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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 5

Lipin 1 deficiency leads to impaired fasting expression levels of RNA binding proteins such as ESRP2, as well as altered splicing of ESRP2 targets.

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Lipin 1 deficiency leads to impaired fasting expression levels of RNA bi...
(A) Volcano plots of differentially expressed genes in liver of refed compared with fasted Lpin1+/+ or Lpin1–/– mice. Red dots represent differentially expressed genes in the refed versus fasted state (P < 1 × 10–6, FDR = 0.1). The numbers of differentially expressed genes that are increased (Up) or decreased (Down) by refeeding are indicated. (B) Genes with increased expression in refed compared with fasted Lpin1–/– liver are functionally enriched for RNA binding and RNA processing proteins (enrichment scores indicated at top). (C) Heatmap of mRNA expression levels of RNA-binding protein (RBP) encoding genes are reduced in fasted Lpin1–/– liver and normalized to Lpin1+/+ levels by refeeding. (D) Expression of the RNA binding protein ESRP2 in fasted and fed liver. Data analyzed by 2-way ANOVA followed by t test (n = 3); *P < 0.05; **P < 0.01. (E) ESRP2 target gene splicing in Lpin1–/– liver is dysregulated in fasting conditions and normalized by feeding. Experimentally determined ESRP2 exon inclusion events (34, 35) were assessed in RNA-Seq data from fasted and refed Lpin1–/– and Lpin1+/+ liver (n = 3). Data are shown as mean ± SD; *P < 0.05 in Lpin1+/+ versus Lpin1–/– liver as determined by RNA-Seq analysis (FDR< 5%). (F) Verification of splicing of representative ESRP2 targets by standard PCR. Splice products were quantitated by densitometry (n = 3). Asterisks indicate significant differences analyzed by 2-way ANOVA followed by t test; **P < 0.01, ****P < 0.0001.

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