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GBshape: a genome browser database for DNA shape annotations.

Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R - Nucleic Acids Res. (2014)

Bottom Line: Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif.Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families.As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

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Variation in Roll (blue), HelT (green) and ProT (red) on average in nucleosome sequences from the (A) Caenorhabditis elegans, (B) Drosophila melanogaster and (C) human genomes. Numbering of the nucleotide position starts with −1 and 1 for the central two base pairs, respectively.
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Figure 4: Variation in Roll (blue), HelT (green) and ProT (red) on average in nucleosome sequences from the (A) Caenorhabditis elegans, (B) Drosophila melanogaster and (C) human genomes. Numbering of the nucleotide position starts with −1 and 1 for the central two base pairs, respectively.

Mentions: We have now used GBshape to predict MGW and compare this structural property to the ORChID2 pattern for these massive lists of 3.6 million from Caenorhabditis elegans, 3.8 million nucleosome-bound sequences from Drosophila melanogaster and 13.1 million from the human genome (Figure 3). The strong correlation between MGW and ORChID2 for all three organisms served as a validation of GBshape due to the independent approaches used to generate these predictions. Whereas the 10-bp periodicity was shared between human, fly and worm, details of the DNA shape profiles of nucleosomal DNA varied across species due to the different nucleotide compositions of these genomes. Analysis of the other DNA shape features Roll, HelT and ProT further confirmed the shared 10-bp periodicity as well as distinctions in DNA shape between nucleosome-bound sequences in these genomes (Figure 4). The maxima and minima of the MGW, Roll and ProT patterns overlapped, whereas the troughs in the HelT patterns matched the peaks in the other parameters, indicating a local helix unwinding at positions where a more positive Roll locally widens the minor groove.


GBshape: a genome browser database for DNA shape annotations.

Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R - Nucleic Acids Res. (2014)

Variation in Roll (blue), HelT (green) and ProT (red) on average in nucleosome sequences from the (A) Caenorhabditis elegans, (B) Drosophila melanogaster and (C) human genomes. Numbering of the nucleotide position starts with −1 and 1 for the central two base pairs, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384032&req=5

Figure 4: Variation in Roll (blue), HelT (green) and ProT (red) on average in nucleosome sequences from the (A) Caenorhabditis elegans, (B) Drosophila melanogaster and (C) human genomes. Numbering of the nucleotide position starts with −1 and 1 for the central two base pairs, respectively.
Mentions: We have now used GBshape to predict MGW and compare this structural property to the ORChID2 pattern for these massive lists of 3.6 million from Caenorhabditis elegans, 3.8 million nucleosome-bound sequences from Drosophila melanogaster and 13.1 million from the human genome (Figure 3). The strong correlation between MGW and ORChID2 for all three organisms served as a validation of GBshape due to the independent approaches used to generate these predictions. Whereas the 10-bp periodicity was shared between human, fly and worm, details of the DNA shape profiles of nucleosomal DNA varied across species due to the different nucleotide compositions of these genomes. Analysis of the other DNA shape features Roll, HelT and ProT further confirmed the shared 10-bp periodicity as well as distinctions in DNA shape between nucleosome-bound sequences in these genomes (Figure 4). The maxima and minima of the MGW, Roll and ProT patterns overlapped, whereas the troughs in the HelT patterns matched the peaks in the other parameters, indicating a local helix unwinding at positions where a more positive Roll locally widens the minor groove.

Bottom Line: Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif.Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families.As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

Show MeSH
Related in: MedlinePlus