Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes

Abstract

The important role that cilia and flagella play in human disease creates an urgent need to identify genes involved in ciliary assembly and function. The strong and specific induction of flagellar-coding genes during flagellar regeneration in Chlamydomonas reinhardtii suggests that transcriptional profiling of such cells would reveal new flagella-related genes. We have conducted a genome-wide analysis of RNA transcript levels during flagellar regeneration in Chlamydomonas by using maskless photolithography method-produced DNA oligonucleotide microarrays with unique probe sequences for all exons of the 19,803 predicted genes. This analysis represents previously uncharacterized whole-genome transcriptional activity profiling study in this important model organism. Analysis of strongly induced genes reveals a large set of known flagellar components and also identifies a number of important disease-related proteins as being involved with cilia and flagella, including the zebrafish polycystic kidney genes Qilin, Reptin, and Pontin, as well as the testis-expressed tubby-like protein TULP2.

Fig. 1.

Measurement of the transcriptional activity for all predicted C. reinhardtii.(a) Fluorescence micrograph of a maskless high-density oligonucleotide array. The array is designed to contain ≈390,000 36-mer features in a 14- × 17.4-mm area, with feature size of ≈15 μm. A control oligonucleotide probe is hybridized to an embedded set of features (Inset), which are used for array identification and extraction of experimental hybridization fluorescence data using software. (b) Analysis of raw data over all time points during flagellar regeneration shows that 41% of the predicted genes were expressed during this study. Median expression levels of all genes are provided in Table 3.