Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis

Abstract

Ciona intestinalis is a useful model organism to analyze chordate development and genetics. However, unlike vertebrates, it shares a unique mechanism called trans-splicing with lower eukaryotes. In the computational analysis of trans-splicing in C. intestinalis we report here, we discovered that although the amount of non-trans-spliced and trans-spliced genes is usually equivalent, the expression ratio between the two groups varies significantly with tissues and developmental stages. Among the seven tissues studied, the observed ratios ranged from 2.53 in "gonad" to 19.53 in "endostyle", and during development they increased from 1.68 at the "egg" stage to 7.55 at the "juvenile" stage. We further hypothesize that this enrichment in trans-spliced mRNAs in early developmental stages might be related to the abundance of trans-spliced mRNAs in "gonad". Our analysis indicates that in C. intestinalis, although there may not exist strong fundamental requirements for genes to be trans-spliced, the populations of non-trans-spliced and trans-spliced genes are likely to be spatially and temporally regulated differently.

High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: Alternative expression modes and gene function correlates

“…These terms fell into several functionally interrelated themes featuring the plasma membrane/endomembrane system, transmembrane Ca 2+ transport, cell-cell signaling/secretion/ transmembrane signal transduction, membrane organization/ transport/endocytosis, cell adhesion, and cytoskeleton. In agreement with the results of Sierro et al (2009), we found the term ''protein transport'' overrepresented. However, we did not observe overrepresentation of terms related to mitochondria or to cell cycle, nor did Sierro and colleagues observe overrepresentation of membrane-or Ca…”

“…Our previous study found no GO terms significantly overrepresented in a small sample (;330) of transspliced genes, but in a related sample of similar size Sierro et al (2009) reported that the terms ''mitochondrion,'' ''protein transport,'' and ''cell cycle'' were overrepresented in the trans-spliced gene class. A significant new finding of our current study was the identification of a large number of GO terms (>100) overrepresented among efficiently trans-spliced and frequently transspliced gene classes.…”

“…Genome-wide knowledge of the trans-splicing status of individual genes would provide a basis for elucidating those aspects of gene structure or function that may affect the ''choice'' of SL transsplicing versus conventional gene expression. Although there have been several studies of individual genes or of small samples of the transspliced or non-trans-spliced gene sets Sierro et al 2009), there has not yet been a genome-wide identification of trans-spliced and non-trans-spliced gene populations in any organism. Because the trans-spliced and non-trans-spliced gene subpopulations represent a significant fraction of the genome, generating a comprehensive overview has been beyond the reach of conventional sequencing methodologies.…”