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Multiple sequence-directed possibilities provide a pool of nucleosome position choices in different states of activity of a gene.

Vinayachandran V, Pusarla RH, Bhargava P - Epigenetics Chromatin (2009)

Bottom Line: While the DNA sequences may help decide their locations, the observed positions in vivo are end-results of chromatin remodeling, the state of gene activity and binding of the sequence-specific factors to the DNA, all of which influence nucleosome positions.Thus, the observed nucleosome locations in vivo do not reflect the true contribution of DNA sequence to the mapped position.On a gene locus, multiple nucleosome positions are directed by a gene sequence to provide a pool of possibilities, out of which the preferred ones are selected by the chromatin remodeler and transcription factor of the gene under different states of activity of the gene.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Hyderabad-500007, India. vinesh@ccmb.res.in

ABSTRACT

Background: Genome-wide mappings of nucleosome occupancy in different species have shown presence of well-positioned nucleosomes. While the DNA sequences may help decide their locations, the observed positions in vivo are end-results of chromatin remodeling, the state of gene activity and binding of the sequence-specific factors to the DNA, all of which influence nucleosome positions. Thus, the observed nucleosome locations in vivo do not reflect the true contribution of DNA sequence to the mapped position. Moreover, the naturally occurring nucleosome-positioning sequences are known to guide multiple translational positionings.

Results: We show that yeast SNR6, a gene transcribed by RNA polymerase III, constitutes nucleosome-positioning sequence. In the absence of a chromatin remodeler or any factor binding, the gene sequence confers a unique rotational phase to nucleosomes in the gene region, and directs assembly of several translationally positioned nucleosomes on approximately 1.2 kb DNA from the gene locus, including the short approximately 250 bp gene region. Mapping of all these gene sequence-directed nucleosome positions revealed that the array of nucleosomes in the gene upstream region occupy the same positions as those observed in vivo but the nucleosomes on the gene region can be arranged in three distinct registers. Two of these arrangements differ from each other in the position of only one nucleosome, and match with the nucleosome positions on the gene in repressed and active states in vivo, where the gene-specific factor is known to occupy the gene in both the states. The two positions are interchanged by an ATP-dependent chromatin remodeler in vivo. The third register represents the positions which block the access of the factor to the gene promoter elements.

Conclusion: On a gene locus, multiple nucleosome positions are directed by a gene sequence to provide a pool of possibilities, out of which the preferred ones are selected by the chromatin remodeler and transcription factor of the gene under different states of activity of the gene.

No MeSH data available.


Related in: MedlinePlus

Sequence-directed nucleosome positions on the yeast SNR6 gene. Numbers denote the positions of the promoter elements and MNase cuts in the genomic DNA in base pairs while ovals represent individual nucleosomes. (A) Schematic representation of reported nucleosome positions in vivo on the gene and its flanking regions. Arrow marks the transcription initiation site. (B) and (C) Indirect end-labeling analysis of the chromatin structure reconstituted on the SNR6 gene in the plasmids in vitro. Naked DNA (lanes 1, 2) and chromatin (lanes 3,4) were digested with MNase and probed with a primer away from the gene region. Positions of the boxes A and B are marked, M denotes molecular size marker and the vertical bar marks the genomic DNA region in the plasmid. (B) Primer hybridizes 1281 bp upstream of the SNR6 TATA box. Bands at -545, -656 and +830 bp map in the vector DNA. As compared with -241 and -453, bands at -368 and -545 are faint (black dots, lanes 3 and 4) and may not be the chromatin-specific cuts (cf. naked DNA cuts at -349 and -517, lanes 1 and 2). Two alternate registers are shown on two sides of lanes 3 and 4. (C) Primer hybridizes 894 bp upstream of the TATA box. Positions -264 and +558 fall in the vector DNA.
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Figure 1: Sequence-directed nucleosome positions on the yeast SNR6 gene. Numbers denote the positions of the promoter elements and MNase cuts in the genomic DNA in base pairs while ovals represent individual nucleosomes. (A) Schematic representation of reported nucleosome positions in vivo on the gene and its flanking regions. Arrow marks the transcription initiation site. (B) and (C) Indirect end-labeling analysis of the chromatin structure reconstituted on the SNR6 gene in the plasmids in vitro. Naked DNA (lanes 1, 2) and chromatin (lanes 3,4) were digested with MNase and probed with a primer away from the gene region. Positions of the boxes A and B are marked, M denotes molecular size marker and the vertical bar marks the genomic DNA region in the plasmid. (B) Primer hybridizes 1281 bp upstream of the SNR6 TATA box. Bands at -545, -656 and +830 bp map in the vector DNA. As compared with -241 and -453, bands at -368 and -545 are faint (black dots, lanes 3 and 4) and may not be the chromatin-specific cuts (cf. naked DNA cuts at -349 and -517, lanes 1 and 2). Two alternate registers are shown on two sides of lanes 3 and 4. (C) Primer hybridizes 894 bp upstream of the TATA box. Positions -264 and +558 fall in the vector DNA.

Mentions: As shown in Figure 1A, the SNR6 gene locus constitutes a TATA box at -30 bp, box A at +21 bp, the terminator at +109 bp, and box B at +233 bp positions (with respect to +1 at transcription initiation site). To find the contribution of the genomic DNA sequence to the nucleosome positions, we used the salt gradient dilution method to deposit nucleosomes on plasmids carrying different parts of genomic DNA from the SNR6 gene region in the absence of any bound transcription factor, and subjected the chromatin to structural analyses for locating the positioned nucleosomes, if any.


