Alan L. Kwan1, Huawen Lin2, and Susan K. Dutcher2
RNA-Seq of Chlamydomonas deflagellation reveals early genetic program for ciliogenesis
1) Department of Computer Science & Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
2) Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA
Chlamydomonas cells shed their flagella upon acid pH shock and most of the known axonemal genes show transcriptional upregulation. These observations have provided a valuable platform for investigations aimed at the elucidation of a flagellar proteome and its regulation. Studies by Schloss, Rosenbaum and colleagues suggest that changes at early time points may elucidate the genetic program used for flagellar assembly and function. We analyzed the Chlamydomonas transcriptome by RNA-Seq with Illumina sequencing on samples from 0, 3, 10, 30, and 60 minutes post-deflagellation using the Cufflinks algorithm. Over 50% of the genes show no changes throughout the time course. A small set (N=21) are upregulated as a single pulse at 10 min and are restored to the basal level by 30 min. This set is enriched in transcription factor and kinase motifs, which may suggest a cascading regulatory network topology. The genes for axonemal proteins and the intraflagellar transport proteins follow distinct expression programs. Axonemal genes are transcribed at basal levels until 30 min while most IFT genes show increased levels by 10 min, reach a maximum at 30 min, and decrease to basal levels by 60 min. These patterns suggest that the different sets show unique blueprint that is consistent with the events in flagellar assembly. In addition, these patterns may help to identify further members of these groups.
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