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Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines

Systematic knockout studies in mice have shown that a large fraction of the gene replacements show no lethal or other overt phenotypes. This has led to the development of more refined analysis schemes, including physiological, behavioral, developmental and cytological tests. However, transcriptomic...

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Autores principales: Xie, Chen, Bekpen, Cemalettin, Künzel, Sven, Keshavarz, Maryam, Krebs-Wheaton, Rebecca, Skrabar, Neva, Ullrich, Kristian K., Zhang, Wenyu, Tautz, Diethard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685438/
https://www.ncbi.nlm.nih.gov/pubmed/33180766
http://dx.doi.org/10.1371/journal.pcbi.1008354
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author Xie, Chen
Bekpen, Cemalettin
Künzel, Sven
Keshavarz, Maryam
Krebs-Wheaton, Rebecca
Skrabar, Neva
Ullrich, Kristian K.
Zhang, Wenyu
Tautz, Diethard
author_facet Xie, Chen
Bekpen, Cemalettin
Künzel, Sven
Keshavarz, Maryam
Krebs-Wheaton, Rebecca
Skrabar, Neva
Ullrich, Kristian K.
Zhang, Wenyu
Tautz, Diethard
author_sort Xie, Chen
collection PubMed
description Systematic knockout studies in mice have shown that a large fraction of the gene replacements show no lethal or other overt phenotypes. This has led to the development of more refined analysis schemes, including physiological, behavioral, developmental and cytological tests. However, transcriptomic analyses have not yet been systematically evaluated for non-lethal knockouts. We conducted a power analysis to determine the experimental conditions under which even small changes in transcript levels can be reliably traced. We have applied this to two gene disruption lines of genes for which no function was known so far. Dedicated phenotyping tests informed by the tissues and stages of highest expression of the two genes show small effects on the tested phenotypes. For the transcriptome analysis of these stages and tissues, we used a prior power analysis to determine the number of biological replicates and the sequencing depth. We find that under these conditions, the knockouts have a significant impact on the transcriptional networks, with thousands of genes showing small transcriptional changes. GO analysis suggests that A930004D18Rik is involved in developmental processes through contributing to protein complexes, and A830005F24Rik in extracellular matrix functions. Subsampling analysis of the data reveals that the increase in the number of biological replicates was more important that increasing the sequencing depth to arrive at these results. Hence, our proof-of-principle experiment suggests that transcriptomic analysis is indeed an option to study gene functions of genes with weak or no traceable phenotypic effects and it provides the boundary conditions under which this is possible.
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spelling pubmed-76854382020-12-02 Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines Xie, Chen Bekpen, Cemalettin Künzel, Sven Keshavarz, Maryam Krebs-Wheaton, Rebecca Skrabar, Neva Ullrich, Kristian K. Zhang, Wenyu Tautz, Diethard PLoS Comput Biol Research Article Systematic knockout studies in mice have shown that a large fraction of the gene replacements show no lethal or other overt phenotypes. This has led to the development of more refined analysis schemes, including physiological, behavioral, developmental and cytological tests. However, transcriptomic analyses have not yet been systematically evaluated for non-lethal knockouts. We conducted a power analysis to determine the experimental conditions under which even small changes in transcript levels can be reliably traced. We have applied this to two gene disruption lines of genes for which no function was known so far. Dedicated phenotyping tests informed by the tissues and stages of highest expression of the two genes show small effects on the tested phenotypes. For the transcriptome analysis of these stages and tissues, we used a prior power analysis to determine the number of biological replicates and the sequencing depth. We find that under these conditions, the knockouts have a significant impact on the transcriptional networks, with thousands of genes showing small transcriptional changes. GO analysis suggests that A930004D18Rik is involved in developmental processes through contributing to protein complexes, and A830005F24Rik in extracellular matrix functions. Subsampling analysis of the data reveals that the increase in the number of biological replicates was more important that increasing the sequencing depth to arrive at these results. Hence, our proof-of-principle experiment suggests that transcriptomic analysis is indeed an option to study gene functions of genes with weak or no traceable phenotypic effects and it provides the boundary conditions under which this is possible. Public Library of Science 2020-11-12 /pmc/articles/PMC7685438/ /pubmed/33180766 http://dx.doi.org/10.1371/journal.pcbi.1008354 Text en © 2020 Xie et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Xie, Chen
Bekpen, Cemalettin
Künzel, Sven
Keshavarz, Maryam
Krebs-Wheaton, Rebecca
Skrabar, Neva
Ullrich, Kristian K.
Zhang, Wenyu
Tautz, Diethard
Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
title Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
title_full Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
title_fullStr Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
title_full_unstemmed Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
title_short Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
title_sort dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685438/
https://www.ncbi.nlm.nih.gov/pubmed/33180766
http://dx.doi.org/10.1371/journal.pcbi.1008354
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