Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation.

Transcriptional initiation is a key step in the control of mRNA synthesis and is intimately related to chromatin structure and histone modification. Here, we show that the ubiquitylation of H2A (ubH2A) correlates with silent chromatin and regulates transcriptional initiation. The levels of ubH2A vary during hepatocyte regeneration, and based on microarray expression data from regenerating liver, we identified USP21, a ubiquitin-specific protease that catalyzes the hydrolysis of ubH2A. When chromatin is assembled in vitro, ubH2A, but not H2A, specifically represses the di- and trimethylation of H3K4. USP21 relieves this ubH2A-specific repression. In addition, in vitro transcription analysis revealed that ubH2A represses transcriptional initiation, but not transcriptional elongation, by inhibiting H3K4 methylation. Notably, ubH2A-mediated repression was not observed when H3 Lys 4 was changed to arginine. Furthermore, overexpression of USP21 in the liver up-regulates a gene that is normally down-regulated during hepatocyte regeneration. Our studies revealed a novel mode of trans-histone cross-talk, in which H2A ubiquitylation controls the di- and trimethylation of H3K4, resulting in regulation of transcriptional initiation.

[1]  Thomas A. Milne,et al.  WDR5 Associates with Histone H3 Methylated at K4 and Is Essential for H3 K4 Methylation and Vertebrate Development , 2005, Cell.

[2]  Stuart L Schreiber,et al.  Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. , 2003, Molecular cell.

[3]  E. Yeh,et al.  Identification of a Novel Isopeptidase with Dual Specificity for Ubiquitin- and NEDD8-conjugated Proteins* , 2000, The Journal of Biological Chemistry.

[4]  Haruhiko Koseki,et al.  Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. , 2004, Developmental cell.

[5]  John R. Yates,et al.  Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation , 2005, Nature.

[6]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[7]  Ali Shilatifard,et al.  Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. , 2006, Annual review of biochemistry.

[8]  R. Baum,et al.  Isolation and characterization of protein A24, a "histone-like" non-histone chromosomal protein. , 1975, The Journal of biological chemistry.

[9]  C. Glass,et al.  A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation. , 2007, Molecular cell.

[10]  G. Orphanides,et al.  A Unified Theory of Gene Expression , 2002, Cell.

[11]  J. T. Kadonaga.  Eukaryotic Transcription: An Interlaced Network of Transcription Factors and Chromatin-Modifying Machines , 1998, Cell.

[12]  Ryuji Kobayashi,et al.  ACF, an ISWI-Containing and ATP-Utilizing Chromatin Assembly and Remodeling Factor , 1997, Cell.

[13]  J. Ausió,et al.  Histone ubiquitination: a tagging tail unfolds? , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[14]  C. Allis,et al.  Histone and chromatin cross-talk. , 2003, Current opinion in cell biology.

[15]  R. Costa,et al.  Transcription factors in liver development, differentiation, and regeneration , 2003, Hepatology.

[16]  David Mangnall,et al.  The molecular physiology of liver regeneration following partial hepatectomy , 2003, Liver international : official journal of the International Association for the Study of the Liver.

[17]  M. Vidal,et al.  Role of histone H2A ubiquitination in Polycomb silencing , 2004, Nature.

[18]  Peter White,et al.  Identification of Transcriptional Networks during Liver Regeneration* , 2005, Journal of Biological Chemistry.

[19]  D. Patel,et al.  Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF , 2006, Nature.

[20]  Danny Reinberg,et al.  Human but Not Yeast CHD1 Binds Directly and Selectively to Histone H3 Methylated at Lysine 4 via Its Tandem Chromodomains* , 2005, Journal of Biological Chemistry.

[21]  Brian D. Strahl,et al.  Gene silencing: Trans-histone regulatory pathway in chromatin , 2002, Nature.

[22]  P. Chambon,et al.  Stability of nucleosomes in native and reconstituted chromatins. , 1976, Nucleic acids research.

[23]  Ali Shilatifard,et al.  Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. , 2003, Genes & development.

[24]  Eric S. Lander,et al.  Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse , 2005, Cell.

