Global Transcriptomics Uncovers Distinct Contributions From Splicing Regulatory Proteins to the Macrophage Innate Immune Response

Overview

Journal Front Immunol

Specialty Allergy & Immunology

Date 2021 Jul 26

PMID 34305890

Citations 14

Authors

Allison R Wagner

Haley M Scott

Kelsi O West

Krystal J Vail

Timothy C Fitzsimons

Aja K Coleman

Kaitlyn E Carter

Robert O Watson

Kristin L Patrick

Affiliations

Soon will be listed here.

Abstract

Pathogen sensing pattern recognition receptors triggers massive reprogramming of macrophage gene expression. While the signaling cascades and transcription factors that activate these responses are well-known, the role of post-transcriptional RNA processing in modulating innate immune gene expression remains understudied. Given their crucial role in regulating pre-mRNA splicing and other RNA processing steps, we hypothesized that members of the SR/hnRNP protein families regulate innate immune gene expression in distinct ways. We analyzed steady state gene expression and alternatively spliced isoform production in ten SR/hnRNP knockdown RAW 264.7 macrophage-like cell lines following infection with the bacterial pathogen serovar Typhimurium (). We identified thousands of transcripts whose abundance is increased or decreased by SR/hnRNP knockdown in macrophages. Notably, we observed that SR and hnRNP proteins influence expression of different genes in uninfected versus -infected macrophages, suggesting functionalization of these proteins upon pathogen sensing. Likewise, we found that knockdown of SR/hnRNPs promoted differential isoform usage (DIU) for thousands of macrophage transcripts and that these alternative splicing changes were distinct in uninfected and -infected macrophages. Finally, having observed a surprising degree of similarity between the differentially expressed genes (DEGs) and DIUs in hnRNP K and U knockdown macrophages, we found that hnRNP K and U knockdown macrophages are both more restrictive to Vesicular Stomatitis Virus (VSV), while hnRNP K knockdown macrophages are more permissive to Typhimurium. Based on these findings, we conclude that many innate immune genes evolved to rely on one or more SR/hnRNPs to ensure the proper magnitude of their induction, supporting a model wherein pre-mRNA splicing is critical for regulating innate immune gene expression and controlling infection outcomes in macrophages .

Citing Articles

Adipocyte-specific Steap4 deficiency reduced thermogenesis and energy expenditure in mice.

Wang H, Zhang L, Chen X, Hong L, Zhao J, Qian W iScience. 2025; 28(2):111903.

PMID: 39995871 PMC: 11848796. DOI: 10.1016/j.isci.2025.111903.

Functional and dynamic profiling of transcript isoforms reveals essential roles of alternative splicing in interferon response.

Ueda M, Inamo J, Miya F, Shimada M, Yamaguchi K, Kochi Y Cell Genom. 2024; 4(10):100654.

PMID: 39288763 PMC: 11602592. DOI: 10.1016/j.xgen.2024.100654.

PRPF40A induces inclusion of exons in GC-rich regions important for human myeloid cell differentiation.

Tan C, Sim D, Zhen Y, Tian H, Koh J, Roca X Nucleic Acids Res. 2024; 52(15):8800-8814.

PMID: 38943321 PMC: 11347146. DOI: 10.1093/nar/gkae557.

What could be the function of the spinal muscular atrophy-causing protein SMN in macrophages?.

Tapken I, Detering N, Claus P Front Immunol. 2024; 15:1375428.

PMID: 38863697 PMC: 11165114. DOI: 10.3389/fimmu.2024.1375428.

hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing.

Zheng R, Dunlap M, Bobkov G, Gonzalez-Figueroa C, Patel K, Lyu J Mol Cell. 2024; 84(11):2087-2103.e8.

PMID: 38815579 PMC: 11204102. DOI: 10.1016/j.molcel.2024.05.004.

