Physical mapping of the globin gene deletion in hereditary persistence of foetal haemoglobin (HPFH)

Bernards, R.; Flavell, R.A.

doi:10.1093/nar/8.7.1521

Cited by 147 publications

(62 citation statements)

References 11 publications

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“…Molecular studies indicate that independent transcriptional units are often separated by large intergenic regions (31). In the yeast mating-type loci (35) and mammalian hemoglobin loci (36,37), sequences at least 800 nucleotides from the transcriptional unit have some effect on expression. The mechanism of these distant effects is not clear.…”

Section: Discussionmentioning

confidence: 99%

Restriction map variation in the Adh region of Drosophila.

Langley¹,

Montgomery²,

Quattlebaum³

1982

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

105

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Restriction maps of a 12,000-nucleotide region containing the alcohol dehydrogenase (Adh) locus of the second chromosome of Drosophila were determined for (i) 18 independent second chromosome stocks of D. melanogaster established from several natural populations and (ii) five closely related Drosophila species. All of the detected map differences appear to lie outside the Adh coding block. Four polymorphic restriction sites and four insertion/deletion variants were identified among D. melanogaster chromosomes. The estimated heterozygosity per nucleotide site was 0.006. The relative distributions of restriction sites and insertion/deletion variations among subpopulations and species suggest that the insertion/deletion variation may be mildly deleterious.In recent years it has become possible to survey organisms for DNA sequence variation detected as differences in distributions of restriction endonuclease sites along specific regions of DNA (1). Both nuclear and cytoplasmic DNAs show variation in laboratory strains. These differences are important in localizing mutational lesions and functional regions. Restriction map variation also has been systematically surveyed in natural populations of several species, including Drosophila melanogaster, simulans, and virilis (2); the deer mouse (3); and man (4). These studies have allowed the estimation of .sequence diversity among individuals, populations, and species in DNA sequences that have been inaccessible (e.g., noncoding regions and mitochondrial genomes).Goldberg reported the cloning ofthe DNA in and around the alcohol dehydrogenase locus (Adh) of D. melanogaster (5). A single transcript was found from this region-that of Adh (5). The availability of this cloned sequence afforded us the opportunity to survey restriction map variation in this region. We report here the restriction maps from 18 independent second chromosome stocks of D. melanogaster established from several natural populations. We also present restriction maps for five other species closely related to D. melanogaster. From these maps, estimates of sequence diversity over a 12,000-nucleotide region can be made. Insertion/deletion variation was found both within and between species. The distribution over individuals, subpopulations, and species suggests some selective effect of insertions/deletions outside the transcriptional unit.MATERIALS AND METHODS Drosophila Stocks. Eighteen stocks of D. melanogaster homozygous for independent second chromosomes isolated from several natural populations were received from C. C. Laurie-Ahlberg (6). Ten

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Section: Discussionmentioning

confidence: 99%

Restriction map variation in the Adh region of Drosophila.

Langley¹,

Montgomery²,

Quattlebaum³

1982

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

105

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“…Blotting was as described by Southern (35) on nitrocellulose (Schleicher & Schuell Co.; ph 79). Nick translation of probes and filter hybridizations were as described previously (2,10). The specific activity of the probes was 2 x 108 to 5 x 108 cpm/,ug.…”

Section: Methodsmentioning

confidence: 99%

The chronic myelocytic cell line K562 contains a breakpoint in bcr and produces a chimeric bcr/c-abl transcript.

Grosveld¹,

Verwoerd²,

Agthoven³

et al. 1986

Mol. Cell. Biol.

