Quantitative Proteomic Analysis of Histone Modifications (original) (raw)
Related papers
Histone structure and nucleosome stability
Expert Review of Proteomics, 2005
Histone proteins play essential structural and functional roles in the transition between active and inactive chromatin states. Although histones have a high degree of conservation due to constraints to maintain the overall structure of the nucleosomal octameric core, variants have evolved to assume diverse roles in gene regulation and epigenetic silencing. Histone variants, post-translational modifications and interactions with chromatin remodeling complexes influence DMA replication, transcription, repair and recombination. The authors review recent findings on the structure of chromatin that confirm previous interparticle interactions observed in crystal structures.
Regulation of Chromatin Structure and Transcription Via Histone Modifications
Post-Translational Modifications in Health and Disease, 2010
Chromatin, which was once considered merely a structural component required for DNA packaging, is now recognized as a dynamic template governed by intricate regulation. Histone post-translational modifications (PTMs) contribute to chromatin dynamics and regulate fundamental biological processes including transcription, mitotic chromatin condensation and DNA repair following damage. To date, histone methylation, acetylation, phosphorylation, ubiquitination, sumoylation and ADP-ribosylation, among others, have
Histone H3 phosphorylation near the nucleosome dyad alters chromatin structure
Nucleic Acids Research, 2014
Nucleosomes contain 146bpofDNAwrappedaroundahistoneproteinoctamerthatcontrolsDNAaccessibilitytotranscriptionandrepaircomplexes.Posttranslationalmodification(PTM)ofhistoneproteinsregulatesnucleosomefunction.Todate,onlymodestchangesinnucleosomestructurehavebeendirectlyattributedtohistonePTMs.HistoneresidueH3(T118)islocatednearthenucleosomedyadandcanbephosphorylated.ThisPTMdestabilizesnucleosomesandisimplicatedintheregulationoftranscriptionandrepair.Here,wereportgelelectrophoreticmobility,sucrosegradientsedimentation,thermaldisassembly,micrococcalnucleasedigestionandatomicforcemicroscopymeasurementsoftwoDNA−histonecomplexesthatarestructurallydistinctfromnucleosomes.WefindthatH3(T118ph)facilitatestheformationofanucleosomeduplexwithtwoDNAmoleculeswrappedaroundtwohistoneoctamers,andanaltosomecomplexthatcontainsoneDNAmoleculewrappedaroundtwohistoneoctamers.Thenucleosomeduplexcomplexformswithinshort146 bp of DNA wrapped around a histone protein octamer that controls DNA accessibility to transcription and repair complexes. Posttranslational modification (PTM) of histone proteins regulates nucleosome function. To date, only modest changes in nucleosome structure have been directly attributed to histone PTMs. Histone residue H3(T118) is located near the nucleosome dyad and can be phosphorylated. This PTM destabilizes nucleosomes and is implicated in the regulation of transcription and repair. Here, we report gel electrophoretic mobility, sucrose gradient sedimentation, thermal disassembly, micrococcal nuclease digestion and atomic force microscopy measurements of two DNA-histone complexes that are structurally distinct from nucleosomes. We find that H3(T118ph) facilitates the formation of a nucleosome duplex with two DNA molecules wrapped around two histone octamers, and an altosome complex that contains one DNA molecule wrapped around two histone octamers. The nucleosome duplex complex forms within short 146bpofDNAwrappedaroundahistoneproteinoctamerthatcontrolsDNAaccessibilitytotranscriptionandrepaircomplexes.Posttranslationalmodification(PTM)ofhistoneproteinsregulatesnucleosomefunction.Todate,onlymodestchangesinnucleosomestructurehavebeendirectlyattributedtohistonePTMs.HistoneresidueH3(T118)islocatednearthenucleosomedyadandcanbephosphorylated.ThisPTMdestabilizesnucleosomesandisimplicatedintheregulationoftranscriptionandrepair.Here,wereportgelelectrophoreticmobility,sucrosegradientsedimentation,thermaldisassembly,micrococcalnucleasedigestionandatomicforcemicroscopymeasurementsoftwoDNA−histonecomplexesthatarestructurallydistinctfromnucleosomes.WefindthatH3(T118ph)facilitatestheformationofanucleosomeduplexwithtwoDNAmoleculeswrappedaroundtwohistoneoctamers,andanaltosomecomplexthatcontainsoneDNAmoleculewrappedaroundtwohistoneoctamers.Thenucleosomeduplexcomplexformswithinshort150 bp DNA molecules, whereas altosomes require at least $250 bp of DNA and form repeatedly along 3000 bp DNA molecules. These results are the first report of a histone PTM significantly altering the nucleosome structure.
Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle
The Journal of Cell Biology
As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulatio...
FEBS Journal, 2014
N-terminal tails of histones are easily accessible outside of the nucleosomal core particle and post-translational modifications (PTMs) of these tails have been the focus of attention in the past 15-20 years. By recruiting (or excluding) specific readers, histone modifications can regulate chromatin dynamics and, by extension, DNA-dependent processes. However, until very recently, the direct impact of histone PTMs on nucleosome structure and thus on chromatin function has remained somewhat elusive. Recent findings of novel sites and types of histone PTMs located within the globular domain of histones and, in particular, on the lateral surface of the histone octamer have changed this. As a result of their structurally important location in close proximity to the DNA molecule, this new class of histone PTMs can have a direct impact on chromatin function. Depending on their precise position at the nucleosome lateral surface (e.g. near the DNA entry/exit sites or in the dyad region), histone PTMs can regulate nucleosome structure and/or stability differently. We review recent progress on how histone PTMs can influence DNA unwrapping and/or nucleosome disassembly and shed light on how these types of novel modifications contribute mechanistically to the regulation of transcriptional activity.
Phosphorylation of histone H3(T118) alters nucleosome dynamics and remodeling
Nucleic Acids Research, 2011
Nucleosomes, the fundamental units of chromatin structure, are regulators and barriers to transcription, replication and repair. Post-translational modifications (PTMs) of the histone proteins within nucleosomes regulate these DNA processes. Histone H3(T118) is a site of phosphorylation [H3(T118ph)] and is implicated in regulation of transcription and DNA repair. We prepared H3(T118ph) by expressed protein ligation and determined its influence on nucleosome dynamics. We find H3(T118ph) reduces DNA-histone binding by 2 kcal/mol, increases nucleosome mobility by 28-fold and increases DNA accessibility near the dyad region by 6-fold. Moreover, H3(T118ph) increases the rate of hMSH2-hMSH6 nucleosome disassembly and enables nucleosome disassembly by the SWI/SNF chromatin remodeler. These studies suggest that H3(T118ph) directly enhances and may reprogram chromatin remodeling reactions.
Histone modifications dictate specific biological readouts
Journal of Genetics and Genomics, 2009
The basic unit of chromatin is the nucleosomal core particle, containing 147 bp of DNA that wraps twice around an octamer of core histones. The core histones bear a highly dynamic N-terminal amino acid tail around 20 35 residues in length and rich in basic amino acids. These tails extending from the surface of nucleosome play an important role in folding of nucleosomal arrays into higher order chromatin structure, which plays an important role in eukaryotic gene regulation. The amino terminal tails protruding from the nuclesomes get modified by the addition of small groups such as methyl, acetyl and phosphoryl groups. In this review, we focus on these complex modification patterns and their biological functions. Moreover, these modifications seem to be part of a complex scheme where distinct histone modifications act in a sequential manner or in combination to form a "histone code" read by other proteins to control the structure and/or function of the chromatin fiber. Errors in this histone code may be involved in many human diseases especially cancer, the nature of which could be therapeutically exploited. Increasing evidence suggests that many proteins bear multiple, distinct modifications, and the ability of one modification to antagonize or synergize the deposition of another can have significant biological consequences.
Chromosomal histone modification patterns – from conservation to diversity
Trends in Plant Science, 2006
The organization of DNA into chromatin regulates expression and maintenance (replication, repair, recombination, segregation) of genetic information in a dynamic manner. The N-terminal tails of the nucleosomal core histones are subjected to post-translational modifications such as acetylation, methylation, phosphorylation, ubiquitination, glycosylation, ADP-ribosylation, carbonylation and sumoylation. These modifications, together with DNA methylation, control the folding of the nucleosomal array into higher order structures and mediate signalling for cellular processes. Although histones and their modifications are highly conserved, recent data show that chromosomal distribution of individual modifications (acetylation, methylation, phosphorylation) can differ along the cell cycle as well as among and between groups of eukaryotes. This implies the possibility of evolutionary divergence in reading the 'histone code'.