Higher-order chromatin organization is presumed to be mediated in part by DNA sequences that bind to the insoluble nuclear matrix. The function of these ‘matrix attachment regions’ (MARs) has been investigated in transgenic plants. The studies indicated that MARs can reduce variation in, and increase, transgene expression levels. However, the hypothesis that MARs fix chromatin loops to the nuclear matrix and insulate regulatory domains presently lacks firm confirmatory evidence, and alternative models and experimental approaches need to be considered.