title: PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings.
abstract: PHYTOCHROME INTERACTING FACTOR3 (PIF3) is a key basic helix-loop-helix transcription factor of Arabidopsis thaliana that negatively regulates light responses, repressing chlorophyll biosynthesis, photosynthesis, and photomorphogenesis in the dark. However, the mechanism for the PIF3-mediated transcription regulation remains largely unknown. In this study, we found that the REDUCED POTASSIUM DEPENDENCY3/HISTONE DEACETYLASE1-type histone deacetylase HDA15 directly interacted with PIF3 in vivo and in vitro. Genome-wide transcriptome analysis revealed that HDA15 acts mainly as a transcriptional repressor and negatively regulates chlorophyll biosynthesis and photosynthesis gene expression in etiolated seedlings. HDA15 and PIF3 cotarget to the genes involved in chlorophyll biosynthesis and photosynthesis in the dark and repress gene expression by decreasing the acetylation levels and RNA Polymerase II-associated transcription. The binding of HDA15 to the target genes depends on the presence of PIF3. In addition, PIF3 and HDA15 are dissociated from the target genes upon exposure to red light. Taken together, our results indicate that PIF3 associates with HDA15 to repress chlorophyll biosynthetic and photosynthetic genes in etiolated seedlings.
authors.affiliation: Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Xuncheng
authors.initials: X
authors.lastname: Liu
authors.forename: Chia-Yang
authors.initials: CY
authors.lastname: Chen
authors.forename: Ko-Ching
authors.initials: KC
authors.lastname: Wang
authors.forename: Ming
authors.initials: M
authors.lastname: Luo
authors.forename: Ready
authors.initials: R
authors.lastname: Tai
authors.forename: Lianyu
authors.initials: L
authors.lastname: Yuan
authors.forename: Minglei
authors.initials: M
authors.lastname: Zhao
authors.forename: Songguang
authors.initials: S
authors.lastname: Yang
authors.forename: Gang
authors.initials: G
authors.lastname: Tian
authors.forename: Yuhai
authors.initials: Y
authors.lastname: Cui
authors.forename: Hsu-Liang
authors.initials: HL
authors.lastname: Hsieh
authors.forename: Keqiang
authors.initials: K
authors.lastname: Wu
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics* / Q000378:metabolism; D002467:Cell Nucleus / Q000378:metabolism; D002734:Chlorophyll / Q000096:biosynthesis*; D064527:Etiolation / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D006655:Histone Deacetylases / Q000235:genetics* / Q000378:metabolism; D018546:Hypocotyl / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D008957:Models, Genetic; D010788:Photosynthesis / Q000235:genetics*; D030821:Plants, Genetically Modified; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D034622:RNA Interference; D020133:Reverse Transcriptase Polymerase Chain Reaction; D036226:Seedlings / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D002734:Chlorophyll; D049452:Green Fluorescent Proteins; D006655:Histone Deacetylases; C116162:PIF3 protein, Arabidopsis; C573088:HDA15 protein, Arabidopsis
references.citation: Plant Cell. 2001 Dec;13(12):2589-607
references.pmid: 11752374
references.citation: EMBO J. 2002 May 15;21(10):2441-50
references.pmid: 12006496
references.citation: Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9437-42
references.pmid: 11481498
references.citation: Plant Cell. 2007 Mar;19(3):731-49
references.pmid: 17337630
references.citation: Plant Cell. 2007 Dec;19(12):3915-29
references.pmid: 18065691
references.citation: Nature. 2007 May 24;447(7143):407-12
references.pmid: 17522673
references.citation: PLoS One. 2012;7(2):e30846
references.pmid: 22363501
references.citation: Nat Methods. 2005 Mar;2(3):213-8
references.pmid: 16163802
references.citation: Plant J. 2005 Mar;41(5):767-78
references.pmid: 15703063
references.citation: Plant Cell. 2004 Jun;16(6):1433-45
references.pmid: 15155879
references.citation: Annu Rev Plant Biol. 2007;58:321-46
references.pmid: 17227226
references.citation: Plant J. 1998 Dec;16(6):735-43
references.pmid: 10069079
references.citation: Plant Physiol. 2002 Nov;130(3):1090-101
references.pmid: 12427976
references.citation: Plant Cell. 2013 Jan;25(1):134-48
references.pmid: 23362207
references.citation: Mol Cell. 2006 Aug 4;23(3):439-46
references.pmid: 16885032
references.citation: J Biol Chem. 2005 Jan 14;280(2):1465-73
references.pmid: 15525647
references.citation: Science. 2000 May 5;288(5467):859-63
references.pmid: 10797009
