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.