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Transcriptional regulatory logic of the diurnal cycle in the mouse liver

Sobel, Jonathan Aryeh ; Krier, Irina ; Andersin, Teemu ; [et al.]

Public Library of Science (PLoS) ; 2017

In: PLOS Biology Vol. 15, No. 4 ( 2017-4-17), p. e2001069-

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In: PLOS Biology, Public Library of Science (PLoS), Vol. 15, No. 4 ( 2017-4-17), p. e2001069-

Type of Medium: Online Resource

ISSN: 1545-7885

URL: Article

DOI: 10.1371/journal.pbio.2001069

DOI: 10.1371/journal.pbio.2001069.g001

DOI: 10.1371/journal.pbio.2001069.g002

DOI: 10.1371/journal.pbio.2001069.g003

DOI: 10.1371/journal.pbio.2001069.g004

DOI: 10.1371/journal.pbio.2001069.g005

DOI: 10.1371/journal.pbio.2001069.g006

DOI: 10.1371/journal.pbio.2001069.s001

DOI: 10.1371/journal.pbio.2001069.s002

DOI: 10.1371/journal.pbio.2001069.s003

DOI: 10.1371/journal.pbio.2001069.s004

DOI: 10.1371/journal.pbio.2001069.s005

DOI: 10.1371/journal.pbio.2001069.s006

DOI: 10.1371/journal.pbio.2001069.s007

DOI: 10.1371/journal.pbio.2001069.s008

DOI: 10.1371/journal.pbio.2001069.s009

DOI: 10.1371/journal.pbio.2001069.s010

DOI: 10.1371/journal.pbio.2001069.s011

DOI: 10.1371/journal.pbio.2001069.s012

DOI: 10.1371/journal.pbio.2001069.s013

DOI: 10.1371/journal.pbio.2001069.s014

DOI: 10.1371/journal.pbio.2001069.s015

DOI: 10.1371/journal.pbio.2001069.s016

DOI: 10.1371/journal.pbio.2001069.s017

DOI: 10.1371/journal.pbio.2001069.s018

DOI: 10.1371/journal.pbio.2001069.s019

DOI: 10.1371/journal.pbio.2001069.s020

DOI: 10.1371/journal.pbio.2001069.s021

DOI: 10.1371/journal.pbio.2001069.s022

DOI: 10.1371/journal.pbio.2001069.s023

DOI: 10.1371/journal.pbio.2001069.s024

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2017

detail.hit.zdb_id: 2126773-X

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Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome

Mauvoisin, Daniel ; Atger, Florian ; Dayon, Loïc ; [et al.]

Elsevier BV ; 2017

In: Cell Reports Vol. 20, No. 7 ( 2017-08), p. 1729-1743

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In: Cell Reports, Elsevier BV, Vol. 20, No. 7 ( 2017-08), p. 1729-1743

Type of Medium: Online Resource

ISSN: 2211-1247

URL: Article

DOI: 10.1016/j.celrep.2017.07.065

Language: English

Publisher: Elsevier BV

Publication Date: 2017

detail.hit.zdb_id: 2649101-1

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Author response image 3. Examples of the gene expression profiles from our database qualified as circadian by JTK_CYCLE.

Perrin, Laurent ; Loizides-Mangold, Ursula ; Chanon, Stéphanie ; [et al.]

eLife Sciences Publications, Ltd ; 2018

In: eLife Vol. 7 ( 2018-04-16)

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In: eLife, eLife Sciences Publications, Ltd, Vol. 7 ( 2018-04-16)

Abstract: Circadian regulation of transcriptional processes has a broad impact on cell metabolism. Here, we compared the diurnal transcriptome of human skeletal muscle conducted on serial muscle biopsies in vivo with profiles of human skeletal myotubes synchronized in vitro. More extensive rhythmic transcription was observed in human skeletal muscle compared to in vitro cell culture as a large part of the in vivo mRNA rhythmicity was lost in vitro. siRNA-mediated clock disruption in primary myotubes significantly affected the expression of ~8% of all genes, with impact on glucose homeostasis and lipid metabolism. Genes involved in GLUT4 expression, translocation and recycling were negatively affected, whereas lipid metabolic genes were altered to promote activation of lipid utilization. Moreover, basal and insulin-stimulated glucose uptake were significantly reduced upon CLOCK depletion. Our findings suggest an essential role for the circadian coordination of skeletal muscle glucose homeostasis and lipid metabolism in humans.

