Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning - PubMed (original) (raw)
Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning
A Thåström et al. J Mol Biol. 2004.
Abstract
DNA sequence is an important determinant of the positioning, stability, and activity of nucleosomes, yet the molecular basis of these effects remains elusive. A "consensus DNA sequence" for nucleosome positioning has not been reported and, while certain DNA sequence preferences or motifs for nucleosome positioning have been discovered, how they function is not known. Here, we report that an unexpected observation concerning the reassembly of nucleosomes during salt gradient dialysis has allowed a breakthrough in our efforts to identify the nucleosomal locations of the DNA sequence motifs that dominate histone-DNA interactions and nucleosome positioning. We conclude that a previous selection experiment for high-affinity, nucleosome-forming DNA sequences exerted selective pressure chiefly on the central stretch of the nucleosomal DNA. This observation implies that algorithms for aligning the selected DNA sequences should seek to optimize the alignment over much less than the full 147 bp of nucleosomal DNA. A new alignment calculation implemented these ideas and successfully aligned 19 of the 41 sequences in a non-redundant database of selected high-affinity, nucleosome-positioning sequences. The resulting alignment reveals strong conservation of several stretches within a central 71 bp of the nucleosomal DNA. The alignment further reveals an inherent palindromic symmetry in the selected DNAs; it makes testable predictions of nucleosome positioning on the aligned sequences and for the creation of new positioning sequences, both of which are upheld experimentally; and it suggests new signals that may be important in translational nucleosome positioning.
Similar articles
- New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning.
Lowary PT, Widom J. Lowary PT, et al. J Mol Biol. 1998 Feb 13;276(1):19-42. doi: 10.1006/jmbi.1997.1494. J Mol Biol. 1998. PMID: 9514715 - Archaeal histone selection of nucleosome positioning sequences and the procaryotic origin of histone-dependent genome evolution.
Bailey KA, Pereira SL, Widom J, Reeve JN. Bailey KA, et al. J Mol Biol. 2000 Oct 13;303(1):25-34. doi: 10.1006/jmbi.2000.4128. J Mol Biol. 2000. PMID: 11021967 - Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences.
Thåström A, Lowary PT, Widlund HR, Cao H, Kubista M, Widom J. Thåström A, et al. J Mol Biol. 1999 Apr 30;288(2):213-29. doi: 10.1006/jmbi.1999.2686. J Mol Biol. 1999. PMID: 10329138 - Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences.
Ioshikhes I, Bolshoy A, Derenshteyn K, Borodovsky M, Trifonov EN. Ioshikhes I, et al. J Mol Biol. 1996 Sep 20;262(2):129-39. doi: 10.1006/jmbi.1996.0503. J Mol Biol. 1996. PMID: 8831784 Review. - Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution.
Korber P. Korber P. Biochem Soc Trans. 2012 Apr;40(2):377-82. doi: 10.1042/BST20110730. Biochem Soc Trans. 2012. PMID: 22435815 Review.
Cited by
- The shelterin component TRF2 mediates columnar stacking of human telomeric chromatin.
Wong SY, Soman A, Korolev N, Surya W, Chen Q, Shum W, van Noort J, Nordenskiöld L. Wong SY, et al. EMBO J. 2024 Jan;43(1):87-111. doi: 10.1038/s44318-023-00002-3. Epub 2023 Dec 14. EMBO J. 2024. PMID: 38177309 Free PMC article. - Interactome of intact chromatosome variants with site-specifically ubiquitylated and acetylated linker histone H1.2.
Saumer P, Scheffner M, Marx A, Stengel F. Saumer P, et al. Nucleic Acids Res. 2024 Jan 11;52(1):101-113. doi: 10.1093/nar/gkad1113. Nucleic Acids Res. 2024. PMID: 37994785 Free PMC article. - Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study.
Oleinikov PD, Fedulova AS, Armeev GA, Motorin NA, Singh-Palchevskaia L, Sivkina AL, Feskin PG, Glukhov GS, Afonin DA, Komarova GA, Kirpichnikov MP, Studitsky VM, Feofanov AV, Shaytan AK. Oleinikov PD, et al. Int J Mol Sci. 2023 Oct 14;24(20):15194. doi: 10.3390/ijms242015194. Int J Mol Sci. 2023. PMID: 37894874 Free PMC article. - Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes.
Sawade K, Marx A, Peter C, Kukharenko O. Sawade K, et al. PLoS Comput Biol. 2023 Aug 1;19(8):e1010531. doi: 10.1371/journal.pcbi.1010531. eCollection 2023 Aug. PLoS Comput Biol. 2023. PMID: 37527265 Free PMC article. - The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics.
Donovan BT, Luo Y, Meng Z, Poirier MG. Donovan BT, et al. Nucleic Acids Res. 2023 Feb 22;51(3):1139-1153. doi: 10.1093/nar/gkac1267. Nucleic Acids Res. 2023. PMID: 36688297 Free PMC article.