Construction of a YAC contig and a STS map spanning at least seven megabasepairs in chromosome 5q34-35

Lu-Kuo, Jennifer M.; Pasller, Denis Le; Welssenbach, Jean; Chumakov, llya; Cohen, D.; Ward, David C.

doi:10.1093/hmg/3.1.99

Cited by 18 publications

(10 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Eight probes map to sites on human chromosome 5. 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(chromosome 4: Myers and Goold, 1992; chromosome 5: Lu-Kuo et al, 1994) and by mapping relative to R-bands (Yokota, H., unpublished data).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).…”

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

View full text Add to dashboard Cite

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-

show abstract

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

View full text Add to dashboard Cite

show abstract

“…Starting drug-sensitive cell lines either arose from a single cell (populations A6, C8, F5; Recombinant Cosmids and Chromosome-Specific Paints. Cosmids c5-4, c5-92, c5-8, and c5-9 were isolated from a chromosome-5-specific cosmid library (Integrated Genetics) and map to 5p15, 5q12-13, 5q21, and 5q35, respectively (38). DHFR-specific clones (191C10.3, 83C2.7.2, 112A3.1, and 325J23) were identified by screening a second chromosome 5-specific cosmid library (39) or a bacterial artificial chromosome (BAC) library (Research Genetics, Huntsville, AL; ref.…”

Section: Cell Lines and Development Of Independent Methotrexate-resismentioning

confidence: 99%

Amplification of the human dihydrofolate reductase gene via double minutes is initiated by chromosome breaks

Singer

Mesner

Friedman

et al. 2000

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

120

View full text Add to dashboard Cite

DNA sequence amplification is one of the most frequent manifestations of genomic instability in human tumors. We have shown previously that amplification of the dihydrofolate reductase (DHFR) gene in Chinese hamster cells is initiated by chromosome breaks, followed by bridge-breakage-fusion cycles that generate large intrachromosomal repeats; these are ultimately trimmed by an unknown process to smaller, more homogenous units manifested as homogenously staining chromosome regions (HSRs). However, in most human tumor cells, amplified DNA sequences are borne on unstable, extrachromosomal double minutes (DMs), which suggests the operation of a different amplification mechanism. In this study, we have isolated a large number of independent methotrexate-resistant human cell lines, all of which contained DHFR-bearing DMs. Surprisingly, all but one of these also had suffered partial or complete loss of one of the parental DHFR-bearing chromosomes. Cells in a few populations displayed what could be transient intermediates in the amplification process, including an initial HSR, its subsequent breakage, the appearance of DHFR-containing fragments, and, finally, DMs. Our studies suggest that HSRs and DMs both are initiated by chromosome breaks, but that cell types differ in how the extra sequences ultimately are processed and͞or maintained.

show abstract

“…YACs comprising the known contigs at 5q31.3-q33, 4,5 at 5q33, 10 and at 5q34-q35.1 11,12 were obtained from CEPH (Centre d'Etude du Polymorphisme Humain). Screening with anonymous markers 27,28 and genes assigned to 5q31.1-qter allowed the extension of these maps.…”

Section: Construction Of Yac Contig Of 5q313-qtermentioning

confidence: 99%

“…10 In addition, there are two YAC contigs spanning 7-10 Mbp of 5q34-q35. 11,12 This region encompasses the disease gene of craniosynostosis Boston type which was identified as the homeotic gene MSX2. 13,14 More than 50 genes [OMIM, http://www3.ncbi.nlm-.nih.gov:80/omim] and more than 130 expressed sequence tags (ESTs) have been assigned to distal 5q (Whitehead Institute/MIT Centre for Genome Research, http://www-genome.wi.mit.edu).…”

Section: Introductionmentioning

confidence: 99%

Integrated physical and transcript map of 5q31.3-qter

Kostrzewa

Dixon

et al. 1998

Eur J Hum Genet

View full text Add to dashboard Cite

We have constructed a physical and transcript map of 5q31.3-qter. The contig comprises 173 yeast artificial chromosomes (YACs) to which 159 sequence tagged sites (STSs), 47 expressed sequence tags (ESTs), and 32 genes were assigned. Previously published partial YAC contigs of the region have been refined and integrated. Given that the region contains 25 Mbp of DNA the average spacing of markers is approximately 100 kb.

show abstract

Construction of a YAC contig and a STS map spanning at least seven megabasepairs in chromosome 5q34-35

Cited by 18 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.

Amplification of the human dihydrofolate reductase gene via double minutes is initiated by chromosome breaks

Integrated physical and transcript map of 5q31.3-qter

Contact Info

Product

Resources

About