In Silico Analysis of BMAL1 and CLOCK SNPs in the Ensembl Database

Year 2022, Volume: 81 Issue: 2, 125 - 135, 29.12.2022

Şeref Gül

https://doi.org/10.26650/EurJBiol.2022.1164864

Abstract

Objective: A circadian rhythm in mammals controls the sleep-wake cycle, blood pressure, hormone secretion, metabolism and many other physiological processes. The circadian clock mechanism is regulated by four genes: Bmal1, Clock, Cry, and Per. Mutations in these regulatory genes are associated with sleep and mood disorders, obesity, and cancer. Several PER2 and CRY2 SNPs are associated with advanced sleep phase syndrome. It is, therefore, critical to understand the effect of clock genes’ SNPs on the circadian clock. In this study, we determined “pathogenic” BMAL1 and CLOCK SNPs in the Ensembl database for biochemical characterization. Materials and Methods: BMAL1 and CLOCK SNPs in the Ensemble database were filtered out for only missense mutations. Among the missense mutations, pathogenic ones were determined according to SIFT, PolyPhen, and CADD scores, REVEL, MetalR, Mutation Assessor, I-Mutant, PROVEAN, and FireDock programs. BMAL1 and CLOCK SNPs were visualized by using PyMol. Results: Thousands of BMAL1 and CLOCK missense SNP mutations were reported in the Ensembl database. After the classification of those SNPs according to their SIFT, PolyPhen, and CADD pathogenicity, twelve SNPs for each protein remained as pathogenic. A further analysis with all in silico tools revealed that BMAL1 SNPs causing Ala154Val, Arg166Gln, and Val440Gly mutations; and CLOCK SNPs causing Gly120Val, Asp119Val, Gly120Ser, Ala117Val, and Cys371Gly mutations were predicted as the most “pathogenic” ones. Conclusion: Overall, by using in silico tools, we provided a starting point for experimental studies for determining the effect of pathogenic BMAL1 and CLOCK SNPs on the circadian clock mechanism.

