GENOME-WIDE RNA/CHROMATIN LINK

Our work on the RNA-mediated chromatin silencing of FLC, both through vernalization and the autonomous pathway, has led into detailed mechanistic analysis of RNA-mediated chromatin regulation. Through collaboration with the group of Prof. Detlef Weigel (Max Planck Institute, Tuebingen) we are exploring the genome-wide consequences of the autonomous pathway and how that is affected by environmental conditions.

With Dr Sascha Laubinger and Prof. Weigel we established that FCA and FPA, both RNA-binding proteins functioning in the autonomous pathway, promote proximal polyadenylation at many loci in the Arabidopsis genome. Loss of their function leads to increased intergenic transcription and a variety of alternatively spliced transcripts polyadenylated at distal sites, often kbs downstream of the proximal site.

With Dr Claude Becker and Prof. Weigel we are using RNA-Seq techniques to explore interaction of the autonomous pathway function with changes in gene and non-coding RNA expression induced by prolonged cold.