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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.

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Poly(dA:dT) elements have a reduced affinity for nucleosome formation in vitro.(A–C) Experimental maps of nucleosome occupancy at three genomic loci for which we measured the relative nucleosome affinity of Poly(dA:dT)-containing sequences (blue triangles). Every cyan oval represents the genomic location of one nucleosome that we sequenced in its entirety. Also shown is the average nucleosome occupancy per basepair predicted by the sequence-based nucleosome model that we developed here (red), the raw hybridization signals of two microarray-based nucleosome maps [5],[10] (green and purple traces), and the locations of nucleosomes that were computationally inferred from these hybridization signals [5],[10] (green and purple ovals). Annotated genes [63], transcription factor binding sites [47], and TATA sequences [53] in the region are indicated. (D) Poly(dA:dT)-containing sequences have low nucleosome affinities. Shown are measurements of relative affinity for nucleosome formation of seven Poly(dA:dT)-containing sequences (blue bar; shown are mean and standard deviation for seven measured sequences: three boundary regions from yeast that each contain multiple Poly(dA:dT) elements, and four sequence variants that disrupt one of the Poly(dA:dT) elements in each sequence). For comparison, also shown are the relative affinities of sequences selected for their relative resistance to nucleosome formation [45] (yellow bars), and of sequences selected for their high nucleosome affinity from the mouse genome [18] (green bars) and from chemically synthesized random sequences [7],[19] (red bars). All results are presented relative to the 5S reference sequence, defined as 0. (E) The sequences of the Poly(dA:dT)-containing elements of (a–c) that we measured, along with their chromosomal locations.
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pcbi-1000216-g008: Poly(dA:dT) elements have a reduced affinity for nucleosome formation in vitro.(A–C) Experimental maps of nucleosome occupancy at three genomic loci for which we measured the relative nucleosome affinity of Poly(dA:dT)-containing sequences (blue triangles). Every cyan oval represents the genomic location of one nucleosome that we sequenced in its entirety. Also shown is the average nucleosome occupancy per basepair predicted by the sequence-based nucleosome model that we developed here (red), the raw hybridization signals of two microarray-based nucleosome maps [5],[10] (green and purple traces), and the locations of nucleosomes that were computationally inferred from these hybridization signals [5],[10] (green and purple ovals). Annotated genes [63], transcription factor binding sites [47], and TATA sequences [53] in the region are indicated. (D) Poly(dA:dT)-containing sequences have low nucleosome affinities. Shown are measurements of relative affinity for nucleosome formation of seven Poly(dA:dT)-containing sequences (blue bar; shown are mean and standard deviation for seven measured sequences: three boundary regions from yeast that each contain multiple Poly(dA:dT) elements, and four sequence variants that disrupt one of the Poly(dA:dT) elements in each sequence). For comparison, also shown are the relative affinities of sequences selected for their relative resistance to nucleosome formation [45] (yellow bars), and of sequences selected for their high nucleosome affinity from the mouse genome [18] (green bars) and from chemically synthesized random sequences [7],[19] (red bars). All results are presented relative to the 5S reference sequence, defined as 0. (E) The sequences of the Poly(dA:dT)-containing elements of (a–c) that we measured, along with their chromosomal locations.

Mentions: If nucleosome exclusion is the primary mechanism by which Poly(dA:dT) elements exert their effect, then we might also expect these elements to show a reduced affinity for nucleosome formation in vitro. One study addressed this question, and demonstrated that incorporating a perfect Poly-A(16) element into a (non-natural) DNA sequence disfavors nucleosome formation, with an effect of about two-fold on DNA accessibility [31]. To examine whether natural boundary sequences also exhibit reduced nucleosome affinity in vitro, we selected three Poly(dA:dT)-containing regions from the yeast genome that each contain multiple Poly(dA:dT) elements and measured the relative affinities of these regions for nucleosome formation along with the relative affinities of four sequence variants that disrupt one of the Poly(dA:dT) elements in each sequence. Like many of the other Poly(dA:dT) elements in the genome, the Poly(dA:dT) elements that we selected exhibit nucleosome depletion in vivo (Figure 8A–C). Consistent with earlier measurements [31], we find that all seven Poly(dA:dT)-containing sequences have significantly reduced affinities, comparable to affinities of DNA sequences that were selected for their ability to resist nucleosome formation [45] (Figure 8D and 8E). These relative affinity measurements for nucleosome formation were performed as previously described [2],[7].


