BET proteins commonly activate cellular gene expression, yet inhibiting their recruitment paradoxically reactivates latent HIV-1 transcription. Here we identify the short isoform of BET family member BRD4 (BRD4S) as a corepressor of HIV-1 transcription. We found that BRD4S was enriched in chromatin fractions of latently infected T cells, and it was more rapidly displaced from chromatin upon BET inhibition than the long isoform. BET inhibition induced marked nucleosome remodeling at the latent HIV-1 promoter, which was dependent on the activity of BRG1-associated factors (BAF), an SWI/SNF chromatin-remodeling complex with known repressive functions in HIV-1 transcription. BRD4S directly bound BRG1, a catalytic subunit of BAF, via its bromodomain and extraterminal (ET) domain, and this isoform was necessary for BRG1 recruitment to latent HIV-1 chromatin. Using chromatin immunoprecipitation sequencing (ChIP-seq) combined with assay for transposase-accessible chromatin coupled to high-throughput sequencing (ATAC-seq) data, we found that the latent HIV-1 promoter phenotypically resembles endogenous long terminal repeat (LTR) sequences, pointing to a select role of BRD4S-BRG1 complexes in genomic silencing of invasive retroelements.

BET蛋白通常会激活细胞基因表达，但反常地抑制其募集会重新激活潜在的HIV-1转录。在这里，我们确定BET家族成员BRD4（BRD4S）的短同工型是HIV-1转录的核心抑制剂。我们发现，BRD4S富集了潜伏感染T细胞的染色质部分，并且与长同种型相比，经BET抑制，BRD4S从染色质中的迁移速度更快。BET抑制在潜在的HIV-1启动子上诱导了明显的核小体重塑，这取决于BRG1相关因子（BAF）的活性，该因子是SWI / SNF染色质重塑复合体，在HIV-1转录中具有已知的抑制功能。BRD4S通过其溴结构域和末端（ET）结构域直接结合BAF的催化亚基BRG1，该同工型对于BRG1募集到潜在的HIV-1染色质是必需的。使用染色质免疫沉淀测序（ChIP-seq）结合转座酶可及的染色质测定与高通量测序（ATAC-seq）数据相结合，我们发现潜在的HIV-1启动子在表型上类似于内源性长末端重复（LTR）序列，指出BRD4S-BRG1复合物在侵入性元件的基因组沉默中的选择性作用。