Search Results - "chromatin"

Nucleosome assembly during DNA replication

Table of Contents: “…Contents: Introduction to chromatin structure -- Primary function of chromatin: DNA compaction -- The nucleosome core particle -- De novo nucleosome assembly during the cell cycle -- Two distinct processes contribute to restoration of chromatin structure during DNA replication -- A fundamental problem in nucleosome assembly: histone-DNA aggregation -- Chromatin Assembly Factor 1 (CAF-1) and PCNA -- ASF1: a multi-talented histone chaperone -- Biomedical implications -- Agents that block the acetylation and deacetylation of new histones may sensitise cells to cancer chemotherapeutic agents -- Genome-wide histone acetylation, deacetylation and epigenetic inheritance -- Epigenetic xerox machines as potential targets for cancer therapy and regenerative medicine.…”
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Modeling the 3D conformation of genomes / by Tiana, G. (Guido), Giorgetti, Luca

Table of Contents: “…Cover; Half Title; Series Page; Title Page; Copyright Page; Contents; Preface; Editor; Contributors; 1: Job Dekker; 1.1 Introduction; 1.2 Chromosome Conformation Capture; 1.3 3C Variants to Obtain Genome-Scale and High-Resolution Chromatin Interaction Matrices; 1.4 Insights Obtained From Chromosome Interaction Data; 1.5 Dynamics and Cell-to-Cell Variation in Chromatin Interactions; 1.6 Polymer Models for Chromosome Folding; 1.7 Mechanisms of Chromosome Folding and Nuclear Organization; 1.8 Future Perspective; Acknowledgments; Part 1: First-Principles Models; 2: Cédric Vaillant and Daniel Jost…”
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DNA methylation and genome defense in Neurospora crassa

Table of Contents: “…Contents: Control of DNA methylation -- repeat-induced point (RIP) mutation -- relationship of chromatin modifications and DNA methylation -- mutants that eliminate DNA methylation -- roles of histone H3 methyltransferase (DIM-5) and heterochromatin protein 1 (HP1) in DNA methylation -- indications of involvement of protein acetylation, methylation and phosphorylation in mechanism of DNA methylation -- propagation of DNA methylation and the associated silenced chromatin state.…”
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DNA methylation and genome defense in Neurospora crassa

Table of Contents: “…Contents: Control of DNA methylation -- repeat-induced point (RIP) mutation -- relationship of chromatin modifications and DNA methylation -- mutants that eliminate DNA methylation -- roles of histone H3 methyltransferase (DIM-5) and heterochromatin protein 1 (HP1) in DNA methylation -- indications of involvement of protein acetylation, methylation and phosphorylation in mechanism of DNA methylation -- propagation of DNA methylation and the associated silenced chromatin state.…”
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DNA methylation and genome defense in Neurospora crassa

Table of Contents: “…Contents: Control of DNA methylation -- repeat-induced point (RIP) mutation -- relationship of chromatin modifications and DNA methylation -- mutants that eliminate DNA methylation -- roles of histone H3 methyltransferase (DIM-5) and heterochromatin protein 1 (HP1) in DNA methylation -- indications of involvement of protein acetylation, methylation and phosphorylation in mechanism of DNA methylation -- propagation of DNA methylation and the associated silenced chromatin state.…”
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Plant genes, genomes, and genetics / by Grotewold, Erich, Chappell, Joseph, Kellogg, Elizabeth Anne

Table of Contents: “…The plant genetic material -- The genome landscape : plastic and dynamic -- Transposable elements -- Centromeres, telomeres and chromatin -- Organelle genomes -- RNA -- The plant RNA polymerases -- Making mRNAs : control of transcription by RNP-II -- Controlling nuclear transcription -- Control of transcription factor function -- Small RNAs -- Chromatin and gene expression -- RNA processing and transport -- Fate of RNA -- Translation of RNA -- Protein folding and transport -- Protein degradation.…”
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Mitotic chromosome condensation

Table of Contents: “…Contents: Evolutionary and developmental comparisons -- Stages of mitosis -- Primary functions of mitosis -- Lower levels of chromatin organization -- Helical folding -- Experimental foundation of textbook model -- Are there specific DNA sequences at the base of chromatin loops? …”
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Epigenetically mediated gene silencing a companion to genetic alterations in driving tumorigenesis /

