\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{Keen1981}Keene MA, Corces V, Lowenhaupt K, Elgin SC. 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}(1):143--146.

\bibitem{McGhee1981}McGhee JD, Wood WI, Dolan M, Engel JD, Felsenfeld G. 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}(1 Pt 2):45--55.

\bibitem{Dorschner2004}Dorschner MO, Hawrylycz M, Humbert R, Wallace JC, Shafer A, Kawamoto J, Mack J, Hall R, Goldy J, Sabo PJ, Kohli A, Li Q, McArthur M, Stamatoyannopoulos JA. 2004. High-throughput localization of functional elements by quantitative chromatin profiling. \textit{Nat Methods} \textbf{1}(3):219--225.

\bibitem{Sabo2006}Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, Dorschner MO, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA. 2006. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. \textit{Nat Methods} \textbf{3}(7):511--518.

\bibitem{Boyle2008}Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. 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{Hesselberth2009}Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA. 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{Buenrostro2013}Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 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}(12):1213--1218. % doi: 10.1038/nmeth.2688. 

\bibitem{Schones2008}Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. \textit{Cell} \textbf{132}(5):887--898. % doi: 10.1016/j.cell.2008.02.022.

\bibitem{Kelly2012}Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. 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{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{Krebs2017}Krebs AR, Imanci D, Hoerner L, Gaidatzis D, Burger L, Sch\"ubeler D. 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{Murray2018}Murray IA, Morgan RD, Luyten Y, Fomenkov A, Corr\^ea IR Jr, Dai N, Allaw MB, Zhang X, Cheng X, Roberts RJ. 2018. The non-specific adenine DNA methyltransferase M.EcoGII. \textit{Nucleic Acids Res} \textbf{46}(2):840--848. % doi: 10.1093/nar/gkx1191.

\bibitem{Simpson2017}Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W. 2017. Detecting DNA cytosine methylation using nanopore sequencing. \textit{Nat Methods} \textbf{14}(4):407--410. %  doi: 10.1038/nmeth.4184. 

\bibitem{Rand2017}Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, Paten B. 2017. Mapping DNA methylation with high-throughput nanopore sequencing. \textit{Nat Methods} \textbf{14}(4):411--413. % doi: 10.1038/nmeth.4189. 

\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{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{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{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{Cole2011}Cole HA, Howard BH, Clark DJ. 2011. The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere. \textit{Proc Natl Acad Sci U S A} \textbf{108}(31):12687--12692. % doi: 10.1073/pnas.1104978108. 

\bibitem{Henikoff2014}Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang JP, Henikoff JG. 2014. The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. \textit{Elife} \textbf{3}:e01861. % doi: 10.7554/eLife.01861.

\bibitem{Merz2008}Merz K, Hondele M, Goetze H, Gmelch K, Stoeckl U, Griesenbeck J. 2008. Actively transcribed rRNA genes in \textit{S. cerevisiae} are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules. \textit{Genes Dev} \textbf{22}(9):1190--1204. % doi: 10.1101/gad.466908.

\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{French2003}French SL, Osheim YN, Cioci F, Nomura M, Beyer AL. 2003. In exponentially growing \textit{Saccharomyces cerevisiae} cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. \textit{Mol Cell Biol} \textbf{23}(5):1558--1568.

\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{Panday2016}Panday A, Grove A. 2016. Yeast HMO1: Linker Histone Reinvented. \textit{Microbiol Mol Biol Rev} \textbf{81}(1). pii: e00037--16.

\bibitem{Jones2007}Jones HS, Kawauchi J, Braglia P, Alen CM, Kent NA, Proudfoot NJ. 2007. RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA. \textit{Nat Struct Mol Biol} \textbf{14}(2):123--130. 

\bibitem{Huang2003}Huang J, Moazed D. 2003. Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing. \textit{Genes Dev} \textbf{17}(17):2162--2176. 

\bibitem{Zhu2018}Zhu F, Farnung L, Kaasinen E, Sahu B, Yin Y, Wei B, Dodonova SO, Nitta KR, Morgunova E, Taipale M, Cramer P, Taipale J. 2018. The interaction landscape between transcription factors and the nucleosome. \textit{Nature} \textbf{562}(7725):76--81. % doi: 10.1038/s41586-018-0549-5. 

\bibitem{OSullivan2004}O'Sullivan JM, Tan-Wong SM, Morillon A, Lee B, Coles J, Mellor J, Proudfoot NJ. 2004. Gene loops juxtapose promoters and terminators in yeast. \textit{Nat Genet} \textbf{36}(9):1014--1018.

\bibitem{Tan2012}Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ. 2012. Gene loops enhance transcriptional directionality. \textit{Science} \textbf{338}(6107):671--675. % doi: 10.1126/science.1224350. 

\bibitem{Hsieh2015}Hsieh TH, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. 2015. Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. \textit{Cell} \textbf{162}(1):108--119. % doi: 10.1016/j.cell.2015.05.048. 

