Exclusion of repetitive DNA elements from gnathostome Hox clusters

Abstract

Despite their homology and analogous function, the Hox gene clusters of vertebrates and invertebrates are subject to different constraints on their structural organization. This is demonstrated by a drastically different distribution of repetitive DNA elements in the Hox cluster regions. While gnathostomes have a strong tendency to exclude repetitive DNA elements from the inside of their Hox clusters, no such trend can be detected in the Hox gene clusters of protostomes. Repeats ''invade'' the gnathostome Hox clusters from the 5 0 and 3 0 ends while the core of the clusters remains virtually free of repetitive DNA. This invasion appears to be correlated with relaxed constraints associated with gene loss after cluster duplications.

Unusual gene order and organization of the sea urchin hox cluster

“…Analyzed with this repeat library the repeat content of the hox region, though a little sparse compared with the currently available BAC sequences, is not otherwise unusual. For example, there is no bias in the distribution of repeats as seen in the repeat-poor gnathostome genomic hox gene sequences (Fried et al, 2003). The remnants of reverse transcriptase coding sequence found in the cluster are far too divergent to have been active recently.…”

Hox clusters as models for vertebrate genome evolution

“…However, not only is the structure of Hox clusters evolutionarily conserved, and possibly constraint, but also there appears to be strong selection against the invasion or spreading of repetitive elements [e.g. short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), long terminal repeats (LTRs) and DNA transposons] in Hox clusters [3,14]. Gene loss, however, is also often accompanied by the invasion of those repetitive elements.…”

“…Gene loss, however, is also often accompanied by the invasion of those repetitive elements. In invertebrates, Hox-cluster structure is less conserved and there is no difference between the number and length of the repetitive sequences within a cluster and those in the surrounding sequences [14]. The compactness of the clusters made it possible to compare, for example, the available HoxA-cluster sequences from shark with those of tetrapods and several other teleost species.…”

Evolution of the vertebrate parahox clusters

“…clusters is relaxed after duplication: repetitive elements, which are otherwise stringently excluded from the Hox clusters have been able to invade in particular regions where genes have been lost (Fried et al, 2004). At least in protostomes, ParaHox genes are furthermore relatively frequently lost: so far all three ParaHox genes have been reported only in two protostome phyla: sipunculans (Ferrier and Holland, 2001) and (basal) molluscs (Barucca et al, 2006).…”