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Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.

Yardımcı GG, Frank CL, Crawford GE, Ohler U - Nucleic Acids Res. (2014)

Bottom Line: DNase-seq footprints were absent under a fraction of ChIP-seq peaks, which we show to be indicative of weaker binding, indirect TF-DNA interactions or possible ChIP artifacts.The modeling approach was also able to detect variation in the consensus motifs that TFs bind to.Finally, cell type specific footprints were detected within DNase hypersensitive sites that are present in multiple cell types, further supporting that footprints can identify changes in TF binding that are not detectable using other strategies.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology and Bioinformatics Program, Duke University, Durham, NC 27708, USA Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA.

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Scenarios relevant to identifying DNase footprints. On the right, representative examples of DNase-seq data from GM12878 cell type and ChIP-seq data for NRSF from ENCODE (34). The location of sequence motif match for the TF NRSF is indicated with a yellow box. On the left, a schematic representation of TF–DNA interaction is shown and whether a footprint is detected or not detected at the motif match. (A) A DNase footprint centered at the motif maps within a ChIP-seq peak indicating a direct binding event. (B) A motif that maps within a DHS site, but has no appreciable ChIP-seq signal, nor footprint, indicating no interaction between TF and sequence motif match. (C) Multiple sequence motif matches within a DHS site may only have a single footprint, showing that TF may be more likely to interact with one of the motif matches. (D) ChIP-seq peak with a sequence motif match that does not have a footprint suggests a possible indirect binding event.
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Figure 1: Scenarios relevant to identifying DNase footprints. On the right, representative examples of DNase-seq data from GM12878 cell type and ChIP-seq data for NRSF from ENCODE (34). The location of sequence motif match for the TF NRSF is indicated with a yellow box. On the left, a schematic representation of TF–DNA interaction is shown and whether a footprint is detected or not detected at the motif match. (A) A DNase footprint centered at the motif maps within a ChIP-seq peak indicating a direct binding event. (B) A motif that maps within a DHS site, but has no appreciable ChIP-seq signal, nor footprint, indicating no interaction between TF and sequence motif match. (C) Multiple sequence motif matches within a DHS site may only have a single footprint, showing that TF may be more likely to interact with one of the motif matches. (D) ChIP-seq peak with a sequence motif match that does not have a footprint suggests a possible indirect binding event.

Mentions: At least four different scenarios arise when searching for bona fide DNase footprints at candidate TF-binding sites, which we define as DNA sequences that match the sequence preferences of a specific TF (i.e. a sequence motif match). We provide examples of these scenarios using NRSF ChIP-seq and DNase-seq data from the GM12878 lymphoblastoid cell line (37,38). First, true positives are sequence motif matches that overlap both a DNase footprint and a ChIP-seq peak for a TF associated with the sequence motif. These are highly likely to represent direct binding sites (Figure 1A). Second, true negatives are sequence motif matches without a DNase-seq footprint that do not map in a ChIP-seq peak (Figure 1B). Third, ChIP may not have the resolution to tell apart which one of two sequence motif matches is indeed bound, but this may be resolved by the presence of a footprint (Figure 1C). Fourth, sequence motif matches that overlap ChIP-seq peaks but do not exhibit a DNase-seq footprint (Figure 1D) may represent weak or indirect binding of TFs, long-range chromatin looping (39) or simply artifacts due to false-positive ChIP-seq peak calls (40,41). Together, these scenarios illustrate the challenges of identifying footprints and the motivation behind our modeling approach.


Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.

Yardımcı GG, Frank CL, Crawford GE, Ohler U - Nucleic Acids Res. (2014)

Scenarios relevant to identifying DNase footprints. On the right, representative examples of DNase-seq data from GM12878 cell type and ChIP-seq data for NRSF from ENCODE (34). The location of sequence motif match for the TF NRSF is indicated with a yellow box. On the left, a schematic representation of TF–DNA interaction is shown and whether a footprint is detected or not detected at the motif match. (A) A DNase footprint centered at the motif maps within a ChIP-seq peak indicating a direct binding event. (B) A motif that maps within a DHS site, but has no appreciable ChIP-seq signal, nor footprint, indicating no interaction between TF and sequence motif match. (C) Multiple sequence motif matches within a DHS site may only have a single footprint, showing that TF may be more likely to interact with one of the motif matches. (D) ChIP-seq peak with a sequence motif match that does not have a footprint suggests a possible indirect binding event.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231734&req=5

Figure 1: Scenarios relevant to identifying DNase footprints. On the right, representative examples of DNase-seq data from GM12878 cell type and ChIP-seq data for NRSF from ENCODE (34). The location of sequence motif match for the TF NRSF is indicated with a yellow box. On the left, a schematic representation of TF–DNA interaction is shown and whether a footprint is detected or not detected at the motif match. (A) A DNase footprint centered at the motif maps within a ChIP-seq peak indicating a direct binding event. (B) A motif that maps within a DHS site, but has no appreciable ChIP-seq signal, nor footprint, indicating no interaction between TF and sequence motif match. (C) Multiple sequence motif matches within a DHS site may only have a single footprint, showing that TF may be more likely to interact with one of the motif matches. (D) ChIP-seq peak with a sequence motif match that does not have a footprint suggests a possible indirect binding event.
Mentions: At least four different scenarios arise when searching for bona fide DNase footprints at candidate TF-binding sites, which we define as DNA sequences that match the sequence preferences of a specific TF (i.e. a sequence motif match). We provide examples of these scenarios using NRSF ChIP-seq and DNase-seq data from the GM12878 lymphoblastoid cell line (37,38). First, true positives are sequence motif matches that overlap both a DNase footprint and a ChIP-seq peak for a TF associated with the sequence motif. These are highly likely to represent direct binding sites (Figure 1A). Second, true negatives are sequence motif matches without a DNase-seq footprint that do not map in a ChIP-seq peak (Figure 1B). Third, ChIP may not have the resolution to tell apart which one of two sequence motif matches is indeed bound, but this may be resolved by the presence of a footprint (Figure 1C). Fourth, sequence motif matches that overlap ChIP-seq peaks but do not exhibit a DNase-seq footprint (Figure 1D) may represent weak or indirect binding of TFs, long-range chromatin looping (39) or simply artifacts due to false-positive ChIP-seq peak calls (40,41). Together, these scenarios illustrate the challenges of identifying footprints and the motivation behind our modeling approach.

Bottom Line: DNase-seq footprints were absent under a fraction of ChIP-seq peaks, which we show to be indicative of weaker binding, indirect TF-DNA interactions or possible ChIP artifacts.The modeling approach was also able to detect variation in the consensus motifs that TFs bind to.Finally, cell type specific footprints were detected within DNase hypersensitive sites that are present in multiple cell types, further supporting that footprints can identify changes in TF binding that are not detectable using other strategies.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology and Bioinformatics Program, Duke University, Durham, NC 27708, USA Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA.

Show MeSH
Related in: MedlinePlus