Erratum to: Singh R.K. and Gunjan A. Histone tyrosine phosphorylation comes of age. Epigenetics 2011; 6:153-60.

We recently noticed that there is a major error in Figure 1 of our review published in Epignetics 2010, Volume 6, Issue 2. During the preparation of the figure, the human and yeast H2B tyrosines were numbered the same, making the human numbering incorrect. The correct Figure 1 with proper numbering of human tyrosines is below.Erratum to:Singh R.K. and Gunjan A. Histone tyrosine phosphorylation comes of age.Epigenetics 2011; 6:153-60.We recently noticed that there is a major error in Figure 1 of our review published in Epignetics 2010, Volume 6, Issue 2. During the preparation of the figure, the human and yeast H2B tyrosines were numbered the same, making the human numbering incorrect. The correct Figure 1 with proper numbering of human tyrosines is below.Open in a separate windowFigure 1. Tyrosine residues are highly conserved between budding yeast and mammalian core histones. The four canonical core histone proteins from the budding yeast Saccharomyces cerevisiae are indicated by the prefix “Sc” and denoted in blue. The mammalian core histones and the mammalian variant histone H2A.X are shown in black. The number of amino acid (aa) residues in each core histone is indicated on the right. The location of the a-helices in the secondary structure of the histone proteins is indicated by cylinders. Tyrosine residues are shown as balloons and the tyrosine residues essential for viability in budding yeast histones are indicated by red balloons. Tyrosines in mammalian histones have not yet been evaluated to determine the residues essential for viability. Note the high degree of conservation of the location as well as the spacing of all but one tyrosine residue between budding yeast and mammalian core histones (H3 Y54 being the exception). Tyrosine residues that have recently been shown to be phosphorylated in vivo are marked by yellow “explosion” signs and the letter “P.” Additional tyrosine residues that are predicted to be reasonably accessible in the nucleosomal context under certain conditions and can be potentially phosphorylated in vivo are indicated by a yellow halo only on the mammalian histones for clarity, but are likely to be just as applicable to the yeast histones. Solid yellow halo indicates higher probability of phosphorylation, while a dashed yellow halo indicates lower probability of phosphorylation.     

Histone tyrosine phosphorylation comes of age

Histones were discovered over a century ago and have since been found to be the most extensively post-translationally modified proteins, although tyrosine phosphorylation of histones had remained elusive until recently. The year 2009 proved to be a landmark year for histone tyrosine (Y) phosphorylation as five research groups independently discovered this modification. Three groups describe phosphorylation of Y142 in the variant histone H2A.X, where it may be involved in the cellular decision making process to either undergo DNA repair or apoptosis in response to DNA damage. Further, one group suggests that phosphorylation of histone H3 on Y99 is crucial for its regulated proteolysis in yeast, while another found that Y41 phosphorylation modulates chromatin architecture and oncogenesis in mammalian cells. These pioneering studies provide the initial conceptual framework for further analyses of the diverse roles of tyrosine phosphorylation on different histones, with far reaching implications for human health and disease.Key words: histones, chromatin, tyrosine phosphorylation, genomic instability, DNA damage, DNA repair, apoptosis, ubiquitylation, proteolysis, cancer     

Histone tyrosine phosphorylation comes of age

Histones were discovered over a century ago and have since been found to be the most extensively posttranslationally modified proteins, although tyrosine phosphorylation of histones had remained elusive until recently. The year 2009 proved to be a landmark year for histone tyrosine (Y) phosphorylation as five research groups independently discovered this modification. Three groups describe phosphorylation of Y142 in the variant histone H2A.X, where it may be involved in the cellular decision making process to either undergo DNA repair or apoptosis in response to DNA damage. Further, one group suggests that phosphorylation of histone H3 on Y99 is crucial for its regulated proteolysis in yeast, while another found that Y41 phosphorylation modulates chromatin architecture and oncogenesis in mammalian cells. These pioneering studies provide the initial conceptual framework for further analyses of the diverse roles of tyrosine phosphorylation on different histones, with far reaching implications for human health and disease.

