% \bibitem{Ma2021}Ma CJ, Li L, Shao WX, Ding JH, Cai XL, Lun ZR, Yuan BF, Feng YQ. 2021. An enzyme-mediated bioorthogonal labeling method for genome-wide mapping of 5-hydroxymethyluracil. \textit{Chem Sci} \textbf{12}(42):14126--14132. % click chemistry, pull down
% https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1150-1
% \bibitem{Irwin2018}Irwin NAT, Martin BJE, Young BP, Browne MJG, Flaus A, Loewen CJR, Keeling PJ, Howe LJ. 2018. Viral proteins as a potential driver of histone depletion in dinoflagellates. \textit{Nat Commun} \textbf{9}(1):1535. % doi: 10.1038/s41467-018-03993-4.
% \bibitem{Siegel2009}Siegel TN, Hekstra DR, Kemp LE, Figueiredo LM, Lowell JE, Fenyo D, Wang X, Dewell S, Cross GA. 2009. Four histone variants mark the boundaries of polycistronic transcription units in \textit{Trypanosoma brucei}. \textit{Genes Dev} \textbf{23}(9):1063--1076.
% \bibitem{Lowell2004}Lowell JE, Cross GA. 2004. A variant histone H3 is enriched at telomeres in \textit{Trypanosoma brucei}. \textit{J Cell Sci} \textbf{117}(Pt 24):5937--5947.



\bibitem{Rizzo1991}Rizzo PJ. 1991. The enigma of the dinoflagellate chromosome. \textit{J Protozool} \textbf{38}(3):246--52.

\bibitem{WargoRizzo2001}Wargo MJ, Rizzo PJ. 2001. Exception to eukaryotic rules. \textit{Science} \textbf{294}:2477.

\bibitem{Rizzo2003}Rizzo PJ. 2003. Those amazing dinoflagellate chromosomes. \textit{Cell Res} \textbf{13}:215--217.

\bibitem{Hackett2004}Hackett JD, Anderson DM, Erdner DL, Bhattacharya D. 2004. Dinoflagellates: a remarkable evolutionary experiment. \textit{Am J Bot} \textbf{91}:1523--1534.

\bibitem{Lin2011}Lin S. 2011. Genomic understanding of dinoflagellates. \textit{Res Microbiol} \textbf{162}(6):551--569.

\bibitem{Wisecaver2011}Wisecaver JH, Hackett JD. 2011. Dinoflagellate genome evolution. \textit{Annu Rev Microbiol} \textbf{65}:369--387.

\bibitem{LaJeunesse2018}LaJeunesse TC, Parkinson JE, Gabrielson PW, Jeong HJ, Reimer JD, Voolstra CR, Santos SR. 2018. Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts. \textit{Curr Biol} \textbf{28}(16):2570--2580.e6. % doi: 10.1016/j.cub.2018.07.008. Epub 2018 Aug 9.

\bibitem{Trench1993}Trench RK. 1993. Microalgal--invertebrate symbiosis: a review. \textit{Endocyt Cell Res} \textbf{9}:135--175

\bibitem{Hoegh1999}Hoegh--Guldberg O. 1999. Climate change, coral bleaching and the future of the world's coral reefs. \textit{Mar Freshw Res} \textbf{50}:839--866

\bibitem{Hoegh2007}Hoegh--Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, Gomez E, Harvell CD, Sale PF, Edwards AJ, Caldeira K, Knowlton N, Eakin CM, Iglesias--Prieto R, Muthiga N, Bradbury RH, Dubi A, Hatziolos ME. 2007. \textit{Science} \textbf{318}(5857):1737--1742. Coral reefs under rapid climate change and ocean acidification.

\bibitem{Rizzo1972}Rizzo PJ, Nooden LD. 1972. Chromosomal proteins in the dinoflagellate alga \textit{Gyrodinium cohnii}. \textit{Science} \textbf{176}:796--797.

\bibitem{Rizzo1987}Rizzo PJ. 1987. Biochemistry of the dinoflagellate nucleus. In Taylor FJR (Ed.) The Biology of Dinoflagellates. \textit{Blackwell, Oxford}, pp.143--173.

