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The analysis of allele-specific gene expression has been of long-standing interest in the study of genomic imprinting, but there is growing awareness that differences in allelic expression are widespread among autosomal nonimprinted genes. Recent research into cis-acting regulatory polymorphisms has utilized the analysis of allele-specific gene expression to identify functionally important regulatory haplotypes and specific genetic polymorphisms. Allele-specific effects are typically of modest magnitude, requiring techniques for analysis of high sensitivity and specificity. Here, strategic approaches to the analysis of allele-specific gene expression are reviewed with protocols for in vivo analysis. These include analysis of the relative allelic abundance of transcribed RNA and of transcription factor recruitment and Pol II loading by chromatin immunoprecipitation.

Original publication




Journal article


Methods Mol Biol

Publication Date





153 - 165


Alleles, Cell Line, Chromatin Immunoprecipitation, DNA, Complementary, Gene Expression, Genetic Techniques, Humans, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, RNA, Transcription, Genetic