<em> Hox </em>Temporal Collinearity: Misleading Fallacy or Essential Developmental Mechanism?

Kondo and collaborators recently reported the absence of Hox temporal collinearity in Xenopus tropicalis. They found none in the initiation of accumulation of&nbsp; Hox transcripts (detected via RNA seq). And none in the initial expression sequence of primary unprorocessed transcripts (Identified by using qRT-PCR against introns or intron-exon boundaries).&nbsp; Nor in the initial acquisition by Hox gene DNA of a mark for active chromatin.&nbsp; These findings are in conflict with the idea that temporal collinearity has to do with the initiation of Hox gene transcription or with the opening of and a progression from repressed to active states in Hox chromatin.&nbsp; But collinear acquisition of the same active chromatin mark has been shown by others in murine 5&rsquo; Hoxd cluster genes.The reason for this difference is unknown . This careful study thus indicated that the initiation phase of Hox expression shows no temporal collinearity in X. tropicalis. A previous study in X. laevis from the same group also showed&nbsp;&nbsp; that the sequence of times for reaching (normalised) half maximal Hox expression showed no temporal collinearity. These conclusions are likely to be correct. These authors do however also conclude that &ldquo;experimental evidence for the temporal collinearity hypothesis is not strong&rdquo; There is however strong evidence that Hox temporal collinearity does occur in early vertebrate embryos.&nbsp;&nbsp; Below. I present and discuss 3 lines of evidence to resolve the present conflict&nbsp;&nbsp; I argue that Hox temporal collinearity actually does exist and that it is part of a central mechanism in early development.