|
Agrestin, A. and Bianchi, M. A. (2003). HMGB proteins and gene expression. Elsevier. 13:170-178. Alinsug, M. V., Yu, C.W., and Wu, K. (2009). Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants. BMC Plant Biol. 9: 37. Assenberg, R., Webb, M., Connolly, E., Stott, K., Watson, M., Hobbs, J., and Thomas, J.O. (2008). A critical role in structure-specific DNA binding for the acetylatable lysine residues in HMGB1. Biochem J. 411: 553-561. Antosch, M., Mortensen, S.A., and Grasser, K. D. (2012). Plant proteins containing high mobility group box DNA-binding domains modulate different nuclear processes. Plant Physiol. 159: 875–883. Bustin, M., and Reeves, R. (1996). High-mobility-group chromosomal proteins: architectural components that facilitate chromatin function. Prog. Nucleic Acids Res. Mol. Bol. 54: 35–100. Bustin, M. (1999). Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins. Mol. Cell. Biol. 19: 5237–5246. Bustin, M. (2001). Revised nomenclature for high mobility group (HMG) chromosomal proteins. Trends Biochem. Sci. 26: 152-153. Berger, S.L. (2007). The complex language of chromatin regulation during transcription. Nature. 447: 407–412. Chen, Z.J., and Tian, L. (2007). Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim. Biophys. Acta. 1769: 295-307.
Earley, K., Lawrence, R. J., Pontes, O., Reuther, R., Enciso, A. J., Silva, M., Neves, N., Gross, M., Viegas, W., and Pikaard, C. S. (2006). Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev. 20: 1283-1293. Elenkov, I., Pelovsky, P., Ugrinova, I., Takahashi, M., and Pasheva, E. (2011). The DNA binding and bending activities of truncated tail-less HMGB1 protein are differentially affected by Lys-2 and Lys-81 residues and their acetylation. Int. J. Biol Sci. 7: 691-699. Grasser, K. D., Grill, S., Duroux, M., Launholt, D., Thomsen, M.S., Nielsen, B.V., Nielsen, H. K., and Merkle, T. (2004). HMGB6 from Arabidopsis thaliana specifies a novel type of plant chromosomal HMGB protein. Biochem. J. 43: 1309-1314. Hansen, F. T., Madsen, C. K., Nordland, A. M., Grasser, M., Merkle, T. and Grasser, K. D. (2008). A novel family of plant DNA-binding proteins containing both HMG-box and AT-rich interaction domains. Biochem. 47: 13207–13214. Iwahara, J., Iwahara, M., Daughdrill, G.W., Ford, J., and Clubb, R.T. (2002). The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA. EMBO J. 21: 1197-1209. Ito I, Fukazawa J, Yoshida M. (2007). Post-translational methylation of high mobility group box 1 (HMGB1) causes its cytoplasmic localization in neutrophils. J. Biol Chem. 282: 16336–16344 Ikeda, Y., Kinoshita, Y., Susaki, D., Ikeda, Y., Iwano, M., Takayama, S., Higashiyama, T., Kakutani, T., and Kinoshita, T. (2011). HMG domain containing SSRP1 is required for DNA demethylation and genomic imprinting in Arabidopsis. Dev. 21: 589–596. Ivan, E., Pelovsky, P., Ugrinova, I., Takahashi, M., and Pasheva, E. (2011). The DNA Binding and Bending Activities of Truncated Tail-less HMGB1 protein are Differentially Affected by Lys-2 and Lys-81 Residues and Their Acetylation. Int. J. Biol. Sci. 7(6): 691-699. Kortschak, R. D., Tucker, P. W., and Saint, R. (2000). ARID proteins come in from the desert. Trends. Biochem. Sci. 25: 294-299. Klosterman, S.J., and Hadwiger, L.A. (2002). Plant HMG proteins bearing the AT-hook motif. Plant Sci. 162: 855–866. Kwak, K. J., Kim, J. Y., Kim, Y. O., and Kang, H. (2007). Characterization of transgenic Arabidopsis plants overexpressing high mobility group B proteins under high salinity, drought or cold stress. Plant Cell Physiol. 48: 221–231. Kim, W., Latrasse, D., Servet, C., and Zhou, D. X. (2012). Arabidopsis histone deacetylase HDA9 regulates flowering time through repression of AGL19. Biochem. Biophys. Res. Commun. 