clone, pG3.9, from gorilla DNA. Fluorescence in situ hybridization on banded chromosomes under high stringency conditions revealed that pG3.9 identifies homologous sequences at the centromeric region of ten gorilla chromosomes, and, with few exceptions, also recognizes the homologous chromosomes in human. A pG3.9-like alphoid DNA is present on a larger number of orangutan chromosomes, but, in contrast, is present on only two chromosomes in the chimpanzee. These results show that the chromosomal subsets of related alpha satellite DNA sequences may undergo different patterns of evolution.

Isolation of large numbers of chromosome 3-specific cosmids containing clusters of rare restriction-endonuclease sites

We tested 519 chromosome 3-specific cosmids for the presence of rare restriction-endonuclease sites in a search for cosmids containing HTF islands. We have identified 49 cosmids (9% of those tested) that contain multiple rare restriction-endonuclease sites. The cosmids were digested with several common cutting restriction endonucleases to liberate small fragments which were tested as unique-sequence chromosome 3-specific hybridization probes and for evolutionary sequence conservation. Unique-sequence hybridization probes isolated from the cosmids were hybridized to a somatic cell hybrid deletion mapping panel to subchromosomally localize the cosmids. Fragments from many of these cosmids demonstrated conservation of sequence through evolution, and these fragments hybridize to distinct transcripts. These cosmids should therefore prove a useful resource for the identification of many chromosome 3-specific genes, in addition to having potential use as linking clones for pulsed-field gel mapping studies.

Isolation of a variant family of mouse minor satellite DNA that hybridizes preferentially to chromosome 4

Two cosmids (HRS-1 and HRS-2) containing mouse minor satellite DNA sequences have been isolated from a mouse genomic library. In situ hybridization under moderate stringency conditions to metaphase chromosomes from RCS-5, a tumor cell line derived from the SJL strain, mapped both HRS-1 and HRS-2 to the centromeric region of chromosome 4. Sequence data indicate that these cloned minor satellite DNA sequences have a basic higher order repeat of 180 bp, composed of three diverged 60-bp monomers. Digestion of mouse genomic DNA with several restriction enzymes produces a ladder of minor satellite fragments based on a 120-bp repeat. The restriction enzyme NlaIII (CATG) digests all the minor satellite DNA into three prominent bands of 120, 240, and 360 bp and a weak band of 180 bp. Thus, the majority of minor satellite sequences in the genome are arranged in repeats based on a 120-bp dimer, while the family of minor satellite sequences described here represents a rare variant of these sequences. Our results raise the possibility that there may be other variant families of minor satellites analogous to those of alphoid DNA present in humans.

A chimpanzee-derived chromosome-specific alpha satellite DNA sequence conserved between chimpanzee and human

We describe a cloned 2.7 kb alpha satellite sequence, Pan-3, from the pygmy chimpanzee (Pan paniscus) that specifically hybridizes in situ to chromosome 19 in the pygmy chimpanzee and to the homeologous human chromosome, no. 17. Using high stringency conditions of hybridization on Southern blots, this sequence hybridized to DNA from both species of chimpanzee (P. paniscus and P. troglodytes) and from human but not to DNA from gorilla (Gorilla gorilla) or orangutan (Pongo pygmaeus). Partial sequence analysis showed that Pan-3 and a previously described human chromosome 17-specific clone have up to 91% sequence identity. To our knowledge this is the highest sequence similarity reported between alphoid subsets from human and any other primate.

Chromosome-specific subsets of human alphoid DNA identified by a chromosome 2-derived clone

We have cloned an alphoid DNA fragment, pBS4D, from the DNA of a human-hamster hybrid cell line containing chromosome 2 as its only cytologically detectable human component. Under high stringency conditions, pBS4D hybridized in situ mostly to chromosome 2 and to a lesser extent to chromosomes 18 and 20. Restriction analysis using the DNA from selected somatic hybrid cell lines revealed that the genomic organization of this alphoid DNA differs on each of these three chromosomes.

A human alpha satellite DNA subset specific for chromosome 12

We have isolated a DNA clone (pBR12, locus D12Z3) which identifies an alphoid subset specific for chromosome 12. This alphoid subset has an EcoRI periodicity of 680 bp and is characterized by a higher-order repeat of about 1.4 kb (eight basic units of about 170 bp each) as revealed by several restriction enzymes. The sequence analysis confirmed the alphoid nature of pBR12 and the dimeric organization.

