Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis

Abstract

The tunicate Ciona intestinalis, an invertebrate chordate, has recently emerged as a powerful model organism for gene regulation analysis. However, few studies have been conducted to identify and characterize its transcription start sites (TSSs) and promoters at the genome-wide level. Here, using TSS-seq, we identified TSSs at the genome-wide scale and characterized promoters in C. intestinalis. Specifically, we identified TSS clusters (TSCs), high-density regions of TSS-seq tags, each of which appears to originate from an identical promoter. TSCs were found not only at known TSSs but also in other regions, suggesting the existence of many unknown transcription units in the genome. We also identified candidate promoters of 79 ribosomal protein (RP) genes, each of which had the major TSS in a polypyrimidine tract and showed a sharp TSS distribution like human RP gene promoters. Ciona RP gene promoters, however, did not appear to have typical TATA boxes, unlike human RP gene promoters. In Ciona non-RP promoters, two pyrimidine-purine dinucleotides, CA and TA, were frequently used as TSSs. Despite the absence of CpG islands, Ciona TATA-less promoters showed low expression specificity like CpG-associated human TATA-less promoters. By using TSS-seq, we also predicted trans-spliced gene TSSs and found that their downstream regions had higher G+T content than those of non-trans-spliced gene TSSs. Furthermore, we identified many putative alternative promoters, some of which were regulated in a tissue-specific manner. Our results provide valuable information about TSSs and promoter characteristics in C. intestinalis and will be helpful in future analysis of transcriptional regulation in chordates.

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

“…In Ciona , the transcripts of approximately half of the protein-coding genes undergo spliced-leader (SL) trans -splicing, causing the 5' end of mRNAs to differ from the transcription start site (TSS) 24,25 . Using annotated TSSs [26][27][28] , RNA-seq datasets 15 , and our ATAC-seq data ( Fig. S2), we determined that promoter regions and 5' untranslated regions (5'UTR) were over-represented in the accessome ( P <0.01, binomial test; Fig.…”

The regulatory pathway from genes directly activated by maternal factors to muscle structural genes in ascidian embryos

“…KH2012.C4.57.v3.A.SL1-1, CG.KH2012.C8.309.v1.A.nonSL1-1, CG.KH2012.C8.477.v1.A.nonSL1-1, CG.KH2012.C8.859.v1.A.nonSL1-1, CG.KH2012.C11.673.v1.A.SL1-1, CG.KH2012.C1.1186.A.SL2-1. Because the transcription start site of Tnc was not determined precisely, we mapped TSS-seq data (Yokomori et al, 2016) and regarded the nucleotide position 15,401 of chromosome 12 as the transcription start site.…”

Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

“…The TOP motif in vertebrate canonical TOP mRNAs (ribosomal proteins and other members of the translational apparatus) is highly conserved and required for growth-dependent translational control via mTOR signalling (Levy et al, 1991). A 5' TOP motif is also enriched in ribosomal protein mRNAs in the ascidian Ciona intestinalis Yokomori et al, 2016). The canonical TOP motif begins with a cytosine and is followed by a stretch of 4-14 pyrimidines (Meyuhas, 2001).…”