\bibitem{Herzog1981}Herzog M, Soyer MO. 1981. Distinctive features of dinoflagellate chromatin. Absence of nucleosomes in a primitive species \textit{Prorocentrum micans} E. \textit{Eur J Cell Biol} \textbf{23}(2):295--302. 

\bibitem{Gornik2012}Gornik SG, Ford KL, Mulhern TD, Bacic A, McFadden GI, Waller RF. 2012. Loss of nucleosomal DNA condensation coincides with appearance of a novel nuclear protein in dinoflagellates. \textit{Curr Biol} \textbf{22}(24):2303--2312.

\bibitem{Jano2017}Janou\v{s}kovec J, Gavelis GS, Burki F, Dinh D, Bachvaroff TR, Gornik SG, Bright KJ, Imanian B, Strom SL, Delwiche CF, Waller RF, Fensome RA, Leander BS, Rohwer FL, Saldarriaga JF. 2017. Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics. \textit{Proc Natl Acad Sci U S A} \textbf{114}(2):E171--E180.

\bibitem{Talbert2019}Talbert PB, Meers MP, Henikoff S. 2019. Old cogs, new tricks: the evolution of gene expression in a chromatin context. \textit{Nat Rev Genet} \textbf{20}(5):283--297.

\bibitem{Jenuwein2001}Jenuwein T, Allis CD. 2001. Translating the histone code. \textit{Science} \textbf{293}(5532):1074--1080.

\bibitem{Marinov2015}Marinov GK, Lynch M. 2015. Diversity and Divergence of Dinoflagellate Histone Proteins. \textit{G3 (Bethesda)} \textbf{6}(2):397--422. % doi: 10.1534/g3.115.023275.

\bibitem{Bachvaroff2008}Bachvaroff TR, Place AR. 2008. From stop to start: tandem gene arrangement, copy number and trans-splicing sites in the dinoflagellate \textit{Amphidinium carterae}. \textit{PLoS One} \textbf{3}(8):e2929. % doi: 10.1371/journal.pone.0002929.

\bibitem{Shoguchi2013}Shoguchi E, Shinzato C, Kawashima T, Gyoja F, Mungpakdee S, Koyanagi R, Takeuchi T, Hisata K, Tanaka M, Fujiwara M, Hamada M, Seidi A, Fujie M, Usami T, Goto H, Yamasaki S, Arakaki N, Suzuki Y, Sugano S, Toyoda A, Kuroki Y, Fujiyama A, Medina M, Coffroth MA, Bhattacharya D, Satoh N. 2013. Draft assembly of the \textit{Symbiodinium minutum} nuclear genome reveals dinoflagellate gene structure. \textit{Curr Biol} \textbf{23}(15):1399--1408. % doi: 10.1016/j.cub.2013.05.062. 

\bibitem{Aranda2016}Aranda M, Li Y, Liew YJ, Baumgarten S, Simakov O, Wilson MC, Piel J, Ashoor H, Bougouffa S, Bajic VB, Ryu T, Ravasi T, Bayer T, Micklem G, Kim H, Bhak J, LaJeunesse TC, Voolstra CR. 2016. Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. \textit{Sci Rep} \textbf{6}:39734.

\bibitem{Lin2015}Lin S, Cheng S, Song B, Zhong X, Lin X, Li W, Li L, Zhang Y, Zhang H, Ji Z, Cai M, Zhuang Y, Shi X, Lin L, Wang L, Wang Z, Liu X, Yu S, Zeng P, Hao H, Zou Q, Chen C, Li Y, Wang Y, Xu C, Meng S, Xu X, Wang J, Yang H, Campbell DA, Sturm NR, Dagenais-Bellefeuille S, Morse D. 2015. The \textit{Symbiodinium kawagutii} genome illuminates dinoflagellate gene expression and coral symbiosis. \textit{Science} \textbf{350}(6261):691--694. % doi: 10.1126/science.aad0408.

\bibitem{Zhang2007}Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S. 2007. Spliced leader RNA trans-splicing in dinoflagellates. \textit{Proc Natl Acad Sci U S A} \textbf{104}(11):4618--4623.

