KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit αclsN (custom)	Eurogentec	N/A
Rabbit αPCNA3 (custom)	CovalAb	N/A
Rabbit αVps4 (custom)	CovalAb	N/A
Rabbit αReptin (custom)	Covance	N/A
Rabbit αRpo2	Qureshi et al., 1997	N/A
Goat αRabbit HRP	Pierce	Cat #65-6120
Archaeal Strains
S. acidocaldarius DSM639	Lab collection	N/A
S. islandicus E233S (ΔpyrEF ΔlacS)	Deng et al., 2009	N/A
S. islandicus Δorc1-1	Samson et al., 2013	N/A
S. islandicus Δorc1-1 Δorc1-3	Samson et al., 2013	N/A
S. islandicus E235 (ΔargD)	Zhang and Whitaker, 2018	N/A
S. acidocaldarius MW001	Wang et al., 2019	N/A
S. acidocaldarius ΔfadR	Wang et al., 2019	N/A
S. islandicus ΔoriC1	This study	N/A
Bacterial Strains
E. coli NEB 10 beta was used for cloning	New England Biolabs	Cat # C3019I
E. coli Rosetta (DE3) was used for protein expression	Millipore Sigma	Cat # 70954
Biological Samples
N/A
Chemicals, Peptides, and Recombinant Proteins
Actinomycin D	Sigma Aldrich	Cat# A1410-2MG
Restriction enzymes	New England Biolabs	N/A
Biotin-14-dCTP	Thermo Fisher Scientific	Cat# 19518018
DNA Polymerase I, Large (Klenow) Fragment	New England Biolabs	Cat# M0210L
T4 DNA ligase	New England Biolabs	Cat# M0202L
Phenol:chloroform:isoamyl alcohol	Sigma Aldrich	Cat# 77618-100ML
BSA	Thermo Fisher Scientific	Cat# B14
T4 DNA polymerase	New England Biolabs	Cat# M0203S
Dynabeads MyOne Streptavidin C1	Thermo Fisher Scientific	Cat# 65001
AMPure XP Beads	Beckman Coulter	Cat# A63880
37 % Formaldehyde	Thermo Fisher Scientific	Cat# BP531-500
nProteinA Sepharose fast Flow	GE Healthcare	Cat# 17-5280-01
HiTrap NHS-activated HP	GE Healthcare	Cat# 17-0716-01
Proteinase K	Thermo Fisher Scientific	Cat# 25530015
Glycogen	Invitrogen	Cat# 10814-010
Critical Commercial Assays
NEBNext Ultra DNA Library Prep Kit for Illumina	New England Biolabs	Cat# E7370S
NEBNex Multiplex Oligos for Illumina	New England Biolabs	Cat# E7335S, E7500S, E7710S
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina	New England Biolabs	Cat# E7760S
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina	New England Biolabs	Cat# E7760S
NEBuilder HiFI DNA Assembly Master Mix	New England Biolabs	Cat# E2621S
TruSeq ChIP Library Preparation Kit	Illumina	IP-202-1012, IP-202-1024
FISH Tag DNA Multicolor Kit	Thermo Fisher Scientific	Cat# F32951
Deposited Data
The NGS datasets generated in this study are available at GEO	https://www.ncbi.nlm.nih.gov/geo/	GSE128063
The ChIP Seq data for fadR were obtained from GEO	https://www.ncbi.nlm.nih.gov/geo/	GSE108039
Experimental Models: Cell Lines
N/A
Experimental Models: Organisms/Strains
Information shown in “Archaeal Strains”
Oligonucleotides
See Table S2
Recombinant DNA
pCR-XL-2-TOPO: DNA FISH P1 probe	This study	pNTB3
pCR-XL-2-TOPO: DNA FISH P2 probe	This study	pNTB4
pCR-XL-2-TOPO: DNA FISH P3 probe	This study	pNTB5
pCR-XL-2-TOPO: DNA FISH P4 probe	This study	pNTB6
pCR-XL-2-TOPO: DNA FISH P5 probe	This study	pNTB7
pET30-SacSMC	This study	pET30-SacSMC
pET33-SisSMC	This study	pET33-SisSMC
pCR-ArgD	This study	pCR-ArgD
pSSRgD	This study	pSSRgD
pSSRgD-ClsN	This study	pSSRgD-ClsN
Software and Algorithms
HiC-Pro	Servant et al., 2015	https://github.com/nservant/HiC-Pro
HiTC	Servant et al., 2012	https://bioconductor.org/packages/release/bioc/html/HiTC.html
ShRec3D	Lesne et al., 2014	https://sites.google.com/site/julienmozziconacci/home/softwares
VMD	Humphrey et al., 1996	https://www.ks.uiuc.edu/Research/vmd/
Bowtie 2	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
deepTools	Ramirez et al., 2016	https://deeptools.readthedocs.io/en/develop/
MACS2	Zhang et al., 2008	https://github.com/taoliu/MACS
Salmon	Patro et al., 2017	https://combine-lab.github.io/salmon/
SpotDistance	Schober et al., 2008	http://bigwww.epfl.ch/sage/soft/spotdistance/
Other