Structure of the terminal 300 kb of DNA from human chromosome 21q

Reston, James; Hu, Xue-Lan; Macina, Roberto A.; Spais, Chrysanthe; Riethman, Harold

doi:10.1016/0888-7543(95)80079-2

Cited by 20 publications

(11 citation statements)

References 22 publications

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“…Data on polymorphic telomeres are from Riethman, unpubl. results;Wilke et al (1991); Ijdo et al (1992); Cook et al (1994); Macina et al (1994Macina et al ( , 1995; Martin-Gallardo et al (1995); Reston et al (1995); Monfouilloux et al (1998);Trask et al (1998);van Overveld et al (2000). sequences were not already identified by the BLAST analysis described above; for the most part, the regions identified by WSSD were consistent with our analyses, although each method missed a small percentage of the duplications.…”

Section: Sequence Organization Of Subtelomeric Dnasupporting

confidence: 80%

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Riethman¹,

Ambrosini²,

Castañeda³

et al. 2004

Genome Res.

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115

119

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Physical mapping data were combined with public draft and finished sequences to derive subtelomeric sequence assemblies for each of the 41 genetically distinct human telomere regions. Sequence gaps that remain on the reference telomeres are generally small,well-defined,and for the most part,restricted to regions directly adjacent to the terminal (TTAGGG)n tract. Of the 20.66 Mb of subtelomeric DNA analyzed, 3.01 Mb are subtelomeric repeat sequences (Srpt),and an additional 2.11 Mb are segmental duplications. The subtelomeric sequence assemblies are enriched >25-fold in short,internal (TTAGGG)n-like sequences relative to the rest of the genome; a total of 114 (TTAGGG)n-like islands were found,55 within Srpt regions,35 within one-copy regions,11 at one-copy/Srpt or Srpt/segmental duplication boundaries,and 13 at the telomeric ends of assemblies. Transcripts were annotated in each assembly,noting their mapping coordinates relative to their respective telomere and whether they originate in duplicated DNA or single-copy DNA. A total of 697 transcripts were found in 15.53 Mb of one-copy DNA,76 transcripts in 2.11 Mb of segmentally duplicated DNA,and 168 transcripts in 3.01 Mb of Srpt sequence. This overall transcript density is similar (within ∼10%) to that found genome-wide. Zinc finger-containing genes and olfactory receptor genes are duplicated within and between multiple telomere regions

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Section: Sequence Organization Of Subtelomeric Dnasupporting

confidence: 80%

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Riethman¹,

Ambrosini²,

Castañeda³

et al. 2004

Genome Res.

Self Cite

115

119

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“…Position effects of telomere proximity upon transcriptional activity have been demonstrated in yeast (Gottschling et al 1990), and position effects have likewise been observed in Drosophila when euchromatic genes are juxtaposed to subtelomeric heterochromatin (Karpen and Spradling 1992). It is possible that the expression of genes located within human subtelomeric regions (Vyas et al 1992;Saccone et al 1993;Cook et al 1994;Reston et al 1995) may also be affected by telomere proximity and the variable presence of heterochromatin-like structures, although at present no direct experimental evidence exists to support this notion.…”

mentioning

confidence: 78%

“…The region of cloned DNA farthest from the molecular telomere is typically least likely to contain subtelomeric repeats and most likely to contain chromosome-specific sequences (Riethman et al 1989;Macina et al 1994;Negorev et al 1994;Reston et al 1995). Therefore, DNA from the centromeric end of each of the five half-YAC inserts was isolated and used to develop both a hybridization probe and a PCR assay (see Methods; summarized in Table 1).…”

Section: Assay Developmentmentioning

confidence: 99%

“…Finely mapped, discrete subtelomeric probes are required for these sorts of studies. to several megabases (Ferrin andCamerini-Otero 1991, 1994), and have provided an efficient means of m a p p i n g DNA from half-YACs (Macina et al 1994;Negorev et al 1994;Reston et al 1995). In this study telomeric fragments of human chromosomes 2p, 6q, 8q, 12q, and 18q cloned using the half-YAC system were analyzed using RecAassisted restriction endonuclease (RARE) cleavage mapping.…”

mentioning

confidence: 99%

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Molecular cloning and RARE cleavage mapping of human 2p, 6q, 8q, 12q, and 18q telomeres.

