Project description:Using nanoproteomics,we profiled the dynamics of proteome and found potentially important proteins in Arabidopsis thaliana early embryogenesis. Combining with RNAs-seq, we unveiled the relationship of protein and mRNA during Arabidopsis embryogenesis.
Project description:In this project, we profiled the dynamics of proteome during Arabidopsis early embryogenesis using nanoproteomics. In addition, we identified some proteins which may be important during this process. Combining with RNA-seq, we unveiled the relationship between RNA and proteins during Arabidopsis early embryogenesis.
Project description:Somatic embryogenesis closely resembles zygotic embryogenesis and hence, it is considered as a model system to explore dynamic events of embryogenesis, at a molecular level. We sequenced three district developmental time points of somatic embryo development in Arabidopsis thaliana with the aim of exploring transcriptomes at a global scale.
Project description:We resolved the RNA secondary structure during zebrafish early embryogenesis based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We analyzed the RNA structure dynamics among different development stages. Also, we studied which factors regulate maternal gene decay by RNA structure switch.
Project description:Early vertebrate embryogenesis is characterized by extensive post-transcriptional regulation during the maternal-to-zygotic transition. The N6-methyladenosine (m6A) modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability, translation efficiency and effect on miR-430 degradation kinetics. Notably, we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. After zygotic genome activation m6A is associated with improved stability and dampens the effect of miR-430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms, for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development.
Project description:To determine the transcriptional effects of lack of Tet proteins during early embryogenesis, we performed single-embryo RNA-sequencing of control and TKO embryos (E6.75; 4 embryos from each group). Genome-wide analyses showed that Tet deficiency promotes the expression of mesoderm-related genes during early embryogenesis in vivo.
Project description:Translational control is critical for early Drosophila embryogenesis and is exerted mainly at the gene-specific level. To understand the post-transcriptional regulation during Drosophila early embryonic development, we used the sucrose polysomal gradient analyses and GeneChip analysis to illustrate the translation profile of individual mRNAs. A paper was published in Genome Biology 2007 under the tile Global analyses of mRNA translational control during early Drosophila embryogenesis". Experiment Overall Design: In this study, we have fractionated embryo extracts from a series of early stages by sedimentation on sucrose density gradients and analyzed the RNA components of these fractions. Our analysis has focused on analyzing ribosomal density, generally and for individual transcripts, global translational activity during the first 10 hours after egg laying and coordination between transcription and translation regulation.