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¹ Laboratory of Molecular Gerontology and ² Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
³ Graduate Program in Molecular Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
⁴ Centre national de la recherche scientifique UMR 5089-IPBS, Université de Toulouse, Toulouse Cedex F-31077, France

CORRESPONDENCE Patricia J. Gearhart: gearhartp{at}grc.nia.nih.gov

Repetitive DNA sequences in the immunoglobulin switch µ region form RNA-containing secondary structures and undergo hypermutation by activation-induced deaminase (AID). To examine how DNA structure affects transcription and hypermutation, we mapped the position of RNA polymerase II molecules and mutations across a 5-kb region spanning the intronic enhancer to the constant µ gene. For RNA polymerase II, the distribution was determined by nuclear run-on and chromatin immunoprecipitation assays in B cells from uracil-DNA glycosylase (UNG)–deficient mice stimulated ex vivo. RNA polymerases were found at a high density in DNA flanking both sides of a 1-kb repetitive sequence that forms the core of the switch region. The pileup of polymerases was similar in unstimulated and stimulated cells from Ung^–/– and Aid^–/–Ung^–/– mice but was absent in cells from mice with a deletion of the switch region. For mutations, DNA was sequenced from Ung^–/– B cells stimulated in vivo. Surprisingly, mutations of A nucleotides, which are incorporated by DNA polymerase , decreased 10-fold before the repetitive sequence, suggesting that the polymerase was less active in this region. We propose that altered DNA structure in the switch region pauses RNA polymerase II and limits access of DNA polymerase during hypermutation.

T. Chakraborty's present address is Immune Disease Institute, Harvard Medical School, Boston, MA 02115.

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This article has been cited by other articles:

• Rajagopal, D., Maul, R. W., Ghosh, A., Chakraborty, T., Khamlichi, A. A., Sen, R., Gearhart, P. J. (2009). Immunoglobulin switch {micro} sequence causes RNA polymerase II accumulation and reduces dA hypermutation. JCB 185: i9-i9 [Full Text]  

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