Digital gene expression profiling by 5'-end sequencing of cDNAs during reprogramming in the moss Physcomitrella patens.

PloS One
Tomoaki NishiyamaTetsuya Kurata

Abstract

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, altho...Continue Reading

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Citations

Nov 7, 2013·Nucleic Acids Research·Ayaka HienoYoshiharu Y Yamamoto
Jul 1, 2015·The Plant Journal : for Cell and Molecular Biology·Margaret H Frank, Michael J Scanlon
Feb 11, 2014·Current Opinion in Plant Biology·Rumiko Kofuji, Mitsuyasu Hasebe
Mar 3, 2015·Journal of Plant Research·Munetaka Sugiyama
Feb 1, 2019·Current Opinion in Plant Biology·Kaoru SugimotoSachihiro Matsunaga

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Datasets Mentioned

BETA
DRA000400

Methods Mentioned

BETA
PCR
dissection
phosphotransfer
protein
enzymatic treatments
histone acetylation
electrophoresis

Software Mentioned

PHYSCObase
BiNGO
Cytoscape
SOLiD3
SOLiD
SOLiD2
GeneSpring
nanoCAGE
BLASTP

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