Epigenetic Distribution of Recombinant Plant Chromosome Fragments in a Human–Arabidopsis Hybrid Cell Line
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Methylation Landscape of Plant Genome Fragments in Human Hybrid Cells
2.2. Patterns of DNA Methylation in Genes and TEs
2.3. Differentially Methylated Arabidopsis Genome Segments in Hybrid Cell Lines
2.4. Hypomethylation of Arabidopsis Repetitive Elements in the Human Genome Background
2.5. Function of Arabidopsis Methyltransferase in Hybrid Cells
2.6. Expression Analysis of Plant-Specific Genes in Hybrid Cells
3. Discussion
3.1. Conservation of Genome-Wide Arabidopsis CG Methylation Level in Human Genome Background
3.2. Hypomethylation of Arabidopsis Centromere in 300-Day-Old Hybrid Cells
3.3. Hypomethylation of Arabidopsis Repetitive Elements in the Human Genome Background
3.4. No Preferential Expression of Original Arabidopsis Genes in Human Genome Background
4. Materials and Methods
4.1. Cell Culture
4.2. Plant Material and DNA Extraction
4.3. Whole-Genome Bisulfite Sequencing (WBGS)
4.4. WGBS Data Processing
4.5. Differential Methylation Analysis
4.6. Gene Expression Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Arabidopsis Methyltransferase | Methylation Context | Presence | Expression |
---|---|---|---|
DDM2/MET1 | CG | Yes | No |
CMT3 | CHG | No | No |
DRM2 | CHH | Yes | No |
Gene | Locus | Encoding Protein | Gene Ontology | Log2 Ratio * | Expression in 60-Day-Old Cells | Expression in 300-Day-Old Cells |
---|---|---|---|---|---|---|
HPR | AT1G68010 | Hydroxyperuvase reductase | Cellular response to light stimulus, photorespiration, chloroplast | 3.22 | N | Gene absent |
NPY4 | AT2G23050 | Naked Pins in YUC Mutants 4 | Positive gravitropism | 7.96 | Y | Y |
LHCB4.3 | AT2G40100 | Light Harvesting Complex Photosystem II | Photosynthesis, light harvesting, response to light stimulus, chloroplast | 4.22 | Y | Y |
CA2 | AT5G14740 | Carbonic anhydrase 2 | Carbon utilization, chloroplast | 9.06 | Y | Y |
APE2 | AT5G46110 | Acclimation of Photosynthesis to Environment 2 | Photosynthetic acclimation, chloroplast | 7.01 | N | N |
CESA4 | AT5G44030 | Cellulose Synthase A4 | Cell wall biogenesis | - | N | N |
GSL8 | AT2G36850 | Glucan Synthase-Like 8 | Pollen development | - | N | N |
AtNADH | AT5G11770 | NADH-ubiquinone oxidoreductase | Aerobic respiration | 11.23 | Y | Y |
GAMMA-TIP | AT2G36830 | Gamma-tonoplast intrinsic protein 1 | Transmembrane transport, response to salt stress | 10.44 | Y | Y |
PLP6 | AT2G39220 | Patatin-like protein 6 | Hydrolase activity | 10.28 | Y | Y |
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Liaw, Y.; Liu, Y.; Teo, C.; Cápal, P.; Wada, N.; Fukui, K.; Doležel, J.; Ohmido, N. Epigenetic Distribution of Recombinant Plant Chromosome Fragments in a Human–Arabidopsis Hybrid Cell Line. Int. J. Mol. Sci. 2021, 22, 5426. https://doi.org/10.3390/ijms22115426
Liaw Y, Liu Y, Teo C, Cápal P, Wada N, Fukui K, Doležel J, Ohmido N. Epigenetic Distribution of Recombinant Plant Chromosome Fragments in a Human–Arabidopsis Hybrid Cell Line. International Journal of Molecular Sciences. 2021; 22(11):5426. https://doi.org/10.3390/ijms22115426
Chicago/Turabian StyleLiaw, YengMun, Yikun Liu, CheeHow Teo, Petr Cápal, Naoki Wada, Kiichi Fukui, Jaroslav Doležel, and Nobuko Ohmido. 2021. "Epigenetic Distribution of Recombinant Plant Chromosome Fragments in a Human–Arabidopsis Hybrid Cell Line" International Journal of Molecular Sciences 22, no. 11: 5426. https://doi.org/10.3390/ijms22115426