Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.

Intronic microRNAs (in-miRNAs) as a class of miRNA family that regulates gene expression are still poorly understood in plants. In this study, we systematically identified rice in-miRNAs by re-mining eight published small RNA-sequencing datasets of rice. Furthermore, based on the collected expressio...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yong-ao Tong, Hua Peng, Cheng Zhan, LinHong Fan, Taobo Ai, Shenghua Wang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/468d76f2f4de4485b7fa7660791c5db1
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:468d76f2f4de4485b7fa7660791c5db1
record_format	dspace
spelling	oai:doaj.org-article:468d76f2f4de4485b7fa7660791c5db12021-11-18T07:44:38ZGenome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.1932-620310.1371/journal.pone.0063938https://doaj.org/article/468d76f2f4de4485b7fa7660791c5db12013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23717514/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Intronic microRNAs (in-miRNAs) as a class of miRNA family that regulates gene expression are still poorly understood in plants. In this study, we systematically identified rice in-miRNAs by re-mining eight published small RNA-sequencing datasets of rice. Furthermore, based on the collected expression, annotation, and putative target data, we investigated the structures, potential functions, and expression features of these in-miRNAs and the expression patterns of their host genes. A total of 153 in-miRNAs, which account for over 1/4 of the total rice miRNAs, were identified. In silico expression analysis showed that most of them (∼63%) are tissue or stage-specific. However, a majority of their host genes, especially those containing clustered in-miRNAs, exhibit stable high-level expressions among 513 microarray datasets. Although in-miRNAs show diversity in function and mechanism, the DNA methylation directed by 24 nt in-miRNAs may be the main pathway that controls the expressions of target genes, host genes, and even themselves. These findings may enhance our understanding on special functions of in-miRNAs, especially in mediating DNA methylation that was concluded to affect the stability of expression and structure of host and target genes.Yong-ao TongHua PengCheng ZhanLinHong FanTaobo AiShenghua WangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e63938 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yong-ao Tong Hua Peng Cheng Zhan LinHong Fan Taobo Ai Shenghua Wang Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.
description	Intronic microRNAs (in-miRNAs) as a class of miRNA family that regulates gene expression are still poorly understood in plants. In this study, we systematically identified rice in-miRNAs by re-mining eight published small RNA-sequencing datasets of rice. Furthermore, based on the collected expression, annotation, and putative target data, we investigated the structures, potential functions, and expression features of these in-miRNAs and the expression patterns of their host genes. A total of 153 in-miRNAs, which account for over 1/4 of the total rice miRNAs, were identified. In silico expression analysis showed that most of them (∼63%) are tissue or stage-specific. However, a majority of their host genes, especially those containing clustered in-miRNAs, exhibit stable high-level expressions among 513 microarray datasets. Although in-miRNAs show diversity in function and mechanism, the DNA methylation directed by 24 nt in-miRNAs may be the main pathway that controls the expressions of target genes, host genes, and even themselves. These findings may enhance our understanding on special functions of in-miRNAs, especially in mediating DNA methylation that was concluded to affect the stability of expression and structure of host and target genes.
format	article
author	Yong-ao Tong Hua Peng Cheng Zhan LinHong Fan Taobo Ai Shenghua Wang
author_facet	Yong-ao Tong Hua Peng Cheng Zhan LinHong Fan Taobo Ai Shenghua Wang
author_sort	Yong-ao Tong
title	Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.
title_short	Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.
title_full	Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.
title_fullStr	Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.
title_full_unstemmed	Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.
title_sort	genome-wide analysis reveals diversity of rice intronic mirnas in sequence structure, biogenesis and function.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/468d76f2f4de4485b7fa7660791c5db1
work_keys_str_mv	AT yongaotong genomewideanalysisrevealsdiversityofriceintronicmirnasinsequencestructurebiogenesisandfunction AT huapeng genomewideanalysisrevealsdiversityofriceintronicmirnasinsequencestructurebiogenesisandfunction AT chengzhan genomewideanalysisrevealsdiversityofriceintronicmirnasinsequencestructurebiogenesisandfunction AT linhongfan genomewideanalysisrevealsdiversityofriceintronicmirnasinsequencestructurebiogenesisandfunction AT taoboai genomewideanalysisrevealsdiversityofriceintronicmirnasinsequencestructurebiogenesisandfunction AT shenghuawang genomewideanalysisrevealsdiversityofriceintronicmirnasinsequencestructurebiogenesisandfunction
_version_	1718423032424300544

Genome-wide analysis reveals diversity of rice intronic miRNAs in sequence structure, biogenesis and function.

Ejemplares similares