Crystal Structures of Nucleosome Core Particles Containing the ‘601’ Strong Positioning Sequence

Vasudevan, Dileep; Chua, Eugene Y.D.; Davey, C.A.

doi:10.1016/j.jmb.2010.08.039

Cited by 395 publications

(493 citation statements)

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“…These major groove blocks contain 6 bp compared with the others, which have 5 bp (Fig. 1), and are the principal sites for DNA stretching previously observed for ASP (PDB ID code 1kx4, 146 bp; PDB ID code 2nzd, 145 bp), NCP146b (PDB ID code 1kx3, 3utb, 146 bp) and nucleosome cores containing three versions of the 601 sequence (e.g., PDB ID code 3lz1, 145 bp) (7,9,14,15).…”

Section: Significancementioning

confidence: 71%

“…A resolution of at least 2.6 Å is necessary to evaluate differences in DNA conformations and assess solvent interactions adequately. To date, this highly reliable "library" of DNA structural information pertinent to the nucleosome core consists primarily of two similar sequences of half α-satellite repeats and half the artificially "evolved" sequence 601 (7)(8)(9)(10). Further investigations have been limited to substitution of short sequence elements in one of the α-satellite sequences (11,12).…”

mentioning

confidence: 99%

“…These high-resolution structures have hinged on using palindromic sequences to avoid twofold averaging imposed by crystal packing. The lack of twofold symmetry in the full 601 sequence, for example, resulted in superposition of the electron density of the two different half-sequences (9).…”

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confidence: 99%

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X-ray structure of the MMTV-A nucleosome core

Frouws

Duda

Richmond

2016

Proc. Natl. Acad. Sci. U.S.A.

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The conformation of DNA bound in nucleosomes depends on the DNA sequence. Questions such as how nucleosomes are positioned and how they potentially bind sequence-dependent nuclear factors require near-atomic resolution structures of the nucleosome core containing different DNA sequences; despite this, only the DNA for two similar α-satellite sequences and a sequence (601) selected in vitro have been visualized bound in the nucleosome core. Here we report the 2.6-Å resolution X-ray structure of a nucleosome core particle containing the DNA sequence of nucleosome A of the 3′-LTR of the mouse mammary tumor virus (147 bp MMTV-A). To our knowledge, this is the first nucleosome core particle structure containing a promoter sequence and crystallized from Mg 2+ ions. It reveals sequence-dependent DNA conformations not seen previously, including kinking into the DNA major groove.chromatin | nucleosome | DNA | X-ray structure | MMTV D NA in eukaryotic cells is wrapped repeatedly in nucleosomes to form chromatin, the substrate engaged by the nuclear machinery to carry out repair, replication, recombination, and transcription of genomes. Nucleosome mapping in situ combined with biochemical studies has revealed that nucleosome positions determine access to DNA regulatory sequences essential to these processes (1, 2). Nucleosome position is determined chiefly by DNA sequence and ATP-dependent chromatin remodeling factors (3-5). The nucleosome includes a linker DNA of variable length and a nucleosome core containing a histone octamer and 147 bp of DNA (6). Many high-resolution structures of nucleosome cores with differing DNA sequences are required to see how the details of DNA conformation could affect nucleosome positioning and dynamics, as well as nuclear factor binding. The DNA studied would most interestingly represent natural sequences of transcription promoters and enhancer elements.Our knowledge of sequence-dependent structure of DNA bound in the nucleosome core relative to the amount of DNA bound in genomes is extremely limited. A resolution of at least 2.6 Å is necessary to evaluate differences in DNA conformations and assess solvent interactions adequately. To date, this highly reliable "library" of DNA structural information pertinent to the nucleosome core consists primarily of two similar sequences of half α-satellite repeats and half the artificially "evolved" sequence 601 (7-10). Further investigations have been limited to substitution of short sequence elements in one of the α-satellite sequences (11, 12). These high-resolution structures have hinged on using palindromic sequences to avoid twofold averaging imposed by crystal packing. The lack of twofold symmetry in the full 601 sequence, for example, resulted in superposition of the electron density of the two different half-sequences (9).We describe here the X-ray structure of a nucleosome core particle (NCP) containing a DNA sequence from mouse mammary tumor virus (MMTV) determined at 2.6 Å resolution. To our knowledge, this is the first NCP structure conta...

