Histone H4 acetylation during interleukin‐2 stimulation of mouse T cells

Taplick, Jan; Kurtev, Vladislav; Lagger, Gerda; Seiser, Christian

doi:10.1016/s0014-5793(98)01164-8

Cited by 34 publications

(21 citation statements)

References 52 publications

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“…Even when the probability assigned to the three preferred states was lowered for a test set, the system preferred the other two states containing lysine acetylation. Such consistent results demonstrate the ability of our model to reproduce the presence of the modifications mentioned above, during transcription, (as reported, (Taplick, 1998;Zhang et al, 2007) in particular, during expression of oncogenes). For higher levels of DNA methylation (>0.85, Figure 6), the preference is more towards choosing methylated histone states leading to reduced transcription rate.…”

Section: Resultssupporting

confidence: 88%

“…For example, histone methylation was found to be important for DNA methylation maintenance at imprinted loci, which could lead to disorders such as the Prader-Willi syndrome, (Chahwan et al, 2011). Such individual experiments have helped unravel the connection step by step between levels of DM and specific histone modifications including special histone variants, (Barber et al, 2004;Ito, 2007;Meng et al, 2009;Sun et al, 2007;Taplick, 1998;Wyrick & Parra, 2008). Hence a complete picture of the molecular communications that control the cellular events is lacking.…”

Section: Histone Modifications -Dimensionmentioning

confidence: 99%

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Modelling DNA Methylation Dynamics

Raghavan¹,

Ruskin²

2012

DNA Methylation - From Genomics to Technology

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Ireland Introduction"Epigenetics" as introduced by Conrad Waddington in 1946, is defined as a set of interactions between genes and the surrounding environment, which determines the phenotype or physical traits in an organism, (Murrell et al., 2005;Waddington, 1942). Initial research focused on genomic regions such as heterochromatin and euchromatin based on dense and relatively loose DNA packing, since these were known to contain inactive and active genes respectively, (Yasuhara et al., 2005). Subsequently, key roles of DNA methylation, Histone Modifications and other assistive proteins such as Methyl Binding Proteins (MBP) during gene expression and suppression were identified, (Baylin & Ohm, 2006;Jenuwein & Allis, 2001). An emergent and persistent view that every epigenetic event affects another, to strengthen or suppress gene expression has made this an active field of research. DNA methylation refers to the modification of DNA by addition of a methyl group to the cytosine base, and is the most stable, heritable and well conserved epigenetic change. It is introduced and maintained, (Riggs & Xiong, 2004;Ushijima et al., 2003) by an enzyme family called DNA Methyl Transferases (DNMT), (Doerfler et al., 1990). Methyl-Cytosine or "mC", often referred to as the fifth type of nucleotide plays an extremely important role in gene expression and other cellular activities. Although DM is defined a simple molecular modification, its effect, can range from altering the state of a single gene to controlling a whole section of chromosome in the human genome.The human genome is largely made of complex sequences evolved over time due to replication, mutations and insertion of foreign DNA. Based on the nucleotide distribution and functional significance, the genome has been categorized into different block of sequences, namely genes or coding and non-coding regions. A special type of sequence located near genes, in relation to spread of DNA methylation and dinucleotide frequencies are the CpG islands 1 . These islands are mostly found near the promoters, (5'end), of genes and their methylation levels are closely monitored to investigate the spread of Cancer. Useful insight on epigenetic mechanisms may be found from analysing the DNA sequence patterns or the genotype of the organism, (Gertz et al., 2011;Glass et al., 2004;Segal & Widom, 2009). Since more than 90% of DM occurs in CG dinucleotides, , knowledge of the distribution and location of CG can be utilized to understand the biological 1 DNA sequences are defined and classified as CpG islands if , (a) length of that DNA sequence >200 bp, (b) Total amount of Guanine and Cytosine nucleotides >50%, and, (c) the observed/expected ratio of CG dinucleotides for that given length of sequence, >60%, (Takai & Jones, 2002)

