% \bibitem{Nabilsi2014}Nabilsi NH, Deleyrolle LP, Darst RP, Riva A, Reynolds BA, Kladde MP. 2014. Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma. \textit{Genome Res} \textbf{24}(2):329--339. % doi: 10.1101/gr.161737.113. %  MAPit-patch
% \bibitem{Feng2010}Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE. 2010. Conservation and divergence of methylation patterning in plants and animals. \textit{Proc Natl Acad Sci U S A} \textbf{107}(19):8689--8694. % doi: 10.1073/pnas.1002720107.
% \bibitem{Zemach2010}Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation.  \textit{Science} \textbf{328}(5980):916--919. % doi: 10.1126/science.1186366.
% \bibitem{Lister2008}Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in \textit{Arabidopsis}. \textit{Cell} \textbf{133}(3):523--536. % doi: 10.1016/j.cell.2008.03.029.
% \bibitem{Fu2015}Fu Y, Luo GZ, Chen K, Deng X, Yu M, Han D, Hao Z, Liu J, Lu X, Dor\'e LC, Weng X, Ji Q, Mets L, He C. 2015. N$^6$-methyldeoxyadenosine marks active transcription start sites in \textit{Chlamydomonas}. \textit{Cell} \textbf{161}(4):879--892. % doi: 10.1016/j.cell.2015.04.010. 
% \bibitem{Wang2017}Wang Y, Chen X, Sheng Y, Liu Y, Gao S. 2017. N$^6$-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in \textit{Tetrahymena}. \textit{Nucleic Acids Res} \textbf{45}(20):11594--11606. % doi: 10.1093/nar/gkx883.
% \bibitem{Luo2018}Luo GZ, Hao Z, Luo L, Shen M, Sparvoli D, Zheng Y, Zhang Z, Weng X, Chen K, Cui Q, Turkewitz AP, He C. 2018. N$^6$-methyldeoxyadenosine directs nucleosome positioning in \textit{Tetrahymena} DNA. \textit{Genome Biol} \textbf{19}(1):200. % doi: 10.1186/s13059-018-1573-3.
% \bibitem{Timinskas1995}Timinskas A, Butkus V, Janulaitis A. 1995. Sequence motifs characteristic for DNA [cytosine-N4] and DNA [adenine-N6] methyltransferases. Classification of all DNA methyltransferases. \textit{Gene} \textbf{157}(1--2):3--11.
% \bibitem{Salter2016}Salter JD, Bennett RP, Smith HC. 2016. The APOBEC Protein Family: United by Structure, Divergent in Function. \textit{Trends Biochem Sci} \textbf{41}(7):578--594. % doi: 10.1016/j.tibs.2016.05.001. 
% \bibitem{Kawasaki2017}Kawasaki F, Beraldi D, Hardisty RE, McInroy GR, van Delft P, Balasubramanian S. 2017. Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite \textit{Leishmania}. \textit{Genome Biol} \textbf{18}(1):23. % doi: 10.1186/s13059-017-1150-1.



\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}(2):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}(7414):75-82.

\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}(7561):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}(6237):910--914. % doi: 10.1126/science.aab1601. Epub 2015 May 7.

\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}(1):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}(1):153--170. % doi: 10.1038/s41596-018-0087-5.

\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}(12):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}(3):411--422.e4. % doi: 10.1016/j.molcel.2017.06.027. 

\bibitem{EMSeq2019}Vaisvila R, Ponnaluri VKC, Sun Z, et al. (2019) EM-seq: Detection of DNA Methylation at Single Base Resolution from Picograms of DNA. \textit{bioRxiv} 2019.12.20.884692 % doi: https://doi.org/10.1101/2019.12.20.884692

\bibitem{Simpson2017}Simpson JT, Workman RE, Zuzarte PC, et al. (2017) Detecting DNA cytosine methylation using nanopore sequencing. \textit{Nat Methods} \textbf{14}, 407--410. %  doi: 10.1038/nmeth.4184. 

