Analysis of the stability of 70 housekeeping genes during iPS reprogramming

Abstract Studies on induced pluripotent stem (iPS) cells highly rely on the investigation of their gene expression which requires normalization by housekeeping genes. Whether the housekeeping genes are stable during the iPS reprogramming, a transition of cell state known to be associated with profou...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yulia Panina, Arno Germond, Tomonobu M. Watanabe
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2606ed6d15814f0fa1186c79082b9a1e
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:2606ed6d15814f0fa1186c79082b9a1e
record_format	dspace
spelling	oai:doaj.org-article:2606ed6d15814f0fa1186c79082b9a1e2021-12-02T16:18:05ZAnalysis of the stability of 70 housekeeping genes during iPS reprogramming10.1038/s41598-020-78863-52045-2322https://doaj.org/article/2606ed6d15814f0fa1186c79082b9a1e2020-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-78863-5https://doaj.org/toc/2045-2322Abstract Studies on induced pluripotent stem (iPS) cells highly rely on the investigation of their gene expression which requires normalization by housekeeping genes. Whether the housekeeping genes are stable during the iPS reprogramming, a transition of cell state known to be associated with profound changes, has been overlooked. In this study we analyzed the expression patterns of the most comprehensive list to date of housekeeping genes during iPS reprogramming of a mouse neural stem cell line N31. Our results show that housekeeping genes’ expression fluctuates significantly during the iPS reprogramming. Clustering analysis shows that ribosomal genes’ expression is rising, while the expression of cell-specific genes, such as vimentin (Vim) or elastin (Eln), is decreasing. To ensure the robustness of the obtained data, we performed a correlative analysis of the genes. Overall, all 70 genes analyzed changed the expression more than two-fold during the reprogramming. The scale of this analysis, that takes into account 70 previously known and newly suggested genes, allowed us to choose the most stable of all genes. We highlight the fact of fluctuation of housekeeping genes during iPS reprogramming, and propose that, to ensure robustness of qPCR experiments in iPS cells, housekeeping genes should be used together in combination, and with a prior testing in a specific line used in each study. We suggest that the longest splice variants of Rpl13a, Rplp1 and Rps18 can be used as a starting point for such initial testing as the most stable candidates.Yulia PaninaArno GermondTomonobu M. WatanabeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-10 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yulia Panina Arno Germond Tomonobu M. Watanabe Analysis of the stability of 70 housekeeping genes during iPS reprogramming
description	Abstract Studies on induced pluripotent stem (iPS) cells highly rely on the investigation of their gene expression which requires normalization by housekeeping genes. Whether the housekeeping genes are stable during the iPS reprogramming, a transition of cell state known to be associated with profound changes, has been overlooked. In this study we analyzed the expression patterns of the most comprehensive list to date of housekeeping genes during iPS reprogramming of a mouse neural stem cell line N31. Our results show that housekeeping genes’ expression fluctuates significantly during the iPS reprogramming. Clustering analysis shows that ribosomal genes’ expression is rising, while the expression of cell-specific genes, such as vimentin (Vim) or elastin (Eln), is decreasing. To ensure the robustness of the obtained data, we performed a correlative analysis of the genes. Overall, all 70 genes analyzed changed the expression more than two-fold during the reprogramming. The scale of this analysis, that takes into account 70 previously known and newly suggested genes, allowed us to choose the most stable of all genes. We highlight the fact of fluctuation of housekeeping genes during iPS reprogramming, and propose that, to ensure robustness of qPCR experiments in iPS cells, housekeeping genes should be used together in combination, and with a prior testing in a specific line used in each study. We suggest that the longest splice variants of Rpl13a, Rplp1 and Rps18 can be used as a starting point for such initial testing as the most stable candidates.
format	article
author	Yulia Panina Arno Germond Tomonobu M. Watanabe
author_facet	Yulia Panina Arno Germond Tomonobu M. Watanabe
author_sort	Yulia Panina
title	Analysis of the stability of 70 housekeeping genes during iPS reprogramming
title_short	Analysis of the stability of 70 housekeeping genes during iPS reprogramming
title_full	Analysis of the stability of 70 housekeeping genes during iPS reprogramming
title_fullStr	Analysis of the stability of 70 housekeeping genes during iPS reprogramming
title_full_unstemmed	Analysis of the stability of 70 housekeeping genes during iPS reprogramming
title_sort	analysis of the stability of 70 housekeeping genes during ips reprogramming
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/2606ed6d15814f0fa1186c79082b9a1e
work_keys_str_mv	AT yuliapanina analysisofthestabilityof70housekeepinggenesduringipsreprogramming AT arnogermond analysisofthestabilityof70housekeepinggenesduringipsreprogramming AT tomonobumwatanabe analysisofthestabilityof70housekeepinggenesduringipsreprogramming
_version_	1718384158645944320

Analysis of the stability of 70 housekeeping genes during iPS reprogramming

Ejemplares similares