Dynamic regulation of a chromatin loop by non-coding RNA

ARIEL, FD; LATRASSE, D; ROMERO-BARRIOS, N; JEGU, T; BENHAMED, M; CRESPI, M

Amsterdam

Congreso; EMBO Meeting; 2013

EMBO

Background  Eukaryotes exhibit a highly structured epigenome shaped in large part by different types of transcriptional activity. However, little is known about how epigenome differs between distinct cell types and developmental stages. Epigenetic dynamics determine genome topology, conditioning transcriptional responses. Non-coding RNAs help to determine the epigenetic landscape, although the mechanisms by which they participate in shaping chromosome conformation remain largely unknown.  Observations  In this work we study the Arabidopsis thaliana long intergenic non-coding RNA APOLO that is dynamically transcribed by the Pol II and the Pol V complexes in response to the phyto-hormone auxins. Chromosome conformation capture served to identify the formation of a chromatin loop between the APOLO locus and its neighbor gene, a key regulator of auxins polar transport. The use of overexpressing, RNAi and mutant lines indicate that APOLO transcript levels affect the loop formation, fine-tuning the promoter activity of the auxin-responsive gene. Chromatin Immunoprecipitation (IP) was performed to determine that auxin treatment alters the whole epigenetic profile of this region, notably modulating certain repressive marks. The analyses of a wide range of mutant lines affecting chromatin modification pathways allowed us to determine what marks result essential for loop formation. Furthermore, we show by RNA IP that APOLO interacts with one component of the plant Ploycomb Repressive Complex 1 (PRC1-like). This interaction correlates with the loop formation dynamics. PRC1-like and PRC2 participate in the accurate dynamism of chromatin conformation.  Conclusions RNA is one of the major components of chromatin and it is thought to exert a key role in chromosome conformation. In this work, we identified a long non-coding RNA that dynamically modulates a chromatin loop, fine-tuning the promoter activity of its neighbor gene.