An exon DNA element modulates heterochromatin spreading in the master regulator for sexual commitment in malaria parasites

Heterochromatin is essential in all eukaryotes to maintain genome integrity, long-term gene repression and to help chromosome segregation during mitosis. However, heterochromatin regions must be restricted by boundary elements to avoid its spreading over actively transcribed loci. In , facultative heterochromatin is important to regulate parasite virulence, antigenic variation and transmission. However, the underlying molecular mechanisms regulating repressive regions remain unknown. To investigate this topic, we chose the gene, which forms a strictly delimited and independent heterochromatin island. Using electrophoretic motility shift assay (EMSA) we identified an exon element at the 3’ end binding nuclear protein complexes. Upon replacement of this region by a gene, we observed a shift in the heterochromatin boundary resulting in HP1 (Heterochromatin Protein 1) spreading over ∼2 additional kb downstream. We used this DNA element to purify candidate proteins followed by proteomic analysis. The identified complexes were found to be enriched in RNA-binding proteins, pointing to a potential role of RNA in the regulation of the 3’ heterochromatin boundary. Our results provide insight into the unexplored topic of heterochromatin biology in and identify a DNA element within the master regulator of sexual commitment modulating heterochromatin spreading.