Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.30.2 (endonuclease)
 18,621 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Ribosomal RNA genes are organized in tandem arrays called nucleolus organizer regions (NORs). In a prior study, RFLP mapping on pulsed-field gels placed NOR2 at the northern tip of Arabidopsis thaliana chromosome 2. New polymorphisms have allowed the other NOR, NOR4, to be mapped to the northern tip of chromosome 4. To map NOR-associated loci, rDNA-specific cleavage by I-Ppol, an endonuclease with a 15 nucleotide recognition sequence involved in rDNA-homing of a mobile, self-splicing Group I intron in Physarum was exploited. I-Ppol digestion of A. thaliana genomic DNA liberated two telomere-containing fragments no larger than 13 kbp, and telomere polymorphisms identified using I-Ppol cosegregated with NOR2 and NOR4. Restriction mapping suggested that telomere-proximal rRNA genes are oriented with their 5' ends nearest the chromosome ends and their 3' ends nearest the centromere. This orientation was confirmed using the polymerase chain reaction to clone one of the telomere-rDNA junctions, most likely the junction on chromosome 4. The telomeric repeats join the terminal rRNA gene downstream of its promoter, suggesting that this first gene is inactive. Subtelomeric repetitive DNAs are absent at the telomere-rDNA junction. Localization of NOR2, NOR4 and their associated telomeres, TEL2N and TEL4N, respectively, provides end points for the genetic and physical maps of chromosomes 2 and 4.
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PMID:RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4. 882 Jun 10

Clonal rearrangements of the Ig heavy chain (IGH) locus consisting of either intrachromosomal (VDJ) rearrangements or interchromosomal translocations are a consistent feature of all B-cell malignancies and may be used both diagnostically and to monitor response to therapy. Many of these rearrangements are targeted to the IGHJ segments, but only some can be amplified with regular polymerase chain reaction (PCR) techniques. To permit PCR amplification of potentially all IGHJ rearrangements, we have devised a method incorporating self-ligation of restriction endonuclease-digested DNA fragments with long-distance PCR (long-distance, inverse PCR [LDI-PCR]). We show here, using only 4 nested oligonucleotide primers, the successful amplification and DNA sequencing of all IGHJ rearrangements up to 5.4 kb in length from a panel of 13 cases and cell lines of various types of B-cell malignancy. In all cases, both VDJ and DJ IGH rearrangements and translocation breakpoints were amplified. Six cases exhibited t(14;18)(q32;q21). All translocation breakpoints were cloned and sequenced. Three cases exhibited a rearrangement to the BCL2 major breakpoint region (MBR). However, 2 other cases exhibited rearrangements between the MBR and the minor cluster region (mcr). These 2 cases broke within 44 bp of each other, confirming the presence of an additional 3' BCL2 breakpoint cluster region. The final case fell immediately 3' of the 3' UTR of the BCL2 gene adjacent to an Alu repeat. No other BCL2 breakpoints within this region have been reported. Four cases exhibited t(11;14)(q13;q32). All 3 cases with translocations targeted to the IGHJ segments were successfully amplified and sequenced, including 1 case in which the BCL1 translocation could not be detected by DNA blot using the currently available probes. All three translocation breakpointsfell outside the BCL1 major translocation cluster between 20 and 40 kb telomeric and showed no clustering. Two of the three fell within or adjacent to Alu repeat regions. LDI-PCR is a simple and robust technique that allows PCR amplification of nearly all IGHJ rearrangements.
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PMID:Rapid molecular cloning of rearrangements of the IGHJ locus using long-distance inverse polymerase chain reaction. 931 Apr 98