\bibitem{Slamovits2008}Slamovits CH, Keeling PJ. 2008. Widespread recycling of processed cDNAs in dinoflagellates. \textit{Curr Biol} \textbf{18}(13):R550--552. % doi: 10.1016/j.cub.2008.04.054.

\bibitem{Marinov2021}Marinov GK, Trevino AE, Xiang T, Kundaje A, Grossman AR, Greenleaf WJ. 2021. Transcription--dependent domain-scale three-dimensional genome organization in the dinoflagellate \textit{Breviolum minutum}. \textit{Nat Genetics} \textbf{53}:613--617.

\bibitem{Nand2021}Nand A, Zhan Y, Salazar OR, Aranda M, Voolstra CR, Dekker J. 2021. Genetic and spatial organization of the unusual chromosomes of the dinoflagellate \textit{Symbiodinium microadriaticum}. \textit{Nat Genet} \textbf{53}(5):618--629.

\bibitem{Lieberman2009}Lieberman--Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. \textit{Science} \textbf{326}(5950):289--293. % doi: 10.1126/science.1181369.

\bibitem{Rae1973}Rae PM. 1973. 5-Hydroxymethyluracil in the DNA of a dinoflagellate. \textit{Proc Natl Acad Sci U S A} \textbf{70}(4):1141--1145.

\bibitem{Rae1976}Rae PM. 1976. Hydroxymethyluracil in eukaryote DNA: a natural feature of the pyrrophyta (dinoflagellates). \textit{Science} \textbf{194}(4269):1062--1064

\bibitem{Rae1978}Rae PM, Steele RE. 1978. Modified bases in the DNAs of unicellular eukaryotes: an examination of distributions and possible roles, with emphasis on hydroxymethyluracil in dinoflagellates. \textit{Biosystems} \textbf{10}(1--2):37--53.

\bibitem{Steele1980}Steele RE, Rae PM. 1980. Ordered distribution of modified bases in the DNA of a dinoflagellate. \textit{Nucleic Acids Res} \textbf{8}(20):4709--4725.

\bibitem{Herzog1982}Herzog M, Soyer MO, Daney de Marcillac G. 1982. A high level of thymine replacement by 5-hydroxymethyluracil in nuclear DNA of the primitive dinoflagellate \textit{Prorocentrum micans} E. \textit{Eur J Cell Biol} \textbf{27}(2):151--155.

\bibitem{Carson2016}Carson S, Wilson J, Aksimentiev A, Weigele PR, Wanunu M. 2016. Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA. \textit{Nucleic Acids Res} \textbf{44}(5):2085--2092.

\bibitem{Davies1988}Davies W, Jakobson KS, Norby {\O}. 1988. Characterization of DNA from the dinoflagellate \textit{Woloszynskia bostoniensis}. \textit{J Protozool} \textbf{35}:418--422.

\bibitem{Pasternack1996}Pasternack LB, Bramham J, Mayol L, Galeone A, Jia X, Kearns DR. 1996. 1H NMR studies of the 5-(hydroxymethyl)-2'-deoxyuridine containing TF1 binding site. \textit{Nucleic Acids Res} \textbf{24}(14):2740--2745.

\bibitem{Vu1999}Vu HM, Pepe A, Mayol L, Kearns DR. 1999. NMR-derived solution structure of a 17mer hydroxymethyluracil-containing DNA. \textit{Nucleic Acids Res} \textbf{27}(21):4143--4150.

\bibitem{Gommer1993}Gommers-Ampt JH, Teixeira AJ, van de Werken G, van Dijk WJ, Borst P. 1993. The identification of hydroxymethyluracil in DNA of \textit{Trypanosoma brucei}. \textit{Nucleic Acids Res} \textbf{21}(9):2039--2043

\bibitem{Lukes2009}Lukes J, Leander BS, Keeling PJ. 2009. Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. \textit{Proc Natl Acad Sci U S A} \textbf{106} Suppl 1:9963--9970. % doi: 10.1073/pnas.0901004106. 

