Transcriptome analysis of HeLa cells upon deprivation of methionine and cysteine (Met/Cys)
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ABSTRACT:
PROVIDER: PRJEB24740 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2276800_1.fastq.gz | Fastqsanger.gz | |||
| ERR2276800_2.fastq.gz | Fastqsanger.gz | |||
| ERR2276801_1.fastq.gz | Fastqsanger.gz | |||
| ERR2276801_2.fastq.gz | Fastqsanger.gz | |||
| ERR2276802_1.fastq.gz | Fastqsanger.gz |
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Project description:We have previously shown that deprivation of essential amino acids, namely methionine/cysteine or tyrosine, leads to the transcriptional reactivation of integrated silenced transgenes, and latent HIV-1 provirus. In an effort to understand the underlying mechanisms, here we investigate the overall transcriptional profile of HeLa cells upon Met/Cys starvation for different time points, including the expression of repeated and transposable elements. HeLa cells carrying a stably integrated and silenced plasmid expressing the OA1/GPR143 gene (pcDNA3.1-OA1) were cultured in regular DMEM medium for 6-30-120 hours, or in absence of Met/Cys for 6-15-30-72-120 hours, and the changes in the expression of genes and repeated elements was evaluated by RNAseq
2018-07-21 | E-MTAB-6452 | biostudies-arrayexpress
Project description:First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys) Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys). Keywords: amino acid deprivation
2007-12-13 | GSE9517 | GEO
Project description:First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys); Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys). Experiment Overall Design: First experiment: Three plates of cells were cultured under each condition. Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys). Experiment Overall Design: Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys).
2008-06-16 | E-GEOD-9517 | biostudies-arrayexpress
Project description:Limitation of essential amino acids, such as tyrosine or methionine/cysteine, causes upregulation of exogenous integrated transgene expression in mammalian cells. This phenomenon is mediated by histone acetylation and chromatin remodelling, since histone deacetylase (HDAC) inhibitors reproduce starvation-induced transgene upregulation and chromatin immunoprecipitation analysis of amino acid-deprived cells reveals significant changes in total core histones detectable at the CMV promoter. Expression profiling of HeLa cells starved for 5 days in medium without tyrosine or methionine/cysteine provides important information on the cellular response to amino acid deprivation and suggests the involvement of HDAC4 (class II HDAC) in transgene derepression during amino acid starvation. Total RNA obtained from HeLa and HeLaOA1myc cells (HeLa cells with a human ocular albinism type 1 (OA1)+myc tag transgene) subjected to 5 days of tyrosine or methionine/cysteine starvation compared to control cells. Twelve samples are analyzed: HeLa and HeLaOA1myc grown for 5 days in RPMI deprived of tyrosine (Y) vs. complete RPMI; technical duplicates of HeLa and HeLaOA1myc grown for 5 days in DMEM deprived of methionine/cysteine (MC) vs. complete DMEM.
2012-07-23 | E-GEOD-35323 | biostudies-arrayexpress
Project description:Limitation of essential amino acids, such as tyrosine or methionine/cysteine, causes upregulation of exogenous integrated transgene expression in mammalian cells. This phenomenon is mediated by histone acetylation and chromatin remodelling, since histone deacetylase (HDAC) inhibitors reproduce starvation-induced transgene upregulation and chromatin immunoprecipitation analysis of amino acid-deprived cells reveals significant changes in total core histones detectable at the CMV promoter. Expression profiling of HeLa cells starved for 5 days in medium without tyrosine or methionine/cysteine provides important information on the cellular response to amino acid deprivation and suggests the involvement of HDAC4 (class II HDAC) in transgene derepression during amino acid starvation.
2012-07-24 | GSE35323 | GEO
Project description:Using RNA-seq to explore the mechanisms underlysing the effects of methionyl-methionine dipeptide (Met-Met) or free methionine (Met) supplementation in Met-restricted mice during pregnancy on mammogenesis and lactation.
