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Global transcriptomics reveals specialized roles for splicing regulatory proteins in the macrophage innate immune response

ABSTRACT: Global transcriptomics reveals specialized roles for splicing regulatory proteins in the macrophage innate immune response

PROVIDER: PRJNA719420 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14137825.fastq.gz	Fastqsanger.gz
	SRR14137825_1.fastq.gz	Fastqsanger.gz
	SRR14137825_2.fastq.gz	Fastqsanger.gz
	SRR14137826.fastq.gz	Fastqsanger.gz
	SRR14137826_1.fastq.gz	Fastqsanger.gz

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Project description:Purpose: The goal of this study is to measure how steady state RNA and alternatively spliced transcript abundance levels are impacted by loss of specific RNA-binding proteins as part of macrophage transcriptional activation upon pathogen sensing. Methods: SRSF 1, 2, 6, 7, 9, and hnRNP C, F, K, U were knockdown using shRNA in RAW 264.7 macrophages. Macrophages were collected as uninfected (resting) cells and infected with Salmonella Typhimuirum for 4HR. mRNA profiles of uninfected (UN) and Salmonella infected (SAL) hnRNP C, F, K, U and SRSF 1, 2, 6, 7, 9 were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the gene expression and transcript expression level with CLC Genomics Workbench. qRT–PCR validation was performed using SYBR Green assays. Results: We identified thousands of transcripts whose abundance is increased or decreased by SR/hnRNP knockdown in macrophages. We observed that different SR/hnRNPs control the ex-pression of distinct gene regulons in uninfected and Salmonella-infected macrophages, with sev-eral key innate immune genes (Nos2, Mx1, Il1a) relying heavily on multiple SR/hnRNPs to main-tain proper induction and/or repression. Knockdown of SR/hnRNPs promoted differential isoform usage (DIU) for a number of key immune sensors and signaling molecules and many of these splicing changes were distinct in uninfected and Salmonella-infected macrophages. After observ-ing a surprising degree of similarity between the differentially expressed genes (DEGs) and DIUs in hnRNP K and U knockdown macrophages, we found that these cells are better able to restrict vesicular stomatitis virus repli-cation than control cells, supporting a role for these hnRNPs in controlling infection outcomes in macrophages ex vivo. Based on these findings, we conclude that many innate immune genes have evolved to rely on one or more splicing regulatory factors to ensure the proper timing and magnitude of their induction, bolstering a model wherein pre-mRNA splicing is a critical regulatory node in the innate immune response. Conclusions: SR and hnRNP proteins have profound impacts on the abundance of innate immune transcripts and seem to contribute to macrophage gene expression via distinct mechanisms

Project description:Pathogen sensing via 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 Salmonella enterica serovar Typhimurium (Salmonella). 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 Salmonella-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 Salmonella-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 Salmonella 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 ex vivo.

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Global transcriptomics reveals specialized roles for splicing regulatory proteins in the macrophage innate immune response

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