Limits...
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.

Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E - PLoS Comput. Biol. (2008)

Bottom Line: The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence.We find that Poly(dA:dT) tracts are an important component of these nucleosome positioning signals and that their nucleosome-disfavoring action results in large nucleosome depletion over them and over their flanking regions and enhances the accessibility of transcription factors to their cognate sites.Our results suggest that the yeast genome may utilize these nucleosome positioning signals to regulate gene expression with different transcriptional noise and activation kinetics and DNA replication with different origin efficiency.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.

ABSTRACT
The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the functional consequences of this encoding. Here, we address this question using a genome-wide map of approximately 380,000 yeast nucleosomes that we sequenced in their entirety. Utilizing the high resolution of our map, we refine our understanding of how nucleosome organizations are encoded by the DNA sequence and demonstrate that the genomic sequence is highly predictive of the in vivo nucleosome organization, even across new nucleosome-bound sequences that we isolated from fly and human. We find that Poly(dA:dT) tracts are an important component of these nucleosome positioning signals and that their nucleosome-disfavoring action results in large nucleosome depletion over them and over their flanking regions and enhances the accessibility of transcription factors to their cognate sites. Our results suggest that the yeast genome may utilize these nucleosome positioning signals to regulate gene expression with different transcriptional noise and activation kinetics and DNA replication with different origin efficiency. These distinct functions may be achieved by encoding both relatively closed (nucleosome-covered) chromatin organizations over some factor binding sites, where factors must compete with nucleosomes for DNA access, and relatively open (nucleosome-depleted) organizations over other factor sites, where factors bind without competition.

Show MeSH

Related in: MedlinePlus

The sequence specificity of micrococcal nuclease is not the cause of nucleosome depletion over Poly(dA:dT) elements.(A) Shown is a standard sequence logo representation of the sequence specificity of micrococcal nuclease, as determined by aligning the ∼1,000,000 cut sites that we obtained in our study. In this standard representation, every position represents the probability distribution over the four possible nucleotides at that position (relative to the yeast genome composition), by the information content contained in that distribution. As can be seen, the information content is low, indicating that although micrococcal nuclease does have detectable sequence specificity, this specificity is low and can thus be found in nearly every small stretch of DNA in the yeast genome. (B) Shown is the ranking of all 4096 possible 6-mers by their preference to be cut by micrococcal nuclease, defined as the ratio between the probability that they appear as a cut site and the probability that they appear in the yeast genome. The top ranking 6-mers are shown, along with the (low ranking) position of AAAAAA and TTTTTT. (C) Shown is the fraction of micrococcal nuclease cut sites in which there is a Poly(dA:dT) element k basepairs away from the cut site, when k ranges from −100 bp (i.e., 100 bp inside the mapped nucleosome) to 250 bp (outside). For this analysis we took perfect Poly(dA:dT) elements of length 6 or greater. Note that the most likely position for Poly(dA:dT) elements is not at the cut site but rather ∼50 bp from the cut site.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2570626&req=5

pcbi-1000216-g006: The sequence specificity of micrococcal nuclease is not the cause of nucleosome depletion over Poly(dA:dT) elements.(A) Shown is a standard sequence logo representation of the sequence specificity of micrococcal nuclease, as determined by aligning the ∼1,000,000 cut sites that we obtained in our study. In this standard representation, every position represents the probability distribution over the four possible nucleotides at that position (relative to the yeast genome composition), by the information content contained in that distribution. As can be seen, the information content is low, indicating that although micrococcal nuclease does have detectable sequence specificity, this specificity is low and can thus be found in nearly every small stretch of DNA in the yeast genome. (B) Shown is the ranking of all 4096 possible 6-mers by their preference to be cut by micrococcal nuclease, defined as the ratio between the probability that they appear as a cut site and the probability that they appear in the yeast genome. The top ranking 6-mers are shown, along with the (low ranking) position of AAAAAA and TTTTTT. (C) Shown is the fraction of micrococcal nuclease cut sites in which there is a Poly(dA:dT) element k basepairs away from the cut site, when k ranges from −100 bp (i.e., 100 bp inside the mapped nucleosome) to 250 bp (outside). For this analysis we took perfect Poly(dA:dT) elements of length 6 or greater. Note that the most likely position for Poly(dA:dT) elements is not at the cut site but rather ∼50 bp from the cut site.

