Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA.
Virol J. 2014 Jan 27;11:15. doi: 10.1186/1743-422X-11-15.
Adeno-associated virus (AAV) serotype 2 prevalently infects humans and is the only described eukaryotic virus that integrates site-preferentially. In a recent high throughput study, the genome wide distribution of AAV-2 integrants was determined using Integrant Capture Sequencing (IC-Seq). Additional insight regarding the integration of AAV-2 into human genomic DNA could be gleaned by low-throughput sequencing of complete viral-chromosomal junctions.
In this study, 140 clones derived from Integrant-Capture Sequencing were sequenced. 100 met sequence inclusion criteria, and of these 39 contained validated junction sequences. These unique sequences were analyzed to investigate the structure and location of viral-chromosomal junctions.
Overall the low-throughput analysis confirmed the genome wide distribution profile gathered through the IC-Seq analysis. We found no unidentifiable sequence inserted at AAV-2 chromosomal junctions. Assessing both left and right ends of the AAV genome, viral breakpoints predominantly occurred in one hairpin of the inverted terminal repeat and AAV genomes were preferentially integrated as single copies.
腺相关病毒(AAV)血清型 2 普遍感染人类,是唯一被描述的具有优先整合位点的真核病毒。在最近的高通量研究中,使用整合子捕获测序(IC-Seq)确定了 AAV-2 整合子的全基因组分布。通过对完整病毒-染色体连接点进行低通量测序,可以进一步了解 AAV-2 整合到人类基因组 DNA 中的情况。
本研究对来自整合子捕获测序的 140 个克隆进行了测序。满足序列纳入标准的有 100 个克隆,其中 39 个包含经验证的连接序列。对这些独特的序列进行了分析,以研究病毒-染色体连接点的结构和位置。
总的来说,低通量分析证实了通过 IC-Seq 分析获得的全基因组分布情况。我们没有发现 AAV-2 染色体连接点插入无法识别的序列。评估 AAV 基因组的左、右端,病毒断点主要发生在反向末端重复的一个发夹结构中,AAV 基因组优先以单拷贝形式整合。