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Section: Significancementioning

confidence: 71%

mentioning

confidence: 99%

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X-ray structure of the MMTV-A nucleosome core

Frouws

Duda

Richmond

2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Two recent crystal structures include the original, higher affinity 601 sequence (Makde et al 2010;Vasudevan et al 2010) and a detailed understanding of the conformation of the 601 sequence has been developed Chua et al 2012).…”

Section: Widom 601 Sequencementioning

confidence: 99%

Principles and practice of nucleosome positioningin vitro

Flaus

2011

Frontiers in Life Science

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“…Current knowledge about the sequence-dependent deformations of DNA adopted in the nucleosome core particle, however, is extremely limited. The characterized DNA pathways include only three classes of sequences-a human a-satellite sequence (26), the high-affinity 601 sequence (45,46), and a sequence from the mouse mammary tumor virus (47)-with the perturbations of DNA structure depending on the sequence pattern. The available high-resolution structures provide similarly sketchy hints as to how pairs of nucleosomes may associate along chromatin fibers.…”

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confidence: 99%

Contributions of Sequence to the Higher-Order Structures of DNA

Todolli

Perez

Clauvelin

et al. 2017

Biophysical Journal

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One of the critical unanswered questions in genome biophysics is how the primary sequence of DNA bases influences the global properties of very-long-chain molecules. The local sequence-dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate the global folding and interactions of double helices with hundreds of basepairs. These features also determine the positions of nucleosomes on DNA and the lengths of the interspersed DNA linkers. Like the patterns of basepair association within DNA, the arrangements of nucleosomes in chromatin modulate the properties of longer polymers. The intrachromosomal loops detected in genomic studies contain hundreds of nucleosomes, and given that the simulated configurations of chromatin depend on the lengths of linker DNA, the formation of these loops may reflect sequence-dependent information encoded within the positioning of the nucleosomes. With knowledge of the positions of nucleosomes on a given genome, methods are now at hand to estimate the looping propensities of chromatin in terms of the spacing of nucleosomes and to make a direct connection between the DNA base sequence and larger-scale chromatin folding.Despite the astonishing amount of information now known about the sequential makeup and spatial organization of genomic DNA, there is much to learn about how the vast numbers of basepairs in these systems contribute to the three-dimensional architectures and workings of long, spatially constrained, double-helical molecules. New biochemical and imaging methodologies, such as proximity-based ligation and fluorescence in situ hybridization (1-3), have shed light on the large-scale organization of genomic DNA, enabling investigators to pinpoint DNA elements in close spatial proximity and follow the course of these associations during cellular processes. The resulting measurements have motivated the study of long genomes in terms of simple polymer models (4,5), which have in turn illuminated the physical nature of the contacted elements and pointed to mechanisms potentially governing genome architecture and dynamics. Although these models are appropriate for the very large scale of the experimental data, they rest on the assumption that the chemical makeup of DNA does not matter, and thus provide no link between the primary sequence of bases and the tertiary structures and interactions of genomic folds.At the other extreme of chain length, the detailed molecular structures of DNA with only tens of basepairs point to various sequence-dependent spatial and energetic codes underlying the three-dimensional organization of the double helix and its susceptibility to interactions with proteins and other molecules (6). The structural data also include more than 100 crystallographic examples of the tight, superhelical wrapping of~150 DNA basepairs (bp) around the core of the histone proteins in the nucleosome core particle, the fundamental packagi...

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Crystal Structures of Nucleosome Core Particles Containing the ‘601’ Strong Positioning Sequence

Cited by 395 publications

References 59 publications

X-ray structure of the MMTV-A nucleosome core

X-ray structure of the MMTV-A nucleosome core

Principles and practice of nucleosome positioningin vitro

Contributions of Sequence to the Higher-Order Structures of DNA

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