Plant homeodomain fingers form a helping hand for transcription

Epigenetics

Volumn 6, Issue 1, 2011, Pages 4-8

  Fortschegger, Klaus ^a,c   Shiekhattar, Ramin ^a,b  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b WISTAR INSTITUTE   (United States)

^c CHILDREN'S CANCER RESEARCH INSTITUTE   (Austria)

Author keywords

Brain development; Epigenetics; Histone demethylase; Neuronal differentiation; RNA polymerase II; Transcription; X linked mental retardation

Indexed keywords

AMINO ACID; DNA; HISTIDINE; HISTONE H3; HISTONE H4; HOMEODOMAIN PROTEIN; LYSINE; THREONINE; TYROSINE; VEGETABLE PROTEIN;

ARTICLE; BINDING AFFINITY; CHROMATIN; DEMETHYLATION; GENE EXPRESSION; GENE REPRESSION; GENETIC TRANSCRIPTION; HISTONE MODIFICATION; IMMUNOPRECIPITATION; NONHUMAN; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING;

DANIO RERIO;

EID: 78651240488     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.6.1.13297     Document Type: Article

References (36)

1. Kouzarides T. Chromatin modifications and their function. Cell 2007; 128:693-705.
2. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007; 129:823-837
3. Allis CD, Berger SL, Cote J, Dent S, Jenuwein T, Kouzarides T, et al. New nomenclature for chroma-tin-modifying enzymes. Cell 2007; 131:633-636.
4. Vermeulen M, Mulder KW, Denissov S, Pijnappel WW, van Schaik FM, Varier RA, et al. Selective anchoring of TFIID to nucleosomes by trimethyl-ation of histone H3 lysine 4. Cell 2007; 131:58-69.
5. Wysocka J, Swigut T, Xiao H, Milne TA, Kwon SY, Landry J, et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 2006; 442:86-90.
6. Klose RJ, Kallin EM, Zhang Y. JmjC-domain-containing proteins and histone demethylation. Nat Rev Genet 2006; 7:715-727
7. Lee MG, Norman J, Shilatifard A, Shiekhattar R. Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein. Cell 2007; 128:877-887.
8. Tahiliani M, Mei P, Fang R, Leonor T, Rutenberg M, Shimizu F, et al. The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation. Nature 2007; 447:601-605.
9. Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 2007; 14:1025-1040.
10. Suganuma T, Workman JL. Crosstalk among histone modifications. Cell 2008; 135:604-607
11. Feng W, Yonezawa M, Ye J, Jenuwein T, Grummt I. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Nat Struct Mol Biol 2010; 17:445-450.
12. Fortschegger K, de Graaf P, Outchkourov NS, van Schaik FMA, Timmers HTM, Shiekhattar R. PHF8 targets histone methylation and RNA polymerase II to activate transcription. Mol Cell Biol 2010; 30:3286-3298.
13. Horton JR, Upadhyay AK, Qi HH, Zhang X, Shi Y, Cheng X. Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Mol Biol 2010; 17:38-43.
14. Kleine-Kohlbrecher D, Christensen J, Vandamme J, Abarrategui I, Bak M, Tommerup N, et al. A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. Mol Cell 2010; 38:165-168.
15. Wen H, Li J, Song T, Lu M, Kan PY, Lee MG, et al. Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation. J Biol Chem 2010; 285:9322-9326.
16. Liu W, Tanasa B, Tyurina OV, Zhou TY, Gassmann R, Liu WT, et al. PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature 2010; 466:508-512.
17. Qi HH, Sarkissian M, Hu GQ, Wang Z, Bhattacharjee A, Gordon DB, et al. Histone H4K20/ H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature 2010; 466:503-507
18. Li H, Ilin S, Wang W, Duncan EM, Wysocka J, Allis CD, et al. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 2006; 442:91-95.
19. Yu L, Wang Y, Huang S, Wang J, Deng Z, Zhang Q, et al. Structural insights into a novel histone demethylase PHF8. Cell Res 2010; 20:166-173.
20. Yue WW, Hozjan V, Ge W, Loenarz C, Cooper CD, Schofield CJ, et al. Crystal structure of the PHF8 Jumonji domain, an Nepsilon-methyl lysine demethylase. FEBS Lett 2010; 584:825-830.
21. Yang Y, Hu L, Wang P, Hou H, Lin Y, Liu Y, et al. Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans. Cell Res 2010; 20:886-898.
22. Tsukada Y, Ishitani T, Nakayama KI. KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development. Genes Dev 2010; 24:432-437
23. Dai J, Sultan S, Taylor SS, Higgins JM. The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment. Genes Dev 2005; 19:472-488.
24. Lin H, Wang Y, Tian F, Pu P, Yu Y, Mao H, et al. Coordinated regulation of active and repressive histone methylations by a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans. Cell Res 2010; 20:899-907
25. Org T, Rebane A, Kisand K, Laan M, Haljasorg U, Andreson R, et al. AIRE activated tissue specific genes have histone modifications associated with inactive chromatin. Hum Mol Genet 2009; 18:4699-4710.
26. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006; 125:315-326.
27. Huang C, Xiang Y, Wang Y, Li X, Xu L, Zhu Z, et al. Dual-specificity histone demethylase KIAA1718 (KDM7A) regulates neural differentiation through FGF4. Cell Res 2010; 20:154-165.
28. Loenarz C, Ge W, Coleman ML, Rose NR, Cooper CD, Klose RJ, et al. PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase. Hum Mol Genet 2010; 19:217-222.
29. Qiu J, Shi G, Jia Y, Li J, Wu M, Dong S, et al. The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation. Cell Res 2010; 20:908-918.
30. Core LJ, Waterfall JJ, Lis JT Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008; 322:1845-1848.
31. Siderius LE, Hamel BC, van Bokhoven H, de Jager F, van den Helm B, Kremer H, et al. X-linked mental retardation associated with cleft lip/palate maps to Xp11.3-q21.3. Am J Med Genet 1999; 85:216-220.
32. Abidi FE, Miano MG, Murray JC, Schwartz CE. A novel mutation in the PHF8 gene is associated with X-linked mental retardation with cleft lip/cleft palate. Clin Genet 2007; 72:19-22.
33. Koivisto AM, Ala-Mello S, Lemmela S, Komu HA, Rautio J, Jarvela I. Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate. Clin Genet 2007; 72:145-149.
34. Laumonnier F, Holbert S, Ronce N, Faravelli F, Lenzner S, Schwartz CE, et al. Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate. J Med Genet 2005; 42:780-786.
35. Qiao Y, Liu X, Harvard C, Hildebrand MJ, Rajcan-Separovic E, Holden JJ, et al. Autism-associated familial microdeletion of Xp11.22. Clin Genet 2008; 74:134-144.
36. Zhu Z, Wang Y, Li X, Xu L, Wang X, Sun T, et al. PHF8 is a histone H3K9me2 demethylase regulating rRNA synthesis. Cell Res 2010; 20:794-801.