New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries

Zabarovsky, Eugene R.; Boldog, Ferenc; Erlandsson, Rikard; Kashuba, Vladimir I.; Allikmets, Rando; Marcsek, Z; Kisselev, Lev L.; Stanbridge, Eric J.; Klein, George; Sümegi, János; Winberg, Gösta

doi:10.1016/0888-7543(91)90029-e

Cited by 30 publications

(23 citation statements)

References 32 publications

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“…The phenotype of the lymphoblastoid cell line (LCL) CBM1-Ral-Sto (CBM1) is nonmalignant, although it is immortalized in vitro by EBV, and it displays an EBV latency type III pattern (19,20). By contrast, in the cell line Rael, the Burkitt's lymphoma (BL) phenotype represents a malignant state (tumorigenic in immunocompromised mice) and is associated with the EBV type I latency pattern (19).…”

Section: Significancementioning

confidence: 99%

Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape

Wennborg

Aurell

et al. 2016

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

107

100

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The observed intercellular heterogeneity within a clonal cell population can be mapped as dynamical states clustered around an attractor point in gene expression space, owing to a balance between homeostatic forces and stochastic fluctuations. These dynamics have led to the cancer cell attractor conceptual model, with implications for both carcinogenesis and new therapeutic concepts. Immortalized and malignant EBV-carrying B-cell lines were used to explore this model and characterize the detailed structure of cell attractors. Any subpopulation selected from a population of cells repopulated the whole original basin of attraction within days to weeks. Cells at the basin edges were unstable and prone to apoptosis. Cells continuously changed states within their own attractor, thus driving the repopulation, as shown by fluorescent dye tracing. Perturbations of key regulatory genes induced a jump to a nearby attractor. Using the Fokker-Planck equation, this cell population behavior could be described as two virtual, opposing influences on the cells: one attracting toward the center and the other promoting diffusion in state space (noise). Transcriptome analysis suggests that these forces result from high-dimensional dynamics of the gene regulatory network. We propose that they can be generalized to all cancer cell populations and represent intrinsic behaviors of tumors, offering a previously unidentified characteristic for studying cancer.cancer cell attractor | cell heterogeneity | edge cells | gene regulatory network | cell population dynamics

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Section: Significancementioning

confidence: 99%

Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape

Wennborg

Aurell

et al. 2016

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

107

100

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“…Clones specific to the 11q23.3-qter region were selected from Alu and L1-positive clones by hybridization to J1-kc DNA. A Not I jumping library of R229-3A was constructed by the method of Zabarovsky et al (1991). Lambda phage clones (LN-, LB-, LJ-numbered clones) were isolated from a total human genomic library (Stratagene) using N-clones, boundary clones, and jumping clones as a probe, respectively.…”

Section: Not I Linking Clonesmentioning

confidence: 99%

A complete Not I restriction map covering the entire long arm of human chromosome 11

et al. 1997

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“…Chromosome 21 is perhaps the most completely mapped autosome, and here macrorestriction mapping has provided a valuable supplement to YAC cloning procedures (22). Construction of maps by correlation of linking and jumping clones with macrorestriction fragments is a theoretically attractive way to construct physical maps (23)(24)(25), although limited by the uneven distribution of rare sites along a chromosome and the tendency of most rare cutting sites to be subject to blocking by methylation in vivo. In this regard the largest jumps reported in the literature are in the range of 0.5 megabase (25,26).…”

Section: Discussionmentioning

confidence: 99%

“…The amplified DNA (0. 25 ,ug/ml) was subjected to a second round of selection hybridization as mentioned above. A second set of primers nested with the previous set of primers (6) was used for this amplification.…”

mentioning

confidence: 99%

Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers.

Kandpal

Weissman

1994

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

203

172

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We describe a simple and rapid method for contructing small-insert genomic libraries highly enriched for dimeric, trimeric,and tetrameric nucleotide repeat motifs. The approach involves use of DNA inserts recovered by PCR amplification of a small-insert sonicated genomic phage library or by a single-primer PCR amplification of Mbo I-digested and adaptor-ligated genomic DNA. The genomic DNA inserts are heat denatured and hybridized to a biotinylated oligonucleotde.

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New strategy for mapping the human genome based on a novel procedure for construction of jumping libraries

Cited by 30 publications

References 32 publications

Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape

Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape

A complete Not I restriction map covering the entire long arm of human chromosome 11

Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers.

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