Using Barcoded HIV Ensembles (B‐HIVE) for Single Provirus Transcriptomics

Current Protocols in Molecular Biology - Tập 122 Số 1 - 2018
Heng‐Chang Chen1,2,3, Eduard Zorita1,2,3, Guillaume J. Filion1,3
1Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
2these authors contributed equally to this work
3University Pompeu Fabra, Barcelona, Spain

Tóm tắt

AbstractThe latent HIV reservoir is the main barrier to curing AIDS, because infected cells escape the immune system and antiretroviral therapies. Developing new treatment strategies requires technologies to trace latent proviruses. Here, we describe a genome‐wide technique called Barcoded HIV Ensembles (B‐HIVE) to measure HIV expression at the single provirus level. The principle of B‐HIVE is to tag the genome of HIV with DNA barcodes to trace viral transcripts produced by single proviruses in an infected cell population. This in turn reveals which proviruses are active and which are latent or expressed at low level. B‐HIVE is a high‐throughput method to identify and quantify thousands of individual viral transcripts per round of infection. It can be applied in different conditions, characterizing the response of single proviruses to different treatments. Overall, B‐HIVE gives unprecedented insight into the expression of single proviruses in populations of HIV‐infected cells. © 2018 by John Wiley & Sons, Inc.

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Tài liệu tham khảo

10.1016/j.cell.2013.07.018

10.1038/nature11286

10.1038/nmeth.2688

10.1002/0471142727.mb2129s109

10.1038/nm.3489

10.1038/nsmb.3328

10.1073/pnas.1402873111

10.1038/nm1329

10.1016/j.tibs.2014.12.001

10.1038/8394

10.1016/S0014-5793(00)01775-0

10.1093/nar/18.7.1687

10.1126/science.2814500

10.1007/978-1-349-20235-5_10

10.1016/j.cell.2014.11.021

Salimullah M., 2011, NanoCAGE: A high‐resolution technique to discover and interrogate cell transcriptomes, Cold Spring Harbor Protocols, 2011, pdb.prot5559, 10.1101/pdb.prot5559

10.1038/nmeth1103

10.1016/S0092-8674(02)00864-4

10.1371/journal.ppat.1003834

10.1093/nar/16.16.8186

10.1101/gr.6286907

10.1002/0471142727.mb2605s65

10.1093/bioinformatics/btv053

www.unaids.org/en/resources/fact‐sheet

https://lab.thegrandlocus.com/protocols/barcoding‐pcr

https://github.com/gui11aume/starcode

https://hub.docker.com/r/gui11aume/bhive/

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Current Protocols in Molecular Biology

Tập 122 Số 1

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