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Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).
- 2.
Ambrosi, C., Manzo, M. & Baubec, T. Dynamics and context-dependent roles of DNA methylation. J. Mol. Biol. 429, 1459–1475 (2017).
- 3.
Luo, C., Hajkova, P. & Ecker, J. R. Dynamic DNA methylation: in the right place at the right time. Science 361, 1336–1340 (2018).
- 4.
Matzke, M. A. & Mosher, R. A. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat. Rev. Genet. 15, 394–408 (2014).
- 5.
Stroud, H. et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat. Struct. Mol. Biol. 21, 64–72 (2014).
- 6.
Heard, E. & Martienssen, R. A. Transgenerational epigenetic inheritance: myths and mechanisms. Cell 157, 95–109 (2014).
- 7.
Kawashima, T. & Berger, F. Epigenetic reprogramming in plant sexual reproduction. Nat. Rev. Genet. 15, 613–624 (2014).
- 8.
Ingouff, M. et al. Live-cell analysis of DNA methylation during sexual reproduction in Arabidopsis reveals context and sex-specific dynamics controlled by noncanonical RdDM. Genes Dev. 31, 72–83 (2017).
- 9.
Ibarra, C. A. et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360–1364 (2012).
- 10.
Calarco, J. P. et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151, 194–205 (2012).
- 11.
Park, K. et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proc. Natl Acad. Sci. USA 113, 15138–15143 (2016).
- 12.
Choi, Y. et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110, 33–42 (2002).
- 13.
Satyaki, P. R. V. & Gehring, M. DNA methylation and imprinting in plants: machinery and mechanisms. Crit. Rev. Biochem. Mol. Biol. 52, 163–175 (2017).
- 14.
Schoft, V. K. et al. Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte. Proc. Natl Acad. Sci. USA 108, 8042–8047 (2011).
- 15.
Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461–472 (2009).
- 16.
Martinez, G., Panda, K., Köhler, C. & Slotkin, R. K. Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nat. Plants 2, 16030 (2016).
- 17.
He, S., Vickers, M., Zhang, J. & Feng, X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. Elife 8, e42530 (2019).
- 18.
Penterman, J. et al. DNA demethylation in the Arabidopsis genome. Proc. Natl Acad. Sci. USA 104, 6752–6757 (2007).
- 19.
Gong, Z. et al. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111, 803–814 (2002).
- 20.
Francis, K. E. et al. Pollen tetrad-based visual assay for meiotic recombination in Arabidopsis. Proc. Natl Acad. Sci. USA 104, 3913–3918 (2007).
- 21.
Hollister, J. D. et al. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl Acad. Sci. USA 108, 2322–2327 (2011).
- 22.
Schmitz, R. J. et al. Patterns of population epigenomic diversity. Nature 495, 193–198 (2013).
- 23.
Gehring, M., Bubb, K. L. & Henikoff, S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324, 1447–1451 (2009).
- 24.
Batista, R. A. et al. The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons. Elife 8, e50541 (2019).
- 25.
Walker, J. et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nat. Genet. 50, 130–137 (2018).
- 26.
Bewick, A. J. et al. On the origin and evolutionary consequences of gene body DNA methylation. Proc. Natl Acad. Sci. USA 113, 9111–9116 (2016).
- 27.
Chang, F., Gu, Y., Ma, H. & Yang, Z. AtPRK2 promotes ROP1 activation via RopGEFs in the control of polarized pollen tube growth. Mol. Plant 6, 1187–1201 (2013).
- 28.
Duckney, P. et al. Actin-membrane interactions mediated by NETWORKED2 in Arabidopsis pollen tubes through associations with Pollen Receptor-Like Kinase 4 and 5. N. Phytol. 216, 1170–1180 (2017).
- 29.
Ge, Z. et al. Arabidopsis pollen tube integrity and sperm release are regulated by RALF-mediated signaling. Science 358, 1596–1600 (2017).
- 30.
Lu, Y. et al. Pollen tubes lacking a pair of K+ transporters fail to target ovules in Arabidopsis. Plant Cell 23, 81–93 (2011).
- 31.
Qin, Y. et al. Penetration of the stigma and style elicits a novel transcriptome in pollen tubes, pointing to genes critical for growth in a pistil. PLoS Genet. 5, e1000621 (2009).
- 32.
Wang, T. et al. A receptor heteromer mediates the male perception of female attractants in plants. Nature 531, 241–244 (2016).
- 33.
Muschietti, J. P. & Wengier, D. L. How many receptor-like kinases are required to operate a pollen tube. Curr. Opin. Plant Biol. 41, 73–82 (2018).
- 34.
Evans, A. R., Hall, D., Pritchard, J. & Newbury, H. J. The roles of the cation transporters CHX21 and CHX23 in the development of Arabidopsis thaliana. J. Exp. Bot. 63, 59–67 (2012).
- 35.
