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Lipin 1 modulates mRNA splicing during fasting adaptation in liver
Huan Wang, Tracey W. Chan, Ajay A. Vashisht, Brian G. Drew, Anna C. Calkin, Thurl E. Harris, James A. Wohlschlegel, Xinshu Xiao, Karen Reue
Huan Wang, Tracey W. Chan, Ajay A. Vashisht, Brian G. Drew, Anna C. Calkin, Thurl E. Harris, James A. Wohlschlegel, Xinshu Xiao, Karen Reue
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Research Article Metabolism

Lipin 1 modulates mRNA splicing during fasting adaptation in liver

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Abstract

Lipin 1 regulates cellular lipid homeostasis through roles in glycerolipid synthesis (through phosphatidic acid phosphatase activity) and transcriptional coactivation. Lipin 1–deficient individuals exhibit episodic disease symptoms that are triggered by metabolic stress, such as stress caused by prolonged fasting. We sought to identify critical lipin 1 activities during fasting. We determined that lipin 1 deficiency induces widespread alternative mRNA splicing in liver during fasting, much of which is normalized by refeeding. The role of lipin 1 in mRNA splicing was largely independent of its enzymatic function. We identified interactions between lipin 1 and spliceosome proteins, as well as a requirement for lipin 1 to maintain homeostatic levels of spliceosome small nuclear RNAs and specific RNA splicing factors. In fasted Lpin1–/– liver, we identified a correspondence between alternative splicing of phospholipid biosynthetic enzymes and dysregulated phospholipid levels; splicing patterns and phospholipid levels were partly normalized by feeding. Thus, lipin 1 influences hepatic lipid metabolism through mRNA splicing, as well as through enzymatic and transcriptional activities, and fasting exacerbates the deleterious effects of lipin 1 deficiency on metabolic homeostasis.

Authors

Huan Wang, Tracey W. Chan, Ajay A. Vashisht, Brian G. Drew, Anna C. Calkin, Thurl E. Harris, James A. Wohlschlegel, Xinshu Xiao, Karen Reue

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Figure 1

Fasting alters mRNA levels and splicing patterns in lipin 1–deficient liver.

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Fasting alters mRNA levels and splicing patterns in lipin 1–deficient li...
(A) t-SNE visualization of top 1000 differentially expressed genes with highest variance in liver of fasted and refed Lpin1+/+ or Lpin1–/– mice (n = 3). Each symbol represents an individual mouse. (B) Volcano plots of differentially expressed genes in liver of fasted compared with refed Lpin1+/+ or Lpin1–/– mice. Blue dots represent differential expression with an absolute value of the Log2 fold-change > 0.05 and adjusted P < 0.05 (Benjamini-Hochberg corrected). Differentially expressed genes are listed in Supplemental Table 1. (C) The number of alternatively spliced transcripts in fasted compared with refed Lpin1+/+ or fasted compared with refed Lpin1–/– liver. Five splice patterns were assessed: A5SS, alternative 5′ splice site; A3SS, alternative 3′ splice site; MXE, mutually exclusive exons; RI, retained intron; and SE, skipped exon. (D) Classes of aberrant splicing events in fasted Lpin1–/– compared with fasted Lpin1+/+ liver. Of the SE events, 74% are predicted to result in frame shifts in protein coding sequence in Lpin1–/– liver. (E) Enrichment analysis (via GO term) of genes undergoing alternative skipped exon events in liver of fasted compared with refed Lpin1+/+ or Lpin1–/– mice. Bubble color indicates log10 (P value); bubble size indicates the frequency of GO term in the Gene Ontology database.

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