In silico prediction and in vivo validation of Daphnia pulex microRNAs.

Daphnia pulex, the crustacean with the first sequenced genome, is an important organism that has been widely used in ecological and toxicological research. MicroRNAs (miRNAs) are 21-25 nucleotide small non-coding RNAs that are involved in a myriad of physiological processes. In this research, we pre...

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Autores principales:	Shuai Chen, Garrett J McKinney, Krista M Nichols, Maria S Sepúlveda
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/62a8a3e2d76345dc8cbb93c4648f59be
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spelling	oai:doaj.org-article:62a8a3e2d76345dc8cbb93c4648f59be2021-11-18T08:38:53ZIn silico prediction and in vivo validation of Daphnia pulex microRNAs.1932-620310.1371/journal.pone.0083708https://doaj.org/article/62a8a3e2d76345dc8cbb93c4648f59be2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24400076/?tool=EBIhttps://doaj.org/toc/1932-6203Daphnia pulex, the crustacean with the first sequenced genome, is an important organism that has been widely used in ecological and toxicological research. MicroRNAs (miRNAs) are 21-25 nucleotide small non-coding RNAs that are involved in a myriad of physiological processes. In this research, we predicted 75 D. pulex miRNAs by sequence homology and secondary structure identification from the full genome sequence. Fourteen predicted miRNAs were selected for quantitative real time polymerase chain reaction (RT-PCR) validation. Out of these, eight (mir-8, mir-9, mir-12, mir-92, mir-100, mir-133, mir-153 and mir-283) were successfully amplified and validated. Next, expression levels were quantified at three different life stages (days 4, 8 and 12 of age) using U6 spliceosomal RNA as a reference gene. The expression of mir-8, mir-9, mir-12, mir-92 and mir-100 significantly differed across time suggesting these microRNAs might play a critical role during D. pulex development. This is the first study to identify and validate miRNAs in D. pulex, which is an important first step in further studies that evaluate their roles in development and response to environmental and ecological stimuli.Shuai ChenGarrett J McKinneyKrista M NicholsMaria S SepúlvedaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e83708 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shuai Chen Garrett J McKinney Krista M Nichols Maria S Sepúlveda In silico prediction and in vivo validation of Daphnia pulex microRNAs.
description	Daphnia pulex, the crustacean with the first sequenced genome, is an important organism that has been widely used in ecological and toxicological research. MicroRNAs (miRNAs) are 21-25 nucleotide small non-coding RNAs that are involved in a myriad of physiological processes. In this research, we predicted 75 D. pulex miRNAs by sequence homology and secondary structure identification from the full genome sequence. Fourteen predicted miRNAs were selected for quantitative real time polymerase chain reaction (RT-PCR) validation. Out of these, eight (mir-8, mir-9, mir-12, mir-92, mir-100, mir-133, mir-153 and mir-283) were successfully amplified and validated. Next, expression levels were quantified at three different life stages (days 4, 8 and 12 of age) using U6 spliceosomal RNA as a reference gene. The expression of mir-8, mir-9, mir-12, mir-92 and mir-100 significantly differed across time suggesting these microRNAs might play a critical role during D. pulex development. This is the first study to identify and validate miRNAs in D. pulex, which is an important first step in further studies that evaluate their roles in development and response to environmental and ecological stimuli.
format	article
author	Shuai Chen Garrett J McKinney Krista M Nichols Maria S Sepúlveda
author_facet	Shuai Chen Garrett J McKinney Krista M Nichols Maria S Sepúlveda
author_sort	Shuai Chen
title	In silico prediction and in vivo validation of Daphnia pulex microRNAs.
title_short	In silico prediction and in vivo validation of Daphnia pulex microRNAs.
title_full	In silico prediction and in vivo validation of Daphnia pulex microRNAs.
title_fullStr	In silico prediction and in vivo validation of Daphnia pulex microRNAs.
title_full_unstemmed	In silico prediction and in vivo validation of Daphnia pulex microRNAs.
title_sort	in silico prediction and in vivo validation of daphnia pulex micrornas.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/62a8a3e2d76345dc8cbb93c4648f59be
work_keys_str_mv	AT shuaichen insilicopredictionandinvivovalidationofdaphniapulexmicrornas AT garrettjmckinney insilicopredictionandinvivovalidationofdaphniapulexmicrornas AT kristamnichols insilicopredictionandinvivovalidationofdaphniapulexmicrornas AT mariassepulveda insilicopredictionandinvivovalidationofdaphniapulexmicrornas
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In silico prediction and in vivo validation of Daphnia pulex microRNAs.

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