Relationship of mouse minor satellite DNA to centromere activity

Chromosomes from a female mouse cell line were identified by Q-banding prior to in situ hybridization with 3H-labeled mouse minor satellite (satellite II) DNA. No cell was found in which every chromosome was labeled, but grain counts showed that every active centromeric region had minor satellite sequences. In the mouse T (10;13)199H translocation, the breakpoint was within the minor satellite array, leaving clusters of minor satellite at the C-bandless active centromere of the 13(10) chromosome and at the interstitial C-band of the 10(13) chromosome, which is not associated with centromeric activity. In a mouse A9 (L-cell derived) marker chromosome with one terminal and two interstitial C-bands, only the terminal C-band was adjacent to an active centromere, but minor satellite DNA was present at all three sites. Minor satellite DNA was not detected on the Y chromosome, although the presence of a small amount of divergent satellite sequences on this chromosome could not be ruled out.

A human alphoid DNA clone from the EcoRI dimeric family: genomic and internal organization and chromosomal assignment

We isolated an alpha satellite DNA clone (pC1.8), 17 kb long, which is composed exclusively of tandemly repeated 340-bp EcoRI fragments. Hybridization studies using 37 random EcoRI dimers subcloned from pC1.8 showed that they are heterogeneous. The sequence of 5 dimers, 3 of them adjacent, confirmed this observation and showed that the heterogeneity is more accentuated among the second monomers. The chromosomal assignment under high stringency conditions showed that this alphoid subset is located on chromosomes 1, 5, and 19. No conditions that eliminate the hybridization on any one of those chromosomes were found. This suggests that, in contrast to many other chromosome-specific alpha satellite subsets, the single chromosome subsets of this family are virtually indistinguishable by hybridization techniques.

The organization of the mouse satellite DNA at centromeres

The mouse genome contains a major and a minor satellite DNA family of repetitive DNA sequences. The use of 5-azacytidine has allowed us to demonstrate that these satellite DNAs are organized in two separate domains at the centromeres of mouse chromosomes. The minor satellite is closer to the short arms of the acrocentric chromosomes than the major satellite. The major satellite is farther away, flanking the minor satellite and adjacent to the euchromatic long arm of each mouse chromosome. At the level of resolution afforded by the in situ hybridization technique it would appear that the organization of the centromeric domain of the mouse is similar to that in man. That is, both contain two repetitive DNA sequence families arranged in major blocks.

Genetic correction of hereditary disease

Several hereditary disorders may be potentially correctable by the introduction and incorporation of the normal gene into human tissues using a variety of systems. Although technical issues surrounding integration, stable expression and potential insertional mutagenesis to the treated cells has not yet been fully resolved, enough scientific progress has already been made to consider somatic cell gene therapy acceptable from both the scientific and ethical viewpoints. Tissue-specific stem cell and embryonic stem cell transplantation will allow therapy earlier in the developing embryo. As technical problems are eliminated, these procedures will become morally permissible, as they will allow the correction of devastating hereditary disease.

Relationship between the number and function of human ribosomal genes

The relative number of ribosomal RNA genes of the acrocentric chromosomes in one individual was measured by counting grains after in situ hybridization of 3H-labeled human 18S rDNA to fixed metaphase chromosomes. The relative amount of ribosomal RNA gene activity of each of the same chromosomes was estimated by determining the frequency with which the chromosome's nucleolus organizer region (NOR) was silver stained, the size of the silver-stained region, and how often the chromosome was found in satellite association. Results were similar in phytohemagglutinin-stimulated T-lymphocytes, Epstein-Barr virus transformed lymphoblasts, and fibroblasts. One chromosome 21 had few gene copies and low activity. One chromosome 22 had many gene copies but low activity. Both chromosomes 14 had few gene copies but high activity. The level of expression that can be achieved by rRNA gene clusters can, therefore, be determined by factors other than the number of gene copies.

p82H identifies sequences at every human centromere

A cloned alphoid sequence, p82H, hybridizes in situ to the centromere of every human chromosome. After washing under stringent conditions, no more than 8% of the grains are located on any specific chromosome. p82H thus differs from other centromeric sequences which are reported to be chromosome specific, because it detects sequences that are conserved among the chromosomes. Two experimental approaches show that the p82H sequences are closely associated with the centromere. First, p82H remains with the relocated centromeres in an inv(19) and an inv(6) chromosome. Second, p82H hybridizes at the centromere but not to the centromeric heterochromatin of chromosomes 1, 9 and 16 that have elongated 1qh, 9qh and 16qh regions produced by short growth in 5-azacytidine. The only noncentromeric site of hybridization is at the distal end of the 9qh region.

