Stage-specific control of early B cell development by the transcription factor Ikaros

Abstract

Ikaros is an essential regulator of lymphopoiesis. Here, we studied the B-cell-specific function of Ikaros by conditional Ikzf1 inactivation in pro-B cells. B-cell development was arrested at an aberrant 'pro-B' cell stage characterized by increased cell adhesion and loss of pre-B cell receptor signaling. Ikaros was found to activate genes coding for pre-BCR signal transducers and to repress genes involved in the downregulation of pre-BCR signaling and upregulation of the integrin signaling pathway. Unexpectedly, derepression of Aiolos expression could not compensate for the loss of Ikaros in pro-B cells. Ikaros induced or suppressed active chromatin at regulatory elements of activated or repressed target genes. Notably, Ikaros binding and target gene expression was dynamically regulated at distinct stages of early B-lymphopoiesis.

Regulation of gene expression dynamics during developmental transitions by the Ikaros transcription factor

“…However, enrichment of Ikaros-binding events in the vicinity of genes that are misregulated in Ikzf1 mutant cells was not observed despite evidence that Ikaros regulates stage-specific genes during two stages of B-cell development, similar to our findings in thymocytes. Instead, the study by Schwickert et al (2014), like our studies and those of others (Zhang et al 2011;Schjerven et al 2013), reported preferential binding in the vicinity of a large percentage of transcriptionally active genes or in the vicinity of control regions that exhibit histone modifications characteristic of transcriptionally active chromatin. These findings raise the possibility that the Ikaros-binding events observed by ChIP-seq may reflect a broader role in genome organization rather than a specific role in regulating genes in the vicinity of the binding sites.…”

“…Schwickert et al (2014) showed that the genomic sites occupied by Ikaros differ at different stages of B-cell development. However, enrichment of Ikaros-binding events in the vicinity of genes that are misregulated in Ikzf1 mutant cells was not observed despite evidence that Ikaros regulates stage-specific genes during two stages of B-cell development, similar to our findings in thymocytes.…”

“…However, the properties of Ikaros observed in vivo and in vitro have made it difficult to obtain a clear view of its full range of targets and mechanisms of action. For example, recent genome-wide chromatin immunoprecipitation (ChIP) combined with deep sequencing (ChIP-seq) experiments revealed the binding of Ikaros to 9878 genomic sites in progenitor B (pro-B) cells, including 60% of all active promoters and 30% of all active enhancers (Schwickert et al 2014). In this same study, 61% of genes misregulated in Ikzf1 mutant cells were bound by Ikaros, demonstrating that Ikaros binding is distributed broadly and exhibits no enrichment at Ikaros-dependent genes.…”

“…In contrast, the dimerization and DNAbinding domains of Ikaros are located at opposite ends of the protein, leading to considerable flexibility in DNA recognition (B Cobb and ST Smale, unpubl.). Indeed, Ikaros ChIP-seq peaks generally exhibit enrichment of only an Ikaros half-site (Zhang et al 2011;Ferreiros-Vidal et al 2013;Schjerven et al 2013;Schwickert et al 2014), raising the possibility that the two subunits associate with sequences separated by large distances or even on different chromosomes. Additional findings suggest that Ikaros dimers assemble into multimeric structures in vivo Trinh et al 2001).…”

The making of a lymphocyte: the choice among disparate cell fates and the IKAROS enigma

“…The NuRD complex is unique, especially in lymphocytes, as it can modulate access to nucleosomes through Mi-2β, restrict chromatin through histone deacetylases (HDAC1-2), and, with the addition of IKAROS proteins, target chromatin in a sequence-and lineage-specific manner (Kim et al 1999;Zhang et al 2011). Indeed, in Tcell and B-cell precursors, Mi-2β is highly enriched at IKAROS-binding sites in the vicinity of transcriptionally active lymphoid genes Schwickert et al 2014). The presence of the NuRD complex at these active regulatory sites may serve as a harbinger for their shutdown at a later differentiation stage (Whyte et al 2012;Yamada et al 2014).…”