% \bibitem{He2014}He HH, Meyer CA, Hu SS, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. 2014. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. \textit{Nat Methods} \textbf{11}(1):73--78. % doi: 10.1038/nmeth.2762. 
% \bibitem{Piper2013}Piper J, Elze MC, Cauchy P, Cockerill PN, Bonifer C, Ott S. 2013. Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data. \textit{Nucleic Acids Res} \textbf{41}(21):e201. % doi: 10.1093/nar/gkt850. 
% \bibitem{Schwessinger2017}Schwessinger R, Suciu MC, McGowan SJ, Telenius J, Taylor S, Higgs DR, Hughes JR. 2017. Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints. \textit{Genome Res} \textbf{27}(10):1730--1742. % doi: 10.1101/gr.220202.117.
% \bibitem{Orchard2020}Orchard P, Kyono Y, Hensley J, Kitzman JO, Parker SCJ. 2020. Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv. \textit{Cell Syst} \textbf{10}(3):298--306.e4
% \bibitem{Koohy2013}Koohy H, Down TA, Hubbard TJ. 2013. Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme. \textit{PLoS One} \textbf{8}(7):e69853
% \bibitem{Marsico2019}Marsico G, Chambers VS, Sahakyan AB, McCauley P, Boutell JM, Antonio MD, Balasubramanian S. 2019. Whole genome experimental maps of DNA G-quadruplexes in multiple species. \textit{Nucleic Acids Res} \textbf{47}(8):3862--3874. % G4-seq
% \bibitem{BL2019}Amemiya HM, Kundaje A, Boyle AP. 2019. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. \textit{Sci Rep} \textbf{9}(1):9354. % doi: 10.1038/s41598-019-45839-z.

\bibitem{Durand2016}Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL. 2016. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. \textit{Cell Syst} \textbf{3}(1):95--98. % doi: 10.1016/j.cels.2016.07.002.

\bibitem{Fulco2019}Fulco CP, Nasser J, Jones TR, Munson G, Bergman DT, Subramanian V, Grossman SR, Anyoha R, Doughty BR, Patwardhan TA, Nguyen TH, Kane M, Perez EM, Durand NC, Lareau CA, Stamenova EK, Aiden EL, Lander ES, Engreitz JM. 2019. Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. \textit{Nat Genet} \textbf{51}(12):1664--1669.

\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, 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{McGhe1981}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{Crawford2006}Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, Zhou D, Luo S, Vasicek TJ, Daly MJ, Wolfsberg TG, Collins FS. 2006. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). \textit{Genome Res} \textbf{16}(1):123--131. 

\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{Thurman2012}Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. 2012. The accessible chromatin landscape of the human genome. \textit{Nature} \textbf{489}(7414):75-82.

\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{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{Shipony2018}Shipony Z, Marinov GK, Swaffer MP, Sinnott-Armstrong NA, Skotheim JM, Kundaje A, Greenleaf WJ. 2020. Long-range single-molecule mapping of chromatin accessibility in eukaryotes. \textit{Nat Methods} \textbf{17}(3):319--327. % SMAC-seq

\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{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{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{Pique2011}Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. 2011. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. \textit{Genome Res} \textbf{21}(3):447--455.

\bibitem{Neph2012a}Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. 2012. Circuitry and dynamics of human transcription factor regulatory networks. \textit{Cell} \textbf{150}(6):1274--1286. % doi: 10.1016/j.cell.2012.04.040. 

\bibitem{Neph2012b}Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA. 2012. An expansive human regulatory lexicon encoded in transcription factor footprints. \textit{Nature} \textbf{489}(7414):83--90. % doi: 10.1038/nature11212.

\bibitem{Stergachis2014}Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA. 2014. Conservation of trans-acting circuitry during mammalian regulatory evolution. \textit{Nature} \textbf{515}(7527):365--370. % doi: 10.1038/nature13972.

\bibitem{Vierstra2016}Vierstra J, Stamatoyannopoulos JA. 2016. Genomic footprinting. \textit{Nat Methods} \textbf{13}(3):213--221.

