, WHO. World malaria report, 2018.

Z. Bozdech, M. Lliná-s, B. L. Pulliam, E. D. Wong, J. Zhu et al., The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum, PLoS Biol, vol.1, 2003.

V. Van-noort and M. A. Huynen, Combinatorial gene regulation in Plasmodium falciparum, Trends Genet, vol.22, pp.73-81, 2006.

A. Scherf, J. J. Lopez-rubio, and L. Riviere, Antigenic variation in Plasmodium falciparum, Annu Rev Microbiol, vol.62, pp.445-470, 2008.

S. M. Kraemer, S. A. Kyes, G. Aggarwal, A. L. Springer, S. O. Nelson et al., Patterns of gene recombination shape var gene repertoires in Plasmodium falciparum: comparisons of geographically diverse isolates, BMC Genomics, vol.8, p.45, 2007.

L. Jiang, J. Mu, Q. Zhang, T. Ni, P. Srinivasan et al., PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum, Nature, vol.499, pp.223-227, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-00842612

J. Lopez-rubio, L. Mancio-silva, and A. Scherf, Genome-wide analysis of heterochromatin associates clonally variant gene regulation with perinuclear repressive centers in malaria parasites, Cell Host Microbe, vol.5, pp.179-190, 2009.

C. Wang, S. R. Adapa, J. Gibbons, S. Sutton, and R. Jiang, Punctuated chromatin states regulate Plasmodium falciparum antigenic variation at the intron and 2 kb upstream regions, BMC Genomics, vol.17, p.27538502, 2016.

I. Amit-avraham, G. Pozner, S. Eshar, Y. Fastman, N. Kolevzon et al., Antisense long noncoding RNAs regulate var gene activation in the malaria parasite Plasmodium falciparum, Proc Natl Acad Sci, vol.112, pp.982-991, 2015.

J. A. Rowe, A. Claessens, R. A. Corrigan, and M. Arman, Adhesion of Plasmodium falciparum-infected erythrocytes to human cells: molecular mechanisms and therapeutic implications, Expert Rev Mol Med, vol.11, 2009.

M. L. Bochman, K. Paeschke, and V. A. Zakian, DNA secondary structures: stability and function of G-quadruplex structures, Nat Rev Genet, vol.13, pp.770-780, 2012.

N. Maizels, Dynamic roles for G4 DNA in the biology of eukaryotic cells, Nat Struct Mol Biol, vol.13, pp.1055-1059, 2006.

N. Maizels and L. T. Gray, The G4 genome, PLoS Genet, vol.9, 2013.

R. Hänsel-hertsch, D. Beraldi, S. Lensing, G. Marsico, K. Zyner et al., G-quadruplex structures mark human regulatory chromatin, Nat Genet, vol.48, pp.1267-1272, 2016.

R. Hänsel-hertsch, D. Antonio, M. Balasubramanian, and S. , DNA G-quadruplexes in the human genome: Detection, functions and therapeutic potential, Nat Rev Mol Cell Biol, vol.18, pp.279-284, 2017.

R. Rodriguez, K. M. Miller, J. Forment, C. R. Bradshaw, M. Nikan et al., Small-molecule-induced DNA damage identifies alternative DNA structures in human genes, Nat Chem Biol, vol.8, pp.301-310, 2012.

A. Siddiqui-jain, C. L. Grand, D. J. Bearss, and L. H. Hurley, Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription, Proc Natl Acad Sci, vol.99, pp.11593-11598, 2002.

A. J. Zaug, E. R. Podell, and T. R. Cech, Human POT1 disrupts telomeric G-quadruplexes allowing telomerase extension in vitro, Proc Natl Acad Sci, vol.102, pp.10864-10869, 2005.

R. Shahid, A. Bugaut, and S. Balasubramanian, The BCL-2 5 0 untranslated region contains an RNA G-quadruplex-forming motif that modulates protein expression, Biochemistry, vol.49, pp.8300-8306, 2010.

S. Balasubramanian, L. H. Hurley, and S. Neidle, Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?, Nat Rev Drug Discov, vol.10, pp.261-275, 2011.

S. Neidle, Quadruplex Nucleic Acids as Novel Therapeutic Targets, J Med Chem, vol.59, pp.5987-6011, 2016.

D. Drygin, A. Siddiqui-jain, O. 'brien, S. Schwaebe, M. Lin et al., Anticancer activity of CX-3543: A direct inhibitor of rRNA biogenesis, Cancer Res, vol.69, pp.7653-7661, 2009.

