Multiple defects in mouse stem cell based embryo models lacking all Hox function [ATAC-seq]

Mammals have four genomic copies of an ancestral Hox cluster, with a total of 39 genes. While gene inactivation approaches and full cluster deletions have revealed their critical functions during early development, the effect of removing all Hox function has remained elusive due to both biological and technological challenges. We have used mouse gastruloids, an ES cells-derived embryo model where Hox genes are properly activated in time and space, to assess the effect of their complete absence. We report that gastruloids lacking Hox function can still elongate and reach a general shape resembling their control counterparts, with a well-established AP polarity. However, unlike controls, they fail to produce any endoderm and are unable to properly segment their presomitic mesoderm into persistent somite-like structures. Instead, they produce a type of mesoderm with a more anterior identity. We thus propose that, in this system at least, HOX proteins are necessary to posteriorize an existing anterior ‘ground-state’ structure, in part by promoting and/or maintaining the epithelialization of cellular condensations. Multiomes analysis revealed range of modifications in chromatin accessibility in the absence of any HOX proteins, involving in particular variations in the binding of the co-factor PBX1. In contrast, neuro-mesodermal progenitor (NMP) cells are not overtly affected in mutant gastruloids, even though they normally initiate strong Hox gene transcription, suggesting that these cells are used as vehicles to translate a temporal sequence of activation into an AP colinear transcript distribution, which becomes functional at a later stage only.