The lncRNA BAMBOO decoys NF-YA2 transcription factor from the promoter of its targets in Arabidopsis lateral roots

In Arabidopsis thaliana, NF-YA2 and NF-YA10 (Nuclear Factor A2 and A10) are TFs post-transcriptionally regulated by microRNAs, participating in a regulatory hub controlling root architecture. Here, RNA-seq and ChIP-seq approaches served to identify NF-YA2 direct target genes involved in lateral root (LR) development, water deprivation and hormone pathways.

Furthermore, we searched for NFYA2 potential RNA partners by using RIP-seq and identified a long noncoding RNA (lncRNA) named BAMBOO after its counterpart PANDA, which interacts with mammalian NF-YA. BAMBOO is dynamically regulated during LR development and bamboo mutant plants exhibit a NF-YA2-related root developmental phenotype. bamboo plants share half of its deregulated genes with the NF-YA2 regulome. Furthermore, overexpressing the lncRNA BAMBOO disturbed NF-YA2 binding to its target promoters suggesting an RNA-based competition of target recognition by NF-YA2 in chromatin.