- ArticleEsrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation
- Nicola Festuccia (n.festuccia{at}lms.mrc.ac.uk)*,1,3,
- Florian Halbritter1,4,6,
- Andrea Corsinotti1,2,
- Alessia Gagliardi1,5,
- Douglas Colby1,
- Simon R Tomlinson1 and
- Ian Chambers (ichambers{at}ed.ac.uk)*,1
- 1MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- 2Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
- 3Present Address: MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine Imperial College London, London, UK
- 4Present Address: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- 5Present Address: Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- 6Present Address: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- ↵*
Corresponding author. Tel: +44 20 8383 8228; E‐mail: n.festuccia{at}lms.mrc.ac.uk
Corresponding author. Tel: +44 131 651 9562; Fax: +44 131 651 9501; E‐mail: ichambers{at}ed.ac.uk
Differential Esrrb transcription factor expression instructs differentiation kinetics of mouse embryonic stem cells.
Synopsis
Embryonic stem cell (ESC) populations cultured in LIF‐containing serum heterogeneously express NANOG and ESRRB transcription factors (TFs), and contain both self‐renewing cells as well as cells initiating differentiation. Using fluorescent knock‐in reporters, mouse ESCs are shown to be heterogeneous in self‐renewal, gene expression, and regulatory element activities during exit from naïve pluripotency.
Downregulation of NANOG is required for loss of ESRRB in LIF/FCS culture of ESCs.
Loss of ESRRB marks commitment to differentiation.
Co‐binding of OCT4 at regulatory sites in ESRRB‐high ESCs is differentially dependent on NANOG and other naïve pluripotency TFs.
Genes proximal to regulatory elements losing OCT4 binding are preferentially expressed in naïve cells.
The EMBO Journal (2018): e95476
- Received December 14, 2016.
- Revision received August 24, 2018.
- Accepted August 27, 2018.
- © 2018 The Authors. Published under the terms of the CC BY 4.0 license
This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
- ArticleNonsense‐mediated mRNA decay involves two distinct Upf1‐bound complexes
- Marine Dehecq1,2,
- Laurence Decourty1,
- Abdelkader Namane1,
- Caroline Proux3,
- Joanne Kanaan4,
- Hervé Le Hir4,
- Alain Jacquier1 and
- Cosmin Saveanu (cosmin.saveanu{at}pasteur.fr)*,1
- 1Génétique des Interactions Macromoléculaires, Genomes and Genetics Department, Institut Pasteur, Paris, France
- 2Université Pierre et Marie Curie, Paris, France
- 3Transcriptome and Epigenome, CITECH, Institut Pasteur, Paris, France
- 4Expression des ARN Messagers Eucaryotes, Biology Department, CNRS UMR8197, Inserm U1024, Institut de Biologie de l'Ecole Normale Supérieure, Paris, France
- ↵*Corresponding author. Tel: +33 1 44 38 92 80; E‐mail: cosmin.saveanu{at}pasteur.fr
Distinct mechanisms for Nonsense‐Mediated mRNA Decay (NMD) have been proposed in different organisms. Proteomics‐based characterization of NMD complexes in yeast reveals the existence of two mutually exclusive complexes that may provide a universal model for NMD.
Synopsis
A number of partly contradictory mechanisms have been proposed for Nonsense‐Mediated RNA Decay (NMD). Proteomics‐based characterization of NMD complexes in Saccharomyces cerevisiae identifies two mutually exclusive complexes that may provide a universal mechanism for NMD.
Enrichment computation based on label‐free quantitative mass‐spectrometry and total protein abundance discriminates between true interacting proteins and contaminants.
NMD factors bind to the core NMD protein Upf1 as two distinct complexes: Upf1‐23 complex (Upf1/2/3) and Upf1‐decapping (Upf1/decapping factors/Ebs1/Nmd4).
The Upf1‐decapping complex binds specifically to NMD target RNAs and is associated with monosomes and polysomes.
Smg‐5/7 (Ebs1) and Smg‐6 (Nmd4) homologues are required for yeast NMD, suggesting that NMD mechanisms are more conserved than previously thought.
The EMBO Journal (2018) e99278
- Received February 20, 2018.
- Revision received August 10, 2018.
- Accepted August 22, 2018.
- © 2018 The Authors
- News & ViewsAlpha‐ketoglutarate: a “magic” metabolite in early germ cell development
- 1Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, USA
- 2Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA, USA
- 3California NanoSystems Institute, UCLA, Los Angeles, CA, USA
- 4Department of Bioengineering, UCLA, Los Angeles, CA, USA
- 5Molecular Biology Institute, UCLA, Los Angeles, CA, USA
- 6Eli and Edythe Broad Center of Regenerative Medicine, UCLA, Los Angeles, CA, USA
- 7Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
A causal relationship between cell metabolism and the fate of pluripotent stem cells through epigenome regulation is emerging. A recent study shows that the tricarboxylic acid cycle intermediate alpha‐ketoglutarate (αKG) can both sustain naïve mouse embryonic stem cell pluripotency and promote primordial germ cell differentiation. This observation together with other studies provides intriguing possibilities for stabilizing ephemeral embryonic cell states and enhancing desired fate transitions through specific metabolite manipulations.
See also: J Tischler et al
Recent implications of a Krebs cycle intermediate in stem cell pluripotency and differentiation suggest possibilities for stabilizing ephemeral embryonic cell states and enhancing desired fate transitions through specific metabolite manipulations.
