What sequencing technologies can teach us about innate immunity*

Abstract

For years, we have taken a reductionist approach to understanding gene regulation through the study of one gene in one cell at a time. While this approach has been fruitful it is laborious and fails to provide a global picture of what is occurring in complex situations involving tightly coordinated immune responses. The emergence of wholegenome techniques provides a system-level view of a response and can provide a plethora of information on events occurring in a cell from gene expression changes to splicing changes and chemical modifications. As with any technology, this often results in more questions than answers, but this wealth of knowledge is providing us with an unprecedented view of what occurs inside our cells during an immune response. In this review, we will discuss the current RNA-sequencing technologies and what they are helping us learn about the innate immune system.

The RNA binding protein, HNRNPA2B1, regulates IFNG signaling in macrophages

“…Macrophages sense danger signals through PRRs (1,2) -such as TLR4-which recognizes lipopolysaccharide (LPS) triggering complex signaling cascades culminating in the production of pro-inflammatory cytokines (1,3–5). Due to the complex nature of these responses there are regulatory steps throughout including at the level of transcription, pre-mRNA splicing, RNA modification, RNA export, and translation (6). In recent years a small number of studies have been carried out to investigate the role that HNRNP proteins play in regulating innate immune responses.…”

Stability and change in epigenetic regulation of immune cells

“…Many of the key findings featured in this issue relied on advances in sequencing methods over the last 20 years that generate billions of short reads or millions of ultra-long reads from single experiments (reviewed by Salih et al 1 ). Rapidly decreasing costs of these techniques has enabled a wide array of labeling and enrichment to isolate chromatin associated with specific biochemical features in small numbers of purified immune cell subsets or, more recently, single cells.…”