\bibitem{Ivens2005}Ivens AC, Peacock CS, Worthey EA, Murphy L, Aggarwal G, Berriman M, Sisk E, Rajandream MA, Adlem E, Aert R, Anupama A, Apostolou Z, Attipoe P, Bason N, Bauser C, Beck A, Beverley SM, Bianchettin G, Borzym K, Bothe G, Bruschi CV, Collins M, Cadag E, Ciarloni L, Clayton C, Coulson RM, Cronin A, Cruz AK, Davies RM, De Gaudenzi J, Dobson DE, Duesterhoeft A, Fazelina G, Fosker N, Frasch AC, Fraser A, Fuchs M, Gabel C, Goble A, Goffeau A, Harris D, Hertz-Fowler C, Hilbert H, Horn D, Huang Y, Klages S, Knights A, Kube M, Larke N, Litvin L, Lord A, Louie T, Marra M, Masuy D, Matthews K, Michaeli S, Mottram JC, M\"uller-Auer S, Munden H, Nelson S, Norbertczak H, Oliver K, O'neil S, Pentony M, Pohl TM, Price C, Purnelle B, Quail MA, Rabbinowitsch E, Reinhardt R, Rieger M, Rinta J, Robben J, Robertson L, Ruiz JC, Rutter S, Saunders D, Sch\"afer M, Schein J, Schwartz DC, Seeger K, Seyler A, Sharp S, Shin H, Sivam D, Squares R, Squares S, Tosato V, Vogt C, Volckaert G, Wambutt R, Warren T, Wedler H, Woodward J, Zhou S, Zimmermann W, Smith DF, Blackwell JM, Stuart KD, Barrell B, Myler PJ. 2005. The genome of the kinetoplastid parasite, \textit{Leishmania major}. \textit{Science} \textbf{309}(5733):436--442.

\bibitem{El-Sayed2005a}El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N. 2005. Comparative genomics of trypanosomatid parasitic protozoa. \textit{Science} \textbf{309}(5733):404--409. 

\bibitem{El-Sayed2005b}El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran AN, Ghedin E, Worthey EA, Delcher AL, Blandin G, Westenberger SJ, Caler E, Cerqueira GC, Branche C, Haas B, Anupama A, Arner E, Aslund L, Attipoe P, Bontempi E, Bringaud F, Burton P, Cadag E, Campbell DA, Carrington M, Crabtree J, Darban H, da Silveira JF, de Jong P, Edwards K, Englund PT, Fazelina G, Feldblyum T, Ferella M, Frasch AC, Gull K, Horn D, Hou L, Huang Y, Kindlund E, Klingbeil M, Kluge S, Koo H, Lacerda D, Levin MJ, Lorenzi H, Louie T, Machado CR, McCulloch R, McKenna A, Mizuno Y, Mottram JC, Nelson S, Ochaya S, Osoegawa K, Pai G, Parsons M, Pentony M, Pettersson U, Pop M, Ramirez JL, Rinta J, Robertson L, Salzberg SL, Sanchez DO, Seyler A, Sharma R, Shetty J, Simpson AJ, Sisk E, Tammi MT, Tarleton R, Teixeira S, Van Aken S, Vogt C, Ward PN, Wickstead B, Wortman J, White O, Fraser CM, Stuart KD, Andersson B. 2005. The genome sequence of \textit{Trypanosoma cruzi}, etiologic agent of Chagas disease. \textit{Science} \textbf{309}(5733):409--415.

\bibitem{Berriman2005}Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, B\"ohme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UC, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, Macleod A, Mooney PJ, Moule S, Martin DM, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CM, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE, El-Sayed NM. The genome of the African trypanosome \textit{Trypanosoma brucei}. \textit{Science} \textbf{309}(5733):416--422

\bibitem{Boothroyd1982}Boothroyd JC, Cross GA. 1982. Transcripts coding for variant surface glycoproteins of \textit{Trypanosoma brucei} have a short, identical exon at their 5' end. \textit{Gene} \textbf{20}(2):281--289.

\bibitem{Nelson1983}Nelson RG, Parsons M, Barr PJ, Stuart K, Selkirk M, Agabian N. 1983. Sequences homologous to the variant antigen mRNA spliced leader are located in tandem repeats and variable orphons in \textit{Trypanosoma brucei}. \textit{Cell} \textbf{34}(3):901--909.

