Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver.

Abstract:

:Diurnal oscillations of gene expression controlled by the circadian clock and its connected feeding rhythm enable organisms to coordinate their physiologies with daily environmental cycles. While available techniques yielded crucial insights into regulation at the transcriptional level, much less is known about temporally controlled functions within the nucleus and their regulation at the protein level. Here, we quantified the temporal nuclear accumulation of proteins and phosphoproteins from mouse liver by SILAC proteomics. We identified around 5,000 nuclear proteins, over 500 of which showed a diurnal accumulation. Parallel analysis of the nuclear phosphoproteome enabled the inference of the temporal activity of kinases accounting for rhythmic phosphorylation. Many identified rhythmic proteins were parts of nuclear complexes involved in transcriptional regulation, ribosome biogenesis, DNA repair, and the cell cycle and its potentially associated diurnal rhythm of hepatocyte polyploidy. Taken together, these findings provide unprecedented insights into the diurnal regulatory landscape of the mouse liver nucleus.

journal_name

Cell Metab

journal_title

Cell metabolism

authors

Wang J,Mauvoisin D,Martin E,Atger F,Galindo AN,Dayon L,Sizzano F,Palini A,Kussmann M,Waridel P,Quadroni M,Dulić V,Naef F,Gachon F

doi

10.1016/j.cmet.2016.10.003

subject

Has Abstract

pub_date

2017-01-10 00:00:00

pages

102-117

issue

1

eissn

1550-4131

issn

1932-7420

pii

S1550-4131(16)30534-4

journal_volume

25

pub_type

杂志文章
  • Comparative metabolomics reveals endogenous ligands of DAF-12, a nuclear hormone receptor, regulating C. elegans development and lifespan.

    abstract::Small-molecule ligands of nuclear hormone receptors (NHRs) govern the transcriptional regulation of metazoan development, cell differentiation, and metabolism. However, the physiological ligands of many NHRs remain poorly characterized, primarily due to lack of robust analytical techniques. Using comparative metabolom...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2013.11.024

    authors: Mahanti P,Bose N,Bethke A,Judkins JC,Wollam J,Dumas KJ,Zimmerman AM,Campbell SL,Hu PJ,Antebi A,Schroeder FC

    更新日期:2014-01-07 00:00:00

  • Glucose-independent glutamine metabolism via TCA cycling for proliferation and survival in B cells.

    abstract::Because MYC plays a causal role in many human cancers, including those with hypoxic and nutrient-poor tumor microenvironments, we have determined the metabolic responses of a MYC-inducible human Burkitt lymphoma model P493 cell line to aerobic and hypoxic conditions, and to glucose deprivation, using stable isotope-re...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2011.12.009

    authors: Le A,Lane AN,Hamaker M,Bose S,Gouw A,Barbi J,Tsukamoto T,Rojas CJ,Slusher BS,Zhang H,Zimmerman LJ,Liebler DC,Slebos RJ,Lorkiewicz PK,Higashi RM,Fan TW,Dang CV

    更新日期:2012-01-04 00:00:00

  • Increased internal and external bacterial load during Drosophila aging without life-span trade-off.

    abstract::The role of microbial load during aging of the adult fruit fly Drosophila melanogaster is incompletely understood. Here we show dramatic increases in aerobic and anaerobic bacterial load during aging, both inside the body and on the surface. Scanning electron microscopy and cell staining analyses of the surface of age...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2007.06.006

    authors: Ren C,Webster P,Finkel SE,Tower J

    更新日期:2007-08-01 00:00:00

  • Ablation of CD11c-positive cells normalizes insulin sensitivity in obese insulin resistant animals.

    abstract::Obese adipose tissue is characterized by infiltration of macrophages. We and others recently showed that a specific subset of macrophages is recruited to obese adipose and muscle tissue. This subset expresses CD11c and produces high levels of proinflammatory cytokines that are linked to the development of obesity-asso...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2008.08.015

    authors: Patsouris D,Li PP,Thapar D,Chapman J,Olefsky JM,Neels JG

    更新日期:2008-10-01 00:00:00

  • Microbial Imidazole Propionate Affects Responses to Metformin through p38γ-Dependent Inhibitory AMPK Phosphorylation.

