Abstract
Advances in molecular and computational biology in recent years have led to the development or the improvement of methods for analyzing global gene expression. In most of these efforts, it is assumed that alleles of different origins contribute equally to the transcript pool. However, accumulating evidence suggests that many genes are not equally expressed from the paternal and maternal chromosomes. In addition to imprinting, the phenomenon of imbalanced allelic expression is widespread in heterozygous individuals. To distinguish transcript pools derived from different alleles present in the same organism, a number of methods have been developed. Here, we describe an oligonucleotide tiling microarray-based assay for analyzing allele-specific gene expression. Specifically targeting single-nucleotide polymorphisms, this two-step assay offers a high-throughput and multiplex method for detecting and quantifying unequal allelic expression that is readily applicable to many experimental systems.
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References
Buckland PR (2004) Allele-specific gene expression in humans. Hum Mol Genet 13:255–260
Milani L, Gupta M, Andersen M et al (2007) Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells. Nucleic Acids Res 35:e34
Springer NM, Stupar RM (2007) Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell 19:2391–2402
Khatib H (2007) Is it genomic imprinting or preferential expression? Bioessays 29:1022–1028
Yan H, Yuan W, Velculescu VE et al (2002) Allelic variation in human gene expression. Science 297:1143
Bray NJ, Buckland PR, Owen MJ et al (2003) Cis-acting variation in the expression of a high proportion of genes in human brain. Hum Genet 113:149–153
Lo HS, Wang Z, Hu Y et al (2003) Allelic variation in gene expression is common in the human genome. Genome Res 13:1855–1862
Ha G, Roth A, Bashashati A et al (2012) Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer. Genome Res. doi:10.1101/gr.137570.112
Guo M, Rupe MA, Zinselmeier C et al (2004) Allelic variation of gene expression in maize hybrids. Plant Cell 16:1707–1716
Stupar RM, Springer NM (2006) Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid. Genetics 173:2199–2210
Adams KL, Cronn R, Percifield R et al (2003) Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 100:4649–4654
Wang J, Tian L, Lee HS et al (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172:507–517
Flagel L, Udall JA, Nettleton D et al (2008) Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biol 6:16
Jeong S, Hahn Y, Rong Q et al (2007) Accurate quantitation of allele-specific expression patterns by analysis of DNA melting. Genome Res 17:1093–1100
Winter E, Yamamoto F, Almoguera C et al (1985) A method to detect and characterize point mutations in transcribed genes: amplification and overexpression of the mutant c-Ki-ras allele in human tumor cells. Proc Natl Acad Sci USA 82:7575–7579
Singer-Sam J, Chapman V, LeBon JM et al (1992) Parental imprinting studied by allele-specific primer extension after PCR: paternal X chromosome-linked genes are transcribed prior to preferential paternal X chromosome inactivation. Proc Natl Acad Sci USA 89:10469–10473
Skelly DA, Johansson M, Madeoy J et al (2011) A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Res 21:1728–1737
Deveale B, van der Kooy D, Babak T (2012) Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PLoS Genet 8:e1002600
Liljedahl U, Fredriksson M, Dahlgren A et al (2004) Detecting imbalanced expression of SNP alleles by minisequencing on microarrays. BMC Biotechnol 4:24
Ronald J, Akey JM, Whittle J et al (2005) Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res 15:284–291
Udall JA, Swanson JM, Nettleton D et al (2006) A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics 173:1823–1827
Yamada K, Lim J, Dale JM et al (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842–846
Li L, Wang XF, Stolc V et al (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38:124–129
Li L, He H, Zhang J et al (2008) Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol 9:R57
Li L, Wang XF, Sasidharan R, Stolc V, Deng W, He H et al (2007) Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One 2:e294
Li L, Wang XF, Xia M, Stolc V, Su N, Peng Z et al (2005) Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol 6:R52
Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR et al (2009) Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol 10:R17
Kurihara Y, Kaminuma E, Matsui A, Kawashima M, Tanaka M, Morosawa T et al (2009) Transcriptome analyses revealed diverse expression changes in ago1 and hyl1 Arabidopsis mutants. Plant Cell Physiol 50:1715–1720
He H, Zhang H, Wang X, Wu N, Yang X, Chen R et al (2010) Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression. Genomics 96:308–315
Yu J, Wang J, Lin W, Li S, Li H, Zhou J et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3:e38
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Zhang, H., Deng, XW., Li, L. (2013). Analysis of Allele-Specific Gene Expression Using a Target-Oriented Tiling Microarray Assay. In: Lee, TL., Shui Luk, A. (eds) Tiling Arrays. Methods in Molecular Biology, vol 1067. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-607-8_5
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DOI: https://doi.org/10.1007/978-1-62703-607-8_5
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