Biochemical analysis of enhancer–promoter communication in chromatin

Polikanov, Y.S.; Rubtsov, Mikhail A.; Studitsky, Vasily M.

doi:10.1016/j.ymeth.2006.11.003

Cited by 15 publications

(20 citation statements)

References 51 publications

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“…1C, which allows for the assembly of saturated nucleosomal arrays and quantitative characterization of the resulting chromatin system (13,14). The DNA plasmids (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Transcription was conducted as described previously (13). In short, all templates were linearized, the closed initiation complexes were formed, and the enhancer-binding protein (NtrC) was prebound to DNA in the absence of ATP.…”

Section: Methodsmentioning

confidence: 99%

“…New experimental approaches that yield quantitative data on the rate of enhancer-promoter communication on nucleosome-bound DNA constructs in vitro (13,14) provide unique information for deciphering the mechanisms of eukaryotic gene expression in chromatin. The levels of RNA detected upon association of regulatory proteins that are bound to the ends of these constructs reveal surprising new information about the intervening DNA.…”

mentioning

confidence: 99%

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Internucleosomal Interactions Mediated by Histone Tails Allow Distant Communication in Chromatin

Kulaeva¹,

Zheng

Polikanov³

et al. 2012

Journal of Biological Chemistry

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Background: Gene expression is regulated by DNA elements that often lie far apart along genomic sequences. Results: Novel computations and experiments provide new structural insights into long-range communication on chromatin. Conclusion: Efficient long-range association of transcriptional elements requires intact tails on the core histones. Significance: The understanding of action-at-a-distance in three dimensions helps to connect nucleosome structure/positioning to chromatin dynamics and gene regulation.

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“…1C, which allows for the assembly of saturated nucleosomal arrays and quantitative characterization of the resulting chromatin system (13,14). The DNA plasmids (Fig.…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Internucleosomal Interactions Mediated by Histone Tails Allow Distant Communication in Chromatin

Kulaeva¹,

Zheng

Polikanov³

et al. 2012

Journal of Biological Chemistry

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“…The normal expression of eukaryotic genes requires stimulation of promoters by enhancers that often exert their eVects over many kilobases of intervening DNA (Tjian and Maniatis 1994;Blackwood and Kadonaga 1998;Szutorisz et al 2005;Zhao and Dean 2005;Polikanov et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Evidences for insulator activity of the 5′UTR of the Drosophila melanogaster LTR-retrotransposon ZAM

et al. 2010

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Insulators or chromatin boundary are DNA elements that organize the genome into discrete regulatory domains by limiting the actions of enhancers and silencers through a "positional-blocking mechanism". The role of these sequences, both in modulation of the enhancers range of action (enhancer-promoter selectivity) and in the organization of the chromatin in functional domains, is emerging strongly in these last years. There is a great interest in identifying new insulators because deeper knowledge of these elements can help understand how cis-regulatory elements coordinate the expression of the target genes. However, while insulators are critical in gene regulation and genome functioning, only a few have been reported so far. Here, we describe a new insulator sequence that is located in the 5'UTR of the Drosophila retrotransposon ZAM. We have used an "enhancer-blocking assay" to test its effects on the activity of the enhancer in transiently transfected Drosophila S2R(+) cell line. Moreover, we show that the new insulator is able to affect significantly the enhancer-promoter interaction in the human cell line HEK293. These results suggest the possibility of employing the ZAM insulator in gene transfer protocols from insects to mammals in order to counteract the transgene positional and genotoxic effects.

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“…Unifying observations in several studies suggest that heparin binds the trypsin-sensitive solvent-phase tails of the core histones (26) and renders the nucleosomes more accessible to nucleases (27,28). Furthermore, heparin increases enhancer-promoter communication (29) by disassembling the chromatin structure (30,31).…”

mentioning

confidence: 99%

Heparin exerts a dual effect on murine lupus nephritis by enhancing enzymatic chromatin degradation and preventing chromatin binding in glomerular membranes

Hedberg¹,

Fismen²,

Fenton³

et al. 2011

Arthritis & Rheumatism

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Objective. Association of nucleosome-IgG immune complexes with glomerular basement membranes (GBMs) is an important event in the development of lupus nephritis. Preventing this binding and/or increasing nuclease sensitivity of nucleosomes may be viable strategies for the prevention of the disease. Theoretically, heparin may alter nucleosomal structure and increase sensitivity to proteinases and nucleases, and may also inhibit binding of nucleosomes and nucleosome-IgG complexes to basement membrane structures. The aim of this study was to investigate whether and eventually how heparin prevents murine lupus nephritis.Methods. Surface plasmon resonance was used to analyze if heparin inhibits binding of nucleosomes to laminin and collagen. The effect of heparin on nucleaseand proteinase-mediated degradation of nucleosomes was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and agarose gel electrophoresis. In vitro results were compared with analyses in vivo in heparin-treated (NZB ؋ NZW)F 1 mice. Anti-doublestranded DNA antibody production, deposition of nucleosome-IgG complexes in GBMs, and development of proteinuria were monitored, and circulating chromatin fragments were quantified using quantitative polymerase chain reaction.Results. In vitro studies demonstrated that heparin increased enzymatic degradation of nucleosomes and almost completely inhibited binding of nucleosomes to laminin and collagen. (NZB ؋ NZW)F 1 mice treated with heparin demonstrated delayed or no antibody production and higher variation of circulating chromatin levels compared with untreated control mice. This effect was accompanied by highly reduced nucleosomeIgG complexes in GBMs and delayed development of nephritis.Conclusion. Increasing the degradation of nucleosomes, reducing their immunogenicity, and preventing binding of nucleosome-IgG complexes in glomeruli together provide an alternative basis for the treatment of lupus nephritis.

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Biochemical analysis of enhancer–promoter communication in chromatin

Cited by 15 publications

References 51 publications

Internucleosomal Interactions Mediated by Histone Tails Allow Distant Communication in Chromatin

Internucleosomal Interactions Mediated by Histone Tails Allow Distant Communication in Chromatin

Evidences for insulator activity of the 5′UTR of the Drosophila melanogaster LTR-retrotransposon ZAM

Heparin exerts a dual effect on murine lupus nephritis by enhancing enzymatic chromatin degradation and preventing chromatin binding in glomerular membranes

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