Limits...
The organization of nucleosomes around splice sites.

Chen W, Luo L, Zhang L - Nucleic Acids Res. (2010)

Bottom Line: Using the computational model of Increment of Diversity with Quadratic Discriminant (IDQD) trained from the microarray data, the nucleosome occupancy score (NOScore) was defined and applied to splice junction regions of constitutive, cassette exon, alternative 3' and 5' splicing events in the human genome.We found an interesting relation between NOScore and RNA splicing: exon regions have higher NOScores compared with their flanking intron sequences in both constitutive and alternative splicing events, indicating the stronger nucleosome occupation potential of exon regions.In addition, NOScore valleys present at approximately 25 bp upstream of the acceptor site in all splicing events.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.

ABSTRACT
The occupancy of nucleosomes along chromosome is a key factor for gene regulation. However, except promoter regions, genome-wide properties and functions of nucleosome organization remain unclear in mammalian genomes. Using the computational model of Increment of Diversity with Quadratic Discriminant (IDQD) trained from the microarray data, the nucleosome occupancy score (NOScore) was defined and applied to splice junction regions of constitutive, cassette exon, alternative 3' and 5' splicing events in the human genome. We found an interesting relation between NOScore and RNA splicing: exon regions have higher NOScores compared with their flanking intron sequences in both constitutive and alternative splicing events, indicating the stronger nucleosome occupation potential of exon regions. In addition, NOScore valleys present at approximately 25 bp upstream of the acceptor site in all splicing events. By defining folding diversity-to-energy ratio to describe RNA structural flexibility, we demonstrated that primary RNA transcripts from nucleosome occupancy regions are relatively rigid and those from nucleosome depleted regions are relatively flexible. The negative correlation between nucleosome occupation/depletion of DNA sequence and structural flexibility/rigidity of its primary transcript around splice junctions may provide clues to the deeper understanding of the unexpected role for nucleosome organization in the regulation of RNA splicing.

Show MeSH

Related in: MedlinePlus

The nucleosome occupancy score around splice junctions in constitutive splicing event. The score was smoothed with a 50-bp sliding window in 10-bp increments from −500 to 500 bp relative to the splice sites and given for the acceptor (top panel) and donor (down panel) sites, respectively. (a–c) correspond to sequences with exons that ranging from 140 to 160 bp, 160 to 180 bp and 190 to 210 bp, respectively. The x-axis gives the position of the sliding window labeled by its center relative to acceptor site AG (denoted as 0) or to donor site GT (denoted as 0) and the y-axis represents the nucleosome occupancy score.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2875036&req=5

Figure 2: The nucleosome occupancy score around splice junctions in constitutive splicing event. The score was smoothed with a 50-bp sliding window in 10-bp increments from −500 to 500 bp relative to the splice sites and given for the acceptor (top panel) and donor (down panel) sites, respectively. (a–c) correspond to sequences with exons that ranging from 140 to 160 bp, 160 to 180 bp and 190 to 210 bp, respectively. The x-axis gives the position of the sliding window labeled by its center relative to acceptor site AG (denoted as 0) or to donor site GT (denoted as 0) and the y-axis represents the nucleosome occupancy score.

Mentions: By using IDQD model, the NOScore was calculated in a 50-bp sliding window with a step size of 10-bp along the 1000 bp regions around the donor and acceptor splice sites. Figure 2 shows the NOScore against the position of sliding windows over the regions around the acceptor (AG) and donor (GT) sites of constitutive splicing event.Figure 2.


The organization of nucleosomes around splice sites.

Chen W, Luo L, Zhang L - Nucleic Acids Res. (2010)

The nucleosome occupancy score around splice junctions in constitutive splicing event. The score was smoothed with a 50-bp sliding window in 10-bp increments from −500 to 500 bp relative to the splice sites and given for the acceptor (top panel) and donor (down panel) sites, respectively. (a–c) correspond to sequences with exons that ranging from 140 to 160 bp, 160 to 180 bp and 190 to 210 bp, respectively. The x-axis gives the position of the sliding window labeled by its center relative to acceptor site AG (denoted as 0) or to donor site GT (denoted as 0) and the y-axis represents the nucleosome occupancy score.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875036&req=5

Figure 2: The nucleosome occupancy score around splice junctions in constitutive splicing event. The score was smoothed with a 50-bp sliding window in 10-bp increments from −500 to 500 bp relative to the splice sites and given for the acceptor (top panel) and donor (down panel) sites, respectively. (a–c) correspond to sequences with exons that ranging from 140 to 160 bp, 160 to 180 bp and 190 to 210 bp, respectively. The x-axis gives the position of the sliding window labeled by its center relative to acceptor site AG (denoted as 0) or to donor site GT (denoted as 0) and the y-axis represents the nucleosome occupancy score.
Mentions: By using IDQD model, the NOScore was calculated in a 50-bp sliding window with a step size of 10-bp along the 1000 bp regions around the donor and acceptor splice sites. Figure 2 shows the NOScore against the position of sliding windows over the regions around the acceptor (AG) and donor (GT) sites of constitutive splicing event.Figure 2.

Bottom Line: Using the computational model of Increment of Diversity with Quadratic Discriminant (IDQD) trained from the microarray data, the nucleosome occupancy score (NOScore) was defined and applied to splice junction regions of constitutive, cassette exon, alternative 3' and 5' splicing events in the human genome.We found an interesting relation between NOScore and RNA splicing: exon regions have higher NOScores compared with their flanking intron sequences in both constitutive and alternative splicing events, indicating the stronger nucleosome occupation potential of exon regions.In addition, NOScore valleys present at approximately 25 bp upstream of the acceptor site in all splicing events.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.

ABSTRACT
The occupancy of nucleosomes along chromosome is a key factor for gene regulation. However, except promoter regions, genome-wide properties and functions of nucleosome organization remain unclear in mammalian genomes. Using the computational model of Increment of Diversity with Quadratic Discriminant (IDQD) trained from the microarray data, the nucleosome occupancy score (NOScore) was defined and applied to splice junction regions of constitutive, cassette exon, alternative 3' and 5' splicing events in the human genome. We found an interesting relation between NOScore and RNA splicing: exon regions have higher NOScores compared with their flanking intron sequences in both constitutive and alternative splicing events, indicating the stronger nucleosome occupation potential of exon regions. In addition, NOScore valleys present at approximately 25 bp upstream of the acceptor site in all splicing events. By defining folding diversity-to-energy ratio to describe RNA structural flexibility, we demonstrated that primary RNA transcripts from nucleosome occupancy regions are relatively rigid and those from nucleosome depleted regions are relatively flexible. The negative correlation between nucleosome occupation/depletion of DNA sequence and structural flexibility/rigidity of its primary transcript around splice junctions may provide clues to the deeper understanding of the unexpected role for nucleosome organization in the regulation of RNA splicing.

Show MeSH
Related in: MedlinePlus