\bibitem{DeLange1984}De Lange T, Michels PA, Veerman HJ, Cornelissen AW, Borst P. 1984. Many trypanosome messenger RNAs share a common 5' terminal sequence. \textit{Nucleic Acids Res} \textbf{12}(9):3777--3790.

\bibitem{DeLange1984B}De Lange T, Berkvens TM, Veerman HJ, Frasch AC, Barry JD, Borst P. 1984. Comparison of the genes coding for the common 5' terminal sequence of messenger RNAs in three trypanosome species. \textit{Nucleic Acids Res} \textbf{12}(11):4431--4443.

\bibitem{Sutton1986}Sutton RE, Boothroyd JC. 1986. Evidence for trans splicing in trypanosomes. \textit{Cell} \textbf{47}(4):527--535.

\bibitem{Dooijes2000}Dooijes D, Chaves I, Kieft R, Dirks-Mulder A, Martin W, Borst P. 2000. Base J originally found in kinetoplastida is also a minor constituent of nuclear DNA of \textit{Euglena gracilis}. \textit{Nucleic Acids Res} \textbf{28}(16):3017--3021.

\bibitem{Gommer1991}Gommers-Ampt J, Lutgerink J, Borst P. 1991. A novel DNA nucleotide in \textit{Trypanosoma brucei} only present in the mammalian phase of the life-cycle. \textit{Nucleic Acids Res} \textbf{19}(8):1745--151.

\bibitem{Gommer1993b}Gommers-Ampt JH, Van Leeuwen F, de Beer AL, Vliegenthart JF, Dizdaroglu M, Kowalak JA, Crain PF, Borst P. 1993. beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan \textit{T. brucei}. \textit{Cell} \textbf{75}(6):1129--1136.

\bibitem{Borst2008}Borst P, Sabatini R. 2008. Base J: discovery, biosynthesis, and possible functions. \textit{Annu Rev Microbiol} \textbf{62}:235--251.

\bibitem{vanLeeuwen1998}van Leeuwen F, Taylor MC, Mondragon A, Moreau H, Gibson W, Kieft R, Borst P. 1998. $\beta$-D-glucosyl-hydroxymethyluracil is a conserved DNA modification in kinetoplastid protozoans and is abundant in their telomeres. \textit{Proc Natl Acad Sci U S A} \textbf{95}(5):2366--2371.

\bibitem{vanLeeuwen1997}van Leeuwen F, Wijsman ER, Kieft R, van der Marel GA, van Boom JH, Borst P. 1997. Localization of the modified base J in telomeric VSG gene expression sites of \textit{Trypanosoma brucei}. \textit{Genes Dev} \textbf{11}(23):3232--3241.

\bibitem{vanLeeuwen1996}van Leeuwen F, Wijsman ER, Kuyl-Yeheskiely E, van der Marel GA, van Boom JH, Borst P. 1996. The telomeric GGGTTA repeats of \textit{Trypanosoma brucei} contain the hypermodified base J in both strands. \textit{Nucleic Acids Res} \textbf{24}(13):2476--2482..

\bibitem{Cliffe2010}Cliffe LJ, Siegel TN, Marshall M, Cross GA, Sabatini R. 2010. Two thymidine hydroxylases differentially regulate the formation of glucosylated DNA at regions flanking polymerase II polycistronic transcription units throughout the genome of \textit{Trypanosoma brucei}. \textit{Nucleic Acids Res} \textbf{38}(12):3923--3935.

\bibitem{vanLuenen2012}van Luenen HG, Farris C, Jan S, Genest PA, Tripathi P, Velds A, Kerkhoven RM, Nieuwland M, Haydock A, Ramasamy G, Vainio S, Heidebrecht T, Perrakis A, Pagie L, van Steensel B, Myler PJ, Borst P. 2012. Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in \textit{Leishmania}. \textit{Cell} \textbf{150}(5):909--921

\bibitem{Reynolds2014}Reynolds D, Cliffe L, F\"orstner KU, Hon CC, Siegel TN, Sabatini R. 2014. Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in \textit{Leishmania major} and \textit{Trypanosoma brucei}. \textit{Nucleic Acids Res} \textbf{42}(15):9717--9729.

