Figure 1

DNA-capture-seq enables the detection of proviral DNA with high sensitivity and the determination of the retroviral integration site. (A) The schematic flow of the experimental procedure following the construction of a new reference genome to be used in the analysis of a novel HIV-1-infected cell line. The alignment to a reference sequence, which was comprised of the human genome that includes the HXB2 HIV-1 sequence as an additional chromosome, allows us to obtain the consensus sequence of the integrated provirus and determine its structure. By using the same dataset to align to hg19 and the proviral sequence separated in two (LTR sequence and non-LTR sequence) we obtain the information of the integration site. With this information, we are able to construct a new reference sequence that is specific for the new cell line. (B) IGV profile for ACH-2 cell line, before (top) and after (bottom) enrichment with the virus-specific DNA probes. The proportion of reads that aligned to the provirus within the total data is also shown. As a reference genome for both mapping and visualization, we used hg19 containing the HIV-1 proviral sequence inserted at the viral integration site determined for ACH-2 cells. The pink and purple lines depict individual reads aligning the sense and anti-sense strands of the genomic DNA, respectively. (C) IGV profile for the J1.1 cell line after enrichment. The initial part of the 5′LTR and the end of the 3′LTR are shown with the details of the reads in the enlarged frames. (D) IGV profiles for J-Lat 9.2 and J-Lat 10.6 cell lines. The coverage for the EGFP region is low compared to the rest of the provirus because probes targeting this sequence were not included in the enrichment.