Structure of RCC1 chromatin factor bound to the nucleosome core particle

Makde, Ravindra D.; England, Joseph R.; Yennawar, Hemant P.; Tan, Song

doi:10.1038/nature09321

Cited by 350 publications

(454 citation statements)

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“…The undertwisted stretch at SHL ±5 is so stable that crystallisation in the standard lattice requires a 145 bp fragment to replicate terminal base pair stacking normally provided by 147 bp DNA ). The stretch is also observed in the RCC1 ternary binding protein, which does not require stacking at all for crystal packing (Makde et al 2010). …”

Section: Widom 601 Sequencementioning

confidence: 97%

“…The stretch phenomenon was originally thought to be induced by crystal packing of exposed 146 bp DNA termini (Luger, Mäder, et al 1997), but a recent structure without end packing also shows the same effect (Makde et al 2010), suggesting that the phenomenon may be inherent to nucleosome wrapping.…”

Section: Dna Twisting and Localised Stretch Sitesmentioning

confidence: 98%

“…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%

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Principles and practice of nucleosome positioningin vitro

Flaus

2011

Frontiers in Life Science

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Section: Widom 601 Sequencementioning

confidence: 97%

Section: Dna Twisting and Localised Stretch Sitesmentioning

confidence: 98%

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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.…”

Section: Todolli Et Almentioning

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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“…Ran can bind directly to histone H3 and histone H4 (Bilbao-Cortes et al 2002) or indirectly to nucleosomes through regulator of chromosome condensation 1 (RCC1), a protein found in animals but not plants. RCC1 is a guanine nucleotide exchange factor of Ran, which efficiently converts Ran from the GDP to GTP state (Makde et al 2010). In the cytoplasm, the GTPase-activating protein RanGAP together with its cofactor RanBP1 or RanBP2 (Bischoff et al 1994(Bischoff et al , 1995 stimulates the reverse reaction and promotes the GDP-bound state.…”

mentioning

confidence: 99%

Mechanisms of plant spindle formation

Zhang

Dawe

2011

Chromosome Res

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In eukaryotes, the formation of a bipolar spindle is necessary for the equal segregation of chromosomes to daughter cells. Chromosomes, microtubules and kinetochores all contribute to spindle morphogenesis and have important roles during mitosis. A unique property of flowering plant cells is that they entirely lack centrosomes, which in animals have a major role in spindle formation. The absence of these important structures suggests that plants have evolved novel mechanisms to assure chromosome segregation. In this review, we highlight some of the recent studies on plant mitosis and argue that plants utilize a variation of "spindle self-organization" that takes advantage of the early polarity of plant cells and accentuates the role of kinetochores in stabilizing the spindle midzone in prometaphase.

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Structure of RCC1 chromatin factor bound to the nucleosome core particle

Cited by 350 publications

References 49 publications

Principles and practice of nucleosome positioningin vitro

Principles and practice of nucleosome positioningin vitro

Contributions of Sequence to the Higher-Order Structures of DNA

Mechanisms of plant spindle formation

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