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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
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A novel method for genome-wide profiling of dynamic host-pathogen interactions using 3' end enriched RNA-seq
Jie Li1,2, Liangliang He1, Yun Zhang1
1State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
Scientific Reports
|August 19, 2017
Summary
This study introduces 3' end enriched RNA-seq to analyze Marek's disease virus (MDV) infection in chickens. The method reveals dynamic host-pathogen interactions and gene regulation during infection.
Area of Science:
- Virology
- Oncology
- Genomics
Background:
- Marek's disease is a contagious viral lymphoproliferative disease in chickens, serving as a model for viral oncogenesis.
- Understanding host-pathogen interactions during infection is crucial for insights into disease dynamics.
- Dynamic changes in host and pathogen gene expression and regulation are key to viral oncogenesis.
Purpose of the Study:
- To introduce and validate 3' end enriched RNA-sequencing (RNA-seq) as a novel method for studying host-pathogen interactions.
- To simultaneously profile gene expression and alternative polyadenylation (APA) in host and pathogen during Marek's disease virus (MDV) infection.
- To identify host genes and APA events involved in the dynamic response to MDV infection.
Main Methods:
- Utilized 3' end enriched RNA-seq on chicken embryo fibroblasts infected with Marek's disease virus.
- Performed simultaneous profiling of host and viral gene expression.
- Analyzed alternative polyadenylation (APA) site usage, including tandem 3' UTRs and coding region/3' UTR switching.
Main Results:
- Identified 476 differentially expressed host genes and 437 host APA switching genes.
- Observed APA switching within tandem 3' UTRs and between coding regions and 3' UTRs.
- Found that differentially expressed and APA-switched genes were primarily related to innate immunity, apoptosis, and metabolism, with limited overlap suggesting complementary regulatory mechanisms.
Conclusions:
- 3' end enriched RNA-seq is a promising method for comprehensive analysis of host-pathogen interactions.
- Dynamic changes in gene expression and APA contribute to host regulation during MDV infection.
- The study provides insights into the intricate molecular interplay governing Marek's disease pathogenesis.
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