The formation of the thumb requires direct modulation of transcription by Hoxa13.

In the tetrapod limb, the digits (fingers or toes) are the elements most subject to morphological diversification in response to functional adaptations. However, despite their functional importance, the mechanisms controlling digit morphology remain poorly understood. Here we have focused on understanding the special morphology of the thumb (digit 1), the acquisition of which was an important adaptation of the human hand. To this end, we have studied the limbs of the mouse mutant that specifically fail to form digit 1. We show that, consistent with the role of Hoxa13 in transcriptional regulation, the expression of in mutant limbs does not extend into the presumptive digit 1 territory, which is therefore devoid of distal transcripts, a circumstance that can explain its agenesis. The loss of expression, exclusively in digit 1 territory, correlates with increased Gli3 repressor activity, a negative regulator, resulting from increased transcription that, in turn, is due to the release from the negative modulation exerted by Hox13 paralogs on regulatory sequences. Our results indicate that Hoxa13 acts hierarchically to initiate the formation of digit 1 by reducing transcription and by enabling expansion of the second expression phase, thereby establishing anterior-posterior asymmetry in the handplate. Our work uncovers a mutual antagonism between Gli3 and Hox13 paralogs that has important implications for and gene regulation in the context of development and evolution.