Matrix attachment regions (MARs) are DNA sequences that bind non-histone proteins in the chromatin scaffold and define discrete loops of DNA containing expressed genes in vivo. I have been studying the effects of flanking transgenes with MARs on transgene expression levels in BMS maize callus. Three MAR elements, two from maize (Adhl 5' MAR and Mhal 5' MAR) and one from yeast (ARS1), have very different effects on transgene expression that bear no relation to their affinity for the nuclear matrix in vitro. The main effect of MARs is to prevent silencing of some (but not all) transgenes, at least when transgene silencing is operative. Additionally, MARs can influence the establishment and heritability of transgene transcription states. During a period of five years, I found that the degree of transgene silencing in BMS cultures was progressively lost. The protective effect of MARs against transgene silencing was also progressively lost, suggesting that trans-acting factors responsible for both effects were gradually lost as the cells aged. This observation is very similar to observations made in yeast where SIR proteins that are responsible for establishment and heritability of gene silencing are lost or rendered functionally inactive as cells age. In yeast, SIR proteins also interact with the machinery responsible for non-homologous recombination (i.e. end-joining), and loss of SIR function is associated with reduced end-joining. Similarly, as transgene silencing was lost in BMS cultures, the levels of end-joining (as measured by stable transformation frequencies) also decreased. Thus, factors involved in cellular aging, transgene silencing, end-joining, and the in vivo effects of matrix attachment regions in a multicellular eukaryotic system may be inter-related, much as they are in yeast.