% Chan, P.P. and Lowe, T. M. (2019) tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. \textit{Methods Mol Biol} \textbf{1962}:1--14.
% Chan, P.P., Lin, B.Y., Mak, A.J., and Lowe, T.M. (2021) tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes. Nucl. Acids Res. 49:9077â€“9096.
% https://www.biorxiv.org/content/10.1101/2023.06.01.543357v2.abstract?%3Fcollection=
% \bibitem{Marinov2016}Marinov GK, Lynch M. 2016. Conservation and divergence of the histone code in nucleomorphs. \textit{Biol Direct} \textbf{11}(1):18.
% \bibitem{Searcy1980a}Searcy DG, Delange RJ. 1980. \textit{Thermoplasma acidophilum} histone-like protein. Partial amino acid sequence suggestive of homology to eukaryotic histones. \textit{Biochim Biophys Acta} \textbf{609}(1):197--200.
% \bibitem{Searcy1980b}Searcy DG, Stein DB. 1980. Nucleoprotein subunit structure in an unusual prokaryotic organism: \textit{Thermoplasma acidophilum}. \textit{Biochim Biophys Acta} \textbf{609}(1):180--195.
% \bibitem{Zhang2012}Zhang Z, Guo L, Huang L. 2012. Archaeal chromatin proteins. \textit{Sci China Life Sci} \textbf{55}(5):377--385.
% \bibitem{Sandman2005}Sandman K, Reeve JN. 2005. Archaeal chromatin proteins: different structures but common function? \textit{Curr Opin Microbiol} \textbf{8}(6):656--661
% \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{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 \textit{Saccharomyces cerevisiae} genome. \textit{Genome Res} \textbf{29}(12):1996--2009.
% \bibitem{Chereji2019}Chereji RV, Eriksson PR, Ocampo J, Prajapati HK, Clark DJ. 2019. Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation. \textit{Genome Res} \textbf{29}(12):1985--1995.
% \bibitem{Xie2004}Xie Y, Reeve JN. 2004. Transcription by an Archaeal RNA Polymerase Is Slowed but Not Blocked by an Archaeal Nucleosome. \textit{J Bacteriol} \textbf{186}:3492--3498.
% \bibitem{Marinov2015piwi}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{Krzywinski2009}Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: an information aesthetic for comparative genomics. \textit{Genome Res} \textbf{19}(9):1639--1645.

\bibitem{Grigoriev1998}Grigoriev A. 1998. Analyzing genomes with cumulative skew diagrams. \textit{Nucleic Acids Res} \textbf{26}(10):2286--2290. 

\bibitem{Lobry1996}Lobry JR. 1996. Asymmetric substitution patterns in the two DNA strands of bacteria. \textit{Mol Biol Evol} \textbf{13}(5):660--65

\bibitem{Kozlov2019}Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. \textit{Bioinformatics} \textbf{35}(21):4453--4455.

\bibitem{AlphaFold}Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, \v{Z}\'idek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, Romera-Paredes B, Nikolov S, Jain R, Adler J, Back T, Petersen S, Reiman D, Clancy E, Zielinski M, Steinegger M, Pacholska M, Berghammer T, Bodenstein S, Silver D, Vinyals O, Senior AW, Kavukcuoglu K, Kohli P, Hassabis D. 2021. Highly accurate protein structure prediction with AlphaFold. \textit{Nature} \textbf{596}(7873):583--589.

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

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

\bibitem{Woese1977}Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. \textit{Proc Natl Acad Sci U S A} \textbf{74}(11):5088--5090.

\bibitem{Lake1984}Lake JA, Henderson E, Oakes M, Clark MW. 1984. Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes. \textit{Proc Natl Acad Sci U S A} \textbf{81}(12):3786--3790.

\bibitem{Lake1988}Lake JA. 1988. Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. \textit{Nature} \textbf{331}(6152):184--186.

