Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1

Abstract

We provide evidence for the location of matrix attachment sites along a contiguous region of 280 kb on maize chromosome 1. We define nine potential loops that vary in length from 6 kb to >75 kb. The distribution of the different classes of DNA within this continuum with respect to the predicted structural loops reveals an interesting correlation: the long stretches of mixed classes of highly repetitive DNAs are often segregated into topologically sequestered units, whereas low-copy-number DNAs (including the alcohol dehydrogenase1 [adh1] gene) are positioned in separate loops. Contrary to expectations, several classes of highly repeated elements with representatives in this region were found to be transcribed, and some of these exhibited tissue-specific patterns of expression.