UMSBP2 is chromatin remodeler that functions in regulation of gene expression and suppression of antigenic variation in trypanosomes [ATAC-seq]

Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of trypanosomatids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and play an essential role in chromosome ends protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its, previously described, DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression that plays a role in the control of antigenic variation in T. brucei. Overall design: To determine the comparative differences between the accessible region of chromatin in the UMSBP2 knockdown Trypanosoma brucei brucei compared to the wild type ( 3 replicates for each of the 2 conditions)

通用微环序列结合蛋白（Universal Minicircle Sequence binding proteins, UMSBPs）是一类CCHC型锌指蛋白，可结合保守存在于动质体DNA（锥虫科寄生虫的线粒体基因组）微环复制起始位点的富含G单链UMS序列。近期研究证实，布氏锥虫UMSBP2（TbUMSBP2）可与端粒共定位，并在染色体末端保护过程中发挥不可或缺的作用。本研究报道，TbUMSBP2能够使由核心组蛋白H2B、H4或连接组蛋白H1凝集的体外DNA分子发生解凝集。该DNA解凝集过程通过TbUMSBP2与上述组蛋白之间的蛋白质-蛋白质相互作用介导，不依赖于其此前已被报道的DNA结合活性。对TbUMSBP2基因进行沉默会导致布氏锥虫染色质中核小体解离程度显著降低，该表型可通过向敲低细胞中补加TbUMSBP2得以恢复。转录组分析结果显示，TbUMSBP2沉默会影响布氏锥虫中多个基因的表达，其中对亚端粒变异表面糖蛋白（variant surface glycoproteins, VSG）基因的上调效应最为显著——这类基因介导非洲锥虫的抗原变异。上述观测结果表明，UMSBP2是一种染色质重塑蛋白，参与调控基因表达，并在布氏锥虫的抗原变异调控中发挥作用。

实验整体设计：为对比UMSBP2敲低的布氏布氏锥虫与野生型布氏布氏锥虫之间染色质可及区域的差异，本研究为两组实验各设置3次生物学重复。