Type of Medium: Online Resource

ISSN: 2050-084X

URL: Article

DOI: 10.7554/eLife.34114

DOI: 10.7554/eLife.34114.001

DOI: 10.7554/eLife.34114.002

DOI: 10.7554/eLife.34114.004

DOI: 10.7554/eLife.34114.005

DOI: 10.7554/eLife.34114.003

DOI: 10.7554/eLife.34114.006

DOI: 10.7554/eLife.34114.009

DOI: 10.7554/eLife.34114.010

DOI: 10.7554/eLife.34114.011

DOI: 10.7554/eLife.34114.007

DOI: 10.7554/eLife.34114.008

DOI: 10.7554/eLife.34114.012

DOI: 10.7554/eLife.34114.013

DOI: 10.7554/eLife.34114.014

DOI: 10.7554/eLife.34114.018

DOI: 10.7554/eLife.34114.019

DOI: 10.7554/eLife.34114.020

DOI: 10.7554/eLife.34114.021

DOI: 10.7554/eLife.34114.015

DOI: 10.7554/eLife.34114.016

DOI: 10.7554/eLife.34114.017

DOI: 10.7554/eLife.34114.022

DOI: 10.7554/eLife.34114.023

DOI: 10.7554/eLife.34114.024

DOI: 10.7554/eLife.34114.025

DOI: 10.7554/eLife.34114.026

DOI: 10.7554/eLife.34114.027

DOI: 10.7554/eLife.34114.029

DOI: 10.7554/eLife.34114.030

DOI: 10.7554/eLife.34114.031

Language: English

Publisher: eLife Sciences Publications, Ltd

Publication Date: 2018

detail.hit.zdb_id: 2687154-3

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Chronotype: Implications for Epidemiologic Studies on Chrono-Nutrition and Cardiometabolic Health

Almoosawi, Suzana ; Vingeliene, Snieguole ; Gachon, Frederic ; [et al.]

Elsevier BV ; 2019

In: Advances in Nutrition Vol. 10, No. 1 ( 2019-01), p. 30-42

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In: Advances in Nutrition, Elsevier BV, Vol. 10, No. 1 ( 2019-01), p. 30-42

Type of Medium: Online Resource

ISSN: 2161-8313

URL: Article

DOI: 10.1093/advances/nmy070

Language: English

Publisher: Elsevier BV

Publication Date: 2019

detail.hit.zdb_id: 2583634-1

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Author response

Gaspar, Ludmila ; Howald, Cedric ; Popadin, Konstantin ; [et al.]

eLife Sciences Publications, Ltd ; 2017

In: eLife Vol. 6 ( 2017-09-04)

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In: eLife, eLife Sciences Publications, Ltd, Vol. 6 ( 2017-09-04)

Abstract: The importance of natural gene expression variation for human behavior is undisputed, but its impact on circadian physiology remains mostly unexplored. Using umbilical cord fibroblasts, we have determined by genome-wide association how common genetic variation impacts upon cellular circadian function. Gene set enrichment points to differences in protein catabolism as one major source of clock variation in humans. The two most significant alleles regulated expression of COPS7B, a subunit of the COP9 signalosome. We further show that the signalosome complex is imported into the nucleus in timed fashion to stabilize the essential circadian protein BMAL1, a novel mechanism to oppose its proteasome-mediated degradation. Thus, circadian clock properties depend in part upon a genetically-encoded competition between stabilizing and destabilizing forces, and genetic alterations in these mechanisms provide one explanation for human chronotype.

