Actin-related protein Arp4 regulates euchromatic gene expression and development by H2A.Z deposition in blood-stage Plasmodium falciparum [H2A.Z ChIP-seq]. Actin-related protein Arp4 regulates euchromatic gene expression and development by H2A.Z deposition in blood-stage Plasmodium falciparum [H2A.Z ChIP-seq]

Chromatin structure is a basal epigenetic mechanism that determines cellular fate by organizing the dynamic gene expression during the cell development and proliferation. The nuclear members of the evolutionarily conserved actin-related protein (ARPs) superfamily are major components of nucleosome remodelingcomplexes in the nucleus. In the human malaria parasites, Plasmodium falciparum, comparative genome analysis reveals that two canonical actins and three orthologues of ARPs including PfArp1, PfArp4, and PfArp6 are encoded in the genome of this parasite. However, little is known about the biological functions of the two nuclear PfArp4 and PfArp6 proteins. Here, by Pfarp4 gene knockdown and comparative transcriptome analysis, we uncovered that PfArp4 correlated positively with the dynamic expression of eukaryotic genes. Genome-wide distribution analysis by ChIP-seq revealed that PfArp4 protein colocalized with the histone 2A variant H2A.Z and euchromatic marker H3K9ac in the intergenic regions. Inducible downregulation of PfArp4 resulted in the depletion of H2A.Z and lower H3K9ac level at the upstream regions of eukaryotic genes, thereby repressing the transcriptional abundances. Moreover, we found a significant enrichment of PfArp4 at the flanking sites of centromeres, which likely shapes the H2A.Z-enriched centromeric chromatin microenvironment as a boundary marker. PfArp4 depletion triggered loss of H2A.Z at the entire centromere regions, and arrested the blood-stage development probably through interference with the schizogony process. Finally, PfArp6 was detected as an interactor of PfArp4 in the nucleus. Taken together, our finding indicates that the nuclear PfArp4/6regulates the cell cycles through controlling H2A.Z deposition and centromere biology, which will contribute to understanding the complex epigenetic regulation of gene expression and development of the malaria parasites. Overall design: Genome-wide location analysis (ChIP-Seq) of H2A.Z in the P. falciparum for wt ,wt_GlcN+,PfArp4 and PfArp4_GlcN+ parasites

染色质结构是一种基础表观遗传机制，通过调控细胞发育与增殖过程中的动态基因表达，决定细胞命运。进化保守的肌动蛋白相关蛋白（actin-related protein, ARPs）超家族的核成员，是细胞核内核小体重塑复合物的核心组分。在人类疟原虫——恶性疟原虫（Plasmodium falciparum）中，比较基因组分析显示，该寄生虫基因组编码两种经典肌动蛋白以及三类肌动蛋白相关蛋白同源物，分别为PfArp1、PfArp4与PfArp6。然而，目前对于这两种核定位的PfArp4与PfArp6蛋白的生物学功能尚不清楚。本研究通过对Pfarp4基因进行敲降并开展比较转录组分析，发现PfArp4与真核生物基因的动态表达呈正相关。通过染色质免疫共沉淀测序（ChIP-seq）进行的全基因组分布分析显示，PfArp4蛋白与组蛋白2A变体H2A.Z以及常染色质标记H3K9ac在基因间区共定位。诱导性下调PfArp4的表达会导致真核基因上游区域的H2A.Z缺失以及H3K9ac水平降低，进而抑制基因转录丰度。此外，我们发现PfArp4在着丝粒侧翼区域存在显著富集，其可能作为边界标记，塑造富含H2A.Z的着丝粒染色质微环境。PfArp4的缺失会导致全着丝粒区域的H2A.Z丢失，并可能通过干扰裂体增殖过程，阻断疟原虫的红内期发育。最后，我们在细胞核中检测到PfArp6与PfArp4存在相互作用。综上，本研究结果表明，核定位的PfArp4/6复合物通过调控H2A.Z的沉积与着丝粒生物学功能，调控疟原虫的细胞周期，这将有助于解析疟原虫基因表达与发育过程中的复杂表观遗传调控机制。实验整体设计：针对恶性疟原虫的H2A.Z开展全基因组定位分析（ChIP-seq），实验样本包括野生型（wt）、wt_GlcN+、PfArp4组与PfArp4_GlcN+寄生虫株