Functional selection of shRNA loops from randomized retroviral libraries.

Gene silencing by RNA interference (RNAi) can be achieved by the ectopic expression of tailored short hairpin RNAs (shRNAs) which after export to the cytoplasm are processed by Dicer and incorporated into the RNA induced silencing complex (RISC). Design rules for shRNAs have been the focus of severa...

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Autores principales:	Stig Mølgaard Rask Jensen, Alexander Schmitz, Finn Skou Pedersen, Jørgen Kjems, Jesper Bertram Bramsen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7ce8f2ace8eb476f81eee2ca98e8ccb5
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spelling	oai:doaj.org-article:7ce8f2ace8eb476f81eee2ca98e8ccb52021-11-18T07:08:27ZFunctional selection of shRNA loops from randomized retroviral libraries.1932-620310.1371/journal.pone.0043095https://doaj.org/article/7ce8f2ace8eb476f81eee2ca98e8ccb52012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22912797/?tool=EBIhttps://doaj.org/toc/1932-6203Gene silencing by RNA interference (RNAi) can be achieved by the ectopic expression of tailored short hairpin RNAs (shRNAs) which after export to the cytoplasm are processed by Dicer and incorporated into the RNA induced silencing complex (RISC). Design rules for shRNAs have been the focus of several studies, but only a few reports have turned the attention to the sequence of the loop-region. In this work we selected high-functional and low-functional shRNA loops from retroviral hairpin-loop-libraries in an RNAi reporter assay. The procedure revealed a very significant and stem sequence-dependent effect of the loop on shRNA function and although neither strong consensus loop sequence nor structural motifs could be identified, a preferred loop sequence (5'-UGUGCUU-3') was found to support robust knock down with little stem sequence dependency. These findings will serve as a guide for designing shRNAs with improved knock down capacity.Stig Mølgaard Rask JensenAlexander SchmitzFinn Skou PedersenJørgen KjemsJesper Bertram BramsenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e43095 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Stig Mølgaard Rask Jensen Alexander Schmitz Finn Skou Pedersen Jørgen Kjems Jesper Bertram Bramsen Functional selection of shRNA loops from randomized retroviral libraries.
description	Gene silencing by RNA interference (RNAi) can be achieved by the ectopic expression of tailored short hairpin RNAs (shRNAs) which after export to the cytoplasm are processed by Dicer and incorporated into the RNA induced silencing complex (RISC). Design rules for shRNAs have been the focus of several studies, but only a few reports have turned the attention to the sequence of the loop-region. In this work we selected high-functional and low-functional shRNA loops from retroviral hairpin-loop-libraries in an RNAi reporter assay. The procedure revealed a very significant and stem sequence-dependent effect of the loop on shRNA function and although neither strong consensus loop sequence nor structural motifs could be identified, a preferred loop sequence (5'-UGUGCUU-3') was found to support robust knock down with little stem sequence dependency. These findings will serve as a guide for designing shRNAs with improved knock down capacity.
format	article
author	Stig Mølgaard Rask Jensen Alexander Schmitz Finn Skou Pedersen Jørgen Kjems Jesper Bertram Bramsen
author_facet	Stig Mølgaard Rask Jensen Alexander Schmitz Finn Skou Pedersen Jørgen Kjems Jesper Bertram Bramsen
author_sort	Stig Mølgaard Rask Jensen
title	Functional selection of shRNA loops from randomized retroviral libraries.
title_short	Functional selection of shRNA loops from randomized retroviral libraries.
title_full	Functional selection of shRNA loops from randomized retroviral libraries.
title_fullStr	Functional selection of shRNA loops from randomized retroviral libraries.
title_full_unstemmed	Functional selection of shRNA loops from randomized retroviral libraries.
title_sort	functional selection of shrna loops from randomized retroviral libraries.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/7ce8f2ace8eb476f81eee2ca98e8ccb5
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Functional selection of shRNA loops from randomized retroviral libraries.

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