Correction to: Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements (PLOS Genetics, (2016), 12, 1, (e1005771), 10.1371/journal.pgen.1005771);Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements

PLoS Genetics

Volumn 12, Issue 1, 2016, Pages

  Wang, Hua ^a   Liu, Chunmei ^a   Cheng, Jingfei ^a   Liu, Jian ^a   Zhang, Lei ^b   He, Chongsheng ^a,e   Shen, Wen Hui ^c,d   Jin, Hong ^b   Xu, Lin ^a   Zhang, Yijing ^a  

^a INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^b FUDAN UNIVERSITY   (China)

^c FUDAN UNIVERSITY   (China)

^d UNIVERSITÉ DE STRASBOURG   (France)

^e UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BMI1 PROTEIN; CURLY LEAF PROTEIN; HISTONE H3; LIKE HETEROCHROMATIN PROTEIN 1; MADS DOMAIN PROTEIN; POLYCOMB GROUP PROTEIN; RING1 PROTEIN; SWINGER PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; ARABIDOPSIS PROTEIN; CARRIER PROTEIN; CURLY LEAF PROTEIN, ARABIDOPSIS; HISTONE; HOMEODOMAIN PROTEIN; RING1A PROTEIN, ARABIDOPSIS; SWINGER PROTEIN, ARABIDOPSIS;

ARABIDOPSIS; ARTICLE; CIS REGULATORY ELEMENT; CONTROLLED STUDY; DEVELOPMENTAL GENE; GENE EXPRESSION; GENE REPRESSION; HISTONE METHYLATION; NONHUMAN; PLANT DEVELOPMENT; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; QUANTITATIVE ANALYSIS; REGULATORY SEQUENCE; SEEDLING; TISSUE SPECIFICITY; BIOSYNTHESIS; FLOWER; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; PLANT LEAF;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CARRIER PROTEINS; FLOWERS; GENE EXPRESSION REGULATION, PLANT; HISTONES; HOMEODOMAIN PROTEINS; PLANT DEVELOPMENT; PLANT LEAVES; POLYCOMB-GROUP PROTEINS; REGULATORY SEQUENCES, NUCLEIC ACID; SEEDLINGS; TRANSCRIPTION FACTORS;

EID: 84957832959     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1006574     Document Type: Erratum

References (82)

