Surprisal analysis of the transcriptomic response of the green microalga Chlamydomonas to the addition of acetate during day/night cycles
| Autor: | Rémi Willamme, Kenny A. Bogaert, Françoise Remacle, Claire Remacle |
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| Rok vydání: | 2018 |
| Předmět: |
2. Zero hunger
0106 biological sciences 0301 basic medicine Cell division biology Surprisal analysis Chemistry Mutant Chlamydomonas Glyoxylate cycle General Physics and Astronomy Isocitrate lyase biology.organism_classification 01 natural sciences Cell biology Transcriptome 03 medical and health sciences 030104 developmental biology Physical and Theoretical Chemistry Gene 010606 plant biology & botany |
| Zdroj: | Chemical Physics. 514:154-163 |
| ISSN: | 0301-0104 |
| DOI: | 10.1016/j.chemphys.2018.04.015 |
| Popis: | Our study aims to find gene pathways that depend on acetate assimilation under diurnal conditions in the microalga Chlamydomonas. We compare the transcriptome of two strains, one control and one mutant deficient for the glyoxylate cycle essential in acetate metabolism, cultivated under day/night cycles with acetate. We apply surprisal analysis, an information-theoretic approach, to the RNA-seq data. Carrying out the analysis on groups of dark and light phase samples separately allows identifying constraints and gene pathways that discriminate between mutant and control samples. Carbon metabolism is the most important in the light phase for the control strain while the dark phase is enriched in cell division pathways. The mutant phenotype includes genes pathways of stress response and autophagy in the two phases. Cell division pathways are found in the light phase and catabolic pathways in the dark phase, highlighting a rewiring of the mutant transcriptome in these cyclic cultivation conditions. |
| Databáze: | OpenAIRE |
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