J. A. Capra, K. Paeschke, M. Singh, and V. A. Zakian, G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae, PLoS Comput Biol, vol.6, p.1000861, 2010.

P. Rawal, V. B. Kummarasetti, J. Ravindran, N. Kumar, K. Halder et al., Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation, Genome Res, vol.16, pp.644-655, 2006.

R. Perrone, E. Lavezzo, E. Riello, R. Manganelli, G. Palu et al., Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions, Sci Rep, vol.7, p.28720801, 2017.

R. Garg, J. Aggarwal, and B. Thakkar, Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants, Sci Rep, vol.6, p.28211, 2016.

E. Lavezzo, M. Berselli, I. Frasson, R. Perrone, G. Palù et al., G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide, PLoS Comput Biol, vol.14, p.1006675, 2018.

E. Belmonte-reche, M. Martinez-garcia, A. Guedin, M. Zuffo, M. Arevalo-ruiz et al., G-Quadruplex Identification in the Genome of Protozoan Parasites Points to Naphthalene Diimide Ligands as New Antiparasitic Agents, J Med Chem, vol.61, pp.1231-1240, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02863564

N. Smargiasso, V. Gabelica, C. Damblon, F. Rosu, D. Pauw et al., Putative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes, BMC Genomics, vol.10, p.362, 2009.

V. S. Chambers, G. Marsico, J. M. Boutell, D. Antonio, M. Smith et al., High-throughput sequencing of DNA G-quadruplex structures in the human genome, Nat Biotechnol, vol.33, pp.877-881, 2015.

G. Marsico, V. S. Chambers, A. B. Sahakyan, P. Mccauley, J. M. Boutell et al., Whole genome experimental maps of DNA G-quadruplexes in multiple species, Nucleic Acids Res, vol.47, pp.3862-3874, 2019.

L. A. Cahoon and H. S. Seifert, An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoeae. Science (80-), vol.325, pp.764-767, 2009.

R. Perrone, M. Nadai, I. Frasson, J. A. Poe, E. Butovskaya et al., A Dynamic G-quadruplex region regulates the HIV-1 Long terminal repeat promoter, J Med Chem, vol.56, pp.6521-6530, 2013.

P. Murat, J. Zhong, L. Lekieffre, N. P. Cowieson, J. L. Clancy et al., G-quadruplexes regulate Epstein-Barr virus-encoded nuclear antigen 1 mRNA translation, Nat Chem Biol, vol.10, pp.358-364, 2014.

B. Biswas, M. Kandpal, U. K. Jauhari, and P. Vivekanandan, Genome-wide analysis of G-quadruplexes in herpesvirus genomes, BMC Genomics, vol.17, p.949, 2016.

L. M. Harris, K. R. Monsell, F. Noulin, T. Famodimu, M. Smargiasso et al., G-quadruplex DNA motifs in the malaria parasite Plasmodium falciparum and their potential as novel antimalarial drug targets, Antimicrob Agents Chemother, vol.62, pp.1828-1845, 2018.

M. Anas, R. Sharma, V. Dhamodharan, P. I. Pradeepkumar, A. Manhas et al., Investigating Pharmacological Targeting of G-Quadruplexes in the Human Malaria Parasite, Biochemistry, vol.56, pp.6691-6699, 2017.

J. Guillon, A. Cohen, R. N. Das, C. Boudot, N. M. Gueddouda et al., Design, synthesis, and antiprotozoal evaluation of new 2,9-bis[(substituted-aminomethyl)phenyl]-1,10-phenanthroline derivatives, Chem Biol Drug Des, vol.91, pp.974-995, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01690455

M. J. Gardner, N. Hall, E. Fung, O. White, M. Berriman et al., Genome sequence of the human malaria parasite Plasmodium falciparum, Nature, vol.19, pp.498-511, 2002.

A. Stanton, L. M. Harris, G. Graham, and C. J. Merrick, Recombination events among virulence genes in malaria parasites are associated with G-quadruplex-forming DNA motifs, BMC Genomics, vol.17, p.27809775, 2016.

A. Bedrat, L. Lacroix, and J. L. Mergny, Re-evaluation of G-quadruplex propensity with G4Hunter, Nucleic Acids Res, vol.44, pp.1746-1759, 2016.

