A comprehensive collection of mouse zinc finger motifs compiled by molecular indexing

Riu Yamashita, Kenichi Matsubara, Kikuya Kato

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

The C2H2 zinc finger motif found in many transcription factors is thought to be for nucleic acid binding and/or dimerization. Nearly 1% of eukaryote genes are estimated to encode this motif. We investigated the gene family encoding this motif in the Mus musculus mRNA by molecular indexing, a technique used to select a subpopulation of cDNA by ligation of adapters to cDNA fragments digested by a class IIS restriction enzyme(s). In place of oligo-dT primers in the original method, a polymerase chain reaction primer designed based on the conserved sequence of the C2H2 zinc finger protein stranded cDNA was made from various mouse tissue mRNAs, digested with FokI and BsmAI, and joined with adapters. Amplification of the cDNA with an adapter primer and zinc finger-specific primer yielded products enriched in zinc finger protein genes. Fragments were separated by subsequent denaturing polyacrylamide gel electrophoresis, and characterized by DNA sequencing. Consequently, 259 C2H2 zinc finger motif sequences were obtained, among which 166 were novel. Combined with the reported sequences, these mouse motif sequences were compared with those of other species such as Saccharomyces cerevisiae and Caenorhabditis elegans. Some of the amino acids in the motif sequence showed strong bias among species. Most of the novel sequences were supposed to be DNA-binding according to the surface potential of predicted tertiary structures.

Original languageEnglish
Pages (from-to)101-110
Number of pages10
JournalGene
Volume274
Issue number1-2
DOIs
Publication statusPublished - 2001 Aug 22

Keywords

  • Molecular indexing
  • Polymerase chain reaction
  • Tertiary structure
  • Transcription factor

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'A comprehensive collection of mouse zinc finger motifs compiled by molecular indexing'. Together they form a unique fingerprint.

Cite this