DOI: 10.1017/s0033583501003699. Role of DNA sequence in nucleosome stability and dynamics

Role of DNA sequence in nucleosome stability and dynamics

10.1017/s0033583501003699

Crossref journal-article

Cambridge University Press (CUP)

Quarterly Reviews of Biophysics (56)

Abstract

1. Introduction 2701.1 Overview of nucleosome structure 2712. Relative equilibrium stability (affinity) of histone–DNA interactions in nucleosomes 2722.1 Relative affinity equals relative equilibrium stability 2722.2 Competition assays for relative free-energy measurements 2732.3 Technical issues in relative free-energy measurements 2752.4 Range of affinities 2783. Relation of nucleosome stability to nucleosome positioning 2793.1 Translational nucleosome positioning 2793.2 Rotational positioning 2803.3 Unfavorable positioning 2813.4 Experiments 2814. Physical basis of DNA sequence preferences 2824.1 Free-energy cost of DNA bending 2834.2 Molecular mechanics of DNA bending and bendability 2844.3 Bent and bendable DNA sequences 2864.4 Parameter sets for prediction of DNA bending and bendability 2884.5 DNA twisting 2904.6 Energetics of nucleosomal DNA packaging 2915. DNA sequence motifs for nucleosome packaging 2925.1 Natural and designed nucleosomal DNAs 2935.2 New rules and reagents from physical selection studies 2945.3 Molecular basis of DNA sequence preferences 2995.4 Special properties of the TA step 3005.5 Unfavorable sequences 3025.6 Natural genomes 3035.7 Evolutionary approach toward an optimal sequence 3055.8 Optimization by design 3056. Dynamic nucleosome instability 3086.1 Site-exposure equilibria 3086.2 DNA sequence-dependence to site-exposure equilibria 3126.3 Nucleosome translocation 3156.4 Action of processive enzymes 3197. Conclusions 3198. Acknowledgements 3209. References 320The nucleosome core particle is the fundamental repeating subunit of chromatin. It consists of two molecules each of the four ‘core histone’ proteins, H2A, H2B, H3 and H4, and a 147 bp stretch of DNA. The lowest level of chromatin organization consists of a repeated array of nucleosome core particles separated by variable lengths of ‘linker DNA’. In many, but not all, cases, each core particle plus its linker DNA is associated with one molecule of a fifth ‘linker’ histone protein, H1. The complex of the core particle plus its linker DNA and H1 (when present) is called a ‘nucleosome’.

Bibliography

Widom, J. (2001). Role of DNA sequence in nucleosome stability and dynamics. Quarterly Reviews of Biophysics, 34(3), 269â324.

Authors 1

J. Widom (first)

References 0 Referenced 310

None

Dates

Type	When
Created	17 years ago (Aug. 14, 2008, 6:20 a.m.)
Deposited	6 years, 4 months ago (March 29, 2019, 3:27 p.m.)
Indexed	5 hours, 38 minutes ago (Aug. 26, 2025, 2:36 a.m.)
Issued	24 years ago (Aug. 1, 2001)
Published	24 years ago (Aug. 1, 2001)
Published Online	23 years, 6 months ago (Jan. 30, 2002)
Published Print	24 years ago (Aug. 1, 2001)

Funders 0

None

BibTeX

@article{Widom_2001, title={Role of DNA sequence in nucleosome stability and dynamics}, volume={34}, ISSN={1469-8994}, url={http://dx.doi.org/10.1017/s0033583501003699}, DOI={10.1017/s0033583501003699}, number={3}, journal={Quarterly Reviews of Biophysics}, publisher={Cambridge University Press (CUP)}, author={Widom, J.}, year={2001}, month=aug, pages={269–324} }

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  "abstract": "<jats:p><jats:bold>1. Introduction 270</jats:bold></jats:p><jats:p>1.1 Overview of nucleosome structure 271</jats:p><jats:p><jats:bold>2. Relative equilibrium stability (affinity) of histone\u2013DNA interactions in \nnucleosomes 272</jats:bold></jats:p><jats:p>2.1 Relative affinity equals relative equilibrium stability 272</jats:p><jats:p>2.2 Competition assays for relative free-energy measurements 273</jats:p><jats:p>2.3 Technical issues in relative free-energy measurements 275</jats:p><jats:p>2.4 Range of affinities 278</jats:p><jats:p><jats:bold>3. Relation of nucleosome stability to nucleosome positioning 279</jats:bold></jats:p><jats:p>3.1 Translational nucleosome positioning 279</jats:p><jats:p>3.2 Rotational positioning 280</jats:p><jats:p>3.3 Unfavorable positioning 281</jats:p><jats:p>3.4 Experiments 281</jats:p><jats:p><jats:bold>4. Physical basis of DNA sequence preferences 282</jats:bold></jats:p><jats:p>4.1 Free-energy cost of DNA bending 283</jats:p><jats:p>4.2 Molecular mechanics of DNA bending and bendability 284</jats:p><jats:p>4.3 Bent and bendable DNA sequences 286</jats:p><jats:p>4.4 Parameter sets for prediction of DNA bending and bendability 288</jats:p><jats:p>4.5 DNA twisting 290</jats:p><jats:p>4.6 Energetics of nucleosomal DNA packaging 291</jats:p><jats:p><jats:bold>5. DNA sequence motifs for nucleosome packaging 292</jats:bold></jats:p><jats:p>5.1 Natural and designed nucleosomal DNAs 293</jats:p><jats:p>5.2 New rules and reagents from physical selection studies 294</jats:p><jats:p>5.3 Molecular basis of DNA sequence preferences 299</jats:p><jats:p>5.4 Special properties of the TA step 300</jats:p><jats:p>5.5 Unfavorable sequences 302</jats:p><jats:p>5.6 Natural genomes 303</jats:p><jats:p>5.7 Evolutionary approach toward an optimal sequence 305</jats:p><jats:p>5.8 Optimization by design 305</jats:p><jats:p><jats:bold>6. Dynamic nucleosome instability 308</jats:bold></jats:p><jats:p>6.1 Site-exposure equilibria 308</jats:p><jats:p>6.2 DNA sequence-dependence to site-exposure equilibria 312</jats:p><jats:p>6.3 Nucleosome translocation 315</jats:p><jats:p>6.4 Action of processive enzymes 319</jats:p><jats:p><jats:bold>7. Conclusions 319</jats:bold></jats:p><jats:p><jats:bold>8. Acknowledgements 320</jats:bold></jats:p><jats:p><jats:bold>9. References 320</jats:bold></jats:p><jats:p>The nucleosome core particle is the fundamental repeating subunit of chromatin. It consists \nof two molecules each of the four \u2018core histone\u2019 proteins, H2A, H2B, H3 and H4, and a \n147 bp stretch of DNA. The lowest level of chromatin organization consists of a repeated \narray of nucleosome core particles separated by variable lengths of \u2018linker DNA\u2019. In many, \nbut not all, cases, each core particle plus its linker DNA is associated with one molecule of \na fifth \u2018linker\u2019 histone protein, H1. The complex of the core particle plus its linker DNA and \nH1 (when present) is called a \u2018nucleosome\u2019.</jats:p>",
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