Identification of putative target genes of the transcription factor RUNX2

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Kuhlwilm, Martin ^a   Davierwala, Armaity ^a   Pääbo, Svante ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR RUNX2; BIRC3 PROTEIN, HUMAN; INHIBITOR OF APOPTOSIS PROTEIN; RUNX2 PROTEIN, HUMAN;

AHNAK GENE; ARTICLE; ATF3 GENE; BIRC3 GENE; CD82 GENE; CELL LINE; CONTROLLED STUDY; DUSP10 GENE; EGR1 GENE; GENE; GENE EXPRESSION; GENE IDENTIFICATION; GENE OVEREXPRESSION; HMOX1 GENE; HUMAN; HUMAN CELL; IL11 GENE; KLF9 GENE; LRP1 GENE; MALAT1 GENE; MEGF10 GENE; MITOCHONDRIAL GENOME; MT ATP6 GENE; MT CO3 GENE; MT CYB GENE; MT ND1 GENE; MT ND4L GENE; MT ND5 GENE; MT ND6 GENE; MTATP6P1 GENE; NEAT1 GENE; NFKBIE GENE; OSSIFICATION; PPP1R15A GENE; PROMOTER REGION; RUNX2 GENE; TOOTH DEVELOPMENT; UNC5B GENE; BIOSYNTHESIS; BONE DEVELOPMENT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HELA CELL LINE; HEPG2 CELL LINE; METABOLISM; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; PHYSIOLOGY; TOOTH;

CORE BINDING FACTOR ALPHA 1 SUBUNIT; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, MITOCHONDRIAL; GENOME, MITOCHONDRIAL; HELA CELLS; HEP G2 CELLS; HUMANS; INHIBITOR OF APOPTOSIS PROTEINS; OSTEOGENESIS; TOOTH;

EID: 84892596990     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0083218     Document Type: Article

References (44)

1. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710-722. doi: 10.1126/science.1188021. PubMed: 20448178.
2. Reich D, Green RE, Kircher M, Krause J, Patterson N et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053-1060. doi:10.1038/nature09710. PubMed: 21179161.
3. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science 338: 222-226. doi:10.1126/science.1224344. PubMed: 22936568.
4. Schlebusch CM, Skoglund P, Sjödin P, Gattepaille LM, Hernandez D et al. (2012) Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338: 374-379. doi: 10.1126/science.1227721. PubMed: 22997136.
5. Otto F, Thornell AP, Crompton T, Denzel A, Gilmour KC et al. (1997) Cbfa1, a candidate gene for cleidocranial dysplasia syndrome, is essential for osteoblast differentiation and bone development. Cell 89: 765-771. doi:10.1016/S0092-8674(00)80259-7. PubMed: 9182764.
6. Komori T, Yagi H, Nomura S, Yamaguchi A, Sasaki K et al. (1997) Targeted disruption of Cbfa1 results in a complete lack of bone formation owing to maturational arrest of osteoblasts. Cell 89: 755-764. doi:10.1016/S0092-8674(00) 80258-5. PubMed: 9182763.
7. Falk D, Zollikofer CP, Morimoto N, de Leon Ponce (2012) Metopic suture of Taung (Australopithecus africanus) and its implications for hominin brain evolution. Proc Natl Acad Sci U S A 109: 8467-8470. doi: 10.1073/pnas. 1119752109. PubMed: 22566620.
8. Bufalino A, Paranaíba LM, Gouvêa AF, Gueiros LA, Martelli-Júnior H et al. (2012) Cleidocranial dysplasia: oral features and genetic analysis of 11 patients. Oral Dis 18: 184-190. doi:10.1111/j. 1601-0825.2011.01862.x. PubMed: 22023169.
9. Mundlos S, Otto F, Mundlos C, Mulliken JB, Aylsworth AS et al. (1997) Mutations involving the transcription factor CBFA1 cause cleidocranial dysplasia. Cell 89: 773-779. doi:10.1016/S0092-8674(00)80260-3. PubMed: 9182765.
10. Kalliala E, Taskinen PJ (1962) Cleidocranial dysostosis: Report of six typical cases and one atypical case. Oral Surg Oral Med Oral Pathol 15: 808-822. doi:10.1016/0030-4220(62)90331-6. PubMed: 14453327.
11. Gunz P, Neubauer S, Maureille B, Hublin JJ (2010) Brain development after birth differs between Neanderthals and modern humans. Curr Biol 20: R921-R922. doi:10.1016/j.cub.2010.03.054. PubMed: 21056830.
12. Lieberman DE, McBratney BM, Krovitz G (2002) The evolution and development of cranial form in Homosapiens. Proc Natl Acad Sci U S A 99: 1134-1139. doi:10.1073/pnas.022440799. PubMed: 11805284.
13. Voisin JL (2008) The Omo I hominin clavicle: archaic or modern? J Hum Evol 55: 438-443. doi:10.1016/j.jhevol.2008.06.001. PubMed: 18692220.
14. Xiao ZS, Thomas R, Hinson TK, Quarles LD (1998) Genomic structure and isoform expression of the mouse, rat and human Cbfa1/Osf2 transcription factor. Gene 214: 187-197. doi:10.1016/S0378-1119(98)00227-3. PubMed: 9651525.
15. Zhang S, Xiao Z, Luo J, He N, Mahlios J et al. (2009) Dose-dependent effects of Runx2 on bone development. J Bone Miner Res 24: 1889-1904. doi:10.1359/jbmr.090502. PubMed: 19419310.
16. Park MH, Shin HI, Choi JY, Nam SH, Kim YJ et al. (2001) Differential expression patterns of Runx2 isoforms in cranial suture morphogenesis. J Bone Miner Res 16: 885-892. doi:10.1359/jbmr. 2001.16.5.885. PubMed: 11341333.
17. van der Deen M, Akech J, Lapointe D, Gupta S, Young DW et al. (2012) Genomic promoter occupancy of runt-related transcription factor RUNX2 in Osteosarcoma cells identifies genes involved in cell adhesion and motility. J Biol Chem 287: 4503-4517. doi:10.1074/ jbc.M111.287771. PubMed: 22158627.
18. Barber RD, Harmer DW, Coleman RA, Clark BJ (2005) GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues. Physiol Genomics 21: 389-395. doi:10.1152/physiolgenomics.00025.2005. PubMed: 15769908.
19. Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010: pdb prot5448.
20. Kircher M, Stenzel U, Kelso J (2009) Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol 10: R83. doi:10.1186/gb-2009-10-8-r83. PubMed: 19682367.
21. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106. doi:10.1186/gb-2010-11-10-r106. PubMed: 20979621.
22. Team RC (2012) R: A Language and Environment for Statistical. Computing.
23. Durinck S, Spellman PT, Birney E, Huber W (2009) Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protocols 4: 1184-1191. doi:10.1038/nprot. 2009.97.
24. Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B et al. (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21: 3439-3440. doi:10.1093/bioinformatics/bti525. PubMed: 16082012.
25. Prüfer K, Muetzel B, Do HH, Weiss G, Khaitovich P et al. (2007) FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8: 41. doi: 10.1186/1471-2105-8-41. PubMed: 17284313.
