Screening for inter-individual splicing differences in human GSTM4 and the discovery of a single nucleotide substitution related to the tandem skipping of two exons.

The glutathione S-transferase Mu class (GSTM) genes encode phase II metabolism enzymes that are involved in the detoxification of various carcinogens and drugs. Some genetic polymorphisms in GSTM genes are related to disease phenotypes and drug-metabolism differences in the population. Polymorphisms that alter gene-splicing patterns are functionally very important because they often lead to the insertion or deletion of many amino acids. To identify inter-individual differences in the splicing pattern of the GSTM4 gene, we used reverse transcriptase polymerase chain reaction (RT-PCR) to screen cDNA from 96 human liver samples. We discovered a novel splice variant of GSTM4 that resulted from tandem skipping of exons 4 and 5. This exon-skipping event is associated with a mutation at the splice acceptor site in intron 4.

[1]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[2]  P K Rogan,et al.  Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites , 1995, Human mutation.

[3]  G. Rijksen,et al.  Ex vivo analysis of aberrant splicing induced by two donor site mutations in PKLR of a patient with severe pyruvate kinase deficiency , 2004, British journal of haematology.

[4]  L. Le Marchand,et al.  Meta- and pooled analyses of the effects of glutathione S-transferase M1 polymorphisms and smoking on lung cancer risk. , 2002, Carcinogenesis.

[5]  Yi Xing,et al.  ASAP: the Alternative Splicing Annotation Project , 2003, Nucleic Acids Res..

[6]  S. Berget.  Exon Recognition in Vertebrate Splicing (*) , 1995, The Journal of Biological Chemistry.

[7]  S. Antonarakis,et al.  Nomenclature for the description of human sequence variations , 2001, Human Genetics.

[8]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[9]  A. Paulussen,et al.  Two linked mutations in transcriptional regulatory elements of the CYP3A5 gene constitute the major genetic determinant of polymorphic activity in humans. , 2000, Pharmacogenetics.

[10]  Ann Daly,et al.  Sequence diversity in CYP3A promoters and characterization of the genetic basis of polymorphic CYP3A5 expression , 2001, Nature Genetics.

[11]  T. D. Schneider,et al.  Information analysis of human splice site mutations , 1998, Human mutation.

[12]  John K Field,et al.  A T2517C polymorphism in the GSTM4 gene is associated with risk of developing lung cancer. , 2002, Lung cancer.

[13]  D. Nickerson,et al.  PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. , 1997, Nucleic acids research.

[14]  Shivendra V. Singh,et al.  Cloning and expression of a novel Mu class murine glutathione transferase isoenzyme. , 2002, The Biochemical journal.

[15]  L. Brooks,et al.  A DNA polymorphism discovery resource for research on human genetic variation. , 1998, Genome research.

[16]  Yongqing Zhang,et al.  Distribution of exonic splicing enhancer elements in human genes. , 2005, Genomics.

[17]  N. Tetlow,et al.  Polymorphism of human mu class glutathione transferases. , 2001, Pharmacogenetics.

[18]  Michael C O'Donovan,et al.  Promoter polymorphisms in glutathione-S-transferase genes affect transcription. , 2004, Pharmacogenetics.

[19]  T. D. Schneider,et al.  Information content of individual genetic sequences. , 1997, Journal of theoretical biology.

[20]  Henry J. Lin,et al.  Pooled analysis and meta-analysis of glutathione S-transferase M1 and bladder cancer: a HuGE review. , 2002, American journal of epidemiology.

[21]  P. Board,et al.  Molecular cloning and heterologous expression of an alternatively spliced human Mu class glutathione S-transferase transcript. , 1993, The Biochemical journal.

[22]  C. Wolf,et al.  Deduced amino acid sequence, gene structure and chromosomal location of a novel human class Mu glutathione S-transferase, GSTM4. , 1993, The Biochemical journal.

[23]  E. Schuetz,et al.  Nonsense mediated decay downregulates conserved alternatively spliced ABCC4 transcripts bearing nonsense codons. , 2003, Human molecular genetics.

[24]  X. Hao,et al.  A comparison of the enzymatic and physicochemical properties of human glutathione transferase M4-4 and three other human Mu class enzymes. , 1994, Archives of biochemistry and biophysics.

[25]  R. Armstrong,et al.  Structure, catalytic mechanism, and evolution of the glutathione transferases. , 1997, Chemical research in toxicology.

[26]  K. Johnson,et al.  Isolation and analysis of the gene and cDNA for a human Mu class glutathione S-transferase, GSTM4. , 1993, The Journal of biological chemistry.

[27]  M. Olivier.  A haplotype map of the human genome , 2003, Nature.

[28]  L. Marchand,et al.  Erratum: Meta- and pooled analyses of the effects of glutathione S-transferase M1 polymorphisms and smoking on lung cancer risk (Carcinogenesis (2002) vol. 23 (1343-1350)) , 2002 .

[29]  C. Burge,et al.  A computational analysis of sequence features involved in recognition of short introns , 2001, Proceedings of the National Academy of Sciences of the United States of America.