\bibitem{Luger1997}Luger K, M\"ader AW, Richmond RK, et al. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. \textit{Nature} 389, 251--260.

\bibitem{Wu1980}Wu C. (1980) The 5$^{\prime}$ ends of \textit{Drosophila} heat shock genes in chromatin are hypersensitive to DNase I. \textit{Nature} \textbf{286}(5776):854--860.

\bibitem{Keene1981}Keene MA, Corces V, Lowenhaupt K, et al. (1981) DNase I hypersensitive sites in Drosophila chromatin occur at the 5$^{\prime}$ ends of regions of transcription. \textit{Proc Natl Acad Sci U S A} \textbf{78}, 143--146.

\bibitem{McGhe1981}McGhee JD, Wood WI, Dolan M, et al. (1981) A 200 base pair region at the 5$^{\prime}$ end of the chicken adult $\beta$-globin gene is accessible to nuclease digestion. \textit{Cell} \textbf{27}, 45--55.

\bibitem{Dorschner2004}Dorschner MO, Hawrylycz M, Humbert R, et al. (2004) High-throughput localization of functional elements by quantitative chromatin profiling. \textit{Nat Methods} \textbf{1}, 219--225.

\bibitem{Sabo2004}Sabo PJ, Humbert R, Hawrylycz M, et al. (2004) Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. \textit{Proc Natl Acad Sci U S A} \textbf{101}, 4537-4542.

\bibitem{Sabo2006}Sabo PJ, Kuehn MS, Thurman R, et al. (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. \textit{Nat Methods} \textbf{3}, 511--518.

\bibitem{Crawford2006}Crawford GE, Holt IE, Whittle J, et al. (2006) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). \textit{Genome Res} \textbf{16}, 123--131. 

\bibitem{Boyle2008}Boyle AP, Davis S, Shulha HP, et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. \textit{Cell} \textbf{132}, 311--322. % doi: 10.1016/j.cell.2007.12.014.

\bibitem{Thurman2012}Thurman RE, Rynes E, Humbert R, et al. (2012) The accessible chromatin landscape of the human genome. \textit{Nature} \textbf{489}, 75-82.

\bibitem{Kelly2012}Kelly TK, Liu Y, Lay FD, et al. (2012) Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. \textit{Genome Res} \textbf{22}, 2497--2506. % doi: 10.1101/gr.143008.112. % NOME-seq

\bibitem{Krebs2017}Krebs AR, Imanci D, Hoerner L, Gaidatzis D, et al. (2017) Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters. \textit{Mol Cell} \textbf{67}, 411--422.e4. % doi: 10.1016/j.molcel.2017.06.027. 

\bibitem{Shipony2018}Shipony Z, Marinov GK, Swaffer MP, et al. (2018) Long-range single-molecule mapping of chromatin accessibility in eukaryotes. \textit{bioRxiv} 504662.

\bibitem{Wang2019}Wang Y, Wang A, Liu Z, et al. (2019) Single-molecule long-read sequencing reveals the chromatin basis of gene expression. \textit{Genome Res} \textbf{29}, 1329--1342. % doi: 10.1101/gr.251116.119.  % MeSMLR-seq

\bibitem{Aughey2018}Aughey GN, Estacio Gomez A, Thomson J, et al. (2018) CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo. \textit{Elife} \textbf{7}, pii: e32341. % doi: 10.7554/eLife.32341.

\bibitem{Chereji2019}Chereji RV, Eriksson PR, Ocampo J, Clark DJ. (2019) DNA accessibility is not the primary determinant of chromatin-mediated gene regulation \textit{bioRxiv} 639971 % doi: https://doi.org/10.1101/639971

\bibitem{Ponnaluri2017}Ponnaluri VKC, Zhang G, Est\'eve PO, et al. (2017) NicE-seq: high resolution open chromatin profiling. \textit{Genome Biol} \textbf{18}(1):122. % doi: 10.1186/s13059-017-1247-6.

