Mathew Thayer, PhD
Chromosome dynamics, replication timing, non-coding RNA,
and genome stability
Mammalian cells initiate DNA replication at multiple sites along each chromosome at different times, following a temporal replication program. The Thayer lab has used a chromosome-engineering strategy to identify cis-acting loci that control this replication-timing program on individual human chromosomes. They found that that Cre/loxP-mediated disruption of the lncRNA genes ASAR6 and ASAR15 result in delayed replication of human chromosomes 6 and 15, respectively. ASAR6 and ASAR15 share numerous characteristics with XIST, including: 1) random mono-allelic expression of lncRNAs that can physically "coat" entire chromosomes in cis; 2) asynchronous replication between alleles; 3) genetic disruption results in structural instability of their respective chromosomes; and 4) ectopic integration of transgenes causes delayed replication and transcriptional silencing of entire chromosomes. Their work, combined with the observation that disruption of XIST results in a phenocopy of the delayed replication and instability phenotype caused by disruption of either ASAR6 or ASAR15, suggests that all mammalian chromosomes are regulated by similar loci. Therefore, they are proposing that all mammalian chromosomes contain "Inactivation/Stability Centers" (I/SCs), which normally function to promote proper replication timing, monoallelic gene expression and structural stability of individual chromosomes. They believe that I/SCs are as fundamentally important to mammalian chromosome biology as telomeres, centromeres, or origins of replication. Thus, under this scenario every mammalian chromosome contains four essential cis-acting elements, origins, centromeres, telomeres, and I/SCs all functioning to ensure proper replication, segregation and stability of each chromosome. The current work in the lab is designed to identify the DNA sequences within ASAR6 and ASAR15 that are necessary and sufficient for their function, elucidate the functional activities of the ASAR6 and ASAR15 lncRNAs, and determine the role that ASAR6 and ASAR15 play in nuclear localization and 3D chromatin interaction maps of their respective chromosomes.