Anna V Klepikova1, Ivan V Kulakovskiy2,3,4, Artem S Kasianov2, Maria D Logacheva1,5,6, Aleksey A Penin7,8. 1. Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051, Russia. 2. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, Moscow, 119991, Russia. 3. Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Vitkevicha 1, Pushchino, Moscow Region, 142290, Russia. 4. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991, Moscow, Russia. 5. Moscow State University, Leninskye gory, build 1, Moscow, 119992, Russia. 6. Skolkovo Institute of Science and Technology, Nobelya Ulitsa 3, Moscow, 121205, Russia. 7. Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051, Russia. alekseypenin@gmail.com. 8. Moscow State University, Leninskye gory, build 1, Moscow, 119992, Russia. alekseypenin@gmail.com.
Abstract
BACKGROUND: Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. RESULTS: The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. CONCLUSIONS: Stress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress .
BACKGROUND: Transcriptome map is a powerful tool for a variety of biological studies; transcriptome maps that include different organs, tissues, cells and stages of development are currently available for at least 30 plants. Some of them include samples treated by environmental or biotic stresses. However, most studies explore only limited set of organs and developmental stages (leaves or seedlings). In order to provide broader view of organ-specific strategies of cold stress response we studied expression changes that follow exposure to cold (+ 4 °C) in different aerial parts of plant: cotyledons, hypocotyl, leaves, young flowers, mature flowers and seeds using RNA-seq. RESULTS: The results on differential expression in leaves are congruent with current knowledge on stress response pathways, in particular, the role of CBF genes. In other organs, both essence and dynamics of gene expression changes are different. We show the involvement of genes that are confined to narrow expression patterns in non-stress conditions into stress response. In particular, the genes that control cell wall modification in pollen, are activated in leaves. In seeds, predominant pattern is the change of lipid metabolism. CONCLUSIONS:Stress response is highly organ-specific; different pathways are involved in this process in each type of organs. The results were integrated with previously published transcriptome map of Arabidopsis thaliana and used for an update of a public database TraVa: http://travadb.org/browse/Species=AthStress .