Keywords

Circadian clock, Ensembl, BMAL1, CLOCK, SNP

References

• 1. Dunlap JC. Molecular bases for circadian clocks. Cell 1999; 96(2): 271-90. google scholar
• 2. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, et al. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 2002; 109(3): 307-20. google scholar
• 3. Sancar G, Brunner M. Circadian clocks and energy metabolism. Cell Mol Life Sci 2014; 71(14): 2667-80. google scholar
• 4. Turek FW, Joshu C, Kohsaka A, Lin E, Ivanova G, McDearmon E, et al. Obesity and metabolic syndrome in circadian Clock mutant mice. Science 2005; 308(5724): 1043-45. google scholar
• 5. Nernpermpisooth N, Qiu SQ, Mintz JD, Suvitayavat W, Thirawarapan S, Rudic DR, et al. Obesity Alters the Peripheral Circadian Clock in the Aorta and Microcirculation. Microcirculation 2015; 22(4): 257-66. google scholar
• 6. Damiola F, Le Minh N, Preitner N, Kornmann B, Fleury-Olela F, Schibler U. Restricted feeding uncouples circadian oscillators in peripheral tissues from the central pacemaker in the suprachias-matic nucleus. Gene Dev 2000; 14(23): 2950-61. google scholar
• 7. Mohawk JA, Takahashi JS. Cell autonomy and synchrony of supra-chiasmatic nucleus circadian oscillators. Trends Neurosci 2011; 34(7): 349-58. google scholar
• 8. Kavakli IH, Sancar A. Circadian photoreception in humans and mice. Mol Interv 2002; 2(8): 484-92. google scholar
• 9. Ko CH, Takahashi JS. Molecular components of the mammalian circadian clock. Hum Mol Genet 2006; 15: R271-R77. google scholar
• 10. Welsh DK, Logothetis DE, Meister M, Reppert SM. Individual Neu-rons Dissociated from Rat Suprachiasmatic Nucleus Express Inde-pendently Phased Circadian Firing Rhythms. Neuron 1995; 14(4): 697-706. google scholar
• 11. King DP, Zhao YL, Sangoram AM, Wilsbacher LD, Tanaka M, Antoch MP, et al. Positional cloning of the mouse circadian Clock gene. Cell 1997; 89(4): 641-53. google scholar
• 12. Vitaterna MH, King DP, Chang AM, Kornhauser JM, Lowrey PL, Mcdonald JD, et al. Mutagenesis and Mapping of a Mouse Gene Clock, Essential for Circadian Behavior. Science 1994; 264 (5159): 719-25. google scholar
• 13. Bunger MK, Wilsbacher LD, Moran SM, Clendenin C, Radcliffe LA, Hogenesch JB, et al. Mop3 is an essential component of the master circadian pacemaker in mammals. Cell 2000; 103(7): 1009-17. google scholar
• 14. Shearman LP, Zylka MJ, Weaver DR, Kolakowski LF, Reppert SM. Two period homologs: Circadian expression and photic regulation in the suprachiasmatic nuclei. Neuron 1997; 19(6): 1261- 69. google scholar
• 15. Griffin EA, Staknis D, Weitz CJ. Light-independent role of CRY1 and CRY2 in the mammalian circadian clock. Science 1999; 286(5440): 768-71. google scholar
• 16. Kume K, Zylka MJ, Sriram S, Shearman LP, Weaver DR, Jin XW, et al. mCRY1 and mCRY2 are essential components of the negative limb of the circadian clock feedback loop. Cell 1999; 98(2): 193-205. google scholar
• 17. Hao HP, Allen DL, Hardin PE. A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster. Mol Cell Biol 1997; 17(7): 3687-93. google scholar
• 18. Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB. A cir-cadian gene expression atlas in mammals: Implications for biology and medicine. P Natl Acad Sci USA 2014; 111(45): 16219-24. google scholar
• 19. Hirano A, Fu YH, Ptacek LJ. The intricate dance of post-translation-al modifications in the rhythm of life. Nat Struct Mol Biol 2016; 23(12): 1053-60. google scholar
• 20. Preitner N, Damiola F, Molina LL, Zakany J, Duboule D, Albrecht U, et al. The orphan nuclear receptor REV-ERB alpha controls circadi-an transcription within the positive limb of the mammalian circa-dian oscillator. Cell 2002; 110(2): 251-60. google scholar
• 21. Sato TK, Panda S, Miraglia LJ, Reyes TM, Rudic RD, McNamara P, et al. A functional genomics strategy reveals rora as a component of the mammalian circadian clock. Neuron 2004; 43(4): 527-37. google scholar
• 22. Kelleher FC, Rao A, Maguire A. Circadian molecular clocks and can-cer. Cancer Lett 2014; 342(1): 9-18. google scholar
• 23. Scheer FAJL, Hilton MF, Mantzoros CS, Shea SA. Adverse metabol-ic and cardiovascular consequences of circadian misalignment. P Natl Acad Sci USA 2009; 106(11): 4453-58. google scholar
• 24. Fu Y, Jones CR, Toh K, Virshup D, Ptacek LJ. An hPer2 phosphory-lation site mutation in familial Advanced Sleep-Phase Syndrome. Am J Hum Genet 2001; 69(4): 597-97. google scholar