Human ribosomal DNA fragments amplified in hamster cells are transcribed only by RNA polymerase II and are not silver stained

Cloned human rRNA gene fragments that included the promoter region were introduced into Chinese hamster dihydrofolate reductase-deficient (dhfr-) cells by cotransformation with a dhfr minigene and amplified by selection for methotrexate resistance. The human ribosomal DNA was transcribed by RNA polymerase II, not RNA polymerase I or III. The metaphase chromosome regions containing the transcriptionally active human ribosomal DNA failed to show silver staining.

Overabundance of rare-cutting restriction endonuclease sites in the human genome

A human chromosome 3-specific cosmid library was constructed from a somatic cell hybrid containing human chromosome 3 as its only human component. This library was screened to identify 230 human recombinants which contained an average insert size of 37 kilobases. DNA prepared from 54 of these cosmids, representing 2000 kilobases of human DNA, was then tested for restriction endonuclease sites for EcoRI, HindIII, KpnI, XhoI, and DraI, as well as those of the rare-cutting restriction endonucleases NotI, SfiI, NruI, MluI, SacII, and BssHII. Sites for the latter enzymes were much more abundant than would be expected from theoretical calculations, reflecting non-random clustering of these sites. This has important implications for the use of these enzymes in the construction of physical maps of chromosomes. Some individual cosmids contained large numbers of rare sites, offering an alternative means of physically mapping chromosomes based upon identifying clusters of rare restriction sites. These clusters appear to be spaced an average of 1000 kb apart.

Generation of human B-cell hybridomas secreting monoclonal anti-myelin-associated glycoprotein antibodies from a patient with neuropathy

Human hybridomas that secrete monoclonal IgM anti-myelin-associated glycoprotein antibodies were generated by fusion with cells from a patient with peripheral neuropathy and IgM monoclonal gammopathy. Karyotypic analysis of the hybridoma cells revealed no chromosomal abnormalities. The cells were positive for cell-surface idiotype HLA-DR and the plasma cell antigen PCA-1, and negative for the B-cell determinant B4 and for Leu-1, which has been postulated to distinguish a subpopulation of B cells that secrete IgM with autoantibody activity.

Gene therapy

Severe genetic disorders are potentially correctable by the addition of a normal gene into tissues. Although the technical problems involving integration, stable expression, and insertional damage to the treated cell are not yet fully solved, enough scientific progress has already been made to consider somatic cell gene therapy acceptable from both the ethical and scientific viewpoints. The resolutions to problems evolving from somatic cell gene therapy will help to overcome the technical difficulties encountered presently with germ line gene manipulation. This procedure would then become morally permissible as it will cause, in time, a reduction in the pool of abnormal genes in the population. Enhancement genetic engineering is technically feasible but morally unacceptable. Eugenic genetic engineering is not technically possible or ethically permissible in the foreseeable future.

Homogeneously staining regions (HSRs) of a rat hepatoma cell line are not early replicating

The rat hepatoma cell line H4-IIE-C3 (H4) has homogeneously staining regions (HSRs) which contain multiple, tandemly repeated copies of ribosomal RNA (rRNA) genes. We determined the time of replication of the DNA within these HSRs autoradiographically after incorporation of [3H]thymidine and by Hoechst 33258 and Giemsa staining after 5-bromodeoxyuridine (5-BrdU) incorporation. The DNA within the H4 HSRs is not early replicating, unlike that in other HSRs. It begins replicating later than much of the other nuclear DNA, continues replicating throughout most of the S phase, and is completed 1-2 h before mitosis.