\bibitem{Cox2008}Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. 2008. The archaebacterial origin of eukaryotes. \textit{Proc Natl Acad Sci U S A} \textbf{105}(51):20356--20361. % doi: 10.1073/pnas.0810647105. 

\bibitem{Spang2015}Spang A, Saw JH, J{{\o}}rgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG. 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. \textit{Nature} \textbf{521}(7551):173--179. % doi: 10.1038/nature14447. 

\bibitem{Koonin2010}Koonin EV. 2010. The origin and early evolution of eukaryotes in the light of phylogenomics. \textit{Genome Biol} \textbf{11}(5):209

\bibitem{Koonin2014}Koonin EV, Yutin N. 2014. The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. \textit{Cold Spring Harb Perspect Biol} \textbf{6}(4):a016188

\bibitem{Sandman2006}Sandman K, Reeve JN. 2006. Archaeal histones and the origin of the histone fold. \textit{Curr Opin Microbiol} \textbf{9}:520--525.

\bibitem{Arents1991}Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN. 1991. The nucleosomal core histone octamer at 3.1 \r{A} resolution: a tripartite protein assembly and a left-handed superhelix. \textit{Proc Natl Acad Sci U S A} \textbf{88}(22):10148--10152

\bibitem{Henneman2018}Henneman B, van Emmerik C, van Ingen H, Dame RT. 2018. Structure and function of archaeal histones. \textit{PLoS Genet} \textbf{14}(9):e1007582.

\bibitem{Stevens2020}Stevens KM, Swadling JB, Hocher A, Bang C, Gribaldo S, Schmitz RA, Warnecke T. 2020. Histone variants in archaea and the evolution of combinatorial chromatin complexity. \textit{Proc Natl Acad Sci U S A} \textbf{117}(52):33384--33395.

\bibitem{Maruyama2013}Maruyama H, Harwood JC, Moore KM, Paszkiewicz K, Durley SC, Fukushima H, Atomi H, Takeyasu K, Kent NA. 2013. An alternative beads-on-a-string chromatin architecture in \textit{Thermococcus kodakarensis}. \textit{EMBO Rep} \textbf{14}(8):711--717.

\bibitem{Mattiroli2017}Mattiroli F, Bhattacharyya S, Dyer PN, White AE, Sandman K, Burkhart BW, Byrne KR, Lee T, Ahn NG, Santangelo TJ, Reeve JN, Luger K. 2017. Structure of histone-based chromatin in Archaea. \textit{Science} \textbf{357}(6351):609--612. % doi: 10.1126/science.aaj1849.

\bibitem{Bowerman2021}Bowerman S, Wereszczynski J, Luger K. 2021. Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways. \textit{Elife} \textbf{10}:e65587

\bibitem{Henneman2021}Henneman B, Brouwer TB, Erkelens AM, Kuijntjes GJ, van Emmerik C, van der Valk RA, Timmer M, Kirolos NCS, van Ingen H, van Noort J, Dame RT. 2021. Mechanical and structural properties of archaeal hypernucleosomes. \textit{Nucleic Acids Res} \textbf{49}(8):4338--4349.

\bibitem{Alva2019}Alva V, Lupas AN. 2019. Histones predate the split between bacteria and archaea. \textit{Bioinformatics} \textbf{35}(14):2349--2353.

\bibitem{Schwab2023}Schwab S, Boyle AL, Dame RT. 2023. Novel histones and histone variant families in prokaryotes. \textit{bioRxiv} 2023.06.01.543357

\bibitem{Hocher2023}Hocher A, Laursen SP, Radford P, Tyson J, Lambert C, Stevens KM, Picardeau M, Sockett RE, Luger K, Warnecke T. 2023. Histone-organized chromatin in bacteria. \textit{bioRxiv} 2023.01.26.525422.