\bibitem{Weber2005}Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Sch\"ubeler D. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. \textit{Nat Genet} \textbf{37}(8):853--862.

\bibitem{Down2008}Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr\"af S, Johnson N, Herrero J, Tomazou EM, Thorne NP, BÃ¤ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar\'e S, Beck S. 2008. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. \textit{Nat Biotechnol} \textbf{26}(7):779--785.

\bibitem{ATAC}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{omniATAC}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{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{Irwin2018}Irwin NAT, Martin BJE, Young BP, Browne MJG, Flaus A, Loewen CJR, Keeling PJ, Howe LJ. 2018. Viral proteins as a potential driver of histone depletion in dinoflagellates. \textit{Nat Commun} \textbf{9}(1):1535. % doi: 10.1038/s41467-018-03993-4.

\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{Swaffer2021}Swaffer MP, Kim J, Chandler-Brown D, Langhinrichs M, Marinov GK, Greenleaf WJ, Kundaje A, Schmoller KM, Skotheim JM. 2021. Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size. \textit{Mol Cell} \textbf{81}(23):4861--4875.e7

\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{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{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

\bibitem{Kawasaki2018}Kawasaki F, Mart\'inez Cuesta S, Beraldi D, Mahtey A, Hardisty RE, Carrington M, Balasubramanian S. 2018. Sequencing 5-Hydroxymethyluracil at Single-Base Resolution. \textit{Angew Chem Int Ed Engl} \textbf{57}(31):9694--9696. 

\bibitem{Oberbeckmann2019}Oberbeckmann E, Wolff M, Krietenstein N, Heron M, Ellins JL, Schmid A, Krebs S, Blum H, Gerland U, Korber P. 2019. Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome. \textit{Genome Res} \textbf{29}(12):1996--2009.

\bibitem{Xiang2013}Xiang T, Hambleton EA, DeNofrio JC, Pringle JR, Grossman AR. 2013. Isolation of clonal axenic strains of the symbiotic dinoflagellate \textit{Symbiodinium} and their growth and host specificity. \textit{J Phycol} \textbf{49}(3):447--458. % doi: 10.1111/jpy.12055. 

\bibitem{Xiang2015}Xiang T, Nelson W, Rodriguez J, Tolleter D, Grossman AR. 2015. \textit{Symbiodinium} transcriptome and global responses of cells to immediate changes in light intensity when grown under autotrophic or mixotrophic conditions. \textit{Plant J} \textbf{82}(1):67--80. % doi: 10.1111/tpj.12789. 

\bibitem{Dudchenko2017}Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. \textit{Science} \textbf{356}(6333):92--95. % doi: 10.1126/science.aal3327. 

\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{Marinov2015b}Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF. 2015. Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. \textit{Dev Cell} \textbf{32}(6):765--771

\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{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{Marinov2017a}Marinov GK. 2017. ChIP-seq for the Identification of Functional Elements in the Human Genome. \textit{Methods Mol Biol} \textbf{1543}:3--18.

\bibitem{Neumann2019}Neumann T, Herzog VA, Muhar M, von Haeseler A, Zuber J, Ameres SL, Rescheneder P. 2019. Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. \textit{BMC Bioinformatics} \textbf{20}(1):258.

\bibitem{Herzog2017}Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL. 2017. Thiol-linked alkylation of RNA to assess expression dynamics. \textit{Nat Methods} \textbf{14}(12):1198--1204. 

\bibitem{Shipony2020}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. 

\bibitem{Marinov2023}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{trimmomatic}Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. \textit{Bioinformatics} \textbf{30}(15):2114--2120. % doi: 10.1093/bioinformatics/btu170. 

\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{Marinov2022}Marinov GK, Shipony Z, Kundaje A, Greenleaf WJ. 2022. Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq. \textit{Methods Mol Biol} \textbf{2458}:269--298.

\bibitem{Marinov2020ATAC}Marinov GK, Shipony Z. 2020. Interrogating the accessible chromatin landscape of eukaryote genomes using ATAC-seq. \textit{Methods Mol Biol} \textbf{2243}:183--226.

