Negative elongation factor controls energy homeostasis in cardiomyocytes

Abstract

Negative elongation factor (NELF) is known to enforce promoter-proximal pausing of RNA polymerase II (Pol II), a pervasive phenomenon observed across multicellular genomes. However, the physiological impact of NELF on tissue homeostasis remains unclear. Here, we show that whole-body conditional deletion of the B subunit of NELF (NELF-B) in adult mice results in cardiomyopathy and impaired response to cardiac stress. Tissue-specific knockout of NELF-B confirms its cell-autonomous function in cardiomyocytes. NELF directly supports transcription of those genes encoding rate-limiting enzymes in fatty acid oxidation (FAO) and the tricarboxylic acid (TCA) cycle. NELF also shares extensively transcriptional target genes with peroxisome proliferator-activated receptor α (PPARα), a master regulator of energy metabolism in the myocardium. Mechanistically, NELF helps stabilize the transcription initiation complex at the metabolism-related genes. Our findings strongly indicate that NELF is part of the PPARα-mediated transcription regulatory network that maintains metabolic homeostasis in cardiomyocytes.

Figure 1. NELF-B KO Leads to Cardiomyopathy

(A) Hematoxylin and eosin staining of left ventricles from control (Ctrl) and NELF-B knockout (KO) mice. The scale bar represents 50 μm. (B) Picrosirius red staining for collagen deposition. The scale bar represents 50 μm. (C) Quantification of picrosirius red staining (n = 5). Here and elsewhere in the figures, *p < 0.05. Error bars represent SEM. (D) Quantification of cell size of over 100 individual cardiomyocytes (n = 3). (E) Relative mRNA levels of two hypertrophy markers (n = 6). (F) Representative left ventricular M-mode echocardiography. The double-headed arrows indicate the left ventricular dimension at diastole (longer arrow) and systole (shorter arrow) (G) Fractional shortening from the left ventricle (LV) at rest (thin lines) and following dobutamine injection (thick lines). Ctrl: n = 11; KO: n = 8.

Figure 2. NELF-B Supports Energy-Metabolism-Related Transcription in Cardiomyocytes

(A and B) Verification of microarray results (n = 3) for genes involved in fatty acid oxidation (FAO) and TCA cycle. (C–E) ChIP of NELF-A (C), NELF-B (D), and NELF-C/NELF-D (E) at the TSS and 1 kb downstream (DS) region of the Cpt1b and Idh3g genes in wild-type myocardium (n = 3). IgG, immunoglobulin G. (F and G) Diagrams of the FAO (F) and TCA cycle (G) with indicated changes in metabolic intermediates and enzymes in KO (red for increase and blue decrease).

Figure 3. NELF-B Is Part of the PPARα Transcriptional Regulatory Network

(A) Overlap in down- and upregulated genes in NELF-B and PPARα KO myocardium. The green and red squares denote the enrichment score (ES)₀ values of down- and upregulated genes, respectively. The diamond-dotted curve is the frequency distribution of ES values for sets of randomly selected genes. (B) Heatmap for the overlapped genes in the NELF-B and PPARα KO mouse myocardium. (C) Venn diagram illustrating the presence of PPARα binding sites at the NELF target genes in myocardium. (D) NELF-A ChIP at the NELF-B and PPARα common target genes listed in (B) (n = 3).

Figure 4. NELF Facilitates Occupancy of the Transcription Initiation Complex

(A) ChIP of total Pol II at TSS. (B) Ratio of total Pol II ChIP at TSS over gene body. (C) TFIIB ChIP at TSS. (D) RXRα ChIP at PPARα binding sites (PBS). (E) Histone H3 ChIP at TSS (n = 3). (F) A proposed role of NELF in controlling chromatin occupancy of the transcription initiation complex.