H3 Lysine 4 Methylation Is Required for Full Activation of Genes Involved in α-Ketoglutarate Availability in the Nucleus of Yeast Cells after Diauxic Shift
Abstract
:1. Introduction
2. Materials and Methods
2.1. Yeast Growth Condition
2.2. Chromatin Immuno-Precipitation on DNA Arrays (ChIP on Chip)
2.3. Western Blot Analysis
2.4. Chromatin Immunoprecipitation (ChIP)
2.5. Real Time RT-PCR
2.6. Statistical Analysis
3. Results
3.1. Expression of Jhd2 and Set1 in Different Phases of Yeast Growht
3.2. H3K4 Tri-Methylation Level during DS
3.3. H3K4 Methylation Stimulates Gene Transcription Induction at DS
3.4. Active Demethylation Is Not Required for DS Genes Repression following Refreshing
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Yeast Strain | Genotype |
---|---|
BY4741 | MATα his3∆ leu2∆0 LYS2 met15∆0 ura3∆0 |
W303 | MATa, his3-11, ade2-1, leu2-3,112, ura3-1, trp1-D2, can1-100 |
Δjhd2 BY4741 | MATa, his3∆ leu2∆0 LYS2 met15∆0 ura3∆0 YJR119c::kanMX4 |
Δset1 W303 | MATa, his3∆ leu2∆0 LYS2 met15∆0 ura3∆0 YJHR119w::kanMX4 |
over-JHD2 | as BY4741 with plasmid pDPM2 |
Gene | Description | Rank Difference (DS-EG) | p |
---|---|---|---|
IDP2 | Isocitrate dehydrogenase (NADP+), cytosolic | 0.78 | <0.001 |
MLS1 | Malate synthase 1, functions in glyoxylate cycle, has near identity to Dal7p | 0.57 | <0.01 |
ECM13 | Protein possibly involved in cell wall structure or biosynthesis | 0.55 | <0.01 |
GND2 | 6-Phosphogluconate dehydrogenase, decarboxylating, converts 6-phosphogluconate + NADP to ribulose-5-phosphate + NADPH + CO2 | 0.49 | <0.001 |
PXA1 | Protein required for long-chain fatty acid transport across the peroxisomal membrane, member of the ATP-binding cassette (ABC) superfamily, has similarity to a human gene associated with adrenoleukodystrophy | 0.49 | <0.001 |
YPT53 | GTP-binding protein involved in endocytosis and transport of proteins to the vacuole, member of the rab family in the ras superfamily | 0.48 | <0.01 |
ODC1 | 2-Oxodicarboxylate transporter, has specificity for 2-oxoadipate and 2-oxoglutarate, member of the mitochondrial carrier (MCF) family of membrane transporters | 0.48 | <0.05 |
ATH1 | Vacuolar acid trehalase, converts alpha, alpha-trehalose to glucose | 0.47 | <0.001 |
GPX1 | Glutathione peroxidase, involved in cellular protection against lipid and non-lipid hydroperoxides | 0.45 | <0.05 |
MTH1 | Repressor of hexose transport genes | 0.45 | <0.05 |
ADY2 | Protein required for proper ascus formation, has strong similarity to Ydr384p and Ynr002p | 0.44 | <0.05 |
HSP26 | Heat shock protein of 26 kDa, expressed during entry to stationary phase and induced by osmostress, may be required for resistance to ethanol and acetaldehyde | 0.42 | <0.001 |
LEE1 | Protein containing two CCCH-type zinc finger domains, which bind DNA or RNA | 0.4 | <0.001 |
TRX3 | Mitochondrial thioredoxin, has similarity to cytoplasmic thioredoxins Trx1p and Trx2p | 0.38 | <0.05 |
CRC1 | Mitochondrial carnitine carrier, member of the mitochondrial carrier family (MCF) of membrane transporters | 0.38 | <0.001 |
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Di Nisio, E.; Danovska, S.; Condemi, L.; Cirigliano, A.; Rinaldi, T.; Licursi, V.; Negri, R. H3 Lysine 4 Methylation Is Required for Full Activation of Genes Involved in α-Ketoglutarate Availability in the Nucleus of Yeast Cells after Diauxic Shift. Metabolites 2023, 13, 507. https://doi.org/10.3390/metabo13040507
Di Nisio E, Danovska S, Condemi L, Cirigliano A, Rinaldi T, Licursi V, Negri R. H3 Lysine 4 Methylation Is Required for Full Activation of Genes Involved in α-Ketoglutarate Availability in the Nucleus of Yeast Cells after Diauxic Shift. Metabolites. 2023; 13(4):507. https://doi.org/10.3390/metabo13040507
Chicago/Turabian StyleDi Nisio, Elena, Svetlana Danovska, Livia Condemi, Angela Cirigliano, Teresa Rinaldi, Valerio Licursi, and Rodolfo Negri. 2023. "H3 Lysine 4 Methylation Is Required for Full Activation of Genes Involved in α-Ketoglutarate Availability in the Nucleus of Yeast Cells after Diauxic Shift" Metabolites 13, no. 4: 507. https://doi.org/10.3390/metabo13040507