Loraine, A. E., McCormick, S., Estrada, A., Patel, K. & Qin, P. RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. Plant Physiol. 162, 1092–1109 (2013).
- 36.
Jones, A. M. et al. Border control–a membrane-linked interactome of Arabidopsis. Science 344, 711–716 (2014).
- 37.
Dong, S. et al. Proteome-wide, structure-based prediction of protein-protein interactions/new molecular interactions viewer. Plant Physiol. 179, 1893–1907 (2019).
- 38.
Tang, K., Lang, Z., Zhang, H. & Zhu, J.-K. The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications. Nat. Plants 2, 16169 (2016).
- 39.
Borges, F. et al. Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis. Nat. Genet. 50, 186–192 (2018).
- 40.
You, W. et al. Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biol. 12, 51 (2012).
- 41.
Dapper, A. L. & Wade, M. J. Relaxed selection and the rapid evolution of reproductive genes. Trends Genet. 36, 640–649 (2020).
- 42.
Ossowski, S. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327, 92–94 (2010).
- 43.
Hesiod. Theogony (Start Publishing, 2017).
- 44.
Higashiyama, T. & Yang, W. C. Gametophytic pollen tube guidance: attractant peptides, gametic controls, and receptors. Plant Physiol. 173, 112–121 (2017).
- 45.
Johnson, M. A., Harper, J. F. & Palanivelu, R. A fruitful journey: pollen ttube navigation from germination to fertilization. Annu. Rev. Plant Biol. 70, 809–837 (2019).
- 46.
Zhong, S. & Qu, L. J. Peptide/receptor-like kinase-mediated signaling involved in male-female interactions. Curr. Opin. Plant Biol. 51, 7–14 (2019).
- 47.
Shirzadi, R. et al. Genome-wide transcript profiling of endosperm without paternal contribution identifies parent-of-origin-dependent regulation of AGAMOUS-LIKE36. PLoS Genet. 7, e1001303 (2011).
- 48.
Lu, Y. RNA isolation from Arabidopsis pollen grains. Bio-protocol e67–e67 (2011).
- 49.
Schoft, V. K. et al. SYBR green-activated sorting of Arabidopsis pollen nuclei based on different DNA/RNA content. Plant Reprod. 28, 61–72 (2015).
- 50.
Borges, F. et al. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei. Plant Methods 8, 44 (2012).
- 51.
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
- 52.
Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).
- 53.
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
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Source: https://www.nature.com/articles/s41467-020-20606-1
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Original Text (This is the original text for your reference.)
- 1.
Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).
- 2.
Ambrosi, C., Manzo, M. & Baubec, T. Dynamics and context-dependent roles of DNA methylation. J. Mol. Biol. 429, 1459–1475 (2017).
- 3.
Luo, C., Hajkova, P. & Ecker, J. R. Dynamic DNA methylation: in the right place at the right time. Science 361, 1336–1340 (2018).
- 4.
Matzke, M. A. & Mosher, R. A. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat. Rev. Genet. 15, 394–408 (2014).
- 5.
Stroud, H. et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat. Struct. Mol. Biol. 21, 64–72 (2014).
- 6.
Heard, E. & Martienssen, R. A. Transgenerational epigenetic inheritance: myths and mechanisms. Cell 157, 95–109 (2014).
- 7.
Kawashima, T. & Berger, F. Epigenetic reprogramming in plant sexual reproduction. Nat. Rev. Genet. 15, 613–624 (2014).
- 8.
Ingouff, M. et al. Live-cell analysis of DNA methylation during sexual reproduction in Arabidopsis reveals context and sex-specific dynamics controlled by noncanonical RdDM. Genes Dev. 31, 72–83 (2017).
- 9.
Ibarra, C. A. et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360–1364 (2012).
- 10.
Calarco, J. P. et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151, 194–205 (2012).
- 11.
Park, K. et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proc. Natl Acad. Sci. USA 113, 15138–15143 (2016).
- 12.
Choi, Y. et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110, 33–42 (2002).
- 13.
Satyaki, P. R. V. & Gehring, M. DNA methylation and imprinting in plants: machinery and mechanisms. Crit. Rev. Biochem. Mol. Biol. 52, 163–175 (2017).
- 14.
Schoft, V. K. et al. Function of the DEMETER DNA glycosylase in the Arabidopsis thaliana male gametophyte. Proc. Natl Acad. Sci. USA 108, 8042–8047 (2011).
- 15.
Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461–472 (2009).
- 16.
Martinez, G., Panda, K., Köhler, C. & Slotkin, R. K. Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nat. Plants 2, 16030 (2016).
- 17.
He, S., Vickers, M., Zhang, J. & Feng, X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. Elife 8, e42530 (2019).
- 18.
Penterman, J. et al. DNA demethylation in the Arabidopsis genome. Proc. Natl Acad. Sci. USA 104, 6752–6757 (2007).
- 19.
Gong, Z. et al. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111, 803–814 (2002).
- 20.
