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Method for predicting functional gene for regulating and controlling yeast autophagy

A technology of autophagy genes and gene regulation, applied in the field of bioinformatics, can solve the problems of long experiment cycle and high cost

Active Publication Date: 2021-07-06
HUAZHONG UNIV OF SCI & TECH
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0003] In view of the traditional experimental method in the prior art to identify functional genes that regulate yeast autophagy, which requires a long experimental cycle and high cost or improvement needs, the purpose of the present invention is to provide a method for predicting functional genes that regulate yeast autophagy, Among them, by improving the overall process design of the method, and selecting the three key characteristics of genes, based on the multi-omics data of transcriptome and quantitative proteome, the prediction of genes regulating autophagy is realized by the integration of multi-omics data

Method used

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  • Method for predicting functional gene for regulating and controlling yeast autophagy
  • Method for predicting functional gene for regulating and controlling yeast autophagy
  • Method for predicting functional gene for regulating and controlling yeast autophagy

Examples

Experimental program
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Embodiment 1

[0048] This example provides a method for predicting functional proteins involved in the regulation of autophagy based on multi-omics integration, such as figure 1 and figure 2 shown, including the following steps:

[0049] The wild-type (BY4741; MATa his3D leu2Dmet15D ura3D) and corresponding atg9 gene knockout yeast cells were treated with nitrogen source-depleted medium as an autophagy inducer for 0 hour, 1 hour, and 4 hours, respectively, and collected 3 hours after treatment Spot the yeast cell sample.

[0050] Using the second-generation gene sequencer HiSeq 4000system, RNA sequencing was performed on yeast cell samples before and after nitrogen-deficient medium treatment to obtain transcriptome data.

[0051] The Bowtie-Tophat-Cufflinks series software was used to analyze and process the transcriptome data to obtain quantitative information of genes.

[0052] Using liquid chromatography-mass spectrometry (LC-MS), the proteome analysis of yeast cell samples before an...

Embodiment 2

[0062] In order to verify whether the gene is involved in the regulation of autophagy, in this example, the potential genes involved in the regulation of autophagy, GLO3 and SCS7 obtained in the above-mentioned Example 1, were taken as examples, combined with the yeast gene knockout library, GFP was detected by Western blotting method -The splicing changes of Atg8 protein to explore the influence of predicted genes on autophagy in yeast cells. At the same time, according to the situation of the GFP-Atg8 protein entering the vacuole, the influence of the predicted gene on the autophagy activity of the cell was judged. like image 3 , Figure 4 As shown, knockdown of GLO3 can block the degree of cleavage of GFP-Atg8 induced by nitrogen source deprivation treatment and reduce the entry of GFP-Atg8 into vacuoles. like Figure 5 , Image 6 As shown, knockdown of SCS7 can reduce the cleavage of GFP-Atg8 induced by nitrogen source deprivation treatment and prevent GFP-Atg8 from e...

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Abstract

The invention belongs to the technical field of biological information, and discloses a method for predicting functional genes for regulating and controlling yeast autophagy, which comprises the following steps: S1, carrying out time sequence transcriptome and proteome analysis on normal yeast samples before and after starvation induction treatment and yeast samples from which autophagy key regulation and control genes are knocked out; s2, screening genes with interaction, and recording the genes as a set A; s3, extracting transcriptional expression change and protein expression change of each gene in the set A, and the interaction degree with the known autophagy gene as features; s4, establishing and training a prediction model; and S5, optimizing the model, and scoring the genes in the set A so as to predict the functional genes for regulating and controlling yeast autophagy. By utilizing the prediction method provided by the invention, the gene screening range can be effectively narrowed before verification of a traditional experimental method, so that the workload of experimental verification is reduced, and the functional gene for regulating and controlling yeast autophagy is accurately predicted.

Description

technical field [0001] The invention belongs to the technical field of biological information, and more specifically relates to a method for predicting functional genes regulating yeast autophagy. Background technique [0002] Autophagy is a lysosome (animal) / vacuole (yeast and plant)-based degradation pathway that engulfs damaged organelles, misfolded proteins, and other cellular materials through the formation of autophagosomes and transports them to lysosomes / Degraded in the vacuole to meet the metabolic needs and the renewal of some organelles. Autophagy can be divided into two types: selective autophagy and non-selective autophagy. Under the conditions of nutrient deficiency and various stimuli, the activity of autophagy increases significantly, thereby exerting the protective function on cells. The occurrence of autophagy includes the formation and extension of autophagosomes, the maturation of autophagosomes, and the fusion of autophagosomes and lysosomes. In the ...

Claims

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Application Information

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IPC IPC(8): G16B20/30G16B25/10G16B40/00
CPCG16B25/10G16B40/00G16B20/30
Inventor 薛宇王晨玮彭迪宁万山付珊珊
Owner HUAZHONG UNIV OF SCI & TECH
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