A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation

Abstract

Two mechanisms that play important roles in cell fate decisions are control of a “core transcriptional network” and repression of alternative transcriptional programs by antagonizing transcription factors. Whether these two mechanisms operate together is not known. Here we report that GATA-1, SCL, and Klf1 form an erythroid core transcriptional network by co-occupying >300 genes. Importantly, we find that PU.1, a negative regulator of terminal erythroid differentiation, is a highly integrated component of this network. GATA-1, SCL, and Klf1 act to promote, whereas PU.1 represses expression of many of the core network genes. PU.1 also represses the genes encoding GATA-1, SCL, Klf1, and important GATA-1 cofactors. Conversely, in addition to repressing PU.1 expression, GATA-1 also binds to and represses >100 PU.1 myelo-lymphoid gene targets in erythroid progenitors. Mathematical modeling further supports that this dual mechanism of repressing both the opposing upstream activator and its downstream targets provides a synergistic, robust mechanism for lineage specification. Taken together, these results amalgamate two key developmental principles, namely, regulation of a core transcriptional network and repression of an alternative transcriptional program, thereby enhancing our understanding of the mechanisms that establish cellular identity.

Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1

“…Moreover, PU.1 also blocks expression of genes associated with other variant cell fates, such as Gata2, Zbtb16, Prf1, and probably Il2rb, which could promote mast cell, innate lymphocyte, or NK cell pathways that are much less Notch-dependent. PU.1 is capable of acting as a direct repressor (Rekhtman et al 2003;Stopka et al 2005;Hu et al 2011;Wontakal et al 2012;de la Rica et al 2013), and our results suggest that it down-regulates Sox13 and Il7r directly. However, its repressive effects on most T-cell genes work through an indirect mechanism.…”

“…In fact, T-lineage cells must silence PU.1 completely before they are mature (Anderson et al 2002). PU.1 binds to tens of thousands of genomic sites, which differ in erythroid cells, myeloid cells, B cells, and early T cells (Ghisletti et al 2010;Heinz et al 2010;Wontakal et al 2011Wontakal et al , 2012Ridinger-Saison et al 2012;Zhang et al 2012;Ostuni et al 2013), but in all of these cases, the majority of the binding sites detected are likely to be nonfunctional. To clarify why this regulatory protein is so important for hematopoiesis, we dissected its role in a developmental pathway where its function is restricted to the earliest uncommitted progenitor states: the T-cell pathway.…”

Extrinsic and intrinsic control by EKLF (KLF1) within a specialized erythroid niche

“…4C). This overlaps with GATA1, TAL1 and p300 binding, consistent with the 'core' transcription factor observations that have been noted at a subset of EKLF binding sites (Li et al, 2013;Su et al, 2013;Tallack et al, 2012;Wontakal et al, 2012). Inspection of the EKLF DNA binding cognate sequence shows that it falls into the 'class I' site category within 5 0 -CCMCRCCCN, and thus should bind the neonatal anemia (Nan) EKLF variant based on our analysis of Nan-EKLF biochemical properties (Siatecka and Bieker, 2011;Siatecka et al, 2010).…”

Erythro-megakaryocytic transcription factors associated with hereditary anemia

“…These changes are believed to regulate its interactions with partner proteins and to control its activity in vivo. 50 In MEPs, KLF1 expression contributes to the specification of erythroid cell fate by competing with the MEG factor FLI1. 1,2 Mutations affecting KLF1 function cause isolated anemia without thrombocytopenia.…”