1. Bemer M, Grossniklaus U, (2012) Dynamic regulation of Polycomb group activity during plant development. Curr Opin Plant Biol 15: 523–529. doi: 10.1016/j.pbi.2012.09.006 22999383
2. Mozgova I, Hennig L, (2015) The Polycomb Group Protein Regulatory Network. Annu Rev Plant Biol.
3. Grossniklaus U, Paro R, (2014) Transcriptional silencing by polycomb-group proteins. Cold Spring Harb Perspect Biol 6: a019331. doi: 10.1101/cshperspect.a019331 25367972
4. Xiao J, Wagner D, (2015) Polycomb repression in the regulation of growth and development in Arabidopsis. Curr Opin Plant Biol 23C: 15–24.
5. Goodrich J, Puangsomlee P, Martin M, Long D, Meyerowitz EM, et al. (1997) A Polycomb-group gene regulates homeotic gene expression in Arabidopsis. Nature 386: 44–51. 9052779
6. Kinoshita T, Harada JJ, Goldberg RB, Fischer RL, (2001) Polycomb repression of flowering during early plant development. Proc Natl Acad Sci U S A 98: 14156–14161. 11698668
7. Yang C, Bratzel F, Hohmann N, Koch M, Turck F, et al. (2013) VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis. Curr Biol 23: 1324–1329. doi: 10.1016/j.cub.2013.05.050 23810531
8. Shen LS, Thong ZH, Gong XM, Shen Q, Gan YB, et al. (2014) The putative PRC1 RING-finger protein AtRING1A regulates flowering through repressing MADS AFFECTING FLOWERING genes in Arabidopsis. Development 141: 1303–U1238. doi: 10.1242/dev.104513 24553292
9. Grossniklaus U, Vielle-Calzada JP, Hoeppner MA, Gagliano WB, (1998) Maternal control of embryogenesis by MEDEA, a polycomb group gene in Arabidopsis. Science 280: 446–450. 9545225
10. Gaudin V, Libault M, Pouteau S, Juul T, Zhao G, et al. (2001) Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development 128: 4847–4858. 11731464
11. Chanvivattana Y, Bishopp A, Schubert D, Stock C, Moon YH, et al. (2004) Interaction of Polycomb-group proteins controlling flowering in Arabidopsis. Development 131: 5263–5276. 15456723
12. Bratzel F, Lopez-Torrejon G, Koch M, Del Pozo JC, Calonje M, (2010) Keeping cell identity in Arabidopsis requires PRC1 RING-finger homologs that catalyze H2A monoubiquitination. Curr Biol 20: 1853–1859. doi: 10.1016/j.cub.2010.09.046 20933424
13. Xu L, Shen WH, (2008) Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis. Curr Biol 18: 1966–1971. doi: 10.1016/j.cub.2008.11.019 19097900
14. Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, et al. (2007) Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 3: e86. 17542647
15. Zhang X, Germann S, Blus BJ, Khorasanizadeh S, Gaudin V, et al. (2007) The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat Struct Mol Biol 14: 869–871. 17676062
16. Chen D, Molitor A, Liu C, Shen WH, (2010) The Arabidopsis PRC1-like ring-finger proteins are necessary for repression of embryonic traits during vegetative growth. Cell Res 20: 1332–1344. doi: 10.1038/cr.2010.151 21060339
17. Derkacheva M, Steinbach Y, Wildhaber T, Mozgova I, Mahrez W, et al. (2013) Arabidopsis MSI1 connects LHP1 to PRC2 complexes. EMBO J 32: 2073–2085. doi: 10.1038/emboj.2013.145 23778966
18. Merini W, Calonje M, (2015) PRC1 is taking the lead in PcG repression. Plant J Accepted Article.
19. Molitor AM, Bu Z, Yu Y, Shen WH, (2014) Arabidopsis AL PHD-PRC1 complexes promote seed germination through H3K4me3-to-H3K27me3 chromatin state switch in repression of seed developmental genes. PLoS Genet 10: e1004091. doi: 10.1371/journal.pgen.1004091 24465219
20. Wang Y, Gu X, Yuan W, Schmitz RJ, He Y, (2014) Photoperiodic control of the floral transition through a distinct polycomb repressive complex. Dev Cell 28: 727–736. doi: 10.1016/j.devcel.2014.01.029 24613395
21. Lodha M, Marco CF, Timmermans MC, (2013) The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes Dev 27: 596–601. doi: 10.1101/gad.211425.112 23468429
22. Liu X, Kim YJ, Muller R, Yumul RE, Liu C, et al. (2011) AGAMOUS terminates floral stem cell maintenance in Arabidopsis by directly repressing WUSCHEL through recruitment of Polycomb Group proteins. Plant Cell 23: 3654–3670. doi: 10.1105/tpc.111.091538 22028461
23. Liu C, Xi W, Shen L, Tan C, Yu H, (2009) Regulation of floral patterning by flowering time genes. Dev Cell 16: 711–722. doi: 10.1016/j.devcel.2009.03.011 19460347
24. Heo JB, Sung S, (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331: 76–79. doi: 10.1126/science.1197349 21127216
25. Swiezewski S, Liu F, Magusin A, Dean C, (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462: 799–802. doi: 10.1038/nature08618 20010688
26. Adrian J, Farrona S, Reimer JJ, Albani MC, Coupland G, et al. (2010) cis-Regulatory elements and chromatin state coordinately control temporal and spatial expression of FLOWERING LOCUS T in Arabidopsis. Plant Cell 22: 1425–1440. doi: 10.1105/tpc.110.074682 20472817