    abstract::Metformin is the first-line therapy for type 2 diabetes, but there are large inter-individual variations in responses to this drug. Its mechanism of action is not fully understood, but activation of AMP-activated protein kinase (AMPK) and changes in the gut microbiota appear to be important. The inhibitory role of mic...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2020.07.012

    authors: Koh A,Mannerås-Holm L,Yunn NO,Nilsson PM,Ryu SH,Molinaro A,Perkins R,Smith JG,Bäckhed F

    更新日期:2020-10-06 00:00:00

  • Branching out for detection of type 2 diabetes.

    abstract::Type 2 diabetes is an epidemic disease worldwide, but it is difficult to predict its appearance in the general population. A recent study demonstrates that circulating concentrations of a small group of essential amino acids predict risk for diabetes, contributing to a recent resurgence of interest in these common ana...

    journal_title:Cell metabolism

    pub_type: 评论,杂志文章

    doi:10.1016/j.cmet.2011.04.003

    authors: Shah SH,Svetkey LP,Newgard CB

    更新日期:2011-05-04 00:00:00

  • Fibrosis and adipose tissue dysfunction.

    abstract::Fibrosis is increasingly appreciated as a major player in adipose tissue dysfunction. In rapidly expanding adipose tissue, pervasive hypoxia leads to an induction of HIF1α that in turn leads to a potent profibrotic transcriptional program. The pathophysiological impact of adipose tissue fibrosis is likely to play an e...

    journal_title:Cell metabolism

    pub_type: 杂志文章,评审

    doi:10.1016/j.cmet.2013.06.016

    authors: Sun K,Tordjman J,Clément K,Scherer PE

    更新日期:2013-10-01 00:00:00

  • ATF4-Induced Metabolic Reprograming Is a Synthetic Vulnerability of the p62-Deficient Tumor Stroma.

    abstract::Tumors undergo nutrient stress and need to reprogram their metabolism to survive. The stroma may play a critical role in this process by providing nutrients to support the epithelial compartment of the tumor. Here we show that p62 deficiency in stromal fibroblasts promotes resistance to glutamine deprivation by the di...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2017.09.001

    authors: Linares JF,Cordes T,Duran A,Reina-Campos M,Valencia T,Ahn CS,Castilla EA,Moscat J,Metallo CM,Diaz-Meco MT

    更新日期:2017-12-05 00:00:00

  • Mast Cell-Derived Histamine Regulates Liver Ketogenesis via Oleoylethanolamide Signaling.

    abstract::The conversion of lipolysis-derived fatty acids into ketone bodies (ketogenesis) is a crucial metabolic adaptation to prolonged periods of food scarcity. The process occurs primarily in liver mitochondria and is initiated by fatty-acid-mediated stimulation of the ligand-operated transcription factor, peroxisome prolif...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2018.09.014

    authors: Misto A,Provensi G,Vozella V,Passani MB,Piomelli D

    更新日期:2019-01-08 00:00:00

  • Mitochondrial phosphatase PTPMT1 is essential for cardiolipin biosynthesis.

    abstract::PTPMT1 was the first protein tyrosine phosphatase found localized to the mitochondria, but its biological function was unknown. Herein, we demonstrate that whole body deletion of Ptpmt1 in mice leads to embryonic lethality, suggesting an indispensable role for PTPMT1 during development. Ptpmt1 deficiency in mouse embr...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2011.04.007

    authors: Zhang J,Guan Z,Murphy AN,Wiley SE,Perkins GA,Worby CA,Engel JL,Heacock P,Nguyen OK,Wang JH,Raetz CR,Dowhan W,Dixon JE

    更新日期:2011-06-08 00:00:00

  • A bitter aftertaste: unintended effects of artificial sweeteners on the gut microbiome.

    abstract::Intestinal microbial communities regulate a range of host physiological functions, from energy harvest and glucose homeostasis to immune development and regulation. Suez et al. (2014) recently demonstrated that artificial sweeteners alter gut microbial communities, leading to glucose intolerance in both mice and human...

