Transcription Factor Access Is Mediated by Accurately Positioned Nucleosomes on the Mouse Mammary Tumor Virus Promoter

Archer, Trevor; Cordingley, Michael G.; Wolford, Ronald G.; Hager, Gordon L.

doi:10.1128/mcb.11.2.688-698.1991

Cited by 43 publications

(31 citation statements)

References 38 publications

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“…In vivo the protamines, which can contain extensive tracts of polyarginine, accumulate to a large excess during spermatogenesis to achieve this displacement of histones. The energetic considerations involved in the binding of single transcription factor to a specific sequence are likely to be insufficient to disrupt all of the histone-DNA interactions in a complete nucleosome core particle; other mechanisms must mediate nucleosome disruption (Pina et al, 1990;Archer et al, 1991;Perlmann, 1992;Hayes & Wolffe, 1992).…”

Section: Discussionmentioning

confidence: 99%

Structure of DNA in a nucleosome core at high salt concentration and at high temperature

Bashkin

Hayes²,

Tullius³

et al. 1993

Biochemistry

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We have used hydroxyl radical cleavage of DNA to probe the organization of the nucleosome core at high salt concentration and high temperature. The rotational and translational positioning of a DNA fragment, containing part of the Xenopus borealis 5S RNA gene, on the histone octamer is maintained between salt concentrations of 0.0 and 0.8 M NaCl and between temperatures of 0 and 75 degrees C. These results provide evidence that the energy of bending DNA around the nucleosome is independent of salt concentration and temperature in this range. They illustrate the severe energetic requirements necessary to displace DNA from previously organized contacts with histones in the nucleosome core.

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Section: Discussionmentioning

confidence: 99%

Structure of DNA in a nucleosome core at high salt concentration and at high temperature

Bashkin

Hayes²,

Tullius³

et al. 1993

Biochemistry

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“…11 Although the nucleosome is stable in physiological conditions, it undergoes large-scale structural rearrangements during different cell cycles. DNAbinding proteins such as transcription factors, 12,13 chromatin remodelers, 14 and polymerases 15,16 need to bind nucleosomal DNA. Furthermore, the sequence of nucleosomal DNA may determine the strength of histone−DNA interactions and may encode organization of the nucleosome at larger length scales.…”

Section: Introductionmentioning

confidence: 99%

Molecular Mechanism for the Role of the H2A and H2B Histone Tails in Nucleosome Repositioning

2018

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The nucleosome core particle (NCP) is the basic packaging unit of DNA. Recently reported structures of the NCP suggest that the histone octamer undergoes conformational changes during the process of DNA translocation around the histone octamer. Herein, we demonstrate with long-time all-atomistic molecular dynamics simulations that the histone tails play a critical role in this nucleosome repositioning. We simulate the NCP at high salt concentrations, an order of magnitude higher than physiological conditions, to screen the electrostatic interactions. We find that the positively charged H2B tail collapses and complexes with the minor groove of nucleosomal DNA. Upon collapse of the tail, counterions are released. This promotes the formation of a ∼10 bp loop of nucleosomal DNA. The complexation of the tail increases the local flexibility of the DNA, as characterized by local force constants. Using normal mode analysis, we identify a “wave-like motion” of nucleosomal DNA. We perform umbrella sampling to characterize two possible pathways of the initial stages of unwrapping, symmetric and asymmetric. These results suggest that regulation of the histone tail interactions with nucleosomal DNA may play a critical role in nucleosomal dynamics by acting as a switch to determine the initial pathway of unwrapping.

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“…The mouse mammary tumor virus (MMTV) LTR has been well characterized as a steroid-inducible transcription unit (Hager, 1988;Beato, 1989;Gunzburg & Salmons, 1992), and more recently has provided the field of chromatin with an important model for the regulation of transcription by histones [see Hager et al (1993) and references cited therein]. Current understanding of the nucleoprotein structure of the MMTV LTR is based on data obtained by low-resolution mapping of nucleosome positions in vivo (Richard-Foy & Hager, 1987;Bresnick et al, 1991;Truss et al, 1993), and by reconstitution of small fragments of the LTR with histones in vitro (Perlmann & Wrange, 1988;Pina et al, 1990a,c; Archer et al, 1991). The resulting model of LTR chromatin structure incorporates the LTR into an array of six phased nucleosomes (Richard-Foy & Hager, 1987;Perlmann & Wrange, 1988;Pina et al, 1990b).…”

mentioning

confidence: 99%

“…In this context, the B nucleosome region contains four hormone response elements (HREs) and a cognate binding site for the NF-1 transcription factor. The nucleoprotein structure in this region of the LTR is observed to undergo a structural transition that increases the accessibility of DNase I (Richard-Foy & Hager, 1987;Sistare et al, 1987;Bresnick et al, 1990), restriction endonucleases (Bresnick et al, 1991;Archer et al, 1991Archer et al, , 1992Archer et al, , 1994, and MPE-Fe(II) (Richard-Foy , in response to treatment with dexamethasone. Data from several laboratories regarding the in vitro reconstitution of nucleosomes containing B region DNA have suggested that a reconstituted nucleosome adopts a single position on the DNA (Perlmann & Wrange, 1988;Pina et al, 1990b;Archer et al, 1991).…”

mentioning

confidence: 99%

Nucleosomes Reconstituted in Vitro on Mouse Mammary Tumor Virus B Region DNA Occupy Multiple Translational and Rotational Frames

Fragoso²,

Gl³

1995

Biochemistry

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The mouse mammary tumor virus acquires a highly reproducible chromatin structure when integrated into cellular DNA. Previous studies have suggested that the LTR is arranged as a series of six phased nucleosomes, that occupy specific positions on the LTR. On the basis of nucleosome reconstitution studies using DNA from the B region of the LTR, it has been argued that this sequence directs a uniquely positioned nucleosome. Here we demonstrate in vitro that reconstituted B region nucleosomes adopt at least five distinct translational positions in two rotational frames on a 206 bp fragment of DNA. We have resolved an initial reconstitute into its component species using nondenaturing gel electrophoresis, and precisely mapped the positions of each species using a hydroxyl radical footprinting assay. To confirm the nucleosome positions determined with the hydroxyl radical assay, nucleosome boundaries were mapped using exonuclease III. Comparison of the results from the hydroxyl radical footprinting and exonuclease III assays revealed a symmetrical pattern of overdigestion by exonuclease III which made unequivocal determination of nucleosome boundaries dubious. We conclude that the general use of exonuclease III to map the positions of nucleosomes may lead to incorrect assignment of position, and that assignment of position through the determination of the nucleosome pseudo-dyad from hydroxyl radical footprinting data represents a superior method of analysis.

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Transcription Factor Access Is Mediated by Accurately Positioned Nucleosomes on the Mouse Mammary Tumor Virus Promoter

Cited by 43 publications

References 38 publications

Structure of DNA in a nucleosome core at high salt concentration and at high temperature

Structure of DNA in a nucleosome core at high salt concentration and at high temperature

Molecular Mechanism for the Role of the H2A and H2B Histone Tails in Nucleosome Repositioning

Nucleosomes Reconstituted in Vitro on Mouse Mammary Tumor Virus B Region DNA Occupy Multiple Translational and Rotational Frames

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