Combined analysis of multiple omics

TECHNOLOGY SERVICES

Animal and plant genomes
Microbial genome
Transcriptional regulation
Microbial diversity
Animal and plant resequencing
Proteomics and metabolomics
Pure sequencing
- Third generation database sequencing
- Second generation database building sequencing

Product introduction
Common problem
Classic case
Result display

Due to the existence of variable shear (variable shear exists in 90% of the RNA expressed by human genes), a gene often corresponds to multiple transcripts (isoforms), so the quantification of transcripts is very necessary. The traditional transcriptome can only quantify the expression of genes (go, KEGG and other analysis based on the longest transcript). Isoform quantitative full-length transcriptome can quantify the transcript and annotate the function of each isoform of the gene.

Multiomics association analysis based on isoform quantitative full-length transcriptome restores the real systems biology process.

Case study: joint analysis of multiomics reveals the regulatory effect of autophagy on Maize metabolism (if = 13.256)

Under nutritional constraints, autophagy is essential for cell life activities. ATG is a series of autophagy related proteins. Atg8 is a ubiquitin protein. Under the action of atg12-atg5-atg16, it binds with PE to form atg8-pe complex, which plays an important role in the process of autophagy.

scientific problems

Mechanism of cell dependent autophagy in Maize

experimental design

Wild type (W22), atg12-1 mutant (Atg8 modification was blocked and inactivated), and atg12-2 (gene knockout) were cultured under nitrogen rich conditions for 2 weeks and under nitrogen deficient conditions for 1 week, respectively. The second and fourth leaves of seedlings at two stages were taken for transcriptome (PCR verification), proteome, metabolome and Ionome detection.

result

Phenotypic nitrogen stress changed the transcriptome and proteome of WT leaves, increased nitrogen metabolism and decreased chlorophyll expression. Nitrogen deficient seedlings showed strong growth inhibition and atg12 mutant senescence.

There were differences in transcriptome, proteome and metabolome (PCA) between multiomic mutants and wild-type under nitrogen rich or nitrogen deficient conditions.

The abundance of proteome Atg8 protein family and total protein increased in atg12, indicating that autophagy is important to maintain normal protein abundance in plants. Atg12 mutant blocks the conversion mediated by Atg8 autophagy.

Transcriptome autophagy significantly affected maize transcriptome, and protease and lipid metabolism transcripts in autophagy mutants were significantly up-regulated in 567 core transcripts.

The metabolites of metabolome were significantly different under nitrogen rich conditions, indicating that autophagy could significantly affect maize metabolism even under normal growth conditions; The relatively small differences during stress, especially lipids, indicate that hunger activates other metabolic pathways other than autophagy to help meet this challenge.

association analysis

There was no significant change in the mRNA corresponding to most of the abundant proteins in atg12-1. On the surface, these changes were caused by autophagy and had nothing to do with synthesis. The increased levels of protein and metabolites are consistent with the increased levels of these metabolites. The consumption of thylakoids in mutants is consistent with the accelerated decomposition of chloroplasts, which may be due to the lack of other decomposition pathways under autophagy conditions.

The changes of major mRNA and protein and metabolites related to lipid metabolism in atg12 indicate that the excessive accumulation of lipid metabolites in the mutant is caused by defects in other metabolic processes regulated by autophagy, which may be related to protein clearance.

Conclusion autophagy essentially changes the protein composition and metabolites of maize, and provides nutrients for plant growth. It is an important part of maintaining cell homeostasis.

reference

Fionn M, Robert C A, Richard S M, et al. Maize multi-omics reveal roles for autophagic recycling in proteome remodelling and lipid turnover. Nature Plants 4, 1056–1070 (2018).