Histone Recognition
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Histone Recognition
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Author : Ming-Ming Zhou
language : en
Publisher: Springer
Release Date : 2015-05-29
Histone Recognition written by Ming-Ming Zhou and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-05-29 with Medical categories.
This book provides a timely review of the role of histone modifications in epigenetic control of gene expression. Topics covered include: basic mechanisms of molecular recognition of histone post-translational modification (PTMs); combinatorial readout of histone PTMs by tandem epigenome reader domains; genome-wide profiling of histone PTM interactions; small molecule modulation of histone PTM interactions and their potential as a new approach to therapeutic intervention in human diseases. All chapters were written by leading scientists who made the original key discoveries of the structure and mechanism of evolutionarily conserved reader domains, which serve to direct gene transcription in chromatin through interactions with DNA-packing histones in a PTM-sensitive manner.
Recognition Of Post Translational Histone Modifications By Antibodies And Epigenetic Reading Domains
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Author : Ina Bock
language : en
Publisher:
Release Date : 2011
Recognition Of Post Translational Histone Modifications By Antibodies And Epigenetic Reading Domains written by Ina Bock and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
Molecular epigenetics is described as the study of heritable changes in gene function without alterations in DNA sequence. Epigenetic phenomena are regulated by three interconnected players: DNA methylation, post-translational histone modifications and non-coding RNAs, which are involved in the regulation of many cellular processes including cellular differentiation and transcription. Post-translational histone modifications either directly modulate chromatin structure or they can serve as binding signals for reading domains, which recognize the modifications and mediate most of the biological functions of these modifications. In the present PhD work, we have introduced Celluspots peptide arrays as a tool for the initial screening of putative reading domains interacting with a diverse set of post-translational histone modifications in one experiment in competition. With this tool, we studied the binding specificities of antibodies and reading domains with known as well as unknown primary targets. Furthermore, we studied differences and similarities in substrate recognition of two histone lysine methyltransferases, MLL3 and MLL1, from the same protein family. Celluspots peptide arrays were first validated with antibodies directed towards post-translational histone tail modifications. In this study, we found that most of the antibodies bound well to the modification they had been raised for, but some failed. Some antibodies showed high cross-reactivity and most of the antibodies were inhibited by additional modifications close to the primary one. Furthermore, the comparison of the specificity profiles of antibodies, which had been raised for the same modification, revealed that the binding profiles sometimes differed greatly. Therefore, we did not only validate the method with this approach, but we further introduced Celluspots peptide arrays as a good tool for the quality control of epigenetic antibodies. Additionally, we applied Celluspots peptide arrays for the investigation of the specificity of the interaction of reading domains with known substrate specificity with histone peptides. The results that we obtained with this approach agreed with literature concerning the primary targets of the reading domains, but we also obtained previously unknown information concerning the influence of secondary modifications for the binding affinity to the primary targets of these reading domains. After validation of Celluspots peptide arrays, we screened approximately 20 reading domain candidates and proceeded with the most promising candidates for further analysis. One such candidate is a human polycomb group protein, which was shown to associate with the core components of the Polycomb repressive complex 2. The Polycomb repressive complex 2 is the major histone 3 lysine 27 methyltransferase-containing complex, which tri-methylates this lysine residue. Tri-methylated histone 3 lysine 27 is a post-translational modification, which is associated with transcriptional repression of developmental genes, especially HOX genes. We found that this polycomb group protein recognizes this histone tail modification in a histone variant specific manner. This histone variant is thought to be exclusively expressed in the mammalian testis and we propose that this polycomb group protein is involved in targeting the complex to this histone variant tri-methylated at lysine 27 in the human testis. The histone lysine methyltransferases of the mixed lineage leukemia (MLL) protein family mono-, di- and tri-methylate histone 3 lysine 4. We studied the substrate specificity for two members of this family, MLL3 and MLL1, and revealed that the preferred substrate sequences are different. With these differences in substrate recognition we searched for non-histone targets and found similar, but also different non-histone targets at the peptide level. This is the first time that differences in substrate recognition was observed for MLL methyltransferases, which do not depend on differing MLL-complex members, which are known to be involved in targeting the methyltransferases to their gene targets.
Reading The Histone Code
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Author : Nataliya Nady
language : en
Publisher:
Release Date : 2012
Reading The Histone Code written by Nataliya Nady and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with categories.
Structural Determinants For Histone And Inhibitor Recognition By The Bromodomain Protein 4
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Author : Marie Jung
language : en
Publisher:
Release Date : 2015
Structural Determinants For Histone And Inhibitor Recognition By The Bromodomain Protein 4 written by Marie Jung and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.
The Role Of Histone Acetylation In Recognition Memory
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Author : Anna Elizabeth Smith
language : en
Publisher:
Release Date : 2016
The Role Of Histone Acetylation In Recognition Memory written by Anna Elizabeth Smith and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Molecular Basis Of Histone Acetyl Lysine Recognition By The Brpf1 Bromodomain
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Author : Mulu Y. Lubula
language : en
Publisher:
Release Date : 2014
Molecular Basis Of Histone Acetyl Lysine Recognition By The Brpf1 Bromodomain written by Mulu Y. Lubula and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.