Table of Contents: “…Contents: Introduction to epigenetic changes in cancer -- defining the process of promoter DNA hypermethylation as a constituent of a broad range of chromatin abnormalities in cancer -- defining the genes aberrantly silenced in cancer including approaches being used to screen the cancer genome for such genes -- defining what is known about the interaction of DNA methylation and chromatin modifications for initiating and maintaining gene silencing in cancer -- outlining the position of aberrant gene silencing in tumor progression and particularly highlighting the key role these changes may play for the earliest steps in tumorigenesis -- defining the potential for using DNA hypermethylated gene promoter sequences as molecular markers for cancer risk assessment, early diagnosis and prognosis -- discussing the possibilities for targeting reversal of gene silencing as a prevention and therapeutic strategy for cancer.…”
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Nuclear receptors transcriptional functions /

Table of Contents: “…Contents: Introduction to transcription factors -- Nuclear receptors as ligand-dependent transcription factors -- Classes of nuclear receptor -- Nuclear receptor ligands: agonists and antagonists -- Nuclear receptor phylogeny -- Nuclear receptor isoforms -- The nuclear receptor DNA-binding domain -- Hormone response elements -- The nuclear receptor ligand-binding domain -- Nuclear receptor mechanism -- Subcellular localization of nuclear receptors -- The effect of ligand binding -- Nuclear receptor coregulators -- Initial discoveries of coregulators -- The SRC/p160 coregulator family -- Nuclear receptor-coregulator interaction motifs -- Histone acetylation and chromatin structure -- The Nuclear Receptor Signaling Atlas (NURSA) -- Chromatin immunoprecipitation as a tool in nuclear receptor mechanism -- Functional differences between type I and type II nuclear receptors -- The coregulator exchange -- DNA-binding independent functions -- Transrepression -- The role of kinases.…”
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Initiation of DNA replication

Table of Contents: “…Contents: Cell cycle control of DNA replication -- Yeast as a model eukaryote -- Control of S-phase entry in yeast -- Characterization of origins of DNA replication -- Modular structure of S. cerevisiae origins -- The budding yeast origin recognition complex (ORC) -- Structure of the ORC-Cdc6 complex -- Evolutionary comparison of ORC AAA+ subunits -- Proteins required for formation of the pre-Replication Complex (pre-RC) -- Cell cycle dependent association of yeast initiation proteins with chromatin -- ATP-dependent assembly of a pre-RC -- Cell cycle regulation of the pre-RC -- The chromosome cycle and establishment of pre-RCs -- Dynamic assembly and stability of ORC in human cells -- Commitment to S-phase and initiation -- Cdc45p is associated with chromatin in a cell cycle-dependent manner -- Temporal regulation of DNA replication -- Dynamics of pre-RC proteins in human cells differ from pre-RC proteins in yeast.…”
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Mitotic chromosome condensation

Table of Contents: “…Contents: Evolutionary and developmental comparisons -- Stages of mitosis -- Primary functions of mitosis -- Lower levels of chromatin organization -- Helical folding -- Experimental foundation of textbook model -- Are there specific DNA sequences at the base of chromatin loops? …”
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Epigenetically mediated gene silencing a companion to genetic alterations in driving tumorigenesis /

Table of Contents: “…Contents: Introduction to epigenetic changes in cancer -- defining the process of promoter DNA hypermethylation as a constituent of a broad range of chromatin abnormalities in cancer -- defining the genes aberrantly silenced in cancer including approaches being used to screen the cancer genome for such genes -- defining what is known about the interaction of DNA methylation and chromatin modifications for initiating and maintaining gene silencing in cancer -- outlining the position of aberrant gene silencing in tumor progression and particularly highlighting the key role these changes may play for the earliest steps in tumorigenesis -- defining the potential for using DNA hypermethylated gene promoter sequences as molecular markers for cancer risk assessment, early diagnosis and prognosis -- discussing the possibilities for targeting reversal of gene silencing as a prevention and therapeutic strategy for cancer.…”
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Nuclear receptors transcriptional functions /

Table of Contents: “…Contents: Introduction to transcription factors -- Nuclear receptors as ligand-dependent transcription factors -- Classes of nuclear receptor -- Nuclear receptor ligands: agonists and antagonists -- Nuclear receptor phylogeny -- Nuclear receptor isoforms -- The nuclear receptor DNA-binding domain -- Hormone response elements -- The nuclear receptor ligand-binding domain -- Nuclear receptor mechanism -- Subcellular localization of nuclear receptors -- The effect of ligand binding -- Nuclear receptor coregulators -- Initial discoveries of coregulators -- The SRC/p160 coregulator family -- Nuclear receptor-coregulator interaction motifs -- Histone acetylation and chromatin structure -- The Nuclear Receptor Signaling Atlas (NURSA) -- Chromatin immunoprecipitation as a tool in nuclear receptor mechanism -- Functional differences between type I and type II nuclear receptors -- The coregulator exchange -- DNA-binding independent functions -- Transrepression -- The role of kinases.…”
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Initiation of DNA replication

