Background: The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene prediction programs and in part to the fragmented nature of the assembly.

No abstract

Bone morphogenetic protein (BMP) was extracted from human dentin matrix with 4 mol/L guanidine-HCl and was purified by liquid chromatography. SDS-PAGE and IEF showed that the purified BMP was homogeneous and induced new bone formation in situ after three weeks when implanted into muscle pouches in Wistar rats. The molecular weight of BMP was estimated to be about 20.0 kDa by SDS-PAGE, and the pI value was 8.8 by IEF. Amino acid analysis suggested that BMP is a protein containing 191 amino acids. A partial amino acid sequence was obtained from the final purified BMP. Dentin-matrix-derived BMP is probably not identical to, but is similar to, bone-matrix-derived BMP, though both types of BMP have the same action in vivo.

Pre-mRNA 59 spliced-leader (SL) trans-splicing occurs in some metazoan groups but not in others. Genome-wide characterization of the trans-spliced mRNA subpopulation has not yet been reported for any metazoan. We carried out a highthroughput analysis of the SL trans-spliced mRNA population of the ascidian tunicate Ciona intestinalis by 454 Life Sciences (Roche) pyrosequencing of SL-PCR-amplified random-primed reverse transcripts of tailbud embryo RNA. We obtained ;250,000 high-quality reads corresponding to 8790 genes, ;58% of the Ciona total gene number. The great depth of this data revealed new aspects of trans-splicing, including the existence of a significant class of ''infrequently trans-spliced'' genes, accounting for ;28% of represented genes, that generate largely non-trans-spliced mRNAs, but also produce trans-spliced mRNAs, in part through alternative promoter use. Thus, the conventional qualitative dichotomy of trans-spliced versus non-trans-spliced genes should be supplanted by a more accurate quantitative view recognizing frequently and infrequently trans-spliced gene categories. Our data include reads representing ;80% of Ciona frequently trans-spliced genes. Our analysis also revealed significant use of closely spaced alternative trans-splice acceptor sites which further underscores the mechanistic similarity of cis-and trans-splicing and indicates that the prevalence of 63-nt alternative splicing events at tandem acceptor sites, NAGNAG, is driven by spliceosomal mechanisms, and not nonsense-mediated decay, or selection at the protein level. The breadth of gene representation data enabled us to find new correlations between trans-splicing status and gene function, namely the overrepresentation in the frequently trans-spliced gene class of genes associated with plasma/endomembrane system, Ca 2+ homeostasis, and actin cytoskeleton.[Supplemental material is available online at http://www.genome.org. The sequence data from this study have been submitted to the NCBI Short Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) under accession no. SRX006190.]A striking evolutionary variation in eukaryotic gene expression mechanisms is the presence or absence in diverse organismal groups of a form of RNA splicing-pre-mRNA spliced leader (SL) trans-splicing (Davis 1996;Nilsen 2001;Hastings 2005). SL transsplicing is closely related to conventional RNA splicing, or cissplicing. The same nucleotide sequence features define donor and acceptor sites, and both processes occur in spliceosomes and involve formation of a 59,39,29 branchpoint upstream of the acceptor site (Agabian 1990;Nilsen 1993). Whereas cis-splicing joins paired donor and acceptor sites within a single RNA molecule, in SL transsplicing the donor exon is the 59-segment of a specialized small 59-capped RNA molecule-the SL RNA-and the target is an unpaired acceptor site near the 59-end of a pre-mRNA molecule.Transfer of the SL RNA 59-segment, the SL sequence, to the pre-mRNA molecule occurs with loss of the pre-mRNA's initial 59-segment ups...