Transcription of mouse rDNA and associated formation of the nucleolus organizer region after gene transfer and amplification in Chinese hamster cells

Mouse rDNA can initiate transcription by using only Chinese hamster cell components, and this is associated with nucleolus organizer activity. To demonstrate this, we transferred a 3.2-kilobase segment of mouse rDNA containing the promoter, the transcription initiation site, and part of the external transcribed spacer to dihydrofolate reductase-deficient Chinese hamster cells by cotransformation with an abbreviated mouse dhfr gene. Stepwise selection for methotrexate resistance produced sublines in which the mouse rDNA was usually coamplified with the donor dhfr DNA and occupied the same site or sites in the hamster genome, as shown by in situ hybridization. Transcription from mouse rDNA was demonstrated in two such lines, and S1 protection mapping indicated faithful initiation of the transcript. In some cells from both lines, the chromosome segments containing amplified mouse rDNA showed multiple silver-staining regions (i.e., active nucleolus organizers). Although the transferred mouse rDNA was able to use the rDNA transcriptional machinery of the Chinese hamster, the level of transcription was much lower than expected from the rDNA copy number, and a large fraction of each amplified region showed no silver staining. Since the absence of silver staining is generally correlated with the absence of transcription, many copies of the amplified mouse rDNA may have been in a chromatin conformation in which they could not be transcribed. This was not associated with the extensive methylation seen in other amplified, inactive rDNA sequences.

Cellular uptake and localization of fluorescent derivatives of phorbol ester tumor promoters

The synthetic fluorescent derivatives of 12-O-tetradecanoylphorbol-13-acetate (TPA), dansyl-TPA, dansyl-TPA-20-acetate and dansyl-TPA-13-desacetate, have ID50 values in the [3H]PDBu binding assay of 2nM, 30nM and 1000nM respectively; the ID50 value of TPA is 4nM. Dansyl-TPA is also equipotent with TPA as an activator of protein kinase C(PKC) producing half maximum stimulation at 2nM. Dansyl-TPA-13-desacetate is almost as potent as dansyl-TPA, while dansyl-TPA-20-acetate is completely inactive as an activator of PKC. The cellular uptake of these fluorescent TPA derivatives tends to parallel their activity in the [3H]PDBu binding assay. Treatment of C3H 10T1/2 cells with 100nM dansyl-TPA results in intense fluorescence of the entire cytoplasm, while the nucleus is virtually devoid of fluorescence. The uptake of fluorescence is quenched by an excess of TPA. Thus, dansyl-TPA rapidly enters cells and binds to specific sites distributed throughout the cytoplasm. Presumably these sites reflect the cellular localization of phorbol ester receptors and protein kinase C.

Pattern of undermethylation of the major satellite DNA of mouse sperm

Enzymatic hydrolysis and base analysis by high performance liquid chromatography showed that mouse satellite DNA had 30-50% less 5-methylcytosine in sperm than in somatic tissue (1.59 mols % vs 2.40-3.11 mols %). Maxam-Gilbert sequencing and analysis of the intensity of the cytosine bands indicated that the level of methylation of the eight CpGs of the consensus sequence in sperm satellite DNA ranged from 0 to about 50%, considerably lower than the levels reported in somatic tissues. The Mn1I site containing one of these CpGs was cut much more extensively in satellite DNA from sperm than from liver, confirming the undermethylation of this site in sperm DNA.

The c-myc oncogene is translocated to the involved chromosome 12 in mouse plasmacytoma

Although it is known that the c-myc oncogene is rearranged in a head-to-head fashion with the immunoglobulin heavy chain locus in mouse plasmacytomas, it has not been clear whether the c-myc oncogene is translocated to the heavy chain locus on mouse chromosome 12 or whether the heavy chain locus is translocated to the c-myc locus on mouse chromosome 15. To determine which of these two possibilities is correct, we hybridized Chinese hamster fibroblasts with J558 mouse plasmacytoma cells that carry a reciprocal chromosome translocation between chromosomes 12 and 15, and we examined the segregating hybrids for the presence of the normal and rearranged mouse c-myc genes, for the presence of different regions of the mouse heavy chain locus, and for the presence of genes located on mouse chromosomes 12 and 15. The results of this analysis indicate that, as in human Burkitt lymphomas with the 8;14 chromosome translocation, the c-myc gene is translocated to the heavy chain locus in mouse plasmacytomas. Thus the orientation of the heavy chain locus on mouse chromosome 12 and of the c-myc gene on mouse chromosome 15 is the same as the orientation of the homologous loci in man.

DNA methylation is not increased in mouse-human somatic cell hybrids

The level of DNA methylation in three mouse-human cell lines that retained different human chromosomes and in the parental mouse and human lines has been determined by high-pressure liquid chromatography (HPLC). The level of methylation is similar in the hybrid and parental cells, indicating that interspecific somatic cell hybridization followed by preferential chromosome segregation can occur without an increase in overall DNA methylation.

