REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
STBL3_pDC2	(Nkrumah et al., 2006)	N/A
STBL3_pOM1	This manuscript	N/A
STBL3_pOM2	This manuscript	N/A
XL10-Gold_attP_minkahrp	This manuscript	N/A
XL10-Gold_attP_minkahrp_PF3D7_1372200	This manuscript	N/A
XL10-Gold_attP_minkahrp_PF3D7_1200700	This manuscript	N/A
XL10-Gold_attP_minkahrp_PF3D7_0719000	This manuscript	N/A
XL10-Gold_attP_minkahrp_PF3D7_1222700	This manuscript	N/A
XL10-Gold_attP_minkahrp_PF3D7_1200700negative	This manuscript	N/A
XL10-Gold_attP_minkahrp_PF3D7_0719000negative	This manuscript	N/A
DH5α_pINT	This manuscript	N/A
STBL3	Thermo Fisher Scienfic	Cat#C7373-03
XL10-Gold	Stratagene	Cat#200314
DH5α	New England Biolabs	Cat#C29871
Chemicals, Peptides, and Recombinant Proteins
Blasticidin-S-HCl	Thermo Fisher Scienfic	Cat#R210-01
WR99210	Jacobus Pharmaceuticals	N/A
Geneticin	Thermo Fisher Scienfic	Cat#11811-031
Proteinase K	Sigma-Aldrich	Cat#P6556
KAPA HiFi HotStart ReadyMix	KAPA Biosystems	Cat#KK2602
TURBO DNase	Ambion (Thermo Fisher Scientific)	Cat#AM2238
NextFlex adapters	Bio Scientific	Cat#514122
Actinomycin D	Thermo Fisher Scientific	Cat#11805017
SuperScript III Reverse Transcriptase	Invitrogen (Thermo Fisher Scientific)	Cat#18080044
RNasin Plus RNase Inhibitor	Promega	Cat#N261B
2x iQ SYBR Green Supermix	BioRad	Cat#170-8887
cOmplete, EDTA-free Protease Inhibitor Cocktail	Roche (Sigma-Aldrich)	Cat#04693132001
Ribonucleic acid, transfer from baker’s yeast (S. cerevisiae)	Sigma-Aldrich	Cat#R5636
Poly(deoxyinosinic-deoxycytidylic) acid sodium salt	Sigma-Aldrich	Cat#P4929
Poly(deoxyadenylic-thymidylic) acid sodium salt	Sigma-Aldrich	Cat#P0883
TCEP	Sigma-Aldrich	Cat#C4706-2G
MMTS	Thermo Fisher Scienfic	Cat#23011
Trypsin/Lys-C Mix, Mass Spec Grade	Promega	Cat#V5072
NaBH3CN	Merck	Cat#818053
NaBD3CN	Sigma-Aldrich	Cat#190020-1G
Trifluoroacetic acid ULC/MS	Biosolve BV	Cat#20234131
Critical Commercial Assays
Wizard Plus SV Minipreps DNA Purification Systems	Promega	Cat#A1460
QIAamp DNA Blood Mini Kit	QIAGEN	Cat#51106
QIAquick PCR Purification Kit	QIAGEN	Cat#28106
MinElute PCR Purification Kit	QIAGEN	Cat#28006
QIAGEN RNeasy Mini Kit	QIAGEN	Cat#74106
Oligotex mRNA Mini Kit	QIAGEN	Cat#70022
Qubit dsDNA HS Assay Kit	Thermo Fisher Scientific	Cat#Q32854
Qubit RNA HS Assay Kit	Thermo Fisher Scientific	Cat#Q32852
Qubit Protein Assay Kit	Thermo Fisher Scientific	Cat#Q33212
Nextera DNA Library Prep Kit	Illumina	Cat#FC-121-1030
Nextera DNA Sample Preparation Index Kit	Illumina	Cat#FC-121-1012
Agilent High Sensitivity DNA Kit	Agilent	Cat#5067-4626
KAPA Library Quantification Kit	KAPA Biosystems	Cat#KR0405
NextSeq500/550 HighOutput kit V2 (75 cycles)	Illumina	Cat# FC-404-2005.