2022-04-02 | GSE129224 | GEO
Project description:Human iPSCs require high amounts of methionine (Met). Met deprivation results in a rapid decrease in intracellular S-adenosyl-methionine (SAM), poising human iPSCs for differentiation and leading to apoptosis of undifferentiated cells. Met deprivation triggers a rapid metabolite change, including SAM, followed by reversible epigenetic modification. We show here that short-term Met deprivation impairs pluripotency network through epigenetic modification. The trimethylation of lysine 4 on histone H3 (H3K4me3) was dramatically affected compared to other histone modifications. Transcription start site (TSS) region of key pluripotent genes such as NANOG and OCT3/4 are specifically impacted upon short-term Met deprivation. Gene expression levels of these genes decreased, correlating to the loss of H3K4me3 marks. Upon differentiation, Met deprivation triggers a loss of the H3K27me3 in many mesendodermal genes, thereby switching from a bivalent to monovalent (H3K4me3) state. We concluded that Met metabolism maintains the pluripotent network with histone marks, and their loss potentiates differentiation.
2022-12-05 | GSE198171 | GEO
Project description:Human iPSCs require high amounts of methionine (Met). Met deprivation results in a rapid decrease in intracellular S-adenosyl-methionine (SAM), poising human iPSCs for differentiation and leading to apoptosis of undifferentiated cells. Met deprivation triggers a rapid metabolite change, including SAM, followed by reversible epigenetic modification. We show here that short-term Met deprivation impairs pluripotency network through epigenetic modification. The trimethylation of lysine 4 on histone H3 (H3K4me3) was dramatically affected compared to other histone modifications. Transcription start site (TSS) region of key pluripotent genes such as NANOG and OCT3/4 are specifically impacted upon short-term Met deprivation. Gene expression levels of these genes decreased, correlating to the loss of H3K4me3 marks. Upon differentiation, Met deprivation triggers a loss of the H3K27me3 in many mesendodermal genes, thereby switching from a bivalent to monovalent (H3K4me3) state. We concluded that Met metabolism maintains the pluripotent network with histone marks, and their loss potentiates differentiation.
2022-12-05 | GSE198160 | GEO
Project description:Staple crops in human and livestock diets suffer from deficiencies in certain “essential” amino acids including methionine. With the goal of increasing methionine in rice seed, we generated a pair of “PushxPull” double transgenic lines, each containing a methionine-dense seed storage protein (2S albumin from sunflower, HaSSA) and an exogenous enzyme for either methionine (feedback desensitized cystathionine gamma synthase from Arabidopsis, AtD-CGS) or cysteine (serine acetyltransferase from E. coli, EcSAT) biosynthesis. In both double transgenic lines, the total seed methionine content was approximately 50% higher than in their untransformed parental line, Oryza sativa ssp. japonica cv. Taipei 309. HaSSA-containing rice seeds were reported to display an altered seed protein profile, speculatively due to insufficient sulfur amino acid content. However, here we present data suggesting that this may result from an overloaded protein folding machinery in the endoplasmic reticulum rather than primarily from redistribution of limited methionine from endogenous seed proteins to HaSSA. We hypothesize that HaSSA-associated endoplasmic reticulum stress results in redox perturbations that negatively impact sulfate reduction to cysteine, and we speculate that this is mitigated by EcSAT-associated increased sulfur import into the seed, which facilitates additional synthesis of cysteine and glutathione. The data presented here reveal challenges associated with increasing the methionine content in rice seed, including what may be relatively low protein folding capacity in the endoplasmic reticulum and an insufficient pool of sulfate available for additional cysteine and methionine synthesis. We propose that future approaches to further improve the methionine content in rice should focus on increasing seed sulfur loading and avoiding the accumulation of unfolded proteins in the endoplasmic reticulum.
2020-06-30 | GSE149252 | GEO
Project description:RNA sequence for mammary gland of ICR mice at pregnant day 17 with supplementation of methionine (Met) alone or with methionyl-methionine (Met-Met) dipeptide.
| PRJNA530552 | ENA