A. Claessens, L. M. Harris, S. Stanojcic, L. Chappell, A. Stanton et al., RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics, PLoS Genet, vol.14, p.1007490, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01989183

D. Bhartiya, V. Chawla, S. Ghosh, R. Shankar, and N. Kumar, Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum, Genomics, vol.108, pp.224-231, 2016.

J. L. Huppert and S. Balasubramanian, Prevalence of quadruplexes in the human genome, Nucleic Acids Res, vol.33, pp.2908-2916, 2005.

O. Kikin, L. Antonio, and P. S. Bagga, QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences, Nucleic Acids Res, vol.34, pp.676-682, 2006.

C. Aurrecoechea, J. Brestelli, B. P. Brunk, J. Dommer, S. Fischer et al., PlasmoDB: A functional genomic database for malaria parasites, Nucleic Acids Res, vol.37, pp.539-543, 2009.

M. Saad, A. Guédin, S. Amor, A. Bedrat, N. J. Tourasse et al., Mapping and characterization of G-quadruplexes in the genome of the social amoeba Dictyostelium discoideum, Nucleic Acids Res, vol.47, pp.4363-4374, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02140699

A. Guédin, L. Y. Lin, S. Armane, L. Lacroix, J. Mergny et al., Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome, Nucleic Acids Res, vol.46, pp.5297-5307, 2018.

J. L. Ruiz, J. J. Tena, C. Bancells, A. Cortés, J. L. Gómez-skarmeta et al., Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum, Nucleic Acids Res, vol.46, pp.9414-9431, 2018.

S. H. Adjalley, C. D. Chabbert, B. Klaus, V. Pelechano, and L. M. Steinmetz, Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum, Cell Rep, vol.14, pp.2463-2475, 2016.

E. P. Calvo, M. Wasserman, and . G-quadruplex-ligands, Potent inhibitors of telomerase activity and cell proliferation in Plasmodium falciparum, Mol Biochem Parasitol, vol.207, pp.33-38, 2016.

A. De-cian, P. Grellier, E. Mouray, D. Depoix, H. Bertrand et al., Plasmodium telomeric sequences: structure, stability and quadruplex targeting by small compounds, Chembiochem, vol.9, pp.2730-2739, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00339356

T. S. Rask, D. A. Hansen, T. G. Theander, A. G. Pedersen, and T. Lavstsen, Plasmodium falciparum erythrocyte membrane protein 1 diversity in seven genomes-divide and conquer, PLoS Comput Biol, vol.6, 2010.

T. D. Otto, A. Gilabert, T. Crellen, U. Böhme, C. Arnathau et al., Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria, Nat Microbiol, vol.3, p.29784978, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01960220

T. L. Bailey, M. Boden, F. A. Buske, M. Frith, C. E. Grant et al., Tools for motif discovery and searching, Nucleic Acids Res, vol.37, pp.202-208, 2009.

C. Ribeyre, J. Lopes, J. Boulé, A. Piazza, A. Gué-din et al., The Yeast Pif1 Helicase Prevents Genomic Instability Caused by G-Quadruplex-Forming CEB1 Sequences In Vivo. Cohen-Fix O, editor, PLoS Genet, vol.5, p.1000475, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02109281

R. Del-villar-guerra, J. O. Trent, and J. B. Chaires, G-Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy, Angew Chemie-Int Ed, vol.57, pp.7171-7175, 2018.

J. L. Mergny, J. Li, L. Lacroix, S. Amrane, and J. B. Chaires, Thermal difference spectra: A specific signature for nucleic acid structures, Nucleic Acids Res, vol.33, p.138, 2005.

A. R. De-la-faverie, A. Guédin, A. Bedrat, L. A. Yatsunyk, and J. L. Mergny, Thioflavin T as a fluorescence light-up probe for G4 formation, Nucleic Acids Res, vol.42, p.65, 2014.

E. Y. Lam, D. Beraldi, D. Tannahill, and S. Balasubramanian, G-quadruplex structures are stable and detectable in human genomic DNA, Nat Commun, vol.4, p.1796, 2013.

M. Frank and K. Deitsch, Activation, silencing and mutually exclusive expression within the var gene family of Plasmodium falciparum, Int J Parasitol, vol.36, pp.975-985, 2006.