\bibitem{Hu2023}Hu Y, Schwab S, Deiss S, Escudeiro P, Joiner JD, Hartmann MD, Lupas AN, Hernandez Alvarez B, Alva V, Dame RT. 2023. Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. \textit{bioRxiv} 2023.02.26.530074

\bibitem{Ammar2012}Ammar R, Torti D, Tsui K, Gebbia M, Durbic T, Bader GD, Giaever G, Nislow C. 2012. Chromatin is an ancient innovation conserved between Archaea and Eukarya. \textit{Elife} \textbf{1}:e00078. 

\bibitem{Nalabothula2013}Nalabothula N, Xi L, Bhattacharyya S, Widom J, Wang JP, Reeve JN, Santangelo TJ, Fondufe-Mittendorf YN. 2013. Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs. \textit{BMC Genomics} \textbf{14}:391. 

\bibitem{Badel2022}Badel C, Samson RY, Bell SD. 2022. Chromosome organization affects genome evolution in \textit{Sulfolobus} archaea. \textit{Nat Microbiol}  doi: 10.1038/s41564-022-01127-7

\bibitem{Marinov2022Haloferax}Marinov GK, Bagdatli ST, Wu T, He C, Kundaje A, Greenleaf WJ. 2022. The chromatin landscape of the euryarchaeon \textit{Haloferax volcanii}. (\textit{bioRxiv} 2022.07.22.501187.)

\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{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{Wu2020}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{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{Stolp1963}Stolp H, Starr MP. 1963. \textit{Bdellovibrio bacteriovorus} gen. et sp. n., a predatory, ectoparasitic, and bacteriolytic microorganism. \textit{Antonie Van Leeuwenhoek} \textbf{29}:217--248.

\bibitem{Stolp1965}Stolp H, Starr MP. 1965. Bacteriolysis. \textit{Annu Rev Microbiol} \textbf{19}:79--104.

\bibitem{Lovering2021}Lovering AL, Sockett RE. 2021. Microbe Profile: \textit{Bdellovibrio bacteriovorus}: a specialized bacterial predator of bacteria. \textit{Microbiology (Reading)} \textbf{167}(4):001043

\bibitem{Tock2005}Tock MR, Dryden DT. 2005. The biology of restriction and anti-restriction. \textit{Curr Opin Microbiol} \textbf{8}(4):466--472.

\bibitem{Oren2021}Oren A, Garrity GM. 2021. Valid publication of the names of forty-two phyla of prokaryotes. \textit{Int J Syst Evol Microbiol} \textbf{71}(10).

\bibitem{Melfi2021}Melfi MD, Lasker K, Zhou X, Shapiro L. 2021. ATAC-seq reveals megabase-scale domains of a bacterial nucleoid. \textit{bioRxiv} 2021.01.09.426053

\bibitem{MarinovShipony2021}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{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. % SMAC-seq

\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{Core2019}Core L, Adelman K. 2019. Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. \textit{Genes Dev} \textbf{33}(15--16):960--982.

\bibitem{Gilmour1986}Gilmour DS, Lis JT. 1986. RNA polymerase II interacts with the promoter region of the noninduced \textit{hsp70} gene in \textit{Drosophila melanogaster} cells. \textit{Mol Cell Biol} \textbf{6}:3984--3989. % 10.1128/MCB.6.11.3984

\bibitem{Rougvie1988}Rougvie AE, Lis JT. 1988. The RNA polymerase II molecule at the 5' end of the uninduced \textit{hsp70} gene of \textit{D. melanogaster} is transcriptionally engaged. \textit{Cell} \textbf{54}:795--804. % 10.1016/S0092-8674(88)91087-2

\bibitem{Muse2007}Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K. 2007. RNA polymerase is poised for activation across the genome. \textit{Nat Genet} \textbf{39}(12):1507--1511.

\bibitem{Nechaev2010}Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K. 2010. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in \textit{Drosophila}. \textit{Science} \textbf{327}:335--338.

\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}:950--953.