27. Berger N, Dubreucq B, Roudier F, Dubos C, Lepiniec L, (2011) Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27. Plant Cell 23: 4065–4078. doi: 10.1105/tpc.111.087866 22080598
28. Sun B, Looi LS, Guo S, He Z, Gan ES, et al. (2014) Timing mechanism dependent on cell division is invoked by Polycomb eviction in plant stem cells. Science 343: 1248559. doi: 10.1126/science.1248559 24482483
29. Crevillen P, Yang H, Cui X, Greeff C, Trick M, et al. (2014) Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state. Nature 515: 587–590. doi: 10.1038/nature13722 25219852
30. Roudier F, Ahmed I, Berard C, Sarazin A, Mary-Huard T, et al. (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30: 1928–1938. doi: 10.1038/emboj.2011.103 21487388
31. Bouyer D, Roudier F, Heese M, Andersen ED, Gey D, et al. (2011) Polycomb repressive complex 2 controls the embryo-to-seedling phase transition. PLoS Genet 7: e1002014. doi: 10.1371/journal.pgen.1002014 21423668
32. Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR, (2012) EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genet 8: e1002512. doi: 10.1371/journal.pgen.1002512 22457632
33. Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ, (2012) MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biol 13: R16. doi: 10.1186/gb-2012-13-3-r16 22424423
34. Xu J, Shao Z, Li D, Xie H, Kim W, et al. (2015) Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Mol Cell 57: 304–316. doi: 10.1016/j.molcel.2014.12.009 25578878
35. Xu J, Shao Z, Glass K, Bauer DE, Pinello L, et al. (2012) Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell 23: 796–811. doi: 10.1016/j.devcel.2012.09.003 23041383
36. Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, et al. (2014) Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol Cell 53: 32–48. doi: 10.1016/j.molcel.2013.11.011 24361252
37. Aubert D, Chen L, Moon YH, Martin D, Castle LA, et al. (2001) EMF1, a novel protein involved in the control of shoot architecture and flowering in Arabidopsis. Plant Cell 13: 1865–1875. 11487698
38. Sneeringer CJ, Scott MP, Kuntz KW, Knutson SK, Pollock RM, et al. (2010) Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas. Proc Natl Acad Sci U S A 107: 20980–20985. doi: 10.1073/pnas.1012525107 21078963
39. Stepanik VA, Harte PJ, (2012) A mutation in the E(Z) methyltransferase that increases trimethylation of histone H3 lysine 27 and causes inappropriate silencing of active Polycomb target genes. Developmental Biology 364: 249–258. 22182520
40. Deng WW, Buzas DM, Ying H, Robertson M, Taylor J, et al. (2013) Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes. Bmc Genomics 14.
41. Lu FL, Cui X, Zhang SB, Jenuwein T, Cao XF, (2011) Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nature Genetics 43: 715–U144. doi: 10.1038/ng.854 21642989
42. Schubert D, Primavesi L, Bishopp A, Roberts G, Doonan J, et al. (2006) Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27. Embo Journal 25: 4638–4649. 16957776
43. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545–15550. 16199517
44. Jia H, Suzuki M, McCarty DR, (2014) Regulation of the seed to seedling developmental phase transition by the LAFL and VAL transcription factor networks. Wiley Interdiscip Rev Dev Biol 3: 135–145. doi: 10.1002/wdev.126 24902838
45. Nambara E, Hayama R, Tsuchiya Y, Nishimura M, Kawaide H, et al. (2000) The role of ABI3 and FUS3 loci in Arabidopsis thaliana on phase transition from late embryo development to germination. Developmental Biology 220: 412–423. 10753527
46. West MAL, Yee KM, Danao J, Zimmerman JL, Fischer RL, et al. (1994) Leafy Cotyledon1 Is an Essential Regulator of Late Embryogenesis and Cotyledon Identity in Arabidopsis. Plant Cell 6: 1731–1745. 12244233
47. Baumbusch LO, Hughes DW, Galau GA, Jakobsen KS, (2004) LEC1, FUS3, ABI3 and Em expression reveals no correlation with dormancy in Arabidopsis. Journal of Experimental Botany 55: 77–87. 14676287
48. Huang H, Mizukami Y, Hu Y, Ma H, (1993) Isolation and characterization of the binding sequences for the product of the Arabidopsis floral homeotic gene AGAMOUS. Nucleic Acids Res 21: 4769–4776. 7901838
49. Riechmann JL, Wang M, Meyerowitz EM, (1996) DNA-binding properties of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA and AGAMOUS. Nucleic Acids Res 24: 3134–3141. 8774892
50. Wang Y, Deng D, Zhang R, Wang S, Bian Y, et al. (2012) Systematic analysis of plant-specific B3 domain-containing proteins based on the genome resources of 11 sequenced species. Mol Biol Rep 39: 6267–6282. doi: 10.1007/s11033-012-1448-8 22302388
51. Pajoro A, Madrigal P, Muino JM, Matus JT, Jin J, et al. (2014) Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol 15: R41. doi: 10.1186/gb-2014-15-3-r41 24581456
52. DS OM, Wuest SE, Rae L, Raganelli A, Ryan PT, et al. (2013) Control of reproductive floral organ identity specification in Arabidopsis by the C function regulator AGAMOUS. Plant Cell 25: 2482–2503. doi: 10.1105/tpc.113.113209 23821642
