Smooth muscle cell genome browser: Enabling the identification of novel serum response factor target genes

PLoS ONE

Volumn 10, Issue 8, 2015, Pages

  Lee, Moon Young ^a,b   Park, Chanjae ^a   Berent, Robyn M ^a   Park, Paul J ^a   Fuchs, Robert ^a   Syn, Hannah ^a   Chin, Albert ^a   Townsend, Jared ^a   Benson, Craig C ^c   Redelman, Doug ^a   Shen, Tsaiwei ^d   Park, Jong Kun ^e   Miano, Joseph M ^c   Sanders, Kenton M ^a   Ro, Seungil ^a  

^a UNIVERSITY OF NEVADA SCHOOL OF MEDICINE   (United States)

^b Wonkwang University School of Medicine   (South Korea)

^c UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

^d LC Sciences   (United States)

^e Wonkwang University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM CHANNEL; CATION; CHLORIDE CHANNEL; POTASSIUM CHANNEL; SERUM RESPONSE FACTOR; SODIUM CHANNEL; CARRIER PROTEIN; GREEN FLUORESCENT PROTEIN; HISTONE; ION CHANNEL; MESSENGER RNA; MUSCLE PROTEIN; TRANSCRIPTOME;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BINDING SITE; CELL DIFFERENTIATION; CELL FUNCTION; CELL ISOLATION; COLON; CONTROLLED STUDY; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE INTERACTION; GENE MAPPING; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; JEJUNUM; MOUSE; NONHUMAN; PROTEIN EXPRESSION; PROTEOMICS; PROTON TRANSPORT; SMOOTH MUSCLE FIBER; SODIUM TRANSPORT; SRF GENE; ANIMAL; ANTIBODY SPECIFICITY; COMPARATIVE STUDY; COMPUTER SIMULATION; CYTOLOGY; DEFICIENCY; GENE LIBRARY; GENETICS; HISTONE CODE; KNOCKOUT MOUSE; METABOLISM; REPORTER GENE; SERUM RESPONSIVE ELEMENT; SMOOTH MUSCLE CELL; TRANSGENIC MOUSE; WEB BROWSER;

ANIMALS; BINDING SITES; CARRIER PROTEINS; COLON; COMPUTER SIMULATION; GENE LIBRARY; GENES, REPORTER; GREEN FLUORESCENT PROTEINS; HISTONE CODE; HISTONES; ION CHANNELS; JEJUNUM; MICE; MICE, KNOCKOUT; MICE, TRANSGENIC; MUSCLE PROTEINS; MYOCYTES, SMOOTH MUSCLE; ORGAN SPECIFICITY; PROTEOMICS; RNA, MESSENGER; SERUM RESPONSE ELEMENT; SERUM RESPONSE FACTOR; TRANSCRIPTOME; WEB BROWSER;

EID: 84942092511     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0133751     Document Type: Article

References (41)

