DNA hypomethylation and unusual chromosome instability in cell lines from ICF syndrome patients

The ICF syndrome (immunodeficiency, centromeric region instability, facial anomalies) is a unique DNA methylation deficiency disease diagnosed by an extraordinary collection of chromosomal anomalies specifically in the vicinity of the centromeres of chromosomes 1 and 16 (Chr1 and Chr16) in mitogen-stimulated lymphocytes. These aberrations include decondensation of centromere-adjacent (qh) heterochromatin, multiradial chromosomes with up to 12 arms, and whole-arm deletions. We demonstrate that lymphoblastoid cell lines from two ICF patients exhibit these Chr1 and Chr16 anomalies in 61% of the cells and continuously generate 1qh or 16qh breaks. No other consistent chromosomal abnormality was seen except for various telomeric associations, which had not been previously noted in ICF cells. Surprisingly, multiradials composed of arms of both Chr1 and Chr16 were favored over homologous associations and cells containing multiradials with 3 or >4 arms almost always displayed losses or gains of Chr1 or Chr16 arms from the metaphase. Our results suggest that decondensation of 1qh and 16qh often leads to unresolved Holliday junctions, chromosome breakage, arm missegregation, and the formation of multiradials that may yield more stable chromosomal abnormalities, such as translocations. These cell lines maintained the abnormal hypomethylation in 1qh and 16qh seen in ICF tissues. The ICF-specific hypomethylation occurs in only a small percentage of the genome, e.g., ICF brain DNA had 7% less 5-methylcytosine than normal brain DNA. The ICF lymphoblastoid cell lines, therefore, retain not only the ICF-specific pattern of chromosome rearrangements, but also of targeted DNA hypomethylation. This hypomethylation of heterochromatic DNA sequences is seen in many cancers and may predispose to chromosome rearrangements in cancer as well as in ICF.     

Bovine DNA contains a single major family of interspersed repetitive sequences

A major family of short, interspersed, repeated sequences in the bovine genome has been characterized. This family makes up the majority of all non-satellite repetitive DNA or about 6% of the bovine genome. It is estimated that there are at least 600 000 copies of this family interspersed among non-repetitive DNA sequences. Sequence analysis shows that this family includes sequences reported previously by Watanabe et al. (Nucleic Acids Res. 10, 1459-1469, 1982) and is distantly related to the human Alu sequence family.     

DNA synthesis in Bloom's syndrome fibroblasts

The relationship between relative rates of DNA synthesis and DNA content in Bloom's syndrome fibroblasts (BS cells) was investigated by flow cytometry. The cells were pulse labelled with 5-bromo-2'-deoxyuridine (BrdU). The BrdU content and cellular DNA content of individual BS cells were simultaneously measured by flow cytometry in which the cells were double-stained by a FITC-conjugated anti BrdU monoclonal antibody (mAb) for the BrdU content (green) and by PI (propidium iodide) (red) for total DNA content. Their red fluorescence histograms were analysed by a microcomputer to evaluate the cell fractions of each S compartment. The BrdU uptake in the early S phase of BS cells was lower than that of normal cells (fibroblasts from skin of a normal human), whereas the uptake in the middle and late S phase was essentially the same as that of normal cells. The early S phase in BS cells accounted for over 50% of the S phase cells. These findings suggest that, in comparison with normal cells, the rate of DNA synthesis in the early S phase of BS cells is lower, but is identical to controls in the middle and late S phases.     

Specific association of repetitive DNA sequences with major histocompatibility genes.

The DNA sequence organization of a 17.8-kilobase segment of porcine DNA, containing a functional major histocompatibility (MHC) gene, has been studied. The DNA flanking the MHC gene contains at least 10 distinct repetitive DNA sequence elements, each of which occurs only once within the 17.8-kilobase DNA segment. Their reiteration frequencies in the genome range from 10(2) to 10(4). The genomic organization of seven of these sequence elements has been examined; all are interspersed with other, unrelated DNA sequences. These seven repeated sequences are not generally associated in the genome. However, they appear to be nonrandomly linked in MHC-associated regions of the genome: at least two additional DNA segments containing MHC-homologous DNA also contain sequences homologous to DNA fragments bearing the seven different repeats. Of the seven sequences, four can be detected in splenic total RNA. These results suggest that these repeated elements are specifically associated with the MHC locus.     

