MULTITUDE OF INVERTED REPEATS CHARACTERIZES A CLASS OF ANCHORAGE SITES OF CHROMATIN LOOPS TO THE NUCLEAR MATRIX

In order to understand the nature of DNA sequences that organize chrom atin into domains or loops, we have cloned the nuclear matrix DNA (1.7 % of the total DNA) from human myelogeneous leukemia cells in culture. Nuclear matrix is formed by interactions between specific stretches o f DNA of about 0.1 to 5.0 kb with protein transcription factors, nucle ar enzymes, and structural proteins. Nuclear matrix is believed to be the exclusive nuclear microenvironment in which initiation of DNA repl ication, transcription, and repair take place. The matrix attachment r egions (MARs) of DNA have transcriptional enhancer activity, harbor th e origins of replication of the human genome and define the borders be tween.neighboring chromatin loops. In this study we report the sequenc e of the human MAR fragment 19.2 of a size of 542 bp. Hum. MAR 19.2 is composed of TG-, CA-, CT-, and GA-rich blocks and shows 8 perfect and imperfect inverted repeats. Thus, we have identified a novel class of MARs with sequence characteristics divergent from the AT-rich class o f MARs. The inverted repeats of the 19.2 sequence might be stabilized into their cruciform configuration by torsional strain and by specific transcription/replication protein factors. This MAR might function in the initiation of replication of the flanking chromatim domain and in the regulation of the transcriptional activity of the gene(s) that re side in this domain. (C) 1993 Wiley-Liss, Inc.