Determinants of expression variability

Nucleic Acids Research

Volumn 42, Issue 6, 2014, Pages 3503-3514

  Alemu, Elfalem Y ^a   Carl Jr , Joseph W ^a   Bravo, Héctor Corrada ^a   Hannenhalli, Sridhar ^a  

^a University of Maryland   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISEASE; EPIGENESIS, GENETIC; GENE EXPRESSION; GENETIC VARIATION; GENOMICS; HUMANS; INTRINSICALLY DISORDERED PROTEINS; POLYMORPHISM, GENETIC; PROMOTER REGIONS, GENETIC; TRANSCRIPTOME;

EID: 84898957989     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1364     Document Type: Article

References (49)

1. Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101, 6062-6067.
2. Sul, J. Y., Kim, T. K., Lee, J. H. and Eberwine, J. (2012) Perspectives on cell reprogramming with RN A. Trends Biotechnol., 30, 243-249.
3. Kim, T. K., Sul, J. Y., Peternko, N. B., Lee, J. H., Lee, M., Patel, V. V., Kim, J. and Eberwine, J. H. (2011) Transcriptome transfer provides a model for understanding the phenotype of cardiomyocytes. Proc. Natl Acad. Sci. USA, 108, 11918-11923.
4. Raj, A. and van Oudenaarden, A. (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell, 135, 216-226.
5. Kaern, M., Elston, T. C., Blake, W. J. and Collins, J. J. (2005) Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet., 6, 451-464.
6. Storey, J. D., Madeoy, J., Strout, J. L., Wurfel, M., Ronald, J. and Akey, J. M. (2007) Gene-expression variation within and among human populations. Am. J. Hum. Genet., 80, 502-509.
7. Stranger, B. E., Montgomery, S. B., Dimas, A. S., Parts, L., Stegle, O., Ingle, C. E., Sekowska, M., Smith, G. D., Evans, D., Gutierrez-Arcelus, M. et al. (2012) Patterns of cis regulatory variation in diverse human populations. PLoS Genet., 8, e1002639.
8. Sun, D., Lennernas, H., Welage, L. S., Barnett, J. L., Landowski, C. P., Foster, D., Fleisher, D., Lee, K. D. and Amidon, G. L. (2002) Comparison of human duodenum and Caco-2 gene expression profiles for 12,000 gene sequences tags and correlation with permeability of 26 drugs. Pharm. Res., 19, 1400-1416.
9. Dong, D., Shao, X., Deng, N. and Zhang, Z. (2011) Gene expression variations are predictive for stochastic noise. Nucleic Acids Res, 39, 403-413.
10. Li, J., Liu, Y., Kim, T., Min, R. and Zhang, Z. (2010) Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Comput. Biol., 6, e1000910.
11. Li, J., Min, R., Vizeacoumar, F. J., Jin, K., Xin, X. and Zhang, Z. (2010) Exploiting the determinants of stochastic gene expression in Saccharomyces cerevisiae for genome-wide prediction of expression noise. Proc. Natl Acad. Sci. USA, 107, 10472-10477.
12. Lehner, B. (2008) Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol. Syst. Biol., 4, 170.
13. Cheung, V. G., Spielman, R. S., Ewens, K. G., Weber, T. M., Morley, M. and Burdick, J. T. (2005) Mapping determinants of human gene expression by regional and genome-wide association. Nature, 437, 1365-1369.
14. Chalancon, G., Ravarani, C. N., Balaji, S., Martinez-Arias, A., Aravind, L., Jothi, R. and Babu, M. M. (2012) Interplay between gene expression noise and regulatory network architecture. Trends Genet, 28, 221-232.
15. Barrett, T., Troup, D. B., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M. et al. (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res, 39, D1005-D1010.
16. McCall, M. N., Bolstad, B. M. and Irizarry, R. A. (2010) Frozen robust multiarray analysis (fRMA). Biostatistics, 11, 242-253.
17. McCall, M. N., Murakami, P. N., Lukk, M., Huber, W. and Irizarry, R. A. (2011) Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics, 12, 137.
18. McCall, M. N., Uppal, K., Jaffee, H. A., Zilliox, M. J. and Irizarry, R. A. (2011) The Gene expression barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res, 39, D1011-D1015.
19. Loader, C. (1999) Local Regression and Likelihood. Springer, New York.
20. Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
21. Matys, V., Kel-Margoulis, O. V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res, 34, D108-D110.
22. Levy, S. and Hannenhalli, S. (2002) Identification of transcription factor binding sites in the human genome sequence. Mamm. Genome, 13, 510-514.
23. Mahony, S., Auron, P. E. and Benos, P. V. (2007) DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput. Biol, 3, e61.