Table of Contents: “…Contents: Cell cycle control of DNA replication -- Yeast as a model eukaryote -- Control of S-phase entry in yeast -- Characterization of origins of DNA replication -- Modular structure of S. cerevisiae origins -- The budding yeast origin recognition complex (ORC) -- Structure of the ORC-Cdc6 complex -- Evolutionary comparison of ORC AAA+ subunits -- Proteins required for formation of the pre-Replication Complex (pre-RC) -- Cell cycle dependent association of yeast initiation proteins with chromatin -- ATP-dependent assembly of a pre-RC -- Cell cycle regulation of the pre-RC -- The chromosome cycle and establishment of pre-RCs -- Dynamic assembly and stability of ORC in human cells -- Commitment to S-phase and initiation -- Cdc45p is associated with chromatin in a cell cycle-dependent manner -- Temporal regulation of DNA replication -- Dynamics of pre-RC proteins in human cells differ from pre-RC proteins in yeast.…”
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Epigenetically mediated gene silencing a companion to genetic alterations in driving tumorigenesis /

Table of Contents: “…Contents: Introduction to epigenetic changes in cancer -- defining the process of promoter DNA hypermethylation as a constituent of a broad range of chromatin abnormalities in cancer -- defining the genes aberrantly silenced in cancer including approaches being used to screen the cancer genome for such genes -- defining what is known about the interaction of DNA methylation and chromatin modifications for initiating and maintaining gene silencing in cancer -- outlining the position of aberrant gene silencing in tumor progression and particularly highlighting the key role these changes may play for the earliest steps in tumorigenesis -- defining the potential for using DNA hypermethylated gene promoter sequences as molecular markers for cancer risk assessment, early diagnosis and prognosis -- discussing the possibilities for targeting reversal of gene silencing as a prevention and therapeutic strategy for cancer.…”
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Nuclear receptors transcriptional functions /

Table of Contents: “…Contents: Introduction to transcription factors -- Nuclear receptors as ligand-dependent transcription factors -- Classes of nuclear receptor -- Nuclear receptor ligands: agonists and antagonists -- Nuclear receptor phylogeny -- Nuclear receptor isoforms -- The nuclear receptor DNA-binding domain -- Hormone response elements -- The nuclear receptor ligand-binding domain -- Nuclear receptor mechanism -- Subcellular localization of nuclear receptors -- The effect of ligand binding -- Nuclear receptor coregulators -- Initial discoveries of coregulators -- The SRC/p160 coregulator family -- Nuclear receptor-coregulator interaction motifs -- Histone acetylation and chromatin structure -- The Nuclear Receptor Signaling Atlas (NURSA) -- Chromatin immunoprecipitation as a tool in nuclear receptor mechanism -- Functional differences between type I and type II nuclear receptors -- The coregulator exchange -- DNA-binding independent functions -- Transrepression -- The role of kinases.…”
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Series

Initiation of DNA replication

Table of Contents: “…Contents: Cell cycle control of DNA replication -- Yeast as a model eukaryote -- Control of S-phase entry in yeast -- Characterization of origins of DNA replication -- Modular structure of S. cerevisiae origins -- The budding yeast origin recognition complex (ORC) -- Structure of the ORC-Cdc6 complex -- Evolutionary comparison of ORC AAA+ subunits -- Proteins required for formation of the pre-Replication Complex (pre-RC) -- Cell cycle dependent association of yeast initiation proteins with chromatin -- ATP-dependent assembly of a pre-RC -- Cell cycle regulation of the pre-RC -- The chromosome cycle and establishment of pre-RCs -- Dynamic assembly and stability of ORC in human cells -- Commitment to S-phase and initiation -- Cdc45p is associated with chromatin in a cell cycle-dependent manner -- Temporal regulation of DNA replication -- Dynamics of pre-RC proteins in human cells differ from pre-RC proteins in yeast.…”
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Mitotic chromosome condensation

Table of Contents: “…Contents: Evolutionary and developmental comparisons -- Stages of mitosis -- Primary functions of mitosis -- Lower levels of chromatin organization -- Helical folding -- Experimental foundation of textbook model -- Are there specific DNA sequences at the base of chromatin loops? …”
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Series

BMC Molecular Biology

Open Access

BMC Molecular Biology

Open Access