432: 394–398. Launholt, D., Grnlund, J.T., Nielsen, H.K., and Grasser, K.D. (2007). Overlapping expression patterns among the genes encoding Arabidopsis chromosomal high mobility group (HMG) proteins. FEBS Lett. 581: 1114-1118. Lildballe, D.L., Pedersen, D.S., Kalamajka, R., Emmersen, J., Houben, A., and Grasser, K.D. (2008). The expression level of the chromatin-associated HMGB1 protein influences growth, stress tolerance and transcriptome in Arabidopsis. J. Mol. Biol. 384: 9–21. Lolas, I.B., Himanen, K., Gronlund, J.T., Lynggaard, C., Houben, A., Melzer, M., Van Lijsebettens, M., and Grasser, K.D. (2010). The transcript elongation factor FACT affects Arabidopsis vegetative and reproductive development and genetically interacts with HUB1/2. Plant J. 61: 686–697. Murfett, J., Wang, X.J., Hagen, G., and Guilfoyle, T.J. (2001). Identification of Arabidopsis histone deacetylase HDA6 mutants that affect transgene expression. Plant Cell. 13: 1047-1061. Orphanides, G., Wu, W. H., Lane, W. S., Hampsey, M., and Reinberg, D. (1999). The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature. 400: 284–288 Pandey, R., Muller, A., Napoli, C. A., Selinger, D. A., Pikaard, C. S., Richards, E. J., Bender, J., Mount, D. W., and Jorgensen, R. A. (2002). Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 30: 5036–5055. Pedersen, D. S., and Grasser, K. D. (2010). The role of chromosomal HMGB proteins in plants. Biochimi. Biophys. Acta. 1799: 171–174. Pedersen, D.S., Coppens, F., Ma, L., Antosch, M., Marktl, B., Merkle, T., Beemster, G.T.S., Houben, A., and Grasser, K.D. (2011). The plant-specific family of DNA-binding proteins containing three HMG-box domains interacts with mitotic and meiotic chromosomes. New Phytol. 192: 577–589. Riechmann, J, L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O, J., Samaha, R, R. (2000). Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science. 290: 2105–2110 Reeves, R. (2010). Nuclear functions of the HMG proteins. Biochim. Biophys. Acta. 1799: 3-14. Stros, M., Launholt, D., and Grasser, K.D. (2007). The HMG-box: a versatile protein domain occurring in a wide variety of DNA-binding proteins. Cell. Mol. Life Sci. 64: 2590–2606. Tian, L., and Chen, Z.J. (2001). Blocking histone deacetylation in Arabidopsis induces pleiotropic effects on plant gene regulation and development. Proc. Natl. Acad. Sci USA. 98: 200-205. Thomas, J.O. (2001). HMG1 and 2: architectural DNA-binding proteins. Biochem. Soc. Trans. 29: 395–401. Ugrinova, I., Pasheva, E. A., Armengaud, J., and Pashev, I. G. (2001). In vivo acetylation of HMG1 protein enhances its binding affinity to distorted DNA structures. Biochemistry. 40: 14655-14660. Ugrinova, I., Mitkova, E., Moskalenko, C., Pashev, I., and Pasheva, E. (2007). DNA bending versus DNA end joining activity of HMGB1 protein is modulated in vitro by acetylation. Biochemistry. 46: 2111-2117. Ueda, T., and Yoshida, M. (2010). HMGB proteins and transcriptional regulation. Biochem. Biophys. Acta. 1799: 114-118. Wilsker, D., Patsialou, A., Dallas, P. B., and Moran, E. (2002). ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development. Cell Growth Differ. 13: 95-106. Wilskera, D., Probstb, L., Wainc, H.M., Maltaisd, L., Tuckerb, P.W., and Moran, E. (2005). Nomenclature of the ARID family of DNA-binding proteins. Genomics. 86: 242 – 251. Wu, K., Malik, K., Tian, L., Brown, D., and Miki, B. (2000). Functional analysis of a RPD3 histone deacetylase homologue in Arabidopsis thaliana. Plant Mol. Biol. 44: 167-176. Wu, K., Zhang, L., Zhou, C., Yu, C. W., and Chaikam, V. (2008). HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J. Exp. Bot. 59:225-234 Xia, C., Wang, Y. J., Liang, Y., Niu, Q. K., Tan, X. Y., Chu, L. C., Chen, L. Q., Zhang, X. Q., and Ye, D. (2014). The ARID-HMG DNA-binding protein AtHMGB15 is required for pollen tube growth in Arabidopsis thaliana. Plant J. 79: 741-756. Yu, C. W., Liu, X., Luo, M., Chen, C., Lin, X., Tian, G., Lu, Q., Cui, Y., and Wu, K. (2011). HISTONE DEACETYLASE6 interacts with FLOWERING LOCUS D and regulates flowering in Arabidopsis. Plant Physiol. 156: 173–184. Yu, C.W., Chang, K.Y., and Wu, K. (2016). Genome-Wide Analysis of Gene Regulatory Networks of the FVE-HDA6-FLD Complex in Arabidopsis. Front Plant Sci. 7: 555.
|