NEW YORK (GenomeWeb) – Some innate immune system genes have evolved rapidly and vary widely in their expression across species and individual cells, while others are more conserved and consistent, according to a new study.

The innate immune response kicks into gear upon infection to both inhibit pathogen replication and raise the alarm. This response has to balance its rapid evolution in the face of pathogens and cell-to-cell variability with the need for regulatory constraints to prevent tissue damage and other pathological effects.

Researchers from the Wellcome Sanger Institute and elsewhere characterized the transcriptomes of fibroblasts and bone marrow-derived phagocytes from various species in response to immune challenges, both in bulk and at the single-cell level. As they reported yesterday in Nature, some genes’ transcription diverged across species and between single cells, while other genes had less changeable expression.

“We think that this pattern of activation – where some genes are under tight control, and others have more variable activity – has evolved as a way to fine-tune the immune response. It is effective, but balanced,” first author Tzachi Hagai from the Wellcome Sanger Institute said in a statement. “Genes can evolve to help a cell control an attacker, and the use of those genes can vary between cells, so surrounding tissues are not affected by a massive fall­out.”

Prior to examining the cells’ transcriptomes, the researchers exposed fibroblasts from primates and rodents to a synthetic double-stranded RNA to mimic a viral infection and exposed phagocytes from rodents and mammals to a bacterial lipopolysaccharide. When they studied the bulk RNA sequencing data, they noted not only the rapid upregulation of expected immune genes like INFB, TNF, and CCL5 across species but also some genes that are expressed in some species but not others. For instance, Ifi27 is upregulated in primates but not rodents, while Daxx is upregulated in rodents but not primates.

In all, they uncovered 955 differentially expressed genes in fibroblasts from different species and 2,336 differentially expressed genes in phagocytes.

Using ChIP-seq, the researchers profiled active histone marks to find that promoter methylation on high-divergence genes was less conserved between humans and rodents than promoter methylation on low-divergence genes. They also noted that genes that highly diverged in expression have higher sequence conservation. This, they said, could be due to the promoters of high- and low-divergence genes having differing architectures: TATA box-enriched and CGI-depleted promoters are linked to transcriptional divergence, but with sequence conservation.

As the researchers reported, genes like those encoding cytokines have diverged faster than genes encoding other immune factors, like those involved in apoptosis. Cytokines also exhibited a higher transcriptional range and were enriched in TATA boxes, while depleted in CGI, suggesting this promoter architecture is associated with a greater difference between species and conditions.

The researchers also performed single-cell RNA-seq across all species and found that genes whose expression in response to bacterial or viral challenges differed between species were also more variable between single cells of the same species. In addition, genes with TATA boxes had higher transcriptional variability, while those with CGI-containing genes varied less in expression. Cytokines, for instance, also exhibited high levels of cell-to-cell variability.

This, the researchers said, suggests transcriptional variability between cells and transcriptional divergence between species are linked to whether these promoter elements are present.

They also suggested that this pattern of conserved and variably expressed genes “has evolved as a mechanism for fine-tuned regulation to achieve an effective but balanced response” by the innate immune system.