Extensive variation between tissues in allele specific expression in an outbred mammal

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Chamberlain, Amanda J ^a,b   Vander Jagt, Christy J ^a,b   Hayes, Benjamin J ^a,b,c   Khansefid, Majid ^a,b,d   Marett, Leah C ^a   Millen, Catriona A ^b,d   Nguyen, Thuy T T ^a   Goddard, Michael E ^a,d  

^a Transport and Resources ^*  (Australia)

^b Dairy Futures Cooperative Research Centre   (Australia)

^c LA TROBE UNIVERSITY   (Australia)

^d UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Allele specific expression; Bovine; Cattle; Differential expression; Gene expression; Regulation; RNA sequencing; Tissue specific expression; Transcriptomics

Indexed keywords

ALLELE; ANIMAL EXPERIMENT; ANIMAL TISSUE; BOVINE; CEREBELLUM; CHROMOSOME; FEMALE; GENE EXPRESSION; GENE FREQUENCY; GENE OVEREXPRESSION; GENOME; GENOTYPE; HETEROZYGOSITY; HOMOZYGOSITY; KIDNEY; LUNG; NONHUMAN; SINGLE NUCLEOTIDE POLYMORPHISM; THYMUS; VALIDATION PROCESS; ANIMAL; ANTIBODY SPECIFICITY; CHROMOSOMAL MAPPING; GENE EXPRESSION PROFILING; GENETICS; GENOME IMPRINTING; MALE; METABOLISM; OUTBRED STRAIN; PROCEDURES; SEQUENCE ANALYSIS;

ALLELES; ANIMALS; ANIMALS, OUTBRED STRAINS; CATTLE; CHROMOSOME MAPPING; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOMIC IMPRINTING; LUNG; MALE; ORGAN SPECIFICITY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, RNA; THYMUS GLAND;

EID: 84947907524     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-2174-0     Document Type: Article

References (41)