DNA synthesis in Bloom's syndrome fibroblasts

Abstract. The relationship between relative rates of DNA synthesis and DNA content in Bloom's syndrome fibroblasts (BS cells) was investigated by flow cytometry. The cells were pulse labelled with 5-bromo-2'-deoxyuridine (BrdU). The BrdU content and cellular DNA content of individual BS cells were simultaneously measured by flow cytometry in which the cells were double-stained by a FITC-conjugated anti BrdU monoclonal antibody (mAb) for the BrdU content (green) and by PI (propidium iodide) (red) for total DNA content. Their red fluorescence histograms were analysed by a microcomputer to evaluate the cell fractions of each S compartment. The BrdU uptake in the early S phase of BS cells was lower than that of normal cells (fibroblasts from skin of a normal human), whereas the uptake in the middle and late S phase was essentially the same as that of normal cells. The early S phase in BS cells accounted for over 50% of the S phase cells. These findings suggest that, in comparison with normal cells, the rate of DNA synthesis in the early S phase of BS cells is lower, but is identical to controls in the middle and late S phases.     

Human chromosome-specific repetitive DNA sequences: novel markers for genetic analysis

Two recombinant DNA clones that are localized to single human chromosomes were isolated from a human repetitive DNA library. Clone pHuR 98, a variant satellite 3 sequence, specifically hybridizes to chromosome position 9qh. Clone pHuR 195, a variant satellite 2 sequence, specifically hybridizes to chromosome position 16qh. These locations were determined by fluorescent in situ hybridization to metaphase chromosomes, and confirmed by DNA hybridizations to human chromosomes sorted by flow cytometry. Pulsed field gel electrophoresis analysis indicated that both sequences exist in the genome as large DNA blocks. In situ hybridization to intact interphase nuclei showed a well-defined, localized organization for both DNA sequences. The ability to tag specific human autosomal chromosomes, both at metaphase and in interphase nuclei, allows novel molecular cytogenetic analyses in numerous basic research and clinical studies.     

The relationship between repetitive DNA and chromosomal bands in man

The relationship between chromosomal bands and repetitious DNA has been investigated by means of the quinacrine fluorescence technique and in situ hybridization with c-RNA to different fractions of repetitive DNA. A comparison of the Q bands with the labelling patterns obtained showed a preferential distribution of repetitive DNA's at Cot's ranging from 0 to 5 in those regions that are Q band positive. A distinct labelling was also observed in the pericentromeric regions and in some telomeres. It is suggested that the distribution of repetitive DNA along the chromosomes plays an important role in band formation.     

Analysis of major repetitive DNA sequences in the dog (Canis familiaris) genome

A systematic screening and analysis of repeated DNA sequences from a dog genomic library composed of small DNA inserts enabled us to characterize abundant canine repetitive DNA families. Four main families were identified: i) a group of highly repeated tRNA-derived short interspersed repetitive DNA elements (tRNA-SINEs); ii) another type of SINE-like element that was mainly found inserted into long interspersed repetitive elements (LINEs); iii) LINEs of the L1 type; and iv) satellite or satellite-like DNA. Surprisingly, no SINEs derived from 7SL RNA were found in the dog genome. These data should help in the analysis of canine DNA sequences and in the design of canine genome mapping reagents. Received: 4 November 1998 / Accepted: 2 February 1999     

Interspersion of repetitive sequences in rat liver DNA

In rat liver DNA, which contains only 20% repetitive sequences, a close interspersion of repetitive and unique sequences is found in about 35 % of the total DNA. The mean length of repetitive and unique alternating sequences is respectively 230 and 400 base pairs.     

Bloom's syndrome: DNA replication in cultured fibroblasts and lymphocytes

Summary Analysis of DNA fiber autoradiograms from Bloom's syndrome skin fibroblasts and blood lymphocytes shows a retarded rate of replication fork movement compared to normal adult controls. Other measurements from the autoradiograms—replication unit length, incidence of bidirectional replication, and degree of initiation synchrony—are normal in Bloom's syndrome cells. These results suggest that a slow rate of fork movement is a specific manifestation of defective DNA synthesis in all Bloom's syndrome cells.     

Homologies of repetitive DNA sequences among Crustacea

The interrelationships of a number of Crustacea were measured by nucleic acid hybridization techniques, with special emphas is on the question of whether GC-rich satellite DNA contains nucleotide sequences homologous to sequences found in other Crustacea with and without similar satellite DNAs. Repetitious sequences from both main-band DNA and GC-rich satellite DNA from the land crab, Gecarcinus lateralis, were hybridized to the total DNAs of crustaceans ranging from the brine shrimp (Subclass: Branchiopoda) to the North American lobster (Homarus americanus, Subclass: Malacostraca; Suborder: Repantia; Section: Macrura) and the true crabs (Subclass: Malacostraca; Suborder: Reptantia; Section: Brachyura). Approximately half of the Gecarcinus repetitious main-band DNA sequences were found to be represented in the DNA of the other true crabs, while a lesser but still significant amount of homology (5 to 10%) to the GC-rich satellite DNA was observed. We also observed a significant amount of homology of the Gecarcinus GC-rich satellite to other crustacean DNAs, even at the level of a different taxonomic Section. This is the first observation of hybrid formation between a purified satellite and DNAs from other organisms under stringent hybridization conditions.Research sponsored by the U.S. Atomic Energy Commission under contact with the Union Carbide Corporation.Research performed while an Oak Ridge Graduate Fellow under appointment from the Oak Ridge Associated Universities in partial fulfillment of the Ph. D. degree from the University of Tennessee, Knoxville, Tennessee.     

