TY - JOUR
T1 - A comprehensive collection of mouse zinc finger motifs compiled by molecular indexing
AU - Yamashita, Riu
AU - Matsubara, Kenichi
AU - Kato, Kikuya
PY - 2001/8/22
Y1 - 2001/8/22
N2 - 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.
AB - 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.
KW - Molecular indexing
KW - Polymerase chain reaction
KW - Tertiary structure
KW - Transcription factor
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U2 - 10.1016/S0378-1119(01)00547-9
DO - 10.1016/S0378-1119(01)00547-9
M3 - Article
C2 - 11675002
AN - SCOPUS:0035934180
VL - 274
SP - 101
EP - 110
JO - Gene
JF - Gene
SN - 0378-1119
IS - 1-2
ER -