IKZF1: born to be the repressor

In this issue of Blood, Zhang et al report that IKZF1 predominantly interacts with corepressors to mediate transcriptional silencing through a rapid loss of chromatin accessibility and reduced levels of H3K27ac, especially at enhancers.¹ The precise mechanisms of how IKZF1 regulates lymphocyte development and serves as a pivotal tumor suppressor² are still incompletely characterized. In this article, the authors employ a range of quantitative and time-sensitive analyses to uncover its key regulatory mechanisms.

Turn on, turn off. Transcription factors are crucial proteins that regulate gene expression. IKZF1, a zinc finger transcription factor, regulates differentiation, proliferation, and survival of lymphoid cells.³ Previous studies have outlined some mechanisms by which IKZF1 decides a pre-B-cell fate, showing that it regulates gene expression through various DNA and chromatin-dependent processes. For example, IKZF1 can dimerize with other factors and complexes, such as the nucleosome remodeling and deacetylase (NuRD) and the positive transcription elongation factor b,⁴ affecting cofactor function and altering chromatin structure, including acetylation and methylation patterns. Despite its known involvement in recruiting coregulators and chromatin remodeling,⁵ the exact role of IKZF1 in modifying chromatin accessibility to activate or repress gene expression is still not fully understood.

Zhang et al took advantage of precise next-generation methodological tools, including chromatin immunoprecipitation mass spectometry, RNA sequencing, assay for transposase-accessible chromatin with sequencing, chromatin immunoprecipitation sequencing, and RNA fluorescence in situ hybridization, to define individual and cooperative functions of IKZF1, as well as the cofactors required for these activities. They identified IKZF1 interacting proteins, revealing that in pre-B cells, IKZF1 interacts far more with corepressors than with coactivators, identifying NuRD as the predominant IKZF1-associated complex. This interaction between IKZF1 and NuRD is mediated by a conserved KRK sequence within the IKZF1 helical motif region and is essential for efficient silencing of target genes and antiproliferative functions of IKZF1 in precursor-B acute lymphoblastic leukemia (B-ALL) cells. They also demonstrated that transcriptional repression is the immediate response to IKZF1 induction, with their data showing a rapid loss of chromatin accessibility and reduced levels of H3K27ac after IKZF1 binding. Notably, this decreased accessibility and H3K27ac occurred more quickly and prominently at enhancers than at promoters. Therefore, the authors suggest that enhancer disruption may be a primary driver of IKZF1-mediated transcriptional repression (see figure). The time-resolved analysis of transcriptional changes following IKZF1 induction was a valuable approach that provided insight into the dynamic nature of gene regulation. It highlighted the rapid repression followed by delayed activation, suggesting a sequential mechanism. Finally, by demonstrating an overlap between genes repressed by IKZF1 in pre-B cells and genes aberrantly expressed in B-ALL with mutant IKZF1, the study strengthens the link between IKZF1 dysregulation and leukemia development.

Together, their findings are novel and advance in the fields of normal B-cell development and of leukemia. Although previous research hinted at some of these results, this work goes beyond previous characterizations of IKZF1 as a dual-function transcription factor, revealing a strong bias toward corepressors, mainly the NuRD complex. The identification of the conserved KRK motif mediating NuRD interaction is particularly novel and could have important implications for understanding the mechanism of IKZF1-mediated gene regulation and its potential as a therapeutic target. This motif is shared with other zinc finger transcription factors,⁶ suggesting a broader mechanism for NuRD recruitment. Although the study provides a convincing argument for NuRD’s role in IKZF1-mediated repression, it does not completely exclude the involvement of other corepressor complexes or the potential for a more complex interplay of corepressors and coactivators in regulating IKZF1’s function. Last, the study demonstrates that IKZF1 reduces the probability of transcriptional bursting, rather than affecting the intensity of bursts. This finding adds a new dimension to the understanding of how transcriptional repression is accomplished.

In addition to the significant experimental results obtained, this work has potential clinical implications. IKZF1 gene alterations in B-ALL are associated with an increased risk of relapse.⁷ Mutations in the IKZF1 helical motif, which are predicted to be highly pathogenic, have been identified in patients with B-ALL.⁸ This suggests that targeting these motifs could be a promising therapeutic strategy. Additionally, the discovery that the IKZF1-NuRD interaction is crucial for gene repression indicates that restoring it could also be a viable treatment approach. The study further reveals that specific genes rapidly repressed by IKZF1 in pre-B cells are aberrantly expressed in IKZF1-mutant B-ALL, highlighting their potential as biomarkers for disease progression and patient outcome. However, these clinical implications require further investigation and validation.

In summary, this work challenges the traditional view of IKZF1 as a dual function “switch” and provides evidence that it primarily acts through repression via its interaction with NuRD. The study identifies the critical KRK motif and highlights how IKZF1 preferentially represses enhancers, adding novel layers to our understanding of how IKZF1 achieves its regulatory role. Although we often think of a switch as being able to turn things on and off, this study shows that IKZF1 is more of an unbalanced “turn off” switch.

Conflict-of-interest disclosure: M.E. declares no competing financial interests.