Genetic and epigenetic dissection of cis regulatory variation

Current Opinion in Plant Biology

Volumn 10, Issue 2, 2007, Pages 142-148

  Zhang, Xu ^a   Richards, Eric J ^b   Borevitz, Justin O ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; GENETIC EPIGENESIS; GENETIC VARIABILITY; GENETICS; QUANTITATIVE TRAIT LOCUS; REGULATORY SEQUENCE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

ARABIDOPSIS; EPIGENESIS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REGULATORY SEQUENCES, NUCLEIC ACID; VARIATION (GENETICS);

EID: 33847296166     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2007.02.002     Document Type: Review

References (56)

1. Yvert G., Brem R.B., Whittle J., Akey J.M., Foss E., Smith E.N., Mackelprang R., and Kruglyak L. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35 (2003) 57-64
2. Brem R.B., Yvert G., Clinton R., and Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science 296 (2002) 752-755
3. Schadt E.E., Monks S.A., Drake T.A., Lusis A.J., Che N., Colinayo V., Ruff T.G., Milligan S.B., Lamb J.R., Cavet G., et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422 (2003) 297-302
4. Ronald J., Brem R.B., Whittle J., and Kruglyak L. Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet 1 (2005) e25
5. Brem R.B., Storey J.D., Whittle J., and Kruglyak L. Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436 (2005) 701-703. A systematic analysis of eQTL epistasis in yeast.
6. Zhang X., Yazaki J., Sundaresan A., Cokus S., Chan S.W., Chen H., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E., et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126 (2006) 1189-1201. The first genome-wide high-density methylation map of an organism.
7. Zilberman D., Gehring M., Tran R.K., Ballinger T., and Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39 (2007) 61-69
8. Borevitz J.O., and Ecker J.R. Plant genomics: the third wave. Annu Rev Genomics Hum Genet 5 (2004) 443-477. A comprehensive review on the application of tiling arrays.
9. Gibson G., Riley-Berger R., Harshman L., Kopp A., Vacha S., Nuzhdin S., and Wayne M. Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster. Genetics 167 (2004) 1791-1799. The authors describe the first study in which non-additivity and maternal effects are tested using large-scale expression data.
10. Wayne M.L., Pan Y.J., Nuzhdin S.V., and McIntyre L.M. Additivity and trans-acting effects on gene expression in male Drosophila simulans. Genetics 168 (2004) 1413-1420
11. Ranz J.M., Namgyal K., Gibson G., and Hartl D.L. Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Res 14 (2004) 373-379
12. Vuylsteke M., van Eeuwijk F., Van Hummelen P., Kuiper M., and Zabeau M. Genetic analysis of variation in gene expression in Arabidopsis thaliana. Genetics 171 (2005) 1267-1275
13. Wang J., Tian L., Lee H.S., Wei N.E., Jiang H., Watson B., Madlung A., Osborn T.C., Doerge R.W., Comai L., et al. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172 (2006) 507-517
14. Auger D.L., Gray A.D., Ream T.S., Kato A., Coe Jr. E.H., and Birchler J.A. Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics 169 (2005) 389-397
15. 1 hybrid. Genetics 173 (2006) 2199-2210
16. 1 hybrid and its inbred parents. Proc Natl Acad Sci USA 103 (2006) 6805-6810
17. Cowles C.R., Hirschhorn J.N., Altshuler D., and Lander E.S. Detection of regulatory variation in mouse genes. Nat Genet 32 (2002) 432-437
18. Doss S., Schadt E.E., Drake T.A., and Lusis A.J. Cis-acting expression quantitative trait loci in mice. Genome Res 15 (2005) 681-691
19. Lo H.S., Wang Z., Hu Y., Yang H.H., Gere S., Buetow K.H., and Lee M.P. Allelic variation in gene expression is common in the human genome. Genome Res 13 (2003) 1855-1862
20. Pastinen T., Sladek R., Gurd S., Sammak A., Ge B., Lepage P., Lavergne K., Villeneuve A., Gaudin T., Brandstrom H., et al. A survey of genetic and epigenetic variation affecting human gene expression. Physiol Genomics 16 (2004) 184-193
21. Wittkopp P.J., Haerum B.K., and Clark A.G. Evolutionary changes in cis and trans gene regulation. Nature 430 (2004) 85-88
22. Wittkopp P.J., Haerum B.K., and Clark A.G. Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting. Genetics 173 (2006) 1817-1821
23. Carrel L., and Willard H.F. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434 (2005) 400-404
24. Jaenisch R., and Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 Suppl (2003) 245-254
25. Caron H., van Schaik B., van der Mee M., Baas F., Riggins G., van Sluis P., Hermus M.C., van Asperen R., Boon K., Voute P.A., et al. The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291 (2001) 1289-1292
26. Zhu T. Global analysis of gene expression using GeneChip microarrays. Curr Opin Plant Biol 6 (2003) 418-425
27. Manning K., Tor M., Poole M., Hong Y., Thompson A.J., King G.J., Giovannoni J.J., and Seymour G.B. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38 (2006) 948-952
