ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis

Plant Journal

Volumn 78, Issue 4, 2014, Pages 706-714

  Li, Guang ^a,b   Liu, Shujing ^a   Wang, Jiawei ^a   He, Jianfeng ^a   Huang, Hai ^a   Zhang, Yijing ^a   Xu, Lin ^a  

^a INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Arabidopsis thaliana; ATP dependent chromatin remodeling; ISWI; MNase seq; Nucleosome distribution; technical advance

Indexed keywords

GENE EXPRESSION;

ARABIDOPSIS THALIANA; CHROMATIN REMODELING; ISWI; MNASE-SEQ; NUCLEOSOMES; TECHNICAL ADVANCES;

CHROMOSOMES;

ANIMALIA; ARABIDOPSIS; ARABIDOPSIS THALIANA;

ADENOSINE TRIPHOSPHATASE; ARABIDOPSIS PROTEIN; CHR11 PROTEIN, ARABIDOPSIS; CHR17 PROTEIN, ARABIDOPSIS; CHROMATIN; ISWI PROTEIN; NUCLEOSOME; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ARABIDOPSIS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MUTATION; NUCLEOSOME; PLANT GENOME;

ADENOSINE TRIPHOSPHATASES; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; MUTATION; NUCLEOSOMES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84900474003     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12499     Document Type: Article

References (32)

1. Aravind, L., and, Iyer, L.M., (2012) The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. Cell Cycle, 11, 119-131.
2. Bai, L., and, Morozov, A.V., (2010) Gene regulation by nucleosome positioning. Trends Genet. 26, 476-483.
3. Chen, K., Xi, Y., Pan, X., Li, Z., Kaestner, K., Tyler, J., Dent, S., He, X., and, Li, W., (2013) DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 23, 341-351.
4. Chodavarapu, R.K., Feng, S., Bernatavichute, Y.V., et al. (2010) Relationship between nucleosome positioning and DNA methylation. Nature, 466, 388-392.
5. Clapier, C.R., and, Cairns, B.R., (2009) The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273-304.
6. Costas, C., de la Paz Sanchez, M., Stroud, H., et al. (2011) Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks. Nat. Struct. Mol. Biol. 18, 395-400.
7. Dong, J., Gao, Z., Liu, S., Li, G., Yang, Z., Huang, H., and, Xu, L., (2013) SLIDE, the protein interacting domain of ISWI remodelers, binds DDT-domain proteins of different subfamilies in chromatin remodeling complexes. J. Integr. Plant Biol. 55, 928-937.
8. Fincher, J.A., Vera, D.L., Hughes, D.D., McGinnis, K.M., Dennis, J.H., and, Bass, H.W., (2013) Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales. Plant Physiol. 162, 1127-1141.
9. Fu, K., Tang, Q., Feng, J., Liu, X.S., and, Zhang, Y., (2012) DiNuP: a systematic approach to identify regions of differential nucleosome positioning. Bioinformatics, 28, 1965-1971.
10. Gaffney, D.J., McVicker, G., Pai, A.A., Fondufe-Mittendorf, Y.N., Lewellen, N., Michelini, K., Widom, J., Gilad, Y., and, Pritchard, J.K., (2012) Controls of nucleosome positioning in the human genome. PLoS Genet. 8, e1003036.
11. Gkikopoulos, T., Schofield, P., Singh, V., Pinskaya, M., Mellor, J., Smolle, M., Workman, J.L., Barton, G.J., and, Owen-Hughes, T., (2011) A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science, 333, 1758-1760.
12. Huanca-Mamani, W., Garcia-Aguilar, M., Leon-Martinez, G., Grossniklaus, U., and, Vielle-Calzada, J.P., (2005) CHR11, a chromatin-remodeling factor essential for nuclear proliferation during female gametogenesis in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 102, 17231-17236.
13. Knizewski, L., Ginalski, K., and, Jerzmanowski, A., (2008) Snf2 proteins in plants: gene silencing and beyond. Trends Plant Sci. 13, 557-565.
14. Langmead, B., Trapnell, C., Pop, M., and, Salzberg, S.L., (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25.
15. Langst, G., and, Becker, P.B., (2001) Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors. J. Cell Sci. 114, 2561-2568.
16. Li, G., Zhang, J., Li, J., Yang, Z., Huang, H., and, Xu, L., (2012a) ISWI chromatin remodeling factors and their interacting RINGLET proteins act together in controlling the plant vegetative phase in Arabidopsis. Plant J. 72, 261-270.
17. Li, Z., Gadue, P., Chen, K., Jiao, Y., Tuteja, G., Schug, J., Li, W., and, Kaestner, K.H., (2012b) Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell, 151, 1608-1616.
18. Narlikar, G.J., (2010) A proposal for kinetic proof reading by ISWI family chromatin remodeling motors. Curr. Opin. Chem. Biol. 14, 660-665.
19. Russo, V.E.A., Martienssen, R.A., and, Riggs, A.D., (1996) Epigenetic Mechanisms of Gene Regulation. Woodbury: Cold Spring Harbor Laboratory Press.
20. Sadeh, R., and, Allis, C.D., (2011) Genome-wide "re"-modeling of nucleosome positions. Cell, 147, 263-266.
21. Sala, A., Toto, M., Pinello, L., Gabriele, A., Di Benedetto, V., Ingrassia, A.M., Lo Bosco, G., Di Gesu, V., Giancarlo, R., and, Corona, D.F., (2011) Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI. EMBO J. 30, 1766-1777.
22. Shivaswamy, S., Bhinge, A., Zhao, Y., Jones, S., Hirst, M., and, Iyer, V.R., (2008) Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol. 6, e65.
23. Smaczniak, C., Immink, R.G., Muino, J.M., et al. (2012) Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development. Proc. Natl Acad. Sci. USA, 109, 1560-1565.
24. Stroud, H., Otero, S., Desvoyes, B., Ramirez-Parra, E., Jacobsen, S.E., and, Gutierrez, C., (2012) Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 109, 5370-5375.
25. Struhl, K., and, Segal, E., (2013) Determinants of nucleosome positioning. Nat. Struct. Mol. Biol. 20, 267-273.
26. van Dijk, K., Ding, Y., Malkaram, S., et al. (2010) Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana. BMC Plant Biol. 10, 238.
27. Weiner, A., Hughes, A., Yassour, M., Rando, O.J., and, Friedman, N., (2010) High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res. 20, 90-100.
28. Xu, L., Xu, Y., Dong, A., Sun, Y., Pi, L., and, Huang, H., (2003) Novel as1 and as2 defects in leaf adaxial-abaxial polarity reveal the requirement for ASYMMETRIC LEAVES1 and 2 and ERECTA functions in specifying leaf adaxial identity. Development, 130, 4097-4107.
29. Yadon, A.N., and, Tsukiyama, T., (2011) SnapShot: chromatin remodeling: ISWI. Cell, 144, 454-454.e451.
30. Yadon, A.N., Van de Mark, D., Basom, R., Delrow, J., Whitehouse, I., and, Tsukiyama, T., (2010) Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription. Mol. Cell. Biol. 30, 5110-5122.
31. Zhang, X., Clarenz, O., Cokus, S., Bernatavichute, Y.V., Pellegrini, M., Goodrich, J., and, Jacobsen, S.E., (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 5, e129.
32. Zhang, W., Zhang, T., Wu, Y., and, Jiang, J., (2012) Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell, 24, 2719-2731.