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Section: Resultssupporting

confidence: 88%

Section: Histone Modifications -Dimensionmentioning

confidence: 99%

Modelling DNA Methylation Dynamics

Raghavan¹,

Ruskin²

2012

DNA Methylation - From Genomics to Technology

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“…Histone preparation and Western blot analyses were performed as previously described (38). All antibodies used in this study were purchased from Upstate Biotechnology, Lake Placid, N.Y.…”

Section: Methodsmentioning

confidence: 99%

Activation of the Mouse Histone Deacetylase 1 Gene by Cooperative Histone Phosphorylation and Acetylation

Hauser

Schuettengruber

Bartl

et al. 2002

Molecular and Cellular Biology

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The amino-terminal tails of core histones are targets for multiple modifications such as acetylation, phosphorylation, and methylation. Generation of modification-specific antibodies and the identification of some of the modifying enzymes allow us to begin to understand the impact of these modifications on several cellular processes, including DNA replication and transcription. Reversible histone acetylation emerged during recent years as an important mechanism for the chromatindependent regulation of gene expression. Acetylation of ε-amino groups of lysine residues results in reduced interaction between positively charged histone tails and negatively charged DNA. Local or wide-range histone deacetylation leads to chromatin condensation, while acetylation is believed to increase the accessibility of particular genomic regions for high-molecular-weight protein complexes, thereby setting the stage for transcription.In addition to acetylation, histone phosphorylation has been recently shown to play an important role for chromatin-associated processes. Distinct sets of kinases have been implicated in these events (references 4 and 41 and references cited therein). On one hand, H3 phosphorylation correlates with entry into mitosis, suggesting a link between chromatin condensation and histone modification by kinases. On the other hand, histone H3 phosphorylation at serine 10 was found to be an important step of the so-called nucleosomal response (26; reviewed in reference 41). This term describes the phosphorylation of histone H3, which leads to the concomitant activation of the immediate-early genes c-fos, c-jun, and c-myc (3, 26). The nucleosomal response can be induced through stimulation of the mitogen-activated protein (MAP) kinase cascade by growth factors, pharmacological agents, or stress. Induction of the MAP kinase pathway leads to the activation of effector kinases (MSK1/Rsk-2) which can phosphorylate histone H3 (33,40).Only a small fraction of histone H3 is transiently phosphorylated at the G 0 /G 1 transition in growth factor-stimulated cells (1). This subset of phosphorylated histone H3 proteins is highly susceptible to hyperacetylation induced by histone deacetylase (HDAC) inhibitors. One possible explanation for this finding is the strong preference in in vitro experiments of several acetylating enzymes for histone H3 phosphorylated at serine 10 (5, 24). Indeed, a number of recent observations strongly suggest the presence of cross talk between the different histone modifying mechanisms (reviewed in references 19, 35, and 43). A link between histone acetylation and phosphorylation is provided by studies reporting the association of simultaneously acetylated and phosphorylated (in this report referred to as "phosphoacetylated") histone H3 with nucleosomes of activated immediate-early genes (5, 6, 23). A concerted action of acetyltransferases and kinases was also demonstrated in yeast (25) and in mammalian cells (28).An alternative model predicts the independent targeting of histone H3 by kinases and ac...

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“…For example, HDAC inhibitors consistently induce the cyclin-dependent kinase inhibitor p21 WAF1/Cip1 (13)(14)(15)(16), which causes cell growth arrest in various tumor cell lines. In general, inhibition of HDAC results in accumulation of acetylated histone protein (15,17,18). Furthermore, inhibition of HDAC is known to affect a variety of biological processes, such as the induction of differentiation (19,20), cell cycle arrest (13, 16 -18, 21), and apoptotic cell death (19,22).…”

Section: Cyclooxygenase (Cox)mentioning

confidence: 99%