African trypanosomes such as Trypanosoma brucei undergo antigenic variation in the bloodstream of their mammalian hosts by regularly changing the variant surface glycoprotein (VSG) gene expressed. The transcribed VSG gene is invariably located in a telomeric expression site. There are multiple expression sites and one way to change the VSG gene expressed is by activating a new site and inactivating the previously active one. The mechanisms that control expression site switching are unknown, but have been suggested to involve epigenetic regulation. We have found previously that VSG genes in silent (but not active) expression sites contain modified restriction endonuclease cleavage sites, and we have presented circumstantial evidence indicating that this is attributable to the presence of a novel modified base beta-D-glucosyl-hydroxymethyluracil, or J. To directly test this, we have generated antisera that specifically recognize J-containing DNA and have used these to determine the precise location of this modified thymine in the telomeric VSG expression sites. By anti J-DNA immunoprecipitations, we found that J is present in telomeric VSG genes in silenced expression sites and not in actively transcribed telomeric VSG genes. J was absent from inactive chromosome-internal VSG genes. DNA modification was also found at the boundaries of expression sites. In the long 50-bp repeat arrays upstream of the promoter and in the telomeric repeat arrays downstream of the VSG gene, J was found both in silent and active expression sites. This suggests that silencing results in a gradient of modification spreading from repetitive DNA flanks into the neighboring expression site sequences. In this paper, we discuss the possible role of J in silencing of expression sites.
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PMID:Localization of the modified base J in telomeric VSG gene expression sites of Trypanosoma brucei. 938 54

In the course of a search for microsatellites as centromeric polymorphic markers at the 3' ends of Alu or L1 elements, we observed a much higher frequency of L1 than Alu elements embedded within alpha satellite DNA. By sequence analysis of the L1 elements at their alphoid locus of insertion, we found that the insertion site was specific, with the consensus being (Py)2-10/ (Pu)3-7. All potential sites within the consensus alphoid 171-bp repeat are occupied by such elements. This confirms the finding by Feng et al. (1996; Human retrotransposon encodes a conserved endonuclease required for retrotransposition, Cell 87:905-916) that the progenitor L1 elements encode a site-specific endonuclease and that they generate copies that are inserted at these specific sites. The analysis of retrotransposed L1 elements within the alphoid domains of the acrocentric chromosomes showed that a number of loci are shared among all five acrocentrics. This sheds light on the manner in which centromeric regions of these chromosomes are exchanging information during evolution.
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PMID:Site-specific retrotransposition of L1 elements within human alphoid satellite sequences. 940 67

In order to elucidate the structural chromosome organization of the heterochromatic regions in sheep, we have used C-banding, silver-staining, sequential CDD technique and restriction endonuclease banding. By these banding techniques we obtained four fractions of repetitive DNA, the autosomal fractions A and B, the C fraction in the X chromosome, and the D fraction in the Y chromosome. Silver staining revealed active nucleolus organizer regions (NOR's) on the telomeric GC-rich areas of chromosomes 1, 2, 3, 4, and 25 which were digested with HaeIII restriction endonuclease.
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PMID:Characterization of the heterochromatic chromosome regions in sheep. 954 6

Telomerase from the ciliate Euplotes crassus incorporates G4T4telomeric repeats onto both telomeric and non-telomeric single-stranded DNA 3'-ends via reverse transcription of a templating domain in its RNA subunit. Here we describe an unusual mode of template copying that is characteristic of DNA synthesis onto non-telomeric 3'-ends in vitro . When dTTP was eliminated from telomerase reactions, telomeric primers or DNA products generated from the telomerase endonuclease were extended by precise copying of the RNA template. In contrast, telomerase catalyzed the addition of up to 13 dG residues onto primers with non-telomeric 3'-ends under the same reaction conditions. Introducing mismatches in the 3'-terminus of telomeric primers that reduced primer complementarity to the RNA template induced reiterative dG incorporation, indicating that the reaction is influenced by Watson-Crick base pair formation between the primer and the RNA template. Unexpectedly, the reiterative dG addition mode was confined to telomerase derived from developing cells that undergo new telomere formation. This reaction was not observed in vegetatively growing cells. We postulate that indiscriminate dG addition by telomerase occurs by reiterative copying of C residues in the telomerase RNA templating domain and reflects lateral instability of the primer-template interaction during de novo telomere formation.
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PMID:Reiterative dG addition by Euplotes crassus telomerase during extension of non-telomeric DNA. 970 11