53. Wuest SE, O'Maoileidigh DS, Rae L, Kwasniewska K, Raganelli A, et al. (2012) Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA. Proc Natl Acad Sci U S A 109: 13452–13457. doi: 10.1073/pnas.1207075109 22847437
54. Smaczniak C, Immink RG, Muino JM, Blanvillain R, Busscher M, et al. (2012) Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development. Proc Natl Acad Sci U S A 109: 1560–1565. doi: 10.1073/pnas.1112871109 22238427
55. Becker B, Marin B, (2009) Streptophyte algae and the origin of embryophytes. Ann Bot 103: 999–1004. doi: 10.1093/aob/mcp044 19273476
56. Theissen G, Melzer R, (2007) Molecular mechanisms underlying origin and diversification of the angiosperm flower. Ann Bot 100: 603–619. 17670752
57. Exner V, Aichinger E, Shu H, Wildhaber T, Alfarano P, et al. (2009) The Chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 Is Essential for H3K27me3 Binding and Function during Arabidopsis Development. Plos One 4.
58. He C, Huang H, Xu L, (2013) Mechanisms guiding Polycomb activities during gene silencing in Arabidopsis thaliana. Front Plant Sci 4: 454. doi: 10.3389/fpls.2013.00454 24312106
59. Gregis V, Andres F, Sessa A, Guerra RF, Simonini S, et al. (2013) Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis. Genome Biol 14: R56. doi: 10.1186/gb-2013-14-6-r56 23759218
60. Gramzow L, Theissen G, (2010) A hitchhiker's guide to the MADS world of plants. Genome Biol 11: 214. doi: 10.1186/gb-2010-11-6-214 20587009
61. Regad F, Lebas M, Lescure B, (1994) Interstitial Telomeric Repeats within the Arabidopsis-Thaliana Genome. Journal of Molecular Biology 239: 163–169. 8196051
62. Tremousaygue D, Garnier L, Bardet C, Dabos P, Herve C, et al. (2003) Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells. Plant Journal 33: 957–966. 12631321
63. Zhou Y, Hartwig B, Velikkakam JG, Schneeberger K, Turck F, (2015) Complementary activities of TELOMERE REPEAT BINDING proteins and Polycomb Group complexes in transcriptional regulation of target genes. Plant Cell.
64. Feng SH, Cokus SJ, Schubert V, Zhai JX, Pellegrini M, et al. (2014) Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis. Molecular Cell 55: 694–707. doi: 10.1016/j.molcel.2014.07.008 25132175
65. Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, et al. (2001) Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410: 120–124. 11242054
66. Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T, (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116–120. 11242053
67. Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, et al. (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298: 1039–1043. 12351676
68. Min J, Zhang Y, Xu RM, (2003) Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17: 1823–1828. 12897052
69. Francis NJ, Kingston RE, Woodcock CL, (2004) Chromatin compaction by a polycomb group protein complex. Science 306: 1574–1577. 15567868
70. Mortz E, Krogh TN, Vorum H, Gorg A, (2001) Improved silver staining protocols for high sensitivity protein identification using matrix-assisted laser desorption/ionization-time of flight analysis. Proteomics 1: 1359–1363. 11922595
71. Bouveret R, Schonrock N, Gruissem W, Hennig L, (2006) Regulation of flowering time by Arabidopsis MSI1. Development 133: 1693–1702. 16554362
72. He CS, Chen XF, Huang H, Xu L, (2012) Reprogramming of H3K27me3 Is Critical for Acquisition of Pluripotency from Cultured Arabidopsis Tissues. Plos Genetics 8.
73. Larsson AS, Landberg K, Meeks-Wagner DR, (1998) The TERMINAL FLOWER2 (TFL2) gene controls the reproductive transition and meristem identity in Arabidopsis thaliana. Genetics 149: 597–605. 9611176
74. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760. doi: 10.1093/bioinformatics/btp324 19451168
75. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14: R36. doi: 10.1186/gb-2013-14-4-r36 23618408
76. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137. doi: 10.1186/gb-2008-9-9-r137 18798982
77. Ji H, Wong WH, (2005) TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 21: 3629–3636. 16046496
78. Thorvaldsdottir H, Robinson JT, Mesirov JP, (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14: 178–192. doi: 10.1093/bib/bbs017 22517427
79. Anders S, Huber W, (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106. doi: 10.1186/gb-2010-11-10-r106 20979621
80. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W, (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136: 2621–2632. 15375207
81. Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, et al. (2014) JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res 42: D142–147. doi: 10.1093/nar/gkt997 24194598
82. Liu Y, Shao Z, Yuan GC, (2010) Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics 96: 17–26. doi: 10.1016/j.ygeno.2010.03.012 20353814