% \bibitem{Horiguchi1994}Horiguchi T, Pienaar R. 1994. Ultrastructure of a new marine sand-dwelling dinoflagellate, \textit{Gymnodinium quadrilobatum} sp. nov. (Dinophyceae) with special reference to its endosymbiotic alga. \textit{Eur J Phyc} \textbf{29}:237--245.
% \bibitem{Horiguchi1991}Horiguchi T, Pienaar R. 1991. Ultrastructure of a marine dinoflagellate, \textit{Peridinium quinquecorne} Abe (Peridiniales) from South Africa with special reference to its chrysophyte endosymbiont. \textit{Bot Mar} \textbf{34}:123--131
% \bibitem{LiB2007}Li B, Carey M, Workman JL. 2007. The role of chromatin during transcription. \textit{Cell} \textbf{128}(4):707--719.
% \bibitem{Hopkins2012}Hopkins JF, Spencer DF, Laboissiere S, Neilson JA, Eveleigh RJ, Durnford DG, Gray MW, Archibald JM. 2012. Proteomics reveals plastid- and periplastid-targeted proteins in the chlorarachniophyte alga Bigelowiella natans. \textit{Genome Biol Evol} \textbf{4}(12):1391--1406.

\bibitem{Blanchard2000}Blanchard JL, Lynch M. 2000. Organellar genes: why do they end up in the nucleus? \textit{Trends Genet} \textbf{16}(7):315--320.

\bibitem{Moran2014}Moran NA, Bennett GM. 2014. The tiniest tiny genomes. \textit{Annu Rev Microbiol} \textbf{68}:195--215.

\bibitem{Keeling2010}Keeling PJ. 2010. The endosymbiotic origin, diversification and fate of plastids. \textit{Philos Trans R Soc Lond B Biol Sci} \textbf{365}(1541):729--748.

\bibitem{Dodge1971}Dodge JD. 1971. A dinoflagellate with both a mesokaryotic and a eukaryotic nucleus: Part 1 fine structure of the nuclei. \textit{Protoplasma} \textbf{73}:145--157.

\bibitem{Figueroa2009}Figueroa RI, Bravo I, Fraga S, Garc\'es E, Llaveria G. 2009. The life history and cell cycle of \textit{Kryptoperidinium foliaceum}, a dinoflagellate with two eukaryotic nuclei. \textit{Protist} \textbf{160}(2):285--300.

\bibitem{Nakayama2020}Nakayama T, Takahashi K, Kamikawa R, Iwataki M, Inagaki Y, Tanifuji G. 2020. Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organisms. \textit{Commun Integr Biol} \textbf{13}(1):84--88. % doi: 10.1080/19420889.2020.1776568.

\bibitem{Sarai2020}Sarai C, Tanifuji G, Nakayama T, Kamikawa R, Takahashi K, Yazaki E, Matsuo E, Miyashita H, Ishida KI, Iwataki M, Inagaki Y. 2020. Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis. \textit{Proc Natl Acad Sci U S A} \textbf{117}(10):5364--5375. % doi: 10.1073/pnas.1911884117. 

\bibitem{Greenwood1974}Greenwood AD. 1974. The Cryptophyta in relation to phylogeny and photosynthesis. \textit{In: Sanders JV, Goodchild DJ, (Eds.). Electron microscopy 1974}. Canberra: Australian Academy of Sciences. p.566--567.

\bibitem{Greenwood1977}Greenwood AD, Griffiths HB, Santore UJ. 1977. Chloroplasts and cell compartments in Cryptophyceae. \textit{Brit Phycol J} \textbf{12}:119.

\bibitem{Archibald2007}Archibald JM. 2007. Nucleomorph genomes: structure, function, origin and evolution. \textit{Bioessays} \textbf{29}(4):392--402.

\bibitem{Archibald2009}Archibald JM, Lane CE. 2009. Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction. \textit{J Hered} \textbf{100}(5):582--590.

\bibitem{Zauner2000}Zauner S, Fraunholz M, Wastl J, Penny S, Beaton M, Cavalier-Smith T, Maier UG, Douglas S. 2000. Chloroplast protein and centrosomal genes, a tRNA intron, and odd telomeres in an unusually compact eukaryotic genome, the cryptomonad nucleomorph. \textit{Proc Natl Acad Sci U S A} \textbf{97}(1):200--205.

\bibitem{Douglas2001}Douglas S, Zauner S, Fraunholz M, Beaton M, Penny S, Deng LT, Wu X, Reith M, Cavalier-Smith T, Maier UG. 2001. The highly reduced genome of an enslaved algal nucleus. \textit{Nature} \textbf{410}(6832):1091--1096.

\bibitem{Tanifuji2011}Tanifuji G, Onodera NT, Wheeler TJ, Dlutek M, Donaher N, Archibald JM. 2011. Complete nucleomorph genome sequence of the nonphotosynthetic alga \textit{Cryptomonas paramecium} reveals a core nucleomorph gene set. \textit{Genome Biol Evol} \textbf{3}:44--54.