references.citation: Plant Physiol. 2011 May;156(1):173-84
references.pmid: 21398257
references.citation: Cell. 1998 Jun 26;93(7):1219-29
references.pmid: 9657154
references.citation: Cell. 1998 Nov 25;95(5):657-67
references.pmid: 9845368
references.citation: EMBO Rep. 2002 Mar;3(3):224-9
references.pmid: 11882541
references.citation: Genes Dev. 2001 Oct 1;15(19):2613-25
references.pmid: 11581165
references.citation: Plant Physiol. 2012 Jan;158(1):119-29
references.pmid: 21994348
references.citation: Nucleic Acids Res. 2002 Dec 1;30(23):5036-55
references.pmid: 12466527
references.citation: Annu Rev Plant Physiol Plant Mol Biol. 1998 Jun;49:525-555
references.pmid: 15012245
references.citation: Cell Res. 2009 Jul;19(7):899-909
references.pmid: 19436261
references.citation: Plant Physiol. 2008 Aug;147(4):2070-83
references.pmid: 18550682
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21431-6
references.pmid: 19948955
references.citation: Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):2053-8
references.pmid: 11172074
references.citation: Plant Cell Physiol. 2004 Aug;45(8):968-75
references.pmid: 15356322
references.citation: PLoS Genet. 2009 Sep;5(9):e1000638
references.pmid: 19730687
references.citation: Plant Cell. 2008 Sep;20(9):2357-71
references.pmid: 18776063
references.citation: Nat Protoc. 2007;2(7):1565-72
references.pmid: 17585298
references.citation: Plant Cell. 2009 Nov;21(11):3535-53
references.pmid: 19920208
references.citation: Plant J. 2010 Jan;61(2):259-70
references.pmid: 19843313
references.citation: Genes Dev. 2008 Sep 15;22(18):2564-77
references.pmid: 18794352
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11626-31
references.pmid: 20534526
references.citation: Plant J. 2005 Dec;44(6):1023-35
references.pmid: 16359394
references.citation: Plant J. 2008 Nov;56(3):493-504
references.pmid: 18644002
references.citation: Annu Rev Cell Dev Biol. 1997;13:203-29
references.pmid: 9442873
references.citation: Trends Plant Sci. 2005 Mar;10(3):103-5
references.pmid: 15749466
references.citation: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7660-5
references.pmid: 19380720
references.citation: Plant Cell. 2001 Mar;13(3):599-612
references.pmid: 11251099
references.citation: Plant Cell. 2003 Oct;15(10):2399-407
references.pmid: 14508006
references.citation: Plant Physiol. 2010 Dec;154(4):1646-58
references.pmid: 20935176
references.citation: PLoS Genet. 2012;8(12):e1003114
references.pmid: 23271976
references.citation: Proc Natl Acad Sci U S A. 2009 May 5;106(18):7654-9
references.pmid: 19380736
references.citation: Plant Cell. 2011 May;23(5):1849-60
references.pmid: 21571951
references.citation: Plant Cell. 2009 Dec;21(12):3732-48
references.pmid: 20008096
references.citation: Plant Cell. 2012 Mar;24(3):1081-95
references.pmid: 22415275
references.citation: Plant Cell. 2005 Dec;17(12):3239-56
references.pmid: 16284311
references.citation: J Exp Bot. 2008;59(2):225-34
references.pmid: 18212027
references.citation: Plant Cell. 2006 Nov;18(11):2893-903
references.pmid: 17085686
references.citation: Plant J. 2007 Mar;49(6):981-94
references.pmid: 17319847
references.citation: Cell. 1998 Jun 26;93(7):1207-17
references.pmid: 9657153
references.citation: Science. 2004 Sep 24;305(5692):1937-41
references.pmid: 15448264
references.citation: Plant Cell. 2011 Nov;23(11):3974-91
references.pmid: 22108407
references.citation: Genes Dev. 1997 Nov 15;11(22):2983-95
references.pmid: 9367981
references.citation: Plant Cell. 2005 Aug;17(8):2384-96
references.pmid: 15994908
references.citation: Plant J. 2012 Aug;71(3):390-401
references.pmid: 22409654
references.citation: Genes Dev. 2002 May 15;16(10):1247-59
references.pmid: 12023303
references.citation: Nat Rev Genet. 2007 Mar;8(3):217-30
references.pmid: 17304247
references.citation: Curr Opin Genet Dev. 2001 Apr;11(2):155-61
references.pmid: 11250138
references.citation: EMBO J. 2000 Sep 15;19(18):4997-5006
references.pmid: 10990463
references.citation: Cell. 1997 May 2;89(3):349-56
references.pmid: 9150134
references.citation: Plant J. 2008 Jan;53(1):172-85
references.pmid: 17999645
references.citation: Proc Natl Acad Sci U S A. 2004 Nov 16;101(46):16091-8
references.pmid: 15505214
references.citation: Mol Cell Biol. 2005 Apr;25(8):2873-84
references.pmid: 15798178
references.citation: Curr Opin Plant Biol. 2009 Feb;12(1):49-56
references.pmid: 19084466
references.citation: Plant Cell. 2003 Jun;15(6):1468-79
references.pmid: 12782737