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)

Poly(dA:dT) elements have a reduced affinity for nucleosome formation in vitro.(A–C) Experimental maps of nucleosome occupancy at three genomic loci for which we measured the relative nucleosome affinity of Poly(dA:dT)-containing sequences (blue triangles). Every cyan oval represents the genomic location of one nucleosome that we sequenced in its entirety. Also shown is the average nucleosome occupancy per basepair predicted by the sequence-based nucleosome model that we developed here (red), the raw hybridization signals of two microarray-based nucleosome maps [5],[10] (green and purple traces), and the locations of nucleosomes that were computationally inferred from these hybridization signals [5],[10] (green and purple ovals). Annotated genes [63], transcription factor binding sites [47], and TATA sequences [53] in the region are indicated. (D) Poly(dA:dT)-containing sequences have low nucleosome affinities. Shown are measurements of relative affinity for nucleosome formation of seven Poly(dA:dT)-containing sequences (blue bar; shown are mean and standard deviation for seven measured sequences: three boundary regions from yeast that each contain multiple Poly(dA:dT) elements, and four sequence variants that disrupt one of the Poly(dA:dT) elements in each sequence). For comparison, also shown are the relative affinities of sequences selected for their relative resistance to nucleosome formation [45] (yellow bars), and of sequences selected for their high nucleosome affinity from the mouse genome [18] (green bars) and from chemically synthesized random sequences [7],[19] (red bars). All results are presented relative to the 5S reference sequence, defined as 0. (E) The sequences of the Poly(dA:dT)-containing elements of (a–c) that we measured, along with their chromosomal locations.
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Related In: Results  -  Collection

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pcbi-1000216-g008: Poly(dA:dT) elements have a reduced affinity for nucleosome formation in vitro.(A–C) Experimental maps of nucleosome occupancy at three genomic loci for which we measured the relative nucleosome affinity of Poly(dA:dT)-containing sequences (blue triangles). Every cyan oval represents the genomic location of one nucleosome that we sequenced in its entirety. Also shown is the average nucleosome occupancy per basepair predicted by the sequence-based nucleosome model that we developed here (red), the raw hybridization signals of two microarray-based nucleosome maps [5],[10] (green and purple traces), and the locations of nucleosomes that were computationally inferred from these hybridization signals [5],[10] (green and purple ovals). Annotated genes [63], transcription factor binding sites [47], and TATA sequences [53] in the region are indicated. (D) Poly(dA:dT)-containing sequences have low nucleosome affinities. Shown are measurements of relative affinity for nucleosome formation of seven Poly(dA:dT)-containing sequences (blue bar; shown are mean and standard deviation for seven measured sequences: three boundary regions from yeast that each contain multiple Poly(dA:dT) elements, and four sequence variants that disrupt one of the Poly(dA:dT) elements in each sequence). For comparison, also shown are the relative affinities of sequences selected for their relative resistance to nucleosome formation [45] (yellow bars), and of sequences selected for their high nucleosome affinity from the mouse genome [18] (green bars) and from chemically synthesized random sequences [7],[19] (red bars). All results are presented relative to the 5S reference sequence, defined as 0. (E) The sequences of the Poly(dA:dT)-containing elements of (a–c) that we measured, along with their chromosomal locations.
Mentions: If nucleosome exclusion is the primary mechanism by which Poly(dA:dT) elements exert their effect, then we might also expect these elements to show a reduced affinity for nucleosome formation in vitro. One study addressed this question, and demonstrated that incorporating a perfect Poly-A(16) element into a (non-natural) DNA sequence disfavors nucleosome formation, with an effect of about two-fold on DNA accessibility [31]. To examine whether natural boundary sequences also exhibit reduced nucleosome affinity in vitro, we selected three Poly(dA:dT)-containing regions from the yeast genome that each contain multiple Poly(dA:dT) elements and measured the relative affinities of these regions for nucleosome formation along with the relative affinities of four sequence variants that disrupt one of the Poly(dA:dT) elements in each sequence. Like many of the other Poly(dA:dT) elements in the genome, the Poly(dA:dT) elements that we selected exhibit nucleosome depletion in vivo (Figure 8A–C). Consistent with earlier measurements [31], we find that all seven Poly(dA:dT)-containing sequences have significantly reduced affinities, comparable to affinities of DNA sequences that were selected for their ability to resist nucleosome formation [45] (Figure 8D and 8E). These relative affinity measurements for nucleosome formation were performed as previously described [2],[7].

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