Raha, D., Hong, M. & Snyder, M. ChIP‐Seq: a method for global identification of regulatory elements in the genome. Curr. Protoc. Mol. Biol. https://doi.org/10.1002/0471142727.mb2119s91 (2010).
Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6, e21856 (2017).
Google Scholar
Song, L. & Crawford, G. E. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harbor Protoc. https://doi.org/10.1101/pdb.prot5384 (2010).
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).
Google Scholar
Reiter, F., Wienerroither, S. & Stark, A. Combinatorial function of transcription factors and cofactors. Curr. Opin. Genet. Dev. 43, 73–81 (2017).
Google Scholar
Morgunova, E. & Taipale, J. Structural perspective of cooperative transcription factor binding. Curr. Opin. Struct. Biol. 47, 1–8 (2017).
Google Scholar
Ibarra, I. L. et al. Mechanistic insights into transcription factor cooperativity and its impact on protein–phenotype interactions. Nat. Commun. 11, 124 (2020).
Google Scholar
Sönmezer, C. et al. Molecular co-occupancy identifies transcription factor binding cooperativity in vivo. Mol. Cell 81, 255–267.e6 (2021).
Google Scholar
Kelly, T. K. et al. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 22, 2497–2506 (2012).
Google Scholar
Krebs, A. R. et al. Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters. Mol. Cell 67, 411–422.e4 (2017).
Google Scholar
Nabilsi, N. H. et al. Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma. Genome Res. 24, 329–339 (2014).
Google Scholar
Stergachis, A. B., Debo, B. M., Haugen, E., Churchman, L. S. & Stamatoyannopoulos, J. A. Single-molecule regulatory architectures captured by chromatin fiber sequencing. Science 368, 1449–1454 (2020).
Google Scholar
Lee, I. et al. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat. Methods 17, 1191–1199 (2020).
Google Scholar
Abdulhay, N. J. et al. Massively multiplex single-molecule oligonucleosome footprinting. eLife 9, e59404 (2020).
Google Scholar
Shipony, Z. et al. Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nat. Methods 17, 319–327 (2020).
Google Scholar
Krebs, A. R. Studying transcription factor function in the genome at molecular resolution. Trends Genet. https://doi.org/10.1016/j.tig.2021.03.008 (2021)
Minnoye, L. et al. Chromatin accessibility profiling methods. Nat. Rev. Methods Prim. 1, 10 (2021).
Google Scholar
Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).
Google Scholar
Cusanovich, D. A. et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910–914 (2015).
Google Scholar
Levo, M. et al. Systematic investigation of transcription factor activity in the context of chromatin using massively parallel binding and expression assays. Mol. Cell 65, 604–617.e6 (2017).
Google Scholar
Oberbeckmann, E. et al. Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome. Genome Res. 29, 1996–2009 (2019).
Google Scholar
Untergasser, A. et al. Primer3—new capabilities and interfaces. Nucleic Acids Res. 40, e115–e115 (2012).
Google Scholar
Gaidatzis, D., Lerch, A., Hahne, F. & Stadler, M. B. QuasR: quantification and annotation of short reads in R. Bioinformatics 31, 1130–1132 (2015).
Google Scholar
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Google Scholar
Barzaghi G, K. A. SingleMoleculeFootprinting. Analysis tools for Single Molecule Footprinting (SMF) data. R package version 1.0.0. (Bioconductor, 2021). https://doi.org/10.18129/B9.bioc.SingleMoleculeFootprinting
Fornes, O. et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. https://doi.org/10.1093/nar/gkz1001 (2019)
Puig, R. R. et al. UniBind: maps of high-confidence direct TF-DNA interactions across nine species. BMC Genomics https://doi.org/10.1186/s12864-021-07760-6 (2021).
Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011).
Google Scholar
Domcke, S. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature 528, 575–579 (2015).
Google Scholar
Nicola, N. A. & Babon, J. J. Leukemia inhibitory factor (LIF). Cytokine Growth Factor Rev. 26, 533–544 (2015).
Google Scholar
GuidoBarzaghi, S. M. & KrebsLab. Krebslabrep/SingleMoleculeFootprinting: SingleMoleculeFootprinting. Zenodo https://doi.org/10.5281/ZENODO.4767134 (2021).

