Fluorescence in Situ Hybridization Mapping of Human Chromosome 19: Cytogenetic Band Location of 540 Cosmids and 70 Genes or DNA Markers

Trask, Barbara J.; Fertitta, Anne; Christensen, Mari; Youngblom, Janey; Bergmann, Anne; Copeland, Alex; Jong, Pieter J. de; Mohrenweiser, Harvey W.; Olsen, Anne S.; Carrano, A.V.; Tynan, Katherine

doi:10.1006/geno.1993.1021

Cited by 78 publications

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“…The figure indicates the range of map position as determined b y measuring the distance between probe hybridization site and the p terminus (chromosome 4: Myers and Goold, 1992; chromosome 5: Lu-Kuo et al, 1994) and by mapping relative to R-bands (Yokota, H., unpublished data). Seven cosmids distributed along human chromosome 19 were chosen on the basis of their map position relative to cytogenetic bands (Trask et al, 1993b). The D N A contents of chromosomes 4, 5, and 19 are estimated to be 200, 190, and 65 Mbp, respectively (Trask et al, 1989b).…”

Section: B) (B) the Y-intercept Of This Relationship Is Approximatelmentioning

confidence: 99%

Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus.

Yokota

Engh

Hearst

et al. 1995

The Journal of Cell Biology

271

200

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Abstract. We determined the folding of chromosomes in interphase nuclei by measuring the distance between points on the same chromosome. Over 25,000 measurements were made in G0/G1 nuclei between DNA sequences separated by 0.15-190 megabase pairs (Mbp) on three human chromosomes. The DNA sequences were specifically labeled by fluorescence in situ hybridization. The relationship between mean-square interphase distance and genomic separation has two linear phases, with a transition at N2 Mbp. This biphasic relationship indicates the existence of two organizational levels at scales >100 kbp. On one level, chromatin appears to be arranged in large loops several Mbp in size. Within each loop, chromatin is randomly folded. On the second level, specific loop-attachment sites are arranged to form a supple, backbonelike structure, which also shows characteristic random walk behavior. This random walk/giant loop model is the simplest model that fully describes the observed large-scale spatial relationships. Additional evidence for large loops comes from measurements among probes in Xq28, where interphase distance increases and then locally decreases with increasing genomic separation. SIaORXLY after cell division, the mitotic chromosomes decondense and diffuse into the interphase nucleus. While individual chromosomes cannot be discerned, important processes related to chromosome function take place. Regulatory factors interact with chromatin, DNA is made accessible for transcription, RNA is produced and processed, DNA is replicated, and repairs are made of DNA strand breaks. When the chromosomes reappear for the next mitosis, they have been duplicated and prepared for rapid partitioning over the daughter cells. The complexity of these processes raises many questions about the large-scale organization of chromosomes and how this organization relates to cell function (e.g., Blobel, 1985;Manuelidis and Chen, 1990;Cook, 1991;Lawrence and Singer, 1991;De Boni, 1994).Diverse models, ranging from highly random to highly organized, have been proposed for the higher-order organization of interphase chromatin. These models variously involve irregularly folded fibers (DuPraw, 1965), radial loop structures (Manuelidis and Chen, 1990), giant loops (Ostashevsky and Lange, 1994), semirigid orientation ("Rabl" configuration) (Rabl, 1885;Comings, 1968), or random polymers confined by tethering or external forces (Hahnfeldt et al., 1993). Some models assign to chromo-

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Section: B) (B) the Y-intercept Of This Relationship Is Approximatelmentioning

confidence: 99%

Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus.

Yokota

Engh

Hearst

et al. 1995

The Journal of Cell Biology

271

200

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“…Gene order was determined by minimizing the number of recombination events required to account for the allele distribution patterns. Fluorescent in situ hybridization of cosmids to metaphase human chromosomes was carried out as described previously (21,22).…”

Section: Methodsmentioning

confidence: 99%

Genomic Organization, Chromosomal Localization, Tissue Distribution, and Biophysical Characterization of a Novel MammalianShaker-related Voltage-gated Potassium Channel, Kv1.7