    journal_title:Cell metabolism

    pub_type: 评论,杂志文章

    doi:10.1016/j.cmet.2014.10.012

    authors: Bokulich NA,Blaser MJ

    更新日期:2014-11-04 00:00:00

  • Differential Metabolic Reprogramming by Zika Virus Promotes Cell Death in Human versus Mosquito Cells.

    abstract::Zika virus is a pathogen that poses serious consequences, including congenital microcephaly. Although many viruses reprogram host cell metabolism, whether Zika virus alters cellular metabolism and the functional consequences of Zika-induced metabolic changes remain unknown. Here, we show that Zika virus infection diff...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2019.01.024

    authors: Thaker SK,Chapa T,Garcia G Jr,Gong D,Schmid EW,Arumugaswami V,Sun R,Christofk HR

    更新日期:2019-05-07 00:00:00

  • ACOT12-Dependent Alteration of Acetyl-CoA Drives Hepatocellular Carcinoma Metastasis by Epigenetic Induction of Epithelial-Mesenchymal Transition.

    abstract::Metabolic reprogramming plays an important role in supporting tumor growth. However, little is known about the metabolic alterations that promote cancer metastasis. In this study, we identify acyl-CoA thioesterase 12 (ACOT12) as a key player in hepatocellular carcinoma (HCC) metastasis. The expression of ACOT12 is sig...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2018.12.019

    authors: Lu M,Zhu WW,Wang X,Tang JJ,Zhang KL,Yu GY,Shao WQ,Lin ZF,Wang SH,Lu L,Zhou J,Wang LX,Jia HL,Dong QZ,Chen JH,Lu JQ,Qin LX

    更新日期:2019-04-02 00:00:00

  • Steroids make you bigger? Fat chance says Myc.

    abstract::In flies, ecdysone integrates growth with developmental transitions by antagonizing insulin signaling, which links growth with nutritional status. Work in Developmental Cell (Delanoue et. al, 2010) finds that ecdysone represses the transcription factor Myc in the larval fat body to inhibit systemic growth, revealing a...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2010.06.003

    authors: Rajan A,Perrimon N

    更新日期:2010-07-07 00:00:00

  • NAD+ Metabolism and Signaling.

    abstract::We caught up with some of the leading researchers in the NAD+ metabolism and signaling field as they gathered in Dublin for the 2019 FASEB Science Research Conference. Here they share their excitement from the rich history of NAD+ biology dating back over 100 years ago to a future of translation benefiting human healt...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2019.06.013

    authors:

    更新日期:2019-07-02 00:00:00

  • AMPK and TOR: The Yin and Yang of Cellular Nutrient Sensing and Growth Control.

    abstract::The AMPK (AMP-activated protein kinase) and TOR (target-of-rapamycin) pathways are interlinked, opposing signaling pathways involved in sensing availability of nutrients and energy and regulation of cell growth. AMPK (Yin, or the "dark side") is switched on by lack of energy or nutrients and inhibits cell growth, whil...

    journal_title:Cell metabolism

    pub_type: 杂志文章,评审

    doi:10.1016/j.cmet.2020.01.015

    authors: González A,Hall MN,Lin SC,Hardie DG

    更新日期:2020-03-03 00:00:00

  • MicroRNA-210 controls mitochondrial metabolism during hypoxia by repressing the iron-sulfur cluster assembly proteins ISCU1/2.

    abstract::Repression of mitochondrial respiration represents an evolutionarily ancient cellular adaptation to hypoxia and profoundly influences cell survival and function; however, the underlying molecular mechanisms are incompletely understood. Primarily utilizing pulmonary arterial endothelial cells as a representative hypoxi...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2009.08.015

    authors: Chan SY,Zhang YY,Hemann C,Mahoney CE,Zweier JL,Loscalzo J

    更新日期:2009-10-01 00:00:00

  • Why Syndrome X? From Harold Himsworth to the insulin resistance syndrome.

    abstract::Although the concept of Syndrome X was introduced in the Banting Medal address of 1988 (Reaven, 1988), the notion that led to its genesis had started approximately 50 years earlier. In this short history, an attempt will be made to trace the two paths of scientific discovery that were formally merged in New Orleans in...