\bibitem{Williams2015}Williams LH, Fromm G, Gokey NG, Henriques T, Muse GW, Burkholder A, Fargo DC, Hu G, Adelman K. 2015. Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks. \textit{Mol Cell} \textbf{58}:311--322.

\bibitem{Chivu2023}Chivu AG, Abuhashem A, Barshad G, Rice EJ, Leger MM, Vill AC, Wong W, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito IL, Ruiz-Trillo I, Hadjantonakis AK, Lis JT, Lewis JJ, Danko CG. 2023. Evolution of promoter-proximal pausing enabled a new layer of transcription control. \textit{bioRxiv} 2023.02.19.529146

\bibitem{Kassavetis1981}Kassavetis GA, Chamberlin MJ. 1981. Pausing and termination of transcription within the early region of bacteriophage T7 DNA in vitro. \textit{J Biol Chem} \textbf{256}:2777--2786.

\bibitem{Yanofsky1981}Yanofsky C. 1981. Attenuation in the control of expression of bacterial operons. \textit{Nature} \textbf{289}:751--758.

\bibitem{Winkler1981}Winkler ME, Yanofsky C. 1981. Pausing of RNA polymerase during in vitro transcription of the tryptophan operon leader region. \textit{Biochemistry} \textbf{20}:3738--3744.

\bibitem{Lau1983}Lau LF, Roberts JW, Wu R. 1983. RNA polymerase pausing and transcript release at the lambda tR1 terminator in vitro. \textit{J Biol Chem} \textbf{258}:9391--9397.

\bibitem{Kireeva2009}Kireeva ML, Kashlev M. 2009. Mechanism of sequence-specific pausing of bacterial RNA polymerase. \textit{Proc Natl Acad Sci U S A} \textbf{106}(22):8900--8905

\bibitem{Kang2019}Kang JY, Mishanina TV, Landick R, Darst SA. 2019. Mechanisms of Transcriptional Pausing in Bacteria. \textit{J Mol Biol} \textbf{431}(20):4007--4029.

\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{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{Dwidar2017}Dwidar M, Im H, Seo JK, Mitchell RJ. 2017. Attack-Phase \textit{Bdellovibrio bacteriovorus} Responses to Extracellular Nutrients Are Analogous to Those Seen During Late Intraperiplasmic Growth. \textit{Microb Ecol} \textbf{74}(4):937--946.

\bibitem{Price2006}Price MN, Arkin AP, Alm EJ. 2006. The life-cycle of operons. \textit{PLoS Genet} \textbf{2}(6):e96.

\bibitem{Koide2009}Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS. 2009. Prevalence of transcription promoters within archaeal operons and coding sequences. \textit{Mol Syst Biol} \textbf{5}:285.

\bibitem{Babski2016}Babski J, Haas KA, N\"ather-Schindler D, Pfeiffer F, F\"orstner KU, Hammelmann M, Hilker R, Becker A, Sharma CM, Marchfelder A, Soppa J. 2016. Genome-wide identification of transcriptional start sites in the haloarchaeon \textit{Haloferax volcanii} based on differential RNA-Seq (dRNA-Seq). \textit{BMC Genomics} \textbf{17}(1):629

\bibitem{Laass2019}Laass S, Monzon VA, Kliemt J, Hammelmann M, Pfeiffer F, F\"orstner KU, Soppa J. 2019. Characterization of the transcriptome of \textit{Haloferax volcanii}, grown under four different conditions, with mixed RNA-Seq. \textit{PLoS ONE} \textbf{14}(4):e0215986

\bibitem{Grunerger2019}Gr\"nberger F, Kn\"uppel R, J\"uttner M, Fenk M, Borst A, Reichelt R, Hausner W, Soppa J, Ferreira-Cerca S, Grohmann D. 2019. Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing. \textit{bioRxiv} 2019.12.18.880849

\bibitem{Le2013}Le TB, Imakaev MV, Mirny LA, Laub MT. 2013. High-resolution mapping of the spatial organization of a bacterial chromosome. \textit{Science} \textbf{342}(6159):731--734

\bibitem{Yildirim2018}Yildirim A, Feig M. 2018. High-resolution 3D models of \textit{Caulobacter crescentus} chromosome reveal genome structural variability and organization. \textit{Nucleic Acids Res} \textbf{46}(8):3937--3952.

