Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2

Pratibha Jagannatha,Elektra K Robinson,Matthew Cattle,Mark Akeson,Barbara Shapleigh,Sergio Covarrubias,Valeriya Smaliy,Rojin Safavi,Susan Carpenter,Suzanne M Cloonan,Robin Abu-Shumays,Angela N Brooks,Miten Jain

doi:10.7554/elife.69431

Pratibha Jagannatha, Elektra K Robinson + Show 11 more

Open Access

https://doi.org/10.7554/elife.69431

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Journal: eLife	Publication Date: May 28, 2021
Citations: 25	License type: CC BY 4.0

Affiliation: University of California, Santa Cruz, Cornell University

Abstract

Determining the layers of gene regulation within the innate immune response is critical to our understanding of the cellular responses to infection and dysregulation in disease. We identified a conserved mechanism of gene regulation in human and mouse via changes in alternative first exon (AFE) usage following inflammation, resulting in changes to the isoforms produced. Of these AFE events, we identified 95 unannotated transcription start sites in mice using a de novo transcriptome generated by long-read native RNA-sequencing, one of which is in the cytosolic receptor for dsDNA and known inflammatory inducible gene, Aim2. We show that this unannotated AFE isoform of Aim2 is the predominant isoform expressed during inflammation and contains an iron-responsive element in its 5'UTR enabling mRNA translation to be regulated by iron levels. This work highlights the importance of examining alternative isoform changes and translational regulation in the innate immune response and uncovers novel regulatory mechanisms of Aim2.

Highlights

Macrophages are critical cells in the innate immune system that combat infection by initiating acute inflammatory responses
Acute inflammation is tightly coordinated and begins with the detection of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs), which include Toll-Like Receptors (TLRs) (Medzhitov and Janeway, 1998; Pai et al, 2016a). These initial steps are followed by the activation of sequestered transcription factors, such as nuclear factor of kappa-B (NF-kB) and interferon regulatory factors (IRFs), which orchestrate pro-inflammatory and antiviral response signals involved in pathogen clearance (Pai et al, 2016a)
We show that this unannotated alternative first exon (AFE) isoform of absent in melanoma 2 (Aim2) is the predominant isoform produced during inflammation and contains an iron-responsive element in its 5′untranslated region (UTR), enabling mRNA translation to be controlled by iron levels

Summary

Introduction

Macrophages are critical cells in the innate immune system that combat infection by initiating acute inflammatory responses. Such an approach is necessary to fully appreciate the extent of alternative transcript isoform usage as we know most transcriptome annotations are incomplete (Workman et al, 2019), and isoforms generated are cell-type and treatment specific (Sapkota et al, 2019; Weirather et al, 2017; Workman et al, 2019; Wu et al, 2018) We used both long and short-read RNA sequencing to uncover novel isoforms and classes of alternative splicing events following inflammation in human and murine macrophages. Understanding the exact isoforms of genes that are expressed during an inflammatory response will enable us to design better targets for therapeutic intervention of these diseases

Results

Materials and Methods

Annotated 5’UTR motifs