Welcome to the PhageExpressionAtlas!

The PhageExpressionAtlas is your platform to interactively explore various phage infections on the transcriptional level based on dual RNA-seq data. The PhageExpressionAtlas currently hosts - publicly available dual RNA-seq datasets of phage infections. In addition to exploring phage-host interactions, the atlas provides a genome viewer that allows to visually explore the phage genome of interest.

Why investigating bacteriophages?

Bacteriophages (or phages) are viruses that infect and ultimately kill their bacterial hosts through cell lysis. Phages exhibit exceptional host specificity, targeting particular bacterial species or even individual strains. They are approximately ten times more abundant than bacteria and play essential roles in regulating and shaping microbial communities.

Phage research has led to a wealth of molecular innovations that have profoundly influenced molecular biology, biotechnology, and medicine. Tools such as T4 DNA ligase, T7 RNA polymerase, and bacterial defense systems like CRISPR-Cas and restriction-modification systems are among the most notable discoveries originating from phage studies. Moreover, due to their ability to selectively target and kill bacteria, phages are increasingly being explored as therapeutic agents – especially in cases where standard antibiotic treatments fail due to antimicrobial resistances. Studying phages and their interactions with bacterial hosts is therefore vital for understanding the regulation and functionality of phage infections, as well as harnessing their full potential for biomedical and biotechnological applications.

The PhageExpressionAtlas offers a possibility to explore diverse phage-host interactions on the transcriptome level.

Dual RNA-seq of phage infections

Dual RNA sequencing (dual RNA-seq) captures the transcriptomes of two interacting biological entities simultaneously. In the context of phage infections, dual RNA-seq is commonly used to study the expression patterns of both the phage and its bacterial host at the RNA level. This approach provides valuable insights into the host's response to phage invasion, as well as the molecular strategies employed by the phage to hijack and replicate within its host.

Time-resolved dual RNA-seq further enhances this analysis by enabling the monitoring of gene expression changes in both organisms throughout the infection process. Typically, phage genes are expressed in distinct temporal phases:

• Early genes encode proteins involved in host takeover and cellular reprogramming.
• Middle genes are primarily associated with phage DNA replication.
• Late genes play key roles in phage particle assembly and host cell lysis, facilitating the release of progeny phages.

The PhageExpressionAtlas enables researchers to explore these gene classes using either predefined criteria or custom classification strategies. This offers an entry point for inferring potential functions of phage genes and study temporal phage gene expression in their genomic context.