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Sci Rep. 2017 Jun 5;7(1):2787. doi: 10.1038/s41598-017-02632-0.

Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells.

Sherstyuk VV1,2,3,4, Medvedev SP1,2,3,4, Elisaphenko EA1,2,3, Vaskova EA1,2,3, Ri MT5,6, Vyatkin YV1,4,5,6, Saik OV1, Shtokalo DN1,5,6,7, Pokushalov EA2, Zakian SM8,9,10,11.

Author information

1
Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., Novosibirsk, 630090, Russia.
2
Siberian Federal Biomedical Research Center, Ministry of Healthcare of the Russian Federation, 15 Rechkunovskaya St., Novosibirsk, 630055, Russia.
3
Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., Novosibirsk, 630090, Russia.
4
Novosibirsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia.
5
AcademGene LLC, 6 Lavrentyeva Ave., Novosibirsk, 630090, Russia.
6
St. Laurent Institute, 317 New Boston St., Woburn, MA, 01801, USA.
7
A.P.Ershov Institute of Informatics Systems, 6 Lavrentyeva Ave., Novosibirsk, 630090, Russia.
8
Federal Research Center Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentyeva Ave., Novosibirsk, 630090, Russia. zakian@bionet.nsc.ru.
9
Siberian Federal Biomedical Research Center, Ministry of Healthcare of the Russian Federation, 15 Rechkunovskaya St., Novosibirsk, 630055, Russia. zakian@bionet.nsc.ru.
10
Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, 8 Lavrentyeva Ave., Novosibirsk, 630090, Russia. zakian@bionet.nsc.ru.
11
Novosibirsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia. zakian@bionet.nsc.ru.

Abstract

MicroRNAs (miRNAs) constitute a class of small noncoding RNAs that plays an important role in the post-transcriptional regulation of gene expression. Much evidence has demonstrated that miRNAs are involved in regulating the human and mouse pluripotency. Nevertheless, to our knowledge, miRNAs in the pluripotent stem cells of one of the most commonly used model organisms - the Rattus norvegicus have not been studied. In the present study, we performed deep sequencing of small RNA molecules in the embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells of laboratory rats. Bioinformatics analysis revealed 674 known miRNAs and 394 novel miRNA candidates in all of the samples. Expression of known pluripotency-associated miRNAs, such as the miR-290-295 and miR-183-96-182 clusters as well as members of the miR-200 family, was detected in rat pluripotent stem cells. Analysis of the targets of differentially expressed known and novel miRNAs showed their involvement in the regulation of pluripotency and the reprogramming process in rats. Bioinformatics and systems biology approaches identified potential pathways that are regulated by these miRNAs. This study contributes to our understanding of miRNAs in the regulation of pluripotency and cell reprogramming in the laboratory rat.

PMID:
28584262
PMCID:
PMC5459850
DOI:
10.1038/s41598-017-02632-0
[Indexed for MEDLINE]
Free PMC Article

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