Regulatory and evolutionary annotation identifies KAN1, MYB44 and PIF4 as regulators of Arabidopsis lincRNAs expressed in root

Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of eight annotation resources, we defined 6,599 high-confidence lincRNA loci in Arabidopsis thaliana . For lincRNAs belonging to different evolutionary age categories, we identified major differences in sequence and chromatin features, as well as in the level of conservation and selection. Spatiotemporal gene expression profiles combined with transcription factor (TF) chromatin immunoprecipitation data was used to construct a TF-lincRNA regulatory network containing 2,659 lincRNAs and 43,233 interactions. We experimentally confirmed the role of three TFs, KAN1, MYB44, and PIF4, as key regulators controlling root-specific lincRNA expression, demonstrating the predictive power of our network. Furthermore, we identified 58 lincRNAs regulated by these TFs showing strong root cell-type specific expression and that are linked with GWAS genetic associations related to root system development and growth. The multi-omics approach applied in this study sheds light on the global regulatory complexity of plant lincRNA networks and pinpoints a role of specific TFs in lincRNA regulation in roots.