Erratum to: Singh R.K. and Gunjan A. Histone tyrosine phosphorylation comes of age. Epigenetics 2011; 6:153-60.     

A new resource for cereal genomics: 22K barley GeneChip comes of age

In recent years, access to complete genomic sequences, coupled with rapidly accumulating data related to RNA and protein expression patterns, has made it possible to determine comprehensively how genes contribute to complex phenotypes. However, for major crop plants, publicly available, standard platforms for parallel expression analysis have been limited. We report the conception and design of the new publicly available, 22K Barley1 GeneChip probe array, a model for plants without a fully sequenced genome. Array content was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley (Hordeum vulgare) gene sequences from the National Center for Biotechnology Information nonredundant database. Conserved sequences expressed in seedlings of wheat (Triticum aestivum), oat (Avena strigosa), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays) were identified that will be valuable in the design of arrays across grasses. To enhance the usability of the data, BarleyBase, a MIAME-compliant, MySQL relational database, serves as a public repository for raw and normalized expression data from the Barley1 GeneChip probe array. Interconnecting links with PlantGDB and Gramene allow BarleyBase users to perform gene predictions using the 21,439 non-redundant Barley1 exemplar sequences or cross-species comparison at the genome level, respectively. We expect that this first generation array will accelerate hypothesis generation and gene discovery in disease defense pathways, responses to abiotic stresses, development, and evolutionary diversity in monocot plants.     

Erratum to H. Frederik Nijhout,et al. Epigenetics Volume 1, Issue 2; pp. 81-87.

In the paper, Long-Range Allosteric Interactions between the Folate and Methionine Cycles Stabilize DNA Methylation Reaction Rate, by H. Frederik Nijhout, Michael C. Reed, David F. Anderson, Jonathan C. Mattingly, S. Jill James and Cornelia M. Ulrich (Epigenetics 2006; 2:81-87), an eqution was misprinted on page 86 of the appendix. The corrected equations can be found in the online pdf.     

p60v-src causes tyrosine phosphorylation and inactivation of the N-cadherin-catenin cell adhesion system.

Transformation of chick embryonic fibroblasts with Rous sarcoma virus strongly suppresses N-cadherin-mediated cell-cell adhesion, without inhibiting its expression. This suppression is correlated with tyrosine phosphorylation of N-cadherin and catenins, the cadherin-associated proteins, which are known to regulate cadherin function. Experiments with non-myristylation and temperature-sensitive mutants of RSV and with herbimycin A, a potent inhibitor of tyrosine kinases, suggest that both the suppression of cell adhesion and tyrosine phosphorylation of catenins are highly transformation-specific.     

A lymphoma protein with an in vitro site of tyrosine phosphorylation homologous to that in pp60src

The major in vitro substrate for a tyrosine protein kinase in the particulate fraction of the lymphoma cell line LSTRA is a protein of molecular weight of 58,000 (pp58) (Casnellie, J. E. Harrison, M. L., Pike, L. J., Hellstrom, K. E., and Krebs, E. G. (1982) Proc. Natl. Acad. Sci. U. S. A. 79, 282-286). In order to determine if this protein was related to pp60src, the transformation-specific protein from Rous sarcoma virus, partial proteolysis maps of in vitro 32P-labeled pp58 and pp60src were prepared using Staphylococcus aureus V8 protease and papain. The maps were clearly different, indicating the pp58 is distinct from pp60src. However characterization of the tryptic fragment containing the single site of in vitro tyrosine phosphorylation in pp58 has revealed that the amino acid sequence around this site is extremely homologous to, if not identical with the sequence around the site of tyrosine phosphorylation in pp60src.     

pp60c-src in human melanocytes and melanoma cells exhibits elevated specific activity and reduced tyrosine 530 phosphorylation compared to human fibroblast pp60c-src.

