Abstract
Although somatic homologous pairing is common in Drosophila it is not generally observed in mammalian cells. However, a number of regions have recently been shown to come into close proximity with their homologous allele, and it has been proposed that pairing might be involved in the establishment or maintenance of monoallelic expression. Here, we investigate the pairing properties of various imprinted and non-imprinted regions in mouse tissues and ES cells. We find by allele-specific 4C-Seq and DNA FISH that the Kcnq1 imprinted region displays frequent pairing but that this is not dependent on monoallelic expression. We demonstrate that pairing involves larger chromosomal regions and that the two chromosome territories come close together. Frequent pairing is not associated with imprinted status or DNA repair, but is influenced by chromosomal location and transcription. We propose that homologous pairing is not exclusive to specialised regions or specific functional events, and speculate that it provides the cell with the opportunity of trans-allelic effects on gene regulation.
Highlights
Tight spatial and temporal regulation of gene expression requires several interleaved layers of control
Since homologous pairing was previously proposed to be linked to monoallelically expressed regions [4,5], we probed the Kcnq1 imprinted region for interactions with its homologous allele
We have demonstrated for the first time by allele specific 4CSeq and by extensive DNA FISH analysis that many loci pair with their homologous allele
Summary
Tight spatial and temporal regulation of gene expression requires several interleaved layers of control. Co-regulated genes are found in the same transcription factory, bringing together various regions from different chromosomes [1]. This is, not limited to heterologous regions. Pairing of homologous chromosomes has long been known in Drosophila. It underlies the phenomenon of transvection which refers to changes in gene activity through interaction of regulatory elements of one allele with its homologue [2]. It has been proposed that somatic pairing is a general feature of regions for which one allele is silenced which might be involved in the establishment or maintenance of monoallelic expression [4,7,8]
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