\bibitem{Moore2012}Moore CE, Curtis B, Mills T, Tanifuji G, Archibald JM. 2012. Nucleomorph genome sequence of the cryptophyte alga \textit{Chroomonas mesostigmatica} CCMP1168 reveals lineage-specific gene loss and genome complexity. \textit{Genome Biol Evol} \textbf{4}(11):1162--1175.

\bibitem{Tanifuji2014}Tanifuji G, Onodera NT, Brown MW, Curtis BA, Roger AJ, Ka-Shu Wong G, Melkonian M, Archibald JM. 2014. Nucleomorph and plastid genome sequences of the chlorarachniophyte \textit{Lotharella oceanica}: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. \textit{BMC Genomics} \textbf{15}:374.

\bibitem{Gilson2006}Gilson PR, Su V, Slamovits CH, Reith ME, Keeling PJ, McFadden GI. 2006. Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus. \textit{Proc Natl Acad Sci U S A} \textbf{103}(25):9566--9571.

\bibitem{Lane2007}Lane CE, van den Heuvel K, Kozera C, Curtis BA, Parsons BJ, Bowman S, Archibald JM. 2007. Nucleomorph genome of \textit{Hemiselmis andersenii} reveals complete intron loss and compaction as a driver of protein structure and function. \textit{Proc Natl Acad Sci U S A} \textbf{104}(50):19908--19913.

\bibitem{Marinov2016}Marinov GK, Lynch M. 2016. Conservation and divergence of the histone code in nucleomorphs. \textit{Biol Direct} \textbf{11}(1):18.

\bibitem{Postberg2010}Postberg J, Forcob S, Chang WJ, Lipps HJ. 2010. The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms. \textit{BMC Evol Biol} \textbf{10}:259.

\bibitem{Marinov2015dino}Marinov GK, Lynch M. 2015. Diversity and Divergence of Dinoflagellate Histone Proteins. \textit{G3 (Bethesda)} \textbf{6}(2):397--422.

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

\bibitem{Hirakawa2011}Hirakawa Y, Burki F, Keeling PJ. 2011. Nucleus- and nucleomorph-targeted histone proteins in a chlorarachniophyte alga. \textit{Mol Microbiol} \textbf{80}(6):1439--1449

\bibitem{Eick2013}Eick D, Geyer M. 2013. The RNA polymerase II carboxy-terminal domain (CTD) code. \textit{Chem Rev} \textbf{113}(11):8456--8490.

\bibitem{Yang2014}Yang C, Stiller JW. 2014. Evolutionary diversity and taxon-specific modifications of the RNA polymerase II C-terminal domain. \textit{Proc Natl Acad Sci U S A} \textbf{111}(16):5920--5925.

\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{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{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{Zhipony2020}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{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{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{Tanifuji2014b}Tanifuji G, Onodera NT, Moore CE, Archibald JM. 2014. Reduced nuclear genomes maintain high gene transcription levels. \textit{Mol Biol Evol} \textbf{31}(3):625--635.

\bibitem{Suzuki2016}Suzuki S, Ishida K, Hirakawa Y. 2016. Diurnal Transcriptional Regulation of Endosymbiotically Derived Genes in the Chlorarachniophyte \textit{Bigelowiella natans}. \textit{Genome Biol Evol} \textbf{8}(9):2672--2682.

\bibitem{Sanita2017}Sanit\'a Lima M, Smith DR. 2017. Pervasive Transcription of Mitochondrial, Plastid, and Nucleomorph Genomes across Diverse Plastid-Bearing Species. \textit{Genome Biol Evol} \textbf{9}(10):2650--2657.

\bibitem{Rangsrikitphoti2019}Rangsrikitphoti P, Durnford DG. 2019. Transcriptome Profiling of \textit{Bigelowiella natans} in Response to Light Stress. \textit{J Eukaryot Microbiol} \textbf{66}(2):316--333.

\bibitem{Rao2014}Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. \textit{Cell} \textbf{159}(7):1665--1680.

\bibitem{Hoencamp2021}Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sede\~no Cacciatore \'A, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, G\'omez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD. 2021. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. \textit{Science} \textbf{372}(6545):984--989. \\

\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{Curtis2012}Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Oborn\'ik M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, H\"oppner MP, Ishida K, Kim E, Ko\v{r}en\'y L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. \textit{Nature} \textbf{492}(7427):59--65.

\bibitem{Hopkins2012}Hopkins JF, Spencer DF, Laboissiere S, Neilson JA, Eveleigh RJ, Durnford DG, Gray MW, Archibald JM. 2012. Proteomics reveals plastid- and periplastid-targeted proteins in the chlorarachniophyte alga Bigelowiella natans. \textit{Genome Biol Evol} \textbf{4}(12):1391--1406.

\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{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 Genet} \textbf{53}(5):613--617.

\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{Marinov2015}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{Durand2016a}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{Payne2021}Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F. 2021. In situ genome sequencing resolves DNA sequence and structure in intact biological samples. \textit{Science} \textbf{371}(6532):eaay3446

\bibitem{Mateo2019}Mateo LJ, Murphy SE, Hafner A, Cinquini IS, Walker CA, Boettiger AN. 2019. Visualizing DNA folding and RNA in embryos at single-cell resolution. \textit{Nature} \textbf{568}(7750):49--54.