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J Biol Chem, Vol. 273, Issue 45, 29838-29846, November 6, 1998

A Nuclear Matrix Attachment Region Upstream of the T Cell Receptor  Gene Enhancer Binds Cux/CDP and SATB1 and Modulates Enhancer-dependent Reporter Gene Expression but Not Endogenous Gene Expression

From the Center for Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139

We have previously identified a DNase I-hypersensitive site in the T cell receptor  locus, designated HS1, that is located 400 base pairs upstream of the transcriptional enhancer E and is induced during CD4CD8 to CD4⁺CD8⁺ thymocyte differentiation. Using electrophoretic mobility shift assays, we show that HS1 induction correlates with increased binding of two nuclear factors, Cux/CDP and SATB1, to a 170-base pair DNA sequence within HS1. Furthermore, we demonstrate that HS1 is a nuclear matrix attachment region, referred to as MAR. These findings demonstrate that an analogous organization of cis-regulatory elements in which a nuclear matrix attachment region is in close proximity to an enhancer is conserved in the immunoglobulin and T cell receptor loci. In addition, we show that MAR represses E-dependent reporter gene expression in transient transfection assays. However, the targeted deletion of MAR from the endogenous locus does not change T cell receptor  gene transcription in developing T cells. These contrasting results suggest a potential pitfall of functional studies of nuclear matrix attachment regions outside of their natural chromosomal context.

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