Type of Medium: Online Resource

ISSN: 2050-084X

URL: Article

DOI: 10.7554/eLife.24994

DOI: 10.7554/eLife.24994.001

DOI: 10.7554/eLife.24994.002

DOI: 10.7554/eLife.24994.006

DOI: 10.7554/eLife.24994.003

DOI: 10.7554/eLife.24994.004

DOI: 10.7554/eLife.24994.005

DOI: 10.7554/eLife.24994.007

DOI: 10.7554/eLife.24994.008

DOI: 10.7554/eLife.24994.009

DOI: 10.7554/eLife.24994.012

DOI: 10.7554/eLife.24994.013

DOI: 10.7554/eLife.24994.010

DOI: 10.7554/eLife.24994.011

DOI: 10.7554/eLife.24994.014

DOI: 10.7554/eLife.24994.015

DOI: 10.7554/eLife.24994.016

DOI: 10.7554/eLife.24994.017

DOI: 10.7554/eLife.24994.018

DOI: 10.7554/eLife.24994.019

DOI: 10.7554/eLife.24994.020

DOI: 10.7554/eLife.24994.021

DOI: 10.7554/eLife.24994.022

DOI: 10.7554/eLife.24994.023

DOI: 10.7554/eLife.24994.024

DOI: 10.7554/eLife.24994.027

DOI: 10.7554/eLife.24994.028

Language: English

Publisher: eLife Sciences Publications, Ltd

Publication Date: 2017

detail.hit.zdb_id: 2687154-3

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Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs

Yeung, Jake ; Mermet, Jérôme ; Jouffe, Céline ; [et al.]

Cold Spring Harbor Laboratory ; 2018

In: Genome Research Vol. 28, No. 2 ( 2018-02), p. 182-191

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In: Genome Research, Cold Spring Harbor Laboratory, Vol. 28, No. 2 ( 2018-02), p. 182-191

Abstract: Temporal control of physiology requires the interplay between gene networks involved in daily timekeeping and tissue function across different organs. How the circadian clock interweaves with tissue-specific transcriptional programs is poorly understood. Here, we dissected temporal and tissue-specific regulation at multiple gene regulatory layers by examining mouse tissues with an intact or disrupted clock over time. Integrated analysis uncovered two distinct regulatory modes underlying tissue-specific rhythms: tissue-specific oscillations in transcription factor (TF) activity, which were linked to feeding-fasting cycles in liver and sodium homeostasis in kidney; and colocalized binding of clock and tissue-specific transcription factors at distal enhancers. Chromosome conformation capture (4C-seq) in liver and kidney identified liver-specific chromatin loops that recruited clock-bound enhancers to promoters to regulate liver-specific transcriptional rhythms. Furthermore, this looping was remarkably promoter-specific on the scale of less than 10 kilobases (kb). Enhancers can contact a rhythmic promoter while looping out nearby nonrhythmic alternative promoters, confining rhythmic enhancer activity to specific promoters. These findings suggest that chromatin folding enables the clock to regulate rhythmic transcription of specific promoters to output temporal transcriptional programs tailored to different tissues.

Type of Medium: Online Resource

ISSN: 1088-9051 , 1549-5469

URL: Article

DOI: 10.1101/gr.222430.117

RVK:

XA 10000

Language: English

Publisher: Cold Spring Harbor Laboratory

Publication Date: 2018

detail.hit.zdb_id: 1483456-X

SSG: 12

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Pancreatic α- and β-cellular clocks have distinct molecular properties and impact on islet hormone secretion and gene expression

Petrenko, Volodymyr ; Saini, Camille ; Giovannoni, Laurianne ; [et al.]

Cold Spring Harbor Laboratory ; 2017

In: Genes & Development Vol. 31, No. 4 ( 2017-02-15), p. 383-398

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In: Genes & Development, Cold Spring Harbor Laboratory, Vol. 31, No. 4 ( 2017-02-15), p. 383-398