\bibitem{Vierstra2020}Vierstra J, Lazar J, Sandstrom R, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Haugen E, Rynes E, Reynolds A, Nelson J, Johnson A, Frerker M, Buckley M, Kaul R, Meuleman W, Stamatoyannopoulos JA. 2020. Global reference mapping of human transcription factor footprints. \textit{Nature} \textbf{583}(7818):729-736

\bibitem{Mortazavi2008}Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. \textit{Nat Methods} \textbf{5}(7):621--628

\bibitem{Nagalakshmi2008}Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. \textit{Science} \textbf{320}(5881):1344--1349. % doi: 10.1126/science.1158441. 

\bibitem{Wilhelm2008}Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, B\"ahler J. 2008. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. \textit{Nature} \textbf{453}(7199):1239--1243. % doi: 10.1038/nature07002. 

\bibitem{Sultan2008}Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML. 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. \textit{Science} \textbf{321}(5891):956--960.

\bibitem{Henikoff2011}Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. 2011. Epigenome characterization at single base-pair resolution. \textit{Proc Natl Acad Sci U S A} \textbf{108}:18318--18323

\bibitem{Batut2013}Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR. 2013. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. \textit{Genome Res} \textbf{23}(1):169-180. 

\bibitem{Churchman2011}Churchman LS, Weissman JS. 2011. Nascent transcript sequencing visualizes transcription at nucleotide resolution. \textit{Nature} \textbf{469}(7330):368--373.

\bibitem{Core2008}Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. \textit{Science} \textbf{322}(5909):1845--1848. % doi: 10.1126/science.1162228. 

\bibitem{Core2012}Core LJ, Waterfall JJ, Gilchrist DA, Fargo DC, Kwak H, Adelman K, Lis JT. 2012. Defining the status of RNA polymerase at promoters. \textit{Cell Rep} \textbf{2}(4):1025--1035

\bibitem{Kwak2013}Kwak H, Fuda NJ, Core LJ, Lis JT. 2013. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. \textit{Science} \textbf{339}(6122):950--953. %  doi: 10.1126/science.1229386.

\bibitem{Tome2018}Tome JM, Tippens ND, Lis JT. 2018. Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers. \textit{Nat Genet} 50(11):1533-1541 % CoPRO

\bibitem{KAS}Wu T, Lyu R, You Q, He C. 2020. Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity \textit{in situ}. \textit{Nat Methods} \textbf{17}(5):515--523. % doi: 10.1038/s41592-020-0797-9. % KAS-seq

\bibitem{Bochman2012}Bochman ML, Paeschke K, Zakian VA. 2012. DNA secondary structures: stability and function of G-quadruplex structures. \textit{Nat Rev Genet} \textbf{13}(11):770--780.

\bibitem{Hayatsu1967}Hayatsu H, Ukita T. 1967. The selective degradation of pyrimidines in nucleic acids by permanganate oxidation. \textit{Biochem Biophys Res Commun} \textbf{29}(4):556--561.

\bibitem{Rubin1980}Rubin CM, Schmid CW. 1980. Pyrimidine-specific chemical reactions useful for DNA sequencing. \textit{Nucleic Acids Res} \textbf{8}(20):4613--4619.

\bibitem{Sasse-Dwight1989}Sasse-Dwight S, Gralla JD. 1989. KMnO$_4$ as a probe for \textit{lac} promoter DNA melting and mechanism \textit{in vivo}. \textit{J Biol Chem} \textbf{264}(14):8074--8081.

\bibitem{Mueller1989}Mueller PR, Wold B. 1989. In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. \textit{Science} \textbf{246}(4931):780--786

\bibitem{Kouzine2013}Kouzine F, Gupta A, Baranello L, Wojtowicz D, Ben-Aissa K, Liu J, Przytycka TM, Levens D. 2013. Transcription-dependent dynamic supercoiling is a short-range genomic force. \textit{Nat Struct Mol Biol} \textbf{20}(3):396--403.

