An autosomal locus that controls chromosome-wide replication timing and mono-allelic expression

Abstract

Mammalian DNA replication initiates at multiple sites along chromosomes at different times, following a temporal replication program. Homologous alleles typically replicate synchronously; however, mono-allelically expressed genes such as imprinted genes, allelically excluded genes and genes on the female X chromosome replicate asynchronously. We have used a chromosome engineering strategy to identify a human autosomal locus that controls this replication timing program in cis. We show that Cre/loxP-mediated rearrangements at a discrete locus at 6q16.1 result in delayed replication of the entire chromosome. This locus displays asynchronous replication timing that is coordinated with other mono-allelically expressed genes on chromosome 6. Characterization of this locus revealed mono-allelic expression of a large intergenic non-coding RNA, which we have named asynchronous replication and autosomal RNA on chromosome 6, ASAR6. Finally, disruption of this locus results in the activation of the previously silent alleles of linked mono-allelically expressed genes. We previously found that chromosome rearrangements involving eight different autosomes display delayed replication timing, and that cells containing chromosomes with delayed replication timing have a 30-80-fold increase in the rate at which new gross chromosomal rearrangements occurred. Taken together, these observations indicate that human autosomes contain discrete cis-acting loci that control chromosome-wide replication timing, mono-allelic expression and the stability of entire chromosomes.

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells

“…However, very few loci in mammalian genomes display asynchronous replication, and so far all of them have been linked to either X Chromosome inactivation in female cells or to parental imprinting/monoallelic gene expression (Reik and Walter 2001;Goldmit and Bergman 2004;Gimelbrant et al 2007;Farkash-Amar et al 2008;Stoffregen et al 2011;DeVeale et al 2012;Koren et al 2014;Mukhopadhyay et al 2014;Donley et al 2015). Moreover, direct comparison of known asynchronously replicated or monoallelically expressed genes to our categories of genes revealed that such genes are mostly constitutively replicated (Supplemental Fig.…”

Chromosome Replicating Timing Combined with Fluorescent <em>In situ</em> Hybridization

“…Accordingly, the banded pattern of BrdU incorporation allows for the detection of actively replicating regions of chromosomes, and differences in replication timing between chromosome pairs are seen as differences in this banding pattern (Figures 2 and 3). Finally, these differences in binding patterns can be compared to known replication timing maps for each chromosome 6,7 , which allows for an estimate of the replication timing difference between homologous chromosomes or chromosome arms 4 . For example, the two chromosome 6's in Figure 3A display a difference in banding pattern of >2 hr when compared to the normal replication timing of chromosome 6 4 .…”

“…In addition, certain chromosome rearrangements found in cancer cells and in cells exposed to ionizing radiation display a significant delay in replication timing of >3 hours that affects the entire chromosome 2,3 . Recent work from our lab indicates that disruption of discrete cis-acting autosomal loci result in an extremely late replicating phenotype that affects the entire chromosome 4 . Additional 'chromosome engineering' studies indicate that certain chromosome rearrangements affecting many different chromosomes result in this abnormal replication-timing phenotype, suggesting that all mammalian chromosomes contain discrete cis-acting loci that control proper replication timing of individual chromosomes 5 .…”

Making a long story short: noncoding RNAs and chromosome change

“…An elegant chromosome engineering strategy showed that rearrangements of chromosome 6q16.1, an EB and a locus carrying monoallelic expression of an intergenic lncRNA called asynchronous replication and autosomal RNA on chromosome 6 (ASAR6), results in delayed DNA replication of the entire chromosome 6 (Stoffregen et al, 2011). Disruption of this locus resulted in activation of previously silenced mono-allelically expressed genes linked to ASAR6, and none of the nine other Cre/loxp-mediated rearranged chromosomes displayed DRT, thus indicating that inactivation of the lncRNA at this site is responsible for the abnormalities observed (Stoffregen et al, 2011).…”