Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA.

Lin, Hong; Schroth, Gary P.; Matthews, Harry R.; Yau, Peter; Bradbury, E. Morton

doi:10.1016/s0021-9258(18)54150-8

Cited by 357 publications

(72 citation statements)

References 36 publications

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“…This is confirmed by the topoisomer composition of the eluted products in figure 2b, c. A similar, although significantly smaller, effect was observed with tetrasomes reconstituted with moderately acetylated tetramers and relaxed in a phosphate-containing relaxation buffer, known to destabilize DNA-tails interactions (Hong et al . 1993).…”

Section: (C) Histone Tail Regulation Of Tetrasome Chiral Transition Through Lateral Openingsupporting

confidence: 75%

Nucleosome conformational flexibility and implications for chromatin dynamics

Sivolob

Prunell

2004

Philosophical Transactions of the Royal Society of London. Seri

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The active role of chromatin in the regulation of gene activity seems to imply a conformational flexibility of the basic chromatin structural unit, the nucleosome. This review is devoted to our recent results pertaining to this subject, using an original approach based on the topology of single particles reconstituted on DNA minicircles, combined with their theoretical simulation. Three types of chromatin particles have been studied so far: a subnucleosome, that is, the (H3-H4)(2) histone tetramer-containing particle, now known as the tetrasome; the nucleosome; and the linker histone H5/H1-bearing nucleosome (the chromatosome). All the particles were found to exist in two to three conformational states, which differ by their topological and mechanical properties. Our approach unveiled the molecular mechanisms of nucleosome conformational dynamics and will help to understand its functional relevance. A most surprising conclusion of the work was perhaps that DNA overall flexibility increases considerably upon particle formation, which might indeed be a requirement of genome function.

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Section: (C) Histone Tail Regulation Of Tetrasome Chiral Transition Through Lateral Openingsupporting

confidence: 75%

Nucleosome conformational flexibility and implications for chromatin dynamics

Sivolob

Prunell

2004

Philosophical Transactions of the Royal Society of London. Seri

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“…Even though a few sequence-specific TFs have also been shown to directly interact with specific histone modifications (Vermeulen et al, 2010), the main impact of chromatin modifications on TF binding is likely mediated through their effect on DNA accessibility. For example, lysine acetylation neutralizes the positive charge of histone residues and thus decreases nucleosome affinity to DNA (Hong et al, 1993;Dion et al, 2005). This effect has theoretically been described by a nucleosomemediated cooperativity model (Mirny, 2010), which proposes competition for DNA binding between nucleosomes and a set of TFs as a dynamic equilibrium.…”

Section: Regulation Of Tf-binding To Chromatin Through Dna-sequence and Epigeneticsmentioning

confidence: 99%

Transcription factors: Bridge between cell signaling and gene regulation

et al. 2021

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Transcription factors (TFs) are key regulators of intrinsic cellular processes, such as differentiation and development, and of the cellular response to external perturbation through signaling pathways. In this review we focus on the role of TFs as a link between signaling pathways and gene regulation. Cell signaling tends to result in the modulation of a set of TFs that then lead to changes in the cell's transcriptional programme. We highlight the molecular layers at which TF activity can be measured and the associated technical and conceptual challenges. These layers include post-translational modifications of the TF, regulation of TF binding to DNA through chromatin accessibility and epigenetics, and expression of target genes. We highlight that a large number of TFs are understudied in both signaling and gene regulation studies, and that our knowledge about known TF targets has a strong literature bias. We argue that TFs serve as a perfect bridge between the fields of gene regulation and signaling, and that separating these fields hinders our understanding of cell functions. Multiomics approaches that measure multiple dimensions of TF activity are ideally suited to study the interplay of cell signaling and gene regulation using TFs as the anchor to link the two fields.

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“…Over the following decades, it was revealed that hyperacetylated histones are abundant near active genes, while heterochromatic regions are hypoacetylated. Early studies of histone acetylation suggested that it facilitates DNA accessibility by neutralizing positively charged lysines, thereby reducing their affinity to DNA [127][128][129][130][131]. A direct link between histone acetylation and transcription was established decades later in the 1990s, with the purification of histone acetyltransferase A (HAT A), a homologue of the yeast transcriptional coactivator Gcn5p, from Tetrahymena macronuclei [132].…”

Section: H3k27acmentioning

confidence: 99%

Establishment and function of chromatin modification at enhancers

Tafessu

Banaszynski

2020

Open Biol.

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How a single genome can give rise to distinct cell types remains a fundamental question in biology. Mammals are able to specify and maintain hundreds of cell fates by selectively activating unique subsets of their genome. This is achieved, in part, by enhancers—genetic elements that can increase transcription of both nearby and distal genes. Enhancers can be identified by their unique chromatin signature, including transcription factor binding and the enrichment of specific histone post-translational modifications, histone variants, and chromatin-associated cofactors. How each of these chromatin features contributes to enhancer function remains an area of intense study. In this review, we provide an overview of enhancer-associated chromatin states, and the proteins and enzymes involved in their establishment. We discuss recent insights into the effects of the enhancer chromatin state on ongoing transcription versus their role in the establishment of new transcription programmes, such as those that occur developmentally. Finally, we highlight the role of enhancer chromatin in new conceptual advances in gene regulation such as condensate formation.

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Studies of the DNA binding properties of histone H4 amino terminus. Thermal denaturation studies reveal that acetylation markedly reduces the binding constant of the H4 “tail” to DNA.

Cited by 357 publications

References 36 publications

Nucleosome conformational flexibility and implications for chromatin dynamics

Nucleosome conformational flexibility and implications for chromatin dynamics

Transcription factors: Bridge between cell signaling and gene regulation

Establishment and function of chromatin modification at enhancers

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