Search for basonuclin target genes

Junwen Wang, Shengliang Zhang, Richard M. Schultz, Hung Tseng

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


Basonuclin (Bnc 1) is a transcription factor that has an unusual ability to interact with promoters of both RNA polymerases I and II. The action of basonuclin is mediated through three pairs of evolutionarily conserved zinc fingers, which produce three DNase I footprints on the promoters of rDNA and the basonuclin gene. Using these DNase footprints, we built a computational model for the basonuclin DNA-binding module, which was used to identify in silico potential RNA polymerase II target genes in the human and mouse promoter databases. The target genes of basonuclin show that it regulates the expression of proteins involved in chromatin structure, transcription/DNA-binding, ion-channels, adhesion/cell-cell junction, signal transduction, and intracellular transport. Our results suggest that basonuclin, like MYC, may coordinate transcriptional activities among the three RNA polymerases. But basonuclin regulates a distinctive set of pathways, which differ from that regulated by MYC.

Original languageEnglish (US)
Pages (from-to)1261-1271
Number of pages11
JournalBiochemical and Biophysical Research Communications
Issue number4
StatePublished - Oct 6 2006


  • Bioinformatics
  • Chromatin immunoprecipitation
  • Computational biology
  • DNA binding
  • Orthologous promoters
  • Pathway analysis
  • RNA polymerase I
  • RNA polymerase II
  • Transcription

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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