Mentions: To confirm that nucleosome depletion over Poly(dA:dT) elements is not a result of the sequence specificity of micrococcal nuclease, we examined the ∼1 million cut sites of micrococcal nuclease provided by our data (since we sequenced ∼500,000 individual nucleosomes altogether, and each nucleosome is sequenced in full, thereby providing two cut sites). By aligning all of these cut sites, we find that the sequence specificity in these cut sites is highly similar to that reported previously [39], and that it has very little information content (i.e., the specificity of the nuclease is low, confined mainly to two basepairs). This means that a preferred sequence for micrococcal nuclease can be found in nearly every small stretch of DNA in the yeast genome (Figure 6A). Moreover, ranking all of the 4096 possible 6-mers by their preference to be cut by micrococcal nuclease, defined as the ratio between the probability that they appear as a cut site and the probability that they appear in the yeast genome, we find that AAAAAA is ranked 1782 out of the 4096 possible 6-mers as a micrococcal nuclease cleavage site (Figure 6B), while it ranks number 1 for its observed in vivo nucleosome depletion (Figure 2A). In addition, plotting the distribution of Poly(dA:dT) elements as a function of their distance from all cut sites obtained in our data, we find that the most likely position for Poly(dA:dT) elements relative to cut sites is ∼50 bp from the cut site, which is consistent with the enrichment of Poly(dA:dT) elements in linker DNA regions, but not with the idea that Poly(dA:dT) elements are preferentially cut by micrococcal nuclease (Figure 6C). Thus, the relative lack of nucleosome occupancy over Poly(dA:dT) elements in vivo is not attributable to these sites being preferentially degraded by the micrococcal nuclease.


Distinct modes of regulation by chromatin encoded through nucleosome positioning signals.

Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E - PLoS Comput. Biol. (2008)

The sequence specificity of micrococcal nuclease is not the cause of nucleosome depletion over Poly(dA:dT) elements.(A) Shown is a standard sequence logo representation of the sequence specificity of micrococcal nuclease, as determined by aligning the ∼1,000,000 cut sites that we obtained in our study. In this standard representation, every position represents the probability distribution over the four possible nucleotides at that position (relative to the yeast genome composition), by the information content contained in that distribution. As can be seen, the information content is low, indicating that although micrococcal nuclease does have detectable sequence specificity, this specificity is low and can thus be found in nearly every small stretch of DNA in the yeast genome. (B) Shown is the ranking of all 4096 possible 6-mers by their preference to be cut by micrococcal nuclease, defined as the ratio between the probability that they appear as a cut site and the probability that they appear in the yeast genome. The top ranking 6-mers are shown, along with the (low ranking) position of AAAAAA and TTTTTT. (C) Shown is the fraction of micrococcal nuclease cut sites in which there is a Poly(dA:dT) element k basepairs away from the cut site, when k ranges from −100 bp (i.e., 100 bp inside the mapped nucleosome) to 250 bp (outside). For this analysis we took perfect Poly(dA:dT) elements of length 6 or greater. Note that the most likely position for Poly(dA:dT) elements is not at the cut site but rather ∼50 bp from the cut site.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2570626&req=5