Elevated levels of pp60c-src tyrosine kinase activity have been implicated in both tumorigenesis and cell differentiation. We have found a 2- to 4-fold elevation in pp60c-src specific activity in certain human melanoma cell lines compared to human foreskin fibroblasts. This activation of pp60c-src did not appear to be related to melanoma tumor progression, because when normal human epidermal melanocytes were examined, it was found that they contained pp60c-src having a 7-fold elevation in specific activity compared to pp60c-src from human fibroblasts. It was determined that pp60c-src from melanocytes was not the neuronal form, pp60c-src+. Melanocyte pp60c-src exhibited a reduced level of phosphorylation on its carboxyl-terminal regulatory site, tyrosine 530, which might be responsible for its elevated specific activity. These results suggest that, in melanocytes, regulation of tyrosine 530 phosphorylation-dephosphorylation favors activation of pp60c-src. This activation may be involved in the growth, differentiation, or function of human melanocytes.     

Isolation and preliminary characterization of R6K plasmid deletion mutants.

Several deletion mutants of R6K have been isolated by mutagen treatment of bacterial host carrying wild type of the plasmid and search for clones that lost ampicillin or streptomycin resistance. The molecular weight of the mutants as estimated by agarose gel electrophoresis was 15 times 10(6) minus 23 times 10(6) compared to 26 times 10(6) for the parental plasmid. The mutants were characterized in respect of the level of resistance to ampicillin and frequency of conjugational transfer. Some of the mutants were found to differ in Eco RI digestion pattern from the wild type.     

EGF-induced tyrosine phosphorylation of Endofin is dependent on PI3K activity and proper localization to endosomes

In our previous study, Endofin was validated to be a novel tyrosine phosphorylation target downstream of EGFR. Here, we attempted to map the signaling events associated with Endofin following activation of EGFR with EGF. Tyrosine phosphorylation of endogenous Endofin peaked around 15 min and was modulated within 30 min of EGF treatment. Phosphatidylinositol 3-kinase (PI3K) activity and FYVE domain-mediated localization of Endofin to EEA1-marked endosomes were shown to be necessary for the tyrosine phosphorylation of Endofin. Tyrosine 515 was mapped to be a major phosphorylation site on Endofin but disruption of phosphorylation at Y515 neither affected Endofin's localization nor its co-localization with EGFR in the endosomes. Instead, abrogation of Y515 phosphorylation and mislocalization of Endofin were found to enhance the amplitude of the MAPK cascade, suggesting a possible role of Endofin in the modulation of MAPK pathway. Our study has identified a novel signaling cascade involving EGFR, PI3K, Endofin and MAPK in the EGFR signaling network.     

The vaccinia virus A33R protein provides a chaperone function for viral membrane localization and tyrosine phosphorylation of the A36R protein

The products of the A33R and A36R genes of vaccinia virus are incorporated into the membranes of intracellular enveloped virions (IEV). When extracts of cells that had been infected with vaccinia virus and labeled with H(3)(32)PO(4) were immunoprecipitated with antibodies against the A33R protein, two prominent bands were resolved. The moderately and more intensely labeled bands were identified as phosphorylated A33R and A36R proteins, respectively. The immunoprecipitated complex contained disulfide-bonded dimers of A33R protein that were noncovalently linked to A36R protein. Biochemical analysis indicated that the two proteins were phosphorylated predominantly on serine residues, with lesser amounts on threonines. The A36R protein was also phosphorylated on tyrosine, as determined by specific binding to an anti-phosphotyrosine antibody. Serine phosphorylation and A33R-A36R protein complex formation occurred even when virus assembly was blocked at an early stage with the drug rifampin. Tyrosine phosphorylation was selectively reduced in cells infected with F13L or A34R gene deletion mutants that were impaired in the membrane-wrapping step of IEV formation. In addition, tyrosine phosphorylation was specifically inhibited in cells infected with an A33R deletion mutant that still formed IEV. Immunofluorescence and immunoelectron microscopy indicated that in the absence of the A33R protein, the A36R protein was localized in Golgi membranes but not in IEV. In the absence of the A36R protein, however, the A33R protein still localized to IEV membranes. These studies together with others suggest that the A33R protein guides the A36R protein to the IEV membrane, where it subsequently becomes tyrosine phosphorylated as a signal for actin tail formation.