Intrinsically Disordered Regions in Chromodomain Helicase DNA-binding (CHD) Proteins Shape Distinct Protein Interaction Networks

Metazoans employ chromodomain helicase DNA-binding (CHD) enzymes to reposition nucleosomal DNA for transcription and replication. The CHD family consists of nine distinct members (CHD1-9) that possess highly conserved chromo and ATPase domains. These domains are flanked by poorly characterised N- and C-termini, which are enriched with intrinsically disordered regions (IDRs) and short aggregation-prone regions (APRs). The contribution of IDRs and APRs to CHD function has remained elusive. In this study we used affinity purification followed by mass spectrometry analysis (AP-MS) to define the protein-protein interaction (PPI) networks within the N- and C-termini of each CHD family member. The results illustrate a comprehensive map of CHD1-9-specific binding proteins that include dozens of novel interactions with transcription regulators and epigenetic factors. Using AlphaFold Multimer we examined the structural predictions of high confidence PPIs from our AP-MS screens and identified APR regions with alpha helical structures that contribute to PPIs. We further investigated a highly conserved APR within the C-terminus of the CHD4 protein and demonstrate that it contributes to the interaction of CHD4 with the nucleosome remodelling and deacetylase (NuRD) and CHD, ADNP, HP1 (ChAHP) complexes. Peptides mimicking this APR effectively disrupt CHD4 binding to both NuRD and ChAHP complexes, consequently triggering the transcriptional activation or repression of hundreds of target genes. Our results emphasise the crucial role that the N- and C-termini of CHD chromatin remodelers play in establishing protein-protein interaction (PPI) networks, which drive unique transcriptional programs. Overall design: G1E-ER4 cells were cultured to a density of 2.5 × 105 in 12-well plates. CHD4-APR (-YWLLAGII-Tat) and CTRL (AAAAAAA-Tat) peptides were added to the culture media each at 10 µM concentration. After 2 h cells were treated with 100 µM of Tamoxifen for another 28 h and cells were collected for RNA extraction. Cell pellets were lysed in 1 mL of TRIzol™ Reagent (Invitrogen).