Bcl11b sets pro-T cell fate by site-specific cofactor recruitment and by repressing Id2 and Zbtb16

Abstract

SUMMARY Multipotent progenitors confirm their T cell-lineage identity in the DN2 pro-T cell stages, when expression of the essential transcription factor Bcl11b begins. In vivo and in vitro stage-specific deletions globally identified Bcl11b-controlled target genes in pro-T cells. Proteomic analysis revealed that Bcl11b associates with multiple cofactors, and that its direct action was needed to recruit these cofactors to selective target sites. These sites of Bcl11b-dependent cofactor recruitment were enriched near functionally regulated target genes, and deletion of individual cofactors relieved repression of many Bcl11b-repressed genes. Runx1 collaborated with Bcl11b most frequently for both activation and repression. In parallel, Bcl11b indirectly regulated a subset of target genes by a gene network circuit via Id2 and Zbtb16 (encoding PLZF), which were directly repressed by Bcl11b and controlled distinct alternative programs. Thus, this study defines the molecular basis of direct and indirect Bcl11b actions that promote T cell identity and block alternative potentials.

Cell type–specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells

“…S1 B). Expression of Id2 was up-regulated by disruption of Bcl11b in DN3 and Scid.adh.2c2 cells as expected (Hosokawa et al, 2018a; Fig. 2 A).…”

“…1 I, green rectangles) and pro-T-specific sites (magenta rectangles). In pro-T cells, Bcl11b directly represses Id2, and we previously determined that one of the Bcl11b binding sites about 40 kb downstream of the Id2 locus transcriptional start site (+40k) mediates significant repressive activity in pro-T cells (Hosokawa et al, 2018a). This site was bound less strongly in the Scid.adh.2C2 cell line, where repression is leaky, than in primary pro-T cells, but it was completely unbound in ILC2/b6 cells ( Fig.…”

“…3 B). Similar to Runx1 (Hosokawa et al, 2018a), Runx3 co-bound with Bcl11b at "pro-T cell sites" in Scid.adh.2c2 cells and a highly overlapping set of sites in primary DN2b/DN3 cells, but was found at the distinct "ILC2" sites of Bcl11b binding in ILC2/b6 cells ( Fig. 3 B and Fig.…”

“…To investigate how Bcl11b could exert such different actions, we examined the binding profiles of known and likely Bcl11b interaction partners that might be differentially active in pro-T and ILC2 cells. We previously reported that Runx1 is one of the most important binding partners of Bcl11b in pro-T cells (Hosokawa et al, 2018a), and Runx factors are important in ILCs as well (Ebihara et al, 2017;Miyamoto et al, 2019). However, ILC2 cells express less Runx1 and more Runx3 than Scid.adh.2c2 ( Fig.…”

Temporal scaling in developmental gene networks by epigenetic timing control

“…To gain insights into these questions, we investigate an epigenetic mechanism controlling the activation timing of Bcl11b , a T-cell lineage commitment regulator that turns on with an extended delay to enable early progenitor expansion (Figure 2A). After entering the thymus, hematopoietic progenitor cells turn on Bcl11b to commit to the T-cell lineage (Hosokawa et al, 2018;Ikawa et al, 2010;Li et al, 2010aLi et al, , 2010b . Bcl11b activation requires Notch signals in the thymus, along with multiple transcription factors that are up-regulated by Notch signaling (García-Ojeda et al, 2013;Germar et al, 2011;Li et al, 2010b;Weber et al, 2011) .…”