\bibitem{Kouzine2017}Kouzine F, Wojtowicz D, Baranello L, Yamane A, Nelson S, Resch W, Kieffer-Kwon KR, Benham CJ, Casellas R, Przytycka TM, Levens D. 2017. Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. \textit{Cell Syst} \textbf{4}(3):344--356.e7.

\bibitem{ENCODE2012}ENCODE Project Consortium, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kelllis M, Khatun J, Kheradpour P, Kundaje A, Lassman T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SC, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M, Pazin MJ, Lowdon RF, Dillon LA, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elinitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guig\'o R, Hardison RC, Hubbard TJ, Kellis M, Kent WJ, Lieb JD, Margulies EH, Myers RM, Snyder M, Starnatoyannopoulos JA, Tennebaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, R\"oder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandu KS, Schaeffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guig\'o R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent WJ, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL, Giresi PG, Lee BK, Battenhouse A, Sheffield NC, Simon JM, Showers KA, Safi A, London D, Bhinge AA, Shestak C, Schaner MR, Kim SK, Zhang ZZ, Mieczkowski PA, Mieczkowska JO, Liu Z, McDaniell RM, Ni Y, Rashid NU, Kim MJ, Adar S, Zhang Z, Wang T, Winter D, Keefe D, Birney E, Iyer VR, Lieb JD, Crawford GE, Li G, Sandhu KS, Zheng M, Wang P, Luo OJ, Shahab A, Fullwood MJ, Ruan X, Ruan Y, Myers RM, Pauli F, Williams BA, Gertz J, Marinov GK, Reddy TE, Vielmetter J, Partridge EC, Trout D, Varley KE, Gasper C, Bansal A, Pepke S, Jain P, Amrhein H, Bowling KM, Anaya M, Cross MK, King B, Muratet MA, Antoshechkin I, Newberry KM, McCue K, Nesmith AS, Fisher-Aylor KI, Pusey B, DeSalvo G, Parker SL, Balasubramanian S, Davis NS, Meadows SK, Eggleston T, Gunter C, Newberry JS, Levy SE, Absher DM, Mortazavi A, Wong WH, Wold B, Blow MJ, Visel A, Pennachio LA, Elnitski L, Margulies EH, Parker SC, Petrykowska HM, Abyzov A, Aken B, Barrell D, Barson G, Berry A, Bignell A, Boychenko V, Bussotti G, Chrast J, Davidson C, Derrien T, Despacio-Reyes G, Diekhans M, Ezkurdia I, Frankish A, Gilbert J, Gonzalez JM, Griffiths E, Harte R, Hendrix DA, Howald C, Hunt T, Jungreis I, Kay M, Khurana E, Kokocinski F, Leng J, Lin MF, Loveland J, Lu Z, Manthravadi D, Mariotti M, Mudge J, Mukherjee G, Notredame C, Pei B, Rodriguez JM, Saunders G, Sboner A, Searle S, Sisu C, Snow C, Steward C, Tanzer A, Tapanan E, Tress ML, van Baren MJ, Walters N, Washieti S, Wilming L, Zadissa A, Zhengdong