Analysis of rat repetitive DNA sequences.

Parameters of repetitive sequence organization have been measured in the rat genome. Experiments using melting, hydroxylapatite binding, and single strand specific nuclease digestion have been used to measure the number, length, and arrangement of repeated DNA sequences. Renaturation and melting or S1 nuclease digestion of 1.0 kbp DNA fragment show about 20% of rat DNA sequences are 3000-fold repeated. Renatured duplexes from 4.0 kbp DNA fragments display two repetitive size fractions after nuclease digestion. About 60% of the repeated sequences are 0.2-0.4 kbp long while the remainder are longer than 1.5 kbp. The arrangement of the repeated sequences has been measured by hydroxylapatite fractionation of DNA fragments of varying lengths bearing a repeated sequence. Repeated DNA sequences are interspersed among 2.5 kbp long nonrepeated sequences throughout more than 70% of the rat genome. There are approximately 350 different 3000-fold short repeated sequences in the rat interspersed among 600,000 nonrepeated DNA sequences.     

Centromeric repetitive DNA sequences in the genus Brassica

Representatives of two major repetitive DNA sequence families from the diploid Brassica species B. campestris and B. oleracea were isolated, sequenced and localized to chromosomes by in situ hybridization. Both sequences were located near the centromeres of many chromosome pairs in both diploid species, but major sites of the two probes were all on different chromosome pairs. Such chromosome specificity is unusual for plant paracentromeric repetitive DNA. Reduction of stringency of hybridization gave centromeric hybridization sites on more chromosomes, indicating that there are divergent sequences present on other chromosomes. In tetraploid species derived from the diploids, the number of hybridization sites was different from the sum of the diploid ancestors, and some chromosomes had both sequences, indicating relatively rapid homogenization and copy number evolution since the origin of the tetraploid species.     

Highly repetitive DNA sequences in cyanobacterial genomes.

We characterized three distinct families of repeated sequences in the genome of the cyanobacterium Calothrix sp. strain PCC 7601. These repeated sequences were present at a level of about 100 copies per Calothrix genome and consisted of tandemly amplified heptanucleotides. These elements were named short tandemly repeated repetitive (STRR) sequences. We used the three different Calothrix STRR sequences as probes to perform Southern hybridization experiments with DNAs extracted from various cyanobacterial strains, Bacillus subtilis, and Escherichia coli. The three different STRR sequences were found as repetitive genomic DNA components specific to the heterocystous strains tested. The role of the STRR sequences, as well as their possible use in taxonomic studies, is discussed.     

Similarity and divergence among rodent repetitive DNA sequences

Summary We have analyzed the sequence of 63 B1 and 71 B2 repetitive elements from published data base sequences. The sequences conform to previously published consensus sequences, but are not identical to them. The B2 sequences show seven regions of high variability between family members, which we show points to the B2 family containing subfamilies; no similar evidence is found for subfamilies of the B1 family. The comparisons show no evidence for the emergence of species-specific variants of B1 or B2 sequences since the separation of murine and hamster lines of descent, nor of their concerted evolution within species in the last 10 million years.     

DNA,FISH and complementation studies in ICF syndrome: DNA hypomethylation of repetitive and single copy loci and evidence for a trans acting factor

ICF syndrome (ICFS) is a rare immunodeficiency disorder characterized by instability of the pericentromeric heterochromatin predominantly of chromosomes 1 and 16. DNA methylation studies in two unrelated ICFS patients provide further evidence for a marked hypomethylation of satellite 2 DNA. The ICFS-specific disturbances of chromatin structure take place within the satellite 2 DNA regions, as demonstrated by fluorescence in situ hybridization analysis. Moreover, methylation studies of genomic imprinted loci D15S63, D15S9, and H19 have revealed hypomethylation to different degrees in both patients; this provides evidence for hypomethylation at autosomal single copy loci in ICFS. Cell fusion experiments have revealed a distinct reduction of chromosomal abnormalities in ICFS cells after fusion with normal cells, suggesting that the abnormalities are caused by the loss of function of an as yet unknown trans acting factor. Although it is now clear that wide-spread DNA hypomethylation is a characteristic feature of ICFS, neither the cause and mechanism of hypomethylation nor their relationship to the clinical symptoms is known. We speculate that a phenotypic effect might result from tissue-dependent abnormal gene expression and/or from a possible structural disturbance of DNA domains, which, with respect to the immunodeficiency, partially prevents the normal somatic recombinations in immunologically active cells.