Macina¹,

Morii²,

Hu³

et al. 1995

Genome Res.

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Large terminal fragments of human chromosomes 2p, 6q, 8q, 12q, and 18q were cloned using yeast artificial chromosomes (YACs). RecA-assisted restriction endonuclease {RARE] cleavage analysis of genomic DNA samples from II unrelated individuals using YAC-derived probes confirmed the telomeric localizations of the half-YACs studied. The cloned fragments provide telomeric closure of maps for the respective chromosome arms and will supply the reagents needed for analyzing and sequencing these distal subtelomeric regions.

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“…These complexes protected the selected sites from enzymatic methylation, and after dissociation of the complexes, restriction enzyme cleavage was limited to the selected unmethylated sites. We later improved the method to cleave fragments greater than a megabase in size (2), and it has been used by numerous investigators to map and manipulate large segments of DNA (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18). We have now developed a complementary method that is functionally the reverse of RARE cleavage, in that the method uses RecA protein and oligonucleotides to direct the sequence-specific ligation of DNA.…”

mentioning

confidence: 99%

Sequence-specific ligation of DNA using RecA protein

Ferrin¹,

Camerini‐Otero²

1998

Proc. Natl. Acad. Sci. U.S.A.

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A method is described that allows the sequence-specific ligation of DNA. The method is based on the ability of RecA protein from Escherichia coli to selectively pair oligonucleotides to their homologous sequences at the ends of fragments of duplex DNA. These three-stranded complexes were protected from the action of DNA polymerase. When treated with DNA polymerase, unprotected duplex fragments were converted to fragments with blunt ends, whereas protected fragments retained their cohesive ends. By using conditions that greatly favored ligation of cohesive ends, a second DNA fragment could be selectively ligated to a previously protected fragment of DNA. When this second DNA was a vector, selected fragments were preferentially cloned. The method had sufficient power to be used for the isolation of single-copy genes directly from yeast or human genomic DNA, and potentially could allow the isolation of much longer fragments with greater fidelity than obtainable by using PCR.In 1991, we described RecA-assisted restriction endonuclease (RARE) cleavage (1). The method was a general and efficient way to target restriction enzyme cleavage to unique, predetermined sites. The method utilized the ability of RecA protein to pair oligonucleotides to homologous sequences in duplex DNA to form three-stranded complexes. These complexes protected the selected sites from enzymatic methylation, and after dissociation of the complexes, restriction enzyme cleavage was limited to the selected unmethylated sites. We later improved the method to cleave fragments greater than a megabase in size (2), and it has been used by numerous investigators to map and manipulate large segments of DNA (3-18). We have now developed a complementary method that is functionally the reverse of RARE cleavage, in that the method uses RecA protein and oligonucleotides to direct the sequence-specific ligation of DNA. It represents the first report of targeting of the action of DNA ligase. When one of the DNA segments is a vector, it is possible to perform sequence-specific cloning of a selected genomic DNA segment. When used in this manner, we refer to the technique as RecA-assisted cloning (RAC).Several methods are available to amplify genomic DNA and to isolate selected fragments in a pure form. The most widely used method is PCR. A major limitation of PCR is the small size that may be reliably amplified, although improvements have allowed amplification of up to 20-30 kb by using human genomic DNA as the template (19-21). The other widely used general method to isolate genomic fragments involves constructing and screening DNA libraries. Libraries based on phage or cosmid vectors have long been in use, and several other vectors are now available for cloning large (Ͼ100 kb) segments of DNA in the form of yeast artificial chromosomes, bacterial artificial chromosomes, and P1 phage-derived artificial chromosomes. Such libraries, however, are tedious to construct and screen.Several groups have described strategies to use RecA protein from E. coli to scr...

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Structure of the terminal 300 kb of DNA from human chromosome 21q

Cited by 20 publications

References 22 publications

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Molecular cloning and RARE cleavage mapping of human 2p, 6q, 8q, 12q, and 18q telomeres.

Sequence-specific ligation of DNA using RecA protein

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