\bibitem{Umeyama2017}Umeyama T, Ito T. (2017) DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers. \textit{Cell Rep} \textbf{21}, 289--300. % doi: 10.1016/j.celrep.2017.09.035.

\bibitem{Timms2019}Timms RT, Tchasovnikarova IA, Lehner PJ. (2019) Differential viral accessibility (DIVA) identifies alterations in chromatin architecture through large-scale mapping of lentiviral integration sites. \textit{Nat Protoc} \textbf{14}, 153--170. % doi: 10.1038/s41596-018-0087-5.

\bibitem{Buenrostro2013}Buenrostro JD, Giresi PG, Zaba LC, et al. (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. \textit{Nat Methods} \textbf{10}, 1213--1218. % doi: 10.1038/nmeth.2688. 

\bibitem{Buenrostro2015}Buenrostro JD, Wu B, Litzenburger UM, et al. (2015) Single-cell chromatin accessibility reveals principles of regulatory variation. \textit{Nature} \textbf{523}, 486--490. % doi: 10.1038/nature14590. Epub 2015 Jun 17.

\bibitem{Cusanovich2015}Cusanovich DA, Daza R, Adey A, et al. (2015) Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. \textit{Science} \textbf{348}, 910--914. % doi: 10.1126/science.aab1601. Epub 2015 May 7.

\bibitem{Corces2017}Corces MR, Trevino AE, Hamilton EG, et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. \textit{Nat Methods} \textbf{14}, 959--962. % doi: 10.1038/nmeth.4396. 

\bibitem{Corces2016}Corces MR, Buenrostro JD, Wu B, et al. (2016) Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. \textit{Nat Genet} \textbf{48}, 1193--1203. % doi: 10.1038/ng.3646. 

\bibitem{Picelli2014}Picelli S, Bj\"orklund AK, Reinius B, et al. (2014) Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. \textit{Genome Res} \textbf{24}, 2033--2040. % doi: 10.1101/gr.177881.114. Epub 2014 Jul 30.

\bibitem{Lu2017}Lu Z, Hofmeister BT, Vollmers C, et al. (2017) Combining ATAC-seq with nuclei sorting for discovery of \textit{cis}-regulatory regions in plant genomes. \textit{Nucleic Acids Res} \textbf{45}, e41. % doi: 10.1093/nar/gkw1179.

\bibitem{Maher2018}Maher KA, Bajic M, Kajala K, et al. (2018) Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules. \textit{Plant Cell} \textbf{30}, 15--36. % doi: 10.1105/tpc.17.00581. 

\bibitem{Bajic2018}Bajic M, Maher KA, Deal RB. (2018) Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq. \textit{Methods Mol Biol} \textbf{1675}, 183--201. % doi: 10.1007/978-1-4939-7318-7_12.

\bibitem{Deal2010}Deal RB, Henikoff S. (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. \textit{Dev Cell} 18, 1030--1040. % doi: 10.1016/j.devcel.2010.05.013.

\bibitem{Daugherty2017}Daugherty AC, Yeo RW, Buenrostro JD, et al. (2017) Chromatin accessibility dynamics reveal novel functional enhancers in \textit{C. elegans}. \textit{Genome Res} \textbf{27}, 2096-2107. % doi: 10.1101/gr.226233.117. 

\bibitem{Schep2015}Schep AN, Buenrostro JD, Denny SK, et al. (2015) Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. \textit{Genome Res} \textbf{25}, 1757--1770. % doi: 10.1101/gr.192294.115.

\bibitem{Cusanovich2018}Cusanovich DA, Reddington JP, Garfield DA, et al. (2018) The \textit{cis}-regulatory dynamics of embryonic development at single-cell resolution. \textit{Nature} \textbf{555}, 538--542. % doi: 10.1038/nature25981. 

\bibitem{Cao2018}Cao J, Cusanovich DA, Ramani V, et al. (2018) Joint profiling of chromatin accessibility and gene expression in thousands of single cells. \textit{Science} 361, 1380--1385. % doi: 10.1126/science.aau0730. 

\bibitem{ENCODE2012}ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. \textit{Nature} \textbf{489}, 57--74.