• 25. Patke A, Murphy PJ, Onat OE, Krieger AC, Ozcelik T, Campbell SS, et al. Mutation of the Human Circadian Clock Gene CRY1 in Familial Delayed Sleep Phase Disorder. Cell 2017; 169(2): 203- 15. google scholar
• 26. Onat OE, Kars ME, Gul S, Bilguvar K, Wu YM, Ozhan A, et al. Human CRY1 variants associate with attention deficit/hyperactivity disor-der. J Clin Invest 2020; 130(7): 3885-900. google scholar
• 27. Gul S, Aydin C, Ozcan O, Gurkan B, Surme S, Baris I, et al. The Arg-293 of Cryptochrome1 is responsible for the allosteric regulation of CLOCK-CRY1 binding in circadian rhythm. J Biol Chem 2020; 295(50): 17187-99. google scholar
• 28. Parlak GC, Camur BB, Gul S, Ozcan O, Baris I, Kavakli IH. The second-ary pocket of Cryptochrome 2 is important for the regulation of its stability and localization. J Biol Chem 2022: 102334. google scholar
• 29. Huang NA, Chelliah Y, Shan YL, Taylor CA, Yoo SH, Partch C, et al. Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcrip-tional Activator Complex. Science 2012; 337(6091): 189-94. google scholar
• 30. Wang ZX, Wu YL, Li LF, Su XD. Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-he-lix domains with E-box DNA. Cell Res 2013; 23(2): 213-24. google scholar
• 31. Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 2003; 31(13): 3812-14. google scholar
• 32. Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 2002; 30(17): 3894-900. google scholar
• 33. Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 2014; 46(3): 310. google scholar
• 34. Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. Am J Hum Genet 2016; 99(4): 877-85. google scholar
• 35. Dong CL, Wei P, Jian XQ, Gibbs R, Boerwinkle E, Wang K, et al. Com-parison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet 2015; 24(8): 2125-37. google scholar
• 36. Li C, Zhi D, Wang K, Liu X. MetaRNN: Differentiating Rare Pathogen-ic and Rare Benign Missense SNVs and InDels Using Deep Learn-ing. bioRxiv 2021. google scholar
• 37. Capriotti E, Fariselli P, Casadio R. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res 2005; 33: W306-W10. google scholar
• 38. Choi Y, Chan AP. PROVEAN web server: a tool to predict the func-tional effect of amino acid substitutions and indels. Bioinformatics 2015; 31(16): 2745-47. google scholar
• 39. Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L. The FoldX web server: an online force field. Nucleic Acids Res 2005; 33: W382-W88. google scholar
• 40. Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ. FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res 2008; 36: W229- W32. google scholar
• 41. Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J, Edbali O, et al. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res 2022; 50(W1): W276-W79. google scholar
• 42. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2-a multiple sequence alignment editor and analy-sis workbench. Bioinformatics 2009; 25(9): 1189-91. google scholar
• 43. Schrodinger L. The PyMOL Molecular Graphics System. 2010. google scholar
• 44. Hua P, Liu WG, Chen DH, Zhao YY, Chen L, Zhang N, et al. Cry1 and Tef gene polymorphisms are associated with major depressive dis-order in the Chinese population. J Affect Disorders 2014; 157: 10003. google scholar
• 45. Hirano A, Shi G, Jones CR, Lipzen A, Pennacchio LA, Xu Y, et al. A Cryptochrome 2 mutation yields advanced sleep phase in hu-mans. Elife 2016; 5. google scholar
• 46. Kwon I, Lee J, Chang SH, Jung NC, Lee BJ, Son GH, et al. BMAL1 shuttling controls transactivation and degradation of the CLOCK/ BMAL1 heterodimer. Mol Cell Biol 2006; 26(19): 7318-30. google scholar
• 47. Pei JF, Li XK, Li WQ, Gao Q, Zhang Y, Wang XM, et al. Diurnal oscilla-tions of endogenous H2O2 sustained by p66(Shc) regulate circadi-an clocks. Nat Cell Biol 2019; 21(12): 1553-64. google scholar
• 48. Shimizu T, Huang D, Yan F, Stranava M, Bartosova M, Fojtikova V, et al. Gaseous O2, NO, and CO in signal transduction: structure and function relationships of heme-based gas sensors and heme-re-dox sensors. Chem Rev 2015; 115(13): 6491-533. google scholar
• 49. Freeman SL, Kwon H, Portolano N, Parkin G, Venkatraman Girija U, Basran J, et al. Heme binding to human CLOCK affects interactions with the E-box. Proc Natl Acad Sci U S A 2019; 116(40): 19911-16. google scholar