Transgene Integration -In general, transgenes integrate at random sites in any of the chromosomes of the genome of host cells., Usually, in a given cell, integration occurs at a single location. As a result, different cells may be expected to show integration of the trans gene at different chromosomal locations.

The number of copies integrated per genome ranges from one to several hundred. In general, multiple copies are integrated when large amounts of DNA are used for transfection, while single copies are integrated with smaller amounts. When multiple copies are integrated, they are mostly integrated at one site joined to each other head-to-tail, i.e., as a concatemer. However, in a small proportion of cases, the multiple copies are located at several sites in the same genome.

This property can be used to obtain highly amplified integration of any gene simply by linking it to such genes. In addition to random integration, a very low frequency of integration occurs through homologous recombination provided the gene construct has sequences which are homologous to some sequences in the host cell genome. The frequency of homologous recombination based integration is only 0.1 to 1 % of that of random integrations.

The sequences flanking a gene on either side influence the expression of this gene. Therefore, the same trans gene integrated at different locations in the genome may show different levels of expression; this is known as position effect.