R. E. Desjardins, C. J. Canfield, J. D. Haynes, and J. D. Chulay, Quantitative assessment of antimalarial activity in vitro by a semiautomated microdilution technique, Antimicrob Agents Chemother, vol.16, pp.710-718, 1979.

H. J. Painter and T. L. Campbell, Lliná s M. The Apicomplexan AP2 family: integral factors regulating Plasmodium development, Mol Biochem Parasitol, vol.176, pp.1-7, 2011.

J. Eddy and N. Maizels, Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes, Nucleic Acids Res, vol.36, pp.1321-1354, 2008.

J. L. Huppert and S. Balasubramanian, G-quadruplexes in promoters throughout the human genome, Nucleic Acids Res, 2007.

J. A. Smestad and L. J. Maher, Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription, BMC Med Genet, vol.16, p.91, 2015.

J. L. Huppert, A. Bugaut, S. Kumari, and S. Balasubramanian, G-quadruplexes: the beginning and end of UTRs, Nucleic Acids Res, vol.36, pp.6260-6268, 2008.

A. Claessens, W. L. Hamilton, M. Kekre, T. D. Otto, A. Faizullabhoy et al., Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis, PLoS Genet, vol.10, p.1004812, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01989273

S. Bopp, M. J. Manary, A. T. Bright, G. L. Johnston, N. V. Dharia et al., Mitotic Evolution of Plasmodium falciparum Shows a Stable Core Genome but Recombination in Antigen Families, PLoS Genet, vol.9, 2013.

A. Verma, V. K. Yadav, R. Basundra, A. Kumar, and S. Chowdhury, Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells, Nucleic Acids Res, vol.37, pp.4194-4204, 2009.

R. Halder, J. F. Riou, M. P. Teulade-fichou, T. Frickey, and J. S. Hartig, Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines, BMC Res Notes, vol.5, p.138, 2012.
URL : https://hal.archives-ouvertes.fr/inserm-00708330

M. Lawrence, W. Huber, H. Pagès, P. Aboyoun, M. Carlson et al., Software for Computing and Annotating Genomic Ranges, PLoS Comput Biol, vol.9, 2013.

M. Lawrence, R. Gentleman, and V. Carey, rtracklayer: an R package for interfacing with genome browsers, Bioinformatics, vol.25, pp.1841-1842, 2009.

P. R. Kensche, W. Hoeijmakers, C. G. Toenhake, M. Bras, L. Chappell et al., The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences, Nucleic Acids Res, vol.44, pp.2110-2124, 2015.

D. Sims, N. E. Ilott, S. N. Sansom, I. M. Sudbery, J. S. Johnson et al., CGAT: Computational genomics analysis toolkit, Bioinformatics, vol.30, pp.1290-1291, 2014.

J. Lelièvre, A. Berry, and F. Benoit-vical, An alternative method for Plasmodium culture synchronization, Exp Parasitol, vol.109, pp.195-197, 2005.

C. Lambros and J. P. Vanderberg, Synchronization of Plasmodium falciparum erythrocytic stages in culture, J Parasitol, vol.65, pp.418-438, 1979.

Y. Wu, C. D. Sifri, H. H. Lei, X. Z. Su, and T. E. Wellems, Transfection of Plasmodium falciparum within human red blood cells, Proc Natl Acad Sci, vol.92, pp.973-980, 1995.

C. Epp, F. Li, C. A. Howitt, T. Chookajorn, and K. W. Deitsch, Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum, RNA, vol.15, pp.116-143, 2009.

A. Salanti, T. Staalsoe, T. Lavstsen, A. Jensen, M. Sowa et al., Selective upregulation of a single distinctly structured var gene in chondroitin sulphate A-adhering Plasmodium falciparum involved in pregnancy-associated malaria, Mol Microbiol, vol.49, pp.179-191, 2003.

R. Dzikowski, M. Frank, and K. Deitsch, Mutually Exclusive Expression of Virulence Genes by Malaria Parasites Is Regulated Independently of Antigen Production, PLoS Pathog, vol.2, p.22, 2006.

T. N. Siegel, C. C. Hon, Q. Zhang, J. J. Lopez-rubio, C. Scheidig-benatar et al., Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum, BMC Genomics, vol.15, p.24559473, 2014.
URL : https://hal.archives-ouvertes.fr/inserm-00981322

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.25516281, 2014.