Promoter architecture and sex-specific gene expression in the microcrustacean Daphnia pulex revealed by large-scale profiling of 5'-mRNA ends

摘要: Large-scale identification of transcription start sites (TSSs) using Cap Analysis Gene Expression (CAGE) has yielded insight into promoter location, architecture, and regulation for a small set taxa representing major model organisms. However, comparative evolutionary genomics studies cis-regulatory control initiation wider spectrum Metazoa are still outstanding. To broaden our understanding core structure in species from metazoan clades with currently scant genome data, we sought to characterize the landscape elements microcrustacean water flea Daphnia pulex, an important organism ecology, toxicology, genetics. We performed CAGE total RNA derived three separate developmental states: sexual females, asexual males, reflecting distinct sexes modes reproduction. mapped over 120 million reads D. generated 'Daphnia Promoter Atlas' containing 12,662 unique promoters. Characterization showed expected enrichment CA-dinucleotide at TSSs [-1,+1] (associated Initiator-motif promoters) but also significant over-representation GN-dinucleotides. Overall, these data suggest that pulex among most GC-rich yet observed any organism. Computational de novo motif discovery around CAGE-identified revealed eight putative elements, including canonical TATA (TATAWAA) Initiator (CAGWY) motifs, as well statistically motifs no obvious orthologs other metazoans. Finally, compared activity across sampled states, revealing sex- condition-specific initiation. deferentially expressed genes suggests number cell cycle (each net negative regulatory effects on meiosis) upregulated providing glimpse molecular events underpin cyclical parthenogenesis pulex. Taken together, this work provides first picture architecture within Crustacea. The Atlas present here basis future study spp. genomic analyses transcriptional control.