Histone Modifications And Nucleosome Core Particle Recognition
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Author : Michael Studer
language : en
Publisher:
Release Date : 2005
Histone Modifications And Nucleosome Core Particle Recognition written by Michael Studer and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005 with categories.
The Molecular Relationship Between Chromatin Reading Modules And Combinatorial Histone Modifications
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Author : Zhangli Su
language : en
Publisher:
Release Date : 2016
The Molecular Relationship Between Chromatin Reading Modules And Combinatorial Histone Modifications written by Zhangli Su and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
The enormous amount of genomic information encoded within our DNA is dynamically regulated by epigenetic mechanisms, to allow different interpretation of the same DNA blueprint. The post-translational modifications (PTMs) of histones are major components of epigenetic mechanisms and have a direct regulatory role in chromatin-dependent processes, such as transcription, DNA replication and DNA repair. Histone modification is also tightly associated with genetics and metabolism, through which it is linked to environment sensing and normal development. The action of histone modifications is mediated by histone-reading modules (reader domains), which are small protein modules that recognize specific histone modifications. Histone-reading modules are often part of large chromatin-modifying complexes, and mediate important biological outputs via the specific interaction with histone PTMs. Over the last decade, people have identified great numbers of histone-reader pairs. Detailed structural analysis revealed delicate intermolecular network that governs the histone recognition by reader domains. The mechanistic study about reader-histone interaction could serve as a springboard for future therapeutic interventions when histone interaction by reader domain is misregulated during disease processes. A missing link in the field is about the combinatorial nature of histone modification patterns. With each individual PTM subject to dynamic regulations, neighboring PTMs are often controlled in concert, giving rise to unique combinatorial PTM patterns. The dynamics of histone PTM landscapes and their recognition mechanism by chromatin-reading modules remain largely uncharacterized in the complete context of native chromatin. The work presented in the following chapters addresses some of these challenges about combinatorial histone modifications and reader domains. Chapter 1 introduces the basic concepts and current views of combinatorial histone modification and reader domains. Chapter 2 highlights the development of a comprehensive histone peptide microarray that encompasses combinations of different histone PTMs. Use of the peptide microarray revealed context-specific recognition by reader domains. Such specific recognitions were employed to develop a chromatin reader-based affinity enrichment platform to reveal interconnections between nucleosomal histone PTMs. In Chapter 3, I further utilized peptide microarray and determined histone-binding preferences among closely related KDM4 (lysine demethylase 4) reader domains. In particular, I followed up on H3K23me3, a poorly understood histone modification. Structural and biochemical analysis of reader-histone interaction discovered molecular determinants for recognizing H3K23me3. Further analysis supports a novel epigenetic mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis. Chapter 4 presents conclusions from this work and provides an outlook for the future research.
Molecular Characterization Of Nucleosome Recognition By Linker Histone H1 0
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Author : Amber Rae Cutter
language : en
Publisher:
Release Date : 2018
Molecular Characterization Of Nucleosome Recognition By Linker Histone H1 0 written by Amber Rae Cutter and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with categories.
Linker histones (H1s) are essential components of metazoan chromatin, facilitating chromatin condensation and regulation of numerous biological processes. However, how H1 binds to nucleosomes and specifically stabilizes chromatin structures is unclear. To provide insight into its role in higher order chromatin structure, this work identifies interactions between H1 globular domain (G) and C-terminal domain (CTD) regions and nucleosomes. Using a strategy of H1 site-specific crosslinking, I mapped interactions of selected globular domain residues with nucleosome DNA to single-base resolution. This information illuminated molecular details of how the H1 globular domain achieves nucleosome structure-specific recognition, and precisely defined the binding orientation of the H1 G domain on the nucleosome. These biochemical analyses complement structural observations, and provided critical constraints for refinement of a model of the nucleosome in complex with H1. Additionally, I investigated the mechanism by which members of the high mobility group nucleosome binding (HMGN) family counteract the propensity of H1 to stabilize formation of higher order chromatin structures, to facilitate transcription. Surprisingly, my data support that HMGNs do not displace H1s from nucleosomes; rather these proteins bind nucleosomes simultaneously with H1s without disturbing specific contacts between GH1 and nucleosomal DNA. Finally, I report the first set of specific contacts identified between the H1 CTD and linker DNA, providing key insights into the role of the H1 CTD in DNA charge neutralization and compaction. To further characterize the chromatin condensation functions of H1, interactions between H1 and oligonucleosome arrays were also studied. Taken together, this work advances our understanding of nucleosome recognition by H1 and will inform future efforts to understand the mechanism for assembly of higher-order chromatin structures.
Molecular Recognition In The Baz2b Bromodomain
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Author : Fleur Marcia Ferguson
language : en
Publisher:
Release Date : 2015
Molecular Recognition In The Baz2b Bromodomain written by Fleur Marcia Ferguson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.