A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation

Cell Research

Volumn 27, Issue 2, 2017, Pages 226-240

  Duan, Cheng Guo ^a,b   Wang, Xingang ^b   Xie, Shaojun ^a   Pan, Li ^b   Miki, Daisuke ^a   Tang, Kai ^b   Hsu, Chuan Chih ^b   Lei, Mingguang ^a   Zhong, Yingli ^a   Hou, Yueh Ju ^b   Wang, Zhijuan ^b,c   Zhang, Zhengjing ^a   Mangrauthia, Satendra K ^b,d   Xu, Huawei ^b,e   Zhang, Heng ^a   Dilkes, Brian ^b   Tao, W Andy ^b   Zhu, Jian Kang ^a,b  

^a Chinese Academy of Sciences   (China)

^b PURDUE UNIVERSITY   (United States)

^c Key Laboratory of Agricultural Water Resources Center for Agricultural Resources Research Institute of Genetics and Developmental Biology   (China)

^d DIRECTORATE OF RICE RESEARCH   (India)

^e HENAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

anti silencing; DNA demethylation; domestication; histone acetylation; transposon

Indexed keywords

ARABIDOPSIS PROTEIN; DNA BINDING PROTEIN; HDP1 PROTEIN, ARABIDOPSIS; HDP2 PROTEIN, ARABIDOPSIS; HISTONE ACETYLTRANSFERASE; NUCLEAR PROTEIN; PLANT DNA; PROTEIN BINDING;

AMINO ACID SEQUENCE; ARABIDOPSIS; CELL NUCLEUS; CHEMISTRY; DNA DEMETHYLATION; DNA METHYLATION; GENE SILENCING; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN DOMAIN; TRANSGENE; TRANSPOSON;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; CELL NUCLEUS; DNA DEMETHYLATION; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; DNA-BINDING PROTEINS; GENE SILENCING; HISTONE ACETYLTRANSFERASES; NUCLEAR PROTEINS; PHYLOGENY; PROTEIN BINDING; PROTEIN DOMAINS; TRANSGENES;

EID: 85004098353     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/cr.2016.147     Document Type: Article

References (41)

1. Britten RJ, Kohne DE. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science 1968; 161: 529-540
2. Wicker T, Sabot F, Hua-Van A, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet 2007; 8: 973-982
3. Mc CB. The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA 1950; 36: 344-355
4. Cui H, Fedoroff NV. Inducible DNA demethylation mediated by the maize suppressor-mutator transposon-encoded TnpA protein. Plant Cell 2002; 14: 2883-2899
5. Sinzelle L, Izsvák, Ivics Z. Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cell Mol Life Sci 2009; 66: 1073-1093
6. Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 2010; 11: 204-220
7. Matzke MA, Mosher RA. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 2014; 15: 394-408
8. Zhu JK. Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet 2009; 43: 143-166
9. He XJ, Chen T, Zhu JK. Regulation and function of DNA methylation in plants and animals. Cell Res 2011; 21: 442-465
10. Wu H, Zhang Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 2014; 156: 45-68
11. Gong Z, Morales-Ruiz T, Ariza RR, Roldan-Arjona T, David L, Zhu JK. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 2002; 111: 803-814
12. Zhu J, Kapoor A, Sridhar VV, Agius F, Zhu JK. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 2007; 17: 54-59
13. Qian W, Miki D, Zhang H, et al. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 2012; 336: 1445-1448
14. Lang Z, Lei M, Wang X, et al. The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing. Mol Cell 2015; 57: 971-983
15. Qian W, Miki D, Lei M, et al. Regulation of active DNA demethylation by an α-crystallin domain protein in Arabidopsis. Mol Cell 2014; 55: 361-371
16. Wang C, Dong X, Jin D, et al. Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis. Plant Physiol 2015; 167: 905-914
17. Kapitonov VV, Jurka J. Harbinger transposons and an ancient HARBI1 gene derived from a transposase. DNA Cell Biol 2004; 23: 311-324
18. Zhang X, Jiang N, Feschotte C, Wessler SR. PIF-and Ponglike transposable elements: distribution, evolution and relationship with tourist-like miniature inverted-repeat transposable elements. Genetics 2004; 166: 971-986
19. Casola C, Lawing AM, Betran E, Feschotte C. PIF-like transposons are common in drosophila and have been repeatedly domesticated to generate new host genes. Mol Biol Evol 2007; 24: 1872-1888
20. Hoen DR, Bureau TE. Discovery of novel genes derived from transposable elements using integrative genomic analysis. Mol Biol Evol 2015; 32: 1487-1506
21. Lei M, Zhang H, Julian R, Tang K, Xie S, Zhu JK. Regulatory link between DNA methylation and active demethylation in Arabidopsis. Proc Natl Acad Sci USA 2015; 112: 3553-3557
22. Tariq M, Paszkowski J. DNA and histone methylation in plants. Trends Genet 2004; 20: 244-251
23. Jones P, Binns D, Chang HY, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 2014; 30: 1236-1240
24. Casola C, Hucks D, Feschotte C. Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol Biol Evol 2008; 25: 29-41
25. Bao W, Kojima KK, Kohany O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mob DNA 2015; 6: 11
26. Yuan YW, Wessler SR. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci USA 2011; 108: 7884-7889
27. Sinzelle L, Kapitonov VV, Grzela DP, et al. Transposition of a reconstructed Harbinger element in human cells and functional homology with two transposon-derived cellular genes. Proc Natl Acad Sci USA 2008; 105: 4715-4720
28. Jurka J, Kapitonov VV. PIFs meet tourists and harbingers: a superfamily reunion. Proc Natl Acad Sci USA 2001; 98: 12315-12316
29. Kaplan-Levy RN, Brewer PB, Quon T, Smyth DR. The trihelix family of transcription factors - light, stress and development. Trends Plant Sci 2012; 17: 163-171
30. Liang SC, Hartwig B, Perera P, et al. Kicking against the PRCs - a domesticated transposase antagonises silencing mediated by polycomb group proteins and is an accessory component of polycomb repressive complex 2. PLoS Genet 2015; 11: e1005660
31. Mateo L, Gonzalez J. Pogo-like transposases have been repeatedly domesticated into CENP-B-related proteins. Genome Biol Evol 2014; 6: 2008-2016
32. DesJarlais R, Tummino PJ. Role of histone-modifying enzymes and their complexes in regulation of chromatin biology. Biochemistry 2016; 55: 1584-1599
33. Siggers T, Gordan R. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res 2014; 42: 2099-2111
34. Scharf KD, Siddique M, Vierling E. The expanding family of Arabidopsis thaliana small heat stress proteins and a new family of proteins containing alpha-crystallin domains (Acd proteins). Cell Stress Chaperones 2001; 6: 225-237
35. Feng Z, Mao Y, Xu N, et al. Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci USA 2014; 111: 4632-4637
36. Wang X, Duan CG, Tang K, et al. RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1. Proc Natl Acad Sci USA 2013; 110: 15467-15472
37. Duan CG, Zhang H, Tang K, et al. Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation. EMBO J 2015; 34: 581-592
38. Yoo SD, Cho YH, Sheen J. Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat Protoc 2007; 2: 1565-1572
39. Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947-2948
40. Duan CG, Fang YY, Zhou BJ, et al. Suppression of Arabidopsis ARGONAUTE1-mediated slicing, transgene-induced RNA silencing, and DNA methylation by distinct domains of the cucumber mosaic virus 2b protein. Plant Cell 2012; 24: 259-274
41. Baubec T, Ivanek R, Lienert F, Schubeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 2013; 153: 480-492