Dosage compensation in mammals: why does a gene on the inactive X yield less product than one on the active X?

An expressed gene on the inactive mammalian X chromosome yields less product than the same gene on the active X. Characteristics of the inactive X which might be responsible for this are late replication, chromatin clumping, and altered patterns of DNA methylation. If an expressed gene on the inactive X is not replicated until late in S, it will be present in two copies for a shorter fraction of the cell cycle than its early replicating homologue and therefore yield less product. Alternatively, transcription may be slowed by a microenvironment of highly condensed chromatin or by an abnormal pattern of methylation of the DNA template. Experiments are proposed by which to test these and related hypotheses.

Restriction enzyme banding of mouse metaphase chromosomes

Fixed metaphase chromosomes from mouse strain RIII embryos or A9 cells were treated with a restriction endonuclease, followed by Giemsa staining. Alu I, Hinf I, or Mbo I treatment produced a C-band pattern, and Eco RII or Hae III produced a G-band plus C-band pattern. Ava II and Bst NI each produced a G-band pattern, but on most chromosomes only a small segment of each C-band, adjacent to the centromere, was stained. These tiny residual C-bands may contain a minor satellite located adjacent to the major satellite clusters.

Occurrence and evolution of homogeneously staining regions may be due to breakage-fusion-bridge cycles following telomere loss

Chromosomes with homogeneously staining regions (HSR) were analysed in a subclone of the H4 rat hepatoma cell line, where they represent amplification of the ribosomal RNA (rRNA) genes. Detailed G-band analysis of the subclone revealed that an HSR on the short arm of chromosome 3 became unstable and changed its position within the chromosome. The evolution of this marker chromosome was associated with the terminal deletion of the normal long arm of the HSR-bearing chromosome 3 and may have involved ring formation as a result of fusion between the HSR on the short arm and the broken end of the long arm. Evidence was obtained for breakage at different sites within the ring, producing chromosomes with HSRs located terminally on either the long arms or both arms. The terminally located HSR underwent elongation in some cells presumably as a result of a breakage-fusion-bridge cycle characteristic of instability due to telomeric loss. It is suggested that terminally located HSRs may generally occur this way.

Chromosome localization of highly repetitive human DNA's and amplified ribosomal DNA with restriction enzymes

Restriction endonucleases cut and partially removed DNA throughout fixed air-dried human metaphase chromosomes. Some enzymes produced a G-banding pattern; some revealed the presence of multiple chromosome-specific classes of highly repetitive DNA in C-band heterochromatin. Enzymes that produced the informative C-band patterns had recognition sequences that were four or five, but not six, base pairs long and did not contain a cytosine-guanine doublet. In both rat and human chromosomes, regions containing amplified ribosomal RNA genes were specifically removed by the restriction endonuclease Msp I.

The rat XC sarcoma cell line: ribosomal RNA gene amplification and banded karyotype

Ribosomal RNA gene amplification has been demonstrated in the rat XC sarcoma cell line. Cells of this rat line have a fairly stable karyotype with several unusual features, which have been clarified by in situ hybridization, silver staining, and binding of antibodies to 5-methylcytosine. There are one or two tiny acrocentric chromosomes containing transcriptionally active 18S and 28S ribosomal RNA (rRNA) genes. The short arm of one chromosome No. 12 has been replaced by a GC-rich, C-band negative, differentially staining region (DSR) containing an increased number of rRNA genes; most of these are transcriptionally inactive and located in regions containing highly methylated DNA. The short are of a small chromosome, probably a No. 20, has been replaced by a GC-rich, C-band negative, homogeneously staining region (HSR) that presumably represents amplification of a DNA sequence other than the 18S and 28S rRNA coding sequences. The DNA in this HSR is not enriched in 5-methylcytosine and neither is that in the HSRs of methotrexate-resistant Syrian hamster cells.

Is DNA methylation responsible for mammalian X chromosome inactivation?

MOHANDAS et al. (1981) have proposed that mammalian X chromosome inactivation involves segmental methylation of cytosine residues in the DNA at multiple sites along the X chromosome. Using antibodies specific for 5-methylcytosine, we have found no detectable difference in the extent of methylation of the DNA in the two X chromosomes of owl monkey or human females. Thus inactivation (facultative heterochromatization) of the X chromosome is not due to, or associated with, intense DNA methylation comparable to that seen in most constitutive heterochromatin.