Finally, there is a hyc locus in M. tuberculosis, M. kansasii, M. marinum and M. ulcerans without features of transposition or homologous recombination.
It has been speculated that this preference for insertion near genes may reflect interactions between the transposition machinery and some features of chromatin structure such as compactness/density of nucleosomes (Hancock et al. 2011).
Other observations also stress transposition as an intrinsic feature of at least some sequences arranged in tandem.
Dicentric chromosome formation is a characteristic feature of alternative transposition reactions, such as RET, involving two nearby Ac/Ds elements (Huang and Dooner, 2008; Yu et al., 2010).
Our results are consistent with that of Kelleher and Barbash (2013) who performed linear regression analysis for a number of different genomic features, including the transposition rate of active TEs, and concluded that there are limits to the optimization of host defense mechanisms.
Thus, this mode of transposition might be a unifying feature of the Mutator superfamily of transposases.
If ZmhelA1 indeed function as an autonomous element, then it would suggest that RPA1 is not an indispensable feature for helitrons transposition.
This approach will take advantage of the well documented Ac/Ds feature of preferential transposition to chromosomally linked positions [ 48], equally observed in barley [ 12, 25].
To further understand the characteristics of helitrons as well as the features of their transpositions, we have again developed a set of PERL scripts to search for additional helitrons in the maize genome.
The preferential insertion into expressed genomic sequences is a feature of Ac/Ds transposition, that has been well documented in barley [ 12, 13, 27], Arabidopsis [ 42, 43] and rice [ 44, 45, 40].