[25]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[26]  Tony Kouzarides,et al.  Reversing histone methylation , 2005, Nature.

[27]  Bing Li,et al.  The Role of Chromatin during Transcription , 2007, Cell.

[28]  P. Meltzer,et al.  Activating Signal Cointegrator 2 Belongs to a Novel Steady-State Complex That Contains a Subset of Trithorax Group Proteins , 2003, Molecular and Cellular Biology.

[29]  T. Kouzarides.  Chromatin Modifications and Their Function , 2007, Cell.

[30]  Hengbin Wang,et al.  Regulation of cell cycle progression and gene expression by H2A deubiquitination , 2007, Nature.

[31]  Munetaka Hashimoto,et al.  Suppression of Pathogenicity of Porphyromonas gingivalis by Newly Developed Gingipain Inhibitors , 2004, Molecular Pharmacology.

[32]  B. Hauser,et al.  The PRETTY FEW SEEDS2 gene encodes an Arabidopsis homeodomain protein that regulates ovule development , 2005, Development.

[33]  Karl Henry,et al.  Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B. , 2004, Genes & development.

[34]  Yi Zhang.  Transcriptional regulation by histone ubiquitination and deubiquitination. , 2003, Genes & development.

[35]  Hiroshi Kimura,et al.  Kinetics of Core Histones in Living Human Cells , 2001, The Journal of cell biology.

[36]  Y. Hayashizaki,et al.  Mechanism of liver regeneration after partial hepatectomy using mouse cDNA microarray. , 2004, Journal of hepatology.

[37]  Zu-Wen Sun,et al.  Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast , 2002, Nature.

[38]  J. Mellor.  The dynamics of chromatin remodeling at promoters. , 2005, Molecular cell.

[39]  M. Pazin,et al.  ATP-dependent nucleosome reconfiguration and transcriptional activation from preassembled chromatin templates. , 1994, Science.

[40]  H. Busch,et al.  Isopeptide linkage between nonhistone and histone 2A polypeptides of chromosomal conjugate-protein A24. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[41]  J. T. Kadonaga,et al.  Assembly of regularly spaced nucleosome arrays by Drosophila chromatin assembly factor 1 and a 56-kDa histone-binding protein. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Thomas A. Milne,et al.  A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling , 2006, Nature.

[43]  V. Chow,et al.  Novel human HALR (MLL3) gene encodes a protein homologous to ALR and to ALL-1 involved in leukemia, and maps to chromosome 7q36 associated with leukemia and developmental defects. , 2001, Cancer detection and prevention.

[44]  R. Taub.  Transcriptional control of liver regeneration , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[45]  R. Tjian,et al.  Diversified transcription initiation complexes expand promoter selectivity and tissue-specific gene expression. , 2003, Genes & development.

[46]  S. Berger,et al.  Histone modifications in transcriptional regulation. , 2002, Current opinion in genetics & development.

[47]  M. Muramatsu,et al.  p300-mediated acetylation facilitates the transfer of histone H2A-H2B dimers from nucleosomes to a histone chaperone. , 2000, Genes & development.

[48]  Mark Johnston,et al.  Methylation of Histone H3 by COMPASS Requires Ubiquitination of Histone H2B by Rad6* , 2002, The Journal of Biological Chemistry.

[49]  G. Felsenfeld,et al.  The organization of histones and DNA in chromatin: Evidence for an arginine-rich histone kernel , 1976, Cell.

[50]  H. Kato,et al.  G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. , 2002, Genes & development.

[51]  Tsutomu Ohta,et al.  Nucleosomal histone kinase-1 phosphorylates H2A Thr 119 during mitosis in the early Drosophila embryo. , 2004, Genes & development.

[52]  G. Higgins,et al.  Experimental pathology of the liver , 1931 .

[53]  Jayadev Raju,et al.  Energy restriction reduces the number of advanced aberrant crypt foci and attenuates the expression of colonic transforming growth factor beta and cyclooxygenase isoforms in Zucker obese (fa/fa) rats. , 2003, Cancer research.