Deposited Data
ATAC-seq data in P. falciparum 3D7	This manuscript	GEO: GSE104075
RNA-seq data in P. falciparum 3D7	This manuscript	GEO: GSE104075
AP2-I-GFP ChIP-seq data in P. falciparum Dd2	(Santos et al., 2017)	GEO: GSE80293
P. falciparum 3D7 reference genome (release 26)	PlasmoDB and GeneDB (Aurrecoechea et al., 2009, Logan-Klumpler et al., 2012)	http://plasmodb.org/common/downloads/release-26/Pfalciparum3D7/fasta/data/PlasmoDB-26_Pfalciparum3D7_Genome.fasta
P. falciparum 3D7 reference annotated transcriptome (realease 26)	PlasmoDB and GeneDB (Aurrecoechea et al., 2009, Logan-Klumpler et al., 2012)	http://plasmodb.org/common/downloads/release-26/Pfalciparum3D7/fasta/data/PlasmoDB-26_Pfalciparum3D7_AnnotatedTranscripts.fasta
P. falciparum 3D7 annotated proteome (release 9.3)	PlasmoDB and GeneDB (Aurrecoechea et al., 2009, Logan-Klumpler et al., 2012)	http://plasmodb.org/common/downloads/release-9.3/Pfalciparum3D7/fasta/data/PlasmoDB-9.3_Pfalciparum3D7_AnnotatedProteins.fasta
Motifs from plants, vertebrates and invertebrates reported in CISBP	(Weirauch et al., 2014)	http://cisbp.ccbr.utoronto.ca/index.php
Experimental Models: Cell Lines
Parasite strain: P. falciparum 3D7	(Walliker et al., 1987)	Alan Cowman, WEHI, Melbourne, Australia
Parasite strain: P. falciparum 3D7 attB(+)	(Nkrumah et al., 2006)	David A. Fidock, Columbia Uni., US
Parasite strain: P. falciparum 3D7 attB::attP_minkahrp	This manuscript	N/A
Parasite strain: P. falciparum 3D7 attB::attP_minkahrp_PF3D7_137220	This manuscript	N/A
Parasite strain: P. falciparum 3D7 attB::attP_minkahrp_PF3D7_1200700	This manuscript	N/A
Parasite strain: P. falciparum 3D7 attB::attP_minkahrp_PF3D7_0719000	This manuscript	N/A
Parasite strain: P. falciparum 3D7 attB::attP_minkahrp_PF3D7_1200700negative	This manuscript	N/A
Parasite strain: P. falciparum 3D7 attB::attP_minkahrp_PF3D7_0719000negative	This manuscript	N/A
Oligonucleotides
See Table S1 for primers used for cloning and RTqPCR	Biolegio B.V.	N/A
See Table S1 for DNA oligo’s used for DNA pull-down experiments	Integrated DNA Technologies	N/A
Random hexamer primers	Roche (Sigma-Aldrich)	Cat#11034731001
OligodT12-18	Invitrogen (Thermo Fisher Scientific)	Cat#18418012
Recombinant DNA
MV163 plasmid	(Vos et al., 2015)	Robert Sauerwein, Radboud UMC, NL
pDC2 (attB containing plasmid)	(Nkrumah et al., 2006)	David A. Fidock, Columbia Uni., US
pINT	(Nkrumah et al., 2006)	David A. Fidock, Columbia Uni., US
pOM1	This manuscript	N/A
pOM2	This manuscript	N/A
attP_minkahrp	This manuscript	N/A
attP_minkahrp_PF3D7_0719000	This manuscript	N/A
attP_minkahrp_PF3D7_1200700	This manuscript	N/A
attP_minkahrp_PF3D7_1222700	This manuscript	N/A
attP_minkahrp_PF3D7_1372200	This manuscript	N/A
attP_minkahrp_PF3D7_0719000negative	This manuscript	N/A
attP_minkahrp_PF3D7_1200700negative	This manuscript	N/A
attP_minkahrp_PF3D7_1222700negative	This manuscript	N/A
Software and Algorithms
FastQC v0.11.2	(Andrew, 2010)	RRID: SCR_014583; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
BWA samse (version 0.7.12-r1039)	(Li and Durbin, 2010)	RRID: SCR_010910; http://bio-bwa.sourceforge.net/bwa.shtml
BWA-mem (version 0.7.10)	(Li, 2013)	RRID: SCR_010910; http://bio-bwa.sourceforge.net/bwa.shtml
Picard tools (version 1.139)	Broad Institute	RRID: SCR_006525; https://broadinstitute.github.io/picard/
Samtools (version 1.2 and 1.3.1)	(Li et al., 2009)	RRID: SCR_002105; http://samtools.sourceforge.net/
Bedtools suite (version 2.20.1)	(Quinlan and Hall, 2010)	RRID: SCR_006646; http://bedtools.readthedocs.io/en/latest/
MACS2 (release 2.7)	(Liu, 2016)	RRID: SCR_013291; https://github.com/taoliu/MACS/wiki/Advanced:-Call-peaks-using-MACS2-subcommands
R package preprocessCore (version 1.36.0)	(Bolstad, 2017)	https://github.com/bmbolstad/preprocessCore
UCSC Genome Browser	(Kent et al., 2002)	RRID: SCR_005780; http://genome.ucsc.edu/
Morpheus tool	Broad Institute	https://software.broadinstitute.org/morpheus/
Trimmomatic (version 0.36)	(Bolger et al., 2014)	RRID: SCR_011848; http://www.usadellab.org/cms/?page=trimmomatic
Fluff	(Georgiou and van Heeringen, 2016)	https://github.com/simonvh/fluff/blob/master/README.md
maxQuant (version 1.5.3.30)	(Cox and Mann, 2008)	RRID: SCR_014485; http://www.coxdocs.org/doku.php?id=maxquant:start
Perseus software package (version 1.4.0.20)	(Tyanova et al., 2016)	RRID: SCR_015753; http://www.coxdocs.org/doku.php?id=perseus:start
R package SeqGL (version 1.1.3)	(Setty and Leslie, 2015)	https://bitbucket.org/leslielab/seqgl/overview
GimmeMotifs package (v0.11.0)	(van Heeringen and Veenstra, 2011)	RRID: SCR_001146; http://gimmemotifs.readthedocs.io/en/master/
Other
Plasmodipur filters	EuroProxima	Cat#8011Filter25u
Agencourt AMPure XP beads	Beckman Coulter	Cat#A63882
Streptavidin Sepharose High Performance	GE Healthcare	Cat#17511301
2% E-Gel Size Select agarose gels	Invitrogen (Thermo Fisher Scientific)	Cat#G6610-02