Rhombomere-specific analysis reveals the repertoire of genetic cues expressed across the developing hindbrain

Abstract

Background: The Hox family of homeodomain transcription factors comprises pivotal regulators of cell specification and identity during animal development. However, despite their well-defined roles in the establishment of anteroposterior pattern and considerable research into their mechanism of action, relatively few target genes have been identified in the downstream regulatory network. We have sought to investigate this issue, focussing on the developing hindbrain and the cranial motor neurons that arise from this region. The reiterated anteroposterior compartments of the developing hindbrain (rhombomeres (r)) are normally patterned by the combinatorial action of distinct Hox genes. Alteration in the normal pattern of Hox cues in this region results in a transformation of cellular identity to match the remaining Hox profile, similar to that observed in Drosophila homeotic transformations. Results:To define the repertoire of genes regulated in each rhombomere, we have analysed the transcriptome of each rhombomere from wild-type mouse embryos and not those where pattern is perturbed by gain or loss of Hox gene function. Using microarray and bioinformatic methodologies in conjunction with other confirmatory techniques, we report here a detailed and comprehensive set of potential Hox target genes in r2, r3, r4 and r5. We have demonstrated that the data produced are both fully reflective and predictive of rhombomere identity and, thus, may represent some the of Hox targets. These data have been interrogated to generate a list of candidate genes whose function may contribute to the generation of neuronal subtypes characteristic of each rhombomere. Interestingly, the data can also be classified into genetic motifs that are predicted by the specific combinations of Hox genes and other regulators of hindbrain anteroposterior identity. The sets of genes described in each or combinations of rhombomeres span a wide functional range and suggest that the Hox genes, as well as other regulatory inputs, exert their influence across the full spectrum of molecular machinery. Conclusion:We have performed a systematic survey of the transcriptional status of individual segments of the developing mouse hindbrain and identified hundreds of previously undescribed genes expressed in this region. The functional range of the potential candidate effectors or upstream modulators of Hox activity suggest multiple unexplored mechanisms. In particular, we present evidence of a potential new retinoic acid signalling system in ventral r4 and propose a model for the refinement of identity in this region. Furthermore, the rhombomeres demonstrate a molecular relationship to each other that is consistent with known observations about neurogenesis in the hindbrain. These findings give the first genome-wide insight into the complexity of gene expression during patterning of the developing hindbrain.

Cyp1b1 deletion and retinol deficiency coordinately suppress mouse liver lipogenic genes and hepcidin expression during post-natal development

“…Cyp1b1 expression corresponds to a key period of retinoid regulation of morphogenic patterning genes and overlaps with expression of the retinoid-responsive transcription factor, Hoxb1 , in the hindbrain and the foregut (Chambers et al, 2007, Chambers et al, 2009, Huang et al, 1998, Stoilov et al, 2004). This connection between retinol and Cyp1b1 has led us to investigate neonatal gene expression patterns that may redirect adult liver function.…”

“…CYP1B1 metabolizes retinol to the bioactive retinoic acid (RA) (Chambers et al, 2007, Chambers et al, 2009). Vitamin A (VA)/retinol is obtained from the diet, absorbed in chylomicra, and stored as retinyl ester (RE) in stellate cells of the liver (Bonet et al, 2012, Harrison, 2012).…”

The Homeodomain Transcription Factor Hoxa2 Interacts with and Promotes the Proteasomal Degradation of the E3 Ubiquitin Protein Ligase RCHY1

“…Hox transcriptional targets were also functionally identified through transcriptomic screenings [16,17] and chromatin immunoprecipitation assays [18-21]. …”

Identification of genes downstream of the Shh signalling in the developing chick wing and syn-expressed with Hoxd13 using microarray and 3D computational analysis

“…LMO1, has a homolog in Drosophila, dLMO which negatively regulates activity of the LIM homeodomain transcription factor, Apterous (Zeng et al, 1998) in wing development. Interestingly, LMO1 was recently identified as a potential Hox gene target in the hindbrain (Chambers et al, 2009).…”