Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

Computer Science Department, Colorado State University, Fort Collins, CO, USA.
BMC Genomics (Impact Factor: 3.99). 02/2010; 11(1):114. DOI: 10.1186/1471-2164-11-114
Source: PubMed


Genome-wide computational analysis of alternative splicing (AS) in several flowering plants has revealed that pre-mRNAs from about 30% of genes undergo AS. Chlamydomonas, a simple unicellular green alga, is part of the lineage that includes land plants. However, it diverged from land plants about one billion years ago. Hence, it serves as a good model system to study alternative splicing in early photosynthetic eukaryotes, to obtain insights into the evolution of this process in plants, and to compare splicing in simple unicellular photosynthetic and non-photosynthetic eukaryotes. We performed a global analysis of alternative splicing in Chlamydomonas reinhardtii using its recently completed genome sequence and all available ESTs and cDNAs.
Our analysis of AS using BLAT and a modified version of the Sircah tool revealed AS of 498 transcriptional units with 611 events, representing about 3% of the total number of genes. As in land plants, intron retention is the most prevalent form of AS. Retained introns and skipped exons tend to be shorter than their counterparts in constitutively spliced genes. The splice site signals in all types of AS events are weaker than those in constitutively spliced genes. Furthermore, in alternatively spliced genes, the prevalent splice form has a stronger splice site signal than the non-prevalent form. Analysis of constitutively spliced introns revealed an over-abundance of motifs with simple repetitive elements in comparison to introns involved in intron retention. In almost all cases, AS results in a truncated ORF, leading to a coding sequence that is around 50% shorter than the prevalent splice form. Using RT-PCR we verified AS of two genes and show that they produce more isoforms than indicated by EST data. All cDNA/EST alignments and splice graphs are provided in a website at
The extent of AS in Chlamydomonas that we observed is much smaller than observed in land plants, but is much higher than in simple unicellular heterotrophic eukaryotes. The percentage of different alternative splicing events is similar to flowering plants. Prevalence of constitutive and alternative splicing in Chlamydomonas, together with its simplicity, many available public resources, and well developed genetic and molecular tools for this organism make it an excellent model system to elucidate the mechanisms involved in regulated splicing in photosynthetic eukaryotes.

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    • "Plants favor intron retention but do vary in levels of AS. Specifically , 61% of multiexonic Arabidopsis thaliana genes were spliced, compared with only 3% of those in the green algae Chlamydomonas reinhardtii (Labadorf et al. 2010; Marquez et al. 2012). In contrast, members of the animal lineage prefer exon skipping and can have extremely high levels of AS which, in Homo sapiens, is often tissue or cell specific (Keren et al. 2010; Pan et al. 2008). "
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    Molecular Plant-Microbe Interactions 11/2014; 28(3). DOI:10.1094/MPMI-09-14-0300-FI · 3.94 Impact Factor
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    • "Although intron retention made up half of the alternative splicing events (305 of 611) in C. reinhardtii (Labadorf et al. 2010), our study shows that constitutively spliced introns are over two times more enriched with poly(A) sites than that of retained introns, suggesting constitutively spliced introns have stronger preference to polyadenylation than retained introns. So it is possible that the preference of polyadenylation to constitutive splicing may be the result of interplay between polyadenylation and splicing. "
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    • "One of the major advances over the past years was the insight that most RNA splicing events occur cotranscriptionally and hence are dependent on DNA and chromatin structure and modifications (reviewed in Braunschweig et al., 2013). Up to 90% of proteincoding and many non-protein-coding genes contain introns in photosynthetic eukaryotes (Hirsch et al., 2006; Szarzynska et al., 2009; Labadorf et al., 2010). Generation of mature mRNAs from these genes requires precise removal of introns from precursor mRNAs (pre-mRNAs) and joining of exons. "
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