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Genes regulated by mitoflash

ABSTRACT: We found mitoflash has function in reprogramming. So we examined the genes expression after activation of mitoflash during somatic cell reprogramming. There are two ways to improve the mitoflash. First we overexpressed CypD, a mPTP component, to improve the mitoflash. Second we used the durgs, mastoparan and paraquat to increase the mitoflash. The MEF cells were reprogrammed, and treatment with mastoparan, paraquat or overexpressed with CypD. After activation of mitoflash at different times, the cells were collected for RNA-Seq.

ORGANISM(S): Mus musculus

PROVIDER: GSE73049 | GEO | 2015/09/16

SECONDARY ACCESSION(S): PRJNA296000

REPOSITORIES: GEO

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genes regulated by mitoflash

Project description:We found mitoflash has function in reprogramming. So we examined the genes expression after activation of mitoflash during somatic cell reprogramming. There are two ways to improve the mitoflash. First we overexpressed CypD, a mPTP component, to improve the mitoflash. Second we used the durgs, mastoparan and paraquat to increase the mitoflash. The MEF cells were reprogrammed, and treatment with mastoparan, paraquat or overexpressed with CypD. After activation of mitoflash at different times, the cells were collected for RNA-Seq. MEF cells were reprogrammed and expressed with CypD and Flag (as control) for 4 days. The cells were collected for RNA-Seq (Samples: Falg-D4, CypD-D4). MEF cells were reprogrammed and treated with mastoparan and paraquat for 8 days. The cells were collected for RNA-Seq (Samples: control-D8, mastoparan-D8 and paraquat-D8).

2015-09-16 | E-GEOD-73049 | biostudies-arrayexpress

genes regulated by mitoflash

Project description:we examine the genes expression after activation of mitoflash. The MEF were expressed with CypD or treated with paraquat and mastoparan. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.RNA libraries were prepared for sequencing using standard Illumina protocols.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2-2.2.5 with parameters -p 8 --bowtie2 -sensitivity-level very_sensitive.

2015-09-26 | E-MTAB-3875 | biostudies-arrayexpress

CircBIRC6-2 inhibits transmissible gastroenteritis virus induced mitochondrial permeability transition pore opening by its encoding protein

Project description:Transmissible gastroenteritis virus (TGEV), a member of coronavirus, is the pathogen of TGE. We previously found 123 circular RNAs (circRNAs) were differential expression during activation of mitochondrial permeability transition in porcine intestinal epithelial cells-jejunum 2 cell line (IPEC-J2) in response to TGEV infection. Mitochondrial permeability transition pore (mPTP) is a transmembrane pore of mitochondria and plays a key role in MPT. mPTP abnormal opening causes MPT. Therefore, we postulated that circRNAs might be related to mPTP abnormal opening induced by TGEV. In this study, we found that circBIRC6-2 could inhibit the mPTP abnormal opening induced by TGEV. Interestingly, circBIRC6-2 encodes protein BIRC6-236aa. An open reading frame (ORF) and internal ribosomal entrance site (IRES) of circBIRC6-2 were identified. We also found that BIRC6-236aa rather than circBIRC6-2 inhibited the mPTP opening by overexpression of circBIRC6-2 related vectors. We obtained 91 proteins that interacted with BIRC6-236aa using immunoprecipitation-mass spectrometry (IP-MS). The interaction between voltage-dependent anion-selective channel protein 1 (VDAC1) and BIRC6-236aa was demonstrated through co-immunoprecipitation (Co-IP). Moreover, BIRC6-236aa could inhibit the formation of VDAC1 and Cyclophilin D (CypD) complexes. Overall, these results indicated that BIRC6-236aa antagonized mPTP opening by interacting with VDAC1 to weaken the extent of interaction between VDAC1 and CypD.

