SATB1-Binding sequences and Alu-like motifs define a unique chromatin context in the vicinity of human immunodeficiency virus type 1 integration sites
SATB1-Binding sequences and Alu-like motifs define a unique chromatin context in the vicinity of human immunodeficiency virus type 1 integration sites
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DOI：
10.1128/jvi.01405-06
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发表时间：
2007-06-01
影响因子：
5.4
通讯作者：
Galande, Sanjeev
中科院分区：
文献类型：
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作者：
Kumar, Pavan P.;Mehta, Sameet;Galande, Sanjeev
逆转录病毒整合最近被证明是非随机的，有利于染色质的转录活性区域。然而，逆转录病毒选择整合位点的机制尚不清楚。我们在这里显示，在侧翼的序列中出现的病毒整合位点，这是显着不同的随机挑选的序列从人类基因组中获得的序列，表明独特的主要序列特征存在于人类免疫缺陷病毒1型（HIV-1）靶向的基因组区域。此外，这些序列优先结合的SATB 1，T谱系限制的染色质组织者，在体外和体内。Alu重复序列占人类基因组的近10%，并与转录调控有关。为了特异性地分离病毒整合位点侧翼的序列，同时也包含了类似重复序列和SATB 1结合位点，我们将染色质免疫沉淀与连续PCR相结合。从HIV-1 NL 4.3感染的Jurkat T细胞染色质中分离的抗SATB 1免疫沉淀基因组DNA片段库中特异性免疫沉淀并扩增HIV-1整合位点侧翼的克隆序列。此外，这些序列中的许多序列优先分配在与核基质紧密相关的DNA中，而不是在染色质环中。引人注目的是，当SATB 1沉默时，这些区域中的许多区域不利于整合，这为它在HIV-1整合位点选择中的作用提供了明确的证据。我们建议，明确的序列特征，如ESTA样的图案和SATB 1结合位点提供了一个独特的染色质背景下，在体内，这是优先针对HIV-1的整合机制。
Retroviral integration has recently been shown to be nonrandom, favoring transcriptionally active regions of chromatin. However, the mechanism for integration site selection by retroviruses is not clear. We show here the occurrence of Alu-like motifs in the sequences flanking the reported viral integration sites that are significantly different from those obtained from the randomly picked sequences from the human genome, suggesting that unique primary sequence features exist in the genomic regions targeted by human immunodeficiency virus type 1 (HIV-1). Additionally, these sequences were preferentially bound by SATB1, the T lineage-restricted chromatin organizer, in vitro and in vivo. Alu repeats make up nearly 10% of the human genome and have been implicated in the regulation of transcription. To specifically isolate sequences flanking the viral integration sites and also harboring both Alu-like repeats and SATB1-binding sites, we combined chromatin immunoprecipitation with sequential PCRs. The cloned sequences flanking HIV-1 integration sites were specifically immunoprecipitated and amplified from the pool of anti-SATB1-immunoprecipitated genomic DNA fragments isolated from HIV-1 NL4.3-infected Jurkat T-cell chromatin. Moreover, many of these sequences were preferentially partitioned in the DNA associated tightly with the nuclear matrix and not in the chromatin loops. Strikingly, many of these regions were disfavored for integration when SATB1 was silenced, providing unequivocal evidence for its role in HIV-1 integration site selection. We propose that definitive sequence features such as the Alu-like motifs and SATB1-binding sites provide a unique chromatin context in vivo which is preferentially targeted by the HIV-1 integration machinery.