pcbi-1000216-g006: The sequence specificity of micrococcal nuclease is not the cause of nucleosome depletion over Poly(dA:dT) elements.(A) Shown is a standard sequence logo representation of the sequence specificity of micrococcal nuclease, as determined by aligning the ∼1,000,000 cut sites that we obtained in our study. In this standard representation, every position represents the probability distribution over the four possible nucleotides at that position (relative to the yeast genome composition), by the information content contained in that distribution. As can be seen, the information content is low, indicating that although micrococcal nuclease does have detectable sequence specificity, this specificity is low and can thus be found in nearly every small stretch of DNA in the yeast genome. (B) Shown is the ranking of all 4096 possible 6-mers by their preference to be cut by micrococcal nuclease, defined as the ratio between the probability that they appear as a cut site and the probability that they appear in the yeast genome. The top ranking 6-mers are shown, along with the (low ranking) position of AAAAAA and TTTTTT. (C) Shown is the fraction of micrococcal nuclease cut sites in which there is a Poly(dA:dT) element k basepairs away from the cut site, when k ranges from −100 bp (i.e., 100 bp inside the mapped nucleosome) to 250 bp (outside). For this analysis we took perfect Poly(dA:dT) elements of length 6 or greater. Note that the most likely position for Poly(dA:dT) elements is not at the cut site but rather ∼50 bp from the cut site.
Mentions: To confirm that nucleosome depletion over Poly(dA:dT) elements is not a result of the sequence specificity of micrococcal nuclease, we examined the ∼1 million cut sites of micrococcal nuclease provided by our data (since we sequenced ∼500,000 individual nucleosomes altogether, and each nucleosome is sequenced in full, thereby providing two cut sites). By aligning all of these cut sites, we find that the sequence specificity in these cut sites is highly similar to that reported previously [39], and that it has very little information content (i.e., the specificity of the nuclease is low, confined mainly to two basepairs). This means that a preferred sequence for micrococcal nuclease can be found in nearly every small stretch of DNA in the yeast genome (Figure 6A). Moreover, ranking all of the 4096 possible 6-mers by their preference to be cut by micrococcal nuclease, defined as the ratio between the probability that they appear as a cut site and the probability that they appear in the yeast genome, we find that AAAAAA is ranked 1782 out of the 4096 possible 6-mers as a micrococcal nuclease cleavage site (Figure 6B), while it ranks number 1 for its observed in vivo nucleosome depletion (Figure 2A). In addition, plotting the distribution of Poly(dA:dT) elements as a function of their distance from all cut sites obtained in our data, we find that the most likely position for Poly(dA:dT) elements relative to cut sites is ∼50 bp from the cut site, which is consistent with the enrichment of Poly(dA:dT) elements in linker DNA regions, but not with the idea that Poly(dA:dT) elements are preferentially cut by micrococcal nuclease (Figure 6C). Thus, the relative lack of nucleosome occupancy over Poly(dA:dT) elements in vivo is not attributable to these sites being preferentially degraded by the micrococcal nuclease.

Bottom Line: The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence.We find that Poly(dA:dT) tracts are an important component of these nucleosome positioning signals and that their nucleosome-disfavoring action results in large nucleosome depletion over them and over their flanking regions and enhances the accessibility of transcription factors to their cognate sites.Our results suggest that the yeast genome may utilize these nucleosome positioning signals to regulate gene expression with different transcriptional noise and activation kinetics and DNA replication with different origin efficiency.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.

ABSTRACT
The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the functional consequences of this encoding. Here, we address this question using a genome-wide map of approximately 380,000 yeast nucleosomes that we sequenced in their entirety. Utilizing the high resolution of our map, we refine our understanding of how nucleosome organizations are encoded by the DNA sequence and demonstrate that the genomic sequence is highly predictive of the in vivo nucleosome organization, even across new nucleosome-bound sequences that we isolated from fly and human. We find that Poly(dA:dT) tracts are an important component of these nucleosome positioning signals and that their nucleosome-disfavoring action results in large nucleosome depletion over them and over their flanking regions and enhances the accessibility of transcription factors to their cognate sites. Our results suggest that the yeast genome may utilize these nucleosome positioning signals to regulate gene expression with different transcriptional noise and activation kinetics and DNA replication with different origin efficiency. These distinct functions may be achieved by encoding both relatively closed (nucleosome-covered) chromatin organizations over some factor binding sites, where factors must compete with nucleosomes for DNA access, and relatively open (nucleosome-depleted) organizations over other factor sites, where factors bind without competition.

Show MeSH
Related in: MedlinePlus