2022-10-13 | PXD029055 | Pride

Tet1 as a Negative Regulator of Somatic Cell Reprogramming

Project description:Tet1 is a hydroxylase known for its role in the conversion of 5-methylcytosines (5mC) to 5-hydroxymethylcytosines (5hmC) involved in the possible active demethylation process and gene expression regulation1-5.M-BM- As somatic cell reprogramming involves the re-activation of pluripotency genes and the silencing of somatic ones6, it remains unclear whether Tet1 plays a positive or negative role in the reprogramming process. Here we show that Tet1 deficiency enhances reprogramming and its overexpression impairs reprogramming. Mechanistically, we demonstrated that Tet1 represses the early obligatory process of mesenchymal to epithelial transition (MET) during reprogramming7,8. Thus, our findings not only define a negative role for Tet1 in somatic cell reprogramming, but also suggest that the Tet enzymes regulate cell fate through distinctive mechanisms. Examination of genome DNA hmC modifications in 2 conditions: individually overexpressed Tet1CD or Tet2CD during MEF reprogramming; Examination of mRNA levels in five different conditions: individually overexpressed DR or Tet1CD or Tet1CDmut or Tet2CD or Tet2CDmut, during MEF reprogrammig.

2013-03-08 | E-GEOD-44935 | biostudies-arrayexpress

Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies

Project description:We report the miRNA profiling in MEF cells, ES cells and three Pluripotent Stem Cells obtained by three different reprogramming approaches from MEF cells based on Solexa sequencing. iPS cells are reprogrammed by four factors (OSKM) from MEF cells. NT-ESCs were established by reprogramming MEF cells into ESCs using nuclear transfer. NT-iPSCs were established to reflect the combination of nuclear transfer and iPS technologies. iPSCs, NT-ESCs, and NT-iPSCs were exactly derived from the same MEF cells. The results indicate NT-ESCs give expression to the unique miRNAs other than both ESCs and iPSCs while pluripotent cells acquire or retain the pluripotent specific miRNAs compared with MEF. Furthermore, the comparison of different reprogramming cells suggests that several miRNAs have key roles in distinctly developmental potential reprogrammine cells.

2014-07-05 | GSE52950 | GEO

Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies

2014-07-05 | E-GEOD-52950 | biostudies-arrayexpress

MEF_OSK_O_KS_T20

Project description:Next Generation Sequencing with differdent pluripotent transcript factor overexpression in MEF Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) by defined factors. The low efficiency of reprogramming limited the potential application of iPSCs. Here we found that knockdown LSD1 , which demethylates histone H3 Lys 4 or 9 , could increase iPSCs generation. It has been reported that LSD1 interaction with Oct4 which is the core factor of reprogramming. So we try to find out the different of overexpression Oct4 or Kllf4/Sox2 in MEF and LSD1 inhibitor. Retrovirus-mediated different pluripotent transcript factor overexpression in MEF cells after 4 days collect mRNA profiles processing with Illumina MiSeq; MEF, Mouse Embryonic Fibroblast O, MEF infected with Oct4 KS,MEF infected with Klf4 and Sox2 OSK, MEF infected with Oct4 Klf4 and Sox2 T20, MEF infected with Oct4 Klf4 and Sox2 and treated with 20nm LSD1 inhibitor Tranylcypromine

2015-09-17 | E-GEOD-61694 | biostudies-arrayexpress

MEF_OSK_O_KS_T20

2015-09-17 | GSE61694 | GEO

Overlapping and distinct roles of LIN28 paralogs

Project description:Lin28a or Lin28b single knockout or double knockout MEF cells reprogrammed to iPS cells Lin28a or Lin28b single knockout or double knockout MEF cells reprogrammed to iPS cells

2016-05-24 | GSE67568 | GEO

Transcription profiling of mouse differentiated, partially- and fully-reprogrammed MEFs/B-cells

Project description:Expression profiles generated during dissection of the molecular mechanisms underlying direct reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells, iPS). Experiment Overall Design: 2 technical replicates of B lymphocytes, partially reprogrammed (MCV8, MCV6, BIV1), MEF-iPS(Oct4) and B-iPS(Nanog) cell lines.

2008-06-18 | E-GEOD-10871 | biostudies-arrayexpress

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