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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

Comparison of the nucleosome positions on the SNR6 gene locus. TFIIIC is omitted for the sake of clarity. Positions of the promoter elements are marked in panel A and described at the bottom of the figure. Numbers in bold and vertical arrows represent the MNase cut sites mapped by the indirect end-labeling technique in the upstream region. The rest of the numbers in panel B mark the positions of nucleosome boundaries mapped by Exo III footprinting. Nucleosomes are color coded, with their positions as given in Table 1. (A) Positions reported in vivo in the presence of TFIIIC [37]. (B) All the in vitro positions in the absence of TFIIIC, as mapped in this study and summarized in Table 1. Positions 1, 2 and 7 are omitted for the sake of clarity. (C, D and E) show three possible registers (R1, R2 and R3) generated by the combinations of positions depicted in the panel (B) under three different conditions. Positions 5 and 6 are mutually exclusive. In vivo, 6 is occupied in repressed state (Panel D), while chromatin remodeler RSC shifts it to position 5 in active state (Panel E). Boundaries of position 12, which is selected after TFIIIC binding and chromatin remodeling in vivo are marked in bold.
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Figure 7: Comparison of the nucleosome positions on the SNR6 gene locus. TFIIIC is omitted for the sake of clarity. Positions of the promoter elements are marked in panel A and described at the bottom of the figure. Numbers in bold and vertical arrows represent the MNase cut sites mapped by the indirect end-labeling technique in the upstream region. The rest of the numbers in panel B mark the positions of nucleosome boundaries mapped by Exo III footprinting. Nucleosomes are color coded, with their positions as given in Table 1. (A) Positions reported in vivo in the presence of TFIIIC [37]. (B) All the in vitro positions in the absence of TFIIIC, as mapped in this study and summarized in Table 1. Positions 1, 2 and 7 are omitted for the sake of clarity. (C, D and E) show three possible registers (R1, R2 and R3) generated by the combinations of positions depicted in the panel (B) under three different conditions. Positions 5 and 6 are mutually exclusive. In vivo, 6 is occupied in repressed state (Panel D), while chromatin remodeler RSC shifts it to position 5 in active state (Panel E). Boundaries of position 12, which is selected after TFIIIC binding and chromatin remodeling in vivo are marked in bold.

Mentions: Most of the positions mapped in this study and summarized in Table 1 can be correlated to the positions reported earlier [3,37,39,59] or predicted by the SNR6 sequence [26]. Figure 7 compares a summary of the results of this study (in vitro, panel B) with the nucleosome positions from our previous study ([37], in vivo, panel A). The striking similarity of the mapped positions in the gene upstream region (in bold, panel A) and less defined rotational phase of the DNA upstream of -100 bp (Figure 3) suggests that the nucleosomes upstream of -70 bp position are directed by the SNR6 sequence. With a strong possibility of multiple sequence-directed positions at uniform intervals on the SNR6 gene region (Figures 4, 5, 6), when both the halves of the SNR6 are together in the gene, the nucleosome positions on the 5' half of the gene may align with those in the downstream region.


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)

Comparison of the nucleosome positions on the SNR6 gene locus. TFIIIC is omitted for the sake of clarity. Positions of the promoter elements are marked in panel A and described at the bottom of the figure. Numbers in bold and vertical arrows represent the MNase cut sites mapped by the indirect end-labeling technique in the upstream region. The rest of the numbers in panel B mark the positions of nucleosome boundaries mapped by Exo III footprinting. Nucleosomes are color coded, with their positions as given in Table 1. (A) Positions reported in vivo in the presence of TFIIIC [37]. (B) All the in vitro positions in the absence of TFIIIC, as mapped in this study and summarized in Table 1. Positions 1, 2 and 7 are omitted for the sake of clarity. (C, D and E) show three possible registers (R1, R2 and R3) generated by the combinations of positions depicted in the panel (B) under three different conditions. Positions 5 and 6 are mutually exclusive. In vivo, 6 is occupied in repressed state (Panel D), while chromatin remodeler RSC shifts it to position 5 in active state (Panel E). Boundaries of position 12, which is selected after TFIIIC binding and chromatin remodeling in vivo are marked in bold.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Comparison of the nucleosome positions on the SNR6 gene locus. TFIIIC is omitted for the sake of clarity. Positions of the promoter elements are marked in panel A and described at the bottom of the figure. Numbers in bold and vertical arrows represent the MNase cut sites mapped by the indirect end-labeling technique in the upstream region. The rest of the numbers in panel B mark the positions of nucleosome boundaries mapped by Exo III footprinting. Nucleosomes are color coded, with their positions as given in Table 1. (A) Positions reported in vivo in the presence of TFIIIC [37]. (B) All the in vitro positions in the absence of TFIIIC, as mapped in this study and summarized in Table 1. Positions 1, 2 and 7 are omitted for the sake of clarity. (C, D and E) show three possible registers (R1, R2 and R3) generated by the combinations of positions depicted in the panel (B) under three different conditions. Positions 5 and 6 are mutually exclusive. In vivo, 6 is occupied in repressed state (Panel D), while chromatin remodeler RSC shifts it to position 5 in active state (Panel E). Boundaries of position 12, which is selected after TFIIIC binding and chromatin remodeling in vivo are marked in bold.
Mentions: Most of the positions mapped in this study and summarized in Table 1 can be correlated to the positions reported earlier [3,37,39,59] or predicted by the SNR6 sequence [26]. Figure 7 compares a summary of the results of this study (in vitro, panel B) with the nucleosome positions from our previous study ([37], in vivo, panel A). The striking similarity of the mapped positions in the gene upstream region (in bold, panel A) and less defined rotational phase of the DNA upstream of -100 bp (Figure 3) suggests that the nucleosomes upstream of -70 bp position are directed by the SNR6 sequence. With a strong possibility of multiple sequence-directed positions at uniform intervals on the SNR6 gene region (Figures 4, 5, 6), when both the halves of the SNR6 are together in the gene, the nucleosome positions on the 5' half of the gene may align with those in the downstream region.

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