Dual RNA Sequencing: Study the Events as Bacteria Infecting the Host

Introduction to Dual RNA Sequencing

The transcriptome is the collection of all RNAs transcribed from a specific cell or tissue at a specific time or state. RNA sequencing is a prevailing research tool for transcriptomics research, which uses next-generation sequencing technology to provide information about the transcription of an organism rapidly and accurately, revealing the gene expression of an organism. In recent years, this method has become very popular in biological sciences and medical research, and its use is gradually moving towards clinical applications.

When studying the events as bacteria infect the host, most focus on either bacterial or host mRNA. Dual RNA sequencing technology allows both to be focused simultaneously to obtain a more complete picture of the events that occur during the early and late stages of infection. It labels the bacteria with fluorescence, enabling the identification of the infected host cell components. This technique allows the study of mRNAs and transcripts of non-coding RNAs from both organisms as the course of the infection progresses.

Workflow of Dual RNA Sequencing

The parallel transcriptomic analysis of bacterial pathogens and their eukaryotic host cells is known as dual RNA-Seq. A full dual RNA-Seq test comprises three phases: (1) total host-bacteria RNA extraction and purification; (2) total RNA next-generation sequencing (NGS); and (3) bioinformatic processing and statistical analysis of the host-bacteria transcriptome.

Dual RNA-Seq entails a standard workflow that includes RNA extraction, rRNA depletion, library preparation, sequencing, and data analysis and interpretation. Meanwhile, data analysis procedures include preprocessing, alignment, and advanced downstream analyses such as alternative and non-linear splicing, differential expression, and epigenetic analyses, all of which lead to quality reports, novel transcript calculations and predictions, differentially expressed transcript probabilities, and transcript characterization.

Like traditional transcriptomic methodologies, dual RNA-seq entails quantification, difference screening, pathway annotation, network construction, and so on.

Applications of Dual RNA Sequencing

By extracting the total RNA from infected cells, dual RNA-Seq can reveal the interaction between pathogens and their hosts. While the mixed sequencing reads are allocated to their originating genomes, the sequencing and analyses of the interested RNAs from bacterial pathogens and infected cells can be accompanied at the same time, benefited from the advancement of library construction and sequencing technologies. Its use can be applied to a variety of research directions, including but not limited to:

1. Variations in host and pathogen gene expression
2. Study infection-related sRNA, mitochondrial RNA, and other RNAs
3. Study of signal path-related non-coding RNA in depth
4. Comparative genomics is being used to investigate the differences between wild and mutant pathogens.
5. Study the gene regulation relationship to expose the interaction mechanism between/among species.
6. In the pathogen-host interaction process, researchers are looking into the regulatory network, pathogenic mechanisms during infection, and host resistance mechanisms.
7. Investigate the evolutionary relationships between pathogens from various species, as well as the discovery of positive selection based on homologous genes.

CD Genomics enjoys a high reputation for sequencing, microarray analysis, library construction and genotyping, providing reliable services to pharmaceutical and biotechnology companies as well as academia and government agencies.