Prevalence, evolution and cis-regulation of diel transcription in Chlamydomonas reinhardtii. Chlamydomonas reinhardtii

Biological rhythms in response to both endogenous (circadian) and exogenous (e.g. diel) cycles, with a period of ~24 hours, are a prominent feature of many living systems. In green algal species, knowledge on the extent of diel rhythmicity of genome wide gene expression, its evolution, and its cis-regulatory mechanism is limited. In this study, we identified cyclically expressed genes under diel conditions in Chlamydomonas reinhardtii and found that ~50% of the 17,114 annotated genes exhibited cyclic expression. The cyclic expression patterns indicate a clear succession of biological processes during the course of a day. Among 237 functional categories enriched in cyclically expressed genes, >90% were phase-specific, including photosynthesis, cell division and motility processes. By contrasting cyclic expression between C. reinhardtii and Arabidopsis thaliana putative orthologs, we found significant but weak conservation in cyclic gene expression patterns. On the other hand, within C. reinhardtii cyclic expression was preferentially maintained, particularly amongst older duplicates, and the evolution of phase between paralogs is limited to relatively minor shifts in time. Finally, to better understand the cis regulatory basis of diel expression, putative cis-regulatory elements were identified that could predict the expression phase of a subset of the cyclic transcriptome. Our findings demonstrate both the prevalence of as well as the complex regulatory circuitry required to control cyclic expression in a green algal model, highlighting the need to consider diel expression in studying algal molecular networks and in future biotechnological applications. Overall design: Total RNA sequences extracted every 3 hours between ZT (Zeitgeber Time, hours since last doawn) 0 and ZT21 from two biological replicates of C. reinhardtiis dw15.1