Project description:The lack of knowledge about extreme conservation in genomes remains a major gap in our understanding of the evolution of gene regulation. Here, we reveal an unexpected role of extremely conserved 5’UTRs in non-canonical translational regulation that is linked to the emergence of essential developmental features in vertebrate species. Endogenous deletion of conserved elements within these 5’UTRs decreased gene expression, and extremely conserved 5’UTRs possess cis-regulatory elements that promote cell-type specific regulation of translation. We further developed in-cell mutate-and-map (icM2), a novel methodology that maps RNA structure inside cells. Using icM2, we determined that an extremely conserved 5’UTR encodes multiple alternative structures and that each single nucleotide within the conserved element maintains the balance of alternative structures important to control the dynamic range of protein expression. These results explain how extreme sequence conservation can lead to RNA-level biological functions encoded in the untranslated regions of vertebrate genomes.
Project description:The lack of knowledge about extreme conservation in genomes remains a major gap in our understanding of the evolution of gene regulation. Here, we reveal an unexpected role of extremely conserved 5’UTRs in non-canonical translational regulation that is linked to the emergence of essential developmental features in vertebrate species. Endogenous deletion of conserved elements within these 5’UTRs decreased gene expression, and extremely conserved 5’UTRs possess cis-regulatory elements that promote cell-type specific regulation of translation. We further developed in-cell mutate-and-map (icM2), a novel methodology that maps RNA structure inside cells. Using icM2, we determined that an extremely conserved 5’UTR encodes multiple alternative structures and that each single nucleotide within the conserved element maintains the balance of alternative structures important to control the dynamic range of protein expression. These results explain how extreme sequence conservation can lead to RNA-level biological functions encoded in the untranslated regions of vertebrate genomes.
Project description:Differential DNA methylation at conserved non-genic elements and transgenerational inheritance following developmental exposure to mono(2-ethylhexyl) phthalate and 5-azacytidine in zebrafish
Project description:Lysine succinylation (Ksu) is a novel identified post-translational modification that conserved from prokaryote to eukaryotes. As a kind of acylation, Ksu was reported to have different functions with others acylation at lysine residue. However, recently studies on the Ksu mainly focus on the plants and bacterial, there are still very rare studies in the vertebrate. Therefore, the biological role of succinylation remains largely unknown in mammal. In this study, we performed global Ksu mapping in Danio rerio (zebrafish) using mass spectrometry-based proteomics with enrichment of Ksu peptides by immunoprecipitation technology. As a result, we totally identified 552 Ksu sites in 164 proteins. Compared with our previous studies on lysine acetylation and crotonylation, Ksu plays a major role in a diverse metabolic process, such as carbon metabolism and tricarboxylic acid circle. In addition, we defined 5 new succinylation motifs: (su)KA, (suc)KxxxxA, (su)KxxxxL, (su)KxA, (su)KxV. In conclusion, our result provides proteome-wide database for study of Ksu in zebrafish and our bioinformatics result facilitated the understanding of the Ksu in the role of central metabolism.