Multiple sequence-directed possibilities provide a pool of nucleosome position choices in different states of activity of a gene.

Vinayachandran V, Pusarla RH, Bhargava P - Epigenetics Chromatin (2009)

Sequence-directed nucleosome positions on the yeast SNR6 gene. Numbers denote the positions of the promoter elements and MNase cuts in the genomic DNA in base pairs while ovals represent individual nucleosomes. (A) Schematic representation of reported nucleosome positions in vivo on the gene and its flanking regions. Arrow marks the transcription initiation site. (B) and (C) Indirect end-labeling analysis of the chromatin structure reconstituted on the SNR6 gene in the plasmids in vitro. Naked DNA (lanes 1, 2) and chromatin (lanes 3,4) were digested with MNase and probed with a primer away from the gene region. Positions of the boxes A and B are marked, M denotes molecular size marker and the vertical bar marks the genomic DNA region in the plasmid. (B) Primer hybridizes 1281 bp upstream of the SNR6 TATA box. Bands at -545, -656 and +830 bp map in the vector DNA. As compared with -241 and -453, bands at -368 and -545 are faint (black dots, lanes 3 and 4) and may not be the chromatin-specific cuts (cf. naked DNA cuts at -349 and -517, lanes 1 and 2). Two alternate registers are shown on two sides of lanes 3 and 4. (C) Primer hybridizes 894 bp upstream of the TATA box. Positions -264 and +558 fall in the vector DNA.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667510&req=5

Figure 1: Sequence-directed nucleosome positions on the yeast SNR6 gene. Numbers denote the positions of the promoter elements and MNase cuts in the genomic DNA in base pairs while ovals represent individual nucleosomes. (A) Schematic representation of reported nucleosome positions in vivo on the gene and its flanking regions. Arrow marks the transcription initiation site. (B) and (C) Indirect end-labeling analysis of the chromatin structure reconstituted on the SNR6 gene in the plasmids in vitro. Naked DNA (lanes 1, 2) and chromatin (lanes 3,4) were digested with MNase and probed with a primer away from the gene region. Positions of the boxes A and B are marked, M denotes molecular size marker and the vertical bar marks the genomic DNA region in the plasmid. (B) Primer hybridizes 1281 bp upstream of the SNR6 TATA box. Bands at -545, -656 and +830 bp map in the vector DNA. As compared with -241 and -453, bands at -368 and -545 are faint (black dots, lanes 3 and 4) and may not be the chromatin-specific cuts (cf. naked DNA cuts at -349 and -517, lanes 1 and 2). Two alternate registers are shown on two sides of lanes 3 and 4. (C) Primer hybridizes 894 bp upstream of the TATA box. Positions -264 and +558 fall in the vector DNA.
Mentions: As shown in Figure 1A, the SNR6 gene locus constitutes a TATA box at -30 bp, box A at +21 bp, the terminator at +109 bp, and box B at +233 bp positions (with respect to +1 at transcription initiation site). To find the contribution of the genomic DNA sequence to the nucleosome positions, we used the salt gradient dilution method to deposit nucleosomes on plasmids carrying different parts of genomic DNA from the SNR6 gene region in the absence of any bound transcription factor, and subjected the chromatin to structural analyses for locating the positioned nucleosomes, if any.

Bottom Line: While the DNA sequences may help decide their locations, the observed positions in vivo are end-results of chromatin remodeling, the state of gene activity and binding of the sequence-specific factors to the DNA, all of which influence nucleosome positions.Thus, the observed nucleosome locations in vivo do not reflect the true contribution of DNA sequence to the mapped position.On a gene locus, multiple nucleosome positions are directed by a gene sequence to provide a pool of possibilities, out of which the preferred ones are selected by the chromatin remodeler and transcription factor of the gene under different states of activity of the gene.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Hyderabad-500007, India. vinesh@ccmb.res.in

ABSTRACT

Background: Genome-wide mappings of nucleosome occupancy in different species have shown presence of well-positioned nucleosomes. While the DNA sequences may help decide their locations, the observed positions in vivo are end-results of chromatin remodeling, the state of gene activity and binding of the sequence-specific factors to the DNA, all of which influence nucleosome positions. Thus, the observed nucleosome locations in vivo do not reflect the true contribution of DNA sequence to the mapped position. Moreover, the naturally occurring nucleosome-positioning sequences are known to guide multiple translational positionings.

Results: We show that yeast SNR6, a gene transcribed by RNA polymerase III, constitutes nucleosome-positioning sequence. In the absence of a chromatin remodeler or any factor binding, the gene sequence confers a unique rotational phase to nucleosomes in the gene region, and directs assembly of several translationally positioned nucleosomes on approximately 1.2 kb DNA from the gene locus, including the short approximately 250 bp gene region. Mapping of all these gene sequence-directed nucleosome positions revealed that the array of nucleosomes in the gene upstream region occupy the same positions as those observed in vivo but the nucleosomes on the gene region can be arranged in three distinct registers. Two of these arrangements differ from each other in the position of only one nucleosome, and match with the nucleosome positions on the gene in repressed and active states in vivo, where the gene-specific factor is known to occupy the gene in both the states. The two positions are interchanged by an ATP-dependent chromatin remodeler in vivo. The third register represents the positions which block the access of the factor to the gene promoter elements.

Conclusion: On a gene locus, multiple nucleosome positions are directed by a gene sequence to provide a pool of possibilities, out of which the preferred ones are selected by the chromatin remodeler and transcription factor of the gene under different states of activity of the gene.

No MeSH data available.


Related in: MedlinePlus