title: Transcriptome Characteristics and X-Chromosome Inactivation Status in Cultured Rat Pluripotent Stem Cells.
abstract: Rat pluripotent stem cells, embryonic stem cells (ESCs), and induced pluripotent stem cells (iPSCs) as mouse and human ones have a great potential for studying mammalian early development, disease modeling, and evaluation of regenerative medicine approaches. However, data on pluripotency realization and self-renewal maintenance in rat cells are still very limited, and differentiation protocols of rat ESCs (rESCs) and iPSCs to study development and obtain specific cell types for biomedical applications are poorly developed. In this study, the RNA-Seq technique was first used for detailed transcriptome characterization in rat pluripotent cells. The rESC and iPSC transcriptomes demonstrated a high similarity and were significantly different from those in differentiated cells. Additionally, we have shown that reprogramming of rat somatic cells to a pluripotent state was accompanied by X-chromosome reactivation. There were two active X chromosomes in XX rESCs and iPSCs, which is one of the key attributes of the pluripotent state. Differentiation of both rESCs and iPSCs led to X-chromosome inactivation (XCI). The dynamics of XCI in differentiating rat cells was very similar to that in mice. Two types of facultative heterochromatin described in various mammalian species were revealed on the rat inactive X chromosome. To explore XCI dynamics, we established a new monolayer differentiation protocol for rESCs and iPSCs that may be applied to study different biological processes and optimized for directed derivation of specific cell types.
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .|3 Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Evgeniya A
authors.initials: EA
authors.lastname: Vaskova
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .|3 Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|4 Novosibirsk State University , Novosibirsk, Russia .
authors.forename: Sergey P
authors.initials: SP
authors.lastname: Medvedev
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .|3 Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Anastasiya E
authors.initials: AE
authors.lastname: Sorokina
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .|3 Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Artem A
authors.initials: AA
authors.lastname: Nemudryy
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .|3 Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Evgeniy A
authors.initials: EA
authors.lastname: Elisaphenko
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .|3 Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Irina S
authors.initials: IS
authors.lastname: Zakharova
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .|3 Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Alexander I
authors.initials: AI
authors.lastname: Shevchenko
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Elena A
authors.initials: EA
authors.lastname: Kizilova
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Antonina I
authors.initials: AI
authors.lastname: Zhelezova
authors.affiliation: 5 Institute of Systems Biology, Ltd. , Novosibirsk, Russia .|6 Design Technological Institute of Digital Techniques, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Ivan S
authors.initials: IS
authors.lastname: Evshin
authors.affiliation: 4 Novosibirsk State University , Novosibirsk, Russia .|5 Institute of Systems Biology, Ltd. , Novosibirsk, Russia .|6 Design Technological Institute of Digital Techniques, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Ruslan N
authors.initials: RN
authors.lastname: Sharipov
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Julia M
authors.initials: JM
authors.lastname: Minina
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Natalia S
authors.initials: NS
authors.lastname: Zhdanova
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Igor I
authors.initials: II
authors.lastname: Khegay
authors.affiliation: 5 Institute of Systems Biology, Ltd. , Novosibirsk, Russia .|6 Design Technological Institute of Digital Techniques, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .
authors.forename: Fedor A
authors.initials: FA
authors.lastname: Kolpakov
authors.affiliation: 7 Research Center for Obstetrics, Gynecology, and Perinatology, Ministry of Healthcare of the Russian Federation , Moscow, Russia .
authors.forename: Gennadiy T
authors.initials: GT
authors.lastname: Sukhikh
authors.affiliation: 2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .
authors.forename: Evgeniy A
authors.initials: EA
authors.lastname: Pokushalov
authors.affiliation: 2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Karaskov
authors.affiliation: 3 Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|4 Novosibirsk State University , Novosibirsk, Russia .
authors.forename: Valentin V
authors.initials: VV
authors.lastname: Vlasov
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|4 Novosibirsk State University , Novosibirsk, Russia .
authors.forename: Ludmila N
authors.initials: LN
authors.lastname: Ivanova
authors.affiliation: 1 The Federal Research Center Institute of Cytology and Genetics , the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|2 State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia .|3 Institute of Chemical Biology and Fundamental Medicine, the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia .|4 Novosibirsk State University , Novosibirsk, Russia .
authors.forename: Suren M
authors.initials: SM
authors.lastname: Zakian
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D053595:Embryonic Stem Cells / Q000166:cytology* / Q000378:metabolism; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism*; D051381:Rats; D059467:Transcriptome; D049951:X Chromosome Inactivation