TY - JOUR
T1 - Digital gene expression profiling by 5′-end sequencing of cdnas during reprogramming in the moss physcomitrella patens
AU - Nishiyama, Tomoaki
AU - Miyawaki, Kaori
AU - Ohshima, Masumi
AU - Thompson, Kari
AU - Nagashima, Akitomo
AU - Hasebe, Mitsuyasu
AU - Kurata, Tetsuya
N1 - Funding Information:
We thank A. Kato, R. Ichikawa for technical suggestions and help and M. Kubo for comments on gene expression analysis. SOLiD experiments, cultivation of the moss, and data analyses were supported in part by the Functional Genomics Facility, Model Plant Research Facility, and Data Integration and Analysis Facility of National Institute for Basic Biology.
PY - 2012/5/4
Y1 - 2012/5/4
N2 - Stem cells self-renew and repeatedly produce differentiated cells during development and growth. The differentiated cells can be converted into stem cells in some metazoans and land plants with appropriate treatments. After leaves of the moss Physcomitrella patens are excised, leaf cells reenter the cell cycle and commence tip growth, which is characteristic of stem cells called chloronema apical cells. To understand the underlying molecular mechanisms, a digital gene expression profiling method using mRNA 5′-end tags (5′-DGE) was established. The 5′-DGE method produced reproducible data with a dynamic range of four orders that correlated well with qRT-PCR measurements. After the excision of leaves, the expression levels of 11% of the transcripts changed significantly within 6 h. Genes involved in stress responses and proteolysis were induced and those involved in metabolism, including photosynthesis, were reduced. The later processes of reprogramming involved photosynthesis recovery and higher macromolecule biosynthesis, including of RNA and proteins. Auxin and cytokinin signaling pathways, which are activated during stem cell formation via callus in flowering plants, are also activated during reprogramming in P. patens, although no exogenous phytohormone is applied in the moss system, suggesting that an intrinsic phytohormone regulatory system may be used in the moss.
AB - Stem cells self-renew and repeatedly produce differentiated cells during development and growth. The differentiated cells can be converted into stem cells in some metazoans and land plants with appropriate treatments. After leaves of the moss Physcomitrella patens are excised, leaf cells reenter the cell cycle and commence tip growth, which is characteristic of stem cells called chloronema apical cells. To understand the underlying molecular mechanisms, a digital gene expression profiling method using mRNA 5′-end tags (5′-DGE) was established. The 5′-DGE method produced reproducible data with a dynamic range of four orders that correlated well with qRT-PCR measurements. After the excision of leaves, the expression levels of 11% of the transcripts changed significantly within 6 h. Genes involved in stress responses and proteolysis were induced and those involved in metabolism, including photosynthesis, were reduced. The later processes of reprogramming involved photosynthesis recovery and higher macromolecule biosynthesis, including of RNA and proteins. Auxin and cytokinin signaling pathways, which are activated during stem cell formation via callus in flowering plants, are also activated during reprogramming in P. patens, although no exogenous phytohormone is applied in the moss system, suggesting that an intrinsic phytohormone regulatory system may be used in the moss.
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U2 - 10.1371/journal.pone.0036471
DO - 10.1371/journal.pone.0036471
M3 - Article
C2 - 22574165
AN - SCOPUS:84860524202
VL - 7
JO - PLoS One
JF - PLoS One
SN - 1932-6203
IS - 5
M1 - e36471
ER -