A Genome-Wide Screen Indicates Correlation between Differentiation and Expression of Metabolism Related Genes

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Roy, Priti ^a   Kumar, Brijesh ^a   Shende, Akhilesh ^a   Singh, Anupama ^a,c   Meena, Anil ^a,b   Ghosal, Ritika ^a   Ranganathan, Madhav ^a   Bandyopadhyay, Amitabha ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY KANPUR   (India)

^b Mphasis Limited   (India)

^c Cactus Communications   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; CHICKEN; CONTROLLED STUDY; DEVELOPMENTAL STAGE; EMBRYO; EMBRYO DEVELOPMENT; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC CORRELATION; GENOME ANALYSIS; GENOMIC IN SITU HYBRIDIZATION; METABOLIC REGULATION; NONHUMAN; ORGANOGENESIS; RNA ANALYSIS; SIGNAL TRANSDUCTION; TISSUE DIFFERENTIATION; TISSUE SPECIFICITY;

ANIMALS; CELL DIFFERENTIATION; CHICK EMBRYO; CHICKENS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME-WIDE ASSOCIATION STUDY; KIDNEY; METABOLIC NETWORKS AND PATHWAYS; ORGANOGENESIS; TRANSCRIPTOME; UP-REGULATION;

EID: 84878162494     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0063670     Document Type: Article

References (49)