24. Di Domenico, T., Walsh, I., Martin, A. J. and Tosatto, S. C. (2012) MobiDB: a comprehensive database of intrinsic protein disorder annotations. Bioinformatics, 28, 2080-2081.
25. Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C. et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res, 41, D808-D815.
26. Oshlack, A. and Wakefield, M. J. (2009) Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct, 4, 14.
27. Carey, L. B., van Dijk, D., Sloot, P. M., Kaandorp, J. A. and Segal, E. (2013) Promoter sequence determines the relationship between expression level and noise. PLoS Biol, 11, e1001528.
28. Deaton, A. M. and Bird, A. (2011) CpG islands and the regulation of transcription. Genes Dev, 25, 1010-1022.
29. Lin, W. H., Liu, W. C. and Hwang, M. J. (2009) Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. BMC Syst. Biol, 3, 32.
30. Lam, K. C., Muhlpfordt, F., Vaquerizas, J. M., Raja, S. J., Holz, H., Luscombe, N. M., Manke, T. and Akhtar, A. (2012) The NSL complex regulates housekeeping genes in Drosophila. PLoS Genet., 8, e1002736.
31. Kittisopikul, M. and Suel, G. M. (2010) Biological role of noise encoded in a genetic network motif. Proc. Natl Acad. Sci. USA, 107, 13300-13305.
32. To, T. L. and Maheshri, N. (2010) Noise can induce bimodality in positive transcriptional feedback loops without bistability. Science, 327, 1142-1145.
33. Benevolenskaya, E. V. (2007) Histone H3K4 demethylases are essential in development and differentiation. Biochem. Cell Biol., 85, 435-443.
34. Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I. and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
35. Edmunds, J. W., Mahadevan, L. C. and Clayton, A. L. (2008) Dynamic histone H3 methylation during gene induction: HYPB/ Setd2 mediates all H3K36 trimethylation. EMBO J, 27, 406-420.
36. Ernst, J. and Kellis, M. (2012) ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods, 9, 215-216.
37. Uversky, V. N., Oldfield, C. J., Midic, U., Xie, H., Xue, B., Vucetic, S., Iakoucheva, L. M., Obradovic, Z. and Dunker, A. K. (2009) Unfoldomics of human diseases: linking protein intrinsic disorder with diseases. BMC Genomics, 10(Suppl. 1), S7.
38. Dunker, A. K., Cortese, M. S., Romero, P., Iakoucheva, L. M. and Uversky, V. N. (2005) Flexible nets. The roles of intrinsic disorder in protein interaction networks. FEBS J, 272, 5129-5148.
39. Dunker, A. K., Silman, I., Uversky, V. N. and Sussman, J. L. (2008) Function and structure of inherently disordered proteins. Curr. Opin. Struct. Biol., 18, 756-764.
40. Batada, N. N. and Hurst, L. D. (2007) Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat. Genet., 39, 945-949.
41. Vavouri, T., Semple, J. I., Garcia-Verdugo, R. and Lehner, B. (2009) Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell, 138, 198-208.
42. Mar, J. C., Matigian, N. A., Mackay-Sim, A., Mellick, G. D., Sue, C. M., Silburn, P. A., McGrath, J. J., Quackenbush, J. and Wells, C. A. (2011) Variance of gene expression identifies altered network constraints in neurological disease. PLoS Genet, 7, e1002207.
43. Bravo, H. C., Pihur, V., McCall, M., Irizarry, R. A. and Leek, J. T. (2012) Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics, 13, 272.
44. Pujadas, E. and Feinberg, A. P. (2012) Regulated noise in the epigenetic landscape of development and disease. Cell, 148, 1123-1131.
45. Feinberg, A. P. (2007) Phenotypic plasticity and the epigenetics of human disease. Nature, 447, 433-440.
46. Shalek, A. K., Satija, R., Adiconis, X., Gertner, R. S., Gaublomme, J. T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D. et al. (2013) Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature, 498, 236-240.
47. Battle, A., Mostafavi, S., Zhu, X., Potash, J. B., Weissman, M. M., McCormick, C., Haudenschild, C. D., Beckman, K. B., Shi, J., Mei, R. et al. (2013) Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res., Nov 27 (doi:10.1101/gr.155192. 113; epub ahead of print).
48. Ansel, J., Bottin, H., Rodriguez-Beltran, C., Damon, C., Nagarajan, M., Fehrmann, S., Francois, J. and Yvert, G. (2008) Cell-to-cell stochastic variation in gene expression is a complex genetic trait. PLoS Genet., 4, e1000049.
49. Choi, S. S. and Hannenhalli, S. (2013) Three independent determinants of protein evolutionary rate. J. Mol. Evol., 76, 98-111.