Control of genetic and epigenetic instabilities by lincRNA genes

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 DESCRIPTION (provided by applicant): Cancer cells differ from their normal cellular counterparts in many important characteristics. These `hallmarks' of cancer affect numerous biological processes, and are acquired during the multistep development of human cancer. Not surprisingly, genetic and/or epigenetic changes are present in most if not all cancers, and are known to be responsible for these phenotypic alterations. In addition, genetic and/or epigenetic instabilities are thought to be present in most cancers and are thought to be required to generate the numerous genetic and/or epigenetic changes that are present in individual tumor cells. Understanding the mechanisms that drive these alterations is clearly an important goal. My lab previously characterized a chromosomal abnormality associated with certain tumor-derived chromosome rearrangements. This abnormal phenotype affects individual chromosomes and is characterized by delayed replication timing (DRT), delayed mitotic chromosome condensation (DMC), and frequent rearrangement of the affected chromosomes. We have developed a `chromosome engineering' system that allows us to generate DRT/DMC chromosomes in an efficient and reproducible manner. Thus, using a Cre/loxP-based strategy to screen for rearrangements in human chromosomes we identified 5 balanced translocations, affecting 8 different autosomes, all displaying DRT/DMC. We also found that the engineered DRT/DMC chromosomes display chromosome structure instability. More recently, we found that Cre/loxP-mediated disruption of a long non-coding RNA gene, which we named ASynchronous replication and Autosomal RNA on chromosome 6 (ASAR6), results in DRT/DMC on human chromosome 6. We also found that ASAR6 shares many characteristics with the Xist non-coding RNA gene, including: random monoallelic expression, asynchronous replication, silencing of other monoallelic genes in cis, and the ability to delay replication of entire chromosomes following ectopic integration of genomic transgenes. Notably, deletion of Xist results in delayed replication, abnormal chromatin structure and secondary rearrangements on the X chromosome. Therefore, disruption of ASAR6 results in a phenocopy of Xist deletion. Furthermore, disruption of Xist was recently shown to cause a 100% penetrant hematopoetic malignancy in mice, indicating that Xist functions as a tumor suppressor. More recently, we identified a second non-coding RNA gene, tentatively named ASAR15, which controls replication timing and stability of human chromosome 15. Taken together, these observations raise the intriguing possibility that all mammalian chromosomes contain `Xist-like' tumor suppressor loci functioning to maintain the genetic and epigenetic stability of individual chromosomes. The experiments that make up this proposal are designed to: 1) characterize the "molecular signature" of structural rearrangements associated with ASAR6, ASAR15 or Xist disruption; 2) elucidate the chromatin and gene expression changes associated with ASAR6 or ASAR15 disruption; and 3) identify human cancer cells with structural rearrangements in ASAR6, ASAR15 or XIST.