TY - JOUR

T1 - Genome-wide profiling and differential expression of microRNA in rat pluripotent stem cells

AU - Sherstyuk, Vladimir V.

AU - Medvedev, Sergey P.

AU - Elisaphenko, Evgeniy A.

AU - Vaskova, Evgeniya A.

AU - Ri, Maxim T.

AU - Vyatkin, Yuri V.

AU - Saik, Olga V.

AU - Shtokalo, Dmitry N.

AU - Pokushalov, Evgeniy A.

AU - Zakian, Suren M.

N1 - Publisher Copyright: © The Author(s) 2017.

PY - 2017/6/5

Y1 - 2017/6/5

N2 - 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.

AB - 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.

KW - Animals

KW - Cell Line

KW - Computational Biology/methods

KW - Gene Expression Profiling

KW - Gene Expression Regulation, Developmental

KW - Genome-Wide Association Study

KW - MicroRNAs/genetics

KW - Molecular Sequence Annotation

KW - Pluripotent Stem Cells/cytology

KW - Rats

KW - Transcriptome

KW - MOUSE EMBRYOS

KW - SELF-RENEWAL

KW - MIR-200 FAMILY

KW - REPRESSORS ZEB1

KW - MURINE

KW - EPITHELIAL-MESENCHYMAL TRANSITION

KW - PATHWAY

KW - TARGETS

KW - BLASTOCYSTS

KW - HUMAN SOMATIC-CELLS

UR - http://www.scopus.com/inward/record.url?scp=85020419666&partnerID=8YFLogxK

U2 - 10.1038/s41598-017-02632-0

DO - 10.1038/s41598-017-02632-0

M3 - Article

C2 - 28584262

AN - SCOPUS:85020419666

VL - 7

SP - 2787

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

M1 - 2787

ER -