1. Moloney DJ, Panin VM, Johnston SH, Chen J, Shao L, et al. (2000) Fringe is a glycosyltransferase that modifies Notch. Nature 406: 369-375.
2. Sen J, Goltz JS, Stevens L, Stein D, (1998) Spatially Restricted Expression of pipe in the Drosophila Egg Chamber Defines Embryonic Dorsal-Ventral Polarity. Cell 95: 471-481.
3. Sohaskey ML, Yu J, Diaz MA, Plaas AH, Harland RM, (2008) JAWS coordinates chondrogenesis and synovial joint positioning. Development 135: 2215-2220.
4. Nurminsky D, Shanmugasundaram S, Deasey S, Michaud C, Allen S, et al. (2011) Transglutaminase 2 regulates early chondrogenesis and glycosaminoglycan synthesis. Mechanisms of Development 128: 234-245.
5. Zou W, Chen X, Shim J-H, Huang Z, Brady N, et al. (2011) The E3 ubiquitin ligase Wwp2 regulates craniofacial development through mono-ubiquitylation of Goosecoid. Nat Cell Biol 13: 59-65.
6. Lapez-Sanchez C, Bãrtulos Ãs, Martãnez-Campos E, Gaããn C, Valenciano AI, et al. (2010) Tyrosine hydroxylase is expressed during early heart development and is required for cardiac chamber formation. Cardiovascular Research 88: 111-120.
7. Zhang Y, Zhang Y, Gao Y, Zhao X, Wang Z, (2011) Drosophila long-chain acyl-CoA synthetase acts like a gap gene in embryonic segmentation. Developmental Biology 353: 259-265.
8. Wistow GJ, Piatigorsky J, (1988) Lens crystallins: the evolution and expression of proteins for a highly specialized tissue. Annu Rev Biochem 57: 479-504.
9. Huberts DH, van der Klei IJ, (2010) Moonlighting proteins: an intriguing mode of multitasking. Biochim Biophys Acta 1803: 520-525.
10. Jeffery CJ, (2009) Moonlighting proteins-an update. Mol Biosyst 5: 345-350.
11. Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, et al. (2004) Regulation of gene expression by a metabolic enzyme. Science 306: 482-484.
12. Kozhevnikova Elena N, van der Knaap Jan A, Pindyurin Alexey V, Ozgur Z, van Ijcken Wilfred FJ, et al. (2012) Metabolic Enzyme IMPDH Is Also a Transcription Factor Regulated by Cellular State. Molecular Cell 47: 133-139.
13. Zheng L, Roeder RG, Luo Y, (2003) S phase activation of the histone H2B promoter by OCA-S, a coactivator complex that contains GAPDH as a key component. Cell 114: 255-266.
14. Jeffery CJ, (2004) Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins. Curr Opin Struct Biol 14: 663-668.
15. Gomez A, Domedel N, Cedano J, Pinol J, Querol E, (2003) Do current sequence analysis algorithms disclose multifunctional (moonlighting) proteins? Bioinformatics 19: 895-896.
16. Dietrich S, Schubert FR, Lumsden A, (1997) Control of dorsoventral pattern in the chick paraxial mesoderm. Development 124: 3895-3908.
17. Murtaugh LC, Chyung JH, Lassar AB, (1999) Sonic hedgehog promotes somitic chondrogenesis by altering the cellular response to BMP signaling. Genes & Development 13: 225-237.
18. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
19. Miki R, Kadota K, Bono H, Mizuno Y, Tomaru Y, et al. (2001) Delineating Developmental and Metabolic Pathways in vivo by Expression Profiling Using the RIKEN Set of 18,816 Full-Length Enriched Mouse cDNA Arrays. Proceedings of the National Academy of Sciences of the United States of America 98: 2199-2204.
20. Hamburger V, (1992) The stage series of the chick embryo. Developmental Dynamics 195: 273-275.
21. Cogburn LA, Porter TE, Duclos MJ, Simon J, Burgess SC, et al. (2007) Functional Genomics of the Chicken-A Model Organism. Poultry Science 86: 2059-2094.
22. Hubbard SJ, Grafham DV, Beattie KJ, Overton IM, McLaren SR, et al. (2005) Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. Genome Res 15: 174-183.
23. Nishimura M, Naito S, (2008) Tissue-specific mRNA Expression Profiles of Human Solute Carrier Transporter Superfamilies. Drug Metabolism and Pharmacokinetics 23: 22-44.
24. Schweitzer R, Chyung JH, Murtaugh LC, Brent AE, Rosen V, et al. (2001) Analysis of the tendon cell fate using Scleraxis, a specific marker for tendons and ligaments. Development 128: 3855-3866.
25. Montero JA, Lorda-Diez CI, Certal AC, Moreno N, Rodriguez-Leon J, et al. (2010) Coordinated and sequential activation of neutral and acidic DNases during interdigital cell death in the embryonic limb. Apoptosis 15: 1197-1210.
26. Kania A, Jessell TM, (2003) Topographic motor projections in the limb imposed by LIM homeodomain protein regulation of ephrin-A:EphA interactions. Neuron 38: 581-596.
27. Mok GF, Sweetman D, (2011) Many routes to the same destination: lessons from skeletal muscle development. Reproduction 141: 301-312.
28. Ozbudak EM, Tassy O, Pourquie O, (2010) Spatiotemporal compartmentalization of key physiological processes during muscle precursor differentiation. Proc Natl Acad Sci U S A 107: 4224-4229.
29. Duncan SA, (2000) Transcriptional regulation of liver development. Dev Dyn 219: 131-142.
30. Si-Tayeb K, Lemaigre FP, Duncan SA, (2010) Organogenesis and development of the liver. Dev Cell 18: 175-189.
31. Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
32. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-360.
33. Steedman HF, (1950) Alcian Blue 8GS: A New Stain for Mucin. Quarterly Journal of Microscopical Science 3-91: 477-479.
34. Silbert JE, Sugumaran G, (2002) Biosynthesis of Chondroitin/Dermatan Sulfate. IUBMB Life 54: 177-186.
35. Ohana E, Shcheynikov N, Park M, Muallem S, (2012) Solute Carrier Family 26 Member a2 (Slc26a2) Protein Functions as an Electroneutral SO42â?'/OHâ?'/Clâ?' Exchanger Regulated by Extracellular Clâ?'. Journal of Biological Chemistry 287: 5122-5132.
36. Hiraoka S, Furuichi T, Nishimura G, Shibata S, Yanagishita M, et al. (2007) Nucleotide-sugar transporter SLC35D1 is critical to chondroitin sulfate synthesis in cartilage and skeletal development in mouse and human. Nat Med 13: 1363-1367.
37. Choi D, Fang Y, Mathers WD, (2006) Condition-specific coregulation with cis-regulatory motifs and modules in the mouse genome. Genomics 87: 500-508.
38. Parviz F, Matullo C, Garrison WD, Savatski L, Adamson JW, et al. (2003) Hepatocyte nuclear factor 4[alpha] controls the development of a hepatic epithelium and liver morphogenesis. Nat Genet 34: 292-296.
39. Ohguchi H, Tanaka T, Uchida A, Magoori K, Kudo H, et al. (2008) Hepatocyte nuclear factor 4alpha contributes to thyroid hormone homeostasis by cooperatively regulating the type 1 iodothyronine deiodinase gene with GATA4 and Kruppel-like transcription factor 9. Mol Cell Biol 28: 3917-3931.
40. Thiagarajan RD, Georgas KM, Rumballe BA, Lesieur E, Chiu HS, et al. (2011) Identification of Anchor Genes during Kidney Development Defines Ontological Relationships, Molecular Subcompartments and Regulatory Pathways. PLoS ONE 6: e17286.
41. Agathocleous M, Love NK, Randlett O, Harris JJ, Liu J, et al. (2012) Metabolic differentiation in the embryonic retina. Nat Cell Biol 14: 859-864.
42. Tsai HM, Garber BB, Larramendi LM, (1981) 3H-thymidine autoradiographic analysis of telencephalic histogenesis in the chick embryo: I. Neuronal birthdates of telencephalic compartments in situ. J Comp Neurol 198: 275-292.
43. Xie Z, Chen Y, Li Z, Bai G, Zhu Y, et al. (2011) Smad6 promotes neuronal differentiation in the intermediate zone of the dorsal neural tube by inhibition of the Wnt/beta-catenin pathway. Proc Natl Acad Sci U S A 108: 12119-12124.
44. Li N, Hornbruch A, Klafke R, Katzenberger B, Wizenmann A, (2005) Specification of dorsoventral polarity in the embryonic chick mesencephalon and its presumptive role in midbrain morphogenesis. Developmental Dynamics 233: 907-920.
45. Hiramatsu H, Yasugi S, (2004) Molecular analysis of the determination of developmental fate in the small intestinal epithelium in the chicken embryo. Int J Dev Biol 48: 1141-1148.
46. Wagner M, Siddiqui MA, (2007) Signal transduction in early heart development (I): cardiogenic induction and heart tube formation. Exp Biol Med (Maywood) 232: 852-865.
47. Lee J-S, Chien C-B, (2004) When sugars guide axons: insights from heparan sulphate proteoglycan mutants. Nat Rev Genet 5: 923-935.
48. Johnson CH, Patterson AD, Idle JR, Gonzalez FJ, (2012) Xenobiotic metabolomics: major impact on the metabolome. Annu Rev Pharmacol Toxicol 52: 37-56.
49. Cankaya M, Hernandez AM, Ciftci M, Beydemir S, Ozdemir H, et al. (2007) An analysis of expression patterns of genes encoding proteins with catalytic activities. BMC Genomics 8: 232.