26. Genomes Project C (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073. doi:10.1038/nature09534. PubMed: 20981092.
27. Zheng C, Kabaleeswaran V, Wang Y, Cheng G, Wu H (2010) Crystal structures of the TRAF2: cIAP2 and the TRAF1: TRAF2: cIAP2 complexes: affinity, specificity, and regulation. Mol Cell 38: 101-113. doi:10.1016/j.molcel.2010.03. 009. PubMed: 20385093.
28. Gyrd-Hansen M, Meier P (2010) IAPs: from caspase inhibitors to modulators of NF-kappaB, inflammation and cancer. Nat Rev Cancer 10: 561-574. doi:10.1038/nrc2889. PubMed: 20651737.
29. Ma O, Cai WW, Zender L, Dayaram T, Shen J et al. (2009) MMP13, Birc2 (cIAP1), and Birc3 (cIAP2), amplified on chromosome 9, collaborate with p53 deficiency in mouse osteosarcoma progression. Cancer Res 69: 2559-2567. doi:10.1158/0008-5472.CAN-08-2929. PubMed: 19276372.
30. Tanaka Y, Nakamura A, Morioka MS, Inoue S, Tamamori-Adachi M et al. (2011) Systems analysis of ATF3 in stress response and cancer reveals opposing effects on pro-apoptotic genes in p53 pathway. PLOS ONE 6: e26848. doi:10.1371/journal.pone.0026848. PubMed: 22046379.
31. Pagel JI, Deindl E (2011) Early growth response 1 - a transcription factor in the crossfire of signal transduction cascades. Indian J Biochem Biophys 48: 226-235. PubMed: 22053691.
32. Nieminen P, Morgan NV, Fenwick AL, Parmanen S, Veistinen L et al. (2011) Inactivation of IL11 signaling causes craniosynostosis, delayed tooth eruption, and supernumerary teeth. Am J Hum Genet 89: 67-81. doi:10.1016/j.ajhg.2011.05. 024. PubMed: 21741611.
33. Kawata K, Kubota S, Eguchi T, Moritani NH, Shimo T et al. (2010) Role of the low-density lipoprotein receptor-related protein-1 in regulation of chondrocyte differentiation. J Cell Physiol 222: 138-148. doi:10.1002/jcp.21930. PubMed: 19795391.
34. Guenebeaud C, Goldschneider D, Castets M, Guix C, Chazot G et al. (2010) The dependence receptor UNC5H2/B triggers apoptosis via PP2A-mediated dephosphorylation of DAP kinase. Mol Cell 40: 863-876. doi:10.1016/j.molcel. 2010.11.021. PubMed: 21172653.
35. Suzuki E, Nakayama M (2007) MEGF10 is a mammalian ortholog of CED-1 that interacts with clathrin assembly protein complex 2 medium chain and induces large vacuole formation. Exp Cell Res 313: 3729-3742. doi:10.1016/j.yexcr.2007. 06.015. PubMed: 17643423.
36. Hollander MC, Zhan Q, Bae I, Fornace AJ Jr. (1997) Mammalian GADD34, an apoptosis- and DNA damage-inducible gene. J Biol Chem 272: 13731-13737. doi:10.1074/jbc.272.21.13731. PubMed: 9153226.
37. Brush MH, Weiser DC, Shenolikar S (2003) Growth arrest and DNA damage-inducible protein GADD34 targets protein phosphatase 1 alpha to the endoplasmic reticulum and promotes dephosphorylation of the alpha subunit of eukaryotic translation initiation factor 2. Mol Cell Biol 23: 1292-1303. doi:10.1128/MCB.23.4.1292-1303.2003. PubMed: 12556489.
38. Krum SA, Chang J, Miranda-Carboni G, Wang CY (2010) Novel functions for NFkappaB: inhibition of bone formation. Nat Rev Rheumatol 6: 607-611. doi:10.1038/nrrheum.2010.133. PubMed: 20703218.
39. Jiménez MJ, Balbín M, López JM, Alvarez J, Komori T et al. (1999) Collagenase 3 is a target of Cbfa1, a transcription factor of the runt gene family involved in bone formation. Mol Cell Biol 19: 4431-4442. PubMed: 10330183.
40. Pratap J, Javed A, Languino LR, van Wijnen AJ, Stein JL et al. (2005) The Runx2 osteogenic transcription factor regulates matrix metalloproteinase 9 in bone metastatic cancer cells and controls cell invasion. Mol Cell Biol 25: 8581-8591. doi:10.1128/MCB. 25.19.8581-8591.2005. PubMed: 16166639.
41. Hayami T, Kapila YL, Kapila S (2011) Divergent upstream osteogenic events contribute to the differential modulation of MG63 cell osteoblast differentiation by MMP-1 (collagenase-1) and MMP-13 (collagenase-3). Matrix Biol 30: 281-289. doi:10.1016/j.matbio.2011.04.003. PubMed: 21539914.
42. Doecke JD, Day CJ, Stephens AS, Carter SL, van Daal A et al. (2006) Association of functionally different RUNX2 P2 promoter alleles with BMD. J Bone Miner Res 21: 265-273. PubMed: 16418782.
43. Bustamante M, Nogués X, Agueda L, Jurado S, Wesselius A et al. (2007) Promoter 2 -1025 T/C polymorphism in the RUNX2 gene is associated with femoral neck bmd in Spanish postmenopausal women. Calcif Tissue Int 81: 327-332. doi:10.1007/s00223-007-9069-2. PubMed: 17878995.
44. Lee HJ, Koh JM, Hwang JY, Choi KY, Lee SH et al. (2009) Association of a RUNX2 promoter polymorphism with bone mineral density in postmenopausal Korean women. Calcif Tissue Int 84: 439-445. doi: 10.1007/s00223-009-9246-6. PubMed: 19424741.