The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia and hepatic steatosis in mice are dependent on LXRs and correlate with an LXR-dependent hepatic induction of lipogenic genes. To further investigate the roles of RXR and LXR in the regulation of hepatic gene expression, we have mapped the ligandregulated genome-wide binding of these factors in mouse liver. We find that the RXR agonist bexarotene primarily increases the genomic binding of RXR, whereas the LXR agonist T0901317 greatly increases both LXR and RXR binding. T he liver plays a central role in the control of whole-body lipid homeostasis, and hepatic lipid metabolism is continuously adjusted to fit the needs of the organism. This adaptation requires major adjustments in the hepatic metabolic gene program, including a strong upregulation of lipogenic gene expression in the fed state, whereas in the fasting state, the expression of genes involved in fatty acid oxidation as well as ketogenesis and hepatic glucose production is highly induced. Class II nuclear receptors (NRs), i.e., NRs forming heterodimers with retinoid X receptor (RXR), play a key role in coordinating these changes. They include the liver X receptor (LXR) (29, 57) and peroxisome proliferatoractivated receptor (PPAR) (32, 34, 41) families as well as farnesoid X receptor (FXR) (44, 55, 88), pregnane X receptor (PXR) (5, 33), vitamin D receptor (VDR) (43), constitutive androstane receptor (CAR) (3, 9, 23), and retinoic acid receptors (RARs) (13).The LXR family consists of the two subtypes, LXR␣ (NR1H3) and LXR␤ (NR1H2), both of which form obligate heterodimers with RXR. LXR-RXR heterodimers are reported to bind to LXR response elements (LXREs) that consist of a direct repeat of the core sequence 5=-AGGTCA-3= spaced by 4 nucleotides (DR4) (2,72,76,79,92). LXRs are activated by oxidized cholesterol derivatives and play an important role in the regulation of cholesterol homeostasis in the liver. Thus, pharmacological activation of LXR leads to the induction of several genes implicated in reverse cholesterol transport and mobilization of cholesterol, such as the ATP binding cassette (ABC) transporter genes Abca1, Abcg1, Abcg5, and Abcg8 and the apolipoprotein E gene (ApoE) (12,31,37,60,63,84). Furthermore, a recent genomewide study of LXR in human hepatoma cells showed that LXR also downregulates expression of the cholesterologenic genes for lanosterol 14␣-demethylase (Cyp51A1) and squalene synthase (Fdst1) (89). Moreover, LXR activation induces triglyceride synthesis partly through induction of the lipogenic transcription factors sterol regulatory element-binding protein 1c (SREBP-1c) (42,61,95) and carbohydrate response element-binding protein (ChREBP) (8) but also by direct activation of genes encoding lipogenic enzymes such as fatty acid synthase (Fasn), stearoyl coenzyme A (CoA) desaturase (Scd1), ...

The clearance of damaged or dysfunctional mitochondria by selective autophagy (mitophagy) is important for cellular homeostasis and prevention of disease. Our understanding of the mitochondrial signals that trigger their recognition and targeting by mitophagy is limited. Here we show that the mitochondrial matrix proteins NIPSNAP1 (4-Nitrophenylphosphatase domain and non-neuronal SNAP25-like protein homolog 1) and NIPSNAP2 accumulate on the mitochondria surface upon mitochondrial depolarization. There they recruit proteins involved in selective autophagy, including autophagy receptors and ATG8 proteins, thereby functioning as an "eat-me signal" for mitophagy. NIPSNAP1 and NIPSNAP2 have a redundant function in mitophagy and are predominantly expressed in different tissues, with NIPSNAP1 being the most abundant in the brain. Zebrafish lacking a functional Nipsnap1 display reduced mitophagy in the brain and parkinsonian phenotypes, including loss of tyrosine hydroxylase (Th1) positive dopaminergic (DA) neurons, reduced motor activity and increased oxidative stress.

The MITF transcription factor is a master regulator of melanocyte development and a critical factor in melanomagenesis. The related transcription factors TFEB and TFE3 regulate lysosomal activity and autophagy processes known to be important in melanoma. Here we show that MITF binds the CLEAR-box element in the promoters of lysosomal and autophagosomal genes in melanocytes and melanoma cells. The crystal structure of MITF bound to the CLEAR-box reveals how the palindromic nature of this motif induces symmetric MITF homodimer binding. In metastatic melanoma tumors and cell lines, MITF positively correlates with the expression of lysosomal and autophagosomal genes, which, interestingly, are different from the lysosomal and autophagosomal genes correlated with TFEB and TFE3. Depletion of MITF in melanoma cells and melanocytes attenuates the response to starvation-induced autophagy, whereas the overexpression of MITF in melanoma cells increases the number of autophagosomes but is not sufficient to induce autophagic flux. Our results suggest that MITF and the related factors TFEB and TFE3 have separate roles in regulating a starvation-induced autophagy response in melanoma. Understanding the normal and pathophysiological roles of MITF and related transcription factors may provide important clinical insights into melanoma therapy.

Here, we report the biochemical characterization of the mono-ADP-ribosyltransferase 2,3,7,8-tetrachlorodibenzo-p-dioxin poly-ADP-ribose polymerase (TIPARP/ARTD14/PARP7), which is known to repress aryl hydrocarbon receptor (AHR)-dependent transcription. We found that the nuclear localization of TIPARP was dependent on a short N-terminal sequence and its zinc finger domain. Deletion and in vitro ADP-ribosylation studies identified amino acids 400–657 as the minimum catalytically active region, which retained its ability to mono-ADP-ribosylate AHR. However, the ability of TIPARP to ADP-ribosylate and repress AHR in cells was dependent on both its catalytic activity and zinc finger domain. The catalytic activity of TIPARP was resistant to meta-iodobenzylguanidine but sensitive to iodoacetamide and hydroxylamine, implicating cysteines and acidic side chains as ADP-ribosylated target residues. Mass spectrometry identified multiple ADP-ribosylated peptides in TIPARP and AHR. Electron transfer dissociation analysis of the TIPARP peptide 33ITPLKTCFK41 revealed cysteine 39 as a site for mono-ADP-ribosylation. Mutation of cysteine 39 to alanine resulted in a small, but significant, reduction in TIPARP autoribosylation activity, suggesting that additional amino acid residues are modified, but loss of cysteine 39 did not prevent its ability to repress AHR. Our findings characterize the subcellular localization and mono-ADP-ribosyltransferase activity of TIPARP, identify cysteine as a mono-ADP-ribosylated residue targeted by this enzyme, and confirm the TIPARP-dependent mono-ADP-ribosylation of other protein targets, such as AHR.