1. Pai AA, Pritchard JK, Gilad Y. The Genetic and Mechanistic Basis for Variation in Gene Regulation. PLoS Genet. 2015;11:e1004857.
2. Kleinjan DA, van Heyningen V. Long-range control of gene expression: Emerging mechanisms and disruption in disease. Am J Hum Genet. 2005;76:8-32.
3. Wray GA. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet. 2007;8:206-16.
4. Guenther CA, Tasic B, Luo L, Bedell MA, Kingsley DM. A molecular basis for classic blond hair color in Europeans. Nat Genet. 2014;46:748-52.
5. Karim L, Takeda H, Lin L, Druet T, Arias JAC, Baurain D, et al. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nat Genet. 2011;43:405-15.
6. Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y et al. Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat Genet. 2015, Advanced online article.
7. GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science. 2015;348:648-60.
8. Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, et al. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009;25:3207-12.
9. Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA et al. The landscape of genomic imprinting across diverse adult human tissues. Genome Res. 2015, Ahead of print.
10. Daetwyler HD, Capitan A, Pausch H, Stothard P, Van Binsbergen R, Brøndum RF, et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet. 2014;46:858-65.
11. MacLeod IM, Larkin DM, Lewin HA, Hayes BJ, Goddard ME. Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors. Mol Biol Evol. 2013;30:2209-23.
12. Wang X, Clark AG. Using next-generation RNA sequencing to identify imprinted genes. Heredity. 2014;113:156-66.
13. Wood DLA, Nones K, Steptoe A, Christ A, Harliwong I, Newell F, et al. Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data. PLoS ONE. 2015;10:e0126911.
14. Pant PVK, Tao H, Beilharz EJ, Ballinger DG, Cox DR, Frazer KA. Analysis of allelic differential expression in human white blood cells. Genome Res. 2006;16:331-9.
15. Gao C, Devarajan K, Zhou Y, Slater CM, Daly MB, Chen X. Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome. BMC Genomics. 2012;13:570.
16. Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, et al. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science. 2010;329:643-8.
17. Asselbergs FW, Guo Y, Van Iperen EPA, Sivapalaratnam S, Tragante V, Lanktree MB, et al. Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci. Am J Hum Genet. 2012;91:823-38.
18. Guo T, Yin RX, Chen X, Bin Y, Nie RJ, Li H. Sex-specific association of the SPTY2D1 rs7934205 polymorphism and serum lipid levels. Int J Clin Exp Pathol. 2015;8:665-81.
19. Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature. 2011;477:289-94.
20. Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E et al. Allelic imbalance is a prevalent and tissue-specific feature of the mouse transcriptome. Genet. 2015, 200:ahead of print.
21. Römer AM, Lühr I, Klein A, Friedl A, Sebens S, Rösel F, et al. Normal mammary fibroblasts induce reversion of the malignant phenotype in human primary breast cancer. Anticancer Res. 2013;33:1525-36.
22. Erkko H, Pylkäs K, Karppinen SM, Winqvist R. Germline alterations in the CLSPN gene in breast cancer families. Cancer Lett. 2008;261:93-7.
23. Pelden S, Insawang T, Thuwajit C, Thuwajit P. The trefoil factor 1 (TFF1) protein involved in doxorubicin-induced apoptosis resistance is upregulated by estrogen in breast cancer cells. Oncol Rep. 2013;30:1518-26.
24. Itsumura N, Inamo Y, Okazaki F, Teranishi F, Narita H, Kambe T, et al. Compound Heterozygous Mutations in SLC30A2/ZnT2 Results in Low Milk Zinc Concentrations: A Novel Mechanism for Zinc Deficiency in a Breast-Fed Infant. PLoS ONE. 2013;8.
25. Wang W, Lv N, Zhang S, Shui G, Qian H, Zhang J, et al. Cidea is an essential transcriptional coactivator regulating mammary gland secretion of milk lipids. Nat Med. 2012;18:235-43.
26. Vestergaard E, Nexo E, Wendt A, Guthmann F. Trefoil factors in human milk. Early Hum Dev. 2008;84:631-5.
27. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A. Widespread monoallelic expression on human autosomes. Science. 2007;318:1136-40.
28. Zwemer LM, Zak A, Thompson BR, Kirby A, Daly MJ, Chess A, et al. Autosomal monoallelic expression in the mouse. Genome Biol. 2012;13:R10.
29. Borel C, Ferreira PG, Santoni F, Delaneau O, Fort A, Popadin KY, et al. Biased Allelic Expression in Human Primary Fibroblast Single Cells. Am J Hum Genet. 2015;96:70-80.
30. Nitta T, Takahama Y. The lymphocyte guard-IANs: regulation of lymphocyte survival by IAN/GIMAP family proteins. Trends Immunol. 2007;28:58-65.
31. Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, et al. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol. 2015;16:57.
32. Cheng HH, Perumbakkam S, Black-Pyrkosz A, Dunn JR, Muir WM. Allele-Specific Expression Screening Demonstrates that Variation in Genetic Resistance to Marek's Disease in Chicken is Mainly Controlled at the Transcriptional Level. In. 10th World Congress of Genetics Applied to Livestock Production Conference Proceedings. Vancouver, Canada; 2014.
33. Muir WM, Perumbakkam S, Black-Pyrkosz A, Dunn JR, Cheng HH. Allele-Specific Expression, a New Genomics Tool for Development of Value-Added SNP chips and to Fine Map QTL. In. 10th World Congress of Genetics Applied to Livestock Production. Vancouver, Canada; 2014.
34. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14.
35. Deluca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012;28:1530-2.
36. Anders S, Theodor Pyl P, Huber W. HTSeq - A Python framework to work with high-throughput sequencing data. bioRxiv. 2014, preprint.
37. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (Oxford, England). 2010;26:139-40.
38. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11.
39. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44-57.
40. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.
41. Sargolzaei M, Chesnais JP, Schenkel FS. A new approach for efficient genotype imputation using information from relatives. BMC Genomics. 2014;15:478.