A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.

Transcription factors (TFs), microRNAs (miRNAs), small interfering RNAs (siRNAs) and other functional non-coding small RNAs (sRNAs) are important gene regulators. Comparison of sRNA expression profiles between transgenic barley over-expressing a drought tolerant TF (TaDREB3) and non-transgenic contr...

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Autores principales:	Michael Hackenberg, Bu-Jun Shi, Perry Gustafson, Peter Langridge
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4bd0c7ac72e8495a9fcd7ad880d10ae3
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spelling	oai:doaj.org-article:4bd0c7ac72e8495a9fcd7ad880d10ae32021-11-18T07:10:06ZA transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.1932-620310.1371/journal.pone.0042030https://doaj.org/article/4bd0c7ac72e8495a9fcd7ad880d10ae32012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22870277/?tool=EBIhttps://doaj.org/toc/1932-6203Transcription factors (TFs), microRNAs (miRNAs), small interfering RNAs (siRNAs) and other functional non-coding small RNAs (sRNAs) are important gene regulators. Comparison of sRNA expression profiles between transgenic barley over-expressing a drought tolerant TF (TaDREB3) and non-transgenic control barley revealed many group-specific sRNAs. In addition, 42% of the shared sRNAs were differentially expressed between the two groups (\|log(2)\| >1). Furthermore, TaDREB3-derived sRNAs were only detected in transgenic barley despite the existence of homologous genes in non-transgenic barley. These results demonstrate that the TF strongly affects the expression of sRNAs and siRNAs could in turn affect the TF stability. The TF also affects size distribution and abundance of sRNAs including miRNAs. About half of the sRNAs in each group were derived from chloroplast. A sRNA derived from tRNA-His(GUG) encoded by the chloroplast genome is the most abundant sRNA, accounting for 42.2% of the total sRNAs in transgenic barley and 28.9% in non-transgenic barley. This sRNA, which targets a gene (TC245676) involved in biological processes, was only present in barley leaves but not roots. 124 and 136 miRNAs were detected in transgenic and non-transgenic barley, respectively. miR156 was the most abundant miRNA and up-regulated in transgenic barley, while miR168 was the most abundant miRNA and up-regulated in non-transgenic barley. Eight out of 20 predicted novel miRNAs were differentially expressed between the two groups. All the predicted novel miRNA targets were validated using a degradome library. Our data provide an insight into the effect of TF on the expression of sRNAs in barley.Michael HackenbergBu-Jun ShiPerry GustafsonPeter LangridgePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e42030 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Michael Hackenberg Bu-Jun Shi Perry Gustafson Peter Langridge A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.
description	Transcription factors (TFs), microRNAs (miRNAs), small interfering RNAs (siRNAs) and other functional non-coding small RNAs (sRNAs) are important gene regulators. Comparison of sRNA expression profiles between transgenic barley over-expressing a drought tolerant TF (TaDREB3) and non-transgenic control barley revealed many group-specific sRNAs. In addition, 42% of the shared sRNAs were differentially expressed between the two groups (\|log(2)\| >1). Furthermore, TaDREB3-derived sRNAs were only detected in transgenic barley despite the existence of homologous genes in non-transgenic barley. These results demonstrate that the TF strongly affects the expression of sRNAs and siRNAs could in turn affect the TF stability. The TF also affects size distribution and abundance of sRNAs including miRNAs. About half of the sRNAs in each group were derived from chloroplast. A sRNA derived from tRNA-His(GUG) encoded by the chloroplast genome is the most abundant sRNA, accounting for 42.2% of the total sRNAs in transgenic barley and 28.9% in non-transgenic barley. This sRNA, which targets a gene (TC245676) involved in biological processes, was only present in barley leaves but not roots. 124 and 136 miRNAs were detected in transgenic and non-transgenic barley, respectively. miR156 was the most abundant miRNA and up-regulated in transgenic barley, while miR168 was the most abundant miRNA and up-regulated in non-transgenic barley. Eight out of 20 predicted novel miRNAs were differentially expressed between the two groups. All the predicted novel miRNA targets were validated using a degradome library. Our data provide an insight into the effect of TF on the expression of sRNAs in barley.
format	article
author	Michael Hackenberg Bu-Jun Shi Perry Gustafson Peter Langridge
author_facet	Michael Hackenberg Bu-Jun Shi Perry Gustafson Peter Langridge
author_sort	Michael Hackenberg
title	A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.
title_short	A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.
title_full	A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.
title_fullStr	A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.
title_full_unstemmed	A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.
title_sort	transgenic transcription factor (tadreb3) in barley affects the expression of micrornas and other small non-coding rnas.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/4bd0c7ac72e8495a9fcd7ad880d10ae3
work_keys_str_mv	AT michaelhackenberg atransgenictranscriptionfactortadreb3inbarleyaffectstheexpressionofmicrornasandothersmallnoncodingrnas AT bujunshi atransgenictranscriptionfactortadreb3inbarleyaffectstheexpressionofmicrornasandothersmallnoncodingrnas AT perrygustafson atransgenictranscriptionfactortadreb3inbarleyaffectstheexpressionofmicrornasandothersmallnoncodingrnas AT peterlangridge atransgenictranscriptionfactortadreb3inbarleyaffectstheexpressionofmicrornasandothersmallnoncodingrnas AT michaelhackenberg transgenictranscriptionfactortadreb3inbarleyaffectstheexpressionofmicrornasandothersmallnoncodingrnas AT bujunshi transgenictranscriptionfactortadreb3inbarleyaffectstheexpressionofmicrornasandothersmallnoncodingrnas AT perrygustafson transgenictranscriptionfactortadreb3inbarleyaffectstheexpressionofmicrornasandothersmallnoncodingrnas AT peterlangridge transgenictranscriptionfactortadreb3inbarleyaffectstheexpressionofmicrornasandothersmallnoncodingrnas
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A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs.

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