MULTIPLE PROMOTERS AND ALTERNATIVE SPLICING: Hoxa5 TRANSCRIPTIONAL COMPLEXITY IN THE MOUSE EMBRYO

DISCUSSION:
This research paper discusses about the Hox clusters and participation of larger transcripts in transcriptional regulation relate to the possibility that Hoxa5 larger transcripts may be involved with the Hox gene expression. The paper starts with the introduction of the Hox clusters, in Mammals it has been observed that there are 39 Hox genes and are spread along four clusters. If the Hox genes are not expressed properly in the animal it may lead to malformations like tumors. The authors of the paper have used Hoxa5 gene as model to study the expression of the Hox gene. This gene plays an important role in the development of embryo and related to formation of tumors. In a growing embryo Hoxa5 is expressed in Neural tube caudal to posterior myelencephalon, in the axial skeleton upto the level of prevertebra and in the mesenchymal components of different organs like kidneys, trachea, and stomach. The paper also shows in the results that loss of this gene in mouse affects well defined structures situated at the cervicothoracic level. The most abundant of all the transcripts in Hoxa5 gene is 1.8 kb which corresponds to two exons and encodes HOXA5 protein of 270 amino acids in length. There are multiple overlapping sites at the Hoxa5 locus and this relates to the theory that the Hoxa5 gene regulation might be very complex. The expression of this gene is involving different DNA elements located upstream and downstream and some of the regulatory sequences are shared with the Hoxa4 gene while the other sequences overlap with the Hoxa 6 coding sequences. Also there are some larger transcripts encompassing the Hoxa5 coding sequences suggesting that there might be more DNA sequences involved in the Hoxa5 gene regulation and they may be present all over the cluster. The authors in this paper have done the molecular characterization of Hoxa5 gene to know the crucial function of the larger transcripts in the gene regulation of Hoxa5 genes that will lead to knowing of how the genes integrate in the development program. They found several transcriptional units of the Hoxa5 and Hoxa 6 loci which results from the use of three promoters and alternative splicing. Although most of the transcripts found produce 270 amino acids, only the 1.8Kb form seems to produce the real protein. Also the functional domain of Hoxa5 along the embryonic axis coincides with the region of protein that actually expresses and at this place the larger transcripts are not there. The D1 promoter which is the distal one is putative Hoxa6 promoter, and D2 promoter present at downstream to the 3 extremity of the Hoxa7 gene generate larger transcripts. Diversity of the transcripts is also provided by the alternative splicing. There is just one polyadenylation site located at the end of the Hoxa5 locus which is utilized by all transcripts encompassing the Hoxa5 and Hoxa6 sequences.The transcriptional units are conserved between mouse and human and a few are polycistronic. According to the paper Hoxa6 gene does not play a role in the axial specification, it may be involved with other functions that are yet to be discovered and larger transcripts cannot produce the HOXA5 protein. Thus disorder of the larger transcripts will

have no relevant effect on the axial specification, whereas transcription of intergenic regions or upstream promoter sequences can affect the expression of the adjacent genes by generating transcriptional interference, or by changing the chromatin structure. At the end the authors conclude with the following question: whether the Hoxa5 larger transcripts represent their transcriptional noise or do they contribute by themselves to the control of Hox gene expression? Eukaryotic transcriptome structure is revealed by the new technologies, the overlap of transcriptional units and the complications involved like multifunctional roles of genomic sequences have led to the re-evaluation of the current concept of the nature of gene. With the help of Hox cluster in which many of these events do happen we can learn the transcriptional complexity and genome organization.