\bibitem{Rand2017}Rand AC, Jain M, Eizenga JM, et al. (2017) Mapping DNA methylation with high-throughput nanopore sequencing. \textit{Nat Methods} \textbf{14}, 411--413. % doi: 10.1038/nmeth.4189. 

\bibitem{Shipony2018}Shipony Z, Marinov GK, Swaffer MP, et al. (2020) Long-range single-molecule mapping of chromatin accessibility in eukaryotes. \textit{Nat Methods} \textbf{17}, 319--327. % doi: 10.1038/s41592-019-0730-2. 

\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. 

\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{Schones2008}Schones DE, Cui K, Cuddapah S, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. \textit{Cell} \textbf{132}, 887--898. % doi: 10.1016/j.cell.2008.02.022.

\bibitem{Hesselberth2009}Hesselberth JR, Chen X, Zhang Z, et al. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. \textit{Nat Methods} \textbf{6}(4):283--289. % doi: 10.1038/nmeth.1313. 

\bibitem{Neph2012b}Neph S, Vierstra J, Stergachis AB, et al. (2012) An expansive human regulatory lexicon encoded in transcription factor footprints. \textit{Nature} \textbf{489}, 83--90. % doi: 10.1038/nature11212.

\bibitem{Murray2018}Murray IA, Morgan RD, Luyten Y, et al. (2018) The non-specific adenine DNA methyltransferase M.EcoGII. \textit{Nucleic Acids Res} \textbf{46}, 840--848. % doi: 10.1093/nar/gkx1191.

\bibitem{ENCODE2012}ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. \textit{Nature} \textbf{489}, 57--74.

\bibitem{Kuhn2013}Kuhn RM, Haussler D, Kent WJ (2013) The UCSC genome browser and associated tools. \textit{Brief Bioinform} \textbf{14}, 144--161.

\bibitem{Kent2010}Kent WJ, Zweig AS, Barber G, et al. (2010) BigWig and BigBed: enabling browsing of large distributed datasets. \textit{Bioinformatics} \textbf{26}, 2204--2207.

\bibitem{Li2016}Li H. 2016. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. \textit{Bioinformatics} \textbf{32}(14):2103--2110. % doi: 10.1093/bioinformatics/btw152. 

\bibitem{Stoiber2017}Stoiber MH, Quick J, Egan R, Lee JE, Celniker SE, Neely R, Loman N, Pennacchio L, Brown JB. 2017. De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. \textit{bioRxiv} 094672 % doi: https://doi.org/10.1101/094672

\bibitem{Krueger2011}Krueger F, Andrews SR. 2011. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. \textit{Bioinformatics} \textbf{27}(11):1571--1572. % doi: 10.1093/bioinformatics/btr167. 

\bibitem{Brogaard2012}Brogaard K, Xi L, Wang JP, Widom J. 2012. A map of nucleosome positions in yeast at base-pair resolution. \textit{Nature} \textbf{486}(7404):496--501. % doi: 10.1038/nature11142. 

\bibitem{Fu2008}Fu Y, Sinha M, Peterson CL, Weng Z. 2008. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. \textit{PLoS Genet} \textbf{4}(7):e1000138. % doi: 10.1371/journal.pgen.1000138.

\bibitem{Conconi1989}Conconi A, Widmer RM, Koller T, Sogo JM. 1989. Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. \textit{Cell} \textbf{57}(5):753--761.

\bibitem{Goetze2010}Goetze H, Wittner M, Hamperl S, Hondele M, Merz K, Stoeckl U, Griesenbeck J. 2010. Alternative chromatin structures of the 35S rRNA genes in \textit{Saccharomyces cerevisiae} provide a molecular basis for the selective recruitment of RNA polymerases I and II. \textit{Mol Cell Biol} \textbf{30}(8):2028--2045. % doi: 10.1128/MCB.01512-09. 

\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.