Association of the thyroid hormone receptor with rat liver chromatin

We have investigated the association of the triiodothyronine (T3) nuclear receptor with rat liver chromatin by the use of selective endonuclease digestion and differential solubilization. The T3 receptor was found in a fraction of chromatin having some of the characteristics of active chromatin: (a) It is highly sensitive to DNase I and micrococcal nuclease digestion; (b) it is enriched in nonhistone proteins and depleted of histone (H-1). Micrococcal nuclease and pancreatic DNase I excised two receptor-containing fragments from chromatin, a minor (12--14 S) form and a major (5.5--6.0 S) form. The latter structure has a Stokes radius of 42 +/- 2 A and an estimated molecular weight of 95400 when a partial specific volume of 0.725 cm3/g for protein is used. It contains DNA but no histones. Similar receptor-containing fragments were excised from chromatin of other rat tissues, including brain, kidney, and heart. Both the 5.5--6 S and the 12--14 S receptor-containing chromatin structures are converted by 0.5 M KCl to the 3.5 S form (R0 35 A molecular weight 50500). Titration with micrococcal nuclease and pancreatic DNase I revealed that the 5.5--6 S form is preferentially excised by endonuclease. Neither receptor occupancy nor thyroidal status had an apparent effect on the susceptibility of chromatin to endonucleolytic digestion nor did they influence the distribution of T3 receptors in chromatin. Our results suggest that T3 receptors are not tightly associated with nucleosomes, the basic subunit of chromatin, but are associated with the DNA-linking nucleosomes in structurally modified regions of chromatin in rat liver nuclei. The T3 receptor-containing fragment may well represent a higher order of structural complexity necessary for T3 action at the cellular level.