\bibitem{Trussart2017}Trussart M, Yus E, Martinez S, BaÃ¹ D, Tahara YO, Pengo T, Widjaja M, Kretschmer S, Swoger J, Djordjevic S, Turnbull L, Whitchurch C, Miyata M, Marti-Renom MA, Lluch-Senar M, Serrano L. 2017. Defined chromosome structure in the genome-reduced bacterium \textit{Mycoplasma pneumoniae}. \textit{Nat Commun} \textbf{8}:14665

\bibitem{Marbouty2014}Marbouty M, Cournac A, Flot JF, Marie-Nelly H, Mozziconacci J, Koszul R. 2014. Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. \textit{Elife} \textbf{3}:e03318

\bibitem{Marbouty2015}Marbouty M, Le Gall A, Cattoni DI, Cournac A, Koh A, Fiche JB, Mozziconacci J, Murray H, Koszul R, Nollmann M. 2015. Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging. \textit{Mol Cell} \textbf{59}(4):588--602.

\bibitem{Marbouty2017}Marbouty M, Baudry L, Cournac A, Koszul R. 2017. Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay. \textit{Sci Adv} \textbf{3}(2):e1602105

\bibitem{Lioy2018}Lioy VS, Cournac A, Marbouty M, Duigou S, Mozziconacci J, Esp\'eli O, Boccard F, Koszul R. 2018. Multiscale Structuring of the \textit{E. coli }Chromosome by Nucleoid-Associated and Condensin Proteins. \textit{Cell} \textbf{172}(4):771--783.e18. % doi: 10.1016/j.cell.2017.12.027

\bibitem{Bohm2020}B\"ohm K, Giacomelli G, Schmidt A, Imhof A, Koszul R, Marbouty M, Bramkamp M. 2020. Chromosome organization by a conserved condensin-ParB system in the actinobacterium \textit{Corynebacterium glutamicum}. \textit{Nat Commun} \textbf{11}(1):1485.

\bibitem{Marbouty2021}Marbouty M, Thierry A, Millot GA, Koszul R. 2021. MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut. \textit{Elife} \textbf{10}:e60608

\bibitem{Lamy-Besnier2023}Lamy-Besnier Q, Bignaud A, Garneau JR, Titecat M, Conti DE, Von Strempel A, Monot M, Stecher B, Koszul R, Debarbieux L, Marbouty M. 2023. Chromosome folding and prophage activation reveal specific genomic architecture for intestinal bacteria. \textit{Microbiome} \textbf{11}(1):111

\bibitem{Wang2017}Wang X, Brand\~ao HB, Le TB, Laub MT, Rudner DZ. 2017. \textit{Bacillus subtilis} SMC complexes juxtapose chromosome arms as they travel from origin to terminus. \textit{Science} \textbf{355}(6324):524--527.

\bibitem{Austin1983a}Austin S, Abeles A. 1983. Partition of unit-copy miniplasmids to daughter cells. II. The partition region of miniplasmid P1 encodes an essential protein and a centromere-like site at which it acts. \textit{J Mol Biol} \textbf{169}(2):373--87.

\bibitem{Austin1983b}Austin S, Abeles A. 1983. Partition of unit-copy miniplasmids to daughter cells. I. P1 and F miniplasmids contain discrete, interchangeable sequences sufficient to promote equipartition. \textit{J Mol Biol} \textbf{169}(2):353--372.

\bibitem{Abeles1985}Abeles AL, Friedman SA, Austin SJ. 1985. Partition of unit-copy miniplasmids to daughter cells. III. The DNA sequence and functional organization of the P1 partition region. \textit{J Mol Biol} \textbf{185}(2):261--272.