Z, Brent M, Haussler D, Kellis M, Valencia A, Gerstein M, Raymond A, Guig\'o R, Harrow J, Hubbard TJ, Landt SG, Frietze S, Abyzov A, Addleman N, Alexander RP, Auerbach RK, Balasubramanian S, Bettinger K, Bhardwaj N, Boyle AP, Cao AR, Cayting P, Charos A, Cheng Y, Cheng C, Eastman C, Euskirchen G, Fleming JD, Grubert F, Habegger L, Hariharan M, Harmanci A, Iyenger S, Jin VX, Karczewski KJ, Kasowski M, Lacroute P, Lam H, Larnarre-Vincent N, Leng J, Lian J, Lindahl-Allen M, Min R, Miotto B, Monahan H, Moqtaderi Z, Mu XJ, O'Geen H, Ouyang Z, Patacsil D, Pei B, Raha D, Ramirez L, Reed B, Rozowsky J, Sboner A, Shi M, Sisu C, Slifer T, Witt H, Wu L, Xu X, Yan KK, Yang X, Yip KY, Zhang Z, Struhl K, Weissman SM, Gerstein M, Farnham PJ, Snyder M, Tenebaum SA, Penalva LO, Doyle F, Karmakar S, Landt SG, Bhanvadia RR, Choudhury A, Domanus M, Ma L, Moran J, Patacsil D, Slifer T, Victorsen A, Yang X, Snyder M, White KP, Auer T, Centarin L, Eichenlaub M, Gruhl F, Heerman S, Hoeckendorf B, Inoue D, Kellner T, Kirchmaier S, Mueller C, Reinhardt R, Schertel L, Schneider S, Sinn R, Wittbrodt B, Wittbrodt J, Weng Z, Whitfield TW, Wang J, Collins PJ, Aldred SF, Trinklein ND, Partridge EC, Myers RM, Dekker J, Jain G, Lajoie BR, Sanyal A, Balasundaram G, Bates DL, Byron R, Canfield TK, Diegel MJ, Dunn D, Ebersol AK, Ebersol AK, Frum T, Garg K, Gist E, Hansen RS, Boatman L, Haugen E, Humbert R, Jain G, Johnson AK, Johnson EM, Kutyavin TM, Lajoie BR, Lee K, Lotakis D, Maurano MT, Neph SJ, Neri FV, Nguyen ED, Qu H, Reynolds AP, Roach V, Rynes E, Sabo P, Sanchez ME, Sandstrom RS, Sanyal A, Shafer AO, Stergachis AB, Thomas S, Thurman RE, Vernot B, Vierstra J, Vong S, Wang H, Weaver MA, Yan Y, Zhang M, Akey JA, Bender M, Dorschner MO, Groudine M, MacCoss MJ, Navas P, Stamatoyannopoulos G, Kaul R, Dekker J, Stamatoyannopoulos JA, Dunham I, Beal K, Brazma A, Flicek P, Herrero J, Johnson N, Keefe D, Lukk M, Luscombe NM, Sobral D, Vaquerizas JM, Wilder SP, Batzoglou S, Sidow A, Hussami N, Kyriazopoulou-Panagiotopoulou S, Libbrecht MW, Schaub MA, Kundaje A, Hardison RC, Miller W, Giardine B, Harris RS, Wu W, Bickel PJ, Banfai B, Boley NP, Brown JB, Huang H, Li Q, Li JJ, Noble WS, Bilmes JA, Buske OJ, Hoffman MM, Sahu AO, Kharchenko PV, Park PJ, Baker D, Taylor J, Weng Z, Iyer S, Dong X, Greven M, Lin X, Wang J, Xi HS, Zhuang J, Gerstein M, Alexander RP, Balasubramanian S, Cheng C, Harmanci A, Lochovsky L, Min R, Mu XJ, Rozowsky J, Yan KK, Yip KY, Birney E. 2012. An integrated encyclopedia of DNA elements in the human genome. \textit{Nature} \textbf{489}(7414):57--74.