Abstract: A critical role of circadian oscillators in orchestrating insulin secretion and islet gene transcription has been demonstrated recently. However, these studies focused on whole islets and did not explore the interplay between α-cell and β-cell clocks. We performed a parallel analysis of the molecular properties of α-cell and β-cell oscillators using a mouse model expressing three reporter genes: one labeling α cells, one specific for β cells, and a third monitoring circadian gene expression. Thus, phase entrainment properties, gene expression, and functional outputs of the α-cell and β-cell clockworks could be assessed in vivo and in vitro at the population and single-cell level. These experiments showed that α-cellular and β-cellular clocks are oscillating with distinct phases in vivo and in vitro . Diurnal transcriptome analysis in separated α and β cells revealed that a high number of genes with key roles in islet physiology, including regulators of glucose sensing and hormone secretion, are differentially expressed in these cell types. Moreover, temporal insulin and glucagon secretion exhibited distinct oscillatory profiles both in vivo and in vitro. Altogether, our data indicate that differential entrainment characteristics of circadian α-cell and β-cell clocks are an important feature in the temporal coordination of endocrine function and gene expression.

Type of Medium: Online Resource

ISSN: 0890-9369 , 1549-5477

URL: Article

DOI: 10.1101/gad.290379.116

RVK:

WA 15000

Language: English

Publisher: Cold Spring Harbor Laboratory

Publication Date: 2017

detail.hit.zdb_id: 1467414-2

SSG: 12

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Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver

Wang, Jingkui ; Mauvoisin, Daniel ; Martin, Eva ; [et al.]

Elsevier BV ; 2017

In: Cell Metabolism Vol. 25, No. 1 ( 2017-01), p. 102-117

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In: Cell Metabolism, Elsevier BV, Vol. 25, No. 1 ( 2017-01), p. 102-117

Type of Medium: Online Resource

ISSN: 1550-4131

URL: Article

DOI: 10.1016/j.cmet.2016.10.003

Language: English

Publisher: Elsevier BV

Publication Date: 2017

detail.hit.zdb_id: 2174469-5

SSG: 12

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USP2-45 Is a Circadian Clock Output Effector Regulating Calcium Absorption at the Post-Translational Level

Pouly, Daniel ; Chenaux, Sébastien ; Martin, Virginie ; [et al.]

Public Library of Science (PLoS) ; 2016

In: PLOS ONE Vol. 11, No. 1 ( 2016-1-12), p. e0145155-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 11, No. 1 ( 2016-1-12), p. e0145155-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0145155

DOI: 10.1371/journal.pone.0145155.g001

DOI: 10.1371/journal.pone.0145155.g002

DOI: 10.1371/journal.pone.0145155.g003

DOI: 10.1371/journal.pone.0145155.g004

DOI: 10.1371/journal.pone.0145155.g005

DOI: 10.1371/journal.pone.0145155.g006

DOI: 10.1371/journal.pone.0145155.g007

DOI: 10.1371/journal.pone.0145155.t001

DOI: 10.1371/journal.pone.0145155.s001

DOI: 10.1371/journal.pone.0145155.s002

DOI: 10.1371/journal.pone.0145155.s003

DOI: 10.1371/journal.pone.0145155.s004

DOI: 10.1371/journal.pone.0145155.s005

DOI: 10.1371/journal.pone.0145155.s006

DOI: 10.1371/journal.pone.0145155.s007

DOI: 10.1371/journal.pone.0145155.s008

DOI: 10.1371/journal.pone.0145155.s009

DOI: 10.1371/journal.pone.0145155.s010

DOI: 10.1371/journal.pone.0145155.s011

DOI: 10.1371/journal.pone.0145155.s012

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2016

detail.hit.zdb_id: 2267670-3

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The Insulin/Insulin‐like Growth Factor signalling connects metabolism with sexual differentiation

Weger, Benjamin D. ; Gachon, Frédéric

Wiley ; 2021

In: Acta Physiologica Vol. 231, No. 3 ( 2021-03)

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In: Acta Physiologica, Wiley, Vol. 231, No. 3 ( 2021-03)

Type of Medium: Online Resource

ISSN: 1748-1708 , 1748-1716

URL: Issue

URL: Article

DOI: 10.1111/apha.2021.231.issue-3

DOI: 10.1111/apha.13576

Language: English

Publisher: Wiley

Publication Date: 2021

detail.hit.zdb_id: 2617148-X

detail.hit.zdb_id: 2219379-0

SSG: 12

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