Indiana University researchers use strand-specific community RNA-seq to reveal antisense transcription in human gut microbiota

Metagenomics and other meta-omics approaches (including metatranscriptomics) provide insights into the composition and function of microbial communities living in different environments or animal hosts. Metatranscriptomics research provides an unprecedented opportunity to examine gene regulation for many microbial species simultaneously, and more importantly, for the majority that are unculturable microbial species, in their natural environments (or hosts). Current analyses of metatranscriptomic datasets focus on the detection of gene expression levels and the study of the relationship between changes of gene expression and changes of environment.

As a demonstration of utilizing metatranscriptomics beyond these common analyses, researchers at Indiana University developed a computational and statistical procedure to analyze the antisense transcripts in strand-specific metatranscriptomic datasets. Antisense RNAs encoded on the DNA strand opposite a gene’s CDS have the potential to form extensive base-pairing interactions with the corresponding sense RNA, and can have important regulatory functions. Most studies of antisense RNAs in bacteria are rather recent, are mostly based on transcriptome analysis, and have been applied mainly to single bacterial species. Application of these approaches to human gut-associated metatranscriptomic datasets allowed the researchers to survey antisense transcription for a large number of bacterial species associated with human beings. The ratio of protein coding genes with antisense transcription ranges from 0 to 35.8% (median = 10.0%) among 47 species.

Highly expressed genes tend to be dominated by sense transcription or antisense transcription. Each circle represents a gene. The y-axis shows the gene expression (log(FPKM)) and the x-axis shows d, which is close to 1 for genes with mostly sense transcription, and -1 with mostly antisense transcription. RNA-seq data from individual 1 (X310763260) was used for this plot. To limit the bias that may be introduced by rare species or genes with low expression levels, we only included the genes (3,689 in total) each supported by at least 20 RNA-seq reads, and are from the species (23 in total) each having at least 100 genes with RNA-seq reads support. See Supplementary Figure S2 for the plot using the original gene expression data, involving 30,493 genes from all 47 strains, one for each species.

These results show that antisense transcription is dynamic, varying between human individuals. Functional enrichment analysis revealed a preference of certain gene functions for antisense transcription, and transposase genes are among the most prominent ones (but antisense transcription in bacterial house-keeping genes was also observed).