References

Krecic A, Swanson M . hnRNP complexes: composition, structure, and function. Curr Opin Cell Biol. 1999; 11(3):363-71. DOI: 10.1016/S0955-0674(99)80051-9. View

Penn B, Netter Z, Johnson J, Von Dollen J, Jang G, Johnson T . An Mtb-Human Protein-Protein Interaction Map Identifies a Switch between Host Antiviral and Antibacterial Responses. Mol Cell. 2018; 71(4):637-648.e5. PMC: 6329589. DOI: 10.1016/j.molcel.2018.07.010. View

Talkish J, Igel H, Perriman R, Shiue L, Katzman S, Munding E . Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome. PLoS Genet. 2019; 15(8):e1008249. PMC: 6726248. DOI: 10.1371/journal.pgen.1008249. View

Fu X, Ares Jr M . Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet. 2014; 15(10):689-701. PMC: 4440546. DOI: 10.1038/nrg3778. View

Richards A, Watza D, Findley A, Alazizi A, Wen X, Pai A . Environmental perturbations lead to extensive directional shifts in RNA processing. PLoS Genet. 2017; 13(10):e1006995. PMC: 5667937. DOI: 10.1371/journal.pgen.1006995. View

Swanson M, Dreyfuss G . Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities. Mol Cell Biol. 1988; 8(5):2237-41. PMC: 363409. DOI: 10.1128/mcb.8.5.2237-2241.1988. View

Bhatt D, Pandya-Jones A, Tong A, Barozzi I, Lissner M, Natoli G . Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell. 2012; 150(2):279-90. PMC: 3405548. DOI: 10.1016/j.cell.2012.05.043. View

Munoz M, Perez Santangelo M, Paronetto M, Mata M, Pelisch F, Boireau S . DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell. 2009; 137(4):708-20. DOI: 10.1016/j.cell.2009.03.010. View

Pourhaghighi R, Ash P, Phanse S, Goebels F, Hu L, Chen S . BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Cell Syst. 2020; 11(2):208. DOI: 10.1016/j.cels.2020.08.006. View

10.

Schoggins J, Rice C . Interferon-stimulated genes and their antiviral effector functions. Curr Opin Virol. 2012; 1(6):519-25. PMC: 3274382. DOI: 10.1016/j.coviro.2011.10.008. View

11.

Shin C, Feng Y, Manley J . Dephosphorylated SRp38 acts as a splicing repressor in response to heat shock. Nature. 2004; 427(6974):553-8. DOI: 10.1038/nature02288. View

12.

Schoggins J, Wilson S, Panis M, Murphy M, Jones C, Bieniasz P . A diverse range of gene products are effectors of the type I interferon antiviral response. Nature. 2011; 472(7344):481-5. PMC: 3409588. DOI: 10.1038/nature09907. View

13.

Pandey A, Ding S, Qin Q, Gupta R, Gomez G, Lin F . Global Reprogramming of Host Kinase Signaling in Response to Fungal Infection. Cell Host Microbe. 2017; 21(5):637-649.e6. PMC: 5538893. DOI: 10.1016/j.chom.2017.04.008. View

14.

Huelga S, Vu A, Arnold J, Liang T, Liu P, Yan B . Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012; 1(2):167-78. PMC: 3345519. DOI: 10.1016/j.celrep.2012.02.001. View

15.

Budzik J, Swaney D, Jimenez-Morales D, Johnson J, Garelis N, Repasy T . Dynamic post-translational modification profiling of -infected primary macrophages. Elife. 2020; 9. PMC: 7030789. DOI: 10.7554/eLife.51461. View

16.

Cao P, Luo W, Li C, Tong Z, Zheng Z, Zhou L . The heterogeneous nuclear ribonucleoprotein hnRNPM inhibits RNA virus-triggered innate immunity by antagonizing RNA sensing of RIG-I-like receptors. PLoS Pathog. 2019; 15(8):e1007983. PMC: 6703689. DOI: 10.1371/journal.ppat.1007983. View

17.

Havugimana P, Hart G, Nepusz T, Yang H, Turinsky A, Li Z . A census of human soluble protein complexes. Cell. 2012; 150(5):1068-81. PMC: 3477804. DOI: 10.1016/j.cell.2012.08.011. View

18.

Munding E, Shiue L, Katzman S, Donohue J, Ares Jr M . Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. Mol Cell. 2013; 51(3):338-48. PMC: 3771316. DOI: 10.1016/j.molcel.2013.06.012. View

19.

Zhong H, May M, Jimi E, Ghosh S . The phosphorylation status of nuclear NF-kappa B determines its association with CBP/p300 or HDAC-1. Mol Cell. 2002; 9(3):625-36. DOI: 10.1016/s1097-2765(02)00477-x. View

20.

Loomis R, Naoe Y, Parker J, Savic V, Bozovsky M, Macfarlan T . Chromatin binding of SRp20 and ASF/SF2 and dissociation from mitotic chromosomes is modulated by histone H3 serine 10 phosphorylation. Mol Cell. 2009; 33(4):450-61. PMC: 2667802. DOI: 10.1016/j.molcel.2009.02.003. View