Kálmán

Nguyen

Tseng-Crank

et al. 1998

Journal of Biological Chemistry

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We report the isolation of a novel mouse voltage-gated Shaker-related K ؉ channel gene, Kv1.7 (Kcna7/KCNA7). Unlike other known Kv1 family genes that have intronless coding regions, the protein-coding region of Kv1.7 is interrupted by a 1.9-kilobase pair intron. The Kv1.7 gene and the related Kv3.3 (Kcnc3/KCNC3) gene map to mouse chromosome 7 and human chromosome 19q13.3, a region that has been suggested to contain a diabetic susceptibility locus. The mouse Kv1.7 channel is voltage-dependent and rapidly inactivating, exhibits cumulative inactivation, and has a single channel conductance of 21 pS. It is potently blocked by noxiustoxin and stichodactylatoxin, and is insensitive to tetraethylammonium, kaliotoxin, and charybdotoxin. Northern blot analysis reveals ϳ3-kilobase pair Kv1.7 transcripts in mouse heart and skeletal muscle. In situ hybridization demonstrates the presence of Kv1.7 in mouse pancreatic islet cells. Kv1.7 was also isolated from mouse brain and hamster insulinoma cells by polymerase chain reaction.Ion channels that exhibit a variety of gating patterns and ion selectivity are critical elements that transduce signals in diverse cell types (1). Voltage-gated potassium-selective (Kv) 1 channels represent the largest family within this class of proteins (2), and perform many vital functions in both electrically excitable and nonexcitable cells. Following initiation of an action potential in nerve and muscle cells, Kv channels play the important role of repolarizing the cell membrane (1). Kv channels can also modulate hormone secretion, for example insulin release from pancreatic islet cells (3-6), and regulate calcium signaling during mitogen-stimulated activation of lymphocytes (7).Kv channels in mammalian cells are encoded by an extended family of at least nineteen genes (2). The largest subfamily, Kv1, is related to the fly Shaker gene and contains six members, Kv1.1-Kv1.6 (2). The Shaker gene has 21 exons, which can be alternatively spliced to generate at least five functionally distinct transcripts (8, 9). In contrast, the protein-coding regions of each of the six known mammalian Kv1 genes and the three known Xenopus homologues are contained in a single exon (2, 10), precluding alternative splicing as a means of generating functionally different proteins. The evolutionary significance of this pattern of organization remains a puzzle.Here we report the identification of a novel mammalian gene, Kv1.7 (Kcna7/KCNA7), that has a genomic organization distinct from the other members of the vertebrate Kv1 subfamily. We have defined the chromosomal location of this gene in the mouse and human genome, determined its tissue distribution, and characterized the biophysical and pharmacological properties of the cloned channel. mKv1.7, hKv1.7, hKv3.3, and hKv3.4 DNA Clones-Three overlapping genomic clones (KC225, KC254, and KC256) were isolated from an AKR/J mouse genomic library screened with a mixture of mKv1.1 and rKv1.5 cDNA probes, as described previously (10), and mapped by multiple and partial restrict...

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“…Four overlapping YAC clones (784E8, 411H1, 138D1 and 60D10) spanning an estimated 1.75 MB of this region were initially used as probes to screen a flow-sorted chromosome 19 arrayed cosmid library. A total of 85 cosmids were identified, assigned to bins and assembled into overlapping sets of cosmid clones based on fluorescent fingerprinting methods (Carrano et al 1989;Trask et al 1993). The location and relative position of each cosmid contig were confirmed using an STS screening strategy and FISH analysis of sperm pronuclei with representative cosmid clones from each contig as probes (Brandriff et al 1994;Brandriff et al 1991) (Figure 1b Since the BAC and chromosome-19 specific cosmid libraries originate from two different genomic sources, comparative EcoR1 digests between these two sources served as an important check-and-balance in confirming the integrity of the genomic clones used in the construction of a physical map of this region.…”

Section: Resultsmentioning

confidence: 99%

“…Comparative EcoR1 fluorescent fingerprinting between cosmid contigs and BACs as well as FISH hybridization on chromosomal preparations from human metaphase and sperm pronuclei (Trask et al 1993) were used as final criteria for assigning BACs to the 19p12 physical map.…”

Section: Physical Map Constructionmentioning

confidence: 99%

Sequence Ready Characterization of the Pericentromeric Region of 19p12

Eichler¹

2006

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Fluorescence in Situ Hybridization Mapping of Human Chromosome 19: Cytogenetic Band Location of 540 Cosmids and 70 Genes or DNA Markers

Cited by 78 publications

References 0 publications

Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus.

Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus.

Genomic Organization, Chromosomal Localization, Tissue Distribution, and Biophysical Characterization of a Novel MammalianShaker-related Voltage-gated Potassium Channel, Kv1.7

Sequence Ready Characterization of the Pericentromeric Region of 19p12

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