PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Wang, Juan ^a   Lin, Xueqiu ^a   Wang, Su ^a   Wang, Chenfei ^a   Wang, Qixuan ^a   Duan, Xikun ^a   Lu, Peng ^b   Wang, Qian ^a   Wang, Chengyang ^a   Liu, X Shirley ^c,d   Huang, Jinyan ^a  

^a TONGJI UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c DANA FARBER CANCER INSTITUTE   (United States)

^d HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN; HISTONE DEMETHYLASE; PHF8 PROTEIN, HUMAN; RE1-SILENCING TRANSCRIPTION FACTOR; REPRESSOR PROTEIN; RNA POLYMERASE II; TRANSCRIPTION FACTOR;

CELL CULTURE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; NUCLEOTIDE MOTIF; PROMOTER REGION;

CELLS, CULTURED; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION REGULATION; HISTONE DEMETHYLASES; HUMANS; NUCLEOTIDE MOTIFS; PROMOTER REGIONS, GENETIC; REPRESSOR PROTEINS; RNA POLYMERASE II; TRANSCRIPTION FACTORS;

EID: 84901386570     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep05008     Document Type: Article

References (28)

1. Ram, O. et al. Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells. Cell 147, 1628-1639 (2011).
2. Yun, M., Wu, J., Workman, J. L. &Li, B. Readers of histone modifications. Cell Res. 21, 564-578 (2011).
3. Hargreaves, D. C. & Crabtree, G. R. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 21, 396-420 (2011).
4. Kleine-Kohlbrecher, D. et al. AFunctional Link between theHistoneDemethylase PHF8 and the Transcription Factor ZNF711 in X-Linked Mental Retardation. Mol. Cell 38, 165-178 (2010).
5. Liu,W. et al. PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature 466, 508-512 (2010).
6. Qi,H. H. et al. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature 466, 503-507 (2010).
7. Qiu, J. et al. The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation. Cell Res. 20, 908-918 (2010).
8. Lee, M. G., Norman, J., Shilatifard, A. & Shiekhattar, R. Physical and Functional Association of a Trimethyl H3K4 Demethylase and Ring6a/MBLR, a Polycomblike Protein. Cell 128, 877-887 (2007).
9. Pasini, D. et al. Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and Polycomb-Repressive Complex 2. Genes & Dev. 22, 1345-1355 (2008).
10. Ziqi, Z. et al. PHF8 is a histone H3K9me2 demethylase regulating rRNA synthesis. Cell Res. 20, 794-801 (2010).
11. Weijun, F., Masato, Y., Jing, Y., Thomas, J. & Ingrid, G. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Nat. Struct. Mol. Biol. 17, 445-450 (2010).
12. Laumonnier, F. et al. Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate. J. Med. Genet. 42, 780-786 (2005).
13. Koivisto, A. M. et al. 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 72, 145-149 (2007).
14. Tahiliani, M. et al. The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation. Nature 447, 601-605 (2007).
15. Fortschegger, K. et al. PHF8 Targets Histone Methylation and RNA Polymerase II To Activate Transcription. Mol. Cell Biol. 30, 3286-3298 (2010).
16. Liu, T. et al. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 12, R83 (2011).
17. Liu, X. S., Brutlag, D. L. &Liu, J. S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nature Biotechnol. 20, 835-839 (2002).
18. Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protoc. 4, 44-57 (2008).
19. Shin, H., Liu, T., Manrai, A. K. & Liu, X. S. CEAS: cis-regulatory element annotation system. Bioinformatics 25, 2605-2606 (2009).
20. Bieda, M. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res. 16, 595-605 (2006).
21. McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnol. 28, 495-501 (2010).
22. Iwase, S. et al. The X-LinkedMental Retardation Gene SMCX/JARID1CDefines a Family of Histone H3 Lysine 4 Demethylases. Cell 128, 1077-1088 (2007).
23. Shi, Y. et al. Histone Demethylation Mediated by the Nuclear Amine Oxidase Homolog LSD1. Cell 119, 941-953 (2004).
24. Roopra, A., Qazi, R., Schoenike, B., Daley, T. J. & Morrison, J. F. Localized Domains of G9a-Mediated Histone Methylation Are Required for Silencing of Neuronal Genes. Mol. Cell 14, 727-738 (2004).
25. Ballas, N. &Mandel, G. Themany faces of REST oversee epigenetic programming of neuronal genes. Curr. Opin. Neurobiol. 15, 500-506 (2005).
26. Zhang, Y. et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
27. Agilent. Agilent Feature Extraction Reference Guide. 2007. URL http://www. chem. agilent. com/Library/usermanuals/Public/G4460-90026-FE- Reference. pdf (last accesses on July 2 2013).
28. Smyth, G. K. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor [397-42] (Springer, New York: 2005).