An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa.
Hao HuangXiaolong ShaoYingpeng XieTingting WangYingchao ZhangXin WangXin DengPublished in: Nature communications (2019)
The virulence of Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen, is regulated by many transcriptional factors (TFs) that control the expression of quorum sensing and protein secretion systems. Here, we report a genome-wide, network-based approach to dissect the crosstalk between 20 key virulence-related TFs. Using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), as well as RNA-seq, we identify 1200 TF-bound genes and 4775 differentially expressed genes. We experimentally validate 347 of these genes as functional target genes, and describe the regulatory relationships of the 20 TFs with their targets in a network that we call 'Pseudomonas aeruginosa genomic regulatory network' (PAGnet). Analysis of the network led to the identification of novel functions for two TFs (ExsA and GacA) in quorum sensing and nitrogen metabolism. Furthermore, we present an online platform and R package based on PAGnet to facilitate updating and user-customised analyses.
Keyphrases
- pseudomonas aeruginosa
- genome wide
- biofilm formation
- rna seq
- transcription factor
- cystic fibrosis
- dna methylation
- copy number
- escherichia coli
- bioinformatics analysis
- gram negative
- gene expression
- single cell
- acinetobacter baumannii
- genome wide identification
- staphylococcus aureus
- antimicrobial resistance
- high throughput sequencing
- dna damage
- candida albicans
- high throughput
- binding protein
- long non coding rna
- working memory
- network analysis
- circulating tumor cells
- heat shock