X-ray structure of the MMTV-A nucleosome core

Frouws, T.D.; Duda, Sylwia; Richmond, Timothy J.

doi:10.1073/pnas.1524607113

Cited by 36 publications

(39 citation statements)

References 42 publications

(73 reference statements)

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“…S5 and S6). Preference for a single orientation has been observed previously for an NCP with a non-palindromic DNA sequence containing a poly (dA·dT) tract as well as for the MMTV-A NCP (29,59). In the Telo-NCP refined map, the electron density showed well-resolved bases as well as distinct densities characterising purines and pyrimidines (Supplementary Figure S7).…”

Section: Crystal Structure Of the Telomeric Ncpsupporting

confidence: 68%

“…By comparison, none of the Arg 17 aa of the H4 tails of the palindromic NCP-601L (62) are in contact with DNA (Figure 5c). We speculate that this strengthened tail interaction with DNA might contribute to the preference for a single orientation in the crystal lattice, as observed in the non-palindromic 147 bp MMTV-A NCP (29).…”

Section: The Basic H4 N-terminal Tail Interacts With the Ho Acidic Pamentioning

confidence: 72%

“…These results specifically highlighted the important role of the most flexible of all base steps, the TA step, occurring with a 10 bp periodicity at inward minor groove registers. The only positioning DNA sequences of natural origin (albeit not fully native NCPs) for which NCP crystal structures have been determined are the centromeric α-satellite and the mouse mammary tumor virus (MMT-V) promoter sequence (27)(28)(29). Two cryo-EM structures of nucleosome formed by native positioning DNA and the native human histone octamer have been solved recently (30,31).…”

Section: Introductionmentioning

confidence: 99%

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The human telomeric nucleosome displays distinct structural and dynamic properties

Soman

Liew

Teo

et al. 2019

Preprint

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ABSTRACTTelomeres protect the ends of our chromosomes and are key to maintaining genomic integrity during cell division and differentiation. However, our knowledge of telomeric chromatin and nucleosome structure at the molecular level is limited. Here, we aimed to define the structure, dynamics as well as properties in solution of the human telomeric nucleosome. We first determined the 2.2 Å crystal structure of a human telomeric nucleosome core particle (NCP) containing 145 bp DNA, which revealed the same helical path for the DNA as well as symmetric stretching in both halves of the NCP as that of the 145 bp ‘601’ NCP. In solution, the telomeric nucleosome exhibited a less stable and a markedly more dynamic structure compared to NCPs containing DNA positioning sequences. These observations provide molecular insights into how telomeric DNA forms nucleosomes and chromatin and advance our understanding of the unique biological role of telomeres.

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Section: Crystal Structure Of the Telomeric Ncpsupporting

confidence: 68%

Section: The Basic H4 N-terminal Tail Interacts With the Ho Acidic Pamentioning

confidence: 72%

Section: Introductionmentioning

confidence: 99%

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The human telomeric nucleosome displays distinct structural and dynamic properties

Soman

Liew

Teo

et al. 2019

Preprint

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“…To determine whether another type of nucleosome positioning sequence has a different sensitivity to the ncRNA, we performed a thermal stability assay using the nucleosome with 147 base pairs of the MMTV (mouse mammary tumor virus)-A DNA sequence 33 ( Supplementary Fig. 1d, e).…”

Section: Resultsmentioning

confidence: 99%

Nucleosome destabilization by nuclear non-coding RNAs

et al. 2020

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In the nucleus, genomic DNA is wrapped around histone octamers to form nucleosomes. In principle, nucleosomes are substantial barriers to transcriptional activities. Nuclear noncoding RNAs (ncRNAs) are proposed to function in chromatin conformation modulation and transcriptional regulation. However, it remains unclear how ncRNAs affect the nucleosome structure. Eleanors are clusters of ncRNAs that accumulate around the estrogen receptor-α (ESR1) gene locus in long-term estrogen deprivation (LTED) breast cancer cells, and markedly enhance the transcription of the ESR1 gene. Here we detected nucleosome depletion around the transcription site of Eleanor2, the most highly expressed Eleanor in the LTED cells. We found that the purified Eleanor2 RNA fragment drastically destabilized the nucleosome in vitro. This activity was also exerted by other ncRNAs, but not by poly(U) RNA or DNA. The RNA-mediated nucleosome destabilization may be a common feature among natural nuclear RNAs, and may function in transcription regulation in chromatin.

