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SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome.

Mulholland N, Xu Y, Sugiyama H, Zhao K - Cell Biosci (2012)

Bottom Line: We previously have shown that activation of the CSF1 gene by a chromatin remodeling event in the promoter results in Z-DNA formation at TG repeats within the promoter.We show that remodeling of a mononucleosome by the human SWI/SNF complex results in Z-DNA formation when the DNA within the mononucleosome contains Z-DNA favoring sequence.We present evidence that Z-DNA can form on nucleosomes though previous observations indicate the occlusion of nucleosome formation from Z-DNA.

View Article: PubMed Central - HTML - PubMed

Affiliation: Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Maryland, USA. zhaok@nhlbi.nih.gov.

ABSTRACT

Background: Z-DNA is a higher-energy, left-handed form of the double helix. A primary function of Z-DNA formation is to facilitate transcriptional initiation and activation. Sequences favoring Z-DNA formation are frequently located in promoter regions and Z-DNA is stabilized by torsional strain resulting from negative supercoiling, such as that generated by an actively transcribing polymerase or by a nucleosome remodeling event. We previously have shown that activation of the CSF1 gene by a chromatin remodeling event in the promoter results in Z-DNA formation at TG repeats within the promoter.

Results: We show that remodeling of a mononucleosome by the human SWI/SNF complex results in Z-DNA formation when the DNA within the mononucleosome contains Z-DNA favoring sequence. Nuclease accessibility patterns of nucleosome core particle consisting of Z-DNA are quite different from counterpart nucleosomes containing classic B-DNA. Z-nucleosomes represent a novel mononucleosome structure.

Conclusions: We present evidence that Z-DNA can form on nucleosomes though previous observations indicate the occlusion of nucleosome formation from Z-DNA.

No MeSH data available.


Related in: MedlinePlus

B-DNA and Z-DNA mononucleosome templates. a. Two series of templates were used for mononucleosome assembly: 140 bp and 177 bp. Each series consists of B-DNA without GC repeats (T140 and T177), B-DNA with GC repeats (B140 and B177) and Z-DNA (Z140 and Z177). All DNAs were generated by PCR amplification of the same parental vector. A PCR primer with GC repeats was used to generate the B-DNA-GC fragment; a primer with 8-me-guanine modified GC repeats was used to generate the Z-DNA fragment. b. Body-labeled PCR fragments described in 1a were challenged with Zaa-Fok (a fusion protein consisting of two highly specific Z-DNA binding domains, Zα, from ADAR1 and the catalytic domain of the restriction enzyme FokI) to assess Z-DNA stability. Arrow heads indicate the cleavage products.
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Figure 1: B-DNA and Z-DNA mononucleosome templates. a. Two series of templates were used for mononucleosome assembly: 140 bp and 177 bp. Each series consists of B-DNA without GC repeats (T140 and T177), B-DNA with GC repeats (B140 and B177) and Z-DNA (Z140 and Z177). All DNAs were generated by PCR amplification of the same parental vector. A PCR primer with GC repeats was used to generate the B-DNA-GC fragment; a primer with 8-me-guanine modified GC repeats was used to generate the Z-DNA fragment. b. Body-labeled PCR fragments described in 1a were challenged with Zaa-Fok (a fusion protein consisting of two highly specific Z-DNA binding domains, Zα, from ADAR1 and the catalytic domain of the restriction enzyme FokI) to assess Z-DNA stability. Arrow heads indicate the cleavage products.

Mentions: The templates used in this study are described in Figure 1. One series of fragments are 140 bp and the other are 177 bp. Each series consist of 'T', 'B' and 'Z' fragments. The 'T' refers to TPT, the nucleosome-positioning sequence originally described by Shrader and Crothers [8]. 'B' refers to B-DNA and consists of the TPT fragment with 12 GC repeats located at the opposite end of the nucleosome positioning sequence. 'Z' refers to Z-DNA fragments which are identical in sequence to 'B' but contain 8-me-Guanine (8meG) in the GC repeats to stabilize Z-DNA structure [9]. The 8meG was incorporated in the fragment by synthesizing an oligonucleotide PCR primer with the 8meG using standard phosphoramidite chemistry [10].


SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome.

Mulholland N, Xu Y, Sugiyama H, Zhao K - Cell Biosci (2012)

B-DNA and Z-DNA mononucleosome templates. a. Two series of templates were used for mononucleosome assembly: 140 bp and 177 bp. Each series consists of B-DNA without GC repeats (T140 and T177), B-DNA with GC repeats (B140 and B177) and Z-DNA (Z140 and Z177). All DNAs were generated by PCR amplification of the same parental vector. A PCR primer with GC repeats was used to generate the B-DNA-GC fragment; a primer with 8-me-guanine modified GC repeats was used to generate the Z-DNA fragment. b. Body-labeled PCR fragments described in 1a were challenged with Zaa-Fok (a fusion protein consisting of two highly specific Z-DNA binding domains, Zα, from ADAR1 and the catalytic domain of the restriction enzyme FokI) to assess Z-DNA stability. Arrow heads indicate the cleavage products.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3293710&req=5

Figure 1: B-DNA and Z-DNA mononucleosome templates. a. Two series of templates were used for mononucleosome assembly: 140 bp and 177 bp. Each series consists of B-DNA without GC repeats (T140 and T177), B-DNA with GC repeats (B140 and B177) and Z-DNA (Z140 and Z177). All DNAs were generated by PCR amplification of the same parental vector. A PCR primer with GC repeats was used to generate the B-DNA-GC fragment; a primer with 8-me-guanine modified GC repeats was used to generate the Z-DNA fragment. b. Body-labeled PCR fragments described in 1a were challenged with Zaa-Fok (a fusion protein consisting of two highly specific Z-DNA binding domains, Zα, from ADAR1 and the catalytic domain of the restriction enzyme FokI) to assess Z-DNA stability. Arrow heads indicate the cleavage products.
Mentions: The templates used in this study are described in Figure 1. One series of fragments are 140 bp and the other are 177 bp. Each series consist of 'T', 'B' and 'Z' fragments. The 'T' refers to TPT, the nucleosome-positioning sequence originally described by Shrader and Crothers [8]. 'B' refers to B-DNA and consists of the TPT fragment with 12 GC repeats located at the opposite end of the nucleosome positioning sequence. 'Z' refers to Z-DNA fragments which are identical in sequence to 'B' but contain 8-me-Guanine (8meG) in the GC repeats to stabilize Z-DNA structure [9]. The 8meG was incorporated in the fragment by synthesizing an oligonucleotide PCR primer with the 8meG using standard phosphoramidite chemistry [10].

Bottom Line: We previously have shown that activation of the CSF1 gene by a chromatin remodeling event in the promoter results in Z-DNA formation at TG repeats within the promoter.We show that remodeling of a mononucleosome by the human SWI/SNF complex results in Z-DNA formation when the DNA within the mononucleosome contains Z-DNA favoring sequence.We present evidence that Z-DNA can form on nucleosomes though previous observations indicate the occlusion of nucleosome formation from Z-DNA.

View Article: PubMed Central - HTML - PubMed

Affiliation: Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Maryland, USA. zhaok@nhlbi.nih.gov.

ABSTRACT

Background: Z-DNA is a higher-energy, left-handed form of the double helix. A primary function of Z-DNA formation is to facilitate transcriptional initiation and activation. Sequences favoring Z-DNA formation are frequently located in promoter regions and Z-DNA is stabilized by torsional strain resulting from negative supercoiling, such as that generated by an actively transcribing polymerase or by a nucleosome remodeling event. We previously have shown that activation of the CSF1 gene by a chromatin remodeling event in the promoter results in Z-DNA formation at TG repeats within the promoter.

Results: We show that remodeling of a mononucleosome by the human SWI/SNF complex results in Z-DNA formation when the DNA within the mononucleosome contains Z-DNA favoring sequence. Nuclease accessibility patterns of nucleosome core particle consisting of Z-DNA are quite different from counterpart nucleosomes containing classic B-DNA. Z-nucleosomes represent a novel mononucleosome structure.

Conclusions: We present evidence that Z-DNA can form on nucleosomes though previous observations indicate the occlusion of nucleosome formation from Z-DNA.

No MeSH data available.


Related in: MedlinePlus