Comparative cytogenetics of human chromosome 3q21.3 reveals a hot spot for ectopic recombination in hominoid evolution

Yue, Y.; Grossmann, Bärbel; Ferguson‐Smith, Malcolm A.; Yang, Fengtang; Haaf, Thomas

doi:10.1016/j.ygeno.2004.10.007

Cited by 20 publications

(21 citation statements)

References 29 publications

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“…Our findings confirm and add more evidence to Haaf and colleagues' hypothesis about evolutionary plasticity of the primate-specific chr 3 breakpoint regions (Tsend-Ayush et al 2004;Yue et al 2005.…”

Section: Tbrs Correspond To Evolutionary Break-prone Regionssupporting

confidence: 91%

“…The second "amplicon" was homologous to several chromosomal regions ( Fig. 2A), which are similar to the described 3q21.3 "SDamplicon" (Yue et al 2005). Three of the homologous segments were at the 75 Mb position (chr3:75), at the 131 Mb position (chr3:131), and at the 127 Mb position (chr3:127).…”

Section: Tumor Break-prone Segmental Duplication (Tbsd)supporting

confidence: 69%

“…4A). According to Yue et al (2005), this SD was missing on homologous chromosomes in siamang and Old World monkey as well, confirming that it expanded after the human-orangutan divergence. The RBSD probe, which was a combination of RP11-666K17 and RP11-139H7 (see Fig.…”

Section: The Tbsd Expanded In Homininaementioning

confidence: 80%

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Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions

Darai‐Ramqvist¹,

Sandlund²,

Müller³

et al. 2008

Genome Res.

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We have previously found that the borders of evolutionarily conserved chromosomal regions often coincide with tumor-associated deletion breakpoints within human 3p12-p22. Moreover, a detailed analysis of a frequently deleted region at 3p21.3 (CER1) showed associations between tumor breaks and gene duplications. We now report on the analysis of 54 chromosome 3 breaks by multipoint FISH (mpFISH) in 10 carcinoma-derived cell lines. The centromeric region was broken in five lines. In lines with highly complex karyotypes, breaks were clustered near known fragile sites, FRA3B, FRA3C, and FRA3D (three lines), and in two other regions: 3p12.3-p13 (∼75 Mb position) and 3q21.3-q22

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Section: Tbrs Correspond To Evolutionary Break-prone Regionssupporting

confidence: 91%

Section: Tumor Break-prone Segmental Duplication (Tbsd)supporting

confidence: 69%

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Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions

Darai‐Ramqvist¹,

Sandlund²,

Müller³

et al. 2008

Genome Res.

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“…For fiber FISH analysis, the chromosome 19-specific probe G248P81017A8: WI2-732B15 (38,354 base pairs [bp]) was used. DNA probe was labeled using a nick translation kit (Invitrogen), following the manufacturer's instructions, and FISH was performed essentially as described previously [27].…”

Section: Fluorescence In Situ Hybridization Analysismentioning

confidence: 99%

Robust, Persistent Transgene Expression in Human Embryonic Stem Cells Is Achieved with AAVS1-Targeted Integration

et al. 2007

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Silencing and variegated transgene expression are poorly understood problems that can interfere with gene function studies in human embryonic stem cells (hESCs). We show that transgene expression (enhanced green fluorescent protein [EGFP]) from random integration sites in hESCs is affected by variegation and silencing, with only half of hESCs expressing the transgene, which is gradually lost after withdrawal of selection and differentiation. We tested the hypothesis that a transgene integrated into the adenoassociated virus type 2 (AAV2) target region on chromosome 19, known as the AAVS1 locus, would maintain transgene expression in hESCs. When we used AAV2 technology to target the AAVS1 locus, 4.16% of hESC clones achieved AAVS1-targeted integration. Targeted clones expressed Oct-4, stage-specific embryonic antigen-3 (SSEA3), and Tra-1-60 and differentiated into all three primary germ layers. EGFP expression from the AAVS1 locus showed significantly reduced variegated expression when in selection, with 90% ؎ 4% of cells expressing EGFP compared with 57% ؎ 32% for randomly integrated controls, and reduced tendency to undergo silencing, with 86% ؎ 7% hESCs expressing EGFP 25 days after withdrawal of selection compared with 39% ؎ 31% for randomly integrated clones. In addition, quantitative polymerase chain reaction analysis of hESCs also indicated significantly higher levels of EGFP mRNA in AAVS1-targeted clones as compared with randomly integrated clones. Transgene expression from the AAVS1 locus was shown to be stable during hESC differentiation, with more than 90% of cells expressing EGFP after 15 days of differentiation, as compared with ϳ30% for randomly integrated clones. These results demonstrate the utility of transgene integration at the AAVS1 locus in hESCs and its potential clinical application. STEM CELLS 2008;26: 496 -504 Disclosure of potential conflicts of interest is found at the end of this article.

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“…The breakpoint syntenic to HSA3p12.3 is located in the 360-kb interval between BACs RP11-642N14 and CTD-2026G6 (Yue et al, 2005a). The breakpoint at HSA3q21.3 is located in a 280-kb interval between RP11-93K22 and RP11-77P16 (Yue et al, 2005b). The 3p12.3 and 3q21.3 breakpoint regions share DNA segments of 1 110 kb length with 1 90 % sequence similarity, containing four and two OR genes of the 7E subfamily, respectively ( Fig.…”

Section: E Or-containing Regions In the Human Genome Are Associated mentioning

confidence: 99%

7E olfactory receptor gene clusters and evolutionary chromosome rearrangements

Yue¹,

Haaf²

2005

Cytogenet Genome Res

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Olfactory receptor (OR) genes of the 7E subfamily have been duplicated to multiple regions throughout the human genome. Segmental duplications containing 7E OR genes have been associated with both pathological and evolutionary chromosome rearrangements. Many of these breakpoint regions coincide with breaks of chromosomal synteny in the mouse, rat and/or chicken genomes. Collectively, these data suggest that 7E OR-containing regions represent hot spots of genomic instability.

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Comparative cytogenetics of human chromosome 3q21.3 reveals a hot spot for ectopic recombination in hominoid evolution

Cited by 20 publications

References 29 publications

Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions

Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions

Robust, Persistent Transgene Expression in Human Embryonic Stem Cells Is Achieved with AAVS1-Targeted Integration

7E olfactory receptor gene clusters and evolutionary chromosome rearrangements

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