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DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum

Affiliations
  • 1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
  • 2Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.
  • 3Huck Institutes Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA.
  • 4Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA.
  • 5Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA.
  • 6Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.
  • 7Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
  • 8Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.
  • 9Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.
  • 10Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
  • 11Department of Computer Science, Duke University, Durham, NC 27708, USA.
  • 12Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA.
  • 13Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.

Published on:

July 5, 2024

Abstract

Development of the malaria parasite, Plasmodium falciparum, is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites is largely unknown. To address TF specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized two additional ApiAP2 TFs, PfAP2-G and PfAP2-EXP, which bind unique DNA motifs (GTAC and TGCATGCA). We also interrogated the impact of DNA sequence and chromatin context on P. falciparum TF binding by integrating high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We found that DNA sequence context minimally impacts binding site selection for paralogous CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization correlate with differential binding. In contrast, GTGCAC-binding TFs prefer different DNA sequence context in addition to chromatin dynamics. Finally, we determined that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms.

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