28. Cubas P., Vincent C., and Coen E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401 (1999) 157-161
29. Bastow R., Mylne J.S., Lister C., Lippman Z., Martienssen R.A., and Dean C. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427 (2004) 164-167
30. Shindo C., Lister C., Crevillen P., Nordborg M., and Dean C. Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response. Genes Dev 20 (2006) 3079-3083
31. Lippman Z., Gendrel A.V., Black M., Vaughn M.W., Dedhia N., McCombie W.R., Lavine K., Mittal V., May B., Kasschau K.D., et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 430 (2004) 471-476
32. Klose R.J., and Bird A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31 (2006) 89-97
33. Tran R.K., Henikoff J.G., Zilberman D., Ditt R.F., Jacobsen S.E., and Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol 15 (2005) 154-159
34. Morgan H.D., Santos F., Green K., Dean W., and Reik W. Epigenetic reprogramming in mammals. Hum Mol Genet 14 Spec No1 (2005) R47-R58
35. Ruiz-Garcia L., Cervera M.T., and Martinez-Zapater J.M. DNA methylation increases throughout Arabidopsis development. Planta 222 (2005) 301-306
36. Steimer A., Schob H., and Grossniklaus U. Epigenetic control of plant development: new layers of complexity. Curr Opin Plant Biol 7 (2004) 11-19
37. Kakutani T., Jeddeloh J.A., Flowers S.K., Munakata K., and Richards E.J. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci USA 93 (1996) 12406-12411
38. Chan S.W., Henderson I.R., Zhang X., Shah G., Chien J.S., and Jacobsen S.E. RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLoS Genet 2 (2006) e83
39. Weber M., Davies J.J., Wittig D., Oakeley E.J., Haase M., Lam W.L., and Schubeler D. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37 (2005) 853-862
40. Khulan B., Thompson R.F., Ye K., Fazzari M.J., Suzuki M., Stasiek E., Figueroa M.E., Glass J.L., Chen Q., Montagna C., et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 16 (2006) 1046-1055
41. Ching T.T., Maunakea A.K., Jun P., Hong C., Zardo G., Pinkel D., Albertson D.G., Fridlyand J., Mao J.H., Shchors K., et al. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet 37 (2005) 645-651
42. Keshet I., Schlesinger Y., Farkash S., Rand E., Hecht M., Segal E., Pikarski E., Young R.A., Niveleau A., Cedar H., et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 38 (2006) 149-153
43. Schadt E.E. Exploiting naturally occurring DNA variation and molecular profiling data to dissect disease and drug response traits. Curr Opin Biotechnol 16 (2005) 647-654
44. Mehrabian M., Allayee H., Stockton J., Lum P.Y., Drake T.A., Castellani L.W., Suh M., Armour C., Edwards S., Lamb J., et al. Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat Genet 37 (2005) 1224-1233
45. Rockman M.V., and Kruglyak L. Genetics of global gene expression. Nat Rev Genet 7 (2006) 862-872
46. Storey J.D., Akey J.M., and Kruglyak L. Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol 3 (2005) e267
47. Zou F., Gelfond J.A., Airey D.C., Lu L., Manly K.F., Williams R.W., and Threadgill D.W. Quantitative trait locus analysis using recombinant inbred intercrosses: theoretical and empirical considerations. Genetics 170 (2005) 1299-1311
48. Riddle N.C., and Richards E.J. Genetic variation in epigenetic inheritance of ribosomal RNA gene methylation in Arabidopsis. Plant J 41 (2005) 524-532
49. Mockler T.C., Chan S., Sundaresan A., Chen H., Jacobsen S.E., and Ecker J.R. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85 (2005) 1-15
50. Schumacher A., Kapranov P., Kaminsky Z., Flanagan J., Assadzadeh A., Yau P., Virtanen C., Winegarden N., Cheng J., Gingeras T., et al. Microarray-based DNA methylation profiling: technology and applications. Nucleic Acids Res 34 (2006) 528-542
51. Cawley S., Bekiranov S., Ng H.H., Kapranov P., Sekinger E.A., Kampa D., Piccolboni A., Sementchenko V., Cheng J., Williams A.J., et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116 (2004) 499-509
52. Borevitz J.O., Liang D., Plouffe D., Chang H.S., Zhu T., Weigel D., Berry C.C., Winzeler E., and Chory J. Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13 (2003) 513-523
53. Rabbee N., and Speed T.P. A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics 22 (2006) 7-12
54. Kirst M., Caldo R., Casati P., Tanimoto G., Walbot V., Wise R.P., and Buckler E.S. Genetic diversity contribution to errors in short oligonucleotide microarray analysis. Plant Biotech J 4 (2006) 489-498
55. Ronald J., Akey J.M., Whittle J., Smith E.N., Yvert G., and Kruglyak L. Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res 15 (2005) 284-291. The authors describe an approach to detect allele-specific expression using mRNA tiling array data.
56. Castle J., Garrett-Engele P., Armour C.D., Duenwald S.J., Loerch P.M., Meyer M.R., Schadt E.E., Stoughton R., Parrish M.L., Shoemaker D.D., et al. Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol 4 (2003) R66