25 years after the nucleosome model: chromatin modifications

Wu, Jiansheng; Grunstein, Michael

doi:10.1016/s0968-0004(00)01718-7

Cited by 329 publications

(268 citation statements)

References 63 publications

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“…Point mutations in menin NLSs do not affect menin association with chromatin ( Figure 6), but abrogate its specific binding to the IGFBP-2 promoter in vivo (Figure 7), suggesting a crucial role of the NLSs in stablizing the binding of menin and perhaps its interacting proteins to the IGFBP-2 locus. Menin represses JunD's transcription activity in a reporter assay, and the repression can be released by an inhibitor (TSA) of histone deacetylases, which are thought to trigger formation of inhibitory chromatin structure by removing the acetyl group in the histone tails (Gobl et al, 1999;Wu and Grunstein, 2000). In addition, menin has also been shown to interact with HDAC1 and 2 and inhibit JunD in reporter gene assays (Kim et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

Tumor suppressor menin: the essential role of nuclear localization signal domains in coordinating gene expression

Desmond

Hou

et al. 2006

Oncogene

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Section: Discussionmentioning

confidence: 99%

Tumor suppressor menin: the essential role of nuclear localization signal domains in coordinating gene expression

Desmond

Hou

et al. 2006

Oncogene

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“…The actual challenge is thus to find a way to extract these structural informations from an appropriate reading of the DNA text. Since the different orders of packaging in the hierarchical structural organization of DNA are implicated in the accessibility of DNA sequence elements to trans-acting factors that control the processes of transcription and replication [27,28,29,30,31,32,33,34], there is actually a wealth of structural and dynamical informations to learn in the primary DNA sequence about how DNA works in a living cell.…”

Section: Introductionmentioning

confidence: 99%

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Audit

Vaillant

Arnéodo

et al. 2004

Journal of Biological Physics

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Abstract. Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called 'wavelet transform microscope' reveals a characteristic scale of 100 − 200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime ( 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called waveletbased multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1,2].

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“…Nucleosomes can impede DNA binding of transcription factors and GTFs and form a transcriptional barrier for RNAP. Thus, chromatin structure can significantly reduce the efficiency of transcription at both the initiation and elongation steps (Wu, 1997;Peterson and Workman, 2000;Wu and Grunstein, 2000;Narlikar et al, 2002;Li et al, 2007). It is well established that genes can be de-repressed when histones are depleted from cells (Han and Grunstein, 1988).…”

Section: Chromatin Remodeling and Modificationsmentioning

confidence: 99%

Transcriptional activators and activation mechanisms

2011

Protein Cell

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25 years after the nucleosome model: chromatin modifications

Cited by 329 publications

References 63 publications

Tumor suppressor menin: the essential role of nuclear localization signal domains in coordinating gene expression

Tumor suppressor menin: the essential role of nuclear localization signal domains in coordinating gene expression

Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences

Transcriptional activators and activation mechanisms

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