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Background  microRNAs (miRNAs) have been found to play an essential role in the modulation of numerous biological processes in eukaryotes.  Chlamydomonas reinhardtii  is an ideal model organism for the study of many metabolic processes including responses to sulfur-deprivation. We used a deep sequencing platform to extensively profile and identify changes in the miRNAs expression that occurred under sulfur-replete and sulfur-deprived conditions. The aim of our research was to characterize the differential expression of  Chlamydomonas  miRNAs under sulfur-deprived conditions, and subsequently, the target genes of miRNA involved in sulfur-deprivation were further predicted and analyzed.    Results  By using high-throughput sequencing, we characterized the microRNA transcriptomes under sulphur-replete and sulfur-deprived conditions in  Chlamydomonas reinhardtii . We predicted a total of 310 miRNAs which included 85 known miRNAs and 225 novel miRNAs. 13 miRNAs were the specific to the sulfur-deprived conditions. 47 miRNAs showed significantly differential expressions responding to sulfur-deprivation, and most were up-regulated in the small RNA libraries with sulfur-deprivation. Using a web-based integrated system (Web MicroRNAs Designer 3) and combing the former information from a transcriptome of  Chlamydomonas reinhardtii , 22 miRNAs and their targets involved in metabolism regulation with sulfur-deprivation were verified.    Conclusions  Our results indicate that sulfur-deprivation may have a significant influence on small RNA expression patterns, and the differential expressions of miRNAs and interactions between miRNA and its targets might further reveal the molecular mechanism responding to sulfur-deprivation in  Chlamydomonas reinhardtii .

Characterization and differential expression of microRNAs elicited by sulfur deprivation in Chlamydomonas reinhardtii