Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends

Abstract Despite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-a...

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Autores principales:	Wojciech Rosikiewicz, Jarosław Sikora, Tomasz Skrzypczak, Magdalena R. Kubiak, Izabela Makałowska
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3981fc0701e4405da1c74d4a50f20d01
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spelling	oai:doaj.org-article:3981fc0701e4405da1c74d4a50f20d012021-12-02T14:53:43ZPromoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends10.1038/s41598-021-87970-w2045-2322https://doaj.org/article/3981fc0701e4405da1c74d4a50f20d012021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87970-whttps://doaj.org/toc/2045-2322Abstract Despite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-antisense gene pairs were analyzed with a particular focus on pairs overlapping at their 5’ ends. Analyses were performed in 73 human transcription start site libraries. The results of our studies showed that the overlap between genes is not a stable feature and depends on which TSSs are utilized in a given cell type. An analysis of gene expression did not confirm that overlap between genes causes downregulation of their expression. This observation contradicts earlier findings. In addition, we showed that the switch from one promoter to another, leading to genes overlap, may occur in response to changing environment of a cell or tissue. We also demonstrated that in transfected and cancerous cells genes overlap is observed more often in comparison with normal tissues. Moreover, utilization of overlapping promoters depends on particular state of a cell and, at least in some groups of genes, is not merely coincidental.Wojciech RosikiewiczJarosław SikoraTomasz SkrzypczakMagdalena R. KubiakIzabela MakałowskaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wojciech Rosikiewicz Jarosław Sikora Tomasz Skrzypczak Magdalena R. Kubiak Izabela Makałowska Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
description	Abstract Despite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-antisense gene pairs were analyzed with a particular focus on pairs overlapping at their 5’ ends. Analyses were performed in 73 human transcription start site libraries. The results of our studies showed that the overlap between genes is not a stable feature and depends on which TSSs are utilized in a given cell type. An analysis of gene expression did not confirm that overlap between genes causes downregulation of their expression. This observation contradicts earlier findings. In addition, we showed that the switch from one promoter to another, leading to genes overlap, may occur in response to changing environment of a cell or tissue. We also demonstrated that in transfected and cancerous cells genes overlap is observed more often in comparison with normal tissues. Moreover, utilization of overlapping promoters depends on particular state of a cell and, at least in some groups of genes, is not merely coincidental.
format	article
author	Wojciech Rosikiewicz Jarosław Sikora Tomasz Skrzypczak Magdalena R. Kubiak Izabela Makałowska
author_facet	Wojciech Rosikiewicz Jarosław Sikora Tomasz Skrzypczak Magdalena R. Kubiak Izabela Makałowska
author_sort	Wojciech Rosikiewicz
title	Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
title_short	Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
title_full	Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
title_fullStr	Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
title_full_unstemmed	Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
title_sort	promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/3981fc0701e4405da1c74d4a50f20d01
work_keys_str_mv	AT wojciechrosikiewicz promoterswitchinginresponsetochangingenvironmentandelevatedexpressionofproteincodinggenesoverlappingattheir5ends AT jarosławsikora promoterswitchinginresponsetochangingenvironmentandelevatedexpressionofproteincodinggenesoverlappingattheir5ends AT tomaszskrzypczak promoterswitchinginresponsetochangingenvironmentandelevatedexpressionofproteincodinggenesoverlappingattheir5ends AT magdalenarkubiak promoterswitchinginresponsetochangingenvironmentandelevatedexpressionofproteincodinggenesoverlappingattheir5ends AT izabelamakałowska promoterswitchinginresponsetochangingenvironmentandelevatedexpressionofproteincodinggenesoverlappingattheir5ends
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Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends

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