161

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In the DNAs of all Ph1-positive chronic myelocytic leukemia patients studied to date, a breakpoint on chromosome 22 (the Ph1 chromosome) can be demonstrated with a probe from the bcr (breakpoint cluster region). Although the K562 cell line was established from cells of a chronic myelocytic leukemia patient, we have been unable to detect the Ph1 chromosome by cytogenetic means. Employing a probe from the 5' region of bcr, we have cloned an amplified Ph1 breakpoint fragment from K562. This demonstrates that K562 contains multiple remnants of a Ph1 chromosome with a breakpoint within bcr and thus may serve as a model system for the study of Ph1-positive chronic myelocytic leukemia at a molecular level. The isolation of bcr cDNA sequences shows that parts of bcr encode a protein. Employing K562, we demonstrate the presence of an abnormally sized mRNA species hybridizing to c-abl and to a bcr cDNA probe, indicating the possible consequence of the Ph1 translocation on a transcriptional level in chronic myelocytic leukemia. The isolation and sequencing of a cDNA containing the breakpoint area of this mRNA provide further evidence for its chimeric structure. Cloning of large stretches of chromosomal DNA flanking bcr and c-abl sequences in K562 and identification of the exons participating in the formation of the chimeric mRNA shows that a splice of at least 99 kilobases is made to fuse the 3' bcr exon to the 5' c-abl exon. Furthermore two chimeric cDNAs were isolated containing chromosome 9 sequences that map 43.5 kilobases downstream from the K562 breakpoint. These chromosome 9 sequences neither hybridize to the 8.5-kilobase chimeric c-abl mRNA nor to normal c-abl mRNAs in Hela cells and probably represent incorrect splicing products present in the K562 cell line.

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“…However, the amples of each form at these two sites. Second, from the discovery of very similar variants in different laboratory strains Genetics: Leigh Brown chromosomal puffing response involves a large region around the locus and there might be signals in flanking DNA-as pos-tulated for the /3-globin gene cluster (58,59)-whose spacing. from the coding region is important.…”

Section: Methodsmentioning

confidence: 99%

Variation at the 87A heat shock locus in Drosophila melanogaster

Brown¹

1983

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

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Restriction maps for 25 kilobases of DNA around the 87A7 heat shock locus have been determined in 29 chromosomes isolated from a natural population. The heterozygosity per nucleotide and the proportion of polymorphic nucleotide sites were estimated to be 0.0024 and 0.007, respectively. The mean number of insertional differences in this region between random pairs of chromosomes was 0.95. A significant amount of this variation was due to the insertion of large transposable elements. All the insertion/deletion events were found in a region less than 2 kilobases in size. This could either be due to nonrandom integration or to differences in the intensity of selection against DNA insertion at different sites.Several estimates of the level of variation in mitochondrial DNA from natural populations have now been made (1)(2)(3)(4)(5). This work has generally involved mapping restriction site polymorphisms and various approaches to the analysis of such data have now been published (6-10). The study of DNA-level variation in nuclear genes is technically more complex and to date three systematic population surveys have been completed-one on the ,B-globin region in man (11) and two on the alcohol dehydrogenase (Adh) locus in Drosophila melanogaster (12, 13). Much information has been collected at other loci in man (14-18) but, in general, those studies were conditioned by the prior discovery of variation and do not provide an unbiased estimate of its overall level. In this paper I present the results of a survey on variation in restriction map at the 87A7 heat shock locus in a single natural population of D. melanogaster.The major, 70,000-dalton, heat-inducible protein (hsp7o) in D. melanogaster is encoded at two cytogenetic loci, 87A7 and 87C1 (19-22). The coding sequence for the hsp70 mRNA is 2.1 kilobases (kb) long, contains no introns, and is duplicated at both loci. The duplicated sequences ("z element") include 400 bases 5' to the transcribed region which is conserved in all copies (20,(23)(24)(25). At 87A7, two z elements are arranged in a diverging orientation separated by a 1.2-kb spacer region (26,27 (28).In this paper I present data that indicate that the conservation of gene arrangement observed in this species subgroup has been achieved in spite of high levels of intraspecific insertion/deletion variation. Although such events may occur outside the regions required for correct expression of heat shock sequences (29, 30), they nevertheless appear to affect fitness sufficiently for them to be screened out by natural selection. MATERIALS AND METHODSTwenty-nine D. melanogaster third chromosomes were obtained from a large collection made in June 1977 from a natural population in Raleigh, N.C. Since that time the chromosomes have been maintained over In (3LR)TM6 Ubx. Methods used for setting up these lines have been described elsewhere (31). Before extracting DNA, the 87A region of each wild-derived chromosome was uncovered by crossing the balanced stock to a deficiency stock DJ(3R)karD3 and selecting +/de...

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Physical mapping of the globin gene deletion in hereditary persistence of foetal haemoglobin (HPFH)

Cited by 147 publications

References 11 publications

Restriction map variation in the Adh region of Drosophila.

Restriction map variation in the Adh region of Drosophila.

The chronic myelocytic cell line K562 contains a breakpoint in bcr and produces a chimeric bcr/c-abl transcript.

Variation at the 87A heat shock locus in Drosophila melanogaster

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