Dynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells

Abstract

Homeobox a1 (Hoxa1) is one of the most rapidly induced genes in ES cell differentiation and it is the earliest expressed Hox gene in the mouse embryo. In this study, we used genomic approaches to identify Hoxa1-bound regions during early stages of ES cell differentiation into the neuro-ectoderm. Within 2 h of retinoic acid treatment, Hoxa1 is rapidly recruited to target sites that are associated with genes involved in regulation of pluripotency, and these genes display early changes in expression. The pattern of occupancy of Hoxa1 is dynamic and changes over time. At 12 h of differentiation, many sites bound at 2 h are lost and a new cohort of bound regions appears. At both time points the genome-wide mapping reveals that there is significant co-occupancy of Nanog (Nanog homeobox) and Hoxa1 on many common target sites, and these are linked to genes in the pluripotential regulatory network. In addition to shared target genes, Hoxa1 binds to regulatory regions of Nanog, and conversely Nanog binds to a 3′ enhancer of Hoxa1. This finding provides evidence for direct cross-regulatory feedback between Hoxa1 and Nanog through a mechanism of mutual repression. Hoxa1 also binds to regulatory regions of Sox2 (sex-determining region Y box 2), Esrrb (estrogen-related receptor beta), and Myc, which underscores its key input into core components of the pluripotential regulatory network. We propose a model whereby direct inputs of Nanog and Hoxa1 on shared targets and mutual repression between Hoxa1 and the core pluripotency network provides a molecular mechanism that modulates the fine balance between the alternate states of pluripotency and differentiation.

Pluripotency factors regulate the onset of Hox cluster activation in the early embryo

“…We propose that at these early stages, Oct4 plays a dual role, first 12 maintaining Hox genes silent before lineage commitment, and later being required for their proper activation. This behavior is specific for Oct4, as in the case of Nanog we only observe initial repression of Hox genes, which agrees with the recent description of the mutual cross-repression of Nanog and Hoxa1 to differentially regulate a common set of downstream target genes involved in early phases of lineage commitment (51).…”

Nanog regulates Pou3f1 expression and represses anterior fate at the exit from pluripotency

“…We also observed a reduction in the expression of Hoxa1, a marker for posterior neural (hindbrain) fate ( Fig. S3), in line with recent findings (De Kumar et al, 2017;Lopez-Jimenez et al, 2019).…”

Hox genes: Downstream “effectors” of retinoic acid signaling in vertebrate embryogenesis

“…In the case of the Hoxd4 RARE element, Pax6 has been identified as a physical interacting partner, which is highly expressed in the dorsal aspect of the neural tube (Nolte et al, 2006). Parker, Parrish, et al, 2017a). As the DE RARE appears to control the expression of several flanking lncRNA loci (Hobbit and HoxBlinc), there is the possibility that these lncRNAs could regulate global HoxB transcription in trans.…”

“…The vertebrate Hox gene complexes arose by duplication and divergence from a common ancestral cluster through processes involving wholegenome duplications and lineage-specific chromosomal duplications during animal evolution (Kuraku & Meyer, 2009;Meyer & Van de Peer, 2005;Smith & Keinath, 2015). Mammalian Hox proteins have a wide range of downstream target genes that coordinate the activation and repression of genes and signaling pathways associated with their roles in specification of cellular identity (De Kumar, Parker, Parrish, et al, 2017a;De Kumar, Parker, Paulson, Parrish, Pushel, et al, 2017b;De Kumar, Parker, Paulson, Parrish, Zeitlinger, et al, 2017c;Donaldson et al, 2012;Huang et al, 2012;Qian et al, 2018). Coordination of the levels, spatial distribution, and temporal dynamics of Hox gene expression must be precisely controlled to facilitate the progressive activation of their downstream target genes and pathways.…”