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* The Scripps Research Institute, La Jolla, CA 92037; and
Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
A major component in controlling V(D)J recombination is
differential accessibility through localized changes in chromatin
structure. Attachment of DNA to the nuclear matrix via matrix
attachment region (MAR) sequences, and interaction with MAR-binding
proteins have been shown to alter chromatin conformation, promote
histone acetylation, and influence gene transcription. In this study,
the flanking regions of several human and mouse Ig VH and
Ig V
genes were analyzed extensively for the presence of MARs by in
vitro matrix-binding assay, and for interaction with the MAR-binding
proteins cut-like protein x/CCAAT-displacement protein (Cux/CDP), B
cell regulator of IgH transcription (Bright), and special AT-rich
sequence-binding protein (SATB1) by EMSA. Cux/CDP and SATB1 are
associated with repression, while Bright is an activator of Ig
transcription. Binding sites were identified in the vicinity of all
analyzed Ig V genes, and were also found flanking TCR V
genes. We
also show that the binding sites of the different factors do not always
occur at MAR sequences. MAR sequences were also found within the Ig V
loci at a much higher frequency than throughout the rest of the genome.
Overall, the frequency and location of binding sites relative to the
coding regions, and the strength of DNA-protein interaction showed much
heterogeneity. Thus, variations in factor binding and MAR activity
could potentially influence the extent of localized accessibility to
V(D)J recombination and thus could play a role in unequal rearrangement
of individual V genes. These sites could also contribute to effective
transcription of Ig genes in mature and/or activated B cells, bringing
both the promoter as well as the enhancer regions into close proximity
at the nuclear matrix.
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