APOLO long noncoding RNA regulates multiple distal loci in Arabidopsis

ARIEL, FEDERICO D.

Buenos Aires

Workshop; Workshop Biologia Celular y Molecular del ARN; 2018

Fundación Instituto Leloir

In Arabidopsis, the lncRNA APOLO was previously shown to modulate the dynamic formation of a chromatin loop encompassing the promoter region of its neighbor gene PID, fine-tuning its response to the phyto-hormone auxin. In this work, we purified APOLO?associated DNA by Chromatin Isolation by RNA purification (ChIRP) followed by library construction and high-throughput sequencing. Together with an RNA-seq approach comparing plants over expressing APOLO versus wild type, we identified bona fide APOLO targets in trans, across the Arabdiopsis genome. A subset of the APOLO targets was also directly regulated by the APOLO protein partner LHP1, a component of the plant Polycomb Repressive Complex 1. We demonstrated that APOLO up- and down-regulation impacts local chromatin looping of multiple target loci, which transpired to be recognized by APOLO sequence complementarity forming DNA-RNA duplexes known as R-loops. The analysis of the APOLO promoter fused to reporter genes revealed that it is expressed during lateral root formation. APOLO turned out to coordinate the transcription of auxin-responsive genes involved in lateral root formation by direct recognition, fine-tuning local chromatin loop formation.