ASAR15, A cis-Acting Locus that Controls Chromosome-Wide Replication Timing and Stability of Human Chromosome 15

Abstract

DNA replication initiates at multiple sites along each mammalian chromosome at different times during each S phase, following a temporal replication program. We have used a Cre/loxP-based strategy to identify cis-acting elements that control this replication-timing program on individual human chromosomes. In this report, we show that rearrangements at a complex locus at chromosome 15q24.3 result in delayed replication and structural instability of human chromosome 15. Characterization of this locus identified long, RNA transcripts that are retained in the nucleus and form a “cloud” on one homolog of chromosome 15. We also found that this locus displays asynchronous replication that is coordinated with other random monoallelic genes on chromosome 15. We have named this locus ASynchronous replication and Autosomal RNA on chromosome 15, or ASAR15. Previously, we found that disruption of the ASAR6 lincRNA gene results in delayed replication, delayed mitotic condensation and structural instability of human chromosome 6. Previous studies in the mouse found that deletion of the Xist gene, from the X chromosome in adult somatic cells, results in a delayed replication and instability phenotype that is indistinguishable from the phenotype caused by disruption of either ASAR6 or ASAR15. In addition, delayed replication and chromosome instability were detected following structural rearrangement of many different human or mouse chromosomes. These observations suggest that all mammalian chromosomes contain similar cis-acting loci. Thus, under this scenario, all mammalian chromosomes contain four distinct types of essential cis-acting elements: origins, telomeres, centromeres and “inactivation/stability centers”, all functioning to promote proper replication, segregation and structural stability of each chromosome.

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.…”

Replication timing and transcriptional control: beyond cause and effect — part III

“…In general, homologues replicate highly synchronously with very few regions showing allelic differences in RT or in origin usage related to DNA sequence variation, although some reach statistical or disease-associated significance worth further investigation [24*,66*,67,68*,69*]. An elegant series of recent papers has revealed a new class of cis -acting elements involved in the regulation of RT, mitotic condensation and chromosome stability [70–72**]. These elements consist of monoallelically expressed long non-coding RNAs that appear to be present on each mammalian chromosome, and interact in cis to regulate RT, monoallelic gene expression and structural stability of the entire chromosome [72**].…”

“…An elegant series of recent papers has revealed a new class of cis -acting elements involved in the regulation of RT, mitotic condensation and chromosome stability [70–72**]. These elements consist of monoallelically expressed long non-coding RNAs that appear to be present on each mammalian chromosome, and interact in cis to regulate RT, monoallelic gene expression and structural stability of the entire chromosome [72**]. Overall, these results uncover specific mechanisms that control intrinsic allelic variation in RT that are certain to be the subject of much investigation in the coming years.…”

RNA as a fundamental component of interphase chromosomes: could repeats prove key?

“…Another particularly promising prospect for an RNA that likely spreads across Chromosome 15 is ASAR15 (Figure 3E), discovered because disruption of this large locus impacts the replication timing and stability of the chromosome [30]. Several published images show an extensive overlap of ASAR15 RNA with chromosome 15 DNA (marked by many loci rather than a DNA library).…”

“…D) An illustration of the amount of interphase X-chromosome territory typically “painted” by XIST RNA (green) and XACT RNA (yellow) in a pluripotent cell (as seen by us and in published images) [28]. E) An illustration of the amount of interphase chromosome-15 territory typically “painted” by ASAR5 RNA (as seen in published images) [30]. F) An illustration of the amount of a human interphase chromosome territory typically “painted” by Cot-1 ecRNA in mouse/human hybrid cells (as seen in our published images) [39].…”