Identification of novel Hoxa1 downstream targets regulating hindbrain, neural crest and inner ear development

Dev Biol. 2011 Sep 15;357(2):295-304. doi: 10.1016/j.ydbio.2011.06.042. Epub 2011 Jul 18.


Hox genes play a crucial role during embryonic patterning and organogenesis. Of the 39 Hox genes, Hoxa1 is the first to be expressed during embryogenesis and the only anterior Hox gene linked to a human syndrome. Hoxa1 is necessary for the proper development of the brainstem, inner ear and heart in humans and mice; however, almost nothing is known about the molecular downstream targets through which it exerts its function. To gain insight into the transcriptional network regulated by this protein, we performed microarray analysis on tissue microdissected from the prospective rhombomere 3-5 region of Hoxa1 null and wild type embryos. Due to the very early and transient expression of this gene, dissections were performed on early somite stage embryos during an eight-hour time window of development. Our array yielded a list of around 300 genes differentially expressed between the two samples. Many of the identified genes play a role in a specific developmental or cellular process. Some of the validated targets regulate early neural crest induction and specification. Interestingly, three of these genes, Zic1, Hnf1b and Foxd3, were down-regulated in the posterior hindbrain, where cardiac neural crest cells arise, which pattern the outflow tract of the heart. Other targets are necessary for early inner ear development, e.g. Pax8 and Fgfr3 or are expressed in specific hindbrain neurons regulating respiration, e.g. Lhx5. These findings allow us to propose a model where Hoxa1 acts in a genetic cascade upstream of genes controlling specific aspects of embryonic development, thereby providing insight into possible mechanisms underlying the human HoxA1-syndrome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Ear, Inner / cytology
  • Ear, Inner / embryology*
  • Ear, Inner / metabolism
  • Embryo, Mammalian / cytology
  • Embryo, Mammalian / metabolism
  • Gene Expression Regulation, Developmental
  • Gene Targeting
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism*
  • Humans
  • In Situ Hybridization
  • Mice
  • Mice, Inbred C57BL
  • Models, Biological
  • Neural Crest / cytology
  • Neural Crest / embryology*
  • Neural Crest / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Organ Specificity / genetics
  • Phenotype
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction
  • Rhombencephalon / cytology
  • Rhombencephalon / embryology*
  • Rhombencephalon / metabolism
  • Time Factors
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*


  • Homeodomain Proteins
  • Transcription Factors
  • homeobox A1 protein