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Genome-wide footprinting: ready for prime time?

Nature Methods volume 13, pages 222–228 (2016)Cite this article

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Abstract

High-throughput sequencing technologies have allowed many gene locus–level molecular biology assays to become genome-wide profiling methods. DNA-cleaving enzymes such as DNase I have been used to probe accessible chromatin. The accessible regions contain functional regulatory sites, including promoters, insulators and enhancers. Deep sequencing of DNase-seq libraries and computational analysis of the cut profiles have been used to infer protein occupancy in the genome at the nucleotide level, a method introduced as 'digital genomic footprinting'. The approach has been proposed as an attractive alternative to the analysis of transcription factors (TFs) by chromatin immunoprecipitation followed by sequencing (ChIP-seq), and in theory it should overcome antibody issues, poor resolution and batch effects. Recent reports point to limitations of the DNase-based genomic footprinting approach and call into question the scope of detectable protein occupancy, especially for TFs with short-lived chromatin binding. The genomics community is grappling with issues concerning the utility of genomic footprinting and is reassessing the proposed approaches in terms of robust deliverables. Here we summarize the consensus as well as different views emerging from recent reports, and we describe the remaining issues and hurdles for genomic footprinting.

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Figure 1: DHSs versus TF footprints.
Figure 2: Comparison of observed and DNA-intrinsic cut profiles averaged over motif elements bound by TFs.
Figure 3: DNase sequence-bias-corrected profiles showing the correlation between footprint depth and TF binding residence time in vivo.
Figure 4: The difficulty of assigning TFs on the basis of motif matches.

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Acknowledgements

Computationally intensive tasks were performed using the US National Institutes of Health (NIH) Biowulf cluster, a GNU-Linux parallel processing system. We thank the NIH Helix systems staff for the management of this system. This work was supported by the Intramural Research Program of the NIH, National Cancer Institute.

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Author notes

  1. Myong-Hee Sung

    Present address: Present address: Transcription Systems Dynamics and Biology Unit, Laboratory of Molecular Biology and Immunology, National Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA.,

  2. Myong-Hee Sung and Songjoon Baek: These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA

    Myong-Hee Sung, Songjoon Baek & Gordon L Hager

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Contributions

M.-H.S. and G.L.H. conceived the project. S.B. and M.-H.S. performed the analysis. M.-H.S. and G.L.H. wrote the manuscript.

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Correspondence to Myong-Hee Sung or Gordon L Hager.

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Sung, MH., Baek, S. & Hager, G. Genome-wide footprinting: ready for prime time?. Nat Methods 13, 222–228 (2016). https://doi.org/10.1038/nmeth.3766

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