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Background  The genomic organization of  Hox  clusters is fundamental for the precise spatio-temporal regulation and the function of each  Hox  gene, and hence for correct embryo patterning. Multiple overlapping transcriptional units exist at the  Hoxa5  locus reflecting the complexity of  Hox  clustering: a major form of 1.8 kb corresponding to the two characterized exons of the gene and polyadenylated RNA species of 5.0, 9.5 and 11.0 kb. This transcriptional intricacy raises the question of the involvement of the larger transcripts in  Hox  function and regulation.    Methodology/Principal Findings  We have undertaken the molecular characterization of the  Hoxa5  larger transcripts. They initiate from two highly conserved distal promoters, one corresponding to the putative  Hoxa6  promoter, and a second located nearby  Hoxa7 . Alternative splicing is also involved in the generation of the different transcripts. No functional polyadenylation sequence was found at the  Hoxa6  locus and all larger transcripts use the polyadenylation site of the  Hoxa5  gene. Some larger transcripts are potential  Hoxa6 / Hoxa5  bicistronic units. However, even though all transcripts could produce the genuine 270 a.a. HOXA5 protein, only the 1.8 kb form is translated into the protein, indicative of its essential role in  Hoxa5  gene function. The  Hoxa6  mutation disrupts the larger transcripts without major phenotypic impact on axial specification in their expression domain. However,  Hoxa5 -like skeletal anomalies are observed in  Hoxa6  mutants and these defects can be explained by the loss of expression of the 1.8 kb transcript. Our data raise the possibility that the larger transcripts may be involved in  Hoxa5  gene regulation.    Significance  Our observation that the  Hoxa5  larger transcripts possess a developmentally-regulated expression combined to the increasing sum of data on the role of long noncoding RNAs in transcriptional regulation suggest that the  Hoxa5  larger transcripts may participate in the control of  Hox  gene expression.

Multiple Promoters and Alternative Splicing: Hoxa5 Transcriptional Complexity in the Mouse Embryo