{"id":338,"date":"2022-08-23T11:05:06","date_gmt":"2022-08-23T02:05:06","guid":{"rendered":"https:\/\/kumamoto-u-jrchri.jp\/satou\/?post_type=topics_en&#038;p=338"},"modified":"2022-08-23T15:04:21","modified_gmt":"2022-08-23T06:04:21","slug":"probe-based-target-enrichment-improves-chip-seq-analysis-of-hiv-1-and-htlv-1-provirus","status":"publish","type":"topics_en","link":"https:\/\/kumamoto-u-jrchri.jp\/satou\/news\/topics_en\/probe-based-target-enrichment-improves-chip-seq-analysis-of-hiv-1-and-htlv-1-provirus\/","title":{"rendered":"Probe-based target enrichment improves ChIP-seq analysis of HIV-1 and HTLV-1 provirus"},"content":{"rendered":"<div class=\"topic_img_box\"><img class=\"alignnone size-full wp-image-203\" src=\"http:\/\/sample.ssrd.jp\/satou\/wp\/wp-content\/uploads\/2022\/07\/20220722_topic_img.png\" alt=\"\" \/><\/div>\n<div class=\"topic_img_suggest\">\u00a0<\/div>\n<p>Retroviruses, like HIV-1 and HTLV-1, integrate DNA copies of their genomes directly into the host cells\u2019 genomic DNA, forming a provirus. Integration allows these proviruses to coopt the molecular machinery of host cells to produce more virus, but the proviruses are subject to the same epigenetic factors that regulate non-viral genes on that chromosome. Understanding the regulation of transcription of these proviruses is valuable to both basic research and treatment of retroviruses that cause life-threatening illness.<\/p>\n<p>Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) has the potential to be an excellent tool for understanding the regulation of provirus transcription. However, these proviruses are only ~9 kb, integrated within the ~3 billion bp human genome. Performing detailed expression analysis on such a small proportion of the total DNA requires further enrichment of the target sequences beyond the ChIP enrichment.<\/p>\n<p>To achieve this, we designed biotinylated target capture probes against the most frequent HIV-1 and HTLV-1 subtypes prevalent in Japan. Then, we perform targeted enrichment on the samples with the relevant probe set after preparing the sequencing library samples.<\/p>\n<p>Analysis performed on non-enriched ChIP samples showed that &gt;99.99% of the reads were of the host genome and not useful for provirus analysis. However, with the probe-based, targeted enrichment, we were able to increase the provirus reads several hundred to several thousand fold over non-enriched samples. We also found that the data for the enriched libraries correlate well with the non-enriched ones, indicating that probe-based enrichment does not introduce any bias.<\/p>\n<p>Thus, we conclude that this probe-based, targeted enrichment method improves analysis of provirus sequences within the genomic context. Furthermore, the probes are easily customizable for the provirus sub-types and reduces the cost of performing deep sequencing runs. We believe that this method of probe-based provirus enrichment should be useful for other applications as well.<\/p>\n<p>[Journal Information]<\/p>\n<p>Title\u00a0\u00a0\u00a0\u00a0\u00a0: Application of targeted enrichment to next-generation sequencing of retroviruses\u00a0<br \/>\nintegrated into the host human genome<br \/>\nJournal: Scientific Reports<\/p>\n","protected":false},"featured_media":0,"template":"","acf":[],"_links":{"self":[{"href":"https:\/\/kumamoto-u-jrchri.jp\/satou\/wp-json\/wp\/v2\/topics_en\/338"}],"collection":[{"href":"https:\/\/kumamoto-u-jrchri.jp\/satou\/wp-json\/wp\/v2\/topics_en"}],"about":[{"href":"https:\/\/kumamoto-u-jrchri.jp\/satou\/wp-json\/wp\/v2\/types\/topics_en"}],"wp:attachment":[{"href":"https:\/\/kumamoto-u-jrchri.jp\/satou\/wp-json\/wp\/v2\/media?parent=338"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}