The EMBO Journal (2018) e100615
- © 2018 The Authors
- News & ViewsEpigenetically jump starting de novo shoot regeneration
The ability to regenerate lost organs or tissues is a central requirement for animals and plants in order to cope with injury. Regeneration of a whole body is rare in animals but is more commonly found in plants where in vitro regeneration has become a widely used tool in plant research. In a new study, Kim et al find that epigenetic changes via the histone acetyltransferase HAG1 establish the competency for shoot regeneration from callus by promoting the expression of root stem cell factors.
See also: JY Kim et al
The histone acetyltransferase HAG1 drives plant regeneration from callus by promoting the expression of root stem cell factors.
The EMBO Journal (2018) e100596
- © 2018 The Authors
- ArticleChemical genetic identification of CDKL5 substrates reveals its role in neuronal microtubule dynamics
- Lucas L Baltussen1,†,
- Priscilla D Negraes2,†,
- Margaux Silvestre1,
- Suzanne Claxton1,
- Max Moeskops1,
- Evangelos Christodoulou3,
- Helen R Flynn4,
- Ambrosius P Snijders4,
- Alysson R Muotri (muotri{at}ucsd.edu)*,2,5 and
- Sila K Ultanir (sila.ultanir{at}crick.ac.uk)*,1
- 1Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
- 2Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- 3Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
- 4Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
- 5Department of Pediatrics/Cellular & Molecular Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, School of Medicine, Rady Children's Hospital San Diego, University of California San Diego, La Jolla, CA, USA
- ↵*
Corresponding author. Tel: +1 858 534 9320; E‐mail: muotri{at}ucsd.edu
Corresponding author. Tel: +44 20 3796 1613; E‐mail: sila.ultanir{at}crick.ac.uk
↵† These authors contributed equally to this work
The finding of decreased microtubule affinity of CDKL5‐phosphorylated MAP1S provides new insights into a possible pathogenic pathway of neurodevelopmental CDKL5 deficiency disorder.
Synopsis
Chemical genetic identification of physiological CDKL5 substrates EB2 and MAP1S reveals its role as a regulator of neuronal microtubule dynamics. MAP1S phosphorylation decreases microtubule affinity, suggesting a possible pathogenic pathway of CDKL5 deficiency disorder (CDD).
CDKL5 directly phosphorylates the RPXS* motif of microtubule‐associated proteins EB2, MAP1S and ARHGEF2.
EB2 and MAP1S phosphorylation is lost in CDKL5 KO mouse brains and human CDD patient‐derived neurons.
MAP1S phosphorylation by CDKL5 directly impairs its microtubule binding and stabilizing properties.
CDKL5 regulates dendritic microtubule dynamics in a MAP1S‐dependent manner, resulting in altered cargo trafficking.
The EMBO Journal (2018) e99763
- Received May 3, 2018.
- Revision received August 7, 2018.
- Accepted August 31, 2018.
- © 2018 The Francis Crick Institute. Published under the terms of the CC BY 4.0 license
This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
- ResourcePhosphoproteomic screening identifies physiological substrates of the CDKL5 kinase
- Ivan M Muñoz1,†,
- Michael E Morgan1,†,
- Julien Peltier1,2,
- Florian Weiland1,
- Mateusz Gregorczyk1,
- Fiona CM Brown1,
- Thomas Macartney1,
- Rachel Toth1,
- Matthias Trost (matthias.trost{at}ncl.ac.uk)*,1,2 and
- John Rouse (j.rouse{at}dundee.ac.uk)*,1
- 1MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
- 2Faculty of Medical Sciences, Institute for Cell and Molecular Biosciences, Newcastle upon Tyne, UK
- ↵*
Corresponding author. Tel: +44 191 2087009; E‐mail: matthias.trost{at}ncl.ac.uk
Corresponding author. Tel: +44 1382 385490; E‐mail: j.rouse{at}dundee.ac.uk
↵† These authors contributed equally to this work
Identification of phosphorylation targets reveals a sequence preference for the neurodevelopmental disease‐linked CDKL5, and that pathogenic mutations decrease activity towards microtubule‐ and centrosome‐associated substrates.
Synopsis
CDKL5 kinase is mutated in a neurodevelopmental disease termed CDKL5 disorder but the cellular targets and functions of CDKL5 are unclear. A phosphoproteomic screen to identify cellular targets of CDKL5 now addresses this gap.
CDKL5 phosphorylates MAP1S, CEP131, and DLG5, proteins involved in regulation of microtubules and centrosomes.
In all three substrates, the phosphorylated serine lies in an RPXSA motif, with in vitro analysis showing certain amino acids other than Ala also tolerated C‐terminal to the phosphoacceptor serine.
CDKL5 activity is controlled by tyrosine auto‐phosphorylation in its T‐loop.
Pathogenic CDKL5 mutations cause severe reduction in kinase activity towards MAP1S and CEP131 in cells and in vitro.
The EMBO Journal (2018) e99559
- Received April 5, 2018.
- Revision received August 14, 2018.
- Accepted September 10, 2018.
- © 2018 The Authors. Published under the terms of the CC BY 4.0 license
This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
- News & ViewsATF4‐amino acid circuits: a recipe for resistance in melanoma
Lactate dehydrogenase A (LDHA) has appropriately received attention as a therapeutic target for the treatment of a broad spectrum of tumor types, yet little is known regarding intrinsic resistance to LDHA inhibitors. Pathria et al (2018) now establish that ATF4‐dependent control of enzymes that direct amino acid metabolism confers resistance to LDHA inhibitors in melanoma and identify chokepoints that can be exploited to overcome metabolic compensation, setting the stage for trials with such combinations.
See also: G Pathria et al
A new study shows that ATF4‐mediated rewiring of amino acid metabolism mediates resistance to lactate dehydrogenase A inhibitors.
The EMBO Journal (2018) e100600
- © 2018 The Authors