\bibitem{ENCODE2020}ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, L\'ecuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guig\'o R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. 2020. Expanded encyclopaedias of DNA elements in the human and mouse genomes. \textit{Nature} \textbf{583}(7818):699--710.

\bibitem{Marinov2014}Marinov GK, Wang YE, Chan D, Wold BJ. 2014. Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors. \textit{PLoS One} \textbf{9}(1):e84713. 

\bibitem{Shadel1997}Shadel GS, Clayton DA. 1997. Mitochondrial DNA maintenance in vertebrates. \textit{Annu Rev Biochem} \textbf{66}:409--435.

\bibitem{Cantatore1980} Cantatore P, Attardi G. 1980. Mapping of nascent light and heavy strand transcripts on the physical map of HeLa cell mitochondrial DNA. \textit{Nucleic Acids Res} \textbf{8}(12):2605--2625.

\bibitem{Montoya1982} Montoya J, Christianson T, Levens D, Rabinowitz M, Attardi G. 1982. Identification of initiation sites for heavy-strand and light-strand transcription in human mitochondrial DNA. \textit{Proc Natl Acad Sci} \textbf{79}(23):7195--7199.

\bibitem{Ernst2012}Ernst J, Kellis M. 2012. ChromHMM: automating chromatin-state discovery and characterization. \textit{Nat Methods} \textbf{9}(3):215--216.

\bibitem{DESeq2}Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. \textit{Genome Biol} \textbf{15}(12):550.

\bibitem{Bell1999}Bell AC, West AG, Felsenfeld G. 1999. The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. \textit{Cell} \textbf{98}(3):387--399.

\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

\bibitem{Wulfridge2023}Wulfridge P, Yan Q, Rell N, Doherty J, Jacobson S, Offley S, Deliard S, Feng K, Phillips-Cremins JE, Gardini A, Sarma K. 2023. G-quadruplexes associated with R-loops promote CTCF binding. \textit{Mol Cell} \textbf{83}(17):3064--3079.e5

\bibitem{Seila2008}Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA. 2008. Divergent transcription from active promoters. \textit{Science} \textbf{322}(5909):1849--1851.

\bibitem{Daley2013}Daley T, Smith AD. 2013. Predicting the molecular complexity of sequencing libraries. \textit{Nat Methods} \textbf{10}(4):325--327. % doi: 10.1038/nmeth.2375. 

\bibitem{CIS-BP}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. % CIS-BP

\bibitem{Sung2016}Sung MH, Baek S, Hager GL. 2016. Genome-wide footprinting: ready for prime time? \textit{Nat Methods} \textbf{13}(3):222--228.

\bibitem{Zhang2021}Zhang H, Lu T, Liu S, Yang J, Sun G, Cheng T, Xu J, Chen F, Yen K. 2021. Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification. \textit{NAR Genom Bioinform} \textbf{3}(4):lqab094

\bibitem{Li2019}Li Z, Schulz MH, Look T, Begemann M, Zenke M, Costa IG. 2019. Identification of transcription factor binding sites using ATAC-seq. \textit{Genome Biol} \textbf{20}(1):45. % doi: 10.1186/s13059-019-1642-2. % HINT

\bibitem{Baek2017}Baek S, Goldstein I, Hager GL. 2017. Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity.  \textit{Cell Rep} \textbf{19}(8):1710--1722. % doi: 10.1016/j.celrep.2017.05.003.

\bibitem{Bentsen2020}Bentsen M, Goymann P, Schultheis H, Klee K, Petrova A, Wiegandt R, Fust A, Preussner J, Kuenne C, Braun T, Kim J, Looso M. 2020. ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. \textit{Nat Commun} \textbf{11}(1):4267 % TOBIAS

\bibitem{Marinov2023}Marinov GK, Kim SH, Bagdatli ST, Higashino SI, Trevino AE, Tycko J, Wu T, Bintu L, Bassik MC, He C, Kundaje A, Greenleaf WJ. 2023. CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping. \textit{Genome Biol} \textbf{24}(1):85

\bibitem{Picelli2014}Picelli S, Bj\"orklund AK, Reinius B, Sagasser S, Winberg G, Sandberg R. 2014. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. \textit{Genome Res} \textbf{24}(12):2033--2040.

\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{Marinov2023ATAC}Marinov GK, Shipony Z, Kundaje A, Greenleaf WJ. 2023. Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq. \textit{Methods Mol Biol} \textbf{2611}:3--19.

\bibitem{Marinov2021}Marinov GK, Shipony Z. 2021. Interrogating the Accessible Chromatin Landscape of Eukaryote Genomes Using ATAC-seq. \textit{Methods Mol Biol} \textbf{2243}:183--226.

\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{MACS2}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{FIMO}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.