\bibitem{Weiner2015}Weiner A, Hsieh TH, Appleboim A, Chen HV, Rahat A, Amit I, Rando OJ, Friedman N. 2015. High-resolution chromatin dynamics during a yeast stress response. \textit{Mol Cell} \textbf{58}(2):371--386. % doi: 10.1016/j.molcel.2015.02.002.

\bibitem{Morano2012}Morano KA, Grant CM, Moye-Rowley WS. 2012. The response to heat shock and oxidative stress in \textit{Saccharomyces cerevisiae}. \textit{Genetics} \textbf{190}(4):1157--1195. % doi: 10.1534/genetics.111.128033. 

\bibitem{Gabrieli2018}Gabrieli T, Sharim H, Fridman D, Arbib N, Michaeli Y, Ebenstein Y. 2018. Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH). \textit{Nucleic Acids Res} \textbf{46}(14):e87. % doi: 10.1093/nar/gky411.

\bibitem{TOPSeq}Sta\v{s}evskij Z, Gibas P, Gordevi\v{c}ius J, Kriukien\.e E, Klima\v{s}auskas S. 2017. Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling. \textit{Mol Cell} \textbf{65}(3):554--564.e6. % doi: 10.1016/j.molcel.2016.12.012. 

\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{Schep2015}Schep AN, Buenrostro JD, Denny SK, Schwartz K, Sherlock G, Greenleaf WJ. 2015. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. \textit{Genome Res} \textbf{25}(11):1757--1770. % doi: 10.1101/gr.192294.115.

\bibitem{Miura2012}Miura F, Enomoto Y, Dairiki R, Ito T. 2012. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. \textit{Nucleic Acids Res} \textbf{40}(17):e136. 

\bibitem{Bismark2011}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{Corces2017}Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY. 2017. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. \textit{Nat Methods} \textbf{14}(10):959--962. % doi: 10.1038/nmeth.4396. 

\bibitem{Bowtie2009}Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. \textit{Genome Biol} \textbf{10}(3):R25. % doi: 10.1186/gb-2009-10-3-r25. 

\bibitem{Hu2015}Hu B, Petela N, Kurze A, Chan KL, Chapard C, Nasmyth K. 2015. Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq. \textit{Nucleic Acids Res} \textbf{43}(20):e132. % doi: 10.1093/nar/gkv670.

\bibitem{Feng2012}Feng J, Liu T, Qin B, Zhang Y, Liu XS. 2012. Identifying ChIP-seq enrichment using MACS. \textit{Nat Protoc} \textbf{7}(9):1728--1740.

\bibitem{Trapnell2012}Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. \textit{Nat Protoc} \textbf{7}(3):562--578.

\bibitem{Langmead2009}Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. \textit{Genome Biol} \textbf{10}(3):R25. % doi: 10.1186/gb-2009-10-3-r25. 

\bibitem{Grant2011}Grant CE, Bailey TL, Noble WS. 2011. FIMO: scanning for occurrences of a given motif. \textit{Bioinformatics} \textbf{27}(7):1017--1018. % doi: 10.1093/bioinformatics/btr064.

\bibitem{Bailey2009}Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. 2009. MEME SUITE: tools for motif discovery and searching. \textit{Nucleic Acids Res} \textbf{37}(Web Server issue):W202--208. % doi: 10.1093/nar/gkp335.

\bibitem{Weirauch2014}Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR. 2014. Determination and inference of eukaryotic transcription factor sequence specificity. \textit{Cell} \textbf{158}(6):1431--1443. % doi: 10.1016/j.cell.2014.08.009.

\bibitem{Pelechano2013}Pelechano V, Wei W, Steinmetz LM. 2013. Extensive transcriptional heterogeneity revealed by isoform profiling. \textit{Nature} \textbf{497}(7447):127--131. % doi: 10.1038/nature12121. 

\bibitem{Ramachandran2015}Ramachandran S, Zentner GE, Henikoff S. 2015. Asymmetric nucleosomes flank promoters in the budding yeast genome. \textit{Genome Res} \textbf{25}(3):381--390. % doi: 10.1101/gr.182618.114. 

\bibitem{Chereji2018}Chereji RV, Ramachandran S, Bryson TD, Henikoff S. 2018. Precise genome-wide mapping of single nucleosomes and linkers in vivo. \textit{Genome Biol} \textbf{19}(1):19. % doi: 10.1186/s13059-018-1398-0.

\bibitem{Liang2018}Liang Z, Shen L, Cui X, Bao S, Geng Y, Yu G, Liang F, Xie S, Lu T, Gu X, Yu H. 2018. DNA N$^6$-Adenine Methylation in \textit{Arabidopsis thaliana}. \textit{Dev Cell} \textbf{45}(3):406--416.e3. % doi: 10.1016/j.devcel.2018.03.012. 

\bibitem{Greer2015}Greer EL, Blanco MA, Gu L, Sendinc E, Liu J, Aristiz\'abal-Corrales D, Hsu CH, Aravind L, He C, Shi Y. 2015. DNA Methylation on N6-Adenine in \textit{C. elegans}. \textit{Cell} \textbf{161}(4):868--878. % doi: 10.1016/j.cell.2015.04.005. 

\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.
