Positive intergenic feedback circuitry, involving EBF1 and FOXO1, orchestrates B-cell fate

Abstract

Recent studies have identified a number of transcriptional regulators, including E2A, early B-cell factor 1 (EBF1), FOXO1, and paired box gene 5 (PAX5), that promote early B-cell development. However, how this ensemble of regulators mechanistically promotes B-cell fate remains poorly understood. Here we demonstrate that B-cell development in FOXO1-deficient mice is arrested in the common lymphoid progenitor (CLP) LY6D + cell stage. We demonstrate that this phenotype closely resembles the arrest in B-cell development observed in EBF1-deficient mice. Consistent with these observations, we find that the transcription signatures of FOXO1-and EBF1-deficient LY6D + progenitors are strikingly similar, indicating a common set of target genes. Furthermore, we found that depletion of EBF1 expression in LY6D + CLPs severely affects FOXO1 mRNA abundance, whereas depletion of FOXO1 activity in LY6D + CLPs ablates EBF1 transcript levels. We generated a global regulatory network from EBF1 and FOXO1 genome-wide transcription factor occupancy and transcription signatures derived from EBF1-and FOXO1-deficient CLPs. This analysis reveals that EBF1 and FOXO1 act in a positive feedback circuitry to promote and stabilize specification to the B-cell lineage.

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

“…These factors set up a self-promoting feed-forward loop that establishes B-cell identity while eliminating differentiation into other affiliated cell lineages Rolink et al 1999;Pongubala et al 2008;Lin et al 2010;Treiber et al 2010;Nechanitzky et al 2013;Boller et al 2016). FOXO1 and EBF1 support each other's expression, while EBF1 also induces PAX5 that further augments EBF1 (Roessler et al 2007;Decker et al 2009;Inlay et al 2009;Mansson et al 2012).…”

“…Key components of the pre-T-cell receptor (pre-TCR) and pre-B-cell receptor (pre-BCR) signaling pathways (recombination factors) as well as transcription and recombination at the antigen receptor loci (Igh and Tcrb) are examples of genes whose transcription is supported by these early T-cell and B-cell transcription factor networks (Schebesta et al 2007;Treiber et al 2010;Welinder et al 2011;Mansson et al 2012).…”

Early B-cell Factor 1 Regulates the Expansion of B-cell Progenitors in a Dose-dependent Manner

“…Furthermore, E-proteins regulate FOXO1 expression in the CLP compartment (7). A lack of FOXO1 results in defective lineage priming in a manner similar to what is observed in EBF1-deficient progenitors (9). The ability of FOXO1 to bind potential regulatory elements in the Ebf1 gene and binding of EBF1 to regions in the FoxO1 gene suggest that these proteins act in a regulatory loop crucial for the specification of early B-cell progenitors (9).…”

“…The understanding of this process has been facilitated by recent advancements in the isolation of early progenitor populations (1) as well as by analysis of gene expression patterns and in vivo protein-DNA interactions (2)(3)(4). The formation of the earliest B-cell committed progenitors is dependent on the transcription factor EBF1 (5, 6) as well as E2a encoded proteins (Tcf3) (7,8) and FOXO1 (9) because in the absence of these factors, the expression of B-lineage genes is dramatically reduced in the lymphoid progenitors, and normal lineage restriction is disrupted (9,10). Commitment to B-lineage development is associated with the expression of the transcription factor PAX5, known to be of critical importance for restriction of alternative cell fates (11)(12)(13).…”

Interaction of CCR4–NOT with EBF1 regulates gene-specific transcription and mRNA stability in B lymphopoiesis

“…In CLPs (consisting of all lymphoid progenitors [ALPs] and B-cell-biased lymphoid progenitors [BLPs]) as well as pre-pro-B cells, multilineage priming of enhancers has been implicated in setting a chromatin state that facilitates the activation of the B-lineage program (Inlay et al 2009;Mercer et al 2011;Zandi et al 2012). B-cell programming requires a complex network of transcription factors (TFs) in which feed-forward loops and synergistic and antagonistic actions allow for a robust implementation of the B-cell program (Zandi et al 2008;Lin et al 2010;Mansson et al 2012;Boller and Grosschedl 2014;Singh et al 2014). In pro-B cells, the repression of genes associated with alternative cell fates stabilizes the lineage decision and commits the cells to the B-cell fate (for review, see Nutt and Kee 2007;Ramírez et al 2010;Boller and Grosschedl 2014).…”