The feasibility of using the fission yeast, Schizosaccharomyces pombe , as a host for the propagation of cloned large fragments of human DNA has been investigated. Two acentric vector arms were utilized; these carry autonomously replicating sequences ( ars elements), selectable markers ( ura4(+) or LEU2 ) and 250 bp of S. pombe terminal telomeric repeats. All cloning was performed between the unique sites in both vector arms for the restriction endonuclease Not I. Initially the system was tested by converting six previously characterized cosmids from human chromosome 11p13 into a form that could be propagated in S.pombe as linear episomal elements of 50-60 kb in length. In all transformants analysed these cosmids were maintained intact. To test if larger fragments of human DNA could also be propagated total human DNA was digested with Not I and size fractionated by pulsed field gel electrophoresis (PFGE). Fractions of 100-1000 kb were ligated to Not I-digested vector arms and transformed into S.pombe protoplasts in the presence of lipofectin. Prototrophic ura+leu+transformants were obtained which upon examination by PFGE were found to contain additional linear chromosomes migrating at between 100 and 500 kb with a copy number of 5-10 copies/cell. Hybridization analyses revealed that these additional bands contained human DNA. Fluorescent in situ hybridization (FISH) analyses of several independent clones indicated that the inserts were derived from single loci within the human genome. These analyses clearly demonstrate that it is possible to clone large fragments of heterologous DNA in fission yeast using this S.p ombe artificial chromosome system which we have called SPARC. This vector-host system will complement the various other systems for cloning large DNA fragments.
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PMID:A Schizosaccharomyces pombe artificial chromosome large DNA cloning system. 980 Dec 99

The pericentromeric heterochromatin contains tandemly repeated alphoid DNA sequences of about 171 bp in length. They are highly divergent from one chromosome to another due to chromosome specific alphoid subsets. In the present investigation, we used chromosome 18-specific centromeric probe (D18Z1) to evaluate the extent of pericentromeric heteromorphism classified by FISH-technique among 25 normal individuals. The hybridization signals were arbitrarily classified into five sizes when compared with the length of the short arm of chromosome 18. These are: negative (1), small (2), medium (3), large (4), and very large (5), with incidence of 0, 12, 24, 42, and 22 percent, respectively. Based on limited data, there were no chromosomes with negative signals while 42% of chromosome 18 had large-sized pericentromeric heterochromatin. The incidence observed earlier by restriction endonuclease Alu1 was different as compared to the present approach suggesting the complex heterogeneity of pericentric region of chromosome 18.
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PMID:Pericentromeric heteromorphism of human chromosome 18 as revealed by FISH-technique. 983 69

The addition of new telomeres to the ends of broken chromosomes, termed chromosome healing, has been extensively studied in unicellular organisms; however, its role in the mammalian cell response to double-strand breaks is unknown. A system for analysis of chromosome healing, which involves the integration of plasmid sequences immediately adjacent to a telomere, has been established in mouse embryonic stem cells. This "marked" telomere contains a neo gene for positive selection in G418, an I-SceI endonuclease recognition sequence for introducing double-strand breaks, and a herpes simplex virus thymidine kinase gene for negative selection with ganciclovir for cells that have lost the telomere. Transient expression of the I-SceI endonuclease results in terminal deletions involving telomeric repeat sequences added directly onto the end of the broken chromosome. The sites of addition of the new telomeres contain short regions of complementarity to telomeric repeat sequences. The most common site of addition is the last A of the ATAA 3' overhang generated by the I-SceI endonuclease, without the loss of a single nucleotide from the end of the chromosome. The next most frequent site involved 5 bp of complementarity, which occurred after the loss of four nucleotides from the end of the chromosome. The new telomeres are generally much shorter than in the parental cell line, and most increase in size with time in culture. These results demonstrate that chromosome healing is a mechanism for repair of chromosome breaks in mammalian cells.
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PMID:Chromosome healing in mouse embryonic stem cells. 1035 89

A half-YAC clone derived from human chromosome 17p was mapped at high resolution using cosmid subclone fingerprint analysis. Colinearity of the half-YAC with the telomeric human genomic DNA fragment was ascertained by RecA-assisted restriction endonuclease cleavage mapping. Previously isolated and radiation hybrid-mapped markers TEL17P37, TEL17P49, and TEL17P80 mapped 30-60 kb from the 17p terminus. This sequence-ready map permits high-resolution integration of genetic maps with the DNA sequences directly adjacent to the tip of human chromosome 17p, and will provide the cloned DNA required for ascertaining the nucleotide sequence of this subtelomeric region.
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PMID:A sequence-ready map of the human chromosome 17p telomere. 1036 53


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