Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress

Abstract Background Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expressi...

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Autores principales:	Fernanda Ferreira Salgado, Letícia Rios Vieira, Vivianny Nayse Belo Silva, André Pereira Leão, Priscila Grynberg, Marcos Mota do Carmo Costa, Roberto Coiti Togawa, Carlos Antônio Ferreira de Sousa, Manoel Teixeira Souza Júnior
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Abiotic stress Elaeis guineensis Transcription factor Transcriptome Non-coding RNA Botany QK1-989
Acceso en línea:	https://doaj.org/article/45c81685a19c449f9c7b14443d54873c
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spelling	oai:doaj.org-article:45c81685a19c449f9c7b14443d54873c2021-11-14T12:09:20ZExpression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress10.1186/s12870-021-03296-91471-2229https://doaj.org/article/45c81685a19c449f9c7b14443d54873c2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03296-9https://doaj.org/toc/1471-2229Abstract Background Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expression, emerging as a regulatory molecule key in the responses to plant stress, such as cold, heat, drought, and salt. This work is a comprehensive and large-scale miRNA analysis performed to characterize the miRNA population present in oil palm (Elaeis guineensis Jacq.) exposed to a high level of salt stress, to identify miRNA-putative target genes in the oil palm genome, and to perform an in silico comparison of the expression profile of the miRNAs and their putative target genes. Results A group of 79 miRNAs was found in oil palm, been 52 known miRNAs and 27 new ones. The known miRNAs found belonged to 28 families. Those miRNAs led to 229 distinct miRNA-putative target genes identified in the genome of oil palm. miRNAs and putative target genes differentially expressed under salinity stress were then selected for functional annotation analysis. The regulation of transcription, DNA-templated, and the oxidation-reduction process were the biological processes with the highest number of hits to the putative target genes, while protein binding and DNA binding were the molecular functions with the highest number of hits. Finally, the nucleus was the cellular component with the highest number of hits. The functional annotation of the putative target genes differentially expressed under salinity stress showed several ones coding for transcription factors which have already proven able to result in tolerance to salinity stress by overexpression or knockout in other plant species. Conclusions Our findings provide new insights into the early response of young oil palm plants to salinity stress and confirm an expected preponderant role of transcription factors - such as NF-YA3, HOX32, and GRF1 - in this response. Besides, it points out potential salt-responsive miRNAs and miRNA-putative target genes that one can utilize to develop oil palm plants tolerant to salinity stress.Fernanda Ferreira SalgadoLetícia Rios VieiraVivianny Nayse Belo SilvaAndré Pereira LeãoPriscila GrynbergMarcos Mota do Carmo CostaRoberto Coiti TogawaCarlos Antônio Ferreira de SousaManoel Teixeira Souza JúniorBMCarticleAbiotic stressElaeis guineensisTranscription factorTranscriptomeNon-coding RNABotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-17 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Abiotic stress Elaeis guineensis Transcription factor Transcriptome Non-coding RNA Botany QK1-989
spellingShingle	Abiotic stress Elaeis guineensis Transcription factor Transcriptome Non-coding RNA Botany QK1-989 Fernanda Ferreira Salgado Letícia Rios Vieira Vivianny Nayse Belo Silva André Pereira Leão Priscila Grynberg Marcos Mota do Carmo Costa Roberto Coiti Togawa Carlos Antônio Ferreira de Sousa Manoel Teixeira Souza Júnior Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress
description	Abstract Background Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expression, emerging as a regulatory molecule key in the responses to plant stress, such as cold, heat, drought, and salt. This work is a comprehensive and large-scale miRNA analysis performed to characterize the miRNA population present in oil palm (Elaeis guineensis Jacq.) exposed to a high level of salt stress, to identify miRNA-putative target genes in the oil palm genome, and to perform an in silico comparison of the expression profile of the miRNAs and their putative target genes. Results A group of 79 miRNAs was found in oil palm, been 52 known miRNAs and 27 new ones. The known miRNAs found belonged to 28 families. Those miRNAs led to 229 distinct miRNA-putative target genes identified in the genome of oil palm. miRNAs and putative target genes differentially expressed under salinity stress were then selected for functional annotation analysis. The regulation of transcription, DNA-templated, and the oxidation-reduction process were the biological processes with the highest number of hits to the putative target genes, while protein binding and DNA binding were the molecular functions with the highest number of hits. Finally, the nucleus was the cellular component with the highest number of hits. The functional annotation of the putative target genes differentially expressed under salinity stress showed several ones coding for transcription factors which have already proven able to result in tolerance to salinity stress by overexpression or knockout in other plant species. Conclusions Our findings provide new insights into the early response of young oil palm plants to salinity stress and confirm an expected preponderant role of transcription factors - such as NF-YA3, HOX32, and GRF1 - in this response. Besides, it points out potential salt-responsive miRNAs and miRNA-putative target genes that one can utilize to develop oil palm plants tolerant to salinity stress.
format	article
author	Fernanda Ferreira Salgado Letícia Rios Vieira Vivianny Nayse Belo Silva André Pereira Leão Priscila Grynberg Marcos Mota do Carmo Costa Roberto Coiti Togawa Carlos Antônio Ferreira de Sousa Manoel Teixeira Souza Júnior
author_facet	Fernanda Ferreira Salgado Letícia Rios Vieira Vivianny Nayse Belo Silva André Pereira Leão Priscila Grynberg Marcos Mota do Carmo Costa Roberto Coiti Togawa Carlos Antônio Ferreira de Sousa Manoel Teixeira Souza Júnior
author_sort	Fernanda Ferreira Salgado
title	Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress
title_short	Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress
title_full	Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress
title_fullStr	Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress
title_full_unstemmed	Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress
title_sort	expression analysis of mirnas and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress
publisher	BMC
publishDate	2021
url	https://doaj.org/article/45c81685a19c449f9c7b14443d54873c
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Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress

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