Abstract
BackgroundmicroRNAs (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.ResultsBy 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.ConclusionsOur 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.
Highlights
MicroRNAs have been found to play an essential role in the modulation of numerous biological processes in eukaryotes
The small RNA profile of Chlamydomonas reinhardtii in both sulfur-replete and sulfur-deprived conditions The equal numbers of algal cells were resuspended under continuous illumination for up to 72 h in TAP or TAP-S
Comparing the common small RNAs sequences between -S and + S libraries, the total small RNAs sequences in both libraries reached 98.01%, the common categories of unique small RNAs were only 24.88%. It indicates that sulfur-deprivation led to a significant influence on the small RNA expression patterns in Chlamydomonas reinhardtii (Figure 2)
Summary
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. Sulfur is an essential trace element for all organisms, and is widely used in biochemical processes. The available pools of sulfate can vary significantly as environmental conditions change. Most organisms have a limited capacity to store sulfur, and require different strategies to optimize sulfur use for survival.
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