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“…1A and Supplementary Table 1). All sequences are able to form nucleosomes of different stabilities and properties and have been extensively characterized (13)(14)(15)(16). In addition, effects into 5-methylcytosine (5mC) (17,18) and 5-hydroxymethylcytosine (5hmC) (19) on nucleosome occupancy have been investigated on the Widom 601 sequence, however it is unclear how 5fC affects nucleosome formation and stability.…”

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confidence: 99%

5-Formylcytosine controls nucleosome positioning through covalent histone-DNA interaction

Raiber

Portella

Cuesta

et al. 2017

Preprint

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Nucleosomes are the basic unit of chromatin that ensure genome integrity and control access to the genetic information. The organization of not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/224444 doi: bioRxiv preprint first posted online Nov. 24, 2017; The organization of nucleosomes is an important feature to the chromatin structure. The DNA sequence itself has been shown to be a determinant of nucleosome positioning raising questions about the effect of DNA modifications on chromatin structure. 5-Formylcytosine is generated by the oxidation of 5mC by TET enzymes. It can undergo base excision repair by the thymine DNA glycosylase (TDG) (5) and it is therefore thought to mark sites that undergo active demethylation (6). However, we have previously shown that the 5fC distribution not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/224444 doi: bioRxiv preprint first posted online Nov. 24, 2017; 3 was tissue-dependent in mice (7) and that 5fC was a stable modification in genomic DNA in vivo (8). Additionally we and others have demonstrated that 5fC can alter the physical properties of the DNA double helix (9, 10) and the identification of 5fC-binding chromatin remodelers and transcription factors in vitro (11,12) raises fundamental questions about its involvement in chromatin biology. Moreover, the nature of the formyl group confers specific chemical properties to 5fC that are unique from other cytosine modifications such as 5-hydroxymethylcytosine (5hmC) and 5-carboxycytosine (5caC). We therefore hypothesized that 5fC may be important in nucleosomal organization, particularly during early development, where increased levels of 5fC have been reported (8).To test this hypothesis, we assessed the impact of 5fC on nucleosome core particles formation and stability. We carried out biochemical studies on three different DNA sequences, Widom 601, MMTV-A and 5SrDNA with varying CpG and GC content ( Fig. 1A and Supplementary Table 1). All sequences are able to form nucleosomes of different stabilities and properties and have been extensively characterized (13-16). In addition, effects into 5-methylcytosine (5mC) (17, 18) and 5-hydroxymethylcytosine (5hmC) (19) on nucleosome occupancy have been investigated on the Widom 601 sequence, however it is unclear how 5fC affects nucleosome formation and stability. To address this, we compared nucleosome occupancy after chaperone-mediated assembly using DNA with unmodified and modified cytosines. We observed that 5mC, 5hmC and 5fC each caused an increase in nucleosome occupancy compared to unmodified Widom 601 DNA (Fig. 1A), with 5fC-DNA significantly (unpaired t-test, p value ≤ 0.0001) displaying the strongest effect (Fig. 1B). Notably we found that only 5fC not peer-reviewed) is the author/funder. All rights reserved. No reuse a...

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X-ray structure of the MMTV-A nucleosome core

Cited by 36 publications

References 42 publications

The human telomeric nucleosome displays distinct structural and dynamic properties

The human telomeric nucleosome displays distinct structural and dynamic properties

Nucleosome destabilization by nuclear non-coding RNAs

5-Formylcytosine controls nucleosome positioning through covalent histone-DNA interaction

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