1. Halayko AJ, Solway J (2001) Molecular mechanisms of phenotypic plasticity in smooth muscle cells. J Appl Physiol (1985) 90: 358-368. PMID: 11133929
2. Owens GK, Kumar MS, Wamhoff BR (2004) Molecular regulation of vascular smooth muscle cell differentiation in development and disease. Physiol Rev 84: 767-801. PMID: 15269336
3. Chen J, Chen H, Sanders KM, Perrino BA (2008) Regulation of SRF/CArG-dependent gene transcription during chronic partial obstruction of murine small intestine. Neurogastroenterol Motil 20: 829-842. doi: 10.1111/j.1365-2982.2008.01149.x PMID: 18557893
4. Kawai-Kowase K, Owens GK (2007) Multiple repressor pathways contribute to phenotypic switching of vascular smooth muscle cells. Am J Physiol Cell Physiol 292: C59-69. PMID: 16956962
5. Shimoda LA (2010) Hypoxic regulation of ion channels and transporters in pulmonary vascular smooth muscle. Adv Exp Med Biol 661: 221-235. doi: 10.1007/978-1-60761-500-2-14 PMID: 20204733
6. Berridge MJ (2008) Smooth muscle cell calcium activation mechanisms. J Physiol 586: 5047-5061. doi: 10.1113/jphysiol.2008.160440 PMID: 18787034
7. Sanders KM, Koh SD, Ro S, Ward SM (2012) Regulation of gastrointestinal motility - insights from smooth muscle biology. Nat Rev Gastroenterol Hepatol 9: 633-645. doi: 10.1038/nrgastro.2012.168 PMID: 22965426
8. Miano JM (2003) Serum response factor: toggling between disparate programs of gene expression. J Mol Cell Cardiol 35: 577-593. PMID: 12788374
9. Sun Q, Chen G, Streb JW, Long X, Yang Y, Stoeckert CJ Jr, et al. (2006) Defining the mammalian CAr-Gome. Genome Res 16: 197-207. PMID: 16365378
10. Ilagan RM, Genheimer CW, Quinlan SF, Guthrie KI, Sangha N, Ramachandrannair S, et al. (2011) Smooth muscle phenotypic diversity is mediated through alterations in myocardin gene splicing. J Cell Physiol 226: 2702-2711. doi: 10.1002/jcp.22622 PMID: 21792927
11. Fisher SA (2010) Vascular smooth muscle phenotypic diversity and function. Physiol Genomics 42A: 169-187. doi: 10.1152/physiolgenomics.00111.2010 PMID: 20736412
12. Park C, Hennig GW, Sanders KM, Cho JH, Hatton WJ, Redelman D, et al. (2011) Serum response factor-dependent MicroRNAs regulate gastrointestinal smooth muscle cell phenotypes. Gastroenterology 141: 164-175. doi: 10.1053/j.gastro.2011.03.058 PMID: 21473868
13. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, et al. (2013) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 41: D64-69. doi: 10.1093/nar/gks1048 PMID: 23155063
14. Xin HB, Deng KY, Rishniw M, Ji G, Kotlikoff MI (2002) Smooth muscle expression of Cre recombinase and eGFP in transgenic mice. Physiol Genomics 10: 211-215. PMID: 12209023
15. Miano JM, Ramanan N, Georger MA, de Mesy Bentley KL, Emerson RL, Balza RO Jr, et al. (2004) Restricted inactivation of serum response factor to the cardiovascular system. Proc Natl Acad Sci U S A 101: 17132-17137. PMID: 15569937
16. Wirth A, Benyo Z, Lukasova M, Leutgeb B, Wettschureck N, Gorbey S, et al. (2008) G12-G13-LARGmediated signaling in vascular smooth muscle is required for salt-induced hypertension. Nat Med 14: 64-68. PMID: 18084302
17. Benson CC, Zhou Q, Long X, Miano JM (2011) Identifying functional single nucleotide polymorphisms in the human CArGome. Physiol Genomics 43: 1038-1048. doi: 10.1152/physiolgenomics.00098. 2011 PMID: 21771879
18. Ro S, Park C, Jin J, Zheng H, Blair PJ, Redelman D, et al. (2010) A model to study the phenotypic changes of interstitial cells of Cajal in gastrointestinal diseases. Gastroenterology 138: 1068-1078. e1061-1062. doi: 10.1053/j.gastro.2009.11.007 PMID: 19917283
19. Park C, Yan W, Ward SM, Hwang SJ, Wu Q, Hatton WJ, et al. (2011) MicroRNAs dynamically remodel gastrointestinal smooth muscle cells. PLoS One 6: e18628. doi: 10.1371/journal.pone.0018628 PMID: 21533178
