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Gene Regulation Section

Ranjan Sen, Ph.D., Chief

Epigenetic changes during VDJ recombination: Multiple epigenetic marks have been proposed to contribute to the regulation of antigen receptor gene assembly via V(D)J recombination. We provide a comprehensive view of DNA methylation at the immunoglobulin heavy chain (IgH) gene locus prior to and during V(D)J recombination. DNA methylation did not correlate with the histone modification state on unrearranged alleles, indicating that these epigenetic marks were regulated independently. Instead, pockets of tissue-specific demethylation were restricted to DNase I hypersensitive sites within this locus. Though unrearranged diversity (D(H)) and joining (J(H)) gene segments were methylated, DJ(H) junctions created after the first recombination step were largely demethylated in pro-, pre-, and mature B cells. Junctional demethylation was highly localized, B-lineage-specific, and required an intact tissue-specific enhancer, Eμ. We propose that demethylation occurs after the first recombination step and may mark the junction for secondary recombination. Three critical constraints govern V(H) recombination. These include timing (V(H) recombination follows D(H) recombination), precision (V(H) gene segments recombine only to DJ(H) junctions) and allele specificity (V(H) recombination is restricted to DJ(H)-recombined alleles). We propose a model for these universal features of V(H) recombination. Analyses of DJ(H)-recombined alleles showed that DJ(H) junctions were selectively epigenetically marked, became nuclease sensitive and bound RAG recombinase proteins, which thereby permitted D(H)-associated recombination signal sequences to initiate the second step of Igh gene assembly. We propose that V(H) recombination is precise, because these changes did not extend to germline D(H) segments located 5' of the DJ(H) junction.

Function of NF-kB Proteins: NF-kB proteins are a family of inducible transcription factors that allow cells to respond to extracellular stimuli. The diverse stimuli that activate NF-kB and the distinct cellular responses that ensue raise the question as to how specificity of the response is regulated. This complexity is most likely a reflection of the several different Rel proteins that constitute the NF-kB family and the several different IkB proteins that inactivate them. For example, there may be differences in the way Rel proteins are sequestered in the cytoplasm, different signals may target different IkBs, and different family members may activate different genes. However, there are very few well characterized examples of such differences and even fewer molecular mechanisms to explain them. Our long-term interest is to attempt to unravel some of this complexity, particularly in cells of the immune system.

Portfolio/Research Areas

  • Molecular Biology/Biochemistry
  • Chromosome Biology/Epigenetics
  • Cell Biology/Cell Signaling
  • Genetics/Genomics
  • Immunology