\bibitem{Jalal2020}Jalal ASB, Le TBK. 2020. Bacterial chromosome segregation by the ParABS system. \textit{Open Biol} \textbf{10}(6):200097

\bibitem{Livny2007}Livny J, Yamaichi Y, Waldor MK. 2007. Distribution of centromere-like parS sites in bacteria: insights from comparative genomics. \textit{J Bacteriol} \textbf{189}(23):8693--8703.

\bibitem{Takemata2019}Takemata N, Samson RY, Bell SD. 2019. Physical and Functional Compartmentalization of Archaeal Chromosomes. \textit{Cell} \textbf{179}(1):165--179.

\bibitem{Cockram2021}Cockram C, Thierry A, Gorlas A, Lestini R, Koszul R. 2021. Euryarchaeal genomes are folded into SMC-dependent loops and domains, but lack transcription-mediated compartmentalization. \textit{Mol Cell} \textbf{81}(3):459--472.e10

\bibitem{Ofer2023}Ofer S, Blombach F, Erkelens AM, Barker D, Soloviev Z, Schwab S, Smollett K, Matelska D, Fouqueau T, van der Vis N, Kent NA, Thalassinos K, Dame RT, Werner F. 2023. DNA-bridging by an archaeal histone variant via a unique tetramerisation interface. \textit{Commun Biol} \textbf{6}(1):968

\bibitem{MarinovSymb}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{Sakrikar2021}Sakrikar S, Schmid AK. 2021. An archaeal histone-like protein regulates gene expression in response to salt stress. \textit{Nucleic Acids Res} \textbf{49}(22):12732--12743.

\bibitem{Jevtic2019}Jevtic Z, Stoll B, Pfeiffer F, Sharma K, Urlaub H, Marchfelder A, Lenz C. 2019. The Response of \textit{Haloferax volcanii} to Salt and Temperature Stress: A Proteome Study by Label-Free Mass Spectrometry. \textit{Proteomics} \textbf{19}(20):e1800491

\bibitem{Dulmage2015}Dulmage KA, Todor H, Schmid AK. 2015. Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein. \textit{mBio} \textbf{6}(5):e00649--15

\bibitem{Bankevich2012}Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. \textit{J Comput Biol} \textbf{19}(5):455--477. % doi: 10.1089/cmb.2012.0021. 

\bibitem{Aziz2008}Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST Server: rapid annotations using subsystems technology. \textit{BMC Genomics} \textbf{9}:75.

\bibitem{infernal}Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. \textit{Bioinformatics} \textbf{29}:2933--2935.

\bibitem{RFAM}Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD. 2015. Rfam 12.0: updates to the RNA families database. \textit{Nucleic Acids Res} \textbf{43}(Database issue):D130--137.

\bibitem{RNAmmer}Lagesen K, Hallin P, R{\o}dland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. \textit{Nucleic Acids Res} \textbf{35}(9):3100--3108.

\bibitem{Edgar2004}Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. \textit{Nucleic Acids Res} \textbf{32}(5):1792--1797.

\bibitem{HMMER3}Eddy SR. 2011. Accelerated Profile HMM Searches. \textit{PLoS Comput Biol} \textbf{7}(10):e1002195.

\bibitem{PFAM}Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. 2014. Pfam: the protein families database. \textit{Nucleic Acids Res} \textbf{42}(Database issue):D222--230.

\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{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{Love2014}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{MarinovNucl}Marinov GK, Chen X, Wu T, He C, Grossman AR, Kundaje A, Greenleaf WJ. 2022. The chromatin organization of a chlorarachniophyte nucleomorph genome. \textit{Genome Biol} \textbf{23}(1):65

\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{Durand2016b}Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, Aiden EL. 2016. Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. \textit{Cell Syst} \textbf{3}(1):99--101. 

