Related Experiment Video
Updated: Oct 17, 2026
Mosaic Zebrafish Transgenesis for Functional Genomic Analysis of Candidate Cooperative Genes in Tumor Pathogenesis
Published on: March 31, 2015
A dual-color FISH framework map for the characterization of the Sai1 tumor suppression region on rat chromosome 5
K Helou1, X C Lü, K Montelius-Alatalo
1CMB-Genetics, Lundberg Laboratory, Göteborg University, Göteborg, Sweden.
Abstract:
The analysis of cell hybrids between malignant mouse hepatoma cells and normal rat fibroblasts has previously demonstrated the critical role of a deletion in rat chromosome 5 (RNO5) that was related to an anchorage independent phenotype. Those hybrids that were anchorage independent displayed loss of the entire RNO5 or an interstitial deletion in RNO5. These findings suggested that a putative tumor suppressor gene, Sai1 (suppression of anchorage independence 1), was located within the deleted region. To explore the molecular basis of the tumor suppressor activity of the Sai1 region, we analyzed the RNO5q23-q36 region with several genes and microsatellite markers that could be assigned to the region, as well as with new markers derived by representational difference analysis (RDA) or by microdissection. Dual-color FISH was used to construct a detailed physical map of the entire RNO5. These new data can be used to connect the physical and linkage maps in the rat, as well as to identify the details of the comparative map with other mammalian species including humans and mice. Using as FISH reagents genomic YAC, P1, or phage lambda clones corresponding to RNO5 markers, the order and unique positions of 18 markers could be established. The map provided a framework for the detailed characterization of the deletion found in anchorage independent hybrids. All markers within the bands RNO5q31.3-q35 were shown to be lost, including known cancer-related genes such as Ifna (5q32), Cdkn2a, -b (5q32), Jun (5q34), and Cdkn2c (5q35). However, the aberration in the deletion chromosome turned out to be more complex than originally thought in that we detected the presence of a paracentric inversion in addition to a deletion. The inversion led to the juxtaposition of the gene markers Tal2 (5q24.1) and Cd30lg (5q24.3). The framework map will provide the basis for the detailed physical YAC clone contig mapping of this region, and facilitate the identification and characterization of the Sai1 locus.
Insights
Researchers identified a tumor suppressor gene, Sai1, on rat chromosome 5. Deletions and inversions in this region are linked to anchorage-independent growth in cancer cells.
Area of Science:
- Genetics
- Cancer Biology
- Molecular Oncology
Background:
- Cell hybrid analysis revealed a critical deletion in rat chromosome 5 (RNO5) associated with anchorage-independent growth.
- This suggested a tumor suppressor gene, Sai1 (suppression of anchorage independence 1), located in the deleted region.
Purpose of the Study:
- To explore the molecular basis of Sai1's tumor suppressor activity.
- To construct a detailed physical map of the RNO5q23-q36 region.
Main Methods:
- Representational difference analysis (RDA) and microdissection to identify new markers.
- Dual-color fluorescence in situ hybridization (FISH) to create a physical map of RNO5.
- Analysis of YAC, P1, and phage lambda clones for marker positioning.
Main Results:
- Established the order and unique positions of 18 markers on RNO5.
- Identified loss of markers in RNO5q31.3-q35, including cancer-related genes (Ifna, Cdkn2a/b, Jun, Cdkn2c).
- Detected a paracentric inversion in addition to deletion, juxtaposing Tal2 and Cd30lg genes.
Conclusions:
- The physical map provides a framework for characterizing the RNO5 deletion.
- The complex aberration (deletion and inversion) impacts anchorage-independent growth.
- Facilitates identification and characterization of the Sai1 tumor suppressor locus.
