The disordered extensions of the Arid5a core ARID domain modulate its DNA- and RNA-binding propensities
ARID (AT-rich interacting domain) proteins are a heterogeneous family of DNA-binding proteins involved in transcriptional regulation. No precise DNA-binding preferences have yet been defined for the aberrant member Arid5a. In addition, the protein binds to mRNA motifs for transcript stabilisation, presumably through the DNA-binding ARID domain. Here we first provide an unbiased definition of RNA motifs and a clear breakdown of nucleic acid binding by the ARID domain. An RNA Bind-n-Seq (RBNS) experiment was performed to find a consensus motif of the Arid5a domain. It reveals a preference for an unexpected CAGGCAG consensus motif, accompanied by a general preference for AU-rich motifs. Overall design: RNA Bind-n-Seq (RBNS) experiment to to test ARID's capability to interact with specific RNA motifs. An RNA pool (1 µM) of 20 random nucleotides flanked by short constant adapter sequences was incubated with different concentrations of the Strep-tagged Arid49-152 domain (0.25, 1, 5 µM)