20. Miano JM, Long X, Fujiwara K (2007) Serum response factor: master regulator of the actin cytoskeleton and contractile apparatus. Am J Physiol Cell Physiol 292: C70-81. PMID: 16928770
21. Shimizu RT, Blank RS, Jervis R, Lawrenz-Smith SC, Owens GK (1995) The smooth muscle alphaactin gene promoter is differentially regulated in smooth muscle versus non-smooth muscle cells. J Biol Chem 270: 7631-7643. PMID: 7706311
22. Spencer JA, Misra RP (1999) Expression of the SRF gene occurs through a Ras/Sp/SRF-mediatedmechanism in response to serum growth signals. Oncogene 18: 7319-7327. PMID: 10602487
23. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837. PMID: 17512414
24. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326. PMID: 16630819
25. Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, et al. (2007) The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res 17: 691-707. PMID: 17567990
26. McDonald OG, Owens GK (2007) Programming smooth muscle plasticity with chromatin dynamics. Circ Res 100: 1428-1441. PMID: 17525382
27. Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, et al. (2012) An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol 13: 418. doi: 10.1186/gb-2012-13-8-418 PMID: 22889292
28. Floyd R, Wray S (2007) Calcium transporters and signalling in smooth muscles. Cell Calcium 42: 467-476. PMID: 17624426
29. Perez CF, Lopez JR, Allen PD (2005) Expression levels of RyR1 and RyR3 control resting free Ca2+ in skeletal muscle. Am J Physiol Cell Physiol 288: C640-649. PMID: 15548569
30. Beavers DL, Wang W, Ather S, Voigt N, Garbino A, Dixit SS, et al. (2013) Mutation E169K in junctophilin-2 causes atrial fibrillation due to impaired RyR2 stabilization. J Am Coll Cardiol 62: 2010-2019. doi: 10.1016/j.jacc.2013.06.052 PMID: 23973696
31. Murer H, Ahearn G, Biber J, Cassano G, Gmaj P, Stieger B (1983) Co-and counter-transport mechanisms in brush border membranes and basal-lateral membranes of intestine and kidney. J Exp Biol 106: 163-180. PMID: 6317788
32. Anders S, Reyes A, HuberW(2012) Detecting differential usage of exons from RNA-seq data. Genome Res 22: 2008-2017. doi: 10.1101/gr.133744.111 PMID: 22722343
33. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415. doi: 10.1038/ng.259 PMID: 18978789
34. Black DL (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72: 291-336. PMID: 12626338
35. Miano JM (2010) Role of serum response factor in the pathogenesis of disease. Lab Invest 90: 1274-1284. doi: 10.1038/labinvest.2010.104 PMID: 20498652
36. Bitar KN, Raghavan S, Zakhem E (2014) Tissue engineering in the gut: developments in neuromusculature. Gastroenterology 146: 1614-1624. doi: 10.1053/j.gastro.2014.03.044 PMID: 24681129
37. Takeshima H, Komazaki S, Hirose K, Nishi M, Noda T, Iino M (1998) Embryonic lethality and abnormal cardiac myocytes in mice lacking ryanodine receptor type 2. EMBO J 17: 3309-3316. PMID: 9628868
38. Garbino A, van Oort RJ, Dixit SS, Landstrom AP, Ackerman MJ, Wehrens XH (2009) Molecular evolution of the junctophilin gene family. Physiol Genomics 37: 175-186. doi: 10.1152/physiolgenomics. 00017.2009 PMID: 19318539
39. Takeshima H (2002) Intracellular Ca2+ store in embryonic cardiac myocytes. Front Biosci 7: d1642-1652. PMID: 12086916
40. Golini L, Chouabe C, Berthier C, Cusimano V, Fornaro M, Bonvallet R, et al. (2011) Junctophilin 1 and 2 proteins interact with the L-type Ca2+ channel dihydropyridine receptors (DHPRs) in skeletal muscle. J Biol Chem 286: 43717-43725. doi: 10.1074/jbc.M111.292755 PMID: 22020936
41. Woo JS, Hwang JH, Ko JK, Kim dH, Ma J, Lee EH (2009) Glutamate at position 227 of junctophilin-2 is involved in binding to TRPC3. Mol Cell Biochem 328: 25-32. doi: 10.1007/s11010-009-0070-0 PMID: 19277847