Francis, K. E. et al. Pollen tetrad-based visual assay for meiotic recombination in Arabidopsis. Proc. Natl Acad. Sci. USA 104, 3913–3918 (2007).
- 21.
Hollister, J. D. et al. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl Acad. Sci. USA 108, 2322–2327 (2011).
- 22.
Schmitz, R. J. et al. Patterns of population epigenomic diversity. Nature 495, 193–198 (2013).
- 23.
Gehring, M., Bubb, K. L. & Henikoff, S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324, 1447–1451 (2009).
- 24.
Batista, R. A. et al. The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons. Elife 8, e50541 (2019).
- 25.
Walker, J. et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nat. Genet. 50, 130–137 (2018).
- 26.
Bewick, A. J. et al. On the origin and evolutionary consequences of gene body DNA methylation. Proc. Natl Acad. Sci. USA 113, 9111–9116 (2016).
- 27.
Chang, F., Gu, Y., Ma, H. & Yang, Z. AtPRK2 promotes ROP1 activation via RopGEFs in the control of polarized pollen tube growth. Mol. Plant 6, 1187–1201 (2013).
- 28.
Duckney, P. et al. Actin-membrane interactions mediated by NETWORKED2 in Arabidopsis pollen tubes through associations with Pollen Receptor-Like Kinase 4 and 5. N. Phytol. 216, 1170–1180 (2017).
- 29.
Ge, Z. et al. Arabidopsis pollen tube integrity and sperm release are regulated by RALF-mediated signaling. Science 358, 1596–1600 (2017).
- 30.
Lu, Y. et al. Pollen tubes lacking a pair of K+ transporters fail to target ovules in Arabidopsis. Plant Cell 23, 81–93 (2011).
- 31.
Qin, Y. et al. Penetration of the stigma and style elicits a novel transcriptome in pollen tubes, pointing to genes critical for growth in a pistil. PLoS Genet. 5, e1000621 (2009).
- 32.
Wang, T. et al. A receptor heteromer mediates the male perception of female attractants in plants. Nature 531, 241–244 (2016).
- 33.
Muschietti, J. P. & Wengier, D. L. How many receptor-like kinases are required to operate a pollen tube. Curr. Opin. Plant Biol. 41, 73–82 (2018).
- 34.
Evans, A. R., Hall, D., Pritchard, J. & Newbury, H. J. The roles of the cation transporters CHX21 and CHX23 in the development of Arabidopsis thaliana. J. Exp. Bot. 63, 59–67 (2012).
- 35.
Loraine, A. E., McCormick, S., Estrada, A., Patel, K. & Qin, P. RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. Plant Physiol. 162, 1092–1109 (2013).
- 36.
Jones, A. M. et al. Border control–a membrane-linked interactome of Arabidopsis. Science 344, 711–716 (2014).
- 37.
Dong, S. et al. Proteome-wide, structure-based prediction of protein-protein interactions/new molecular interactions viewer. Plant Physiol. 179, 1893–1907 (2019).
- 38.
Tang, K., Lang, Z., Zhang, H. & Zhu, J.-K. The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications. Nat. Plants 2, 16169 (2016).
- 39.
Borges, F. et al. Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis. Nat. Genet. 50, 186–192 (2018).
- 40.
You, W. et al. Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biol. 12, 51 (2012).
- 41.
Dapper, A. L. & Wade, M. J. Relaxed selection and the rapid evolution of reproductive genes. Trends Genet. 36, 640–649 (2020).
- 42.
Ossowski, S. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327, 92–94 (2010).
- 43.
Hesiod. Theogony (Start Publishing, 2017).
- 44.
Higashiyama, T. & Yang, W. C. Gametophytic pollen tube guidance: attractant peptides, gametic controls, and receptors. Plant Physiol. 173, 112–121 (2017).
- 45.
Johnson, M. A., Harper, J. F. & Palanivelu, R. A fruitful journey: pollen ttube navigation from germination to fertilization. Annu. Rev. Plant Biol. 70, 809–837 (2019).
- 46.
Zhong, S. & Qu, L. J. Peptide/receptor-like kinase-mediated signaling involved in male-female interactions. Curr. Opin. Plant Biol. 51, 7–14 (2019).
- 47.
Shirzadi, R. et al. Genome-wide transcript profiling of endosperm without paternal contribution identifies parent-of-origin-dependent regulation of AGAMOUS-LIKE36. PLoS Genet. 7, e1001303 (2011).
- 48.
Lu, Y. RNA isolation from Arabidopsis pollen grains. Bio-protocol e67–e67 (2011).
- 49.
Schoft, V. K. et al. SYBR green-activated sorting of Arabidopsis pollen nuclei based on different DNA/RNA content. Plant Reprod. 28, 61–72 (2015).
- 50.
Borges, F. et al. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei. Plant Methods 8, 44 (2012).
- 51.
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
- 52.
Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).
- 53.
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
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