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Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo

(2017) NATURE PLANTS. 3(11). p.894-904
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Abstract
During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue-and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.
Keywords
LASER CAPTURE MICRODISSECTION, LIGATION-INDEPENDENT CLONING, GENOME-WIDE ANALYSIS, EARLY EMBRYOGENESIS, GLOBAL ANALYSIS, ROOT-MERISTEM, INTACT METHOD, CELL-TYPES, THALIANA, NUCLEI

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MLA
Palovaara, Joakim, et al. “Transcriptome Dynamics Revealed by a Gene Expression Atlas of the Early Arabidopsis Embryo.” NATURE PLANTS, vol. 3, no. 11, 2017, pp. 894–904, doi:10.1038/s41477-017-0035-3.
APA
Palovaara, J., Saiga, S., Wendrich, J., van ’t Hofland, N., van Schayck, J. P., Hater, F., … Weijers, D. (2017). Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. NATURE PLANTS, 3(11), 894–904. https://doi.org/10.1038/s41477-017-0035-3
Chicago author-date
Palovaara, Joakim, Shunsuke Saiga, Jos Wendrich, Nicole van ’t Hofland, J Paul van Schayck, Friederike Hater, Sumanth Mutte, et al. 2017. “Transcriptome Dynamics Revealed by a Gene Expression Atlas of the Early Arabidopsis Embryo.” NATURE PLANTS 3 (11): 894–904. https://doi.org/10.1038/s41477-017-0035-3.
Chicago author-date (all authors)
Palovaara, Joakim, Shunsuke Saiga, Jos Wendrich, Nicole van ’t Hofland, J Paul van Schayck, Friederike Hater, Sumanth Mutte, Jouke Sjollema, Mark Boekschoten, Guido J Hooiveld, and Dolf Weijers. 2017. “Transcriptome Dynamics Revealed by a Gene Expression Atlas of the Early Arabidopsis Embryo.” NATURE PLANTS 3 (11): 894–904. doi:10.1038/s41477-017-0035-3.
Vancouver
1.
Palovaara J, Saiga S, Wendrich J, van ’t Hofland N, van Schayck JP, Hater F, et al. Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. NATURE PLANTS. 2017;3(11):894–904.
IEEE
[1]
J. Palovaara et al., “Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo,” NATURE PLANTS, vol. 3, no. 11, pp. 894–904, 2017.
@article{8549440,
  abstract     = {{During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue-and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.}},
  author       = {{Palovaara, Joakim and Saiga, Shunsuke and Wendrich, Jos and van 't Hofland, Nicole and van Schayck, J Paul and Hater, Friederike and Mutte, Sumanth and Sjollema, Jouke and Boekschoten, Mark and Hooiveld, Guido J and Weijers, Dolf}},
  issn         = {{2055-0278}},
  journal      = {{NATURE PLANTS}},
  keywords     = {{LASER CAPTURE MICRODISSECTION,LIGATION-INDEPENDENT CLONING,GENOME-WIDE ANALYSIS,EARLY EMBRYOGENESIS,GLOBAL ANALYSIS,ROOT-MERISTEM,INTACT METHOD,CELL-TYPES,THALIANA,NUCLEI}},
  language     = {{eng}},
  number       = {{11}},
  pages        = {{894--904}},
  title        = {{Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo}},
  url          = {{http://doi.org/10.1038/s41477-017-0035-3}},
  volume       = {{3}},
  year         = {{2017}},
}

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