Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, United States of America.
Broad Institute of MIT and Harvard, Cambridge, MA, United States of America.
PLoS One. 2019 Dec 30;14(12):e0216515. doi: 10.1371/journal.pone.0216515. eCollection 2019.
The HIV genome is rich in A but not G or U and deficient in C. This nucleotide bias controls HIV phenotype by determining the highly unusual composition of all major HIV proteins. The bias is also responsible for the high frequency of narrow DNA minor groove sites in the double-stranded HIV genome as compared to cellular protein coding sequences and the bulk of the human genome. Since drugs that bind in the DNA minor groove disrupt nucleosomes on sequences that contain closely spaced oligo-A tracts which are prevalent in HIV DNA because of its bias, it was of interest to determine if these drugs exert this selective inhibitory effect on HIV chromatin. To test this possibility, nucleosomes were reconstituted onto five double-stranded DNA fragments from the HIV-1 pol gene in the presence and in the absence of several minor groove binding drugs (MGBDs). The results demonstrated that the MGBDs inhibited the assembly of nucleosomes onto all of the HIV-1 segments in a manner that was proportional to the A-bias, but had no detectable effect on the formation of nucleosomes on control cloned fragments or genomic DNA from chicken and human. Nucleosomes preassembled onto HIV DNA were also preferentially destabilized by the drugs as evidenced by enhanced nuclease accessibility in physiological ionic strength and by the preferential loss of the histone octamer in hyper-physiological salt solutions. The drugs also selectively disrupted HIV-containing nucleosomes in yeast as revealed by enhanced nuclease accessibility of the in vivo assembled HIV chromatin and reductions in superhelical densities of plasmid chromatin containing HIV sequences. A comparison of these results to the density of A-tracts in the HIV genome indicates that a large fraction of the nucleosomes that make up HIV chromatin should be preferred in vitro targets for the MGBDs. These results show that the MGBDs preferentially disrupt HIV-1 chromatin in vitro and in vivo and raise the possibility that non-toxic derivatives of certain MGBDs might serve as a novel class of anti-HIV agents.
HIV 基因组富含 A，但不含 G 或 U，且 C 含量不足。这种核苷酸偏向性通过决定所有主要 HIV 蛋白的非常特殊的组成来控制 HIV 表型。这种偏向性还导致双链 HIV 基因组中 DNA 小沟的窄位点的高频出现，与细胞蛋白编码序列和大部分人类基因组相比。由于结合 DNA 小沟的药物会破坏含有紧密间隔的寡 A 片段的核小体，而 HIV DNA 由于其偏向性而富含这些片段，因此人们有兴趣确定这些药物是否对 HIV 染色质产生这种选择性抑制作用。为了检验这种可能性，在存在和不存在几种小沟结合药物 (MGBD) 的情况下，将核小体重新组装到来自 HIV-1 pol 基因的五个双链 DNA 片段上。结果表明，MGBD 以与 A 偏向性成比例的方式抑制所有 HIV-1 片段上核小体的组装，但对对照克隆片段或来自鸡和人的基因组 DNA 上核小体的形成没有可检测的影响。如在生理离子强度下增加核酸酶可及性和组蛋白八聚体优先丢失所证明的那样，预先组装到 HIV DNA 上的核小体也被药物优先去稳定。药物还通过增强体内组装的 HIV 染色质的核酸酶可及性和降低含有 HIV 序列的质粒染色质的超螺旋密度，选择性地破坏酵母中的含 HIV 核小体。将这些结果与 HIV 基因组中的 A 片段密度进行比较表明，构成 HIV 染色质的核小体的很大一部分应该是 MGBD 的体外优先靶标。这些结果表明，MGBD 优先体外和体内破坏 HIV-1 染色质，并提出某些 MGBD 的无毒衍生物可能作为一类新型抗 HIV 药物的可能性。
