Conserved helical motifs in the IKZF1 disordered region mediate NuRD interaction and transcriptional repression

Abstract

The transcription factor IKZF1 is essential for B cell development, and recurrently mutated in human B-ALL. IKZF1 has been ascribed both activating and repressive functions via interactions with coactivator and corepressor complexes, but the relative abundance of IKZF1-associated coregulators and their contribution to IKZF1-mediated gene regulation are not well understood. To address this, we performed an unbiased identification of IKZF1-interacting proteins in pre-B cells and found that IKZF1 interacts overwhelmingly with corepressors and heterochromatin-associated proteins. Time-resolved analysis of transcription and chromatin state identified transcriptional repression as the immediate response to IKZF1 induction. Transcriptional repression preceded transcriptional activation by several hours, manifesting as a decrease in the fraction of transcriptional bursts at the single molecule level. Repression was accompanied by a rapid loss of chromatin accessibility and reduced levels of H3K27ac particularly at enhancers. We identified highly conserved helical motifs within the intrinsically disordered region in IKZF1 that mediate its association with the NuRD corepressor complex through critical “KRK” residues that bind the NuRD subunit RBBP4, a mechanism shared with the TFs FOG1, BCL11A, and SALL4. Functional characterization reveals this region is necessary for to the efficient silencing of target genes and antiproliferative functions of IKZF1 in B-ALL.