    journal_title:Cell metabolism

    pub_type: 历史文章,杂志文章

    doi:10.1016/j.cmet.2004.12.001

    authors: Reaven GM

    更新日期:2005-01-01 00:00:00

  • Tyk2 and Stat3 regulate brown adipose tissue differentiation and obesity.

    abstract::Mice lacking the Jak tyrosine kinase member Tyk2 become progressively obese due to aberrant development of Myf5+ brown adipose tissue (BAT). Tyk2 RNA levels in BAT and skeletal muscle, which shares a common progenitor with BAT, are dramatically decreased in mice placed on a high-fat diet and in obese humans. Expressio...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2012.11.005

    authors: Derecka M,Gornicka A,Koralov SB,Szczepanek K,Morgan M,Raje V,Sisler J,Zhang Q,Otero D,Cichy J,Rajewsky K,Shimoda K,Poli V,Strobl B,Pellegrini S,Harris TE,Seale P,Russell AP,McAinch AJ,O'Brien PE,Keller SR,Cronig

    更新日期:2012-12-05 00:00:00

  • Lipotoxicity, β cell dysfunction, and gestational diabetes.

    abstract::Gestational diabetes (GDM) is caused by failure of islet β cells to meet the increased insulin requirements of pregnancy. Recently, Prentice et al. (2014) discovered a 7-fold elevation of the furan fatty acid metabolite 3-carboxy-4-methyl-5-propyl-2-furanopropanoic acid (CMPF) in plasma of women with GDM and showed th...

    journal_title:Cell metabolism

    pub_type: 评论,杂志文章

    doi:10.1016/j.cmet.2014.03.020

    authors: Nolan CJ

    更新日期:2014-04-01 00:00:00

  • Bypassing Intestinal Sugar Enhancement of Sweet Appetite.

    abstract::Intestinal sugar sensing has an appetite-stimulating action that enhances preferences for sweets. Han et al. (2016) report that duodenal-jejunal bypass surgery reduces sweet appetite by reducing sugar-induced dopamine release in the dorsal striatum. ...

    journal_title:Cell metabolism

    pub_type: 评论,杂志文章

    doi:10.1016/j.cmet.2015.12.013

    authors: Sclafani A

    更新日期:2016-01-12 00:00:00

  • miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting.

    abstract::Current understanding of microRNA (miRNA) biology is limited, and antisense oligonucleotide (ASO) inhibition of miRNAs is a powerful technique for their functionalization. To uncover the role of the liver-specific miR-122 in the adult liver, we inhibited it in mice with a 2'-O-methoxyethyl phosphorothioate ASO. miR-12...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2006.01.005

    authors: Esau C,Davis S,Murray SF,Yu XX,Pandey SK,Pear M,Watts L,Booten SL,Graham M,McKay R,Subramaniam A,Propp S,Lollo BA,Freier S,Bennett CF,Bhanot S,Monia BP

    更新日期:2006-02-01 00:00:00

  • Energy intake and exercise as determinants of brain health and vulnerability to injury and disease.

    abstract::Evolution favored individuals with superior cognitive and physical abilities under conditions of limited food sources, and brain function can therefore be optimized by intermittent dietary energy restriction (ER) and exercise. Such energetic challenges engage adaptive cellular stress-response signaling pathways in neu...

    journal_title:Cell metabolism

    pub_type: 杂志文章,评审

    doi:10.1016/j.cmet.2012.08.012

    authors: Mattson MP

    更新日期:2012-12-05 00:00:00

  • Aging-Dependent Demethylation of Regulatory Elements Correlates with Chromatin State and Improved β Cell Function.

    abstract::Aging is driven by changes of the epigenetic state that are only partially understood. We performed a comprehensive epigenomic analysis of the pancreatic β cell, key player in glucose homeostasis, in adolescent and very old mice. We observe a global methylation drift resulting in an overall more leveled methylome in o...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2015.07.025

    authors: Avrahami D,Li C,Zhang J,Schug J,Avrahami R,Rao S,Stadler MB,Burger L,Schübeler D,Glaser B,Kaestner KH

