The kappa B transcriptional enhancer motif and signal sequences of V(D)J recombination are targets for the zinc finger protein HIVEP3/KRC: a site selection amplification binding study.
BACKGROUND
The ZAS family is composed of proteins that regulate transcription via specific gene regulatory elements. The amino-DNA binding domain (ZAS-N) and the carboxyl-DNA binding domain (ZAS-C) of a representative family member, named kappaB DNA binding and recognition component (KRC), were expressed as fusion proteins and their target DNA sequences were elucidated by site selection amplification binding assays, followed by cloning and DNA sequencing. The fusion proteins-selected DNA sequences were analyzed by the MEME and MAST computer programs to obtain consensus motifs and DNA elements bound by the ZAS domains.


RESULTS
Both fusion proteins selected sequences that were similar to the kappaB motif or the canonical elements of the V(D)J recombination signal sequences (RSS) from a pool of degenerate oligonucleotides. Specifically, the ZAS-N domain selected sequences similar to the canonical RSS nonamer, while ZAS-C domain selected sequences similar to the canonical RSS heptamer. In addition, both KRC fusion proteins selected oligonucleoties with sequences identical to heptamer and nonamer sequences within endogenous RSS.


CONCLUSIONS
The RSS are cis-acting DNA motifs which are essential for V(D)J recombination of antigen receptor genes. Due to its specific binding affinity for RSS and kappaB-like transcription enhancer motifs, we hypothesize that KRC may be involved in the regulation of V(D)J recombination.
Allen
Carl E
CE
Department of Pediatrics, College of Medicine and Public Health, The Ohio State University, Columbus, OH 43210, USA. allen.111@osu.edu
Mak
Chi-ho
CH
Wu
Lai-Chu
LC
D000818:Animals; D000916:Antibody Diversity / Q000235:genetics; D001482:Base Composition; D018983:DNA Footprinting / Q000379:methods; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D030541:Databases, Genetic; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007128:Immunoglobulin Fragments / Q000235:genetics / Q000378:metabolism*; D007133:Immunoglobulin Joining Region / Q000235:genetics / Q000378:metabolism; D007135:Immunoglobulin Variable Region / Q000235:genetics / Q000378:metabolism; D051379:Mice; D016328:NF-kappa B / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D021382:Protein Sorting Signals / Q000235:genetics*; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D011995:Recombination, Genetic; D012984:Software; D014158:Transcription, Genetic; D016335:Zinc Fingers / Q000235:genetics*
D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C425103:HIVEP3 protein, human; C084779:Hivep3 protein, mouse; D007128:Immunoglobulin Fragments; D007133:Immunoglobulin Joining Region; D007135:Immunoglobulin Variable Region; D016328:NF-kappa B; D021382:Protein Sorting Signals; D011994:Recombinant Proteins