Epigenetics Chromatin 4:21 (2011)
Enhancer-Driven ChromatinIinteractions during Development Promote Escape from Silencing by a Long Non-Coding RNA.
Korostowski L, Raval A, Breuer G, Engel N
BACKGROUND: Gene regulation in eukaryotes is a complex process entailing the establishment of transcriptionally silent chromatin domains interspersed with regions of active transcription. Imprinted domains consist of clusters of genes, some of which exhibit parent-of-origin dependent mono-allelic expression, while others are biallelic. The Kcnq1 imprinted domain illustrates the complexities of long-range regulation that co-exists with local exceptions. A paternally expressed repressive non-coding RNA, Kcnq1ot1, regulates a domain of up to 750 kb, encompassing 14 genes. We study how the Kcnq1 gene, initially silenced by Kcnq1ot1, undergoes tissue-specific escape from imprinting during development. Specifically, we uncover the role of chromosome conformation during these events.
RESULTS: We show that Kcnq1 transitions from mono- to bi-allelic expression during mid-gestation in the developing heart. This transition is not associated with the loss of methylation on the Kcnq1 promoter. However, by exploiting Chromosome Conformation Capture (3C) technology, we find tissue- and stage-specific chromatin loops between the Kcnq1 promoter and newly identified DNA regulatory elements. These regulatory elements showed in vitro activity in a luciferase assay and in vivo activity in transgenic embryos.
CONCLUSIONS: By exploring the spatial organization of the Kcnq1 locus, our results reveal a novel mechanism by which local activation of genes can override the regional silencing effects of non-coding RNAs