    更新日期:2015-10-06 00:00:00

  • Tumor necrosis factor alpha-induced skeletal muscle insulin resistance involves suppression of AMP-kinase signaling.

    abstract::Elevated levels of tumor necrosis factor (TNFalpha) are implicated in the development of insulin resistance, but the mechanisms mediating these chronic effects are not completely understood. We demonstrate that TNFalpha signaling through TNF receptor (TNFR) 1 suppresses AMPK activity via transcriptional upregulation o...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2006.11.005

    authors: Steinberg GR,Michell BJ,van Denderen BJ,Watt MJ,Carey AL,Fam BC,Andrikopoulos S,Proietto J,Görgün CZ,Carling D,Hotamisligil GS,Febbraio MA,Kay TW,Kemp BE

    更新日期:2006-12-01 00:00:00

  • Ctr1 drives intestinal copper absorption and is essential for growth, iron metabolism, and neonatal cardiac function.

    abstract::The trace element copper (Cu) is a cofactor for biochemical functions ranging from energy generation to iron (Fe) acquisition, angiogenesis, and free radical detoxification. While Cu is essential for life, the molecules that mediate dietary Cu uptake have not been identified. Ctr1 is a homotrimeric protein, conserved ...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2006.08.009

    authors: Nose Y,Kim BE,Thiele DJ

    更新日期:2006-09-01 00:00:00

  • CRFR1 in AgRP Neurons Modulates Sympathetic Nervous System Activity to Adapt to Cold Stress and Fasting.

    abstract::Signaling by the corticotropin-releasing factor receptor type 1 (CRFR1) plays an important role in mediating the autonomic response to stressful challenges. Multiple hypothalamic nuclei regulate sympathetic outflow. Although CRFR1 is highly expressed in the arcuate nucleus (Arc) of the hypothalamus, the identity of th...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2016.04.017

    authors: Kuperman Y,Weiss M,Dine J,Staikin K,Golani O,Ramot A,Nahum T,Kühne C,Shemesh Y,Wurst W,Harmelin A,Deussing JM,Eder M,Chen A

    更新日期:2016-06-14 00:00:00

  • Rewiring of Glutamine Metabolism Is a Bioenergetic Adaptation of Human Cells with Mitochondrial DNA Mutations.

    abstract::Using molecular, biochemical, and untargeted stable isotope tracing approaches, we identify a previously unappreciated glutamine-derived α-ketoglutarate (αKG) energy-generating anaplerotic flux to be critical in mitochondrial DNA (mtDNA) mutant cells that harbor human disease-associated oxidative phosphorylation defec...

    journal_title:Cell metabolism

    pub_type: 杂志文章

    doi:10.1016/j.cmet.2018.03.002

    authors: Chen Q,Kirk K,Shurubor YI,Zhao D,Arreguin AJ,Shahi I,Valsecchi F,Primiano G,Calder EL,Carelli V,Denton TT,Beal MF,Gross SS,Manfredi G,D'Aurelio M

    更新日期:2018-05-01 00:00:00

  • SHIPing news: a new way to keep your weight down.

    abstract::Almost always, obesity is an obligate prerequisite for the development of type 2 diabetes mellitus. Loss of a well-known lipid phosphatase appears to prevent insulin-resistant diabetes in mice by removal of a positive regulator of adiposity. ...

    journal_title:Cell metabolism

    pub_type: 评论,杂志文章

    doi:10.1016/j.cmet.2005.01.007

    authors: Birnbaum MJ

    更新日期:2005-02-01 00:00:00

  • Reproduction, fat metabolism, and life span: what is the connection?

    abstract::Reduced reproduction is associated with increased fat storage and prolonged life span in multiple organisms, but the underlying regulatory mechanisms remain poorly understood. Recent studies in several species provide evidence that reproduction, fat metabolism, and longevity are directly coupled. For instance, germlin...

    journal_title:Cell metabolism

    pub_type: 杂志文章,评审

    doi:10.1016/j.cmet.2012.12.003

    authors: Hansen M,Flatt T,Aguilaniu H

    更新日期:2013-01-08 00:00:00