Resumen de Characterization of the molecular mechanisms used by jmjc-lysine demethylases to regulate gene expression
Mammalian neurodevelopment is dictated by the crosstalk of developmental signals, specific transcription factors and epigenetic regulators. Their close coordination activates cis-regulatory elements that will determine cell-type specific gene expression programs. Enhancers are key regulatory regions of the genome that respond to developmental signals to activate their target genes in a spatial-temporal specific manner, constituting the major regulatory unit during development. It is well known that mammalian promoters are usually regulated by multiple enhancers, and it has been demonstrated that chromatin is reorganized to establish enhancer-enhancer contacts, forming enhancer clusters that activate promoters to drive gene expression. What is still an open debate is how these cis-regulatory hubs are orchestrated.
To deepen into this open field, the present work examined the crosstalk between the TGFβ pathway and the JmjC-containing demethylase (JMJCKDM) JMJD3 to regulate gene expression upon the commitment of neural stem cells (NSCs) to the neuronal lineage. Specifically, we studied the formation of an enhancer cluster in the Chst8 locus. Through 4C-seq experiments we observed that the TGFβ pathway promotes the establishment of contacts between cis-regulatory elements, ensuring the activation of their regulated gene. The formation of this enhancer cluster and the expression of Chst8 depended on the TGFβ coactivator JMJD3, which promoted the activation of the locus in a catalytic-independent manner. Apart from the JmjC domain, the demethylase just contains a strikingly large intrinsically disordered region (IDR) enriched in prolines and low complexity regions. These domains are widely involved in the formation of liquid-liquid phase separated (LLPS) condensates, a process that has been recently demonstrated to play a role in enhancer clustersdriven transcription. Indeed, we showed that JMJD3 participates in a LLPS process to form condensates in an IDR-dependent manner, and this correlates with the observed transcriptional regulation of the Chst8 locus.
Not only JMJD3, but many others JMJC-KDMs are widely involved in transcriptional regulatory processes. So, considering our findings for JMJD3 and the recently described phase separated transcriptional condensates, we wondered about the universality of the phase separation process as a general mechanism used by JMJC-KDMs. This way, we came to discover that these proteins are enriched in large IDRs, and that representative examples from different families, namely KDM2A, KDM4B and PHF2, are able to form phase separated condensates that correlate with their transcriptional features. Thus, our results suggest that phase separation is a common mechanism that JMJC-KDMs utilize, in addition to their catalytic activity, to promote their biological functions
