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

• Published in: PloS one Vol. 7; no. 5; p. e36471
• Main Authors: Nishiyama, Tomoaki, Miyawaki, Kaori, Ohshima, Masumi, Thompson, Kari, Nagashima, Akitomo, Hasebe, Mitsuyasu, Kurata, Tetsuya
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04.05.2012; Public Library of Science (PLoS)
• Subjects: Arabidopsis; Arabidopsis - cytology; Arabidopsis - genetics; Arabidopsis thaliana; Auxins; Biology; Biosynthesis; Bryophyta; Bryopsida - cytology; Bryopsida - genetics; Callus; Cell cycle; Cell Differentiation - genetics; Cell Division - genetics; Cell Proliferation; Chloronema; Chloroplasts; Correlation analysis; Cytokinins; Data processing; Deoxyribonucleic acid; Development; DNA; DNA, Complementary - genetics; DNA, Plant - genetics; Epigenesis, Genetic - genetics; Evolution; Flowering; Flowers & plants; Gene expression; Gene Expression Profiling - methods; Gene Library; Gene sequencing; Genes; Genes, Plant - genetics; Genetic research; Genomes; High-Throughput Nucleotide Sequencing; Leaves; Macromolecules; Metabolism; Metazoa; Molecular biology; Molecular modelling; Mosses; Mutagenesis; Oryza; Photosynthesis; Physcomitrella patens; Plant Growth Regulators - genetics; Plant Growth Regulators - metabolism; Plants (botany); Profiling; Proteins; Proteolysis; Ribonucleic acid; RNA; RNA, Messenger - genetics; RNA, Messenger - metabolism; Science; Selaginella; Sequence Analysis, DNA - methods; Signal transduction; Signal Transduction - genetics; Signaling; Stem cells; Stem Cells - cytology; Stress; Time Factors; Transcription factors; Transcription Factors - metabolism; United States > US; Japan; California
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0036471

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.